Cross Species use of Human Microarray Genotyping Technology for Bornean Orangutan (Pongo pygmaeus) SNP Discovery

Previous genetic studies of orangutans (Pongo spp.) have relied mainly upon mitochondrial DNA or microsatellite short tandem repeats (STR) for genomic genotyping analysis. Scientists have yet to take advantage of the genetic closeness of the great apes to humans for genomic analysis by using advanced techniques available for human genotyping. To genotype orangutans at Tanjung Puting National Park, we developed a novel combination of a methyl-based magnetic enrichment capture of genomic fecal DNA with genotyping on a human targeted single nucleotide polymorphism (SNP) microarray, and compared this to additional microsatellite (STR) micro-capillary genotyping. We successfully isolated 125 known human genomic SNP loci (0.08% of those targeted) which hybridized orangutan DNA on the human targeted Illumina Infinium QC array. We estimated genetic diversity and relatedness (r) using three estimators for a total of 32 (21 female and 9 male) wild orangutans at the Camp Leakey study site. Average TrioML relatedness within the sample, estimated from our combo SNP/STR dataset, was at a range consistent with half and first cousins (r = .082). All sampled males and females had relatives within the study site indicating we have verified a local, closely related community of wild orangutans at Camp Leakey.

Immunoinformatics mapping of potential epitopes in SARS-CoV-2 structural proteins

All approved coronavirus disease 2019 (COVID-19) vaccines in current use are safe, effective, and reduce the risk of severe illness. Although data on the immunological presentation of patients with COVID-19 is limited, increasing experimental evidence supports the significant contribution of B and T cells towards the resolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Despite the availability of several COVID-19 vaccines with high efficacy, more effective vaccines are still needed to protect against the new variants of SARS-CoV-2. Employing a comprehensive immunoinformatic prediction algorithm and leveraging the genetic closeness with SARS-CoV, we have predicted potential immune epitopes in the structural proteins of SARS-CoV-2. The S and N proteins of SARS-CoV-2 and SARS-CoVs are main targets of antibody detection and have motivated us to design four multi-epitope vaccines which were based on our predicted B- and T-cell epitopes of SARS-CoV-2 structural proteins. The cardinal epitopes selected for the vaccine constructs are predicted to possess antigenic, non-allergenic, and cytokine-inducing properties. Additionally, some of the predicted epitopes have been experimentally validated in published papers. Furthermore, we used the C-ImmSim server to predict effective immune responses induced by the epitope-based vaccines. Taken together, the immune epitopes predicted in this study provide a platform for future experimental validations which may facilitate the development of effective vaccine candidates and epitope-based serological diagnostic assays.

Variation in helminth susceptibility of indigenous chickens in Kano and Jigawa States of Nigeria

This study was carried out to identify the helminth parasites and burden associated with five indigenous chicken strains namely normal feathered Fulani ecotypes, naked neck, dwarf and frizzle kept under free- range system in six local government areas of Kano and Jigawa States. A total of 540 fresh faecal samples were collected from the gastrointestinal tract. Faecal egg count (quantitative examination) was carried out using the modified McMaster technique with flotation solution. All the helminths (cestodes and nematodes) were examined under light microscope and identified on the basis of helminthological keys. Worm count, EPG, Packed cell volume (PCV), total serum proteins and albumin were used to assess chicken susceptibility to worm infection. Significant differences were observed among the chicken strains for egg per gramme (EPG), cestodes and nematodes. The highest EPG (119.80) was observed in naked neck chickens, followed by frizzled (114.18), dwarf (62.86), normal feathered (30.80) and Fulani ecotypes (0.71). Frizzled chickens had higher mean cestode (7.96) count than the other strains. Dwarf chickens were significantly (P<0.05) more susceptible to nematode infection. Higher EPG (60.55) and worm burden (cestode, 6.08) was found in males than females. The high gene flow and low differentiation between Fulani ecotype and normal feathered and, naked neck and frizzled buttressed the assertion that the similarity in EPG between them were because of genetic closeness. Susceptibility to worm infection in the study measured by the prevalence and EPG was therefore genetically controlled. There were generally negative and low correlations between egg and adult worm counts with haematological indices considered. Thus, blood parameters do vary in response to helminth infection and could be good measures of susceptibility. Cette étude a été réalisée pour identifier les parasites de Helminthe et le fardeau associé à cinq souches de poulet autochtones, à savoir des écotypes Fulani à plumes normaux, un nuque nu, un nain et une frisée maintenus sous un système de liberté dans six zones gouvernementales locales des États de Kano et Jigawa. Un total de 540 échantillons fécaux frais ont été collectés à partir du tractus gastro-intestinal. Le nombre d'œufs fécaux (examen quantitatif) a été réalisé en utilisant la technique modifiée McMaster avec une solution de flottation. Tous les helminthes (cestodes et nématodes) ont été examinés sous un microscope léger et identifiés sur la base de clés helminthologiques. Le nombre de ver, ŒPG, volume de cellules emballé (VCE), les protéines sériques totales et l'albumine ont été utilisées pour évaluer la sensibilité au poulet à une infection de vers. Des différences significatives ont été observées parmi les souches de poulet pour l'œuf par gramme (ŒPG), des cestodes et des nématodes. Le plus haut ŒPG (119,80) a été observé dans des poulets de cou nu, suivis de frisanges (114,18), de nains (62,86), d'écotypes normaux à plumes (30,80) et de Fulani (0,71). Les poulets frongettes avaient une cestode moyenne moyenne (7,96) comptant que les autres souches. Les poulets nains étaient significativement (p <0,05) plus susceptibles d'infection nématode. L'ŒPG (60,55) et la charge de ver supérieur (CESTOD, 6,08) ont été trouvés chez les poulets que les poules. Le flux de gènes élevé et la faible différenciation entre les écotypes Fulani et la normale à plumes normaux et à la nuque nue et à contreforts librizatés l'affirmation selon laquelle la similitude dans ŒPG entre elles étaient à cause de la proximité génétique. La susceptibilité à une infection de vers dans l'étude mesurée par la prévalence et l'ŒPG a donc été contrôlée génétiquement. Il y avait généralement des corrélations négatives et faibles entre le nombre de ver d'œufs et d'adultes avec des indices hématologiques considérés. Ainsi, les paramètres sanguins varient en réponse à l'infection d'helminthe et pourraient être de bonnes mesures de susceptibilité.

