Showing papers by "Central University of Kerala published in 2019"

The unique composition of Indian gut microbiome, gene catalogue, and associated fecal metabolome deciphered using multi-omics approaches

Abstract: BACKGROUND Metagenomic studies carried out in the past decade have led to an enhanced understanding of the gut microbiome in human health; however, the Indian gut microbiome has not been well explored. We analyzed the gut microbiome of 110 healthy individuals from two distinct locations (North-Central and Southern) in India using multi-omics approaches, including 16S rRNA gene amplicon sequencing, whole-genome shotgun metagenomic sequencing, and metabolomic profiling of fecal and serum samples. RESULTS The gene catalogue established in this study emphasizes the uniqueness of the Indian gut microbiome in comparison to other populations. The gut microbiome of the cohort from North-Central India, which was primarily consuming a plant-based diet, was found to be associated with Prevotella and also showed an enrichment of branched chain amino acid (BCAA) and lipopolysaccharide biosynthesis pathways. In contrast, the gut microbiome of the cohort from Southern India, which was consuming an omnivorous diet, showed associations with Bacteroides, Ruminococcus, and Faecalibacterium and had an enrichment of short chain fatty acid biosynthesis pathway and BCAA transporters. This corroborated well with the metabolomics results, which showed higher concentration of BCAAs in the serum metabolome of the North-Central cohort and an association with Prevotella. In contrast, the concentration of BCAAs was found to be higher in the fecal metabolome of the Southern-India cohort and showed a positive correlation with the higher abundance of BCAA transporters. CONCLUSIONS The study reveals the unique composition of the Indian gut microbiome, establishes the Indian gut microbial gene catalogue, and compares it with the gut microbiome of other populations. The functional associations revealed using metagenomic and metabolomic approaches provide novel insights on the gut-microbe-metabolic axis, which will be useful for future epidemiological and translational researches.

Association of Flavonifractor plautii, a Flavonoid-Degrading Bacterium, with the Gut Microbiome of Colorectal Cancer Patients in India.

Abstract: Recently, dysbiosis in the human gut microbiome and shifts in the relative abundances of several bacterial species have been recognized as important factors in colorectal cancer (CRC). However, these studies have been carried out mainly in developed countries where CRC has a high incidence, and it is unclear whether the host-microbiome relationships deduced from these studies can be generalized to the global population. To test if the documented associations between the microbiome and CRC are conserved in a distinct context, we performed metagenomic and metabolomic association studies on fecal samples from 30 CRC patients and 30 healthy controls from two different locations in India, followed by a comparison of CRC data available from other populations. We confirmed the association of Bacteroides and other bacterial taxa with CRC that have been previously reported in other studies. However, the association of CRC with Flavonifractor plautii in Indian patients emerged as a novel finding. The plausible role of F. plautii appears to be linked with the degradation of beneficial anticarcinogenic flavonoids, which was also found to be significantly correlated with the enzymes and modules involved in flavonoid degradation within Indian CRC samples. Thus, we hypothesize that the degradation of beneficial flavonoids might be playing a role in cancer progression within this Indian cohort. We also identified 20 potential microbial taxonomic markers and 33 potential microbial gene markers that discriminate the Indian CRC from healthy microbiomes with high accuracy based on machine learning approaches.IMPORTANCE This study provides novel insights on the CRC-associated microbiome of a unique cohort in India, reveals the potential role of a new bacterium in CRC, and identifies cohort-specific biomarkers, which can potentially be used in noninvasive diagnosis of CRC. The study gains additional significance, as India is among the countries with a very low incidence of CRC, and the diet and lifestyle in India have been associated with a distinct gut microbiome in healthy Indians compared to other global populations. Thus, in this study, we hypothesize a unique relationship between CRC and the gut microbiome in an Indian population.

Role of the Gut Microbiome in Autism Spectrum Disorders.

