Relevant bibliographies by topics / Ph-Coding

Academic literature on the topic 'Ph-Coding'

Author: Grafiati
Published: 10 December 2022
Last updated: 28 January 2023

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Journal articles on the topic "Ph-Coding"

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Tessema, Girum Tadesse, Trond Møretrø, Lars Snipen, Even Heir, Askild Holck, Kristine Naterstad, and Lars Axelsson. "Microarray-based transcriptome ofListeria monocytogenesadapted to sublethal concentrations of acetic acid, lactic acid, and hydrochloric acid." Canadian Journal of Microbiology 58, no. 9 (September 2012): 1112–23. http://dx.doi.org/10.1139/w2012-091.

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Listeria monocytogenes , an important foodborne pathogen, commonly encounters organic acids in food-related environments. The transcriptome of L. monocytogenes L502 was analyzed after adaptation to pH 5 in the presence of acetic acid, lactic acid, or hydrochloric acid (HCl) at 25 °C, representing a condition encountered in mildly acidic ready-to-eat food kept at room temperature. The acid-treated cells were compared with a reference culture with a pH of 6.7 at the time of RNA harvesting. The number of genes and magnitude of transcriptional responses were higher for the organic acids than for HCl. Protein coding genes described for low pH stress, energy transport and metabolism, virulence determinates, and acid tolerance response were commonly regulated in the 3 acid-stressed cultures. Interestingly, the transcriptional levels of histidine and cell wall biosynthetic operons were upregulated, indicating possible universal response against low pH stress in L. monocytogenes. The opuCABCD operon, coding proteins for compatible solutes transport, and the transcriptional regulator sigL were significantly induced in the organic acids, strongly suggesting key roles during organic acid stress. The present study revealed the complex transcriptional responses of L. monocytogenes towards food-related acidulants and opens the roadmap for more specific and in-depth future studies.
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Zhang, Hui, R. Dale Brown, Kurt R. Stenmark, and Cheng-Jun Hu. "RNA-Binding Proteins in Pulmonary Hypertension." International Journal of Molecular Sciences 21, no. 11 (May 26, 2020): 3757. http://dx.doi.org/10.3390/ijms21113757.

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Pulmonary hypertension (PH) is a life-threatening disease characterized by significant vascular remodeling and aberrant expression of genes involved in inflammation, apoptosis resistance, proliferation, and metabolism. Effective therapeutic strategies are limited, as mechanisms underlying PH pathophysiology, especially abnormal expression of genes, remain unclear. Most PH studies on gene expression have focused on gene transcription. However, post-transcriptional alterations have been shown to play a critical role in inflammation and metabolic changes in diseases such as cancer and systemic cardiovascular diseases. In these diseases, RNA-binding proteins (RBPs) have been recognized as important regulators of aberrant gene expression via post-transcriptional regulation; however, their role in PH is less clear. Identifying RBPs in PH is of great importance to better understand PH pathophysiology and to identify new targets for PH treatment. In this manuscript, we review the current knowledge on the role of dysregulated RBPs in abnormal mRNA gene expression as well as aberrant non-coding RNA processing and expression (e.g., miRNAs) in PH.
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PAŘENICOVÁ, Lucie, Jacques A. E. BENEN, Harry C. M. KESTER, and Jaap VISSER. "pgaA and pgaB encode two constitutively expressed endopolygalacturonases of Aspergillus niger." Biochemical Journal 345, no. 3 (January 25, 2000): 637–44. http://dx.doi.org/10.1042/bj3450637.

