gebhart/patrepeval huggingface dataset:
Protein modifications related to phage resistance in a marine roseobacter (2009)

AME Aquatic Microbial Ecology Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials AME 55:203-207 (2009) - DOI: https://doi.org/10.3354/ame01304 NOTE Protein modifications related to phage resistance in a marine roseobacter Yongyu Zhang1,2, Nianzhi Jiao2,*, David R. Colquhoun3, Rolf U. Halden3,4, Feng Chen1,** 1Center of Marine Biotechnology, University of Maryland Biotechnology Institute, Baltimore, Maryland 21202, USA 2State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361005, PR China 3Department of Environmental Health Sciences, Center for Water and Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205–2179, USA 4Center for Environmental Biotechnology, The Biodesign Institute at Arizona State University, Tempe, Arizona 85287–5701, USA **Email: jiao@xmu.edu.cn**Email: chenf@umbi.umd.edu ABSTRACT: The Roseobacter lineage is an important group of bacteria in the marine environment. Silicibacter pomeroyi DSS-3 has been used as a model strain for understanding the biological and ecological relevance of this group. Recently, a phage (Φ1) which infects S. pomeroyi DSS-3 was isolated in our laboratory. Mutants of DSS-3 that are resistant to phage Φ1 were also obtained. A comparison of the protein expression profiles of the wild type, DSS-3, and the phage Φ1-resistant mutant M1 identified a potential phage resistance response due to the modification of 4 highly expressed proteins. One of these 4 proteins was successfully identified via mass spectrometry, and matched a hypothetical protein (SPOA0343) in the S. pomeroyi DSS-3 genome. Although the type of protein modification has not yet been determined, our results suggest that bacteria could become resistant to phage infection via protein modification. Studies on phage resistance of S. pomeroyi DSS-3 could provide new insight into the complex relationship between marine bacteria and their viruses in the natural environment. KEY WORDS: Silicibacter pomeroyi DSS-3 · Phage resistance · Two-dimensional polyacrylamide gel electrophoresis · Mass spectrometry · Protein modification Full text in pdf format PreviousCite this article as: Zhang Y, Jiao N, Colquhoun DR, Halden RU, Chen F (2009) Protein modifications related to phage resistance in a marine roseobacter. Aquat Microb Ecol 55:203-207. https://doi.org/10.3354/ame01304 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in AME Vol. 55, No. 2. Online publication date: April 28, 2009 Print ISSN: 0948-3055; Online ISSN: 1616-1564 Copyright © 2009 Inter-Research.
Inhibition of Macrophage Migration Inhibitory Factor or Its Receptor (CD74) Attenuates Growth and Invasion of DU-145 Prostate Cancer Cells (2006)

Macrophage migration inhibitory factor (MIF), a proinflammatory cytokine, is overexpressed in prostate cancer, but the mechanism by which MIF exerts effects on tumor cells remains undetermined. MIF interacts with its identified membrane receptor, CD74, in association with CD44, resulting in ERK 1/2 activation. Therefore, we hypothesized that increased expression or surface localization of CD74 and MIF overexpression by prostate cancer cells regulated tumor cell viability. Prostate cancer cell lines (LNCaP and DU-145) had increased MIF gene expression and protein levels compared with normal human prostate or benign prostate epithelial cells (p < 0.01). Although MIF, CD74, and CD44 variant 9 expression were increased in both androgen-dependent (LNCaP) and androgen-independent (DU-145) prostate cancer cells, cell surface of CD74 was only detected in androgen-independent (DU-145) prostate cancer cells. Therefore, treatments aimed at blocking CD74 and/or MIF (e.g., inhibition of MIF or CD74 expression by RNA interference or treatment with anti-MIF- or anti-CD74- neutralizing Abs or MIF-specific inhibitor, ISO-1) were only effective in androgen-independent prostate cancer cells (DU-145), resulting in decreased cell proliferation, MIF protein secretion, and invasion. In DU-145 xenografts, ISO-1 significantly decreased tumor volume and tumor angiogenesis. Our results showed greater cell surface CD74 in DU-145 prostate cancer cells that bind to MIF and, thus, mediate MIF-activated signal transduction. DU-145 prostate cancer cell growth and invasion required MIF activated signal transduction pathways that were not necessary for growth or viability of androgen-dependent prostate cells. Thus, blocking MIF either at the ligand (MIF) or receptor (CD74) may provide new, targeted specific therapies for androgen-independent prostate cancer.
A sensitive and specific ELISA detects methionine sulfoxide-containing apolipoprotein A-I in HDL (2008)

