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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Xu, Junhua, John Linneman, Yanfeng Zhong, Haoyang Yin, Qinyi Xia, Kang Kang, and Deming Gou. "MicroRNAs in Pulmonary Hypertension, from Pathogenesis to Diagnosis and Treatment." Biomolecules 12, no. 4 (March 24, 2022): 496. http://dx.doi.org/10.3390/biom12040496.
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Pulmonary hypertension (PH) is a fatal and untreatable disease, ultimately leading to right heart failure and eventually death. microRNAs are small, non-coding endogenous RNA molecules that can regulate gene expression and influence various biological processes. Changes in microRNA expression levels contribute to various cardiovascular disorders, and microRNAs have been shown to play a critical role in PH pathogenesis. In recent years, numerous studies have explored the role of microRNAs in PH, focusing on the expression profiles of microRNAs and their signaling pathways in pulmonary artery smooth muscle cells (PASMCs) or pulmonary artery endothelial cells (PAECs), PH models, and PH patients. Moreover, certain microRNAs, such as miR-150 and miR-26a, have been identified as good candidates of diagnosis biomarkers for PH. However, there are still several challenges for microRNAs as biomarkers, including difficulty in normalization, specificity in PH, and a lack of longitudinal and big sample-sized studies. Furthermore, microRNA target drugs are potential therapeutic agents for PH treatment, which have been demonstrated in PH models and in humans. Nonetheless, synthetic microRNA mimics or antagonists are susceptible to several common defects, such as low drug efficacy, inefficient drug delivery, potential toxicity and especially, off-target effects. Therefore, finding clinically safe and effective microRNA drugs remains a great challenge, and further breakthrough is urgently needed.
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Revyatskyy, I. Yu, and A. I. Boiko. "Theoretical and applied aspects of creating a unified information accounting system of pharmaceutical and medical products in Ukraine." Farmatsevtychnyi zhurnal, no. 6 (December 9, 2020): 26–36. http://dx.doi.org/10.32352/0367-3057.6.20.03.
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In modern conditions of reforming the Ukrainian Health Care system based on the introduction of innovative digital information technologies, the development of a methodology for the computerization of pharmaceutical information exchange processes is relevant.
The purpose of our study was to develop a methodology for creating a unified accounting system (UAS) of information on pharmaceutical and medical products (Ph&MP) in Ukraine (taking into account the current standards of computer systems for structuring and fixing information, as well as in accordance with international standards for automated identification of information about Ph&MP.
The objects of the research were: scientific and specialized publications devoted to the issue of the implementation of a system of accounting and tracking of medical and health care in the EU, USA, Canada;pharmaceutical information with tracking and recording the established information flows in computer databases.The main research is based on the methodology of pharmaceutical informatics: creation of pharmaceutical computer databases, coding of pharmaceutical products. The method of system analysis processed publications on the types of Ph&MP encodings in the EU, USA, Canada.
In the scientific work, the international standards for the sale of information in two-dimensional shaded codes of the DataMatrixECC 200 standard are highlighted, which is one of the information blocks on the basis of which the development of the UAS Ph&MP database structure should be based.The structure and interconnection of information blocks for the accounting of Ph&MP units using GTIN and serial numbers in the database of structural units of business entities of the pharmaceutical market of Ukraine have been developed.
A systematic analysis of the types of Ph&MP encodings in the EU countries, the USA, and Canada has been carried out.Highlighted rational approaches to the formation of coding and accounting for Ph & MP, taking into account national characteristics. The basis of the integral structure of the UAS Ph&MP with basic information blocks has been developed.Approaches and principles to the methodology of its formation are given, taking into account the current standards of computer systems for the structuring and fixing of information, as well as in accordance with international standards for automated identification of information about Ph&MP. The requirements for the compliance of computer databases of structural units of business entities with modern standards for preserving pharmaceutical information necessary about medicines when accounting are presented.
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Wei, Lanjing, Huitao Liu, Kimia Alizadeh, Maria D. Juarez-Rodriguez, and Roman R. Ganta. "Functional Characterization of Multiple Ehrlichia chaffeensis Sodium (Cation)/Proton Antiporter Genes Involved in the Bacterial pH Homeostasis." International Journal of Molecular Sciences 22, no. 16 (August 5, 2021): 8420. http://dx.doi.org/10.3390/ijms22168420.
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Ehrlichia chaffeensis causes human monocytic ehrlichiosis. Little is known about how this and other related tick-borne rickettsia pathogens maintain pH homeostasis in acidified phagosomes and the extracellular milieu. The membrane-bound sodium (cation)/proton antiporters are found in a wide range of organisms aiding pH homeostasis. We recently reported a mutation in an antiporter gene of E. chaffeensis (ECH_0379) which causes bacterial in vivo attenuation. The E. chaffeensis genome contains 10 protein coding sequences encoding for predicted antiporters. We report here that nine of these genes are transcribed during the bacterial growth in macrophages and tick cells. All E. chaffeensis antiporter genes functionally complemented antiporter deficient Escherichia coli. Antiporter activity for all predicted E. chaffeensis genes was observed at pH 5.5, while gene products of ECH_0179 and ECH_0379 were also active at pH 8.0, and ECH_0179 protein was complemented at pH 7.0. The antiporter activity was independently verified for the ECH_0379 protein by proteoliposome diffusion analysis. This is the first description of antiporters in E. chaffeensis and demonstrates that the pathogen contains multiple antiporters with varying biological functions, which are likely important for the pH homeostasis of the pathogen’s replicating and infectious forms.
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Sun, Yi Fei, Yasunori Kobori, Anna Kuwana, and Haruo Kobayashi. "Pulse Coding Controlled Switching Converter with Notch Generation and its Conversion Voltage Ratio Analysis." Advanced Engineering Forum 38 (November 2020): 171–78. http://dx.doi.org/10.4028/www.scientific.net/aef.38.171.
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This paper proposes an EMI spread spectrum technology with automatically setting the notch frequency using the pulse coding controlled method of the DC-DC switching converter. In the automatic notch generation method, by usage of the input frequency Fin, the clock frequency Fckand the coding pulses PH, PL are generated automatically using the equation (see formula in the paper). Here the conversion voltage ratio is given by (see formula in the paper) . If shifts, the balance of the inductor current is shifted and then the output voltage ripple is influenced. Moreover, as the power supply IC, it is necessary to automatically detect or set the conditions for Vin and Vout, and hence we also provide discussion about the conversion voltage ratio Do in many situations.
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Kurniawan, Lutfi Athanuzul, and Amirullah Amirullah. "Monitoring and Controlling of pH Levels and Plant Nutrition Supplied by Standalone Photovoltaic in a Greenhouse Hydroponic System using Arduino Uno." ELKHA 13, no. 1 (April 20, 2021): 69. http://dx.doi.org/10.26418/elkha.v13i1.45657.
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This paper aims to implement the prototype model to monitor and control the pH levels and nutrition plant (electrical conductivity-EC) supplied by a standalone photovoltaic (PV) module-connected battery (Lithium-Ion) on the greenhouse hydroponic systems. The pH and EC sensors are connected to the Arduino Uno circuit as a relay control to drive four pumps, i.e. the water flow pump, EC pump, pH up pump, and pH down pump. The greenhouse function to control pests and the impact of environmental non-uniformity caused by variation of wind speed, temperature, or sunlight so that hydroponic plants can grow in an appropriate environment. The Arduino Uno circuit with a 20 × 4 liquid crystal display (LCD) order four relays to monitor and control the four pumps of the greenhouse hydroponic system based on the coding which has been programmed previously. The prototype model is able to monitor and control the pH of hydroponic plant water at the level between 6-7 using a pH-up and pH-down sensor. This model is also able to monitor and control nutrition plant water over 1 mS/cm using an EC sensor. Finally, the proposed prototype is able to monitor and control EC and pH level to regulate plant growth in the greenhouse hydroponic system normally and in real-time.
