Neoechinulin A as a Promising SARS-CoV-2 Mpro Inhibitor: In Vitro and In Silico Study Showing the Ability of Simulations in Discerning Active from Inactive Enzyme Inhibitors

The COVID-19 pandemic and its continuing emerging variants emphasize the need to discover appropriate treatment, where vaccines alone have failed to show complete protection against the new variants of the virus. Therefore, treatment of the infected cases is critical. This paper discusses the bio-guided isolation of three indole diketopiperazine alkaloids, neoechinulin A (1), echinulin (2), and eurocristatine (3), from the Red Sea-derived Aspergillus fumigatus MR2012. Neoechinulin A (1) exhibited a potent inhibitory effect against SARS-CoV-2 M^pro with IC₅₀ value of 0.47 μM, which is comparable to the reference standard GC376. Despite the structural similarity between the three compounds, only 1 showed a promising effect. The mechanism of inhibition is discussed in light of a series of extensive molecular docking, classical and steered molecular dynamics simulation experiments. This paper sheds light on indole diketopiperazine alkaloids as a potential structural motif against SARS-CoV-2 M^pro. Additionally, it highlights the potential of different molecular docking and molecular dynamics simulation approaches in the discrimination between active and inactive structurally related M^pro inhibitors.     

Global Bibliometric Analysis of the Research in Biochar

Global interest in studying biochar stems from its ability to sequester carbon in soil and render nutrients and moisture more readily available to root systems. Therefore, a bibliometric analysis was conducted to investigate global scientific publications related to biochar research, providing insight into the number of articles published, journal platforms, subjects, citations, and overall trends. The primary databases employed were the Web of Science and Science Citation Index. A total of 1,697 articles published between 2000 and 2015 were evaluated. This systematic bibliometric analysis will assist research groups and individuals to understand global biochar research trends and focus future research. The influence of biochar on soil, plants, and the environment continues to require greater attention.     

Identification of Co-dominant SSR Markers Associated with Genes Controlling α′-and α-subunit-null β-conglycinin Phenotypes in Soybean (Glycine max (L.) Merr.)

Studies have shown that the three subunits of β-conglycinin are the main potential allergens of soybean sensitive patients.And β-conglycinin has adverse effects on nutrition and food processing.So solation and production of lines with lower β-conglycinin content has been the focus of recent soybean breeding projects.Soybean lines with deficiency in one or all subunits of β-conglycinin have been obtained.An effective and rapid system to identify such mutations will facilitate genetic manipulation of the β-conglycinin subunit composition.Here,two segregating F_2 populations were developed from crosses between Cgy-1/cgy-1 (CC),an α′-lacking line (Δα′),and DongNong 47 (DN47),a wild-type (Wt) Chinese soybean cultivar with normal globulin components,and Cgy-2/cgy-2 (CB),an α-lacking line (Δα),and DN47.These populations were used to estimate linkage among the cgy-1 (conferring α′-null) and cgy-2 (α-null) loci and simple sequence repeat (SSR) markers.Seven SSR markers (Sat_038,Satt243,Sat_307,Sat_109,Sat_231,Sat_108 and Sat_190) were determined to co-segregate with cgy-1,and six SSR markers (Satt650,Satt671,Sat_418,Sat_170,Satt292 and Sat_324) co-segregated with cgy-2.Linkage maps being composed of seven SSR markers and cgy-1 locus,and six SSR markers and the cgy-2 locus were then constructed.It assigned that the cgy-1 gene to chromosome 10 at a position between Sat_307 and Sat_231,and the cgy-2 gene to chromosome 20 at a position between Satt650 and Satt671.These markers should enable map-based cloning of the cgy-1 and cgy-2 genes.For different subunit-deficiency types[α′-null,α-null and (α′+α)-null types],the two sets of SSR markers could also detect of polymorphism between three normal cultivars and seven related mutant lines.The identification of these markers is great significance to the molecular marker-assisted breeding of soybean β-conglycinin subunits.     

