Whole-genome sequencing of three local rice varieties (Oryza sativa L.) in Vietnam

Recently, a new technology, Next-generation sequencing (NGS) has been launched and providing whole-genome sequences that helps identify molecular markers across the genome. DNA markers such as single nucleotides and insertion – deletion (InDel) polymorphisms were widely used for plant breeding particularly to distinguish important traits in rice. These PCR-based markers can be used for the precision detection of polymorphisms. Moreover, PCR-based approaches are simple and effective methods for dealing with the issue of fraudulent labeling and adulteration in the global rice industry. In this study, three local varieties of Oryza sativa L. in Vietnam were sequenced with up to ten times genome depth and at least four times coverage (~83%) using the Illumina HiSeq2000™ system, with an average of 6.5 GB clean data per sample, generated after filtering low-quality data. The data was approximately mapped up to 95% to the reference genome IRGSP 1.0. The results obtained from this study will contribute to a wide range of valuable information for further investigation into this germplasm

Ranking load in microgrid based on fuzzy analytic hierarchy process and technique for order of preference by similarity to ideal solution algorithm for load shedding problem

This paper proposes a method to rank the loads in the microgrid by means of a weight that combines the criteria together in terms of both technical and economic aspects. The fuzzy analytic hierarchy process technique for order of preference by similarity to ideal solution (fuzzy AHP TOPSIS) algorithm is used to calculate this combined weight. The criteria to be considered are load importance factor (LIF), voltage electrical distance (VED) and voltage sensitivity index (VSI). The fuzzy algorithm helps to fuzzy the judgment matrix of the analytic hierarchy process (AHP) method, making it easier to compare objects with each other and remove the uncertainty of the AHP method. The technique for order of preference by similarity to ideal solution (TOPSIS) algorithm is used to normalize the decision matrix, determine the positive and negative ideal solutions to calculate the index of proximity to the ideal solution, and finally rank all the alternatives. The combination of fuzzy AHP and TOPSIS algorithms is the optimal combination for decision making and ranking problems in a multi-criteria environment. The 19-bus microgrid system is applied to calculate and demonstrate the effectiveness of the proposed method

Stimulation of shoot regeneration through leaf thin cell layer culture of Passiflora edulis Sims.

Passiflora edulis Sims. belonged to the genus Passiflora, is one of the important economic crops of the world as well as Vietnam. Nowadays, the commercial P. edulis is mainly propagated by seeds, cuttings and grafting; however, these methods still have some limitations such as genetic degradation and heterogeneity and the spread of pathogenic viruses. Micro-propagation has been used for clonal breeding and disease-free plant breeding, as well as providing a source of materials for Passiflora breeding. In this study, leaf explants of P. edulis Sims. (2.0-month-old) excised from the in vitro culture of ex vitro axillary buds cut longitudinally and transversally into thin cell layers (lTCL and tTCL) were used as plant materials to evaluate the shoot regeneration. In addition, the effects of explant age and lighting condition on shoot regeneration were also investigated. After 8 weeks of culture, the results showed that shoot regeneration rate (100%) and shoot multiplication coefficient (13.33) of the in vitro leaf-tTCL-4 were higher than those of other treatments and control. The shoot regeneration rate of P. edulis Sims. also varied with the change of explant age. The highest shoot regeneration rate (100%) was obtained from leaf explants of 1.5-month-old shoots after 8 weeks of culture. Moreover, the light (fluorescent lamps with photoperiod of 16 hours/day and lighting intensity of 40 - 45 μmol.m-2.s-1) improved not only morphogenesis rate, but also shoot regeneration rate (100%) of leaf explants after 8 weeks of culture. This study provided a novel method for rapid micro-propagation of P. edulis Sims

Assessment of pesticide safety knowledge and practices in Vietnam: A cross-sectional study of smallholder farmers in the Mekong Delta

Over the past three decades, the Vietnamese Mekong Delta has experienced a significant increase in agricultural productivity, partly achieved through increased agrochemical use. To abate negative effects on human and environmental health, several national programs were launched to enhance safer pesticide use. This study aimed to assess the patterns and relationships of official sustainable agriculture educational programs, pesticide safety knowledge, and practices of smallholder farmers in the Mekong Delta. A cross-sectional survey was conducted with 400 smallholder farmers from three communes in Thoi Lai district (Can Tho province) from March to May 2020. Twenty-four questions on pesticide safety knowledge and practices were used to identify traits using latent class analysis. Adjusted generalized linear regression was used to assess determinants of pesticide safety knowledge and estimate associations of pesticide safety knowledge with pesticide practices. 96.2% of participants have used at least one WHO class II pesticide during the past year while the use of specific personal protective equipment was limited mainly due to unavailability (37.0%) or discomfort (83.0%). High education (Odds Ratio (OR), 95% Confidence Interval; 3.84, 1.70–9.45), exposure to official educational programs (1.87, 1.13–3.12), peer-to-peer knowledge exchange (3.58, 2.18–6.00), and learning from governmental extension services (2.31, 1.14–4.98) were positively associated with increased pesticide safety knowledge. Compared to poor practices, pesticide safety knowledge was increasingly positively associated with intermediate (1.65, 1.02–2.66) and good pesticide practices (8.96, 2.58–31.12). These findings highlight the importance of school education and educational programs, access to PPE, and addressing discomforts of PPE to improve the protection of farmers from pesticide exposures. Simultaneously, pesticide market authorization processes should be reconsidered to promote the authorization of less toxic products. Further indepth studies on the nature of pesticides used, nonuse of personal protective equipment, and effectiveness of educational programs will further define leverage points for safer pesticide use

