SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation.

RNA-directed DNA methylation in Arabidopsis thaliana depends on the upstream synthesis of 24-nucleotide small interfering RNAs (siRNAs) by RNA POLYMERASE IV (Pol IV) and downstream synthesis of non-coding transcripts by Pol V. Pol V transcripts are thought to interact with siRNAs which then recruit DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) to methylate DNA. The SU(VAR)3-9 homologues SUVH2 and SUVH9 act in this downstream step but the mechanism of their action is unknown. Here we show that genome-wide Pol V association with chromatin redundantly requires SUVH2 and SUVH9. Although SUVH2 and SUVH9 resemble histone methyltransferases, a crystal structure reveals that SUVH9 lacks a peptide-substrate binding cleft and lacks a properly formed S-adenosyl methionine (SAM)-binding pocket necessary for normal catalysis, consistent with a lack of methyltransferase activity for these proteins. SUVH2 and SUVH9 both contain SRA (SET- and RING-ASSOCIATED) domains capable of binding methylated DNA, suggesting that they function to recruit Pol V through DNA methylation. Consistent with this model, mutation of DNA METHYLTRANSFERASE 1 (MET1) causes loss of DNA methylation, a nearly complete loss of Pol V at its normal locations, and redistribution of Pol V to sites that become hypermethylated. Furthermore, tethering SUVH9 [corrected] with a zinc finger to an unmethylated site is sufficient to recruit Pol V and establish DNA methylation and gene silencing. These results indicate that Pol V is recruited to DNA methylation through the methyl-DNA binding SUVH2 and SUVH9 proteins, and our mechanistic findings suggest a means for selectively targeting regions of plant genomes for epigenetic silencing.

Biological evaluation of 3-hydroxybenzyl alcohol, an extrolite produced by Aspergillus nidulans strain KZR-132.

AIMS: The aim of the study was to purify and characterize a bioactive compound from Aspergillus nidulans strain KZR-132 and its biological evaluation. METHODS AND RESULTS: A bioactive extolite was purified from A. nidulans strain KZR-132, and its chemical structure was elucidated as 3-hydroxylbenzyl alcohol (3-HBA) based on 1 H and 13 C NMR, FT-IR and mass spectroscopic analysis. The antimicrobial efficacy of 3-HBA was established against Gram-positive, Gram-negative bacteria and different Candida strains. It also showed promising antibiofilm activity against various tested microbial strains. Reactive oxygen species induced by 3-HBA treatment on different Candida strains killed most of the cells and showed necrotic effect. It also exhibited dose-dependent antioxidant and anti-inflammatory activities. CONCLUSIONS: This bioactive extrolite produced by A. nidulans isolated from a niche habitat was demonstrated to possess significant biotechnological and pharmacological potential since it exhibited broad-spectrum antimicrobial and antibiofilm activities which are reported for the first time. SIGNIFICANCE AND IMPACT OF THE STUDY: The overall study demonstrates that 3-HBA produced by A. nidulansKZR-132 is a promising bioactive metabolite and possibly can function as a pharmacologically suitable broad-spectrum antimicrobial drug candidate against various dreaded human-related bacterial and fungal pathogens.

Incidence & prognosis of acute kidney injury in individuals of snakebite in a tertiary care hospital in India.

