Journal articles: 'PHOG'

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Imantoko, Imantoko, Arief Hermawan, and Donny Avianto. "Comparative analysis of support vector machine and k-nearest neighbors with a pyramidal histogram of the gradient for sign language detection." Matrix : Jurnal Manajemen Teknologi dan Informatika 11, no. 2 (July 15, 2021): 107–18. http://dx.doi.org/10.31940/matrix.v11i2.2433.

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The communication method using sign language is very efficient considering that the speed of information delivery is closer to verbal communication (speaking) compared to writing or typing. Because of this, sign language is often used by people who are deaf, speech impaired, and normal people to communicate. To make sign language translation easier, a system is needed to translate symbols formed from hand movements (in the form of images) into text or sound. This study aims to compare performance such as accuracy and computation time of Support Vector Machine (SVM) and K-Nearest Neighbors (KNN) with Pyramidal Histogram of Gradient (PHOG) for feature extraction, to know which one is better at recognizing sign language. Yield, both combined methods PHOG-SVM and PHOG-KNN can recognize images from hand movements that form certain symbols. The system built using the SVM classification produces the highest accuracy of 82% at PHOG level 3, while the system built with the KNN classification produces the highest accuracy of 78% at PHOG level 2. The total computation time of the fastest training and testing by the SVM model is 236.53 seconds at PHOG level 3, while the KNN model is 78.27 seconds at PHOG level 3. In terms of accuracy, PHOG-SVM is better, but in terms of computation time, PHOG-KNN takes the place.

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Spencer, John. "Blowing away the PHOG." Clinical Teacher 4, no. 1 (February 23, 2007): 1. http://dx.doi.org/10.1111/j.1743-498x.2007.00146.x.

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Ghorbel, Sofiane, Jan Kormanec, Alexandra Artus, and Marie-Joelle Virolle. "Transcriptional Studies and Regulatory Interactions between the phoR-phoP Operon and the phoU, mtpA, and ppk Genes of Streptomyces lividans TK24." Journal of Bacteriology 188, no. 2 (January 15, 2006): 677–86. http://dx.doi.org/10.1128/jb.188.2.677-686.2006.

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ABSTRACT The PhoR/PhoP two-component system of Streptomyces lividans was previously shown to allow the growth of the bacteria at low Pi concentrations and to negatively control antibiotic production. The present study focuses on the transcriptional analysis of phoR and phoP, along with the phoU and mtpA genes that are transcribed divergently from the phoRP operon in S. lividans. The effect of phoR, phoP, phoU, and ppk mutations on transcription of these genes was examined under phosphate-replete and phosphate-limited conditions. We demonstrated that phoR and phoP were cotranscribed as a leaderless bicistronic transcript cleaved at discrete sites toward the 3′ end of phoR. In addition, phoP could also be transcribed alone from a promoter located at the 3′ end of phoR. The phoU and mtpA genes, predicted to encode metal binding proteins, were shown to be transcribed as monocistronic transcripts. The expression of phoR-phoP, phoP, and phoU was found to be induced under conditions of Pi limitation in S. lividans TK24. This induction, requiring both PhoR and PhoP, was significantly weaker in the phoU mutant but much stronger in the ppk mutant than in the parental strain. The expression of mtpA was also shown to be up-regulated when Pi was limiting but independently of PhoR/PhoP. The induction of mtpA expression was much stronger in the phoU mutant strain than in the other strains. This study revealed interesting regulatory interactions between the different genes and allowed us to propose putative roles for PhoU and MtpA in the adaptation to phosphate scarcity.

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Antelmann, Haike, Christian Scharf, and Michael Hecker. "Phosphate Starvation-Inducible Proteins ofBacillus subtilis: Proteomics and Transcriptional Analysis." Journal of Bacteriology 182, no. 16 (August 15, 2000): 4478–90. http://dx.doi.org/10.1128/jb.182.16.4478-4490.2000.

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ABSTRACT The phosphate starvation response in Bacillus subtiliswas analyzed using two-dimensional (2D) polyacrylamide gel electrophoresis of cell extracts and supernatants from phosphate-starved cells. Most of the phosphate starvation-induced proteins are under the control of ςB, the activity of which is increased by energy depletion. In order to define the proteins belonging to the Pho regulon, which is regulated by the two-component regulatory proteins PhoP and PhoR, the 2D protein pattern of the wild type was compared with those of a sigB mutant and aphoR mutant. By matrix-assisted laser desorption ionization–time of flight mass spectrometry, two alkaline phosphatases (APases) (PhoA and PhoB), an APase-alkaline phosphodiesterase (PhoD), a glycerophosphoryl diester phosphodiesterase (GlpQ), and the lipoprotein YdhF were identified as very strongly induced PhoPR-dependent proteins secreted into the extracellular medium. In the cytoplasmic fraction, PstB1, PstB2, and TuaD were identified as already known PhoPR-dependent proteins, in addition to PhoB, PhoD, and the previously described PstS. Transcriptional studies of glpQ and ydhFconfirmed the strong PhoPR dependence. Northern hybridization and primer extension experiments showed that glpQ is transcribed monocistronically from a ςA promoter which is overlapped by four putative TT(A/T)ACA-like PhoP binding sites. Furthermore, ydhF might be cotranscribed withphoB initiating from the phoB promoter. Only a small group of proteins remained phosphate starvation inducible in bothphoR and sigB mutant and did not form a unique regulation group. Among these, YfhM and YjbC were controlled by ςB-dependent and unknown PhoPR-independent mechanisms. Furthermore, YtxH and YvyD seemed to be induced after phosphate starvation in the wild type in a ςB-dependent manner and in the sigB mutant probably via ςH. YxiE was induced by phosphate starvation independently of ςB and PhoPR.

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Vogel, K., W. Hörz, and A. Hinnen. "The two positively acting regulatory proteins PHO2 and PHO4 physically interact with PHO5 upstream activation regions." Molecular and Cellular Biology 9, no. 5 (May 1989): 2050–57. http://dx.doi.org/10.1128/mcb.9.5.2050-2057.1989.

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The repressible acid phosphatase gene PHO5 of Saccharomyces cerevisiae requires the two positively acting regulatory proteins PHO2 and PHO4 for expression. pho2 or pho4 mutants are not able to derepress the PHO5 gene under low-Pi conditions. Here we show that both PHO2 and PHO4 bind specifically to the PHO5 promoter in vitro. Gel retardation assays using promoter deletions revealed two regions involved in PHO4 binding. Further characterization by DNase I footprinting showed two protected areas, one located at -347 to -373 (relative to the ATG initiator codon) (UASp1) and the other located at -239 to -262 (UASp2). Exonuclease III footprint experiments revealed stops at -349 and -368 (UASp1) as well as at -245 and -260 (UASp2). Gel retardation assays with the PHO2 protein revealed a binding region that lay between the two PHO4-binding sites. DNase I footprint analysis suggested a PHO2-binding site covering the region between -277 and -296.

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Vogel, K., W. Hörz, and A. Hinnen. "The two positively acting regulatory proteins PHO2 and PHO4 physically interact with PHO5 upstream activation regions." Molecular and Cellular Biology 9, no. 5 (May 1989): 2050–57. http://dx.doi.org/10.1128/mcb.9.5.2050.

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The repressible acid phosphatase gene PHO5 of Saccharomyces cerevisiae requires the two positively acting regulatory proteins PHO2 and PHO4 for expression. pho2 or pho4 mutants are not able to derepress the PHO5 gene under low-Pi conditions. Here we show that both PHO2 and PHO4 bind specifically to the PHO5 promoter in vitro. Gel retardation assays using promoter deletions revealed two regions involved in PHO4 binding. Further characterization by DNase I footprinting showed two protected areas, one located at -347 to -373 (relative to the ATG initiator codon) (UASp1) and the other located at -239 to -262 (UASp2). Exonuclease III footprint experiments revealed stops at -349 and -368 (UASp1) as well as at -245 and -260 (UASp2). Gel retardation assays with the PHO2 protein revealed a binding region that lay between the two PHO4-binding sites. DNase I footprint analysis suggested a PHO2-binding site covering the region between -277 and -296.

