Molecular evolution

Molecular evolution is the process of change in the sequence composition of cellular molecules such as DNA, RNA, and proteins across generations. The field of molecular evolution uses principles of evolutionary biology and population genetics to explain patterns in these changes. Major topics in molecular evolution concern the rates and impacts of single nucleotide changes, neutral evolution vs. natural selection, origins of new genes, the genetic nature of complex traits, the genetic basis of speciation, evolution of development, and ways that evolutionary forces influence genomic and phenotypic changes.
History.
The history of molecular evolution starts in the early 20th century with comparative biochemistry, and the use of "fingerprinting" methods such as immune assays, gel electrophoresis and paper chromatography in the 1950s to explore homologous proteins.
The field of molecular evolution came into its own in the 1960s and 1970s, following the rise of molecular biology. The advent of protein sequencing allowed molecular biologists to create phylogenies based on sequence comparison, and to use the differences between homologous sequences as a molecular clock to estimate the time since the last universal common ancestor. In the late 1960s, the neutral theory of molecular evolution provided a theoretical basis for the molecular clock, though both the clock and the neutral theory were controversial, since most evolutionary biologists held strongly to panselectionism, with natural selection as the only important cause of evolutionary change. After the 1970s, nucleic acid sequencing allowed molecular evolution to reach beyond proteins to highly conserved ribosomal RNA sequences, the foundation of a reconceptualization of the early history of life.
Forces in molecular evolution.
The content and structure of a genome is the product of the molecular and population genetic forces which act upon that genome. Novel genetic variants will arise through mutation and will spread and be maintained in populations due to genetic drift or natural selection.
Mutation.
Mutations are permanent, transmissible changes to the genetic material (DNA or RNA) of a cell or virus. Mutations result from errors in DNA replication during cell division and by exposure to radiation, chemicals, and other environmental stressors, or viruses and transposable elements. Most mutations that occur are single nucleotide polymorphisms which modify single bases of the DNA sequence, resulting in point mutations. Other types of mutations modify larger segments of DNA and can cause duplications, insertions, deletions, inversions, and translocations.
Most organisms display a strong bias in the types of mutations that occur with strong influence in GC-content. Transitions (A ↔ G or C ↔ T) are more common than transversions (purine (adenine or guanine)) ↔ pyrimidine (cytosine or thymine, or in RNA, uracil)) and are less likely to alter amino acid sequences of proteins.
Mutations are stochastic and typically occur randomly across genes. Mutation rates for single nucleotide sites for most organisms are very low, roughly 10−9 to 10−8 per site per generation, though some viruses have higher mutation rates on the order of 10−6 per site per generation. Among these mutations, some will be neutral or beneficial and will remain in the genome unless lost via genetic drift, and others will be detrimental and will be eliminated from the genome by natural selection.
Because mutations are extremely rare, they accumulate very slowly across generations. While the number of mutations which appears in any single generation may vary, over very long time periods they will appear to accumulate at a regular pace. Using the mutation rate per generation and the number of nucleotide differences between two sequences, divergence times can be estimated effectively via the molecular clock.
Recombination.
Recombination is a process that results in genetic exchange between chromosomes or chromosomal regions. Recombination counteracts physical linkage between adjacent genes, thereby reducing genetic hitchhiking. The resulting independent inheritance of genes results in more efficient selection, meaning that regions with higher recombination will harbor fewer detrimental mutations, more selectively favored variants, and fewer errors in replication and repair. Recombination can also generate particular types of mutations if chromosomes are misaligned.
Gene conversion.
Gene conversion is a type of recombination that is the product of DNA repair where nucleotide damage is corrected using an homologous genomic region as a template. Damaged bases are first excised, the damaged strand is then aligned with an undamaged homolog, and DNA synthesis repairs the excised region using the undamaged strand as a guide. Gene conversion is often responsible for homogenizing sequences of duplicate genes over long time periods, reducing nucleotide divergence.
Genetic drift.
Genetic drift is the change of allele frequencies from one generation to the next due to stochastic effects of random sampling in finite populations. Some existing variants have no effect on fitness and may increase or decrease in frequency simply due to chance. "Nearly neutral" variants whose selection coefficient is close to a threshold value of 1 / the effective population size will also be affected by chance as well as by selection and mutation. Many genomic features have been ascribed to accumulation of nearly neutral detrimental mutations as a result of small effective population sizes. With a smaller effective population size, a larger variety of mutations will behave as if they are neutral due to inefficiency of selection.
Selection.
Selection occurs when organisms with greater fitness, i.e. greater ability to survive or reproduce, are favored in subsequent generations, thereby increasing the instance of underlying genetic variants in a population. Selection can be the product of natural selection, artificial selection, or sexual selection. Natural selection is any selective process that occurs due to the fitness of an organism to its environment. In contrast sexual selection is a product of mate choice and can favor the spread of genetic variants which act counter to natural selection but increase desirability to the opposite sex or increase mating success. Artificial selection, also known as selective breeding, is imposed by an outside entity, typically humans, in order to increase the frequency of desired traits.
The principles of population genetics apply similarly to all types of selection, though in fact each may produce distinct effects due to clustering of genes with different functions in different parts of the genome, or due to different properties of genes in particular functional classes. For instance, sexual selection could be more likely to affect molecular evolution of the sex chromosomes due to clustering of sex specific genes on the X, Y, Z or W.
Intragenomic conflict.
Selection can operate at the gene level at the expense of organismal fitness, resulting in intragenomic conflict. This is because there can be a selective advantage for selfish genetic elements in spite of a host cost. Examples of such selfish elements include transposable elements, meiotic drivers, killer X chromosomes, selfish mitochondria, and self-propagating introns.
Genome architecture.
Genome size.
Genome size is influenced by the amount of repetitive DNA as well as number of genes in an organism. The C-value paradox refers to the lack of correlation between organism 'complexity' and genome size. Explanations for the so-called paradox are two-fold. First, repetitive genetic elements can comprise large portions of the genome for many organisms, thereby inflating DNA content of the haploid genome. Secondly, the number of genes is not necessarily indicative of the number of developmental stages or tissue types in an organism. An organism with few developmental stages or tissue types may have large numbers of genes that influence non-developmental phenotypes, inflating gene content relative to developmental gene families.
Neutral explanations for genome size suggest that when population sizes are small, many mutations become nearly neutral. Hence, in small populations repetitive content and other 'junk' DNA can accumulate without placing the organism at a competitive disadvantage. There is little evidence to suggest that genome size is under strong widespread selection in multicellular eukaryotes. Genome size, independent of gene content, correlates poorly with most physiological traits and many eukaryotes, including mammals, harbor very large amounts of repetitive DNA.
