biological processes that systematically vary over a 24-hour cycle are called
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Biological rhythms are repetitive biological processes. Some types of biological rhythms have been described as biological clocks. They can range in frequency from microseconds to less than one repetitive event per decade. Biological rhythms are studied by chronobiology. In the biochemical context biological rhythms are called biochemical oscillations. The variations of the timing and duration of biological activity in living organisms occur for many essential biological processes. These occur (a) in animals (eating, sleeping, mating, hibernating, migration, cellular regeneration, etc.), (b) in plants (leaf movements, photosynthetic reactions, etc.), and in microbial organisms such as fungi and protozoa. They have even been found in bacteria, especially among the cyanobacteria (aka blue-green algae, see bacterial circadian rhythms). Circadian rhythm The best studied rhythm in chronobiology is the circadian rhythm, a roughly 24-hour cycle shown by physiological processes in all these organisms. The term circadian comes from the Latin circa, meaning "around" and dies, "day", meaning "approximately a day." It is regulated by circadian clocks. The circadian rhythm can further be broken down into routine cycles during the 24-hour day: Diurnal, which describes organisms active during daytime Nocturnal, which describes organisms active in the night Crepuscular, which describes animals primarily active during the dawn and dusk hours (ex: white-tailed deer, some bats) While circadian rhythms are defined as regulated by endogenous processes, other biological cycles may be regulated by exogenous signals. In some cases, multi-trophic systems may exhibit rhythms driven by the circadian clock of one of the members (which may also be influenced or reset by external factors). The endogenous plant cycles may regulate the activity of the bacterium by controlling availability of plant-produced photosynthate. Other cycles Many other important cycles are also studied, including: Infradian rhythms, which are cycles longer than a day. Examples include circannual or annual cycles that govern migration or reproduction cycles in many plants and animals, or the human menstrual cycle. Ultradian rhythms, which are cycles shorter than 24 hours, such as the 90-minute REM cycle, the 4-hour nasal cycle, or the 3-hour cycle of growth hormone production. Tidal rhythms, commonly observed in marine life, which follow the roughly 12.4-hour transition from high to low tide and back. Lunar rhythms, which follow the lunar month (29.5 days). They are relevant e.g. for marine life, as the level of the tides is modulated across the lunar cycle. Gene oscillations – some genes are expressed more during certain hours of the day than during other hours. Within each cycle, the time period during which the process is more active is called the acrophase. When the process is less active, the cycle is in its bathyphase or trough phase. The particular moment of highest activity is the peak or maximum; the lowest point is the nadir. How high (or low) the process gets is measured by the amplitude. Biochemical basis of biological rhythms Goldbeter's book provides a thorough analysis of the biochemical mechanisms and their kinetic properties that underlie biological rhythms. References External links Society for Research on Biological Rhythms
Biological rhythm
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Circadian rhythm sleep disorders (CRSD), also known as circadian rhythm sleep-wake disorders (CRSWD), are a family of sleep disorders which affect the timing of sleep. CRSDs arise from a persistent pattern of sleep/wake disturbances that can be caused either by dysfunction in one's biological clock system, or by misalignment between one's endogenous oscillator and externally imposed cues. As a result of this mismatch, those affected by circadian rhythm sleep disorders have a tendency to fall asleep at unconventional time points in the day. These occurrences often lead to recurring instances of disturbed rest, where individuals affected by the disorder are unable to go to sleep and awaken at "normal" times for work, school, and other social obligations. Delayed sleep phase disorder, advanced sleep phase disorder, non-24-hour sleep–wake disorder and irregular sleep–wake rhythm disorder represents the four main types of CRSD. Overview Humans, like most living organisms, have various biological rhythms. These biological clocks control processes that fluctuate daily (e.g., body temperature, alertness, hormone secretion), generating circadian rhythms. Among these physiological characteristics, the sleep-wake propensity can also be considered one of the daily rhythms regulated by the biological clock system. Human's sleeping cycles are tightly regulated by a series of circadian processes working in tandem, allowing for the experience of moments of consolidated sleep during the night and a long wakeful moment during the day. Conversely, disruptions to these processes and the communication pathways between them can lead to problems in sleeping patterns, which are collectively referred to as circadian rhythm sleep disorders. Normal rhythm A circadian rhythm is an entrainable, endogenous, biological activity that has a period of roughly twenty-four hours. This internal time-keeping mechanism is centralized in the suprachiasmatic nucleus (SCN) of humans, and allows for the internal physiological mechanisms underlying sleep and alertness to become synchronized to external environmental cues, like the light-dark cycle. The SCN also sends signals to peripheral clocks in other organs, like the liver, to control processes such as glucose metabolism. Although these rhythms will persist in constant light or dark conditions, different Zeitgebers (time givers such as the light-dark cycle) give context to the clock and allow it to entrain and regulate expression of physiological processes to adjust to the changing environment. Genes that help control light-induced entrainment include positive regulators BMAL1 and CLOCK and negative regulators PER1 and CRY. A full circadian cycle can be described as a twenty-four hour circadian day, where circadian time zero (CT 0) marks the beginning of a subjective day for an organism and CT 12 marks the start of subjective night. Humans with regular circadian function have been shown to maintain regular sleep schedules, regulate daily rhythms in hormone secretion, and sustain oscillations in core body temperature. Even in the absence of Zeitgebers, humans will continue to maintain a roughly 24-hour rhythm in these biological activities. Regarding sleep, normal circadian function allows people to maintain balance rest and wakefulness that allows people to work and maintain alertness during the day's activities, and rest at night. Some
Circadian rhythm sleep disorder
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A diurnal cycle (or diel cycle) is any pattern that recurs every 24 hours as a result of one full rotation of the planet Earth around its axis. Earth's rotation causes surface temperature fluctuations throughout the day and night, as well as weather changes throughout the year. The diurnal cycle depends mainly on incoming solar radiation. Climate and atmosphere In climatology, the diurnal cycle is one of the most basic forms of climate patterns, including variations in diurnal temperature and rainfall. Diurnal cycles may be approximately sinusoidal or include components of a truncated sinusoid (due to the Sun's rising and setting) and thermal relaxation (Newton cooling) at night. The diurnal cycle also has a great impact on carbon dioxide levels in the atmosphere, due to processes such as photosynthesis and cellular respiration. Biological effects Diurnal cycles of light and temperature can result in similar cycles in biological processes, such as photosynthesis in plants and clinical depression in humans. Plant responses to environmental cycles may even induce indirect cycles in rhizosphere microbial activities, including nitrogen fixation. Semi-diurnal cycle A semi-diurnal cycle refers to a pattern that occurs about every twelve hours or about twice a day. Often these can be related to lunar tides, in which case the interval is closer to 12 hours and 25 minutes. See also Chronotype Circadian rhythm Diel vertical migration Diurnality References Climate patterns Day
Diurnal cycle
315998
Biological clock may refer to: Age and female fertility, decrease of female fertility with advancing maternal age Ageing, biological program that limits the lifespan of an individual Biological rhythms Internal clock, the timeframe sensed by the individual's body which is largely affected by the light-dark cycle Circadian clock, a molecular mechanism that results in a circadian rhythm in a living organism Circadian rhythm, biological process that displays an oscillation about 24 hours, such as the human sleep-wake cycle (the "body clock") Epigenetic clock, a set of DNA sites whose methylation levels can be used to measure aging throughout the body Molecular clock, a technique that uses the mutation rate of a biomolecule to deduce the time in prehistory when two life forms diverged Vernalisation, the induction of flowering by prolonged exposure to low temperatures, as during the winter in a temperate climate Menstrual cycle, the regular natural change that occurs in the female reproductive system that makes pregnancy possible
Biological clock
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A phase response curve (PRC) illustrates the transient change (phase response) in the cycle period of an oscillation induced by a perturbation as a function of the phase at which it is received. PRCs are used in various fields; examples of biological oscillations are the heartbeat, circadian rhythms, and the regular, repetitive firing observed in some neurons in the absence of noise. In circadian rhythms In humans and animals, there is a regulatory system that governs the phase relationship of an organism's internal circadian clock to a regular periodicity in the external environment (usually governed by the solar day). In most organisms, a stable phase relationship is desired, though in some cases the desired phase will vary by season, especially among mammals with seasonal mating habits. In circadian rhythm research, a PRC illustrates the relationship between a chronobiotic's time of administration (relative to the internal circadian clock) and the magnitude of the treatment's effect on circadian phase. Specifically, a PRC is a graph showing, by convention, time of the subject's endogenous day along the x-axis and the amount of the phase shift (in hours) along the y-axis. Each curve has one peak and one trough in each 24-hour cycle. Relative circadian time is plotted against phase-shift magnitude. The treatment is usually narrowly specified as a set intensity and colour and duration of light exposure to the retina and skin, or a set dose and formulation of melatonin. These curves are often consulted in the therapeutic setting. Normally, the body's various physiological rhythms will be synchronized within an individual organism (human or animal), usually with respect to a master biological clock. Of particular importance is the sleep–wake cycle. Various sleep disorders and externals stresses (such as jet lag) can interfere with this. Humans with non-24-hour sleep–wake disorder often experience an inability to maintain a consistent internal clock. Extreme chronotypes usually maintain a consistent clock, but find that their natural clock does not align with the expectations of their social environment. PRC curves provide a starting point for therapeutic intervention. The two common treatments used to shift the timing of sleep are light therapy, directed at the eyes, and administration of the hormone melatonin, usually taken orally. Either or both can be used daily. The phase adjustment is generally cumulative with consecutive daily administrations, and — at least partially — additive with concurrent administrations of distinct treatments. If the underlying disturbance is stable in nature, ongoing daily intervention is usually required. For jet lag, the intervention serves mainly to accelerate natural alignment, and ceases once desired alignment is achieved. Note that phase response curves from the experimental setting are usually aggregates of the test population, that there can be mild or significant variation within the test population, that individuals with sleep disorders often respond atypically, and that the formulation of the chronobiotic might be specific to the experimental setting and not generally available in clinical practice (e.g. for melatonin, one sustained-release formulation might differ in its release rate as compared to another);
Phase response curve
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A circadian advantage is an advantage gained when an organism's biological cycles are in tune with its surroundings. It is not a well studied phenomenon, but it is known to occur in certain types of cyanobacteria, whose endogenous cycles, or circadian rhythm, "resonates" or aligns with their environment. It is known to occur in plants also, suggesting that any organism which is able to attune its natural growth cycles with its environment will have a competitive advantage over those that do not. Circadian advantage may also refer to sporting teams gaining an advantage by acclimatizing to the time zone where a match is played. In organisms In the context of bacterial circadian rhythms, specifically in cyanobacteria, circadian advantage refers to the improved survival of strains of cyanobacteria whose endogenous cycles "resonate" or align with the environmental circadian rhythm. For example, consider a strain with a free-running period (FRP) of 24 hours that is co-cultured with a strain that has a free-running period (FRP) of 30 hours in a light-dark cycle of 12 hours light and 12 hours dark (LD 12:12). The strain that has a 24 hour FRP will out-compete the 30 hour strain over time. Competition studies in plants provide another example of circadian advantage. These studies have shown that an endogenous clock that resonates with environmental cycles leads to a competitive advantage in Arabidopsis thaliana. Experiments with wild type, short circadian period mutants, and long circadian period mutants demonstrated that plants with a circadian period that is optimally synchronized to the environment grew fastest. The same study also showed that photosynthetic carbon fixation was directly correlated to “circadian resonance”. A different study discovered that genes involved in photosynthetic reactions of A. thaliana are under clock control. mRNAs that encode chlorophyll binding proteins and the enzyme protoporphyrin IX magnesium chelatase involved in chlorophyll synthesis were cycling. The “circadian resonance” increase in productivity may arise from appropriate anticipation of sunrise and sunset, allowing for timely synthesis of light-harvesting complex proteins and chlorophyll. Therefore, the competitive advantage in A. thaliana further supports the idea that anticipation of environmental changes leads to enhanced fitness. Rhodopseudomonas palustris is another example of the advantage in having a biological timing system that interacts with the environmental cycles. While the only prokaryotic group with a well-known circadian timekeeping mechanism is the cyanobacteria, recent discoveries involving R. palustris have suggested alternative timekeeping mechanisms among the prokaryotes. R. palustris is a purple non-sulfur bacterium that has KaiB and KaiC genes and exhibit adaptive kaiC-dependent growth in 24h cyclic environments. However, R. palustris was reported to show a poorly self-sustained intrinsic rhythm, and kaiC-dependent growth enhancement was not present under constant conditions. The R. palustris system was proposed as a “proto” circadian timekeeper that exhibit some parts of circadian systems (kaiB and kaiC homologs), but not all. Likewise, research on the endogenous circadian timekeeping mechanisms in mice further supports that “circadian resonance” is evolutionarily adaptive. One study in particular compared the fitness of wild-type mice with mutant mice which
Circadian advantage
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Period circadian protein homolog 1 is a protein in humans that is encoded by the PER1 gene. Function The PER1 protein is important to the maintenance of circadian rhythms in cells, and may also play a role in the development of cancer. This gene is a member of the period family of genes. It is expressed with a daily oscillating circadian rhythm, or an oscillation that cycles with a period of approximately 24 hours. PER1 is most notably expressed in the region of the brain called the suprachiasmatic nucleus (SCN), which is the primary circadian pacemaker in the mammalian brain. PER1 is also expressed throughout mammalian peripheral tissues. Genes in this family encode components of the circadian rhythms of locomotor activity, metabolism, and behavior. Circadian expression of PER1 in the suprachiasmatic nucleus will free-run in constant darkness, meaning that the 24-hour period of the cycle will persist without the aid of external light cues. Subsequently, a shift in the light/dark cycle evokes a proportional shift of gene expression in the suprachiasmatic nucleus. The time of gene expression is sensitive to light, as light during a mammal's subjective night results in a sudden increase in per expression and thus a shift in phase in the suprachiasmatic nucleus. Alternative splicing has been observed in this gene; however, these variants have not been fully described. There is some disagreement between experts over the occurrence of polymorphisms with functional significance. Many scientists state that there are no known polymorphisms of the human PER1 gene with significance at a population level that results in measurable behavioral or physiological changes. Still, some believe that even silent mutations can cause significant behavioral phenotypes, and result in major phase changes. Functional conservation of the PER gene is shown in a study by Shigeyoshi et al. 2002. In this study, mouse mPer1 and mPer2 genes were driven by Drosophila timeless promoter in Drosophila melanogaster. They found that both mPer constructs could restore rhythm to arrhythmic flies (per01 flies). Thus mPer1 and mPer2 can function as clock components in flies and may have implications concerning the homology of per genes. Role in chronobiology The PER1 gene, also called rigui, is a characteristic circadian oscillator. PER1 is rhythmically transcribed in the SCN, keeping a period of approximately 24 hours. This rhythm is sustained in constant darkness, and can also be entrained to changing light cycles. PER1 is involved in generating circadian rhythms in the SCN, and also has an effect on other oscillations throughout the body. For example, PER1 knockouts affect food entrainable oscillators and methamphetamine-sensitive circadian oscillators, whose periods are altered in the absence of PER1. In addition, mice with knockouts in both the PER1 and PER2 genes show no circadian rhythmicity. Phase shifts in PER1 neurons can be induced by a strong, brief light stimulus to the SCN of rats. This light exposure causes increases in PER1 mRNA, suggesting that the PER1 gene plays an important role in entrainment of the mammalian biological clock to the light-dark cycle. Feedback
Period circadian protein homolog 1