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Nagano, Celso S., Juan J. Calvete, Domingo Barettino, Alicia Pérez, Benildo S. Cavada, and Libia Sanz. "Insights into the structural basis of the pH-dependent dimer–tetramer equilibrium through crystallographic analysis of recombinant Diocleinae lectins." Biochemical Journal 409, no. 2 (December 21, 2007): 417–28. http://dx.doi.org/10.1042/bj20070942.
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The structural ground underlying the pH-dependency of the dimer–tetramer transition of Diocleinae lectins was investigated by equilibrium sedimentation and X-ray crystal structure determination of wild-type and site-directed mutants of recombinant lectins. Synthetic genes coding for the full-length α-chains of the seed lectins of Dioclea guianensis (termed r-αDguia) and Dioclea grandiflora (termed r-αDGL) were designed and expressed in Escherichia coli. This pioneering approach, which will be described in detail in the present paper, yielded recombinant lectins displaying carbohydrate-binding activity, dimer–tetramer equilibria and crystal structures indistinguishable from their natural homologues. Conversion of the pH-stable tetrameric r-αDGL into a structure exhibiting pH-dependent dimer–tetramer transition was accomplished through mutations that abolished the interdimeric interactions at the central cavity of the tetrameric lectins. Both the central and the peripheral interacting regions bear structural information for formation of the canonical legume lectin tetramer. We hypothesize that the strength of the ionic contacts at these sites may be modulated by the pH, leading to dissociation of those lectin structures that are not locked into a pH-stable tetramer through interdimeric contacts networking the central cavity loops.
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Choi, Eunna, Eduardo A. Groisman, and Dongwoo Shin. "Activated by Different Signals, the PhoP/PhoQ Two-Component System Differentially Regulates Metal Uptake." Journal of Bacteriology 191, no. 23 (October 2, 2009): 7174–81. http://dx.doi.org/10.1128/jb.00958-09.
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ABSTRACT The PhoP/PhoQ two-component system controls several physiological and virulence functions in Salmonella enterica. This system is activated by low Mg2+, acidic pH, and antimicrobial peptides, but the biological consequences resulting from sensing multiple signals are presently unclear. Here, we report that the PhoP/PhoQ system regulates different Salmonella genes depending on whether the inducing signal is acidic pH or low Mg2+. When Salmonella experiences acidic pH, the PhoP/PhoQ system promotes Fe2+ uptake in a process that requires the response regulator RstA, activating transcription of the Fe2+ transporter gene feoB. In contrast, the PhoP-induced RstA protein did not promote feoB expression at neutral pH with low Mg2+. The PhoP/PhoQ system promotes the expression of the Mg2+ transporter mgtA gene only when activated in bacteria starved for Mg2+. This is because mgtA transcription promoted at high Mg2+ concentrations by the acidic-pH-activated PhoP protein failed to reach the mgtA coding region due to the mgtA leader region functioning as a Mg2+ sensor. Our results show that a single two-component regulatory system can regulate distinct sets of genes in response to different input signals.
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Garrett, April D., Reid S. Brennan, Anya L. Steinhart, Aubrey M. Pelletier, and Melissa H. Pespeni. "Unique Genomic and Phenotypic Responses to Extreme and Variable pH Conditions in Purple Urchin Larvae." Integrative and Comparative Biology 60, no. 2 (May 27, 2020): 318–31. http://dx.doi.org/10.1093/icb/icaa072.
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Synopsis Environmental variation experienced by a species across space and time can promote the maintenance of genetic diversity that may be adaptive in future global change conditions. Selection experiments have shown that purple sea urchin, Strongylocentrotus purpuratus, populations have adaptive genetic variation for surviving pH conditions at the “edge” (pH 7.5) of conditions experienced in nature. However, little is known about whether populations have genetic variation for surviving low-pH events beyond those currently experienced in nature or how variation in pH conditions affects organismal and genetic responses. Here, we quantified survival, growth, and allele frequency shifts in experimentally selected developing purple sea urchin larvae in static and variable conditions at three pH levels: pH 8.1 (control), pH 7.5 (edge-of-range), and pH 7.0 (extreme). Variable treatments recovered body size relative to static treatments, but resulted in higher mortality, suggesting a potential tradeoff between survival and growth under pH stress. However, within each pH level, allele frequency changes were overlapping between static and variable conditions, suggesting a shared genetic basis underlying survival to mean pH regardless of variability. In contrast, genetic responses to pH 7.5 (edge) versus pH 7.0 (extreme) conditions were distinct, indicating a unique genetic basis of survival. In addition, loci under selection were more likely to be in exonic regions than regulatory, indicating that selection targeted protein-coding variation. Loci under selection in variable pH 7.5 conditions, more similar to conditions periodically experienced in nature, performed functions related to lipid biosynthesis and metabolism, while loci under selection in static pH 7.0 conditions performed functions related to transmembrane and mitochondrial processes. While these results are promising in that purple sea urchin populations possess genetic variation for surviving extreme pH conditions not currently experienced in nature, they caution that increased acidification does not result in a linear response but elicits unique physiological stresses and survival mechanisms.
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Wang, Zhongshan, Meng Zhang, Xiaodong Shi, and Quanju Xiang. "Purification and Characterization of an ATPase GsiA from Salmonella enterica." BioMed Research International 2017 (2017): 1–8. http://dx.doi.org/10.1155/2017/3076091.
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The coding sequence of Salmonella enterica gsiA was cloned and expressed in E. coli. The protein was purified and ATPase activity was characterized by NADH oxidation method. GsiA exhibited optimum activity at 30°C and at pH 8 in Tris/HCl buffer. GsiA protein was stable at 20°C. 66% and 44% activity remained after incubation at 30°C and 40°C for 30 min. pH 7 and pH 9 incubation would obviously reduce the ATPase activity. In vivo functionality of gsiA was determined by constructing gene deletion strains. gsiA was shown to be essential for GSI mediated glutathione uptake and gsiA deletion could decrease the virulence of Salmonella enterica. Interactions of glutathione import proteins GsiA, GsiB, GsiC, and GsiD were investigated by using bacterial two-hybrid system. GsiA could interact with itself and inner membrane proteins GsiC and GsiD. This report provides the first description of gsiA functions in Salmonella enterica. The results could help elucidating the glutathione uptake mechanism and glutathione functions in bacteria.
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Fernández, Ana I., Raquel Yotti, Ana González-Mansilla, Teresa Mombiela, Enrique Gutiérrez-Ibanes, Candelas Pérez del Villar, Paula Navas-Tejedor, et al. "The Biological Bases of Group 2 Pulmonary Hypertension." International Journal of Molecular Sciences 20, no. 23 (November 23, 2019): 5884. http://dx.doi.org/10.3390/ijms20235884.
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Pulmonary hypertension (PH) is a potentially fatal condition with a prevalence of around 1% in the world population and most commonly caused by left heart disease (PH-LHD). Usually, in PH-LHD, the increase of pulmonary pressure is only conditioned by the retrograde transmission of the left atrial pressure. However, in some cases, the long-term retrograde pressure overload may trigger complex and irreversible biomechanical and biological changes in the pulmonary vasculature. This latter clinical entity, designated as combined pre- and post-capillary PH, is associated with very poor outcomes. The underlying mechanisms of this progression are poorly understood, and most of the current knowledge comes from the field of Group 1-PAH. Treatment is also an unsolved issue in patients with PH-LHD. Targeting the molecular pathways that regulate pulmonary hemodynamics and vascular remodeling has provided excellent results in other forms of PH but has a neutral or detrimental result in patients with PH-LHD. Therefore, a deep and comprehensive biological characterization of PH-LHD is essential to improve the diagnostic and prognostic evaluation of patients and, eventually, identify new therapeutic targets. Ongoing research is aimed at identify candidate genes, variants, non-coding RNAs, and other biomarkers with potential diagnostic and therapeutic implications. In this review, we discuss the state-of-the-art cellular, molecular, genetic, and epigenetic mechanisms potentially involved in PH-LHD. Signaling and effective pathways are particularly emphasized, as well as the current knowledge on -omic biomarkers. Our final aim is to provide readers with the biological foundations on which to ground both clinical and pre-clinical research in the field of PH-LHD.