However, birds likely have experienced strong selection for reduced genome size, in response to changing energetic needs for flight. Birds, unlike humans, produce nucleated red blood cells, and larger nuclei lead to lower levels of oxygen transport. Bird metabolism is far higher than that of mammals, due largely to flight, and oxygen needs are high. Hence, most birds have small, compact genomes with few repetitive elements. Indirect evidence suggests that non-avian theropod dinosaur ancestors of modern birds also had reduced genome sizes, consistent with endothermy and high energetic needs for running speed. Many bacteria have also experienced selection for small genome size, as time of replication and energy consumption are so tightly correlated with fitness.
Repetitive elements.
Transposable elements are self-replicating, selfish genetic elements which are capable of proliferating within host genomes. Many transposable elements are related to viruses, and share several proteins in common.
Chromosome number and organization.
The number of chromosomes in an organism's genome also does not necessarily correlate with the amount of DNA in its genome. The ant "Myrmecia pilosula" has only a single pair of chromosomes whereas the Adders-tongue fern "Ophioglossum reticulatum" has up to 1260 chromosomes. Cilliate genomes house each gene in individual chromosomes, resulting in a genome which is not physically linked. Reduced linkage through creation of additional chromosomes should effectively increase the efficiency of selection.
Changes in chromosome number can play a key role in speciation, as differing chromosome numbers can serve as a barrier to reproduction in hybrids. Human chromosome 2 was created from a fusion of two chimpanzee chromosomes and still contains central telomeres as well as a vestigial second centromere. Polyploidy, especially allopolyploidy, which occurs often in plants, can also result in reproductive incompatibilities with parental species. "Agrodiatus" blue butterflies have diverse chromosome numbers ranging from n=10 to n=134 and additionally have one of the highest rates of speciation identified to date.
Gene content and distribution.
Different organisms house different numbers of genes within their genomes as well as different patterns in the distribution of genes throughout the genome. Some organisms, such as most bacteria, "Drosophila", and "Arabidopsis" have particularly compact genomes with little repetitive content or non-coding DNA. Other organisms, like mammals or maize, have large amounts of repetitive DNA, long introns, and substantial spacing between different genes. The content and distribution of genes within the genome can influence the rate at which certain types of mutations occur and can influence the subsequent evolution of different species. Genes with longer introns are more likely to recombine due to increased physical distance over the coding sequence. As such, long introns may facilitate ectopic recombination, and result in higher rates of new gene formation.
Organelles.
In addition to the nuclear genome, endosymbiont organelles contain their own genetic material typically as circular plasmids. Mitochondrial and chloroplast DNA varies across taxa, but membrane-bound proteins, especially electron transport chain constituents are most often encoded in the organelle. Chloroplasts and mitochondria are maternally inherited in most species, as the organelles must pass through the egg. In a rare departure, some species of mussels are known to inherit mitochondria from father to son.
Origins of new genes.
New genes arise from several different genetic mechanisms including gene duplication, de novo origination, retrotransposition, chimeric gene formation, recruitment of non-coding sequence, and gene truncation.
Gene duplication initially leads to redundancy. However, duplicated gene sequences can mutate to develop new functions or specialize so that the new gene performs a subset of the original ancestral functions. In addition to duplicating whole genes, sometimes only a domain or part of a protein is duplicated so that the resulting gene is an elongated version of the parental gene.
Retrotransposition creates new genes by copying mRNA to DNA and inserting it into the genome. Retrogenes often insert into new genomic locations, and often develop new expression patterns and functions.
Chimeric genes form when duplication, deletion, or incomplete retrotransposition combine portions of two different coding sequences to produce a novel gene sequence. Chimeras often cause regulatory changes and can shuffle protein domains to produce novel adaptive functions.
"De novo" gene birth can also give rise to new genes from previously non-coding DNA. For instance, Levine and colleagues reported the origin of five new genes in the "D. melanogaster" genome from noncoding DNA. Similar de novo origin of genes has been also shown in other organisms such as yeast, rice and humans. De novo genes may evolve from transcripts that are already expressed at low levels. Mutation of a stop codon to a regular codon or a frameshift may cause an extended protein that includes a previously non-coding sequence. The formation of novel genes from scratch typically can not occur within genomic regions of high gene density. The essential events for de novo formation of genes is recombination/mutation which includes insertions, deletions, and inversions. These events are tolerated if the consequence of these genetic events does not interfere in cellular activities. Most genomes comprise prophages wherein genetic modifications do not, in general, affect the host genome propagation. Hence, there is higher probability of genetic modifications, in regions such as prophages, which is proportional to the probability of de novo formation of genes.
"De novo" evolution of genes can also be simulated in the laboratory. For example, semi-random gene sequences can be selected for specific functions. More specifically, they selected sequences from a library that could complement a gene deletion in "E. coli". The deleted gene encodes ferric enterobactin esterase (Fes), which releases iron from an iron chelator, enterobactin. While Fes is a 400 amino acid protein, the newly selected gene was only 100 amino acids in length and unrelated in sequence to Fes.
"In vitro" molecular evolution experiments.
Principles of molecular evolution have also been discovered, and others elucidated and tested using experimentation involving amplification, variation and selection of rapidly proliferating and genetically varying molecular species outside cells. Since the pioneering work of Sol Spiegelmann in 1967 [ref], involving RNA that replicates itself with the aid of an enzyme extracted from the Qß virus [ref], several groups (such as Kramers [ref] and Biebricher/Luce/Eigen [ref]) studied mini and micro variants of this RNA in the 1970s and 1980s that replicate on the timescale of seconds to a minute, allowing hundreds of generations with large population sizes (e.g. 10^14 sequences) to be followed in a single day of experimentation. The chemical kinetic elucidation of the detailed mechanism of replication [ref, ref] meant that this type of system was the first molecular evolution system that could be fully characterised on the basis of physical chemical kinetics, later allowing the first models of the genotype to phenotype map based on sequence dependent RNA folding and refolding to be produced [ref, ref]. Subject to maintaining the function of the multicomponent Qß enzyme, chemical conditions could be varied significantly, in order to study the influence of changing environments and selection pressures [ref]. Experiments with "in vitro" RNA quasi species included the characterisation of the error threshold for information in molecular evolution [ref], the discovery of "de novo" evolution [ref] leading to diverse replicating RNA species and the discovery of spatial travelling waves as ideal molecular evolution reactors [ref, ref]. Later experiments employed novel combinations of enzymes to elucidate novel aspects of interacting molecular evolution involving population dependent fitness, including work with artificially designed molecular predator prey and cooperative systems of multiple RNA and DNA [ref, ref]. Special evolution reactors were designed for these studies, starting with serial transfer machines, flow reactors such as cell-stat machines, capillary reactors, and microreactors including line flow reactors and gel slice reactors. These studies were accompanied by theoretical developments and simulations involving RNA folding and replication kinetics that elucidated the importance of the correlation structure between distance in sequence space and fitness changes [ref], including the role of neutral networks and structural ensembles in evolutionary optimisation.
