gebhart/patrepeval huggingface dataset:
MalI, a novel protein involved in regulation of the maltose system of Escherichia coli, is highly homologous to the repressor proteins GalR, CytR, and LacI (1989)

The maltose regulon of Escherichia coli comprises several operons that are under common regulatory control of the MalT activator protein. Five mal genes, organized in two divergent operons, code for a binding-protein-dependent transport system specific for maltose and maltodextrins. MalK, one of the subunits of this transport system, not only is essential for transport but also plays a role in regulation. Mutations abolishing MalK function not only result in inability to transport maltose but also cause constitutive expression of the maltose regulon. For this constitutivity to be exerted, the function of an additional gene product, MalI, is necessary. Using the constitutive expression of a malK-lacZ fusion as a signal, we cloned the malI gene, expressed it in minicells, and determined its DNA sequence. The sequence predicted a protein of 34,729 molecular weight, in agreement with the apparent molecular weight of the protein (35,000) when expressed in minicells and analyzed by polyacrylamide gel electrophoresis and autoradiography. MalI exhibited high homology to the repressor proteins GalR, CytR, and LacI. When the amino acid sequences were appropriately aligned, MalI showed 28% identity to GalR, 21% to CytR, and 24% to LacI. Including conservative amino acid exchanges, these numbers increased to 69, 56, and 58%, respectively. The regions of high homology were clustered in particular at the N-terminal portion of the protein that includes the helix-turn-helix motif thought to be involved in DNA binding. The protein contained a short stretch of 30 amino acids that was surprisingly homologous to a sequence in MalT. The amino-terminal half of the protein exhibited significant homology with MalK. The transcriptional start of malI was determined by reverse transcriptase and by S1 nuclease mapping. We found a possible binding site for cyclic AMP receptor protein in the promoter region of malI as well as two perfect direct repeats of 14 base pairs with twofold symmetry indicating their possible role as operator sites. Upstream to malI we observed a divergent open reading frame that extended to the end of the sequenced DNA.
MicroRNA-126 Regulates HOXA9 by Binding to the Homeobox (2008)

The PicTar program predicted that microRNA-126 (miR-126), miR-145, and let-7s target highly conserved sites within the Hoxa9 homeobox. There are increased nucleotide constraints in the three microRNA seed sites among Hoxa9 genes beyond that required to maintain protein identity, suggesting additional functional conservation. In preliminary experiments, forced expression of these microRNAs in Hoxa9-immortalized bone marrow cells downregulated the HOXA9 protein and caused loss of biological activity. The microRNAs were shown to target their predicted sites within the homeobox. miR-126 and Hoxa9 mRNA are coexpressed in hematopoietic stem cells and downregulated in parallel during progenitor cell differentiation; however, miR-145 is barely detectable in hematopoietic cells, and let-7s are highly expressed in bone marrow progenitors, suggesting that miR-126 may function in normal hematopoietic cells to modulate HOXA9 protein. In support of this hypothesis, expression of miR-126 alone in MLL-ENL-immortalized bone marrow cells decreased endogenous HOXA9 protein, while inhibition of endogenous miR-126 increased expression of HOXA9 in F9 cells.
Hepatitis C virus antibodies in dialysis patients in Tunisia: a single center study. (2012)

Fifty-eight patients on maintenance hemodialysis in a dialysis unit at Tunis, Tunisia were tested for anti-hepatitis C virus (anti-HCV) antibodies by second generation ELISA test, and for HCV-RNA by nested reverse transcriptase polymerase chain reaction (RT-PCR) of 5' non-coding region. Specificity of the antibodies was confirmed by immunoblot test. HCV genotype was defined using INNO-LIPA test. Twenty-seven out of 58 patients (46.5%) were reactive by ELISA. Transaminase levels were assessed over a six-month period and showed normal average values. Fourteen of the 27 anti-HCV positive patients (51%) were positive by RT-PCR. Type 1b HCV genotype was the most prevalent, seen in all the dialysis patients and one patient in addition, was co-infected with genotype 4. There was a significant correlation between the duration on dialysis (over five years) and the prevalence of anti-HCV-positive patients (P< 0.005) while no correlation existed between the number of blood transfusions and the presence of anti-HCV antibodies. The present study illustrates the high prevalence of HCV infection among Tunisian dialysis patients (51%) and indicates that the spread may be nosocomial rather than transfusion-related.
Evaluation of hot-melt extrusion technology to improve dissolution rates of poorly water soluble drugs (2004)

