Epigenetic dysregulation in cancers by isocitrate dehydrogenase 2 (IDH2).

Recent advances in genome-wide studies have revealed numerous epigenetic regulations brought about by genes involved in cellular metabolism. Isocitrate dehydrogenase (IDH), an essential enzyme, that converts isocitrate into -ketoglutarate (KG) predominantly in the tricarboxylic acid (TCA) cycle, has gained particular importance due to its cardinal role in the metabolic pathway in cells. IDH1, IDH2, and IDH3 are the three isomeric IDH enzymes that have been shown to regulate cellular metabolism. Of particular importance, IDH2 genes are associated with several cancers, including gliomas, oligodendroglioma, and astrocytomas. These mutations lead to the production of oncometabolite D-2-hydroxyglutarate (D-2-HG), which accumulates in cells promoting tumor growth. The enhanced levels of D-2-HG competitively inhibit α-KG dependent enzymes, inhibiting cell TCA cycle, upregulating the cell growth and survival relevant HIF-1α pathway, promoting DNA hypermethylation related epigenetic activity, all of which synergistically contribute to carcinogenesis. The present review discusses epigenetic mechanisms inIDH2 regulation in cells and further its clinical implications.

Disturbance and vegetational structure in an urban forest of Indian Siwaliks: an ecological assessment.

Urban forests face multiple human-mediated pressures leading to compromised ecosystem structure and functioning. Therefore, understanding ecosystem structure in response to ongoing pressures is crucial for sustaining ecological integrity and human well-being. We aim to assess the disturbance and its effects on the vegetation structure of urban forests in Chandigarh using a combination of remote sensing techniques and vegetation surveys. The disturbance was evaluated as a change in NDVI (Normalised Difference Vegetation Index) from 2001 to 2021 by applying the BFAST (Breaks For Additive Season and Trend) algorithm to the MODIS satellite imagery data. A vegetation survey was conducted to compare the species composition, taxonomic and phylogenetic diversity as measures of forest vegetational structure. While signals of disturbance were evident, the changes in vegetation structure were not well established from our study. Further, this analysis indicated no significant differences in vegetation composition due to disturbance (F1,12 = 0.91, p = 0.575). However, the phylogenetic diversity was substantially lower for disturbed plots than undisturbed plots, though the taxonomic diversity was similar among the disturbed and undisturbed plots. Our results confirmed that disturbance effects are more prominent on the phylogenetic than taxonomic diversity. These findings can be considered early signals of disturbance and its impact on the vegetation structure of urban forests and contribute to the knowledge base on urban ecosystems. Our study has implications for facilitating evidence-based decision-making and the development of sustainable management strategies for urban forest ecosystems.

Culture-Free Whole Genome Sequencing of Mycobacterium tuberculosis Using Ligand-Mediated Bead Enrichment Method.

Background: Direct whole genome sequencing (WGS) of Mycobacterium tuberculosis (Mtb) can be used as a tool to study drug resistance, mixed infections, and within-host diversity. However, WGS is challenging to obtain from clinical samples due to low number of bacilli against a high background. Methods: We prospectively collected 34 samples (sputum, n = 17; bronchoalveolar lavage, n = 13; and pus, n = 4) from patients with active tuberculosis (TB). Prior to DNA extraction, we used a ligand-mediated magnetic bead method to enrich Mtb from clinical samples and performed WGS on Illumina platform. Results: Mtb was definitively identified based on WGS from 88.2% (30/34) of the samples, of which 35.3% (12/34) were smear negative. The overall median genome coverage was 15.2% (interquartile range [IQR], 7.7%-28.2%). There was a positive correlation between load of bacilli on smears and genome coverage (P < .001). We detected 58 genes listed in the World Health Organization mutation catalogue in each positive sample (median coverage, 85% [IQR, 61%-94%]), enabling the identification of mutations missed by routine diagnostics. Mutations causing resistance to rifampicin, isoniazid, streptomycin, and ethambutol were detected in 5 of 34 (14.7%) samples, including the rpoB S441A mutation that confers resistance to rifampicin, which is not covered by Xpert MTB/RIF. Conclusions: We demonstrate the feasibility of magnetic bead-based enrichment for culture-free WGS of Mtb from clinical specimens, including smear-negative samples. This approach can also be integrated with low-cost sequencing workflows such as targeted sequencing for rapid detection of Mtb and drug resistance.

