A biogeographic 16S rRNA survey of bacterial communities of ureolytic biomineralization from California public restrooms

In this study, we examined the total bacterial community associated with ureolytic biomineralization from urine drainage systems. Biomineral samples were obtained from 11 California Department of Transportation public restrooms fitted with waterless, low-flow, or conventional urinals in 2019. Following high throughput 16S rRNA Illumina sequences processed using the DADA2 pipeline, the microbial diversity assessment of 169 biomineral and urine samples resulted in 3,869 reference sequences aggregated as 598 operational taxonomic units (OTUs). Using PERMANOVA testing, we found strong, significant differences between biomineral samples grouped by intrasystem sampling location and urinal type. Biomineral microbial community profiles and alpha diversities differed significantly when controlling for sampling season. Observational statistics revealed that biomineral samples obtained from waterless urinals contained the largest ureC/16S gene copy ratios and were the least diverse urinal type in terms of Shannon indices. Waterless urinal biomineral samples were largely dominated by the Bacilli class (86.1%) compared to low-flow (41.3%) and conventional samples (20.5%), and had the fewest genera that account for less than 2.5% relative abundance per OTU. Our findings are useful for future microbial ecology studies of urine source-separation technologies, as we have established a comparative basis using a large sample size and study area.

Population-level genome-wide STR discovery and validation for population structure and genetic diversity assessment of Plasmodium species

Short tandem repeats (STRs) are highly informative genetic markers that have been used extensively in population genetics analysis. They are an important source of genetic diversity and can also have functional impact. Despite the availability of bioinformatic methods that permit large-scale genome-wide genotyping of STRs from whole genome sequencing data, they have not previously been applied to sequencing data from large collections of malaria parasite field samples. Here, we have genotyped STRs using HipSTR in more than 3,000 Plasmodium falciparum and 174 Plasmodium vivax published whole-genome sequence data from samples collected across the globe. High levels of noise and variability in the resultant callset necessitated the development of a novel method for quality control of STR genotype calls. A set of high-quality STR loci (6,768 from P. falciparum and 3,496 from P. vivax) were used to study Plasmodium genetic diversity, population structures and genomic signatures of selection and these were compared to genome-wide single nucleotide polymorphism (SNP) genotyping data. In addition, the genome-wide information about genetic variation and other characteristics of STRs in P. falciparum and P. vivax have been available in an interactive web-based R Shiny application PlasmoSTR (https://github.com/bahlolab/PlasmoSTR).

AVIFAUNISTIC DIVERSITY OF MERINE FOREST, NORTH-WEST ALGERIA

This study is an avifaunistic diversity assessment was carried out in the Merine forest, Sidi Bel Abbes (Northwest Algeria). During three years (2019-2021). The major objective of our investigation is to inventory avian species and to define their phenological categories. Among the important results is a record of, 71 species of bird, belonging to 17 orders and 28 families. The Passeriformes are the most noted with 43 species, distributed across 15 families, of which the Muscicapidae is the most represented with 10 species. The phenological categories indicates that the majority of this species are resident breeders (65 %), 21% are migrant breeders and 14% are passing visitors. Depending on trophic status, 32% are polyphagous, 27% insectivorous, 17% carnivorous, 15% granivorous and 8% omnivorous. In addition, we noted that, 31 species are protected by Flat 12-235 in Algeria, with one species (Falco naumanni) protected by the Ordinance 06-05. Internationally and one species protected according of the IUCN red list (Streptopelia turtur). The Merine forest is shelter to five species endemic to North Africa: Barbary Partridge (Alectoris barbara), Levaillant's Woodpecker (Picus vaillantii), Moussier's Redstart (Phoenicurus moussieri), Tristram's Warbler (Sylvia deserticola), African Blue Tit (Cyanistes teneriffae).

