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PubMed Journal Database | Journal of biochemistry RSS

07:52 EDT 24th May 2019 | BioPortfolio

The US National Library of Medicine and National Institutes of Health manage PubMed.gov which comprises of more than 29 million records, papers, reports for biomedical literature, including MEDLINE, life science and medical journals, articles, reviews, reports and  books.

BioPortfolio aims to cross reference relevant information on published papers, clinical trials and news associated with selected topics - speciality.

For example view all recent relevant publications on Epigenetics and associated publications and clincial trials.

Showing PubMed Articles 1–25 of 170 from Journal of biochemistry

Glycoengineering of HEK293 cells to produce high-mannose-type N-glycan structures.

Therapeutic proteins are a developing part of the modern biopharmaceutical industry, providing novel therapies to intractable diseases including cancers and autoimmune diseases. The human embryonic kidney 293 (HEK293) cell line has been widely used to produce recombinant proteins in both basic science and industry. The heterogeneity of glycan structures is one of the most challenging issues in the production of therapeutic proteins. Previously, we knocked out genes encoding α1,2-mannosidase-Is, MAN1A1, MAN...

Characterization of monoclonal antibodies recognizing each extracellular loop domain of occludin.

The tight junction protein occludin (OCLN) is a four-pass transmembrane protein with two extracellular loops (ELs), and also functions as a co-receptor for hepatitis C virus (HCV). Recently, we reported the establishment of monoclonal antibodies (mAbs) recognizing each intact EL domain of OCLN that can strongly prevent HCV infection in vitro and in vivo and these mAbs were applicable for flow cytometric analysis, immunocytochemistry, and cell-based enzyme-linked immunosorbent assay. In the present study, we...

A novel angiotensin-I converting enzyme inhibitory peptide derived from the glutelin of vinegar soaked black soybean and its antihypertensive effect in spontaneously hypertensive rats.

Vinegar soaked black soybean is a traditional Chinese food widely used for the treatment of hypertension. While its pharmacodynamic substance wasn't fully unveiled. It contained abundant glutelin, thus the purpose of this study was to obtain potent antihypertensive peptides from vinegar soaked black soybean. Black soybean was soaked with vinegar and then glutelin was first catalyzed by alcalase. Ultrafitration, ion exchange chromatography and reversed-phase high performance liquid chromatography were sequen...

Stable mutants of restriction-deficient/modification-proficient Bacillus subtilis 168: Hub strains for giant DNA engineering.

Bacillus subtilis 168 has been explored as a platform for the synthesis and transmission of large DNA. Two inherent DNA incorporation systems, natural transformation and pLS20-based conjugation transfer, enable rapid handling of target DNA. Both systems are affected by the Bsu restriction-modification system that recognizes and cleaves unmethylated XhoI sites, limiting the choice of target DNA. We constructed B. subtilis 168 with stable mutation for restriction-deficient and modification-proficient (r-m+). ...

Age- and gender-dependent D-amino acid oxidase activity in mouse brain and peripheral tissues: implication for aging and neurodegeneration.

D-amino acid oxidase (DAO) is a flavoenzyme, catalyzing oxidative deamination of D-amino acids to produce corresponding α-keto acids, ammonia and hydrogen peroxide. In our search for DAO activity among various tissues, we developed a sensitive assay based on hydrogen peroxide production involving enzyme-coupled colorimetric assay with peroxidase. We first optimized buffer components to extract DAO protein from mouse tissues. Here we show that DAO activity was detected in kidney, cerebellum, medulla oblonga...

Metal binding to cutinase-like enzyme from Saccharomonospora viridis AHK190 and its effects on enzyme activity and stability.

A cutinase from Saccharomonospora viridis AHK190, Cut190, can hydrolyze polyethylene terephthalate and has a unique feature that the activity and stability are regulated by Ca2+ binding. Our recent structural and functional analyses showed three Ca2+ binding sites and their respective roles. Here, we analyzed the binding thermodynamics of Mn2+, Zn2+, and Mg2+ to Cut190 and their effects on the catalytic activity and thermal stability. The binding affinities of Mn2+ and Zn2+ were higher than that of Mg2+ and...

Cellular and molecular mechanisms of sterile inflammation in ischemic stroke.

Cerebral inflammation is a promising therapeutic target for ischemic stroke. After ischemic stroke, inflammatogenic self molecules, which originate from damaged brain tissue due to ischemia, activate infiltrating immune cells (neutrophils, macrophages, and lymphocytes) and thereby trigger sterile inflammation. Innate immunity plays the central role in sterile inflammation at the acute phase of brain ischemia, although immune response by T lymphocytes (innate or acquired immunity) is also implicated in infla...

Distinct molecular assembly of homologous peroxiredoxins from Pyrococcus horikoshii and Thermococcus kodakaraensis.