Sustainable soil management under drought stress through biochar application: Immobilizing arsenic, ameliorating soil quality, and augmenting plant growth.

Rise in climate change-induced drought occurrences have amplified pollution of metal(loid)s, deteriorated soil quality, and deterred growth of crops. Rice straw-derived biochars (RSB) and cow manure-enriched biochars (CEB) were used in the investigation (at doses of 0%, 2.5%, 5%, and 7.5%) to ameliorate the negative impacts of drought, improve soil fertility, minimize arsenic pollution, replace agro-chemical application, and maximize crop yields. Even in soils exposed to severe droughts, 3 months of RSB and CEB amendment (at 7.5% dose) revealed decreased bulk density (13.7% and 8.9%), and increased cation exchange capacity (6.0% and 6.3%), anion exchange capacity (56.3% and 28.0%), porosity (12.3% and 7.9%), water holding capacity (37.5% and 12.5%), soil respiration (17.8% and 21.8%), and nutrient contents (especially N and P). Additionally, RSB and CEB decreased mobile (30.3% and 35.7%), bio-available (54.7% and 45.3%), and leachable (55.0% and 56.5%) fractions of arsenic. Further, pot experiments with Bengal gram and coriander plants showed enhanced growth (62-188% biomass and 90-277% length) and reduced arsenic accumulation (49-54%) in above ground parts of the plants. Therefore, biochar application was found to improve physico-chemical properties of soil, minimize arsenic contamination, and augment crop growth even in drought-stressed soils. The investigation suggests utilisation of cow manure for eco-friendly fabrication of nutrient-rich CEB, which could eventually promote sustainable agriculture and circular economy. With the increasing need for sustainable agricultural practices, the use of biochar could provide a long-term solution to enhance soil quality, mitigate the effects of climate change, and ensure food security for future generations. Future research should focus on optimizing biochar application across various soil types and climatic conditions, as well as assessing its long-term effectiveness.

Systematic comparison of sequencing-based spatial transcriptomic methods.

Recent developments of sequencing-based spatial transcriptomics (sST) have catalyzed important advancements by facilitating transcriptome-scale spatial gene expression measurement. Despite this progress, efforts to comprehensively benchmark different platforms are currently lacking. The extant variability across technologies and datasets poses challenges in formulating standardized evaluation metrics. In this study, we established a collection of reference tissues and regions characterized by well-defined histological architectures, and used them to generate data to compare 11 sST methods. We highlighted molecular diffusion as a variable parameter across different methods and tissues, significantly affecting the effective resolutions. Furthermore, we observed that spatial transcriptomic data demonstrate unique attributes beyond merely adding a spatial axis to single-cell data, including an enhanced ability to capture patterned rare cell states along with specific markers, albeit being influenced by multiple factors including sequencing depth and resolution. Our study assists biologists in sST platform selection, and helps foster a consensus on evaluation standards and establish a framework for future benchmarking efforts that can be used as a gold standard for the development and benchmarking of computational tools for spatial transcriptomic analysis.

Effect of Biofouling on the Sorption of Organic Contaminants by Microplastics.

Microplastics in the aquatic environment are susceptible to colonization by surrounding microorganisms, which form biofilms over the microplastic's surface. These biofilm-laden microplastics can then interact with a diverse array of contaminants. In the present study, biofilms were grown on microplastics in a laboratory setting using Pseudomonas aeruginosa as a model biofilm-forming bacterium for periods of 5 to 15 days. The sorption of three organic compounds representing different levels of hydrophobicity, namely methylene blue (MB), phenanthrol, and phenanthrene, was used to evaluate the effect of biofilm biomass on the adsorption of organic contaminants to microplastics. The sorption of MB and phenanthrol was found to increase with biofouling time, indicating affinity between these contaminants and the biofilm biomass on the particle. However, the presence of a biofilm did not influence the sorption of phenanthrene on the microplastics. These results suggest that the hydrophobicity of organic contaminants plays a major role in how biofouling of microplastics will influence contaminant sorption by microplastics. For some contaminants, biofilm can enhance the role of microplastics as contaminant vectors. These findings emphasize the need to understand the biomass load on environmental microplastics and the contaminants that associate with it for an accurate representation of the risk associated with microplastics in the environment. Environ Toxicol Chem 2024;00:1-9. © 2024 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Bilateral peripapillary choroidal neovascular membranes in Vogt-Koyanagi-Harada disease.

Choroidal neovascular membrane (CNVM) in Vogt-Koyanagi-Harada disease (VKH) is a known entity, observed primarily during the chronic convalescent and chronic-recurrent phases of the disease. However, the peripapillary location of CNVM is a rare finding.We describe a case of chronic VKH with bilateral peripapillary CNVM detected using multimodal imaging and the associated differential diagnoses and treatment approach.A combination of anti-vascular endothelial growth factor injections, systemic steroids and immunosuppressants is often required to manage the aggressive course of this choroidal neovascularisation.

Linking orthodontic treatment and sleep apnea among adult Indian patients.

The differences in the effects of orthodontic treatment on airway and craniocervical posture in patients with OSA (obstructive sleep apnea) having skeletal class II high-angle malocclusion is of interest. Hence, 48 individuals with OSA and skeletal class II high-angle malocclusion were chosen from among all patients in need of orthodontic therapy. Every patients had CBCT (cone beam computed tomography) taken both before and after receiving orthodontic therapy. All parameters were assessed on the lateral cephalogram from CBCT in order to assess the indices of craniocervical posture, hyoid position, skeletal and dental conditions. Parameters of upper airway (position of hyoid) showed statistically significant increase in values after orthodontic treatments. Thus, there was increase in values of dimensions of upper airway, post orthodontic treatment. Hence, orthodontic therapy help improve the upper airway morphology and craniocervical posture in patients of OSA with hyperdivergent skeletal class II malocclusion.

Assessment of three-dimensional (3-D) left ventricular ejection fraction and speckled tracking echocardiographic strain parameters in non-ischemic left bundle branch block (LBBB) patients and their association with cardiovascular events - A prospective observational study.

OBJECTIVE: To investigate the association between three-dimensional (3-D) left ventricular ejection fraction (LVEF) and various speckle tracking echocardiographic (STE) strain parameters in non-ischemic left bundle branch block (LBBB) patients with major adverse cardiovascular events (MACE) during a one-year follow-up phase. METHOD: A total of 50 patients with non-ischemic LBBB were assessed using various parameters of 3-D echocardiography. They were compared with their same-age and sex control group and then followed up with repeat 3-D echocardiography for MACE for one year. RESULTS: Composite outcomes were seen in (n = 11 [22 %], including cardiovascular mortality (n = 2 [4.0 %]) and hospitalization for heart failure (n = 9 [18.0 %]). Mean values of the left ventricle (LV) global longitudinal (GLS), circumferential (GCS), and radial (GRS) strains were -14.4 ± 5.6, -14.3 ± 5.8, and 15.3 ± 5.9 respectively in the study cases. Initial GLS values were significantly impaired among those who had clinical events (-9.2 vs -15.9). Also, significant worsening of GLS (p value < 0.001) was seen in patients with composite outcomes on follow-up. Cut-off values in receiver operating characteristic analyses for composite outcomes were: GLS more than -13.5, GCS more than -12.5, and GRS less than 14.5. Intra-class correlations for both intra-observer and inter-observer variability were found to be good. CONCLUSION: Impaired LV GLS and low 3-D LVEF are significantly associated with the occurrence of MACE in patients with non-ischemic LBBB. This strong association of LV GLS with outcomes can aid in risk stratification, prognostication, and clinical decision-making in non-ischemic LBBB.