Abstract: Autism spectrum disorder (ASD) is a severe neurodevelopmental or neuropsychiatric disorder with elusive etiology and obscure pathophysiology. Cognitive inabilities, impaired communication, repetitive behavior pattern, and restricted social interaction and communication lead to a debilitating situation in autism. The pattern of co-occurrence of medical comorbidities is most intriguing in autism, compared to any other neurodevelopmental disorders. They have an elevated comorbidity burden among which most frequently are seizures, psychiatric illness, and gastrointestinal disorders. The gut microbiota is believed to play a pivotal role in human health and disease through involvement in physiological homoeostasis, immunological development, glutathione metabolism, amino acid metabolism, etc., which in a reasonable way explain the role of gut-brain axis in autism. Branded as a neurodevelopmental disorder with psychiatric impairment and often misclassified as a mental disorder, many experts in the field think that a therapeutic solution to autism is unlikely to emerge. As the pathophysiology is still elusive, taking into account of the various symptoms that are concurrent in autism is important. Gastrointestinal problems that are seen associated with most of the autism cases suggest that it is not just a psychiatric disorder as many claim but have a physiological base, and alleviating the gastrointestinal problems could help alleviating the symptoms by bringing out the much needed overall improvement in the affected victims. A gut disorder akin to Crohn’s disease is, sometimes, reported in autistic children, an extremely painful gastrointestinal disease which is named as autistic enterocolitis. This disturbed situation hypothesized to be initiated by dysbiosis or microbial imbalance could in turn perturb the coordination of microbiota-gut-brain axis which is important in human mental health as goes the popular dictum: “fix your gut, fix your brain.”

Lanatoside C Induces G2/M Cell Cycle Arrest and Suppresses Cancer Cell Growth by Attenuating MAPK, Wnt, JAK-STAT, and PI3K/AKT/mTOR Signaling Pathways.

Abstract: Cardiac glycosides (CGs) are a diverse family of naturally derived compounds having a steroid and glycone moiety in their structures. CG molecules inhibit the α-subunit of ubiquitous transmembrane protein Na+/K+-ATPase and are clinically approved for the treatment of cardiovascular diseases. Recently, the CGs were found to exhibit selective cytotoxic effects against cancer cells, raising interest in their use as anti-cancer molecules. In this current study, we explored the underlying mechanism responsible for the anti-cancer activity of Lanatoside C against breast (MCF-7), lung (A549), and liver (HepG2) cancer cell lines. Using Real-time PCR, western blot, and immunofluorescence studies, we observed that (i) Lanatoside C inhibited cell proliferation and induced apoptosis in cell-specific and dose-dependent manner only in cancer cell lines; (ii) Lanatoside C exerts its anti-cancer activity by arresting the G2/M phase of cell cycle by blocking MAPK/Wnt/PAM signaling pathways; (iii) it induces apoptosis by inducing DNA damage and inhibiting PI3K/AKT/mTOR signaling pathways; and finally, (iv) molecular docking analysis shows significant evidence on the binding sites of Lanatoside C with various key signaling proteins ranging from cell survival to cell death. Our studies provide a novel molecular insight of anti-cancer activities of Lanatoside C in human cancer cells.

Low genetic variation is associated with low mutation rate in the giant duckweed.

Abstract: Mutation rate and effective population size (Ne) jointly determine intraspecific genetic diversity, but the role of mutation rate is often ignored. Here we investigate genetic diversity, spontaneous mutation rate and Ne in the giant duckweed (Spirodela polyrhiza). Despite its large census population size, whole-genome sequencing of 68 globally sampled individuals reveals extremely low intraspecific genetic diversity. Assessed under natural conditions, the genome-wide spontaneous mutation rate is at least seven times lower than estimates made for other multicellular eukaryotes, whereas Ne is large. These results demonstrate that low genetic diversity can be associated with large-Ne species, where selection can reduce mutation rates to very low levels. This study also highlights that accurate estimates of mutation rate can help to explain seemingly unexpected patterns of genome-wide variation.