The bioavailability of orally administered drugs mainly depends on solubility and permeability. Since the advent of high throughput screening (HTS) in drug discovery process the resultant compounds are often high molecular weight and highly lipophilic, that show poor solubility. Scientists have tried to address solubility issues by various pharmaceutical interventions. Today amongst many methods available to improve solubility and dissolution rate, preparation of solid dispersions and solid solutions has gained enormous attention. Hot-melt extrusion is one of the most widely applied processing technologies in the plastic, rubber and food industry. Today this technology has found its place in the array of pharmaceutical manufacturing operations. Melt extrusion processes are currently applied in the pharmaceutical field for the manufacture of a verity of dosage forms and formulations such as granules, pellets, tablets, implants, transdermal systems and ophthalmic inserts. In this study the melt extrusion process is evaluated to formulate solid dispersion and solid solution of poorly water soluble model drug. The primary objective of this study is to evaluate the utility of hot-melt extrusion (HME) in improving the dissolution rate of a poorly water-soluble model drug (Indomethacin) using suitable hydrophilic polymers such as Eudragit EPO (EPO), Polyvinyl pyrrolidone-vinyl acetate copolymer (PVP-VA), Polyvinylpyrrolidone K30 (PVPK30), Poloxamer 188 (P188). The secondary objective is to characterize physical and viscoelastic properties of materials prior to the actual melt extrusion process to assess their suitability for HME process and to establish correlation between these assessments with HME process parameters. To achieve these objectives, the research plan is mainly divided in to three broad sections: (1) Physico-mechanical evaluation of drug and polymer binary mixtures prior to hot-melt extrusion (thermal analysis, viscoelastic evaluation and solubility parameters). (2) Evaluation of hot-melt extrusion process parameters (such as barrel temperatures, motor load, screw speed, feed rate, melt pressure etc.) for the various formulations. (3) The performance attributes of hot-melt extrudate such as solid state characterization (differential scanning calorimetry, powder x-ray diffraction, FTIR spectroscopy), intrinsic dissolution rate studies and stability studies.
Human neutrophil collagenase. A distinct gene product with homology to other matrix metalloproteinases. (1990)

We have identified and sequenced a cDNA encoding human neutrophil collagenase from a lambda gt11 cDNA library constructed from mRNA extracted from the peripheral leukocytes of a patient with chronic granulocytic leukemia. The library was screened with an oligonucleotide probe constructed from the putative zinc-binding region of fibroblast collagenase. Eleven positive clones were identified, of which the one bearing the largest insert (2.2 kilobases (kb)) was sequenced. From the nucleotide sequence of the 2.2-kb cDNA clone we have deduced a 467-amino acid sequence representing the entire coding sequence of the enzyme. The deduced protein was confirmed as neutrophil collagenase by conformity with the amino-terminal sequence analyses of three tryptic peptides of purified neutrophil collagenase. The cDNA clone hybridizes to a 3.3-kb mRNA present in RNA extracted from human bone marrow but did not hybridize with RNA isolated from U937 cells induced to differentiate with phorbol myristate acetate. Neutrophil collagenase was found to possess 57% identity with the deduced protein sequence for fibroblast collagenase with 72% chemical similarity. Certain regions of the molecule, including the putative zinc-binding region, are highly conserved. When compared with the published sequence for fibroblast collagenase, neutrophil collagenase contains four additional sites for glycosylation. Medium from COS-7 cells transfected with a pcDNA1 eucaryotic expression vector containing cDNA for neutrophil collagenase degraded type I collagen into the three-quarter, one-quarter fragments characteristic of mammalian interstitial collagenase activity. Thus, definitive evidence based on the cDNA sequence confirms the neutrophil collagenase is a distinct gene product and a member of the family of matrix metalloproteinases.
Changes in laminin isoforms associated with brain tumor invasion and angiogenesis (2006)

