Twist1 induces chromosomal instability (CIN) in colorectal cancer cells.

Twist1 is a basic helix-loop-helix transcription factor, essential during early development in mammals. While Twist1 induces epithelial-to-mesenchymal transition (EMT), here we show that Twist1 overexpression enhances nuclear and mitotic aberrations. This is accompanied by an increase in whole chromosomal copy number gains and losses, underscoring the role of Twist1 in inducing chromosomal instability (CIN) in colorectal cancer cells. Array comparative genomic hybridization (array CGH) analysis further shows sub-chromosomal deletions, consistent with an increased frequency of DNA double strand breaks (DSBs). Remarkably, Twist1 overexpression downmodulates key cell cycle checkpoint factors-Bub1, BubR1, Mad1 and Mad2-that regulate CIN. Mathematical simulations using the RACIPE tool show a negative correlation of Twist1 with E-cadherin and BubR1. Data analyses of gene expression profiles of patient samples from The Cancer Genome Atlas (TCGA) reveal a positive correlation between Twist1 and mesenchymal genes across cancers, whereas the correlation of TWIST1 with CIN and DSB genes is cancer subtype-specific. Taken together, these studies highlight the mechanistic involvement of Twist1 in the deregulation of factors that maintain genome stability during EMT in colorectal cancer cells. Twist1 overexpression enhances genome instability in the context of EMT that further contributes to cellular heterogeneity. In addition, these studies imply that Twist1 downmodulates nuclear lamins that further alter spatiotemporal organization of the cancer genome and epigenome. Notwithstanding their genetic background, colorectal cancer cells nevertheless maintain their overall ploidy, while the downstream effects of Twist1 enhance CIN and DNA damage enriching for sub-populations of aggressive cancer cells.

Identification of New KRAS G12D Inhibitors through Computer-Aided Drug Discovery Methods.

Owing to several mutations, the oncogene Kirsten rat sarcoma 2 viral oncogene homolog (KRAS) is activated in the majority of cancers, and targeting it has been pharmacologically challenging. In this study, using an in silico approach comprised of pharmacophore modeling, molecular docking, and molecular dynamics simulations, potential KRAS G12D inhibitors were investigated. A ligand-based common feature pharmacophore model was generated to identify the framework necessary for effective KRAS inhibition. The chemical features in the selected pharmacophore model comprised two hydrogen bond donors, one hydrogen bond acceptor, two aromatic rings and one hydrophobic feature. This model was used for screening in excess of 214,000 compounds from InterBioScreen (IBS) and ZINC databases. Eighteen compounds from the IBS and ten from the ZINC database mapped onto the pharmacophore model and were subjected to molecular docking. Molecular docking results highlighted a higher affinity of four hit compounds towards KRAS G12D in comparison to the reference inhibitor, BI-2852. Sequential molecular dynamics (MD) simulation studies revealed all four hit compounds them possess higher KRAS G12D binding free energy and demonstrate stable polar interaction with key residues. Further, Principal Component Analysis (PCA) analysis of the hit compounds in complex with KRAS G12D also indicated stability. Overall, the research undertaken provides strong support for further in vitro testing of these newly identified KRAS G12D inhibitors, particularly Hit1 and Hit2.

Computational Simulations Highlight the IL2Rα Binding Potential of Polyphenol Stilbenes from Fenugreek.

Widely used in global households, fenugreek is well known for its culinary and medicinal uses. The various reported medicinal properties of fenugreek are by virtue of the different natural phytochemicals present in it. Regarded as a promising target, interleukin 2 receptor subunit alpha (IL2Rα) has been shown to influence immune responses. In the present research, using in silico techniques, we have demonstrated the potential IL2Rα binding properties of three polyphenol stilbenes (desoxyrhaponticin, rhaponticin, rhapontigenin) from fenugreek. As the first step, molecular docking was performed to assess the binding potential of the fenugreek phytochemicals with IL2Rα. All three phytochemicals demonstrated interactions with active site residues. To confirm the reliability of our molecular docking results, 100 ns molecular dynamics simulations studies were undertaken. As discerned by the RMSD and RMSF analyses, IL2Rα in complex with the desoxyrhaponticin, rhaponticin, and rhapontigenin indicated stability. The RMSD analysis of the phytochemicals alone also demonstrated no significant structural changes. Based on the stable molecular interactions and comparatively slightly better MM/PBSA binding free energy, rhaponticin seems promising. Additionally, ADMET analysis performed for the stilbenes indicated that all of them obey the ADMET rules. Our computational study thus supports further in vitro IL2Rα binding studies on these stilbenes, especially rhaponticin.