Identification of glycinin and beta-conglycinin subunits that contribute to the increased protein content of high-protein soybean lines

Seed protein concentration of commercial soybean cultivars calculated on a dry weight basis ranges from approximately 37 to 42% depending on genotype and location. A concerted research effort is ongoing to further increase protein concentration. Several soybean plant introductions (PI) are known to contain greater than 50% protein. These PIs are exploited by breeders to incorporate the high-protein trait into commercial North American cultivars. Currently, limited information is available on the biochemical and genetic mechanisms that regulate high-proteins. In this study, we have carried out proteomic and molecular analysis of seed proteins of LG00-13260 and its parental high-protein lines PI 427138 and BARC-6. Sodium dodecyl sulfate polyacrylamide gel electrophoresis analysis revealed that the high-protein lines accumulated increased amounts of beta-conglycinin and glycinins, when compared with Williams 82. High-resolution two-dimensional electrophoresis utilizing pH 4-7 and pH 6-11 ampholytes enabled improved resolution of soybean seed proteins. A total of 38 protein spots, representing the different subunits of beta-conglycinin and glycinin, were identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. High-protein was correlated with an increase in the accumulation of most of the subunits representing beta-conglycinin and glycinin. Comparisons of the amino acid profiles of high-protein soybean lines revealed that the concentration of sulfur amino acids, a reflection of protein quality, was not influenced by the protein concentration. Southern blot analysis showed the presence of genotypic variation at the DNA level between PI 427138 and BARC-6 for the genes encoding group1 glycinin, beta-conglycinin, Bowman-Birk inhibitor (BBI), and the Kunitz trypsin inhibitor (KTI). LG00-13260 inherited the allelic variants of the parental line PI 427138 for glycinin, beta-conglycinin, and KTI, while BBI was inherited from the parental line BARC-6. The results of our study indicate that high-seed protein concentration is attributed to greater accumulation of specific components of beta-conglycinin and glycinin subunits presumably mediated by preferential expression of these genes during seed development.     

Exploring tree diversity and stand structure of savanna woodlands in southeastern Sudan

Savanna woodlands in Sudan host great biodiversity, provide a plethora of ecosystem goods and services to local communities, and sustain numerous ecological functions. Although the importance of the Acacia trees in these areas is well known, up-to-date information about these woodlands' diversity is limited and changes in their woody vegetation composition, density, diversity and relative frequency are not monitored over time. This study explored tree diversity and stand stage structure in Nuara Reserved Forest, a typical savanna woodland ecosystem in southeastern Sudan. A total of 638 circular sample plots (1000 m² for each) were established using a systematic sampling grid method. The distance between plots was 200 m. In each plot, all living trees with diameter at breast height (DBH) ≥5.00 cm were identified and counted, and their DBH values were recorded. From these data, tree composition, diversity, density and stage structure were assessed. There were 12,259 individual trees representing four species (Acacia seyal, Balanites aegyptiaca, Acacia Senegal and Acacia mellifera) that belong to two families. The dominant species was Acacia seyal. Average tree density was 191 trees/hm² and the Shannon-Weiner index for trees diversity was 0.204. Overall, young trees comprised 86.30% of the forest. The state of tree richness and density in the study area was low compared to other similar environments in the region and around the world. We recommended adoption of a proper management system that includes monitoring of woody vegetation diversity in this forest, and management actions to enhance tree diversity and sustain ecosystem services to local communities. In addition to care for the dominant Acacia seyal stands, more attention and conservation should be devoted to reestablishing Acacia senegal and Acacia mellifera trees because of their high ecological and economic values for local communities.     

Etiology of potato soft rot and blackleg diseases complex in Egypt

Journal of Plant Diseases and Protection - Recent observations of increasing incidences of potato plants showing blackleg symptoms have caused serious concern for potato growers and traders in...     

Growth,yield and water productivity of dry direct seeded rice and transplanted aromatic rice under different irrigation management regimes

Sustainability of traditionally cultivated rice in the rice-wheat cropping zone (RWCZ) of Pakistan is dwindling due to the high cost of production, declining water resources and escalating labour availability. Thus, farmers and researchers are compelled to find promising alternatives to traditional transplanted rice (TPR). A field study was conducted in Punjab, Pakistan, in 2017 and 2018 to explore the trade-offs between water saving and paddy yield, water productivity and economics of two aromatic rice varieties under dry direct seeded rice (DDSR) and TPR. The experiment was comprised of three irrigation regimes on the basis of soil moisture tension (SMT) viz., continuous flooded (>−10 kPa SMT), alternate wetting and drying (AWD) (−20 kPa SMT) and aerobic rice (−40 kPa SMT), maintained under TPR and DDSR systems. Two aromatic rice verities: Basmati-515 and Chenab Basmati-2016 were used during both years of study. In both years, DDSR produced higher yields (13–18%) and reduced the total water inputs (8–12%) in comparison to TPR. In comparison to traditional continuous flooded (CF), AWD under DDSR reduced total water input by 27–29% and improved the leaf area index (LAI), tillering, yield (7–9%), and water productivity (44–50%). The performance of AWD with regard to water savings and increased productivity was much higher in DDSR system as compared to AWD in TPR system. Cultivation of DDSR with aerobic irrigation improved water savings (49–55%) and water productivity (22–30%) at the expense of paddy yield reduction (36–39%) and spikelet sterility. With regard to variety, the highest paddy yield (6.6 and 6.7 t ha⁻¹) was recorded in DDSR using Chenab Basmati-2016 under AWD irrigation threshold that attributed to high tiller density and LAI. The economic analysis showed DDSR as more beneficial rice establishment method than TPR with a high benefit-cost ratio (BCR) when the crop was irrigated with AWD irrigation threshold. Our results highlighted that with the use of short duration varieties, DDSR cultivation in conjunction with AWD irrigation can be more beneficial for higher productivity and crop yield.     

