Haematopoietic chimerism expressivity in bovine heterosexual twins

The aim of the experiment was to study the haematopoietic chimerism in bovine heterosexual twins conceived through artificial insemination and post-embryo transfer. Both animal groups were revealed to have a wide individual range of variability for the expressivity of chimerism that varied from 0 to 96% of cells with the chromosomes of an opposite sex. The study also revealed the tendency towards increased frequency of cytogenetic anomalies in immigrant cells

Detection of Biochemical Pathways by Probabilistic Matching of Phyletic Vectors

A phyletic vector, also known as a phyletic (or phylogenetic) pattern, is a binary representation of the presences and absences of orthologous genes in different genomes. Joint occurrence of two or more genes in many genomes results in closely similar binary vectors representing these genes, and this similarity between gene vectors may be used as a measure of functional association between genes. Better understanding of quantitative properties of gene co-occurrences is needed for systematic studies of gene function and evolution. We used the probabilistic iterative algorithm Psi-square to find groups of similar phyletic vectors. An extended Psi-square algorithm, in which pseudocounts are implemented, shows better sensitivity in identifying proteins with known functional links than our earlier hierarchical clustering approach. At the same time, the specificity of inferring functional associations between genes in prokaryotic genomes is strongly dependent on the pathway: phyletic vectors of the genes involved in energy metabolism and in de novo biosynthesis of the essential precursors tend to be lumped together, whereas cellular modules involved in secretion, motility, assembly of cell surfaces, biosynthesis of some coenzymes, and utilization of secondary carbon sources tend to be identified with much greater specificity. It appears that the network of gene coinheritance in prokaryotes contains a giant connected component that encompasses most biosynthetic subsystems, along with a series of more independent modules involved in cell interaction with the environment

Extensive Gains and Losses of Olfactory Receptor Genes in Mammalian Evolution

Odor perception in mammals is mediated by a large multigene family of olfactory receptor (OR) genes. The number of OR genes varies extensively among different species of mammals, and most species have a substantial number of pseudogenes. To gain some insight into the evolutionary dynamics of mammalian OR genes, we identified the entire set of OR genes in platypuses, opossums, cows, dogs, rats, and macaques and studied the evolutionary change of the genes together with those of humans and mice. We found that platypuses and primates have <400 functional OR genes while the other species have 800–1,200 functional OR genes. We then estimated the numbers of gains and losses of OR genes for each branch of the phylogenetic tree of mammals. This analysis showed that (i) gene expansion occurred in the placental lineage each time after it diverged from monotremes and from marsupials and (ii) hundreds of gains and losses of OR genes have occurred in an order-specific manner, making the gene repertoires highly variable among different orders. It appears that the number of OR genes is determined primarily by the functional requirement for each species, but once the number reaches the required level, it fluctuates by random duplication and deletion of genes. This fluctuation seems to have been aided by the stochastic nature of OR gene expression

A Dual Origin of the Xist Gene from a Protein-Coding Gene and a Set of Transposable Elements

X-chromosome inactivation, which occurs in female eutherian mammals is controlled by a complex X-linked locus termed the X-inactivation center (XIC). Previously it was proposed that genes of the XIC evolved, at least in part, as a result of pseudogenization of protein-coding genes. In this study we show that the key XIC gene Xist, which displays fragmentary homology to a protein-coding gene Lnx3, emerged de novo in early eutherians by integration of mobile elements which gave rise to simple tandem repeats. The Xist gene promoter region and four out of ten exons found in eutherians retain homology to exons of the Lnx3 gene. The remaining six Xist exons including those with simple tandem repeats detectable in their structure have similarity to different transposable elements. Integration of mobile elements into Xist accompanies the overall evolution of the gene and presumably continues in contemporary eutherian species. Additionally we showed that the combination of remnants of protein-coding sequences and mobile elements is not unique to the Xist gene and is found in other XIC genes producing non-coding nuclear RNA

Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals

A common assumption in comparative genomics is that orthologous genes share greater functional similarity than do paralogous genes (the “ortholog conjecture”). Many methods used to computationally predict protein function are based on this assumption, even though it is largely untested. Here we present the first large-scale test of the ortholog conjecture using comparative functional genomic data from human and mouse. We use the experimentally derived functions of more than 8,900 genes, as well as an independent microarray dataset, to directly assess our ability to predict function using both orthologs and paralogs. Both datasets show that paralogs are often a much better predictor of function than are orthologs, even at lower sequence identities. Among paralogs, those found within the same species are consistently more functionally similar than those found in a different species. We also find that paralogous pairs residing on the same chromosome are more functionally similar than those on different chromosomes, perhaps due to higher levels of interlocus gene conversion between these pairs. In addition to offering implications for the computational prediction of protein function, our results shed light on the relationship between sequence divergence and functional divergence. We conclude that the most important factor in the evolution of function is not amino acid sequence, but rather the cellular context in which proteins act

МОЛЕКУЛЯРНАЯ ИДЕНТИФИКАЦИЯ ИЗОЛЯТОВ Anaplasmamarginale, ОБНАРУЖЕННЫХ В КРОВИ КРУПНОГО РОГАТОГО СКОТА НА ТЕРРИТОРИИ МОСКОВСКОЙ ОБЛАСТИ

