Teaching transposon classification as a means to crowd source the curation of repeat annotation - a tardigrade perspective.

BACKGROUND: The advancement of sequencing technologies results in the rapid release of hundreds of new genome assemblies a year providing unprecedented resources for the study of genome evolution. Within this context, the significance of in-depth analyses of repetitive elements, transposable elements (TEs) in particular, is increasingly recognized in understanding genome evolution. Despite the plethora of available bioinformatic tools for identifying and annotating TEs, the phylogenetic distance of the target species from a curated and classified database of repetitive element sequences constrains any automated annotation effort. Moreover, manual curation of raw repeat libraries is deemed essential due to the frequent incompleteness of automatically generated consensus sequences. RESULTS: Here, we present an example of a crowd-sourcing effort aimed at curating and annotating TE libraries of two non-model species built around a collaborative, peer-reviewed teaching process. Manual curation and classification are time-consuming processes that offer limited short-term academic rewards and are typically confined to a few research groups where methods are taught through hands-on experience. Crowd-sourcing efforts could therefore offer a significant opportunity to bridge the gap between learning the methods of curation effectively and empowering the scientific community with high-quality, reusable repeat libraries. CONCLUSIONS: The collaborative manual curation of TEs from two tardigrade species, for which there were no TE libraries available, resulted in the successful characterization of hundreds of new and diverse TEs in a reasonable time frame. Our crowd-sourcing setting can be used as a teaching reference guide for similar projects: A hidden treasure awaits discovery within non-model organisms.

A comprehensive investigation on alleviating oxidative stress and inflammation in hyperglycaemic conditions through in vitro experiments and computational analysis.

Protein glycation, hyper-inflammatory reactions, and oxidative stress play a crucial role in the pathophysiology of numerous diseases. The current work evaluated the protective ability of ethyl alcohol extract of leaves from holy basil (Ocimum sanctum Linn) against inflammation, oxidative stress, glycation and advanced glycation endproducts formation. Various in vitro assays assessed prementioned properties of holy basil. In addition, molecular docking was conducted. The highest hydrogen peroxide reduction activity (72.7 %) and maximum percentage of DPPH scavenging (71.3 %) depicted its vigorous antioxidant abilities. Furthermore, it showed the most excellent protection against proteinase activity (67.247 %), prevention of denaturation of egg albumin (65.29 %), and BSA (bovine serum albumin) (68.87 %) with 600 µg/ml. Percent aggregation index (57.528 %), browning intensity (56.61 %), and amyloid structure (57.0 %) were all reduced significantly using 600 µg/ml of extract. Additionally, the antimicrobial potential was also confirmed. According to a molecular docking study, active leaf extract ingredients were found to bind with superoxide dismutase, catalase, and carbonic anhydrase. As a conclusion, O. sanctum has a variety of health-promoting properties that may reduce the severity of many diseases in diabetic patients. However, in order to ascertain the mechanisms of action of the components of its leaves in disease prevention, more thorough research based on pharmacological aspects is needed.

Role of Ajwa Date Fruit Pulp and Seed in the Management of Diseases through In Vitro and In Silico Analysis.

This study investigated the health-promoting activities of methanolic extracts of Ajwa date seed and fruit pulp extracts through in vitro studies. These studies confirmed potential antioxidant, anti-hemolytic, anti-proteolytic, and anti-bacterial activities associated with Ajwa dates. The EC50 values of fruit pulp and seed extracts in methanol were reported to be 1580.35 ± 0.37 and 1272.68 ± 0.27 µg/mL, respectively, in the DPPH test. The maximum percentage of hydrogen peroxide-reducing activity was 71.3 and 65.38% for both extracts at 600 µg/mL. Fruit pulp and seed extracts inhibited heat-induced BSA denaturation by 68.11 and 60.308%, heat-induced hemolysis by 63.84% and 58.10%, and hypersalinity-induced hemolysis by 61.71% and 57.27%, and showed the maximum anti-proteinase potential of 56.8 and 51.31% at 600 µg/mL, respectively. Seed and fruit pulp inhibited heat-induced egg albumin denaturation at the same concentration by 44.31 and 50.84%, respectively. Ajwa seed showed minimum browning intensity by 63.2%, percent aggregation index by 64.2%, and amyloid structure by 63.8% at 600 µg/mL. At 100 mg/mL, Ajwa seed extract exhibited good antibacterial activity. Molecular docking analysis showed that ten active constituents of Ajwa seeds bind with the critical antioxidant enzymes, catalase (1DGH) and superoxide dismutase (5YTU). The functional residues involved in such interactions include Arg72, Ala357, and Leu144 in 1DGH, and Gly37, Pro13, and Asp11 in 5YTU. Hence, Ajwa dates can be used to develop a suitable alternative therapy in various diseases, including diabetes and possibly COVID-19-associated complications.

