bluuebunny/crossref_metadata_2025 huggingface dataset:
Orthologues, Paralogues and Xenologues in Human and Other Genomes
Authors: Zhaxybayeva Olga , Gogarten J Peter , Olendzenski Lorraine
Published: October 2009

Homologous genes share a common evolutionary ancestor and can be orthologues (derived from speciation events), paralogues (derived from gene duplication events) or xenologues (derived from horizontal transfer or lineage fusion). Comparative analysis of the human genome indicates high levels of recent and ancient duplication at the level of nucleotides, genes and chromosome segments, and no unambiguous examples of recent transfer from bacteria.
Modern Humans: Origin and Evolution
Authors: Disotell Todd R
Published: October 2009

Modern humans originated recently in geological time from a diverse African gene pool. Very little if any interbreeding probably occurred with existing archaic human populations outside of Africa such as the Neanderthals of Europe.
Male‐driven Evolution
Authors: Ellegren Hans
Published: October 2009

If the number of germ‐line cell divisions has an effect on the mutation rate, for example owing to replication errors, we might expect the mutation rate of the two sexes to differ. Recent estimates from human and other primates suggest that this difference corresponds to a male bias of a factor of approximately 5.
Population History and Linkage Disequilibrium
Authors: Zöllner Sebastian
Published: October 2009

Population history and demographic structure influence the evolution of linkage disequilibrium between loci. Besides recombination and mutation, processes like selection, genetic drift, bottlenecks, admixture, population substructure and population expansion fundamentally influence the association of linked loci.
Genetic Drift in Human Populations
Authors: Bohonak Andrew J
Published: October 2009

Genetic drift consists of changes in allele frequencies due to sampling error. Even if all individuals in a population have the same opportunities to mate, their reproductive contributions to the next generation will vary due to random chance alone. In any population of finite size, this sampling error will cause gene frequencies to fluctuate from generation to generation. Genetic changes due to drift are neither directional nor predictable in any deterministic way. Nonetheless, genetic drift leads to evolutionary change even in the absence of mutation, natural selection or gene flow.
Fixation Probabilities and Times
Authors: Otto Sarah P , Whitlock Michael C
Published: October 2009

The fixation probability of an allele is the probability that it will eventually be the ancestor of all the alleles within a population at that locus. The time to fixation is the number of generations that it takes for the allele to progress from its initial frequency to fixation.
Inherited Neuromuscular Disease
Authors: Ferguson Toby A , Lynch David R
Published: October 2009

Inherited neuromuscular disease encompasses a broad array of diseases afflicting many people at all stages of life. The main categories of inherited neuromuscular disease are diseases of peripheral nerve (neuropathy), diseases of muscle (myopathy and dystrophy) and diseases of spinal cord motoneurons (motor neuron disease).
Predictive Genetic Testing: Psychological Impact
Authors: Evers‐Kiebooms Gerry , Denayer Lieve
Published: October 2009

Predictive genetic tests aredeoxyribonucleic acid(DNA) tests that predict the future of an asymptomatic person in regard to a specific disease that runs in the family. They require an adequate multidisciplinary counselling approach because the test result has consequences for the psychological well‐being of those tested and their families.
Gene Distribution in Human Chromosomes
Authors: Bernardi Giorgio , Saccone Salvatore
Published: October 2009

The distribution of genes in the human genome is strikingly nonuniform. Gene density is very high in GC (G, guanine; C, cytosine)‐rich isochores and very low in GC‐poor isochores (isochores are long
deoxyribonucleic acid
(DNA) regions characterized by a fairly homogeneous GC level). Since GC‐rich and GC‐poor isochores can be localized on human chromosomes, this ‘chromosomal compositional mapping’ provides information on the distribution of genes on chromosomes. The completion of the human genome sequence and the mapping of isochores on chromosomes have recently confirmed these results.
Chromosomes in Mammals: Diversity and Evolution
Authors: Wienberg Johannes , Müller Stefan
Published: October 2009

Inspecting the morphology of chromosomes in different species has been a classical tool for evolutionary biologists. DNA probes ranging in size from whole chromosomes to a few hundred base pairs can be seen under the microscope and assigned to unique regions of the genomes of different species. They have different resolutions and, in analogy, delineate entire continents, countries or even villages, streets and houses of the genome. Here we describe recent insights into the mode and tempo of mammalian chromosomes evolution using molecular cytogenetic approaches.
Sociobiology, Evolutionary Psychology and Genetics
Authors: Bateson Patrick
Published: October 2009

Much of human behaviour, including violence and those activities thought to be characteristic of each sex, has been attributed to the heritage of human evolution. These ideas have stimulated much discussion but have been criticized for playing down the interplay between the developing individual and the environment. In modern times, their clearest expression has been in the writings of the sociobiologists and the evolutionary psychologists.
Thrifty Genotype Hypothesis and Complex Genetic Disease
Authors: Vardi Pnina , Bloch Konstantin
Published: October 2009