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Shi, Xiao-Wei, Ming-Lv Sun, Bo Zhou, and Xiao-Yun Wang. "Identification, characterization, and overexpression of a phytase with potential industrial interest." Canadian Journal of Microbiology 55, no. 5 (May 2009): 599–604. http://dx.doi.org/10.1139/w09-008.
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A high phytase-producing strain of Aspergillus niger N-3 was identified by screening 104 microbial strains. The gene for A. niger N-3 was cloned and expressed in Pichia pastoris . The coding region without the introns and putative signal sequence was comprised of 1347 nucleotides. It encoded a polypeptide of 448 amino acids, exhibiting high amino acid sequence homologies (94.87%) with the typical phytase of A. niger NRRL 3135. The molecular mass of the recombinant phytase as determined by SDS–PAGE was 60–70 kDa, with maximum activity at ~55 °C (after incubation at 10 min). The phytase retained about 45% of its enzymatic activity under heat treatment at 90 °C for 5 min. It showed a greater affinity for sodium phytate than for p-nitrophenyl phosphate. Dual optima pH (2.0 and 5.5) was gained. The activity at pH 2.0 was about 30% higher than at pH 5.5, which was more suitable to the circumstance of the stomachs of monogastric animals. The extent of glycosylation influenced the characterization of phytase. The deglycosylated phytase showed pH optima at 3.5 and 5.5, and the molecular mass had dropped to 50 kDa.
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Subramanian, Shoba, Carol A. Woolford, Jigar V. Desai, Frederick Lanni, and Aaron P. Mitchell. "cis - and trans -Acting Localization Determinants of pH Response Regulator Rim13 in Saccharomyces cerevisiae." Eukaryotic Cell 11, no. 10 (August 3, 2012): 1201–9. http://dx.doi.org/10.1128/ec.00158-12.
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ABSTRACT The Rim101/PacC pathway governs adaptation to alkaline pH in many fungi. Output of the pathway is mediated by transcription factors of the Rim101/PacC family, which are activated by proteolytic cleavage. The proteolytic complex includes scaffold protein Rim20 and endosome-associated subunits of the endosomal sorting complex required for transport (ESCRT). We provide here evidence that Saccharomyces cerevisiae Rim13, the protease that is implicated in Rim101 cleavage, is associated with the Rim20-ESCRT complex, and we investigate its regulation. Rim13-GFP is dispersed in cells grown in acidic medium but forms punctate foci when cells encounter alkaline conditions. A vps4Δ mutant, which accumulates elevated levels of endosomal ESCRT, also accumulates elevated levels of Rim13-GFP foci, independently of external pH. In the vps4Δ background, mutation of ESCRT subunit Snf7 or of Rim20 blocks the formation of Rim13 foci, and we found that Rim13 and Rim20 are colocalized. The Rim13 ortholog PalB of Aspergillus nidulans has been shown to undergo ESCRT and membrane association through an N-terminal MIT domain, but Rim13 orthologs in the Saccharomyces clade lack homology to this N-terminal region. Instead, there is a clade-limited C-terminal region, and we show that point mutations in this region prevent punctate localization and impair Rim13 function. We suggest that RIM13 arose from its ancestral gene through two genome rearrangements. The ancestor lost the coding region for its MIT domain through a 5′ rearrangement and acquired the coding region for the Saccharomyces -specific functional equivalent through a 3′ rearrangement.
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Estephan, Leonard E., Michael V. Genuardi, Chad M. Kosanovich, Michael G. Risbano, Yingze Zhang, Nancy Petro, Annie Watson, et al. "Distinct plasma gradients of microRNA-204 in the pulmonary circulation of patients suffering from WHO Groups I and II pulmonary hypertension." Pulmonary Circulation 9, no. 2 (March 28, 2019): 204589401984064. http://dx.doi.org/10.1177/2045894019840646.
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Pulmonary hypertension (PH), a heterogeneous vascular disease, consists of subtypes with overlapping clinical phenotypes. MicroRNAs, small non-coding RNAs that negatively regulate gene expression, have emerged as regulators of PH pathogenesis. The muscle-specific micro RNA (miR)-204 is known to be depleted in diseased pulmonary artery smooth muscle cells (PASMCs), furthering proliferation and promoting PH. Alterations of circulating plasma miR-204 across the trans-pulmonary vascular bed might provide mechanistic insights into the observed intracellular depletion and may help distinguish PH subtypes. MiR-204 levels were quantified at sequential pulmonary vasculature sites in 91 patients with World Health Organization (WHO) Group I pulmonary arterial hypertension (PAH) (n = 47), Group II PH (n = 22), or no PH (n = 22). Blood from the right atrium/superior vena cava, pulmonary artery, and pulmonary capillary wedge was collected. Peripheral blood mononuclear cells (PBMCs) were isolated (n = 5/group). Excretion of miR-204 by PAH-PASMCs was also quantified in vitro. In Group I patients only, miR-204 concentration increased sequentially along the pulmonary vasculature (log fold-change slope = 0.22 [95% CI = 0.06–0.37], P = 0.008). PBMCs revealed insignificant miR-204 variations among PH groups ( P = 0.12). Cultured PAH-PAMSCs displayed a decrease of intracellular miR-204 ( P = 0.0004), and a converse increase of extracellular miR-204 ( P = 0.0018) versus control. The stepwise elevation of circulating miR-204 across the pulmonary vasculature in Group I, but not Group II, PH indicates differences in muscle-specific pathobiology between subtypes. Considering the known importance of miR-204 in PH, these findings may suggest pathologic excretion of miR-204 in Group I PAH by PASMCs, thereby accounting for decreased intracellular miR-204 concentration.
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Kobayashi, Hatasu, Risako Kabata, Hideyuki Kinoshita, Takaaki Morimoto, Koh Ono, Midori Takeda, Jungmi Choi, et al. "Rare variants in RNF213, a susceptibility gene for moyamoya disease, are found in patients with pulmonary hypertension and aggravate hypoxia-induced pulmonary hypertension in mice." Pulmonary Circulation 8, no. 3 (May 2, 2018): 204589401877815. http://dx.doi.org/10.1177/2045894018778155.
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Ring finger 213 ( RNF213) is a susceptibility gene for moyamoya disease (MMD), a progressive cerebrovascular disease. Recent studies suggest that RNF213 plays an important role not only in MMD, but also in extracranial vascular diseases, such as pulmonary hypertension (PH). In this study, we undertook genetic screening of RNF213 in patients with PH and performed functional analysis of an RNF213 variant using mouse models. Direct sequencing of the exons in the C-terminal region of RNF213, where MMD-associated mutations are highly clustered, and of the entire coding exons of BMPR2 and CAV1, the causative genes for PH, was performed in 27 Japanese patients with PH. Two MMD-associated rare variants (p.R4810K and p.A4399T) in RNF213 were identified in two patients, three BMPR2 mutations (p.Q92H, p.L198Rfs*4, and p.S930X) were found in three patients, whereas no CAV1 mutations were identified. To test the effect of the RNF213 variants on PH, vascular endothelial cell (EC)-specific Rnf213 mutant transgenic mice were exposed to hypoxia. Overexpression of the EC-specific Rnf213 mutant, but neither Rnf213 ablation nor EC-specific wild-type Rnf213 overexpression, aggravated the hypoxia-induced PH phenotype (high right ventricular pressure, right ventricular hypertrophy, and muscularization of pulmonary vessels). Under hypoxia, electron microscopy showed unique EC detachment in pulmonary vessels, and western blots demonstrated a significant reduction in caveolin-1 (encoded by CAV1), a key molecule involved in EC functions, in lungs of EC-specific Rnf213 mutant transgenic mice, suggestive of EC dysfunction. RNF213 appears to be a genetic risk factor for PH and could play a role in systemic vasculopathy.