Molecular phylogenetics.
Molecular systematics is the product of the traditional fields of systematics and molecular genetics. It uses DNA, RNA, or protein sequences to resolve questions in systematics, i.e. about their correct scientific classification or taxonomy from the point of view of evolutionary biology.
Molecular systematics has been made possible by the availability of techniques for DNA sequencing, which allow the determination of the exact sequence of nucleotides or "bases" in either DNA or RNA. At present it is still a long and expensive process to sequence the entire genome of an organism, and this has been done for only a few species. However, it is quite feasible to determine the sequence of a defined area of a particular chromosome. Typical molecular systematic analyses require the sequencing of around 1000 base pairs.
The driving forces of evolution.
Depending on the relative importance assigned to the various forces of evolution, three perspectives provide evolutionary explanations for molecular evolution.
Selectionist hypotheses argue that selection is the driving force of molecular evolution. While acknowledging that many mutations are neutral, selectionists attribute changes in the frequencies of neutral alleles to linkage disequilibrium with other loci that are under selection, rather than to random genetic drift. Biases in codon usage are usually explained with reference to the ability of even weak selection to shape molecular evolution.
Neutralist hypotheses emphasize the importance of mutation, purifying selection, and random genetic drift. The introduction of the neutral theory by Kimura, quickly followed by King and Jukes' own findings, led to a fierce debate about the relevance of neodarwinism at the molecular level. The Neutral theory of molecular evolution proposes that most mutations in DNA are at locations not important to function or fitness. These neutral changes drift towards fixation within a population. Positive changes will be very rare, and so will not greatly contribute to DNA polymorphisms. Deleterious mutations do not contribute much to DNA diversity because they negatively affect fitness and so are removed from the gene pool before long. This theory provides a framework for the molecular clock. The fate of neutral mutations are governed by genetic drift, and contribute to both nucleotide polymorphism and fixed differences between species.
In the strictest sense, the neutral theory is not accurate. Subtle changes in DNA very often have effects, but sometimes these effects are too small for natural selection to act on. Even synonymous mutations are not necessarily neutral because there is not a uniform amount of each codon. The nearly neutral theory expanded the neutralist perspective, suggesting that several mutations are nearly neutral, which means both random drift and natural selection is relevant to their dynamics. The main difference between the neutral theory and nearly neutral theory is that the latter focuses on weak selection, not strictly neutral.
Mutationists hypotheses emphasize random drift and biases in mutation patterns. Sueoka was the first to propose a modern mutationist view. He proposed that the variation in GC content was not the result of positive selection, but a consequence of the GC mutational pressure.
Protein evolution.
Evolution of proteins is studied by comparing the sequences and structures of proteins from many organisms representing distinct evolutionary clades. If the sequences/structures of two proteins are similar indicating that the proteins diverged from a common origin, these proteins are called homologous proteins. More specifically, homologous proteins that exist in two distinct species are called orthologs. Whereas, homologous proteins encoded by the genome of a single species are called paralogs.
The phylogenetic relationships of proteins are examined by multiple sequence comparisons. Phylogenetic trees of proteins can be established by the comparison of sequence identities among proteins. Such phylogenetic trees have established that the sequence similarities among proteins reflect closely the evolutionary relationships among organisms.
Protein evolution describes the changes over time in protein shape, function, and composition. Through quantitative analysis and experimentation, scientists have strived to understand the rate and causes of protein evolution. Using the amino acid sequences of hemoglobin and cytochrome c from multiple species, scientists were able to derive estimations of protein evolution rates. What they found was that the rates were not the same among proteins. Each protein has its own rate, and that rate is constant across phylogenies (i.e., hemoglobin does not evolve at the same rate as cytochrome c, but hemoglobins from humans, mice, etc. do have comparable rates of evolution.). Not all regions within a protein mutate at the same rate; functionally important areas mutate more slowly and amino acid substitutions involving similar amino acids occurs more often than dissimilar substitutions. Overall, the level of polymorphisms in proteins seems to be fairly constant. Several species (including humans, fruit flies, and mice) have similar levels of protein polymorphism.
In his Dublin 1943 lectures, “What Is Life?”, Erwin Schrodinger proposed that we could progress in answering this question by using statistical mechanics and partition functions, but not quantum mechanics and his wave equation. He described an “aperiodic crystal” which could carry genetic information, a description credited by Francis Crick and James D. Watson with having inspired their discovery of the double helical structure of DNA. Twenty fractals were discovered in solvent associated surface areas of > 5000 protein segments. The existence of these fractals proves that proteins function near critical points of second-order phase transitions, realizing Schrodinger's conjecture. It opens a new biophysics field of accurate thermodynamic analysis of protein evolution based primarily on amino acid sequences
Relation to nucleic acid evolution.
Protein evolution is inescapably tied to changes and selection of DNA polymorphisms and mutations because protein sequences change in response to alterations in the DNA sequence. Amino acid sequences and nucleic acid sequences do not mutate at the same rate. Due to the degenerate nature of DNA, bases can change without affecting the amino acid sequence. For example, there are six codons that code for leucine. Thus, despite the difference in mutation rates, it is essential to incorporate nucleic acid evolution into the discussion of protein evolution. At the end of the 1960s, two groups of scientists—Kimura (1968) and King and Jukes (1969)—independently proposed that a majority of the evolutionary changes observed in proteins were neutral. Since then, the neutral theory has been expanded upon and debated.
Discordance with morphological evolution.
There are sometimes discordances between molecular and morphological evolution, which are reflected in molecular and morphological systematic studies, especially of bacteria, archaea and eukaryotic microbes. These discordances can be categorized as two types: (i) one morphology, multiple lineages (e.g. morphological convergence, cryptic species) and (ii) one lineage, multiple morphologies (e.g. phenotypic plasticity, multiple life-cycle stages). Neutral evolution possibly could explain the incongruences in some cases.
Journals and societies.
The Society for Molecular Biology and Evolution publishes the journals "Molecular Biology and Evolution" and "Genome Biology and Evolution" and holds an annual international meeting. Other journals dedicated to molecular evolution include "Journal of Molecular Evolution" and "Molecular Phylogenetics and Evolution". Research in molecular evolution is also published in journals of genetics, molecular biology, genomics, systematics, and evolutionary biology.