Anti-Inflammatory Cembranoids from a Formosa Soft Coral Sarcophyton cherbonnieri

The present investigation on chemical constituents of the soft coral Sarcophyton cherbonnieri resulted in the isolation of seven new cembranoids, cherbonolides F–L (1–7). The chemical structures of 1–7 were determined by spectroscopic methods, including infrared, one- and two-dimensional (1D and 2D) NMR (COSY, HSQC, HMBC, and NOESY), MS experiments, and a chemical reduction of hydroperoxide by triphenylphosphine. The anti-inflammatory activities of 1–7 against neutrophil proinflammatory responses were evaluated by measuring their inhibitory ability toward N-formyl-methionyl-leucyl-phenylalanine/cytochalasin B (fMLF/CB)-induced superoxide anion generation and elastase release in primary human neutrophils. The results showed that all isolates exhibited moderate activities, while cherbonolide G (2) and cherbonolide H (3) displayed a more active effect than others on the inhibition of elastase release (48.2% ± 6.2%) and superoxide anion generation (44.5% ± 4.6%) at 30 µM, respectively.     

Bacterial diversity of tilapia (Oreochromis niloticus) cultured in brackish water in Saudi Arabia

The bacterial flora occurring in brackish pond water, sediment, gills and intestine of healthy tilapia cultured in Saudi Arabia were estimated both quantitatively and qualitatively, and the isolates were identified to genus or species level. Total viable count of bacteria ranged from 1.4±1.5×10³ to 8.6±2.7×10³ cfu ml⁻¹; 1.2±3.1×10⁶ to 7.3±1.1×10⁷ cfu g⁻¹; 8.7±1.9×10⁵ to 2.1±0.9×10⁶ cfu g⁻¹; and 2.8±2.4×10⁷ to 1.0±1.6×10⁸ cfu g⁻¹ in the pond water, sediment, gills and intestine of brackish water tilapia, respectively. In total, 19 bacterial species were identified. The bacteria were predominantly Gram-negative rods (87%). Pond water and sediment bacteria influenced the bacterial composition of gills and intestine of tilapia. In contrast to gill bacteria, more diversification was observed in intestinal bacteria. The predominant (prevalence >10%) bacterial species were Vibrio parahaemolyticus, Vibrio carchariae, Vibrio alginolyticus, Chryseomonas sp., Vibrio vulnificus, and Streptococcus sp. in all the populations with the exception of the sediment population where Streptococcus sp. was replaced by Shewanella putrefaciens. Vibrio spp. (58% of the total isolates) dominated the total bacterial population.     

The impacts of aquaculture development on food security: lessons from Bangladesh

Fish contribute a significant amount of animal protein to the diets of people in Bangladesh, about 63% of which comes from aquatic animals. In Bangladesh, fish is mainly derived from two sources: capture and culture. Aquaculture has shown tremendous growth in the last two decades, exhibiting by about 10% average annual growth in production. Capture fisheries, although still the major source of supply of fish, have become static or are in decline due to over‐fishing and environmental degradation, and it is now believed that aquaculture has the greatest potential to meet the growing demand for fish from the increasing population. At present, aquaculture production accounts for about one‐third of the total fish production in Bangladesh. This paper examines the impact of an aquaculture development project in Bangladesh on food security, with particular emphasis on the poor. The analysis shows a positive impact of aquaculture development on employment, income and consumption. A number of implications for policy in areas that might strengthen these outcomes are discussed and recommendations are presented.