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S-nitrosylation is a well-known post-translational modification that modulates nitric oxide-dependent cell signaling. NADH-dependent S-nitrosoglutathione reductase (GSNOR) and NADPH-dependent thioredoxin reductase (NTR) enzymes are essential for nitric oxide/S-nitrosothiol (NO/SNO) homeostasis. GSNOR and NTR regulate denitrosylation by reducing S-nitrosoglutathione (GSNO) and thioredoxins, respectively. Genome-wide identification yielded 4 GSNOR and 12 NTR (4 each of NTRA, NTRB, and NTRC) genes in Brassica juncea. Syntenic relationship showed whole genome triplication (WGT) and tandem duplications. The phylogenetic analysis revealed clustering of BjGSNORs and BjNTRs with Arabidopsis homologs suggesting high sequence similarity within groups. Subcellular localization prediction suggested BjGSNOR localizes not only to the cytosol, but also to the Golgi apparatus and endoplasmic reticulum. BjNTRA and BjNTRB were localized in the cytoplasm and mitochondria, respectively, whereas BjNTRC localized in the chloroplast and nucleus. Several cis-acting elements involved in light responsiveness and expression analysis suggested the regulation of denitrosylation by light. The analysis of the promoter region also showed various phytohormone-regulated elements, suggesting the involvement of these enzymes in plant growth. Furthermore, GSNOR and NTR activities were higher in early growth stages. Differential spatial distributions of both the enzymes were observed with higher activity in hypocotyl in comparison with roots and cotyledons of the seedling. In flower, the highest activities were observed in carpel and least in stamens. Collectively, these findings provide an understanding of the structure, localization, and evolution of multiple copies of denitrosylases BjGSNOR and BjNTR, along with their possible roles in plant development. [ABSTRACT FROM AUTHOR]

The Coronavirus Disease 2019 (COVID-19) spread rapidly from China to most other countries around the world in early 2020 killing millions of people. To prevent virus spread, world governments implemented a variety of response measures. This paper's objectives were to discuss the country's adopted measures to combat the virus through June 2020, identify gaps in the measures' effectiveness, and offer possible mitigations to those gaps. The measures taken included screening device deployment across international air and land ports, flight suspensions and closures from COVID-19 affected countries, and declaration and extension of a national public holiday (equivalent to lockdowns in other countries). Identified gaps were test kit, PPE, ICU beds, and ventilator shortages, limited public awareness, and insufficient coordination and collaboration among national and international partners. Proper and timely risk mapping, preparedness, communication, coordination, and collaboration among governments and organizations, and public awareness and engagement would have provided sufficient COVID-19 mitigation in Bangladesh. [ABSTRACT FROM AUTHOR]

Commonly, environmental processes are observed across different locations, and observations present skewed distributions. Recent proposals for analyzing data in their original scale, accommodating spatial structure and skewness, involve two independent Gaussian processes (GP). We focus on a skewed spatial process defined through a convolution of Gaussian and log Gaussian (GLGC) processes. Because of the inclusion of two GPs, the inference procedure quickly becomes challenging as the sample size increases. We aim to investigate how recently developed approximate GPs perform in modeling high-dimensional GLGC processes. Three methods are formulated based on the nearest neighbor (NN) and Hilbert space (HS) methods, and their performances are investigated in comparison with the exact inference using simulation studies. All the approximate methods yield results comparable to exact inference, but the HS-based method provides the fastest inference of moderate to very smooth processes. A hybrid approach incorporating NN and HS methods is preferred for faster inference with improved MCMC efficiency for a wiggly process.Supplementary materials accompanying this paper appear online. [ABSTRACT FROM AUTHOR]