Laminins are the major constituents of blood vessel basement membranes (BMs). Each laminin is a trimer consisting of three assembled polypeptide chains, alpha, beta and gamma. More than 15 laminin isoforms are known to date and the expression of specific isoforms may change in certain pathological conditions. Here we show that during progression of glial tumors laminin-9 (alpha4beta2gamma1) is switched to laminin-8 (alpha4beta1gamma1), which is dramatically increased in glial brain tumors. Laminin-8 overproduction by glial tumor cells facilitates spread of glioma. Brain tumors with laminin-8 overexpression recur faster after standard treatment and patients have shorter survival time. Laminin-8 may be thus used as a predictor of tumor recurrence, patient survival and as a potential molecular target for glioma therapy.
Evidence for the presence of a phosphatidylinositol anchor on the lipoarabinomannan and lipomannan of Mycobacterium tuberculosis. (1990)

The recent availability (Hunter, S.W., Gaylord, H., and Brennan, P.J. (1986) J. Biol. Chem. 261, 12345-12351) of the well known arabinomannan of Mycobacterium leprae and Mycobacterium tuberculosis as the pure native lipoarabinomannan has resulted in its implication in key aspects of the immunopathogenesis of leprosy and tuberculosis. We had indicated that the lipid moiety of lipoarabinomannan is probably based on a diacylglycerol unit in that glycerol and the two fatty acids, hexadecanoate and 10-methyloctadecanoate, were identified. In addition, lipoarabinomannan was also shown to contain myo-inositol 1-phosphate. Evidence is now presented, based on selective radiolabeling and analysis of various cleavage fragments, that the inositol phosphate exists as both an alkalilable phosphodiester and as part of a phosphatidylinositol "membrane anchor." The mannan of M. tuberculosis was also isolated as the native lipomannan. It also apparently contains a phosphatidylinositol unit but is devoid of the alkali-labile inositol phosphate residues. These lipopolysaccharides are apparently multiglycosylated versions of the well known myocobacterial mannosyl phosphatidylinositols and are prokaryotic versions of the growing list of phosphatidylinositol-anchored macromolecules. Immunogold labeling demonstrates that lipoarabinomannan is a true antigenic capsular or extracellular product of M. tuberculosis. The presence of a phosphatidylinositol residue on lipoarabinomannan may explain its interaction with macrophage membranes and role in mycobacterial pathogenesis.
Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli (1992)

Fis is a small basic DNA-binding protein from Escherichia coli that was identified because of its role in site-specific DNA recombination reactions. Recent evidence indicates that Fis also participates in essential cell processes such as rRNA and tRNA transcription and chromosomal DNA replication. In this report, we show that Fis levels vary dramatically during the course of cell growth and in response to changing environmental conditions. When stationary-phase cells are subcultured into a rich medium, Fis levels increase from less than 100 to over 50,000 copies per cell prior to the first cell division. As cells enter exponential growth, nascent synthesis is largely shut off, and intracellular Fis levels decrease as a function of cell division. Fis synthesis also transiently increases when exponentially growing cells are shifted to a richer medium. The magnitude of the peak of Fis synthesis appears to reflect the extent of the nutritional upshift. fis mRNA levels closely resemble the protein expression pattern, suggesting that regulation occurs largely at the transcriptional level. Two RNA polymerase-binding sites and at least six high-affinity Fis-binding sites are present in the fis promoter region. We show that expression of the fis operon is negatively regulated by Fis in vivo and that purified Fis can prevent stable complex formation by RNA polymerase at the fis promoter in vitro. However, autoregulation only partially accounts for the expression pattern of Fis. We suggest that the fluctuations in Fis levels may serve as an early signal of a nutritional upshift and may be important in the physiological roles Fis plays in the cell.
Effect of surface reconstruction on the structural prototypes of ultrasmall ultrabright Si29 nanoparticles (2001)