Peroxiredoxins from Pyrococcus horikoshii (PhPrx) and Thermococcus kodakaraensis (TkPrx) are highly homologous proteins sharing 196 of the 216 residues. We previously reported a pentagonal ring-type decameric structure of PhPrx. Here, we present the crystal structure of TkPrx. Despite their homology, unlike PhPrx, the quaternary structure of TkPrx was found to be a dodecamer comprised of six homodimers arranged in a hexagonal ring-type assembly. The possibility of the redox-dependent conversion of the molec...

Identification and characterization of cytochrome P450 1232A24 and 1232F1 from Arthrobacter sp. and their role in the metabolic pathway of papaverine.

Cytochrome P450 monooxygenases (P450s) play crucial roles in the cell metabolism and provide an unsurpassed diversity of catalyzed reactions. Here, we report the identification and biochemical characterization of two P450s from Arthrobacter sp., a gram-positive organism known to degrade the opium alkaloid papaverine. Combining phylogenetic and genomic analysis suggested physiological roles for P450s in metabolism, and revealed potential gene clusters with redox partners facilitating the reconstitution of th...

Calcium signaling: a key regulator of neuronal migration.

Neuronal migration is a crucial event in neuronal development for the construction of brain architecture and neuronal networks. Newborn neurons proliferate in the germinal zone and start migration toward their final destination. Migrating neurons adopt different routes, cell shapes, and migratory modes depending on extracellular factors and outer physical substrates. Intracellular Ca2+ is an essential second messenger that regulates diverse cellular functions by activating Ca2+-dependent signaling molecules...

Multiple functions of the ER-resident VAP and its extracellular role in neural development and disease.

VAP (VAMP-associated protein) is a type Ⅱ integral membrane protein of the endoplasmic reticulum (ER), and its N-terminal MSP domain faces the cytoplasmic side. VAP functions as a tethering molecule at the membrane contact sites between the ER and intracellular organelles and regulates a wide variety of cellular functions, including lipid transport, membrane trafficking, microtubule reorganization, and unfolded protein response. VAP-point mutations in human vapb are strongly associated with amyotrophic la...

Identification of a Chemical Modulator of EZH2-mediated Silencing by Cell-based High-throughput Screening Assay.

Dysregulation of enhancer of zeste homolog 2 (EZH2), a methyltransferase component of polycomb repressive complex 2 (PRC2), is found in many types of cancers especially those that are highly progressive and aggressive. Specific catalytic inhibitors of EZH2 have high anti-tumor activity, particularly in lymphomas with EZH2 activating mutations. However, the clinical benefits of EZH2 catalytic inhibitors in tumors overexpressing EZH2 are still limited. Here, we identified NPD13668, a novel modulator of EZH2-m...

Roles of angiopoietin-like proteins in regulation of stem cell activity.

Various types of stem cells reside in the body and self-renew thoughout an organism's lifetime. Such self-renewal is essential for maintenance of tissue homeostasis and is coordinately regulated by stem cell-intrinsic signals and signals from stem cell niche. Angiopoietin is a niche-derived signaling molecule well known to contribute to maintenance of hematopoietic stem cells. Angiopoietin-like proteins (ANGPTLs) are structurally similar to angiopoietin, and recent studies reveal that they function in angio...

Hepatitis B virus x protein accelerated the proliferation of hepatocellular carcinoma cell through lncRNA SNHG20/PTEN pathway.

This study investigated the underlying mechanism of long noncoding RNA (lncRNA) small nucleolar RNA host gene 20 (SNHG20) in hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC).

Domains two and three of Escherichia coli ribosomal S1 protein confers 30S subunits a high affinity for downstream A/U-rich mRNAs.

S1, a multi-domain ribosomal protein associated with the 30S subunit, is essential for translation initiation. S1 binds with high affinity to single-stranded mRNA containing AU-rich patches upstream of the start codon. It was previously reported that domains 1-3 of S1 protein play a role in the docking and unfolding of structured mRNAs to the ribosome. Moreover, S1-deficient 30S subunits are still able to bind to low structured mRNAs. However, mRNAs containing AU-rich patches in the early base positions aft...

A DNA-binding domain in the C-terminal region of Cdt2 enhances the DNA synthesis-coupled CRL4Cdt2 ubiquitin ligase activity for Cdt1.

The Cullin-RING ubiquitin ligase CRL4Cdt2 maintains genome integrity by mediating the cell cycle- and DNA damage-dependent degradation of proteins such as Cdt1, p21, and Set8. Human Cdt2 has two regions, a conserved N-terminal seven WD40 repeat region and a less conserved C-terminal region. Here, we showed that the N-terminal region is sufficient for complex formation with CRL4, but the C-terminal region is required for the full ubiquitin ligase activity. UV irradiation-induced polyubiquitination and degrad...

Identification and biochemical characterization of a second zebrafish autotaxin gene.