BACKGROUND & OBJECTIVES: The snakebites are considered to be an occupational hazard in agriculture workers and the snake handlers, resulting in a considerable morbidity, mortality and economical implications. This study was conducted to determine the incidence, clinical presentation, renal injury and clinical outcome in snakebite victims who developed acute kidney injury (AKI). METHODS: This hospital-based prospective, observational study was done on 100 cases who were admitted for the management of snakebite and found to develop AKI in a tertiary care hospital at Hyderabad, India. Renal function tests, complete blood picture, urine routine examination, ultrasound examination of abdomen and coagulation profile were done and the prognosis was assessed by noting recovery, mortality, morbidity and/or progress to chronic stage. RESULTS: A total of 100 patients with a mean age of 43.80±12.63 yr (range 18-70); 62 males and 38 females were studied. All had bites on lower limbs. A total of 86 patients arrived in the hospital within 24 h, and 14 arrived after 24 h. Oliguria was found in 60, bleeding tendencies in 64, haemodynamic instability noted - tachycardia in 86. Systolic blood pressure (BP) was <120 mm Hg in 68 and BP was not recordable in four patients. Twelve patients were in stage III kidney disease and needed haemodialysis. Of the 100 cases of snakebite-induced acute kidney failure, 86 recovered and six died. On follow up, after six months eight patients developed chronic kidney failure. INTERPRETATION & CONCLUSIONS: A cascade of events tends to occur in severe haemotoxic envenomation such as bleeding disorders, hypotension/circulatory shock, intravascular haemolysis, disseminated intravascular coagulation and acute respiratory disease syndrome (ARDS). The findings of this study showed that early hospitalization, quick antisnake venom administration and adequate supporting care provided promising results.

Sequencing Analysis of NS3/4A, NS5A, and NS5B Genes from Patients Infected with Hepatitis C Virus Genotypes 5 and 6.

Direct-acting antivirals (DAAs) with activity against multiple genotypes of the hepatitis C virus (HCV) were recently developed and approved for standard-of-care treatment. However, sequencing assays to support HCV genotype 5 and 6 analysis are not widely available. Here, we describe the development of a sequencing assay for the NS3/4A, NS5A, and NS5B genes from HCV genotype 5 and 6 patient isolates. Genotype- and subtype-specific primers were designed to target NS3/4A, NS5A, and NS5B for cDNA synthesis and nested PCR amplification. Amplification was successfully performed for a panel of 32 plasma samples from HCV-infected genotype 5 and 6 patients with sequencing data obtained for all attempted samples. LiPA 2.0 (Versant HCV genotype 2.0) is a reverse hybridization line probe assay that is commonly used for genotyping HCV-infected patients enrolled in clinical studies. Using NS3/4A, NS5A, and NS5B consensus sequences, HCV subtypes were determined that were not available for the initial LiPA 2.0 result for genotype 6 samples. Samples amplified here included the following HCV subtypes: 5a, 6a, 6e, 6f, 6j, 6i, 6l, 6n, 6o, and 6p. The sequencing data generated allowed for the determination of the presence of variants at amino acid positions previously characterized as associated with resistance to DAAs. The simple and robust sequencing assay for genotypes 5 and 6 presented here may lead to a better understanding of HCV genetic diversity and prevalence of resistance-associated variants.

A diastereoselective synthesis of tetrahydro- and dihydro-pyrido[2,3-c]coumarin derivatives via a one-pot three-component Povarov reaction catalyzed by bismuth(III) chloride.

A diastereoselective synthesis of tetrahydro- and dihydro-pyrido[2,3-c]coumarin derivatives has been achieved via a one-pot three-component aza-Diels-Alder reaction of aromatic aldehydes, 3-aminocoumarin and dienophiles catalyzed by BiCl3. NOE studies proved that exo-isomers were obtained in all cases with high selectivity. The reaction proceeded at room temperature providing good yields of products as well as applicability on a wide range of substrates. Among all the synthesized derivatives, compounds 4i and 4k showed promising DPPH radical scavenging activity as compared to other tested derivatives.

Relationship between nucleosome positioning and DNA methylation.

Nucleosomes compact and regulate access to DNA in the nucleus, and are composed of approximately 147 bases of DNA wrapped around a histone octamer. Here we report a genome-wide nucleosome positioning analysis of Arabidopsis thaliana using massively parallel sequencing of mononucleosomes. By combining this data with profiles of DNA methylation at single base resolution, we identified 10-base periodicities in the DNA methylation status of nucleosome-bound DNA and found that nucleosomal DNA was more highly methylated than flanking DNA. These results indicate that nucleosome positioning influences DNA methylation patterning throughout the genome and that DNA methyltransferases preferentially target nucleosome-bound DNA. We also observed similar trends in human nucleosomal DNA, indicating that the relationships between nucleosomes and DNA methyltransferases are conserved. Finally, as has been observed in animals, nucleosomes were highly enriched on exons, and preferentially positioned at intron-exon and exon-intron boundaries. RNA polymerase II (Pol II) was also enriched on exons relative to introns, consistent with the hypothesis that nucleosome positioning regulates Pol II processivity. DNA methylation is also enriched on exons, consistent with the targeting of DNA methylation to nucleosomes, and suggesting a role for DNA methylation in exon definition.

Transcriptome and methylome interactions in rice hybrids.

DNA methylation is a heritable epigenetic mark that controls gene expression, is responsive to environmental stresses, and, in plants, may also play a role in heterosis. To determine the degree to which DNA methylation is inherited in rice, and how it both influences and is affected by transcription, we performed genome-wide measurements of these patterns through an integrative analysis of bisulfite-sequencing, RNA-sequencing, and siRNA-sequencing data in two inbred parents of the Nipponbare (NPB) and indica (93-11) varieties of rice and their hybrid offspring. We show that SNPs occur at a rate of about 1/253 bp between the two parents and that these are faithfully transmitted into the hybrids. We use the presence of these SNPs to reconstruct the two chromosomes in the hybrids according to their parental origin. We found that, unlike genetic inheritance, epigenetic heritability is quite variable. Cytosines were found to be differentially methylated (epimutated) at a rate of 7.48% (1/15 cytosines) between the NPB and 93-11 parental strains. We also observed that 0.79% of cytosines were epimutated between the parent and corresponding hybrid chromosome. We found that these epimutations are often clustered on the chromosomes, with clusters representing 20% of all epimutations between parental ecotypes, and 2-5% in F1 plants. Epimutation clusters are also strongly associated with regions where the production of siRNA differs between parents. Finally, we identified genes with both allele-specific expression patterns that were strongly inherited as well as those differentially expressed between hybrids and the corresponding parental chromosome. We conclude that much of the misinheritance of expression levels is likely caused by epimutations and trans effects.

Development and validation of an LC-MSMS method for the quantitation of pacritinib; application of kinetics in rabbits.

BACKGROUND: Accurate and selective LC/ESI-MSMS method development and validation for the quantitation of pacritinib is the primary goal of this study to perform kinetic studies in the healthy rabbit. METHODS: Chromatographic resolution was accomplished with a hypersil/ODS (50 mm × 4.6 mm, 3 µ) analytical C18 column and a mobile phase composition of 0.1% formic acid and ACN in the proportion of 25:75 with a 0.6 ml/min flow of the mobile phasic system from the analytical column. The method was employed by monitoring the established ionic transitions of m/z-473.25/98.09 for Pacritinib and 506.18/57.12 for the internal standard (Amprenavir) in multiple reaction monitoring. RESULTS: The calibration plot regression line was y = 0.0002× + 0.007, with a correction coefficient (r2) of 0.9989. The CV outcomes for the matrix effect at low-QC and high-QC levels were 4.79% and 4.91%, respectively. The percentage average recoveries for Pacritinib in High-QC (12.70 µg/ml), MQC (8.50 µg/ml), and Low-QC (1.19 µg/ml) were 95.87%, 103.64%, and 94.32%, respectively. The obtained values were found between 2.98 and 5.07% for the QC (1.19, 8.50, and 12.70 µg/ml) samples. The established procedure was subjected to kinetics study of Pacritinib after oral administration in rabbits. Cmax, Tmax, and T1/2, of the Pacritinib tablets were 247.25 ±â€¯3.32 ng/ml, 6.0 ±â€¯0.03 h, and 12.24 ±â€¯0.53 h, respectively. AUC0-∞ infinity for Pacritinib tablets was 1691.74 ±â€¯3.67 ng h/ml. CONCLUSION: After oral administration of Pacritinib to healthy rabbits, pharmacokinetic characteristics were presented, and the established technique was effectively verified.

Precolumn o-phthalaldehyde-N-acetyl-L-cysteine derivatization followed by RP-HPLC separation and fluorescence detection of sitagliptin enantiomers in rat plasma.

An indirect reversed-phase high-performance liquid chromatographic separation and fluorescence detection of sitagliptin enantiomers in rat plasma was developed and validated. Deproteinized rat plasma containing racemic sitagliptin was derivatized with o-phthalaldehyde and N-acetyl-L-cysteine under alkaline conditions, converted to diastereomers, and separated on a Lichrospher 100 RP-18e column using 20 mM phosphate buffer and methanol (45:55 v/v) as a mobile phase under isocratic mode of elution at a flow rate of 1.0 mL/min. Fluorescence detection was performed at 330 and 450 nm as excitation and emission wavelengths, respectively. The method was linear in the range of 50-5000 ng/ mL for both enantiomers. The intra- and interday accuracy and precision were within the predefined limits of ≤15% at all concentrations. The method was successfully applied to a pharmacokinetic study of sitagliptin after 5 mg/kg oral administration to Wistar rats. Robustness of the method was evaluated using design of experiments.

Examining the Triple Burden of Malnutrition: Insights from a Community-Based Comprehensive Nutrition Survey among Indigenous Tribal Children (0-19 Years) in the Western Ghats Hills of India.

This article presents findings from a community-based cross-sectional study conducted in Attappadi, Kerala, India, aimed at assessing the prevalence of the triple burden of malnutrition among indigenous children aged 0-19 years. Historically, the indigenous population in Attappadi has faced significant developmental challenges, including high rates of malnutrition, infant mortality, and neonatal mortality. This study revealed alarming rates of undernutrition among children aged 0-59 months, with 40.9% experiencing stunting, 27.4% wasting, and 48.3% being underweight. Adolescent girls also suffered from undernutrition, with 21% classified as underweight and 43.3% experiencing stunting. Surprisingly, overweight or obesity was identified as a nutritional problem, affecting 1.4% of children aged 0-59 months, 4.2% of children aged 5-9 years, and 10.5% of adolescent girls. Additionally, a distressing proportion of young children aged 12-59 months (91.2%) were anaemic, with 50% diagnosed specifically with iron deficiency anaemia (IDA). Nearly all adolescent girls (96.6%) were reportedly suffering from anaemia. Deficiencies in vitamin B12, vitamin D, folate, and vitamin-A were prevalent among 35%, 20%, 16%, and 12% of children aged 12-59 months, respectively. The study underscores the urgent need for comprehensive interventions to address this triple burden of malnutrition. Recommendations include promoting culturally appropriate local food-based solutions, establishing participatory and community-led systems for health and nutrition information dissemination, and strengthening the nutrition surveillance system through village-level health and nutrition workers. By adopting a holistic approach, these interventions can help improve the nutritional status and well-being of the indigenous tribal children in Attappadi.

Separation, identification and characterization of stress degradation products of bortezomib using HPLC and LC-MS.

Bortezomib (BT) is a reversible inhibitor of proteasome which is used in the treatment of hematological cancers. To study the degradation behavior, BT was subjected to acidic, basic, neutral, photolytic, oxidative and thermal degradation conditions as per ICH guideline Q1A (R2). A gradient HPLC method has been developed for separating all the degradation products formed under various degradation conditions on Waters XBridge C18 column (150 mm × 4.6 mm × 3.5 µm) using the mobile phase composed of ammonium formate and acetonitrile. A total of six degradation products were formed in various stress conditions and these were separated identified, and characterized using high performance liquid chromatography in combination with electrospray ionization tandem mass spectrometric studies.

Objective evaluation of stubble emission of North India and quantifying its impact on air quality of Delhi.

Crop residue burning during post monsoon season in the neighboring provinces leads to frequent episodes of extreme pollution events, associated with premature morbidity and mortality. A synergistic use of multiple satellite measurements in conjunction with actual field incidences data at the ground led us to develop the realistic high-resolution emission inventory of the hazardous pollutant PM2.5 due to stubble burning. We quantify the share of biomass burning in deteriorating Delhi's air quality during 2018 using the SAFAR chemical transport model that has been validated with dense observational network of Delhi. The impact of biomass burning on Delhi's PM2.5 is found to vary on day-to day basis (peaking at 58%) as it is highly dependent on transportation pathway of air mass, controlled by meteorological parameters from source to target region. Comprehending the multi-scale nature of such events is crucial to plan air quality improvement strategies.

Demonstration of X-ray Thomson scattering as diagnostics for miscibility in warm dense matter.

The gas and ice giants in our solar system can be seen as a natural laboratory for the physics of highly compressed matter at temperatures up to thousands of kelvins. In turn, our understanding of their structure and evolution depends critically on our ability to model such matter. One key aspect is the miscibility of the elements in their interiors. Here, we demonstrate the feasibility of X-ray Thomson scattering to quantify the degree of species separation in a 1:1 carbon-hydrogen mixture at a pressure of ~150 GPa and a temperature of ~5000 K. Our measurements provide absolute values of the structure factor that encodes the microscopic arrangement of the particles. From these data, we find a lower limit of [Formula: see text]% of the carbon atoms forming isolated carbon clusters. In principle, this procedure can be employed for investigating the miscibility behaviour of any binary mixture at the high-pressure environment of planetary interiors, in particular, for non-crystalline samples where it is difficult to obtain conclusive results from X-ray diffraction. Moreover, this method will enable unprecedented measurements of mixing/demixing kinetics in dense plasma environments, e.g., induced by chemistry or hydrodynamic instabilities.

Development and validation of RP-HPLC method for the determination of genotoxic alkyl benzenesulfonates in amlodipine besylate.

The present paper describes a simple isocratic reverse phase HPLC method for the determination of four genotoxic alkyl benzenesulfonates (ABSs) viz. methyl, ethyl, n-propyl and isopropyl benzenesulfonates (MBS, EBS, NPBS and IPBS) in amlodipine besylate (ADB). Good resolution between benzene sulfonic acid (BSA), MBS, EBS, NPBS, IPBS and ADB was achieved with Inertsil ODS 3V (150 mmx4.6 mm, 5 microm) column using a 65:35 (v/v) mixture of 1% triethyl amine, pH adjusted to 3.0 with orthophosphoric acid and acetonitrile as mobile phase. The flow rate was 1.0 ml/min and the elution was monitored at 220 nm. The factors involved in the method development are discussed. This method was validated as per International Conference on Harmonization (ICH) guidelines and is able to quantitate MBS, EBS, NPBS and IPBS at 21, 32, 35 and 28 ppm levels, respectively with respect to 5 mg/ml of ADB. The method is linear in range of 75-180 ppm of ABSs, which matches the range of 50-120% of estimated permitted level (150 ppm) of ABSs. ABSs were not present in the three studied pure and tablet batches of ADB.

Development and validation of GC-MS method for the determination of methyl methanesulfonate and ethyl methanesulfonate in imatinib mesylate.

A gas chromatography-mass spectrometry (GC-MS) method has been developed for the identification and determination of two carcinogenic and genotoxic mesylate esters viz. methyl methanesulfonate (MMS) and ethyl methanesulfonate (EMS) in imatinib mesylate (INM). The method was optimized based on the peak shapes and resolution of MMS and EMS. The method was validated as per International Conference of Harmonization (ICH) guidelines in terms of limits of detection (LOD), limit of quantitation (LOQ), linearity, precision, accuracy, specificity and robustness. The LOD and LOQ values were found to be 0.3 and 1.0 microg/ml, respectively. The method is linear within the range of 1-15 microg/ml for both the compounds. These mesylate esters were not found in three different batches of pure and pharmaceutical formulations of INM.

Isolation and evolutionary analysis of Australasian topotype of bluetongue virus serotype 4 from India.