Duckweed (Lemnaceae): Its Molecular Taxonomy

Abstract: Duckweeds include the world’s smallest and fastest growing flowering plants that have the capacity to produce huge biomass with a broad range of potential applications like production of feed and food, biofuel and biogas. In order to achieve optimal and sustainable commercial system, it is necessary that suitable species and clones of duckweeds be identified and selected based on appropriate strategies. However, a high degree of reduction in their structural complexity poses serious problems in identification of closely related species of duckweeds, on a morphological basis. Use of molecular taxonomic tools is the present solution. The state of the art of molecular taxonomy of all the five genera of duckweeds (Spirodela, Landoltia, Lemna, Wolffiella and Wolffia) is based mainly on the techniques of fingerprinting by amplified fragment length polymorphism (AFLP) and barcoding using sequences of plastidic DNA fragments. After more than 15 years of molecular taxonomic investigations, a certain viewpoint is now available demonstrating all five genera to be monophyletic. Also, the phenetic analyses had made huge progress in delineating the currently defined 36 species of duckweeds, although, all species cannot yet be defined with confidence. Wolffiella has turned out to be the most complicated genus as only 6 to 7 species out of the 10 can be reliably delineated. Further progress in the phylogenetic and phenetic analyses requires more advanced methods like next generation and/or whole genome sequencing. First results using the method genotyping-by-sequencing in the genus Lemna (in combination with metabolomic profiling by matrix-assisted laser desorption ionization time-of-flight mass-spectrometry (MALDI-TOF-MS) as well as AFLP and barcoding by plastidic sequences) are more promising: The species Lemna valdiviana and Lemna yungensis were united to one species, Lemna valdiviana. This reduced the total number of Lemnaceae species to 36.

Carbon Quantum Dot-Modified Carbon Paste Electrode-Based Sensor for Selective and Sensitive Determination of Adrenaline.

Abstract: A carbon quantum dot-based carbon paste electrode was fabricated and used for the determination of adrenaline (AD) at the nanomolar level. This fabricated electrode exhibited tremendous electrocatalytic activity for the oxidation of adrenaline in supporting electrolyte (PBS of pH 7.4). Scan rate variation studies with the modified electrode revealed that the overall electrode process was controlled by a diffusion process. A lower detection limit of 6 nM was achieved by chronoamperometry. Interference by biological molecules such as serotonin (5-HT) and ascorbic acid (AA) in the electrochemical oxidation of AD on the fabricated electrode was tested. It was observed that with the modified electrode, the selective determination of AD was possible. Further, with the fabricated electrode, simultaneous analysis of AA, AD, and 5-HT was performed, and it was observed that the overlapped peaks of these analytes on the naked electrode were well resolved into three peaks on the modified electrode. Along with decent ...

Anticancer effect of fucoidan on cell proliferation, cell cycle progression, genetic damage and apoptotic cell death in HepG2 cancer cells.

