The Millennium Ecosystem Assessment focuses on the benefits people obtain from ecosystems and aims to improve ecosystem management and contribute to human well-being and poverty alleviation Nobody questions the importance of good scientific information for sound environmental decision-making. But designing mechanisms to link scientific research to the decision-making process is no easy matter. Research and decision-making often seem to operate in different worlds. Policy-makers' needs for applied findings and best judgment typically clash with scientists' pursuit of basic research and statistical significance.Despite this challenge, as needs for scientific input into decision-making arise, a number of institutions have been established to help bridge the science–policy divide. Regulatory agencies like the United States' Food and Drug Administration have met this need in areas of public health, for example, and Environmental Impact Assessment procedures have helped to introduce better science into project-level decisions. At the scale of global environmental challenges, highly regarded mechanisms have been established such as the Scientific Assessment of Ozone Depletion, which has guided decisions by governments, the private sector, and nongovernmental organizations (NGOs), and the Intergovernmental Panel on Climate Change, which has become the authoritative source of policy-relevant information on climate science.But a significant gap remains in the landscape of institutions designed to link science with policy-making: no mechanism has existed to provide decision-makers with authoritative information on the causes and consequences of changes in the planet's ecosystems and on the options for response.Human well-being and progress toward sustainable development are vitally dependent upon improving the management of Earth's ecosystems to ensure their conservation and sustainable use. The benefits that human beings extract from nature are the foundation of all economies and the basis of major industries, are sources of knowledge, and are central to many cultures. While demands for ecosystem services such as food and clean water are growing, human actions are at the same time diminishing the capability of many ecosystems to meet these demands. And while many of the changes to ecosystems, such as increased agricultural production, have greatly enhanced human well-being, many others have not. World fisheries are now declining due to overfishing, for instance, and some 40% of agricultural land has been degraded in the past half-century. Other human-induced impacts on ecosystems include alteration of the nitrogen, phosphorous, sulfur, and carbon cycles, causing acid rain, algal blooms, and fish kills in rivers and coastal waters, along with contributions to climate change.The benefits that human beings extract from nature are the foundation of all economies and the basis of major industries, are sources of knowledge, and are central to many cultures.www.millenniumassessment.org) was launched one year later, in 2001. More than 700 authors from 80 countries are now involved in the expert working groups preparing the global assessment; 100 experts will serve on the Editorial Review Board; more than 1,000 experts will be asked to review the materials, and hundreds more are undertaking subglobal assessments as part of the MA.Recognizing the growing scale of these problems, United Nations Secretary General Kofi Annan, in his 2000 Millennium Report to the General Assembly, called for a Millennium Assessment of Global Ecosystems to provide definitive information on the consequences of ecosystem change for human well-being. With further authorization received through three international conventions  and with financial support from the Global Environment Facility, the United Nations Foundation, the David and Lucile Packard Foundation, and the World Bank, the Millennium Ecosystem Assessment (MA) (The MA focuses on ecosystem services (the benefits people obtain from ecosystems), how changes in ecosystem services have affected human well-being, how ecosystem changes may affect people in future decades, and response options that might be adopted at local, national, or global scales to improve ecosystem management and thereby contribute to human well-being and poverty alleviation .Ecosystems and Human Well-Being: A Framework for Assessment—was published in 2003 and describes the approach and methods used in the MA. The four main assessment volumes—Conditions and Trends, Scenarios, Response Options, and Subglobal Assessments—began the first of two rounds of peer review in January 2004, and the final assessment reports will be published in early 2005.The first report—Unlike previous global scientific assessments, the MA is a “multiscale” assessment. Assessments at subglobal scales are needed because ecosystems are highly differentiated in space and time and because sound management requires careful local planning and action. Local assessments alone are insufficient, however, because some processes are global and because local goods, services, matter, and energy are often transferred across regions. The MA subglobal assessments will directly meet needs of decision-makers at the scale at which they are undertaken, strengthen the global findings with on-the-ground reality, and reinforce the local findings with global perspectives, data, and models.In Southern Africa, for example, a series of community-level assessments are being conducted using the MA conceptual framework. The findings from these assessments inform, and are informed by, assessments underway in the Gariep and Zambezi river basins. These local and river basin assessments, in turn, are linked to a regional assessment encompassing the countries in the Southern African Development Community. Other subglobal assessments are now underway in such regions as São Paulo, Brazil; coastal British Columbia, Canada; the Caribbean Sea; western China; Colombia; the Sinai Peninsula, Egypt; several regions within India; Indonesia; the Laguna Lake Basin, the Philippines; Portugal; and Sweden.The ultimate impact of the MA will depend on its credibility, legitimacy, and utility. To ensure its scientific credibility, the assessment involves leading scientists from around the world and has established an independent peer-review process. To ensure the political legitimacy, all of the stakeholders—governments, the private sector, and NGOs—have a role in governing the process, and governments themselves have approved the process through decisions in international conventions. And, to ensure its utility, ongoing interactions with stakeholders are designed to ensure a focus on their questions and issues.The scientific information now available concerning ecosystems and human development holds the promise of significantly improving the choices that the public and decision-makers take concerning the environment. But for that promise to be fulfilled, a bridge needs to be built between the research community holding this information and the decision-makers seeking it. The MA is an attempt to establish that bridge.


This study uses cigarette price elasticity to evaluate the effect of a new excise tax increase on cigarette consumption and to investigate responses from various types of smokers.Our sample consisted of current smokers between 17 and 69 years old interviewed during an annual face-to-face survey conducted by Taiwan National Health Research Institutes between 2000 to 2003. We used Ordinary Least Squares (OLS) procedure to estimate double logarithmic function of cigarette demand and cigarette price elasticity.In 2002, after Taiwan had enacted the new tax scheme, cigarette price elasticity in Taiwan was found to be -0.5274. The new tax scheme brought about an average annual 13.27 packs/person (10.5%) reduction in cigarette consumption. Using the cigarette price elasticity estimate from -0.309 in 2003, we calculated that if the Health and Welfare Tax were increased by another NT$ 3 per pack and cigarette producers shifted this increase to the consumers, cigarette consumption would be reduced by 2.47 packs/person (2.2%). The value of the estimated cigarette price elasticity is smaller than one, meaning that the tax will not only reduce cigarette consumption but it will also generate additional tax revenues. Male smokers who had no income or who smoked light cigarettes were found to be more responsive to changes in cigarette price.An additional tax added to the cost of cigarettes would bring about a reduction in cigarette consumption and increased tax revenues. It would also help reduce incidents smoking-related illnesses. The additional tax revenues generated by the tax increase could be used to offset the current financial deficiency of Taiwan's National Health Insurance program and provide better public services. One of the problems in controlling tobacco in Taiwan is that cigarette prices are lower in Taiwan than in most countries ,2. In InThe smoking population increased to 4.5 million persons  in 2002 . One outBecause high excise taxes on cigarettes have been found able to reduce cigarette consumption -8, such The government should take elasticity of demand into consideration when deciding whether to increase or add an excise tax levy. If there is a price elasticity below 1, a tax increase brings about a decline in consumption and an increase in total tax revenues. Since Hsieh, Hu and Lin (1999) found that figure to be -0.6 in Taiwan, it can be reasonable to assume that a tax increase would be more likely to reduce cigarette consumption more significantly in Taiwan than in other countries with lower price elasticities at least in the short-term and medium term . Higher Taiwan's Tobacco and Wine Tax Law is currently under review in the Legislative Yuan of Taiwan. Some legislators are seeking to increase the Tobacco Health and Welfare Tax by NT $3 per pack, raising it from NT $5 to NT $8 per pack. Just as they have done in the past, cigarette sellers will probably shift the tax increase to the consumers letting them be responsible for the increase. The effect of the price increase on demand depends on cigarette price elasticity – the larger the elasticity, the larger the reduction in consumption. Therefore, an estimation of price elasticity for domestic cigarettes could be a very important indicator of the possible effect a "Tobacco Health and Welfare Tax" would have on cigarette consumption and could be used to adjust Tobacco Health and Welfare Tax accordingly.Price elasticity of cigarette in Taiwan has been mostly estimated using time-series data ,13, thouThis study uses data on current smokers from 17 to 69 years of age during years 2000 to 2003. First, the demand function of the current smokers was established. Respondents who answered "everyday" or "some of the days" to the question how often you smoke were classified as "current smokers". Then, we used a random sampling of how they consumed and how much they paid for it between 2000 to 2003 to calculate cigarette price elasticity. We then analyzed differences in cigarette price elasticity in smokers categorized according to gender, age, education, income standard, and how much they smoked.Cigarette demand function was estimated by OLS and expressed by double logarithm function. The estimated demand function we used was:Qig = α0 + β1 ln Pig + γ2 ln Iig     (1)ln whereig is i'th current smokers' logarithm representing monthly amount smokers consumed per person in group g. Current smokers were categorized according to age, gender, education, monthly income, and amount smoked. lnPig is i'th current smokers' logarithm representing cigarette price per pack (NT$) for smoking characteristics group g. lnIig is i'th current smokers' logarithm representing income per capita (NT$) for various