bluuebunny/crossref_metadata_2025_split huggingface dataset:
Streptomycetaceae: Life Style, Genome, Metabolism and Habitats
Authors: Schrempf Hildgund 
Published: October 2009

Abstract

A huge number of

Streptomyces

species belong to the family Streptomycetaceae. They are abundant soil bacteria with a highly complex life cycle. They have a large linear chromosomal
deoxyribonucleic acid
(DNA) which can be accompanied by circular and linear plasmids. They have an amazing capacity to contribute to the bioconversion of many different compounds including biopolymers, which are important for recycling processes in nature and have many biotechnological applications. They modify and synthesize thousands of chemically diverged secondary metabolites, many of which inhibit various cellular processes. Numerous of these are in use to cure diseases which are due to pathogenic microorganisms, parasites or the proliferation of tumour cells. Designed tailoring of genes encoding these metabolites has begun to complement traditional screening methods for new biologically active substances.
Reconstructing Ancient
DNA
Sequences
in Silico
Authors: Ma Jian 
Published: October 2009

Abstract
The increasing number of mammalian genome sequences becoming available provides scientists with dramatic opportunities to computationally reconstruct ancestral mammalian genomic sequences by comparing the genomes of living descendants. In this article, we review computational genome reconstruction methods in different scales, from base‐level reconstruction to chromosomal rearrangement reconstruction.
Evolution of the MammalianXChromosome
Authors: Waters Paul D , Robinson Terence J 
Published: October 2009

AbstractThe mammalian X chromosome has a fascinating evolutionary history which is intimately linked to that of the Y chromosome, since both evolved in concert from identical chromosomes. Teasing apart the events of this evolution (and their timing) has been helped greatly by identifying similarities and differences between the X and Y, and by comparing the sex chromosomes of different species.
Comparing the Human and Canine Genomes
Authors: Switonski Marek , Szczerbal Izabela 
Published: October 2009

Abstract
The dog is a unique species due to its phenotypic variability, exceptional among mammals. From the point of view of comparative biomedicine it needs to be emphasized that in numerous breeds specific hereditary diseases occur with high prevalence and many of them have molecular and clinical counterparts in humans. Thus, the dog is a very useful model to study human hereditary diseases and their therapy, including gene therapy. Knowledge on the human and dog genomes is very advanced. Both genomes were sequenced, their high‐density marker genome maps are available and evolutionary conserved segments (CSs) were identified by comparative chromosome painting, marker genome mapping and sequencing.
Comparing the Human and Chimpanzee Genomes
Authors: Uddin Monica , Wildman Derek E , Goodman Morris 
Published: October 2009

Abstract
The idea that chimpanzees share a close relationship with humans extends as far back as the early nineteenth century. However, only during the last 50 years has mounting genetic evidence demonstrated that chimpanzees are more closely related to humans than to gorillas or other apes. Whole‐genome sequences now available for both human and common chimpanzee confirm their close genetic relationship, whereas also identifying differences that may have contributed to the emergence of species‐specific phenotypes. To better understand the potential phenotypic significance of these differences, additional comparative genomic data from other primate, mammalian and vertebrate taxa are required.
The Sequencing of the Rhesus Macaque Genome and its Comparison with the Genome Sequences of Human and Chimpanzee
Authors: Gibbs Richard A , Worley Kim C , Kehrer‐Sawatzki Hildegard , Cooper David N 
Published: October 2009

Abstract

The rhesus macaque (

Macaca mulatta

) diverged from the ancestors of

Homo sapiens

about 25 million years ago. The macaque's genetic and physiological similarity to human is the basis for it becoming the most widely used nonhuman primate in basic and applied biomedical research. The genome sequence of a female rhesus macaque of Indian origin has been determined and compared with the genome sequences of chimpanzee and human. Those studies have revealed the likely structure of ancestral primate genomes and provided evidence both for positive selection and for the lineage‐specific expansion and contraction of gene families during primate evolution. The complete description of the macaque genome has greatly increased the utility of this animal model for biomedical research at the same time as improving our understanding of the basic biology of this highly successful species of Old World monkey.
Comparing the Human and Sea Urchin Genomes
Authors: Cameron R Andrew 
Published: October 2009