Bluetongue (BT) is a Culicoides-borne disease caused by several serotypes of bluetongue virus (BTV). Similar to other insect-borne viral diseases, distribution of BT is limited to distribution of Culicoides species competent to transmit BTV. In the tropics, vector activity is almost year long, and hence, the disease is endemic, with the circulation of several serotypes of BTV, whereas in temperate areas, seasonal incursions of a limited number of serotypes of BTV from neighbouring tropical areas are observed. Although BTV is endemic in all the three major tropical regions (parts of Africa, America and Asia) of the world, the distribution of serotypes is not alike. Apart from serological diversity, geography-based diversity of BTV genome has been observed, and this is the basis for proposal of topotypes. However, evolution of these topotypes is not well understood. In this study, we report the isolation and characterization of several BTV-4 isolates from India. These isolates are distinct from BTV-4 isolates from other geographical regions. Analysis of available BTV seg-2 sequences indicated that the Australasian BTV-4 diverged from African viruses around 3,500 years ago, whereas the American viruses diverged relatively recently (1,684 CE). Unlike Australasia and America, BTV-4 strains of the Mediterranean area evolved through several independent incursions. We speculate that independent evolution of BTV in different geographical areas over long periods of time might have led to the diversity observed in the current virus population.

Mangiferin from Pueraria tuberosa reduces inflammation via inactivation of NLRP3 inflammasome.

Recent reports have demonstrated the role of phyto-constituents in modulating inflammatory responses. Mangiferin isolated from Mangifera indica is known to induce potent anti-oxidative, anti-diabetic and anti-inflammatory activity. However, the molecular mechanism of its anti-inflammatory activity is not properly understood. In this study we have isolated Mangiferin from the tubers of Pueraria tuberosa (PT-Mangiferin) and analysed the mechanism of its potent anti-inflammatory effects in LPS stimulated RAW 264.7 mouse macrophage cell line and in a carrageenan induced air pouch model. PT-Mangiferin was non-toxic to primary cells but showed significant toxicity and apoptotic effect on cancerous cells. It significantly reduced the production of pro-inflammatory mediators (COX-2, iNOS and TNF-α) in LPS stimulated RAW 264.7 cells. Further, it has also reduced the generation of ROS and inhibited LPS induced NF-kB translocation in these cells. Additionally, PT-Mangiferin significantly reduced inflammation in a mouse air pouch model by inhibiting the infiltration of monocytes and neutrophils and reducing the production of cytokines. These effects were mediated via inactivation of NLRP3 inflammasome complex and its downstream signalling molecules. Taken together these results suggest that PT-Mangiferin is potent anti-inflammatory compound that reduces inflammation and holds promise in development of herbal based anti-inflammatory therapeutics in future.

Acylated 5,7,2',6'-oxygenated flavone glycosides from Andrographis alata.

Five acylated 5,7,2',6'-oxygenated flavone glycosides along with the known 5,2',6'-trihydroxy-7-methoxyflavone-2'-O-beta-d-glucopyranoside have been isolated from the whole plant of Andrographis alata. The structures of the compounds were established from spectral (mainly 1D and 2D NMR) and chemical studies.

Antitumor effect of a copper coordination compound with superoxide dismutase-like activity.

Growth of Ehrlich carcinomas in inbred CBA mice was retarded by im administration of Cu(II)(3,5-diisopropylsalicylate)2 (CuDIPS). CuDIPS is a low molecular weight (mol wt = 503) copper coordination compound that exhibits superoxide dismutase (SOD)-like activity. It has been used as an anti-inflammatory agent and is lipid-soluble. This property enables the compound to penetrate membranes, thus becoming an intracellular O2- scavenger. In the tumor system studied, the amounts of both copper- and zinc-containing SOD (CuZnSOD) and manganese-containing SOD are reduced. Injection of Orgotein (CuZnSOD from bovine liver) had no significant effect on tumor growth and host survival. When CuDIPS was administered at various doses, reduction in tumor size, delay of metastasis, and a significant increase in survival of the hosts were observed.