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1
Zheng, Wangyang, Yuling Zheng, Xue Bai, et al. "RPNs Levels Are Prognostic and Diagnostic Markers for Hepatocellular Carcinoma." Journal of Oncology 2022 (August 29, 2022): 1–17. http://dx.doi.org/10.1155/2022/7270541.
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The ribophorin family (RPN) is an essential regulatory subunit of the proteasome. By influencing the ubiquitin-proteasome system activity, ribophorins (RPNs) are responsible for almost all physiology and pathology processes of mammalian cells. Nevertheless, little is known about the role of RPNs in HCC. In this work, we first evaluated the transcriptional levels and the prognostic and diagnostic value of RPNs based on the public database. Firstly, we found all RPNs were surprisingly consistently upregulated in HCC tissues. Moreover, the RPNs’ expression pattern is correlated with HCC tumor grade. The TCGA HCC platforms’ data indicated that RPN2, RPN3, RPN6, RPN9, RPN10, RPN11, and RPN12 have robust diagnosis values. Then, survival analysis revealed that the high expression of RPN1, RPN2, RPN4, RPN5, RPN6, RPN9, and RPN11 was correlated with unfavourable HCC overall survival. Then, genetic alteration, immune infiltration feature, gene-genes network, and functional enrichment for RPNs indicated that RPNs have many potential biosynthesis activities expert for UPS functions. Moreover, western blot and qRT-PCR results confirmed these results. The silencing of RPN6 and RPN9 significantly reduced HCC cells’ proliferation, migration, and invasion ability in vitro. An in vivo tumor model further validated the oncogene effect of RPN6 on HCC cell growth. Moreover, RPN6 and RPN9 could promote cell migratory and invasive potential by affecting the epithelial-mesenchymal transition (EMT) process. In summary, this study suggests that the RPN family has the potential to be potential biomarkers and targets for HCC.
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Chen, Ching-Han, Chien-Chun Wang, and Yan-Zhen Chen. "Intelligent Brushing Monitoring Using a Smart Toothbrush with Recurrent Probabilistic Neural Network." Sensors 21, no. 4 (2021): 1238. http://dx.doi.org/10.3390/s21041238.
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Smart toothbrushes equipped with inertial sensors are emerging as high-tech oral health products in personalized health care. The real-time signal processing of nine-axis inertial sensing and toothbrush posture recognition requires high computational resources. This paper proposes a recurrent probabilistic neural network (RPNN) for toothbrush posture recognition that demonstrates the advantages of low computational resources as a requirement, along with high recognition accuracy and efficiency. The RPNN model is trained for toothbrush posture recognition and brushing position and then monitors the correctness and integrity of the Bass Brushing Technique. Compared to conventional deep learning models, the recognition accuracy of RPNN is 99.08% in our experiments, which is 16.2% higher than that of the Convolutional Neural Network (CNN) and 21.21% higher than the Long Short-Term Memory (LSTM) model. The model we used can greatly reduce the computing power of hardware devices, and thus, our system can be used directly on smartphones.
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Schweitzer, Andreas, Antje Aufderheide, Till Rudack, et al. "Structure of the human 26S proteasome at a resolution of 3.9 Å." Proceedings of the National Academy of Sciences 113, no. 28 (2016): 7816–21. http://dx.doi.org/10.1073/pnas.1608050113.
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Protein degradation in eukaryotic cells is performed by the Ubiquitin-Proteasome System (UPS). The 26S proteasome holocomplex consists of a core particle (CP) that proteolytically degrades polyubiquitylated proteins, and a regulatory particle (RP) containing the AAA-ATPase module. This module controls access to the proteolytic chamber inside the CP and is surrounded by non-ATPase subunits (Rpns) that recognize substrates and deubiquitylate them before unfolding and degradation. The architecture of the 26S holocomplex is highly conserved between yeast and humans. The structure of the human 26S holocomplex described here reveals previously unidentified features of the AAA-ATPase heterohexamer. One subunit, Rpt6, has ADP bound, whereas the other five have ATP in their binding pockets. Rpt6 is structurally distinct from the other five Rpt subunits, most notably in its pore loop region. For Rpns, the map reveals two main, previously undetected, features: the C terminus of Rpn3 protrudes into the mouth of the ATPase ring; and Rpn1 and Rpn2, the largest proteasome subunits, are linked by an extended connection. The structural features of the 26S proteasome observed in this study are likely to be important for coordinating the proteasomal subunits during substrate processing.
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Chen, Ching-Han, Pi-Wei Chen, Pi-Jhong Chen, and Tzung-Hsin Liu. "Indoor Positioning Using Magnetic Fingerprint Map Captured by Magnetic Sensor Array." Sensors 21, no. 17 (2021): 5707. http://dx.doi.org/10.3390/s21175707.
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By collecting the magnetic field information of each spatial point, we can build a magnetic field fingerprint map. When the user is positioning, the magnetic field measured by the sensor is matched with the magnetic field fingerprint map to identify the user’s location. However, since the magnetic field is easily affected by external magnetic fields and magnetic storms, which can lead to “local temporal-spatial variation”, it is difficult to construct a stable and accurate magnetic field fingerprint map for indoor positioning. This research proposes a new magnetic indoor positioning method, which combines a magnetic sensor array composed of three magnetic sensors and a recurrent probabilistic neural network (RPNN) to realize a high-precision indoor positioning system. The magnetic sensor array can detect subtle magnetic anomalies and spatial variations to improve the stability and accuracy of magnetic field fingerprint maps, and the RPNN model is built for recognizing magnetic field fingerprint. We implement an embedded magnetic sensor array positioning system, which is evaluated in an experimental environment. Our method can reduce the noise caused by the spatial-temporal variation of the magnetic field, thus greatly improving the indoor positioning accuracy, reaching an average positioning accuracy of 0.78 m.
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Isono, Erika, Kiyoshi Nishihara, Yasushi Saeki, et al. "The Assembly Pathway of the 19S Regulatory Particle of the Yeast 26S Proteasome." Molecular Biology of the Cell 18, no. 2 (2007): 569–80. http://dx.doi.org/10.1091/mbc.e06-07-0635.
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The 26S proteasome consists of the 20S proteasome (core particle) and the 19S regulatory particle made of the base and lid substructures, and it is mainly localized in the nucleus in yeast. To examine how and where this huge enzyme complex is assembled, we performed biochemical and microscopic characterization of proteasomes produced in two lid mutants, rpn5-1 and rpn7-3, and a base mutant ΔN rpn2, of the yeast Saccharomyces cerevisiae. We found that, although lid formation was abolished in rpn5-1 mutant cells at the restrictive temperature, an apparently intact base was produced and localized in the nucleus. In contrast, in ΔN rpn2 cells, a free lid was formed and localized in the nucleus even at the restrictive temperature. These results indicate that the modules of the 26S proteasome, namely, the core particle, base, and lid, can be formed and imported into the nucleus independently of each other. Based on these observations, we propose a model for the assembly process of the yeast 26S proteasome.
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Pakan, Prisca, and Rocky Yefrenes Dillak. "KLASIFIKASI MUSIK MENGGUNAKAN POLYNOMIAL NEURAL NETWORK." Jurnal Ilmiah Flash 3, no. 2 (2017): 94. http://dx.doi.org/10.32511/jiflash.v3i2.144.
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Penelitian ini bertujuan mengembangkan suatu metode yang dapat digunakan untuk melakukanklasifikasi terhadap jenis musik berdasarkan file audio dengan format wav menggunakan algoritmaRidge Polynomial Neural Network (RPNN). Pengklasifikasian file audio ke dalam suatu kelompokatau kelas, memerlukan ciri atau fitur dari file audio tersebut. Metode ekstrak fitur yang digunakanuntuk memperoleh ciri atau fitur dari file yang dimaksud adalah Spectral Centroid (SC), SortTime Energy (STE) dan Zero Crossing Rate (ZCR) yang diturunkan dalam domain waktu (timedomain) yang merupakan salah satu komponen data audio. Berdasarkan hasil dari penelitian inimenunjukkan bahwa pendekatan yang diusulkan mampu melakukan klasifikasi terhadap jenis musikberdasarkan file audio berformat wav dengan akurasi sebesar 90%
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Pakan, Prisca, and Rocky Yefrenes Dillak. "KLASIFIKASI MUSIK MENGGUNAKAN POLYNOMIAL NEURAL NETWORK." Jurnal Ilmiah Flash 3, no. 2 (2017): 94. http://dx.doi.org/10.32511/flash.v3i2.144.
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Penelitian ini bertujuan mengembangkan suatu metode yang dapat digunakan untuk melakukanklasifikasi terhadap jenis musik berdasarkan file audio dengan format wav menggunakan algoritmaRidge Polynomial Neural Network (RPNN). Pengklasifikasian file audio ke dalam suatu kelompokatau kelas, memerlukan ciri atau fitur dari file audio tersebut. Metode ekstrak fitur yang digunakanuntuk memperoleh ciri atau fitur dari file yang dimaksud adalah Spectral Centroid (SC), SortTime Energy (STE) dan Zero Crossing Rate (ZCR) yang diturunkan dalam domain waktu (timedomain) yang merupakan salah satu komponen data audio. Berdasarkan hasil dari penelitian inimenunjukkan bahwa pendekatan yang diusulkan mampu melakukan klasifikasi terhadap jenis musikberdasarkan file audio berformat wav dengan akurasi sebesar 90%
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Cresti, Julianna R., Abramo J. Manfredonia, Christopher E. Bragança, et al. "Proteasomal conformation controls unfolding ability." Proceedings of the National Academy of Sciences 118, no. 25 (2021): e2101004118. http://dx.doi.org/10.1073/pnas.2101004118.
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The 26S proteasome is the macromolecular machine responsible for the bulk of protein degradation in eukaryotic cells. As it degrades a ubiquitinated protein, the proteasome transitions from a substrate-accepting conformation (s1) to a set of substrate-processing conformations (s3 like), each stabilized by different intramolecular contacts. Tools to study these conformational changes remain limited, and although several interactions have been proposed to be important for stabilizing the proteasome’s various conformations, it has been difficult to test these directly under equilibrium conditions. Here, we describe a conformationally sensitive Förster resonance energy transfer assay, in which fluorescent proteins are fused to Sem1 and Rpn6, which are nearer each other in substrate-processing conformations than in the substrate-accepting conformation. Using this assay, we find that two sets of interactions, one involving Rpn5 and another involving Rpn2, are both important for stabilizing substrate-processing conformations. Mutations that disrupt these interactions both destabilize substrate-processing conformations relative to the substrate-accepting conformation and diminish the proteasome’s ability to successfully unfold and degrade hard-to-unfold substrates, providing a link between the proteasome’s conformational state and its unfolding ability.