Abstract
Sea urchins belong to a group of animals that diverged from the lineage leading to humans very early. In that capacity their genomes reflect basic qualities of this lineage and inform to a deep reach of time the evolutionary changes leading to in the human genome. Surprisingly, the invention of new genes in this evolutionary path is subordinate to the diverse changes in the abundance of genes in existing families.
Evolution of Common Fragile Sites
Authors: Helmrich Anne 
Published: October 2009

Abstract

Common fragile sites are specific
deoxyribonucleic acid
(DNA) breakage‐prone genomic regions in all healthy humans. Their instability is provoked by replication stress combined with an escape of cell cycle checkpoints. Common fragile sites are favoured regions of chromosomal aberration formation in the neoplastic process. They are inherent parts of the genomes of all so far analysed mammalian species, and recent data support their existence also in yeast. The common fragile site locations are highly conserved between human and other primates as well as between human and mouse. There is no evidence of an involvement of common fragile sites as ‘hotspots’ in chromosome evolution.
Nucleotide Sequence Divergence between Humans and Chimpanzees
Authors: Chen Feng‐Chi , Chuang Trees‐Juen 
Published: October 2009

Abstract
Chimpanzee, as the closest relative of human, has long been a focus of molecular evolution. In this article, we review recent findings of five major categories of human–chimpanzee genomic divergence, namely nucleotide substitution, insertion/deletion, duplication, pseudogenization and rearrangement. It is demonstrated that nonsubstitution variations greatly increase the complexity and play a critical role in human–chimpanzee genome evolution. These genetic changes may provide some clues to the evolutionary origins of human‐specific traits.
The Rat Genome as a Rodent Model in Evolutionary Studies
Authors: Fechtel Kim 
Published: October 2009

Abstract

The genome sequence of the Brown Norway rat,

Rattus norvegicus

, revealed the precision with which genome analysis could trace the imprint of nucleotide changes associated with the radiation of mammalian species. Analysis of the protein‐coding repertoire and noncoding conserved elements (NCEs) including viable and decayed transposable elements, viruses and simple repeats provide landmarks for reconstructing past evolutionary events. From this analysis, it was possible to posit the configuration of genomes of long‐extinct mammalian ancestors. Application of evolutionary methods to subsets of the rat genome, the orthologues of human disease genes, permits the further validation of the laboratory rat as a model for studies of human pathogenesis.
Transposable Element‐driven Duplications during Hominoid Genome Evolution
Authors: Mishra Bud 
Published: October 2009

AbstractHominoid genomes exhibit a significant number of large segmental duplications; these and other similar duplications in mammalian genomes are hypothesized to be mediated by transposable elements such as Alus or L1s in hominoids and rodents, respectively. The true evolutionary mechanisms that sculpted these duplications are emerging to be much more subtle and complex.
Balancing Selection in Human Evolution
Authors: Vallender Eric J , Johnson Welkin E 
Published: October 2009

Abstract
Selection can act to maintain alleles within a population through many mechanisms that, taken together, constitute balancing selection. Over the course of primate and human evolution, balancing selection has repeatedly acted upon the species. Though ancient causes and effects may never be fully known or appreciated, current, ongoing, balancing selection can be observed in the human genome today. This is particularly true in genes related to immune response and pathogen defence, reproductive fitness and environmental stressors. In understanding balancing selection, it is possible to see the history of humanity's natural challenges as well as evolution's response.
Single Nucleotide Polymorphisms in Human Disease and Evolution: Phylogenies and Genealogies
Authors: Thomas Paul D 
Published: October 2009

Abstract

Single nucleotide polymorphisms (SNPs) are common genetic variants within a population. Several SNPs have been implicated directly in human diseases, but their biggest promise lies in their potential as genetic markers for discovering genetic factors in a wide variety of human diseases and other traits. There are two methods for modeling the processes by which population genetic variation has evolved: genealogy, the actual family tree in which genetic variants arose and were inherited from parents to children and phylogeny, a compressed history of how these genetic variants accumulated in lineages of successive copies of
deoxyribonucleic acid
(DNA) sequences. Genealogies and phylogenies are two ways to view the same evolutionary process, and each has specific applications to the discovery of genetic factors in human disease, especially relevant in the genomic era.
Alternative Polyadenylation in the Human Genome: Evolution
Authors: Tian Bin 
Published: October 2009