categories of smokers in group g.lnQα0, β1, and γ2 are parameters to be estimated. In order to measure how price change might affect cigarette consumption, the determination of price elasticity was particularly important. Price elasticity of demand for cigarettes is defined as the percent change in consumption resulting from a price increase. Cigarette price elasticity of demand β1 and income elasticity of demand γ2 can be derived from logarithmically differentiation (1) according to price and income.The Using an annual face-to-face survey on cigarette consumption from 2000 to 2003 by Taiwan National Health Research Institutes, we collected data on how many packs current smokers consumed, how much they paid for a pack of cigarettes, how much they earned per month and how much they spent on cigarettes per month. Current smokers were categorized into gender, age, education, income, and amount smoked. Calculations of cigarette price were based on the average retail price of the top 3 most consumed cigarettes, calculations of number of packs smoked per month were done by dividing the monthly cigarette consumption by the average retail price. Calculations of income were based on personal monthly income.Certain background characteristics are listed in Table Cigarette consumption, retail price and personal monthly income were used in equation (1), the OLS method, to calculate cigarette price and income elasticities. The overall cigarette price elasticity was negative, less than one, indicating that cigarette consumption or demand in Taiwan was inelastic during the study period Table . Taken iAfter Taiwan's accession to WTO in 2002, Taiwan's first Tobacco Health and Welfare Tax added NT $5 the price of cigarettes, resulting in an increase in cigarette retail price from NT $35.2 in 2001 to NT $42.2 in 2002, about an NT $7 increase. In 2001, smokers 15 years old or older consumed an average 126.52 packs/person . In 2002However, the tax has been in force for two years, and a significant reduction in consumption has been shown to date. Cigarette taxes accounted for 40% of the retail price in 2002. Although forty percent sounds high, this proportion is still rather low when, as mentioned earlier, comparing it with the 66% or more of the retail price going for cigarettes prices in high-income countries (with the notable exception of the United States). ConsequInter-party negotiations at the Legislative Yuan resulted in changes to Tobacco and Liquor Tax Law which led to a NT $3 rise in the health tax levied on cigarettes, from NT$5 to NT$8 per pack. The cigarette industry is likely to pass the tax increase in the form of higher prices on to the consumer. A price increase of 3 NT per pack in cigarette would reflect a consumption reduction of 2.47 packs per capita, totaling 44.7 million packs, 2.2% per capita, in cigarette consumption. Cigarette consumption would be reduced to 2 billion packs (based on a population count of 2003), and the government tax revenue would be 33.46 billion, including the Health and Welfare Tax of 16 billion. We estimate that with a Health and Welfare Tax increase from 5 NT to 8 NT per pack, there would be a 6 billion NT increase in revenue from the Health and Welfare Tax.In 2000 and 2001, the cigarette price elasticities of the current smokers were -0.3134 and -0.3684, respectively. In 2002, it had reached its maximum of -0.5274, indicating that as cigarette prices increased, so did the price elasticity. Consumers responded to the higher prices by cutting consumption. Then in 2003, after Taiwan's accession to WTO, cigarette price elasticity then lowered to -0.309, indicating that the effect of a cigarette price hike can diminish over time.Two sets of previous data concerning the cigarette consumption, retail price and personal monthly income of the current smokers obtained during 2000–2001 and during 2002–2003, were made available to us. Using the OLS method and the rise of cigarette price in 2002 as the baseline, we computed the cigarette price and income elasticities for these two sets of data. Table Cigarette price elasticity for the male smokers reached statistically significance (5%), which was higher than the price elasticity of the female smokers, indicating that men were more responsive to price elasticity than the women. The cigarette price elasticity of the male smokers in 2002–2003 was -0.393, which was higher than -0.3107 male smokers in 2000–2001. The income elasticity of male smokers in 2002–2003 was 0.0194, reaching statistical significance (5%). There was no statistical difference found in estimated cigarette price and income elasticity of smokers among the different age sub-groups, though, according to some reports in foreign countries, teenagers are more sensitive changes to cigarette prices than adults -17.Education level seemed to make a difference. The price elasticity smokers with junior high school educations was -0.5766 in 2000–2001, which was higher than that of senior high school level smokers, -0.2772. In 2002-2003, the price elasticity of college level smokers was -0.7007, which was higher than that of the smokers of senior high school level, -0.5369. Therefore, between 2000 and 2001, the more educated group had a larger price elasticity, though the less educated group had the higher coefficient in 2002–2003. Our findings cover two time spans and are different from those reported by foreign researchers who have found that consumers at lower education levels respond stronger to the change of cigarette price . In our In this study, we evaluate the effect of a new tax on the consumption of tobacco by calculating the cigarette price elasticities of various kinds of smokers and comparing those values with their reactions to an increase cigarette, and then using knowledge gained from that study, we assess the possible effect of another increase on consumption. We found that the new tax scheme implemented after Taiwan joined the WTO reduced cigarette consumption by 13.27 packs/person (10.5%). We estimated that an additional NT $3 increase in Taiwan's Health and Welfare Tax would reduce cigarette consumption here by 2.47 packs/person (2.2%).In this study, cigarette price elasticity was less than one, meaning that in addition to reducing cigarette consumption, an additional tax would also generate additional tax revenues. Continuing price increases should reduce cigarette consumption significantly. Provided that the tax increases are proportionately larger than the resulting reduction in cigarette consumption, cigarette tax revenues will increase and can be used to reduce current National Health Insurance deficits and possibly reduce the damage and death caused by smoking related diseases.Based on estimated cigarette price elasticities for various kinds of current smokers, we found that male smokers without income and light smokers were more sensitive to changes in cigarette prices. Teenagers (17 – 24 years old), however, were not found to be significantly influenced by the change in cigarette price, which means it will take more than just tax increases to decrease consumption among our youth. Schools will need to commit to preventive education by inculcating the students with the knowledge of tobacco hazards. Only through early preventive education starting from their childhood can we expect to see significant reduction in cigarette consumption.Finally, the R-squared statistics of the each empirical estimation was below 0.1 for probably sake of to calculate elasticity and exclude variables like advertisement. Future research should also attempt to include these factors with cigarette demand function.The author(s) declare that they have no competing interests.JML performed physical measurements, collected data, and drafted the manuscript. TCH reviewed the manuscript. CYY and SHC carried out the statistical analysis and participated in data collection. All authors read and approved the final manuscript.The pre-publication history for this paper can be accessed here:


Our sense of taste begins with taste buds and ends in the brain. Researchers are beginning to unravel the mechanisms and connections that lie in between The ability to taste food is a life-and-death matter. Failure to recognise food with a high enough caloric content could mean a slow death from malnutrition. Failure to detect a poison could result in near-instant expiration. And now, as researchers begin to understand some of the nuts and bolts of taste perception, it seems that the sense of taste may also have more subtle effects on health.At the front line of the taste sensory system are the taste buds—onion-shaped structures on the tongue and elsewhere in the mouth . Up to 1Taste is the sense by which the chemical qualities of food in the mouth are distinguished by the brain, based on information provided by the taste buds. Quality or ‘basic taste’, explains Bernd Lindemann, now retired but an active taste researcher in Germany for many years, is a psychophysical term. Large numbers of people describe different tastants and then statistical analyses are used to define the important tastes. ‘The number of taste qualities has varied over the years’, says Lindemann. ‘We are now settling at around five, though I would not be surprised if some additional qualities pop up’.The five qualities that Lindemann refers to are salty, sour, bitter, sweet, and umami, the last being the Japanese term for a savoury sensation. Salty and sour detection is needed to control salt and acid balance. Bitter detection warns of foods containing poisons—many of the poisonous compounds produced by plants for defence are bitter. The quality sweet provides a guide to calorie-rich foods. And umami (the taste of the amino acid glutamate) may flag up protein-rich foods. Our sense of taste has a simple goal, explains Lindemann: ‘Food is already in the mouth. We just have to decide whether to swallow or spit it out. It's an extremely important decision, but it can be made based on a few taste qualities’.Taste has been actively researched for many decades. During the 20th century, electrophysiologists and other researchers worked hard to understand this seemingly simple sense system. Then, in 1991, the first olfactory receptors were described. These proteins, which are exposed on the surface of cells in the nose, bind to volatile chemicals and allow us to detect smells. This landmark discovery, in part, encouraged many established taste researchers to investigate the molecular aspects of taste.The olfaction results also enticed researchers from other disciplines into the taste field, including collaborators Charles Zuker  and Nick Ryba . About six years ago, explains Zuker, who previously worked on other sensory systems in flies, ‘there was a disconnect between our understanding of sensations in the case of photoreception, mechanoreception, touch, and so on and what we knew about taste’. There was evidence, says Ryba, that a class of protein receptors called G-protein-coupled receptors (GPCRs) were involved in sweet and bitter taste, ‘but the receptors weren't known, so we started to look for them …. These molecules are intrinsically interesting, but more importantly, they provide tools with which we can dissect out how taste works’.The bitter receptors fell first to the onslaught of the UCSD–NIDCR team and other molecular biologists. In 1999, the ability to taste propylthiouracil, a bitter tasting compound, had been linked to a locus on human Chromosome 5p15. Reasoning that this variation might be due to alterations in the coding sequence for a bitter receptor, the UCSD–NIDCR researchers used the draft of the human genome to search for sequences that resembled GPCRs on Chromosome 5p15. ‘That was how we found T2R1, the first bitter receptor, and, subsequently, a whole family of T2Rs’, says