Topical collection on Chromatin Biology and Epigenetics.
PMID: 31965979 [PubMed - in process] (Source: Journal of Biosciences)
Source: Journal of Biosciences - January 24, 2020 Category: Biomedical Science Authors: Narlikar G, Galande S Tags: J Biosci Source Type: research

A novel role of tumor suppressor ZMYND8 in inducing differentiation of breast cancer cells through its dual-histone binding function.
Abstract Accumulating evidences indicate the involvement of epigenetic deregulations in cancer. While some epigenetic regulators with aberrant functions in cancer are targeted for improving therapeutic outcome in patients, reinstating the functions of tumor-suppressor-like epigenetic regulators might further potentiate anti-cancer therapies. Epigenetic reader zinc-finger MYND-type-containing 8 (ZMYND8) has been found to be endowed with multiple anti-cancer functions like inhibition of tumor cell migration and proliferation. Here, we report another novel tumor suppressor role of ZMYND8 as an inducer of differentiat...
Source: Journal of Biosciences - January 24, 2020 Category: Biomedical Science Authors: Mukherjee S, Sen S, Adhikary S, Sengupta A, Mandal P, Dasgupta D, Chakrabarti P, Roy S, DAS C Tags: J Biosci Source Type: research

Hypoxia-induced changes in intragenic DNA methylation correlate with alternative splicing in breast cancer.
Abstract The tumor microenvironment is marked by gradients in the level of oxygen and nutrients, with oxygen levels reaching a minimum at the core of the tumor, a condition known as tumor hypoxia. Mediated by members of the HIF family of transcription factors, hypoxia leads to a more aggressive tumor phenotype by transactivation of several genes as well as reprogramming of pre-mRNA splicing. Intragenic DNA methylation, which is known to affect alternative splicing in cancer, could be one of several reasons behind the changes in splicing patterns under hypoxia. Here, we have tried to establish a correlation between...
Source: Journal of Biosciences - January 24, 2020 Category: Biomedical Science Authors: Pant D, Narayanan SP, Vijay N, Shukla S Tags: J Biosci Source Type: research

Histone H2A isoforms: Potential implications in epigenome plasticity and diseases in eukaryotes.
Abstract Epigenetic mechanisms including the post-translational modifications of histones, incorporation of histone variants and DNA methylation have been suggested to play an important role in genome plasticity by allowing the cellular environment to define gene expression and the phenotype of an organism. Studies over the past decade have elucidated how these epigenetic mechanisms are significant in orchestrating various biological processes and contribute to different pathophysiological states. However, the role of histone isoforms and their impact on different phenotypes and physiological processes associated ...
Source: Journal of Biosciences - January 24, 2020 Category: Biomedical Science Authors: Shah S, Verma T, Rashid M, Gadewal N, Gupta S Tags: J Biosci Source Type: research

Phase-separation in chromatin organization.
Abstract The organization of chromatin into different types of compact versus open states provides a means to fine tune gene regulation. Recent studies have suggested a role for phase-separation in chromatin compaction, raising new possibilities for regulating chromatin compartments. This perspective discusses some specific molecular mechanisms that could leverage such phase-separation processes to control the functions and organization of chromatin. PMID: 31965983 [PubMed - in process] (Source: Journal of Biosciences)
Source: Journal of Biosciences - January 24, 2020 Category: Biomedical Science Authors: Narlikar GJ Tags: J Biosci Source Type: research

The role of histone modifications in leukemogenesis.
Abstract Histone modifications play a critical role in coordinating accurate gene expression. Aside from genetic mutations which cause altered DNA sequence, it has become increasingly clear that aberrant post-translational modifications of histone tails are also associated with leukemogenesis. The functional roles of specific histone marks has informed the basis of our understanding for underlying mechanisms of leukemia, while global analyses of interacting histone modifications has begun to distinguish subtypes of leukemia with prognostic and therapeutic implications. In this current era of personalized and preci...
Source: Journal of Biosciences - January 24, 2020 Category: Biomedical Science Authors: Birch NW, Shilatifard A Tags: J Biosci Source Type: research

Metabolic choreography of gene expression: nutrient transactions with the epigenome.
Abstract Eukaryotic complexity and thus their ability to respond to diverse cues are largely driven by varying expression of gene products, qualitatively and quantitatively. Protein adducts in the form of post-translational modifications, most of which are derived from metabolic intermediates, allow fine tuning of gene expression at multiple levels. With the advent of high-throughput and high-resolution mapping technologies there has been an explosion in terms of the kind of modifications on chromatin and other factors that govern gene expression. Moreover, even the classical notion of acetylation and methylation ...
Source: Journal of Biosciences - January 24, 2020 Category: Biomedical Science Authors: Maniyadath B, Sandra US, Kolthur-Seetharam U Tags: J Biosci Source Type: research