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Cafaro, Valeria, Viviana Izzo, Roberta Scognamiglio, Eugenio Notomista, Paola Capasso, Annarita Casbarra, Piero Pucci, and Alberto Di Donato. "Phenol Hydroxylase and Toluene/o-Xylene Monooxygenase from Pseudomonas stutzeri OX1: Interplay between Two Enzymes." Applied and Environmental Microbiology 70, no. 4 (April 2004): 2211–19. http://dx.doi.org/10.1128/aem.70.4.2211-2219.2004.
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ABSTRACT Degradation of aromatic hydrocarbons by aerobic bacteria is generally divided into an upper pathway, which produces dihydroxylated aromatic intermediates by the action of monooxygenases, and a lower pathway, which processes these intermediates down to molecules that enter the citric acid cycle. Bacterial multicomponent monooxygenases (BMMs) are a family of enzymes divided into six distinct groups. Most bacterial genomes code for only one BMM, but a few cases (3 out of 31) of genomes coding for more than a single monooxygenase have been found. One such case is the genome of Pseudomonas stutzeri OX1, in which two different monooxygenases have been found, phenol hydroxylase (PH) and toluene/o-xylene monooxygenase (ToMO). We have already demonstrated that ToMO is an oligomeric protein whose subunits transfer electrons from NADH to oxygen, which is eventually incorporated into the aromatic substrate. However, no molecular data are available on the structure and on the mechanism of action of PH. To understand the metabolic significance of the association of two similar enzymatic activities in the same microorganism, we expressed and characterized this novel phenol hydroxylase. Our data indicate that the PH P component of PH transfers electrons from NADH to a subcomplex endowed with hydroxylase activity. Moreover, a regulatory function can be suggested for subunit PH M. Data on the specificity and the kinetic constants of ToMO and PH strongly support the hypothesis that coupling between the two enzymatic systems optimizes the use of nonhydroxylated aromatic molecules by the draining effect of PH on the product(s) of oxidation catalyzed by ToMO, thus avoiding phenol accumulation.
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Fletcher, Kedung, Anding Nyuak, and Phei Yee Tan. "PH MONITORING FOR LIQUID FERTILIZER MANAGEMENT IN BLACK PEPPER FARMING." International Journal of Innovation and Industrial Revolution 3, no. 6 (March 10, 2021): 01–12. http://dx.doi.org/10.35631/ijirev.36001.
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There is lacking technology application in black pepper farming to automate daily routine activities in monitoring black pepper vines growth and nutrient need. With the revolution of Industry 4.0 (IR4.0), and tremendous improvement in the internet of things (IoT), the application of precision agriculture to pepper farming is a thing to consider for its benefit. This paper to explore the use of IoT to monitor fertilizer requirement for pepper vines using pH sensor. The pH sensor attached to Raspberry Pi 3 will be collecting the data and forwarding it to the cloud database for farmer reference and take decision based on data presented in form of a digital report from the database. The Python environment provides the space for coding in Raspberry Pi. SQL and PHP software is used to design the user interface and data management in the relational database management system. The information about pH provides a better understanding of how pH parameter affects the growth of pepper vines. The farmer will be able to access the information anywhere and anytime. Therefore, our proposed system will greatly help the pepper farmers in Sarawak in managing the usage of fertilizer as a way to minimize farm inputs, thus increase their profit.
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Sohlenkamp, Christian, Kanaan A. Galindo-Lagunas, Ziqiang Guan, Pablo Vinuesa, Sally Robinson, Jane Thomas-Oates, Christian R. H. Raetz, and Otto Geiger. "The Lipid Lysyl-Phosphatidylglycerol Is Present in Membranes of Rhizobium tropici CIAT899 and Confers Increased Resistance to Polymyxin B Under Acidic Growth Conditions." Molecular Plant-Microbe Interactions® 20, no. 11 (November 2007): 1421–30. http://dx.doi.org/10.1094/mpmi-20-11-1421.
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Lysyl-phosphatidylglycerol (LPG) is a well-known membrane lipid in several gram-positive bacteria but is almost unheard of in gram-negative bacteria. In Staphylococcus aureus, the gene product of mprF is responsible for LPG formation. Low pH-inducible genes, termed lpiA, have been identified in the gram-negative α-proteobacteria Rhizobium tropici and Sinorhizobium medicae in screens for acid-sensitive mutants and they encode homologs of MprF. An analysis of the sequenced bacterial genomes reveals that genes coding for homologs of MprF from S. aureus are present in several classes of organisms throughout the bacterial kingdom. In this study, we show that the expression of lpiA from R. tropici in the heterologous hosts Escherichia coli and Sinorhizobium meliloti causes formation of LPG. A wild-type strain of R. tropici forms LPG (about 1% of the total lipids) when the cells are grown in minimal medium at pH 4.5 but not when grown in minimal medium at neutral pH or in complex tryptone yeast (TY) medium at either pH. LPG biosynthesis does not occur when lpiA is deleted and is restored upon complementation of lpiA-deficient mutants with a functional copy of the lpiA gene. When grown in the low-pH medium, lpiA-deficient rhizobial mutants are over four times more susceptible to the cationic peptide polymyxin B than the wild type.
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Albers, Sonja-V., Marieke G. L. Elferink, Robert L. Charlebois, Christoph W. Sensen, Arnold J. M. Driessen, and Wil N. Konings. "Glucose Transport in the Extremely Thermoacidophilic Sulfolobus solfataricus Involves a High-Affinity Membrane-Integrated Binding Protein." Journal of Bacteriology 181, no. 14 (July 15, 1999): 4285–91. http://dx.doi.org/10.1128/jb.181.14.4285-4291.1999.
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ABSTRACT The archaeon Sulfolobus solfataricus grows optimally at 80°C and pH 2.5 to 3.5 on carbon sources such as yeast extracts, tryptone, and various sugars. Cells rapidly accumulate glucose. This transport activity involves a membrane-bound glucose-binding protein that interacts with its substrate with very high affinity (Kd of 0.43 μM) and retains high glucose affinity at very low pH values (as low as pH 0.6). The binding protein was extracted with detergent and purified to homogeneity as a 65-kDa glycoprotein. The gene coding for the binding protein was identified in the S. solfataricus P2 genome by means of the amino-terminal amino acid sequence of the purified protein. Sequence analysis suggests that the protein is anchored to the membrane via an amino-terminal transmembrane segment. Neighboring genes encode two membrane proteins and an ATP-binding subunit that are transcribed in the reverse direction, whereas a homologous gene cluster inPyrococcus horikoshii OT3 was found to be organized in an operon. These data indicate that S. solfataricus utilizes a binding-protein-dependent ATP-binding cassette transporter for the uptake of glucose.
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Sala-Newby, G. B., and A. K. Campbell. "Engineering a bioluminescent indicator for cyclic AMP-dependent protein kinase." Biochemical Journal 279, no. 3 (November 1, 1991): 727–32. http://dx.doi.org/10.1042/bj2790727.
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cDNA coding for the luciferase in the firefly Photinus pyralis was amplified in vitro to generate cyclic AMP-dependent protein kinase phosphorylation sites. The DNA was transcribed and translated to generate light-emitting protein. A valine at position 217 was mutated to arginine to generate a site RRFS and the heptapeptide kemptide, the phosphorylation site of the porcine pyruvate kinase, was added at the N- or C-terminus of the luciferase. The proteins carrying phosphorylation sites were characterized for their specific activity, pI, effect of pH on the colour of the light emitted and effect of the catalytic subunit of protein kinase A in the presence of ATP. Only one of the recombinant proteins (RRFS) was significantly different from wild-type luciferase. The RRFS mutant had a lower specific activity, lower pH optimum, emitted greener light at low pH and when phosphorylated it decreased its activity by up to 80%. This latter effect was reversed by phosphatase. This recombinant protein is a good candidate to measure for the first time cyclic AMP-dependent phosphorylation in live cells.