Zuker.Researchers want to know: how is taste coded?All these receptors, says Zuker, are coexpressed in bitter taste receptor cells, a result that contradicts other research showing that different bitter-responsive cells react to different bitter molecules. ‘To me’, says Zuker, ‘it makes sense that all the bitter receptors would be expressed in each bitter taste cell. We just need to know if something is bitter to avoid death’, not the exact identity of the bitter tastant.Sac locus, which determines the ability of mice to detect saccharin, and T1R3, a third member of the T1R family. The UCSD–NIDCR team subsequently showed that the T1R2 and T1R3 heterodimer (a complex of one T1R2 and one T1R3 molecule) forms a broadly tuned sweet receptor, responsive to natural sugars and artificial sweeteners, and that a homodimer of two T1R3 molecules forms a low-affinity sugar receptor that responds to high concentrations of natural sugars only. All sweet detection, concludes Zuker, is via the T1R2 and T1R3 receptors.The sweet receptor story started in 1999 with the identification of two putative mammalian taste receptors, GPCRs now known as T1R1 and T1R2. In early 2001, four groups reported an association between the mouse And umami? A truncated glutamate receptor was identified as an umami receptor by researchers at the University of Miami (Florida, United States) School of Medicine in 2000. Zuker, however, believes that the one and only umami receptor is a heterodimer of T1R1 and T1R3. In October 2003, Zuker and his coworkers reported that mice in which either T1R1 or T1R3 has been knocked out show no preference for monosodium glutamate (MSG), an umami tastant. However, other researchers reported in August 2003 that T1R3 knockouts retain some preference for MSG. ‘We believe this is due either to the truncated glutamate receptor or another unknown receptor’, says lead author Sami Damak (Mount Sinai School of Medicine, New York, New York, United States). Damak says he does not know why the two sets of T1R3 knockout mice behaved differently, but the UCSD–NIDCR researchers suggest that the residual response to MSG seen by Damak et al. is a response to the sodium content of MSG. Damak is not alone, however, in thinking there may be more than one umami receptor .Commenting on these recent discoveries, taste expert Linda Bartoshuk  says that ‘it is lovely to see all these details, especially as they confirm what we already believed conceptually’. For example, she says, it is no surprise that there are many bitter receptors but probably only one sweet receptor. ‘There are so many poisons and it makes perfect sense to have lots of receptors feeding into a common transduction pathway. Sweet is a different problem. In nature, there are many molecules with structures similar to sugar that we must not eat because we cannot metabolise them. So I would have predicted one or at most a few highly specific sweet receptors’.The salty and sour receptors may be very different from the GPCRs involved in bitter, sweet, and umami perception, which bind complex molecules on the outside of the cell and transmit a signal into the cell. For salty and sour perception, the taste cell only needs to detect simple ions. One way to do this may be to use ion channels—proteins that form a channel through which specific inorganic ions can diffuse. Changes in cellular ion concentrations could then be detected and transmitted to the nervous system.Physiologist John DeSimone  says there are at least two ion channel receptors for salt in rodent taste receptor cells. The first of these is the epithelial sodium channel, a widely expressed channel that can be blocked specifically with the drug amiloride. In rats, says DeSimone, only 75% of the nerve response to salt can be blocked by amiloride, so there is probably a second receptor. This, he says, seems to be a generalist salt receptor—the amiloride-sensitive channel only responds to sodium chloride—and may be the more important receptor in people.Sour tastants are acids, often found in spoiled or unripe food. DeSimone's current idea is that strong acids enter taste cells through a proton channel (probably a known channel present on other cell types) while weak acids, like acetic acid (vinegar), enter as neutral molecules and then dissociate to lower intracellular pH. DeSimone believes that he has identified the proton channel involved in sour taste as well as an ion channel that could be the second salt receptor, and he plans to do knockout experiments on both. If these channels are essential elsewhere in the body, as DeSimone suspects, to avoid lethality he will need to construct conditional knockouts in which the channel is lost only in the taste receptor cells.Zuker, meanwhile, is not convinced that the current ion channel candidates for salt and sour perception are correct. And, he says, GPCRs could also be involved in these modalities. ‘There is a precedent for that’, he claims, noting that extracellular calcium is sensed by a GPCR.With many taste receptors now identified, researchers are turning to a long-standing question in taste perception: how is taste coded? When we eat, our tongue is bombarded with tastants. How is their detection and transduction of information organised so that the appropriate response is elicited? Taste physiologist Sue Kinnamon (Colorado State University, Fort Collins, Colorado, United States) explains the two theories of taste-coding. In the ‘labelled-line’ model, sweet-sensitive cells, for example, are hooked up to sweet-sensitive nerve fibres that go to the brain and code sweet. If you stimulate that pathway, says Kinnamon, ‘you should elicit the appropriate behavioural response without any input from other cell types’. In the ‘cross-fibre’ model, the pattern of activity over many receptors codes taste. This model predicts that taste receptor cells are broadly tuned, responding to many tastants. Support for this theory, says Kinnamon, comes from electrical recordings from receptor cells and from nerves innervating the taste buds that show that one cell can respond to more than one taste quality.Zuker and Ryba's recent work strongly suggests that taste-coding for bitter, sweet, and umami fits the labelled-line model in the periphery of the taste system. Their expression data show that receptors for these qualities are expressed in distinct populations of taste cells. In addition, in early 2003, they reported that, as in other sensory systems, a single signalling pathway involving the ion channel TRPM5 and PLCβ2, a phospholipase that produces a TRPM5 activator, lies downstream of the bitter, sweet, and umami receptors. When the UCSD–NIDCR researchers took PLCβ2 knockout mice, which did not respond to bitter, sweet, or umami, and engineered them so that PLCβ2 was only expressed in bitter receptor-expressing cells, only the ability to respond to bitter tastants was regained. These data, says Zuker, support the labelled-line model.The latest data supporting the labelled-line model came last October when Zuker and colleagues described mice in which a non-taste receptor—a modified κ-opioid receptor that can only be activated by a synthetic ligand—was expressed only in cells expressing T1R2, sweet-responsive cells. The mice were attracted to the synthetic ligand, which they normally ignore, indicating that dedicated pathways mediate attractive behaviours. The researchers plan similar experiments to see whether the same is true for aversive behaviours.Even with all these molecular data, the cross-fibre model of taste-coding still has its supporters—just how many depends on whom one talks to. Both Damak and Kinnamon, for example, believe that there is at least some involvement of cross-fibre patterning even in the taste receptor cells. But, says neurobiologist and olfaction expert Lawrence C. Katz (Duke University, Durham, North Carolina, United States), ‘the onus is now on people who believe otherwise [than the labelled-line model] to provide compelling proof for the cross-fibre theory because now, at least at the periphery, the evidence is compelling for a labelled line for bitter, sweet, and umami’. Bartoshuk also says the debate is decided in favour of the labelled-line model in the periphery. The crossfibre model is an interesting historical footnote, she comments.Whether this putative link between taste perception and health can be confirmed and whether it will be possible to manipulate food preferences to improve health remain to be seen. However, it seems certain that, as in the past five years, the next five years will see large advances in our knowledge of many aspects of taste, a fascinating and important sensory system.The periphery of the taste sensory system has yielded many of its secrets, but relatively little is known about the transduction pathways in taste, how taste cells talk to the nervous system, or about events further downstream in the brain. How are signals from taste receptors integrated with those from olfactory receptors to form a representation of complex food flavours, for example? With their expanding molecular toolbox, researchers can now delve deeper into these aspects of taste perception. This may tell us not only about taste but about how the nervous system in general is put together, says Ryba.But understanding taste is not just an academic exercise. It has practical uses too. DeSimone suggests that by understanding salt receptors, it may be possible to design artificial ligands to help people lower their salt intake. As Kinnamon succinctly puts it, ‘Can you imagine eating potato chips and not having the salty component?’ An artificial salt receptor ligand could make salt-free foods a palatable option for people with high blood pressure. Lindemann also sees a great future in artificial ligands for taste receptors. The sense of taste is partly lost in elderly people, he says, so better tastants—effectively ‘chemical spectacles’—might give them back their pleasure of eating and thereby improve their quality of life.Finally, some aspects of taste may be inextricably tied up with general health, says Bartoshuk. Many people who can taste propylthiouracil are also ‘supertasters’—they have more fungiform papillae, structures containing taste buds, on their tongues than non-tasters . Superta


