Conditional RNA interference (RNAi) enables spatial and/or temporal control over gene silencing. The currently available methods require coexpression of engineered proteins and/or modified promoters which may limit their applications. We designed a novel RNA architecture that combines a drug-inducible allosteric ribozyme with a microRNA precursor analogue that allows chemical induction of RNAi in mammalian cells. The compact and highly modular RNA design should facilitate the construction of conditional RNAi systems that can sense and respond to a variety of molecules recognized by RNA aptamers to regulate virtually any desired genes sensitive to RNAi.

Allosteric hammerhead ribozymes (aptazymes) that are activated by guanine were used to control mammalian gene expression in cis and in trans. Coexpression of the two mechanistically distinct riboswitches resulted in an improved dynamic range of gene expression.

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Chemically inducible RNA interference (RNAi) enables temporal and/or spatial control of virtually any gene, making it useful for study of gene functions, discovery of potential drug targets, and gene therapy applications. Here we describe a new inducible RNAi platform in which orthogonal chemically modified oligonucleotides are used to trigger silencing of two genes in a combinatorial manner. We developed a modular RNA architecture consisting of an oligonucleotide sensor stem-loop and an RNAi effector domain that is designed to undergo a structural shift upon addition of an oligonucleotide inducer. The induced structural change allows the RNA to be processed by the RNAi machinery, ultimately resulting in gene silencing of the target encoded by the RNAi effector module. Combinatorial regulation of multiple genes should accelerate studies of complex gene-gene interactions and screening of new drug targets.

We recently developed a database for hexaploid wheat QTL (WheatQTLdb; www.wheatqtldb.net) that included 11,552 QTL affecting various traits of economic importance. However, that database did not include valuable QTL from other wheat species and/or progenitors of bread wheat. Therefore, an updated and wider version of wheat QTL database (WheatQTLdb V2.0) was developed in this study which now includes information on hexaploid wheat (Triticum aestivum) as well as seven other related species: T. durum, T. turgidum, T. dicoccoides, T. dicoccum, T. monococcum, T. boeoticum, and Aegilops tauschii. WheatQTLdb V2.0 includes a much improved list of QTL, so that V2.0 now has 27,518 main-effect QTL, 202 epistatic QTL, and 1,321 metaQTL. This newly released WheatQTLdb V2.0 will provide plant breeders and geneticists much more valuable options to search and choose the category-wise and trait-wise data for their research or breeding programmes.

Root lesion nematode (RLN; Pratylenchus thornei) causes extensive yield losses in wheat worldwide and thus pose serious threat to global food security. Reliance on fumigants (such as methyl bromide) and nematicides for crop protection has been discouraged due to environmental concerns. Hence, alternative environment friendly control measures like finding and deployment of resistance genes against Pratylenchus thornei are of significant importance. In the present study, genome-wide association study (GWAS) was performed using single-locus and multi-locus methods. In total, 143 wheat genotypes collected from pan-Indian wheat cultivation states were used for nematode screening. Genotypic data consisted of  > 7K SNPs with known genetic positions on the high-density consensus map was used for association analysis. Principal component analysis indicated the existence of sub-populations with no major structuring of populations due to the origin. Altogether, 25 significant marker trait associations were detected with − log10 (p value) > 4.0. Three large linkage disequilibrium blocks and the corresponding haplotypes were found to be associated with significant SNPs. In total, 37 candidate genes with nine genes having a putative role in disease resistance (F-box-like domain superfamily, Leucine-rich repeat, cysteine-containing subtype, Cytochrome P450 superfamily, Zinc finger C2H2-type, RING/FYVE/PHD-type, etc.) were identified. Genomic selection was conducted to investigate how well one could predict the phenotype of the nematode count without performing the screening experiments. Prediction value of r = 0.40 to 0.44 was observed when 56 to 70% of the population was used as a training set. This is the first report where GWAS has been conducted to find resistance against root lesion nematode (P. thornei) in Indian wheat germplasm.

The genus Rotavirus comprises eight species, designated A to H, and two recently identified tentative species I in dogs and J in bats. Species Rotavirus A, B, C and H (RVA, RVB, RVC and RVH) have been detected in humans and animals. While human and animal RVA are well characterized and defined, complete porcine genome sequences in the GenBank are limited compared to human strains. Here, we used a metagenomic approach to sequence the 11 segments of RVA, RVC and RVH strains from piglets in the United States (US) and explore the evolutionary relations of these RV species. Metagenomics identified Astroviridae, Picornaviridae, Caliciviridae, Coronoviridae in samples MN9.65 and OK5.68 while Picobirnaviridae and Arteriviridae were only identified in sample OK5.68. Whole genome sequencing and phylogenetic analyses identified multiple genotypes with the RVA of strain MN9.65 and OK5.68, with the genome constellation of G5/G9-P[7]/P[13]-I5/I5- R1/R1-C1-M1-A8-N1-T7-E1/E1-H1 and G5/G9-P[6]/P[7]-I5-R1/R1-C1-M1-A8-N1-T1/T7-E1/E1-H1, respectively. The RVA strains had a complex evolutionary relationship with other mammalian strains. The RVC strain OK5.68 had a genome constellation of G9-P[6]-I1-R1-C5-M6-A5-N1-T1-E1-H1, and shared an evolutionary relationship with porcine strains from the US. The RVH strains MN9.65 and OK5.68 had the genome constellation of G5-P1-I1-R1-C1-M1-A5-N1-T1-E4-H1 and G5-P1-I1-R1-C1-M1-A5-N1-T1-E1-H1, indicating multiple RVH genome constellations are circulating in the US. These findings allow us to understand the complexity of the enteric virome, develop improved screening methods for RVC and RVH strains, facilitate expanded rotavirus surveillance in pigs, and increase our understanding of the origin and evolution of rotavirus species.

A distinct Russian Mammalian orthorubulavirus 5 (PIV5) was detected in cell culture exhibiting cytopathic effect and hypothesized to be contaminated by a scientist with respiratory symptoms. The identification of the divergent strain indicated a lack of knowledge on the diversity of PIV5 strains and calls for surveillance of global PIV5 strains.