Northeast India, Nepal, Bhutan, and Bangladesh form a continuum of 11.55 million hectare wheat growing area with similar production situations. Additionally, wheat cultivation in some of the traditional rice growing areas of far Northeast India has started only few years ago. To explore the virulence structure of Puccinia triticina, these areas were surveyed for the first time. Virulence analyses of P. triticina populations have revealed the occurrence of five new pathotypes in these areas. Pathotypes 20 − 1 (93R57 = NHKTL), 49 (93R49 = NHKTN), 52 − 3 (121R60 = MHKTN) were identified from Northeast India, 143 (61R47 = KHTPM) from Nepal and 10 − 1 (56R27 = SGJPN) from Bangladesh. These pathotypes are quite diverse in their virulence on leaf rust resistance genes. For identifying rust resistance sources, a set of 600 wheat lines containing predominant cultivars, pipeline material and Near Isogenic Lines (NILs), was evaluated at the seedling stage against the new and closely related previously documented pathotypes under greenhouse conditions. Seventy one wheat lines were resistant to all new pathotypes. Leaf rust resistance genes Lr1, Lr3a, Lr10, Lr11, Lr14a, Lr15, Lr16, Lr17, Lr20, Lr23, and Lr26 occurring in Indian wheat cultivars were ineffective to most of the new pathotypes. In contrast Lr9, Lr19, Lr24, Lr25, Lr28, Lr32, Lr39, Lr45, and Lr47 were effective against these pathotypes. Based on the 25 pairs of SSR primers, these pathotypes were found distinct and broadly categorized into two groups. [ABSTRACT FROM AUTHOR]

Salmonella is a globally distributed major food-borne pathogen and poultry is one of the predominant sources of salmonellosis in humans. To investigate the presence of motile Salmonella in the poultry hatchery environment, we collected 97 fluff samples from four selected broiler breeder chicken hatcheries from Chattogram, Bangladesh during July-December 2015. To isolate motile Salmonella enterica, we used conventional bacteriological techniques followed by serological verification using anti-Salmonella Poly A-E serum and species confirmation by conventional PCR assay. Antimicrobial susceptibility testing by Kirby-Bauer disc diffusion method for 10 commonly used antibiotics was performed on all isolates. Isolates displaying phenotypic resistance to ampicillin were tested by PCR for blaTEM gene, whereas those resistant to tetracycline were tested for the presence of tetA, tetB and tetC genes. A total of 24 samples (24.7%; 95% CI: 16.5–34.5, N = 97) from 3 hatcheries were positive for motile Salmonella. Of them, 21 (87.5%) and 12 (50.0%) were resistant to ampicillin and tetracycline, respectively, 9 (37.5%) to nalidixic acid and sulphamethoxazole/trimethoprim. No resistance was detected to ceftriaxone, cefoxitin, gentamicin, neomycin, ciprofloxacin and colistin. Ten (42%) of 24 isolates from 2 hatcheries were multi-drug resistant (i.e. resistant to ≥ 3 antimicrobial classes). Six of 21 ampicillin resistant isolates contained blaTEM gene and 10 of 12 tetracycline resistant isolates contained tetA gene. This study highlights the circulation of multi-drug resistant motile Salmonella in the hatchery environment for the first time in Bangladesh. Further epidemiological and molecular studies are therefore needed to identify the serotypes and source of the bacteria in hatcheries. [ABSTRACT FROM AUTHOR]

Live animal markets are known hotspots of zoonotic disease emergence. To mitigate those risks, we need to understand how networks shaped by trading practices influence disease spread. Yet, those practices are rarely recorded in high-risk settings. Through a large cross-sectional study, we assessed the potential impact of live poultry trading networks' structures on avian influenza transmission dynamics in Bangladesh. Networks promoted mixing between chickens sourced from different farming systems and geographical locations, fostering co-circulation of viral strains of diverse origins in markets. Viral transmission models suggested that the observed rise in viral prevalence from farms to markets was unlikely explained by intra-market transmission alone, but substantially influenced by transmission occurring in upstream network nodes. Disease control interventions should therefore alter the entire network structures. However, as networks differed between chicken types and city supplied, standardised interventions are unlikely to be effective, and should be tailored to local structural characteristics. [ABSTRACT FROM AUTHOR]