Oxidized HDL has been proposed to play a key role in atherogenesis. A wide range of reactive intermediates oxidizes methionine residues to methionine sulfoxide (MetO) in apolipoprotein A-I (apoA-I), the major HDL protein. These reactive species include those produced by myeloperoxidase, an enzyme implicated in atherogenesis. The aim of the present study was to develop a sensitive and specific ELISA for detecting MetO residues in HDL. We therefore immunized mice with HPLC-purified human apoA-I containing MetO(86) and MetO(112) (termed apoA-I(+32)) to generate a monoclonal antibody termed MOA-I. An ELISA using MOA-I detected lipid-free apoA-I(+32), apoA-I modified by 2e-oxidants (hydrogen peroxide, hypochlorous acid, peroxynitrite), and HDL oxidized by 1e- or 2e-oxidants and present in buffer or human plasma. Detection was concentration dependent, reproducible, and exhibited a linear response over a physiologically plausible range of concentrations of oxidized HDL. In contrast, MOA-I failed to recognize native apoA-I, native apoA-II, apoA-I modified by hydroxyl radical or metal ions, or LDL and methionine-containing proteins other than apoA-I modified by 2e-oxidants. Because the ELISA we have developed specifically detects apoA-I containing MetO in HDL and plasma, it should provide a useful tool for investigating the relationship between oxidized HDL and coronary artery disease.
The Battle for Iron between Bacterial Pathogens and Their Vertebrate Hosts (2010)

Iron is a vital nutrient for virtually all forms of life. The requirement for iron is based on its role in cellular processes ranging from energy generation and DNA replication to oxygen transport and protection against oxidative stress. Bacterial pathogens are not exempt from this iron requirement, as these organisms must acquire iron within their vertebrate hosts in order to replicate and cause disease.
Binary‐Metal Perovskites Toward High‐Performance Planar‐Heterojunction Hybrid Solar Cells (2014)

A simple, low temperature solution process for Pb/Sn binary-metal perovskite planar-heterojunction solar cells is demonstrated. Sn inclusion substantially influences the band-gap, crystallization kinetics, and thin-film formation leading to a broadened light absorption and enhanced film coverage on ITO/PEDOT:PSS. As a result, the optimized device shows a PCE exceeding 10%, which is the best result for binary-metal perovskite solar cells so far.
Nanosecond switching in GeTe phase change memory cells (2009)

The electrical switching behavior of GeTe-based phase change memory devices is characterized by time resolved experiments. SET pulses with a duration of less than 16 ns are shown to crystallize the material. Depending on the resistance of the RESET state, the minimum SET pulse duration can even be reduced down to 1 ns. This finding is attributed to the increasing impact of crystal growth upon decreasing switchable volume. Using GeTe or materials with similar crystal growth velocities, hence promises nonvolatile phase change memories with dynamic random access memorylike switching speeds.
Adenoviruses Activate Human Dendritic Cells without Polarization toward a T-Helper Type 1-Inducing Subset (1999)

Human monocyte-derived dendritic cells (DC) infected with recombinant adenoviruses (rAd) are promising candidate vaccines for inducing protective immunity against pathogens and tumors. However, since some viruses are known to negatively affect DC function, it is important to investigate the interactions between rAd and DC. We now show that infection by rAd enhances the immunostimulatory capacity of immature human monocyte-derived DC through the upregulation of the costimulatory molecules CD80, CD86, and CD40 and the major histocompatibility complex class I and II molecules. Although rAd infection fails to induce the secretion of interleukin-12 (IL-12) and only marginally induces the expression of the DC maturation marker CD83, it acts in synergy with CD40 triggering in rendering DC fully mature. rAd-infected DC triggered through CD40 produce more IL-12 and are more efficient in eliciting T-helper type 1 responses than DC activated by CD40 triggering only. rAd lacking one or more of the early regions, E1, E2A, E3, and E4, which play an important role in virus-host cell interactions are equally capable of DC activation. Efficient DC infection requires a high multiplicity of infection (>1,000), a fact which can be attributed to the absence of the coxsackievirus and adenovirus receptor on this cell type. Despite the poor ability of DC to be infected by rAd, which may be improved by targeting rAd to alternative DC surface molecules, DC infected with all currently tested rAd constitute potent immunostimulators. Our study provides new insights into the interactions between two highly promising vaccine components, rAd and DC, and indicates that their combination into one vaccine may be very advantageous for the stimulation of T-cell immunity.
Wnt/β-Catenin Signaling Modulates Survival of High Glucose–Stressed Mesangial Cells (2006)

