[Evolutionary-clinical analysis of blood circulation in the vertebrobasilar arterial system].
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Basilar Artery↗
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Results for “evolutionary analysis”
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[An evolutionary-dissolutive analysis of the wakefulness-sleep cycle in Tourette syndrome patients].
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Adolescent↗
[Evolutionary and conformational analysis of a family of globins. The evolutionary role of deletions and insertions].
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Amino Acid Sequence↗
Molecular evolution of the GATA family of transcription factors: conservation within the DNA-binding domain.
The GATA-binding transcription factors comprise a protein family whose members contain either one or two highly conserved zinc finger DNA-binding domains. Members of this group have been identified in organisms ranging from cellular slime mold to vertebrates, including plants, fungi, nematodes, insects, and echinoderms. While much work has been done describing the expression patterns, functional aspects, and target genes for many of these proteins, an evolutionary analysis of the entire family has been lacking. Herein we show that only the C-terminal zinc finger (Cf) and basic domain, which together constitute the GATA-binding domain, are conserved throughout this protein family. Phylogenetic analyses of amino acid sequences demonstrate distinct evolutionary pathways. Analysis of GATA factors isolated from vertebrates suggests that the six distinct vertebrate GATAs are descended from a common ancestral sequence, while those isolated from nonvertebrates (with the exception of the fungal AREA orthologues and Arabidopsis paralogues) appear to be related only within the DNA-binding domain and otherwise provide little insight into their evolutionary history. These results suggest multiple modes of evolution, including gene duplication and modular evolution of GATA factors based upon inclusion of a class IV zinc finger motif. As such, GATA transcription factors represent a group of proteins related solely by their homologous DNA-binding domains. Further analysis of this domain examines the degree of conservation at each amino acid site using the Boltzmann entropy measure, thereby identifying residues critical to preservation of structure and function. Finally, we construct a predictive motif that can accurately identify potential GATA proteins.
Amino Acid Motifs↗
Step-wise analysis of polymorphisms in the human dopamine D2 receptor gene.
Evolutionary analysis of neurotransmitter receptor systems has previously focused on interspecies differentiation. Recently, emphasis has shifted to intragenic evolution within a single species and the functional relevance associated with intraspecies variations. For example, multiple polymorphisms have been identified within the human dopamine D2 receptor (DRD2) gene, many of which have been used in clinical association studies. In an attempt to evaluate the intragenic evolution of the DRD2 gene, genotypes from 116 humans were determined using five biallelic markers which reside within a 30 kb span of the DRD2 gene, that are non-polymorphic in other higher order primates. Only seven different haplotypes, out of a theoretical maximum of 32, were present in the study group of 232 chromosomes. Moreover, five of the seven haplotypes accounted for 99% (n = 230/232) of the human haplotypes. A phylogenetic tree was generated from the haplotypic data using a maximum parsimony algorithm. The relationship of the haplotypes within the phylogenetic tree is consistent with a progressive step-wise nucleotide conversion within the human gene. These data indicate that specific haplotypic subtypes of the human DRD2 gene exist within the human population and allow for the possibility that functional differences may exist between the DRD2 subtypes. Therefore, future studies focused on a functional analysis of the entire human DRD2 haplotype, as opposed to individual polymorphisms, may provide important insights into the functional relevance of molecular variations within the human DRD2 gene.
Europe↗
Coracoacromial ligament function: a phylomorphic analysis.
Various morphologic parameters of the coracoacromial region were quantified for five hominoid genera to examine the evolutionary development of the coracoacromial ligament (CAL) and its significance and relationship to shoulder function. No evolutionary correlation within the family Hominoidea was found for several calculated parameters obtained from osseous dimensions and CAL length. However, from an evolutionary analysis of the order Anthropoidea, it appears that the CAL is not solely a vestigial structure in humans but rather represents a stage in the development of the hominoid shoulder with the function of providing increased mechanical stability to the superior bony vault.
Animals↗
Antigenicities of Group I and II hepatitis C virus polypeptides--molecular basis of diagnosis.