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Adkins, Melissa W., Stephanie K. Williams, Jeffrey Linger, and Jessica K. Tyler. "Chromatin Disassembly from the PHO5 Promoter Is Essential for the Recruitment of the General Transcription Machinery and Coactivators." Molecular and Cellular Biology 27, no. 18 (July 9, 2007): 6372–82. http://dx.doi.org/10.1128/mcb.00981-07.

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ABSTRACT The disassembly of promoter nucleosomes appears to be a general property of highly transcribed eukaryotic genes. We have previously shown that the disassembly of chromatin from the promoters of the Saccharomyces cerevisiae PHO5 and PHO8 genes, mediated by the histone chaperone anti-silencing function 1 (Asf1), is essential for transcriptional activation upon phosphate depletion. This mechanism of transcriptional regulation is shared with the ADY2 and ADH2 genes upon glucose removal. Promoter chromatin disassembly by Asf1 is required for recruitment of TBP and RNA polymerase II, but not the Pho4 and Pho2 activators. Furthermore, accumulation of SWI/SNF and SAGA at the PHO5 promoter requires promoter chromatin disassembly. By contrast, the requirement for SWI/SNF and SAGA to facilitate Pho4 activator recruitment to the nucleosome-buried binding site in the PHO5 promoter occurs prior to chromatin disassembly and is distinct from the stable recruitment of SWI/SNF and SAGA that occurs after chromatin disassembly.

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Mutia, Cut, Fitri Arnia, and Rusdha Muharar. "Improving the Performance of CBIR on Islamic Women Apparels Using Normalized PHOG." Bulletin of Electrical Engineering and Informatics 6, no. 3 (September 1, 2017): 271–80. http://dx.doi.org/10.11591/eei.v6i3.657.

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The designs of Islamic women apparels is dynamically changing, which can be shown by emerging of online shops selling clothing with fast updates of newest models. Traditionally, buying the clothes online can be done by querying the keywords to the retrieval system. The approach has a drawback that the keywords cannot describe the clothes designs precisely. Therefore, a searching based on content–known as content-based image retrieval (CBIR)–is required. One of the features used in CBIR is the shape. This article presents a new normalization approach to the Pyramid Histogram of Oriented Gradients (PHOG) as a mean for shape feature extraction of women Islamic clothing in a retrieval system. We refer to the proposed approach as normalized PHOG (NPHOG). The Euclidean distance measured the similarity of the clothing. The performance of the system was evaluated by using 340 clothing images, comprised of four clothing categories, 85 images for each category: blouse-pants, long dress, outerwear, and tunic. The recall and precision parameters measured the retrieval performance; the Histogram of Oriented Gradients (HOG) and PHOG were the methods for comparison. The experiments showed that NPHOG improved the HOG and PHOG performance in three clothing categories.

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Mutia, Cut, and Muhammad Akmal. "Content Based Image Retrieval Busana Muslimah Menggunakan Fitur Kombinasi PHOG dan DCD." Jurnal Teknologi Informasi 5, no. 1 (June 29, 2021): 70–76. http://dx.doi.org/10.36294/jurti.v5i1.2021.

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Abstract - The development of Muslim clothing has increased significantly, especially in Indonesia, where the majority of the population is Muslim. Designers have appeared with a variety of fashion styles that attract consumers, especially young consumers. Technological developments have also influenced the way designers promote and sell their work by utilizing online commerce. So that consumers can search and find various models and colors of clothing that interest them. In this study, the search for Muslim clothing was carried out using the visual content of images or also known as features. The features used in this study are a combination of color and shape features, because shape and color are an attraction for consumers in choosing clothes. Search using image content as a query is known as CBIR. This study applies the PHOG as a shape feature extraction method and the DCD for the extraction of color features. The dataset used is 180 images of Muslim clothing. The performance of CBIR Muslim clothing using a combination of PHOG and DCD features is measured with recall, precision, and f-measure parameters. The results of the performance measurement show that the combination of PHOG and DCD features is better applied to blouse pants clothing. The highest scores were obtained from the red clothing group of 68% (P), 22.2%, and 33.3% (F). Then followed by a group of robes, and outerwear. Keywords - CBIR, PHOG, DCD, Feature and Clothing. Abstrak - Busana muslimah memiliki bentuk dan warna yang beragam dan menarik minat konsumen, banyak situs belanja online yang mempromosikan dan menjual produknya. Namun, pencarian busana muslimah pada situs tersebut masih menggunakan teks, sehingga hasil pencarian produknya sering tidak sesuai dengan harapan konsumen.Pada penelitian ini, pencarian busana muslimah dilakukan dengan menggunakan isi visual citra atau disebut juga sebagai fitur, adapun fitur yang digunakan adalah kombinasi fitur warna dan bentuk, karena bentuk (model) dan warna merupakakan daya tarik bagi konsumen dalam memilih busana. Pencarian menggunakan isi gambar sebagai query dikenal dengan Content Based Image Retrieval (CBIR). Penelitian ini menerapkan Pyramid Histogram of Oriented Gradient (PHOG) sebagai metode ekstraksi fitur bentuk dan Dominant Color Descriptor (DCD) untuk ekstraksi fitur warna. Dataset yang digunakan ada 180 citra busana muslimah, terdiri dari 60 citra blus celana, 60 gamis, dan 60 outerwear. Kemiripan query dengan dataset dilakukan dengan menghitung jarak Euclidean. Pengukuran Kinerja CBIR busana muslimah menggunakan kombinasi fitur PHOG dan DCD dilakukan dengan menghitung nilai recall, precision, dan f-measure. Hasil pengukuran kinerja menunjukkan bahwa kombinasi fitur PHOG dan DCD lebih baik diterapkan pada busana blus-celana. Berdasarkan pengukuruan kinerja dengan precision (P), recall (R0, dan f-measure (F). Nilai tertinggi diperoleh dari kelompok busana berwarna merah sebesar 68 % (P), 22.2%, dan 33.3 % (F). Kemudian diikuti dengan kelompok busana gamis, dan outerwear. Kata Kunci - CBIR, PHOG, DCD, Fitur dan Busana.

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Haldimann, Andreas, Larry L. Daniels, and Barry L. Wanner. "Use of New Methods for Construction of Tightly Regulated Arabinose and Rhamnose Promoter Fusions in Studies of theEscherichia coli Phosphate Regulon." Journal of Bacteriology 180, no. 5 (March 1, 1998): 1277–86. http://dx.doi.org/10.1128/jb.180.5.1277-1286.1998.

