bluuebunny/crossref_metadata_2025_split huggingface dataset:
Major Histocompatibility Complex Genes: Mouse H‐2
Authors: Hatina Jiří 
Published: October 2009

AbstractMouse major histocompatibility complex genes are arranged in a complex gene cluster – the H2 complex, coding for proteins either directly performing or associated with antigen presentation to T lymphocytes. The principal level of the regulation of the expression of H2 genes is the level of transcription. The major histocompatibility complex genes are the most polymorphic genes known, both within the coding and regulatory sequences. The genetic manipulation of H2 genes is very useful for creating mouse models of human immune‐related functions and pathologies. H2‐associated disease susceptibility is used as a model to understand similar human diseases.
Human and Chimpanzee Nucleotide Diversity
Authors: Kaessmann Henrik 
Published: October 2009

Abstract

Nucleotide diversity is a measure of
deoxyribonucleic acid
(DNA) polymorphism in a population that is based on pairwise DNA sequence comparisons. The extent of nucleotide diversity is shaped by the mutation rate and selection but also by the demographic history of a population. Thus, studies of nucleotide diversity in humans and their closest evolutionary relative, the chimpanzee, shed light on the population history of these species.
Introns: Phase Compatibility
Authors: Patthy László 
Published: October 2009

AbstractIntrons that lie between coding regions of protein‐coding genes may be assigned to three different phase classes, depending on their position relative to the reading frame of the translated protein: phase 0 (located between two codons), phase 1 (splitting codons between the first and second nucleotides) or phase 2 (splitting codons between the second and third nucleotides). In the case of protein‐coding genes with a unique pattern of pre‐messengerribonucleic acid(mRNA) splicing (and a unique protein product), the 5′ and 3′ splice junctions of an intron always belong to the same phase class (as defined by the unique protein product).
Exons and Protein Modules
Authors: Patthy László 
Published: October 2009

AbstractModules are versatile protein domains that are frequently used as building blocks in the construction of diverse multidomain proteins. The assembly of multidomain proteins from modules is facilitated by recombination in introns flanking the exons that encode the modules, but it may also occur by recombination in exons or through cotranscription of tandem genes.
Molecular Clocks
Authors: Li Wen‐Hsiung , Makova Kateryna D 
Published: October 2009

Abstract
The molecular clock hypothesis postulates that the rate of evolution in a macromolecule is approximately constant per year over time and among different evolutionary lineages. While local clocks in closely related organisms with similar generation times can be useful for dating evolutionary events, strong evidence now suggests that no global or universal clock exists in mammals.
Pax
Genes: Evolution and Function
Authors: Bouchard Maxime , Schleiffer Alexander , Eisenhaber Frank , Busslinger Meinrad 
Published: October 2009

Abstract

The transcription factors of the Pax protein family have been conserved throughout metazoan evolution and play essential roles in brain development and organogenesis. Loss‐of‐function and gain‐of‐function mutations in

PAX

genes cause inherited disease syndromes and tumor formation respectively.
Gene Families: Multigene Families and Superfamilies
Authors: Ohta Tomoko 
Published: October 2009

Abstract
Multigene families are defined as groups of genes with sequence homology and related overlapping functions, whereas superfamilies are defined as a group of proteins or genes of common origin with nonoverlapping functions. If a group of proteins or genes contains a domain of common origin, it is a superfamily; a protein or a gene may belong to two or more superfamilies.
Concerted Evolution
Authors: Liao Daiqing 
Published: October 2009

Abstract
Concerted evolution is a genetic process by which repetitive deoxyribonucleic acid (DNA) sequences are homogenized so that the sequence of a given multigene family within a species shares much higher sequence identity than that of the homologous gene family between two different species. Concerted evolution occurs in all living organisms, from bacteria to humans. DNA recombination mechanisms, especially unequal crossover and gene conversion, are responsible for concerted evolution.
Ancient
DNA
: Phylogenetic Applications
Authors: Knapp Michael , Vigilant Linda , Hofreiter Michael 
Published: October 2009