Stealth Nanocarriers in Cancer Therapy: a Comprehensive Review of Design, Functionality, and Clinical Applications.

Nanotechnology has significantly transformed cancer treatment by introducing innovative methods for delivering drugs effectively. This literature review provided an in-depth analysis of the role of nanocarriers in cancer therapy, with a particular focus on the critical concept of the 'stealth effect.' The stealth effect refers to the ability of nanocarriers to evade the immune system and overcome physiological barriers. The review investigated the design and composition of various nanocarriers, such as liposomes, micelles, and inorganic nanoparticles, highlighting the importance of surface modifications and functionalization. The complex interaction between the immune system, opsonization, phagocytosis, and the protein corona was examined to understand the stealth effect. The review carefully evaluated strategies to enhance the stealth effect, including surface coating with polymers, biomimetic camouflage, and targeting ligands. The in vivo behavior of stealth nanocarriers and their impact on pharmacokinetics, biodistribution, and toxicity were also systematically examined. Additionally, the review presented clinical applications, case studies of approved nanocarrier-based cancer therapies, and emerging formulations in clinical trials. Future directions and obstacles in the field, such as advancements in nanocarrier engineering, personalized nanomedicine, regulatory considerations, and ethical implications, were discussed in detail. The review concluded by summarizing key findings and emphasizing the transformative potential of stealth nanocarriers in revolutionizing cancer therapy. This review enhanced the comprehension of nanocarrier-based cancer therapies and their potential impact by providing insights into advanced studies, clinical applications, and regulatory considerations.

Impact of the Timing of Percutaneous Catheter Drainage following Endoscopic Drainage on Outcomes in Acute Necrotizing Pancreatitis.

Background The role of dual-modality drainage of walled-off necrosis (WON) in patients with acute pancreatitis (AP) is established. However, there are no data on the association of clinical outcomes with the timing of percutaneous catheter drainage (PCD). We investigated the impact of the timing of PCD following endoscopic drainage of WON on clinical outcomes in AP. Materials and Methods This retrospective study comprised consecutive patients with necrotizing AP who underwent endoscopic cystogastrostomy (CG) of WON followed by PCD between September 2018 and March 2023. Based on endoscopic CG to PCD interval, patients were divided into groups (≤ and >3 days, ≤ and >1 week, ≤ and >10 days, and ≤ and >2 weeks). Baseline characteristics and indications of CG and PCD were recorded. Clinical outcomes were compared between the groups, including length of hospitalization, length of intensive care unit stay, need for surgical necrosectomy, and death during hospitalization. Results Thirty patients (mean age ± standard deviation, 35.5 ± 12.7 years) were evaluated. The mean CG to PCD interval was 11.2 ± 7.5 days. There were no significant differences in baseline characteristics and indications of CG and PCD between the groups. The mean pain to CG interval was not significantly different between the groups. Endoscopic necrosectomy was performed in a significantly greater proportion of patients undergoing CG after 10 days ( p = 0.003) and after 2 weeks ( p = 0.032). There were no significant differences in the complications and clinical outcomes between the groups. Conclusion The timing of PCD following endoscopic CG does not affect clinical outcomes.

Engineering circular RNA for molecular and metabolic reprogramming.

The role of messenger RNA (mRNA) in biological systems is extremely versatile. However, it's extremely short half-life poses a fundamental restriction on its application. Moreover, the translation efficiency of mRNA is also limited. On the contrary, circular RNAs, also known as circRNAs, are a common and stable form of RNA found in eukaryotic cells. These molecules are synthesized via back-splicing. Both synthetic circRNAs and certain endogenous circRNAs have the potential to encode proteins, hence suggesting the potential of circRNA as a gene expression machinery. Herein, we aim to summarize all engineering aspects that allow exogenous circular RNA (circRNA) to prolong the time that proteins are expressed from full-length RNA signals. This review presents a systematic engineering approach that have been devised to efficiently assemble circRNAs and evaluate several aspects that have an impact on protein production derived from. We have also reviewed how optimization of the key components of circRNAs, including the topology of vector, 5' and 3' untranslated sections, entrance site of the internal ribosome, and engineered aptamers could be efficiently impacting the translation machinery for molecular and metabolic reprogramming. Collectively, molecular and metabolic reprogramming present a novel way of regulating distinctive cellular features, for instance growth traits to neoplastic cells, and offer new possibilities for therapeutic inventions.

Latrophilin-2 mediates fluid shear stress mechanotransduction at endothelial junctions.

Endothelial cell responses to fluid shear stress from blood flow are crucial for vascular development, function, and disease. A complex of PECAM-1, VE-cadherin, VEGF receptors (VEGFRs), and Plexin D1 located at cell-cell junctions mediates many of these events. However, available evidence suggests that another mechanosensor upstream of PECAM-1 initiates signaling. Hypothesizing that GPCR and Gα proteins may serve this role, we performed siRNA screening of Gα subunits and found that Gαi2 and Gαq/11 are required for activation of the junctional complex. We then developed a new activation assay, which showed that these G proteins are activated by flow. We next mapped the Gα residues required for activation and developed an affinity purification method that used this information to identify latrophilin-2 (Lphn2/ADGRL2) as the upstream GPCR. Latrophilin-2 is required for all PECAM-1 downstream events tested. In both mice and zebrafish, latrophilin-2 is required for flow-dependent angiogenesis and artery remodeling. Furthermore, endothelial-specific knockout demonstrates that latrophilin plays a role in flow-dependent artery remodeling. Human genetic data reveal a correlation between the latrophilin-2-encoding Adgrl2 gene and cardiovascular disease. Together, these results define a pathway that connects latrophilin-dependent G protein activation to subsequent endothelial signaling, vascular physiology, and disease.

Icariin Ameliorates D-galactose-induced Cell Injury in Neuron-like PC12 Cells by Inhibiting MPTP Opening.

OBJECTIVE: Icariin (ICA) has a good neuroprotective effect and can upregulate neuronal basal autophagy in naturally aging rats. Mitochondrial dysfunction is associated with brain aging-related neurodegenerative diseases. Abnormal opening of the mitochondrial permeability transition pore (mPTP) is a crucial factor in mitochondrial dysfunction and is associated with excessive autophagy. This study aimed to explore that ICA protects against neuronal injury by blocking the mPTP opening and down-regulating autophagy levels in a D-galactose (D-gal)-induced cell injury model. METHODS: A cell model of neuronal injury was established in rat pheochromocytoma cells (PC12 cells) treated with 200 mmol/L D-gal for 48 h. In this cell model, PC12 cells were pre-treated with different concentrations of ICA for 24 h. MTT was used to detect cell viability. Senescence associated ß-galactosidase (SA-ß-Gal) staining was used to observe cell senescence. Western blot analysis was performed to detect the expression levels of a senescence-related protein (p21), autophagy markers (LC3B, p62, Atg7, Atg5 and Beclin 1), mitochondrial fission and fusion-related proteins (Drp1, Mfn2 and Opa1), and mitophagy markers (Pink1 and Parkin). The changes of autophagic flow were detected by using mRFP-GFP-LC3 adenovirus. The intracellular ultrastructure was observed by transmission electron microscopy. Immunofluorescence was used to detect mPTP, mitochondrial membrane potential (MMP), mitochondrial reactive oxygen species (mtROS) and ROS levels. ROS and apoptosis levels were detected by flow cytometry. RESULTS: D-gal treatment significantly decreased the viability of PC12 cells, and markedly increased the SA-ß-Gal positive cells as compared to the control group. With the D-gal stimulation, the expression of p21 was significantly up-regulated. Furthermore, D-gal stimulation resulted in an elevated LC3B II/I ratio and decreased p62 expression. Meanwhile, autophagosomes and autolysosomes were significantly increased, indicating abnormal activation of autophagy levels. In addition, in this D-gal-induced model of cell injury, the mPTP was abnormally open, the ROS generation was continuously increased, the MMP was gradually decreased, and the apoptosis was increased. ICA effectively improved mitochondrial dysfunction to protect against D-gal-induced cell injury and apoptosis. It strongly inhibited excessive autophagy by blocking the opening of the mPTP. Cotreatment with ICA and an mPTP inhibitor (cyclosporin A) did not ameliorate mitochondrial dysfunction. However, the protective effects were attenuated by cotreatment with ICA and an mPTP activator (lonidamine). CONCLUSION: ICA inhibits the activation of excessive autophagy and thus improves mitochondrial dysfunction by blocking the mPTP opening.