The Mammalian Phenotype (MP) Ontology enables robust annotation of mammalian phenotypes in the context of mutations, quantitative trait loci and strains that are used as models of human biology and disease. The Mammalian Phenotype (MP) Ontology enables robust annotation of mammalian phenotypes in the context of mutations, quantitative trait loci and strains that are used as models of human biology and disease. The MP Ontology supports different levels and richness of phenotypic knowledge and flexible annotations to individual genotypes. It continues to develop dynamically via collaborative input from research groups, mutagenesis consortia, and biological domain experts. The MP Ontology is currently used by the Mouse Genome Database and Rat Genome Database to represent phenotypic data. Mammalian phenotypes are complex and the term itself is imprecise. Generally, we use the word phenotype in referring to the appearance or manifestation of a set of traits in an individual that result from the combined action and interaction of genotype and environment.Because mouse is the premier model organism for the study of human biology and disease, the goal of comparative phenotyping and building new animal models through genetic engineering holds great promise. The mouse has distinct advantages for studies that translate to humans. It is a small, short-lived mammal with a fully sequenced genome in which all life stages can be accessed, and for which myriad tools are available for precisely experimentally manipulating its genome. Further, the large collection of inbred strains of mice and the controlled environment in which the animals live provides the ability to confirm phenotype observations and to systematically perturb environmental factors and genetic input to measure effects under defined conditions. Current international efforts to 'make a mutation' for every gene through mutagenesis  and geneMammalian phenotypes are frequently genetically complex. Mutation of even a single gene almost always produces pleiotropic effects. Conversely, non-allelic mutations can produce indistinguishable phenotypes. Modifier genes and epistatic interactions can markedly alter the phenotype. Combining different allelic combinations of different genes can produce unique phenotypes not found in the single-gene mutation genotype. Imprinting of genes can dramatically affect phenotype. Mutations expressed in different inbred strains of mice can manifest as an increase or decrease of severity or penetrance of the corresponding phenotype. Quantitative trait loci (QTL) can contribute in complex nonlinear ways to the phenotype. In addition, mutations that are 'genomic' in nature, either disrupting or deleting multiple genes or occurring in intergenic regions, can produce distinct phenotypes and challenge us to think beyond gene effects to genomic effects. The outcome of these complex interactions can be dissected and reproducibly examined by characterizing inbred strains that represent the combined phenotype of the 'whole-genome' genotype in its environmental context.The Mouse Genome Database (MGD) at the Mouse Genome Informatics website ,5 servesWritten descriptions of phenotypes in higher organisms reflect the complexity of the subject, the richness of language, and the phenomenal diversity that these data represent. While text descriptions are commonly used in publications describing phenotype, and have been the basis of electronically accessible phenotypic descriptions (for example, Online Mendelian Inheritance in Man (OMIM)  and the Consider the example in Table A further detriment to database text records is their difficulty to update and maintain. As new information is learned about a phenotypic mutant, the record must be continually rewritten. Although this practice might be sustained for a small number of records, it does not scale when thousands of mutant records are considered. The alternative of simply adding on another paragraph to existing text records becomes confusing, with potentially conflicting information and different writing styles appearing in one textual description, and unwieldy, with more and more text that may no longer represent a logical synthesis.Formal nomenclatures for genes, mutant alleles and inbred strains of mice have existed since the 1940s ,9. The MBeyond nomenclatures, which are key to object identities and relationships, are vocabularies that can be used to describe broader concepts and categorizations. Vocabularies can take many forms, including simple lists of controlled terms, such as the cytogenetic band designations used to name the bands defined by chromosome staining or the classes of genetic markers, such as gene, pseudogene, expressed sequence tag (EST), and so forth.The annotation of complex biological data and concepts requires more than lists and simple vocabularies. Ontologies, or 'descriptions of what there is', contain both concepts, with precise meanings, and relationships among those concepts. As such ontologies are able to support descriptions of complex biology and are useful in making these data more amenable to computational analyses. The first widely used ontology developed and adopted in the biological domain is the Gene Ontology (GO) -13 whichAlthough the need for vocabularies as key components to consistent phenotype annotations for mammals has been recognized for some time , and manOur goal is to describe the richness of phenotypes as precisely as they are known, recognizing that phenotype data are by nature complex and usually incomplete. Taking advantage of structural properties of a DAG, we have the ability to annotate phenotypes to the level of data resolution available, whether general or very specific and the ability to query with a high-level term, returning all phenotypes containing annotations to that term or to terms more specific than the query term. Thus, one can query for 'respiratory signs/symptoms' and retrieve all phenotypes annotated to this term and its hierarchical 'children' , or specifically request annotations to any of these sub-terms.The top level terms of the MP Ontology include physiological systems, behavior, developmental phenotypes and survival/aging. Physiological systems branch into morphological and physiological phenotypes at the level immediately below. A browser to view the ontology is available at  Figure . In thisEach MP ontology term has a unique identifier, a definition and synonyms. In the term detail pages, these data and the number of hierarchical paths of the vocabulary where the terms appear are displayed. A plus sign following the term indicates that children of this term exist. In this figure, displayed next to the term, is a link indicating the number of annotation instances in MGD using this term or children of this term. This feature, due to be publicly available in early 2005, will greatly improve phenotype-centric searching in MGD.To initiate the vocabulary, we first developed a high-level categorization of phenotypes consisting of approximately 100 terms, such as heart/cardiovascular dysmorphology and skeletal axial defects. As we used this list for annotations, terms were refined and general organizing principles for the MP vocabulary were developed.An important component of our approach has been to address two practical implementation questions. From the biologist's perspective, the question is what term would be used to describe a specific phenotypic trait. From the curation perspective, we ask what terms reflect biological reality and maximize curator productivity.From a purely ontological perspective, every trait could be broken down into a core object, such as 'cornea' or 'gastrulation', defined by anatomical, behavioral or physiological terms, and a series of attribute vocabularies that describe the quality, quantity and character of a trait. For the practical reason of needing robust terms to describe phenotypes up-front to speed curation and the problem of losing biological meaning, particularly for clinical or dysmorphology terms, when terms are completely deconstructed (that is, the sum of the parts is less than the term itself), we have chosen to use compound terms in the MP Ontology. A few examples of terms where it is difficult to preserve the full biological meaning once they are deconstructed are shown in Table pheno@informatics.jax.org.Three major strategies are being pursued to further develop the vocabulary itself. First and most important is through the ongoing process of curating phenotype data. As new phenotypic traits are described and published, the need for new terms is recognized. New terms added in this way may be a simple addition to an existing hierarchical path or may result in the addition of entire new branches in the hierarchy. Second, collaborative efforts between the MGD phenotype curators, the mouse mutagenesis centers and the rat genetics community identify new specific terms and suggest improved organization of terms within particular hierarchical branches. Third, we are recruiting individuals with expertise in specific biological domains to review and evaluate sections of the vocabulary for accuracy, completeness and systematic arrangement. The MP Ontology is a work in progress and remains incomplete in some areas. We welcome the participation of the mammalian research community so that the most useful, definitive and universally applicable terms will be included. Information can be obtained by sending e-mail to While common pathological and clinical terms are used in the MP Ontology, considerations for term placement within the structure and for precise terminology is often derived from comparison with other open biological ontologies (OBO) . RecentlThe MP Ontology was built as a DAG using the DAG-Edit software written by John Richter and Suzanna Lewis . The MP Phenotypes are described in the MGD relative to the genotype of the individual. Genotype objects specifically consist of one or more allele pairs describing mutations or QTLs and the genetic background strain(s) where the phenotype was observed. Each phenotype annotation associates a MP Ontology term with a genotype/strain and the reference or data source supporting this assertion. Additional modifying text may be annotated to describe detail that is not easily standardized. Examples include experimental conditions, age of onset and incidence, and trait penetrance, among others. The annotation note may also include specifics of the phenotype where such details are deemed to be too case specific to be a MP term. In addition, genotypes are associated with OMIM where a particular mouse genotype is a model for human diseases and syndromes. Figure The MP Ontology and annotation schema was designed to minimize curatorial time, yet remain precise enough to describe phenotypic data. It supports robust phenotypic annotations and querying capabilities for mouse phenotype data. While this vocabulary is far from complete, we have designed strategies for its continued development as a collaborative effort for supporting the representation of existing mutations and those that continue to be created.As of 1 November 2004, over 11,150 phenotypic alleles representing mutations in 5,214 unique genes had been catalogued in MGD. For these alleles, 9,696 genotype records exist, with 21,556 phenotypic annotation instances. The MP Ontology is also used in phenotypic data annotations at the RGD . As our


In the recent years, several cytokines have been associated with Alzheimer's disease (AD) development and progression and many studies have correlated this risk with polymorphisms in the genes encoding these molecules. Also the type 1 cytokine interferon (IFN)-γ belongs to a cytokine class that affects the immune function; in fact it plays a major role in defence against viruses and intracellular pathogens but also in the induction of the immune-mediated inflammatory response. The aim of this study was to evaluate the role of IFN-γ in AD by studying the association of +874T→A IFN-γ gene polymorphism with AD. We included in this study 115 AD patients (70 women, 45 men, mean age 80) and 90 sex and age-matched healthy controls (HC, 51 women, 39 men, mean age 82) from northern Italy. Genomic DNA was extracted with the salting-out method from whole blood of all subjects; the genotyping at IFN-γ loci was assessed with ARMS-PCR. The data obtained from the +874T→A IFN-γ gene polymorphism analysis of AD patients and HC lack of any statistically significant differences also when stratified according to gender. In conclusion these results confirm the previous shown lack of association between +874T→A IFN-γ gene polymorphism and the risk of AD. However, other polymorphisms have been demonstrated to influence IFN-γ transcription and since natural killer cells of AD patients show higher production of the cytokine, further analysis will be necessary to clarify the role of this gene in the pathogenesis of the disease. In the human brain several cell types are responsible for initiating and amplifying a specific inflammatory response. In Alzheimer disease (AD) signs of an inflammatory activation of microglia and astroglia are present both inside and outside amyloid deposits. Cell cultures and animal models suggest an interactive relationship between inflammatory response activation, reduced neuronal functioning and amyloid deposition. Furthermore cells associated with extracellular plaques within AD brains can produce a variety of cytokines, chemokines and other related proteins that influence plaque and tangle formation . For the