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ABSTRACT Escherichia coli genes regulated by environmental inorganic phosphate (Pi) levels form the phosphate (Pho) regulon. This regulation requires seven proteins, whose synthesis is under autogenous control, including response regulator PhoB, its partner, histidine sensor kinase PhoR, all four components of the Pi-specific transport (Pst) system (PstA, PstB, PstC, and PstS), and a protein of unknown function called PhoU. Here we examined the effects of uncoupling PhoB synthesis and PhoR synthesis from their normal controls by placing each under the tight control of the arabinose-regulated ParaB promoter or the rhamnose-regulated PrhaB promoter. To do this, we made allele replacement plasmids that may be generally useful for construction of ParaB orPrhaB fusions and for recombination of them onto the E. coli chromosome at the araCBAD orrhaRSBAD locus, respectively. Using strains carrying such single-copy fusions, we showed that a PrhaB fusion is more tightly regulated than a ParaB fusion in that a PrhaB-phoR + fusion but not a ParaB-phoR + fusion shows a null phenotype in the absence of its specific inducer. Yet in the absence of induction, bothParaB-phoB + andPrhaB-phoB + fusions exhibit a null phenotype. These data indicate that less PhoR than PhoB is required for transcriptional activation of the Pho regulon, which is consistent with their respective modes of action. We also used these fusions to study PhoU. Previously, we had constructed strains with precise ΔphoU mutations. However, we unexpectedly found that such ΔphoU mutants have a severe growth defect (P. M. Steed and B. L. Wanner, J. Bacteriol. 175:6797–6809, 1993). They also readily give rise to compensatory mutants with lesions inphoB, phoR, or a pst gene, making their study particularly difficult. Here we found that, by usingParaB-phoB +,PrhaB-phoB +, orPrhaB-phoR + fusions, we were able to overcome the extremely deleterious growth defect of a Pst+ ΔphoU mutant. The growth defect is apparently a consequence of high-level Pst synthesis resulting from autogenous control of PhoB and PhoR synthesis in the absence of PhoU.

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Abdel-Fattah, Wael R., Yinghua Chen, Amr Eldakak, and F. Marion Hulett. "Bacillus subtilis Phosphorylated PhoP: Direct Activation of the EσA- and Repression of the EσE-Responsive phoB-PS+V Promoters during Pho Response." Journal of Bacteriology 187, no. 15 (August 1, 2005): 5166–78. http://dx.doi.org/10.1128/jb.187.15.5166-5178.2005.

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ABSTRACT The phoB gene of Bacillus subtilis encodes an alkaline phosphatase (PhoB, formerly alkaline phosphatase III) that is expressed from separate promoters during phosphate deprivation in a PhoP-PhoR-dependent manner and at stage two of sporulation under phosphate-sufficient conditions independent of PhoP-PhoR. Isogenic strains containing either the complete phoB promoter or individual phoB promoter fusions were used to assess expression from each promoter under both induction conditions. The phoB promoter responsible for expression during sporulation, phoB-PS, was expressed in a wild-type strain during phosphate deprivation, but induction occurred >3 h later than induction of Pho regulon genes and the levels were approximately 50-fold lower than that observed for the PhoPR-dependent promoter, phoB-PV. EσE was necessary and sufficient for PS expression in vitro. PS expression in a phoPR mutant strain was delayed 2 to 3 h compared to the expression in a wild-type strain, suggesting that expression or activation of σE is delayed in a phoPR mutant under phosphate-deficient conditions, an observation consistent with a role for PhoPR in spore development under these conditions. Phosphorylated PhoP (PhoP∼P) repressed PS in vitro via direct binding to the promoter, the first example of an EσE-responsive promoter that is repressed by PhoP∼P. Whereas either PhoP or PhoP∼P in the presence of EσA was sufficient to stimulate transcription from the phoB-PV promoter in vitro, roughly 10- and 17-fold-higher concentrations of PhoP than of PhoP∼P were required for PV promoter activation and maximal promoter activity, respectively. The promoter for a second gene in the Pho regulon, ykoL, was also activated by elevated concentrations of unphosphorylated PhoP in vitro. However, because no Pho regulon gene expression was observed in vivo during Pi -replete growth and PhoP concentrations increased only threefold in vivo during phoPR autoinduction, a role for unphosphorylated PhoP in Pho regulon activation in vivo is not likely.

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Kaneko, Y., Y. Tamai, A. Toh-e, and Y. Oshima. "Transcriptional and post-transcriptional control of PHO8 expression by PHO regulatory genes in Saccharomyces cerevisiae." Molecular and Cellular Biology 5, no. 1 (January 1985): 248–52. http://dx.doi.org/10.1128/mcb.5.1.248-252.1985.

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A DNA fragment bearing the PHO8 gene, which encodes repressible alkaline phosphatase of Saccharomyces cerevisiae, was cloned. Northern hybridizations with the PHO8 DNA as probe indicated that the PHO8 transcript is 1.8 kilobases in length and is more abundant in cells grown in low-phosphate medium than in high-phosphate medium. The pho9 mutant, whose phenotype is defective in the activity of repressible alkaline phosphatase, produced as much of the PHO8 transcript as did the PHO9+ cells. Hence, the PHO9 product should act at the post-transcriptional level. The pho4 mutant could not derepress the PHO8 transcript, whereas the pho80 mutant could, irrespective of the amount of Pi in the medium, as has been suggested by genetic study.

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Kaneko, Y., Y. Tamai, A. Toh-e, and Y. Oshima. "Transcriptional and post-transcriptional control of PHO8 expression by PHO regulatory genes in Saccharomyces cerevisiae." Molecular and Cellular Biology 5, no. 1 (January 1985): 248–52. http://dx.doi.org/10.1128/mcb.5.1.248.

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A DNA fragment bearing the PHO8 gene, which encodes repressible alkaline phosphatase of Saccharomyces cerevisiae, was cloned. Northern hybridizations with the PHO8 DNA as probe indicated that the PHO8 transcript is 1.8 kilobases in length and is more abundant in cells grown in low-phosphate medium than in high-phosphate medium. The pho9 mutant, whose phenotype is defective in the activity of repressible alkaline phosphatase, produced as much of the PHO8 transcript as did the PHO9+ cells. Hence, the PHO9 product should act at the post-transcriptional level. The pho4 mutant could not derepress the PHO8 transcript, whereas the pho80 mutant could, irrespective of the amount of Pi in the medium, as has been suggested by genetic study.

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Lubin, Emma A., Jonathan T. Henry, Aretha Fiebig, Sean Crosson, and Michael T. Laub. "Identification of the PhoB Regulon and Role of PhoU in the Phosphate Starvation Response of Caulobacter crescentus." Journal of Bacteriology 198, no. 1 (October 19, 2015): 187–200. http://dx.doi.org/10.1128/jb.00658-15.

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ABSTRACTAn ability to sense and respond to changes in extracellular phosphate is critical for the survival of most bacteria. ForCaulobacter crescentus, which typically lives in phosphate-limited environments, this process is especially crucial. Like many bacteria,Caulobacterresponds to phosphate limitation through a conserved two-component signaling pathway called PhoR-PhoB, but the direct regulon of PhoB in this organism is unknown. Here we used chromatin immunoprecipitation-DNA sequencing (ChIP-Seq) to map the global binding patterns of the phosphate-responsive transcriptional regulator PhoB under phosphate-limited and -replete conditions. Combined with genome-wide expression profiling, our work demonstrates that PhoB is induced to regulate nearly 50 genes under phosphate-starved conditions. The PhoB regulon is comprised primarily of genes known or predicted to helpCaulobacterscavenge for and import inorganic phosphate, including 15 different membrane transporters. We also investigated the regulatory role of PhoU, a widely conserved protein proposed to coordinate phosphate import with expression of the PhoB regulon by directly modulating the histidine kinase PhoR. However, our studies show that it likely does not play such a role inCaulobacter, as PhoU depletion has no significant effect on PhoB-dependent gene expression. Instead, cells lacking PhoU exhibit striking accumulation of large polyphosphate granules, suggesting that PhoU participates in controlling intracellular phosphate metabolism.IMPORTANCEThe transcription factor PhoB is widely conserved throughout the bacterial kingdom, where it helps organisms respond to phosphate limitation by driving the expression of a battery of genes. Most of what is known about PhoB and its target genes is derived from studies ofEscherichia coli. Our work documents the PhoB regulon inCaulobacter crescentus, and comparison to the regulon inE. colireveals significant differences, highlighting the evolutionary plasticity of transcriptional responses driven by highly conserved transcription factors. We also demonstrated that the conserved protein PhoU, which is implicated in bacterial persistence, does not regulate PhoB activity, as previously suggested. Instead, our results favor a model in which PhoU affects intracellular phosphate accumulation, possibly through the high-affinity phosphate transporter.