Glomerulosclerosis and diabetic nephropathy are attributable to high glucose induction of mesangial cell apoptosis. Whereas Wnt signaling has been found to regulate renal morphogenesis and pathogenesis, the biologic role of Wnt/beta-catenin signaling in controlling high glucose-induced mesangial cell apoptosis is not well defined. Herein is reported that Wnt/beta-catenin signaling is required for protecting glomerular mesangial cells from high glucose-mediated cell apoptosis. High glucose downregulated Wnt4 and Wnt5a expression and the subsequent nuclear translocation of beta-catenin, whereas it increased glycogen synthase kinase-3beta (GSK-3beta) and caspase-3 activities and apoptosis of glomerular mesangial cells. Suppression of GSK-3beta activation or increase in nuclear beta-catenin by transfection of Wnt4 or Wnt5a or stable beta-catenin (S33Y) reversed Akt activation and reduced the high glucose-mediated caspase-3 cleavage and cell apoptosis. Pharmacologic inhibition of GSK-3beta by recombinant Wnt5a or bromoindirubin-3'-oxime or LiCl increased Akt phosphorylation and beta-catenin translocation and abrogated high glucose-mediated proapoptotic activities. Exogenous bromoindirubin-3'-oxime treatment reduced phospho-Ser(9)-GSK-3beta and beta-catenin expression and apoptosis of cells adjacent to glomeruli in diabetic kidneys and attenuated urinary protein secretion in diabetic rats. Taken together, mesangial cells responded to high glucose by impairing that canonical Wnt pathway to increase proapoptotic activities. Sustaining Wnt/beta-catenin signaling is beneficial for promoting survival of mesangial cells that are exposed to high glucose stress.
Electricity Production Coupled to Ammonium in a Microbial Fuel Cell (2009)

The production of electricity from ammonium was examined using a rotating-cathode microbial fuel cell (MFC). The addition of ammonium chloride, ammonium sulfate, or ammonium phosphate (monobasic) resulted in electricity generation, while adding sodium chloride, nitrate, or nitrite did not cause any increase in current production. The peak current increased with increasing amount of ammonium addition up to 62.3 mM of ammonium chloride, suggesting that ammonium was involved in electricity generation either directly as the anodic fuel or indirectly as substrates for nitrifiers to produce organic compounds for heterotrophs. Adding nitrate or nitrite with ammonium increased current production compared to solely ammonium addition. Using 16S rRNA-linked molecular analyses, we found ammonium-oxidizing bacteria and denitrifying bacteria on both the anode and cathode electrodes, whereas no anammox bacteria were detected. The dominant ammonium-oxidizing bacteria were closely related to Nitrosomonas europaea. The present MFC achieved an ammonium removal efficiency of 49.2 +/- 5.9 or 69.7 +/- 3.6%, depending on hydraulic retention time, but exhibited a very low Coulombic efficiency.
The heparin-binding site in tetranectin is located in the N-terminal region and binding does not involve the carbohydrate recognition domain (2000)

Tetranectin is a homotrimeric plasma and extracellular-matrix protein that binds plasminogen and complex sulphated polysaccharides including heparin. In terms of primary and tertiary structure, tetranectin is related to the collectin family of Ca2+-binding C-type lectins. Tetranectin is encoded in three exons. Exon 3 encodes the carbohydrate recognition domain, which binds to kringle 4 in plasminogen at low levels of Ca2+. Exon 2 encodes an α-helix, which is necessary and sufficient to govern the trimerization of tetranectin by assembling into a triple-helical coiled-coil structural element. Here we show that the heparin-binding site in tetranectin resides not in the carbohydrate recognition domain but within the N-terminal region, comprising the 16 amino acid residues encoded by exon 1. In particular, the lysine residues in the decapeptide segment KPKKIVNAKK (tetranectin residues 6-15) are shown to be of primary importance in heparin binding.
Functionalization of Inorganic Nanoparticles for Bioimaging Applications (2011)