Thrifty genes might be responsible for the appearance and increasing frequency of diseases that were uncommon before the emergence of the affluent Western life style. Evolutionary selection of such genes enabled metabolic adaptation to disadvantageous conditions, but now thrifty gene expression is detrimental to health.
Serpins: Evolution
Authors: Silverman Gary A , Askew David J , Irving James A , Luke Cliff J , Kaiserman Dion , Bird Phillip I , Whisstock James C
Published: October 2009

The serpin superfamily of
serine
(and
cysteine
) proteinase inhibitors contains over 750 members represented in Bacteria, Archaea and Eukarya. All members of the serpin family share a unique tertiary structure that is critical to both inhibitory and noninhibitory functions. Serpins are involved in a vast array of biological processes, including the regulation of thrombosis, fibrinolysis and inflammation, and host defense.
Nuclear Receptor Genes: Evolution
Authors: Owen Gareth I
Published: October 2009

The evolutionary origins and diversification of the nuclear receptor superfamily gene structure in the Metazoa.
Fugu
: The Pufferfish Model Genome
Authors: Venkatesh B
Published: October 2009

The genome of the Japanese pufferfish,
Fugu rubripes
, which is among the smallest vertebrate genomes, is an attractive model vertebrate genome, and was the first vertebrate genome to be sequenced after the human genome. It has proved to be valuable for discovering novel genes and evolutionarily conserved gene regulatory elements in the human genome, and continues to serve as a ‘reference’ genome for understanding the evolution of vertebrate genomes.
Protein Glycosylation, an Overview
Authors: Lisowska Elwira
Published: October 2009

Glycosylation is the most common posttranslational modification of proteins. It is a complex process involving many functional proteins and resulting in a great diversity of structures. Biological role of glycosylation and molecular and genetic basis of glycosylation disorders have recently been extensively explored. The goal of this short article is to signalize the variety of problems of this vast field of research.
DELLA
Proteins in Signalling
Authors: Alvey Liz , Boulton Margaret I
Published: October 2009

DELLAs are a family of nuclear proteins that act as growth repressors throughout the life cycle of higher plants. Derepression is mediated through the gibberellic acid (GA)‐dependent degradation of DELLAs and the key components of the GA‐DELLA signalling pathway (the GA receptor and the F‐box protein involved in DELLA destruction) have recently been identified. It is becoming increasingly clear that DELLAs promote a plant's survival by integrating its growth responses to a wide range of endogenous and environmental signals.
Disorders of Cholesterol Biosynthesis, Genetics of
Authors: Phillipi Carrie A , Steiner Robert D
Published: October 2009

Smith‐Lemli‐Opitz syndrome (SLOS) is the most common and best understood of the inborn errors of cholesterol metabolism. Comprising a heterogeneous group of disorders, inborn errors in cholesterol biosynthesis result in characteristic but variable phenotypes. SLOS is an inherited disorder caused by mutations inDHCR7which encodes the final enzyme in the cholesterol synthetic pathway. The features of SLOS are thought to be related to cholesterol deficiency and/or accumulation of cholesterol precursors and their metabolites. Therefore, supplementation of cholesterol is a commonly employed potential therapy. A better understanding of SLOS and other inborn errors of cholesterol biosynthesis may shed light on the importance of cholesterol biosynthesis in embryo‐ and morphogenesis and provide clues to treatment.
Alzheimer Disease, Genetics of
Authors: Kehoe Patrick G
Published: October 2009

In almost 20 years of ongoing research, the genetic cause of Alzheimer disease (AD) is understood for less than 5% of all cases. For the remainder of AD sufferers, multiple genetic and environmental factors probably play a role in contributing to disease onset, severity and progression. To date, only the gene encoding apolipoprotein E (APOE) is recognized as a major genetic risk factor, but numerous other candidates have emerged. What we have learned from these findings is discussed as are the results from recent genome linkage studies on affected sibling pairs which have yielded new chromosomal regions of interest and in turn new candidate genes alongside those reported from ongoing candidate gene association studies.
Actinobacteria
Authors: Trujillo Martha E
Published: October 2009

Actinobacteria are Gram‐positive bacteria with a high mol% G+C composition, widely distributed in soil where they play an important part in the decomposition of organic matter. These bacteria are responsible for the distinctive scent of freshly exposed, moist soil. Actinobacteria are morphologically diverse ranging from coccoid, fragmenting hyphal forms to those with a highly differentiated branched mycelium. Many of these bacteria also produce external spores. Several actinobacteria are important human, animal and plant pathogens. However, they are major producers of medically important antibiotics, especially members of the genus

Streptomyces

, the most abundant group.
Convention on Biological Diversity
Authors: Höft Robert
Published: October 2009