Celsense

Celsense, Inc. is a privately held biotechnology company offering pre-clinical and clinical-grade imaging agents used to non-invasively detect, identify, quantify, and monitor cells and cellular activity. The company is based in Pittsburgh, Pennsylvania. It was founded in 2005 to commercialize imaging platforms developed at Carnegie Mellon University.
Celsense makes proprietary imaging agents for cell trafficking using magnetic resonance imaging (MRI) techniques. The company's products are used primarily to understand regenerative medicine, immunotherapy, inflammation, and immune system response. There are over 100 peer reviewed articles in the academic literature describing cell trafficking in vivo using Celsense products. The first clinical trial involving the use of Cell Sense CS-1000 was completed in 2014. Additional clinical trials are pending in the US and Canada.
Corporate structure.
Current members of the board of directors of Celsense are: Charles F. O’Hanlon, III, Thomas Petzinger, Jr., Abby Lembersky, L. Gerald Tarantino, and Gregory T. Hebrank.


Chan King-ming

Chan King-ming is a Hong Kong politician and academic. He served as the vice-chairman of the Democratic Party of Hong Kong from 2004 to 2006. He is also an associate professor in the department of biochemistry and Environmental Science Program of the Chinese University of Hong Kong.
Academic career.
Chan King-ming earned his Bachelor of Science and Master of Philosophy degrees at the Chinese University of Hong Kong, and his doctoral degree from Memorial University of Newfoundland in St. John's, Newfoundland, Canada.
He is now director of the Environmental Science Program at the Chinese University of Hong Kong. He teaches many different courses including Current Environmental Issues, Biochemical Toxicology and Introduction to Environmental Science in the Environmental Science Program and Molecular Endocrinology in the Biochemistry Programme. Trained as a molecular biologist for his PhD and post-doctoral research, Professor Chan's research interests include gene regulation, aquatic toxicology, marine biotechnology and environmental biochemistry and environmental policy. Prof. Chan is also chairman of CUTA (Chinese University Teachers Association), trustee of Shaw College Board of trustees, Member of Assembly of Fellows, Shaw College, and warden of Hostel 2, Shaw College.
Political career.
Chan is a founding member of the Democratic Party. He was elected as chairman of the New Territories East Branch in 1999, and later became the party's minister of organization affairs and central committee member. He ran for the chairmanship election in 2004 but lost to Lee Wing-tat. He was then elected vice-chairman of the party. He also served as a part-time member of Central Policy Unit of the Hong Kong Government between 2004 and 2006.
He ran again for the chairmanship in December 2006, but lost to Albert Ho. He did not seek to run for the vice-chairmanship in the 2006 election. In 2010, the Democratic Party decided to support the government's proposal of the political reform package to expand the numbers of legislative council members from 30 to 35 in Geographical Constituency and 30 to 35 of Functional Constituency by adopting the idea of the "Super-district Councillors" which will be voted across the territory after nominations by District Councillors. Younger members of the Democratic Party including Chan believed that such proposal could not provide any significant progress towards democratic development in local political agenda.
In December 2010, Chan quit the party due to the electoral reform to found the Neo Democrats and is the incumbent convenor of the party. The Neo Democrats campaigned in the 2011 District Council election and won a total of 8 seats.
Affiliations.
Chan is a current member of the Professional Teachers' Union (HK), Hong Kong Marine Biological Association, Society of Toxicology (SOT) in the US, American Fisheries Society, American Physiological Society, etc.
He is now chairman (elected) of the Teachers' Association of Chinese University (2011–12). He also serves as warden of Student Hostel 2 of Shaw College, member of the board of trustees of Shaw College, and member of the Assembly of Fellows, Shaw College, Chinese University.


Negative regulatory element

A Negative regulatory element (NRE) is a sequence of DNA that represses the expression of certain genes, for example that of the insulin gene.


NBUMP

NBUMP is a highly selective 5-HT1A receptor partial agonist (Ki = 0.1 nM; IA = 40%) with an arylpiperazine structure. It is one of the highest affinity ligands for the 5-HT1A receptor known. It displays 460- and 260-fold selectivity for 5-HT1A over the α1-adrenergic and D2 receptors, respectively.


Shotgun lipidomics

In lipidomics, the process of shotgun lipidomics (named by analogy with shotgun sequencing) uses analytical chemistry to investigate the biological function, significance, and sequelae of alterations in lipids and protein constituents mediating lipid metabolism, trafficking, or biological function in cells.
Lipidomics has been greatly facilitated by recent advances in, and novel applications of, electrospray ionization mass spectrometry (ESI/MS).
Lipidomics is a research field that studies the pathways and networks of cellular lipids in biological systems (i.e., lipidomes) on a large scale. It involves the identification and quantification of the thousands of cellular lipid molecular species and their interactions with other lipids, proteins, and other moieties in vivo. Investigators in lipidomics examine the structures, functions, interactions, and dynamics of cellular lipids and the dynamic changes that occur during pathophysiologic perturbations. Lipidomic studies play an essential role in defining the biochemical mechanisms of lipid-related disease processes through identifying alterations in cellular lipid metabolism, trafficking and homeostasis. The two major platforms currently used for lipidomic analyses are HPLC-MS and shotgun lipidomics.
History.
Shotgun lipidomics was developed by Richard W. Gross and Xianlin Han, by employing ESI intrasource separation techniques. Individual molecular species of most major and many minor lipid classes can be fingerprinted and quantitated directly from biological lipid extracts without the need for chromatographic purification.
Advantages.
Shotgun lipidomics is fast, highly sensitive, and it can identify hundreds of lipids missed by other methods — all with a much smaller tissue sample so that specific cells or minute biopsy samples can be examined.