Insights on COVID-19 impacts, challenges and opportunities for India's biodiversity research: From complexity to building adaptations.

The COVID-19 pandemic has impacted every sphere of human society. The paradigm shift of focus to COVID-related research and management has significantly affected various scientific domains, including biodiversity conservation. We assessed the perceptions of early-career researchers working for biodiversity conservation across India, to understand the impacts of the ongoing pandemic on their research. We administered an online questionnaire survey to 565 respondents, who identified four key areas that are affected by the pandemic: (1) research, (2) conservation (3) education, and (4) communication and networking. Respondents (89.2%) perceived that their fieldwork, followed by travel for meetings and funding were the most affected due to COVID-19 outbreak and subsequent lockdown. Nonetheless, responses on the impact varied between different professional categories and were disproportionate. Our study highlights that majority of the respondents (80%) advocate for stakeholder-driven policies and management practices as the most effective strategy to promote biodiversity conservation, in the post-COVID-19 world. To this end, as a post-pandemic response, we propose holistic solutions such as optimising research funding and collaborations, and supporting and strengthening them by citizen science and big data analytics. Our findings and recommendations will also serve as a paradigm for post-COVID-19 biodiversity policy, advocacy and implementation of the post 2020 biodiversity action plan that supports eco civilization.

Our experience of laparoscopic pyloromyotomy with ultrasound-guided parameters.

Traditional management of infantile Hypertrophic Pyloric Stenosis is open pyloromyotomy after initial adequate resuscitation of the patient. From 1991, laparoscopic approach is considered feasible and safe. Today, diagnosis of hypertrophic pyloric stenosis is made most often made by ultrasound. With use of ultrasound-guided parameters (length of pyloric tumour and thickness of pyloric tumour), we could avoid 'incomplete pyloromyotomy' and 'mucosal perforation' (most common complications in laparoscopic approach) to achieve 100% adequacy and safety in laparoscopic pyloromyotomy.

Total laparoscopic repair of Spigelian hernia with undescended testis.

Spigelian hernia is very rare in the paediatric age group. We present the case of an 11-month-old male child who presented with left Spigelian hernia with the left undescended testis in its sac. Hernia repair with orchidopexy was done using total laparoscopic approach. It is the first reported case of total laparoscopic repair of Spigelian hernia with undescended testis in the paediatric age group.

The PE_PGRS Proteins of Mycobacterium tuberculosis Are Ca(2+) Binding Mediators of Host-Pathogen Interaction.

The phenomenal success of Mycobacterium tuberculosis (M.tb) as a pathogen is primarily based on its ability to modulate host immune responses. The genome of M.tb encodes multiple immunomodulatory proteins, including several members of the multigenic PE_PPE family of which the PE_PGRS proteins are a subset. Curiously, 56 of the 61 PE_PGRS proteins contain multiple copies of the glycine-rich sequence motif GGXGXD/NXUX, a nonapeptide sequence predicted to bind Ca(2+), but the functional significance of these motifs remains a mystery. Here we provide evidence via isothermal titration calorimetry, (45)Ca blotting, fluorescence, and circular dichroism spectroscopy that Ca(2+) binds to the PE_PGRS proteins, PE_PGRS33 (Rv1818c) (10 motifs) and PE_PGRS61 (Rv3653) (one motif). Ca(2+) was observed not to bind to PE_PGRS8 (Rv0742), which lacks nonapeptide motifs. Using recombinant Mycobacterium smegmatis strains expressing Rv1818c and Rv3653 and the THP-1 macrophage model of infection, we show that the two proteins mediate Ca(2+)-dependent upregulation of the anti-inflammatory cytokine IL-10, events critical to the pathogenesis of M.tb. Both Rv1818c and Rv3653 interact with TLR2 in a Ca(2+)-dependent manner, providing a novel mechanistic basis for their immunomodulatory effects. Mutations in the nonapeptide motif of Rv3653 led to compromised Ca(2+) binding, validating the functional criticality of this motif. This study demonstrates for the first time not only their Ca(2+) binding properties but also an essential role for Ca(2+) in the functioning of the M.tb PE_PGRS proteins, opening up the possibility of developing novel anti-tuberculosis therapeutics that inhibit Ca(2+)-PE_PGRS binding.

The Mycobacterium tuberculosis desaturase DesA1 (Rv0824c) is a Ca2+ binding protein.

The hallmark feature of Mycobacterium tuberculosis (M.tb) the causative agent of human tuberculosis, is its complex lipid rich cell wall comprised primarily of mycolic acids, long chain fatty acids that play a key role in structural stability and permeability of the cell wall. In addition, they are involved in inhibiting phagosome-lysosome fusion and aid in granuloma formation during the pathogenic process. M.tb DesA1 is an essential acyl-acyl carrier protein desaturase predicted to catalyze the introduction of position specific double bonds during the biosynthesis of mycolic acids. This protein is one among three annotated desaturases (DesA1-3) in the M.tb genome but is unique in containing a ßγ-crystallin Greek key signature motif, a well-characterized fold known to mediate Ca2+ binding in both prokaryotic and eukaryotic organisms. Using Isothermal Titration Calorimetry and 45CaCl2 overlay, we demonstrate that Ca2+ binds to DesA1. Spectroscopic measurements suggested that this binding induces changes in protein conformation but does not lead to significant alterations in the secondary structure of the protein, a feature common to several ßγ-crystallins. An M. smegmatis strain over-expressing M.tb desA1 showed a Ca2+ dependent variation in surface phenotype, revealing a functional role for Ca2+in DesA1 activity. This study represents the first identification of a Ca2+ binding ßγ-crystallin in M.tb, emphasizing the implicit role of Ca2+ in the pathogenesis of M.tb.

A comparative study of the toxicological aspects of vanadium pentoxide and vanadium oxide nanoparticles.

Indiscriminate use of vanadium oxide nanoparticles (NPs) in steel industries and their release during combustion of fossil fuels makes it essential to study their toxic potential. Herein, we assessed the toxicological effects of two types of in-house synthesized vanadium oxide NPs in Wistar rats exposed to NPs through inhalation route. V2O5 and VO2 NPs exhibited rod and spherical symmetry, respectively with a mean diameter of 50±20 and 30±10 nm. Assessment of bronchoalveolar lavage fluid parameters demonstrated that VO2 NP-exposed animals had higher levels of lactate dehydrogenase, gamma-glutamyl transpeptidase and alkaline phosphatase as compared to V2O5 NP-exposed animals. The levels of oxidative stress markers malondialdehyde and reduced glutathione also indicated higher toxic potential of VO2 NPs. Moreover, after 7-day recovery, the levels of the above parameters were closer to normal levels only in V2O5-exposed animals. Interestingly, histopathological and immune-histopathology analysis (TNF-α) of lung tissue showed higher damage and inflammatory response in VO2 NP-exposed animals, which persisted even after 7 days of recovery period. Surprisingly, the carcinogenic potential of vanadium oxide NPs came into light which was indicated by terminal deoxynucleotidyl transferase dUTP nick-end labeling assay as well as the decreased levels of p53 and Bax, in lung tissue of NP-exposed animals. Notably, the physiochemical characterization of NPs, especially the shape and the size, play a central role in shaping the toxicity of these NPs and thus should be extensively evaluated for outlining the regulatory guidelines.

Antimicrobial Solid Starch-Iodine Complex via Reactive Extrusion and Its Application in PLA-PBAT Blown Films.

In this study, a solid masterbatch of starch-iodine complex with 6.7 wt.% iodine was prepared in pellet form using a ZSK-30 twin-screw extruder. Thermogravimetric (TGA) and isothermal TGA analysis of the pellets revealed that there was no significant loss of iodine due to sublimation during reactive extrusion. These solid pellets demonstrated antifungal properties when applied to strawberries via dip coating in an aqueous solution, extending their shelf life from two days to eight days, thereby reducing fungal growth and visual decay. Furthermore, the solid pellets displayed antibacterial activity against E. coli, as evidenced by the clear zone of inhibition observed in the Kirby-Bauer test. To enhance practical application, these pellets were further blended with PLA-PBAT film formulations at 10 and 18% by wt. to make blown films with effective iodine loadings of 0.7 and 1.3% by wt. These films showed superior antibacterial activity against E. coli compared with PLA control films and the commercial silver antimicrobial-containing films during direct inoculation tests as per ISO 22196. Tensile strength and elongation at break in machine direction (MD) for the starch-iodine-containing blown films were comparable to the control films in MD, but tensile strength was reduced to 37-40% in the transverse direction (TD). This was due to a non-uniform dispersion of the starch-iodine complex in the films, as confirmed by the visual and SEM analyses. Thus, this study illustrates the practical utility of the solid starch-iodine complex as a safe and efficient means of introducing iodine into an environment, mitigating the typical hazards associated with handling solid iodine.

Pulmonary fibrotic response to inhalation of ZnO nanoparticles and toluene co-exposure through directed flow nose only exposure chamber.

The increasing use of Zinc Oxide nanoparticles (ZnONPs) in paint industry is not supplemented with adequate toxicology data. This report focuses on the fibrogenic toxicity caused due to co-exposure of ZnONPs and toluene in male Wistar rats, exposed for 28 days, through directed flow nose only exposure chamber. The rats were grouped as air control, toluene control (200 ppm), zinc oxide control (10 mg/m(3)), low dose co-exposed (5 mg/m(3) ZnO and 200 ppm of toluene) and high dose co-exposed (10 mg/m(3) of ZnO and 200 ppm of toluene). Our study demonstrates that co-exposure of ZnONPs and toluene (as in paint industry), even at their respective permissible exposure level (5 mg/m(3) for ZnO and 200 ppm for toluene) have the potential to produce a progressive inflammatory and fibrotic response in the alveolar tissues of the lungs. We observed a significant increase in inflammatory markers in BAL fluid and elevated malondialdehyde (MDA) levels with lower levels of intracellular reduced glutathione (GSH) in lungs of rats of co-exposed group. Significant increase in the levels of pro-inflammatory mediators (IL-6, Ikßα, Cox-II, p-NF-κB) in lung tissues also indicated pulmonary damage. To best of our knowledge this is the first study which highlights the toxicity of co-exposed ZnO NPs and toluene.

Pantoprazole associated dyspepsia hypocalcemia and hyponatremia: A disproportionality analysis in FDA adverse event reporting system (FAERS) database.

BACKGROUND AND STUDY AIM: The study was designed to detect novel Adverse Events (AEs) of pantoprazole by disproportionality analysis in the FDA (Food and Drug Administration) database of Adverse Event Reporting System (FAERS) using Data Mining Algorithms (DMAs). Pantoprazole, the most commonly over-utilized Over The Counter (OTC) medication, was selected to assess any short-term or long-term AEs. The study aimed to analyze the novel adverse events of pantoprazole using the FAERS database. MATERIALS AND METHODS: A retrospective case/non-case disproportionality analysis was performed in the FAERS database. This study was based on AEs reported to FAERS from 2006Q1-2021Q3. Openvigil 2.1 was used for data extraction. Reporting Odds Ratio (ROR), Proportional Reporting Ratio (PRR), and Information Component (IC) were applied to measure the disproportionality in reporting. A value of ROR-1.96SE > 1, PRR ≥ 2, and IC-2SD > 0 were considered as the threshold for a positive signal. RESULTS: A total of 1050 reports of dyspepsia, 7248 reports of hypocalcemia and 995 reports of hyponatremia were identified. A potential positive signal for dyspepsia (ROR-1.96SE = 2.231, PRR = 2.359, IC-2SD = 1.13), hypocalcemia (4.961, 5.45, 2.23) and hyponatremia (3.948, 4.179, 1.92) were identified for pantoprazole. CONCLUSION: Data mining in the FAERS database produced three potential signals associated with pantoprazole. As a result, further clinical surveillance is needed to quantify and validate potential hazards associated with pantoprazole-related adverse events.

Bilateral single system ectopic ureters - A rare variant.

Bilateral single system ectopic ureters are a rare entity in paediatric urology. We report a girl child with bilateral single system ectopic ureters with right system opening into the vagina, who presented at 3.5 years with continuous dribbling of urine & a small capacity bladder. Renal scans and MRI were done which indicated bilateral single system ectopic ureters with hydroureteronephrosis. We managed her surgically by a right nephro-ureterectomy, bladder augmentation, left ureteric reimplantation and Mitrofanoff. Post op patient had acute on chronic renal failure, stabalised by haemodialysis. It is a rare presentation if managed promptly can prevent renal replacement therapy.

Triosmium clusters on a support: determination of structure by X-ray absorption spectroscopy and high-resolution microscopy.

The structures of small, robust metal clusters on a solid support were determined by a combination of spectroscopic and microscopic methods: extended X-ray absorption fine structure (EXAFS) spectroscopy, scanning transmission electron microscopy (STEM), and aberration-corrected STEM. The samples were synthesized from [Os(3) (CO)(12) ] on MgO powder to provide supported clusters intended to be triosmium. The results demonstrate that the supported clusters are robust in the absence of oxidants. Conventional high-angle annular dark-field (HAADF) STEM images demonstrate a high degree of uniformity of the clusters, with root-mean-square (rms) radii of 2.03±0.06 Å. The EXAFS OsOs coordination number of 2.1±0.4 confirms the presence of triosmium clusters on average and correspondingly determines an average rms cluster radius of 2.02±0.04 Å. The high-resolution STEM images show the individual Os atoms in the clusters, confirming the triangular structures of their frames and determining OsOs distances of 2.80±0.14 Å, matching the EXAFS value of 2.89±0.06 Å. IR and EXAFS spectra demonstrate the presence of CO ligands on the clusters. This set of techniques is recommended as optimal for detailed and reliable structural characterization of supported clusters.

Effects of Modified Thermoplastic Starch on Crystallization Kinetics and Barrier Properties of PLA.

This study reports on using reactive extrusion (REX) modified thermoplastic starch particles as a bio-based and biodegradable nucleating agent to increase the rate of crystallization, percent crystallinity and improve oxygen barrier properties while maintaining the biodegradability of PLA. Reactive blends of maleated thermoplastic starch (MTPS) and PLA were prepared using a ZSK-30 twin-screw extruder; 80% glycerol was grafted on the starch during the preparation of MTPS as determined by soxhlet extraction with acetone. The crystallinity of PLA was found to increase from 7.7% to 28.6% with 5% MTPS. The crystallization temperature of PLA reduced from 113 °C to 103 °C. Avrami analysis of the blends showed that the crystallization rate increased 98-fold and t1/2 was reduced drastically from 20 min to <1 min with the addition of 5% MTPS compared to neat PLA. Observation from POM confirmed that the presence of MTPS in the PLA matrix significantly increased the rate of formation and density of spherulites. Oxygen and water vapor permeabilities of the solvent-casted PLA/MTPS films were reduced by 33 and 19% respectively over neat PLA without causing any detrimental impacts on the mechanical properties (α = 0.05). The addition of MTPS to PLA did not impact the biodegradation of PLA in an aqueous environment.

Computer-Aided Drug Discovery Identifies Alkaloid Inhibitors of Parkinson's Disease Associated Protein, Prolyl Oligopeptidase.

Parkinson's disease is a common neurodegenerative disorder marked by the accumulation of the protein alpha synuclein. Studies have indicated the role of prolyl oligopeptidase (POP), a serine protease, in alpha synuclein accumulation. Therefore, POP emerges as an attractive medicinal target. Traditionally, most of the early medicines have been plant-based owing to their ready availability and negligible side effects. Alkaloids owing to their neurotransmitter modulatory, anti-amyloid, anti-oxidant, and anti-inflammatory activities have shown potential in neurodegenerative disease. In this work, we computationally evaluated alkaloid class of phytochemicals for their therapeutic efficacy against POP. Alkaloids were retrieved from the publically available database, Chemical Entities of Biological Interest (ChEBI), and screened for their drug likeness (Lipinski's rule of 5) and absorption, distribution, metabolism, and excretion, and toxicity (ADMET) in Discovery Studio by ensuring parameters suitable for a central nervous system disease such as blood-brain barrier (BBB) level set to ≤2, absorption level set to 0 and solubility level permitted set to 2, 3, or 4. Next, molecular docking was performed to learn about the affinity of the filtered alkaloids with the POP. Subsequently, molecular dynamic simulations were conducted to assess the reliability and stability of the alkaloid-protein complex. Our study identified metergoline, pipercallosine, celacinnine, lobeline, cystodytin G, lycoperine A, hookerianamide J, and martefragin A as putative lead compounds against POP. Among these, metergoline, pipercallosine, hookerianamide J, and lobeline showed the most promising results. These compounds demonstrated better or equivalent molecular docking scores in comparison to three POP inhibitors that had reached clinical trials, i.e., Z-321, S-17092, and JTP-4819. MD simulations indicated that these compounds remained intact at the active site while adhering to the binding mode and interaction patterns as that of the reported inhibitors. The research conducted here, therefore, provides evidence for conducting in vitro POP inhibitory studies of these newly identified plant-based POP inhibitors.