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Chronotherapy is a behavioural treatment that attempts to move bedtime and rising time later and later each day, around the clock, until a person is sleeping on a normal schedule. This treatment can be used by people with delayed sleep phase disorder (DSPD), who generally cannot reset their circadian rhythm by moving their bedtime and rising time earlier. DSPD is a circadian rhythm sleep disorder, characterised by a mismatch between a person's internal biological clock and societal norms. Chronotherapy uses the human phase response to light or melatonin. The American Academy of Sleep Medicine has recommended chronotherapy for the treatment of circadian rhythm and sleep disorders. Example Here is an example of how chronotherapy could work over a week's course of treatment, with the patient going to sleep 3 hours later every day until the desired sleep and wake time is reached. Day 1: sleep 3:00 am to 11:00 am Day 2: sleep 6:00 am to 2:00 pm Day 3: sleep 9:00 am to 5:00 pm Day 4: sleep 12:00 pm to 8:00 pm Day 5: sleep 3:00 pm to 11:00 pm Day 6: sleep 6:00 pm to 2:00 am next day Day 7: sleep 9:00 pm to 5:00 am next day Day 8 and thereafter: sleep 12:00 am to 8:00 am next day While this technique can provide respite from sleep deprivation for people who must wake early for school or work, the new sleep and wake times can only be maintained by following a strictly disciplined timetable for sleeping and rising. Other forms of sleep phase chronotherapy A modified chronotherapy is called controlled sleep deprivation with phase advance, SDPA. One stays awake one whole night and day, then goes to bed 90 minutes earlier than usual and maintains the new bedtime for a week. This process is repeated weekly until the desired bedtime is reached. Sometimes, although extremely infrequently, "reverse" chronotherapy – i.e., gradual movements of bedtime and rising time earlier each day – has been used in treatment of patients with abnormally short circadian rhythms, in an attempt to move their bedtimes to later times of the day. Because circadian rhythms substantially shorter than 24 hours are extremely rare, this type of chronotherapy has remained largely experimental. Side effects The safety of chronotherapy is not fully known. While chronotherapy has been successful for some, it is necessary to rigidly maintain the desired sleep/wake cycle thenceforth. Any deviation in schedule tends to allow the body clock to shift later again. Chronotherapy has been known to cause non-24-hour sleep–wake disorder in at least three recorded cases, as reported in the New England Journal of Medicine in 1992. Animal studies have suggested that such lengthening could "slow the intrinsic rhythm of the body clock to such an extent that the normal 24-hour day no longer lies within its range of entrainment." References Further reading Czeisler CA, Richardson GS, Coleman RM, Zimmerman JC, Moore-Ede MC, Dement WC, & Weitzman ED. (1981). Chronotherapy: Resetting the circadian clocks of patients with delayed sleep
Chronotherapy (sleep phase)
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A circadian clock, or circadian oscillator, also known as one’s internal alarm clock is a biochemical oscillator that cycles with a stable phase and is synchronized with solar time. Such a clock's in vivo period is necessarily almost exactly 24 hours (the earth's current solar day). In most living organisms, internally synchronized circadian clocks make it possible for the organism to anticipate daily environmental changes corresponding with the day–night cycle and adjust its biology and behavior accordingly. The term circadian derives from the Latin circa (about) dies (a day), since when taken away from external cues (such as environmental light), they do not run to exactly 24 hours. Clocks in humans in a lab in constant low light, for example, will average about 24.2 hours per day, rather than 24 hours exactly. The normal body clock oscillates with an endogenous period of exactly 24 hours, it entrains, when it receives sufficient daily corrective signals from the environment, primarily daylight and darkness. Circadian clocks are the central mechanisms that drive circadian rhythms. They consist of three major components: a central biochemical oscillator with a period of about 24 hours that keeps time; a series of input pathways to this central oscillator to allow entrainment of the clock; a series of output pathways tied to distinct phases of the oscillator that regulate overt rhythms in biochemistry, physiology, and behavior throughout an organism. The clock is reset as an organism senses environmental time cues of which the primary one is light. Circadian oscillators are ubiquitous in tissues of the body where they are synchronized by both endogenous and external signals to regulate transcriptional activity throughout the day in a tissue-specific manner. The circadian clock is intertwined with most cellular metabolic processes and it is affected by organism aging. The basic molecular mechanisms of the biological clock have been defined in vertebrate species, Drosophila melanogaster, plants, fungi, bacteria, and presumably also in Archaea. In 2017, the Nobel Prize in Physiology or Medicine was awarded to Jeffrey C. Hall, Michael Rosbash and Michael W. Young "for their discoveries of molecular mechanisms controlling the circadian rhythm" in fruit flies. Vertebrate anatomy In vertebrates, the master circadian clock is contained within the suprachiasmatic nucleus (SCN), a bilateral nerve cluster of about 20,000 neurons. The SCN itself is located in the hypothalamus, a small region of the brain situated directly above the optic chiasm, where it receives input from specialized photosensitive ganglion cells in the retina via the retinohypothalamic tract. The SCN maintains control across the body by synchronizing "slave oscillators", which exhibit their own near-24-hour rhythms and control circadian phenomena in local tissue. Through intercellular signalling mechanisms such as vasoactive intestinal peptide, the SCN signals other hypothalamic nuclei and the pineal gland to modulate body temperature and production of hormones such as cortisol and melatonin; these hormones enter the circulatory system, and induce clock-driven effects throughout the organism. It is not, however, clear precisely what signal (or signals) enacts principal entrainment to the many biochemical clocks contained
Circadian clock
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A chronotype is the behavioral manifestation of underlying circadian rhythm's myriad of physical processes. A person's chronotype is the propensity for the individual to sleep at a particular time during a 24-hour period. Eveningness (delayed sleep period; most active and alert in the evening) and morningness (advanced sleep period; most active and alert in the morning) are the two extremes with most individuals having some flexibility in the timing of their sleep period. However, across development there are changes in the propensity of the sleep period with pre-pubescent children preferring an advanced sleep period, adolescents preferring a delayed sleep period and many elderly preferring an advanced sleep period. The causes and regulation of chronotypes, including developmental change, individual propensity for a specific chronotype, and flexible versus fixed chronotypes have yet to be determined. However, research is beginning to shed light on these questions, such as the relationship between age and chronotype. There are candidate genes (called CLOCK genes) that exist in most cells in the body and brain, referred to as the circadian system that regulate physiological phenomena (hormone levels, metabolic function, body temperature, cognitive faculties, and sleeping). With the exception of the most extreme and rigid chronotypes, regulation is likely due to gene-environment interactions. Important environmental cues (zeitgebers) include light, feeding, social behavior, and work and school schedules. Additional research has proposed an evolutionary link between chronotype and nighttime vigilance in ancestral societies. Humans are normally diurnal creatures that are active in the daytime. As with most other diurnal animals, human activity-rest patterns are endogenously regulated by biological clocks with a circadian (~24-hour) period . Chronotypes have also been investigated in other species, such as fruit flies and mice. Normal variation in chronotype encompasses sleep–wake cycles that are two to three hours later in evening types than morning types. Extremes outside of this range can cause a person difficulty in participating in normal work, school, and social activities. If a person's "lark" or (more commonly) "owl" tendencies are strong and intractable to the point of disallowing normal participation in society, the person is normally considered to have a circadian rhythm sleep disorder. History Physiology professor Nathaniel Kleitman's 1939 book Sleep and Wakefulness, revised 1963, summarized the existing knowledge of sleep, and it was he who proposed the existence of a basic rest-activity cycle. Kleitman, with his students including William C. Dement and Eugene Aserinsky, continued his research throughout the 1900s. O. Öquist's 1970 thesis at the Department of Psychology, University of Göteborg, Sweden, marks the beginning of modern research into chronotypes, and is entitled Kartläggning av individuella dygnsrytmer, or "Charting Individual Circadian Rhythms". Measurement Morningness–eveningness questionnaire Olov Östberg modified Öquist's questionnaire and in 1976, together with J.A. (Jim) Horne, he published the 19-item morningness–eveningness questionnaire, MEQ, which is still used and referred to in virtually all research on this topic. Researchers in many countries have worked on validating the MEQ with regard to their local cultures. A revision of the scoring of the MEQ as well as a component
Chronotype
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Familial sleep traits are heritable variations in sleep patterns, resulting in abnormal sleep-wake times and/or abnormal sleep length. Circadian rhythms are coordinated physiological and biological changes that oscillate on an approximately 24-hour cycle. Disruptions to these rhythms in humans may affect the duration, onset, and/or quality of sleep during this cycle, resulting in familial sleep traits. These traits are not necessarily syndromes because they do not always cause distress among individuals. Instead of being disorders, familial sleep traits are variations in an individual's biological tendencies of sleep-wake times, and are only considered syndromes if affected individuals complain about life interference, in which case they may fall under the category of Circadian Rhythm Sleep Disorders (CRSD) that affect sleep timing and circadian rhythms. Some of these circadian disorders include Advanced Sleep Phase Disorder (ASPD) and Delayed Sleep Phase Disorder (DSPD). Familial sleep traits are more specific than CRSD because they are heritable and involve a wide range of Mendelian genes. Evidence has shown that genes significantly influence sleep schedules in mammals, including humans, and account for one-third of the variation in sleep quality and duration. Studies in human monozygotic twins have provided evidence that genetic factors affect "normal" sleep patterns as well, meaning ones where no individual has been diagnosed with an altered phenotypic sleep trait. Sleep timing is controlled by the circadian clock, which can entrain to environmental stimuli (usually a light-dark cycle) and is regulated by a transcription-translation feedback loop (TTFL). In humans, there are multiple genes involved in this molecular biological clock, which when mutated may result in sleep disorders such as Familial Advanced Sleep Phase (FASP), Familial Delayed Sleep Phase (FDSP), and Familial Natural Short Sleep (FNSS). Some mutations in Mendelian genes that are involved in the TTFL have been identified as the causes of these sleep traits, including PER2, PER3, CRY2, CRY1. Other Mendelian genes that are not known to play a core role in the TTFL but are involved in FNSS include DEC2 and ADRB1. With some familial sleep traits, there may be a shift in an individual's chronotype, which describes the time of sleep-wake behaviors that result from circadian rhythms. Chronotype may shift depending on multiple factors including gender and age. Individuals with FASP have earlier chronotypes and individuals with FDSP have later chronotypes compared to a conventional sleep period which runs from approximately 10pm to 7am. Individuals may meet the criteria for FASP or FDSP if they have Advanced Sleep Phase or Delayed Sleep Phase and at least one first degree relative with the trait. Researchers have examined the human prevalence of FASP to be 0.33-0.5% by including individuals who have a sleep onset at approximately 8:30pm and offset at 5:30am. FDSP, which includes individuals who have a delayed sleep onset and offset, has an unknown human prevalence and may vary based on location, definition, and age. History of discoveries Familial sleep traits have been difficult to study due to the various environmental influences (such as entraining daily alarms, artificial light at night,
Familial sleep traits
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Somnolence (alternatively sleepiness or drowsiness) is a state of strong desire for sleep, or sleeping for unusually long periods (compare hypersomnia). It has distinct meanings and causes. It can refer to the usual state preceding falling asleep, the condition of being in a drowsy state due to circadian rhythm disorders, or a symptom of other health problems. It can be accompanied by lethargy, weakness and lack of mental agility. Somnolence is often viewed as a symptom rather than a disorder by itself. However, the concept of somnolence recurring at certain times for certain reasons constitutes various disorders, such as excessive daytime sleepiness, shift work sleep disorder, and others; and there are medical codes for somnolence as viewed as a disorder. Sleepiness can be dangerous when performing tasks that require constant concentration, such as driving a vehicle. When a person is sufficiently fatigued, microsleeps may be experienced. In individuals deprived of sleep, somnolence may spontaneously dissipate for short periods of time; this phenomenon is the second wind, and results from the normal cycling of the circadian rhythm interfering with the processes the body carries out to prepare itself to rest. The word "somnolence" is derived from the Latin "somnus" meaning "sleep". Causes Circadian rhythm disorders Circadian rhythm ("biological clock") disorders are a common cause of drowsiness as are a number of other conditions such as sleep apnea, insomnia and narcolepsy. The body clock disorders are classified as extrinsic (externally caused) or intrinsic. The former type is, for example, shift work sleep disorder, which affects people who work nights or rotating shifts. The intrinsic types include: Advanced sleep phase disorder (ASPD) – A condition in which patients feel very sleepy and go to bed early in the evening and wake up very early in the morning Delayed sleep phase disorder (DSPD) – Faulty timing of sleep, peak period of alertness, the core body temperature rhythm, hormonal and other daily cycles such that they occur a number of hours late compared to the norm, often misdiagnosed as insomnia Non-24-hour sleep–wake disorder – A faulty body clock and sleep-wake cycle that usually is longer than (rarely shorter than) the normal 24-hour period causing complaints of insomnia and excessive sleepiness Irregular sleep–wake rhythm – Numerous naps throughout the 24-hour period, no main nighttime sleep episode and irregularity from day to day Physical illness Sleepiness can also be a response to infection. Such somnolence is one of several sickness behaviors or reactions to infection that some theorize evolved to promote recovery by conserving energy while the body fights the infection using fever and other means. Other causes include: Anxiety Brain tumor Chronic pains Concussion – a mild traumatic brain injury Diabetes Fibromyalgia Head injury Hypercalcemia – too much calcium in the blood Hypermagnesemia Hyponatremia – low blood sodium Hypothyroidism – the body doesn't produce enough hormones that control how cells use energy Meningitis Mood disorders – depression Multiple sclerosis Narcolepsy – disorder of the nervous system Skull fractures Sleeping sickness – caused by a specific parasite
Somnolence
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In chronobiology, photoentrainment refers to the process by which an organism's biological clock, or circadian rhythm, synchronizes to daily cycles of light and dark in the environment. The mechanisms of photoentrainment differ from organism to organism. Photoentrainment plays a major role in maintaining proper timing of physiological processes and coordinating behavior within the natural environment. Studying organisms’ different photoentrainment mechanisms sheds light on how organisms may adapt to anthropogenic changes to the environment. Background 24-hour physiological rhythms, known now as circadian rhythms, were first documented in 1729 by Jean Jacques d'Ortous de Mairan, a French astronomer who observed that mimosa plants (Mimosa pudica) would orient themselves to be toward the position of the sun despite being in a dark room. That observation spawned the field of chronobiology, which seeks to understand the mechanisms that underly endogenously expressed daily rhythms in organisms from cyanobacteria to mammals, which includes understanding and modeling the process of photoentrainment. Two prominent 20th century chronobiologists, Jürgen Aschoff and Colin Pittendrigh, both worked throughout the 1960s to model of the process of photoentrainment, and despite examining the same subject, they arrived at different conclusions. Aschoff proposed a parametric model of entrainment, which assumed that organisms entrained to environmental timing cues (often referred to as zeitgebers, or "time givers" in German) gradually, changing their internal "circadian" period to be greater or less than 24 hours until it became aligned with the zeitgeber time. Conversely, Pittendreigh proposed a non-parametric model of entrainment, which assumed that organisms adjusted their internal clocks instantaneously when confronted with a light signal, or zeitgeber, that was out of sync with when their internal circadian time expected to see light. Pittendrigh developed his model based on the phase-response curve, which visualizes the effect of short light pulses on organisms that were free-running (not entrained to a zeitgeber). Pittendrigh determined that an organism’s response to light depended on when the signal was presented. It was determined that exposure to light in the organism’s early subjective night (the early portion of an organism’s “normal” dark period) produced a delay in onset of activity in the following day (phase delay). Additionally, light exposure in the late subjective night resulted in advanced activity in the following day (phase advance). The phase changes experienced by the organism could be represented by a phase-response curve consisting of portions including the advance zone, delay zone, and dead zone. This model became widely accepted over Aschoff's parametric model, but it is still unclear which model most effectively explains the process of photoentrainment. Light intensity in conditions of constant light was found to also modulate an organism’s response. Exposure to higher-intensity light was found to either extend or shorten an organism’s period depending on species, dubbed Aschoff’s rule. Mechanism The molecular mechanism for photoentrainment in multicellular organisms such as in fungi and animals has been linked to the transcription-translation feedback loop (TTFL), where translated protein products influence gene transcription. The TTFL is composed of both a positive and negative arm, where the positive arm