Metabolite damage

Metabolite damage can occur through enzyme promiscuity or spontaneous chemical reactions. Many metabolites are chemically reactive and unstable and can react with other cell components or undergo unwanted modifications. Enzymatically or chemically damaged metabolites are always useless and often toxic. To prevent toxicity that can occur from the accumulation of damaged metabolites, organisms have damage-control systems that:
Damage-control systems can involve one or more specific enzymes.
Types of damage.
Similarly to DNA and proteins, metabolites are prone to damage, which can occur chemically or through enzyme promiscuity. Much less is known about metabolite damage than about DNA and protein damage, in part due to the huge variety and number of damage-prone metabolites.
Chemical damage.
Many metabolites are chemically reactive and unstable, and thus prone to chemical damage. In general, any reaction that occurs "in vitro" under physiological conditions can also occur "in vivo". Some metabolites are so reactive that their half-life in a cell is measured in minutes. For example, the glycolytic intermediate 1,3-bisphosphoglyceric acid has a half-life of 27 minutes "in vivo". Typical types of chemical damage reactions that can occur to metabolites are racemization, rearrangement, elimination, photodissociation, addition, and condensation.
Enzymatic damage.
Although enzymes are generally specific towards their substrate, enzymatic side activities (enzyme promiscuity) can lead to toxic or useless products. These side reactions proceed at much lower rates than their normal physiological reactions, but build-up of damaged metabolites can still be significant over time. For example, the mitochondrial malate dehydrogenase reduces alpha-ketoglutarate to L-2-hydroxyglutarate 107 times less efficiently than its regular substrate oxaloacetate, but L-2-hydroxyglutarate can still accumulate to several grams per day in a human adult.
Damage control.
Metabolite damage-control systems fall into three different categories:
Damage repair.
Damage repair is the conversion of a damaged metabolite back to its original state via one or more enzymatic reactions; the concept is similar to DNA repair and protein repair. For example, the promiscuous activity of malate dehydrogenase causes reduction of alpha-ketoglutarate to L-2-hydroxyglutarate. This compound is a dead-end metabolite and is not a substrate for any other enzyme in central metabolism, and its accumulation in humans causes L-2-Hydroxyglutaric aciduria. The repair enzyme L-2-hydroxyglutarate dehydrogenase oxidizes L-2-hydroxyglutarate back to alpha-ketoglutarate, thus repairing this metabolite. In humans, L-2-hydroxyglutarate dehydrogenase uses FAD as the cofactor, while the "E. coli" enzyme reduces molecular oxygen.
Damage pre-emption.
Pre-emption prevents damage from happening. This is done either by converting reactive metabolites to less harmful ones, or by speeding up an insufficiently fast chemical reaction. The reactive metabolite can be either a side product, or a normal, but highly reactive intermediate.
For example, a side activity of Rubisco yields small amounts of xylulose-1,5-bisphosphate, which can inhibit Rubisco activity. The CbbY enzyme dephosphorylates xylulose-1,5-bisphosphate to the natural metabolite xylulose-5-phosphate, thereby preventing inhibition of Rubisco.
Directed overflow.
Directed overflow is a special case of damage pre-emption, where excess of a normal, but reactive metabolite could lead to toxic products. Preventing this excess is thus pre-emption of potential damage.
The first two intermediates in riboflavin biosynthesis are highly reactive and can spontaneously break down to 5-phosphoribosylamine and Maillard reaction products, which are highly reactive and harmful. The enzyme COG3236 hydrolyzes these two first intermediates into two less harmful products, thus preventing the harm they would otherwise cause.
Disease.
In humans, L-2-Hydroxyglutaric aciduria was the first disease linked to a missing metabolite repair enzyme. Mutations in the "L2HGDH" gene cause accumulation of L-2-hydroxyglutarate, which is a structural analog to glutamate and alpha-ketoglutarate and presumably inhibits other enzymes or transporters.
Systems biology.
Metabolic network modelling aims at reproducing cellular metabolism "in silico". Metabolite damage and repair create cellular energy costs, and consequently need to be incorporated into genome-scale metabolic models so that these models can more effectively guide metabolic engineering design.
In addition, genes encoding so-far unrecognized metabolite damage-control systems may constitute a significant fraction of the many conserved genes of unknown function found in the genomes of all organisms.
Synthetic biology / metabolic engineering.
When an alien pathway is installed in a host ('chassis') organism, and even when a native pathway is massively upregulated, reactive intermediates may accumulate to levels that negatively impact viability, growth, and flux through the pathway because a matching damage-control system is absent or has been overwhelmed. Engineering damage-control systems may thus be needed to support synthetic biology and metabolic engineering projects.


Chrysochloridae


Dapiprazole

Dapiprazole (Rev-Eyes) is an alpha blocker. It is used to reverse mydriasis after eye examination.


Hao Ying

Hao Ying (; born 1958) is a professor of electrical and computer engineering at Wayne State University in Detroit, Michigan. He was named a Fellow of the Institute of Electrical and Electronics Engineers (IEEE) in 2012 for his contributions to the theory and biomedical applications of fuzzy control.


