Managing Ethical Challenges to Mental Health Research in Post‐Conflict Settings

Recently the World Health Organization (WHO) has highlighted the need to strengthen mental health systems following emergencies, including natural and manmade disasters. Mental health services need to be informed by culturally attuned evidence that is developed through research. Therefore, there is an urgent need to establish rigorous ethical research practice to underpin the evidence‐base for mental health services delivered during and following emergencies.     

Exclusion of chromosome 6 and 8 locations in nonrhodopsin autosomal dominant retinitis pigmentosa families: further locus heterogeneity in adRP.

Genetic studies have revealed that 25 to 30% of autosomal dominant retinitis pigmentosa (adRP) families have mutations in the rhodopsin gene, while the remainder do not. More recently linkage data and mutation detection have demonstrated two further loci implicated in adRP, at an as yet unidentified gene on chromosome 8p and at the human gene homologue of the mouse Rds (Retinal Degeneration Slow) gene on chromosome 6p. We have previously reported exclusion of adRP from the rhodopsin locus on 3q in two large adRP families. We now report exclusion data for both families, on chromosomes 6 and 8, demonstrating that the adRP phenotype results from mutations in at least four locations.     

Genome-Wide Analysis of Potassium Transport-Related Genes in Chickpea (<Emphasis Type="Italic">Cicer arietinum</Emphasis> L.) and Their Role in Abiotic Stress Responses

Potassium is the most abundant inorganic cation that constitutes up to 10% of the total plant dry weight and plays a prominent role in plant growth and development. Plants exhibit a complex but highly organized system of channels and transporters, which are involved in absorption and distribution of K⁺ from soil to different parts of plants. In this study, we explored the K⁺ transport system in chickpea genome and identified 36 genes encoding potassium channels and transporters. The identified genes were further classified on the basis of their domain structure and conserved motifs. It includes K⁺ transporters (23 genes: 2 HKTs, 6 KEAs, and 15 KUP/HAK/KTs) and K⁺ channels (13 genes: 8 Shakers and 5 TPKs). Chromosomal localization of these genes demonstrated that various K⁺ transporters and channels are randomly distributed across all the eight chromosomes. Comparative phylogenetic analysis of K⁺ transport system genes from Arabidopsis thaliana, Glycine max, Medicago truncatula, and Oryza sativa revealed their strong conservation in different plant species. Similarly, gene structure analysis displayed conservation of family-specific intron/exon organization in the K⁺ transport system genes. Evolutionary analysis of these genes suggested the segmental duplication as principal route of expansion for this family in chickpea. Several abiotic stress-related cis-regulatory elements were also identified in promoter regions suggesting their role in abiotic stress tolerance. Expression analysis of selected genes under drought, heat, osmotic, and salt stress demonstrated their differential expression in response to these stresses. This signifies the importance of these genes in the modulation of stress response in chickpea. Present study provides the first insight into K⁺ transport system in chickpea and can serve as a basis for their functional analysis.     

An in silico analytical study of lung cancer and smokers datasets from gene expression omnibus (GEO) for prediction of differentially expressed genes

Smoking is the leading cause of lung cancer development and several genes have been identified as potential biomarker for lungs cancer. Contributing to the present scientific knowledge of biomarkers for lung cancer two different data sets, i.e. GDS3257 and GDS3054 were downloaded from NCBI׳s GEO database and normalized by RMA and GRMA packages (Bioconductor). Diffrentially expressed genes were extracted by using and were R (3.1.2); DAVID online tool was used for gene annotation and GENE MANIA tool was used for construction of gene regulatory network. Nine smoking independent gene were found whereas average expressions of those genes were almost similar in both the datasets. Five genes among them were found to be associated with cancer subtypes. Thirty smoking specific genes were identified; among those genes eight were associated with cancer sub types. GPR110, IL1RN and HSP90AA1 were found directly associated with lung cancer. SEMA6A differentially expresses in only non-smoking lung cancer samples. FLG is differentially expressed smoking specific gene and is related to onset of various cancer subtypes. Functional annotation and network analysis revealed that FLG participates in various epidermal tissue developmental processes and is co-expressed with other genes. Lung tissues are epidermal tissues and thus it suggests that alteration in FLG may cause lung cancer. We conclude that smoking alters expression of several genes and associated biological pathways during development of lung cancers.     

Protective effect of jasmonic acid and potassium against cadmium stress in peas (Pisum sativum L.)