Modern biomedical imaging technologies have led to significant advances in diagnosis and therapy. Because most disease processes occur at the molecular and cellular levels, researchers continue to face challenges in viewing and understanding these processes precisely and in real time. The ideal imaging resolution would be in nanometers, because most biological processes take place on this length scale. Therefore, the functionalization of nanoparticles (NPs) and their use in therapeutic and diagnostic applications are of great interest. Molecular and cellular imaging agents made from inorganic NPs have been developed to probe such biological events noninvasively. The conjugation of tiny NPs with specific biomolecules allows researchers to target the desired location, reduce overall toxicity, and boost the efficiency of the imaging probes. In this Account, we review recent research on the functionalization of NPs for bioimaging applications. Several types of NPs have been employed for bioimaging applications, including metal (Au, Ag), metal oxide (Fe(3)O(4)), and semiconductor nanocrystals (e.g. quantum dots (QDs) and magnetic quantum dots (MQDs)). The preparation of NPs for bioimaging applications can include a variety of steps: synthesis, coating, surface functionalization, and bioconjugation. The most common strategies of engineering NP surfaces involve physical adsorption or chemisorption of the desired ligands onto the surface. Chemisorption or covalent linkages are preferred, and the coated NPs should possess high colloidal stability, biocompatibility, water solubility, and functional groups for further bioconjugation. Many of the functionalization techniques that have been reported in the literature suffer from limitations such as complex synthesis steps, poor biocompatibility, low stability, and hydrophobic products. Coating strategies based on chemisorption and ligand exchange often provide a better way to tailor the surface properties of NPs. After conjugation with the appropriate targeting ligands, antibodies, or proteins, the NPs may exhibit highly selective binding, making them useful for fluorescence imaging, magnetic resonance imaging (MRI), positron emission tomography (PET) imaging, and multimodal imaging.
Examination and improvement of reading disturb characteristics of a surrounded gate STTM memory cell (2004)

This paper introduces a novel surrounded gate STTM cell technology to improve retention and read disturb characteristics. In the memory cells previously reported, the device structures limits the CMOS-compatible memory integration and the operation voltage scaling of the memory cells. The proposed cell architecture overcomes this problem and also improves the read disturb characteristics. The proposed memory cell was fabricated using the 0.18 um design rule based on the low power SRAM process technology. This paper demonstrate an the device characteristics of the proposed memory cell and the improvement of tin a read disturb characteristics.
Estrogen receptors α and β in the rodent mammary gland (2000)

An obligatory role for estrogen in growth, development, and functions of the mammary gland is well established, but the roles of the two estrogen receptors remain unclear. With the use of specific antibodies, it was found that both estrogen receptors, ERalpha and ERbeta, are expressed in the rat mammary gland but the presence and cellular distribution of the two receptors are distinct. In prepubertal rats, ERalpha was detected in 40% of the epithelial cell nuclei. This decreased to 30% at puberty and continued to decrease throughout pregnancy to a low of 5% at day 14. During lactation there was a large induction of ERalpha with up to 70% of the nuclei positive at day 21. Approximately 60-70% of epithelial cells expressed ERbeta at all stages of breast development. Cells coexpressing ERalpha and ERbeta were rare during pregnancy, a proliferative phase, but they represented up to 60% of the epithelial cells during lactation, a postproliferative phase. Western blot analysis and sucrose gradient centrifugation confirmed this pattern of expression. During pregnancy, the proliferating cell nuclear antigen was not expressed in ERalpha-positive cells but was observed in 3-7% of ERbeta-containing cells. Because more than 90% of ERbeta-bearing cells do not proliferate, and 55-70% of the dividing cells have neither ERalpha nor ERbeta, it is clear that the presence of these receptors in epithelial cells is not a prerequisite for estrogen-mediated proliferation.
A Dexterous System for Laryngeal Surgery Multi-Backbone Bending Snake-like Slaves for Teleoperated Dexterous Surgical Tool Manipulation (2004)