Maria Falkenberg

Maria Falkenberg is a professor of medical biochemistry at the Sahlgrenska Academy of the University of Gothenburg, Sweden. She has made important contributions to understanding how the mitochondrial genome is maintained in health and disease.
Career.
Falkenberg received her doctorate from the University of Gothenburg in 2000 for her work on the molecular aspects of DNA replication in Herpes Simplex virus type 1 in the Per Elias group in Gothenburg and the Robert Lehman group at Stanford University. She studied the mechanisms of mitochondrial DNA replication during her postdoctoral fellowship from 2001-2003 in the Nils-Göran Larsson laboratory at the Karolinska Institute, where she then established her own group in 2003. She was the first to set up a cell-free system to study human mitochondrial DNA replication. Her research is funded by among others, the European Research Council (ERC), the Swedish Research Council (VR), and the Knut and Alice Wallenberg Foundation (KAW).
Selected publications.
Copy-choice recombination during mitochondrial L-strand synthesis causes DNA deletions.
Persson Ö, Muthukumar Y, Basu S, Jenninger L, Uhler JP, Berglund AK, McFarland R, Taylor RW, Gustafsson CM, Larsson E, Falkenberg M.
"Nat Commun". 2019 Feb 15;10(1):759. doi: 10.1038/s41467-019-08673-5.
Nucleotide pools dictate the identity and frequency of ribonucleotide incorporation in mitochondrial DNA.
Berglund AK, Navarrete C, Engqvist MK, Hoberg E, Szilagyi Z, Taylor RW, Gustafsson CM, Falkenberg M, Clausen AR.
"PLoS Genet". 2017 Feb 16;13(2):e1006628. doi: 10.1371/journal.pgen.1006628.
Maintenance and Expression of Mammalian Mitochondrial DNA.
Gustafsson CM, Falkenberg M, Larsson NG.
"Annu Rev Biochem". 2016 Jun 2;85:133-60. doi: 10.1146/annurev-biochem-060815-014402.
In vitro-reconstituted nucleoids can block mitochondrial DNA replication and transcription
Géraldine Farge, Majda Mehmedovic, Marian Baclayon, Siet MJL van den Wildenberg, Wouter H Roos, Claes M Gustafsson, Gijs JL Wuite, Maria Falkenberg
"Cell Rep." 2014 Jul 10;8(1):66-74. doi: 10.1016/j.celrep.2014.05.046.
In vivo occupancy of mitochondrial single-stranded DNA binding protein supports the strand displacement mode of DNA replication.
Miralles Fusté J, Shi Y, Wanrooij S, Zhu X, Jemt E, Persson Ö, Sabouri N, Gustafsson CM, Falkenberg M.
"PLoS Genet." 2014 Dec 4;10(12):e1004832. doi: 10.1371/journal.pgen.1004832.


GlySens ICGM

GlySens, a biomedical technology company, is a privately owned corporation developing a long term internal continuous glucose monitor in order to effectively manage and observe glucose levels in real time. The GlySens ICGM system is the world's first surgically implanted continuous glucose monitoring system to demonstrate an 18-month performance in a preclinical setting. GlySens Incorporated was founded in 1998 by David A. Gough and Joseph Lucisano, a bioengineering graduate at the University of California, San Diego. The implanted continuous glucose monitoring system system uses an internal sensor equipped with electrochemical detectors to measure glucose readings via a chemical reaction between enzymes and oxygen. The GlySens ICGM system will be the first publicly available glucose monitor capable of withstanding 12+ months of continual use. As the global population of diabetics approached 400 million, this device can dramatically improve the quality of diabetic care.
Technology.
The technology that goes into the ICGM system consists of two parts. Primarily is the internal sensor which utilizes chemical reactions to determine blood glucose levels. Additionally is an external receiver used to display glucose readings and patterns in real-time, helping reduce the level of care needed in diabetics.
Internal sensor.
An internal glucose sensor, measuring at 38mm across and 16 mm thick. The implant consists of an integrated glucose sensor with signal conditioning circuits, a wireless communications circuit, and a 1-year lifetime battery, all housed in a hermetically sealed (airtight) titanium housing. The sensor is surgically implanted under the skin, at the waist or upper arm, and continuously monitors the glucose levels in the subcutaneous (under the skin) tissue. Data is then relayed to the receiver via wireless telemetry, the automatic measurement and transmission of data by wire, radio, or other means from remote sources. The ICGM system is as accurate as any other CGM device, however unlike similar products, the GlySens ICGM sensor works by detecting oxygen, allowing the system to be more stable in the interstitial fluid environment, the fluid surrounding tissue cells, than traditional CGMs. It has an outer membrane with electro-chemical detectors primed with enzymes to interact with the oxygen. The extent of the enzyme reaction and the concentration of glucose can be calculated by measuring the amount of remaining oxygen from the enzyme reaction. It is ensured the sensors are working properly through multiple built-in checks. The sensor may also have applications for glucose monitoring in type 2 diabetes including caloric and activity management, and prevention of type 2 diabetes in susceptible individuals.
External receiver.
The monitor provides a digital readout and graphical display of the glucose levels, alerting the user to hypoglycemic and hyperglycemic glucose levels, trending patterns and a series of directional buttons to access settings, history and calibration. Calibrating the receiver and sensor is necessary in order to ensure accurate readings and is as simple as taking a transdermal blood sample and entering it into the receiver. Lucisano, GlySens Chief Technology Officer, announced that in a future iteration the receiver should be converted to a software application that can run on a cell phone.
Competition.
The two primary competitors of GlySens include: DexCom and Medtronic. These CGM's utilize thin wire sensors that must be inserted just under the surface of the skin and replaced at least once a week. These companies currently are turning their attention away from long-term implantable sensors, while concepts may still be in development, they aren't immediate priorities. This makes the GlySens ICGM sensor the first long-term implantable glucose sensor that will be available to the public.
Studies.
Science Translational Medicine reported success on long-term glucose monitoring with the sensor-telemetry system implanted in the tissues of pigs. Monitoring was carried out while the pigs were initially non diabetic and continued for 6 months after the pigs had been made diabetic by administration of a laboratory drug. The long-term animal results reported by David Gough provide a foundation for human trials, which began in January, 2015 and is expected to conclude in early 2016.The first round of human trials includes a group of 20 individuals, both male and female, from the age of 21 to 65 years old. Each subject was implanted with the GlySens ICGM monitor under the skin of the upper arm and monitored over the course of 18 months. The GlySens ICGM system is currently undergoing clinical evaluation, the initial human implant trials have been completed, and preparations for additional human trials are underway.
Market.
In 2014 worldwide, an estimated 382 million people had diabetes, and this number is expected to double by the year 2030. In the United States alone, nearly 29 million people have been diagnosed with diabetes, and an additional 79 million people are classified as pre-diabetic. The World Health Organization projects that diabetes will be the 7th leading cause of death in 2030. The worldwide annual expenditure on home and self blood glucose monitoring products has been estimated at $7 to $10 billion with half of the sales occurring in the U.S. The total economic impact of diabetes in the U.S. is estimated at $245 billion each year.


Dihydroxyphenylethylene glycol

Dihydroxyphenylethylene glycol (DOPEG) is a metabolite of norepinephrine through monoamine oxidase.


MRGPRD

Mas-related G-protein coupled receptor member D is a protein that in humans is encoded by the "MRGPRD" gene.