Identification of Genes Related to Cold Tolerance and Novel Genetic Markers for Molecular Breeding in Taiwan Tilapia (Oreochromis spp.) via Transcriptome Analysis

Taiwan tilapia is one of the primary species used in aquaculture practices in Taiwan. However, as a tropical fish, it is sensitive to cold temperatures that can lead to high mortality rates during winter months. Genetic and broodstock management strategies using marker-assisted selection and breeding are the best tools currently available to improve seed varieties for tilapia species. The purpose of this study was to develop molecular markers for cold stress-related genes using digital gene expression analysis of next-generation transcriptome sequencing in Taiwan tilapia (Oreochromis spp.). We constructed and sequenced cDNA libraries from the brain, gill, liver, and muscle tissues of cold-tolerance (CT) and cold-sensitivity (CS) strains. Approximately 35,214,833,100 nucleotides of raw sequencing reads were generated, and these were assembled into 128,147 unigenes possessing a total length of 185,382,926 bp and an average length of 1446 bp. A total of 25,844 unigenes were annotated using five protein databases and Venny analysis, and 38,377 simple sequence repeats (SSRs) and 65,527 single nucleotide polymorphisms (SNPs) were identified. Furthermore, from the 38-cold tolerance-related genes that were identified using differential gene expression analysis in the four tissues, 13 microsatellites and 37 single nucleotide polymorphism markers were identified. The results of the genotype analysis revealed that the selected markers could be used for population genetics. In addition to the diversity assessment, one of the SNP markers was determined to be significantly related to cold-tolerance traits and could be used as a molecular marker to assist in the selection and verification of cold-tolerant populations. The specific genetic markers explored in this study can be used for the identification of genetic polymorphisms and cold tolerance traits in Taiwan tilapia, and they can also be used to further explore the physiological and biochemical molecular regulation pathways of fish that are involved in their tolerance to environmental temperature stress.

Qur’an Translation and the Semantic Diversity: Assessment of Urdu Quran Translations (Application of Julian House Model of Quality Assessment)

The research study aims at evaluating the Urdu translation of Qur’an by Pakistani scholars according to the latest assessment models of translation. As different Models of Assessment and Evaluation have been devised for the translations of various types of text such as literary, religious, and technical, hence translation is not mere transfer of words and meanings but the whole culture and connotations of the text need to be transferred. The research study is unique in that it deals with the evaluation of the holy Words of Allah, the Qur’an. To assess the Urdu Translations of the Qur’an, we have selected Julian House Model for Assessment and Evaluation. Furthermore, the study has been narrowed down to Surat Dhuha (93). Rationally, all assessment model cannot be applied for the evaluation of Qur’an Translation, so we have selected the most recent translations of the Qur’an rendered by Mufti Taqi Usmani, Dr. Tahirul Qadri,Pir Karam Shah Azhari, Muhammad Hussain Najfi, Hafiz Salahudin Yousaf, Abul Ala Moudoodi, and Dr. Israr Ahmad.

Agro-morphological traits-based genetic diversity assessment in Ethiopian barley (Hordeum vulgare L.) landrace collections from Bale highlands, Southeast Ethiopia

Background Cultivated barley (Hordeum vulgare L.) is one of the world’s important cereal crops. Ethiopia is claimed to be the centre of origin due to its high phenotypic diversity and flavonoid patterns. It is widely cultivated on subsistence bases and important in supporting the livelihood of local poor. However, the local landraces are currently under threat of severing genetic erosion. Hence, assessing the extents of its genetic diversity is timely in improvement and conservation. Methodology 120 representative cultivated barley landraces have been collected from Bale highlands, Ethiopia, and tested at two locations using alpha lattice design. Data were collected on 21 agro-morphometric traits and analysed using MINITAB 19, SAS 9.4 and FigTree v1.4.3. Results Most morphotypes in each of the qualitative traits considered and mean performance values in most of the quantitative traits revealed wide range of variations suggesting existence of phenotypic diversity among the landraces. Analysis of variance also showed significant variations among the landraces. All the traits, except days to maturity and plant height showed a significant variation for location and treatment-location interactions revealing the high impact of environmental conditions on the variations. Estimates of the variance components also revealed a wider range of variations in most of the traits considered with eventual medium to low genotypic (GCV), phenotypic (PCV) and genotype–environment coefficients of variation (GECV). Estimates of heritability in broad sense (H2) is low (< 40%) in all the traits except in days to maturity. Grouping of the landraces showed poor geographic areas of collection-based pattern suggesting extensive gene flow among the areas. Conclusion The landraces evaluated in the present study showed high morphological diversity. However, the effect of environment factor is pronounced and thus, multiple locations and years with large number of samples must be considered to exploit the available genetic-based variations for breeding and conservation of the crop.