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Kalkanlı Genç, Şerife, Maria J. Diamantopoulou, and Ramazan Özçelik. "Tree Biomass Modeling Based on the Exploration of Regression and Artificial Neural Networks Approaches." Forests 14, no. 12 (2023): 2429. http://dx.doi.org/10.3390/f14122429.
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Understanding the dynamics of tree biomass is a significant factor in forest ecosystems, and accurate quantitative knowledge of its development provides support for the optimization of forest management. This work aimed to employ innovative practices in tree biomass modeling, artificial neural network approaches along with the least-squares regression methodology, in order to construct reliable and accurate estimation and prediction models that contribute to solving the emerging problems in the field of sustainable forest management. Based on this aim, different modeling strategies were developed and explored. The nonlinear seemingly unrelated regression (NSUR) methodology, the generalized regression (GRNN), the resilient propagation (RPNN) and the Bayesian regularization (BRNN) artificial neural network algorithms were utilized for the construction of reliable biomass models to attain the most accurate and reliable tree biomass components and total tree biomass estimations. The work showed that GRNN models provided a significantly better performance compared with the other modeling methodologies tested. Considering the non-parametric nature of the GRNN neural network algorithm, the fact that it was designed for nonlinear regression-type problems capable of dealing with small datasets, this modeling approach warrants consideration as an effective alternative to nonlinear regression or to other neural network approaches to the field of tree biomass modeling.
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Rosenzweig, Rina, Vered Bronner, Daoning Zhang, David Fushman, and Michael H. Glickman. "Rpn1 and Rpn2 Coordinate Ubiquitin Processing Factors at Proteasome." Journal of Biological Chemistry 287, no. 18 (2012): 14659–71. http://dx.doi.org/10.1074/jbc.m111.316323.
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Kajava, Andrey V. "What Curves α-Solenoids?" Journal of Biological Chemistry 277, № 51 (2002): 49791–98. http://dx.doi.org/10.1074/jbc.m204982200.
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The α-helical solenoid proteins adopt a variety of elongated curved structures. They have been examined to identify the interactions that determine their curvature. A sequence pattern characteristic for strongly curved α-helical solenoids has been constructed and was found to match protein sequences containing the proteasome/cyclosome repeats. Based on this, a structural model of the repeat-containing domains of the Rpn1/S2 and Rpn2/S1 proteins, which represent the largest subunits of the 26 S proteasome, has been proposed. The model has a novel architecture resembling an α-helical toroid. Molecular modeling shows that these toroids have a central pore that would allow passage of an unfolded protein substrate through it. This implies that the Rpn1 and Rpn2 toroids are aligned along the common axial pores of the ATPase hexamer and form an “antechamber” of the 26 S proteasome. The proposed quaternary structure agrees with the available experimental data. It is suggested that the function of this antechamber is assistance to the ATPases in the unfolding of protein substrates prior to proteolysis. An evolutionary link between the PC repeat-containing proteins and tetratricopeptide repeat proteins is proposed.
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Glickman, Michael H., David M. Rubin, Victor A. Fried, and Daniel Finley. "The Regulatory Particle of the Saccharomyces cerevisiae Proteasome." Molecular and Cellular Biology 18, no. 6 (1998): 3149–62. http://dx.doi.org/10.1128/mcb.18.6.3149.
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ABSTRACT The proteasome is a multisubunit protease responsible for degrading proteins conjugated to ubiquitin. The 670-kDa core particle of the proteasome contains the proteolytic active sites, which face an interior chamber within the particle and are thus protected from the cytoplasm. The entry of substrates into this chamber is thought to be governed by the regulatory particle of the proteasome, which covers the presumed channels leading into the interior of the core particle. We have resolved native yeast proteasomes into two electrophoretic variants and have shown that these represent core particles capped with one or two regulatory particles. To determine the subunit composition of the regulatory particle, yeast proteasomes were purified and analyzed by gradient sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Resolution of the individual polypeptides revealed 17 distinct proteins, whose identities were determined by amino acid sequence analysis. Six of the subunits have sequence features of ATPases (Rpt1 to Rpt6). Affinity chromatography was used to purify regulatory particles from various strains, each of which expressed one of the ATPases tagged with hexahistidine. In all cases, multiple untagged ATPases copurified, indicating that the ATPases assembled together into a heteromeric complex. Of the remaining 11 subunits that we have identified (Rpn1 to Rpn3 and Rpn5 to Rpn12), 8 are encoded by previously described genes and 3 are encoded by genes not previously characterized for yeasts. One of the previously unidentified subunits exhibits limited sequence similarity with deubiquitinating enzymes. Overall, regulatory particles from yeasts and mammals are remarkably similar, suggesting that the specific mechanistic features of the proteasome have been closely conserved over the course of evolution.
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Effantin, Grégory, Rina Rosenzweig, Michael H. Glickman та Alasdair C. Steven. "Electron Microscopic Evidence in Support of α-Solenoid Models of Proteasomal Subunits Rpn1 and Rpn2". Journal of Molecular Biology 386, № 5 (2009): 1204–11. http://dx.doi.org/10.1016/j.jmb.2009.01.039.
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Li, Ming, Anqing Chen, Peixiong Liu, Wenbo Ren, and Chenghao Zheng. "Multivariable Algorithm Using Signal-Processing Techniques to Identify Islanding Events in Utility Grid with Renewable Energy Penetration." Energies 17, no. 4 (2024): 877. http://dx.doi.org/10.3390/en17040877.
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This paper designs a multi-variable hybrid islanding-detection method (HIDM) using signal-processing techniques. The signals of current captured on a test system where the renewable energy (RE) penetration level is between 50% and 100% are processed by the application of the Stockwell transform (ST) to compute the Stockwell islanding-detection factor (SIDF) and the co-variance islanding-detection factor (CIDF). The signals of current are processed by the application of the Hilbert transform (HT), and the Hilbert islanding-detection factor (HIDF) is computed. The signals of current are also processed by the application of the Alienation Coefficient (ALC), and the Alienation Islanding Detection Factor (AIDF) is computed. A hybrid islanding-detection indicator (HIDI) is derived by multiplying the SIDF, CIDF, AIDF, and an islanding weight factor (IWF) element by element. Two thresholds, designated as the hybrid islanding-detection indicator threshold (HIDIT) and the hybrid islanding-detection indicator fault threshold (HIDIFT), are selected to detect events of islanding and also to discriminate such events from fault events and operational events. The HIDM is effectively tested using an IEEE-13 bus power network, where solar generation plants (SGPs) and wind generation plants (WGPs) are integrated. The HIDM effectively identified and discriminated against events such as islanding, faults, and operational. The HIDM is also effective at identifying islanding events on a real-time distribution feeder. The HIDM is also effective at detecting islanding events in the scenario of a 20dB signal-to-noise ratio (SNR). It is established that the HIDM has a small non-detection zone (NDZ). The effectiveness of the HIDM is better relative to the islanding-detection method (IDM) supported by the discrete wavelet transform (DWT), an IDM using a hybridization of the slantlet transform, and the Ridgelet probabilistic neural network (RPNN). An IDM using wavelet transform multi-resolution (WT-MRA)-based image data and an IDM based on the use of a deep neural network (DNN) were used. The study was performed using the MATLAB software (2017a) and validated in real-time using the data collected from a practical distribution power system network.
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Bai, Minghui, Xian Zhao, Kazutaka Sahara, et al. "In-depth Analysis of the Lid Subunits Assembly Mechanism in Mammals." Biomolecules 9, no. 6 (2019): 213. http://dx.doi.org/10.3390/biom9060213.
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The 26S proteasome is a key player in the degradation of ubiquitinated proteins, comprising a 20S core particle (CP) and a 19S regulatory particle (RP). The RP is further divided into base and lid subcomplexes, which are assembled independently from each other. We have previously demonstrated the assembly pathway of the CP and the base by observing assembly intermediates resulting from knockdowns of each proteasome subunit and the assembly chaperones. In this study, we examine the assembly pathway of the mammalian lid, which remains to be elucidated. We show that the lid assembly pathway is conserved between humans and yeast. The final step is the incorporation of Rpn12 into the assembly intermediate consisting of two modular complexes, Rpn3-7-15 and Rpn5-6-8-9-11, in both humans and yeast. Furthermore, we dissect the assembly pathways of the two modular complexes by the knockdown of each lid subunit.
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Ren, Jinhai, Ying Wang, Lihua Wang, Xiaoling Guo, and Xiaonan Guo. "Ribophorin II is upregulated in myelodysplastic syndromes and prevents apoptosis and cell cycle progression." Experimental Biology and Medicine 245, no. 12 (2020): 1009–15. http://dx.doi.org/10.1177/1535370220927996.
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Myelodysplastic syndromes (MDSs) are a series of heterogeneous diseases affecting hematopoietic stem cells that result in hematopoiesis disturbance and leukemic transformation. As an essential cell cycle regulator, ribophorin II (RPN2) has been extensively identified as a prospective predictor of prognosis in diverse malignant tumors. However, its effects on MDS are unclear. We observed increased mRNA expression RPN2 in samples from MDS patients, compared with samples from normal healthy controls. RPN2 overexpression promoted the proliferation of Ontario Cancer Institute OCI-acute myeloid leukemia 3 (OCI-AML3) cells, whereas RPN2 silencing clearly suppressed the proliferation of OCI-AML3 cells. Furthermore, RPN2 silencing caused G1/S cell cycle arrest and cell apoptosis. In addition, RPN2 overexpression led to a higher proportion of cells in the G2/M phase and reduced cell apoptosis. RPN2 overexpression downregulated enhancer of zeste homolog-2 (EZH2) expression, whereas RPN2 downregulation increased EZH2 expression in a dose-dependent manner. Co-immunoprecipitation showed an interaction between RPN2 and EZH2. Additionally, the administration of 3-deazaneplanocin A, an EZH2 inhibitor, reversed the function of RPN2 silencing in cell cycle arrest and apoptosis induction in OCI-AML3 cells. Hence, RPN2 is an essential regulator of cell proliferation. This study described the etiology of OCI-AML3 cell proliferation regulated by RPN2 and EZH2. Impact statement This study explored the role of ribophorin II (RPN2) in myelodysplastic syndromes (MDSs) cell proliferation and growth and revealed that RPN2 knockdown suppressed OCI-AML3 cell growth and proliferation and triggered cell cycle arrest and elicited apoptosis in OCI-AML3 cells. In addition, it shed light on the etiology of RPN2’s role in MDS cell proliferation that RPN2 can negatively impact enhancer of zeste homolog-2 (EZH2) expression, which in turn is able to modulate the cell cycle location and death in OCI-AML3 cells. Hence, RPN2 expression could be a latent predictor of prognosis in patients with MDS.