The Convention on Biological Diversity is the key global instrument on the conservation and sustainable use of biological diversity and the fair and equitable sharing of the benefits from the use of genetic resources. Through a globally agreed target aimed to reduce the loss of biodiversity the Convention promotes the maintenance of healthy ecosystems, the protection of threatened species and the conservation of the genetic material that underpins populations of wild and domesticated species. Increasingly, nongovernmental organizations, civil society groups and indigenous and local communities work through the Convention to urge countries to live up to their commitments and to support them, for example in the establishment and effective management of protected area networks. As population growth and economic pressures enlarge humanity's ecological footprint it remains to be seen whether the Convention is an effective tool for conserving the beauty, diversity and inspiring nature of our living environment for future generations to enjoy.
Millennium Ecosystem Assessment
Authors: Mace Georgina M
Published: October 2009

The Millennium Ecosystem Assessment was a scientifically based global review of the state of the world's ecosystems and their ability to meet the needs of a growing human population. Requested by governments through four international conventions, the assessment examined a broad suite of ecosystem services. Sixty per cent of 24 ecosystem services assessed at the global scale were degraded or overused. Using various modelling approaches, future prospects were found to improve only where policies related to environmental management were radically altered, in particular towards proactive planning for ecosystem services, and with the implementation of economic, political and technological incentives at scales ranging from global to local.
Amphibian Decline
Authors: Halliday Tim
Published: October 2009

Amphibians are susceptible to changes to both aquatic and terrestrial habitats caused by human activities. Amphibians are declining throughout the world and 32% of species are threatened with extinction. Most disturbingly, many declines, and some extinctions, have occurred in locations where they are supposedly protected. Habitat destruction is the most significant cause of amphibian declines, but other factors, including ultraviolet radiation, contamination by agricultural and industrial chemicals, climate change, introduced predators and overexploitation also play an important role. The most dramatic declines and extinctions have been caused by a fungal disease, chytridiomycosis, which has recently become globally distributed.
Water Transport across Cell Membranes
Authors: Reuss Luis
Published: October 2009

The focus of this article is on the pathways and molecular mechanisms of water transport across the plasma membrane. We discuss basic principles of water transport, including diffusion and osmosis and apply these concepts to the case of water permeation across the cell membrane. The general conclusion is that diffusion and osmosis can explain water transport and that other mechanisms (e.g. cotransport) are less likely. Concerning the pathways for water movement across the plasma membrane, we consider the lipid bilayer, water‐selective pores (aquaporins, AQPs), nonselective larger pores, ion channels and membrane carriers. We conclude that the lipid bilayers and AQPs are the main pathways for transmembrane water fluxes, by solubility–diffusion and single‐file transport, respectively.
Plant Viruses as Gene Expression and Silencing Vectors
Authors: Lomonossoff George P , Montague Nicholas P
Published: October 2009

It has proven possible to introduce foreign sequences into the genomes of plant viruses in such a way that their ability to replicate is retained. As a result, the foreign sequence is amplified resulting in either the high‐level expression of a foreign protein or virus‐induced gene silencing of an endogenous plant gene. This has meant that plant virus‐based vectors have found widespread application both as a means of protein expression and as a tool in functional genomics.
Insect Viruses
Authors: Christian Peter D , Possee Robert D
Published: October 2009

Viruses from over 16 families have been isolated from insects to date and show as much variation in structural and organizational paradigms as viruses from most other animal classes. Unique to the insect viruses is the ability of several virus families to produce a large pseudocrystalline occlusion body that protects the mature virus particles in the environment. Such occlusion bodies have led to these viruses evolving a complex array of associations with their insect host and in many cases causing large‐scale disease epizootics. Among the remaining nonoccluded insect viruses all of the basic structural and organizational paradigms are present in different families. However, the life history strategies of their insect hosts has led the insect viruses to evolve some intriguing replicative strategies of their own that have few, if any, counterparts among the other animal viruses.
Varicella Zoster: Virus and Disease
Authors: McDonald Suzanna LR , Breuer Judith
Published: October 2009

Varicella zoster virus

(VZV), also known as

human herpes virus 3

(HHV3), causes varicella (chicken pox) upon primary infection, establishes latency in dorsal root ganglia (DRG) and can later reactivate to cause herpes zoster (shingles). Difficulties in studying the pathogenesis of VZV; because of its high cell association and narrow host range, have been overcome through the development of the VZV severe combined immunodeficient (SCID) mouse model carrying human tissue implants. VZV is the first human herpes virus for which a live attenuated vaccine has been developed.
Chromosomal Rearrangements in the Human and Chimpanzee Lineages
Authors: Kehrer‐Sawatzki Hildegard , Cooper David N
Published: October 2009

Among the structural differences evident between humans and chimpanzees are large chromosomal rearrangements which are visible by cytogenetic analysis. These include the fusion that created human chromosome 2, nine pericentric inversions and numerous chromatin additions at the telomeres. Recently performed genome‐wide comparative analyses have also revealed a considerable number of submicroscopic structural variations which contribute significantly to the chromosomal divergence between humans and chimpanzees. This microheterogeneity comprises inversions, duplications and deletions ranging in size from a few base pairs up to several megabases. These copy number differences appear to have given rise to several hundred megabases of genomic
deoxyribonucleic acid
(DNA) sequence that are either present or absent in humans as compared to chimpanzees. Since many of these lineage‐specific copy number differences contain genes, humans and chimpanzees may differ significantly with respect to their gene content, and some of these differences could have influenced the evolution of lineage‐specific traits.
Alternative Splicing in the Human Genome and its Evolutionary Consequences
Authors: Florea Liliana
Published: October 2009