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Datta, Ruchira S., Christopher Meacham, Bushra Samad, Christoph Neyer, and Kimmen Sjölander. "Berkeley PHOG: PhyloFacts orthology group prediction web server." Nucleic Acids Research 37, suppl_2 (May 12, 2009): W84—W89. http://dx.doi.org/10.1093/nar/gkp373.

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Barbaric, Slobodan, Martin Münsterkötter, Colin Goding, and Wolfram Hörz. "Cooperative Pho2-Pho4 Interactions at thePHO5 Promoter Are Critical for Binding of Pho4 to UASp1 and for Efficient Transactivation by Pho4 at UASp2." Molecular and Cellular Biology 18, no. 5 (May 1, 1998): 2629–39. http://dx.doi.org/10.1128/mcb.18.5.2629.

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ABSTRACT The activation of the PHO5 gene in Saccharomyces cerevisiae in response to phosphate starvation critically depends on two transcriptional activators, the basic helix-loop-helix protein Pho4 and the homeodomain protein Pho2. Pho4 acts through two essential binding sites corresponding to the regulatory elements UASp1 and UASp2. Mutation of either of them results in a 10-fold decrease in promoter activity, and mutation of both sites renders the promoter totally uninducible. The role of Pho4 appears relatively straightforward, but the mechanism of action of Pho2 had remained elusive. By in vitro footprinting, we have recently mapped multiple Pho2 binding sites adjacent to the Pho4 sites, and by mutating them individually or in combination, we now show that each of them contributes toPHO5 promoter activity. Their function is not only to recruit Pho2 to the promoter but to allow cooperative binding of Pho4 together with Pho2. Cooperativity requires DNA binding of Pho2 to its target sites and Pho2-Pho4 interactions. A Pho4 derivative lacking the Pho2 interaction domain is unable to activate the promoter, but testing of UASp1 and UASp2 individually in a minimal CYC1 promoter reveals a striking difference between the two UAS elements. UASp1 is fully inactive, presumably because the Pho4 derivative is not recruited to its binding site. In contrast, UASp2 activates strongly in a Pho2-independent manner. From in vivo footprinting experiments and activity measurements with a promoter variant containing two UASp2 elements, we conclude that at UASp2, Pho2 is mainly required for the ability of Pho4 to transactivate.

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Ertel, Franziska, A. Barbara Dirac-Svejstrup, Christina Bech Hertel, Dorothea Blaschke, Jesper Q. Svejstrup, and Philipp Korber. "In Vitro Reconstitution of PHO5 Promoter Chromatin Remodeling Points to a Role for Activator-Nucleosome Competition In Vivo." Molecular and Cellular Biology 30, no. 16 (June 21, 2010): 4060–76. http://dx.doi.org/10.1128/mcb.01399-09.

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ABSTRACT The yeast PHO5 promoter is a classical model for studying the role of chromatin in gene regulation. To enable biochemical dissection of the mechanism leading to PHO5 activation, we reconstituted the process in vitro. Positioned nucleosomes corresponding to the repressed PHO5 promoter state were assembled using a yeast extract-based in vitro system. Addition of the transactivator Pho4 yielded an extensive DNase I-hypersensitive site resembling induced PHO5 promoter chromatin. Importantly, this remodeling was energy dependent. In contrast, little or no chromatin remodeling was detected at the PHO8 or PHO84 promoter in this in vitro system. Only the PHO5 promoter harbors a high-affinity intranucleosomal Pho4 binding site (UASp) where Pho4 binding can compete with nucleosome formation, prompting us to test the importance of such competition for chromatin remodeling by analysis of UASp mutants in vivo. Indeed, the intranucleosomal location of the UASp element was critical, but not essential, for complete remodeling at the PHO5 promoter in vivo. Further, binding of just the Gal4 DNA binding domain to an intranucleosomal site could increase PHO5 promoter opening. These data establish an auxiliary role for DNA binding competition between Pho4 and histones in PHO5 promoter chromatin remodeling in vivo.

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Swarnkar, SK, A. Khunteta, MK Gupta, P. Jain, and S. Paliwal. "Pharmacognostic, Phytochemical and Pharmacological Review of “Phog”- Calligonum polygonoides L." Journal of Drug Delivery and Therapeutics 9, no. 2 (March 15, 2019): 469–73. http://dx.doi.org/10.22270/jddt.v9i2.2384.

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Calligonum polygonoides (Phog) belongs to family Polygonaceae. It is a geographically widely distributed shrub seen from the arctic to the tropics. This endangered plant (included in Red data book of IUCN) is morphologically having stem with nodes and internodes, white flowers in spike inflorescence and needle like leaves. It is traditionally used to stabilize sand dunes, as fuel, and in treatment of heat-stroke by mixing with curd or “Rayata”. It is also reported as antidote for opium poisoning. Various phyto-chemicals present include butanolides- calligonolides A and B, various flavanoids like kaempferol, quercetin and their derivatives. Various steroidal compounds are reported in roots. Pharmacologicallly, its cytotoxic, anti-inflammatory, antioxidant, antifungal and biosorbent potentials are reported by various researchers. Therefore, an attempt has been made to accumulate properties of this potential herb. Keywords: Calligonum, Phog, biosorbent, heat-stroke, calligonolides, kaempferol

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Monds, Russell D., Peter D. Newell, Julia A. Schwartzman, and George A. O'Toole. "Conservation of the Pho regulon in Pseudomonas fluorescens Pf0-1." Applied and Environmental Microbiology 72, no. 3 (March 2006): 1910–24. http://dx.doi.org/10.1128/aem.72.3.1910-1924.2006.

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ABSTRACT The Pho regulon integrates the sensing of environmental inorganic phosphate (Pi) availability with coregulation of gene expression, mediating an adaptive response to Pi limitation. Many aspects of the Pho regulon have been addressed in studies of Escherichia coli; however, it is unclear how transferable this knowledge is to other bacterial systems. Here, we report work to discern the conservation of the Pho regulon in Pseudomonas fluorescens Pf0-1. We demonstrate by mutational studies that PhoB/PhoR and the Pst system have conserved functions in the regulation of Pi-induced phosphatase activities, as well as expression of other Pi-regulated genes. A genetic screen was carried out to isolate factors that affect Pho-regulated phosphatase activity. We identified the Pho-regulated phosphatases PhoX and PhoD and present evidence that these enzymes are exported via the Tat system. The phoX and phoD genes were shown to be members of the Pho regulon by reverse transcription-PCR, as well as by functional assessment of putative PhoB binding sites (Pho boxes). Our data also suggested that at least one other non-Tat-secreted Pho-regulated phosphatase exists. From the genetic screen, numerous siderophore mutants that displayed severe defects in Pho-activated phosphatase activity were isolated. Subsequently, iron was shown to be important for modulating the activity of Pho-regulated phosphatases, but it does not regulate this activity at the level of transcription. We also identify and demonstrate a novel role in siderophore production and Pho-regulated phosphatase activity for ApaH, the hydrolase for the nucleotide-signaling molecule AppppA. Finally, numerous mutations in multiple cellular pathways were recovered that may be required for maximal induction of the Pho regulon under Pi-limiting conditions.

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Zhao, Zheng-Yang, Wen-Zhun Huang, Xin-Ke Zhan, Jie Pan, Yu-An Huang, Shan-Wen Zhang, and Chang-Qing Yu. "An Ensemble Learning-Based Method for Inferring Drug-Target Interactions Combining Protein Sequences and Drug Fingerprints." BioMed Research International 2021 (April 24, 2021): 1–12. http://dx.doi.org/10.1155/2021/9933873.

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Identifying the interactions of the drug-target is central to the cognate areas including drug discovery and drug reposition. Although the high-throughput biotechnologies have made tremendous progress, the indispensable clinical trials remain to be expensive, laborious, and intricate. Therefore, a convenient and reliable computer-aided method has become the focus on inferring drug-target interactions (DTIs). In this research, we propose a novel computational model integrating a pyramid histogram of oriented gradients (PHOG), Position-Specific Scoring Matrix (PSSM), and rotation forest (RF) classifier for identifying DTIs. Specifically, protein primary sequences are first converted into PSSMs to describe the potential biological evolution information. After that, PHOG is employed to mine the highly representative features of PSSM from multiple pyramid levels, and the complete describers of drug-target pairs are generated by combining the molecular substructure fingerprints and PHOG features. Finally, we feed the complete describers into the RF classifier for effective prediction. The experiments of 5-fold Cross-Validations (CV) yield mean accuracies of 88.96%, 86.37%, 82.88%, and 76.92% on four golden standard data sets (enzyme, ion channel, G protein-coupled receptors (GPCRs), and nuclear receptor, respectively). Moreover, the paper also conducts the state-of-art light gradient boosting machine (LGBM) and support vector machine (SVM) to further verify the performance of the proposed model. The experimental outcomes substantiate that the established model is feasible and reliable to predict DTIs. There is an excellent prospect that our model is capable of predicting DTIs as an efficient tool on a large scale.

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Zhang, Likun, Xiaoyan Li, Yi Tang, Fangbin Song, Tian Xia, and Wei Wang. "Contemporary Advertising Text Art Design and Effect Evaluation by IoT Deep Learning under the Smart City." Security and Communication Networks 2022 (July 22, 2022): 1–14. http://dx.doi.org/10.1155/2022/5161398.

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This work intends to solve the problem that the current artistic typeface generation methods rely too much on manual intervention, lack novelty, and the single font local feature and the global feature extraction method cannot fully describe the font features. Firstly, it proposes a handwritten word recognition model based on generalized search trees (GIST) and the pyramid histogram of oriented gradient (PHOG). The local features and global features of the font are fused. Secondly, a model of automatic artistic typeface generation based on generative adversarial networks (GAN) is constructed, which can use hand-drawn fonts to automatically generate artistic typefaces in the desired style through training as needed. Finally, the generation of the huaniao typeface is used as an example. By constructing the dataset, the effectiveness of the two models is verified. The experimental results show the following: (1) The proposed handwritten character recognition model based on GIST and PHOG has a higher recognition rate of different fonts than the single GIST and PHOG features by more than 5.8%. The total recognition time is reduced by more than 49.4%, and the performance is improved significantly. (2) Compared with other popular algorithms, the constructed GAN-based automatic artistic typeface generation model has the best quality of the generation of huaniao on both the pencil sketch and the calligraphy character image dataset. Models have broad application prospects in contemporary advertising text art design. This study aims to provide important technical support for the automation of contemporary advertising text art design and the improvement of overall efficiency.

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Biasotti, S., A. Cerri, D. Giorgi, and M. Spagnuolo. "PHOG: Photometric and geometric functions for textured shape retrieval." Computer Graphics Forum 32, no. 5 (August 2013): 13–22. http://dx.doi.org/10.1111/cgf.12168.

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ZHANG, BAILING, and YIFAN ZHOU. "VEHICLE TYPE AND MAKE RECOGNITION BY COMBINED FEATURES AND ROTATION FOREST ENSEMBLE." International Journal of Pattern Recognition and Artificial Intelligence 26, no. 03 (May 2012): 1250004. http://dx.doi.org/10.1142/s0218001412500048.

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Vehicle type/make recognition based on images captured by surveillance cameras is a challenging task in intelligent transportation system and automatic surveillance. In this paper, we comparatively studied two feature extraction methods for image description, i.e. a new multiresolution analysis tool called Fast Discrete Curvelet Transform and the pyramid histogram of oriented gradients (PHOG). Curvelet Transform has better directional and edge representation abilities than widely used wavelet transform, which is particularly appropriate for the description of images rich with edges. PHOG represents the local shape by a histogram of edge orientations computed for each image sub-region, quantized into a number of bins, thus has the ascendency in its description of more discriminating information. A composite feature description from PHOG and Curvelet can further increase the accuracy of classification by taking their complementary information. We also investigated the applicability of the Rotation Forest (RF) ensemble method for vehicle classification based on the combined features. The RF ensemble contains a set of base multilayer perceptrons which are trained using principal component analysis to rotate the original axes of combined features of vehicle images. The class label is assigned by the ensemble via majority voting. Experimental results using more than 600 images from 21 makes of cars/vans show the effectiveness of the proposed approach. The composite feature is better than any single feature in the classification accuracy and the ensemble model produces better performance compared to any of the individual neural network base classifier. With a moderate ensemble size of 20, the Rotation Forest ensembles offers a classification rate close to 96.5%, exhibiting promising potentials for real-life applications.

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Gupta, Sankalp, Anuj Pathak, Akesh Sinha, and Dibyendu Sarkar. "Mycobacterium tuberculosis PhoP Recognizes Two Adjacent Direct-Repeat Sequences To Form Head-to-Head Dimers." Journal of Bacteriology 191, no. 24 (October 9, 2009): 7466–76. http://dx.doi.org/10.1128/jb.00669-09.

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ABSTRACT Mycobacterium tuberculosis PhoP of the PhoP-PhoR two-component signaling system orchestrates a complex transcription program and is essential for the growth and virulence of the tubercle bacillus. PhoP comprises a phosphorylation domain at the amino-terminal half and a DNA-binding domain in the carboxy-terminal half of the protein. We show here that the protein recognizes a 23-bp sequence of the phoP upstream region comprising two adjacent direct repeat motifs believed to promote transcription regulation. DNA binding, which involves the recruitment of two monomeric PhoP molecules, was dependent on conserved adenines of the repeat sequences and the orientation of the repeat motifs relative to each other. Although response regulators such as PhoB and FixJ dimerize upon phosphorylation, we demonstrate here that PhoP dimerization can also be stimulated by DNA binding. Using the established asymmetric tandem binding model by members of the OmpR/PhoB protein family as a guide, we set out to examine intermolecular interactions between PhoP dimers by protein cross-linking. Our results are consistent with a model in which two PhoP protomers bind the duplex DNA with a symmetric head-to-head orientation to project their N termini toward one another, arguing against previously proposed head-to-tail tandem dimer formation for members of the OmpR/PhoB protein subfamily.

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Sharan, Ankit. "Finger Print Matching Based on Miniature and Phog Feature Extraction." International Journal for Research in Applied Science and Engineering Technology 10, no. 4 (April 30, 2022): 1816–18. http://dx.doi.org/10.22214/ijraset.2022.41635.

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Zhou, Yanwen, Tingxi Zhang, Shengyan Jin, Siyu Chen, and Yinlong Zhang. "Effects of Escherichia coli Alkaline Phosphatase PhoA on the Mineralization of Dissolved Organic Phosphorus." Water 13, no. 23 (November 23, 2021): 3315. http://dx.doi.org/10.3390/w13233315.