Genetic differentiation of Coregonus muksun in natural populations and broodstocks of fish rearing farms “Forvat” and “Sobsky” in relation to the problem of restoring the species population in Western Siberia

With regard to the problem of restoring the muksun (Coregonus muksun) population in Western Siberia by means of artificial regeneration, the genetic differentiation of natural populations and broodstocks of fish rearing farms “Forvat” and “Sobsky” was studied. Eighty-four sequences of mtDNA (3,006 bp) containing the highly polymorphic genes ND1 and ND2 were analysed. The differences between the populations of Western and Eastern Siberia were revealed. These findings must be taken into account when attempting to restore the species population in each particular region. The genetic closeness of the muksun from fish rearing farms “Forvat” and “Sobsky” with muksun from the Ob-Taz basin gives grounds for using these broodstocks for seeding the Ob and Taz rivers.

Genetic Diversity of Meat Quality Related Genes in Argentinean Pigs

Background: The genetic influence on pork quality exists between breeds and within a breed. The variation is caused by a large set of genes and pork quality traits have a multi factorial background. Research into the genetics of meat quality found causative mutations associated with marked effects on pig meat value. The main objective of this study was to investigate the diversity of single nucleotide polymorphisms (SNPs) of meat quality-related genes in pigs from commercial and family farms in the North-West of Argentina. A screen for SNPs in RYR1, RN, CAST, and SOX6 candidate genes and the differentiation of their genotypes by PCR–RFLP was conducted. Results: All genes were characterized by a high level of polymorphism and heterozygosity. Additionally, both populations, commercial and Creole pigs, showed genetic closeness for the analyzed SNPs and a moderate selection for RYR1 and RN loci consistent with their allele´s adverse effects. Conclusions: The results obtained here highlighted the role of pig genotypes as a source of basic variability potentially affecting processed meat products as well as fresh meat.

The phenomenon of “female erudition” in the works by German-language authors in the second half of the 18th century

The article focuses on analysis of some German philosophers and publicists’ views on the phenomenon of female erudition in the second half of the 18th century. In the present article, genetic closeness of the mentioned authors’ ideas to educational program by Jean-Jacques Rousseau is stressed. The author makes attempts to put the phenomenon of female erudition in the wide context that included such issues as functioning of equal cross-gender communication in the frameworks of «mixed societies», crucial tends of female education development, key features of reading culture in the German-speaking space in the period under review, as well as enlightened discourse on the rights and duties of women in the second half of the 18th century.

Genome based analyses reveals the presence of heterotypic synonyms and subspecies in Bacteria and Archaea

Term heterotypic synonym refers to different names have been associated with different type strains, however from the opinion of a bacteriologist, different names belongs to the same taxon and term subspecies refers to strains and genetically close organisms that were diverging phenotypically. In this study, sequenced and publicly available genomes in the Edgar 2.0 server were carefully analysed and based on high (>98 %) amino acid identity value, synonyms were putatively identified. The 16S rRNA gene sequence of those species were used for the construction of maximum likelihood based phylogenetic trees to infer the genetic closeness or distance by examining the tree topology and clustering of the organisms within clades. They were further subjected to overall genome related indices like digital DNA-DNA hybridization, average nucleotide identity to confirm the presence of synonyms or subspecies with phenotypic data support. The outcome of this polyphasic taxonomic re-analysis was identification of 40 later heterotypic synonyms and 13 subspecies spread over phylum Actinobacteria, Bacteroidetes, Firmicutes, Nitrospirae, Proteobacteria and Thermotogae and in domain Archaea.

