Length–weight relationships of nine freshwater fishes from six rivers of the Western Ghats of India

Length–weight relationships (LWRs) were estimated for nine freshwater fish species collected three times using a scoop net (mesh size 0.3–0.5 cm), cast net (mesh size 1–1.5 cm) and gillnet (mesh size 2.5–4.5 cm) from six rivers of the Western Ghats of India during August 2017–October 2018. The b values for LWRs varied from 2.862 to 3.656 (R² > 0.916 and p < 0.0001 for all species).     

Insights into the structure–function relationship of brown plant hopper resistance protein,Bph14 of rice plant: a computational structural biology approach

Brown plant hopper (BPH) is one of the major destructive insect pests of rice, causing severe yield loss. Thirty-two BPH resistance genes have been identified in cultivated and wild species of rice Although, molecular mechanism of rice plant resistance against BPH studied through map-based cloning, due to non-existence of NMR/crystal structures of Bph14 protein, recognition of leucine-rich repeat (LRR) domain and its interaction with different ligands are poorly understood. Thus, in the present study, in silico approach was adopted to predict three-dimensional structure of LRR domain of Bph14 using comparative modelling approach followed by interaction study with jasmonic and salicylic acids. LRR domain along with LRR-jasmonic and salicylic acid complexes were subjected to dynamic simulation using GROMACS, individually, for energy minimisation and refinement of the structure. Final binding energy of jasmonic and salicylic acid with LRR domain was calculated using MM/PBSA. Free-energy landscape analysis revealed that overall stability of LRR domain of Bph14 is not much affected after forming complex with jasmonic and salicylic acid. MM/PBSA analysis revealed that binding affinities of LRR domain towards salicylic acid is higher as compared to jasmonic acid. Interaction study of LRR domain with salicylic acid and jasmonic acid reveals that THR987 of LRR form hydrogen bond with both complexes. Thus, THR987 plays active role in the Bph14 and phytochemical interaction for inducing resistance in rice plant against BPH. In future, Bph14 gene and phytochemicals could be used in BPH management and development of novel resistant varieties for increasing rice yield.     

Seed Priming with Iron Oxide Nanoparticles Triggers Iron Acquisition and Biofortification in Wheat (Triticum aestivum L.) Grains

Iron deficiency anaemia is a major challenge among consumers in developing countries. Given the deficiency of iron in the diet, there is an urgent need to devise a strategy for providing the required iron in the daily diet to counter the iron deficiency anaemia. We propose that iron biofortification of wheat (Triticum aestivum L.) through seed priming would be an innovative strategy to address this issue. This investigation attempts to find the interaction of iron oxide nanoparticles on germination, growth parameters and accumulation of grain iron in two contrasting wheat genotypes WL711 (low-iron genotype) and IITR26 (high-iron genotype). Wheat seeds were primed with different concentrations of iron oxide nanoparticles in the range of 25–600 ppm, resulting in differential accumulation of grain iron contents. We observed a pronounced increase in germination percentage and shoot length at 400 and 200 ppm treatment concentrations in IITR26 and WL711 genotypes, respectively. Intriguingly, the treatment concentration of 25 ppm demonstrated higher accumulation with a significant increase in grain iron contents to 45.7% in IITR26 and 26.8% in WL711 genotypes, respectively. Seed priming represents an innovative and user-friendly approach for wheat biofortification which triggers iron acquisition and accumulation in grains.

     

How Do Different Watering Regimes Affect the Growth,Chlorophyll Fluorescence,Phytohormone, and Phenolic Acid Content of Greenhouse-Grown Ceratotheca triloba?

We evaluated the effect of different watering regimes on the growth, chlorophyll fluorescence, phytohormones, and phenolic acids in Ceratotheca triloba (Bernh.) Hook.f., a commonly consumed African indigenous leafy vegetable. The study was conducted in the greenhouse under different watering regimes [seven (daily); three (thrice); two (twice); one (once) day(s) per week] for a period of 2 and 4-months. In each pot (7.5 cm diameter; 150 ml volume), 50 ml of water was applied per treatment. At the end of the experiment, plant growth, chlorophyll fluorescence, phytohormones, and phenolic acids were determined. A decrease in water availability resulted in a consistent decline in plant growth after a 4-month growth period. The severity of reduced water availability was more noticeable in plants watered once a week with a 1.4-fold reduction in growth and quantum efficiency of PSII (Fv/Fm) value of 0.80. The significant decline in growth and chlorophyll fluorescence was probably due to the increased production of abscisic acid (ABA) and cytokinin (CK) content together with the detected phytohormones in plants with restricted water supply. Furthermore, plants watered once a week had a trade-off between growth and phenolic acid production, with significantly higher (threefolds) concentrations of vanillic, ferulic, caffeic, and 4-coumaric acids in 4-month-old plants. Even though C. triloba grew best in well-watered soil, the plant had the potential to adapt and survive in soils with limited water supply for longer periods of growth. These findings suggest that regulation of phytohormones and phenolic acids played an important role in improving the growth of C. triloba under limited water conditions.