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pgaA and pgaB, two genes encoding endopolygalacturonases (PGs, EC 3.2.1.15) A and B, were isolated from a phage genomic library of Aspergillusniger N400. The 1167 bp protein coding region of the pgaA gene is interrupted by one intron, whereas the 1234 bp coding region of the pgaB gene contains two introns. The corresponding proteins, PGA and PGB, consist of 370 and 362 amino acid residues respectively. Northern-blot analysis revealed that pgaA- and pgaB-specific mRNA accumulate in mycelia grown on sucrose. mRNAs are also present upon transfer to media containing D-galacturonic acid and pectin. Recombinant PGA and PGB were characterized with respect to pH optimum, activity on polygalacturonic acid, and mode of action and kinetics on oligogalacturonates of different chain length (n = 3-7). At their pH optimum the specific activities in a standard assay for PGA (pH 4.2) and PGB (pH 5.0) were 16.5 μkat·mg-1 and 8.3 μkat·mg-1 respectively. Product progression analysis, using polygalacturonate as a substrate, revealed a random cleavage pattern for both enzymes and indicated processive behaviour for PGA. This result was confirmed by analysis of the mode of action using oligogalacturonates. Processivity was observed when the degree of polymerization of the substrate exceeded 6. Using pectins of various degrees of methyl esterification, it was shown that PGA and PGB both preferred partially methylated substrates.
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Lai, Vicky C. H., Weidong Zhong, Angela Skelton, Paul Ingravallo, Venteislav Vassilev, Ruben O. Donis, Zhi Hong, and Johnson Y. N. Lau. "Generation and Characterization of a Hepatitis C Virus NS3 Protease-Dependent Bovine Viral Diarrhea Virus." Journal of Virology 74, no. 14 (July 15, 2000): 6339–47. http://dx.doi.org/10.1128/jvi.74.14.6339-6347.2000.

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ABSTRACT Unique to pestiviruses, the N-terminal protein encoded by the bovine viral diarrhea virus (BVDV) genome is a cysteine protease (Npro) responsible for a self-cleavage that releases the N terminus of the core protein (C). This unique protease is dispensable for viral replication, and its coding region can be replaced by a ubiquitin gene directly fused in frame to the core. To develop an antiviral assay that allows the assessment of anti-hepatitis C virus (HCV) NS3 protease inhibitors, a chimeric BVDV in which the coding region of Npro was replaced by that of an NS4A cofactor-tethered HCV NS3 protease domain was generated. This cofactor-tethered HCV protease domain was linked in frame to the core protein of BVDV through an HCV NS5A-NS5B junction site and mimicked the proteolytic function of Npro in the release of BVDV core for capsid assembly. A similar chimeric construct was built with an inactive HCV NS3 protease to serve as a control. Genomic RNA transcripts derived from both chimeric clones, PH/B(wild-type HCV NS3 protease) and PH/B(S139A) (mutant HCV NS3 protease) were then transfected into bovine cells (MDBK). Only the RNA transcripts from the PH/B clone yielded viable viruses, whereas the mutant clone, PH/B(S139A), failed to produce any signs of infection, suggesting that the unprocessed fusion protein rendered the BVDV core protein defective in capsid assembly. Like the wild-type BVDV (NADL), the chimeric virus was cytopathic and formed plaques on the cell monolayer. Sequence and biochemical analyses confirmed the identity of the chimeric virus and further revealed variant viruses due to growth adaptation. Growth analysis revealed comparable replication kinetics between the wild-type and the chimeric BVDVs. Finally, to assess the genetic stability of the chimeric virus, an Npro-null BVDV (BVDV−Npro in which the entire Npro coding region was deleted) was produced. Although cytopathic, BVDV−Npro was highly defective in viral replication and growth, a finding consistent with the observed stability of the chimeric virus after serial passages.
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Zhang, Xiaodong, Caixia Li, Xuantong Chen, Chonlong Chio, Sarita Shrestha, and Wensheng Qin. "Bacillus velezensis Identification and Recombinant Expression, Purification, and Characterization of Its Alpha-Amylase." Fermentation 7, no. 4 (October 11, 2021): 227. http://dx.doi.org/10.3390/fermentation7040227.

