Intra-species Genetic Variations Research Articles

Lower viral evolutionary pressure under stable versus fluctuating conditions in subzero Arctic brines

BackgroundClimate change threatens Earth’s ice-based ecosystems which currently offer archives and eco-evolutionary experiments in the extreme. Arctic cryopeg brine (marine-derived, within permafrost) and sea ice brine, similar in subzero temperature and high salinity but different in temporal stability, are inhabited by microbes adapted to these extreme conditions. However, little is known about their viruses (community composition, diversity, interaction with hosts, or evolution) or how they might respond to geologically stable cryopeg versus fluctuating sea ice conditions.ResultsWe used long- and short-read viromics and metatranscriptomics to study viruses in Arctic cryopeg brine, sea ice brine, and underlying seawater, recovering 11,088 vOTUs (~species-level taxonomic unit), a 4.4-fold increase of known viruses in these brines. More specifically, the long-read-powered viromes doubled the number of longer (≥25 kb) vOTUs generated and recovered more hypervariable regions by >5-fold compared to short-read viromes. Distribution assessment, by comparing to known viruses in public databases, supported that cryopeg brine viruses were of marine origin yet distinct from either sea ice brine or seawater viruses, while 94% of sea ice brine viruses were also present in seawater. A virus-encoded, ecologically important exopolysaccharide biosynthesis gene was identified, and many viruses (~half of metatranscriptome-inferred “active” vOTUs) were predicted as actively infecting the dominant microbial genera Marinobacter and Polaribacter in cryopeg and sea ice brines, respectively. Evolutionarily, microdiversity (intra-species genetic variations) analyses suggested that viruses within the stable cryopeg brine were under significantly lower evolutionary pressures than those in the fluctuating sea ice environment, while many sea ice brine virus-tail genes were under positive selection, indicating virus-host co-evolutionary arms races.ConclusionsOur results confirmed the benefits of long-read-powered viromics in understanding the environmental virosphere through significantly improved genomic recovery, expanding viral discovery and the potential for biological inference. Evidence of viruses actively infecting the dominant microbes in subzero brines and modulating host metabolism underscored the potential impact of viruses on these remote and underexplored extreme ecosystems. Microdiversity results shed light on different strategies viruses use to evolve and adapt when extreme conditions are stable versus fluctuating. Together, these findings verify the value of long-read-powered viromics and provide foundational data on viral evolution and virus-microbe interactions in Earth’s destabilized and rapidly disappearing cryosphere.B3KUN5MJ8EAz4vqucsgZtLVideo

Renal Hypoxic Reperfusion Injury-on-Chip Model for Studying Combinational Vitamin Therapy.

Renal ischemic-reperfusion injury decreases the chances of long-term kidney graft survival and may lead to the loss of a transplanted kidney. During organ excision, the cycle of warm ischemia from the donor and cold ischemia is due to storage in a cold medium after revascularization following organ transplantation. The reperfusion of the kidney graft activates several pathways that generate reactive oxygen species, forming a hypoxic-reperfusion injury. Animal models are generally used to model and investigate renal hypoxic-reperfusion injury. However, these models face ethical concerns and present a lack of robustness and intraspecies genetic variations, among other limitations. We introduce a microfluidics-based renal hypoxic-reperfusion (RHR) injury-on-chip model to overcome current limitations. Primary human renal proximal tubular epithelial cells and primary human endothelial cells were cultured on the apical and basal sides of a porous membrane. Hypoxic and normoxic cell culture media were used to create the RHR injury-on-chip model. The disease model was validated by estimating various specific hypoxic biomarkers of RHR. Furthermore, retinol, ascorbic acid, and combinational doses were tested to devise a therapeutic solution for RHR. We found that combinational vitamin therapy can decrease the chances of RHR injury. The proposed RHR injury-on-chip model can serve as an alternative to animal testing for injury investigation and the identification of new therapies.