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Lathrop, W. F., E. P. Carmichael, D. G. Myles, and P. Primakoff. "cDNA cloning reveals the molecular structure of a sperm surface protein, PH-20, involved in sperm-egg adhesion and the wide distribution of its gene among mammals." Journal of Cell Biology 111, no. 6 (December 1, 1990): 2939–49. http://dx.doi.org/10.1083/jcb.111.6.2939.
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Sperm binding to the egg zona pellucida in mammals is a cell-cell adhesion process that is generally species specific. The guinea pig sperm protein PH-20 has a required function in sperm adhesion to the zona pellucida of guinea pig eggs. PH-20 is located on both the sperm plasma membrane and acrosomal membrane. We report here the isolation and sequence of a full-length cDNA for PH-20 (available from EMBL/GenBank/DDBJ under accession number X56332). The derived amino acid sequence shows a mature protein of 468 amino acids containing six N-linked glycosylation sites and twelve cysteines, eight of which are tightly clustered near the COOH terminus. The sequence indicates PH-20 is a novel protein with no relationship to the mouse sperm adhesion protein galactosyl transferase and no significant homology with other known proteins. The two PH-20 populations, plasma membrane and acrosomal membrane, could arise because one form of PH-20 is encoded and differentially targeted at different spermatogenic stages. Alternatively, two different forms of PH-20 could be encoded. Our evidence thus far reveals only one sequence coding for PH-20: Southern blots of guinea pig genomic DNA indicated there is a single PH-20 gene, Northern blots showed a single size PH-20 message (approximately 2.2 kb), and no sequence variants were found among the sequenced cDNA clones. Cross-species Southern blots reveal the presence of a homologue of the PH-20 gene in mouse, rat, hamster, rabbit, bovine, monkey, and human genomic DNA, showing the PH-20 gene is conserved among mammals. Since genes for zona glycoproteins are also conserved among mammals, the general features of sperm and zona proteins involved in mammalian sperm-egg adhesion may have been evolutionarily maintained. Species specificity may result from limited changes in these molecules, either in their binding domains or in other regions that affect the ability of the binding domains to interact.
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Hauton, C., T. Tyrrell, and J. Williams. "The subtle effects of sea water acidification on the amphipod <i>Gammarus locusta</i>." Biogeosciences Discussions 6, no. 1 (January 15, 2009): 919–46. http://dx.doi.org/10.5194/bgd-6-919-2009.
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Abstract. We report an investigation of the effects of increases in pCO2 on the growth and molecular physiology of the neritic amphipod Gammarus locusta, which has a cosmopolitan distribution in estuaries. Amphipods were reared from juvenile to mature adult in laboratory microcosms at three different levels of pH in nominal range 8.1–7.6. Growth rate was estimated from weekly measures of body length. At sexual maturity the amphipods were sacrificed and assayed for changes in the expression of genes coding for a heat shock protein (hsp70 gene) and the metabolic enzyme glyceraldehyde-3-phosphate dehydrogenase (gapdh gene). The data show that the growth and survival rate of this species is not significantly impacted by a decrease in sea water pH of up to 0.5 units. Quantitative real-time PCR analysis indicated that there was no significant effect of growth in acidified sea water on the expression of the hsp70 gene. However, there was a consistent and significant increase in the expression of the gapdh gene at a pH of ~7.5 which indicated a possible disruption to oxidative metabolic processes. It was concluded that future predicted changes in sea water pH may have subtle effects on the physiology and metabolism of coastal and marine species which may be overlooked in studies of whole organism response.
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Krishnaswamy, Rahul, and David B. Wilson. "Construction and Characterization of anEscherichia coli Strain Genetically Engineered for Ni(II) Bioaccumulation." Applied and Environmental Microbiology 66, no. 12 (December 1, 2000): 5383–86. http://dx.doi.org/10.1128/aem.66.12.5383-5386.2000.
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ABSTRACT An Escherichia coli strain that accumulated Ni(II) was constructed by introducing the nixA gene (coding for a nickel transport system) from Helicobacter pylori into JM109 cells that expressed a glutathione S-transferase–pea metallothionein fusion protein. The resulting strain accumulated 15 μmol of Ni(II) per g (dry weight) from a 10 μM Ni(II) solution, four times the level taken up by JM109 cells. Ni(II) accumulation did not require an energy source, was inhibited by only 50% by 0.1 M NaCl, and occurred over the pH range from 3 to 9.
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STEPHENSON, DENNIS A., EDWARD K. NOVAK, and VERNE M. CHAPMAN. "Analysis of the Kit and Pdgfra genes in the patch-extended (Phe) mutation." Genetical Research 72, no. 3 (December 1998): 205–10. http://dx.doi.org/10.1017/s0016672398003425.
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The patch (Ph) locus allele, patch-extended (Phe), has significantly less pigmentation than the original mutation and homozygotes have been known to survive to term. Analysing inter- subspecific F1 hybrids, we were able to demonstrate that Phe is a deletional mutation encompassing the platelet-derived growth factor receptor alpha subunit (Pdgfra). The deletion does not appear to extend into the coding sequence of the Kit gene (a related tyrosine kinase receptor). However, we were able to demonstrate that, while the Kit gene is transcribed, it does not encode a functionally active receptor.
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Song, Shaojie, Meng Gao, Weiqi Xu, Jingyuan Shao, Guoliang Shi, Shuxiao Wang, Yuxuan Wang, Yele Sun, and Michael B. McElroy. "Fine-particle pH for Beijing winter haze as inferred from different thermodynamic equilibrium models." Atmospheric Chemistry and Physics 18, no. 10 (May 28, 2018): 7423–38. http://dx.doi.org/10.5194/acp-18-7423-2018.
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Abstract. pH is an important property of aerosol particles but is difficult to measure directly. Several studies have estimated the pH values for fine particles in northern China winter haze using thermodynamic models (i.e., E-AIM and ISORROPIA) and ambient measurements. The reported pH values differ widely, ranging from close to 0 (highly acidic) to as high as 7 (neutral). In order to understand the reason for this discrepancy, we calculated pH values using these models with different assumptions with regard to model inputs and particle phase states. We find that the large discrepancy is due primarily to differences in the model assumptions adopted in previous studies. Calculations using only aerosol-phase composition as inputs (i.e., reverse mode) are sensitive to the measurement errors of ionic species, and inferred pH values exhibit a bimodal distribution, with peaks between −2 and 2 and between 7 and 10, depending on whether anions or cations are in excess. Calculations using total (gas plus aerosol phase) measurements as inputs (i.e., forward mode) are affected much less by these measurement errors. In future studies, the reverse mode should be avoided whereas the forward mode should be used. Forward-mode calculations in this and previous studies collectively indicate a moderately acidic condition (pH from about 4 to about 5) for fine particles in northern China winter haze, indicating further that ammonia plays an important role in determining this property. The assumed particle phase state, either stable (solid plus liquid) or metastable (only liquid), does not significantly impact pH predictions. The unrealistic pH values of about 7 in a few previous studies (using the standard ISORROPIA model and stable state assumption) resulted from coding errors in the model, which have been identified and fixed in this study.
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Mathlouthi, A., E. Pennacchietti, and D. De Biase. "Effect of Temperature, pH and Plasmids on In Vitro Biofilm Formation in Escherichia coli." Acta Naturae 10, no. 4 (December 15, 2018): 129–32. http://dx.doi.org/10.32607/20758251-2018-10-4-129-132.
