Genome-Wide Expression Profiling of Small RNAs in Indian Strain of Rhizoctonia solani AG1-1A Reveals Differential Regulation of milRNAs during Pathogenesis and Crosstalk of Gene Regulation

Rhizoctonia solaniAG1-1A is a necrotrophic fungus that causes sheath blight disease in rice. The reliable resistant source against this phytopathogenic fungus is not available in the gene pool of rice. Better understanding of pathogen genomics and gene regulatory networks are critical to devise alternate strategies for developing resistance against this noxious pathogen. In this study, miRNA-like RNAs (milRNAs) of an Indian strain of R. solani were identified by deep sequencing of small RNAs. We identified 128 known and 22 novel milRNAs from 20,963,123 sequence reads. These milRNAs showed 1725 target genes in the fungal genome which include genes associated with growth, development, pathogenesis and virulence of R. solani. Notably, these fungal milRNAs showed their target genes in host (rice) genome also which were later verified by qRT-PCR. The host target genes are associated with auxin metabolism, hypersensitive response, defense genes, and genes related to growth and development of rice. Osa-vacuolar-sorting receptor precursor: Rhi-milR-13, Osa-KANADI1:Rhi-milR-124, Osa-isoflavone reductase: Rhi-milR-135, Osa-nuclear transcription factor Y:Rhi-milR-131, Osa-NB-ARC domain containing protein: Rhi-milR-18, and Osa-OsFBX438: Rhi-milR-142 are notable potential regulons of host target genes: fungal milRNAs that need to be investigated for better understanding of the crosstalk of RNAi pathways between R. solani and rice. The detailed expression analysis of 17 milRNAs by qRT-PCR was analysed during infection at different time points of inoculation, at different growth stages of the host, in four different genotypes of the host, and also in four different strains of fungi which revealed differential regulation of milRNAs associated with pathogenesis and virulence. This study highlights several important findings on fungal milRNAs which need to be further studied and characterized to decipher the gene expression and regulation of this economically important phytopathogen.

Influence of COVID-19 on the poultry production and environment

Although chickens are not susceptible to SARS-CoV-2, several coronavirus disease outbreaks have been described concerning poultry processing facilities in different countries. The COVID-19 pandemic and the developed strain caused 2nd, 3rd, and recent Indian strain waves of epidemics that have led to unexpected consequences, such as forced reductions in demands for some industries, transportation systems, employment, and businesses due to public confinement. Besides, poultry processing plants' conditions exacerbate the risks due to the proximity on the line, cold, and humidity. Most workers do not have access to paid sick time or adequate health care, and because of the low wages, they have limited reserves to enable them to leave steady employment. In addition, workers in meat and poultry slaughterhouses may be infected through respiratory droplets in the air and/or from touching dirty surfaces or objects such as workstations, break room tables, or tools. Egg prices have increased dramatically during the lockdown as consumers have started to change their behaviors and habits. The COVID pandemic might also substantially impact the international poultry trade over the next several months. This review will focus on the effect of COVID-19 on poultry production, environmental sustainability, and earth systems from different process points of view.

Breakthrough COVID-19 infection rate with Indian strain in Single-center Healthcare Workers: A real world data.

Introduction: It is observed that many healthcare workers got COVID19 infection despite of completing both doses of Covishield vaccine. This study aimed to find real incidence of vaccine breakthrough infection. Material and methods: All hospital employees, who were fully vaccinated were included in study. Details about their vaccine side effects, infection prior to vaccination, post vaccination infection, severity of infection, hospital and ICU admission were noted. Results: None encountered any significant side effects of vaccine. Of the 461 participants, 86 (18.65%) got infection average 38 days (range 14 to 70days) after vaccination. As per the NIH classification, out of 86, disease was mild in 69(80.2%), moderate in 10(11.62%), severe in 6(6.97%) and critical in 1(1.16%). Of these, 10(11.62%) required hospital admission. Of these 10, 2 were shifted to ICU. Of the 2, One recovered while one died. Thus mortality was 1/86(1.6%). Conclusion: Breakthrough infection rate in health care workers was 18.65%. Moderate, severe or critical disease occurred in 19.7% participants even after two doses of vaccine. Mortality due to disease cannot be completely obviated due to vaccine. The vaccine was safe without any significant adverse events.

