Prospecting for scarabid specific Bacillus thuringiensis crystal toxin cry8 gene in sugarcane ecosystem of Tamil Nadu, India

In the present study, we report the occurrence of cry8 positive isolates of Bacillus thuringiensis (Bt) in selected white grub, Holotrichia serrata F. (Coleoptera: Scarabaeidae), endemic soils of sugarcane ecosystem and other places in Tamil Nadu. Out of the 66 soil samples collected and screened for white grub specific Bt, 74 isolates of the bacterium, all containing only spherical crystal toxin, were identified. PCR screening of these isolates with cry8 gene universal primer revealed six isolates to be positive. Further, the amplicon of a 370 bp band, amplified with another set of degenerate primer designed based on the conserved sequence of cry8 genes, was sequenced from four isolates. Multiple sequence alignment revealed the gene sequences to be the same for all the isolates. The present report of the availability of cry8 positive Bt isolates opens the avenue for controlling white grubs through transgenic research

South Africa's salt reduction strategy: Are we on track, and what lies ahead?

On 2 September 2016, 25 local and international participants from various sectors met in Cape Town to take stock of South Africa (SA)’s progress in salt reduction and develop a roadmap for action. SA is centre stage on salt reduction globally, being the first country to mandate salt reduction across a wide range of processed foods. Excessive salt intake contributed by processed foods and discretionary sources motivated SA to implement a public awareness campaign in parallel with legislation to reduce salt intake to the World Health Organization target of 5 g per day. Five priority areas were identified for continued action on salt reduction, including obtaining research funds for continued monitoring and compliance of salt reduction targets. Determining the contribution of foods eaten out of home to total salt intake and implementing strategies to address this sector were also highlighted as key actions. Lastly, implementing the next stage of the Salt Watch awareness campaign to change

Genome-Wide Tissue-Specific Occupancy of the Hox Protein Ultrabithorax and Hox Cofactor Homothorax in Drosophila

The Hox genes are responsible for generating morphological diversity along the anterior-posterior axis during animal development. The Drosophila Hox gene Ultrabithorax (Ubx), for example, is required for specifying the identity of the third thoracic (T3) segment of the adult, which includes the dorsal haltere, an appendage required for flight, and the ventral T3 leg. Ubx mutants show homeotic transformations of the T3 leg towards the identity of the T2 leg and the haltere towards the wing. All Hox genes, including Ubx, encode homeodomain containing transcription factors, raising the question of what target genes Ubx regulates to generate these adult structures. To address this question, we carried out whole genome ChIP-chip studies to identify all of the Ubx bound regions in the haltere and T3 leg imaginal discs, which are the precursors to these adult structures. In addition, we used ChIP-chip to identify the sites bound by the Hox cofactor, Homothorax (Hth). In contrast to previous ChIP-chip studies carried out in Drosophila embryos, these binding studies reveal that there is a remarkable amount of tissue- and transcription factor-specific binding. Analyses of the putative target genes bound and regulated by these factors suggest that Ubx regulates many downstream transcription factors and developmental pathways in the haltere and T3 leg. Finally, we discovered additional DNA sequence motifs that in some cases are specific for individual data sets, arguing that Ubx and/or Hth work together with many regionally expressed transcription factors to execute their functions. Together, these data provide the first whole-genome analysis of the binding sites and target genes regulated by Ubx to specify the morphologies of the adult T3 segment of the fly

Whole genome analysis and functional characterization of a novel Bacillus thuringiensis (Bt 62) isolate against sugarcane white grub Holotrichia serrata (F)

In this study, we report the whole genome assembly of Bt 62, a novel isolate harbouring cry8 holotype gene identified by us earlier. Sequencing was carried out using a combination of Illumina NextSeq 500 and Oxford Nanopore sequencing Technologies (ONT). The final assembled genome was 6.13 Mb comprising a circular chromosome and four plasmids. The bioassay studies against Holotrichia serrata (F.) (Coleoptera: Scarabaeidae), a polyphagous pest infesting sugarcane and other crops, indicated significant toxicity to first instar grubs over untreated larvae achieving a highest mean mortality of 91.11% for various doses tested. In vitro proteolytic assay and histopathological studies of the midgut of infected white grubs revealed proteolytic processing of the protoxin and extensive degeneration of larval midgut epithelial cells. The results demonstrate that this novel isolate could be used as a biopesticide or its crystal toxin genes could be expressed in sugarcane and other crops for resistance against H. serrata

Development and validation of real-time PCR screening methods for detection of cry1A.105 and cry2Ab2 genes in genetically modified organisms

Primers and probes were developed for the element-specific detection of cry1A.105 and cry2Ab2 genes, based on their DNA sequence as present in GM maize MON89034. Cry genes are present in many genetically modified (GM) plants and they are important targets for developing GMO element-specific detection methods. Element-specific methods can be of use to screen for the presence of GMOs in food and feed supply chains. Moreover, a combination of GMO elements may indicate the potential presence of unapproved GMOs (UGMs). Primer-probe combinations were evaluated in terms of specificity, efficiency and limit of detection. Except for specificity, the complete experiment was performed in 9 PCR runs, on 9 different days and by testing 8 DNA concentrations. The results showed a high specificity and efficiency for cry1A.105 and cry2Ab2 detection. The limit of detection was between 0.05 and 0.01 ng DNA per PCR reaction for both assays. These data confirm the applicability of these new primer-probe combinations for element detection that can contribute to the screening for GM and UGM crops in food and feed samples

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2–4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

Genetic mechanisms of critical illness in COVID-19.

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice