Characterization, validation and application of a DNA microarray for the detection of mandatory and other waterborne pathogens
Culture methods for the detection of indicator bacteria are currently used for detection of waterborne bacteria. The need for an increased range of analyzed bacteria coupled with the obtainment of rapid and early results justify the development of a DNA microarray for the identification of waterborne pathogens. This DNA microarray has 16 implanted probes with a median size of 147 bases, targeting 12 different parameters, including all mandatory indicator microorganisms, such as Escherichia coli, Clostridium perfringens, Pseudomonas aeruginosa, Staphylococcus aureus, total and fecal coliforms and enterococci. The validation...
Source: Journal of Biochemistry - October 30, 2015 Category: Biochemistry Authors: Gomes, M., Vieira, H., Vale, F. F. Tags: Regular Papers Source Type: research
Functional analysis of conserved motifs in a bacterial tyrosine kinase, BtkB, from Myxococcus xanthus
Myxococcus xanthus has two bacterial protein-tyrosine (BY) kinases, BtkA and BtkB. Autophosphorylation in C-terminal tyrosine-rich clusters and poly(Glu, Tyr) kinase activities of cytoplasmic catalytic domains of BtkA and BtkB were activated by the intracellular juxtamembrane regions of the second transmembrane helices. Protein kinase activity against poly(Glu, Tyr) of cytoplasmic fragment of BtkB (CF-BtkB) containing an activator region was not inhibited by serine/threonine protein kinase inhibitors. However, addition of tyrosine protein kinase inhibitors, genistein and 4-amino-5-(4-chlorophenyl)-7-(t-butyl)pyrazolo[3,4-d...
Source: Journal of Biochemistry - October 30, 2015 Category: Biochemistry Authors: Kato, T., Shirakawa, Y., Takegawa, K., Kimura, Y. Tags: Regular Papers Source Type: research
Mediator complex cooperatively regulates transcription of retinoic acid target genes with Polycomb Repressive Complex 2 during neuronal differentiation
The Mediator complex (Mediator) plays key roles in transcription and functions as the nexus for integration of various transcriptional signals. Previously, we screened for Mediator cyclin-dependent kinase (CDK)-interacting factors and identified three proteins related to chromatin regulation. One of them, SUZ12 is required for both stability and activity of Polycomb Repressive Complex 2 (PRC2). PRC2 primarily suppresses gene expression through histone H3 lysine 27 trimethylation, resulting in stem cell maintenance and differentiation; perturbation of this process leads to oncogenesis. Recent work showed that Mediator contr...
Source: Journal of Biochemistry - October 30, 2015 Category: Biochemistry Authors: Fukasawa, R., Iida, S., Tsutsui, T., Hirose, Y., Ohkuma, Y. Tags: Regular Papers Source Type: research
Cellular misfolded proteins rescued from degradation by MHC class II molecules are possible targets for autoimmune diseases
The major function of major histocompatibility complex (MHC) class II molecules is the presentation of peptide antigens to helper T cells. However, when misfolded proteins are associated with MHC class II molecules in the endoplasmic reticulum, they are transported to the cell surface by MHC class II molecules without processing to peptides. Of note, misfolded proteins complexed with MHC class II molecules are specifically recognized by autoantibodies produced in patients with autoimmune diseases such as rheumatoid arthritis and antiphospholipid syndrome. Furthermore, autoantibody binding to misfolded proteins complexed wi...
Source: Journal of Biochemistry - October 30, 2015 Category: Biochemistry Authors: Arase, N., Arase, H. Tags: JB Reviews Source Type: research
Non-canonical WNT signalling in the lung
The role of WNT signalling in metazoan organogenesis has been a topic of widespread interest. In the lung, while the role of canonical WNT signalling has been examined in some detail by multiple studies, the non-canonical WNT signalling has received limited attention. Reliable evidence shows that this important signalling mechanism constitutes a major regulatory pathway in lung development. In addition, accumulating evidence has also shown that the non-canonical WNT pathway is critical for maintaining lung homeostasis and that aberrant activation of this pathway may underlie several debilitating lung diseases. Functional a...