Genetic diversity and species identity of the critically endangered Rote Island snake-necked turtle, Chelodina mccordi Rhodin, 1994

The endemic Chelodina mccordi is considered extinct in the wild; however, ex-situ populations are thriving and sampled for our genetic diversity assessment. We used three sequences resulting from blood and tissue samples of five individual turtles amplified for 650-bp cytochrome oxidase I (COI) fragment of the mitochondrial DNA. We analysed a total of 30 barcoding DNA sequences for phylogenetic relationships and genetic distances among Chelodina spp. Nucleotide diversity of eight C. mccordi samples is 0.007 ± 0.001 with a haplotype diversity of 0.893 ± 0.086. All these samples form a monophyletic clade that is sister to a clade of Australian and New Guinean long-necked turtles. Genetic distances calculated using Kimura 2-paramater model among C. mccordi sequences range between 0.2% and 1.5%, while a few others are without distance. The shortest genetic distance is between individuals from Rote Island, whereas the longest distance was found between individuals, each of which was derived from parental stocks originating in Rote and Timor islands. A genetic distance of 1.1% - 1.5% is likely to denote distinction at subspecies level. Results of this study could help in reintroducing captive individuals into their natural habitats. Thus, captive breeding programme of this species may help its conservation.

Genetic diversity assessment of neem (Azadirachta indica A. Juss) in northern Nigeria

Neem is a tropical tree that can adapt to a wide range of places and particularly to semi- arid conditions. As at present, it is grown in many Asian countries and also in the tropical regions of the western hemisphere. Genetic variability and diversity are a major requirement needed for both immediate results and the one ones thereafter adaptation of plant types in their original domain. The evaluation of genetic diversity of any species is extremely crucial for their sustainability, continuity, survival and gene manipulation. Major breakthroughs in the field of molecular biology was able to develop several tools for the investigation of genetic diversity at the genome level to determine phylogenetic relationships among inter or intra-species. The advent of molecular markers for the detection and exploitation of DNA polymorphism is one of the major breakthroughs in the world of molecular genetics. The importance of genetic diversity in plant germplasm conservation, especially in economically important species such as Azadirachtaindica, is enormous, particularly in Nigeria. The question is whether A. indica from different Agro-ecological zones have genetic variations or similarities. This was the bane of the current study, which used RAPD to look atgenetic diversity of 27 randomly selected neem trees within the agro-ecological zones in Northern Nigeria. A total of 9 primers were employed out of which only 5 were responsive (OPA-02, OPA-03, OPA-15 and OPA-19). These primers showed dissimilarities in the visible DNA bands among the various tree samples. There was evidence of genetic dissimilarities among the trees sampled. Differences in percentage polymorphism was reported, where it was reportedly highest among the Borno State tree samples (97.44%), compared to those in Yobe State with no polymorphism.

Rendering Multivariate Statistical Models for Genetic Diversity Assessment in a A-Genome Diploid Wheat Population

Diversifying available natural resources to cope with abrupt climatic changes and the necessity to equalize rising agricultural production with improved ability to endure environmental influence is the dire need of the day. Inherent allelic variability regarding significant economic traits featuring both enhanced productivity and environmental adaptability is one such prominent need. To address this requirement, a series of analyses were conducted in this study for exploring natural diploid wheat germplasm resources. The current study involved 98 Recombinant Inbred Lines (RILs) populations developed by crossing two diploid ‘A’ sub-genome wheat species, Triticummonococcum and Triticum boeoticum, enriched with valuable alleles controlling, in particular, biotic and abiotic stresses tolerance. Their 12 phenotypic traits were explored to reveal germplasm value. All traits exhibited vast diversity among parents and RILs via multivariate analysis. Most of the investigated traits depicted significant (p < 0.05) positive correlations enlightening spikelet per spike, total biomass, seed weight per spike, number of seeds per spike, plant height, and days to heading as considerably focused traits for improving hexaploid wheat. Principal component analysis (PCA) exhibited 61.513% of total variation with three PCs for 12 traits. Clustering of genotypes happened in three clades, and the two parents were separated into two extreme clusters, validating their enrichment of diversity. This study provided beneficial aspects of parental resources rich in diverse alleles. They can be efficiently exploited in wheat improvement programs focusing on introgression breeding and the recovery of eroded genetic factors in currently available commercial wheat cultivars to sustain calamities of environmental fluctuations.