Objective of research: To detect and identify by molecular and genetic methods isolates Anaplasma marginale circulating on the territory of Moscow region. Materials and methods: Blood samples were taken from cattle on the territory of Moscow region in 2015. DNA was isolated from whole blood by the kit «Sorb-M». Identification of animals infected with A. marginale and estimation of the parasitemia level were carried out by real-time PCR methods. Typing of A. marginale strains was performed by modifying the primer structure. The received gene fragments were cloned in Escherichia сoli cells. Targeted selection of recombinant clones of E. coli was conducted by PCR methods using standard primers M13 with the following analysis of reaction products by 1,5% agarose gel electrophoresis. Results and discussion: It was shown that seven of thirty animals were carriers of A. marginale strains; levels of parasitemia range from 3,6 × 103 to 5,4 × 105 per 1 ml blood. The analysis of msp4 gene sequence of A. marginale isolates shows their belonging to two already known genotypes. The results obtained can be used for epidemiological monitoring of anaplasmosis on the territory of Moscow region as well as taken into account for development of vaccines.Цель исследования - выявить и идентифицировать с помощью молекулярно-генетических методов изоляты Anaplasma marginale, циркулирующие на территории Московской области. Материалы и методы. Образцы крови крупного рогатого скота были отобраны в 2015 г. на территории Московской области. ДНК выделяли из цельной крови с помощью набора Sorb-M. Выявление животных, инфицированных A. marginale , и оценку уровня паразитемии проводили методом ПЦР в реальном времени, разработанным нами ранее. Типирование штаммов A. marginale осуществляли на основе метода с модификацией в части структуры праймеров. Полученные фрагменты гена были клонированы в клетках Escherichia сoli . Поиск целевых рекомбинантных клонов E. coli проводили методом ПЦР с использованием стандартных праймеров M13 с последующим анализом продуктов реакции электрофорезом в 1,5%-ном агарозном геле. Результаты и обсуждение. Показано, что семь из тридцати исследованных животных являлись носителями A. marginale с уровнем паразитемии в пределах 3,6 × 103-5,4 × 105 на 1мл крови. Типирование обнаруженных изолятов на основе нуклеотидных последовательностей гена msp4 выявило их принадлежность к двум уже известным генотипам. Полученные результаты могут быть использованы при проведении эпидемиологического мониторинга анаплазмоза на территории Московской области, а также учитываться при разработке вакцин

Chemical characterization of oligosaccharides in the milk of six species of New and Old world monkeys

Human and great ape milks contain a diverse array of milk oligosaccharides, but little is known about the milk oligosaccharides of other primates, and how they differ among taxa. Neutral and acidic oligosaccharides were isolated from the milk of three species of Old World or catarrhine monkeys (Cercopithecidae: rhesus macaque (Macaca mulatta), toque macaque (Macaca sinica) and Hamadryas baboon (Papio hamadryas)) and three of New World or platyrrhine monkeys (Cebidae: tufted capuchin (Cebus apella) and Bolivian squirrel monkey (Saimiri boliviensis); Atelidae: mantled howler (Alouatta palliata)). The milks of these species contained 6–8% total sugar, most of which was lactose: the estimated ratio of oligosaccharides to lactose in Old World monkeys (1:4 to 1:6) was greater than in New World monkeys (1:12 to 1:23). The chemical structures of the oligosaccharides were determined mainly by 1H-NMR spectroscopy. Oligosaccharides containing the type II unit (Gal(β1-4)GlcNAc) were found in the milk of the rhesus macaque, toque macaque, Hamadryas baboon and tufted capuchin, but oligosaccharides containing the type I unit (Gal(β1-3)GlcNAc), which have been found in human and many great ape milks, were absent from the milk of all species studied. Oligosaccharides containing Lewis x (Gal(β1-4)[Fuc(α1-3)]GlcNAc) and 3-fucosyl lactose (3-FL, Gal(β1-4)[Fuc(α1-3)]Glc) were found in the milk of the three cercopithecid monkey species, while 2-fucosyl lactose (5'-FL, Fuc(α1-2)Gal(β1-4)Glc) was absent from all species studied. All of these milks contained acidic oligosaccharides that had N-acetylneuraminic acid as part of their structures, but did not contain oligosaccharides that had N-glycolylneuraminic acid, in contrast to the milk or colostrum of great apes which contain both types of acidic oligosaccharides. Two GalNAc-containing oligosaccharides, lactose 3′-O-sulfate and lacto-N-novopentaose I (Gal(β1-3)[Gal(β1-4)GlcNAc(β1-6)]Gal(β1-4)Glc) were found only in the milk of rhesus macaque, hamadryas baboon and tufted capuchin, respectively. Further research is needed to determine the extent to which the milk oligosaccharide patterns observed among these taxa represent wider phylogenetic trends among primates and how much variation occurs among individuals or species

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

Pathway analysis has become the first choice for gaining insight into the underlying biology of differentially expressed genes and proteins, as it reduces complexity and has increased explanatory power. We discuss the evolution of knowledge base–driven pathway analysis over its first decade, distinctly divided into three generations. We also discuss the limitations that are specific to each generation, and how they are addressed by successive generations of methods. We identify a number of annotation challenges that must be addressed to enable development of the next generation of pathway analysis methods. Furthermore, we identify a number of methodological challenges that the next generation of methods must tackle to take advantage of the technological advances in genomics and proteomics in order to improve specificity, sensitivity, and relevance of pathway analysis