A nursery comprising 25 elite bread wheat genotypes were evaluated to identify the sources of resistance to wheat blast caused by Magnaporthe oryzae pathotype Triticum (MoT), under artificial and natural infection experiments in three consecutive years from 2018 to 2020 in two different locations of Bangladesh. Seedling evaluation results revealed the absence of resistant and most genotypes displayed moderately susceptible to susceptible reaction. In the adult-plant field testing, six genotypes namely Borlaug 100, BARI Gom 33, BAW 1272, BAW 1280, BAW 1286, and BAW 1297 consistently showed resistant response to wheat head blast (WHB) infection with low levels of disease severity ranging from 0.2 to 8.1%. Among the remaining genotypes, some were moderately resistant, and the others exhibited various levels of susceptibility. The resistant genotypes that were most promising showed good agronomic performance under inoculated field trials. A significant positive correlation was observed between seedling and adult plant resistance. The above mentioned six genotypes also showed resistant reaction to WHB infection under controlled conditions when tested with three selected MoT isolates. The presence of 2NS/2AS translocation conferring WHB resistance was confirmed in four of the tested genotypes. Three (BAW 1272, BAW 1286, and BAW 1297) lines having non-2NS background exhibited good blast resistance under both the field and controlled conditions. These results will be useful for breeders and pathologists in exploiting the 2NS and non-2NS based resistant sources to pyramid and develop broad genetic based resistant germplasm. [ABSTRACT FROM AUTHOR]

Magnaporthe oryzae pathotype Triticum (MoT) was shown for the first time to cause barley blast in Bangladesh after distinct partially or fully bleached heads were observed in barley fields in Jashore and Meherpur in April 2019. The fungus isolated from diseased spikes was identified as Magnaporthe oryzae based on conidial morphology. MoT was confirmed based on results of ITS sequencing and a MoT3-specific molecular marker assay. Symptoms identical to those in the field were developed on leaves and spikes inoculated with the isolate. [ABSTRACT FROM AUTHOR]

Key message: BjuWRR1, a CNL-type R gene, was identified from an east European gene pool line of Brassica juncea and validated for conferring resistance to white rust by genetic transformation. White rust caused by the oomycete pathogen Albugo candida is a significant disease of crucifer crops including Brassica juncea (mustard), a major oilseed crop of the Indian subcontinent. Earlier, a resistance-conferring locus named AcB1-A5.1 was mapped in an east European gene pool line of B. juncea—Donskaja-IV. This line was tested along with some other lines of B. juncea (AABB), B. rapa (AA) and B. nigra (BB) for resistance to six isolates of A. candida collected from different mustard growing regions of India. Donskaja-IV was found to be completely resistant to all the tested isolates. Sequencing of a BAC spanning the locus AcB1-A5.1 showed the presence of a single CC-NB-LRR protein encoding R gene. The genomic sequence of the putative R gene with its native promoter and terminator was used for the genetic transformation of a susceptible Indian gene pool line Varuna and was found to confer complete resistance to all the isolates. This is the first white rust resistance-conferring gene described from Brassica species and has been named BjuWRR1. Allelic variants of the gene in B. juncea germplasm and orthologues in the Brassicaceae genomes were studied to understand the evolutionary dynamics of the BjuWRR1 gene. [ABSTRACT FROM AUTHOR]

Anther and tapetum-specific genes are important for understanding male gametophyte development, as well as for their use in the development of barnase/barstar-gene based male sterility and restorer system for hybrid seed production. An essential component of the system is the availability of tapetum-specific promoters. In the present study, anther-specific genes were identified in cotton using microarray-based differential expression analysis, some of which show expression specific to the anthers at a stage where tapetum tissue was fully developed. Validation of the identified genes using RT-PCR and in situ hybridization identified one novel gene (AEG—Anther Expressing Gene) encoding a putative lipid binding protein as having a tapetum-specific expression. Further, three paralogs of the gene were identified in the cotton genome out of which the gene AEG1 (Anther Expressing Gene1) was found to express in the tapetum layer. Analysis of transgenic plants developed in cotton using 1.5 Kb promoter region of the of AEG1 gene fused upstream to the reporter gene β-glucuronidase revealed a broad window of expression of the AEG1 promoter in the tapetum tissue from the tetrad stage of anthers till the degeneration of the tapetum cells. Low levels of expression were also observed in the root tissues. Expression was not observed in the stem and leaves. The broad window of expression of AEG1 promoter in the tapetum tissue makes it a suitable candidate for the expression of the barstar gene for effective fertility restoration in the barnase/barstar system. [ABSTRACT FROM AUTHOR]