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Alkaline phosphatases, which play the key role in the mineralization of organic phosphorus, have been grouped into three distinct families, PhoA, PhoX, and PhoD. PhoA is still an important component of the Pho regulon for many microbes although its distribution is not as wide as that of PhoX and PhoD. However, several questions remain unclear about the effect of PhoA mineralization of dissolved organic phosphorus. In this study, the role of Escherichia coli alkaline phosphatase PhoA (hereinafter referred to as PhoA) in the mineralization of different organic phosphorus including phosphate monoesters, phosphate diesters, and phytic acids was investigated. The influence of the reaction time, organic phosphorus concentration, and L-amino acid on PhoA mineralization was examined. The results show that PhoA specifically hydrolyzes phosphate monoesters except for phytic acid and the optimal reaction time is around 12 h. The PhoA mineralization rate of glucose 6-phosphate disodium (G6P), 5′-adenosine monophosphate (AMP), and sodium glycerophosphate (BGP) significantly decreased by 38.01%, 55.31%, and 57.08%, respectively (p < 0.01), while the concentration of organic phosphorus increased from 0.50 to 5.00 mg/L. Overall, L-amino acids inhibited PhoA mineralization in a concentration-independent manner. The inhibitory effect of neutral amino acids serine (L-Ser) and tyrosine (L-Tyr) was significantly higher than that of basic amino acids arginine (L-Arg), lysine (L-Lys), and histidine (L-His). All the five amino acids can inhibit PhoA mineralization of AMP, with the highest inhibition rate observed for L-Tyr (23.77%), the lowest—for L-Arg (1.54%). Compared with other L-amino acids, L-Tyr has the highest G6P and BGP mineralization inhibition rate, with the average inhibition rates of 12.89% and 11.65%, respectively. This study provides meaningful information to better understand PhoA mineralization.

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Bardin, Sylvie D., and Turlough M. Finan. "Regulation of Phosphate Assimilation in Rhizobium (Sinorhizobium) meliloti." Genetics 148, no. 4 (April 1, 1998): 1689–700. http://dx.doi.org/10.1093/genetics/148.4.1689.

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Abstract We report the isolation of phoB and phoU mutants of the bacterium Rhizobium (Sinorhizobium) meliloti. These mutants form N2-fixing nodules on the roots of alfalfa plants. R. meliloti mutants defective in the phoCDET (ndvF) encoded phosphate transport system grow slowly in media containing 2 mm Pi, and form nodules which fail to fix nitrogen (Fix−). We show that the transfer of phoB or phoU insertion mutations into phoC mutant strains restores the ability of these mutants to: (i) form normal N2-fixing root-nodules, and (ii) grow like the wild type in media containing 2 mm Pi. We also show that expression of the alternate orfA pit encoded Pi transport system is negatively regulated by the phoB gene product, whereas phoB is required for phoCDET expression. We suggest that in R. meliloti cells growing under Pi limiting conditions, PhoB protein activates phoCDET transcription and represses orfA pit transcription. Our results suggest that there are major differences between the Escherichia coli and R. meliloti phosphate regulatory systems.

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Bachhawat, Priti, and Ann M. Stock. "Crystal Structures of the Receiver Domain of the Response Regulator PhoP from Escherichia coli in the Absence and Presence of the Phosphoryl Analog Beryllofluoride." Journal of Bacteriology 189, no. 16 (June 1, 2007): 5987–95. http://dx.doi.org/10.1128/jb.00049-07.

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ABSTRACT The response regulator PhoP is part of the PhoQ/PhoP two-component system involved in responses to depletion of extracellular Mg2+. Here, we report the crystal structures of the receiver domain of Escherichia coli PhoP determined in the absence and presence of the phosphoryl analog beryllofluoride. In the presence of beryllofluoride, the active receiver domain forms a twofold symmetric dimer similar to that seen in structures of other regulatory domains from the OmpR/PhoB family, providing further evidence that members of this family utilize a common mode of dimerization in the active state. In the absence of activating agents, the PhoP receiver domain crystallizes with a similar structure, consistent with the previous observation that high concentrations can promote an active state of PhoP independent of phosphorylation.

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Zhang, Shanwen, Yihai Zhu, Zhuhong You, and Xiaowei Wu. "Fusion of superpixel, expectation maximization and PHOG for recognizing cucumber diseases." Computers and Electronics in Agriculture 140 (August 2017): 338–47. http://dx.doi.org/10.1016/j.compag.2017.06.016.

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Chen, Jun, Li Hua Guo, and Yang Bai. "A Fusion Method of Smile and Laugh Expression Classification." Applied Mechanics and Materials 58-60 (June 2011): 2364–69. http://dx.doi.org/10.4028/www.scientific.net/amm.58-60.2364.

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This paper proposed to build a smile expression classification system on data sets of GENKI that can represent real-world environments, and tested its implementation, in which we got the optimal recognition rate up to 86.197%. To deal with the features extraction problems, hybrid features (i.e., Gabor, PHOG, PLBP) are used, using hybrid recognition algorithms (i.e., GentleBoost, SVM) to classify, in this paper. Experiments showed the effectiveness of our methods.

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Jia, Shi Jie, Yan Ping Yang, Jian Ying Zhao, and Nan Xiao. "Pyramid Histograms of Orientated Gradients for Product Image Retrieval." Advanced Materials Research 383-390 (November 2011): 5712–16. http://dx.doi.org/10.4028/www.scientific.net/amr.383-390.5712.

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Traditional text-based image retrieval methods are hard to meet the requirements of on-line product search. This paper applied Content Based Image Retrieval (CBIR) technologies to e-commerce field and designed a product image retrieval algorithm based on Pyramid Histograms of Orientated Gradients (PHOG) descriptor and chi-square distance. By constructing the image retrieval system, we made retrieval tests on PI100 dataset from Microsoft Research Asia. The experimental results proved the efficiency of this algorithm.

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Sugiharto, Aris, Agus Harjoko, and Suharto Suharto. "Indonesian traffic sign detection based on Haar-PHOG features and SVM classification." International Journal on Smart Sensing and Intelligent Systems 13, no. 1 (2020): 1–15. http://dx.doi.org/10.21307/ijssis-2020-026.

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Jia, Shi Jie, Yu Ting Zhai, and Xiao Wei Jia. "Detection of Traffic and Road Condition Based on Adaboost." Applied Mechanics and Materials 433-435 (October 2013): 1357–60. http://dx.doi.org/10.4028/www.scientific.net/amm.433-435.1357.

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In order to avoid the drawbacks of physical detection methods, such as spoiling the road, having complex algorithms and affected by weather factors, the detection methods of traffic and road condition are explored using the Adaboost algorithm and its three variants based on PHOG (pyramid histogram of edge orientation gradients) image feature. Experimental results show that this method can effectively classify 4 types of traffic and road condition images, and Gentle Adaboost algorithm has the best performance for the noisy samples.

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Lejona, Sergio, Andrés Aguirre, María Laura Cabeza, Eleonora García Véscovi, and Fernando C. Soncini. "Molecular Characterization of the Mg2+-Responsive PhoP-PhoQ Regulon in Salmonella enterica." Journal of Bacteriology 185, no. 21 (November 1, 2003): 6287–94. http://dx.doi.org/10.1128/jb.185.21.6287-6294.2003.

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ABSTRACT The PhoP/PhoQ two-component system controls the extracellular magnesium deprivation response in Salmonella enterica. In addition, several virulence-associated genes that are mainly required for intramacrophage survival during the infection process are under the control of its transcriptional regulation. Despite shared Mg2+ modulation of the expression of the PhoP-activated genes, no consensus sequence common to all of them could be detected in their promoter regions. We have investigated the transcriptional regulation and the interaction of the response regulator PhoP with the promoter regions of the PhoP-activated loci phoPQ, mgtA, slyB, pmrD, pcgL, phoN, pagC, and mgtCB. A direct repeat of the heptanucleotide sequence (G/T)GTTTA(A/T) was identified as the conserved motif recognized by PhoP to directly control the gene expression of the first five loci, among which the first four are ancestral to enterobacteria. On the other hand, no direct interaction of the response regulator with the promoter of phoN, pagC, or mgtCB was apparent by either in vitro or in vivo assays. These loci are Salmonella specific and were probably acquired by horizontal DNA transfer. Besides, sequence analysis of pag promoters revealed the presence of a conserved PhoP box in 6 out of the 12 genes analyzed. Our results strongly suggest that the expression of a set of Mg2+-controlled genes is driven by PhoP via unknown intermediate regulatory mechanisms that could also involve ancillary factors.