Abstract

Studies of ancient human
deoxyribonucleic acid
(DNA) attempt to shed light on the genetic relationships among individuals representing archaic or extinct human populations, and between these individuals and modern humans. These studies are limited by several factors, including the contamination of ancient samples with modern human DNA, the limited availability of nuclear DNA and difficulties in interpretation of results, due to the fact that modern, typically geographically defined human populations are not associated with diagnostic mitochondrial DNA (mtDNA) sequences.
Gene Structure: Evolution
Authors: Ohta Tomoko 
Published: October 2009

Abstract
Two fundamental processes in the evolution of gene structure in populations are the production of variations by mutations and the natural selection that filters these variations. Mutations occur randomly in genomes of germ cell lineages and are rejected or selected for, so that genes perform needed functions. As a result of minute effects of most mutations, both genetic drift and natural selection influence their fate in a population.
Long Interspersed Nuclear Elements (LINEs): Evolution
Authors: Furano Anthony V , Boissinot Stéphane 
Published: October 2009

AbstractLINE‐1 (long interspersed nuclear element‐1, L1) repeateddeoxyribonucleic acid(DNA) elements are non‐long terminal repeat (LTR) group of retrotransposons that replicate by copying (reverse transcribing) theirribonucleic acid(RNA) transcript into genomic DNA. LINE‐1 elements, which can also copy other RNAs into genomic DNA, are the dominant (and in some species the only) active clade of retrotransposons in mammals, where they have been replicating and evolving since before the mammalian radiation approximately 100 million years ago.
Risks to Relatives
Authors: Hopper John L , Dite Gillian S , Byrnes Graham B 
Published: October 2009

AbstractStudying risks to relatives can reveal important information on the likely causes of diseases. Even a modest increased risk for relatives of individuals with the disease (affected probands) compared with relatives of individuals without the disease (unaffected probands) cannot exist without there being strong underlying familial risk factors. Studying risks to relatives as a function of the strength of genetic, environmental and cohabitational relationships to the probands can help resolve whether the familial risk factors are likely to have a genetic and/or environmental aetiology, the more so if specific genes and environmental exposures are measured for one or more of the family members. Because only a small proportion of the familial aggregations of common diseases can be explained by known genes and other familial causes, there is scope for greatly expanding our knowledge of disease aetiology through information that can be gained from studying risks to relatives.
Linkage Disequilibrium
Authors: Croucher Peter JP 
Published: October 2009

AbstractWhen two or more polymorphic loci are studied in a population, the interaction between the loci is often expressed in terms of linkage disequilibrium (LD). The loci are in LD if their respective alleles do not associate independently (randomly). The degree of over‐ or underrepresentation of the expected haplotypes measures the extent of LD. Recombination acts to reduce LD.
Genetics of Large Populations and Association Studies
Authors: Garnier‐Géré Pauline Hélène , Chikhi Lounès 
Published: October 2009

Abstract
Association studies aim to discover the genetic basis of genetic diseases or drug responses through the comparison of unrelated affected and nonaffected individuals in large populations assumed to be at Hardy–Weinberg equilibrium (HWE). The HWE principle and the main causes of departures are first described with a focus on population stratification (Wahlund effect), which is one of the major problems in association studies. Recent statistical methods developed to detect and control for it are briefly reviewed.
Polymorphisms: Origins and Maintenance
Authors: Weiss Kenneth M 
Published: October 2009

Abstract

Polymorphism is variation in specific locations in the
deoxyribonucleic acid
(DNA) sequence. Some authors use the term only for variant alleles with at least 1% frequency in a population. This shows the population dependence of the concept itself. Variation arises initially by some form of mutation in a single individual but, because DNA is transmitted from parent to offspring, over time the frequency and geographical distribution of a genetic variant is essentially a population concept that depends on history.
Migration
Authors: Barbujani Guido 
Published: October 2009

Abstract
Migration is the movement of individuals in geographic space. When that movement has genetic consequences, migration determines gene flow. By introducing new genes where they were previously absent, migration increases genetic diversity within populations and reduces the differences among them. As a rule, groups that dwell close to each other tend to exchange more migrants than distant or isolated groups. But there are exceptions, especially during demographic expansions and when the populations are subdivided by geographic or cultural barriers. Rates and patterns of migration can be reconstructed from the analysis of genetic data.
Human Genome Project: Importance in Clinical Genetics
Authors: Little Peter FR , Williams Rohan BH 
Published: October 2009