Photoentrainment (chronobiology)
23670760
A lark, early bird, morning person, or (in Scandinavian countries) an A-person, is a person who usually gets up early in the morning and goes to bed early in the evening. The term relates to the birds known as larks, which are known to sing before dawn. Human "larks" may sleep from around 10 p.m. to 6 a.m. (or earlier), and tend to feel most energetic just after they get up in the morning. They are thus well-suited for working the day shift. The opposite of the lark is the owl, often awake at night. A person called a night owl is someone who usually stays up late and may feel most awake in the evening and at night. Researchers have traditionally used the terms morningness and eveningness to describe these two chronotypes. Charting chronotypes Till Roenneberg, a chronobiologist in Munich, has mapped the circadian rhythms of more than 200,000 people. Biological processes, including sleep-wake patterns, that display an oscillation of about 24 hours are called circadian rhythms. According to Roenneberg, the distribution of circadian rhythms spans from the very early to the very late chronotypes, similarly to how height varies from short to tall. As circadian rhythm is independent of the number of hours of sleep a person needs, Roenneberg calculates the rhythm based on the midpoint of the sleep period. A person who goes to bed at midnight and rises at 8 thus has the same chronotype as a person who goes to bed at 1 a.m. and rises at 7; the midpoint of sleep is 4 a.m. for both of these individuals. People with early chronotypes will usually not be able to "sleep in", even if they have stayed up later than usual. While fit for a "lark-like" societal framework, they find it hard to adapt to a context where "sleeping in" is common: despite feeling refreshed in the morning, they may feel hampered socially when confronted with some kinds of social gatherings (such as soirées) that are often scheduled for the evening, even if most kinds of social events are not. People with late chronotypes go to bed late and rise late. Forced to arise earlier than their circadian rhythm dictates, they have a low body temperature and may require a few hours to feel really awake. They are unable to fall asleep as early as "larks" can. Prevalence A 2007 survey of over 55,000 people found that chronotypes tend to follow a normal distribution, with extreme morning and evening types on the far ends. There are studies that suggest genes determine whether a person is a lark or an evening person in the same way it is implicated in people's attitude toward authority, unconventional behavior, as well as reading and television viewing habits. For instance, there is the case of the Per2 gene on chromosome 2, which was discovered in the early 1990s by Urs Albrecht and colleagues at the University of Fribourg in Switzerland. This gene regulates the circadian clock and a variant of
Lark (person)
54046997
In chronobiology, the circannual cycle is characterized by biological processes and behaviors recurring on an approximate annual basis, spanning a period of about one year. This term is particularly relevant in the analysis of seasonal environmental changes and their influence on the physiology, behavior, and life cycles of organisms. Adaptations observed in response to these circannual rhythms include fur color transformation, molting, migration, breeding, fattening and hibernation, all of which are inherently driven and synchronized with external environmental changes. The regulation of these cycles is linked to internal biological clocks, akin to the circadian rhythm, which respond to external cues such as variations in temperature, daylight length (photoperiod), and food availability. Such environmental signals enable organisms to anticipate seasonal variations and adjust their behaviors and physiological states, thereby optimizing evolutionary fitness and reproductive success. Circannual rhythms are evident in a range of organisms, including birds, mammals, fish, and insects, facilitating their adaptation to the cyclical nature of their habitats. Circannual cycles can be defined by three primary characteristics: ersistence in the absence of apparent time cues, the capacity for phase shifting, and stability against temperature fluctuations. Classified as an infradian rhythm, it occurs less frequently than a circadian rhythm. This cycle was first discovered by Ebo Gwinner and Canadian biologist Ted Pengelley. Derived from Latin, the term circannual combines circa, meaning approximately, with annual, referring to a period of one year. Examples In one study performed by Eberhard Gwinner, two species of birds were born in a controlled environment without ever being exposed to external stimuli. They were presented with a fixed Photoperiod of 10 hours of light and 14 hours of darkness each day. The birds were exposed to these conditions for eight years and consistently molted at the same time as they would have in the wild, indicating that this physiological cycle is innate rather than governed environmentally. Researchers Ted Pengelley and Ken Fisher studied the circannual clock in the golden-mantled ground squirrel. They exposed the squirrels to twelve hours of light and 12 hours of darkness and at a constant temperature for three years. Despite this constant cycle, they continued to hibernate once a year with each episode preceded by an increase in body weight and food consumption. During the first year, the squirrels began hibernation in late October. They started hibernating in mid August and early April respectively for the following two years, displaying a circannual rhythm with a period of about 10 months. An annual rhythm has been observed in humans diagnosed with obsessive compulsive tic disorder (OCTD). The study focused on observing the patients’ seasonal patterns and how the cycle of seasons affected their behaviors. They observed that there was a statistically significant annual rhythm in patients with OC symptoms but not in patients with tic symptoms. As a result of the study, the researchers concluded that treatments for this disorder can be implemented following an observation of the patient’s cycle and annual rhythm that they follow. Gwinner observed the willow warbler (Phylloscopus trochilus)
Circannual cycle
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Period (per) is a gene located on the X chromosome of Drosophila melanogaster. Oscillations in levels of both per transcript and its corresponding protein PER have a period of approximately 24 hours and together play a central role in the molecular mechanism of the Drosophila biological clock driving circadian rhythms in eclosion and locomotor activity. Mutations in the per gene can shorten (perS), lengthen (perL), and even abolish (per0) the period of the circadian rhythm. Discovery The period gene and three mutants (perS, perL, and per0) were isolated in an EMS mutagenesis screen by Ronald Konopka and Seymour Benzer in 1971. The perS, perL, and per0 mutations were found to not complement each other, so it was concluded that the three phenotypes were due to mutations in the same gene. The discovery of mutants that altered the period of circadian rhythms in eclosion and locomotor activity (perS and perL) indicated the role of the per gene in the clock itself and not an output pathway. The period gene was first sequenced in 1984 by Michael Rosbash and colleagues. In 1998, it was discovered that per produces two transcripts (differing only by the alternative splicing of a single untranslated intron) which both encode the PER protein. Function Circadian clock In Drosophila, per mRNA levels oscillate with a period of approximately 24 hours, peaking during the early subjective night. The per product PER also oscillates with a nearly 24-hour period, peaking about six hours after per mRNA levels during the middle subjective night. When PER levels increase, the inhibition of per transcription increases, lowering the protein levels. However, because PER protein cannot directly bind to DNA, it does not directly influence its own transcription; alternatively, it inhibits its own activators. After PER is produced from per mRNA, it dimerizes with Timeless (TIM) and the complex goes into the nucleus and inhibits the transcription factors of per and tim, the CLOCK/CYCLE heterodimer. This CLOCK/CYCLE complex acts as a transcriptional activator for per and tim by binding to specific enhancers (called E-boxes) of their promoters. Therefore, inhibition of CLK/CYC lowers per and tim mRNA levels, which in turn lower the levels of PER and TIM. Now, cryptochrome (CRY) is a light sensitive protein which inhibits TIM in the presence of light. When TIM is not complexed with PER, another protein, doubletime, or DBT, phosphorylates PER, targeting it for degradation. In mammals, an analogous transcription-translation negative feedback loop is observed. Translated from the three mammalian homologs of drosophila-per, one of three PER proteins (PER1, PER2, and PER3) dimerizes via its PAS domain with one of two cryptochrome proteins (CRY1 and CRY2) to form a negative element of the clock. This PER/CRY complex moves into the nucleus upon phosphorylation by CK1-epsilon (casein kinase 1 epsilon) and inhibits the CLK/BMAL1 heterodimer, the transcription factor that is bound to the E-boxes of the three per and two cry promoters by basic helix-loop-helix (BHLH) DNA-binding domains. The mammalian period 1 and period 2 genes play key roles in photoentrainment
Period (gene)
240228
The biological pump (or ocean carbon biological pump or marine biological carbon pump) is the ocean's biologically driven sequestration of carbon from the atmosphere and land runoff to the ocean interior and seafloor sediments. In other words, it is a biologically mediated process which results in the sequestering of carbon in the deep ocean away from the atmosphere and the land. The biological pump is the biological component of the "marine carbon pump" which contains both a physical and biological component. It is the part of the broader oceanic carbon cycle responsible for the cycling of organic matter formed mainly by phytoplankton during photosynthesis (soft-tissue pump), as well as the cycling of calcium carbonate (CaCO3) formed into shells by certain organisms such as plankton and mollusks (carbonate pump). Budget calculations of the biological carbon pump are based on the ratio between sedimentation (carbon export to the ocean floor) and remineralization (release of carbon to the atmosphere). The biological pump is not so much the result of a single process, but rather the sum of a number of processes each of which can influence biological pumping. Overall, the pump transfers about 10.2 gigatonnes of carbon every year into the ocean's interior and a total of 1300 gigatonnes carbon over an average 127 years. This takes carbon out of contact with the atmosphere for several thousand years or longer. An ocean without a biological pump would result in atmospheric carbon dioxide levels about 400 ppm higher than the present day. Overview The element carbon plays a central role in climate and life on Earth. It is capable of moving among and between the geosphere, cryosphere, atmosphere, biosphere and hydrosphere. This flow of carbon is referred to as the Earth's carbon cycle. It is also intimately linked to the cycling of other elements and compounds. The ocean plays a fundamental role in Earth's carbon cycle, helping to regulate atmospheric CO2 concentration. The biological pump is a set of processes that transfer organic carbon from the surface to the deep ocean, and is at the heart of the ocean carbon cycle. The biological pump depends on the fraction of primary produced organic matter that survives degradation in the euphotic zone and that is exported from surface water to the ocean interior, where it is mineralized to inorganic carbon, with the result that carbon is transported against the gradient of dissolved inorganic carbon (DIC) from the surface to the deep ocean. This transfer occurs through physical mixing and transport of dissolved and particulate organic carbon (POC), vertical migrations of organisms (zooplankton, fish) and through gravitational settling of particulate organic carbon. The biological pump can be divided into three distinct phases, the first of which is the production of fixed carbon by planktonic phototrophs in the euphotic (sunlit) surface region of the ocean. In these surface waters, phytoplankton use carbon dioxide (CO2), nitrogen (N), phosphorus (P), and other trace elements (barium, iron, zinc, etc.) during photosynthesis to make carbohydrates, lipids, and proteins. Some plankton, (e.g. coccolithophores
Biological pump
37689509
The neuroscience of rhythm refers to the various forms of rhythm generated by the central nervous system (CNS). Nerve cells, also known as neurons in the human brain are capable of firing in specific patterns which cause oscillations. The brain possesses many different types of oscillators with different periods. Oscillators are simultaneously outputting frequencies from .02 Hz to 600 Hz. It is now well known that a computer is capable of running thousands of processes with just one high-frequency clock. Humans have many different clocks as a result of evolution. Prior organisms had no need for a fast-responding oscillator. This multi-clock system permits quick response to constantly changing sensory input while still maintaining the autonomic processes that sustain life. This method modulates and controls a great deal of bodily functions. Autonomic rhythms The autonomic nervous system is responsible for many of the regulatory processes that sustain human life. Autonomic regulation is involuntary, meaning we do not have to think about it for it to take place. A great deal of these are dependent upon a certain rhythm, such as sleep, heart rate, and breathing. Circadian rhythms Circadian literally translates to "about a day" in Latin. This refers to the human 24-hour cycle of sleep and wakefulness. This cycle is driven by light. The human body must photoentrain or synchronize itself with light in order to make this happen. The rod cells are the photoreceptor cells in the retina capable of sensing light. However, they are not what sets the biological clock. The photosensitive retinal ganglion cells contain a pigment called melanopsin. This photopigment is depolarized in the presence of light, unlike the rods which are hyperpolarized. Melanopsin encodes the day-night cycle to the suprachiasmatic nucleus (SCN) via the retinohypothalamic tract. The SCN evokes a response from the spinal cord. Preganglionic neurons in the spinal cord modulate the superior cervical ganglia, which synapses on the pineal gland. The pineal gland synthesizes the neurohormone melatonin from tryptophan. Melatonin is secreted into the bloodstream where it affects neural activity by interacting with melatonin receptors on the SCN. The SCN is then able to influence the sleep wake cycle, acting as the "apex of a hierarchy" that governs physiological timing functions. "Rest and sleep are the best example of self-organized operations within neuronal circuits". Sleep and memory have been closely correlated for over a century. It seemed logical that the rehearsal of learned information during the day, such as in dreams, could be responsible for this consolidation. REM sleep was first studied in 1953. It was thought to be the sole contributor to memory due to its association with dreams. It has recently been suggested that if sleep and waking experience are found to be using the same neuronal content, it is reasonable to say that all sleep has a role in memory consolidation. This is supported by the rhythmic behavior of the brain. Harmonic oscillators have the capability to reproduce a perturbation that happened in previous cycles. It follows that when the brain
Neuroscience of rhythm
398638
A biogeochemical cycle, or more generally a cycle of matter, is the movement and transformation of chemical elements and compounds between living organisms, the atmosphere, and the Earth's crust. Major biogeochemical cycles include the carbon cycle, the nitrogen cycle and the water cycle. In each cycle, the chemical element or molecule is transformed and cycled by living organisms and through various geological forms and reservoirs, including the atmosphere, the soil and the oceans. It can be thought of as the pathway by which a chemical substance cycles (is turned over or moves through) the biotic compartment and the abiotic compartments of Earth. The biotic compartment is the biosphere and the abiotic compartments are the atmosphere, lithosphere and hydrosphere. For example, in the carbon cycle, atmospheric carbon dioxide is absorbed by plants through photosynthesis, which converts it into organic compounds that are used by organisms for energy and growth. Carbon is then released back into the atmosphere through respiration and decomposition. Additionally, carbon is stored in fossil fuels and is released into the atmosphere through human activities such as burning fossil fuels. In the nitrogen cycle, atmospheric nitrogen gas is converted by plants into usable forms such as ammonia and nitrates through the process of nitrogen fixation. These compounds can be used by other organisms, and nitrogen is returned to the atmosphere through denitrification and other processes. In the water cycle, the universal solvent water evaporates from land and oceans to form clouds in the atmosphere, and then precipitates back to different parts of the planet. Precipitation can seep into the ground and become part of groundwater systems used by plants and other organisms, or can runoff the surface to form lakes and rivers. Subterranean water can then seep into the ocean along with river discharges, rich with dissolved and particulate organic matter and other nutrients. There are biogeochemical cycles for many other elements, such as for oxygen, hydrogen, phosphorus, calcium, iron, sulfur, mercury and selenium. There are also cycles for molecules, such as water and silica. In addition there are macroscopic cycles such as the rock cycle, and human-induced cycles for synthetic compounds such as for polychlorinated biphenyls (PCBs). In some cycles there are geological reservoirs where substances can remain or be sequestered for long periods of time. Biogeochemical cycles involve the interaction of biological, geological, and chemical processes. Biological processes include the influence of microorganisms, which are critical drivers of biogeochemical cycling. Microorganisms have the ability to carry out wide ranges of metabolic processes essential for the cycling of nutrients and chemicals throughout global ecosystems. Without microorganisms many of these processes would not occur, with significant impact on the functioning of land and ocean ecosystems and the planet's biogeochemical cycles as a whole. Changes to cycles can impact human health. The cycles are interconnected and play important roles regulating climate, supporting the growth of plants, phytoplankton and other organisms, and maintaining the health of ecosystems generally. Human activities such as burning fossil fuels and using large amounts of fertilizer
Biogeochemical cycle
7001234