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Milcamps, Anne, Anne Van Dommelen, John Stigter, Jos Vanderleyden, and Frans J. de Bruijn. "TheAzospirillum brasilense rpoNgene is involved in nitrogen fixation, nitrate assimilation, ammonium uptake, and flagellar biosynthesis." Canadian Journal of Microbiology 42, no. 5 (1996): 467–78. http://dx.doi.org/10.1139/m96-064.
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The rpoN (ntrA) gene (encoding sigma 54) of Azospirillum brasilense Sp7 was isolated by using conserved rpoN primers and the polymerase chain reaction, and its nucleotide sequence was determined. The deduced amino acid sequence of the RpoN protein was found to share a high degree of homology with other members of the sigma 54 family. Two additional open reading frames were found in the Azospirillum brasilense rpoN region, with significant similarity to equivalent regions surrounding the rpoN locus in other bacteria. An rpoN mutant of Azospirillum brasilense Sp7 was constructed by gene replacement and found to be defective in nitrogen fixation, nitrate assimilation, and ammonium uptake. Lack of ammonium uptake was also found in previously isolated Azospirillum brasilense ntrB and ntrC mutants, further supporting the role of the ntr system in this process. In addition, the rpoN mutant was found to be nonmotile, suggesting a role of RpoN in Azospirillum brasilense flagellar biosynthesis.Key words: Azospirillum brasilense, sigma factor, nitrogen fixation, ammonium assimilation, motility.
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Sanchez-Bilbao, L., M. De Cos-Gómez, J. C. Ruiz-San Millán, M. A. González-Gay, and R. Blanco. "THU0320 RENAL TRANSPLANTATION DUE TO RAPIDLY PROGRESSIVE GLOMERULONEPHRITIS (RPGN) AND SYSTEMIC AUTOIMMUNE DISORDERS. STUDY OF 42 PATIENTS FROM A SINGLE CENTER." Annals of the Rheumatic Diseases 79, Suppl 1 (2020): 389–90. http://dx.doi.org/10.1136/annrheumdis-2020-eular.4858.
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Background:Rapidly Progressive Glomerulonephritis (RPGN) is characterized by a rapid and severe decline in kidney function that may lead to a kidney transplantation. RPGN is classified in three groups:a) Type I or associated to anti-glomerular basement membrane antibodies (RPGN-GBMa),b) Type II or associated to immunocomplexes (RGPN-immunocomplexes), andc) Type III or pauci-immune (RPGN-pauci-immune). RPGN can be primary, without extra-renal involvement (RPGN-renal-limited), or secondary to systemic autoimmune disorders (RPGN-SAD), infectious diseases or drugs. Kidney transplantation in RPGN-SAD may be associated to a worse outcome.Objectives:To assessa) clinical features of the three types of RPGN,b) comparison of post-transplant survival and graft survival between these three types.Methods:We studied three groups of patients according to renal biopsy:a) RPGN-GBMa (n = 11),b) RPGN-immunocomplexes (n = 2) and c) RPGN-pauci-immune (n=29). All these patients were transplanted in a single reference University Hospital. The main outcome variables werea) graft survival up to 15 years and patient survival up to 30 years andb) evolution of renal function (serum creatinine and proteinuria) in the first 5 years of follow-up.Results:We included a total of 42 patients with renal transplant due to RPGN, mean age at diagnosis 44.87±17.01 years (48.53±17.45 at the time of the transplant). No significant differences at baseline were observed between the three RPGN groups regarding sex, age and cardiovascular risk factors. Renal biopsy had been performed in the 42 patients with RPGN: type I or RPGN-GBMa (n=11, 26.2%), type II or RPGN-immunocomplexes (n=2, 4.8%) and type III or RPGN-pauci-immune (n=29, 69.0%).It was also reported the presence or absence of systemic autoimmune disorders (31% RPGN-SAD and 69% RPGN-renal-limited). According to the presentation and the clinical characteristics of the patients, another classification has been established:a) type I (18.2% (n = 2) Goodpasture-syndrome),b) type II (100% renal-limited),c) type III (13.8% (n = 4) granulomatosis with polyangiitis) and 20.70% (n = 6) microscopic polyangiitis. The evolution of serum creatinine and the proteinuria after the transplant is shown in TABLE 1and 1.1. Neither differences were found in terms of graft and patient survival between the 3 groups (Figures 1 and 2).TABLE 1.1 Month6 Months1 YearSerum Creatinine mg/dLRPGN-type IRPGN-type IIRPGN-type IIIRPGN-type IRPGN-type IIRPGN-type IIIRPGN-type IRPGN-type IIRPGN-type IIIN112261022210222Mean±SD1.78±0.83.85±.4.031.64±0.671.59±0.731.45±0.771.99±1.311.55±0.621.50±0.701.77±1.10Proteinuria mg/24 hRPGN-type IRPGN-type IIRPGN-type IIIRPGN-type IRPGN-type IIRPGN-type IIIRPGN-type IRPGN-type IIRPGN-type IIIN92231011910ND19Mean±SD470.00±566.85400.00±565.68408.22±449.00611.87±832.20*797.00±556.29*362.98±323.38*656.10±1206.68ND282.54±272.35*p<0.05Figure 1.Graft survival.Conclusion:Our study has shown similar graft and patient survival as well as renal outcome in renal transplant due to the three types of RPGN. Renal transplantation could be the best option for patients with end stage renal disease due to RPGN regardless of systemic manifestations.TABLE 1.13 Years5 YearsSerum Creatinine mg/dLRPGN-type IRPGN-type IIRPGN-type IIIRPGN-type IRPGN-type IIRPGN-type IIIN112208218Mean±SD1.64±0.741.70±0.691.85±1.341.55±0.861.60±0.841.72±0.82Proteinuria mg/24 hRPGN-type IRPGN-type IIRPGN-type IIIRPGN-type IRPGN-type IIRPGN-type IIIN112178216Mean±SD510.79±832.90272.57±291.20340.65±344.17238.23±311.19443.88±300.87579.26±1114.5*p<0.05Figure 2.Patient survival.Disclosure of Interests:Lara Sanchez-Bilbao Grant/research support from: Pfizer, Marina de Cos-Gómez: None declared, Juan Carlos Ruiz-San Millán: None declared, Miguel A González-Gay Grant/research support from: Pfizer, Abbvie, MSD, Speakers bureau: Pfizer, Abbvie, MSD, Ricardo Blanco Grant/research support from: AbbVie, MSD, and Roche, Speakers bureau: AbbVie, Pfizer, Roche, Bristol-Myers, Janssen, and MSD
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Ju, Donghong, Xiaogang Wang, Haiming Xu, and Youming Xie. "Genome-Wide Analysis Identifies MYND-Domain Protein Mub1 as an Essential Factor for Rpn4 Ubiquitylation." Molecular and Cellular Biology 28, no. 4 (2007): 1404–12. http://dx.doi.org/10.1128/mcb.01787-07.
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ABSTRACT The proteasome homeostasis in Saccharomyces cerevisiae is regulated by a negative feedback circuit in which the Rpn4 transcription factor upregulates the proteasome genes and is rapidly degraded by the proteasome. Previous work has identified Ubr2 and Rad6 as the cognate E3 and E2 enzymes for Rpn4 ubiquitylation. However, our recent attempts to ubiquitylate Rpn4 using purified Ubr2 and Rad6 proteins in a reconstitution system have been unsuccessful, suggesting that an additional factor is required for Rpn4 ubiquitylation. Here, we screened the entire collection of the single-gene-deletion yeast mutants generated by the Saccharomyces Genome Deletion Project and identified the mub1Δ mutant defective in ubiquitin-dependent degradation of Rpn4. An in vitro reconstitution ubiquitylation assay confirms that Mub1 is the missing factor for Rpn4 ubiquitylation. We further show that Mub1 directly interacts with Ubr2 and Rpn4. The MYND domain of Mub1 may play an important role in Rpn4 ubiquitylation. Interestingly, Mub1 itself is a short-lived protein and its degradation is dependent on the Ubr2/Rad6 ubiquitin ligase. Together, these data suggest that Mub1 and Ubr2 cooperate to transfer ubiquitin to Rpn4 from Rad6 and that Mub1 may switch from a partner to a substrate of the Ubr2/Rad6 ubiquitin ligase.
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Hendrickson, Erik L., Pablo Guevera, Alejandro Peñaloza-Vàzquez, Jing Shao, Carol Bender, and Frederick M. Ausubel. "Virulence of the Phytopathogen Pseudomonas syringae pv. Maculicola Is rpoN Dependent." Journal of Bacteriology 182, no. 12 (2000): 3498–507. http://dx.doi.org/10.1128/jb.182.12.3498-3507.2000.
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ABSTRACT We cloned the rpoN (ntrA andglnF) gene encoding ς54 from the phytopathogen Pseudomonas syringae pv. maculicola strain ES4326. The P. syringae ES4326 rpoN gene complemented Pseudomonas aeruginosa, Escherichia coli, and Klebsiella aerogenes rpoN mutants for a variety of rpoN mutant phenotypes, including the inability to utilize nitrate as sole nitrogen source. DNA sequence analysis of the P. syringae ES4326 rpoN gene revealed that the deduced amino acid sequence was most similar (86% identity; 95% similarity) to the ς54 protein encoded by thePseudomonas putida rpoN gene. A marker exchange protocol was used to construct an ES4326 rpoN insertional mutation,rpoN::Kmr. In contrast to wild-type ES4326, ES4326 rpoN::Kmr was nonmotile and could not utilize nitrate, urea, C4-dicarboxylic acids, several amino acids, or concentrations of ammonia below 2 mM as nitrogen sources.rpoN was essential for production of the phytotoxin coronatine and for expression of the structural genes encoding coronamic acid. In addition, ES4326rpoN::Kmr did not multiply or elicit disease symptoms when infiltrated into Arabidopsis thalianaleaves, did not elicit the accumulation of severalArabidopsis defense-related mRNAs, and did not elicit a hypersensitive response (HR) when infiltrated into tobacco (Nicotiana tabacum) leaves. Furthermore, whereas P. syringae ES4326 carrying the avirulence gene avrRpt2elicited an HR when infiltrated into Arabidopsis ecotype Columbia leaves, ES4326 rpoN::Kmrcarrying avrRpt2 elicited no response. Constitutive expression of ES4326 hrpL in ES4326rpoN::Kmr partially restored defense-related mRNA accumulation, showing a direct role for thehrp cluster in host defense gene induction in a compatible host-pathogen interaction. However, constitutive expression ofhrpL in ES4326 rpoN::Kmrdid not restore coronatine production, showing that coronatine biosynthesis requires factors other than hrpL.
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Péchy-Tarr, Maria, Mélanie Bottiglieri, Sophie Mathys та ін. "RpoN (σ54) Controls Production of Antifungal Compounds and Biocontrol Activity in Pseudomonas fluorescens CHA0". Molecular Plant-Microbe Interactions® 18, № 3 (2005): 260–72. http://dx.doi.org/10.1094/mpmi-18-0260.
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Pseudomonas fluorescens CHA0 is an effective biocontrol agent of root diseases caused by fungal pathogens. The strain produces the antibiotics 2,4-diacetylphloroglucinol (DAPG) and pyoluteorin (PLT) that make essential contributions to pathogen suppression. This study focused on the role of the sigma factor RpoN (σ54) in regulation of antibiotic production and biocontrol activity in P. fluorescens. An rpoN in-frame-deletion mutant of CHA0 had a delayed growth, was impaired in the utilization of several carbon and nitrogen sources, and was more sensitive to salt stress. The rpoN mutant was defective for flagella and displayed drastically reduced swimming and swarming motilities. Interestingly, the rpoN mutant showed a severalfold enhanced production of DAPG and expression of the biosynthetic gene phlA compared with the wild type and the mutant complemented with monocopy rpoN+. By contrast, loss of RpoN function resulted in markedly lowered PLT production and plt gene expression, suggesting that RpoN controls the balance of the two antibiotics in strain CHA0. In natural soil microcosms, the rpoN mutant was less effective in protecting cucumber from a root rot caused by Pythium ultimum. Remarkably, the mutant was not significantly impaired in its root colonization capacity, even at early stages of root infection by Pythium spp. Taken together, our results establish RpoN for the first time as a major regulator of biocontrol activity in Pseudomonas fluorescens.
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Saldías, M. Soledad, Julie Lamothe, Robert Wu, and Miguel A. Valvano. "Burkholderia cenocepacia Requires the RpoN Sigma Factor for Biofilm Formation and Intracellular Trafficking within Macrophages." Infection and Immunity 76, no. 3 (2008): 1059–67. http://dx.doi.org/10.1128/iai.01167-07.
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ABSTRACT Chronic respiratory infections by Burkholderia cenocepacia in cystic fibrosis patients are associated with increased morbidity and mortality, but virulence factors determining the persistence of the infection in the airways are not well characterized. Using a chronic pulmonary infection model, we previously identified an attenuated mutant with an insertion in a gene encoding an RpoN activator protein, suggesting that RpoN and/or components of the RpoN regulon play a role in B. cenocepacia virulence. In this study, we demonstrate that a functional rpoN gene is required for bacterial motility and biofilm formation in B. cenocepacia K56-2. Unlike other bacteria, RpoN does not control flagellar biosynthesis, as evidenced by the presence of flagella in the rpoN mutant. We also demonstrate that, in macrophages, the rpoN mutant is rapidly trafficked to lysosomes while intracellular wild-type B. cenocepacia localizes in bacterium-containing vacuoles that exhibit a pronounced delay in phagolysosomal fusion. Rapid trafficking to the lysosomes is also associated with the release of red fluorescent protein into the vacuolar lumen, indicating loss of bacterial cell envelope integrity. Although a role for RpoN in motility and biofilm formation has been previously established, this study is the first demonstration that the RpoN regulon in B. cenocepacia is involved in delaying phagolysosomal fusion, thereby prolonging bacterial intracellular survival within macrophages.
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Miletic-Drakulic, Svetlana, and Dejan Aleksic. "Recurrent painful ophthalmoplegic neuropathy: A report on the patient from the Romani population and 82-year-old patient." Vojnosanitetski pregled 77, no. 11 (2020): 1231–34. http://dx.doi.org/10.2298/vsp171225023m.
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Introduction. The current diagnostic criteria for recurrent painful ophthalmoplegic neuropathy (RPON) are at least two attacks of unilateral headache, associated with ipsilateral paresis of one, two or all three cranial nerves (III, IV or VI). There is no case report about RPON in the Romany population. The oldest patient with RPON, published in the literature, was 74 years old. Case report. The first patient was a 31-year-old man from the Romani population who was treated during three episodes of RPON, with III nerve palsy during one episode and with alternating VI nerve palsy during two episodes. All examination were normal except serum lipid levels and Cytomegalovirus immunoglobulin G (CMV IgG), Toxoplasma gondii IgG, Epstein?Barr virus (EVB) IgG and Varicella zoster IgG which were elevated. The second patient was a 82-year-old male patient with two RPON episodes with alternating VI nerve palsy. All examinations were normal, except Herpes simplex type 1 virus IgG, CMV IgG, Toxoplasma gondii IgG, EBV IgG and Varicella zoster IgG which were elevated, and his brain magnetic resonance imaging (MRI) showed lacunar ischemic lesions. Both patients were started on corticosteroid. Recovery was completed after all five episodes of RPON. Conclusion. There are no data on the frequency of RPON among the Romani population. The presentation of RPON in the oldest age is rare. RPON should be considered as a diagnostic option in these minorities. New case reports or systematic review articles about RPON are necessary to create a new insight into the nature of the disease.
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Spasskaya, Daria S., Nonna I. Nadolinskaia, Vera V. Tutyaeva, Yuriy P. Lysov, Vadim L. Karpov, and Dmitry S. Karpov. "Yeast Rpn4 Links the Proteasome and DNA Repair via RAD52 Regulation." International Journal of Molecular Sciences 21, no. 21 (2020): 8097. http://dx.doi.org/10.3390/ijms21218097.
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Environmental and intracellular factors often damage DNA, but multiple DNA repair pathways maintain genome integrity. In yeast, the 26S proteasome and its transcriptional regulator and substrate Rpn4 are involved in DNA damage resistance. Paradoxically, while proteasome dysfunction may induce hyper-resistance to DNA-damaging agents, Rpn4 malfunction sensitizes yeasts to these agents. Previously, we proposed that proteasome inhibition causes Rpn4 stabilization followed by the upregulation of Rpn4-dependent DNA repair genes and pathways. Here, we aimed to elucidate the key Rpn4 targets responsible for DNA damage hyper-resistance in proteasome mutants. We impaired the Rpn4-mediated regulation of candidate genes using the CRISPR/Cas9 system and tested the sensitivity of mutant strains to 4-NQO, MMS and zeocin. We found that the separate or simultaneous deregulation of 19S or 20S proteasome subcomplexes induced MAG1, DDI1, RAD23 and RAD52 in an Rpn4-dependent manner. Deregulation of RAD23, DDI1 and RAD52 sensitized yeast to DNA damage. Genetic, epigenetic or dihydrocoumarin-mediated RAD52 repression restored the sensitivity of the proteasome mutants to DNA damage. Our results suggest that the Rpn4-mediated overexpression of DNA repair genes, especially RAD52, defines the DNA damage hyper-resistant phenotype of proteasome mutants. The developed yeast model is useful for characterizing drugs that reverse the DNA damage hyper-resistance phenotypes of cancers.
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Leal, Sérgio Roberto Moura, Rochana Campos de Andrade Lima Santos, and Tereza Cristina Calado. "Inventário ecoturístico da reserva particular (RPPN) Fazenda Santa Tereza, Atalaia, Alagoas." Nature and Conservation 1, no. 1 (2008): 57. http://dx.doi.org/10.6008/ess1983-8344.2008.001.0009.
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A Reserva Particular do Patrimônio Natural (RPPN) Fazenda Santa Tereza localiza-se na microrregião da mata alagoana no município de Atalaia, Estado de Alagoas. Sua área é de 100,3 hectares. No ano de 2003 foi reconhecida com posto avançado da Reserva da Biosfera da Mata Atlântica. O objetivo deste estudo foi realizar um inventário sobre o potencial ecoturístico da RPPN, mapear os espaços potenciais para prática do ecoturismo, identificar trilhas com potenciais faunisticos e florísticos, e os atrativos naturais e sugerir opções de visitação ordenada à reserva. O inventário levou em consideração os níveis de atratividade e singularidade da área, identificadas através de excursões feitas às localidades do entorno e à área da RPPN, como também pesquisa bibliográfica; visitação aos locais com potencial ecoturístico; visitação à cidade de Atalaia; demarcação de trilhas com o auxilio de GPS e trena; levantamento de infra-estrutura turística; levantamento fotográfico; avaliação das condições em que se encontram os atrativos; e entrevistas com pessoas que trabalham na RPPN Fazenda Santa Tereza. A atratividade para o ecoturismo na RPPN está distribuída em quatro trilhas: a da Copiuba, da Barragem, da Mineral e das Piscinas. Apenas a trilha da Copiuba não dispõe de recursos hídricos. Constatou-se que a RPPN dispõe de um rico acervo natural representado pela fauna, a exemplo de aves como a Penelope superciliaris alagoensis (Jacupemba) e a Diopsittaca nobilis (Maracanã-pequena), de mamíferos, como o Callithrix jacchus (Sagui-de-tufos-brancos) e a Dasyprocta prymnolopha (Cutia) e de répteis como o Tupinambis merianae (Tejo). Estes animais foram encontrados nas 04 trilhas existentes na RPPN. Foi realizado também o cálculo de Capacidade de Carga Real (CCR) das trilhas. O resultado mostrou que a RPPN só poderá receber 72 pessoas por dia com o objetivo de utilização das trilhas. Atualmente a RPPN Fazenda Santa Tereza não dispõe de um parâmetro para definir a quantidade de pessoas que poderão acessar as trilhas da RPPN, neste sentido a CCR servirá para ordenar o acesso à área da RPPN. Portanto, a área dispõe de um acervo diversificado que reúne potencialidade e singularidade à infra-estrutura local, confirmando a tendência da RPPN para a prática do ecoturismo.