Abstract
The Human Genome Project is impacting upon clinical genetics by defining the complexity of genes in humans, by developing technology at ‘genome‐wide’ scale, by underpinning the search for the genetic origins of complex disorders and by driving the development of new sequencing technologies of great power. Here we review these developments and argue that the greatest benefit of the Human Genome Project is yet to come.
Deafness: Hereditary
Authors: Hardelin Jean‐Pierre , Levilliers Jacqueline , Petit Christine 
Published: October 2009

Abstract
There are 45 genes known to cause nonsyndromic hearing impairment, and more are expected to be discovered in the next few years. However, difficulties in genetic linkage analysis, coupled with the possible involvement of environmental causes, have prevented the characterization of the main genes that are causative or predisposing to the late‐onset forms of deafness.
Pharmacogenetics and Pharmacogenomics
Authors: Nebert Daniel W 
Published: October 2009

Abstract

Between 1930 and 1990, several dozen
high‐penetrance predominantly monogenic
(hPpM) disorders in drug metabolism were identified and characterized, leading many to expect that the field of pharmacogenetics would very soon be able to provide us with ‘individualized drug therapy’. However, then came the Human Genome Project and the field of pharmacogenomics. We now realize that the genome is exceedingly complex and that the likelihood of ever achieving individualized drug therapy – for every person and every drug – is not scientifically or financially feasible. Perhaps genomics – in combination with transcriptomics, proteomics and metabonomics – will provide some degree of success, within the next several decades.
Clinical Genetic Services in the United Kingdom
Authors: Fryer Alan 
Published: October 2009

Abstract
The aim of Clinical Genetic Services is to help individuals or families with, or at risk of, conditions which may have a genetic basis to live and reproduce as normally as possible. In the UK, such specialist genetic services have, in general, developed as a network of Regional Genetics Centres, each serving populations of approximately 2–5 million people. Clinical geneticists work within these regional centres in multidisciplinary teams together with genetic counsellors and laboratory scientists. The clinical services are delivered through a network of central and district clinics and, in some cases, joint clinics with other specialists.
Newborn Screening Programmes
Authors: Parsons Evelyn P , Bradley Don M 
Published: October 2009

AbstractNewborn screening programmes are used to detect diseases in neonates by analysing a blood sample collected by heel‐prick, usually during the first week of life. Whereas early programmes were started with the aim of preventing mental retardation, advances in technology now mean that a variety of disorders, where treatment is more problematic, or even nonexistent, can be identified. This has broadened the scope of newborn screening and presents service providers with an increasing need to address issues about consent.
Synthetic Nucleic Acid Delivery Systems in Gene Therapy
Authors: Miller Andrew David 
Published: October 2009

Abstract

Synthetic nucleic acid delivery systems also known as synthetic nonviral vectors, are prepared primarily using synthetic organic chemistry expertise for the delivery of therapeutic nucleic acids to cells
in vitro
,
ex vivo
and
in vivo
. In clinical trials, simple cationic liposomes/micelles or simple cationic polymers have been the most widely used synthetic nucleic acid delivery systems. Problems were encountered and solutions are now in development. Consequently, there is no currently marketed gene therapy that makes use of synthetic nucleic acid delivery systems (synthetic nonviral vectors). Given latest developments, this situation should be reversed given time.
Telomere
Authors: Martin Christa Lese , Ledbetter David H 
Published: October 2009

Abstract
Telomeres, the ‘caps’ at the ends of human chromosomes, consist of specialized DNA and protein complexes that help to protect chromosomes from degradation. Other unique characteristics of telomeric DNA include the sequence homology shared between subtelomeric DNA regions, a high gene density and an increased frequency of chromosomal imbalances.
Mammalian Sex Chromosome Evolution
Authors: Wyckoff Gerald J , Malcom Christine M 
Published: October 2009