Redescription and synonymization of Oscheius citri Tabassum, Shahina, Nasira and Erum, 2016 (Rhabditida, Rhabditidae) from India and its taxonomical consequences

A population of a nematode species belonging to the genus Oscheius was isolated in western Uttar Pradesh, India. Morphological and morphometrical studies on this species showed its high similarity with six species described previously from Pakistan (Oscheius citri, O. cobbi, O. cynodonti, O. esculentus, O. punctatus and O. sacchari). The molecular analysis of the ITS1-5.8S-ITS2 rDNA sequences of the Indian population and the six species described from Pakistan showed that all the sequences are almost identical. Thus, based on morphological and molecular characteristics, all of the six above-mentioned Pakistani species and Indian strain do not differ from each other, hence can be considered synonyms. The correct name for this taxon is the first described species O. citri. Additionally, the phylogenetic analysis of the 18S rDNA and the 28S rDNA sequences showed that Oscheius citri is sister to the clade formed by O. chongmingensis and O. rugaoensis from China. The high similarity of morphological and morphometric characteristics of O. citri and other species, O. maqbooli, O. nadarajani, O. niazii, O. shamimi and O. siddiqii, suggest their conspecificity; however, lack of molecular data for these species does not allow this hypothesis to be tested.

The Frequency of G614 SARS-CoV-2 Variant in India

As reported by us and others previously (1, 2), the D614G mutation appeared in the spike glycoprotein (SPG) of the SARS-CoV-2 (the pathogen behind COVID-19) at the early stages of the pandemic and then G614 containing variant of SARS-CoV-2 became the predominant strain in most human populations across the world. However, one of the most recent reports from India (3) stated the incidence of G614 to be only 26% in the Indian population. This report is contradictory to the information available through the GenBank (4) SARS-CoV-2 sequence deposits made by various laboratories from India. The above stated report currently circulating in the Indian media is likely to create a public perception that the Indian strain is less contagious and such a notion could be harmful to people’s welfare. In view of this concern we have re-evaluated, updated and recalculated the incidence of the G614 variant in the Indian population by analyzing 395 Indian SARS-CoV-2 genomic sequences available in the GenBank as of June 26, 2020. In our analysis we have categorized the samples by the month in which the samples were collected. We have used an alignment-free software tool named Compare (5, 6), and the Basic Local Alignment Search Tool (BLAST) (7) in the present analysis. We finally inspected each of the 395 sequences physically for the presence of aspartic acid (D) or glycine (G) at the 614th position of the spike glycoprotein. We analyzed an Australian cohort in parallel for comparison. We have found that the prevalence of G614 variant in the Indian samples for the month of June 2020 is 90.6%. The trends are similar with the Australian samples.

Reaction of Indian Chicks to Klebsiella Pneumoniae Strain Borkar, a Plant Pathogen Causing Pneumonia in Plants

Klebsiella pneumoniae is emerging as an important bacterial plant pathogen in Asia region particularly in China and India. The Chinese strain of Klebsiella pneumoniae causing top rot of maize is reported to be pathogenic on mice also. The Indian strain of Klebsiella pneumoniae causing root bark necrosis and wilt in pomegranate is found non- pathogenic on Indian bird chicken, thereby indicating it to be plant host specific.

A rational drug designing: What bioinformatics approach tells about the wisdom of practicing traditional medicines for screening the potential of Ayurvedic and natural compounds for their inhibitory effect against COVID-19 Spike, Indian strain Spike, Papain-like protease and Main Protease protein

The new outbreak of Coronavirus disease (COVID-19) has been entitled as a pandemic by W.H.O. It spreads to almost 211 countries due to its contagious nature. There is an urgent need for developing specific therapeutic agents against COVID-19. We have performed virtual screening of 52 ligands; most of which are essential components of traditional Ayurvedic medicine as well as natural compounds and three were standard repurposing drugs against COVID-19 Spike, Indian strain Spike (IS-Spike), PL-Pro and M-Pro to find potential inhibitor effects. Based on the docking results, it is estimated that compounds have a better binding affinity with M-Pro and PL-Pro than Spike as well as IS-Spike so it can be beneficial as therapeutics against COVID-19. We also conclude that the binding affinity of ligands with IS-Spike gets low as compared to Spike so the inhibitory potential of drugs may get weak. Based on the calculation of average binding energy (B.E) with the three targets, Spike, PL-Pro, and M-Pro, we found10 best ligands viz. (1) Punicafolin (2) Emblicanin A (3) Punigluconin (4) Lopinavir (5) Kuwanon X (6) Rutin (7) Lithospermic Acid (8) Phyllanemblinin A (9) Amarogentin and (10) Amaroswerin for inhibition. These ligands may act as potential inhibitors against COVID-19 druggable tri-targets. Network analysis revealed that four ligands out of 10 leading compounds are common in all four different networks (Spike, IS-Spike, PL-Pro, and M-Pro) which come under Phyllanthus emblica. Notably, a compound of Azadirachta indica out of 4 and a single compound of Swertia chirata was found common in all networks. Additionally, a standard drug Lopinavir and a compound of Salvia miltiorrhiza are frequently found in all networks. In principle, it appears plausible that the compounds which are common in the entire network should have more inhibitory potential against COVID19 due to the better binding potential among all targets, thus providing better candidacy for drug development.