Alternative splicing, or the ability of genes to produce multiple
messenger ribonucleic acid
(mRNA) and protein isoforms by using different combinations of a gene's segments (exons), has recently been regarded as a mechanism that can explain how functional diversity in higher organisms can be achieved from a small number of genes, and thus can ultimately contribute to the increase in organism complexity during evolution.
Evolution of Gene Expression in Human and Chimpanzee Brains
Authors: Osada Naoki , Sumio Sugano , Suzuki Yutaka
Published: October 2009

The
deoxyribonucleic acid
(DNA) microarray technique enables us to gauge the difference in gene expression level between human and chimpanzee brains at a genome‐wide level. Several studies have shown that (1) gene expression is more conservative in the brain than in other tissues, (2) the divergence rate of gene expression in the brain is higher in the lineage of humans than in the chimpanzees and (3) more genes are up‐regulated in human brains.
Hotspots of Mammalian Chromosome Evolution
Authors: Froenicke Lutz , Lyons Leslie A
Published: October 2009

The emergence of high‐quality mammalian whole genome sequence data has enabled for the first time a comprehensive investigation of the molecular mechanisms of mammalian chromosome evolution. New sequence data reveal an unexpected degree of chromosomal plasticity, both in the healthy human population and in cross‐species evolutionary comparisons. In the context of the evolutionary framework established by comparative cytogenetics, the new data reveal lineage‐specific chromosomal rearrangement pattern often linked to particular duplicated or repetitive sequences. Multispecies comparisons indicate evolutionary reuse of certain chromosomal breakpoints as well as some associations of breakpoints to cytogenetic chromosomal landmarks.
Reconstruction of Ancestral Genomes
Authors: Stanyon Roscoe , Garofalo Fiorella , Bigoni Francesca
Published: October 2009

Comparative genomics allow speculation about the content of the genome of ancestral species and for many major branching points on the tree of life, hypothetical ancestral genomes can be reconstructed. These reconstructions provide insight into evolutionary forces that have sculpted the genomes of extant species.
Susceptibility to Human Infectious Diseases, Genetics of
Authors: Kaslow Richard A , Shrestha Sadeep , Tang Jianming ‘James’
Published: October 2009

Microbial pathogens have shaped portions of the human genome over the millennia of its evolution, resulting in human genetic diversity and differential susceptibility to infectious diseases. Distinguishing characteristics of infectious diseases permit and require specific approaches to the investigation of genetic influences that can differ substantially from highly favourable to highly unfavourable. Expanding knowledge and improved technology are revealing importantdeoxyribonucleic acid(DNA) sequence and structural polymorphism in critical pathways of the innate and acquired immune systems. Reports are proliferating on relationships of responses to infection with variants of genes that encode secreted cytokines and lectins along with their receptors, intracellular signalling molecules, components of the antigen‐presenting machinery and other effector or regulatory products. These notable accomplishments foreshadow both revelations and challenges in dissecting the complex host genetic mediation of differential responses to infectious diseases in individuals and populations.
Structural Diversity of the Human Genome and Disease Susceptibility
Authors: Smith Richard S , Gutiérrez‐Arcelus María , Tran Charles W , Park Stephanie , Couter Cheryn J , Lee Charles
Published: October 2009

Structural genomic variants (SGVs) can span in size from the large microscopically visible chromosomal aberrations (>5 Mb) to variants identified at the DNA (deoxyribonucleic acid) sequence level (e.g. small insertions/deletions of a few base pairs). It has recently been shown that SGVs are widespread among humans, have some degree of specificity within human continental groups, and likely contribute significantly to differential disease susceptibility. Currently, the most common prevalent form of SGVs is copy number variants (CNVs), which are defined as DNA segments greater than 1 kb in length that exist in variable copy numbers between individuals. In this review, we provide an overview of our current understanding of human structural genomic variation, with a particular focus on CNVs and their associations in disease susceptibility.
The Evolution of Fatness and Susceptibility to Obesity
Authors: Wells Jonathan CK
Published: October 2009

Efforts to address the obesity epidemic require that we understand the impact of our modern environment on the human phenotype. An evolutionary approach can be used to address two questions. First, we need to understand what kind of animal we are, so that we comprehend why environmental changes induce increased fat deposition. Second, we need to understand what kind of environments our species evolved in, to identify what exactly we are altering in the twentieth and twenty‐first centuries.
Malarial Resistance and Susceptibility, Genetics of
Authors: Verrelli Brian C
Published: October 2009