Sediment traps are instruments used in oceanography and limnology to measure the quantity of sinking particulate organic (and inorganic) material in aquatic systems, usually oceans, lakes, or reservoirs. This flux of material is the product of biological and ecological processes typically within the surface euphotic zone, and is of interest to scientists studying the role of the biological pump in the carbon cycle. Sediments traps normally consist of an upward-facing funnel that directs sinking particulate matter (e.g. marine snow) towards a mechanism for collection and preservation. Typically, traps operate over an extended period of time (weeks to months) and their collection mechanisms may consist of a series of sampling vessels that are cycled through to allow the trap to record the changes in sinking flux with time (for instance, across a seasonal cycle). Preservation of collected material is necessary because of these long deployments, and prevents sample decomposition and its consumption by zooplankton "swimmers". Traps are often moored at a specific depth in the water column (usually below the euphotic zone or mixed layer) in a particular location, but some are so-called Lagrangian traps that drift with the surrounding ocean currents (though they may remain at a fixed depth). These latter traps travel with the biological systems that they study, while moored traps are subject to variability introduced by different systems (or states of systems) "passing by". However, because of their fixed location moored traps are straightforward to recover for analysis of their measurements. Lagrangian traps must surface at a pre-determined time, and report their position (usually via satellite) in order to be recovered. See also Biological pump f-ratio Marine snow Mooring (oceanography) Primary production References Oceanographic instrumentation Limnology
Sediment trap
44419868
In cell biology, single-cell variability occurs when individual cells in an otherwise similar population differ in shape, size, position in the cell cycle, or molecular-level characteristics. Such differences can be detected using modern single-cell analysis techniques. Investigation of variability within a population of cells contributes to understanding of developmental and pathological processes, Single-cell analysis A sample of cells may appear similar, but the cells can vary in their individual characteristics, such as shape and size, mRNA expression levels, genome, or individual counts of metabolites. In the past, the only methods available for investigating such properties required a population of cells and provided an estimate of the characteristic of interest, averaged over the population, which could obscure important differences among the cells. Single-cell analysis allows scientists to study the properties of a single cell of interest with high accuracy, revealing individual differences among populations and offering new insights in molecular biology. These individual differences are important in fields such as developmental biology, where individual cells can take on different "fates" - become specialized cells such as neurons or organ tissue - during the growth of an embryo; in cancer research, where individual malignant cells can vary in their response to therapy; or in infectious disease, where only a subset of cells in a population become infected by a pathogen. Population-level views of cells can offer a distorted view of the data by averaging out the properties of distinct subsets of cells. For example, if half the cells of a particular group are expressing high levels of a given gene, and the rest are expressing low levels, results from a population-wide analysis may appear as if all cells are expressing a medium level of the given gene. Thus, single-cell analysis allows researchers to study biological processes in finer detail and answer questions that could not have been addressed otherwise. Types of variation Variation in gene expression Cells with identical genomes may vary in the expression of their genes due to differences in their specialized function in the body, their timepoint in the cell cycle, their environment, and also noise and stochastic factors. Thus, accurate measurement of gene expression in individual cells allows researchers to better understand these critical aspects of cellular biology. For example, early study of gene expression in individual cells in fruit fly embryos allowed scientists to discover regularized patterns or gradients of specific gene transcription during different stages of growth, allowing for a more detailed understanding of development at the level of location and time. Another phenomenon in gene expression which could only be identified at the single cell level is oscillatory gene expression, in which a gene is expressed on and off periodically. Single-cell gene expression is typically assayed using RNA-seq. After the cell has been isolated, the RNA-seq protocol typically consists of three steps: the RNA is reverse transcribed into cDNA, the cDNA is amplified to make more material available for the sequencer, and the cDNA is sequenced. Variation in DNA sequence A population of single celled
Single-cell variability
7556348
Phytomorphology is the study of the physical form and external structure of plants. This is usually considered distinct from plant anatomy, which is the study of the internal structure of plants, especially at the microscopic level. Plant morphology is useful in the visual identification of plants. Recent studies in molecular biology started to investigate the molecular processes involved in determining the conservation and diversification of plant morphologies. In these studies transcriptome conservation patterns were found to mark crucial ontogenetic transitions during the plant life cycle which may result in evolutionary constraints limiting diversification. Scope Plant morphology "represents a study of the development, form, and structure of plants, and, by implication, an attempt to interpret these on the basis of similarity of plan and origin". There are four major areas of investigation in plant morphology, and each overlaps with another field of the biological sciences. First of all, morphology is comparative, meaning that the morphologist examines structures in many different plants of the same or different species, then draws comparisons and formulates ideas about similarities. When structures in different species are believed to exist and develop as a result of common, inherited genetic pathways, those structures are termed homologous. For example, the leaves of pine, oak, and cabbage all look very different, but share certain basic structures and arrangement of parts. The homology of leaves is an easy conclusion to make. The plant morphologist goes further, and discovers that the spines of cactus also share the same basic structure and development as leaves in other plants, and therefore cactus spines are homologous to leaves as well. This aspect of plant morphology overlaps with the study of plant evolution and paleobotany. Secondly, plant morphology observes both the vegetative (somatic) structures of plants, as well as the reproductive structures. The vegetative structures of vascular plants includes the study of the shoot system, composed of stems and leaves, as well as the root system. The reproductive structures are more varied, and are usually specific to a particular group of plants, such as flowers and seeds, fern sori, and moss capsules. The detailed study of reproductive structures in plants led to the discovery of the alternation of generations found in all plants and most algae. This area of plant morphology overlaps with the study of biodiversity and plant systematics. Thirdly, plant morphology studies plant structure at a range of scales. At the smallest scales are ultrastructure, the general structural features of cells visible only with the aid of an electron microscope, and cytology, the study of cells using optical microscopy. At this scale, plant morphology overlaps with plant anatomy as a field of study. At the largest scale is the study of plant growth habit, the overall architecture of a plant. The pattern of branching in a tree will vary from species to species, as will the appearance of a plant as a tree, herb, or grass. Fourthly, plant morphology examines the pattern of development, the process by which structures originate and mature as a
Plant morphology
4493
Biology – The natural science that studies life. Areas of focus include structure, function, growth, origin, evolution, distribution, and taxonomy. History of biology History of anatomy History of biochemistry History of biotechnology History of ecology History of genetics History of evolutionary thought: The eclipse of Darwinism – Catastrophism – Lamarckism – Orthogenesis – Mutationism – Structuralism – Vitalism Modern (evolutionary) synthesis History of molecular evolution History of speciation History of medicine History of model organisms History of molecular biology Natural history History of plant systematics Overview Biology Science Life Properties: Adaptation – Energy processing – Growth – Order – Regulation – Reproduction – Response to environment Biological organization: atom – molecule – cell – tissue – organ – organ system – organism – population – community – ecosystem – biosphere Approach: Reductionism – emergent property – mechanistic Biology as a science: Natural science Scientific method: observation – research question – hypothesis – testability – prediction – experiment – data – statistics Scientific theory – scientific law Research method List of research methods in biology Scientific literature List of biology journals: peer review Chemical basis Outline of biochemistry Atoms and molecules matter – element – atom – proton – neutron – electron– Bohr model – isotope – chemical bond – ionic bond – ions – covalent bond – hydrogen bond – molecule Water: properties of water – solvent – cohesion – surface tension – Adhesion – pH Organic compounds: carbon – carbon-carbon bonds – hydrocarbon – monosaccharide – amino acids – nucleotide – functional group – monomer – adenosine triphosphate (ATP) – lipids – oil – sugar – vitamins – neurotransmitter – wax Macromolecules: polysaccharide: cellulose – carbohydrate – chitin – glycogen – starch proteins: primary structure – secondary structure – tertiary structure – conformation – native state – protein folding – enzyme – receptor – transmembrane receptor – ion channel – membrane transporter – collagen – pigments: chlorophyll – carotenoid – xanthophyll – melanin – prion lipids: cell membrane – fats – phospholipids nucleic acids: DNA – RNA Cells Outline of cell biology Cell structure: Cell coined by Robert Hooke Techniques: cell culture – microscope – light microscope – electron microscopy – SEM – TEM Organelles: Cytoplasm – Vacuole – Peroxisome – Plastid Cell nucleus Nucleoplasm – Nucleolus – Chromatin – Chromosome Endomembrane system Nuclear envelope – Endoplasmic reticulum – Golgi apparatus – Vesicles – Lysosome Energy creators: Mitochondrion and Chloroplast Biological membranes: Plasma membrane – Mitochondrial membrane – Chloroplast membrane Other subcellular features: Cell wall – pseudopod – cytoskeleton – mitotic spindle – flagellum – cilium Cell transport: Diffusion – Osmosis – isotonic – active transport – phagocytosis Cellular reproduction: cytokinesis – centromere – meiosis Nuclear reproduction: mitosis – interphase – prophase – metaphase – anaphase – telophase programmed cell death – apoptosis – cell senescence Metabolism: enzyme - activation energy - proteolysis – cooperativity Cellular respiration Glycolysis – Pyruvate dehydrogenase complex – Citric acid cycle – electron transport chain – fermentation Photosynthesis light-dependent reactions – Calvin cycle Cell
Outline of biology
22241441
The selenium cycle is a biological cycle of selenium similar to the cycles of carbon, nitrogen, and sulfur. Within the cycle, there are organisms which reduce the most oxidized form of the element and different organisms complete the cycle by oxidizing the reduced element to the initial state. In the selenium cycle it has been found that bacteria, fungi, and plants, especially species of Astragalus, metabolize the most oxidized forms of selenium, selenate or selenite, to selenide. It is also thought that microorganisms may be able to oxidize selenium of valence zero to selenium of valence +6. Evidence for a selenium cycle is found through the study of selenium accumulator plants. These plants are found in semi-arid, seleniferous soils. The plants biosynthesize forms of organic selenium compounds and release the compounds into the soil when they decay. If the compounds were not oxidized, then an increase in organic selenium would be seen, but selenium in these areas is mainly inorganic. Aquatic ecosystems There are three fates of dissolved selenium in an aquatic ecosystem: 1. it can be absorbed or ingested by organisms; 2. it can bind with suspended solids or sediments; or 3. it can remain in free solution. Over time, most of the selenium is taken in by organisms or bound to other solids. As the suspended material settles, the selenium accumulates in the top layer of sediment. Due to the dynamic flow in an aquatic ecosystem, selenium is usually only in the sediments temporarily before being cycled back into the system. Immobilization processes Selenium can be removed from the ecosystem and bound in sediment through natural processes of chemical and microbial reduction of the selenate form to the selenite form. The reduction is followed by adsorption to clay, reaction with iron species, and coprecipitation or settling. After selenium is in the sediment, other chemical and microbial reduction may occur, causing insoluble organic, mineral, elemental, or adsorbed selenium. Some organic forms may be released into the atmosphere from volatilization by chemical or microbial activity in the water and sediment or by direct release from plants. Immobilization processes effectively remove selenium from the ecosystem, especially in slow-moving or still-water areas. Mobilization processes Selenium is made available to the food chain through four oxidation and methylation processes. The first process is oxidation and methylation of inorganic and organic selenium by plant roots and microorganisms. The second process is biological mixing and associated oxidation of sediments from the burrowing of benthic invertebrates and feeding of fish and wildlife. The third process is represented by physical movement and chemical oxidation from water circulation and mixing, such as current, wind, precipitation, and upwelling. The fourth process is from oxidation by plant photosynthesis. References Biogeochemical cycle Selenium
Selenium cycle
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Photosynthesis converts carbon dioxide to carbohydrates via several metabolic pathways that provide energy to an organism and preferentially react with certain stable isotopes of carbon. The selective enrichment of one stable isotope over another creates distinct isotopic fractionations that can be measured and correlated among oxygenic phototrophs. The degree of carbon isotope fractionation is influenced by several factors, including the metabolism, anatomy, growth rate, and environmental conditions of the organism. Understanding these variations in carbon fractionation across species is useful for biogeochemical studies, including the reconstruction of paleoecology, plant evolution, and the characterization of food chains. Oxygenic photosynthesis is a metabolic pathway facilitated by autotrophs, including plants, algae, and cyanobacteria. This pathway converts inorganic carbon dioxide from the atmosphere or aquatic environment into carbohydrates, using water and energy from light, then releases molecular oxygen as a product. Organic carbon contains less of the stable isotope Carbon-13, or 13C, relative to the initial inorganic carbon from the atmosphere or water because photosynthetic carbon fixation involves several fractionating reactions with kinetic isotope effects. These reactions undergo a kinetic isotope effect because they are limited by overcoming an activation energy barrier. The lighter isotope has a higher energy state in the quantum well of a chemical bond, allowing it to be preferentially formed into products. Different organisms fix carbon through different mechanisms, which are reflected in the varying isotope compositions across photosynthetic pathways (see table below, and explanation of notation in "Carbon Isotope Measurement" section). The following sections will outline the different oxygenic photosynthetic pathways and what contributes to their associated delta values. Carbon isotope measurement Carbon on Earth naturally occurs in two stable isotopes, with 98.9% in the form of 12C and 1.1% in 13C. The ratio between these isotopes varies in biological organisms due to metabolic processes that selectively use one carbon isotope over the other, or "fractionate" carbon through kinetic or thermodynamic effects. Oxygenic photosynthesis takes place in plants and microorganisms through different chemical pathways, so various forms of organic material reflect different ratios of 13C isotopes. Understanding these variations in carbon fractionation across species is applied in isotope geochemistry and ecological isotope studies to understand biochemical processes, establish food chains, or model the carbon cycle through geological time. Carbon isotope fractionations are expressed in using delta notation of δ13C ("delta thirteen C"), which is reported in parts per thousand (per mille, ‰). δ13C is defined in relation to the Vienna Pee Dee Belemnite (VPDB, 13C/12C = 0.01118) as an established reference standard. This is called a "delta value" and can be calculated from the formula below: Photosynthesis reactions The chemical pathway of oxygenic photosynthesis fixes carbon in two stages: the light-dependent reactions and the light-independent reactions. The light-dependent reactions capture light energy to transfer electrons from water and convert NADP+, ADP, and inorganic phosphate into the energy-storage molecules NADPH and ATP. The overall equation for the light-dependent reactions is generally:2 H2O + 2 NADP+ + 3 ADP + 3 Pi + light → 2 NADPH + 2 H+ +
Fractionation of carbon isotopes in oxygenic photosynthesis
71508082
The Coppermills Water Treatment Works is a large water treatment works in the Lea Valley in east London. Completed in 1969 by the Metropolitan Water Board, it is now owned and operated by Thames Water. In 2009, Coppermills was connected to the Thames Water Ring Main via the Northern Extension Tunnel, enabling the facility to be a major supplier of water to the whole London area. It is capable of supplying a maximum of of water per day. Water source The facility draws water from the Lee Valley Reservoir Chain located directly to the north, which sources its water from the River Lea, the New River, and the River Thames (via the Thames-Lee Water Main). Water flows to Coppermills directly through channels from the East Warwick, Low Maynard, and Walthamstow No. 5 reservoirs. It is also supplied via the Coppermill Stream and the ‘Spine Tunnel’ which is fed from the Lockwood, King George V, William Girling and Banbury reservoirs further north. Operations The first water treatment process at Coppermills works is rapid gravity filtration. There are 24 rectangular open topped tanks containing sand. Water enters the top of the tanks and flows down through the sand layer under gravity. The water residence time in the filters is about 15 minutes. The filters remove particulates and the cleaned water flows from the bottom of the filters. Periodically, every 6 to 24 hours each filter is shut in and clean water is pumped up through the bed together with compressed air to scour the sand and remove material caught during the filtration phase. When the backwashing process is complete the filter is bought back into service. Ozone gas is then added to the water to oxidise contaminants such as pesticides and organic material. The process of ozonization also kills bacteria. Water then flows to the next stage Slow Sand Filtration. There are 33 slow sand filter beds at Coppermills water treatment works, which occupy much of the site. The sand bed in the filters support a gelatinous biofilm or hypogeal layer in the top few millimetres of the sand. The surface biofilm provides an effective biological treatment. Water passes through the hypogeal layer where contaminants are retained and metabolised by the bacteria, fungi and protozoa. Over several weeks the biofilm becomes thicker and the flow of water reduces. The filter bed is drained and the biofilm layer is scraped off and replaced with fresh sand. The water then passes through fine 400-micron (400 μm) stainless steel mesh screens. The water is then dosed with chlorine in contact tanks which contain baffles to ensure that chlorine is completely mixed with the water. Chlorine destroys harmful micro-organisms. The water is pumped into the distribution system supplying customers directly or through covered service reservoirs. Problems occur at treatment works during periods of algal bloom in the reservoirs, which reduce the cycle time of the rapid gravity filters. At Coppermills works this reduces the capacity of the plant from its normal throughput of 560 million litres