Molecular analysis of internal transcribed spacer 2 of Dicrocoelium dendriticum isolated from cattle, sheep, and goat in Iran

BackgroundDicrocoelium dendriticum is a broadly distributed zoonotic helminth, which is mainly reported from domesticated and wild ruminants. There is little data covering the molecular features of this trematode; therefore, current study aimed to molecularly analyze D. dendriticum in livestock.MethodsTotally, 23 samples of D. dendriticum were collected from cattle, sheep, and goat from Ilam, Lorestan, and Khuzestan, three west and south-west provinces of Iran from February to August 2018. After genomic DNA extraction, the internal transcribed spacer (ITS) 2 fragment was amplified and sequenced in samples. To investigate genetic variations through the ITS 2 fragment of obtained D. dendriticum, phylogenetic tree and network analysis were employed.ResultsAll 23 samples were successfully amplified and sequenced. Phylogenetic tree showed that our samples were clearly grouped in a clade together with reference sequences. There was no grouping based on either geographical regions or hosts. Network analysis confirmed the phylogenetic findings and showed the presence of nine distinct haplotypes, while our samples together most of sequences, which were previously submitted to the GenBank, were grouped in the Hap1.ConclusionsOur findings indicated that although ITS 2 fragment discriminate D. dendriticum, this fragment is not suitable to study intra-species genetic variations. Therefore, exploring and describing new genetic markers could be more appropriate to provide new data about the genetic distribution of this trematode.

Genetic analysis of mitochondrial pcox1 and ribosomal 18S rRNA genes in Eurytrema pancreaticum isolates from goats in Huaihua City, Hunan Province

To investigate the genetic variation of Eurytrema pancreaticum isolated from goats in Huaihua City, Hunan Province. The partial sequence of mitochondrial cytochrome I (pcox1) and ribosomal 18S rRNA genes were amplified using a PCR assay in E. pancreaticum isolates from goats in Huaihua City, Hunan Province, and the PCR amplification products were sequenced. Then, the gene sequences were subjected to genetic variation and phylogenetic analyses. The sequences of the pcox1 and 18S rRNA genes were 430 bp and 1 857 bp in length in 18 E. pancreaticum isolates from goats in Huaihua City, Hunan Province, and there were 14 and 35 variation sites in pcox1 and 18S rRNA gene sequences, with intra-species genetic variations of 0 to 1.4% and 0 to 0.8%, respectively. The sequences of pcox1 and 18S rRNA genes had 99.0% to 99.8% and 99.5% to 99.8% homologies with those from E. pancreaticum Chinese strain recorded in the GenBank database. Consistent phylogenetic analysis results were found based on pcox1 and 18S rRNA genes. The 18 E. pancreaticum isolates from goats in Huaihua City were clustered into a clade with the known E. pancreaticum isolates registered in GenBank, and the clade with these 18 E. pancreaticum isolates was close to the clades with Eurytrema species and far from the clades with other trematodes. The E. pancreaticum isolates from goats have a low genetic variation in Huaihua City, Hunan Province. Mitochondrial pcox1 and ribosomal 18S rRNA genes may serve as molecular markers for the studies on the genetic variation in goat-derived E. pancreaticum.

DNA Barcoding Markers and Next Generation Sequence Analysis of Rbcl in Intraspecies Genetic Variations of Three Varieties of Cissus quadrangularis L.

Cissus quadrangularis L. is a well-known plant used in Ayurveda. It is also called Asthisamharaka. The etymology of its name indicates its use in the healing of the fractured bone. It is a widely growing plant belonging to the family of vitaceae. C. quadrangularis (Family: Vitaceae) is commonly distributed throughout the hotter parts of India and Sri Lanka. C. quadrangularis is mentioned in classical literature like Bhava Prakash and Chakra Dutta. The present study design to compare three different varieties of C. quadrangularis which includes the species of quadrangular, round and flat types are used to study DNA barcoding marker and phylogenetic analysis. Whole-genome was isolated from the stem parts of three varieties of C. quadrangularis ; quadrangular, round and flat. The PCR amplification of DNA barcoding markers (rbcl, mat k and ITS) was analyzed by DNA electrophoresis. The DNA barcoding markers and next-generation sequencing are able to identify the intraspecies genetic variations among these closely related plant varieties of C. quadrangularis of quadrangular, round and flat.