Origin of RNA Polymerase II pause in eumetazoans: Insights from Hydra.
Abstract Multicellular organisms have evolved sophisticated mechanisms for responding to various developmental, environmental and physical stimuli by regulating transcription. The correlation of distribution of RNA Polymerase II (RNA Pol II) with transcription is well established in higher metazoans, however genome-wide information about its distribution in early metazoans, such as Hydra, is virtually absent. To gain insights into RNA Pol II-mediated transcription and chromatin organization in Hydra, we performed chromatin immunoprecipitation (ChIP)-coupled high-throughput sequencing (ChIP-seq) for RNA Pol II and ...
Source: Journal of Biosciences - January 24, 2020 Category: Biomedical Science Authors: Reddy PC, Pradhan SJ, Karmodiya K, Galande S Tags: J Biosci Source Type: research

Mining histone methyltransferases and demethylases from whole genome sequence.
Abstract Epigenetic regulation through post-translational modification of histones, especially methylation, is well conserved in evolution. Although there are several insect genomes sequenced, an analysis with a focus on their epigenetic repertoire is limited. We have utilized a novel work-flow to identify one or more domains as highpriority domain (HPD), if present in at least 50% of the genes of a given functional class in the reference genome, namely, that of Drosophila melanogaster. Based on this approach, we have mined histone methyltransferases and demethylases from the whole genome sequence of Aedes aegypti...
Source: Journal of Biosciences - January 24, 2020 Category: Biomedical Science Authors: Gulati P, Kohli S, Narang A, Brahmachari V Tags: J Biosci Source Type: research

The conserved aspartate in motif III of b family AdoMet-dependent DNA methyltransferase is important for methylation.
Abstract S-adenosyl-L-methionine (AdoMet)-dependent methyltransferases (MTases) are involved in diverse cellular functions. These enzymes show little sequence conservation but have a conserved structural fold. The DNA MTases have characteristic motifs that are involved in AdoMet binding, DNA target recognition and catalysis. Motif III of these MTases have a highly conserved acidic residue, often an aspartate, whose functional significance is not clear. Here, we report a mutational study of the residue in the β family MTase of the Type III restriction-modification enzyme EcoP15I. Replacement of this residue by...
Source: Journal of Biosciences - January 24, 2020 Category: Biomedical Science Authors: Gopinath A, Kulkarni M, Ahmed I, Chouhan OP, Saikrishnan K Tags: J Biosci Source Type: research

Role of PfGCN5 in nutrient sensing and transcriptional regulation in Plasmodium falciparum.
In this study, we show upregulation of PfGCN5 upon nutrient stress condition. With the help of chromatin immunoprecipitation coupled high-throughput sequencing (ChIP-seq) and transcriptomic (RNA-sequencing) analyses, we show that PfGCN5 is associated with the genes that are important for the maintenance of parasite cellular homeostasis upon nutrient stress condition. Furthermore, we identified various metabolic enzymes as interacting partners of PfGCN5 by immunoprecipitation coupled with mass spectroscopy, possibly acting as a sensor of nutrient conditions in the environment. We also demonstrated that PfGCN5 interacts and ...
Source: Journal of Biosciences - January 24, 2020 Category: Biomedical Science Authors: Rawat M, Malhotra R, Shintre S, Pani S, Karmodiya K Tags: J Biosci Source Type: research

Genomic organization of Polycomb Response Elements and its functional implication in Drosophila and other insects.
Abstract The epigenetic memory is an essential aspect of multicellular organisms to maintain several cell types and their gene expression pattern. This complex process uses a number of protein factors and specific DNA elements within the developmental cues to achieve this. The protein factors involved in the process are the Polycomb group (PcG) members, and, accordingly, the DNA sequences that interact with these proteins are called Polycomb Response Elements (PREs). Since the PcG proteins are highly conserved among higher eukaryotes, including insects, and function at thousands of sites in the genomes, it is expe...
Source: Journal of Biosciences - January 24, 2020 Category: Biomedical Science Authors: Srinivasan A, Mishra RK Tags: J Biosci Source Type: research

Picking a nucleosome lock: Sequence- and structure-specific recognition of the nucleosome.
Abstract The nucleosome presents a formidable barrier to DNA-templated transcription by the RNA polymerase II machinery. Overcoming this transcriptional barrier in a locus-specific manner requires sequence-specific recognition of nucleosomal DNA by 'pioneer' transcription factors (TFs). Cell fate decisions, in turn, depend on the coordinated action of pioneer TFs at cell lineage-specific gene regulatory elements. Although it is already appreciated that pioneer factors play a critical role in cell differentiation, our understanding of the structural and biochemical mechanisms by which they act is still rapidly expa...
Source: Journal of Biosciences - January 24, 2020 Category: Biomedical Science Authors: Makowski MM, Gaullier G, Luger K Tags: J Biosci Source Type: research