Abstract

Messenger
ribonucleic acid
(mRNA) polyadenylation is an essential step for the maturation of most eukaryotic mRNAs, and is tightly coupled with termination of transcription. Over half of all human genes have alternative polyadenylation sites, resulting in transcript variants with different 3′ UTR (untranslated region) sequences and, in some cases, protein‐coding regions. Comparative genomic studies are beginning to elucidate the phylogenetics of
cis
‐elements and protein factors involved in the regulation of mRNA polyadenylation, and shed light on the evolution of alternative polyadenylation.
MicroRNAEvolution in the Human Genome
Authors: Su Bing , Zhang Rui 
Published: October 2009

AbstractMicroribonucleic acids(miRNAs) are a growing class of small RNA [∼22 nucleotide (nt)] that function as negative regulators in the genome by targeting messenger RNA (mRNA) for translational repression, cleavage and destabilization. Hundreds of miRNAs have been identified in the human genome. miRNAs can be conserved or nonconserved according to their cross‐species sequence conservation, and these two classes of miRNAs in the human genome are subject to distinct evolutionary patterns.
Positive Selection and the Evolution of Prodynorphin
Authors: Rockman Matthew V 
Published: October 2009

AbstractPositive natural selection has shaped thecis‐regulation of humanprodynorphin, the precursor molecule for a suite of opioid neuropeptides with roles in perception. Population genetic data suggest that after the split between the human and chimpanzee lineages, selection drove multiple substitutions in a regulatory element upstream ofprodynorphin. The substitutions fall within acis‐regulatory tandem repeat polymorphism segregating in contemporary populations. The repeat polymorphism is also seen by selection, and differing repeat allele frequencies in different parts of the globe reflect the varying pattern of positive selection.
Selection Operating on Protein‐coding Genes in the Human Genome
Authors: Meyer Diogo , Harris Eugene E 
Published: October 2009

Abstract
The dominant selective force acting on protein‐coding regions throughout the human genome is purifying selection, which removes deleterious mutations. The fraction of substitutions that were positively selected, and can therefore be considered to be adaptive, can be estimated using methods based on comparisons of the relative amounts of change at two classes of sites – sites which if changed produce amino acid changes and sites which if changed do not lead to amino acid changes. Current estimates find very low estimates of adaptive evolution in protein‐coding regions during human evolution.
The Contribution of Transposable Elements to Human Proteins
Authors: Volff Jean‐Nicolas 
Published: October 2009

Abstract
The human genome contains hundreds of genes with protein‐coding exons and even complete open reading frames derived from transposable elements. These genes are involved in major biological processes such as immunity, replication, reproduction, cell proliferation and apoptosis. This demonstrates the importance of transposable elements as a genomic pool of coding sequences for the creation and evolution of gene functions.
Are Humans Still Evolving?
Authors: Reed Floyd A 
Published: October 2009

Abstract
The question of whether or not humans are still evolving often captures the popular imagination and regularly leads to conflicting claims. Here, some of the evolutionary forces predicted to act upon current and future human populations are reviewed. It is postulated that the increasing movement and panmixia of humans, coupled with an unprecedented increase in the global size of the human population, are predictive of an unparalleled intensification of natural selection in the near future. However, regardless of which forces eventually prevail in the coming millennia, the idea that human evolution will somehow cease is one that is increasingly difficult to sustain.
Genetic Disease in the Ashkenazim: Role of a Founder Effect
Authors: Kedar‐Barnes Inbal , Rozen Paul , Shohat Mordechai , Baris Hagit N 
Published: October 2009

