Potentials of genotypes, morpho-physio-biochemical traits, and growing media on shelf life and future prospects of gene editing in tomatoes.

Background: To study the genetic basis of the impact of genotypes and morpho-physio-biochemical traits under different organic and inorganic fertilizer doses on the shelf life attribute of tomatoes, field experiments were conducted in randomized block designs during the rabi seasons of 2018-2019 and 2019-2020. The experiment comprised three diverse nutrient environments [T1-organic; T2-inorganic; T3-control (without any fertilizers)] and five tomato genotypes with variable growth habits, specifically Angoorlata (Indeterminate), Avinash-3 (semi-determinate), Swaraksha (semi-determinate), Pusa Sheetal (semi-determinate), and Pusa Rohini (determinate). Results: The different tomato genotypes behaved apparently differently from each other in terms of shelf life. All the genotypes had maximum shelf life when grown in organic environments. However, the Pusa Sheetal had a maximum shelf life of 8.35 days when grown in an organic environment and showed an increase of 12% over the control. The genotype Pusa Sheetal, organic environment and biochemical trait Anthocyanin provides a promise as potential contributor to improve the keeping quality of tomatoes. Conclusion: The genotype Pusa Sheetal a novel source for shelf life, organic environment, and anthocyanin have shown promises for extended shelf life in tomatoes. Thus, the identified trait and genotype can be utilized in tomato improvement programs. Furthermore, this identified trait can also be targeted for its quantitative enhancement in order to increase tomato shelf life through a genome editing approach. A generalized genome editing mechanism is consequently suggested.

Genetic Mechanisms for Hybrid Breeding in Vegetable Crops.

To address the complex challenges faced by our planet such as rapidly changing climate patterns, food and nutritional insecurities, and the escalating world population, the development of hybrid vegetable crops is imperative. Vegetable hybrids could effectively mitigate the above-mentioned fundamental challenges in numerous countries. Utilizing genetic mechanisms to create hybrids not only reduces costs but also holds significant practical implications, particularly in streamlining hybrid seed production. These mechanisms encompass self-incompatibility (SI), male sterility, and gynoecism. The present comprehensive review is primarily focused on the elucidation of fundamental processes associated with floral characteristics, the genetic regulation of floral traits, pollen biology, and development. Specific attention is given to the mechanisms for masculinizing and feminizing cucurbits to facilitate hybrid seed production as well as the hybridization approaches used in the biofortification of vegetable crops. Furthermore, this review provides valuable insights into recent biotechnological advancements and their future utilization for developing the genetic systems of major vegetable crops.

Understanding the self-assembly dynamics of A/T absent 'four-way DNA junctions with sticky ends' at altered physiological conditions through molecular dynamics simulations.

Elucidation of structure and dynamics of alternative higher-order structures of DNA such as in branched form could be targeted for therapeutics designing. Herein, we are reporting the intrinsically dynamic and folds transitions of an unusual DNA junction with sequence d(CGGCGGCCGC)4 which self-assembles into a four-way DNA junction form with sticky ends using long interval molecular simulations under various artificial physiological conditions. The original crystal structure coordinates (PDB ID: 3Q5C) for the selected DNA junction was considered for a total of 1.1 µs molecular dynamics simulation interval, including different temperature and pH, under OPLS-2005 force field using DESMOND suite. Following, post-dynamics structure parameters for the DNA junction were calculated and analyzed by comparison to the crystal structure. We show here that the self-assembly dynamics of DNA junction is mitigated by the temperature and pH sensitivities, and discloses peculiar structural properties as function of time. From this study it can be concluded on account of temperature sensitive and pH dependent behaviours, DNA junction periodic arrangements can willingly be synthesized and redeveloped for multiple uses like genetic biomarkers, DNA biosensor, DNA nanotechnology, DNA Zipper, etc. Furthermore, the pH dis-regulation behaviour may be used to trigger the functionality of DNA made drug-releasing nanomachines.

Gharial (Gavialis gangeticus, Gmelin, 1789) abundance in the Rapti River, Chitwan National Park, Nepal.