We propose, using density functional, configuration interaction, and quantum Monte Carlo calculations, structural prototypes of ultrasmall ultrabright particles prepared by dispersion from bulk. We constructed near spherical structures (Td point group symmetry) that contain 29 Si atoms, five of which constitute a tetrahedral core and the remaining 24 constitute a hydrogen terminated reconstructed Si surface. The surface is a highly wrinkled or puckered system of hexagons and pentagons (as in a filled fullerene). We calculated, for several surface reconstruction models, the coordinates of atoms, the absorption spectrum, the absorption edge, polarizability, and the electron diffraction pattern. The Si29H24 (six reconstructed surface dimers) gives a size of 0.9 nm, an absorption spectrum and bandgap (3.5±0.3 eV), in fair agreement with measurement. The structure yields a polarizability of 830 a.u. with an effective “dielectric” constant of ∼6.0. The calculated electron diffraction of single particles shows residual crystalline coherent scattering for large but not small scattering angles.
Transforming growth factor-beta: the key to understanding lipoprotein(a)? (1995)

Most large studies of the blood parameters that act as risk factors for myocardial infarction, stroke and atherosclerosis have identified elevated circulating levels of lipoprotein(a) as an important risk factor. Lipoprotein(a) consists of an LDL particle that is covalently bound to the distinguishing protein component apolipoprotein(a). Ever since apolipoprotein(a) was cloned in 1987 and the marked sequence homology to plasminogen was noted, mechanisms for the atherogenic activity of lipoprotein(a), based on the competitive inhibition of plasminogen activity, have been proposed. However, with the availability of transgenic mice expressing both human apolipoprotein(a) and lipoprotein(a), recent studies have demonstrated that lipoprotein(a) acts to inhibit plasminogen activation in vivo. One consequence of this is reduced activation of the cytokine transforming growth factor-beta, an important regulator of vessel wall structure.
Flow Cytometric Diagnosis of the Cell Lineage and Developmental Stage of Acute Lymphoblastic Leukemia by Novel Monoclonal Antibodies Specific to Human Pre–B-Cell Receptor (1998)

Three novel monoclonal antibodies (MoAbs) have been established that recognize distinct epitopes of a human pre–B-cell receptor (pre-BCR) composed of a μ heavy (μH) chain and a λ5/VpreB surrogate light (SL) chain. HSL11 reacts with λ5 whereas HSL96 reacts with VpreB. Intriguingly, HSL2 does not bind to each component of the pre-BCR but does bind to the completely assembled pre-BCR complex. Flow cytometric analyses with cytoplasmic staining of a panel of human cell lines showed that HSL11 and HSL96 specifically stained cell lines derived from the pro–B and pre–B-cell stages of B-cell development. In contrast, HSL2 stained exclusively cell lines derived from the pre–B-cell stage. These results prompted us to explore the possibility of clinical application of these MoAbs for the determination of the cell lineage and developmental stage of acute lymphoblastic leukemia (ALL). Whereas none of mature B-lineage ALLs (B-ALLs), T-lineage ALLs (T-ALLs), and acute myeloid leukemias analyzed were stained in the cytoplasm with these three MoAbs, the vast majority of non–B- and non–T-ALLs (53 out of 56 cases) were found positive for either λ5, Vpre-B, or both in their cytoplasm. Among these 53 cytoplasmic SL chain-positive ALLs, 19 cases were also positive for cytoplasmic μH chain, indicative of pre–B-cell origin. Interestingly, 6 out of these 19 pre–B-ALL cases were found negative for cytoplasmic staining with HSL2. From these results, we propose a novel classification of B-ALL in which five subtypes are defined on the basis of the differential expression of SL chain, μH chain, pre-BCR, and light chain along the B-cell development.
Expression of epithelial membrane protein‐2 is associated with endometrial adenocarcinoma of unfavorable outcome (2006)

EMP2 expression is a feature of some prognostically unfavorable endometrial cancers. Its utility for clinical decision making and its biologic role in endometrial cancer deserves further study in a larger series of patients.
RGS4 and GAIP are GTPase-activating proteins for G qα and block activation of phospholipase Cβ by γ-thio-GTP-G qα (1997)