The TM4SF10 gene encodes a putative four-transmembrane domains protein of unknown function termed Brain Cell Membrane Protein 1 (BCMP1), and is abundantly expressed in the brain. This gene is located on the short arm of human chromosome X at p21.1. The hypothesis that mutations in the TM4SF10 gene are associated with impaired brain function was investigated by sequencing the gene in individuals with hereditary X-linked mental retardation (XLMR).The coding region (543 bp) of TM4SF10, including intronic junctions, and the long 3' untranslated region (3 233 bp), that has been conserved during evolution, were sequenced in 16 male XLMR patients from 14 unrelated families with definite, or suggestive, linkage to the TM4SF10 gene locus, and in 5 normal males.Five sequence changes were identified but none was found to be associated with the disease. Two of these changes correspond to previously known SNPs, while three other were novel SNPs in the TM4SF10 gene.We have investigated the majority of the known MRX families linked to the TM4SF10 gene region. In the absence of mutations detected, our study indicates that alterations of TM4SF10 are not a frequent cause of XLMR. Caenorhabditis elegans VAB-9 protein, a protein that has recently been shown to be involved in the control of cell adhesion and epidermal morphology [Brain Cell Membrane Protein 1 (BCMP1) cDNA was fortuitously isolated from a thyroid cDNA library [rphology . The proInitial Northern blot analysis of TM4SF10/BCMP1 gene transcripts distribution in adult dog tissues revealed very high expression in the brain, and lower but clearly detectable levels of expression in most of the tissues examined  confirmeInitially, the TM4SF10 gene was assigned to Xp11.4 . Recent Blood genomic DNA was collected from 16 patients (14 unrelated) and 5 unrelated healthy volunteers using a standard procedure . The patPCR reactions were performed in a final volume of 100 μl containing 200 ng of genomic DNA, 1 μg of each primer  on an Applied Biosystems 3100 automatic DNA sequencer. The sequences of the primers are given in table rd base of the codon Arg59, where a C residue was present in half of the sequences and a G residue in the other half. Individual single nucleotide polymorphism (SNP) data are shown in table The human TM4SF10 gene is composed of 3 exons and produces a 4 kb-long mRNA. The short coding region (543 bp) is interrupted by 2 introns and the last and the largest exon also contains a 3 233 bp-long 3'UTR (see Figure The long 3'UTR sequence of the TM4SF10/BCMP1 transcript is highly conserved, with an overall score of 72% when human, dog, mouse and rat sequences are compared. As the 3'UTR of mRNAs may contain regulatory sequences that participate in the control of gene expression, we decided to screen this part of the gene as well. The entire region, including the sequences around the polyadenylation site, was subdivided into four overlapping fragments of approximately 1 kb in length (3'UTR F1–F4, Figure TM4SF10 sequence was obtained from 16 patients and 5 controls. Four SNPs were identified in the non-coding part of the gene: 3 of them were located in the 3'UTR of the mRNA while the fourth one was located downstream of the polyadenylation site (Figure In this study, we have investigated the majority of the known MRX families linked to the TM4SF10 gene region. In the absence of mutations detected, our results indicate that alterations in the transcribed region of TM4SF10 are not a frequent cause of XLMR. Although the gene promoter has not been identified and screened yet, it appears very unlikely that all mutations would be there.This work also identified three novel SNPs in the TM4SF10 gene, which adds to our knowledge of SNP occurrence within this gene.None declared.CCH performed/managed the PCR and sequencing reactions, and analyzed the DNA sequences. FK, JG, MJA, EHF and CS provided the DNA samples. These authors also participated in the writing of the manuscript. DC conceived and supervised the study, and drafted the manuscript. All authors read and approved the final manuscript.The pre-publication history for this paper can be accessed here:


Chemical reactions lie at the heart of many biological processes, from photosynthesis and respiration to cell signaling and drug metabolism. Thanks to an atmosphere rich in oxygen, many organisms use oxygen to carry out these life processes. But oxygen metabolism produces highly toxic by-products called reactive oxygen species. When oxidation outpaces detoxifying reactions, oxidative stress occurs, and accumulating reactive oxygen species are free to wreak havoc on cellular machinery.PLoS Biology, Lars Leichert and Ursula Jakob describe a novel method to monitor thiol modifications in proteins subjected to varying redox conditions in a living organism, the bacteria Escherichia coli. This technique is capable of providing a global snapshot of the redox state of protein cysteines during normal and oxidative stress conditions in the cell.Cysteine, one of the 20 different amino acids that make up proteins, contains a thiol group, which can be modified upon oxidation. A thiol group can stabilize protein structures by forming covalent disulfide bonds and can mediate cysteine-regulated redox reactions. At the same time, however, the high reactivity of thiol groups makes them also particularly vulnerable to nonspecific reactions during conditions of oxidative stress. Over the past few years, an increasing number of proteins have been discovered that use oxidative thiol chemistry to regulate their protein activity. In E. coli periplasm (the region between the cell's membrane layers), and they were.To detect proteins that have the ability to undergo stress-induced thiol modifications, Leichert and Jakob differentially labeled the thiol groups of thiol-modified and non-thiol-modified proteins. The proteins were then separated on two-dimensional gels based on their charge and molecular weight. If the technique worked, most thiol-modified proteins should be detected in the oxidizing environment of the E. coli periplasm—was targeting. In E. coli mutant strains that lack DsbA, Leichert and Jakob identified a number of proteins with either substantially less or no thiol modification as compared to wild-type (non-mutant) strains, suggesting that these proteins are indeed DsbA substrates.After proving the method's ability to detect proteins whose thiol groups were oxidized, the next logical step was to determine what proteins DsbA—the enzyme that catalyzes disulfide bond formation in the E. coli cytoplasm contains several reducing systems. When the researchers tested a mutant strain that lacked the gene for the reducing enzyme thioredoxin, they found that a large number of proteins accumulated in an oxidized state. Many of these proteins have cysteines and require a reduced thiol status for their activity. These results demonstrated that under normal growing conditions, many proteins contain cysteine residues that are vulnerable to even small amounts of reactive oxygen species and so require the constant attention of detoxifying enzymes.In contrast to the periplasm, the In a final set of experiments, Leichert and Jakob discovered a number of proteins whose thiol groups get specifically modified in the presence of reactive oxygen species. These results start to explain some of the many metabolic changes that occur in oxidatively stressed cells.Leichert and Jakob's technique should be applicable to many different cell types and organisms and can be used to investigate the in vivo thiol status of cellular proteins exposed to virtually any physiological or pathological condition that is accompanied by oxidative stress. The next step will be to investigate just how thiol modifications mediate the various functions of redox-regulated proteins.


Science, Stuart Kim, a Stanford developmental biologist, made the case for laying down the broad strokes of a complex physiological process before defining its mechanisms. “A powerful, top-down, holistic approach,” he wrote, “is to identify all of the components of a particular cellular process, so that one can define the global picture first and then use it as a framework to understand how the individual components of the process fit together.” To get a broad view of gene expression in the aging nematode, Kim's lab turned to DNA microarrays and functional genomics. In a new study, Kim and colleagues apply this same approach to the decidedly more complex problem of human aging and “present a molecular portrait” of the aging kidney.Four years ago in Scientists have identified a wide range of molecular pathways and mechanisms associated with aging. Many have been found in evolutionarily distant organisms, suggesting they have been conserved and could shed light on human aging. Yet other studies suggest that since few animals reach old age in the wild, any aging-related physiological changes aren't likely to impact the fitness of a population and so aren't likely to be conserved. Consequently, aging pathways in worms, for example, would have little bearing on humans. To investigate the molecular pathways associated with human aging, the authors focused on human tissue—in this case, the kidney.Kidneys came from 74 patients, ranging in age from 27 to 92. Samples were extracted from donated kidneys or “meticulously harvested” from kidneys with localized disease to ensure only normal tissue was taken. Two structures that are critical to kidney function (removing toxins from blood) were removed from each sample: the renal cortex, which filters plasma, and the medulla, which alters urine composition to maintain fluid balance. Both deteriorate with age. An extensive clinical history was noted for each sample to account for any potentially confounding medical factors.Kim and colleagues then isolated RNA transcripts from the samples to determine the activity of every gene, broken down by age and kidney section, through microarray analysis. Looking for differences in gene expression across the genome, they identified genes that showed a statistically significant change in expression as a function of age. Of 33,000 known human genes on the microarray, 985 showed age-related changes, most showing increased activity. These changes are truly age-regulated, the authors conclude, since none of the medical factors impacted the observed changes in gene expression.Although cortex and medulla have different cell types and perform different functions, their genetic aging profile was very similar, suggesting a common aging mechanism operates in both structures. In fact, these mechanisms may function broadly, as most of the age-regulated kidney genes were also active in a wide range of human tissues. Other organisms appear to lack these changes, however, prompting the authors to argue that understanding aging in humans will require human subjects.Most importantly, the genetic profile of the tissue samples correlated with the physiological and morphological decline of an aging kidney. An 81-year-old patient with an unusually healthy kidney had a molecular profile typical of someone much younger, while a 78-year-old with a damaged kidney had the profile of a much older person. Using the power of functional genomics, this study has identified a set of genes that can serve as molecular markers for various stages of a deteriorating kidney and predict the relative health of a patient compared to their age group. These gene sets can also serve as probes to shed light on the molecular pathways at work in the aging kidney, and possibly on the process of aging itself.