Comparative nucleotide sequence studies on the putative NS3 and NS4 regions of the genomes of hepatitis C viruses (HCV) have revealed that there are at least two groups of HCV, group I and group II. The cDNA clone E, corresponding to a boundary between the NS3 and NS4 (NS3-4) region of the group II HCV genome, encodes antigens that react to antibodies specific to group II HCV (Tsukiyama-Kohara et al. (1991) Virus Genes 5, 243-254). To understand the molecular basis of the group-specific antigenicity of HCV peptides, the predicted amino acid sequences around the NS3-4 region of our group II HCV cDNAs were compared with those of other HCV isolates. The analysis revealed the presence of group-specific amino acids in this peptide region. Evolutionary analysis of nucleotide sequences within this region of these HCV isolates also led to the same classification. A similar result was obtained by sequence analysis of cloned cDNAs corresponding to the core region. A cDNA of the group II HCV core region was prepared by polymerase chain reaction from the cDNA synthesized with group II-specific primer complementary to the NS3-4 region. The products directed by the cDNA of the core region did not have group-specific antigenicity. The NS3 peptide region also appeared not to carry group-specific antigens. Our results indicate that most HCV isolates can be classified into either group I or II, and that the existence of two groups of HCV does not disturb HCV diagnosis as long as core and/or NS3 peptides are used to detect HCV antibodies.
Amino Acid Sequence↗
Molecular evolution of serine protease and its inhibitor with special reference to domain evolution.
The evolution of serine protease and its inhibitor are discussed with special reference to domain evolution. It is now known that most proteins are composed of more than one functional domain. Because serine proteases such as urokinase and plasminogen are made of various functional domains, these proteins are typical examples of the so-called mosaic proteins. When Kringle domains in serine proteases and a Kunitz-type protease inhibitor domain in the amyloid beta precursor protein in Alzheimer's disease patients were examined by the molecular evolutionary analysis, the phylogenetic trees constructed showed that these functional domains had undergone dynamic changes in the evolutionary process. In particular, these domains are evolutionarily movable. Thus, it is concluded that various functional domains evolved independently of each other and that they have been shuffled to create the existent mosaic proteins. This conclusion leads us to the reasonable speculation that those functional domains must have been minigenes possibly at the time of primordial life or the origin of life. We call these minigenes 'ancestral minigenes'. Every effort should be made to answer the question about the minimum set of ancestral minigenes that must have existed and must have been needed for maintaining life forms. The DNA sequence database is useful for making attempts to answer such difficult but significant questions.
Alzheimer Disease↗
Natural variation in the cytokinin oxidase gene ZmCKX6 influences leaf morphology and yield-related traits in maize.
Leaf width (LW) is a critical determinant of maize architecture and yield. To uncover its genetic basis, we performed a genome-wide association study (GWAS) on 348 maize inbred lines and identified ZmCKX6, encoding cytokinin oxidase/dehydrogenase, as a key gene associated with LW. Natural variation in the ZmCKX6 promoter significantly influenced its expression levels, leading to differences in LW across various haplotypes. Functional validation using CRISPR/Cas9 revealed that ZmCKX6 knockout results in pleiotropic effects, including narrower leaves, reduced plant height, and decreased grain yield components. These phenotypes were accompanied by elevated levels of active cytokinins but reduced levels of auxin, gibberellins, and salicylic acid. Transcriptome analysis revealed a significant downregulation of photosynthesis-related genes, corresponding to reduced photosynthetic rates in knockout lines. Evolutionary analysis demonstrated that the allele associated with narrower leaves were preferentially selected during maize domestication and breeding. This study highlights the role of ZmCKX6 in modulating cytokinin homeostasis and its subsequent impact on multiple agronomic traits in maize, providing insights into the complex genetic control of plant architecture and yield. The identified natural variations could be valuable for marker-assisted selection aimed at optimizing plant architecture and improving yield.
Zea mays↗
Evolution and sequence analysis of a human Y-chromosomal DNA fragment.
A Y-chromosomal DNA fragment has been isolated from a human Y-Charon 21A recombinant library. Evolutionary analysis of 1F5 indicates that the size and sequence of this fragment have been conserved in higher primates. Deletion mapping and in situ hybridization analysis have localized 1F5 to the middle euchromatic portion of the long arm of the human Y chromosome at Yq11.2. Sequence analysis revealed the presence of an atypical Alu element and two regions rich in polypyrimidine-polypurine residues.
Base Sequence↗
The homoerotic behavior that never evolved.
The emerging field of evolutionary psychology provides fascinating new insights into many salient human behaviors, but homosexual behavior is not among these. The new field perpetuates old stereotypes, and useful evolutionary analysis of homosexual behavior is largely nonexistent. In this article, the treatment of homosexual behavior in the field of evolutionary psychology is reviewed, and the factors contributing to this treatment are identified. Recommendations are made to help foster the development of alternative evolutionary models of homosexual behavior.
Biological Evolution↗
A high-quality draft genome assembly of Johnsongrass illuminates relationships between polyploidization, crop-wild hybridization, and reproductive biology.