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Amylases account for about 30% of the global market of industrial enzymes, and the current amylases cannot fully meet industrial needs. This study aimed to identify a high α-amylase producing bacterium WangLB, to clone its α-amylase coding gene, and to characterize the α-amylase. Results showed that WangLB belonged to Bacillus velezensis whose α-amylase gene was 1980 bp coding 659 amino acids designated as BvAmylase. BvAmylase was a hydrophilic stable protein with a signal peptide and a theoretical pI of 5.49. The relative molecular weight of BvAmylase was 72.35 kDa, and was verified by SDS-PAGE. Its modeled structure displayed that it was a monomer composed of three domains. Its optimum temperature and pH were 70 °C and pH 6.0, respectively. It also showed high activity in a wide range of temperatures (40–75 °C) and a relatively narrow pH (5.0–7.0). It was a Ca2+-independent enzyme, whose α-amylase activity was increased by Co2+, Tween 20, and Triton X-100, and severely decreased by SDS. The Km and the Vmax of BvAmylase were 3.43 ± 0.53 and 434.19 ± 28.57 U/mg. In conclusion, the α-amylase producing bacterium WangLB was identified, and one of its α-amylases was characterized, which will be a candidate enzyme for industrial applications.
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Reeves, Rosalind A., Moreland D. Gibbs, Daniel D. Morris, Katherine R. Griffiths, David J. Saul, and Peter L. Bergquist. "Sequencing and Expression of Additional Xylanase Genes from the Hyperthermophile Thermotoga maritimaFjSS3B.1." Applied and Environmental Microbiology 66, no. 4 (April 1, 2000): 1532–37. http://dx.doi.org/10.1128/aem.66.4.1532-1537.2000.

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ABSTRACT Two genes, xynB and xynC, coding for xylanases were isolated from Thermotoga maritima FjSS3B.1 by a genomic-walking–PCR technique. Sequencing of the genes showed that they encode multidomain family 10 xylanases. Only XynB exhibited activity against xylan substrates. The temperature optimum (87°C) and pH optimum (pH 6.5) of XynB are different from the previously reported xylanase, XynA (also a family 10 enzyme), from this organism. The catalytic domain expressed without other domains has a lower temperature optimum, is less thermostable, and has optimal activity at pH 6.5. Despite having a high level of sequence similarity toxynB, xynC appears to be nonfunctional since its encoded protein did not show significant activity on xylan substrates.
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Lassen, Kara G., Craig I. McKenzie, Muriel Mari, Tatsuro Murano, Jakob Begun, Leigh A. Baxt, Gautam Goel, et al. "Genetic Coding Variant in GPR65 Alters Lysosomal pH and Links Lysosomal Dysfunction with Colitis Risk." Immunity 44, no. 6 (June 2016): 1392–405. http://dx.doi.org/10.1016/j.immuni.2016.05.007.

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Pajor, Ana M., Rama Gangula, and Xiaozhou Yao. "Cloning and functional characterization of a high-affinity Na+/dicarboxylate cotransporter from mouse brain." American Journal of Physiology-Cell Physiology 280, no. 5 (May 1, 2001): C1215—C1223. http://dx.doi.org/10.1152/ajpcell.2001.280.5.c1215.

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Neurons contain a high-affinity Na+/dicarboxylate cotransporter for absorption of neurotransmitter precursor substrates, such as α-ketoglutarate and malate, which are subsequently metabolized to replenish pools of neurotransmitters, including glutamate. We have isolated the cDNA coding for a high-affinity Na+/dicarboxylate cotransporter from mouse brain, called mNaDC-3. The mRNA coding for mNaDC-3 is found in brain and choroid plexus as well as in kidney and liver. The mNaDC-3 transporter has a broad substrate specificity for dicarboxylates, including succinate, α-ketoglutarate, fumarate, malate, and dimethylsuccinate. The transport of citrate is relatively insensitive to pH, but the transport of succinate is inhibited by acidic pH. The Michaelis-Menten constant for succinate in mNaDC-3 is 140 μM in transport assays and 16 μM at −50 mV in two-electrode voltage clamp assays. Transport is dependent on sodium, although lithium can partially substitute for sodium. In conclusion, mNaDC-3 likely codes for the high-affinity Na+/dicarboxylate cotransporter in brain, and it has some unusual electrical properties compared with the other members of the family.
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Cafaro, Valeria, Eugenio Notomista, Paola Capasso, and Alberto Di Donato. "Regiospecificity of Two Multicomponent Monooxygenases from Pseudomonas stutzeri OX1: Molecular Basis for Catabolic Adaptation of This Microorganism to Methylated Aromatic Compounds." Applied and Environmental Microbiology 71, no. 8 (August 2005): 4736–43. http://dx.doi.org/10.1128/aem.71.8.4736-4743.2005.