Although the poles are less diverse than the tropics, this decline shows substantial asymmetries between the hemispheres, suggesting that responses to environmental change may differ substantially in the north and the south. Penguins have been receiving a lot of bad press lately. They are considered somehow counter, spare, strange. Unlike most plant and animal groups, they do not show a peak of species richness towards the equator and a decline towards the poles. This more conventional spatial pattern is conveniently known as the latitudinal diversity gradient because of the strong covariance of richness and other measures of biodiversity that it describes. It is one of the most venerable, well-documented, and controversial large-scale patterns in macroecology . EquatorAlthough spatial patterns in biodiversity, and particularly the latitudinal gradient, are increasingly well documented for a range of taxa, the proposed mechanisms underlying these gradients remain controversial. In essence, the multitude of mechanisms proposed to explain diversity gradients can be reduced to three categories: historical, ecological, or null. Most significant in raising the temperature of recent discussions is the question of the relative importance of each of these major categories. Historical mechanisms are those that suggest that earth history (e.g., the opening of the Drake Passage and the cooling of Antarctica) and phylogenetic history have played major roles in generating current patterns in diversity, and tend to emphasise regional  differences therein . ExplanaNonetheless, juxtaposing these three major mechanisms raises several questions that could substantially inform the debate in many ways, but have enjoyed far less attention than debating the relative merits of each of them. The geometric constraints model suggests that, to the extent that there is symmetry in the continuity of land (or water) about the equator, declines in richness from the tropical peak should also be symmetrical, with any asymmetries in the latter matching those in the former. Indeed, most texts and reviews dealing with latitudinal diversity gradients only briefly mention hemisphere-related differences and focus instead on the general decline of diversity away from the tropics in both directions e.g., . HoweverThe last 100 million years have seen both a substantial steepening in latitudinal diversity gradients and the fragmentation of continental land masses . By 15 mMean annual precipitation is spatially more complex. Overall, precipitation is slightly higher in the south than in the north, at least below 60° latitude. However, much of this precipitation falls over the ocean in the south, leaving the more temperate parts of the southern continents as dry as their northern counterparts . SpatialClearly, the spatial complexity of climatic variation is much greater than the present overview would suggest. However, these broad brush strokes capture the hemisphere-related variation that might be most significant from a biological perspective.If differences in climates do cascade upwards to influence individuals, species, and broader scale patterns in diversity, their influence should be readily detectable at the level of species' life histories and distributions. In birds, large-scale geographic variation in life history variables, such as the incidence of cooperative breeding, extent of parental care, survival, and the timing of reproduction, has been studied for at least the past 50 years, and the mechanisms underlying this variation have been much debated. Taking phylogeny and the idiosyncrasies of the Australian avifauna into account, southern species typically lay small clutches and have long fledging periods, and it is often difficult to predict their date of first laying or, indeed, whether they will lay in a particular year at all . By contThese kinds of differences extend to other taxa. Thus, although the variation of metabolic rate with latitude is becoming increasingly well known for a variety of groups, Insect life histories also show hemisphere-related variation. Low-temperature-related diapause is virtually absent in southern species e.g., , and metNorth–south asymmetries also show up in snowlines, treelines, the frost tolerance of trees, and the proportion of winter deciduous species . Indeed,In the years since By contrast, it appears that proximate ecological correlates of diversity gradients differ considerably between north and south. Although both historical and ecological factors have led to variation in the numbers and identity of species across the globe , climateOf course, biodiversity is not just species richness, but also encompasses the ecological complexes of which species are a part. Although potential north–south asymmetries in interactions have not been widely explored, recent work is providing tantalising glimpses of such variation. Thus, it appears that on the basis of a straightforward  comparative analysis, specialisation in plant–pollinator relationships is much greater in the south than in the north. European and North American orchids are typically visited by five species of insects, whereas in southern Africa the median is a single pollinator species per species of orchid  Figure . Insect–Despite considerable spatial complexity, there do seem to be regular north–south differences in species life histories and patterns of range size variation that are consistent with disparities in the climates of the two hemispheres . These dFirst, both phylogenetically independent and non-independent comparisons of life history traits and physiological variables across a variety of groups are required. Contrasting these approaches will provide considerable insight into how much of the signal is based on phylogenetic patterns, and how much on current ecological responses. Whilst in some cases data may be obtained from the literature, it is likely that new work will have to be undertaken, especially in the southern hemisphere, where the number of past investigations of such traits is generally much lower than in the north. Moreover, replicated studies using similar methods might substantially improve the signal-to-noise ratio, which can be weakened in “macrophysiological” or large-scale life history and physiological comparisons by the fact that different methods often lead to different outcomes.Second, there is much to be said for the application of similar methods to investigations of large-scale, hemisphere-related patterns of species interactions. Differences like those in plant–pollinator systems discussed here might extend to other interactions in marine and terrestrial systems. Contrasting phylogenetically independent and non-independent comparisons are likely to provide much insight into the reasons for those asymmetries that are found.Finally, comparisons of latitudinal gradients and their underlying correlates in the two hemispheres for the same taxon, sampled using similar methods, and investigated with methods that take cognisance of likely confounding effects are required. This approach will provide a means of determining whether asymmetries in the climates of the two hemispheres really do translate into differences in biodiversity patterns. Such an approach goes to the heart of the question of the processes underlying the latitudinal gradient in species richness, and could go a considerable way to teasing apart the importance of historical, ecological, and null explanations, and identifying the mechanisms that underlie them.In our view, clarifying these issues is of considerable importance. What is at stake is not a set of arcane ecological questions, but rather questions that are central to determining whether ecological and conservation lessons learnt in one area can be applied more broadly. For example, it has been suggested that climate change will cause substantial extinctions in the near future . Indeed,


Caenorhabditis elegans, combining genetics, gas chromatography, and DNA microarray analysis. We show that C. elegans synthesizes mmBCFAs de novo and utilizes the long-chain fatty acid elongation enzymes ELO-5 and ELO-6 to produce two mmBCFAs, C15ISO and C17ISO. These mmBCFAs are essential for C. elegans growth and development, as suppression of their biosynthesis results in a growth arrest at the first larval stage. The arrest is reversible and can be overcome by feeding the arrested animals with mmBCFA supplements. We show not only that the levels of C15ISO and C17ISO affect the expression of several genes, but also that the activities of some of these genes affect biosynthesis of mmBCFAs, suggesting a potential feedback regulation. One of the genes, lpd-1, encodes a homolog of a mammalian sterol regulatory element-binding protein (SREBP 1c). We present results suggesting that elo-5 and elo-6 may be transcriptional targets of LPD-1. This study exposes unexpected and crucial physiological functions of C15ISO and C17ISO in C. elegans and suggests a potentially important role for mmBCFAs in other eukaryotes.Monomethyl branched-chain fatty acids (mmBCFAs) are commonly found in many organisms from bacteria to mammals. In humans, they have been detected in skin, brain, blood, and cancer cells. Despite a broad distribution, mmBCFAs remain exotic in eukaryotes, where their origin and physiological roles are not understood. Here we report our study of the function and regulation of mmBCFAs in  C. elegans produces two mmBCFAs that are essential for growth, suggesting an important role in other eukaryotesMonomethyl branched chain fatty acids (mmBCFAs) are found in bacteria and up through mammals.  Fatty acids (FAs) belong to a physiologically important class of molecules involved in energy storage, membrane structure, and various signaling pathways. Different FAs have different physical properties that determine their unique functions. Among the most abundant in animal cells as well as the most studied are those of long-chain even-numbered saturated and unsaturated FAs.C15ISO and C17ISO are saturated tetradecanoic and hexadecanoic FAs with a single methyl group appended on the carbon next to the terminal carbon . MonometVernix caseosa , elo-4 (C40H1.4), elo-7 (F56H11.3), and elo-8 (Y47D3A.30)—did not produce any notable phenotypes, whereas suppression of elo-1 (F56H11.4) and elo-2 (F11E6.5) affected the elongation of straight long-chain saturated and polyunsaturated FAs (In characterizing FA elongation in  enzymes . To testated FAs .elo-5 (F41H10.7) and elo-6 (F41H10.8), affected the levels of branched-chain FA. Transcriptional reporter constructs (elo-5Prom::GFP and elo-6Prom::GFP) indicated that both genes are expressed in the gut . RNAi of Y39E4A.3 led to a significant decrease in C15ISO and C17ISO production  to wild-type animals did not cause obvious morphological or growth defects, the suppression of elo-5 resulted in more pronounced phenotypes (elo-5(RNAi) plates displayed no obvious growth or morphological abnormality until the second day of adulthood, when they developed an egg-laying defect , their progeny did not arrest in L1 but continued to develop into adulthood. These animals had no obvious defects in locomotion, pharyngeal pumping, intestinal contractions, chemotaxis response, touch sensitivity, or general anatomy (unpublished data). However, the growing worms became progressively sick , which has a 245-bp deletion eliminating the predicted first exon (Genome Science Center, BC Cancer Research Center, Vancouver, British Columbia, Canada). This allele phenocopies the L1 arrest phenotype of the elo-5(RNAi) animals.We also obtained a likely null mutant of the elo-5(RNAi) animals resulted directly from the deficiency of C15ISO and C17ISO, then feeding these worms with C15ISO and C17ISO should mask a shortage of endogenous C15ISO and C17ISO and permit the animals to grow normally. As predicted, the C17ISO and C17anteISO supplements rescued the elo-5 RNAi defects (in 52 of 60 and 58 of 60 plates, respectively). A partial rescue was observed on the plates supplemented with C15ISO and C15anteISO (23 of 38 and 20 of 28 plates, respectively). Corroborating results were obtained when homozygous elo-5(gk208) animals supplied with C17ISO grew normally. In sharp contrast, neither saturated or mono- or polyunsaturated