Transcriptome diversity assessment of Gossypium arboreum (FDH228) leaves under control, drought and whitefly infestation using PacBio long reads.

Alternative splicing (AS) and alternative polyadenylation (APA) are common mechanisms in eukaryotes to increase the complexity of transcriptomes and subsequently proteomes. Analysis of long reads transcriptomics data can result in the discovery of novel transcripts, splice sites, AS or APA events. Gossypium arboreum is an important cultivated cotton species and a putative contributor of the A sub-genome to the modern tetraploid cotton; and inherently tolerant to several biotic and abiotic stresses. Specifically, its variety 'FDH228' is considered to be an important resistance source. In this study, we sequenced the G. arboreum (var. FDH228) transcriptome using PacBio IsoSeq and illumina short read sequencing under three different conditions i.e. untreated/healthy, treated with biotic stress through whitefly infestation, and treated with abiotic stress via water deprivation, for the discovery and surveying of canonical and non-canonical AS, APA and transcript fusion events. We were able to obtain 15,419 unique transcripts from all samples representing 11,343 genes, out of which 10,832 were annotated and 520 were novel with respect to the published reference genome. These transcripts were grouped into different structural categories including 60 Antisense, 11,959 having a full-splice match, 999 with incomplete-splice match, 30 fusion transcripts, 177 genic, 479 intergenic, 771 novels in the catalog, and 944 Novel but not found in the catalog. Subsequently, randomly selected candidate transcripts were experimentally validated using qRT-PCR. Our comprehensive identification of canonical and non-canonical splicing events, and novel and fusion transcripts aids in the understanding of the resistance mechanisms for this specific germplasm.

Establishment of Transcriptional Gene Silencing Targeting the Promoter Regions of GFP, PDS, and PSY Genes in Cotton using Virus-Induced Gene Silencing.

Virus-induced gene silencing (VIGS) by deploying viral-based vectors such as tobacco rattle virus (TRV) is a homology-based gene silencing technique in post-transcriptional gene silencing (PTGS) and transcriptional gene silencing (TGS) to validate the function of particular genes. The study presented here showed the induction of DNA methylation in the promoter regions of three phenotypic marker genes in different cotton accessions, including two endogenous genes such as phytoene desaturase (PDS) and phytoene synthase (PSY), and an exogenous gene, such as green fluorescent protein (GFP). First, DNA methylation was established in transgenic GFP cotton where methylation persisted up to S3 generation. Afterward, the promoter of PSY was targeted following the same conditions. Significant silencing of PSY was observed and methylation of the promoter was found up to S2 generation in red leaf cotton as detected in GFP cotton. Silencing of PDS resulted in a photobleaching phenotype; interestingly, the strength of this phenotype was diverse within the plants and was not observed in the next generation. Bisulfite sequencing results showed methylation percentage of the cytosine residues was high at CG and CHG sites of the targeted promoter sequences in the silenced plants. The findings of this paper suggest that TRV-based vector system can be used to monitor DNA methylation for both exogenous and endogenous gene levels in cotton and offer a very useful tool for plant epigenetic modification.

RELATIONSHIP BETWEEN NEGATIVE COGNITIVE STYLE AND DEPRESSION AMONG MEDICAL STUDENTS.

BACKGROUND: Depression is one of the major problems faced by medical students, which have significant adverse effects on their social, academic and occupational functioning. The objectives of the study were to estimate the prevalence of depression and to explore the gender differences and interrelationship between the depression and negative cognitive style among medical students of First year (FY) Last year (LY) MBBS. METHODS: A Cross sectional questionnaire based study was conducted in Ayub medical college Abbottabad; Khyber medical college Peshawar; Bannu medical college; Rawalpindi medical college; Punjab medical college Faisalabad and Allama Iqbal medical college Lahore, Pakistan. Applying stratified sampling technique a battery of questionnaires naming depression screening test, self-report depression scale and cognitive style questionnaire was filed by a sample of 1000 (first and last year) medical students. The data was analysed by SPSS 16. RESULTS: Positive relationship exists between depression and negative cognitive style (r = .57, p < .05) among medical students. Forty one percent male and 61% female students of FY and 58% males and 69% female of LY students exhibited depressive symptoms. Females have higher scores on cognitive style questionnaire t (998) = 3.70, p < .05, and depression t (998) = 4.28, p < .05. The t-test analysis also revealed that FY students were holding more negative cognitive style t (998) = 6.21, p < .05, whereas LY medical students to be more depressed t (998) = 5.43, p < .05. CONCLUSIONS: The study revealed significant distress among medical students. Negative cognitive style positively correlates with depression among medical students. Furthermore, it is noticed that among female students the prevalence of depressive symptoms and negative cognitive style was higher. Moreover, it is concluded that the prevalence of depression in LY and negative cognitive styles among FY was higher respectively. Students should be provided proper counselling to avoid and cope with faulty thought patterns leading to depression. Keywords: negative cognitive style, depression, gender.