Coppermills Water Treatment Works
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Transportation in San Diego consists of a variety of air, road, sea, and public transportation options. Public transportation San Diego is served by the San Diego Trolley, bus (operated by the San Diego Metropolitan Transit System), COASTER, and Amtrak. The trolley primarily serves downtown and surrounding urban communities, Mission Valley, east county, the coastal south bay, and the international border. A planned Mid-Coast line will operate from Old Town to University City along the Interstate 5 Freeway. There are also plans for a Silver Line to expand trolley service downtown. The Amtrak and COASTER trains currently run along the coastline and connect San Diego with Los Angeles, Orange County, San Bernardino, Riverside, and Ventura via Metrolink. There are two Amtrak stations in San Diego, in Old Town and Downtown. The bus is available along almost all major routes; however, a large number of bus stops are concentrated in central San Diego. Typical wait times vary from 15 to 60 minutes, depending on the location and route . Trolleys arrive at each station every 7 to 30 minutes (depending on time of day and which trolley line is used). Ferries are also available every half hour crossing San Diego Bay to Coronado. Public transportation statistics The average amount of time people spend commuting with public transit in San Diego, CA, for example to and from work, on a weekday is 70 min. 23% of public transit riders, ride for more than 2 hours every day. The average amount of time people wait at a stop or station for public transit is 16 min, while 29% of riders wait for over 20 minutes on average every day. The average distance people usually ride in a single trip with public transit is 11.2 km, while 30% travel for over 12 km in a single direction. Cycling The dry and mild climate of San Diego makes cycling a convenient and pleasant year-round option. The city has some segregated cycle facilities, particularly in newer developments, however the majority of road facilities specifically for bicycles are painted on regular roadways, covering over 1,570 miles throughout San Diego County. The city's hilly, canyoned terrain and long average trip distances—brought about by strict low-density zoning laws—somewhat restrict cycling for utilitarian purposes. In 2014 of .9% of commuters traveled by bicycle, below the average 1% for large U.S. cities. Also in 2014, San Diego experienced 6.8 bicyclist fatalities per 10,000 cyclist commuters, the average for all large cities was 4.7. A bicycle sharing system called Decobike was instituted in 2015. Air San Diego has two major international airports entirely or extending into its city limits: San Diego International Airport, also known as Lindbergh Field, is the primary commercial airport serving San Diego. It is the busiest single-runway airport in the world. It serves over 24 million passengers every year, and is located on San Diego Bay three miles (4.8 km) from downtown. There are scheduled flights to the rest of the United States, Canada, Japan, Mexico, United Kingdom, Germany,
Transportation in San Diego
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In biology, taxonomy () is the scientific study of naming, defining (circumscribing) and classifying groups of biological organisms based on shared characteristics. Organisms are grouped into taxa (singular: taxon) and these groups are given a taxonomic rank; groups of a given rank can be aggregated to form a more inclusive group of higher rank, thus creating a taxonomic hierarchy. The principal ranks in modern use are domain, kingdom, phylum (division is sometimes used in botany in place of phylum), class, order, family, genus, and species. The Swedish botanist Carl Linnaeus is regarded as the founder of the current system of taxonomy, as he developed a ranked system known as Linnaean taxonomy for categorizing organisms and binomial nomenclature for naming organisms. With advances in the theory, data and analytical technology of biological systematics, the Linnaean system has transformed into a system of modern biological classification intended to reflect the evolutionary relationships among organisms, both living and extinct. Definition The exact definition of taxonomy varies from source to source, but the core of the discipline remains: the conception, naming, and classification of groups of organisms. As points of reference, recent definitions of taxonomy are presented below: Theory and practice of grouping individuals into species, arranging species into larger groups, and giving those groups names, thus producing a classification. A field of science (and a major component of systematics) that encompasses description, identification, nomenclature, and classification The science of classification, in biology the arrangement of organisms into a classification "The science of classification as applied to living organisms, including the study of means of formation of species, etc." "The analysis of an organism's characteristics for the purpose of classification" "Systematics studies phylogeny to provide a pattern that can be translated into the classification and names of the more inclusive field of taxonomy" (listed as a desirable but unusual definition) The varied definitions either place taxonomy as a sub-area of systematics (definition 2), invert that relationship (definition 6), or appear to consider the two terms synonymous. There is some disagreement as to whether biological nomenclature is considered a part of taxonomy (definitions 1 and 2), or a part of systematics outside taxonomy. For example, definition 6 is paired with the following definition of systematics that places nomenclature outside taxonomy: Systematics: "The study of the identification, taxonomy, and nomenclature of organisms, including the classification of living things with regard to their natural relationships and the study of variation and the evolution of taxa". In 1970, Michener et al. defined "systematic biology" and "taxonomy" (terms that are often confused and used interchangeably) in relation to one another as follows: Systematic biology (hereafter called simply systematics) is the field that (a) provides scientific names for organisms, (b) describes them, (c) preserves collections of them, (d) provides classifications for the organisms, keys for their identification, and data on their distributions, (e) investigates their evolutionary histories, and (f) considers their environmental adaptations. This is a field with a long history that in recent years has experienced a notable renaissance,
Taxonomy (biology)
21051206
The carbonate–silicate geochemical cycle, also known as the inorganic carbon cycle, describes the long-term transformation of silicate rocks to carbonate rocks by weathering and sedimentation, and the transformation of carbonate rocks back into silicate rocks by metamorphism and volcanism. Carbon dioxide is removed from the atmosphere during burial of weathered minerals and returned to the atmosphere through volcanism. On million-year time scales, the carbonate-silicate cycle is a key factor in controlling Earth's climate because it regulates carbon dioxide levels and therefore global temperature. The rate of weathering is sensitive to factors that change how much land is exposed. These factors include sea level, topography, lithology, and vegetation changes. Furthermore, these geomorphic and chemical changes have worked in tandem with solar forcing, whether due to orbital changes or stellar evolution, to determine the global surface temperature. Additionally, the carbonate-silicate cycle has been considered a possible solution to the faint young Sun paradox. Overview of the cycle The carbonate-silicate cycle is the primary control on carbon dioxide levels over long timescales. It can be seen as a branch of the carbon cycle, which also includes the organic carbon cycle, in which biological processes convert carbon dioxide and water into organic matter and oxygen via photosynthesis. Physical and chemical processes The inorganic cycle begins with the production of carbonic acid (H2CO3) from rainwater and gaseous carbon dioxide. Due to this process, normal rain has a pH of around 5.6. Carbonic acid is a weak acid, but over long timescales, it can dissolve silicate rocks (as well as carbonate rocks). Most of the Earth's crust (and mantle) is composed of silicates. These substances break down into dissolved ions as a result. For example, calcium silicate (CaSiO3), or wollastonite, reacts with carbon dioxide and water to yield a calcium ion, Ca2+, a bicarbonate ion, HCO3−, and dissolved silica. This reaction structure is representative of general silicate weathering of calcium silicate minerals. The chemical pathway is as follows: 2CO2 + H2O + CaSiO3 -> Ca^2+ + 2HCO3- + SiO2 River runoff carries these products to the ocean, where marine calcifying organisms use Ca2+ and HCO3− to build their shells and skeletons, a process called carbonate precipitation: Ca^2+ + 2HCO3- -> CaCO3 + CO2 + H2O Two molecules of CO2 are required for silicate rock weathering; marine calcification releases one molecule back to the atmosphere. The calcium carbonate (CaCO3) contained in shells and skeletons sinks after the marine organism dies and is deposited on the ocean floor. The final stage of the process involves the movement of the seafloor. At subduction zones, the carbonate sediments are buried and forced back into the mantle. Some carbonate may be carried deep into the mantle where high pressure and temperature conditions allow it to combine metamorphically with SiO2 to form CaSiO3 and CO2, which is released from the interior into the atmosphere via volcanism, thermal vents in the ocean, or soda springs, which are natural springs that contain carbon dioxide gas or soda water: CaCO3 + SiO2 -> CaSiO3 +
Carbonate–silicate cycle
33826069
Viral neuronal tracing is the use of a virus to trace neural pathways, providing a self-replicating tracer. Viruses have the advantage of self-replication over molecular tracers but can also spread too quickly and cause degradation of neural tissue. Viruses that can infect the nervous system, called neurotropic viruses, spread through spatially close assemblies of neurons through synapses, allowing for their use in studying functionally connected neural networks. The use of viruses to label functionally connected neurons stems from the work and bioassay developed by Albert Sabin. Subsequent research allowed for the incorporation of immunohistochemical techniques to systematically label neuronal connections. To date, viruses have been used to study multiple circuits in the nervous system. Neuronal Cartography The individual connections of neurons have long evaded neuroanatomists. Neuronal tracing methods offer an unprecedented view into the morphology and connectivity of neural networks. Depending on the tracer used, this can be limited to a single neuron or can progress trans-synoptically to adjacent neurons. After the tracer has spread sufficiently, the extent may be measured either by fluorescence (for dyes) or by immunohistochemistry (for biological tracers). An important innovation in this field is the use of neurotropic viruses as tracers. These not only spread throughout the initial site of infection but can jump across synapses. Virus life cycle The life cycle of viruses, such as those used in neuronal tracing, is different from cellular organisms. Viruses are parasitic in nature and cannot proliferate on their own. Therefore, they must infect another organism and effectively hijack cellular machinery to complete their life cycle. The first stage of the viral life cycle is called viral entry. This defines the manner in which a virus infects a new host cell. In nature, neurotropic viruses are usually transmitted through bites or scratches, as in the case of the rabies virus or certain strains of herpes viruses. In tracing studies, this step occurs artificially, typically through the use of a syringe. The next stage of the viral life cycle is called viral replication. During this stage, the virus takes over the host cell's machinery to cause the cell to create more viral proteins and assemble more viruses. Once the cell has produced a sufficient number of viruses, the virus enters the viral shedding stage. During this stage, viruses leave the original host cell in search of a new host. In the case of neurotropic viruses, this transmission typically occurs at the synapse. Viruses can jump across a relatively short space from one neuron to the next. This trait is what makes viruses so useful in tracer studies. Once the virus enters the next cell, the cycle begins anew. The original host cell begins to degrade after the shedding stage. In tracer studies, this is the reason the timing must be tightly controlled. If the virus is allowed to spread too far, the original microcircuitry of interest is degraded, and no useful information can be retrieved. Typically, viruses can infect only a small number of organisms, and even then, only
Viral neuronal tracing
1586039
Menstrual synchrony, also called the McClintock effect, or the Wellesley effect, is a contested process whereby women who begin living together in close proximity would experience their menstrual cycle onsets (the onset of menstruation or menses) becoming more synchronized together in time than when previously living apart. "For example, the distribution of onsets of seven female lifeguards was scattered at the beginning of the summer, but after 3 months spent together, the onset of all seven cycles fell within a 4-day period." Martha McClintock's 1971 paper, published in Nature, says that menstrual cycle synchronization happens when the menstrual cycle onsets of two or more women become closer together in time than they were several months earlier. After the initial studies, several papers were published reporting methodological flaws in studies reporting menstrual synchrony including McClintock's study. In addition, other studies were published that failed to find synchrony. The proposed mechanisms have also received scientific criticism. Reviews in 2006 and 2013 concluded that menstrual synchrony likely does not exist. Overview Original study by Martha McClintock Martha McClintock published the first study on menstrual synchrony among women living together in dormitories at Wellesley College, a women's liberal arts college in Massachusetts, US. Proposed causes McClintock hypothesized that pheromones could cause menstrual cycle synchronization. However, other mechanisms have been proposed, most prominently synchronization with lunar phases. Efforts to replicate McClintock's results No scientific evidence supports the lunar hypothesis, and doubt has been cast on pheromone mechanisms. After the initial studies reporting menstrual synchrony began to appear in the scientific literature, other researchers began reporting the failure to find menstrual synchrony. These studies were followed by critiques of the methods used in early studies, which argued that biases in the methods used produced menstrual synchrony as an artifact. More recent studies, which took into account some of these methodological criticisms, failed to find menstrual synchrony. Terminology The term synchrony has been argued to be misleading because no study has ever found that menstrual cycles become strictly concordant, nevertheless menstrual synchrony is used to refer the phenomenon of menstrual cycle onsets becoming closer to each other over time. Status of the hypothesis In a 2013 systematic review of menstrual synchrony, Harris and Vitzthum concluded, "In light of the lack of empirical evidence for MS [menstrual synchrony] sensu stricto, it seems there should be more widespread doubt than acceptance of this hypothesis" (pp. 238–239). The experience of synchrony may be the result of the mathematical fact that menstrual cycles of different frequencies repeatedly converge and diverge over time and not due to a process of synchronization, and the probability of encountering such overlaps by chance is high. Evolutionary perspective Researchers are divided on whether menstrual synchrony would be adaptive. McClintock has suggested that menstrual synchrony may not be adaptive but rather epiphenomenonal, lacking any biological function. Among those who postulate an adaptive function, one argument is that menstrual synchrony is only a particular aspect of the much more general phenomenon of reproductive synchrony, an occurrence familiar to
Menstrual synchrony
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Gastrointestinal physiology is the branch of human physiology that addresses the physical function of the gastrointestinal (GI) tract. The function of the GI tract is to process ingested food by mechanical and chemical means, extract nutrients and excrete waste products. The GI tract is composed of the alimentary canal, that runs from the mouth to the anus, as well as the associated glands, chemicals, hormones, and enzymes that assist in digestion. The major processes that occur in the GI tract are: motility, secretion, regulation, digestion and circulation. The proper function and coordination of these processes are vital for maintaining good health by providing for the effective digestion and uptake of nutrients. Motility The gastrointestinal tract generates motility using smooth muscle subunits linked by gap junctions. These subunits fire spontaneously in either a tonic or a phasic fashion. Tonic contractions are those contractions that are maintained from several minutes up to hours at a time. These occur in the sphincters of the tract, as well as in the anterior stomach. The other type of contractions, called phasic contractions, consist of brief periods of both relaxation and contraction, occurring in the posterior stomach and the small intestine, and are carried out by the muscularis externa. Motility may be overactive (hypermotility), leading to diarrhea or vomiting, or underactive (hypomotility), leading to constipation or vomiting; either may cause abdominal pain. Stimulation The stimulation for these contractions likely originates in modified smooth muscle cells called interstitial cells of Cajal. These cells cause spontaneous cycles of slow wave potentials that can cause action potentials in smooth muscle cells. They are associated with the contractile smooth muscle via gap junctions. These slow wave potentials must reach a threshold level for the action potential to occur, whereupon Ca2+ channels on the smooth muscle open and an action potential occurs. As the contraction is graded based upon how much Ca2+ enters the cell, the longer the duration of slow wave, the more action potentials occur. This, in turn, results in greater contraction force from the smooth muscle. Both amplitude and duration of the slow waves can be modified based upon the presence of neurotransmitters, hormones or other paracrine signaling. The number of slow wave potentials per minute varies based upon the location in the digestive tract. This number ranges from 3 waves/min in the stomach to 12 waves/min in the intestines. Contraction patterns The peristalsis and segmentation, detailed below and pendular movement are famous examples of distinct patterns of GI contraction. Occurring between meals, the migrating motor complex is a series of peristaltic wave cycles in distinct phases starting with relaxation, followed by an increasing level of activity to a peak level of peristaltic activity lasting for 5–15 minutes. This cycle repeats every 1.5–2 hours but is interrupted by food ingestion. The role of this process is likely to clean excess bacteria and food from the digestive system. Peristalsis Peristalsis is one of the patterns that occur during and shortly after a meal. The contractions occur in wave patterns
