Monkeypox genome mutation analysis using a timeseries model based on long short-term memory.

Monkeypox is a double-stranded DNA virus with an envelope and is a member of the Poxviridae family's Orthopoxvirus genus. This virus can transmit from human to human through direct contact with respiratory secretions, infected animals and humans, or contaminated objects and causing mutations in the human body. In May 2022, several monkeypox affected cases were found in many countries. Because of its transmitting characteristics, on July 23, 2022, a nationwide public health emergency was proclaimed by WHO due to the monkeypox virus. This study analyzed the gene mutation rate that is collected from the most recent NCBI monkeypox dataset. The collected data is prepared to independently identify the nucleotide and codon mutation. Additionally, depending on the size and availability of the gene dataset, the computed mutation rate is split into three categories: Canada, Germany, and the rest of the world. In this study, the genome mutation rate of the monkeypox virus is predicted using a deep learning-based Long Short-Term Memory (LSTM) model and compared with Gated Recurrent Unit (GRU) model. The LSTM model shows "Root Mean Square Error" (RMSE) values of 0.09 and 0.08 for testing and training, respectively. Using this time series analysis method, the prospective mutation rate of the 50th patient has been predicted. Note that this is a new report on the monkeypox gene mutation. It is found that the nucleotide mutation rates are decreasing, and the balance between bi-directional rates are maintained.

Analysis of qualitative and quantitative morphological traits related to yield in country bean (Lablab purpureus L. sweet) genotypes.

Country bean is a grain legume extensively farmed for its multi-purpose uses, yet the traits related to yield are are poorly studied and yet unexplored. A study on the diversity of qualitative and quantitative morphological characteristics concerning yield among the country bean germplasms collected from Bangladesh identified considerable variation in the studied traits across the germplasms and identified a complex correlation between the qualitative and quantitative traits. Principal Component Analysis (PCA) detected five components that contributed 66.38% qualitative traits and six components contributed 74.49% quantitative traits to total variations. Eigenvalues indicated that a majority of color-related qualitative traits included cotyledon, leaf, vein, seed, flower, and petals contributed, in contrast,a majority of the seed, leaf, flower, and inflorescence-related quantitative traits contributed to the total diversity of the Lablab germplasms. Among the quantitative traits, the highest coefficient of variation (CV%) was found in average pod weight (50.98%), followed by the total number of spikes per plant (43.82%), while seed length, pod weight, length, width, thickness, number of flower/spike, spike length, and total no of spikes/plant all had more than 20.00 percent CV, suggesting suitability to use in the breeding of high yielding genotypes. The germplasms are grouped into four and three clusters based on quantitative and qualitative traits, suggesting quantitative characters offer better clustering of genotypes. Considering the above traits, our research found that the BD-10804, BD-10807, BD-11091, BD-10808, BD-10815, and BD-11089 and cultivar Goal Goda Lablab beans germplasms produced higher pod weight with corresponding higher pod length, width, and thickness suggesting to use them as high yielding genotypes for food and fodder purposes.

A Review of Integrative Omic Approaches for Understanding Rice Salt Response Mechanisms.

Soil salinity is one of the most serious environmental challenges, posing a growing threat to agriculture across the world. Soil salinity has a significant impact on rice growth, development, and production. Hence, improving rice varieties' resistance to salt stress is a viable solution for meeting global food demand. Adaptation to salt stress is a multifaceted process that involves interacting physiological traits, biochemical or metabolic pathways, and molecular mechanisms. The integration of multi-omics approaches contributes to a better understanding of molecular mechanisms as well as the improvement of salt-resistant and tolerant rice varieties. Firstly, we present a thorough review of current knowledge about salt stress effects on rice and mechanisms behind rice salt tolerance and salt stress signalling. This review focuses on the use of multi-omics approaches to improve next-generation rice breeding for salinity resistance and tolerance, including genomics, transcriptomics, proteomics, metabolomics and phenomics. Integrating multi-omics data effectively is critical to gaining a more comprehensive and in-depth understanding of the molecular pathways, enzyme activity and interacting networks of genes controlling salinity tolerance in rice. The key data mining strategies within the artificial intelligence to analyse big and complex data sets that will allow more accurate prediction of outcomes and modernise traditional breeding programmes and also expedite precision rice breeding such as genetic engineering and genome editing.

Diagnosis, genetic variations, virulence, and toxicity of AHPND-positive Vibrio parahaemolyticus in Penaeus monodon.