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Acid resistance (AR) in Escherichia coli is an important trait that protects this microorganism from the deleterious effect of low-pH environments. Reports on biofilm formation in E. coli K12 showed that the genes participating in AR were differentially expressed. Herein, we investigated the relationship between AR genes, in particular those coding for specific transcriptional regulators, and their biofilm-forming ability at the phenotypic level. The latter was measured in 96-well plates by staining the bacteria attached to the well, following 24-hour growth under static conditions, with crystal violet. The growth conditions were as follows: Luria Bertani (LB) medium at neutral and acidic pH, at 37C or 25C. We observed that the three major transcriptional regulators of the AR genes (gadX, gadE, gadW) only marginally affected biofilm formation in E. coli. However, a striking and novel finding was the different abilities of all the tested E. coli strains to form a biofilm depending on the temperature and pH of the medium: LB, pH 7.4, strongly supported biofilm formation at 25C, with biofilm being hardly detectable at 37C. On the contrary, LB, pH 5.5, best supported biofilm formation at 37C. Moreover, we observed that when E. coli carried a plasmid, the presence of the plasmid itself affected the ability to develop a biofilm, typically by increasing its formation. This phenomenon varies from plasmid to plasmid, depends on growth conditions, and, to the best of our knowledge, remains largely uninvestigated.
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Chalfant, Michael L., Jerod S. Denton, Bakhram K. Berdiev, Iskander I. Ismailov, Dale J. Benos, and Bruce A. Stanton. "Intracellular H+ regulates the α-subunit of ENaC, the epithelial Na+ channel." American Journal of Physiology-Cell Physiology 276, no. 2 (February 1, 1999): C477—C486. http://dx.doi.org/10.1152/ajpcell.1999.276.2.c477.
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Protons regulate electrogenic sodium absorption in a variety of epithelia, including the cortical collecting duct, frog skin, and urinary bladder. Recently, three subunits (α, β, γ) coding for the epithelial sodium channel (ENaC) were cloned. However, it is not known whether pH regulates Na+ channels directly by interacting with one of the three ENaC subunits or indirectly by interacting with a regulatory protein. As a first step to identifying the molecular mechanisms of proton-mediated regulation of apical membrane Na+ permeability in epithelia, we examined the effect of pH on the biophysical properties of ENaC. To this end, we expressed various combinations of α-, β-, and γ-subunits of ENaC in Xenopusoocytes and studied ENaC currents by the two-electrode voltage-clamp and patch-clamp techniques. In addition, the effect of pH on the α-ENaC subunit was examined in planar lipid bilayers. We report that α,β,γ-ENaC currents were regulated by changes in intracellular pH (pHi) but not by changes in extracellular pH (pHo). Acidification reduced and alkalization increased channel activity by a voltage-independent mechanism. Moreover, a reduction of pHi reduced single-channel open probability, reduced single-channel open time, and increased single-channel closed time without altering single-channel conductance. Acidification of the cytoplasmic solution also inhibited α,β-ENaC, α,γ-ENaC, and α-ENaC currents. We conclude that pHi but not pHo regulates ENaC and that the α-ENaC subunit is regulated directly by pHi.
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MERKEL, Olaf, Olga V. OSKOLKOVA, Florian RAAB, Rosemarie EL-TOUKHY, and Fritz PALTAUF. "Regulation of activity in vitro and in vivo of three phospholipases B from Saccharomyces cerevisiae." Biochemical Journal 387, no. 2 (April 5, 2005): 489–96. http://dx.doi.org/10.1042/bj20041272.
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The genome of the yeast, Saccharomyces cerevisiae, contains three highly similar genes coding for phospholipases B/lysophospholipases. These enzymes behave differently with respect to substrate preferences in vitro and relative contributions to phospholipid catabolism in vivo [Merkel, Fido, Mayr, Prüger, Raab, Zandonella, Kohlwein and Paltauf (1999) J. Biol. Chem. 274, 28121–28127]. It is shown in the present study that, in vitro, pH markedly affects the substrate preference of Plb1p and Plb2p, but not of Plb3p. At the pH optimum of 2.5–3.5, the order of substrate preference of Plb1p and Plb2p is PtdSer (phosphatidylserine)>PtdIns>PtdCho (phosphatidylcholine>PtdEtn (phosphatidylethanolamine). At pH values of 5 and above, the substrate preferences change to PtdCho=PtdEtn for Plb1p and PtdSer=PtdEtn for Plb2p. Accordingly, with cultured cells the ratio of PtdIns/PtdCho breakdown, as reflected in the ratio of GroPIns (glycerophosphoinositol)/GroPCho (glycerophosphocholine) released into the culture medium, is inversely related to the pH of the growth medium. This effect is ascribed to the pH response of Plb1p, because Plb2p does not contribute to the degradation of PtdIns and PtdCho in vivo. Bivalent and tervalent cations activate phospholipases B at pH 5.5, but are inhibitory at pH 2.5. Al3+ at a concentration of 20 mM increases Plb1p activity in vitro by 8-fold and leads to a 9-fold increase in GroPCho release by whole cells. In vivo, cycloheximide strongly inhibits the breakdown of PtdIns, and to a lesser extent PtdCho. However, Al3+-stimulated GroPCho release is almost completely inhibited by cycloheximide. Deletion of PLB3 leads to increased sensitivity to toxic Al3+. Addition of SDS or melittin to cultured cells leads to a significant increase in phospholipid degradation, which is insensitive to inhibition by cycloheximide. Deletion mutants defective in the PLB1 gene are significantly more resistant to SDS than are wild-type cells.
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Joshi, Sachindra Raj, Atsushi Kitagawa, Christina Jacob, Ryota Hashimoto, Vidhi Dhagia, Amrit Ramesh, Connie Zheng, et al. "Hypoxic activation of glucose-6-phosphate dehydrogenase controls the expression of genes involved in the pathogenesis of pulmonary hypertension through the regulation of DNA methylation." American Journal of Physiology-Lung Cellular and Molecular Physiology 318, no. 4 (April 1, 2020): L773—L786. http://dx.doi.org/10.1152/ajplung.00001.2020.
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Metabolic reprogramming is considered important in the pathogenesis of the occlusive vasculopathy observed in pulmonary hypertension (PH). However, the mechanisms that link reprogrammed metabolism to aberrant expression of genes, which modulate functional phenotypes of cells in PH, remain enigmatic. Herein, we demonstrate that, in mice, hypoxia-induced PH was prevented by glucose-6-phosphate dehydrogenase deficiency (G6PDDef), and further show that established severe PH in Cyp2c44−/− mice was attenuated by knockdown with G6PD shRNA or by G6PD inhibition with an inhibitor (N-ethyl-N′-[(3β,5α)-17-oxoandrostan-3-yl]urea, NEOU). Mechanistically, G6PDDef, knockdown and inhibition in lungs: 1) reduced hypoxia-induced changes in cytoplasmic and mitochondrial metabolism, 2) increased expression of Tet methylcytosine dioxygenase 2 ( Tet2) gene, and 3) upregulated expression of the coding genes and long noncoding (lnc) RNA Pint, which inhibits cell growth, by hypomethylating the promoter flanking region downstream of the transcription start site. These results suggest functional TET2 is required for G6PD inhibition to increase gene expression and to reverse hypoxia-induced PH in mice. Furthermore, the inhibitor of G6PD activity (NEOU) decreased metabolic reprogramming, upregulated TET2 and lncPINT, and inhibited growth of control and diseased smooth muscle cells isolated from pulmonary arteries of normal individuals and idiopathic-PAH patients, respectively. Collectively, these findings demonstrate a previously unrecognized function for G6PD as a regulator of DNA methylation. These findings further suggest that G6PD acts as a link between reprogrammed metabolism and aberrant gene regulation and plays a crucial role in regulating the phenotype of cells implicated in the pathogenesis of PH, a debilitating disorder with a high mortality rate.
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Korbsrisate, Sunee, Nuttiga Suwanasai, Amornrut Leelaporn, Takayuki Ezaki, Yoshiaki Kawamura, and Suttipant Sarasombath. "Cloning and Characterization of a Nonhemolytic Phospholipase C Gene from Burkholderia pseudomallei." Journal of Clinical Microbiology 37, no. 11 (1999): 3742–45. http://dx.doi.org/10.1128/jcm.37.11.3742-3745.1999.