Gastrointestinal physiology
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Komagataella is a methylotrophic yeast within the order Saccharomycetales. It was found in the 1960s as Pichia pastoris, with its feature of using methanol as a source of carbon and energy. In 1995, P. pastoris was reassigned into the sole representative of genus Komagataella, becoming Komagataella phaffii. Later studies have further distinguished new species in this genus, resulting in a total of 7 recognized species. It is not uncommon to see the old name still in use in the context of protein production, as of 2023; in less formal use, the yeast may confusingly be referred to as pichia. After years of study, Komagataella is widely used in biochemical research and biotech industries. With strong potential for being an expression system for protein production, as well as being a model organism for genetic study, Komagataella phaffii has become important for biological research and biotech applications. Taxonomy According to GBIF: Komagataella kurtzmanii Komagataella mondaviorum Komagataella pastoris Komagataella phaffii – responsible for most, if not all, industrial & research use Komagataella populi Komagataella pseudopastoris Komagataella ulmi Komagataella in nature Natural habitat In nature, Komagataella is found on trees, such as chestnut trees. They are heterotrophs and they can use several carbon sources for living, like glucose, glycerol and methanol. However, they cannot use lactose. Reproduction Komagataella can undergo both asexual reproduction and sexual reproduction, by budding and ascospore. In this case, two types of cells of Komagataella exist: haploid and diploid cells. In the asexual life cycle, haploid cells undergo mitosis for reproduction. In the sexual life cycle, diploid cells undergo sporulation and meiosis. The growth rate of its colonies can vary by a large range, from near to 0 to a doubling time of one hour, which is suitable for industrial processes. Komagataella as a model organism In the last few years, Komagataella was investigated and identified as a good model organism with several advantages. First of all, Komagataella can be grown and used easily in lab. Like other widely used yeast models, it has relatively short life span and fast regeneration time. Moreover, some inexpensive culture media have been designed, so that Komagataella can grow quickly on them, with high cell density. Whole genome sequencing for Komagataella had been performed. The K. phaffii GS115 genome has been sequenced by the Flanders Institute for Biotechnology and Ghent University, and published in Nature Biotechnology. The genome sequence and gene annotation can be browsed through the ORCAE system. The complete genomic data allows scientists to identify homologous proteins and evolutionary relationships between other yeast species and Komagataella. In addition, all seven species were sequenced by 2022. Furthermore, Komagataella are single eukaryotic cells, which means researchers could investigate the proteins inside Komagataella. Then the homologous comparison to other more complicated eukaryotic species can be processed, to obtain their functions and origins. Another advantage of Komagataella is its similarity to the well-studied yeast model — Saccharomyces cerevisiae. As a model organism for biology, S. cerevisiae have been well studied for decades and used by researchers
Komagataella
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The following outline is provided as an overview of and topical guide to evolution: In biology, evolution is change in the heritable characteristics of biological organisms over generations due to natural selection, mutation, gene flow, and genetic drift. Also known as descent with modification. Over time these evolutionary processes lead to formation of new species (speciation), changes within lineages (anagenesis), and loss of species (extinction). "Evolution" is also another name for evolutionary biology, the subfield of biology concerned with studying evolutionary processes that produced the diversity of life on Earth. Fundamentals about evolution Introduction Basic principles Natural speciation Artificial speciation Subfields History By period or event By field Evolutionary theory and modelling See also Basic principles (above) Population genetics Process Variation Key concepts Effects of selection Related topics Evolutionary phenomena Modelling Taxonomy, systematics, and phylogeny Fundamentals Basic concepts of phylogenetics Inference methods Probabilistic methods Current topics Group Traits Group Types Evolution of biodiversity Origin and evolutionary history of life Evolution of organisms Evolution of tetrapods Evolution of other animals Evolution of plants Evolution of other taxa Evolution of cells, organs, and systems Evolution of molecules and genes Evolution of behaviour Evolution of other processes s Applications in other disciplines Evolutionary issues Controversy about evolution Religious and philosophical views of evolution Influence of evolutionary theory See also Applications in other disciplines Publications and organizations concerning evolution Books Evolution: The Modern Synthesis – book by Julian Huxley (grandson of Thomas Henry Huxley); one of the most important books of modern evolutionary synthesis, published in 1942 The Genetical Theory of Natural Selection – book by R.A. Fisher important in modern evolutionary synthesis, first published in 1930 Genetics and the Origin of Species – 1937 book by Ukrainian-American evolutionary biologist Theodosius Dobzhansky On the Origin of Species – seminal book by Charles Darwin concerning evolution by natural selection, first published in 1859 Systematics and the Origin of Species from the Viewpoint of a Zoologist – book by zoologist and evolutionary biologist Ernst Mayr, canonical publication of modern evolutionary synthesis, first published in 1942 by Columbia University Press The Structure of Evolutionary Theory – technical book on macroevolutionary theory by the Harvard paleontologist Stephen Jay Gould Journals Organizations Evolution scholars and researchers Prominent evolutionary biologists See also External links General information Human Timeline (Interactive) – Smithsonian, National Museum of Natural History (August 2016). Experiments concerning the process of biological evolution Algorithms, games, and evolution, Proceedings of the National Academy of Sciences of the USA Online lectures Evolution Evolution
Outline of evolution
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A river plume is a freshened water mass that is formed in the sea as a result of mixing of river discharge and saline seawater. River plumes are formed in coastal sea areas at many regions in the World. River plumes generally occupy wide-but-shallow sea surface layers bounded by sharp density gradients. The area of a river plume is 3-5 orders of magnitude greater than its depth; therefore, even small rivers with discharge rates ~1–10 m/s form river plumes with horizontal spatial extents ~10–100 m. Areas of river plumes formed by the largest rivers are ~100–1000 km2. Despite the relatively small volume of total freshwater runoff to the World Ocean, river plumes occupy up to 21% of shelf areas of the ocean, i.e., several million square kilometers. In some occasions river plumes are spoken of as regions of fresh water influence (ROFIs), although it is preferred to use this term for regions in which multiple sources add to the fresh water input of the zone or for shallow, frictional shelves. ROFIs and river plumes differ in the variation at temporal and spatial scales. The river plume can be identified as a buoyant water mass that emerges due to river discharge into the coastal ocean and varies over diurnal to synoptic timescales. At the edges of this water mass mixing takes place, creating a region adjacent to the river plume which is diluted and fresher compared to the open ocean, but does not have a clear boundary. This extended region is called the region of freshwater influence, ROFI. Due to the indirect influence of freshwater discharge, ROFIs incorporate the dynamics and spatial extent of the river plumes but are typically assessed on seasonal, annual, and decadal timescales. Processes River plumes play an important role in global and regional land-ocean interactions. River discharges provide large fluxes of buoyancy, heat, terrigenous sediments, nutrients, and anthropogenic pollutants to the ocean. River plumes strongly influence many physical, biological, and geochemical processes in the coastal and shelf sea areas including stratification of seawater, coastal currents, carbon and biogeochemical cycles, primary production, and seabed morphology. A river plume is a dynamical system influenced by processes with a wide range of temporal and spatial scales, which depend on the size and shape of the estuary as well as on the type and variation of the forcing from the estuary and the ocean. Feedback mechanisms between sediment deposited by the plume at the submarine delta and the geometry of the delta make for a complex system. Due to this complexity there is not (yet) a general, simple theory that offers quantitative predictability for the motion of particles and the structure of river plumes; however, some theories incorporating simplified assumptions have helped in understanding the important aspects of buoyancy-influenced coastal flows. As is commonly used in fluid dynamics, the description of these complex flows is aided by scaling analysis to determine the relevant processes. The primary parameters which define the structure and scale of an individual river plume are freshwater
River plume
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An actogram is a plot that shows rhythms in biological variables throughout the day. Traditionally, actograms describe phases of activity and rest, but they have also been used to visualize rhythms in protein phosphorylation, gene expression, and hormone secretion. Actograms are commonly used to study the underlying circadian rhythms of animals in fields such as ecology, reproductive biology, and sleep medicine. History One of the first examples of actograms being used in circadian biology was by Maynard Johnson. Johnson compared the daily rhythms of different species of mice. One of the benefits noted about the actogram as a representation of animal activity was that it was easy to see rhythms in activity. An early criticism of actograms was that the level of activity of the test subject could not be seen in an actogram. This was because the Esterline-Angus chart recorders that were used could not give a reliable measure of the amplitude of activity. In the 1960s, Colin Pittendrigh was one of the first biologists to use a double-plotted actogram. Pittendrigh used double-plotted actograms when exploring the "after-effects". The benefit to the double-plotted actogram was that Pittendrigh was able to notice rhythms that extended beyond 24 hours and the existence of two oscillators within organisms. Graph interpretation Actograms typically have a bar above the graph that indicates the lighting conditions that the subject was exposed to. Dark bars indicate periods of total darkness, and white bars indicate periods of light. On the graph itself, the x-axis indicates the time of day, typically in 24-hour cycles. The y-axis indicates the days of the experiment. The graph either plots periods of activity or of rest, as specified by the author. If periods of activity and rest align with the lighting conditions, then the subject is assumed to be entrained to those conditions. If there is a clear rhythm in activity that does not correspond to lighting conditions, or exists in constant darkness, the subject is said to be free-running. In free-running actograms, the period of activity is typically offset each day from the previous day, due to the fact that biological clocks rarely follow an exactly 24-hour cycle. If data points shift to the left, the subject is running on a cycle less than 24 hours. If they shift to the right, it is running on a greater than 24-hour cycle. If the graph shows arrhythmicity with no clear pattern, then the subject may not have a functioning internal biological clock or may have a disruption in the clock's output. Double-plotted actogram While actograms typically plot one 24-hour cycle at a time, double-plotted actograms plot two 24-hour cycles side by side. Double-plotted actograms are interpreted in the same way as single-plotted actograms. However, double-plotted graphs can make it easier to read and interpret data, especially from free-running organisms. Phase response curves derived from actograms A common way that actograms are utilized in chronobiology is by translating the actogram's data into phase response curves (PRCs). PRCs are a way of showing the
Actogram
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Morphogenesis (from the Greek morphê shape and genesis creation, literally "the generation of form") is the biological process that causes a cell, tissue or organism to develop its shape. It is one of three fundamental aspects of developmental biology along with the control of tissue growth and patterning of cellular differentiation. The process controls the organized spatial distribution of cells during the embryonic development of an organism. Morphogenesis can take place also in a mature organism, such as in the normal maintenance of tissue by stem cells or in regeneration of tissues after damage. Cancer is an example of highly abnormal and pathological tissue morphogenesis. Morphogenesis also describes the development of unicellular life forms that do not have an embryonic stage in their life cycle. Morphogenesis is essential for the evolution of new forms. Morphogenesis is a mechanical process involving forces that generate mechanical stress, strain, and movement of cells, and can be induced by genetic programs according to the spatial patterning of cells within tissues. Abnormal morphogenesis is called dysmorphogenesis. History Some of the earliest ideas and mathematical descriptions on how physical processes and constraints affect biological growth, and hence natural patterns such as the spirals of phyllotaxis, were written by D'Arcy Wentworth Thompson in his 1917 book On Growth and Form and Alan Turing in his The Chemical Basis of Morphogenesis (1952). Where Thompson explained animal body shapes as being created by varying rates of growth in different directions, for instance to create the spiral shell of a snail, Turing correctly predicted a mechanism of morphogenesis, the diffusion of two different chemical signals, one activating and one deactivating growth, to set up patterns of development, decades before the formation of such patterns was observed. The fuller understanding of the mechanisms involved in actual organisms required the discovery of the structure of DNA in 1953, and the development of molecular biology and biochemistry. Genetic and molecular basis Several types of molecules are important in morphogenesis. Morphogens are soluble molecules that can diffuse and carry signals that control cell differentiation via concentration gradients. Morphogens typically act through binding to specific protein receptors. An important class of molecules involved in morphogenesis are transcription factor proteins that determine the fate of cells by interacting with DNA. These can be coded for by master regulatory genes, and either activate or deactivate the transcription of other genes; in turn, these secondary gene products can regulate the expression of still other genes in a regulatory cascade of gene regulatory networks. At the end of this cascade are classes of molecules that control cellular behaviors such as cell migration, or, more generally, their properties, such as cell adhesion or cell contractility. For example, during gastrulation, clumps of stem cells switch off their cell-to-cell adhesion, become migratory, and take up new positions within an embryo where they again activate specific cell adhesion proteins and form new tissues and organs. Developmental signaling pathways implicated in morphogenesis include Wnt, Hedgehog, and ephrins. Cellular basis At a tissue level, ignoring
Morphogenesis
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A day is the time period of a full rotation of the Earth with respect to the Sun. On average, this is 24 hours (86,400 seconds). As a day passes at a given location it experiences morning, noon, afternoon, evening, and night. This daily cycle drives circadian rhythms in many organisms, which are vital to many life processes. A collection of sequential days is organized into calendars as dates, almost always into weeks, months and years. A solar calendar organizes dates based on the Sun's annual cycle, giving consistent start dates for the four seasons from year to year. A lunar calendar organizes dates based on the Moon's lunar phase. In common usage, a day starts at midnight, written as 00:00 or 12:00 am in 24- or 12-hour clocks, respectively. Because the time of midnight varies between locations, time zones are set up to facilitate the use of a uniform standard time. Other conventions are sometimes used, for example the Jewish religious calendar counts days from sunset to sunset, so the Jewish Sabbath begins at sundown on Friday. In astronomy, a day begins at noon so that observations throughout a single night are recorded as happening on the same day. In specific applications, the definition of a day is slightly modified, such as in the SI day (exactly 86,400 seconds) used for computers and standards keeping, local mean time accounting of the Earth's natural fluctuation of a solar day, and stellar day and sidereal day (using the celestial sphere) used for astronomy. In most countries outside of the tropics, daylight saving time is practiced, and each year there will be one 23-hour civil day and one 25-hour civil day. Due to slight variations in the rotation of the Earth, there are rare times when a leap second will get inserted at the end of a UTC day, and so while almost all days have a duration of 86,400 seconds, there are these exceptional cases of a day with 86,401 seconds (in the half-century spanning 1972 through 2022, there have been a total of 27 leap seconds that have been inserted, so roughly once every other year). Etymology The term comes from the Old English term dæġ (), with its cognates such as dagur in Icelandic, Tag in German, and dag in Norwegian, Danish, Swedish and Dutch – all stemming from a Proto-Germanic root *dagaz. , day is the 205th most common word in American English, and the 210th most common in English English. Definitions Apparent and mean solar day Several definitions of this universal human concept are used according to context, need, and convenience. Besides the day of 24 hours (86,400 seconds), the word day is used for several different spans of time based on the rotation of the Earth around its axis. An important one is the solar day, the time it takes for the Sun to return to its culmination point (its highest point in the sky). Due to an orbit's eccentricity, the Sun resides in one of