Acute hepatopancreatic necrosis disease (AHPND) is an emerging shrimp (Penaeus monodon) disease caused by Vibrio parahaemolyticus (VP) since 2013 in Bangladesh. The aim of this work was to evaluate a PCR and RT-PCR techniques as rapid methods for detecting V. parahaemolyticus AHPND-positive P. monodon using genetic markers. Healthy and diseased shrimp (P. monodon) samples were collected from three monitoring stations. The samples were enriched in TCBS plates and DNA extraction from the cultured bacteria. DNA quantifications, PCR amplification, RT-PCR, and gene sequencing were done for the detection of V. parahaemolyticus AHPND-positive P. monodon. The sequence of PCR amplicons showed 100% identity and significant alignment with V. parahaemolyticus. The primers used provided high specificity for V. parahaemolyticus in PCR detection compared with another Vibrio species. In the PCR, amplification resulted positive amplicons, whereas, non-AHPND isolates showed no amplicons. Neighbor-joining methods indicated that all genes evolved from a common ancestor and clades have different traits with very low genetic distance and low variability. The pairwise alignment scores of atpA, tox, blaCARB, 16S rRNA, and pirA genes were 100.0, 98.90, 98.89, 95.53, and 41.42, respectively. The RT-qPCR exposed variable expression levels for all genes in the AHPND-positive strain. Homology analysis and distance matrix exhibited all genes to have the lowest similarity and most divergence, offering the highest specificity. In this study, the expression and variability of target genes confirmed the presence of V. parahaemolyticus in all sampling sites. The results suggested that PCR amplification, RT-qPCR, and gene sequencing can be used for the rapid detection of V. parahaemolyticus in AHPND-positive P. monodon that may lead to subsequent prevention and treatment research in the future for managing this disease.

Overexpression of dehydroascorbate reductase, but not monodehydroascorbate reductase, confers tolerance to aluminum stress in transgenic tobacco.

Aluminum (Al) inhibits plant growth partly by causing oxidative damage that is promoted by reactive oxygen species and can be prevented by improving antioxidant capacity. Ascorbic acid (AsA), the most abundant antioxidant in plants, is regenerated by the action of monodehydroascorbate reductase (MDAR) and dehydroascorbate reductase (DHAR). We investigated the role of MDAR and DHAR in AsA regeneration during Al stress using transgenic tobacco (Nicotiana tabacum) plants overexpressing Arabidopsis cytosolic MDAR (MDAR-OX) or DHAR (DHAR-OX). DHAR-OX plants showed better root growth than wild-type (SR-1) plants after exposure to Al for 2 weeks, but MDAR-OX plants did not. There was no difference in Al distribution and accumulation in the root tips among SR-1, DHAR-OX, and MDAR-OX plants after Al treatment for 24 h. However, DHAR-OX plants showed lower hydrogen peroxide content, less lipid peroxidation and lower level of oxidative DNA damage than SR-1 plants, whereas MDAR-OX plants showed the same extent of damage as SR-1 plants. Compared with SR-1 plants, DHAR-OX plants consistently maintained a higher AsA level both with and without Al exposure, while MDAR-OX plants maintained a higher AsA level only without Al exposure. Also, DHAR-OX plants maintained higher APX activity under Al stress. The higher AsA level and APX activity in DHAR-OX plants contributed to their higher antioxidant capacity and higher tolerance to Al stress. These findings show that the overexpression of DHAR, but not of MDAR, confers Al tolerance, and that maintenance of a high AsA level is important to Al tolerance.

Overexpression of a new rice vacuolar antiporter regulating protein OsARP improves salt tolerance in tobacco.

We examined the function of the rice (Oryza sativa L.) antiporter-regulating protein OsARP by overexpressing it in tobacco (Nicotiana tabacum L.). In public databases, this protein was annotated as a putative Os02g0465900 protein of rice. The OsARP gene was introduced into tobacco under the control of the cauliflower mosaic virus 35S promoter. The transformants were selected for their ability to grow on medium containing kanamycin. Incorporation of the transgene in the genome of tobacco was confirmed by PCR, and its expression was confirmed by Western blot analysis. Transgenic plants had better growth and vigor than non-transgenic plants under salt stress in vitro. Overexpression of OsARP in transgenic tobacco plants resulted in salt tolerance, and the plants had a higher rate of photosynthesis and effective PSII photon yield when compared with the wild type. The OsARP protein was localized in the tonoplast of rice plants. Transgenic plants accumulated more Na+ in their leaf tissue than did wild-type plants. It is conceivable that the toxic effect of Na+ in the cytosol might be reduced by sequestration into vacuoles. The rate of water loss was higher in the wild type than in transgenic plants under salt stress. Increased vacuolar solute accumulation and water retention could confer salt tolerance in transgenic plants. Tonoplast vesicles isolated from OsARP transgenic plants showed Na+/H+ exchange rates 3-fold higher than those of wild-type plants. These results suggest that OsARP on the tonoplasts plays an important role in compartmentation of Na+ into vacuoles. We suggest that OsARP is a new type of protein participating in Na+ uptake in vacuoles.