InGeneron

InGeneron Inc. is a private multinational medical device and biotechnology company headquartered in Houston, Texas, United States, and with European headquarters in Munich, Germany. InGeneron develops, manufactures, licenses and sells regenerative cell separation and diagnostics tools. InGeneron's technologies enable the preparation of adipose-derived regenerative cells (ADRC) that contain progenitor and stem cells in humans and animals for autologous use.
History.
InGeneron was founded in 2006, through a recapitalization of aDEPtas, Inc. in Houston, Texas with the focus on translating fundamental research in the regenerative medicine field into clinical practice. Over 40 peer-reviewed studies have been published by InGeneron's team in collaboration with various renowned academic facilities. In 2010, the fully owned subsidiary InGeneron GmbH in Munich was founded to serve as its European headquarters. In 2015, InGeneron Equine GmbH was founded in Germany, which focuses on treating orthopedic indications of sports horses. In 2015, the German-based stem cell banking company eticur) was acquired with the idea of supporting eticur) with scientific evidence from InGeneron's laboratory. In 2012, InGeneron's technology was also used to treat a Malayan tiger at the Houston zoo. In March 2017, InGeneron raised $20 million in Series D funding from Sanford Health.
Products.
InGeneron develops and manufactures biomedical equipment that is designed to fit into the workflow of an operating physician for the easy recovery of regenerative cells from the adipose tissue.
An efficient point-of-care processing system that isolates regenerative cells from adipose tissue has been developed. This system relies on a proprietary enzyme blend and centrifuge technology to isolate and prepare regenerative cells with high yield from adipose tissue within one hour after extraction.
Initial results in the veterinary space show that possible treatment areas include orthopedic injuries, osteoarthritis, incontinence, soft tissue reconstruction and non-healing wounds in animals.
Transpose RT System.
Consisting of the disposables for processing and the Tissue Processing Unit, the Transpose RT System is InGeneron's system that allows for point-of-care preparation of regenerative cells. The collected tissue is processed with the InGeneron Tissue Processing Unit, which is a semi-automated, heatable centrifuge that is developed to process tissue prior to stem cell extraction and uses proprietary agitation to assist in the separation of the regenerative cells.
This system is used in conjunction with the Matrase enzyme that ensures a high yield of regenerative cells. The proprietary enzyme is designed to quickly and gently release from adipose tissue the adult regenerative cells.
Accessories.
For the extraction and processing, InGeneron provides:
For veterinarian use, InGeneron provides:
Regulatory.
The InGeneron Processing Unit as well as disposable packs such as the Lipoaspiration Collection Kit, Transpose RT Lipoaspirate Processing Kit and the SmartGraft Systems are CE marked and meet the requirements of the applicable EC directive.
The Matrase enzymatic agent is manufactured mammalian origin free and in strict compliance with cGMP guidelines.
The SmartGraft 30 and SmartGraft 200 System have 510(k) approval in the US market.


DnaX ribosomal frameshifting element

The DnaX ribosomal frameshifting element is a RNA element found in the mRNA of the dnaX gene in "E. coli". The dnaX gene has two encoded products, tau and gamma, which are produced in a 1:1 ratio. The gamma protein is synthesised due to programmed frameshifting and is shorter than tau. The two products of the dnaX gene are DNA polymerase III subunits.


Hebeloma vinosophyllum

Hebeloma vinosophyllum is a toxic species of agaric fungus in the family Hymenogastraceae. It contains eleven poisonous compounds collectively known as hebevinosides. An ammonia fungus, it tends to grow on the corpses of animals. The species was described by Japanese mycologist Tsuguo Hongo in 1965. It was recorded from Vietnamese "Pinus kesiya" forests in 2014, its first record in Southeast Asia.


Cyanopeptolin

Cyanopeptolins are a class of oligopeptides produced by Microcystis and Planktothrix algae strains, and can be neurotoxic. The production of cyanopeptolins occurs through nonribosomal peptides synthases (NRPS).
Characteristics.
Increased water temperatures, because of climate change and eutrophication of inland waters promote blooms of cyanobacteria, potentially threaten water contamination by the production of the toxic cyanopeptolin (CP1020).
Exposure.
Cyanopeptolin (CP1020) exposure in zebrafish affected pathways related to DNA damage, the circadian rhythm and response to light.


Tenrecomorpha

Tenrecomorpha is the suborder of otter shrews and tenrecs, a group of afrotherian mammals indigenous to equatorial Africa and Madagascar, respectively. The two families are thought to have split about 47–53 million years ago. Potamogalid otter shrews were formerly considered a subfamily of Tenrecidae. The suborder is also presumed to contain the extinct genus "Plesiorycteropus", a group of possibly fossorial insectivores similar to aardvarks, which is known to be more closely related to tenrecs of subfamily Tenrecinae than to golden moles of suborder Chrysochloridea.
Otter shrews are carnivorous and semiaquatic, preying on any aquatic animal they can find with their sensitive whiskers. All tenrecs are believed to descend from a common ancestor that lived 29–37 million years (Ma) ago after rafting from Africa to Madagascar in a single event. Tenrecs are widely diverse; as a result of convergent evolution they resemble hedgehogs, shrews, opossums or mice. All tenrecs appear to be at least somewhat omnivorous, with invertebrates forming the largest part of their diets.


Deoxycytidine monophosphate

Deoxycytidine monophosphate (dCMP), also known as deoxycytidylic acid or deoxycytidylate in its conjugate acid and conjugate base forms, respectively, is a deoxynucleotide, and one of the four monomers that make up DNA. In a DNA double helix, it will base pair with deoxyguanosine monophosphate.


Acrosphaera

Acrosphaera is a radiolarian genus in the Collosphaeridae. The genus contains bioluminescent species. It is a genus of colonial radiolarians (as opposed to solitary).
Species.
The following species are recognized:


Rubp Carboxylase/Oxygenase


Crown Bioscience International

Crown Bioscience International, also known as CrownBio, is a contract research organization focused on patient derived xenografts used in drug screening. The company was acquired by JSR Corporation in January 2018.
Company profile.
CrownBio was founded in 2006 on a drug-testing platform centered around xenografts. The company keeps a library of cancer models used for drug-testing that precedes clinical trials. The company applied for listing on the Taipei Exchange in 2016 as part of its integration into Asian markets, and continued to expand its operations from higher revenues.
In 2018, CrownBio merged with JSR Corporation as part of JSR Corporation's expansion into the therapeutic market.
Products.
CrownBio's signature products include a library of xenograft models used for drug testing and contract research services for experimental drug screening. The company has at least 8,000 viable human tumors that can be used for the evaluation of drugs used in oncology studies.