Abstract
Although they are highly dissimilar in sequence content in extant organisms, the mammalian sex chromosomes (i.e. the X and Y) evolved from a pair of autosomes. Differentiation of the sex chromosomes during evolution was initiated by the suppression of X–Y recombination. This was followed by the general degeneration of genes on the Y‐chromosome, with specific instances of gene specialization on the nonrecombining portion of the Y.
XandYChromosomes: Homologous Regions
Authors: El‐Mogharbel Nisrine , Graves Jennifer AM 
Published: October 2009

AbstractThe human X and Y chromosomes have quite different deoxyribonucleic acid (DNA) and gene contents, and appear completely cytologically nonhomologous. However, they share many homologous regions, the relics of a process of gradual evolution from a homologous autosomal pair into the differentiated sex chromosome pair they are today.
X‐chromosome Inactivation
Authors: Hore Timothy A , Wakefield Matthew J , Graves Jennifer AM 
Published: October 2009

AbstractX‐chromosome inactivation is an epigenetic process that silences the majority of genes on one of the two X‐chromosomes in female mammals. This silencing effectively equalizes dosage of X‐linked genes in females with that of males, who only possess one X‐chromosome and a sex‐determining Y‐chromosome.
Chromosome Rearrangement Patterns in Mammalian Evolution
Authors: Wienberg Johannes , Müller Stefan 
Published: October 2009

Abstract

Closely related species often have the same or similar karyotypes. This has been demonstrated in classical genetics with salivary gland chromosomes of different

Drosophila

species, in which the sequence of rearrangements that occurred during evolution can often be traced. Recently, molecular cytogenetics has proved that this is also true for mammalian chromosomes. The inspection of chromosomal changes with molecular defined probes by fluorescence

in situ

hybridization (FISH) allows the interpretation of the single or multiple steps that changed genomes during evolution. Comparative chromosome painting or ‘Zoo‐FISH’ and related techniques are now considered as one of the most powerful approaches in comparative genome studies for the understanding of the mode and tempo of gross genomic changes in primates and other mammals. For many nodes in mammalian phylogeny landmark chromosome rearrangements have now been identified that would discriminate ancestral versus derived chromosome changes and help to elucidate species phylogenies.
Comparative Cytogenetics
Authors: Breen Matthew , Langford Cordelia 
Published: October 2009

Abstract

In the pre‐genomics era, the field of comparative cytogenetics was restricted to the comparison of banded chromosome preparations of the species being studied. The development of molecular biology and subsequent convergence of this field with conventional cytogenetics led to the development of molecular cytogenetics. The application of molecular cytogenetics, in particular multicolour fluorescence
in situ
hybridization (MFISH), has revolutionized our ability to compare genomes at the chromosomal, subchromosomal and molecular levels, leading to much more defined knowledge about the processes of chromosomal rearrangement that have occurred during evolution. In this article we review very briefly some of the work that has led to a greater understanding of the comparative cytogenetics of mammals, in the context of their relationship to the human karyotype.
Chromosomal Rearrangements in Primates
Authors: Stanyon Roscoe , Bigoni Francesca 
Published: October 2009

Abstract

Comparative molecular cytogenetics techniques allow us to trace the chromosome rearrangements which have occurred during primate and human evolution. Technique such as fluorescence

in situ

hybridization (FISH) of whole chromosome paints (WCP) allows us to track interchromosomal rearrangements (translocations). FISH with smaller probes such as bacterial artificial chromosomes (BAC) allows us to study intrachromosomal rearrangements such as inversions. These data show that human chromosomes are amazingly similar to those of great apes and most Old World monkeys. Human chromosomes can be derived from the ancestral primate karyotype by a limited number of rearrangements.
Primate Phylogenetics
Authors: Disotell Todd R 
Published: October 2009

Abstract
Hypotheses of primate phylogenetic relationships have been greatly influenced by molecular systematic approaches. Improved methods of obtaining and amplifying deoxyribonucleic acid (DNA) from a greater number of sources from more species and subspecies, high‐throughput sequencing techniques, the characterization of genomic events such as the insertion of retrotransposons, along with new analytical techniques have allowed inferences to be drawn for most genus‐level branches of the primate phylogenetic tree.
Clustering of Highly Expressed Genes in the Human Genome
Authors: Gierman Hinco J , Versteeg Rogier 
Published: October 2009