Day
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Biogeochemistry is the scientific discipline that involves the study of the chemical, physical, geological, and biological processes and reactions that govern the composition of the natural environment (including the biosphere, the cryosphere, the hydrosphere, the pedosphere, the atmosphere, and the lithosphere). In particular, biogeochemistry is the study of biogeochemical cycles, the cycles of chemical elements such as carbon and nitrogen, and their interactions with and incorporation into living things transported through earth scale biological systems in space and time. The field focuses on chemical cycles which are either driven by or influence biological activity. Particular emphasis is placed on the study of carbon, nitrogen, oxygen, sulfur, iron, and phosphorus cycles. Biogeochemistry is a systems science closely related to systems ecology. History Early Greek Early Greeks established the core idea of biogeochemistry that nature consists of cycles. 18th-19th centuries Agricultural interest in 18th-century soil chemistry led to better understanding of nutrients and their connection to biochemical processes. This relationship between the cycles of organic life and their chemical products was further expanded upon by Dumas and Boussingault in a 1844 paper that is considered an important milestone in the development of biogeochemistry. Jean-Baptiste Lamarck first used the term biosphere in 1802, and others continued to develop the concept throughout the 19th century. Early climate research by scientists like Charles Lyell, John Tyndall, and Joseph Fourier began to link glaciation, weathering, and climate. 20th century The founder of modern biogeochemistry was Vladimir Vernadsky, a Russian and Ukrainian scientist whose 1926 book The Biosphere, in the tradition of Mendeleev, formulated a physics of the Earth as a living whole. Vernadsky distinguished three spheres, where a sphere was a concept similar to the concept of a phase-space. He observed that each sphere had its own laws of evolution, and that the higher spheres modified and dominated the lower: Abiotic sphere – all the non-living energy and material processes Biosphere – the life processes that live within the abiotic sphere Nöesis or noosphere – the sphere of human cognitive process Human activities (e.g., agriculture and industry) modify the biosphere and abiotic sphere. In the contemporary environment, the amount of influence humans have on the other two spheres is comparable to a geological force (see Anthropocene). The American limnologist and geochemist G. Evelyn Hutchinson is credited with outlining the broad scope and principles of this new field. More recently, the basic elements of the discipline of biogeochemistry were restated and popularized by the British scientist and writer, James Lovelock, under the label of the Gaia Hypothesis. Lovelock emphasized a concept that life processes regulate the Earth through feedback mechanisms to keep it habitable. The research of Manfred Schidlowski was concerned with the biochemistry of the Early Earth. Biogeochemical cycles Biogeochemical cycles are the pathways by which chemical substances cycle (are turned over or moved through) the biotic and the abiotic compartments of Earth. The biotic compartment is the biosphere and the abiotic compartments are the atmosphere, hydrosphere and lithosphere. There are biogeochemical cycles for chemical elements,
Biogeochemistry
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Phase resetting in neurons is a behavior observed in different biological oscillators and plays a role in creating neural synchronization as well as different processes within the body. Phase resetting in neurons is when the dynamical behavior of an oscillation is shifted. This occurs when a stimulus perturbs the phase within an oscillatory cycle and a change in period occurs. The periods of these oscillations can vary depending on the biological system, with examples such as: (1) neural responses can change within a millisecond to quickly relay information; (2) In cardiac and respiratory changes that occur throughout the day, could be within seconds; (3) circadian rhythms may vary throughout a series of days; (4) rhythms such as hibernation may have periods that are measured in years. This activity pattern of neurons is a phenomenon seen in various neural circuits throughout the body and is seen in single neuron models and within clusters of neurons. Many of these models utilize phase response (resetting) curves where the oscillation of a neuron is perturbed and the effect the perturbation has on the phase cycle of a neuron is measured. History Leon Glass and Michael Mackey (1988) developed the theory behind limit cycle oscillators to observe the effects of perturbing oscillating neurons under the assumption the stimulus applied only affected the phase cycle and not the amplitude of response. Phase resetting plays a role in promoting neural synchrony in various pathways in the brain, from regulating circadian rhythms and heartbeat via cardiac pacemaker cells to playing significant roles in memory, pancreatic cells and neurodegenerative diseases such as epilepsy. Burst of activity in patterns of behaviors occur through coupled oscillators using pulsatile signals, better known as pulse-coupled oscillators. Methodology of study Phase response curve Shifts in phase (or behavior of neurons) caused due to a perturbation (an external stimulus) can be quantified within a Phase Response Curve (PRC) to predict synchrony in coupled and oscillating neurons. These effects can be computed, in the case of advances or delays to responses, to observe the changes in the oscillatory behavior of neurons, pending on when a stimulus was applied in the phase cycle of an oscillating neuron. The key to understanding this is in the behavioral patterns of neurons and the routes neural information travels. Neural circuits are able to communicate efficiently and effectively within milliseconds of experiencing a stimulus and lead to the spread of information throughout the neural network. The study of neuron synchrony could provide information on the differences that occur in neural states such as normal and diseased states. Neurons that are involved significantly in diseases such as Alzheimer's disease or Parkinson's disease are shown to undergo phase resetting before launching into phase locking where clusters of neurons are able to begin firing rapidly to communicate information quickly. A phase response curve can be calculated by noting changes to its period over time depending on where in the cycle the input is applied. The perturbation left by the stimulus moves the stable cycle
Phase resetting in neurons
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Weight cycling, also known as yo-yo dieting, is the repeated loss and gain of weight, resembling the up-down motion of a yo-yo. The purpose of the temporary weight loss the yo-yo diet delivers is to lure the dieting into the illusion of success, but due to the nature of the diet, they are impossible to sustain, therefore the dieter gives up, often due to hunger or discomfort, and gains the weight back. The dieter then seeks to lose the regained weight, and the cycle begins again. Other individuals cycle weight deliberately in service of bodybuilding or athletic goals. Weight cycling contributes to increased risk of later obesity, due to repeated signals being sent to the body signalling that it's in starvation mode; therefore it learns to be better and better at storing fat, and increases the strain on vital organs, likely promoting cardiometabolic disease. Causes Dieting The reasons for yo-yo dieting are varied but often include embarking upon a hypocaloric diet too extreme to maintain. At first the dieter may experience elation at the thought of weight loss and pride in their self-control for resisting certain foods, e.g. junk food, desserts, and sweets. Over time, however, the limits imposed by such extreme diets cause effects such as depression or fatigue that make the diet impossible to sustain. Ultimately, the dieter reverts to their old eating habits, now with the added emotional effects of failing to lose weight by the restrictive diet. Such an emotional state leads many people to eating more than they would have before dieting, especially the 'forbidden' foods e.g. junk food, desserts, and sweets, causing them to rapidly regain weight. Sports In some sports where an athlete's weight is important, such as those that use weight classes or aesthetics, it is common for athletes to engage in weight cycling. Weight cycling is common among competitive combat sports athletes, including minors. In bodybuilding and strength sports, weight cycling is often used as a way to take advantage of the increased ability to gain muscle while in a caloric surplus by cyclically going through periods of intentional weight gain, followed by a period of weight loss to prevent excessive body fat accumulation. Mechanism The process of regaining weight and especially body fat is further promoted by the high metabolic plasticity of skeletal muscle. The Summermatter cycle explains how skeletal muscle persistently reduces energy expenditure during dieting. In addition, food restriction increases physical activity which further supports body weight loss initially. Such weight regain in the form of preferential catch-up-fat is well documented after weight loss due to malnutrition, cancer, septic shock or AIDS and thus constitutes a general phenomenon related to weight loss. Health effects Weight cycling certainly has negative health effects from repeated strain on the body, confusing the metabolism, and stress on vital organs. A 2019 systematic review and meta-analysis found that "Body-weight fluctuation was associated with higher mortality due to all causes and CVD and a higher morbidity of CVD and hypertension." A 2019 review found
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In meteorology, eyewall replacement cycles, also called concentric eyewall cycles, naturally occur in intense tropical cyclones, generally with winds greater than , or major hurricanes (Category 3 or above). When tropical cyclones reach this intensity, and the eyewall contracts or is already small, some of the outer rainbands may strengthen and organize into a ring of thunderstorms—a new, outer eyewall—that slowly moves inward and robs the original, inner eyewall of its needed moisture and angular momentum. Since the strongest winds are in a tropical cyclone's eyewall, the storm usually weakens during this phase, as the inner wall is "choked" by the outer wall. Eventually the outer eyewall replaces the inner one completely, and the storm may re-intensify. The discovery of this process was partially responsible for the end of the U.S. government's hurricane modification experiment Project Stormfury. This project set out to seed clouds outside the eyewall, apparently causing a new eyewall to form and weakening the storm. When it was discovered that this was a natural process due to hurricane dynamics, the project was quickly abandoned. Almost every intense hurricane undergoes at least one of these cycles during its existence. Recent studies have shown that nearly half of all tropical cyclones, and nearly all cyclones with sustained winds over , undergo eyewall replacement cycles. Hurricane Allen in 1980 went through repeated eyewall replacement cycles, fluctuating between Category 5 and Category 4 status on the Saffir-Simpson Hurricane Scale several times. Typhoon June (1975) was the first reported case of triple eyewalls, and Hurricane Juliette and Iris (2001) were documented cases of such. History The first tropical system to be observed with concentric eyewalls was Typhoon Sarah by Fortner in 1956, which he described as "an eye within an eye". The storm was observed by a reconnaissance aircraft to have an inner eyewall at and an outer eyewall at . During a subsequent flight 8 hours later, the inner eyewall had disappeared, the outer eyewall had reduced to and the maximum sustained winds and hurricane intensity had decreased. The next hurricane observed to have concentric eyewalls was Hurricane Donna in 1960. Radar from reconnaissance aircraft showed an inner eye that varied from at low altitude to near the tropopause. In between the two eyewalls was an area of clear skies that extended vertically from to . The low-level clouds at around were described as stratocumulus with concentric horizontal rolls. The outer eyewall was reported to reach heights near while the inner eyewall only extended to . 12 hours after identifying concentric eyewalls, the inner eyewall had dissipated. Hurricane Beulah in 1967 was the first tropical cyclone to have its eyewall replacement cycle observed from beginning to end. Previous observations of concentric eyewalls were from aircraft-based platforms. Beulah was observed from the Puerto Rico land-based radar for 34 hours during which time a double eyewall formed and dissipated. It was noted that Beulah reached maximum intensity immediately prior to undergoing the eyewall replacement cycle, and that it was "probably more than a
Eyewall replacement cycle
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Hot air ovens are electrical devices which use dry heat to sterilize. They were originally developed by Louis Pasteur. Generally, they use a thermostat to control the temperature. Their double walled insulation keeps the heat in and conserves energy, the inner layer being a poor conductor and outer layer being metallic. There is also an air filled space in between to aid insulation. An air circulating fan helps in uniform distribution of the heat. These are fitted with the adjustable wire mesh plated trays or aluminium trays and may have an on/off rocker switch, as well as indicators and controls for temperature and holding time. The capacities of these ovens vary. Power supply needs vary from country to country, depending on the voltage and frequency (hertz) used. Temperature sensitive tapes or biological indicators using bacterial spores can be used as controls, to test for the efficacy of the device during use. Advantages and disadvantages They do not require water and there is not much pressure build up within the oven, unlike an autoclave, making them safer to work with. This also makes them more suitable to be used in a laboratory environment. They are much smaller than autoclaves but can still be as effective. They can be more rapid than an autoclave and higher temperatures can be reached compared to other means. As they use dry heat instead of moist heat, some pathogens like prions, may not be killed by them every time, based on the principle of thermal inactivation by oxidation. Usage A complete cycle involves heating the oven to the required temperature, maintaining that temperature for the proper time interval for that temperature, turning the machine off and cooling the articles in the closed oven till they reach room temperature. The standard settings for a hot air oven are: 1.5 to 2 hours at 6 to 12 minutes at ....plus the time required to preheat the chamber before beginning the sterilization cycle. If the door is opened before time, heat escapes and the process becomes incomplete. Thus the cycle must be properly repeated all over. These are widely used to sterilize articles that can withstand high temperatures and not get burnt, like glassware and powders. Linen gets burnt and surgical sharps lose their sharpness. References Textbook of Microbiology by Prof. C P Baveja, Textbook of Microbiology by Ananthanarayan and Panikar, External links http://www.tpub.com/content/medical/14274/css/14274_146.htm Laboratory equipment Medical equipment Medical hygiene Microbiology equipment
Hot air oven
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Erectile tissue is tissue in the body with numerous vascular spaces, or cavernous tissue, that may become engorged with blood. However, tissue that is devoid of or otherwise lacking erectile tissue (such as the labia minora, the vestibule/vagina and the urethra) may also be described as engorging with blood, often with regard to sexual arousal. In sex organs Erectile tissue exists in external genitals such as the corpora cavernosa of the penis and their homologs in the clitoris, also called the corpora cavernosa. During penile or clitoral erection, the corpora cavernosa will become engorged with arterial blood, a process called tumescence. This may result from any of various physiological stimuli which can be internal or external. This process of stimulation, due to internal or external stimuli, is also known as sexual arousal. The corpus spongiosum is a single tubular structure located just below the corpora cavernosa in males. This may also become slightly engorged with blood, but less so than the corpora cavernosa. In the nose Erectile tissue is present in the anterior part of the nasal septum and is attached to the turbinates of the nose. The nasal cycle occurs as the erectile tissue on one side of the nose congests and the other side decongests. This process is controlled by the autonomic nervous system with parasympathetic dominance being associated with congestion and sympathetic with decongestion. The time of one cycle may vary greatly between individuals with Kahana-Zweig et al. finding a range between 15 minutes and 10.35 hours though the average was noted as 2.15 ± 1.84 hours. Other types Erectile tissue is also found in the nose (turbinates), urethral sponge and perineal sponge. The erection of nipples is not due to erectile tissue, but rather due to the contraction of smooth muscle under the control of the autonomic nervous system. References Sexual anatomy ru:Пещеристое тело
Erectile tissue