     

Fine‐scale ecological and anthropogenic variables predict the habitat use and detectability of sloth bears in the Churia habitat of east Nepal

Once widespread throughout the tropical forests of the Indian Subcontinent, the sloth bears have suffered a rapid range collapse and local extirpations in the recent decades. A significant portion of their current distribution range is situated outside of the protected areas (PAs). These unprotected sloth bear populations are under tremendous human pressures, but little is known about the patterns and determinants of their occurrence in most of these regions. The situation is more prevalent in Nepal where virtually no systematic information is available for sloth bears living outside of the PAs. We undertook a spatially replicated sign survey‐based single‐season occupancy study intending to overcome this information gap for the sloth bear populations residing in the Trijuga forest of southeast Nepal. Sloth bear sign detection histories and field‐based covariates data were collected between 2 October and 3 December 2020 at the 74 randomly chosen 4‐km² grid cells. From our results, the model‐averaged site use probability (ψ ± SE) was estimated to be 0.432 ± 0.039, which is a 13% increase from the naïve estimate (0.297) not accounting for imperfect detections of sloth bear signs. The presence of termite mound and the distance to the nearest water source were the most important variables affecting the habitat use probability of sloth bears. The average site‐level detectability (p ± SE) of sloth bear signs was estimated to be 0.195 ± 0.003 and was significantly determined by the index of human disturbances. We recommend considering the importance of fine‐scale ecological and anthropogenic factors in predicting the sloth bear‐habitat relationships across their range in the Churia habitat of Nepal, and more specifically in the unprotected areas.     

The Slowing Rate of CpG Depletion in SARS-CoV-2 Genomes Is Consistent with Adaptations to the Human Host

Depletion of CpG dinucleotides in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genomes has been linked to virus evolution, host-switching, virus replication, and innate immune responses. Temporal variations, if any, in the rate of CpG depletion during virus evolution in the host remain poorly understood. Here, we analyzed the CpG content of over 1.4 million full-length SARS-CoV-2 genomes representing over 170 million documented infections during the first 17 months of the pandemic. Our findings suggest that the extent of CpG depletion in SARS-CoV-2 genomes is modest. Interestingly, the rate of CpG depletion is highest during early evolution in humans and it gradually tapers off, almost reaching an equilibrium; this is consistent with adaptations to the human host. Furthermore, within the coding regions, CpG depletion occurs predominantly at codon positions 2-3 and 3-1. Loss of ZAP (Zinc-finger antiviral protein)-binding motifs in SARS-CoV-2 genomes is primarily driven by the loss of the terminal CpG within the motifs. Nonetheless, majority of the CpG depletion in SARS-CoV-2 genomes occurs outside ZAP-binding motifs. SARS-CoV-2 genomes selectively lose CpGs-motifs from a U-rich context; this may help avoid immune recognition by TLR7. SARS-CoV-2 alpha-, beta-, and delta-variants of concern have reduced CpG content compared to sequences from the beginning of the pandemic. In sum, we provide evidence that the rate of CpG depletion in virus genomes is not uniform and it greatly varies over time and during adaptations to the host. This work highlights how temporal variations in selection pressures during virus adaption may impact the rate and the extent of CpG depletion in virus genomes.     

How do plants defend themselves against pathogens-Biochemical mechanisms and genetic interventions

In agro-ecosystem, plant pathogens hamper food quality, crop yield, and global food security. Manipulation of naturally occurring defense mechanisms in host plants is an effective and sustainable approach for plant disease management. Various natural compounds, ranging from cell wall components to metabolic enzymes have been reported to protect plants from infection by pathogens and hence provide specific resistance to hosts against pathogens, termed as induced resistance. It involves various biochemical components, that play an important role in molecular and cellular signaling events occurring either before (elicitation) or after pathogen infection. The induction of reactive oxygen species, activation of defensive machinery of plants comprising of enzymatic and non-enzymatic antioxidative components, secondary metabolites, pathogenesis-related protein expression (e.g. chitinases and glucanases), phytoalexin production, modification in cell wall composition, melatonin production, carotenoids accumulation, and altered activity of polyamines are major induced changes in host plants during pathogen infection. Hence, the altered concentration of biochemical components in host plants restricts disease development. Such biochemical or metabolic markers can be harnessed for the development of “pathogen-proof” plants. Effective utilization of the key metabolites-based metabolic markers can pave the path for candidate gene identification. This present review discusses the valuable information for understanding the biochemical response mechanism of plants to cope with pathogens and genomics-metabolomics-based sustainable development of pathogen proof cultivars along with knowledge gaps and future perspectives to enhance sustainable agricultural production.     