Role of nucleosome positioning in 3D chromatin organization and loop formation.
We present a physics-based polymer model that can investigate 3D organization of chromatin accounting for DNA elasticity, DNA-bending due to nucleosomes, and 1D organization of nucleosomes along DNA. We find that the packing density of chromatin oscillates between densities corresponding to highly folded and extended configurations as we change the nucleosome organization (length of linker DNA). We compute the looping probability of chromatin and show that the presence of nucleosomes increases the looping probability of the chain compared to that of a bare DNA. We also show that looping probability has a large variability ...
Source: Journal of Biosciences - January 24, 2020 Category: Biomedical Science Authors: Kharerin H, Bhat PJ, Padinhateeri R Tags: J Biosci Source Type: research

Regulation of epigenetic state by non-histone chromatin proteins and transcription factors: Implications in disease.
Abstract Besides the fundamental components of the chromatin, DNA and octameric histone, the non-histone chromatin proteins and non-coding RNA play a critical role in the organization of functional chromatin domains. The non-histone chromatin proteins therefore regulate the transcriptional outcome in both physiological and pathophysiological state as well. They also help to maintain the epigenetic state of the genome indirectly. Several transcription factors and histone interacting factors also contribute in the maintenance of the epigenetic states, especially acetylation by the induction of autoacetylation abilit...
Source: Journal of Biosciences - January 24, 2020 Category: Biomedical Science Authors: Sikder S, Kaypee S, Kundu TK Tags: J Biosci Source Type: research

The CBX family of proteins in transcriptional repression and memory.
Abstract For mammals to develop properly, master regulatory genes must be repressed appropriately in a heritable manner. This review concerns the Polycomb Repressive Complex 1 (PRC1) family and the relationship between the establishment of repression and memory of the repressed state. The primary focus is on the CBX family of proteins in PRC1 complexes and their role in both chromatin compaction and phase separation. These two activities are linked and might contribute to both repression and memory. PMID: 31965994 [PubMed - in process] (Source: Journal of Biosciences)
Source: Journal of Biosciences - January 24, 2020 Category: Biomedical Science Authors: Kim J, Kingston RE Tags: J Biosci Source Type: research

When histones are under glucose starvation.
Abstract Under nutritional stress, cells undergo metabolic rewiring that results in changes of various cellular processes that include gene transcription. This transcriptional regulation requires dynamic chromatin remodeling that involves histone post-translational modifications. There are several histone marks that may act as switches upon starvation for stress-response pathways. PMID: 31965995 [PubMed - in process] (Source: Journal of Biosciences)
Source: Journal of Biosciences - January 24, 2020 Category: Biomedical Science Authors: Lee J, Oh S, Abmayr SM, Workman JL Tags: J Biosci Source Type: research

Recent advances in the spatial organization of the mammalian genome.
Abstract The mammalian genome is complex and presents a dynamic structural organization that reflects function. Organization of the genome inside the mammalian nucleus impacts all nuclear processes including but not limited to transcription, replication and repair, and in many biological contexts such as early development, differentiation and physiological adaptations. However, there is limited understating of how 3D organization of the mammalian genome regulates different nuclear processes. Recent advances in microscopy and a myriad of genomics methods -- ropelled by next-generation sequencing -- have advanced ou...
Source: Journal of Biosciences - January 24, 2020 Category: Biomedical Science Authors: Kumar Y, Sengupta D, Bickmore W Tags: J Biosci Source Type: research

Cellular environment controls the dynamics of histone H3 lysine 56 acetylation in response to DNA damage in mammalian cells.
Abstract Epigenetic changes play a crucial role in sensing signals and responding to fluctuations in the extracellular environment. How the cellular micro-environment affects DNA damage response signalling in chromatin context is not extensively studied. Histone acetylation is dynamic and very sensitive to changes in the extracellular environment. Existing literature on H3 lysine 56 acetylation (H3K56ac) levels upon DNA damage in mammals presents a conflicting picture. The occurrence of both increased and decreased H3K56ac upon DNA damage in our experiments led us to investigate the role of the micro-environment o...
Source: Journal of Biosciences - January 24, 2020 Category: Biomedical Science Authors: Vadla R, Chatterjee N, Haldar D Tags: J Biosci Source Type: research

Role of genomic imprinting in mammalian development.
Abstract Non-mendelian inheritance refers to the group of phenomena and observations related to the inheritance of genetic information that cannot be merely explained by Mendel's laws of inheritance. Phenomenon including Genomic imprinting, X-chromosome Inactivation, Paramutations are some of the best studied examples of non-mendelian inheritance. Genomic imprinting is a process that reversibly marks one of the two homologous loci, chromosome or chromosomal sets during development, resulting in functional non-equivalence of gene expression. Genomic imprinting is known to occur in a few insect species, plants, and ...
Source: Journal of Biosciences - January 24, 2020 Category: Biomedical Science Authors: Thamban T, Agarwaal V, Khosla S Tags: J Biosci Source Type: research

