High-Quality Genome Resource of Ustilaginoidea virens (UV2_4G), Causal Agent of an Emerging False Smut Disease in Rice.

Ustilaginoidea virens is the fungal pathogen causing an emerging false smut disease that affects crop yield as well as deteriorates quality of the grains by producing mycotoxins. A high quality genome of U. virens isolate UV2_4G was sequenced using Nanopore and Illumina HiSeq 2,000 sequencing platforms. The total assembled genome of Indian isolate UV2_4G was 35.9 Mb, which comprised 89 scaffolds with N50 of 700,296 bp. A total of 358,697 variants were identified in the genome, out of which 355,173 were SNPs and 3,524 were INDELS. Further, 7,390 SSRs belonging to different repeat types were also identified in the genome. Out of 7,444 proteins predicted, 7,206 were functionally annotated. A total of 1,307 CAZymes, 501 signal peptides, 1,876 effectors, and 2,709 genes involved in host-pathogen interactions were identified. Comparative analysis revealed isolate UV2_4G is distinct with 31 unique clusters and placed distantly in phylogenetic analysis. Taken together, this high-quality genome assembly and sequence annotation resource can give an improved insight for characterizing the biological and pathogenic mechanisms of U. virens.

Transcriptomic analysis of bakanae disease resistant and susceptible rice genotypes in response to infection by Fusarium fujikuroi.

BACKGROUND: Fusarium fujikuroi causing bakanae is one of the most significant pathogens of rice and much responsible for yield losses thereby emerging as a major risk to food security. METHODS: In the present study transcriptomic analysis was conducted between two contrasting resistant (C101A51) and susceptible (Rasi) genotypes of rice with the combinations of C101A51 control (CC) vs. C101A51 inoculated (CI); Rasi control (RC) vs. Rasi inoculated (RI) and C101A51 inoculated (CI) vs. Rasi inoculated (RI). RESULTS: In CC vs. CI commonly expressed genes were 12,764. Out of them 567 (4%) were significantly upregulated and 1399 (9%) genes were downregulated. For the RC vs. RI 14, 333 (79%) genes were commonly expressed. For CI vs. RI 13,662 (72%) genes were commonly expressed. Genes related to cysteine proteinase inhibitor 10, disease resistance protein TAO1-like, oleosin 16 kDa-like, pathogenesis-related protein (PR1), (PR4), BTB/POZ and MATH domain-containing protein 5-like, alpha-amylase isozyme were upregulated in resistant genotype C101A51. Whereas, genes related to GDSL esterase/lipase, serine glyoxylate aminotransferase, CASP-like protein 2C1, WAT1-related protein, Cytoplasmic linker associated proteins, xyloglucan endotransglucosylase/hydrolase protein and ß-D xylosidase 7 were upregulated in susceptible genotype Rasi. Gene ontology analysis showed functions related to defence response (GO:0006952), regulation of plant hypersensitive type response (GO:0010363), Potassium ion transmembrane activity (GO:0015079), chloroplast (GO:0009507), response to wounding (GO:0009611), xylan biosynthetic process (GO:0045492) were upregulated in resistant genotype C101A51 under inoculated conditions. CONCLUSION: Real time PCR based validation of the selected DEGs showed that the qRT-PCR was consistent with the RNA-Seq results. This is the first transcriptomic study against bakanae disease of rice in Indian genotypes. Further, functional studies on identified genes and their utilization through different methodology will be helpful for the development of bakanae disease management strategies.

Hodgkin Lymphoma-related Vanishing Bile Duct Syndrome Cholestasis Resolved After Chemotherapy.

Vanishing bile duct syndrome is a rare paraneoplastic syndrome occasionally seen in pediatric Hodgkin lymphoma. It is usually regarded as a fatal disorder. Here, we present a case of vanishing bile duct syndrome cholestasis related to Hodgkin lymphoma that resolved after chemotherapy and radiation.