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ABSTRACT The pathways for degradation of aromatic hydrocarbons are constantly modified by a variety of genetic mechanisms. Genetic studies carried out with Pseudomonas stutzeri OX1 suggested that the tou operon coding for toluene o-xylene monooxygenase (ToMO) was recently recruited into a preexisting pathway that already possessed the ph operon coding for phenol hydroxylase (PH). This apparently resulted in a redundancy of enzymatic activities, because both enzymes are able to hydroxylate (methyl)benzenes to (methyl)catechols via the intermediate production of (methyl)phenols. We investigated the kinetics and regioselectivity of toluene and o-xylene oxidation using Escherichia coli cells expressing ToMO and PH complexes. Our data indicate that in the recombinant system the enzymes act sequentially and that their catalytic efficiency and regioselectivity optimize the degradation of toluene and o-xylene, both of which are growth substrates. The main product of toluene oxidation by ToMO is p-cresol, the best substrate for PH, which catalyzes its transformation to 4-methylcatechol. The sequential action of the two enzymes on o-xylene leads, via the intermediate 3,4-dimethylphenol, to the exclusive production of 3,4-dimethylcatechol, the only dimethylcatechol isomer that can serve as a carbon and energy source after further metabolic processing. Moreover, our data strongly support a metabolic explanation for the acquisition of the ToMO operon by P. stutzeri OX1. It is possible that using the two enzymes in a concerted fashion confers on the strain a selective advantage based on the ability of the microorganism to optimize the efficiency of the use of nonhydroxylated aromatic hydrocarbons, such as benzene, toluene, and o-xylene.
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Maccheroni Jr., Walter, Welington Luiz Araújo, and João Lúcio Azevedo. "Ambient pH-regulated enzime secretion in endophytic and pathogenic isolates of the fungal genus Colletotrichum." Scientia Agricola 61, no. 3 (June 2004): 298–302. http://dx.doi.org/10.1590/s0103-90162004000300010.

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In fungi a genetic system ensures that enzymes are secreted mainly at ambient pH values corresponding to their optima of activity. Although a great deal of information has been obtained concerning this environmental response, there is a lack of studies involving phytopathogenic, endophytic and entomopathogenic fungi as well as different aspects of fungus-host interactions. This study compares in a plate-clearing assays, the effect of ambient pH in the secretion of amylase, cellulase, lipase, pectinase and protease by endophytic, phytopathogenic, and entomopathogenic isolates belonging to several species of Colletotrichum. All enzymes were secreted in a pH-dependent manner by all isolates. Endophytes and pathogens showed distinct patterns of protease secretion, with optima at alkaline and acid growth conditions, respectively. In liquid medium, a Pi-repressible acid phosphatase of an endophytic isolate responded to ambient pH, having a 14-fold increase in secreted specific activity at acid pH, as compared to alkaline pH. Furthermore, part of a Colletotrichum pacC homologue gene, coding for a transcriptional factor responsible for pH-regulated gene expression, was cloned. Ambient pH seems to be a general factor controlling enzyme secretion in fungus-host interactions through a conserved genetic circuit.
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Book chapters on the topic "Ph-Coding"

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Stockdale, Elizabeth, Paul Hargreaves, and Anne Bhogal. "Developing soil health indicators for improved soil management on farm." In Advances in measuring soil health, 289–328. Burleigh Dodds Science Publishing, 2021. http://dx.doi.org/10.19103/as.2020.0079.22.