Identification of genes involved in the evolution of human intelligence through combination of inter-species and intra-species genetic variations.

Understanding the evolution of human intelligence is an important undertaking in the science of human genetics. A great deal of biological research has been conducted to search for genes which are related to the significant increase in human brain volume and cerebral cortex complexity during hominid evolution. However, genetic changes affecting intelligence in hominid evolution have remained elusive. We supposed that a subset of intelligence-related genes, which harbored intra-species variations in human populations, may also be evolution-related genes which harbored inter-species variations between humans (Homo sapiens) and great apes (including Pan troglodytes and Pongo abelii). Here we combined inter-species and intra-species genetic variations to discover genes involved in the evolution of human intelligence. Information was collected from published GWAS works on intelligence and a total of 549 genes located within the intelligence-associated loci were identified. The intelligence-related genes containing human-specific variations were detected based on the latest high-quality genome assemblies of three human’s closest species. Finally, we identified 40 strong candidates involved in human intelligence evolution. Expression analysis using RNA-Seq data revealed that most of the genes displayed a relatively high expression in the cerebral cortex. For these genes, there is a distinct expression pattern between humans and other species, especially in neocortex tissues. Our work provided a list of strong candidates for the evolution of human intelligence, and also implied that some intelligence-related genes may undergo inter-species evolution and contain intra-species variation.

DNA barcoding markers to identify intraspecies genetic variations in three ecotypes of Abrus Precatorius L.

Background: Abrus precatorius is also called as Gunja in Ayurveda. It is a commonly grown plant belonging to the family of Fabaceae. It is characterized under the Upavisha (semi-poisonous drugs) and used widely in various Ayurvedic formulations with great beneficial significance. It is used in the treatment of various diseases such as alopecia, edema, helminthiasis, skin diseases, itching, and urinary disorders after being passed through specific purification procedures. Objectives: The present study aims to compare three different varieties of A. precatorius which includes the species of white, black, and red which are used to study DNA barcoding marker and phylogenetic analysis. Materials and Methods: Whole genomic isolated DNA from three varieties (white, black, and red) of A. precatorius leaves and subjected to analysis of the polymerase chain reaction of rbcL, maturase K, and internal transcribed spacer 4,5 using 0.8% agarose gel electrophoresis. Results: The DNA barcoding markers and next-generation sequencing can identify the intraspecies genetic variations among these closely related plant varieties of A. precatorius of white, black, and red. Conclusion: The intraspecies genetic variations among these three varieties of A. precatorius white, black, and red are closely related with A. precatorius isolate TMP 144 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit gene 99.81%.

Comparative Genotyping of Echinococcus granulosus Infecting Livestock in Turkey and Iran