Transcriptome Reprogramming of Tomato Orchestrate the Hormone Signaling Network of Systemic Resistance Induced by Chaetomium globosum.

Chaetomium globosum is a potential biological control agent effective against various plant pathogens. Several reports are available on the mycoparastism and antibiosis mechanisms of C. globosum against plant pathogenic fungi, whereas a few states induced resistance. The potential induced defense component of C. globosum (Cg-2) was evaluated against early blight disease of tomato (Solanum lycopersicum) and further, global RNA sequencing was performed to gain deep insight into its mechanism. The expression of marker genes of hormone signaling pathways, such as PR1, PiII, PS, PAL, Le4, and GluB were analyzed using real-time quantitative reverse transcription PCR (qRT-PCR) to determine the best time point for RNA sequencing. The transcriptome data revealed that 22,473 differentially expressed genes (DEGs) were expressed in tomato at 12 h post Cg-2 inoculation as compared with control plants and among these 922 DEGs had a fold change of -2 to +2 with p < 0.05. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that most of the DEGs were belonging to metabolic pathways, biosynthesis of secondary metabolites, plant-pathogen interaction, chlorophyll metabolism, and plant hormone signal transduction. Gene Ontology (GO) analysis revealed that DEGs were enriched mainly related to binding activity (GO:0005488), catalytic activity (GO:0003824), metabolic process (GO:0008152), cellular process (GO:0009987), response to stimulus (GO:0050896), biological regulation (GO:0065007), and transcription regulator activity (GO:0140110). The gene modulations in hormone signaling transduction, phenylpropanoid biosynthesis, and mitogen-activated protein kinases (MPK) signaling indicated the upregulation of genes in these pathways. The results revealed active participation of jasmonic acid (JA) and salicylic acid (SA) signaling transduction pathways which further indicated the involvement of induced systemic resistance (ISR) and systemic acquired resistance (SAR) in the systemic resistance induced by Cg-2 in tomato.

Molecular Programming of Drought-Challenged Trichoderma harzianum-Bioprimed Rice (Oryza sativa L.).

Trichoderma biopriming enhances rice growth in drought-stressed soils by triggering various plant metabolic pathways related to antioxidative defense, secondary metabolites, and hormonal upregulation. In the present study, transcriptomic analysis of rice cultivar IR64 bioprimed with Trichoderma harzianum under drought stress was carried out in comparison with drought-stressed samples using next-generation sequencing techniques. Out of the 2,506 significant (p < 0.05) differentially expressed genes (DEGs), 337 (15%) were exclusively expressed in drought-stressed plants, 382 (15%) were expressed in T. harzianum-treated drought-stressed plants, and 1,787 (70%) were commonly expressed. Furthermore, comparative analysis of upregulated and downregulated genes under stressed conditions showed that 1,053 genes (42%) were upregulated and 733 genes (29%) were downregulated in T. harzianum-treated drought-stressed rice plants. The genes exclusively expressed in T. harzianum-treated drought-stressed plants were mostly photosynthetic and antioxidative such as plastocyanin, small chain of Rubisco, PSI subunit Q, PSII subunit PSBY, osmoproteins, proline-rich protein, aquaporins, stress-enhanced proteins, and chaperonins. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis states that the most enriched pathways were metabolic (38%) followed by pathways involved in the synthesis of secondary metabolites (25%), carbon metabolism (6%), phenyl propanoid (7%), and glutathione metabolism (3%). Some of the genes were selected for validation using real-time PCR which showed consistent expression as RNA-Seq data. Furthermore, to establish host-T. harzianum interaction, transcriptome analysis of Trichoderma was also carried out. The Gene Ontology (GO) analysis of T. harzianum transcriptome suggested that the annotated genes are functionally related to carbohydrate binding module, glycoside hydrolase, GMC oxidoreductase, and trehalase and were mainly upregulated, playing an important role in establishing the mycelia colonization of rice roots and its growth. Overall, it can be concluded that T. harzianum biopriming delays drought stress in rice cultivars by a multitude of molecular programming.