Johnsongrass [Sorghum halepense (L.) Pers.] is an allopolyploid, rhizomatous, perennial grass species and one of the most troublesome weeds in global agriculture. We assembled the first Johnsongrass genome to clarify poorly understood genetic factors influencing variable rates of crop-wild hybridization with cultivated sorghum [S. bicolor (L.) Moench]. The draft genome assembly has a total size of 3.26 Gb and BUSCO completeness of 95.3%. We also report the first evolutionary analysis of INHIBITION OF ALIEN POLLEN (IAP), the only known cross-(in)compatibility locus in the genus. Our results reveal an evolutionary history of genome instability, including the loss of distinct parental subgenomes, and suggest that Nebraska accession 'J-37,' the genome donor, is a segmental allotetraploid that may function as a diploid or aneuploid during meiosis. Genome instability could explain observations of variable ploidies in Johnsongrass and facilitate ongoing hybridization with sorghum where gamete ploidies and IAP alleles match. Given this information, we provide a suggested research framework for studying evolution and gene expression in the Sorghum genus where crop-wild hybridization occurs and for predicting the potential for hybridization between specific crossing partners. Collectively, this work will bolster efforts to study and manage reproductive biology in other crop-wild polyploid complexes.
Sorghum↗
Expanding the human proteome with microproteins and peptideins.
A major scientific drive is to characterize the protein-coding genome, which is a primary basis for studying human health. But the fundamental question remains of what has been missed in previous analyses. Over the past decade, the translation of non-canonical open reading frames (ncORFs) has been observed across human cell types and disease states1-3, with major implications for biomedical science. However, a key gap in knowledge has been which ncORFs produce small microproteins or alternative protein molecules that contribute to the human proteome. Here we report the collaborative efforts of the TransCODE Consortium4 to produce a consensus landscape of protein-level evidence for ncORFs. We show that about 25% of a set of 7,264 ncORFs gives rise to detectable peptides in a large-scale analysis of 95,520 proteomics experiments. We develop an annotation framework for ncORF-encoded microproteins as human proteins and codify the new conceptual model of 'peptideins' as microproteins that have indeterminate potential as functional proteins. To probe the biological implications of peptideins, we create an evolutionary analysis approach, termed ORF relative branch length (ORBL), and determine that evolutionary constraint is common and associates with observation of ncORF-derived peptides. We then characterize a pan-essential cellular phenotype for one peptidein from the OLMALINC long non-coding RNA. Overall, we generate public research tools supported by GENCODE and PeptideAtlas and advance biomedical discovery for understudied components of the human proteome.
Humans↗
The genes of Na,K-ATPase, a selfreview.
The review is devoted to analysis of research carried out in the author's laboratory on structure-function relationships in genes coding for Na,K-ATPases. Also considered are problems related to molecular evolution of ion-transporting ATPases. This brief review is devoted to a fragment of research carried out in my laboratory, the Laboratory of Human Genes Structure and Function at the Shemyakin Institute of Bioorganic Chemistry, USSR Academy of Sciences. The area of the review may be named as structural-evolutionary analysis of functional anatomies of genes. The approach is fairly standard and its essence was formulated long ago: evolution decides 'to be or not to be' based on usefulness or lack of it. The elements of genes that are important for the gene function are retained in the course of evolution, and a comparison of genes having similar functions in different species should, hopefully, reveal different behavior of gene blocks, conservation of functionally significant blocks and variability of less significant or insignificant ones. An approach like this has been widely used in comparing proteins. However, a study of genes gives the investigator yet another tool of structural and evolutionary import: the exon structure may be relevant to the gene's evolutionary history, with exons corresponding to the functional domains (arguments for and against this fascinating hypothesis have been reviewed by Blake (Blake, 1985). However, even if the exon-domain correlation does not hold in the general case, a similarity in the exon-intron pattern of genes from different species is indicative of their common evolutionary origin and is enforcing the logic of variability analysis, provided, of course, that the compared genes have a common predecessor. A few years ago we employed this approach to analyze the functional structure of genes coding for subunits of bacterial DNA-dependent RNA polymerases and constructed functional maps of the enzyme. After that, a similar study of Na,K-ATPase genes to be reviewed here was started. The entire project became possible through collaboration with the lab of Dr. N. N. Modyanov, an eminent specialist in protein chemistry who had already accumulated considerable information on Na,K-ATPase from pig kidneys by that time. I would also like to stress that the work has been started on the initiative of the deceased Director of the Institute, Yu. A. Ovchinnikov. Since this is a self-review, I am asking my colleagues whose work will not be cited here to excuse me.(ABSTRACT TRUNCATED AT 400 WORDS)
Animals↗
Evolution of genes and taxa: a primer.
