Toxicogenomics Analysis of Non-Model Transcriptomes Using Next-Generation Sequencing and Microarray

With the advent of next generation technologies like Roche/454 Life Sciences that require low cost and less time for sequencing will help in providing a workable draft of non-model species genomes. Availability of high throughput microarray technologies for gene expression profiling provides low-cost tools for investigation of highly-integrated responses to various stimuli. These advancements along with bioinformatics processing have led to an increasing number of non-model species having well-annotated transcriptomes. The project focuses on the life cycle of development, functional annotation, and utilization of genomic tools for the avian wildlife species to determine the molecular impacts of exposure to munitions constituents (MCs). Massively parallel pyrosequencing is created from the normalized multi-tissue library of Northern bobwhite (Colinus virginianus) and Japanese quail (Coturnix coturnix) cDNAs. The assembly of next generation sequencing for transcriptomes of these organisms is challenging. High number of ESTs and longer read length require high computational memory and management between the sensitivity and accuracy to assemble correctly. The researcher developed a new pipeline “Contigs Assembly Pipeline using Reference Genome” (CAPRG) to assemble long reads for non-model organisms that have available reference genome. The results were benchmarked by employing parameter space for different available methods that utilize de novo strategies like overlap-layout-consensus (OLC) and graphs for long reads. It was observed that CAPRG performance was better or near equivalent in the two transcriptomic datasets based on different benchmarks but also completes the assembly in a fraction of the time as compared to assemblers that yield competitive results. The researcher performed statistical analysis to generate differentially expressed genes and utilized metabolic maps, biological networks, pathway analysis and GO enrichment to the differentially-expressed genes in the livers of birds exposed for 60 days (d) to 10 and 60 mg/kg/d 2,6-DNT. These revealed insights into the metabolic perturbations underlying several observed toxicological phenotypes. The impacts were validated by RT-qPCR including: a shift in energy metabolism toward protein catabolism via inhibition of control points for glucose and lipid metabolic pathways, PCK1 and PPARGC1, respectively. To greatly expand the information-base for Northern bobwhite that has little supporting information in Genbank, the researcher initiated and developed the web-based knowledgebase (www.quailgenomics.info). The Quail genomics share and develop functional genomic data for Northern bobwhite to allow researchers to perform analysis and curate genomic information for this non-model species

Novel Implementation of Conditional Co-Regulation by Graph Theory to Derive Co-Expressed Genes from Microarray Data

BackgroundMost existing transcriptional databases like Comprehensive Systems-Biology Database (CSB.DB) and Arabidopsis Microarray Database and Analysis Toolbox (GENEVESTIGATOR) help to seek a shared biological role (similar pathways and biosynthetic cycles) based on correlation. These utilize conventional methods like Pearson correlation and Spearman rank correlation to calculate correlation among genes. However, not all are genes expressed in all the conditions and this leads to their exclusion in these transcriptional databases that consist of experiments performed in varied conditions. This leads to incomplete studies of co-regulation among groups of genes that might be linked to the same or related biosynthetic pathway. ResultsWe have implemented an alternate method based on graph theory that takes into consideration the biological assumption – conditional co-regulation is needed to mine a large transcriptional data bank and properties of microarray data. The algorithm calculates relationships among genes by converting discretized signals from the time series microarray data (AtGenExpress) to output strings. A \u27score\u27 is generated by using a similarity index against all the other genes by matching stored strings for any gene queried against our database. Taking carbohydrate metabolism as a test case, we observed that those genes known to be involved in similar functions and pathways generate a high \u27score\u27 with the queried gene. We were also able to recognize most of the randomly selected correlated pairs from Pearson correlation in CSB.DB and generate a higher number of relationships that might be biologically important. One advantage of our method over previously described approaches is that it includes all genes regardless of its expression values thereby highlighting important relationships absent in other contemporary databases. ConclusionBased on promising results, we understand that incorporating conditional co-regulation to study large expression data helps us identify novel relationships among genes. The other advantage of our approach is that mining expression data from various experiments, the genes that do not express in all the conditions or have low expression values are not excluded, thereby giving a better overall picture. This results in addressing known limitations of clustering methods in which genes that are expressed in only a subset of conditions are omitted. Based on further scope to extract information, ASIDB implementing above described approach has been initiated as a model database. ASIDB is available at http://www.asidb.co

Effect of Plasma Irradiation on CdI2Cd I_2 films

The effect of plasma irradiation is studied systematically on a 4H polytype (002) oriented ${\rm CdI_2}$ stoichiometric film having compressive residual stress. Plasma irradiation was found to change the orientation to (110) of the film at certain moderate irradiation distances. A linear decrease in grain size and residual stress was observed with decreasing irradiation distance (or increasing ion energy) consistent with both structural and morphological observations. The direct optical energy gap ${\rm E_g}$ was found to increase linearly at the rate ${\rm 15\mu eV/atm}$ with the compressive stress. The combined data of present compressive stress and from earlier reported tensile stress show a consistent trend of ${\rm E_g}$ change with stress. The iodine-iodine distance in the unit cell could be responsible for the observed change in ${\rm E_g}$ with stress.Comment: 13 pages and 10 fi

Type A4 truncus arteriosus: series of 3 cases focused on dual source multidetector CT angiogram findings