TET methylcytosine oxidases: new insights from a decade of research.
Abstract In mammals, DNA methyltransferases transfer a methyl group from S-adenosylmethionine to the 5 position of cytosine in DNA. The product of this reaction, 5-methylcytosine (5mC), has many roles, particularly in suppressing transposable and repeat elements in DNA. Moreover, in many cellular systems, cell lineage specification is accompanied by DNA demethylation at the promoters of genes expressed at high levels in the differentiated cells. However, since direct cleavage of the C-C bond connecting the methyl group to the 5 position of cytosine is thermodynamically disfavoured, the question of whether DNA meth...
Source: Journal of Biosciences - January 24, 2020 Category: Biomedical Science Authors: Lio CJ, Yue X, Lopez-Moyado IF, Tahiliani M, Aravind L, Rao A Tags: J Biosci Source Type: research

MiR-506-3p suppresses the proliferation of ovarian cancer cells by negatively regulating the expression of MTMR6.
Abstract MicroRNAs have been reported to play a crucial role in ovarian cancer (OC) as the most lethal malignancy of the women. Here, we found miR-506-3p was significantly down-regulated in OC tissues compared with corresponding adjacent nontumor tissues. Ectopic miR-506-3p expression inhibited OC cell growth and proliferation using MTT and colony formation assay. Additionally, flow cytometry analysis showed that the overexpression of miR-506-3p induced cell cycle G0/G1 phase arrest and cell apoptosis in OC cells. A luciferase reporter assay confirmed that the myotubularin-related protein 6 (MTMR6) was the target ...
Source: Journal of Biosciences - December 1, 2019 Category: Biomedical Science Authors: Wang Y, Lei X, Gao C, Xue Y, Li X, Wang H, Feng Y Tags: J Biosci Source Type: research

Sp7/osterix positively regulates dlx2b and bglap to affect tooth development and bone mineralization in zebrafish larvae.
Abstract Osterix (or Sp7) is an important transcription factor that promotes osteoblast differentiation by modulating the expression of a range of target genes. Although many studies have focused on Osterix/Sp7 regulatory mechanisms, the detailed functions have not been fully elucidated. Toward this end, in this study, we used CRISPR/Cas9 technology to knock out the zebrafish sp7 gene, and then analyzed its phenotype and biological function. Two knockout sp7 mutant lines were successfully obtained. The bone mineralization level was significantly reduced in the zebrafish sp7-/- homozygote, resulting in abnormal too...
Source: Journal of Biosciences - December 1, 2019 Category: Biomedical Science Authors: Chen Z, Song Z, Yang J, Huang J, Jiang H Tags: J Biosci Source Type: research

Long non-coding RNA H19 modulates proliferation and apoptosis in osteoarthritis via regulating miR-106a-5p.
Abstract Osteoarthritis (OA), a type of joint diseases, could result in breakdown of joint cartilage and underlying bone. Accumulating evidences suggested that long non-coding RNAs play important roles in OA progression. However, the underlying mechanism of H19 in OA is still not fully explored. The expression levels of H19 and miR-106a-5p in OA samples from patients or cultured chondrocytes were examined by quantitative real time polymerase chain reaction. Cell proliferation and apoptosis were analysed by MTT assay and flow cytometry, respectively. Western blotting was employed to detect the expression levels of ...
Source: Journal of Biosciences - December 1, 2019 Category: Biomedical Science Authors: Zhang X, Liu X, Ni X, Feng P, Wang YU Tags: J Biosci Source Type: research

Arabidopsis SIMILAR TO RCD-ONE genes are ubiquitous and respond to multiple abiotic stresses through diverse signaling pathways.
Abstract The SIMILAR TO RCD-ONE (SROs) have been characterized as a group of plant-specific proteins which play important functions in stress responses and development. Here, we analyze the expression profiles of six SRO genes under different stress treatments in Arabidopsis. Our results revealed that RCD1 play an essential role in plant responses to various environmental stresses. SRO1 has partially overlapping functions with RCD1 in plant response to HgCl2 and H2O2 stress. Analysis of the transcriptional expression of SROs indicated that both of the RCD1 and SRO1 transcripts were up-regulated by HgCl2 and light,...
Source: Journal of Biosciences - December 1, 2019 Category: Biomedical Science Authors: Zhao X, Gao L, Ren J, Pan F Tags: J Biosci Source Type: research