Transcriptome analysis of sinensetin-treated liver cancer cells guided by biological network analysis.

Hepatocellular carcinoma is recognized as one of the most frequently occurring malignant types of liver cancer globally, making the identification of biomarkers critically important. The aim of the present study was to identify the genes involved in the anticancer effects of flavonoid compounds so that they may be used as targets for cancer treatment. Sinensetin (SIN), an isolated polymethoxyflavone monomer compound, possesses broad antitumor activities in vitro. Therefore, the identification of a transcriptome profile on the condition of cells treated with SIN may aid to better understand the genes involved and its mechanism of action. Genomic profiling studies of cancer are increasing rapidly in order to provide gene expression data that can reveal prognostic biomarkers to combat liver cancer. In the present study, high-throughput RNA sequencing (RNA-seq) was performed to reveal differential gene expression patterns between SIN-treated and SIN-untreated human liver cancer HepG2 cells. A total of 43 genes were identified to be differentially expressed (39 downregulated and 4 upregulated in the SIN-treated group compared with the SIN-untreated group). An extensive network analysis for these 43 genes resulted in the identification of 10 upregulated highly interconnected hub genes that contributed to the progression of cancer. Functional enrichment analysis of these 10 hub genes revealed their involvement in the regulation of apoptotic processes, immune response and tumor necrosis factor production. Additionally, the mRNA expression levels of these 10 genes were evaluated using reverse transcription-quantitative PCR, and the results were consistent with the RNA-seq data. Overall, the results of the present study revealed differentially expressed genes involved in cancer after SIN treatment in HepG2 cells and may help to develop strategies targeting these genes for treating liver cancer.

Computational Approaches to Discover Novel Natural Compounds for SARS-CoV-2 Therapeutics.

Scientists all over the world are facing a challenging task of finding effective therapeutics for the coronavirus disease (COVID-19). One of the fastest ways of finding putative drug candidates is the use of computational drug discovery approaches. The purpose of the current study is to retrieve natural compounds that have obeyed to drug-like properties as potential inhibitors. Computational molecular modelling techniques were employed to discover compounds with potential SARS-CoV-2 inhibition properties. Accordingly, the InterBioScreen (IBS) database was obtained and was prepared by minimizing the compounds. To the resultant compounds, the absorption, distribution, metabolism, excretion and toxicity (ADMET) and Lipinski's Rule of Five was applied to yield drug-like compounds. The obtained compounds were subjected to molecular dynamics simulation studies to evaluate their stabilities. In the current article, we have employed the docking based virtual screening method using InterBioScreen (IBS) natural compound database yielding two compounds has potential hits. These compounds have demonstrated higher binding affinity scores than the reference compound together with good pharmacokinetic properties. Additionally, the identified hits have displayed stable interaction results inferred by molecular dynamics simulation results. Taken together, we advocate the use of two natural compounds, STOCK1N-71493 and STOCK1N-45683 as SARS-CoV-2 treatment regime.

A Small Molecule for Controlled Generation of Peroxynitrite.

2-Methyl-3-[1-(N,N-dimethylamino)diazen-1-ium-1,2-diol-2-ato-methyl]-naphthalene-1,4-dione 1 (HyPR-1), a small molecule containing a superoxide generator strategically linked to a diazeniumdiolate-based nitric oxide donor, is reported. Evidence for HyPR-1's ability to generate peroxynitrite in the presence of an enzyme as well as enhance peroxynitrite within cells is provided. The utility of this tool in generating peroxynitrite for cellular studies is demonstrated.