Resistance to malaria in humans, as well as drug and insecticide resistance by the malarial parasite and the mosquito that acts as its vector, respectively, is the result of adaptation by all three organisms. Characterization of the function and evolution of the genes underlying this resistance and susceptibility is paramount to our understanding of malarial treatment and eradication.
Evolution of Human Gene Expression Control
Authors: Babbitt Courtney C , Wray Gregory A
Published: October 2009

The evolutionary history of

Homo sapiens

has been influenced by selection acting not only on coding regions of the genome, but also on regulatory sequences which control the timing, location and magnitude of gene expression. As the mutations affecting the timing and level of gene expression may be responsible for many of the traits that distinguish us from our closest relatives, selection on regulatory elements of the genome also may have had a large role in shaping recent human evolutionary change.
Human and Macaque Transcriptomes: A Comparison
Authors: Walker Stephen J
Published: October 2009

The initial deciphering of entire genomes from several mammalian species including human, chimpanzee and macaque has now been accomplished and the massive datasets are publicly available in the form of high‐quality draft sequences. As a direct result, the development and commercialization of an ever‐increasing number of sensitive tools to measure global gene expression (the ‘transcriptome’) is providing unique opportunities to evaluate and compare biological systems. One particularly important application is to use tissues derived from macaque models of toxicity and disease to infer responses in their human counterparts. Understanding the similarities and differences in how macaques and humans respond, at the functional genomic level, to perturbations in their environments has significant relevance in biomedical research.
Adaptive Evolution of Primate Sperm Proteins
Authors: Clark Nathaniel L
Published: October 2009

Adaptive pressures throughout primate evolution have shaped sperm and seminal fluid proteins, causing them to change more rapidly than most other proteins. The adaptations are thought to be in response to sperm competition, sexual conflict, pathogen evasion and reinforcement.
Bidirectional Gene Pairs in the Human Genome
Authors: Koyanagi Kanako O , Imanishi Tadashi , Gojobori Takashi
Published: October 2009

Bidirectional gene pairs, also called head‐to‐head gene pairs, are defined as two genes on different strands with adjacent 5′‐ends. They are transcribed divergently in a variety of coordinated fashion. The region between two transcription start sites of a bidirectional gene pair is designated as a putative bidirectional promoter.
Bitter Taste Sensitivity in Humans and Chimpanzees
Authors: Behrens Maik , Meyerhof Wolfgang
Published: October 2009

Bitter taste receptors serve an important function during evolution. They are designed to detect toxic plant metabolites before ingestion. With respect to bitter taste receptors the genetic repertoire of animal species is highly diverse reflecting species differences in their metabolic requirements, the variety of habitats, and evolutionary history. By comparing the bitter taste receptor genes of humans with our closest relative, the chimpanzee, we learn about some of the evolutionary forces that shaped the development modern human beings. This review discusses the current knowledge on bitter taste physiology,
TAS2R
function, and evolutionary conservation of human and chimpanzee TAS2R genes.
Evolution of the Human Immune System
Authors: Danilova Nadia
Published: October 2009

Human immune system is an orchestra of various defence mechanisms functioning at different levels, from individual cells to the whole body. They evolve interactively in concordance with human environment and history.
Evolutionary Conservation of Splice Sites
Authors: Hastings Michelle L. , Sachidanandam Ravi
Published: October 2009

The evolution of splice sites (both 5′ and 3′) is constrained. The results of the constraints are observed in conserved signatures exhibited by splice sites across species.
HapMap Project
Authors: Traynor Bryan J , Singleton Andrew
Published: October 2009

The inception of the International Haplotype Map Project (
http://www.hapmap.org/
) and completion of stages I and II of this project has led to the production and public dissemination of a map of patterns of human genetic diversity in four populations; Japanese from Tokyo, Central Europeans from Utah, Han Chinese and Yorubans from Nigeria. These data present unprecedented opportunities in human genetics; they provide invaluable information on human evolutionary history and for the first time present a roadmap for mapping genetic variability that underlies complex traits. The invention and application of ultra‐high throughput genotyping technologies is beginning to realize this latter goal, even in the early days of this effort the HapMap Project is proving worth the time and resources invested thus far.
Genetics and the History of the Basque People
Authors: Alonso Santos
Published: October 2009

The linguistic peculiarity of the Basques raised the expectation that a similar situation could be found at the biological level. Recent debate has focused mainly on two points: the genetic heterogeneity of the Basque population and whether Basques are the best representative population of Palaeolithic Europe. Several lines of evidence indicate that at least some Basque DNA (
deoxyribonucleic acid
) lineages (alleles) have evolved
in situ
, probably since pre‐Neolithic times. In this regard, we must bear in mind that the term ‘Basque’ is a present‐day cultural concept and we should be cautious in projecting current cultural affiliations into the past.
Genetics and the Origins of the British Population
Authors: Richards Martin , Capelli Cristian , Wilson James F
Published: October 2009