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Chen, Wei-Shan, Sheng-Dean Luo, Tai-Jan Chiu, et al. "Ribophorin II Overexpression Is Associated with Poor Response to Induction Chemotherapy with Docetaxel, Cisplatin, and Fluorouracil in P16-Negative Locally Advanced Head and Neck Squamous Cell Carcinoma." Journal of Clinical Medicine 10, no. 18 (2021): 4118. http://dx.doi.org/10.3390/jcm10184118.
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This study aims to evaluate the relationship between human ribophorin II (RPN2) and the effect of treatment using induction therapy with docetaxel, cisplatin, and fluorouracil (TPF) for p-16 negative locally advanced head and neck squamous cell carcinoma (HNSCC). A total of 203 patients with locally advanced p-16 negative HNSCC who received induction chemotherapy with TPF at the Kaohsiung Chang Gung Memorial Hospital between 2009 and 2014 were enrolled. Immunohistochemistry (IHC) for RPN2 was examined and correlated with treatment outcome. Our study showed that RPN2 overexpression was significantly correlated with a poor response to induction chemotherapy with TPF. Both RPN2 overexpression and clinical N1 to N3 stages represented adverse prognostic factors for progression-free survival (PFS) and overall survival (OS). RPN2 might be a predictive marker for treatment response to induction chemotherapy. Further clinical trials are needed to determine the therapeutic significance of RPN2 in patients with HNSCC.
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GN, Chaudhury, Chowdhury RA, Khondoker T, Ferdous T, Afroz S, and Hanif M. "Etiology and Morphological Pattern in Rapidly Progressive Glomerulonephritis." Scholars Academic Journal of Biosciences 9, no. 6 (2021): 166–70. http://dx.doi.org/10.36347/sajb.2021.v09i06.004.
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Introduction: Rapidly progressive glomerulonephritis (RPGN) is a type of GN disease of the kidney. It is clinically characterized by a rapid decrease in the glomerular filtration rate (GFR) of at least 50% over a short period, from a few days to 3 months. The main pathologic finding is extensive glomerular crescent formation. The present study was conducted to recognize the morphological pattern in RPGN, underlying causes, and the outcome of RPGN in children. Aim of the study: To assess the histopathology of Rapidly Progressive Glomerulonephritis (RPGN), as RPGN can cause rapid irreversible damage to renal glomeruli in the form of crescents. Methods: This study was done on 34 RPGN children at the department of pediatric Nephrology in Dhaka Shishu (Children) Hospital over the period of June 2017 to December 2019. Result: The etiology of RPGN in this study showed, HSP nephritis was the commonest (23.5%) followed by IgA nephropathy (21.9%) and postinfectious glomerulonephritis (17.64%). Hematuria, proteinuria, and edema were present in almost all cases. The proportion of glomeruli displaying cellular crescent was 21%, fibrous crescent 7.1%, and fibrocellular crescent was 35% respectively. In terms of outcome, 61.7% of patients exhibited total recovery of renal function, 14.7% of patients were lost during follow-up, 5.8% were dialysis dependant, 5.8% patients developed chronic kidney disease and 11.7% died during hospitalization. Conclusion: RPGN is one of the important causes of unexplained acute kidney injury (AKI). Rapid and irreversible loss of renal function and remarkable mortality consider the need for awareness and development of a specific registry for Pediatric RPGN in hospitals.
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Albert-Weissenberger, Christiane, Tobias Sahr, Odile Sismeiro, Jörg Hacker, Klaus Heuner, and Carmen Buchrieser. "Control of Flagellar Gene Regulation in Legionella pneumophila and Its Relation to Growth Phase." Journal of Bacteriology 192, no. 2 (2009): 446–55. http://dx.doi.org/10.1128/jb.00610-09.
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ABSTRACT The bacterial pathogen Legionella pneumophila responds to environmental changes by differentiation. At least two forms are well described: replicative bacteria are avirulent; in contrast, transmissive bacteria express virulence traits and flagella. Phenotypic analysis, Western blotting, and electron microscopy of mutants of the regulatory genes encoding RpoN, FleQ, FleR, and FliA demonstrated that flagellin expression is strongly repressed and that the mutants are nonflagellated in the transmissive phase. Transcriptome analyses elucidated that RpoN, together with FleQ, enhances transcription of 14 out of 31 flagellar class II genes, which code for the basal body, hook, and regulatory proteins. Unexpectedly, FleQ independent of RpoN enhances the transcription of fliA encoding sigma 28. Expression analysis of a fliA mutant showed that FliA activates three out of the five remaining flagellar class III genes and the flagellar class IV genes. Surprisingly, FleR does not induce but inhibits expression of at least 14 flagellar class III genes on the transcriptional level. Thus, we propose that flagellar class II genes are controlled by FleQ and RpoN, whereas the transcription of the class III gene fliA is controlled in a FleQ-dependent but RpoN-independent manner. However, RpoN and FleR might influence flagellin synthesis on a posttranscriptional level. In contrast to the commonly accepted view that enhancer-binding proteins such as FleQ always interact with RpoN to fullfill their regulatory functions, our results strongly indicate that FleQ regulates gene expression that is RpoN dependent and RpoN independent. Finally, FliA induces expression of flagellar class III and IV genes leading to the complete synthesis of the flagellum.
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Pejkova, Sofija, Bisera Nikolovska, Blagoja Srbov, et al. "Prophylactic Regenerative Peripheral Nerve Interfaces in Elective Lower Limb Amputations." PRILOZI 43, no. 1 (2022): 41–48. http://dx.doi.org/10.2478/prilozi-2022-0004.
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Abstract Regenerative peripheral nerve interface (RPNI) is a relatively new surgical technique to manage neuromas and phantom pain after limb amputation. This study evaluates prophylactic RPNI efficacy in managing post-amputation pain and neuroma formation in amputees compared with patients in which lower limb amputation was performed without this procedure. We included 28 patients who underwent above the knee amputation (AKA) or below the knee amputation (BKA) for severe soft tissue infection from July 2019 till December 2020. All patients had insulin-dependent diabetes. The patients were divided into two groups, 14 patients with primary RPNI and 14 patients without. We analyzed the demographic data, level of amputation, number of RPNIs, operative time, postoperative complications and functional outcome on the defined follow up period. The mean patient age was 68.6 years (range 49–85), 19 (67.9 %) male and 9 (32.1 %) female patients. In this study 11 (39.3 %) AKA and 17 (60.7 %) BKA were performed. Overall, 37 RPNIs were made. The mean follow-up period was 49 weeks. PROMIS T-score decreased by 15.9 points in favor for the patients with RPNI. The VAS score showed that, in the RPNI group, all 14 patients were without pain compared to the group of patients without RPNI, where the 11 (78.6 %) patients described their pain as severe. Patients with RPNI used prosthesis significantly more (p < 0.005). Data showed significant reduction in pain and high patient satisfaction after amputation with RPNIs. This technique is oriented as to prevent neuroma formation with RPNI surgery, performed at the time of amputation. RPNI surgery did not provoke complications or significant lengthening of operative time and it should be furthermore exploited as a surgical technique.
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Putri, Sandra, Nadhila Aditiyaputri, and Amanukarti Oetomo. "Acute Kidney Injury with Characteristics of Rapidly Progressive Glomerulonephritis Due to Suspected IgA Nephropathy: A Case Report." Indonesian Journal of Kidney and Hypertension 1, no. 3 (2024): 70–74. https://doi.org/10.32867/inakidney.v1i3.141.
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Acute kidney damage (AKI) in glomerular disease is typically characterized by rapidly progressive glomerulonephritis (RPGN). RPGN in IgA nephropathy is uncommon, occurring in less than 10% of patients. RPGN presents diagnostic issues in resource-limited settings. A 34-year-old male patient had acute kidney injury with RPGN characteristics based on clinical symptoms of hypertension, pitting edema, anuria, and hematuria after an upper respiratory tract infection, as well as laboratory findings of proteinuria, persistent microscopic hematuria, and positive erythrocyte casts. Serum creatinine levels rose sharply. Corticosteroids, antihypertensives, and hemodialysis resulted in clinical improvement and fast kidney function recovery. Due to limited resources, no kidney biopsy was conducted. This case provides a diagnostic approach to RPGN in IgA nephropathy in resource-limited settings, along with comprehensive therapy.
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Ho, Philip Levy, Daniel Levi Willis, Jeevitha Patil, et al. "Outcome of patients with clinically node-positive bladder cancer who undergo consolidative surgery after preoperative chemotherapy: MD Anderson Cancer Center experience." Journal of Clinical Oncology 32, no. 4_suppl (2014): 318. http://dx.doi.org/10.1200/jco.2014.32.4_suppl.318.
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318 Background: We previously reported results of our phase II study in patients with retroperitoneal lymph node (RPLN) metastasis from bladder cancer (BC) undergoing consolidative surgery after preoperative chemotherapy. Here we present an expanded cohort of patients who underwent consolidative surgery after chemotherapy for clinically node-positive BC. Methods: We reviewed results of patients from our IRB approved protocol including those with clinical evidence of nodal metastasis in the pelvis or retroperitoneum (M1), without visceral metastasis, from 1995-2010. Endpoint of the study was cancer-specific survival (CSS) calculated from time of surgery. Results: 55 patients with either clinical pelvic lymph node (PLN) metastasis (n=29) or PLN and RPLN metastasis (n=26) were identified. Median CSS was 19 months for all patients; 21 for PLN alone and 16 for PLN and RPLN disease. Kaplan-Meier estimate of 5-year CSS was 31% with no difference between PLN alone and PLN with RPLN disease. Clinical nodal stage was N1: 16, N2: 5, N3: 8, and M1 (RPLN): 26. Majority (94%) of patients received cisplatinum-based chemotherapy. At cystectomy, all patients underwent a PLN dissection with 12 patients (all clinical M1 RPLN) undergoing concurrent RPLN dissection (RPLND). In all, 30 of 55 (55%) patients were pN0 at the time of surgical extirpation while 26% (5 of 19) were pN+ despite radiologic complete response after chemotherapy. 5-year CSS was 57% for pN0 and 9% for pN+ disease (p<0.0001). Median survival in patients with residual tumor in PLN (n=17) was 10.5 months vs. 7 months for RPLN (n=8) (median survival not reached in pN0 patients, p< 0.001). 17 patients developed recurrences outside the surgical field after a median of 8 months. While no recurrences occurred within the lymphadenectomy template, 14% of patients with clinical M1 RPLN disease who did not undergo RPLND had recurrences in RPLN basin. Conclusions: Post-chemotherapy consolidative surgical resection may result in 5-year disease-free survival in patients with clinical evidence of node-positive disease, including those with RPLN positive disease, who have major response to chemotherapy.