RGS proteins constitute a newly appreciated and large group of negative regulators of G protein signaling. Four members of the RGS family act as GTPase-activating proteins (GAPs) with apparent specificity for members of the Gi alpha subfamily of G protein subunits. We demonstrate here that two RGS proteins, RGS4 and GAIP, also act as GAPs for Gq alpha, the G alpha protein responsible for activation of phospholipase C beta. Furthermore, these RGS proteins block activation of phospholipase C beta by guanosine 5'-(3-O-thio) triphosphate-Gq alpha. GAP activity does not explain this effect, which apparently results from occlusion of the binding site on G alpha for effector. Inhibitory effects of RGS proteins on G protein-mediated signaling pathways can be demonstrated by simple mixture of RGS4 or GAIP with plasma membranes.
Antagonistic effects of TGF-β1 and MSF on fibroblast migration and hyaluronic acid synthesis: Possible implications for dermal wound healing (1992)

The migration of adult skin fibroblasts into three-dimensional collagen gel matrices is differentially affected by cell density, with subconfluent cells displaying a significantly elevated level of migration compared to confluent ones. Fetal fibroblasts differ from adult cells in that they display an elevated level of migration at both subconfluent and confluent cell densities. We have previously reported that this difference in behaviour results from the secretion by fetal fibroblasts of a 'migration stimulating factor' (MSF) which is not made by their normal adult counterparts, and that MSF appears to act by stimulating the synthesis of hyaluronic acid (HA). Data presented in this communication indicate that (a) MSF specifically stimulates the synthesis of high molecular weight species of HA, (b) TGF-beta 1 inhibits the elevated migration of adult fibroblasts plated at subconfluent cell density, (c) under these conditions, TGF-beta 1 induces a parallel decrease in the synthesis of high molecular weight HA and increase in the synthesis of low molecular weight HA, (d) TGF-beta 1 is a potent antagonist of MSF, effectively blocking its stimulation of cell migration and synthesis of high molecular weight HA, and (e) the inhibition of fibroblast migration by TGF-beta 1 does not appear to be a chemotactic response dependent upon the existence of a concentration gradient of the cytokine. Our observations regarding the inhibitory effects of TGF-beta 1 on fibroblast migration into 3D collagen gels stand in marked contrast to various published reports indicating that this cytokine stimulates the migration of human skin fibroblasts through the pores of polycarbonate filters as used in modified Boyden chamber assays; this discrepancy underscores the importance of the substratum in modulating cellular response to cytokines. Our results are discussed in terms of the possible combined contribution of MSF and TGF-beta 1 to wound healing.
A brominated (aminoimidazolinyl)indole from the sponge Discodermia polydiscus (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA brominated (aminoimidazolinyl)indole from the sponge Discodermia polydiscusHao H. Sun and Shinichi SakemiCite this: J. Org. Chem. 1991, 56, 13, 4307–4308Publication Date (Print):June 1, 1991Publication History Published online1 May 2002Published inissue 1 June 1991https://pubs.acs.org/doi/10.1021/jo00013a045https://doi.org/10.1021/jo00013a045research-articleACS PublicationsRequest reuse permissionsArticle Views203Altmetric-Citations33LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Control of Crystal Nucleation and Growth of Calcium Carbonate by Synthetic Substrates (2001)

Construction of organic−inorganic hybrid materials with controlled mineralization analogous to those produced by nature is now of current interest for both organic and inorganic chemists to understand the mechanism of the natural biomineralization process as well as to seek industrial and technological applications. This review provides a general survey of recent research on control of crystal nucleation and growth of calcium carbonate by synthetic substrates from the viewpoint of organic and polymer chemistry. Model systems in which low-molecular-weight, linear polymeric, and dendritic organic additives are used to study the effect of molecular properties such as charge and functionality on inorganic crystallization are providing insights into the possible mechanisms operating in biology. To probe the organic−inorganic interface and resolve some of the molecular events mediating template-directed crystal nucleation and growth, a simple model surface, that is, compressed monolayers at the air/water interface and self-assembled monolayers on a solid surface, was used for the nucleation of oriented inorganic materials. The template-inhibition strategy for the synthesis of CaCO3 thin film has also been reported. Microscale phase separation in reaction media has importance in the synthesis of inorganic materials with unusual form and hierarchical structure. These interesting efforts have led to fundamental developments in areas relating to the biomineralization process, which is expected to be the impetus for the next industrial revolution.