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The carbon cycle is that part of the biogeochemical cycle by which carbon is exchanged among the biosphere, pedosphere, geosphere, hydrosphere, and atmosphere of Earth. Other major biogeochemical cycles include the nitrogen cycle and the water cycle. Carbon is the main component of biological compounds as well as a major component of many minerals such as limestone. The carbon cycle comprises a sequence of events that are key to making Earth capable of sustaining life. It describes the movement of carbon as it is recycled and reused throughout the biosphere, as well as long-term processes of carbon sequestration (storage) to and release from carbon sinks. To describe the dynamics of the carbon cycle, a distinction can be made between the fast and slow carbon cycle. The fast carbon cycle is also referred to as the biological carbon cycle. Fast carbon cycles can complete within years, moving substances from atmosphere to biosphere, then back to the atmosphere. Slow or geological cycles (also called deep carbon cycle) can take millions of years to complete, moving substances through the Earth's crust between rocks, soil, ocean and atmosphere. Humans have disturbed the carbon cycle for many centuries. They have done so by modifying land use and by mining and burning carbon from ancient organic remains (coal, petroleum and gas). Carbon dioxide in the atmosphere has increased nearly 52% over pre-industrial levels by 2020, resulting in global warming. The increased carbon dioxide has also caused a reduction in the ocean's pH value and is fundamentally altering marine chemistry. Main compartments The carbon cycle was first described by Antoine Lavoisier and Joseph Priestley, and popularised by Humphry Davy. The global carbon cycle is now usually divided into the following major reservoirs of carbon (also called carbon pools) interconnected by pathways of exchange: Atmosphere Terrestrial biosphere Ocean, including dissolved inorganic carbon and living and non-living marine biota Sediments, including fossil fuels, freshwater systems, and non-living organic material. Earth's interior (mantle and crust). These carbon stores interact with the other components through geological processes. The carbon exchanges between reservoirs occur as the result of various chemical, physical, geological, and biological processes. The ocean contains the largest active pool of carbon near the surface of the Earth. The natural flows of carbon between the atmosphere, ocean, terrestrial ecosystems, and sediments are fairly balanced; so carbon levels would be roughly stable without human influence. Atmosphere Carbon in the Earth's atmosphere exists in two main forms: carbon dioxide and methane. Both of these gases absorb and retain heat in the atmosphere and are partially responsible for the greenhouse effect. Methane produces a larger greenhouse effect per volume as compared to carbon dioxide, but it exists in much lower concentrations and is more short-lived than carbon dioxide. Thus, carbon dioxide contributes more to the global greenhouse effect than methane. Carbon dioxide is removed from the atmosphere primarily through photosynthesis and enters the terrestrial and oceanic biospheres. Carbon dioxide also dissolves directly from the atmosphere into bodies of water (ocean, lakes, etc.), as
Carbon cycle
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Ovulation is the release of eggs from the ovaries. In women, this event occurs when the ovarian follicles rupture and release the secondary oocyte ovarian cells. After ovulation, during the luteal phase, the egg will be available to be fertilized by sperm. In addition, the uterine lining (endometrium) is thickened to be able to receive a fertilized egg. If no conception occurs, the uterine lining as well as the egg will be shed during menstruation. Process Ovulation occurs about midway through the menstrual cycle, after the follicular phase. The days in which a woman is most fertile can be calculated based on the date of the last menstrual period and the length of a typical menstrual cycle. The few days surrounding ovulation (from approximately days 10 to 18 of a 28-day cycle), constitute the most fertile phase. The time from the beginning of the last menstrual period (LMP) until ovulation is, on average, 14.6 days, but with substantial variation among females and between cycles in any single female, with an overall 95% prediction interval of 8.2 to 20.5 days. The process of ovulation is controlled by the hypothalamus of the brain and through the release of hormones secreted in the anterior lobe of the pituitary gland, luteinizing hormone (LH) and follicle-stimulating hormone (FSH). In the preovulatory phase of the menstrual cycle, the ovarian follicle will undergo a series of transformations called cumulus expansion, which is stimulated by FSH. After this is done, a hole called the stigma will form in the follicle, and the secondary oocyte will leave the follicle through this hole. Ovulation is triggered by a spike in the amount of FSH and LH released from the pituitary gland. During the luteal (post-ovulatory) phase, the secondary oocyte will travel through the fallopian tubes toward the uterus. If fertilized by a sperm, the fertilized secondary oocyte or ovum may implant there 6–12 days later. Follicular phase The follicular phase (or proliferative phase) is the phase of the menstrual cycle during which the ovarian follicles mature. The follicular phase lasts from the beginning of menstruation to the start of ovulation. For ovulation to be successful, the ovum must be supported by the corona radiata and cumulus oophorous granulosa cells. The latter undergo a period of proliferation and mucification known as cumulus expansion. Mucification is the secretion of a hyaluronic acid-rich cocktail that disperses and gathers the cumulus cell network in a sticky matrix around the ovum. This network stays with the ovum after ovulation and has been shown to be necessary for fertilization. Ovulation Estrogen levels peak towards the end of the follicular phase, around 12 and 24 hours. This, by positive feedback, causes a surge in levels of luteinizing hormone (LH) and follicle-stimulating hormone (FSH). This lasts from 24 to 36 hours, and results in the rupture of the ovarian follicles, causing the oocyte to be released from the ovary. Through a signal transduction cascade initiated by LH, which activates the pro-inflammatory genes through cAMP secondary messenger, proteolytic enzymes
Ovulation
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The chlorine cycle (Cl) is the biogeochemical cycling of chlorine through the atmosphere, hydrosphere, biosphere, and lithosphere. Chlorine is most commonly found as inorganic chloride ions, or a number of chlorinated organic forms. Over 5,000 biologically-produced chlorinated organics have been identified. The cycling of chlorine into the atmosphere and creation of chlorine compounds by anthropogenic sources has major impacts on climate change and depletion of the ozone layer. Chlorine plays essential roles in many biological processes, including numerous roles in the human body. It also acts as an essential co-factor in enzymes involved in plant photosynthesis. Troposphere Chlorine plays a large role in atmospheric cycling and climate, including, but not limited to chlorofluorocarbons (CFCs). The major flux of chlorine into the troposphere comes from sea salt aerosol spray. Both organic and inorganic chlorine is transferred into the troposphere from the oceans. Biomass combustion is another source of both organic and inorganic forms of chlorine to the troposphere from the terrestrial reservoir. Typically, organic chlorine forms are highly un-reactive and will be transferred to the stratosphere from the troposphere. The major flux of chlorine from the troposphere is via surface deposition into water systems. Hydrosphere Oceans are the largest source of chlorine in the Earth's hydrosphere. In the hydrosphere, chlorine exists primarily as chloride due to the high solubility of the Cl− ion. The majority of chlorine fluxes are within the hydrosphere due to chloride ions' solubility and reactivity within water systems. The cryosphere is able to retain some chlorine deposited by rainfall and snow, but the majority is eluted into oceans. Lithosphere The largest reservoir of chlorine resides in the lithosphere, where of global chlorine is found in Earth's mantle. Volcanic eruptions will sporadically release high levels of chlorine as HCl into the troposphere, but the majority of the terrestrial chlorine flux comes from seawater sources mixing with the mantle. Organically bound chlorine is as abundant as chloride ions in terrestrial soil systems, or the pedosphere. Discovery of multiple Cl-mediating genes in microorganisms and plants indicate that numerous biotic processes use chloride and produce organic chlorinated compounds, as well as many abiotic processes. These chlorinated compounds can then be volatilized or leached out of soils, which makes the overall soil environment a global sink of chlorine. Multiple anaerobic prokaryotes have been found to contain genes and show activity for chlorinated organic volatilization Biological processes Chlorine's ability to completely dissociate in water is also why it is an essential electrolyte in many biological processes. Chlorine, along with phosphorus, is the sixth most common element in organic matter. Cells utilize chloride to balance pH and maintain turgor pressure at equilibrium. The high electrical conductivity of Cl− ions are essential for neuron signalling in the brain and regulate many other essential functions in biology Anthropogenic chlorinated compounds The depleting effects of chlorofluorocarbons (CFCs) on ozone over Antarctica has been studied extensively since the 1980s. The low reactivity of CFCs allow it to reach the upper stratosphere, where it interacts with UV-C radiation and
Chlorine cycle
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Sustainable engineering is the process of designing or operating systems such that they use energy and resources sustainably, in other words, at a rate that does not compromise the natural environment, or the ability of future generations to meet their own needs. Common engineering focuses Sustainable Engineering focuses on the following - Water supply Food production Housing and shelter Sanitation and waste management Energy development Transportation Industrial processing Development of natural resources Cleaning up polluted waste sites Planning projects to reduce environmental and social impacts Restoring natural environments such as forests, lakes, streams, and wetlands Providing medical care to those in need Minimizing and responsibly disposing of waste to benefit all Improving industrial processes to eliminate waste and reduce consumption Recommending the appropriate and innovative use of technology Aspects of engineering disciplines Every engineering discipline is engaged in sustainable design, employing numerous initiatives, especially life cycle analysis (LCA), pollution prevention, Design for the Environment (DfE), Design for Disassembly (DfD), and Design for Recycling (DfR). These are replacing or at least changing pollution control paradigms. For example, concept of a "cap and trade" has been tested and works well for some pollutants. This is a system where companies are allowed to place a "bubble" over a whole manufacturing complex or trade pollution credits with other companies in their industry instead of a "stack-by-stack" and "pipe-by-pipe" approach, i.e. the so-called "command and control" approach. Such policy and regulatory innovations call for some improved technology based approaches as well as better quality-based approaches, such as leveling out the pollutant loadings and using less expensive technologies to remove the first large bulk of pollutants, followed by higher operation and maintenance (O&M) technologies for the more difficult to treat stacks and pipes. But, the net effect can be a greater reduction of pollutant emissions and effluents than treating each stack or pipe as an independent entity. This is a foundation for most sustainable design approaches, i.e. conducting a life-cycle analysis, prioritizing the most important problems, and matching the technologies and operations to address them. The problems will vary by size (e.g. pollutant loading), difficulty in treating, and feasibility. The most intractable problems are often those that are small but very expensive and difficult to treat, i.e. less feasible. Of course, as with all paradigm shifts, expectations must be managed from both a technical and an operational perspective. Historically, sustainability considerations have been approached by engineers as constraints on their designs. For example, hazardous substances generated by a manufacturing process were dealt with as a waste stream that must be contained and treated. The hazardous waste production had to be constrained by selecting certain manufacturing types, increasing waste handling facilities, and if these did not entirely do the job, limiting rates of production. Green engineering recognizes that these processes are often inefficient economically and environmentally, calling for a comprehensive, systematic life cycle approach. Green engineering attempts to achieve four goals: Waste reduction Materials management Pollution prevention and Product enhancement. Green engineering encompasses numerous ways to improve
Sustainable engineering
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Ecology () is the natural science of the relationships among living organisms, including humans, and their physical environment. Ecology considers organisms at the individual, population, community, ecosystem, and biosphere levels. Ecology overlaps with the closely related sciences of biogeography, evolutionary biology, genetics, ethology, and natural history. Ecology is a branch of biology, and is the study of abundance, biomass, and distribution of organisms in the context of the environment. It encompasses life processes, interactions, and adaptations; movement of materials and energy through living communities; successional development of ecosystems; cooperation, competition, and predation within and between species; and patterns of biodiversity and its effect on ecosystem processes. Ecology has practical applications in conservation biology, wetland management, natural resource management (agroecology, agriculture, forestry, agroforestry, fisheries, mining, tourism), urban planning (urban ecology), community health, economics, basic and applied science, and human social interaction (human ecology). The word ecology () was coined in 1866 by the German scientist Ernst Haeckel. The science of ecology as we know it today began with a group of American botanists in the 1890s. Evolutionary concepts relating to adaptation and natural selection are cornerstones of modern ecological theory. Ecosystems are dynamically interacting systems of organisms, the communities they make up, and the non-living (abiotic) components of their environment. Ecosystem processes, such as primary production, nutrient cycling, and niche construction, regulate the flux of energy and matter through an environment. Ecosystems have biophysical feedback mechanisms that moderate processes acting on living (biotic) and abiotic components of the planet. Ecosystems sustain life-supporting functions and provide ecosystem services like biomass production (food, fuel, fiber, and medicine), the regulation of climate, global biogeochemical cycles, water filtration, soil formation, erosion control, flood protection, and many other natural features of scientific, historical, economic, or intrinsic value. Levels, scope, and scale of organization The scope of ecology contains a wide array of interacting levels of organization spanning micro-level (e.g., cells) to a planetary scale (e.g., biosphere) phenomena. Ecosystems, for example, contain abiotic resources and interacting life forms (i.e., individual organisms that aggregate into populations which aggregate into distinct ecological communities). Because ecosystems are dynamic and do not necessarily follow a linear successional route, changes might occur quickly or slowly over thousands of years before specific forest successional stages are brought about by biological processes. An ecosystem's area can vary greatly, from tiny to vast. A single tree is of little consequence to the classification of a forest ecosystem, but is critically relevant to organisms living in and on it. Several generations of an aphid population can exist over the lifespan of a single leaf. Each of those aphids, in turn, supports diverse bacterial communities. The nature of connections in ecological communities cannot be explained by knowing the details of each species in isolation, because the emergent pattern is neither revealed nor predicted until the ecosystem is studied as an integrated whole. Some ecological principles, however, do exhibit collective properties where the sum of the components explain the properties of the whole, such as birth rates of
Ecology
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Entomopathogenic nematodes (EPN) are a group of nematodes (thread worms), that cause death to insects. The term entomopathogenic has a Greek origin, with entomon, meaning insect, and pathogenic, which means causing disease. They are animals that occupy a bio control middle ground between microbial pathogens and predator/parasitoids. Although many other parasitic thread worms cause diseases in living organisms (sterilizing or otherwise debilitating their host), entomopathogenic nematodes are specific in only infecting insects. Entomopathogenic nematodes (EPNs) live parasitically inside the infected insect host, and so they are termed as endoparasitic. They infect many different types of insects living in the soil like the larval forms of moths, butterflies, flies and beetles as well as adult forms of beetles, grasshoppers and crickets. EPNs have been found all over the world in a range of ecologically diverse habitats. They are highly diverse, complex and specialized. The most commonly studied entomopathogenic nematodes are those that can be used in the biological control of harmful insects, the members of Steinernematidae and Heterorhabditidae. They are the only insect-parasitic nematodes possessing an optimal balance of biological control attributes. Classification Life cycle Because of their economic importance, the life cycles of the genera belonging to families Heterorhabditidae and Steinernematidae are well studied. Although not closely related, phylogenetically, both share similar life histories (Poinar 1993). The cycle begins with an infective juvenile, whose only function is to seek out and infect new hosts. When a host has been located, the nematodes penetrate into the insect body cavity, usually via natural body openings (mouth, anus, spiracles) or areas of thin cuticle. (Shapiro-Ilan, David I., and Randy Gaugler. "Nematodes.") After entering an insect, infective juveniles release an associated mutualistic bacterium from their gut which multiplies rapidly. These bacteria of the genus Xenorhabdus or Photorhabdus, for steinerernematides and heterorhabditids, respectively—cause host mortality within 24–48 hours. The nematodes provide shelter to the bacteria, which, in return, kill the insect host and provide nutrients to the nematode. Without this mutualism no nematode is able to act as an entomoparasite. Together, the nematodes and bacteria feed on the liquefying host, and reproduce for several generations inside the cadaver maturing through the growth stages of J2-J4 into adults. Steinernematids infective juveniles may become males or females, whereas heterorhabditids develop into self-fertilizing hermaphrodites with later generations producing two sexes. When food resources in the host become scarce, the adults produce new infective juveniles adapted to withstand the outside environment. The life cycles of the EPNs are completed within a few days.(Shapiro-Ilan, David I., and Randy Gaugler. "Nematodes.") After about a week, hundreds of thousands of infective juveniles emerge and leave in search of new hosts, carrying with them an inoculation of mutualistic bacteria, received from the internal host environment (Boemare 2002, Gaugler 2006). Their growth and reproduction depends upon conditions established in the host cadaver by the bacterium. The nematodes bacterium contributes anti-immune proteins to assist in overcoming their host defenses (Shapiro-Ilan, David I., and Randy Gaugler. "Nematodes."). Foraging strategies The foraging strategies of entomopathogenic nematodes vary
Entomopathogenic nematode