Rational design of type-IA receptor-derived cyclic peptides to target human bone morphogenic protein 2.
Abstract Human bone morphogenetic protein 2 (BMP2) is a bone-growth regulatory factor involved in the formation of bone and cartilage, and has been recogn ized as an attractive therapeutic target for a variety of bone diseases and defects. Here, we report successful design of a head-to-tail cyclic peptide based on crystal structure to target BMP2. Computational alanine scanning identifies two hotspot regions at the crystal complex interface of BMP2 with its type-IA receptor; promising one is stripped from the interface to derive a linear self-inhibitory peptide RPS2[r78-94] that covers residues 78-94 of the recept...
Source: Journal of Biosciences - December 1, 2019 Category: Biomedical Science Authors: Fan X, Xia H, Liu X, Li B, Fang J Tags: J Biosci Source Type: research

Correction to: Protein-rich extract of Musca domestica larvae alleviated metabolic disorder in STZ-induced type 2 diabetic rat model via hepatoprotective and pancreatic β-cell protective activities.
Correction to: Protein-rich extract of Musca domestica larvae alleviated metabolic disorder in STZ-induced type 2 diabetic rat model via hepatoprotective and pancreatic β-cell protective activities. J Biosci. 2019 Dec;44(6): Authors: Mei H, Xu J, He Y, Yang X, Liu W, Tian W, Zeng YU, Zhu J PMID: 31894112 [PubMed - in process] (Source: Journal of Biosciences)
Source: Journal of Biosciences - December 1, 2019 Category: Biomedical Science Authors: Mei H, Xu J, He Y, Yang X, Liu W, Tian W, Zeng YU, Zhu J Tags: J Biosci Source Type: research

Overcoming randomness does not rule out the importance of inherent randomness for functionality.
Abstract Randomness is intrinsic to many natural processes. It is also clear that, under certain conditions, disorders are not associated with functionality. Several examples in which overcoming, suppressing, or combining both randomness and non-randomness is required are drawn from various fields. However, the need to suppress or overcome randomness does not negate its importance under certain conditions and its significance in valid processes and organ functions. Randomness should be acknowledged rather than ignored or suppressed; it can be viewed, at worst, as a disturbing disorder that may be treated to produc...
Source: Journal of Biosciences - December 1, 2019 Category: Biomedical Science Authors: Ilan Y Tags: J Biosci Source Type: research

Rapid burst of ethylene evolution by premature seed: A warning sign for the onset of spongy tissue disorder in Alphonso mango fruit?
Abstract Moisture stress induced in premature seeds due to the breakdown of funiculus in Alphonso mango led to the burst of ethylene evolution, which in turn caused a sudden increase of polyphenol oxidase activity in the pulp, resulting in the development of a black spot near the seed base. Reduced levels of very long chain fatty acids in 70% mature seeds with black spots were associated with a sudden increase of cytokinins followed by a rapid rise of starch-metabolizing enzymes culminating in the onset of pre-germination events. Concurrently, an overproduction of p-OH benzoic acid inhibited amylase and polygalact...
Source: Journal of Biosciences - December 1, 2019 Category: Biomedical Science Authors: Shivashankar S, Sumathi M Tags: J Biosci Source Type: research

A cross-eyed geneticist's view V. How Sydney Brenner, Leslie Barnett, Eugene Katz, and Francis Crick inferred that UGA is a nonsense codon.
PMID: 31894115 [PubMed - in process] (Source: Journal of Biosciences)
Source: Journal of Biosciences - December 1, 2019 Category: Biomedical Science Authors: Kasbekar DP Tags: J Biosci Source Type: research

Laser-ablation-synthesized nanoparticles and animal cell lines studies.
Abstract Nanoparticles (NPs) synthesized by laser ablation in distilled water were used to study their biological effect on normal and cancer cells. Parameters such as cell morphology, cell proliferation and viability were examined for treated cell lines, and the effect was represented in terms of cells cytotoxicity using standard procedures. The study reveals the higher cytotoxic effect of nanoparticles on cancerous cells of breast, melanoma and colon origin compared to normal fibroblast cells NIH- 3T3. Furthermore, DNA fragmentation assay results demonstrated the apoptosis mediated cell death in nanoparticle-tre...
Source: Journal of Biosciences - December 1, 2019 Category: Biomedical Science Authors: Mahadevaiah, Kurrey NK, Gowtham GK, Somshekar R Tags: J Biosci Source Type: research

Involvement of putrescine in osmotic stress-induced ABA signaling in leaves of wheat seedlings.
Abstract To elucidate one mechanism by which putrescine (Put) functions in plant signaling under osmotic stress, Put and ABA contents, and plasma membrane-NADPH oxidase (PM-NOX) activity were detected in wheat seedling leaves. Under osmotic stress, ABA and Put contents, PM-NOX activity, and PM-NOX-dependent O2.- production all increased. The inhibitor tungstate (T) of ABA bio-synthesis reduced the increases in ABA and Put contents under osmotic stress. The inhibitor D-arginine (D-Arg) of Put bio-synthesis didn't reduce osmotic-induced increase of ABA, but it inhibited the increases of PM-NOX activity and O2 . - pr...
Source: Journal of Biosciences - December 1, 2019 Category: Biomedical Science Authors: DU HY, Chen GS, Yu JM, Bao YY, Liu GT, Liu HP, Gupta R Tags: J Biosci Source Type: research