Abstract: The centre of the attraction of this article is inevitably associated with fucoidan polymers in terms of brown seaweed such as Turbinaria conoides. Fucoidan is a sulphated polysaccharide constitutes fucose as a major principle sugar along with other monosugars such as glucuronic acid, xylose and galactose. The core value of fucoidan in terms of various cancer types were substantially exhibited through targeting the key apoptotic molecules and subsequently mitigate the toxicity that are essentially included in the chemotherapeutic agents and radiation. The pragmatic investigation about the anti-cancer effect of fucoidan in a hepatoblastoma-derived (HepG2) cell line was thoroughly analyzed by the typical techniques such as cell viability, colony formation, cell migration, cell cycle progression, genetic damage and apoptosis along with their nuclear morphology and mitochondrial membrane potential. Following the analyzes, the cell viability was precisely evaluated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. And hence, cell cycle arrest and apoptosis was appropriately examined staining with propidium iodide (PI) and annexin V-fluorescein isothiocyante (FITC) by flowcytometer, respectively. Primarily, genetic damage by fucoidan in HepG2 cell line was evaluated by following Trevigen’s comet assay kit. In addition, alteration of nuclear content and mitochondrial membrane potential were also detected with Hoechst and mitochondrial membrane potential dye (JC-1: 5,5′6,6′-tetrachloro-1,1′3,3′tetraethylbenzimi-dazolycarbocyanine iodide) by fluorescence microscopy, respectively. The results of the present study showed that cells constituted with fucoidan/quercetin standard at 50, 100 and 200 μg/ml exhibited cell viability about 71, 60 & 40/80, 65 & 45%, respectively. The above recorded effect of fucoidan was a concentration-dependant inhibition on the basis of decline in colony forming and cell migration potential of HepG2 cancer cells. Compared with untreated control, fucoidan consituted cells were significantly (p ≤ 0.05) accumulated proliferative cells in the G0/G1 phase of the cell cycle in a concentration dependent manner. Increasing concentration of fucoidan (50,100 and 200 μg/ml) was remarkably enhanced the DNA damage which reflected through tail moment value of 3.8, 7.1 & 12.8 folds with respect to the untreated control. Fucoidan induced total apoptotic cells were observed ∼20–40% at 50–200 μg/ml concentrations. The apoptotic cell formation effected by change in the nuclear content and mitochondrial membrane potential was confirmed in HepG2 cancer cells under fluorescence microscopy. It was eventually concluded that the fucoidan display promising anti-cancer activity against HepG2 cancer cells by promoting the inhibition of cell proliferation, migration and cell arrest on concentration dependent-manner that was well correlated with genetic damage and apoptosis.

Resveratrol modulates epigenetic regulators of promoter histone methylation and acetylation that restores BRCA1, p53, p21CIP1 in human breast cancer cell lines.

Abstract: The epigenetic enzymes catalyze posttranslational modifications (PTMs) of histones, which functionally determine gene expression at the chromatin level. Resveratrol (RVT) a much studied anti-cancer natural molecule is known for restoration of BRCA1, p53, and p21 in cancer cells. We aimed to investigate the role of histone methylation and acetylation on upregulation of these tumor suppressor genes. Our results suggest RVT significantly increase expression of BRCA1, p53, and p21, while decreased expression of protein arginine methyltransferase 5 (PRMT5) and enhancer of Zeste homolog 2 (EZH2) at a 20 μM concentration by 48 hr in both MCF-7 and MDA-MB-231 breast cancer cells. Also, there was an overall loss of H4R3me2s (catalytic product of PRMT5) and H3K27me3 (catalytic product of PRMT5). In contrast, RVT exposure caused a significant decrease in lysine deacetylase (KDAC) activity and expression of KDAC1-3, whereas the expression of lysine acetyltransferase KAT2A/3B was increased compared to the unexposed cells. As an outcome, RVT increased global level of H3K9ac and H3K27ac marks. The chromatin immunoprecipitation showed 20 μM RVT exposure significantly reduced the enrichment of repressive histone marks (H4R3me2s and H3K27me3) while the abundance of activating histone marks (H3K9/27ac) within the proximal promoter region of BRCA1, p53, and p21 was increased. We hypothesize RVT by affecting the expression and function of methylation and acetylation enzymes altered the epigenetic modifications on promoter histones that restored expression of these critically important tumor suppressor genes.