Abstract — This paper presents a design overview of a novel high DoF (Degrees-of-Freedom) system being developed for minimally invasive surgery of the throat. The system is designed to allow remote operation of 2-3 tools with high tip dexterity to enable suturing and soft-tissue manipulation while using the patient’s mouth as the only entry port. The slave is a 34 DoF unit equipped with three snake-like distal dexterity units for surgical tool manipulation. Each of these units is a multi-backbone snakelike mechanism equipped with a detachable milli parallel manipulator allowing interchangeable tools to be used. The paper presents the outline of the kinematic analysis of the snake-like units and proposes one possible actuation redundancy resolution to allow further downsize scalability while reducing the risk of buckling of the primary backbone of the snake-like units. Finally, the paper presents a first early experiment with a prototype of the snake-like unit. Keywords- NiTi, multy backbone robot, snake robots, surgical assistant, master-slave mode. I.
ZINC: A Free Tool to Discover Chemistry for Biology (2012)

ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site also enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number. Small custom subsets may be created, edited, shared, docked, downloaded, and conveyed to a vendor for purchase. The database is maintained and curated for a high purchasing success rate and is freely available at zinc.docking.org.
Cell adhesiveness and the cell cycle: correlation in synchronized Balb/c 3T3 cells (1984)

The adhesiveness of Balb/c 3T3 cells partially synchronized either by drug treatment or by the mitotic cell shake-off procedure was assessed by following the aggregation kinetics of aliquots of the cells suspended under defined conditions within the confines of a cone and plate viscometer. M phase cells synchronized by either method were significantly more adherent than appropriate control cells. Cells arrested in S phase following drug treatment were found to be poorly adhesive whereas G1 phase cells prepared by allowing drug treated M phase cells to proceed through mitosis or by treating them with L-histidinol did not differ in their adhesiveness from appropriate control cells. The adhesiveness of control cell populations was found to vary with the extent of re-feeding indicating a possible metabolic dependency of cell adhesion. It is suggested that although M phase cells are poorly adherent to the substrate they are nevertheless considerably adherent in an aggregation system. There was no apparent correlation of the observed increase in intercellular adhesion with any particular stage of M phase (prophase, metaphase, anaphase, telophase). We propose that Balb/c 3T3 cells show an increase in cell-cell adhesiveness as they proceed into M phase and that this is maintained until after division is complete. Our suggestion that certain cell types may interact differently with each other and with the substrate in different stages of the cell cycle could have in vivo relevance in those processes such as tumour spread where considerable cell division is involved.
Prognostic factors in medullary thyroid carcinomas.Survival in relation to age, sex, stage, histology, immunocytochemistry, and DNA content (1988)

Patients with medullary thyroid carcinomas (MTC) were analyzed according to age, sex, and tumor stage. In addition, the MTC were screened for the predominant histologic pattern, immunocytochemical spectrum (60 tumors), and DNA content (DNA cytophotometry and DNA flow cytometry, 25 tumors). These findings were correlated with follow-up data available for 45 of these patients. Forty-eight percent of the tumors revealed a polygonal cell pattern, whereas 22% showed spindle-cell predominance. All tumors contained cytokeratin, chromogranin A, and calcitonin (CT). Calcitonin gene-related peptide (CGRP) was present in 92%, carcinoembryonic antigen (CEA) in 77%, neuron-specific enolase (NSE) in 75%, and vimentin in 53% of cases. Positivity for neurotensin, somatostatin, neurofilaments, bombesin, and alpha human chorionic gonadotropin (a-hCG) and serotonin ranged between 3% and 27%. All MTC were negative for substance P, adrenocorticotropic hormone (ACTH), thyroglobulin (TG), or S-100 protein. Local recurrences and regional lymph node metastases revealed identical staining patterns as the primaries. Prognosis of MTC was found not to be related to histologic features (dominant architectural pattern, cellular shape, presence of amyloid deposits) or immunocytochemical pattern. Instead, survival was significantly correlated to age, sex, and stage of disease. The best prognosis was seen in women younger than 40 years and revealing an early stage of disease. DNA measurements added valuable information in assessing the prognosis of MTC.