Molecular cloning and characterization of genes related to the ethylene signal transduction pathway in pomegranate (Punica granatum L.) under different temperature treatments.
Abstract Low temperature storage is a common method for storing pomegranates post-harvest; however, unsuitable low temperatures can cause fruit chilling injuries, the molecular mechanism of which is as yet unclear. Ethylene is a major factor affecting the post-harvest storage quality of pomegranates, and functions mainly through the ethylene signal transduction pathway. ERF1, ERF2 and ETR are key genes in the ethylene signal transduction pathway. Here, we used RACE and homologous cloning techniques to obtain PgERF1 (KU058889), PgERF2 (KU058890) and PgETR (KU058891) from Punica granatum cv. Yushizi. Sequence alignm...
Source: Journal of Biosciences - December 1, 2019 Category: Biomedical Science Authors: Huang R, Li W, Guan XW, Xie B, Zhang SM Tags: J Biosci Source Type: research

Presence of carbohydrate binding modules in extracellular region of class C G-protein coupled receptors (C GPCR): An in silico investigation on sweet taste receptor.
In conclusion, presence of CBM in STR and, by extrapolation, in other C GPCR family members is suggested, similar to previously proposed sites in gut fungal C GPCRs, through transcriptome analyses. STR modes of interaction with carbohydrates are also discussed and characteristics of non-covalent interactions in C GPCR family are highlighted. PMID: 31894119 [PubMed - in process] (Source: Journal of Biosciences)
Source: Journal of Biosciences - December 1, 2019 Category: Biomedical Science Authors: Kashani-Amin E, Sakhteman A, Larijani B, Ebrahim-Habibi A Tags: J Biosci Source Type: research

Translin: A multifunctional protein involved in nucleic acid metabolism.
Abstract Translin, a highly conserved, DNA/RNA binding protein, is abundantly expressed in brain, testis and in certain malignancies. It was discovered initially in the quest to find proteins that bind to alternating polypurines-polypyrimidines repeats. It has been implicated to have a role in RNA metabolism (tRNA processing, RNAi, RNA transport, etc.), transcription, DNA damage response, etc. Studies from human, mice, drosophila and yeast have revealed that it forms an octameric ring, which is important for its function. Translin is a cytoplasmic protein, but under genotoxic stress, it migrates into the nucleus, ...
Source: Journal of Biosciences - December 1, 2019 Category: Biomedical Science Authors: Gupta A, Pillai VS, Chittela RK Tags: J Biosci Source Type: research

Biophysical methods for quality evaluation of decellularized and recellularized tissue-engineered constructs of organs and tissues.
Abstract Tissue engineering is rapidly growing now and can become a promising alternative to transplantation of organs and tissues, as it is devoid of major shortcomings of transplantology, such as acute shortage, complexity of selection, delivery and storage of donor material, lifelong immunosuppressive therapy. One of the most widely known methods of obtaining biological scaffolds for the subsequent creation of tissue-engineered constructs of organs and tissues is decellularization. The evaluation of the quality of the obtained scaffolds, based on the study of the viability of cell structures in decellularized a...
Source: Journal of Biosciences - December 1, 2019 Category: Biomedical Science Authors: Gubareva EA, Kuevda EV, Basov AA, Sotnichenko AS, Bolotin SN, Dzhimak SS Tags: J Biosci Source Type: research

Investigation of the response to salinity of transgenic potato plants overexpressing the transcription factor StERF94.
In this study, transgenic potato plants overexpressing StERF94 were produced and submitted to salt treatment (100 mM NaCl) in vitro and under greenhouse culture conditions. StERF94 transgenic lines showed lower decrease of stem elongation under salt treatment in comparison to non-transgenic wild-type plants. Moreover, these plants showed a low level of H2O2 and Malondialdehyde content, and an increase in catalase and GPX (Gluthation peroxidase) activities compared to non-transgenic plants. In a second step, enhanced expression of some target genes for example CuZn-SOD, DHN25 (Dehydrin) and ERD (Early Responsive to Dehydrat...
Source: Journal of Biosciences - December 1, 2019 Category: Biomedical Science Authors: Charfeddine M, Charfeddine S, Ghazala I, Bouaziz D, Bouzid RG Tags: J Biosci Source Type: research