Pedestrian Detection in Automotive Safety: Understanding State-of-the-Art

Abstract: Pedestrian detection is one of the important computer vision problems in automotive safety and driver assistance domain. It is a major component of the advanced driver assistance system (ADAS) which help the driver to drive safely. Recent literature shows a number of research activities addressing object detection/tracking in general and pedestrian detection in particular. The solutions proposed by different researchers vary in detection methods, detection scenario, feature descriptors, classification schemes, detection performance, as well as computational complexity. However, the average detection accuracy is not much promising even after many years of research. The fail-safe and real-time human detection from real life road scenes, even in standard resolution, is far from reality. Safety critical systems in the automotive industry have to follow well established stringent safety standards like ISO26262. Since the pedestrian detection system deals with human safety, it also has to follow these standards before integrating to the vehicle electronics. This paper is a study of different techniques used in pedestrian detection specific to the automotive application, along with a description of generic pedestrian detection solution architecture.

Duckweed biomarkers for identifying toxic water contaminants

Abstract: Surface or ground waters can be contaminated with numerous toxic substances. The duckweeds Lemna minor and Lemna gibba are widely used for assaying waterborne toxicity to higher plants in terms of growth inhibition and photosynthetic pigment reduction. These tests cannot, however, in themselves determine the nature of the agents responsible for toxicity. Morphological, developmental, physiological, biochemical, and genetic responses of duckweeds to exposure to toxic water contaminants constitute biomarkers of toxic effect. In principle, the very detection of these biomarkers should enable the contaminants having elicited them (and being responsible for the toxicity) to be identified. However, in practice, this is severely compromised by insufficient specificity of biomarkers for their corresponding toxicants and by the lack of documentation of biomarker/toxin relationships. The present contribution illustrates the difficulties of using known water contaminant-related duckweed biomarkers to identify toxins, and discusses possibilities for achieving this goal.

Importance of Long Non-coding RNAs in the Development and Disease of Skeletal Muscle and Cardiovascular Lineages.

Abstract: The early mammalian embryo is characterized by the presence of three germ layers-the outer ectoderm, middle mesoderm and inner endoderm. The mesoderm is organized into paraxial, intermediate and lateral plate mesoderm. The musculature, vasculature and heart of the adult body are the major derivatives of mesoderm. Tracing back the developmental process to generate these specialized tissues has sparked much interest in the field of regenerative medicine focusing on generating specialized tissues to treat patients with degenerative diseases. Several Long Non-Coding RNAs (lncRNAs) have been identified as regulators of development, proliferation and differentiation of various tissues of mesodermal origin. A better understanding of lncRNAs that can regulate the development of these tissues will open potential avenues for their therapeutic utility and enhance our knowledge about disease progression and development. In this review, we aim to summarize the functions and mechanisms of lncRNAs regulating the early mesoderm differentiation, development and homeostasis of skeletal muscle and cardiovascular system with an emphasis on their therapeutic potential.

Adsorption and kinetic behavior of Cu(II) ions from aqueous solution on DMSA functionalized magnetic nanoparticles

Abstract: In this work, magnetic nanoparticles (MNPs) synthesized by the solvothermal method and functionalized by meso-2,3-dimercaptosuccinic acid (DMSA) by ligand-exchange protocol were used as nanoadsorbents to remove Cu(II) ions from aqueous solution. The magnetic nanoadsorbents were characterized by X-ray diffraction (XRD), transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FTIR) and vibrating sample magnetometer (VSM). The functionalized MNPs were used for removal of Cu(II) by batch adsorption technique under different influencing parameters such as contact time, adsorbent dose, initial Cu(II) concentration, and pH. The adsorption behaviour of Cu(II) on MNP-DMSA follows Pseudo-first-order kinetic model. Removal efficiency was found to decrease from 98 to 64% by increasing the Cu(II) concentration in the solution from 50 to 300 ppm. The experimental data for the adsorption of Cu(II) were found to follow the Langmuir isotherm and the maximum adsorption capacity was 25.44 mg/g.

Curcumin-mediated demethylation of the proximal promoter CpG island enhances the KLF4 recruitment that leads to increased expression of p21Cip1 in vitro.