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A range of chemical, physical and biological processes are important for sustained productivity and environmental quality in agricultural systems. Farmers and scientists share a concern with soil health, and this leads to questions for both measurement and management. An essential step is to define the context and the key functions required of a soil at the scale of interest (e.g. farm, drinking water catchment, region). Only then can appropriate indicator measurements be selected. Current soil health frameworks across the world commonly use organic matter (carbon), pH, extractable phosphorus, and various indicators of soil structure/water storage. A framework of interpretation shows whether the measured values are acceptable or whether one or more soil functions are constrained. A number of the soil health frameworks in practical use present the soil health indicators in a scorecard using traffic light coding to direct users towards guidance for improved soil management on-farm.
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Mandal, Supriya, and Junaid Jibran Jawed. "Alkaliphiles: Diversity, Adaptation and Applications." In Extremophiles: Diversity, Adaptation and Applications, 120–45. BENTHAM SCIENCE PUBLISHERS, 2022. http://dx.doi.org/10.2174/9789815080353122010009.

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Alkaliphiles are some of the major extremophiles which occupy a certain niche of the globe where the pH values are usually two unit higher that the neutrality. Although abundantly found in rare geographical regions, these organisms are of immense importance in terms of their enzymatic activities which enable them to be functional under extreme alkaline conditions and therefore have numerous industrial and biotechnological applications. Their unique mode of adaptation and exclusive ability of resource utilisation make their existence interesting for biotechnological research. The study of alkaliphiles revealed the potential of these microorganisms in the bioremediation of the soda lake, their efficiency to degrade complex organic compounds and a certain class of antibiotics produced by them are of immense importance for the pharmaceutical industries. Recent advancements in genetic studies and recombinant DNA technology allowed the understanding of their genetic modifications which are unique to their taxa and helped researchers to utilise their coding sequence for isolation and purification of commercially important alkaline active enzymes. Despite all the beneficial effects, the isolation, culturing and study of alkaliphiles are among the most challenging tasks and matters of continuous research. This chapter will elaborate on the existence of some important alkaliphilic bacteria in the rare alkaline region of the globe, the diversities among them, their metabolic activities, unique adaptation and modifications in their structural and genomic profile and also summarises the commercially important product isolated from them.
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Conference papers on the topic "Ph-Coding"

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Morinaga, T., Y. Itagaki, A. Suzuki, H. Yasuda, and K. Higashio. "PURIFICATION AND CHARACTERIZATION OF TISSUE PLASMINOGEN ACTIVATOR PRODUCED BY IMR-90 CELLS." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644393.

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Tissue plasminogen activator ( t-PA ) produced by IMR-90 ( human embryonic fibroblast ) cells cultured in the serum-free medium ( DMEM ) containing 1% proteos^e peptone and 1.6 - 3.6mM CaCl2 was purified by the procedure consisted of ultrafiltration, immunoadsorpt ion chromatography, HPLC and lysine-Sepharose chromatography. The yield of t-PA from the culture broth was approximately 47%. The purified t-PA migrated as a single band on SDS-polyacrylamide gels. The molecular weight of the t-PA was estimated to be 66,000 by SDS-polyacrylamide gel electrophoresis and 69,000 by gel filtration method. Purified t-PA had a specific activity of 36 × 104 IU/mg protein by fiblin plate method or 54 - 56 X 104 IU/mg protein by clot lysis method using t-PA obtained from WHO as a standard. The amino acid composition of fibroblast t-PA was very similar to those of melanoma t-PA and uterine t-PA. Isoelectric point of fibroblast t-PA ranged from 5-7 to 8.2. The t-PA had twice as much affinity for fiblin as did high molecular weight urokinase ( UK ). Both t-PA and UK had optimum temperature at 41°C and optimum pH between 8.0 - 9.0. The polyclonal and monoclonal antibodies raised against t-PA quenched t-PA activity but had no effect on UK activity. The inhibitors of serine proteases, difluorophos-phate and gabexate mesilate, strongly inhibited the activities of fibroblast t-PA and UK. The nucleotide sequence analysis of the t-PA cDNA isolated from the cDNA library prepared from IMR-90 mRNA revealed the nucleotide changes at two positions in the coding region as compared to that of melanoma t-PA cDNA. Neither of the changes replaced the coded amino acid. The N-terminal amino acid of fibroblast t-PA was determined to be valine, indicatig the structural similarity of fibroblast t-PA to uterine t-PA.
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