Iris yellow spot virus-induced chloroplast malformation results in male sterility.
Abstract Iris yellow spot virus (IYSV) is one of the most devastating viral pathogens, which causes high economic losses in the onion yield. Physiological and genetic changes are associated with the appearance of chlorotic symptom in the infected plants. IYSV-N gene sequence analysis revealed that it shared sequence identity of 99% with other Egyptian isolates, at both genomic and proteomic levels. In addition, N protein sequence with computational examination indicated many motifs involved and played different roles in the virus activity and its regulation and stability were detected. In the Differential Display-...
Source: Journal of Biosciences - December 1, 2019 Category: Biomedical Science Authors: Abdelkhalek A, Qari SH, Hafez E Tags: J Biosci Source Type: research

A review of computational algorithms for CpG islands detection.
Abstract CpG islands are generally known as the epigenetic regulatory regions in accordance with histone modifications, methylation, and promoter activity. There is a significant need for the exact mapping of DNA methylation in CpG islands to understand the diverse biological functions. However, the precise identification of CpG islands from the whole genome through experimental and computational approaches is still challenging. Numerous computational methods are being developed to detect the CpG-enriched regions, effectively, to reduce the time and cost of the experiments. Here, we review some of the latest compu...
Source: Journal of Biosciences - December 1, 2019 Category: Biomedical Science Authors: Tahir RA, Zheng DA, Nazir A, Qing H Tags: J Biosci Source Type: research

Isoflurane preconditioning protects hepatocytes from oxygen glucose deprivation injury by regulating FoxO6.
In this study, we explored the role and mechanism of FoxO6 in the protective effect of isoflurane preconditioning during hepatocyte injury caused by oxygen-glucose deprivation (OGD). Cells from the human fetal hepatocyte (LO2) line were incubated with 0%, 1%, 2%, 2.5%, 3%, 3.5%, 4%, or 5% isoflurane for 3 h and then exposed to OGD. Data showed that 3% isoflurane preconditioning inhibited FoxO6 expression, caspase-3 activity, and reactive oxygen species production and promoted cell viability. FoxO6 overexpression abolished the effects of 3% isoflurane preconditioning on caspase-3 activity, reactive oxygen species production...
Source: Journal of Biosciences - December 1, 2019 Category: Biomedical Science Authors: Zhong Y, Hu X, Miao L Tags: J Biosci Source Type: research

Investigation of axonal regeneration of Triturus ivanbureschi by using physiological and proteomic strategies.
This study showed that the expression levels of certain proteins differ between distal and proximal nerve endings during the regeneration period. In distal nerve stumps, transport proteins, growth factors, signal, and regulatory molecules are highly expressed, whereas in proximal nerve stumps, neurite elongation proteins, and cytoskeletal proteins are highly expressed. PMID: 31894126 [PubMed - in process] (Source: Journal of Biosciences)
Source: Journal of Biosciences - December 1, 2019 Category: Biomedical Science Authors: Turan SK, Onur MA, Demiralp FDO Tags: J Biosci Source Type: research

MiR-195 inhibits migration, invasion and epithelial-mesenchymal transition (EMT) of endometrial carcinoma cells by targeting SOX4.
In conclusion, our study suggested that miR-195 inhibited the migration, invasion and epithelial mesenchymal transition (EMT) of EC cells at least partly by targeting SOX4. Our study provided a novel underlying mechanism for EC metastasis and a promising therapeutic target for EC management. PMID: 31894127 [PubMed - in process] (Source: Journal of Biosciences)
Source: Journal of Biosciences - December 1, 2019 Category: Biomedical Science Authors: Zhao X, Dai L, Yue Q, Wang H, Wang XU, Li Y, Chen R Tags: J Biosci Source Type: research

Haploinsufficient tumor suppressor Tip60 negatively regulates oncogenic Aurora B kinase.
We report that AurkB undergoes acetylation in vitro by lysine acetyltransferases (KATs) belonging to different families, namely by p300 and Tip60. The haploinsufficient tumor suppressor Tip60 acetylates two highly conserved lysine residues within the kinase domain of AurkB which not only impinges the protein stability but also its kinase activity. These results signify a probable outcome on the increase in "overall activity" of AurkB upon Tip60 downregulation, as observed under cancerous conditions. The present work, therefore, uncovers an important functional interplay between AurkB and Tip60, frailty of which m...
Source: Journal of Biosciences - December 1, 2019 Category: Biomedical Science Authors: Bose A, Sudevan S, Rao VJ, Shima H, Trivedi AK, Igarashi K, Kundu TK Tags: J Biosci Source Type: research

A critical analysis of state-of-the-art metagenomics OTU clustering algorithms.
In this study five current state-of-the-art OTU clustering algorithms (CDHIT, Mothur's Average Neighbour, SUMACLUST, Swarm, and UCLUST) have been comprehensively evaluated on the metagenomics sequencing data. It was found that in all the datasets, Mothur's average neighbour and Swarm created more number of OTU clusters. Based on normalized mutual information (NMI) and normalized information difference (NID), Swarm and Mothur's average neighbour showed better clustering qualities than others. But in terms of time complexity the greedy algorithms (SUMACLUST, CDHIT, and UCLUST) performed well. So there is a trade-off between ...
Source: Journal of Biosciences - December 1, 2019 Category: Biomedical Science Authors: Bhat AH, Prabhu P, Balakrishnan K Tags: J Biosci Source Type: research