FA molecules (C16:0, C16:1 n7, C17:0, C18:3 n6), mmBCFAs with shorter or longer backbones (C13ISO, C18ISO, C19ISO), nor polymethyl branched phytanic acid were able to rescue or reduce defects (0 of 30 plates in each experiment). Therefore, we have determined that only dietary 17-carbon mmBCFAs are competent to bypass the biochemical defect caused by loss of ELO-5 function.We reasoned that if the defects observed in the elo-5(RNAi) worms grown on supplemented plates revealed that only C17ISO and C17anteISO are significantly incorporated into lipids (elo-5(RNAi) feeding Escherichia coli strain (HT115), which lacks mmBCFAs. This mmBCFA-producing strain was identified by chance; we noticed that in the presence of a certain bacterial contaminant the animals could overcome the elo-5(RNAi) effects. Using a rapid bacterial identification method  animals fed with S. maltophilia indicated that they not only accumulated bacterial C15ISO and C15anteISO but also efficiently elongated these FA species to C17ISO and C17anteISO, which are absent in S. maltophilia (elo-5(RNAi) animals. Therefore, ELO-6 function remains intact in elo-5(RNAi). Apparently, C15ISO added to the plates could not be utilized by ELO-6 whereas C15ISO-CoA and/or C15anteISO-CoA originating from the bacterial food could, suggesting that free and esterified mmBCFAs were likely to enter alternative pathways.GC analysis of FA composition in o lipids A–6C. Beco lipids A, we wann method , we dete mmBCFAs D. GC anatophilia D and 6E.elo-5(gk208) deletion mutant. The homozygous mutants grew without any obvious morphological defects when maintained on the plates supplemented with C17ISO or seeded with S. maltophilia. However, removal of the FA supplements or S. maltophilia by bleaching resulted in the same L1 arrest phenotype seen for the elo-5(RNAi) worms.The essential roles of C15ISO and C17ISO were also supported through an examination of the elo-5(RNAi) animals arrested at the L1 stage could be recovered by adding the 17-carbon mmBCFA supplements. Indeed, C17ISO and C17anteISO could effectively release L1 larvae from the developmental arrest; about 50% of 2-d-arrested and 1% of 4-d-old L1 were rescued to full growth and proliferation. Since C17anteISO could not be detected in the laboratory animals under normal conditions of culturing, C17ISO appeared to be the principal molecule conveying the ELO-5 function. Therefore, the L1 arrest of the C17ISO-depleted worms is both completely penetrant and reversible, indicating that C17ISO plays a critical role in growth and development at the L1 stage.We then asked if elo-5 nor elo-6 is significantly expressed in eggs or L1. Therefore, C17ISO likely accumulates in embryos during oogenesis. It may be directly transported from gut to gonads, since both ELO-5 and ELO-6 were expressed mainly in the gut and since feeding C17ISO rescued the elo-5 mutant phenotypes. When RNAi-mediated disruption of elo-5 occurs at the L1 stage of a parent and consequently blocks C17ISO synthesis from that stage on, the eggs and L1 animals of the next generation are expected to contain a critically low concentration of C17ISO, halting further development. Because the arrested L1 can be rescued by a dietary supply of the mmBCFA, the deficiency is not likely to cause critical defects during the embryonic and early postembryonic periods.The analysis of the FA levels of staged worms revealed that the C17ISO level increases gradually from a relatively low level at L1 to its peak in gravid adults containing eggs A. Based elo-5 RNAi is applied to the parent worms at or after the L2 larval stage, when the amount of C17ISO has already been elevated and/or the RNAi effect is less penetrant, the progeny may receive sufficient C17ISO to pass the L1 arrest stage. The resulting animals, however, become visibly unhealthy at the L4 and adult stages as mentioned earlier, suggesting that C17ISO also plays a role in late developmental stages.If Based on these results, we propose a relationship between the amounts of C17ISO and developmental stages B. In thin = 50) obtained from mixed populations of wild-type animals where the fractions of eggs, larvae, and adults randomly varied. We also included GC data separately obtained from staged worms: eggs, L1, L2, L3, L4, and gravid adults. We found that the amounts of C17ISO significantly correlated with only two other FA molecules: linoleic acid (C18:2 n6) and vaccenic acid (C18:1 n7)  . A potenStreptomyces avermitilis -treated worms, a substantial loss of C15ISO and C17ISO is also accompanied by a change in the FA composition, most noticeably by the elevation in C18:1 n7 (see elo-5(RNAi) worm compared to wild type (SI = 0.325 ± 0.011 [n = 6] and SI = 0.320 ± 0.032 [n = 5], respectively). Therefore, elo-5(RNAi) may not cause massive cell membrane dysfunction.In the 1 n7 see C, a resuA positive correlation between the amounts of C17ISO and C18:2 n6 may suggest a potential common function during development. In addition to the importance of linoleic acid as a substrate for polyunsaturated FA biosynthesis, its hydroxylated fatty acid derivative (HODEs) is known as a signaling molecule affecting chemotaxis , cell prelo-5(RNAi) animals fed with C15ISO or C15anteISO containing bacterial supplement , the FA composition was significantly altered  , FAS, and glycerol 3-phosphate acyltransferase (G3PA) , which promotes the expression of FA metabolic enzymes . There ieted 1”) . McKay ae (G3PA) . Thus, slpd-1 also plays a role in mmBCFA metabolism. We first applied RNAi to lpd-1 and determined the FA composition of the mutant worms. As expected, the FA content of treated animals was significantly changed, but surprisingly the most reduced were the levels of C15ISO and C17ISO . McKay and coauthors have shown that the lpd-2(RNAi) and lpd-1(RNAi) phenotypes are quite similar; affected worms are defective in growth, pale and scrawny in appearance, and lacking in fat content (lpd-1(RNAi), the FA composition in lpd-2(RNAi) worms was not significantly different from that of wild-type animals even though these animals had a noticeably sick appearance (unpublished data). This result suggested that, in addition to having some common targets, LPD-1 and LPD-2 have distinct functions. LPD-1 is important for production of mmBCFAs as well as other very-long-chain FAs, whereas LPD-2 has no specificity for any particular type of FA.LPD-2 (C48E7.3) is another  content . They halpd-1(RNAi) would be consistent with downregulation of elo-5, elo-6 (decrease in mmBCFA), elo-2 (increase in C16:0) (9- and/or Δ12-desaturase genes (decrease in C18:2 n6). The genes encoding mammalian orthologs of the C. elegans elo-2 and Δ9-desaturase genes are known targets of SREBP-1c  , and Δ9-SREBP-1c . To examlpd-1Prom::GFP fusion construct (a gift of J. Graff) in transgenic animals revealed that, in addition to the previously reported expression in intestinal cells  plates, the expression was noticeably weakened, suggesting a downregulation of the promoter activities .If LPD-1 promotes tivities A–11D. Nolpd-1(RNAi), we analyzed FA composition in FAS(RNAi) strains. There is one predicted FAS gene, F32H2.5, and its shorter homolog, F32H2.6, in the C. elegans genome. The latter can only encode the N-terminal portion of the protein. These genes share extended nucleotide identity, and RNAi of one could thus possibly affect the other. Consistent with a critical role for FAS in the first steps of FA biosynthesis, the RNAi-mediated disruption of F32H2.5 and F32H2.6 resulted in multiple defects and a lethal growth arrest (unpublished data). The FA composition (the content and relative amounts of various FA species) of the affected animals remained, however, unchanged. This suggests that disruption of FAS does not selectively alter FA biosynthesis and that neither FAS protein is specific for mmBCFA. Therefore, downregulation of FAS by loss of lpd-1 cannot account for the severe deficiency of mmBCFA in lpd-1(RNAi).To test if the disruption of FAS, a target of LPD-1 , could clpd-1 affects C15ISO and C17ISO biosynthesis. The fact that lpd-1, elo-5, and elo-6 are expressed in the same cells concurrently and that the GFP reporter analysis indicated that elo-5 and elo-6 transcription is downregulated in the absence of lpd-1 suggests that elo-5 and elo-6 are likely to be the targets of lpd-1.Thus, we have shown that disruption of C. elegans.Since ACC and FAS catalyze the first steps in the biosynthesis of straight-chain FAs while ELO-5 and ELO-6 extend mmBCFA molecules, LPD-1 appears to integrate conventional and “unusual” FA biosyntheses. It seems reasonable to predict that in order to differentiate between these metabolic pathways and mediate compensatory or adaptive changes in FA composition, LPD-1 must interact with other factors such as nuclear receptors activated by specific FA ligands. It is thus important to screen for such interactions to better understand FA homeostasis in lpd-1 could be regulated by mmBCFAs at the transcriptional level. Our microarray data (discussed below) indicated a 1.68-fold upregulation of lpd-1 in the elo-5(RNAi) animals, while no changes were detected in its levels between samples from wild-type animals at different developmental stages  and control plates to compare GFP fluorescence. No obvious difference in the GFP expression driven by the lpd-1 promoter in intestinal cells was detected on the elo-5(RNAi) plates versus the control plates. A modest change in the transcription level (1.68-fold) could be masked by a variability of the expression between individual animals and even between individual cells (unpublished data). In contrast to the observation for the intestinal cells, a strong induction of GFP was detected in amphid neurons of lpd-1Prom::GFP;elo-5(RNAi) animals (elo-5(RNAi) animals may transcriptionally stimulate LPD-1 production, at least in neuronal cells.To examine the influence of the mmBCFA deficiency on  animals E–11H. Thlpd-1 and C15ISO/C17ISO is reciprocal; while downregulation of lpd-1 transcription results in the C17ISO deficiency, the C15ISO and C17ISO deficiency upregulates lpd-1 transcription at least in a subset of cells. Therefore, the worm SREBP homolog, LPD-1, may play an important role in mmBCFA homeostasis.Collectively, our results suggest that the relationship between Because C15ISO and C17ISO play critical roles in animal development and growth, we suspected mechanisms might exist to respond to and regulate their levels. Regulation of mmBCFA homeostasis may involve transcription factors, metabolic enzymes, and transport and binding proteins. It is reasonable to suggest that a deficiency of mmBCFA triggers a compensatory alteration in the expression of these genes. It is also possible that a comparative analysis of global gene expressions between wild-type and mmBCFA-deficient animals may reveal these potential changes and the changes underlying developmental and growth functions of mmBCFA.elo-5(RNAi) and wild-type animals. To select candidate genes, we applied restrictive criteria and excluded genes of which the expression was also changed in the spt-1(RNAi) strain (spt-1 (C23H3.4) gene encodes a predicted C. elegans homolog of serine-palmitoyl transferase subunit 1. RNAi of spt-1 strongly affects the FA composition without reducing the C15ISO or C17ISO levels (unpublished data). The F1 generation of spt-1(RNAi) animals developed gonadal and egg-laying defects that were similar to the phenotype of F1 animals from parents treated with elo-5(RNAi) at a late larval stage , we would be able to eliminate variations in gene expressions unrelated to the mmBCFA deficiency. Such variations might emerge from altered straight-chain FA metabolism and from general sickness. Here, we discuss the analysis of the first set of candidate genes that are differentially expressed in elo-5(RNAi) and may relate to the C15ISO and C17ISO homeostasis.We used DNA microarray analysis to compare the total gene expression in ) strain . The sptpnk-1 [C10G11.5], nhr-49 [K10C3.6], acs-1 [F46E10.1], and C27H6.2) significantly affected the FA composition .Twenty-five genes were selected in the screen  and eachposition . All foupnk-1, nhr-49, and acs-1 were upregulated in C17ISO-deficient elo-5(RNAi). Lastly, a functional analysis shows that