Truncus arteriosus (TA) is a rare congenital cardiac anomaly caused by failure of normal conotruncal septation during the fetal development. This aberration leads to a common ventricular outflow artery over the malaligned large ventricular septal defect (VSD), supplying systemic, coronary and pulmonary circulation. People with such anomalous anatomy show variable presentation from early childhood to adult life depending on the severity of defects. We here present three cases of truncus arteriosus with aortic interruption / hypoplasia-coarctation (type A4 truncus arteriosus) with focus on relevant dual source MDCTA findings

Study of CdI2{\rm CdI_2} nanocrystals dispersed in amorphous Sb2S3{\rm Sb_2S_3} matrix

Crystalline nanoparticles of cadmium iodide where suspended in the amorphous matrix of antimony trisulphide. Both materials are layered structured and have large band-gaps however cadmium iodide exhibits polytypism, i.e. it exists in various different crystalline states. Different crystalline states are marked by wholely different dielectric constants which give rise to sharp surface plasmon resonance (SPR) peaks in the UV-visible. The manuscript details the variation in SPR's with heat-treatment of the films.Comment: 10 pages 8 figures submitted to PR

On the Structure of ZnI2{\rm ZnI_2}

A new structure for ${\rm ZnI_2}$ is proposed which it exists in tetragonal state. In this structure the ${\rm ZnI_2}$ molecule exists in a nonlinear array and forms the basis of the tetragonal unit cell with one basis per unit cell. The structural analysis based on the reflections listed in ASTM 30-1479 shows that the proposed structure is correct.Comment: six pages and four figures. Manuscript prepared in RevTe

Assessment of Antioxidant Properties in Fruits of Myrica esculenta: A Popular Wild Edible Species in Indian Himalayan Region

Crude extract of Myrica esculenta fruits, a wild edible species of Indian Himalayan Region, was evaluated for phenolic compounds and antioxidant properties. Results revealed significant variation in total phenolic and flavonoid contents across populations. Among populations, total phenolic content varied between 1.78 and 2.51 mg gallic acid equivalent/g fresh weight (fw) of fruits and total flavonoids ranged between 1.31 and 1.59 mg quercetin equivalent/g fw. Antioxidant activity determined by 2,2′-azinobis(3-ethylbenzothiazoline-6-sulphonic acid) radical scavenging, 1,1-diphenyl-2-picrylhydrazyl radical scavenging and ferric reducing antioxidant power (FRAP) exhibited considerable antioxidant potential and showed significant positive correlation with total phenolic and total flavonoids content. High performance liquid chromatography analysis revealed significant variation (P <  .01) in phenolic compounds (i.e., gallic acid, catechin, hydroxybenzioc acid and ρ-coumaric acid) across populations. This study provides evidences to establish that consumption of M. esculenta fruits while providing relished taste would also help in reduction of free radicals. Therefore, this wild edible species deserves promotion in the region through horticulture and forestry interventions

The potential role of vitamin D supplementation as a gut microbiota modifier in healthy individuals

Vitamin D deficiency affects approximately 80% of individuals in some countries and has been linked with gut dysbiosis and inflammation. While the benefits of vitamin D supplementation on the gut microbiota have been studied in patients with chronic diseases, its effects on the microbiota of otherwise healthy individuals is unclear. Moreover, whether effects on the microbiota can explain some of the marked inter-individual variation in responsiveness to vitamin D supplementation is unknown. Here, we administered vitamin D to 80 otherwise healthy vitamin D-deficient women, measuring serum 25(OH) D levels in blood and characterizing their gut microbiota pre- and post- supplementation using 16S rRNA gene sequencing. Vitamin D supplementation significantly increased gut microbial diversity. Specifically, the Bacteroidetes to Firmicutes ratio increased, along with the abundance of the health-promoting probiotic taxa Akkermansia and Bifidobacterium. Significant variations in the two-dominant genera, Bacteroides and Prevotella, indicated a variation in enterotypes following supplementation. Comparing supplementation responders and non-responders we found more pronounced changes in abundance of major phyla in responders, and a significant decrease in Bacteroides acidifaciens in non-responders. Altogether, our study highlights the positive impact of vitamin D supplementation on the gut microbiota and the potential for the microbial gut signature to affect vitamin D response. 2020, The Author(s).Scopu

CAPRG: Sequence Assembling Pipeline for Next Generation Sequencing of Non-Model Organisms

Our goal is to introduce and describe the utility of a new pipeline “Contigs Assembly Pipeline using Reference Genome” (CAPRG), which has been developed to assemble “long sequence reads” for non-model organisms by leveraging a reference genome of a closely related phylogenetic relative. To facilitate this effort, we utilized two avian transcriptomic datasets generated using ROCHE/454 technology as test cases for CAPRG assembly. We compared the results of CAPRG assembly using a reference genome with the results of existing methods that utilize de novo strategies such as VELVET, PAVE, and MIRA by employing parameter space comparisons (intra-assembling comparison). CAPRG performed as well or better than the existing assembly methods based on various benchmarks for “gene-hunting.” Further, CAPRG completed the assemblies in a fraction of the time required by the existing assembly algorithms. Additional advantages of CAPRG included reduced contig inflation resulting in lower computational resources for annotation, and functional identification for contigs that may be categorized as “unknowns” by de novo methods. In addition to providing evaluation of CAPRG performance, we observed that the different assembly (inter-assembly) results could be integrated to enhance the putative gene coverage for any transcriptomics study