Effect of FIGF overexpression on liver cells transforming to insulin-producing cells.
Abstract Limitation in the number of insulin-producing pancreatic β-cells is a typical feature of diabetes. It has been indicated that activating pancreatic transcription factors can promote the transformation of hepatocytes into insulin-secreting β-like cells, indicating that direct hepatocyte differentiation seems promising as a treatment for diabetes. Nevertheless, the reprogramming efficiency still remains low. Our previous study found that the expression of c-fos-induced growth factor (FIGF) was increased in the pancreatic tissues in partial pancreatectomy mice compared to that in normal mice. Here,...
Source: Journal of Biosciences - December 1, 2019 Category: Biomedical Science Authors: He Y, Xie X, Li X, Rong S, Li Y, Lu Z Tags: J Biosci Source Type: research

Type II diabetes mellitus and obesity: Common links, existing therapeutics and future developments.
Abstract Type II diabetes mellitus (T2DM) and obesity are two common pathophysiological conditions of metabolic syndrome (MetS), a collection of similar metabolic dysfunctions due to sedentary lifestyle and overnutrition. Obesity arises from improper adipogenesis which otherwise has a crucial role in maintaining proper metabolic functions. Downstream events arising from obesity have been linked to T2DM. The nuclear receptor peroxisome proliferator activator gamma (PPAR-γ), responsible for maintaining lipid and glucose homeostasis, is down-regulated under obesity leading to a weakened insulin sensitivity of t...
Source: Journal of Biosciences - December 1, 2019 Category: Biomedical Science Authors: Banerjee S, Talukdar I, Banerjee A, Gupta A, Balaji A, Aduri R Tags: J Biosci Source Type: research

Microbiota of spent nuclear fuel pool water with emphasis on their biofilm forming ability on stainless steel (SS-304L).
This study explored the presence of bacteria in SNF pool water with emphasis on their capability to form biofilms on pool wall cladding material stainless steel (SS-304L). Bacteria were isolated from SNF pool water and were characterized using 16S rRNA gene sequencing. The six bacterial isolates (Bacillus subtilis, Staphylococcus sps., S. arlettae, S. epidermidis, S. auricularis and Chryseobacterium gleum) can grow and form biofilms at very low nutrient condition as well as in chronic radioactivity. The bacterial isolates formed biofilm on SS-304L and glass. However, the biofilm parameters assessed by CLSM microscopy showe...
Source: Journal of Biosciences - October 1, 2019 Category: Biomedical Science Authors: Karley D, Shukla SK, Rao TS Tags: J Biosci Source Type: research

Linking microbial diversity with ecosystem functioning through a trait framework.
Abstract Trait-based microbial biogeography provides a path for the mechanistic understanding of relationships between microbial diversity and ecosystem functioning. In this mini-review, we identify the scenarios in which to use traits to characterize the microbial community and propose a simple trait-based conceptual framework to link microbial communities with ecosystem functions. PMID: 31719218 [PubMed - in process] (Source: Journal of Biosciences)
Source: Journal of Biosciences - October 1, 2019 Category: Biomedical Science Authors: Wang JT, Egidi E, Li J, Singh BK Tags: J Biosci Source Type: research

Connect between gut microbiome and diseases of the human eye.
Abstract Implicating dysbiosis of gut microbiome in digestive tract diseases/diet-related diseases (obesity, inflammatory bowel disease, enterocolitis, diabetes, etc.) may be expected. However, when gut microbiome dysbiosis is implicated in extraintestinal diseases like cancers, muscular dystrophy, mental disorders, vaginosis, etc., it is all the more challenging. An additional challenge would be to ascertain the role of gut microbiome in ocular diseases, which are as remote as the brain. The present review highlights studies that establish the connect between gut microbiome dysbiosis and inflammatory ocular disea...
Source: Journal of Biosciences - October 1, 2019 Category: Biomedical Science Authors: Shivaji S Tags: J Biosci Source Type: research

Successful strategies for human microbiome data generation, storage and analyses.
Abstract Current interest in the potential for clinical use of new tools for improving human health are now focused on techniques for the study of the human microbiome and its interaction with environmental and clinical covariates. This review outlines the use of statistical strategies that have been developed in past studies and can inform successful design and analyses of controlled perturbation experiments performed in the human microbiome. We carefully outline what the data are, their imperfections and how we need to transform, decontaminate and denoise them. We show how to identify the important unknown param...
Source: Journal of Biosciences - October 1, 2019 Category: Biomedical Science Authors: Holmes S Tags: J Biosci Source Type: research