A combination of archaeology and evolutionary genetics has led to a reappraisal of the major demographic transitions in British prehistory. The role of ‘Celtic’ migrations has been questioned, with the aboriginal population of the islands seen largely as the result of settlement at the end of the last Ice Age, probably augmented by further settlement during the Neolithic. The demographic impact of the Anglo‐Saxons, considered minor by archaeologists, has been estimated to be high by some geneticists, but this is the result of implausible assumptions about the preceding genetic composition of the islands and overinterpretation of poorly resolved genetic data.
Genetics and the Origins of the Irish
Authors: McEvoy Brian , Bradley Daniel G
Published: October 2009

Population genetics, principally using Y‐chromosome and mitochondrialdeoxyribonucleic acid(DNA), has provided many novel insights into Ireland's past. These inlcude broad issues of early time‐frame including the origin of the first Irish 9000 years before present, as well as the population impact associated with later events such as the appearance of Celtic culture and the Viking invasions. Furthermore, the Y‐chromosome in combination with surname information has also allowed questions of more recent nature and smaller scale to be addresssed including the levels of patrilineal kinship in early medieval Irish kingdoms and the origin and subsequent history of Irish surnames themselves.
Epigenetic Variation in Humans
Authors: Wilkins Jon F
Published: October 2009

Epigenetic modifications alter the expression behaviour of genes without involving changes to the DNA (
deoxyribonucleic acid
) sequence itself. These modifications take a variety of forms, most notably DNA methylation and histone modification. Epigenetic differences allow alleles, cells or even individuals that are genetically identical to exhibit radically different phenotypes. Differentiation among cells underlies tissue differentiation and development. Differentiation between alleles within a cell is used to enhance clonal diversity, as in the immune system, and has been highjacked in the service of evolutionary genetic conflicts, as seen in the phenomenon of genomic imprinting. Epigenetic differences among individuals may account for some of the differences between monozygotic (identical) twins. Some recent studies have even suggested that these epigenetic mechanisms may allow organisms to adapt to environmental changes on very short timescales. Environmental adaptations could be epigenetically encoded and passed on to offspring, providing a potential mechanism for a neo‐Lamarckian mode of evolution.
On the Number of Ancestral Human Species
Authors: Curnoe Darren
Published: October 2009

The number of species within the human evolutionary tree remains a major point of debate. Genomic distances for living humans and other apes may be used to estimate hominin diversity and therefore to set boundaries for palaeontological scenarios. A minimum of five species is recognizable but scenarios involving much higher estimates of diversity cannot be ruled out.
Population Genetics of the Ashkenazim
Authors: Faerman Marina
Published: October 2009

Ashkenazi Jews represent the largest Jewish community and traditionally trace their origin to the ancient Hebrews who lived in the Holy Land over 3000 years ago. Ashkenazi Jews are among the groups most intensively studied by population geneticists. Here, main genetic findings and their implications to the history of Ashkenazim are presented reflecting in a way major developments in population genetics as a discipline. Altogether, Ashkenazi Jews appear as a relatively homogenous population which has retained its identity despite nearly 2000 years of isolation and is closely related to other Jewish communities tracing their common origin to the Middle East.
Reconstructing Human History Using Autosomal, Y‐Chromosomal and Mitochondrial Markers
Authors: Yngvadottir Bryndis , Carvalho‐Silva Denise R
Published: October 2009

By analysing genetic variation between and within extant human populations it is possible to make inferences about the origins and relationships of our ancestors. Although the autosomes give us a representative account of genomic history in humans, the unique characteristics of the maternally inherited mitochondrial
deoxyribonucleic acid
(mtDNA) and the paternally inherited Y chromosome can provide information about the histories specific to women and men. Current evidence suggests a recent African origin for modern humans <200 thousand years ago (KYA) and a single small migration out of Africa 50–70 KYA, with progressive loss of diversity with distance from Africa, somewhat complicated by sex‐specific effects and natural selection.
The Peopling of the Americas as Revealed by Molecular Genetic Studies
Authors: Schurr Theodore G
Published: October 2009

Molecular genetic studies of Siberian and Native American populations indicate that ancestral Native Americans originated in south‐central Siberia and entered the New World between 20 000 and 15 000 years before present (ybp), after thousands of years of isolation in Beringia. These early immigrants probably followed a coastal route into the New World, where they expanded into all continental regions. A second expansion, possibly coming from the same area of Siberia, may have entered the Americas, and genetically influenced North American populations. Beringian populations moved into northern North America after the Last Glacial Maximum (LGM) and gave rise to Aleuts, Eskimos and Na‐Dené Indians.
The Evolution of CentromericDNASequences
Authors: Bayes Joshua J , Malik Harmit S
Published: October 2009

Human centromeres are comprised of millions of base pairs of tandemly repeateddeoxyribonucleic acid(DNA) sequences. Contrary to the expectation that centromeric sequences would be extremely constrained for centromere function throughout primate evolution, these sequences represent some of the most rapidly evolving sequences in the genome. This rapid evolution in spite of conserved function has been referred to as the ‘centromere paradox’, and it is hypothesized that an ancient, ongoing genetic conflict is at the heart of this rapid evolution.
The Biological Significance of Conserved Nongenic
DNA
Authors: Dermitzakis Emmanouil T
Published: October 2009