Echinococcus granulosus contains a complex of different strains that represent diversity in the pattern of the life cycle and also their host types. So far 10 genotypes of this parasite have been identified, using molecular methods. The current study aimed to evaluate and compare the genotypic diversity of E. granulosus metacestodes from livestock of Turkey and Iran. A total of 90 livestock liver and lung organs infected with hydatid cyst from industrial slaughterhouses of Bonab Province in the East Azerbaijan Province in Iran (60 samples, including 30 sheep and 30 cattle) and Van Province in Turkey (30 samples, including 15 sheep and 15 cattle) were collected. DNA was extracted from the protoscolices or germinal layers and polymerase chain reaction (PCR) were utilized, targeting the partial mitochondrial cytochrome c oxidase subunit 1 (cox1) and NADH dehydrogenase 1 (nad1) genes. PCR products were isolated from the electrophoresis gels and sequenced. The sequences were compared with each other, as well as with those related available sequences in the GenBank, using the BioEdit software and the BLAST algorithm. Finally, the phylogenetic trees were constructed by comparing sequences of cox1 and nad1 fragments, using the MEGA7 software and the maximum likelihood method. All samples sequenced from Iran corresponded to the genotype G1 (100%). Among the samples from Turkey, 15 samples (78.9%) were identified as G1 while only one sample (5.3%) corresponded to the genotype G3 and 3 isolates (15.8%) were defined as genotypes G1/G3. Five distinct haplotypes were determined within the examined isolates from sheep and cattle in both countries and all isolates clustered in one group. Phylogenetic analysis revealed that the intra-species genetic variations were 0.0-0.6% and 0.0-1.4% for cox1 and nad1, respectively. The dominant genotype of E. granulosus sensu stricto of livestock in both countries was the G1 (sheep strain) genotype. Our findings indicate that the sheep-dog cycle is the leading cycle of E. granulosus in these two areas. Hence, adopting regional common policies and bilateral cooperation helps to control the disease in livestock as well as in human in these two regions. Further study is required to compare the genetic diversity of human isolates of E. granulosus in these two countries.

Implications of High Molecular Divergence of Nuclear rRNA and Phylogenetic Structure for the Dinoflagellate Prorocentrum (Dinophyceae, Prorocentrales).

The small and large nuclear subunit molecular phylogeny of the genus Prorocentrum demonstrated that the species are dichotomized into two clades. These two clades were significantly different (one-factor ANOVA, p < 0.01) with patterns compatible for both small and large subunit Bayesian phylogenetic trees, and for a larger taxon sampled dinoflagellate phylogeny. Evaluation of the molecular divergence levels showed that intraspecies genetic variations were significantly low (t-test, p < 0.05), than those for interspecies variations (> 2.9% and > 26.8% dissimilarity in the small and large subunit [D1/D2], respectively). Based on the calculated molecular divergence, the genus comprises two genetically distinct groups that should be considered as two separate genera, thereby setting the pace for major systematic changes for the genus Prorocentrum sensu Dodge. Moreover, the information presented in this study would be useful for improving species identification, detection of novel clades from environmental samples.

Genetic Diversity of the Sable (Martes zibellina, Mustelidae) in Russian Far East and Hokkaido Inferred from Mitochondrial NADH Dehydrogenase Subunit 2 Gene Sequences

Abstract. Intra-species genetic variations of the sable Martes zibellina (Carnivora, Mustelidae), originating from Russian Far East and Hokkadio, were assessed by using nucleotide sequences of the mitochondrial NADH dehydrogenase subunit 2 gene (976 base pairs). Evaluation of the genetic diversity of the sables demonstrated that populations in the southern Primorsky territory in Russian Far East harbors high genetic diversity. We assumed that the high genetic variations might have been due to effects of refugia, secondary admixture of allopatrically differentiated lineages, or massive anthropogenic introductions. Molecular phylogenetic (maximum likelihood and Bayesian inference approaches) and network (median joining method) analyses clarified that sables in Hokkaido was monophyletic. Bayesian-relaxed molecular dating approach estimated the date for migration of sables into Hokkaido to lie between 0.10–0.27 Myr BP. Considering the geological evidence, the Late Pleistocene was presumed to be the plausible ...

Geographical Variation in Multiple Lectins of the Acorn Barnacle Megabalanus rosa.

The multiple lectins in the acorn barnacle Megabalanus rosa collected from Sukumo Bay, Kochi, and Okirai Bay, Iwate, were analyzed for seasonal dynamics, agglutinating activities against animal erythrocytes, and peptide maps. Although there was no recognizable morphological difference between specimens collected from the two localities, heterogeneity in amino acid sequence was observed for the multiple lectins isolated from the barnacles. The present study shows that there is intraspecies genetic variations within M. rosa populations distributed along the Japanese coast.