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Smith, Alexandra H., Jon S. Blevins, Gulnaz N. Bachlani, Xiaofeng F. Yang та Michael V. Norgard. "Evidence that RpoS (σS) in Borrelia burgdorferi Is Controlled Directly by RpoN (σ54/σN)". Journal of Bacteriology 189, № 5 (2006): 2139–44. http://dx.doi.org/10.1128/jb.01653-06.
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ABSTRACT The alternative sigma factor (RpoN-RpoS) pathway controls the expression of key virulence factors in Borrelia burgdorferi. However, evidence to support whether RpoN controls rpoS directly or, perhaps, indirectly via a transactivator has been lacking. Herein we provide biochemical and genetic evidence that RpoN directly controls rpoS in B. burgdorferi.
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Salazar, Emmanuel, J. Javier Díaz-Mejía, Gabriel Moreno-Hagelsieb, et al. "Characterization of the NifA-RpoN Regulon in Rhizobium etli in Free Life and in Symbiosis with Phaseolus vulgaris." Applied and Environmental Microbiology 76, no. 13 (2010): 4510–20. http://dx.doi.org/10.1128/aem.02007-09.
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ABSTRACT The NifA-RpoN complex is a master regulator of the nitrogen fixation genes in alphaproteobacteria. Based on the complete Rhizobium etli genome sequence, we constructed an R. etli CFN42 oligonucleotide (70-mer) microarray and utilized this tool, reverse transcription (RT)-PCR analysis (transcriptomics), proteomics, and bioinformatics to decipher the NifA-RpoN regulon under microaerobic conditions (free life) and in symbiosis with bean plants. The R. etli NifA-RpoN regulon was determined to contain 78 genes, including the genes involved in nitrogen fixation, and the analyses revealed 42 new NifA-RpoN-dependent genes. More importantly, this study demonstrated that the NifA-RpoN regulon is composed of genes and proteins that have very diverse functions, that play fundamental and previously less appreciated roles in regulating the normal physiology of the cell, and that have important functions in providing adequate conditions for efficient nitrogen fixation in symbiosis. The R. etli NifA-RpoN regulon defined here has some components in common with other NifA-RpoN regulons described previously, but the vast majority of the components have been found only in the R. etli regulon, suggesting that they have a specific role in this bacterium and particular requirements during nitrogen fixation compared with other symbiotic bacterial models.
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Wang, Xinyue, Siyi Feng, and Hongdong Song. "Caffeic Acid Phenethyl Ester Encapsulated in Self-Assemble Rice Peptides Nanoparticles: Storage Stability, In Vitro Release, and Their Interaction Mechanisms." Foods 13, no. 5 (2024): 755. http://dx.doi.org/10.3390/foods13050755.
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Caffeic acid phenethyl ester (CAPE) is an important active component of propolis with many bioactivities. However, its efficiency and practical application are restricted due to its poor aqueous solubility and storage stability. In this study, a nanocarrier was fabricated to encapsulate CAPE using self-assembled rice peptides obtained by controllable enzymolysis. The physicochemical properties, encapsulation efficiency, and loading capacity of rice peptides nanoparticles (RPNs) were characterized. The storage stability, in vitro release, and interaction mechanisms between CAPE and RPNs were investigated. The results showed that RPNs, mainly assembled by disulfide bonds and hydrogen bonds, possessed an effective diameter of around 210 nm and a high encapsulation efficiency (77.77%) and loading capacity (3.89%). Importantly, the water solubility of CAPE was increased by 45 times after RPNs encapsulation. Moreover, RPNs encapsulation also significantly increased CAPE stability, about 1.4-fold higher than that of unencapsulated CAPE after 18-day storage. An in vitro release study demonstrated that RPNs could delay the release of CAPE, implying a better CAPE protection against extreme environments during digestion. Hydrogen bond and van der Waals force are the predominant interaction forces between RPNs and CAPE. Therefore, the newly developed nanoparticle is a potential delivery system that could effectively improve the aqueous solubility and stability of CAPE.
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Isoda, Kyosuke, and Ayumi Ikenaga. "Synthesis of Furan-Substituted N-Heteroacene-Based Liquid Material and Its Acid-Recognizing Behavior." Crystals 9, no. 1 (2019): 51. http://dx.doi.org/10.3390/cryst9010051.
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In this study, we synthesized a novel N-heteroacene-based liquid material 6,7-bis(3,7,11-trimethyl-1-dodecyloxy)-2,3-difurylquinoxaline (RPNL 1), containing two furan rings. We revealed that RPNL 1 adopted a disordered liquid at 25 ∘ C, determined by polarized optical microscopic observation, differential scanning calorimetry, and X-ray diffraction measurements. The fluorescent spectrum measurement revealed that RPNL 1 showed a blue emission at 25 ∘ C. Dissolving benzene sulfonic acid (BSA) in RPNL 1 brought about dramatic changes in its physical properties, such as emission colors, as well as sample states. Upon recognizing BSA, photoluminescent color was changed into orange, as well as phase transition occurred from liquid to a liquid-crystalline phase. RPNL 1 can function as an acid-recognizing material, accompanied with the color changes in emission.
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Kim, Ryul, Jae-Hyoung Kim, Eunhee Kim, Hee-Kyung Yang, Jeong-Min Hwang, and Ji-Soo Kim. "Oculomotor nerve tumors masquerading as recurrent painful ophthalmoplegic neuropathy: Report of two cases and review of the literature." Cephalalgia 35, no. 9 (2014): 825–30. http://dx.doi.org/10.1177/0333102414558886.
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Background In recurrent painful ophthalmoplegic neuropathy (RPON) that was previously termed as ophthalmoplegic migraine, enhancement of the ocular motor cranial nerves could be seen in the cisternal segment during the acute phase. However, various tumors involving the oculomotor nerve may mimic RPON. Methods We report two patients with MRI findings of oculomotor nerve schwannoma who initially presented with RPON, and found through the literature review five more patients with oculomotor nerve tumors that masqueraded as RPON. Results All patients showed an involvement of the oculomotor nerve. The radiological or pathological diagnosis included schwannoma in five, venous angioma in one, and neuromuscular harmatoma in another one. MRIs with gadolinium documented an enhancing nodule involving the cisternal portion of the oculomotor nerve in six of them, which was also observed on follow-up MRIs without an interval change. Conclusions It should be recognized that an incomplete recovery may occur during future attacks in patients with otherwise uncomplicated RPON. Follow-up MRIs are required to detect tumors involving the ocular motor cranial nerves, especially in patients with suspected RPON when the recovery is incomplete.
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Härtig, Elisabeth, та Walter G. Zumft. "The Requirement of RpoN (Sigma Factor ς54) in Denitrification by Pseudomonas stutzeri Is Indirect and Restricted to the Reduction of Nitrite and Nitric Oxide". Applied and Environmental Microbiology 64, № 8 (1998): 3092–95. http://dx.doi.org/10.1128/aem.64.8.3092-3095.1998.
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ABSTRACT The rpoN region of Pseudomonas stutzeri was cloned, and an rpoN null mutant was constructed. RpoN was not essential for denitrification in this bacterium but affected the expression levels and enzymatic activities of cytochromecd 1 nitrite reductase and nitric oxide reductase, whereas those of respiratory nitrate reductase and nitrous oxide reductase were comparable to wild-type levels. Since the transcription of the structural genes nirS andnorCB, coding for nitrite reductase and the nitric oxide reductase complex, respectively, proceeded unabated, our data indicate a posttranslational process for the two key enzymes of denitrification depending on RpoN.
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Mahovic, Darija, and Matea Bracic. "Erenumab as treatment for recurrent painful ophthalmoplegic neuropathy." Progress in Neurology and Psychiatry 27, no. 4 (2023): 19–22. http://dx.doi.org/10.1002/pnp.810.
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Recurrent painful ophthalmoplegic neuropathy (RPON), formerly known as ophthalmoplegic migraine, is a rare condition characterised by recurrent attacks of unilateral headache with ipsilateral ophthalmoplegia. Although classified as a cranial neuralgia, the exact pathophysiology behind RPON is unclear and the clinical presentation often resembles migraine headaches. Here, the authors present the case of a patient with RPON who, after numerous therapeutic failures, received erenumab and experienced significant improvement. This case supports the argument that RPON should be reclassified as a migraine variant, which would enable the use of specific prophylactic medication in patients suffering from this disorder.
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Iyizoba-Ebozue, Zsuzsanna, Louise J. Murray, Moses Arunsingh, et al. "Retropharyngeal Lymph Node Involvement in Oropharyngeal Carcinoma: Impact upon Risk of Distant Metastases and Survival Outcomes." Cancers 12, no. 1 (2019): 83. http://dx.doi.org/10.3390/cancers12010083.