Although the completion of the human genome was a landmark in genomics, the availability of a single genome did not offer the opportunity to detect most of the functional part of the genome. With the completion of the mouse genome and the subsequent release of additional mammalian and other vertebrate genomes, a large number of conserved nonprotein‐coding sequences were discovered. The most surprising discovery was that the nongenic fraction of the genome that is under purifying selection is larger than the coding fraction of the genome. In this article we review some of the key discoveries in the field and discuss methodologies for the computational and functional interpretation of nongenic
deoxyribonucleic acid
(DNA).
Evolution of Alpha Satellite
DNA
Authors: Ugarković Đurđica
Published: October 2009

Alpha satellite
deoxyribonucleic acid
(DNA) is based on 171‐bp tandem repeats located in the centromeric regions of all primate chromosomes. It evolves through a series of amplification events resulting in the spreading of ‘new’ subfamilies which replace the ‘old’ ones and confer centromere function. Alpha satellite transcripts play an important role in kinetochore formation and the establishment of pericentromeric heterochromatin.
Inferring the Process of Human–Chimpanzee Speciation
Authors: Takahasi K Ryo , Innan Hideki
Published: October 2009

By examining
deoxyribonucleic acid
(DNA) sequence data from closely related species, we may gain insights into the genetic mechanism and process leading to the formation of new species. Recently, several interesting hypotheses have been proposed independently that maintain a complex mode of speciation of humans and chimpanzees, but at present, there does not seem to be any compelling evidence to support this provoking scenario.
Human Lineage‐specific Gene Inactivation
Authors: Grus Wendy E , Zhang Jianzhi
Published: October 2009

Pseudogenes are nonfunctional vestiges of genes. Investigating genes that were inactivated specifically on the human lineage can reveal the genetic basis of inter‐species differences between humans and chimpanzees and inter‐individual differences within humans. It can also help to understand the specific selective pressures that were altered during human evolution.
Segmental Duplications and Their Role in the Evolution of the Human Genome
Authors: Xue Yali , Tyler‐Smith Chris
Published: October 2009

Segmental duplications are unusually abundant in the human genome, perhaps because they carry genes whose amplification has been selectively advantageous during primate and human evolution. Their presence leads to genome instability, and so they are associated with genomic disorders, but they are also involved in the continuing evolution of the genome, for example by leading to increases in gene product, variant gene copies and fusion genes.
Human‐specific Accelerated Evolution of Noncoding Sequences
Authors: Webster Matthew T
Published: October 2009

Mutations in noncoding elements that regulate gene expression are likely to be responsible for a large fraction of phenotypic evolution. Hundreds of putative regulatory elements have been identified with accelerated evolutionary rates in the human lineage, which could be involved in human‐specific adaptations. However, instead of being driven by natural selection, the elevated rates of sequence evolution appear to be largely governed by neutral processes.
The Evolution of Introns in Human Genes
Authors: Gazave Elodie , Fernando Olga , Navarro Arcadi
Published: October 2009

Introns, which constitute the largest fraction of most eukaryotic genes and which had been considered to be neutral sequences, are increasingly acknowledged as functionally important parts of our genomes. For quite some time, research on levels of nucleotide substitution in human introns has been incomplete and yielded contradictory results, but the finishing of the chimpanzee genome allowed for new and more detailed studies that are proving to be key to unveil intronic functions.
Selection against Amino Acid Replacements in Human Proteins
Authors: Subramanian Sankar
Published: October 2009

The similarity of a large fraction of amino acid residues of human protein sequences with that of other species implies that the mutations altering those amino acids were purged through natural selection during the evolution of the human lineage. The deleterious effect of amino acid replacement mutations in human population is manifested by the association of many of these with genetic diseases.
Quality Control of Protein Folding in the Cytosol
Authors: McClellan Amie J
Published: October 2009

In order to function properly, newly synthesized proteins must rapidly and efficiently attain their native conformations. If they fail to do so, the cell may be adversely affected due to loss of function or toxic gain of function effects of misfolded polypeptides. Effective quality control mechanisms to recognize and eliminate misfolded proteins are thus critical for cell viability.
High‐throughput ‘On Chip’ Protein and Nucleic Acid Transfection
Authors: Herrmann Frank , Isalan Mark
Published: October 2009

Transfection describes the nonviral introduction of exogenous molecules into eukaryotic cells. Several transfection methods have been developed to transfer nucleic acids, proteins and other macromolecules across the plasma membrane efficiently. To facilitate large‐scale genomic and proteomic studies there is an increasing need for automated high‐throughput transfection platforms.
Positional Information
Authors: Wolpert Lewis
Published: October 2009

Pattern formation in development can be based on the cells acquiring positional values as in a coordinate system, and then interpreting these values with appropriate cell differentiation. Whether morphogen gradients specify position remains unclear.
Processed Pseudogenes and Their Functional Resurrection in the Human and Mouse Genomes
Authors: Sakai Hiroaki , Itoh Takeshi , Gojobori Takashi
Published: October 2009