A combination of mineral nutrients and plant growth regulators should be assessed to improve crop performance under various abiotic stresses. There is a need to include plant growth regulators in fertilization regime of various crops along with essential mineral nutrients, especially when they are irrigated with polluted water with higher levels of heavy metals. The performance of pea was evaluated under cadmium (Cd) stress coupled with potassium (K) and jasmonic acid (JA) supplementation. The Cd stress (50 μM) was applied to soil (sandy loam) grown pea plants as basal dose after a month of sowing. The control and stressed plants were then supplemented with K (5 M), JA (0.5 mM) and their collective application along with control as distilled water. Cd stress showed a marked reduction in growth pattern, however, the collective supplementation sufficiently improved the growth pattern of stressed peas plants as evidenced by improvement in shoot length (cm), root length (cm), number of leaves per plant, leaf area (cm²), plant fresh and dry weight (gm). Potassium application under Cd stress significantly enhanced internodal distance (cm) while the number of seeds per pod and relative water contents remained nonsignificant. The applied treatment (JA + K) under Cd stress prominently improved enzymatic activities, which were measured as nitrate reductase activity (NRA), nitrite reductase activity (NiRA), superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT). Cd stress impacted the biochemical profile by enhancing antioxidant capacity (AC), antioxidant activity (AA), total phenols (TP), while reducing total soluble protein (TSP), chlorophyll ‘a’, chlorophyll ‘b’ and carotenoids. The combined application of JA and K under Cd stress enhanced AC, AA, TP, Chl a and b, TSP and carotenoids. The results indicate that foliar application of JA and K efficiently negated the harmful effects of Cd stress on peas.     

Deciphering distinct biological control and growth promoting potential of multi-stress tolerant Bacillus subtilis PM32 for potato stem canker

Plant growth-promoting rhizobacteria (PGPR) represent a set of microorganisms that play significant role in improving plant growth and controlling the phytopathogens. Unpredictable performance after the application of PGPR has been observed when these were shifted from in-vitro to in-vivo conditions due to the prevalence of various abiotic stress conditions. During growing period, the potato crop is subjected to a combination of biotic and abiotic stresses. Rhizoctonia solani, a soil-borne plant pathogen, causes reduced vigor and yield of potato crop worldwide. In the current study, multi-stress-tolerant rhizobacterial strain, Bacillus subtilis PM32, was isolated from field-grown potato with various plant growth promoting (PGP) traits including zinc and potassium solubilization, biological nitrogen fixation, ammonia and siderophore, as well as extracellular enzyme productions (cellulase, catalase, amylase, protease, pectinase, and chitinase). The strain PM32 exhibited a distinct potential to support plant growth by demonstrating production of indole-3-acetic acid (102.6 μM/mL), ACC-deaminase activity (1.63 μM of α-ketobutyrate/h/mg protein), and exopolysaccharides (2.27 mg/mL). By retarding mycelial growth of R. solani the strain PM32 drastically reduced pathogenicity of R. solani. The strain PM32 also suppressed the pathogenic activity significantly by impeding mycelial expansion of R. solani with inhibition co-efficient of 49.87. The B. subtilis PM32 also depicted significant tolerance towards salt, heavy metal (Pb), heat and drought stress. PCR based amplification of ituC and acds genes coding for iturin and ACC-deaminase activity respectively indicated potential of strain PM32 for lipopeptides production and ACC deaminase enzyme activity. Results of both in-vitro and pot experiments under greenhouse conditions depicted the efficiency of B. subtilis PM32 as a promising bio-control agent for R. solani infection together with enhanced growth of potato plants as deciphered from biomass accumulation, chlorophyll a, b, and carotenoid contents. Therefore, it was envisioned that application of indigenous multi-stress tolerant PGPR may serve to induce biotic and abiotic stress tolerance in crops/plants for pathogen control and sustainable global food supply.Supplementary InformationThe online version contains supplementary material available at 10.1007/s12298-021-01067-2.     

SWALO: scaffolding with assembly likelihood optimization

Scaffolding, i.e. ordering and orienting contigs is an important step in genome assembly. We present a method for scaffolding using second generation sequencing reads based on likelihoods of genome assemblies. A generative model for sequencing is used to obtain maximum likelihood estimates of gaps between contigs and to estimate whether linking contigs into scaffolds would lead to an increase in the likelihood of the assembly. We then link contigs if they can be unambiguously joined or if the corresponding increase in likelihood is substantially greater than that of other possible joins of those contigs. The method is implemented in a tool called Swalo with approximations to make it efficient and applicable to large datasets. Analysis on real and simulated datasets reveals that it consistently makes more or similar number of correct joins as other scaffolders while linking very few contigs incorrectly, thus outperforming other scaffolders and demonstrating that substantial improvement in genome assembly may be achieved through the use of statistical models. Swalo is freely available for download at https://atifrahman.github.io/SWALO/.