Abstract
A dual mechanism of gene regulation exists in the human genome: Transcription factors determine whether a gene will be expressed and establish a basic level of transcription. In addition, the chromosomal domain in which a gene is positioned exerts a substantial effect and potentiates the ultimate expression level.
Surnames and Genetics
Authors: Jobling Mark A 
Published: October 2009

Abstract
Heritable surnames contain information about the relatedness of individuals within and between populations, and thus can be used to estimate human inbreeding and population structure. These estimates are affected adversely by the failure of underlying assumptions: many surnames have several founders, and the link between surname and inheritance can be broken by nonpaternity and other factors. Associations between patrilinearly inherited surnames and paternally inherited Y‐chromosome haplotypes are now allowing the histories of names to be investigated using molecular genetic methods.
Systemic Lupus Erythematosus: Genetic and Epigenetic View
Authors: Nath Swapan K , Sawalha Amr H 
Published: October 2009

AbstractSystemic lupus erythematosus (SLE) is a common systemic autoimmune disease with complex aetiology, in which susceptibility is determined by the combination of genetic, environmental, epigenetic and stochastic factors. SLE is very heterogeneous in its clinical manifestations and the presence of different autoantibodies may predict different set of clinical outcome. However, despite considerable accumulated knowledge, the detailed pathogenesis of SLE still remains unknown. Several studies have indicated the importance ofdeoxyribonucleic acid(DNA) hypomethylation in the aetiology of SLE. Recent advances in high‐throughput genotyping technologies and high‐density genetic association studies have identified and replicated many SLE susceptibility genes in different populations. In this article, we outline our current understanding of some genetic and epigenetic aspects of SLE.
Genetic Redundancy
Authors: Krakauer David C 
Published: October 2009

AbstractGenetic redundancy typically relates to the duplication of an open reading frame within a genome. Genetic redundancy is often inferred when the modification or deletion of a portion of genetic material in a duplicated genome results in minimal changes in trait or organismal phenotype in reference to the nonduplicated wildtype. This invariance has been attributed to buffering mechanisms promoted by duplicates and to a number of compensatory pathways independent of the duplicate. Most duplicates are rapidly lost from genomes by mutation and drift.
Somatic Hypermutation of Antigen Receptor Genes: Evolution
Authors: Diaz Marilyn , Verkoczy Laurent K 
Published: October 2009

Abstract
Analysis of the pattern of immunoglobulin mutation across species has helped to reveal some of the molecular properties of this process. Strong evidence for the involvement of a cytosine deaminase and error‐prone deoxyribonucleic acid (DNA) polymerases on the DNA encoding the immunoglobulin variable regions confirms earlier predictions made from phylogenetic studies.
Dosage Compensation Mechanisms: Evolution
Authors: Marín Ignacio 
Published: October 2009

Abstract

Degeneration of sex‐limited chromosomes favours the emergence of dosage compensation mechanisms able to equalize in both sexes the amount of products derived from sex‐linked genes. These mechanisms are understood in detail in the fly

Drosophila melanogaster

, the nematode

Caenorhabditis elegans

and in eutherian mammals. The three systems, biochemically and evolutionarily unrelated, share a common logic.
Major Histocompatibility Complex (MHC) Genes: Polymorphism
Authors: Meyer Diogo , Mack Steven J 
Published: October 2009

AbstractThe major histocompatibility complex (MHC) contains genes that code for glycoproteins that play key roles in the immune response. Several features of MHC gene polymorphism indicate that diversifying natural selection has acted upon these genes. Different models of diversifying selection may explain the observed variation.
Low‐density Lipoprotein Receptor (
LDLR
) Family: Genetics and Evolution
Authors: Schneider Wolfgang Johann 
Published: October 2009

Abstract
The low‐density lipoprotein receptor family comprises a large and growing number of genes, whose products contain a characteristic set of structural domains. Attempts to delineate the evolutionary history of this gene family must take into consideration newly discovered functions, ranging from ligand binding by the extracellular domains to signal transduction through the cytoplasmic regions of the receptors.