Autotaxin (ATX) is a secreted enzyme that produces a bioactive lysophospholipid, lysophosphatidic acid (LPA). ATX plays a role in vascular and neural development in embryos but its mechanisms remain unclear. At the beginning of this study, only one zebrafish atx gene (atxa) was known and had been investigated. In this study, we generated ATX knockout (KO) fish by TALEN targeting atxa. Unexpectedly, atxa KO fish showed neither vascular defects nor reduction of ATX activity, implying the existence of one or m...

Epigenetic interplays between DNA demethylation and histone methylation for protecting oncogenesis.

Epigenetic systems are organized by different types of modifications on histones and DNA. To determine how epigenetic systems can produce variable, yet stable cellular outcomes, understanding the collaboration between these modifications is the key. A recent study by Yamagata and Kobayashi revealed the direct interplay between the regulation of two epigenetic modifications: DNA de-methylation by TET2 and histone H3-K36 methylation. Mechanistically, this finding could explain how cells are protected from onc...

A novel splicing variant of small nucleolar RNA host gene 4 is a podocyte-selective non-coding RNA upregulated in response to puromycin aminonucleoside-induced podocyte injury.

Podocytes are terminally differentiated cells that function as the glomerular filtration barrier in the kidney, and podocyte injury leads to serious proteinuria and podocyte leakage into urine. Recent studies have demonstrated that the number of urinary podocytes is correlated with the progression of glomerular diseases. Therefore, urinary podocytes may serve as an indicator of podocyte injury. In this study, to explore podocyte injury-related genes, we performed comprehensive transcriptome analysis of prim...

A novel method for chemo-enzymatic synthesis of chitin oligosaccharide catalyzed by the mutant of inverting family GH19 chitinase using 4,6-dimethoxy-1,3,5-triazin-2-yl α-chitobioside as a glycosyl donor.

A novel method for the chemo-enzymatic synthesis of chitin oligosaccharide catalyzed by mutants of BcChi-A, an inverting family GH19 chitinase from Bryum coronatum, has been developed using 4,6-dimethoxy-1,3,5-triazin-2-yl α-chitobioside [DMT-α-(GlcNAc)2)] as a donor substrate. Based on the glycosynthase derived from BcChi-A, Glu70, which acts as a catalytic base, and Ser102, which fixes a nucleophilic water molecule, were changed to generate several single and double mutants of BcChi-A, which were employ...

Fine epitope mapping of a human disulfide-stabilized diabody against fibroblast growth factor-2.

The human fibroblast growth factor-2 (FGF-2) highly expressed in tumors is an important factor to promote tumor angiogenesis and lymphangiogensis. A disulfide-stabilized diabody (ds-Diabody) could specifically target FGF-2 and show its advantages in inhibition of tumor angiogenesis and growth. It is very important for antibody drugs to confirm the fine epitope. Here, theoretical structure models of FGF-2 and antibody were built by homology modeling. The amino acid residues in the interaction interface of an...

Mitotic phosphorylation of HP1α regulates its cell cycle-dependent chromatin binding.

Heterochromatin protein 1 (HP1) is an evolutionarily conserved chromosomal protein that plays a crucial role in heterochromatin-mediated gene silencing. We previously showed that mammalian HP1α is constitutively phosphorylated at its N-terminal serine residues by casein kinase II (CK2), and that this phosphorylation enhances HP1α's binding specificity for nucleosomes containing lysine 9-methylated histone H3 (H3K9me). Although the presence of additional HP1α phosphorylation during mitosis was reported mo...

Comprehensive analysis of kinase-oriented phospho-signaling pathways.

Accumulating information on eukaryotic protein phosphorylation implies a large and complicated phospho-signaling network in various cellular processes. Although a large number of protein phosphorylation sites have been detected, their physiological consequences and the linkage between each phosphorylation site and the responsible protein kinase remain largely unexplored. To understand kinase-oriented phospho-signaling pathways, we have developed novel substrate screening technologies. In this review, we des...

Lactate Dehydrogenase C Is Required for the Protein Expression of a Sperm-specific Isoform of Lactate Dehydrogenase A.

Metabolites are sensitive indicators of moment-to-moment cellular status and activity. Expecting that tissue-specific metabolic signatures unveil a unique function of the tissue, we examined metabolomes of mouse liver and testis and found that an unusual metabolite, 2-hydroxyglutarate (2-HG), was abundantly accumulated in the testis. 2-HG can exist as D- or L-enantiomer, and both enantiomers interfere with the activities of 2-oxoglutarate (2-OG)-dependent dioxygenases, such as the Jumonji family of histone ...

KDM5D-mediated H3K4 demethylation is required for sexually dimorphic gene expression in mouse embryonic fibroblasts.

Males and females share the same genetic code, but gene expression profile often displays differences between two sexes. Mouse embryonic fibroblasts (MEFs) have been used to experiment as a useful tool to test gene function. They have also been characterized by gender-based differences in expressed genes such as Y-linked Sry or X-linked Hprt. However, there is no report on sex differences in global gene expression. Here, using the next-generation RNA sequencing, we compared the comprehensive transcriptome o...


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