The genomes of human and mouse contain thousands of pseudogenes. Processed pseudogenes, which were derived through retrotransposition, were recognized as ‘dead on arrival’ elements in the genomes, and they have been thought to have no contribution to genome evolution. However, several recent studies have shown that a significant portion of processed pseudogenes were transcribed and were able to function as noncoding
ribonucleic acid
(RNA) genes. Since the transcription mechanism and functions of transcribed processed pseudogenes still remain unknown, it is of great importance to elucidate the biological roles of processed pseudogenes by both approaches of experiments and bioinformatics.
Comparing the Human and Medaka Genomes
Authors: Sasaki Takashi , Shimizu Nobuyoshi
Published: October 2009

Medaka (

Oryzias latipes

) is a small teleost fish for which well‐established resources for genetic and genomic studies are available, hence, medaka has become an excellent laboratory model animal for life sciences. Comparing the human and medaka genomes provided novel information on the sets of genes, repetitive elements, gene regulatory elements and the evolutionary conserved elements at the nucleotide sequence level. The genomic information implied chromosomal evolution in the vertebrate lineage and the use of medaka for medical science.
AMP
‐Activated Protein Kinase (
AMPK
)
Authors: Hardie D Grahame
Published: October 2009

AMPK (AMP‐activated protein kinase) is a protein kinase that acts as a sensor of cellular energy status by monitoring the levels of adenine nucleotides, especially adenosine monophosphate (AMP) and adenosine‐5′‐triphosphate (ATP). When activated by falling cellular energy status, it acts to restore energy balance by switching on ATP‐producing catabolic pathways, while switching off any energy‐requiring processes (such as biosynthesis, cell growth and division) that are not essential for short‐term survival. AMPK is also regulated by hormones and cytokines that control energy balance at the whole body level.
Nitrogen Fixation in Cyanobacteria
Authors: Stal Lucas J
Published: October 2009

Cyanobacteria are oxygenic photosynthetic bacteria that are widespread in marine, freshwater and terrestrial environments and many of them are capable of fixing atmospheric nitrogen. But ironically, nitrogenase, the enzyme that is responsible for the reduction of N
2
, is extremely sensitive to O
2
. Therefore, oxygenic photosynthesis and N
2
fixation are not compatible. Hence, cyanobacteria had to evolve a variety of strategies circumventing this paradox allowing them to grow at the expense of N
2
, a ubiquitous source of nitrogen.
Effectiveness of an occupational health intervention program to reduce whole body vibration exposure: An evaluation study with a controlled pretest–post‐test design
Authors: Tiemessen Ivo J.H. , Hulshof Carel T.J. , Frings‐Dresen Monique H.W.
Published: October 2009

Background

An effective intervention program aiming to reduce whole body vibration (WBV) exposure at work will reduce the number of low back complaints in the near future.

Methods

An evaluation study with a controlled pretest–post‐test design. Nine companies and 126 drivers were included in the study. Cluster randomization on company level divided the drivers and their employers in an intervention group and a “care‐as‐usual” group. At baseline (T0) and intervention program was implemented and evaluated after 7 months (T1). The main outcome measure was WBV exposure. Process measures included knowledge, attitude, and (intended) behavior towards reduction of WBV exposure for the drivers and knowledge and WBV policy for the employers.

Results

At T1, no significant reduction was found in WBV exposure within both groups compared with T0.

Conclusions

Probably due to poor to moderate compliance, the intervention program was not effective in reducing the WBV exposure on group level but small reductions in WBV exposure are possible when intervention compliance is high. Am. J. Ind. Med. 52:943–952, 2009. © 2009 Wiley‐Liss, Inc.
Exploring social capital in rural settlements of an islander region in Greece
Authors: Zissi Anastasia , Tseloni Andromachi , Skapinakis Petros , Savvidou Maria , Chiou Mihaela
Published: November 2009

This paper reports on a large scale cross‐sectional study examining subjective perceptions of community social life held by a randomly selected sample of residents (n = 428) in all small rural settings (n = 89) of the region of North Aegean Sea. The notion of social capital was used as a conceptual tool in order to explore different aspects of the relational life of contemporary rural communities. This study has two aims: First to provide an account of rural residents' perceptions of village life in terms of interpersonal support, mutual aid, trust, social cohesion and community competence, and second to examine the suitability of the social capital notion within the specific cultural context. A combination of data collection procedures and a range of sources were employed, such as key informants, rural residents and researchers' field observations. The findings indicate that small farming communities of high devotion with deep roots and strong sense of belonging face severe demographic imbalance and experience low civic power given the limited links with external agents. The mainstream notion of social capital as an unconditionally beneficial factor is thus questioned. The findings call for revisiting its relevance across communities with varying capacities and needs. Copyright © 2009 John Wiley & Sons, Ltd.