Gharial (Gavialis gangeticus) is a Critically Endangered crocodilian species whose abundance in Nepalese rivers is low due to the threat they face. We estimated gharial abundance in the Rapti River, one of the major rivers in Chitwan National Park (CNP) holding the largest numbers of gharials in Nepal. The Rapti River, running across the CNP, was divided into 18 segments, each measuring ~4 km, and gharials were counted directly with three replicates. Gharial count data were analyzed using an N-mixture model (negative binomial) and the overall occupancy of gharials was estimated using a single season occupancy model. Covariate effects were also investigated on gharial abundance. Our findings revealed that the Rapti River is home to 150 gharials (119-181), with a mean abundance of 8.3 (SD = 3.45) across each segment. The presence of humans and square of Rapti River depth were the significant covariates that had a negative and positive impact on gharial abundance, respectively. Similarly, the number of sandbank present influenced the detection probability of gharials. Our study shows that gharial population estimation can be improved using the N-mixture model. The overall gharial occupancy estimated using single season occupancy model was 0.84 (SD = 0.08), with a detection probability of 0.37 (SD = 0.02). The management authority should concentrate on segments to minimize human disturbance (e.g., fishing, washing clothes, extraction of riverbed materials). If the gharial population in this river declines, their population in central Nepal will be threatened. Hence, we suggest designating the Rapti River section that passes across the CNP as a "no extraction zone."

Computational investigations and molecular dynamics simulations envisioned for potent antioxidant and anticancer drugs using indole-chalcone-triazole hybrids.

Cancer, also called malignancy, is a disease which is closely related with the oxidative stress instigated by the overproduction of vulnerable oxygen and nitrogen species. Available drugs are relatively painful and toxic and so are trailing their captivation. Keeping this in mind, we have attempted to reach a novel anti-cancer drug by taking a set of nineteen ligands which are hybrids of Indole-chalcone and triazole. These ligands were allowed to interact with the DNA dodecamer 5'(CGCGAATTCGCG)3' one by one using various docking protocols of Glide. Better docked complexes screened through docking scores and reported activity data were selected and exposed to molecular dynamics run of 20 ns. The dynamical pathways were investigated for each complex comparing the pre- and post- dynamics run. The outcome of the work is discussed in this paper. Among the better hybrids of this series, one of the molecules has shown interesting features, confirming its non-toxic nature and working as intercalator as well minor groove binder, perhaps making it suitable as a potent drug for further pharmacological use.

Electronic structure, vibrational assignments and simulation studies with A/T rich DNA duplex of an aromatic bis-amidine derivative.

In this paper, computational investigations have been carried out on an aromatic bis-amidine which is considered to be crucial due to its peculiar properties including anti-Pneumocystis carinii pneumonia(PCP), anti-inflammatory and anticancer activities. The raw structure of an aromatic bis-amidine namely; 2,5-bis[4-(N-cyclohexyl-amidino)phenyl]furan was retrieved, optimized and geometrical parameters were computed. The computational results have been compared with those of reported experimental values. In order to check its binding capability, we pave the way a step further by the interaction of the molecule with DNA duplex, 5'(CGCGAATTCGCG)3', which consisted of A/T base pairs in its central region. In addition to geometrical, MEP, HOMO-LUMO analyses and IR assignments, molecular docking with DNA has also been performed. The best docked complex was subjected to molecular dynamics simulation for 50ns using AMBER force field. Free energy of binding has been calculated using MM/PBSA method. The outcomes demonstrate that the molecule recognizes both the strands of DNA duplex through hydrogen bonding within the minor groove side, preferably at A/T rich region and remains stable during the course of dynamics. It may be concluded that the compound shows better binding capability with duplex under study and may be used as a drug lead against Pneumocystis carinii pneumonia.

Molecular modeling and structural studies of 12-mer immobile four-way DNA junction in solution.