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Apel, Alexander K., Alberto Sola-Landa, Antonio Rodríguez-García, and Juan F. Martín. "Phosphate control of phoA, phoC and phoD gene expression in Streptomyces coelicolor reveals significant differences in binding of PhoP to their promoter regions." Microbiology 153, no. 10 (October 1, 2007): 3527–37. http://dx.doi.org/10.1099/mic.0.2007/007070-0.

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Fernanda Januar Pratama, Wikky Fawwaz Al Maki, and Febryanti Sthevanie. "Big Cats Classification Based on Body Covering." Jurnal RESTI (Rekayasa Sistem dan Teknologi Informasi) 5, no. 5 (October 31, 2021): 984–91. http://dx.doi.org/10.29207/resti.v5i5.3328.

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The reduced habitat owned by an animal has a very bad impact on the survival of the animal, resulting in a continuous decrease in the number of animal populations especially in animals belonging to the big cat family such as tigers, cheetahs, jaguars, and others. To overcome the decline in the animal population, a classification model was built to classify images that focuses on the pattern of body covering possessed by animals. However, in designing an accurate classification model with an optimal level of accuracy, it is necessary to consider many aspects such as the dataset used, the number of parameters, and computation time. In this study, we propose an animal image classification model that focuses on animal body covering by combining the Pyramid Histogram of Oriented Gradient (PHOG) as the feature extraction method and the Support Vector Machine (SVM) as the classifier. Initially, the input image is processed to take the body covering pattern of the animal and converted it into a grayscale image. Then, the image is segmented by employing the median filter and the Otsu method. Therefore, the noise contained in the image can be removed and the image can be segmented. The results of the segmentation image are then extracted by using the PHOG and then proceed with the classification process by implementing the SVM. The experimental results showed that the classification model has an accuracy of 91.07%.

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MA Shi-wei, 马世伟, 刘丽娜 LIU Li-na, 傅. 琪. FU Qi, and 温加睿 WEN Jia-rui. "Using PHOG fusion features and multi-class Adaboost classifier for human behavior recognition." Optics and Precision Engineering 26, no. 11 (2018): 2827–37. http://dx.doi.org/10.3788/ope.20182611.2827.

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Ellison, J. "PHOG, a candidate gene for involvement in the short stature of Turner syndrome." Human Molecular Genetics 6, no. 8 (August 1, 1997): 1341–47. http://dx.doi.org/10.1093/hmg/6.8.1341.

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Li, Zisheng, Jun-ichi Imai, and Masahide Kaneko. "Facial Expression Recognition Using Facial-component-based Bag of Words and PHOG Descriptors." Journal of The Institute of Image Information and Television Engineers 64, no. 2 (2010): 230–36. http://dx.doi.org/10.3169/itej.64.230.

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Gour, Neha, and Pritee Khanna. "Automated glaucoma detection using GIST and pyramid histogram of oriented gradients (PHOG) descriptors." Pattern Recognition Letters 137 (September 2020): 3–11. http://dx.doi.org/10.1016/j.patrec.2019.04.004.

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Sarangi, Partha Pratim, Bhabani Shankar Prasad Mishra, and Satchidanand Dehuri. "Fusion of PHOG and LDP local descriptors for kernel-based ear biometric recognition." Multimedia Tools and Applications 78, no. 8 (August 25, 2018): 9595–623. http://dx.doi.org/10.1007/s11042-018-6489-0.

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Haswell, Elizabeth S., and Erin K. O’Shea. "An In Vitro System Recapitulates Chromatin Remodeling at the PHO5 Promoter." Molecular and Cellular Biology 19, no. 4 (April 1, 1999): 2817–27. http://dx.doi.org/10.1128/mcb.19.4.2817.

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ABSTRACT The Saccharomyces cerevisiae gene PHO5 is an excellent system with which to study regulated changes in chromatin structure. The PHO5 promoter is packaged into four positioned nucleosomes under repressing conditions; upon induction, the structure of these nucleosomes is altered such that the promoter DNA becomes accessible to nucleases. We report here the development and characterization of an in vitro system in which partially purified PHO5 minichromosomes undergo promoter chromatin remodeling. Several hallmarks of thePHO5 chromatin transition in vivo were reproduced in this system. Chromatin remodeling of PHO5minichromosomes required the transcription factors Pho4 and Pho2, was localized to the promoter region of PHO5, and was independent of the chromatin-remodeling complex Swi-Snf. In vitro chromatin remodeling also required the addition of fractionated nuclear extract and hydrolyzable ATP. This in vitro system should serve as a useful tool for identifying the components required for this reaction and for elucidating the mechanism by which the PHO5promoter chromatin structure is changed.

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Kageyama, Hakuto, Keshawanand Tripathi, Ashwani K. Rai, Suriyan Cha-um, Rungaroon Waditee-Sirisattha, and Teruhiro Takabe. "An Alkaline Phosphatase/Phosphodiesterase, PhoD, Induced by Salt Stress and Secreted Out of the Cells of Aphanothece halophytica, a Halotolerant Cyanobacterium." Applied and Environmental Microbiology 77, no. 15 (June 10, 2011): 5178–83. http://dx.doi.org/10.1128/aem.00667-11.

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ABSTRACTAlkaline phosphatases (APases) are important enzymes in organophosphate utilization. Three prokaryotic APase gene families, PhoA, PhoX, and PhoD, are known; however, their functional characterization in cyanobacteria largely remains to be clarified. In this study, we cloned thephoDgene from a halotolerant cyanobacterium,Aphanothece halophytica(phoDAp). The deduced protein, PhoDAp, contains Tat consensus motifs and a peptidase cleavage site at the N terminus. The PhoDApenzyme was activated by Ca2+and exhibited APase and phosphodiesterase (APDase) activities. Subcellular localization experiments revealed the secretion and processing of PhoDApin a transformed cyanobacterium. Expression of thephoDApgene inA. halophyticacells was upregulated not only by phosphorus (P) starvation but also under salt stress conditions. Our results suggest thatA. halophyticacells possess a PhoD that participates in the assimilation of P under salinity stress.

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Sanowar, Sarah, Alexandre Martel, and Hervé Le Moual. "Mutational Analysis of the Residue at Position 48 in the Salmonella enterica Serovar Typhimurium PhoQ Sensor Kinase." Journal of Bacteriology 185, no. 6 (March 15, 2003): 1935–41. http://dx.doi.org/10.1128/jb.185.6.1935-1941.2003.

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ABSTRACT The PhoP/PhoQ two-component regulatory system of Salmonella enterica serovar Typhimurium plays an essential role in controlling virulence by mediating the adaptation to Mg2+ depletion. The pho-24 allele of phoQ harbors a single amino acid substitution (T48I) in the periplasmic domain of the PhoQ histidine kinase sensor. This mutation has been shown to increase net phosphorylation of the PhoP response regulator. We analyzed the effect on signaling by PhoP/PhoQ of various amino acid substitutions at this position (PhoQ-T48X [X = A, S, V, I, or L]). Mutations T48V, T48I, and T48L were found to affect signaling by PhoP/PhoQ both in vivo and in vitro. Mutations PhoQ-T48V and PhoQ-T48I increased both the expression of the mgtA::lacZ transcriptional fusion and the net phosphorylation of PhoP, conferring to cells a PhoP constitutively active phenotype. In contrast, mutation PhoQ-T48L barely responded to changes in the concentration of external Mg2+, in vivo and in vitro, conferring to cells a PhoP constitutively inactive phenotype. By analyzing in vitro the individual catalytic activities of the PhoQ-T48X sensors, we found that the PhoP constitutively active phenotype observed for the PhoQ-T48V and PhoQ-T48I proteins is solely due to decreased phosphatase activity. In contrast, the PhoP constitutively inactive phenotype observed for the PhoQ-T48L mutant resulted from both decreased autokinase activity and increased phosphatase activity. Our data are consistent with a model in which the residue at position 48 of PhoQ contributes to a conformational switch between kinase- and phosphatase-dominant states.