Manganese-catalyzed C-C and C-N bond formation with alcohols via borrowing hydrogen or hydrogen auto-transfer.

Transition-metal-mediated "borrowing hydrogen" also known as hydrogen auto-transfer reactions allow the sustainable construction of C-C and C-N bonds using alcohols as hydrogen donors. In recent years, manganese complexes have been explored as efficient catalysts in these reactions. This review highlights the significant progress made in manganese-catalyzed C-C and C-N bond-formation reactions via hydrogen auto-transfer, emphasizing the importance of this methodology and manganese catalysts in sustainable synthesis strategies.

Brain Chimeroids reveal individual susceptibility to neurotoxic triggers.

Interindividual genetic variation affects the susceptibility to and progression of many diseases1,2. However, efforts to study how individual human brains differ in normal development and disease phenotypes are limited by the paucity of faithful cellular human models, and the difficulty of scaling current systems to represent multiple people. Here we present human brain Chimeroids, a highly reproducible, multidonor human brain cortical organoid model generated by the co-development of cells from a panel of individual donors in a single organoid. By reaggregating cells from multiple single-donor organoids at the neural stem cell or neural progenitor cell stage, we generate Chimeroids in which each donor produces all cell lineages of the cerebral cortex, even when using pluripotent stem cell lines with notable growth biases. We used Chimeroids to investigate interindividual variation in the susceptibility to neurotoxic triggers that exhibit high clinical phenotypic variability: ethanol and the antiepileptic drug valproic acid. Individual donors varied in both the penetrance of the effect on target cell types, and the molecular phenotype within each affected cell type. Our results suggest that human genetic background may be an important mediator of neurotoxin susceptibility and introduce Chimeroids as a scalable system for high-throughput investigation of interindividual variation in processes of brain development and disease.

Latrophilin-2 mediates fluid shear stress mechanotransduction at endothelial junctions.

Endothelial cell responses to fluid shear stress from blood flow are crucial for vascular development, function and disease. A complex of PECAM-1, VE-cadherin, VEGF receptors (VEGFRs) and PlexinD1 located at cell-cell junctions mediates many of these events. But available evidence suggests that another mechanosensor upstream of PECAM-1 initiates signaling. Hypothesizing that GPCR and Gα proteins may serve this role, we performed siRNA screening of Gα subunits and found that Gαi2 and Gαq/11 are required for activation of the junctional complex. We then developed a new activation assay, which showed that these G proteins are activated by flow. We next mapped the Gα residues required for activation and developed an affinity purification method that used this information to identify latrophilin-2 (Lphn-2/ADGRL2) as the upstream GPCR. Latrophilin-2 is required for all PECAM-1 downstream events tested. In both mice and zebrafish, latrophilin-2 is required for flow-dependent angiogenesis and artery remodeling. Furthermore, endothelial specific knockout demonstrates that latrophilin plays a role in flow-dependent artery remodeling. Human genetic data reveal a correlation between the latrophilin-2-encoding Adgrl2 gene and cardiovascular disease. Together, these results define a pathway that connects latrophilin-dependent G protein activation to subsequent endothelial signaling, vascular physiology and disease.