Source: Journal of Biochemistry - October 30, 2015 Category: Biochemistry Authors: Li, C., Bellusci, S., Borok, Z., Minoo, P. Tags: JB Reviews Source Type: research
Desmocollin-2 alone forms functional desmosomal plaques, with the plaque formation requiring the juxtamembrane region and plakophilins
The role of the juxtamembrane region of the desmocollin-2 cytoplasmic domain in desmosome formation was investigated by using gene knockout and reconstitution experiments. When a deletion construct of the desmocollin-2 juxtamembrane region was expressed in HaCaT cells, the mutant protein became localized linearly at the cell–cell boundary, suggesting the involvement of this region in desmosomal plaque formation. Then, desmocollin-2 and desmoglein-2 genes of epithelial DLD-1 cells were ablated by using the CRISPR/Cas9 system. The resultant knockout cells did not form desmosomes, but re-expression of desmocollin-2 in t...
Source: Journal of Biochemistry - September 29, 2015 Category: Biochemistry Authors: Fujiwara, M., Nagatomo, A., Tsuda, M., Obata, S., Sakuma, T., Yamamoto, T., Suzuki, S. T. Tags: Regular Papers Source Type: research
Lysophosphatidylcholine promotes SREBP-2 activation via rapid cholesterol efflux and SREBP-2-independent cytokine release in human endothelial cells
In conclusion, LPC activated SREBP-2 via enhancement of cholesterol efflux, which was suppressed by 25-HC. The release of inflammatory cytokines such as IL-6 and IL-8 in endothelial cells was SREBP-2-independent. LPC and 25-HC may act competitively in cholesterol homeostasis but additively in inflammatory cytokine release. (Source: Journal of Biochemistry)
Source: Journal of Biochemistry - September 29, 2015 Category: Biochemistry Authors: Morita, M., Sekine, A., Urano, Y., Nishimura, T., Takabe, W., Arai, H., Hamakubo, T., Kodama, T., Noguchi, N. Tags: Regular Papers Source Type: research
Cholesterol mobilization from hepatic lipid droplets during endotoxemia is altered in obese ob/ob mice
The innate immune response to pathogens during the acute phase response includes lipid metabolism adaptations. Hepatic triacylglycerol (TG) and cholesteryl ester (CE) storage in and mobilization from lipid droplets (LDs) respond to metabolic changes under the control of liver X receptor (LXR) transactivation and cytokine transduction. To evaluate whether alterations of these mechanisms have an impact in the adaptive response to endotoxemia, we analysed liver metabolism changes in lipopolysaccharide (LPS)-treated ob/ob mice, which show altered metabolic and innate responses and a higher sensitivity to sepsis. Lipid composit...
Source: Journal of Biochemistry - September 29, 2015 Category: Biochemistry Authors: Arisqueta, L., Navarro-Imaz, H., Rueda, Y., Fresnedo, O. Tags: Regular Papers Source Type: research
Increased acid ceramidase expression depends on upregulation of androgen-dependent deubiquitinases, USP2, in a human prostate cancer cell line, LNCaP
Acid ceramidase (ACDase) metabolizes ceramide to sphingosine, leading to sphingosine 1-phosphate production. Reportedly, ACDase has been upregulated in prostate cancer. However, its regulatory mechanism remains unclear. LNCaP (androgen-sensitive prostate cancer cell line) but not PC3 and DU-145, (androgen-unresponsive cell lines) exhibited the highest ACDase protein. Among three cell lines, ASAH1 mRNA level was not correlated with ACDase protein expression, and the 5'-promoter activity did not show androgen dependency, suggesting the post-transcriptional regulation of ACDase in LNCaP cells. Based on these results, LNCaP wa...