The rapidly growing fields of molecular evolution and systematics have much to offer to molecular biology, but like any field have their own repertoire of terms and concepts. Homology, for example, is a central theme in evolutionary biology whose definition is complex and often controversial. Homology extends to multigene families, where the distinction between orthology and paralogy is key. Nucleotide sequence alignment is also a homology issue, and is a key stage in any evolutionary analysis of sequence data. Models based on our understanding of the processes of nucleotide substitution are used both in the estimation of the number of evolutionary changes between aligned sequences and in phylogeny reconstruction from sequence data. The three common methods of phylogeny reconstruction--parsimony, distance and maximum likelihood--differ in their use of these models. All three face similar problems in finding optimal--and reliable--solutions among the vast number of possible trees. Moreover, even optimal trees for a given gene may not reflect the relationships of the organisms from which the gene was sampled. Knowledge of how genes evolve and at what rate is critical for understanding gene function across species or within gene families. The Neutral Theory of Molecular Evolution serves as the null model of molecular evolution and plays a central role in data analysis. Three areas in which the Neutral Theory plays a vital role are: interpreting ratios of nonsynonymous to synonymous nucleotide substitutions, assessing the reliability of molecular clocks, and providing a foundation for molecular population genetics.
Base Sequence↗
Molecular classification of living organisms.
Recent studies in molecular evolution have generated strong conflicts in opinion as to how world living organisms should be classified. The traditional classification of life into five kingdom has been challenged by the molecular analysis carried out mostly on rRNA sequences, which supported the division of the extant living organisms into three major groups: Archaebacteria, Eubacteria, and Eukaryota. As to the problem of placing the root of the tree of life, the analysis carried out on a few genes has provided discrepant results. In order to measure the genetic distances between species, we have carried out an evolutionary analysis of the glutamine synthetase genes, which previously have been revealed to be good molecular clocks, and of the small and large rRNA genes. All data demonstrate that archaebacteria are more closely related to eubacteria than to eukaryota, thus supporting the classical division of living organisms into two main superkingdoms, Prokaryota and Eukaryota.
Archaea↗
Polymorphic DNA haplotypes at the LDL receptor locus.
Mutations in the low-density lipoprotein (LDL) receptor gene result in the autosomal dominant disorder familial hypercholesterolemia (FH). Many different LDL receptor mutations have been identified and characterized, demonstrating a high degree of allelic heterogeneity at this locus. The ability to identify mutant LDL receptor genes for prenatal diagnosis of homozygous FH or to study the role of the LDL receptor gene in polygenic hypercholesterolemia requires the use of closely linked RFLPs. In the present study we used 10 different RFLPs, including three newly described polymorphisms, to construct 123 independent haplotypes from 20 Caucasian American pedigrees. Our sample contained 31 different haplotypes varying in frequency from 0.8% to 29.3%; the five most common haplotypes account for 67.5% of the sample. The heterozygosity and PIC of each site were determined, and these values disclosed that eight of the RFLPs were substantially polymorphic. Linkage-disequilibrium analysis of the haplotype data revealed strong nonrandom associations among all 10 RFLPs, especially among those sites clustered in the 3' region of the gene. Evolutionary analysis suggests the occurrence of both mutational and recombinational events in the generation of the observed haplotypes. A strategy for haplotype analysis of the LDL receptor gene in individuals of Caucasian American descent is presented.
Computer Simulation↗
An analysis of retroposition in plants based on a family of SINEs from Brassica napus.
The identification of a family of SINE retroposons dispersed in the genome of oilseed rape Brassica napus has provided the basis for an evolutionary analysis of retroposition in plants. The repetitive elements (called S1Bn) are 170 bp long and occupy roughly 500 loci by haploid genome. They present characteristic features of SINE retroposons such as a 3' terminal A-rich region, two conserved polymerase III motifs (box A and B), flanking direct repeats of variable sizes, and a primary and secondary sequence homology to several tRNA species. A consensus sequence was made from the alignment of 34 members of the family. The retroposon population was divided into five subfamilies based on several correlated sets of mutations from the consensus. These precise separations in subfamilies based on "diagnostic" mutations and the random distribution of mutations observed inside each subfamily are consistent with the master sequence model proposed for the dispersion of mammalian retroposons. An independent analysis of each subfamily provides strong evidence for the coexpression of at least three subfamily master sequences (SMS). In contrast to mammalian retroposition, diagnostic positions are not shared between SMS. We therefore propose that SMS were all derived from a general master sequence (GMS) and independently activated for retroposition after a variable period of random drift. Possible models for plant retroposition are discussed.
Base Sequence↗