Clathrin exchange during clathrin-mediated endocytosis

During clathrin-mediated endocytosis, clathrin-coated pits invaginate to form clathrin-coated vesicles (CVs). Since clathrin-coated pits are planar structures, whereas CVs are spherical, there must be a structural rearrangement of clathrin as invagination occurs. This could occur through simple addition of clathrin triskelions to the edges of growing clathrin-coated pits with very little exchange occurring between clathrin in the pits and free clathrin in the cytosol, or it could occur through large scale exchange of free and bound clathrin. In the present study, we investigated this question by studying clathrin exchange both in vitro and in vivo. We found that in vitro clathrin in CVs and clathrin baskets do not exchange with free clathrin even in the presence of Hsc70 and ATP where partial uncoating occurs. However, surprisingly FRAP studies on clathrin-coated pits labeled with green fluorescent protein-clathrin light chains in HeLa cells show that even when endocytosis is blocked by expression of a dynamin mutant or depletion of cholesterol from the membrane, replacement of photobleached clathrin in coated pits on the membrane occurs at almost the same rate and magnitude as when endocytosis is occurring. Furthermore, very little of this replacement is due to dissolution of old pits and reformation of new ones; rather, it is caused by a rapid ATP-dependent exchange of clathrin in the pits with free clathrin in the cytosol. On the other hand, consistent with the in vitro data both potassium depletion and hypertonic sucrose, which have been reported to transform clathrin-coated pits into clathrin cages just below the surface of the plasma membrane, not only block endocytosis but also block exchange of clathrin. Taken together, these data show that ATP-dependent exchange of free and bound clathrin is a fundamental property of clathrin-coated pits, but not clathrin baskets, and may be involved in a structural rearrangement of clathrin as clathrin-coated pits invaginate.     

Opto-electrical processes in a conducting polymer-bacteriorhodopsin system

In this report, we highlight the opto-electrical processes at a conducting polymer-bacteriorhodopsin (bR) interface in presence of a voltage bias. Oriented bR on a conducting polymer substrate forms a unique hybrid system where the oxidation state of the polymer controls the optically activated proton gradient in the bR side. The internal conversion of the intermediate deprotonated M-state and the proton transfer/transport of bR at the interface can be controlled by the electrostatic environment and leads to interesting device features in this process.     

Long-term hypoxia alters ovine fetal endocrine and physiological responses to hypotension

Exposure to long-term hypoxia (LTH) results in altered cortisol responses in the ovine fetus. The present study was designed to test the hypothesis that LTH alters adrenal responsiveness to fetal hypotension. Pregnant ewes were maintained at high altitude (3,820 meters) from day 30 of gestation. Normoxic control and LTH fetuses were catheterized on day 132 of gestation. In the LTH group, maternal Po(2) was maintained comparable to that observed at altitude ( approximately 60 mmHg) by nitrogen infusion through a tracheal catheter. On day 137, fetuses received a 5-h saline infusion followed by infusion of sodium nitroprusside to reduce fetal arterial pressure by 30-35% for 10 min. The study was repeated on day 139 of gestation with a continuous cortisol infusion (10 microg/min). Hypothalamic and pituitary tissues were collected from additional fetuses for assessment of glucocorticoid receptors. During the saline infusion in response to hypotension, plasma ACTH increased over preinfusion mean values in both groups (P < 0.05). Plasma cortisol concentrations increased in both groups concomitant with increased ACTH secretion. However, peak values in the LTH fetuses were significantly higher compared with controls (P < 0.05). During the cortisol infusion, the ACTH response was eliminated in both groups, with ACTH levels significantly lower in the LTH group (P < 0.05). Glucocorticoid receptor binding was not different between groups. These results demonstrate an enhanced cortisol response to hypotension in LTH fetuses that does not appear to be the result of an increase in negative feedback sensitivity of the hypothalamic-pituitary-adrenal axis.