Source: Journal of Biochemistry - September 29, 2015 Category: Biochemistry Authors: Mizutani, N., Inoue, M., Omori, Y., Ito, H., Tamiya-Koizumi, K., Takagi, A., Kojima, T., Nakamura, M., Iwaki, S., Nakatochi, M., Suzuki, M., Nozawa, Y., Murate, T. Tags: Regular Papers Source Type: research
SIRT1-related inhibition of pro-inflammatory responses and oxidative stress are involved in the mechanism of nonspecific low back pain relief after exercise through modulation of Toll-like receptor 4
This study demonstrates that exercise intervention improves low back pain symptoms through regulation of the SIRT1 axis with repression of oxidative stress and TLR-4 inhibition. (Source: Journal of Biochemistry)
Source: Journal of Biochemistry - September 29, 2015 Category: Biochemistry Authors: Cheng, Y.-Y., Kao, C.-L., Ma, H.-I., Hung, C.-H., Wang, C.-T., Liu, D.-H., Chen, P.-Y., Tsai, K.-L. Tags: Regular Papers Source Type: research
Structural insights into the O2 reduction mechanism of multicopper oxidase
Multicopper oxidases are ubiquitous enzymes that catalyse the oxidation of various substrates via the reduction of O2 to H2O. The enzymes contain a common active centre consisting of four copper ions. The key component for O2 reduction is the trinuclear copper centre comprising one type II and a pair of type III copper ions. Although the crystal structures of many multicopper oxidases have been determined by X-ray crystallography, the geometric parameters in the trinuclear copper centre are different for each study. Recent studies have revealed that the redox state of copper ions is altered by X-ray irradiation. The report...
Source: Journal of Biochemistry - September 29, 2015 Category: Biochemistry Authors: Komori, H., Higuchi, Y. Tags: JB Reviews Source Type: research
Molecular architectures and functions of radical enzymes and their (re)activating proteins
Certain proteins utilize the high reactivity of radicals for catalysing chemically challenging reactions. These proteins contain or form a radical and therefore named ‘radical enzymes’. Radicals are introduced by enzymes themselves or by (re)activating proteins called (re)activases. The X-ray structures of radical enzymes and their (re)activases revealed some structural features of these molecular apparatuses which solved common enigmas of radical enzymes—i.e. how the enzymes form or introduce radicals at the active sites, how they use the high reactivity of radicals for catalysis, how they suppress undes...
Source: Journal of Biochemistry - September 29, 2015 Category: Biochemistry Authors: Shibata, N., Toraya, T. Tags: JB Reviews Source Type: research
Human FAN1 promotes strand incision in 5'-flapped DNA complexed with RPA
In this study, we purified human FAN1, as a bacterially expressed recombinant protein. FAN1 exhibited robust endonuclease activity with 5'-flapped DNA, which is formed at the stalled replication fork. We found that FAN1 efficiently promoted DNA incision at the proper site of RPA-coated 5'-flapped DNA. Therefore, FAN1 possesses the ability to promote the ICL repair of 5'-flapped DNA covered by RPA. (Source: Journal of Biochemistry)
Source: Journal of Biochemistry - August 29, 2015 Category: Biochemistry Authors: Takahashi, D., Sato, K., Hirayama, E., Takata, M., Kurumizaka, H. Tags: Regular Papers Source Type: research
Involvement of thioredoxin on the scaffold activity of NifU in heterocyst cells of the diazotrophic cyanobacterium Anabaena sp. strain PCC 7120
In this study, we investigated thioredoxin (Trx) networks in Anabaena using TrxM, and identified 16 and 38 candidate target proteins in heterocysts and vegetative cells, respectively, by Trx affinity chromatography (Motohashi et al. (Comprehensive survey of proteins targeted by chloroplast thioredoxin. Proc Natl Acad Sci USA, 2001;98, 11224–11229)). Among these, the Fe–S cluster scaffold protein NifU that facilitates functional expression of nitrogenase in heterocysts was found to be a potential TrxM target. Subsequently, we observed that the scaffold activity of N-terminal catalytic domain of NifU is enhanced ...
Source: Journal of Biochemistry - August 29, 2015 Category: Biochemistry Authors: Nomata, J., Maeda, M., Isu, A., Inoue, K., Hisabori, T. Tags: Regular Papers Source Type: research
Eph/ephrin reverse signalling induces axonal retraction through RhoA/ROCK pathway
In this study, we revealed that stimulation with the extracellular domain of EphB2 to activate Eph/ephrin reverse signalling induced axonal retraction in hippocampal neurons. The reduction of axonal length and branching by Eph/ephrin reverse signalling was blocked by inhibition of RhoA or Rho-associated coiled-coil-containing protein kinase (ROCK). These results suggest that Eph/ephrin reverse signalling negatively regulates axonal outgrowth and branching through RhoA/ROCK pathway in hippocampal neurons. (Source: Journal of Biochemistry)
Source: Journal of Biochemistry - August 29, 2015 Category: Biochemistry Authors: Takeuchi, S., Katoh, H., Negishi, M. Tags: Regular Papers Source Type: research