LeanXcam

The leanXcam is an open source based smart camera which is used for industrial applications in the field of machine vision. The hardware design is available for free. It can be downloaded free of charge, making it possible to make the board oneself.
In a presentation at the Vision 2008 exhibition in Stuttgart, leanXcam met with a great positive resonance in the media.
Application.
The leanXcam is used by various universities, government agencies, industrial companies and private clients worldwide. The open source philosophy is encountered, especially in the universities, with great interest. Each also has its own library files freely available on the Internet.
Of the known applications of the leanXcam, it is used to automate production processes, quality controls, and to operate autonomously. In security, the camera is used to recognize objects within the viewing window, and if necessary to trigger an alarm. The leanXcam can also be used as a simple webcam for motion pictures on the internet.
Hardware.
The smart camera contains a Blackfin Blackfin DSP processor (ADSP-BF537), which can analyze the image data directly and evaluate. The camera sensor provides 60 images per second with a resolution of 752x480 pixels. This combination allows operation without an external PC. Communication is made available through the Ethernet port on the camera or, for small amounts of data, via RS-232 and I2C.
Software.
The freely available operating system uClinux is used. This allows the use of various standard programs, such as web servers, directly on the camera. An open source software library (Oscar) allows the control of hardware through the appropriate drivers. Several sample applications in C and C++ are available on the Internet and can be used as a basis for implementing one's own projects.
Technical Data.
Dimensions.
 (L x W x H)
Community.
The open source project is kept alive by a large community which is supported by the development portal of ETH Zurich. Under https://github.com/scs/leanXcam/wiki the resources for the developments and enhancements of the software package can be found. Numerous examples of software, documentation, and libraries are freely available online.
Awards.
2008 marked the most important exhibition for industrial image processing (VISION) of the leanXcam with the "Vision Award 2008".


Certify Data Systems

Certify Data Systems, Inc. founded in 2004, was a healthcare information technology (IT) company located in Campbell, California, that developed an interoperability platform to enable health information exchange (HIE) between healthcare entities, such as integrated health organizations, hospitals, multi-specialty centers, clinics, laboratories and physicians. The company was acquired by Humana Inc. (NYSE: HUM) in 2012. In March 2015, Certify Data Systems integrated with Anvita Health and nliven systems to form Transcend Insights, a population health management (PHM) technology company.
History.
In November 2012, Humana announced its acquisition of Certify Data Systems.
In March 2015, Humana announced the formation of Transcend Insights, a convergence of its three California-based subsidiaries: Certify Data Systems, Anvita Health and nliven systems. The merge brought together more than 30 years of collective experience in the healthcare IT space.
Awards and Accolades.
In August 2009, Certify Data Systems was selected as a semifinalist for the Adaptive Business Leaders Organization's Innovative Approach to the Delivery of Healthcare award.
In December 2009, Cerner Corporation signed an agreement with Certify Data Systems to resell Certify Data Systems' HealthDock appliance to supplement its Cerner Hub connectivity services.
In May 2012, Chilmark Research ranked Certify Data Systems as a "tier one enterprise HIE vendor" in the "2012 HIE Market Report: Analysis & Trends of the Health Information Exchange Market." A representative of Chilmark Research stated, "It is hard to find fault with this company. Certify Data Systems has a clear product vision for a novel, innovative HIE product portfolio and [their] HIE solution suite is elegant in its simplicity and ability to bring up an HIE quickly with deep integration to a wide range of ambulatory EHR solutions in the market."
In June 2012, Certify Data Systems ranked among top three private HIE Vendors In Black Book Market Research 2012 User Survey, recognized as one of the top three private HIE vendors according to the Black Book Healthcare Information 2012 Rankings. Certify was ranked third out of 20 top private Core HIE Systems vendors. In addition, the company ranked within the top 10 percent in a high majority of criteria used to judge vendors in this survey.


Branch migration

Branch migration is the process by which base pairs on homologous DNA strands are consecutively exchanged at a Holliday junction, moving the branch point up or down the DNA sequence. Branch migration is the second step of genetic recombination, following the exchange of two single strands of DNA between two homologous chromosomes. The process is random, and the branch point can be displaced in either direction on the strand, influencing the degree of which the genetic material is exchanged. Branch migration can also be seen in DNA repair and replication, when filling in gaps in the sequence. It can also be seen when a foreign piece of DNA invades the strand.
Mechanism.
The mechanism for branch migration differs between prokaryotes and eukaryotes.
Prokaryotes.
The mechanism for prokaryotic branch migration has been studied many times in "Escherichia coli". In "E. coli," the proteins RuvA and RuvB come together and form a complex that facilitates the process in a number of ways. RuvA is a tetramer and binds to the DNA at the Holliday junction when it is in the open X form. The protein binds in a way that the DNA entering/departing the junction is still free to rotate and slide through. RuvA has a domain with acidic amino acid residues that interfere with the base pairs in the centre of the junction. This forces the base pairs apart so that they can re-anneal with base pairs on the homologous strands.
In order for migration to occur, RuvA must be associated with RuvB and ATP. RuvB has the ability to hydrolyze ATP, driving the movement of the branch point. RuvB is a hexamer with helicase activity, and also binds the DNA. As ATP is hydrolyzed, RuvB rotates the recombined strands while pulling them out of the junction, but does not separate the strands as helicase would.
The final step in branch migration is called resolution and requires the protein RuvC. The protein is a dimer, and will bind to the Holliday junction when it takes on the stacked X form. The protein has endonuclease activity, and cleaves the strands at exactly the same time. The cleavage is symmetrical, and gives two recombined DNA molecules with single stranded breaks. The breaks are then ligated together to complete the process.
Eukaryotes.
The eukaryotic mechanism is much more complex involving different and additional proteins, but follows the same general path. Rad54, a highly conserved eukaryotic protein, is reported to oligomerize on Holliday junctions to promote branch migration.
Control.
The rate of branch migration is dependent on the amount of divalent ions, specifically magnesium ions (Mg2+), present during recombination. The ions determine which structure the Holliday junction will adopt, as they play a stabilizing role. When the ions are absent, the backbones repel each other and the junction takes on the open X structure. In this condition, migration is optimal and the junction will be free to move up and down the strands. When the ions are present, they neutralize the negatively charged backbone. This allows the strands to move closer together and the junction adopts the stacked X structure. It is during this state that resolution will be optimal, allowing RuvC to bind to the junction.