Abstract
One in four Ashkenazi Jews is a carrier of a genetic disorder. More than 20 recessive genetic disorders are known to be prevalent in this population. Among these are four lysosomal storage diseases (LSD) and it has been suggested that carrier advantage is the driving force. For the most part the prevalence can be explained by genetic drift and consanguinity. Here we define the origin of the Ashkenazi Jews and the histories of some of the common genetic disorders. Nowadays, we will also outline the common practice for genetic screening in the Ashkenazi Jewish population in Israel nowadays.
Genetic Diversity in Africa
Authors: Sanchez‐Mazas Alicia , Poloni Estella S 
Published: October 2009

AbstractAfrica exhibits a high level of human genetic variation, the origin of which is still not fully understood. However, the results brought by the study of several independent genetic polymorphisms in relation to other disciplines indicate that this continent has undergone major population movements possibly linked to the diffusion of the main linguistic phyla.
Genetic Diversity in the German Population
Authors: Krawczak Michael , Lu Timothy T , Willuweit Sascha , Roewer Lutz 
Published: October 2009

AbstractThroughout most of recent human history, Germany has experienced major demographic transitions that are also reflected by its current population genetic structure. While the Y‐chromosomal gene pool appears to be considerably stratified and the mitochondrial genome is highly homogeneous, variation on autosomes and on the X‐chromosome both exhibit an intermediate level of heterogeneity between subpopulations.
Genetics and the Origins of the Finns
Authors: Norio Reijo 
Published: October 2009

Abstract
The population of Finland initiated from neighbouring south‐eastern areas 10 000 years ago when the glacial ice melted, and it developed further from several European sources, among them the Ukrainian and Iberian refuges.

According to nuclear gene studies, the Finns belong to the European family, with some eastern components. In mitochondrial
deoxyribonucleic acid
(mtDNA) studies, the Finns are indistinguishable from other Europeans. High values of Y‐chromosomal C>T transition point to male population movements on the east–west axis.

The Finnish Disease Heritage (FDH) means overrepresentation of approximately 40 rare recessive disorders. It is due to national isolation between Sweden and Russia and regional isolation from 500‐year‐old internal migrations. This rare disease flora enjoys favourable conditions for clinical and molecular genetic research.
Genetics and the Origins of the Polynesians
Authors: Chambers Geoffrey K 
Published: October 2009

AbstractThe origin of the Polynesian people who settled in Remote Oceania is a long‐standing mystery. Surveys of genetic variation in these populations have helped to distinguish between competing theories arising from anthropology and linguistics. The genetic data show how maternal and paternal lineages combined around 3000 ybp (years before present) giving rise to a new people who spoke Austronesian languages and developed a sophisticated technology for oceanic voyaging.
An Evolutionary Genetic Framework for Heritable Disorders
Authors: Keller Matthew C 
Published: October 2009

AbstractNatural selection is expected to drive the frequencies of heritable, fitness‐harming states to very low levels, yet many heritable disorders – and especially mental disorder – are common in the human population. These two statements are sometimes interpreted to imply that disorders have not been under natural selection, but this need not be the case. Evolutionary genetics provides three broad classes of models, none of them mutually exclusive, for understanding why disorder risk alleles have persisted in the human population despite natural selection.
Human Genetics and Languages
Authors: Comas David , Bosch Elena , Calafell Francesc 
Published: October 2009

Abstract
The similarities between the mode of inheritance and evolution of genes and languages have fostered interest in the joint analysis of both disciplines. The correlation between genes and languages was firstly demonstrated by Cavalli‐Sforza and collaborators comparing a tree build from ‘classical’ genetic markers to a linguistic tree of languages. Several criticisms to this correlation have been raised and a large number of exceptions have been described. It has been shown that the most plausible factor that influences in the correlation of genes and languages is geography. However, the information provided by genetics and linguistics, as well as the one provided by other disciplines, will allow us to reconstruct the history of humankind.
Molecular Clocks: Determining the Age of the Human–Chimpanzee Divergence
Authors: Jensen‐Seaman Michael I , Hooper‐Boyd Kathryn A 
Published: October 2009