Key message: Genetic locus for tetralocular ovary ( tet - o ) in Brassica rapa was identified and it was shown that the number of locules and width of silique are associated. Abstract: Brassica rapa is a highly polymorphic species containing many vegetables and oleiferous types. An interesting group of oleiferous types is the yellow sarson group (subspecies trilocularis) grown mostly in eastern India. This group contains lines that have bilocular ovaries, a defining trait of Brassicaceae, but also lines that have tetralocular ovaries. Yellow sarson lines commonly have high silique width which is further enhanced in the tetralocular types. We mapped the locus influencing tetralocular ovary in B. rapa using three mapping populations (F, F and F) derived from a cross between Chiifu (subspecies pekinensis, having bilocular ovary) and Tetralocular (having tetralocular ovary). QTL mapping of silique width was undertaken using the three mapping populations and a F population derived from a cross between Chiifu and YSPB-24 (a bilocular line belonging to yellow sarson group). Qualitative mapping of the trait governing locule number ( tet- o) in B. rapa mapped the locus to linkage group A4. QTL mapping for silique width detected a major QTL on LG A4, co-mapping with the tet- o locus in bilocular/tetralocular cross. This QTL was not detected in the bilocular/bilocular cross. Saturation mapping of the tet- o region with SNP markers identified Bra034340, a homologue of CLAVATA3 of Arabidopsis thaliana, as the candidate gene for locule number. A C → T transition at position 176 of the coding sequence of Bra034340 revealed co-segregation with the tetralocular phenotype. The study of silique related traits is of interest both for understanding evolution under artificial selection and for breeding of cultivated Brassica species. [ABSTRACT FROM AUTHOR]

Ribulose bis-carboxylase/oxygenase small subunit genes ( rbcS) are found to be highly expressed in most plant species. Promoters of rbcS genes have been isolated, characterized, and used to enhance expression of transgenes in transgenic lines. In this study, we have identified five different members of the rbcS gene family in cotton ( Gossypium hirsutum). All five genes contain three exons and two introns. Nucleotide sequences of the rbcS genes are conserved in their coding regions, but exhibit considerable sequence divergence in both introns and in upstream and downstream flanking sequences. Based on sequence identity, these genes are grouped into two subfamilies. Promoters of all rbcS genes have been isolated, and their cis-acting motifs, exhibiting different arrangements, have been identified. All five rbcS genes are differentially expressed in leaf and boll tissues of cotton plants at different stages of plant development. Three of the five isolated rbcS genes are found to be highly expressed in analyzed tissues. Multiple transcriptional start sites of all members of the gene family have been identified in leaf and boll tissues of cotton plants. Moreover, different members of the rbcS gene family from the two progenitor diploid species of G. hirsutum, namely, Gossypium herbaceum and Gossypium raimondii, have also been isolated to identify the lineage of the five rbcS genes. In addition, a total of three candidate promoters that can be used to enhance expression of transgenes in cotton have been identified. [ABSTRACT FROM AUTHOR]

Colistin is a last-resort antimicrobial used for the treatment of human infections caused by multidrug-resistant Gram-negative bacteria. However, colistin is still widely used in intensive poultry production in Bangladesh. We aimed to investigate the dynamics and genetic diversity of colistin-resistant commensal Escherichia coli from broiler chickens. A total of 1200 E. coli strains were characterized from 20 broiler farms at three-time points along the production period. All strains were screened for mcr-1 to mcr-5 genes by a multiplex PCR, and their genetic diversity was measured by repetitive extragenic palindromic (REP)-PCR fingerprinting. Genomic diversity and characterization were performed by whole genome sequencing (WGS). Twenty-five percent of the commensal E. coli strains harbored mcr-1 genes. Frequency of mcr-1 gene detection correlated positively (odds ratio 1.71; 95% CI 0.96–3.06; p = 0.068) with the use of colistin in poultry flocks. REP-PCR profiles and WGS analysis showed diverse E. coli population carrying multiple antimicrobial resistance genes. Phylogenetic comparison of mcr-1-bearing strains recovered from this study with a global strain collection revealed wide phylogenetic relationship. This study identified a high prevalence of mcr-1 gene among genetically diverse E. coli populations from broiler chickens in Bangladesh suggesting a massive horizontal spread of mcr-1 rather than by clonal expansion. [ABSTRACT FROM AUTHOR]