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The influence of retropharyngeal lymph node (RPLN) involvement on prognosis in oropharyngeal carcinoma remains poorly defined. The aim of this study was to assess the impact of RPLN involvement upon outcomes. A single-centre retrospective analysis of 402 patients with oropharyngeal carcinoma treated nonsurgically between 2010 and 2017 was performed. All had a baseline 2-[fluorine-18]-fluoro-2-deoxy-d-glucose (FDG) PET-CT and contrast-enhanced MRI and/or CT. RPLN status was determined by radiology review of cases with reported abnormal RPLN. Multivariate backwards logistic regression was used to examine impact on outcomes of factors. Abnormal RPLNs were identified in 40/402 (10%) of patients. Median follow up was 42.9 months. RPLN involvement was associated with inferior 3 year outcomes for overall survival (OS) (67.1% vs. 79.1%, p = 0.006) and distant metastases-free survival (DMFS) (73.9% versus 88.0%, p = 0.011), with no significant difference in local control (81.6% vs. 87.7%, p = 0.154) or regional control (80.7% vs. 85.4%, p = 0.252). On multivariate analysis abnormal RPLN, no concurrent chemotherapy and ongoing smoking were associated with inferior DMFS and OS, while advanced T stage was also associated with inferior OS. In summary, RPLN involvement, present in 10% of patients, was an independent prognostic factor for the development of distant disease failure translating into inferior OS. These findings need confirmation in future studies.
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Hemmis, Casey W., Stephanie C. Heard, and Christopher P. Hill. "Phosphorylation of Tyr-950 in the proteasome scaffolding protein RPN2 modulates its interaction with the ubiquitin receptor RPN13." Journal of Biological Chemistry 294, no. 25 (2019): 9659–65. http://dx.doi.org/10.1074/jbc.ac119.008881.
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Protein substrates are targeted to the 26S proteasome through several ubiquitin receptors. One of these receptors, RPN13, is recruited to the proteasome by binding of its N-terminal pleckstrin-like receptor of ubiquitin (PRU) domain to C-terminal residues of the scaffolding protein RPN2. The RPN13 PRU domain is followed by a flexible linker and a C-terminal deubiquitylase adaptor (DEUBAD) domain, which recruits and activates the deubiquitylase UCH37. Both RPN13 and UCH37 have been implicated in human cancers, and inhibitors of the RPN2–RPN13 interaction are being developed as potential therapeutic anticancer agents. Our current study builds on the recognition that a residue central to the RPN2–RPN13 interaction, RPN2 Tyr-950, is phosphorylated in Jurkat cells. We found that the Tyr-950 phosphorylation enhances binding to RPN13. The crystal structure of the RPN2–RPN13 pTyr-950–ubiquitin complex was determined at 1.76-Å resolution and reveals specific interactions with positively charged side chains in RPN13 that explain how phosphorylation increases binding affinity without inducing conformational change. Mutagenesis and quantitative binding assays were then used to validate the crystallographic interface. Our findings support a model in which RPN13 recruitment to the proteasome is enhanced by phosphorylation of RPN2 Tyr-950, have important implications for efforts to develop specific inhibitors of the RPN2–RPN13 interaction, and suggest the existence of a previously unknown stress-response pathway.
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Tran, Ben, Malcolm J. Moore, Eitan Amir, et al. "Large retroperitoneal lymph nodes (RPLN) as a predictor for venous thromboembolism (VTE) in patients (pts) with germ cell tumor (GCT) receiving first-line chemotherapy (chemo)." Journal of Clinical Oncology 30, no. 5_suppl (2012): 332. http://dx.doi.org/10.1200/jco.2012.30.5_suppl.332.
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332 Background: VTE causes significant morbidity and mortality in GCT pts. While an existing and validated predictive model identifies VTE risk in chemo pts with any cancer (Khorana model), a predictive model specific to GCT does not exist. Many GCT pts present with bulky RPLN that produce venous stasis in the lower extremities. The objective of this study was to explore the association between large RPLN and VTE in GCT pts receiving chemo and compare large RPLN as a predictor for VTE in GCT pts to the non-GCT specific Khorana model. Methods: Clinical data from our institutional GCT database was complemented by review of radiology, pharmacy and medical records. All GCT pts receiving 1st line chemo between 1-Jan-00 and 31-Dec-10 were included. Large RPLN were defined as ≥5cm in maximal diameter. Factors used in the Khorana model (baseline BMI, hemoglobin, white cell count and platelets) were collected. We compared the predictive accuracy of large RPLN versus Khorana score ≥3 using receiver operator characteristic (ROC) curve statistical analyses. Results: The cohort consisted of 260 GCT pts, median age 31.5 years, predominantly testis primary (235, 90%) and good risk (171, 66%). 17 (7%) developed VTE prior to the start of chemo. 19 (7%) were given prophylactic anticoagulation, none of whom developed VTE. Of the remaining 224 pts, 20 (9%) developed VTE during chemo. In a univariate analysis, large RPLN was strongly associated with VTE (OR 7.74, p<0.001), as were Khorana score ≥3 (OR 9.81, p<0.001) and hospital admission during chemo (OR 3.96, p=0.004). ROC curve analyses demonstrated large RPLN was a significant individual predictor for VTE (AUC 0.588, p=0.03), however, Khorana score ≥3 was a better predictor (AUC 0.664, p=0.02). Adding large RPLN to create a modified Khorana score provided marginal gains (AUC 0.682, p=0.02). Conclusions: Although large RPLN at diagnosis predicts for VTE in GCT pts, the Khorana predictive model is superior. Given the high rate of VTE in GCT pts receiving chemo, we recommend prophylactic anticoagulation for pts at increased risk, including pts with Khorana score ≥3, pts requiring hospital admission or pts with large RPLN.
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Mayer, Ulrike, Jan Bräsen, and Lars Pape. "Die Rasch Progessive Glomerulonephritis im Kindesalter." Klinische Pädiatrie 231, no. 01 (2018): 4–13. http://dx.doi.org/10.1055/a-0669-9271.
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ZusammenfassungDie rasch progressive Glomerulonephritis (RPGN) im Kindesalter stellt eine seltene aber schwere Erkrankung dar, die häufig zu einer dialysepflichtigen Niereninsuffizienz führt. In diesem Review wird die Definition der RPGN dargestellt und das grundsätzliche diagnostische und therapeutische Vorgehen inklusive Nierenbiopsie werden diskutiert. Darüber hinaus werden die Besonderheiten einzelner Krankheitsentitäten beschrieben, die eine RPGN verursachen können und entsprechende diagnostische und therapeutische Besonderheiten dargestellt.
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Srikanthan, Amirrtha, Ben Tran, Michel Beausoleil, et al. "Large Retroperitoneal Lymphadenopathy As a Predictor of Venous Thromboembolism in Patients With Disseminated Germ Cell Tumors Treated With Chemotherapy." Journal of Clinical Oncology 33, no. 6 (2015): 582–87. http://dx.doi.org/10.1200/jco.2014.58.6537.
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Purpose Cisplatin-based chemotherapy, a mainstay of treatment for disseminated germ cell tumors (GCTs), is associated with venous thromboembolism (VTE). Many patients with disseminated GCTs have large retroperitoneal lymph node (RPLN) metastases that may cause venous stasis and increase the risk of VTE development. We hypothesized that there was an association between large RPLN and chemotherapy-associated VTE risk. Patients and Methods The training cohort was composed of patients with disseminated GCT receiving first-line chemotherapy at Princess Margaret Cancer Centre between January 2000 and December 2010. Large RPLN was defined as more than 5 cm in maximal axial diameter. The predictive and discriminatory accuracies of a model using large RPLN in predicting VTE were compared with high-risk Khorana score (≥ 3) using logistic regression and area under receiver operator characteristic curves (AUROCs). The model was externally validated in a cohort of patients treated at the London Health Sciences Centre. Results The training cohort comprised 216 patients, 21 (10%) of whom developed VTE during chemotherapy. VTE was associated with large RPLN (odds ratio [OR], 5.26; P = .001), high-risk Khorana score (OR, 11.8; P < .001), intermediate-/poor-risk disease (OR, 3.76; P = .005), and hospitalization during chemotherapy (OR, 4.24; P = .002). Large RPLN showed higher discriminatory accuracy than high-risk Khorana score (AUROC, 0.71 v 0.67, respectively). Superior discriminatory accuracy of large RPLN over high-risk Khorana score was validated in the London cohort (AUROC, 0.61 v 0.57, respectively). Conclusion Large RPLN is associated with VTE in patients with disseminated GCT and provides higher discriminatory accuracy than high-risk Khorana score. Results should be validated in larger, prospective studies. Prophylactic anticoagulation may be considered in high-risk patients.
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Petruzzelli, Maria Giuseppina, Mariella Margari, Flora Furente, et al. "Recurrent Painful Ophthalmoplegic Neuropathy and Oculomotor Nerve Schwannoma: A Pediatric Case Report with Long-Term MRI Follow-Up and Literature Review." Pain Research and Management 2019 (September 25, 2019): 1–11. http://dx.doi.org/10.1155/2019/5392945.
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Background. Recurrent painful ophthalmoplegic neuropathy (RPON), previously known as ophthalmoplegic migraine (OM), is an uncommon disorder with repeated episodes of ocular cranial nerve neuropathy associated with ipsilateral headache. The age of presentation is most often during childhood or adolescence. MRI has a central role in the assessment of the RPON, especially to distinguish orbital, parasellar, or posterior fossa lesions that mimic symptoms of RPON. Actually, oculomotor nerve tumors may be masquerade as RPON so that MRI follow-ups are required to detect the possibility of tumor etiology. Case presentation. We report a 16-year-old boy with a 7-year follow-up and multiple brain MRI data, previously diagnosed as OM. The last brain MRI, performed during an acute phase of oculomotor paresis with ipsilateral headache, showed a nodular lesion described as schwannoma of III cranial nerve. Then, we reviewed the literature on OM and RPON in pediatric age with a focus on brain MRI findings. Conclusions. This review highlights the important role of serial brain MRIs in the long-term follow-up of RPON, especially in the cases with childhood onset, in order to not delay the diagnosis of a possible oculomotor nerve schwannoma.
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Yu, Chao, Fenghuan Yang, Dingrong Xue, Xiuna Wang та Huamin Chen. "The Regulatory Functions of σ54 Factor in Phytopathogenic Bacteria". International Journal of Molecular Sciences 22, № 23 (2021): 12692. http://dx.doi.org/10.3390/ijms222312692.