Of Great Apes and Magpies: Initiations into Animal Behaviour

This paper presents three case studies of exceptional human encounters with animals. These particular examples were selected because they enabled analysis of the underlying reasons that led the human participants to respond in new ways to their animal counterparts. The question asked here is whether sudden insights into the needs and abilities of an animal arises purely from an anthropocentric position as empathy because of genetic closeness (e.g., chimpanzees) or is something else and whether new insights can be applied to other phylogenetic orders not close to us, e.g., birds, and change research questions and implicit prejudices and stereotypes. Particularly in avian species, phylogenetically distant from humans, the prejudices (anthroprocentric position) and the belief in human uniqueness (human exceptionalism) might be greater than in the reactions to primates. Interestingly, in studies of great apes, contradictory opinions and controversies about cognitive abilities, especially when compared with humans, tend to be pronounced. Species appropriateness in test designs are desirable present and future goals but here it is suggested how different experiences can also lead to different questions that explode the myth of human uniqueness and then arrive at entirely different and new results in cognitive and affective abilities of the species under investigation.

The novel Coronavirus enigma: Phylogeny and mutation analyses of SARS-CoV-2 viruses circulating in India during early 2020

BackgroundThis is a comprehensive analysis of 46 Indian SARS-CoV-2 genome sequences available from the NCBI and GISAID repository during early 2020. Evolutionary dynamics, gene-specific phylogeny and emergence of the novel co-evolving mutations in nine structural and non-structural genes among circulating SARS-CoV-2 strains in ten states of India have been assessed.Materials and methods46 SARS-CoV-2 nucleotide sequences submitted from India were downloaded from the GISAID (39/46) or from NCBI (7/46) database. Phylogenetic study and analyses of mutation were based on the nine structural and non-structural genes of SARS-CoV-2 strains. Secondary structure of RdRP/NSP12 protein was predicted with respect to the novel A97V mutation.ResultsPhylogenetic analyses revealed the evolution of “genome-type clusters” and adaptive selection of “L” type SARS-CoV-2 strains with genetic closeness to the bat SARS-like coronaviruses than pangolin or MERS-CoVs. With regards to the novel co-evolving mutations, 2 groups are seen to circulate in India at present: the “major group” (52.2%) and the “minor group” (30.4%), harboring four and five co-existing mutations, respectively. The “major group” mutations fall in the A2a clade. All the minor group mutations, except 11083G>T (L37F, NSP6) were unique to the Indian isolates.ConclusionThe study highlights rapidly evolving SARS-CoV-2 virus and co-circulation of multiple clades and sub-clades, driving this pandemic worldwide. This comprehensive study is a potential resource for monitoring the novel mutations in the viral genome, changes in viral pathogenesis, for designing vaccines and other therapeutics.

Genomic differentiation among varieties of Iberian pig

Aim of study: The objective of this study was to identify the autosomal genomic regions associated with genetic differentiation between three commercial strains of Iberian pig.Area of study: Extremadura (Spain).Material and methods: We used the Porcine v2 BeadChip to genotype 349 individuals from three varieties of Iberian pig (EE, Entrepelado; RR, Retinto; and TT, Torbiscal) and their crosses. After standard filtering of the Single Nucleotide Polymorphism (SNP) markers, 47, 67, and 123 haplotypic phases from EE, RR, and TT origins were identified. The allelic frequencies of 31,180 SNP markers were used to calculate the fixation index (FST) that were averaged in sliding windows of 2Mb.Main results: The results confirmed the greater genetic closeness of the EE and RR varieties, and we were able to identify several genomic regions with a divergence greater than expected. The genes present in those genomic regions were used to perform an Overrepresentation Enrichment Analysis (ORA) for the Gene Ontology (GO) terms for biological process. The ORA indicated that several groups of biological processes were overrepresented: a large group involving morphogenesis and development, and others associated with neurogenesis, cellular responses, or metabolic processes. These results were reinforced by the presence of some genes within the genomic regions that had the highest genomic differentiation.Research highlights: The genomic differentiation among varieties of the Iberian pig is heterogeneous along the genome. The genomic regions with the highest differentiation contain an overrepresentation of genes related with morphogenesis and development, neurogenesis, cellular responses and metabolic processes.