Genetic variation of Nang Thom Cho Dao rice variety based on whole genome sequencing

High-performance sequences are generating increasingly comprehensive catalogs of crop genetic variation. To make optimal use of this vast collection of data for research purposes, a robust and reproducible analytical pipeline discipline is required that is capable of accurately detecting and favoring variants. The entire genome sequencing data from the rice variety Nang Thom Cho Dao was analyzed using the appropriate bioinformatic pipeline. A total of 21 million reads with 6,6 GB of data were analyzed. SNPs and indels from the Nang Thom Cho Dao genome were found to be variable when compared to the Nipponbare reference rice genome. The result showed that the novel Indel of BADH2 gene in Nang Thom Cho Dao genome. The study will contribute valuable information to the development of genetic markers for rice breeding strategies using Nang Thom Cho Dao rice varieties

Extract and fraction of cashew nut testa ameliorate the hyperglycemic mice induced by Streptozotocin and high-fat diet

Drug strategy is a standard method for treating type 2 diabetes mellitus (T2D), a non-communicable disease with increasing prevalence, which may cause side effects. Therefore, natural compounds with limited adverse effects have come back into vogue for treating T2D. This study aims to evaluate the effects on rehabilitating hyperglycemic mice of cashew nut testa (husk) extract and fraction known as potential bio-substances for improvement in T2D. First, the hyperglycemic mice were induced with a high-fat diet (HFD) for 4 weeks and then were injected with streptozotocin (STZ, dozen for injection was 40 mg/kg/week) for 2 weeks. Next, the confirmed hyperglycemic mice were treated with pioglitazone (HG+PG group), total extract (HG+TE group), and saponin-rich fraction (HG+SRF group) for 3 weeks. Then, the evaluation was based on body mass; blood glucose (BG) level; BG tolerance, lipid profile, pancreatic histology and the expression IRS-1 in the pancreas. The results showed that body mass and BG level significantly increased in hyperglycemic mice. After substance treatment, there was no change in body mass in TE and SRF groups. However, BG level of HG+TE group mice significantly decreased compared to hyperglycemic mice and only BG tolerance of HG+SRF group was improved. Besides, HG+TE and HG+SRF groups modulated the triglyceride, HDL and LDL close to those expressed in normal mice. In addition, histological images of the pancreas revealed the restoration in both HG+TE and HG+SRF groups. Simultaneously, the IRS-1 expression in HG+TE group pancreas was restored to its expression in normal mice. These results demonstrate that the TE and SRF of cashew nut testa could ameliorate BG, lipid profile and pancreatic IRS-1 expression and restore the damaged pancreas and islets in hyperglycemic mice

Spatiotemporal evolution of SARS-CoV-2 Alpha and Delta variants during large nationwide outbreak of COVID-19, Vietnam, 2021

We analyzed 1,303 SARS-CoV-2 whole-genome sequences from Vietnam, and found the Alpha and Delta variants were responsible for a large nationwide outbreak of COVID-19 in 2021. The Delta variant was confined to the AY.57 lineage and caused >1.7 million infections and >32,000 deaths. Viral transmission was strongly affected by nonpharmaceutical interventions

In silico design and biological evaluation of a dual specificity kinase inhibitor targeting cell cycle progression and angiogenesis

Methodology: We have utilized a rational in silico-based approach to demonstrate the design and study of a novel compound that acts as a dual inhibitor of vascular endothelial growth factor receptor 2 (VEGFR2) and cyclin-dependent kinase 1 (CDK1). This compound acts by simultaneously inhibiting pro-Angiogenic signal transduction and cell cycle progression in primary endothelial cells. JK-31 displays potent in vitro activity against recombinant VEGFR2 and CDK1/cyclin B proteins comparable to previously characterized inhibitors. Dual inhibition of the vascular endothelial growth factor A (VEGF-A)-mediated signaling response and CDK1-mediated mitotic entry elicits anti-Angiogenic activity both in an endothelial-fibroblast co-culture model and a murine ex vivo model of angiogenesis