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σ54 factor (RpoN), a type of transcriptional regulatory factor, is widely found in pathogenic bacteria. It binds to core RNA polymerase (RNAP) and regulates the transcription of many functional genes in an enhancer-binding protein (EBP)-dependent manner. σ54 has two conserved functional domains: the activator-interacting domain located at the N-terminal and the DNA-binding domain located at the C-terminal. RpoN directly binds to the highly conserved sequence, GGN10GC, at the −24/−12 position relative to the transcription start site of target genes. In general, bacteria contain one or two RpoNs but multiple EBPs. A single RpoN can bind to different EBPs in order to regulate various biological functions. Thus, the overlapping and unique regulatory pathways of two RpoNs and multiple EBP-dependent regulatory pathways form a complex regulatory network in bacteria. However, the regulatory role of RpoN and EBPs is still poorly understood in phytopathogenic bacteria, which cause economically important crop diseases and pose a serious threat to world food security. In this review, we summarize the current knowledge on the regulatory function of RpoN, including swimming motility, flagella synthesis, bacterial growth, type IV pilus (T4Ps), twitching motility, type III secretion system (T3SS), and virulence-associated phenotypes in phytopathogenic bacteria. These findings and knowledge prove the key regulatory role of RpoN in bacterial growth and pathogenesis, as well as lay the groundwork for further elucidation of the complex regulatory network of RpoN in bacteria.
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زيدان, ابراهيم محمد, та د. سمير كامل سعيد الخطيب. "تقييم المخاطر البيئية بإستعمال اداة FMEA دراسة حالة في شركة مصافي الوسط / مصفى الدورة". Journal of Petroleum Research and Studies 11, № 3 (2021): 1–19. http://dx.doi.org/10.52716/jprs.v11i3.535.
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يعد نظام الإدارة البيئية (EMS) من الانظمة الإدارية الحديثة والمهمة في وقتنا الحالي، ويعد مدخلاً لمعالجة أو الحد من المخاطر البيئية وآثارها، إذ يتم التركيز على كيفية زيادة الانتاج وتعظيم الارباح دون الاكتراث لما يترتب عليه من آثار بيئية مستقبلية على المجتمع نتيجة استنزاف ونفاد الموارد الطبيعية وزيادة حجم التلوث والانبعاثات السامة الذي بدوره سينعكس على طبيعة ونوع الحياة للجيل الحالي والقادم.
 تتجلى مشكلة الدراسة في تشخيص وتقييم والحد من مخاطر الجوانب البيئية وماينتج عنها من آثار بيئية ذات أثر واضح على حياة العاملين والبيئة العامة.
 التعرف من خلال هذه الدراسة على مدى تطبيق نظام الإدارة البيئية في (شركة مصافي الوسط/ مصفى الدورة) وتشخيص الجوانب البيئية وتقييمها على وفق إداةFMEA .
 توصلت هذه الدراسة الى جملة من النتائج من استعمال أداة FMEA متعلقة بتقييم درجة أولوية الخطر (RPN1) الخاص بالجوانب البيئية المتولدة في هيئة المشتقات الخفيفة كلها، إذ بلغ مجموع الجوانب البيئية (228) مقسمة الى }خطر كبير (39)، خطر متوسط (126)، خطر بسيط (63){ وبعد تطبيق الاجراءات الموصى بها واتخاذ الافعال العلاجية اصبحت النتائج الخاصة بدرجة أولوية الخطر (RPN2) مقسمة الى }خطر كبير (0)، خطر متوسط (83)، خطر بسيط (145){.
 إن القيمة المضافة في هذه الدراسة تتضح في كيفية توظيف هذه الاداة في تقييم المخاطر البيئية وتحويل الجوانب البيئية المشخصة في القطاع النفطي الى قيم رقمية يسهل التعامل معها بشكل اكثر واقعية من حيث الشدة والحدوث والكشف، التي تكون محصلتها معرفة درجة اولوية الخطر ووضع الاجراءات اللازمة لمعالجته في الشركة المبحوثة.
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Riordan, James T., Jillian A. Tietjen, Coilin W. Walsh, John E. Gustafson, and Thomas S. Whittam. "Inactivation of alternative sigma factor 54 (RpoN) leads to increased acid resistance, and alters locus of enterocyte effacement (LEE) expression in Escherichia coli O157 : H7." Microbiology 156, no. 3 (2010): 719–30. http://dx.doi.org/10.1099/mic.0.032631-0.
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Alternative sigma factor 54 (RpoN) is an important regulator of stress resistance and virulence genes in many bacterial species. In this study, we report on the gene expression alterations that follow rpoN inactivation in Escherichia coli O157 : H7 strain Sakai (SakairpoN : : kan), and the influence of RpoN on the acid resistance phenotype. Microarray gene expression profiling revealed the differential expression of 103 genes in SakairpoN : : kan relative to Sakai. This included the growth-phase-dependent upregulation of genes required for glutamate-dependent acid resistance (GDAR) (gadA, gadB, gadC and gadE), and the downregulation of locus of enterocyte effacement (LEE) genes, which encode a type III secretion system. Upregulation of gad genes in SakairpoN : : kan during exponential growth correlated with increased GDAR and survival in a model stomach system. Complementation of SakairpoN : : kan with a cloned version of rpoN restored acid susceptibility. Genes involved in GDAR regulation, including rpoS (sigma factor 38) and gadE (acid-responsive regulator), were shown to be required for the survival of SakairpoN : : kan by the GDAR mechanism. This study describes the contribution of rpoN to acid resistance and GDAR gene regulation, and reveals RpoN to be an important regulator of stress resistance and virulence genes in E. coli O157 : H7.
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Tran, Ben, Michel S. Beausoleil, Eitan Amir, et al. "Large retroperitoneal lymph nodes (RPLN) as a novel risk factor for venous thromboembolism (VTE) in germ cell tumor (GCT) patients (pts) receiving first-line chemotherapy (chemo)." Journal of Clinical Oncology 30, no. 15_suppl (2012): 4535. http://dx.doi.org/10.1200/jco.2012.30.15_suppl.4535.
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4535 Background: VTE causes substantial morbidity and mortality in GCT pts. The Khorana model is a validated predictive model that stratifies VTE risk in cancer pts receiving chemo; Khorana score ≥3 (K3) identifies pts at high risk. Many GCT pts have bulky RPLN that can cause venous stasis in the lower limbs. This study examines the incidence of VTE in GCT pts and assesses large RPLN as a novel predictor of VTE risk. Methods: Retrospective data from the Princess Margaret Hospital GCT database was complemented by review of medical records. GCT pts receiving 1st line chemo between 2000-2010 were included. Pts diagnosed with VTE prior to chemo and pts receiving thromboprophylaxis (TP) were excluded. Pts diagnosed with VTE during or within 3 months of completing chemo were identified. Large RPLN were defined as having maximal diameter ≥5cm. Odds ratios for VTE risk with large RPLN and K3 were calculated. Discriminatory accuracy (DA) of each predictor was calculated using area under the receiver operating characteristic curves (AUROC). An external cohort from London Regional Cancer Program, with similarly collected data, was used to validate results. Results: In the test cohort 21 (10%) of 216 pts developed VTE. Both large RPLN (OR 6.2, p<0.001) and K3 (OR 11.8, p<0.001) were significantly associated with VTE. Positive predictive value (PPV) was lower for large RPLN compared to K3 (21% v 44%, p<0.014) but sensitivity was greater (71% v 40%, p=0.001), while DA showed no difference (AUROC 0.73 v 0.67, p=0.46). In the validation cohort 10 (9%) of 111 pts developed VTE. There was a non significant trend for associations between VTE and both large RPLN (OR 2.54, p=0.16) and K3 (OR 4.5, p=0.13). When compared to K3, sensitivity was greater for large RPLN (60% v 20%, p=0.003), but there was no difference in PPV (14% v 29%, p=0.25) or DA (AUROC 0.61 v 0.57, p=0.72). Conclusions: VTE occurs in 1 in 10 GCT pts receiving curative chemotherapy. Large RPLN is a novel and clinically applicable predictor of VTE risk, although prospective validation would be beneficial. Randomized controlled trials of TP in GCT pts should be considered in pts at high risk of VTE, identified by large RPLN or K3.
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Wang, Zheng, Xiaolei Chen, Dongmei Zhang, Yiling Cao, Liang Zhang, and Wanxin Tang. "PYCARD Gene Plays a Key Role in Rapidly Progressive Glomerulonephritis: Results of a Weighted Gene Co-Expression Network Analysis." American Journal of Nephrology 48, no. 3 (2018): 193–204. http://dx.doi.org/10.1159/000492725.
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Background: Rapidly progressive glomerulonephritis (RPGN) is caused by various diseases process, thereby resulting in extensive crescent formation, which could lead to a rapid loss of kidney function. The molecular pathogenesis of RPGN remains largely unknown and requires clarification. The weighted gene co-expression network analysis (WGCNA) is a powerful bioinformatics tool to identify meaningful molecules in diseases. Methods: The dataset of GSE104948, which contains 22 RPGN and 18 normal samples, was obtained from Gene Expression Omnibus database. After data pre-processing, the WGCNA was performed to successfully cluster several significant modules. The most significant module was selected for further Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Visualization of network and screening of hub genes were performed by using Cytoscape software. Results: A total of 11 modules were clustered by WGCNA, and the most significant module-turquoise module was selected. As discovered via GO enrichment and KEGG pathway analysis, the turquoise module was mainly associated with neutrophil activation and degranulation. After visualization and calculation for the network, the PYCARD gene has higher relationship score in 2 clusters, namely, neutrophil activation and degranulation. In accordance with the literature review, the hub gene could be closely related to the inflammation response and could act as the potential therapeutic targets in RPGN. Conclusions: WGCNA in RPGN expression profiling was used for the first time in this paper. A novel hub gene closely associated with RPGN was screened out, thereby providing the brand-new molecular candidate for RPGN.
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Amitabh, Wahi, and S. Sundaramurthy. "Wavelet - Based Classification of Outdoor Natural Scenes by Resilient Neural Network." September 4, 2014. https://doi.org/10.5281/zenodo.1096055.
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Natural outdoor scene classification is active and promising research area around the globe. In this study, the classification is carried out in two phases. In the first phase, the features are extracted from the images by wavelet decomposition method and stored in a database as feature vectors. In the second phase, the neural classifiers such as back-propagation neural network (BPNN) and resilient back-propagation neural network (RPNN) are employed for the classification of scenes. Four hundred color images are considered from MIT database of two classes as forest and street. A comparative study has been carried out on the performance of the two neural classifiers BPNN and RPNN on the increasing number of test samples. RPNN showed better classification results compared to BPNN on the large test samples.