A Review of Methods for Monitoring Adverse Events in Pediatric Psychopharmacology Clinical Trials.

Pediatric psychotropic prescription rates are rising, emphasizing the need for careful monitoring of drug safety in this population. Currently, no standardized assessments are used in clinical trials for adverse event (AE) elicitation focused on long-term drug treatment in pediatric patients. Despite a lack of standardized AE elicitation methods in psychiatric clinical trials, it is clear that psychiatric medications have developmentally dependent AEs that differ from those observed in adults. In this review, we discuss the use of general inquiry elicitation, drug-specific checklists, and systematic elicitation scales for AE reporting in pediatric psychopharmacology trials. The checklists evaluated include the Barkley Side Effect Rating Scales (SERS), the Pittsburg side effect rating scale, and the Systematic Monitoring of Adverse events Related to TreatmentS (SMARTS) checklist. The systematic assessment scales discussed include the Systematic Assessment for Treatment of Emergent Events (SAFTEE) and the Safety Monitoring Uniform Report Form (SMURF). We review the advantages and disadvantages of each method and discuss the need for optimal assessment of AEs. AE instruments that are created and utilized for pediatric psychiatric trials must begin to incorporate symptoms that are relevant to this population and account for the nature of the disorders to better characterize treatment-emergent AEs and monitor long-term safety.

Structural and functional alterations in photosynthetic apparatus of plants under cadmium stress.

Cadmium is a potentially toxic heavy metal that hampers plant productivity by interfering with their photochemistry. Cd causes disturbances in a range of physiological processes of plants such as photosynthesis, water relations, ion metabolism and mineral uptake. Cd pronouncedly affects photosynthesis by alteration of its vital machinery in all aspects. Photosynthesis is a well organised and sequential process fundamental to all green plants and microorganisms which involves various components, including photosynthetic pigments and photosystems, the electron transport system and CO2 reduction pathways. Any damage at any level caused by Cd, critically affects overall photosynthetic capacity. Present review focuses on key effects of Cd on photosynthetic apparatus including chloroplast structure, photosynthetic pigments, Chl-protein complexes and photosystems resulting in overall decrease in efficiency of carbon assimilation pathway.

High resistance to antiretroviral drugs: the Indian experience.

Effective antiretroviral treatment (ART) has significantly reduced the morbidity and mortality among people living with HIV/AIDS. The emergence of drug resistance is the major obstacle to the successful implementation of long-term treatment strategy of HIV disease. Hence, monitoring the resistance to ART is an essential task. The MGM Medical College in Navi Mumbai is the only national facility with the capacity to monitor ART resistance using tissue culture technique. The main objective of the study was to determine the prevalence of primary and secondary resistance between May 1997 and April 2003. Four hundred and sixty viral isolates of 74 individuals were tested for ART resistance using tissue culture-based protocol (McGill University, Canada). These included 287 primary and 173 follow-up viral isolates. Following activation of tissue culture, a panel of 12 antiretroviral drugs in concentrations from 0.038 mg/mL to 0.090 mg/mL was tested. The resistance was determined on the basis of the production of p24 antigen at the end of 72 and 144 hours of incubation. The overall resistance against reverse transcriptase inhibitors (RTIs) was 33.7% and that to protease inhibitors (PIs) was 21.5%. However, prevalence of primary resistance among ART näive to RTIs was 14/208 (6.7%) of isolates and that to (PIs) was 2/79(2.5%) of isolates. The incidence of resistance to RTI was 22/500 years (4.4/100 years) and that to PIs was 8/253.6 years (3.2/100 years). It is possible that non-B subtypes of HIV-1 that are prevalent in most developing countries are likely to develop resistance rapidly after ART. However, common factors that influence development of resistance such as poor adherence, inadequate 'wild' doses and regimens, and poor monitoring were not validated in the study. Unless active surveillance is instituted, these factors can pose major challenge for the management of people on ART in developing countries.