Molecular modelling and structural studies of 12-mer immobile four-way DNA junction model is reported here. The DNA junction which was built and investigated, consisted of the following sequences 5'd(GGAAGGGGCTGG), 5'd(CCAGCCTGAGCC), 5'd(GGCTCAACTCGG) and 5'd(CCGAGTCCTTCC). The model was made in such a way that the junction may lack two-fold sequence symmetry at the crossover point. A new version of the AMBER force field has been used, in addition to the Particle Mesh Ewald (PME) method which deals with the refinement treatment of the long range interaction potentials, the well known limitation in MD protocol. After molecular dynamics simulation the backbone parameters and helical parameters of the DNA junction model is calculated and its dynamical pathway is discussed. A close observation near the junction point reveals the shifting in the orientation of some of the P-O bonds from the usual π3 turn for A- and B- DNA to either π1 or π2 type of turn in order to achieve conformational stability. With this study it seems possible to derivatize synthetic DNA molecules with special functional groups both on the bases and at the backbones as in the case of some natural processes by which drugs, particular proteins etc. recognizes and binds to the specific sites of DNA.

Iron status at birth and at 4 weeks in preterm-SGA infants in comparison with preterm and term-AGA infants.

OBJECTIVE: To determine the iron status at birth in preterm small for gestational age (SGA) in comparison with preterm appropriate for gestation (AGA) and term-AGA infants. METHODS: Mother-infant pairs with gestation of < 37 weeks, both SGA, and preterm-AGA and term-AGA as control were enrolled. Maternal, cord blood and infant blood samples at 4 weeks were obtained for various iron indices - cord serum ferritin, proportion of infants with "low" serum ferritin, serum ferritin at 4 weeks and correlation among maternal and neonatal iron indices - hemoglobin,serum ferritin and total iron-binding capacity. RESULTS: There were 50 mother-infant pairs in each group. Cord serum ferritin levels were less in preterm-SGA group as compared to preterm-AGA group (median [interquartile range]: 68 [30 113] vs. 120 [73 127], p = 0.002) and preterm-AGA had less cord ferritin than term-AGA (141 [63 259], p = 0.006). The proportion of the infants with "low" serum ferritin was more in preterm-SGA than in preterm-AGA (16 [32%] vs. 5 [10%], p = 0.01). The serum ferritin levels at follow-up were also less in preterm-SGA as compared to preterm-AGA (143.5 ± 101 vs. 235.1 ± 160, p = 0.004). Other cord blood iron indices and follow-up serum ferritin levels were similar. There was no correlation among various maternal and neonatal cord iron parameters. CONCLUSIONS: Preterm-SGA infants have lesser total iron stores as compared to gestation-matched AGA infants, which is again lesser than term infants. Future studies can be planned to look at iron status at 12 months as well as their neurodevelopmental outcome.

Iron status at birth and at 4 weeks in term small-for-gestation infants in comparison with appropriate-for-gestation infants.

OBJECTIVE: To determine body iron stores at birth in term small-for-gestational age (SGA) infants as compared to appropriate-for-gestational age (AGA) infants. METHODS: In this prospective study, mother-infant pairs with gestation of  ≥ 37 weeks and birth weight of at least 1.5 kg were enrolled. Asymmetric SGA infants were taken as cases and term AGA infants as controls. Maternal, cord blood, and infant blood samples at 4 weeks were obtained for measurement of various iron indices - cord serum ferritin, serum ferritin at 4 weeks, and correlation among maternal and neonatal iron indices - Hb, serum iron, ferritin, and total iron binding capacity (TIBC). RESULTS: There were 50 SGA and 50 AGA mother-infant pairs. Cord serum ferritin levels were low in SGA group as compared to AGA [median (IQR): 68 (30,136) vs. 141 (63,259), p = 0.007]. The proportion of infants with 'low' cord ferritin (< 40 µg/l) were more in SGA [p = 0.05]. There was no correlation among various maternal and neonatal cord iron parameters. The serum ferritin levels at 4 weeks were similar in both the groups (p = 0.16). CONCLUSIONS: Term SGA infants have lesser total iron stores as compared to AGA infants at birth. Future studies can be designed to look at long-term neurodevelopmental outcome of the SGA babies with low as well as normal ferritin and also the role of early iron supplementation in term SGA neonates.