Intramolecularly Double-Donor-Stabilized Stannylene and Its Coordination towards Ag(I) and Au(I) Centers.

The intramolecularly double-donor-stabilized stannylene 1 has been synthesized from the salt-metathesis reaction between two equivalents of lithium pyridine ene-amide L1 and SnCl2 . Compound 1 exhibits dipolar behavior when reacted with B(C6 F5 )3 leading to the zwitterionic compound 2. The reaction of 1 with one equivalent and 0.5 equivalent of AgOTf (OTf=trifluoromethane sulfonate) result in the formation of a stannylene-AgOTf complex 3 and a homoleptic distannylene-silver ionic complex 4, respectively. Analogous to complex 4, the gold(I) complex 5 has been synthesized from the reaction between two equivalents of 1 and 0.5 equivalent of AuCl.SMe2 /Me3 SiOTf. Complex 5 is the first example of homoleptic stannylene-Au(I) ionic complex among the very scarce reports on stannylene-gold(I) coordination complexes. All compounds have been structurally characterized using single crystal X-ray crystallography. Solution-state characterization have been performed using multinuclear NMR techniques. Detailed DFT calculations on the optimized geometries 1 o, 3 o-5 o reveal the change in sp- hybridization on the pyramidal Sn(II) center upon metal coordination and their bonding overlaps.

Versatile coordinating abilities of acyclic N4 and N2P2 ligand frameworks in conjunction with Sn[N(SiMe3)2]2.

The adaptability of three acyclic tetradentate ligands with the -CHR-CHR- (R = H or alkyl substituent) linker in the backbone: bis(α-iminopyridine) L1 and the reduced form L2 and diaminodiphosphine L3 to stabilize various stannylenes has been explored. The reaction of L1 with two equivalents of Sn[N(SiMe3)2]2 led to the stabilization of a bisstannylene 1 through the ene-amide transformation of L1. The reaction of bisstannylene 1 with B(C6F5)3 and silver trifluoromethane sulfonate led to the formation of ligand stabilized Sn(ii) dications 2 and 3 respectively. A mixture of Sn(ii) dication 3 and a Sn(ii) monocation 4 has been obtained from the reaction between 1 and trimethylsilyl trifluoromethane sulfonate. A 1 : 1 stoichiometric reaction between L3 and Sn[N(SiMe3)2]2 led to the isolation of a dimeric monostannylene 5 having a step-like structure with a Sn2N2 central ring. The reaction of L2 with Sn[N(SiMe3)2]2 underwent an electron transfer reaction ultimately leading to bis(α-iminopyridine) isolation.

Stabilization of bis(chlorogermyliumylidene)s within bifunctional PNNP ligand frameworks and their reactivity studies.

The diiminodiphosphine (Lim) and diaminodiphosphines (l-NH and l-NMe) with a bifunctional PNNP ligand framework have been employed to host two [GeCl]+ units leading to the formation of bis(chlorogermyliumylidene) 1-3, respectively. The synthetic route involves a 1 : 2 stoichiometric reaction between the PNNP ligand and GeCl2·dioxane and the subsequent addition of two equivalents of chloride abstracting agent. Compound 1 is unstable towards coordinating solvents and Lewis bases, resulting in the displacement of the GeCl unit and the formation of rearranged products 4 and 5. However, the diaminodiphosphine coordinated Ge(ii) bis(monocation)s 2 and 3 proved to be stable and revealed their electrophilic behaviour towards the Lewis bases studied.

Bis(chlorogermyliumylidene) and its significant role in elusive reductive cyclization.

Bis(chlorogermyliumylidene) 2 has been strategically obtained within redox-active bis(α-iminopyridine). Metal-free reduction of 2 followed by protonation led to elusive 2,3-di(pyridin-2-yl)piperazine with meso-stereoselectivity. Formation of persistent triplet diradicals upon reduction and isolation of piperazine stabilized Ge(ii) dication intermediates provide convincing evidence for the crucial role of [GeCl]+ units in reductive cyclization.

Direct coordination of a germanium(ii) dicationic center to transition metals.

The germanium(ii) center of dicationic compound 1 donates an electron pair to transition metal Ag(i) and Au(i) cations, leading to complexes 2 and 3 respectively. Complex 3 is stabilized by [Ge:]2+→Au(i) σ-donation and π-back donation from filled d-orbitals of Au(i) to the two sets of p-orbitals available on Ge(ii) centers.