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We cloned and characterized a phosphatidylcholine-hydrolyzing phospholipase C (PC-PLC) gene from Burkholderia pseudomallei. DNA sequence analysis of the gene indicated an open reading frame coding for 700 amino acids with a 34-amino-acid signal peptide. When cleaved, this yields a secreted 73-kDa mature protein. The deduced amino acid sequence exhibited 48% similarity to that of a nonhemolytic PLC from Pseudomonas aeruginosa. The expressed PC-PLC was heat stable, nonhemolytic for sheep erythrocytes, and active between pH 2 and 8. Western blot analysis with sera from melioidosis patients indicated that they produced immunoglobulin M antibodies against this PC-PLC protein.
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Transy, C., S. R. Nash, B. David-Watine, M. Cochet, S. W. Hunt, L. E. Hood, and P. Kourilsky. "A low polymorphic mouse H-2 class I gene from the Tla complex is expressed in a broad variety of cell types." Journal of Experimental Medicine 166, no. 2 (August 1, 1987): 341–61. http://dx.doi.org/10.1084/jem.166.2.341.
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We have previously described the isolation of pH-2d-37, a cDNA clone that encodes a so far unknown, poorly polymorphic, class I surface molecule. We report here the isolation of the corresponding gene, its nucleotide sequence, and its localization in the Tla region of the murine MHC. Using a RNase mapping assay, we have confirmed that the second domain coding region of the 37 gene displays very limited polymorphism, and that the gene is transcribed in a broad variety of cell types, in contrast to the genes encoding the known Qa and TL antigens. Possible functions are discussed.
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Meschaninova, Mariya I., Nina S. Entelis, Elena L. Chernolovskaya, and Alya G. Venyaminova. "A Versatile Solid-Phase Approach to the Synthesis of Oligonucleotide Conjugates with Biodegradable Hydrazone Linker." Molecules 26, no. 8 (April 7, 2021): 2119. http://dx.doi.org/10.3390/molecules26082119.
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One of the ways to efficiently deliver various drugs, including therapeutic nucleic acids, into the cells is conjugating them with different transport ligands via labile or stable bonds. A convenient solid-phase approach for the synthesis of 5′-conjugates of oligonucleotides with biodegradable pH-sensitive hydrazone covalent bonds is proposed in this article. The approach relies on introducing a hydrazide of the ligand under aqueous/organic media to a fully protected support-bound oligonucleotide containing aldehyde function at the 5′-end. We demonstrated the proof-of-principle of this approach by synthesizing 5′-lipophilic (e.g., cholesterol and α-tocopherol) conjugates of modified siRNA and non-coding RNAs imported into mitochondria (antireplicative RNAs and guide RNAs for Mito-CRISPR/system). The developed method has the potential to be extended for the synthesis of pH-sensitive conjugates of oligonucleotides of different types (ribo-, deoxyribo-, 2′-O-methylribo-, and others) with ligands of different nature.
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Dmitryjuk, M., M. Dopieralska, E. Łopieńska-Biernat, and R. J. Frączek. "Purification and partial biochemical–genetic characterization of trehalose 6-phosphate synthase from muscles of adult femaleAscaris suum." Journal of Helminthology 87, no. 2 (May 9, 2012): 212–21. http://dx.doi.org/10.1017/s0022149x12000259.
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AbstractTrehalose 6-phosphate (T6P) synthase (TPS;EC2.4.1.15) was isolated from muscles ofAscaris suumby ammonium sulphate fractionation, ion-exchange DEAE SEPHACELTManion exchanger column chromatography and Sepharose 6B gel filtration. On sodium dodecyl sulphate–polyacrylamide gel electrophoresis (SDS–PAGE), 265-fold purified TPS exhibited a molecular weight of 66 kDa. The optimum pH and temperature of the purified enzyme were 3.8–4.2 and 35°C, respectively. The isoelectric point (pI) of TPS was pH 5.4. The studied TPS was not absolutely substrate specific. Besides glucose 6-phosphate, the enzyme was able to use fructose 6-phosphate as an acceptor of glucose. TPS was activated by 10 mMMgCl2, 10 mMCaCl2and 10 mMNaCl. In addition, it was inhibited by ethylenediaminetetra-acetic acid (EDTA), KCl, FeCl3and ZnCl2. Two genes encoding TPS were isolated and sequenced from muscles of the parasite. Complete coding sequences fortps1(JF412033.2) andtps2(JF412034.2) were 3917 bp and 3976 bp, respectively. Translation products (AEX60788.1 and AEX60787.1) showed expression to the glucosyltransferase-GTB-type superfamily.
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Ma, Wanpeng, Haifeng Lu, and Bing Yan. "A new strategy to fabricate multifunctional luminescent MOFs, extending their application range from pH sensing to amino acid information coding." Journal of Colloid and Interface Science 601 (November 2021): 427–36. http://dx.doi.org/10.1016/j.jcis.2021.05.136.
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Sakoda, H., and T. Imanaka. "Cloning and sequencing of the gene coding for alcohol dehydrogenase of Bacillus stearothermophilus and rational shift of the optimum pH." Journal of Bacteriology 174, no. 4 (1992): 1397–402. http://dx.doi.org/10.1128/jb.174.4.1397-1402.1992.
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Tummala, Seshu B., Neil E. Welker, and Eleftherios T. Papoutsakis. "Development and Characterization of a Gene Expression Reporter System for Clostridium acetobutylicumATCC 824." Applied and Environmental Microbiology 65, no. 9 (September 1, 1999): 3793–99. http://dx.doi.org/10.1128/aem.65.9.3793-3799.1999.
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ABSTRACT A gene expression reporter system (pHT3) for Clostridium acetobutylicum ATCC 824 was developed by using thelacZ gene from Thermoanaerobacterium thermosulfurogenes EM1 as the reporter gene. In order to test the reporter system, promoters of three key metabolic pathway genes,ptb (coding for phosphotransbutyrylase), thl(coding for thiolase), and adc (coding for acetoacetate decarboxylase), were cloned upstream of the reporter gene in pHT3 in order to construct vectors pHT4, pHT5, and pHTA, respectively. Detection of β-galactosidase activity in time course studies performed with strains ATCC 824(pHT4), ATCC 824(pHT5), and ATCC 824(pHTA) demonstrated that the reporter gene produced a functional β-galactosidase in C. acetobutylicum. In addition, time course studies revealed differences in the β-galactosidase specific activity profiles of strains ATCC 824(pHT4), ATCC 824(pHT5), and ATCC 824(pHTA), suggesting that the reporter system developed in this study is able to effectively distinguish between different promoters. The stability of the β-galactosidase produced by the reporter gene was also examined with strains ATCC 824(pHT4) and ATCC 824(pHT5) by using chloramphenicol treatment to inhibit protein synthesis. The data indicated that the β-galactosidase produced by the lacZgene from T. thermosulfurogenes EM1 was stable in the exponential phase of growth. In pH-controlled fermentations of ATCC 824(pHT4), the kinetics of β-galactosidase formation from theptb promoter and phosphotransbutyrylase formation from its own autologous promoter were found to be similar.
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Pajor, Ana M., and Nina N. Sun. "Molecular cloning, chromosomal organization, and functional characterization of a sodium-dicarboxylate cotransporter from mouse kidney." American Journal of Physiology-Renal Physiology 279, no. 3 (September 1, 2000): F482—F490. http://dx.doi.org/10.1152/ajprenal.2000.279.3.f482.