Abstract
The approximate clocklike nature of the accumulation of nucleotide substitutions (the ‘molecular clock’) allows for the estimation of the time of divergence between modern species, dependent on calibrating the clock with known divergence dates from the fossil record. The molecular clock gives dates of approximately 6–8 million years ago for the human–chimpanzee divergence, in general agreement with the palaeontological evidence.
Origins of the Australian and New Guinean Aborigines
Authors: van Holst Pellekaan Sheila M 
Published: October 2009

Abstract

Mitochondrial
deoxyribonucleic acid
(mtDNA) and Y chromosome studies indicate deep ancestry for both Australia and New Guinea peoples, with evidence for limited, shared genetic connection as well as ancient maternal lineages specific to both places. Several entry points into Sahul might explain haplotype distribution. Migration by northern as well as by a southern coastal route remain possible scenarios, as no single regional source population is identifiable.
Origins of the Austro‐Asiatic Populations
Authors: Mohan Reddy B , Kumar Vikrant 
Published: October 2009

AbstractThe Austro‐Asiatic linguistic family, which is considered to be the oldest of all the families in South Asia, has substantial presence in Southeast Asia. The origin and expansion of the Austro‐Asiatic populations have been a contentious issue and so far there has been no formidable archaeological or linguistic evidence in favour of any of the hypotheses suggested. In recent years there has been a couple of genetic studies assessing the genetic unity, history and migration of Austro‐Asiatic groups. In this article we examine different hypotheses, based on both the genetic and nongenetic evidences. We infer a common paternal origin of Austro‐Asiatics and the migration of paternal ancestors of Austro‐Asiatic populations from East to South Asia, followed by the origin of Austro‐Asiatic languages which subsequently spread to Southeast Asia, with primarily male‐mediated migrations.
On Sequence Variants that Influence the Risk of Common Diseases
Authors: Stefánsson Kári , Gulcher Jeffrey R 
Published: October 2009

Abstract
Sequence variants impacting risk of common diseases have the following characteristics: Most of the risk of common diseases is conferred by common variants of modest effect although there are rare variants of large effect that account for a small minority of cases. The risk variants are rarely in coding sequences. They generally influence expression of genes and in that determine where on the spectrum of physiologic function an individual falls. The risk variants are common because they have been under selection and carried with them advantage at some point in time or other alleles at their loci have conferred disadvantage.
Gene Conversion during Primate Evolution
Authors: Satta Yoko 
Published: October 2009

Abstract

Gene conversion is a nonreciprocal recombination process. This originally represented a distortion of segregation of alleles in gametocytes. In evolutionary studies, however, this often means ‘the transfer of
deoxyribonucleic acid
(DNA) sequence information from one locus to another’. In evolutionary processes the gene conversion is frequently observed between tandemly duplicated sequences or between homologous sequences on a same chromosome. Significant roles of gene conversion between functional loci are generally in keeping their sequence and functional similarity in the ‘coevolution’ of interacting molecules. In addition, gene conversion often takes place between a functional gene and pseudogene. This mainly causes diseases, especially in humans.
Biased Gene Conversion and its Impact on Human Genome Evolution
Authors: Galtier Nicolas , Duret Laurent 
Published: October 2009

Abstract
Gene conversion between the maternal and paternal alleles occurs during meiosis as part of the complex molecular process of homologous recombination. Consequently, the transmission of alleles can be non‐Mendelian for loci located near recombination initiation sites. A large body of evidence suggests that such events of meiotic gene conversion are GC‐biased: AT/GC heterozygotes produce an elevated proportion of GC gametes, resulting in an evolutionary advantage for GC over AT alleles. This neutral biased gene conversion (BGC) process has surprisingly strong consequences on the evolution of genomic landscapes in human.
Pseudogene Evolution in the Human Genome
Authors: Zhang Zhaolei , Zheng Deyou 
Published: October 2009

Abstract
Pseudogenes are those regions in the genome that have sequence similarity to functional genes but have decayed and do not have obvious functions. It is estimated that the human genome contain more than 10 000 easily recognizable pseudogenes and many more fragmented sequences, mainly arose through one of the following three mechanisms: duplication, retrotranposition and spontaneous loss of function.