Abstract: Curcumin, the active component of the spice turmeric, induce global DNA hypomethylation as it has been shown to inhibit DNA methyltransferases It promotes cell death in cancer cells by arresting in the G1 phase It was explained to cause increased expression of cell cycle regulator, p21 (WAF1/Cip1); however, the mechanism remains not clear The p21 promoter harvests a CpG island (CGI) in the proximal region enriched with CG dinucleotide clusters with Kruppel-like factor 4 (KLF4) transcription factor binding site We probed the p21 promoter CGI (spanning from -135 to +12, respective to the transcription start site) to detect alterations in cytosine methylation level in response to curcumin exposure in four different human cancer cell lines: A431, A549, MCF7, and HeLa We observed curcumin (20 µM) treatment significantly increased the expression of p21, and the promoter CGI was demethylated in a dose-dependent manner The curcumin significantly raised the level KLF4 and enhanced the p21 promoter occupancy by KLF4 From our results we hypothesize that curcumin-mediated demethylation of the p21 proximal promoter and increased KLF4 expression as well as its binding to its proximal promoter could serve as a mechanism that could be hypothesized to cause upregulation of p21 in presence of curcumin and thus its therapeutic implications could further be investigated

Dynamic Interactions between Autophagosomes and Lipid Droplets in Chlamydomonas reinhardtii.

Abstract: Autophagy is a highly conserved catabolic process in eukaryotic cells by which waste cellular components are recycled to maintain growth in both favorable and stress conditions. Autophagy has been linked to lipid metabolism in microalgae; however, the mechanism underlying this interaction remains unclear. In this study, transgenic Chlamydomonas reinhardtii cells that stably express the red fluorescent protein (mCherry) tagged-ATG8 as an autophagy marker were established. By using this tool, we were able to follow the autophagy process in live microalgal cells under various conditions. Live-cell and transmission electron microscopy (TEM) imaging revealed physical contacts between lipid droplets and autophagic structures during the early stage of nitrogen starvation, while fusion of these two organelles was observed in prolonged nutritional deficiency, suggesting that an autophagy-related pathway might be involved in lipid droplet turnover in this alga. Our results thus shed light on the interplay between autophagy and lipid metabolism in C. reinhardtii, and this autophagy marker would be a valuable asset for further investigations on autophagic processes in microalgae.

Curcumin ameliorates PRMT5-MEP50 arginine methyltransferase expression by decreasing the Sp1 and NF-YA transcription factors in the A549 and MCF-7 cells

Abstract: The protein arginine methyltransferase 5 (PRMT5) and its catalytic partner methylosome protein MEP50 (WDR77) catalyse the mono- and symmetric di-methylation of selective arginines in various histones and non-histone target proteins. It has emerged as a crucial epigenetic regulator in cell proliferation and differentiation; which also reported to be overexpressed in many forms of cancers in humans. In this study, we aimed to assess the modulations in the expression of this enzyme upon exposure to the well-studied natural compound from the spice turmeric, curcumin. We exposed the lung and breast cancer cell lines (A549 and MCF-7) to curcumin (2 and 20 μM) and observed a highly significant inhibitory effect on the expression of both PRMT5 and MEP50. The level of symmetrical dimethylarginine (SDMA) in multiple proteins, and more specifically, the H4R3me2s mark (which predominates in GC-rich motifs in nucleosomal DNA) was also diminished significantly. We also found that curcumin significantly reduced the level and enrichment of the transcription factors Sp1 and NF-YA which shares their binding sites within the GC-rich region of the PRMT5 proximal promoter. Furthermore, the involvement of both PKC-p38-ERK-cFos and AKT-mTOR signalling was observed in reducing the Sp1 and NF-YA expression by curcumin. Therefore, we propose curcumin decreased the expression of PRMT5 in these cells by affecting at least these two transcription factors. Altogether, we report a new molecular target of curcumin and further elucidation of this proposed mechanism through which curcumin affects the PRMT5-MEP50 methyltransferase expression might be explored for its therapeutic application.