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The sodium-dicarboxylate cotransporter of the renal proximal tubule, NaDC-1, reabsorbs filtered Krebs cycle intermediates and plays an important role in the regulation of urinary citrate concentrations.1 Low urinary citrate is a risk factor for the development of kidney stones. As an initial step in the characterization of NaDC-1 regulation, the genomic structure and functional properties of the mouse Na+-dicarboxylate cotransporter (mNaDC-1) were determined. The gene coding for mNaDC-1, Slc13a2, is found on chromosome 11. The gene is ∼24.9 kb in length and contains 12 exons. The mRNA coding for mNaDC-1 is found in kidney and small intestine. Expression of mNaDC-1 in Xenopus laevis oocytes results in increased transport of di- and tricarboxylates. The Michaelis-Menten constant ( K m) for succinate was 0.35 mM, and the K m for citrate was 0.6 mM. The transport of citrate was stimulated by acidic pH, whereas the transport of succinate was insensitive to pH changes. Transport by mNaDC-1 is electrogenic, and substrates produced inward currents in the presence of sodium. The sodium affinity was relatively high in mNaDC-1, with half-saturation constants for sodium of 10 mM (radiotracer experiments) and 28 mM at −50 mV (2-electrode voltage clamp experiments). Lithium acts as a potent inhibitor of transport, but it can also partially substitute for sodium. In conclusion, the mNaDC-1 is related in sequence and function to the other NaDC-1 orthologs. However, its function more closely resembles the rabbit and human orthologs rather than the rat NaDC-1, with which it shares higher sequence similarity.
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Zhang, Shilong, Yujiao Li, Feng Han, and Wengong Yu. "YsHyl8A, an Alkalophilic Cold-Adapted Glycosaminoglycan Lyase Cloned from Pathogenic Yersinia sp. 298." Molecules 27, no. 9 (May 2, 2022): 2897. http://dx.doi.org/10.3390/molecules27092897.
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A high enzyme-yield strain Yersinia sp. 298 was screened from marine bacteria harvested from the coastal water. The screening conditions were extensive, utilizing hyaluronic acid (HA)/chondroitin sulfate (CS) as the carbon source. A coding gene yshyl8A of the family 8 polysaccharide lyase (PL8) was cloned from the genome of Yersinia sp. 298 and subjected to recombinant expression. The specific activity of the recombinase YsHyl8A was 11.19 U/mg, with an optimal reaction temperature of 40 °C and 50% of its specific activity remaining after thermal incubation at 30 °C for 1 h. In addition, its optimal reaction pH was 7.5, and while it was most stable at pH 6.0 in Na2HPO4-citric acid buffer, it remained highly stable at pH 6.0–11.0. Further, its enzymatic activity was increased five-fold with 0.1 M NaCl. YsHyl8A, as an endo-lyase, can degrade both HA and CS, producing disaccharide end-products. These properties suggested that YsHyl8A possessed both significant alkalophilic and cold-adapted features while being dependent on NaCl, likely resulting from its marine source. Yersinia is a typical fish pathogen, with glycosaminoglycan lyase (GAG lyase) as a potential pathogenic factor, exhibiting strong hyaluronidase and chondroitinase activity. Further research on the pathogenic mechanism of GAG lyase may benefit the prevention and treatment of related diseases.
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Marshall, Aaron J., Hiroaki Niiro, Cara G. Lerner, Theodore J. Yun, Sushma Thomas, Christine M. Disteche, and Edward A. Clark. "A Novel B Lymphocyte–Associated Adaptor Protein, Bam32, Regulates Antigen Receptor Signaling Downstream of Phosphatidylinositol 3-Kinase." Journal of Experimental Medicine 191, no. 8 (April 17, 2000): 1319–32. http://dx.doi.org/10.1084/jem.191.8.1319.
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We have identified and characterized a novel src homology 2 (SH2) and pleckstrin homology (PH) domain–containing adaptor protein, designated Bam32 (for B cell adaptor molecule of 32 kD). cDNAs encoding the human and mouse Bam32 coding sequences were isolated and the human bam32 gene was mapped to chromosome 4q25–q27. Bam32 is expressed by B lymphocytes, but not T lymphocytes or nonhematopoietic cells. Human germinal center B cells show increased Bam32 expression, and resting B cells rapidly upregulate expression of Bam32 after ligation of CD40, but not immunoglobulin M. Bam32 is tyrosine-phosphorylated upon B cell antigen receptor (BCR) ligation or pervanadate stimulation and associates with phospholipase Cγ2. After BCR ligation, Bam32 is recruited to the plasma membrane through its PH domain. Membrane recruitment requires phosphatidylinositol 3-kinase (PI3K) activity and an intact PI(3,4,5)P3-binding motif, suggesting that membrane association occurs through binding to 3-phosphoinositides. Expression of Bam32 in B cells leads to a dose-dependent inhibition of BCR-induced activation of nuclear factor of activated T cells (NF-AT), which is blocked by deletion of the PH domain or mutation of the PI(3,4,5)P3-binding motif. Thus, Bam32 represents a novel B cell–associated adaptor that regulates BCR signaling downstream of PI3K.
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Shibata, Mari, Hiroshi Ohkawa, Hirokazu Katoh, Masaya Shimoyama, and Teruo Ogawa. "Two CO2 uptake systems in cyanobacteria: four systems for inorganic carbon acquisition in Synechocystis sp. strain PCC6803." Functional Plant Biology 29, no. 3 (2002): 123. http://dx.doi.org/10.1071/pp01188.
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The cyanobacterium Synechocystis sp. strain PCC6803 possesses two CO2 uptake systems; one constitutive, dependent on NdhD3/NdhF3/CupA (Sll1734), and one low-CO2 inducible, dependent on NdhD4/NdhF4/CupB (Slr1302). Homologues of these genes are present in pairs in most cyanobacterial strains. Synechocystis PCC6803 also possesses two types of HCO3– transporters; an ATP-binding cassette (ABC)-type transporter encoded by the cmp operon, and a novel sodium-dependent transporter encoded byslr1512(sbtA) that plays a central role in HCO3– uptake. Mutants impaired for one of these four inorganic-carbon acquisition systems did not show mutant phenotype. Mutants inactivated for both CO2 uptake systems were unable to grow at pH 7.0 in air, although they grew normally at pH 9.0 in air. Additional inactivation of the SbtA-type HCO3– transporter abolished growth at pH 9.0 in air. A fragment containing the promoter region of ndhF3 fused to the coding region of luxAB was inserted into a neutral site of the ΔndhD4 mutant to construct apF3-lux/ ΔndhD4 strain. The luminescence intensity of this strain was low in high-CO2 grown cells, and was increased about 100 times after acclimation to air. Inactivation of the pF3-lux/ ΔndhD4 strain with a transposon-tagging library enabled us to isolate mutants incapable of acclimation to low CO2.
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Hartwich-Young, Rosi, Jon S. Nelson, and David L. Sparks. "The perihypoglossal projection to the superior colliculus in the rhesus monkey." Visual Neuroscience 4, no. 1 (January 1990): 29–42. http://dx.doi.org/10.1017/s0952523800002741.
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AbstractThe projection of the perihypoglossal (PH) complex to the superior colliculus (SC) in the rhesus monkey was investigated using the retrograde transport of wheat germ agglutinin conjugated to horseradish peroxidase (WGA-HRP). Following physiological identification by electrical stimulation and multiunit recording, small injections of the tracer were placed within the SC of three monkeys. The largest numbers of retrogradely labeled neurons within the PH complex were found in the contralateral nucleus prepositus hypoglossi (NPH), in the laterally adjacent medial vestibular nucleus, and in the ventrally adjacent reticular formation (the nucleus reticularis supragigantocellularis). These labeled neurons are strikingly heterogeneous in size and morphology. The nuclei supragenualis and intercalatus also contain numerous labeled neurons in the 2 cases in which the injections involve the caudal SC. Large numbers of retrogradely labeled neurons as well as anterogradely transported WGA-HRP are observed alo throughout the pontine and medullary reticular formation, including the midline raphe. The PH complex, particularly the NPH, is known to be involved in the coding of eye position and has been hypothesized to be a critical component of the “neural integrator.” Our data demonstrate the existence of a robust projection from the PH complex to the contralateral SC in the rhesus monkey. This projection may serve as the anatomical substrate by which a corollary of eye position could reach the SC. Such a signal is a prerequisite for the computation, at the collicular level, of saccadic motor error signals observed in the SC of rhesus monkeys.