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Tait-Kamradt, A. G., K. J. Turner, R. A. Kramer, Q. D. Elliott, S. J. Bostian, G. P. Thill, D. T. Rogers, and K. A. Bostian. "Reciprocal regulation of the tandemly duplicated PHO5/PHO3 gene cluster within the acid phosphatase multigene family of Saccharomyces cerevisiae." Molecular and Cellular Biology 6, no. 6 (June 1986): 1855–65. http://dx.doi.org/10.1128/mcb.6.6.1855-1865.1986.

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We characterized the organization and expression of PHO5 and PHO3, the tightly linked repressible and constitutive acid phosphatase genes of Saccharomyces cerevisiae. The "constitutive" gene, PHO3, is expressed only when PHO5 is not. Altering PHO5 expression, either through promoter deletions or through mutations in trans-acting regulatory genes, showed that PHO5 expression is sufficient to block transcription of PHO3. An active genomic copy of PHO5 was able to block expression of PHO3 from a high-copy-number plasmid, showing that some trans-acting product of PHO5 is involved. This is probably a translation product, since the presence of a nontranslatable PHO5 RNA did not inhibit transcription of PHO3.

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Tait-Kamradt, A. G., K. J. Turner, R. A. Kramer, Q. D. Elliott, S. J. Bostian, G. P. Thill, D. T. Rogers, and K. A. Bostian. "Reciprocal regulation of the tandemly duplicated PHO5/PHO3 gene cluster within the acid phosphatase multigene family of Saccharomyces cerevisiae." Molecular and Cellular Biology 6, no. 6 (June 1986): 1855–65. http://dx.doi.org/10.1128/mcb.6.6.1855.

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We characterized the organization and expression of PHO5 and PHO3, the tightly linked repressible and constitutive acid phosphatase genes of Saccharomyces cerevisiae. The "constitutive" gene, PHO3, is expressed only when PHO5 is not. Altering PHO5 expression, either through promoter deletions or through mutations in trans-acting regulatory genes, showed that PHO5 expression is sufficient to block transcription of PHO3. An active genomic copy of PHO5 was able to block expression of PHO3 from a high-copy-number plasmid, showing that some trans-acting product of PHO5 is involved. This is probably a translation product, since the presence of a nontranslatable PHO5 RNA did not inhibit transcription of PHO3.

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Ahmad, Saeed, and Muhammad Akram. "Antifungal activity in the methanolic, aqueous and hexane extracts of Calligonum polygonoides." International Journal of Immunopathology and Pharmacology 33 (January 2019): 205873841882127. http://dx.doi.org/10.1177/2058738418821275.

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Calligonum polygonoides is locally called as Phog which belongs to the Polygonaceae family. It is traditionally used as an antifungal. The methanolic extract, hexane extract, ethyl acetate extract and aqueous extract were screened against Candida albicans and Aspergillus niger in seven concentrations, that is, 1.8, 2.9, 6.5, 12.6, 25, 50 and 75 µg/mL/disc. Calligonum polygonoides showed significant activity against Candida albicans as the observed minimum inhibitory concentration (MIC) is 6.5 µg/mL for methanolic extract, 9.8 µg/mL for ethyl acetate extract, whereas aqueous and hexane extracts showed no activity. Calligonum polygonoides did not show any significant activity against Aspergillus niger.

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Neef, Daniel W., and Michael P. Kladde. "Polyphosphate Loss Promotes SNF/SWI- and Gcn5-Dependent Mitotic Induction of PHO5." Molecular and Cellular Biology 23, no. 11 (June 1, 2003): 3788–97. http://dx.doi.org/10.1128/mcb.23.11.3788-3797.2003.

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ABSTRACT Approximately 800 transcripts in Saccharomyces cerevisiae are cell cycle regulated. The oscillation of ∼40% of these genes, including a prominent subclass involved in nutrient acquisition, is not understood. To address this problem, we focus on the mitosis-specific activation of the phosphate-responsive promoter, PHO5. We show that the unexpected mitotic induction of the PHO5 acid phosphatase in rich medium requires the transcriptional activators Pho4 and Pho2, the cyclin-dependent kinase inhibitor Pho81, and the chromatin-associated enzymes Gcn5 and Snf2/Swi2. PHO5 mitotic activation is repressed by addition of orthophosphate, which significantly increases cellular polyphosphate. Polyphosphate levels also fluctuate inversely with PHO5 mRNA during the cell cycle, further substantiating an antagonistic link between this phosphate polymer and PHO5 mitotic regulation. Moreover, deletion of PHM3, required for polyphosphate accumulation, leads to premature onset of PHO5 expression, as well as an increased rate, magnitude, and duration of PHO5 activation. Orthophosphate addition, however, represses mitotic PHO5 expression in a phm3Δ strain. Thus, polyphosphate per se is not necessary to repress PHO transcription but, when present, replenishes cellular phosphate during nutrient depletion. These results demonstrate a dynamic mechanism of mitotic transcriptional regulation that operates mostly independently of factors that drive progression through the cell cycle.

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Rice, Christopher D., Jacob E. Pollard, Zachery T. Lewis, and William R. McCleary. "Employment of a Promoter-Swapping Technique Shows that PhoU Modulates the Activity of the PstSCAB2 ABC Transporter in Escherichia coli." Applied and Environmental Microbiology 75, no. 3 (December 1, 2008): 573–82. http://dx.doi.org/10.1128/aem.01046-08.

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ABSTRACT Expression of the Pho regulon in Escherichia coli is induced in response to low levels of environmental phosphate (Pi). Under these conditions, the high-affinity PstSCAB2 protein (i.e., with two PstB proteins) is the primary Pi transporter. Expression from the pstSCAB-phoU operon is regulated by the PhoB/PhoR two-component regulatory system. PhoU is a negative regulator of the Pho regulon; however, the mechanism by which PhoU accomplishes this is currently unknown. Genetic studies of phoU have proven to be difficult because deletion of the phoU gene leads to a severe growth defect and creates strong selection for compensatory mutations resulting in confounding data. To overcome the instability of phoU deletions, we employed a promoter-swapping technique that places expression of the phoBR two-component system under control of the Ptac promoter and the lacO ID regulatory module. This technique may be generally applicable for controlling expression of other chromosomal genes in E. coli. Here we utilized PphoB ::Ptac and PpstS ::Ptac strains to characterize phenotypes resulting from various ΔphoU mutations. Our results indicate that PhoU controls the activity of the PstSCAB2 transporter, as well as its abundance within the cell. In addition, we used the PphoB ::Ptac ΔphoU strain as a platform to begin characterizing new phoU mutations in plasmids.

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Shang, Jinxia, Hua-Ping Guan, Yun Liu, Hongbo Bi, Lina Yang, and Minghui Wang. "A novel method for vehicle headlights detection using salient region segmentation and PHOG feature." Multimedia Tools and Applications 80, no. 15 (January 22, 2021): 22821–41. http://dx.doi.org/10.1007/s11042-020-10501-8.

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Journal articles on the topic 'PHOG'

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