these three candidate genes are required for the normal level of mmBCFA production (RNAi of the genes affects mmBCFA production). The fourth candidate gene, C27H6.2, affects the level of vaccenic acid (C18:1 n7), which is related to the levels of mmBCFA  plates indicated a significantly brighter fluorescence in the RNAi worms (see acs-1and pnk-1 under C15ISO or C17ISO deficiency. These results were in concordance with the microarray data. Moreover, pnk-1, but not acs-1, seemed to be regulated by LPD-1 because pnk-1Prom::GFP expression was significantly reduced on lpd-1(RNAi)  see L and 11Npnk-1 and acs-1 genes were previously selected in two different screens as potential targets of the daf-2/daf-16 (Y55D5A.5 and R13H8.1, respectively) pathway. pnk-1 had been identified in a screen for genes affecting the life span and metabolism of C. elegans through analysis of promoter regions, and it was confirmed as a direct target of DAF-16, a forkhead transcriptional factor (acs-1 had been identified in a microarray screen for DAF-16 targets that influence life span (nhr-49, had been previously selected in a screen for fat regulatory genes (nhr-49(RNAi) animals showed that reduction of nhr-49 activity results in upregulation of saturated FA biosynthesis that may contribute to fat accumulation. Although the regulatory path for this process remains unknown, the involvement of daf-2 has not been ruled out.It was interesting to note that the l factor . acs-1 hife span . A thirdry genes . It was C. elegans insulin-signaling pathway is involved in sensing nutritional state and metabolic conditions as well as controlling growth and diapause  animals . Second, worms may obtain mmBCFAs from their diet (bacteria). Therefore, C. elegans is able to produce, activate, transport, and utilize mmBCFAs and is vitally dependent on this system.Two mmBCFAs are normally detected in The level of C15ISO and C17ISO in eggs appears to be critical for growth and development, as animals depleted of C15ISO or C17ISO completely arrest at the L1 stage. The uniformity and reversibility of the arrest would be consistent with a regulatory role in growth and development for these mmBCFAs or for more complex lipid molecules containing them. However, it cannot be ruled out that the arrest is due to the failure of a metabolic or structural function that is essential for growth and development at the first larval stage. In addition, C15ISO and C17ISO may directly or indirectly regulate genes involved in FA homeostasis. Consistent with this, their deficiency triggers a large alteration in gene expression that may reflect a complex feedback mechanism. Among the potentially responsive genes are transcription factors and metabolic genes.Ubiquitous and unattended mmBCFAs come forth as physiologically important molecules that regulate essential functions in eukaryotes. Many interesting questions regarding mmBCFAs remain to be addressed. What are the other components of the mmBCFA biosynthetic machinery? What are the components of their transport system? Does an organism have a mechanism by which the mmBCFA level is measured? What are the signaling pathways involved in the mmBCFA responses? How do mmBCFAs exert their physiological function? Do mmBCFAs act alone or as parts of more complex lipids? How are mmBCFAs synthesized in mammals? Lastly, what are the specific physiological functions of mmBCFAs in mammals? Both genetic and biochemical approaches will be taken to address these questions.C. elegans whole genome RNAi feeding library (J. Ahringer, MRC Geneservice, Cambridge, United Kingdom).The RNAi feeding vectors were either made in our laboratory using Taq PCR and cloning genomic fragments into a double T7 vector, pPD129.36 (gift of A. Fire), or obtained from the E. coli HT115 transformed with either empty pPD129.36 vector (controls) or with dsRNA-producing constructs. Plates were prepared as described in The RNAi feeding strain was A mixed population of well-fed worms were washed off the plates with water, rinsed 3–4 times, and, after aspirating away water, frozen at −80 °C. FA methyl esters and lipid extraction were performed as described in After bleaching gravid adults, an aliquot of the eggs was set apart, and the rest was incubated overnight in M9 at room temperature. On the next day, an aliquot of L1 was frozen for GC analysis. The rest of L1 was plated on agar plates. Subsequently, L2, L3, L4, young adults, and adults along with hatched L1 were collected as the separate samples. Mixed populations of worms starved for 24–100 h were included in the experiment to monitor a possible effect of the starvation.elo-5 dsRNA-producing plasmid or the control HT115 vector. Two synchronized young adults were plated and their progeny was scored 4 and 5 d later. Each experiment was performed in at least 30 replicates. For recovering elo-5(RNAi) worms from L1 arrest, wild-type adults were placed on the elo-5(RNAi) plates. Four days later, their progeny was removed and eggs of the next generation were left on the plates. Hatched L1 were kept for 2 or 4 d before transferring as agar chunks to new elo-5(RNAi) plates. FA supplements were added to spots next to the chunks. Ten plates were prepared for each FA supplement. Control plates contained no supplements. To verify that an addition of supplements did not affect RNA interference per se, we used let-418(RNAi) animals, which have a sterile phenotype, as a control. Neither C15 nor C17 mmBCFA added to let-418(RNAi) plates modified the expected phenotype.Ninety microliters of the 4 mM solution of FA (Sigma, St. Louis, Missouri, United States) in 1% NP40 was dropped on the side of the bacterial lawn that contained either To prepare the GFP fusion constructs, genomic fragments were PCR amplified and cloned in frame into one of the GFP fusion vectors (gift of A. Fire). The locations of the genomic fragments and PCR primers used are listed below:elo-5Prom::GFP, starting at 3.894 kb genomic upstream of the first codon and ending 4 bp into the first exon; primers, F-BamHI-TTTAGGTCATTTTTTGAGTCGCCA and R-BamHI-TAGTCTGGAATTTTGAAATTGAACGG; vector, pPD95.69;(1) elo-6Prom::GFP, a 4.764-kb fragment covering 3,104 bp upstream and 1,660 bp downstream of the predicted start codon and ending 14 bp into the third exon; primers, F-Sph1-GCCCTTGGAAACCATCTACGACGAATC and R-Sma1-TCCGAACAGAACGACATAAGAGATTTCC; vector, pPD95.77;(2) acs-1Prom::GFP, a 3.142-kb genomic fragment containing 3,048 kb upstream of the first predicted ATG and ending 24 bp into the second predicted exon; primers, F-SphI-CATAATTACTATTGCGTCACATG and R-SphI-CTCTTCCAAACTGGCGATGTCGA; vector, pPD95.69;(3) pnk-1Prom::GFP, a 1.14-kb fragment that includes 937 bp upstream of the first predicted codon of the C10G11.5 and 203 bp downstream, ending 24 bp into the second exon; primers, F-SphI-TCGTACGATCGGACCATAGGCTAA and R-SphI-CTGATCCTCTGTAGCAGCGGCCCT; vector, pPD95.69.(4) C. elegans at 10–50 ng/μl to form extrachromosomal arrays. In the case of acs-1, the extrachromosomal array had been integrated into the C. elegans genome.These constructs were injected into Worms were soaked in a 5-μg/ml solution of DiI (Molecular Probes, Eugene, Oregon, United States) in M9 buffer for 1 h. They were then rinsed three times with M9 and visualized by fluorescence using the Texas Red filter.t test (two-tailed distribution) and correlation analysis were performed using the Microsoft Excel program.The FA quantities obtained by GC were expressed as a percentage of the total. Synchronized adults were placed on control  and RNAi  plates. Several worms of the next generation were picked from the control and RNAi plates and mounted on the same microscopic slide. GFP images were obtained with the fixed settings and exposure.E. coli HT115 strain transformed with empty pPD129.36 vector. Experimental RNAi plates contained E. coli HT115 transformed with corresponding dsRNA constructs. The growth conditions, RNA preparations, and data analyses are described in detail in One young adult of the N2 Bristol strain was plated on each control and RNAi feeding plate. Control plates contained the Dataset S1(1.8 MB TXT).Click here for additional data file.Figure S1elo-5(RNAi) phenotype have a lower number of the changed collagen genes, suggesting that populations on these experimental and control plates are similar.Samples I, II, and III represent mixed populations of wild-type animals started simultaneously from one young adult. Each was harvested at three time points, when mostly adults represented the F1 generation and the embryos and larvae in different proportions represented the F2 generation see . Sample (24 KB PPT).Click here for additional data file.Protocol S1(37 KB DOC).Click here for additional data file.Table S1(28 KB DOC).Click here for additional data file.


Given the overwhelming complexity of the immune system, it's no wonder that unraveling the mechanisms responsible for immunological disease has proved so difficult. The factors that trigger autoimmunity—which involves a breakdown in the body's ability to tolerate its own molecules—are not well understood, though animal studies show that genetic predisposition greatly increases risk. And that's where the real challenge begins. For certain diseases, individuals with defects in both copies of a specific gene invariably develop the disease. But more often, diseases with an inherited component result from the complex interplay of a variety of genes, each contributing a small effect that is typically dependent both on the expression of other genes and on both random and environmental factors.Researchers have increasingly turned to mice to model autoimmunity in humans and have found the same genetic complexity at work, with different strains of lupus-prone mice having different genes predisposing them to autoimmune disease. One model involves targeted disruption of candidate immune system genes to study their role in disease. Gene targeting experiments modify or remove a gene of interest and then watch for corresponding effects on the organism's physiology. Interpretations of results from these experiments have traditionally been predicated on the assumption that the “background,” or nontargeted, genes do not contribute to observed physiological changes. Yet in some studies, mice without targeted mutations develop an unexpected susceptibility to the autoimmune disease under study.Apcs gene, was chosen as an example of a gene-targeted model that develops a lupus-like disease, offering an opportunity to examine the relative contributions of the targeted versus background genes. Apcs is a candidate gene for human systemic lupus erythematosus (SLE), a form of autoimmunity marked by chronic inflammation resulting from a sustained attack on antibodies throughout the body.To investigate what effects background genes might be having in these mouse models, Marina Botto and colleagues compared the genomes of three hybrid strains of the most commonly used genetic background—the 129 and C57BL/6 hybrid mice. One of the hybrids, which carries a mutation in both copies of the Apcs mutations. Disease outcome in gene-targeted mice, it turns out, can be influenced not just by disease-susceptible (or disease-resistant) gene variants near the targeted gene (in this case, Apcs) but by the random heterogeneity of the hybrid genetic background: multiple combinations of genes in the hybrids can produce the same result.Botto and colleagues found that several genomic regions from both the 129 and C57BL/6 mice contributed to autoimmunity, even in the absence of gene-targeted mutations. All of the hybrid strains developed autoimmunity, though disease was more severe in mice with These results fall in line with mounting evidence that background genes are not silent partners in gene-targeted disease models, but can themselves facilitate expression of the disease. This finding underscores the notion that genes are not solitary, static entities; their expression often depends on context. With genetically complex diseases, having the requisite combination of susceptibility genes does not always lead to disease. Much work remains to be done to identify the triggers that cause the immune system to turn on itself. For more on mouse models and autoimmunity, see the primer by Morel in this issue.