gebhart/patrepeval huggingface dataset:
Primary structure of human nuclear ribonucleoprotein particle C proteins: conservation of sequence and domain structures in heterogeneous nuclear RNA, mRNA, and pre-rRNA-binding proteins. (1987)

In the eucaryotic nucleus, heterogeneous nuclear RNAs exist in a complex with a specific set of proteins to form heterogeneous nuclear ribonucleoprotein particles (hnRNPs). The C proteins, C1 and C2, are major constituents of hnRNPs and appear to play a role in RNA splicing as suggested by antibody inhibition and immunodepletion experiments. With the use of a previously described partial cDNA clone as a hybridization probe, full-length cDNAs for the human C proteins were isolated. All of the cDNAs isolated hybridized to two poly(A)+ RNAs of 1.9 and 1.4 kilobases (kb). DNA sequencing of a cDNA clone for the 1.9-kb mRNA (pHC12) revealed a single open reading frame of 290 amino acids coding for a protein of 31,931 daltons and two polyadenylation signals, AAUAAA, approximately 400 base pairs apart in the 3' untranslated region of the mRNA. DNA sequencing of a clone corresponding to the 1.4-kb mRNA (pHC5) indicated that the sequence of this mRNA is identical to that of the 1.9-kb mRNA up to the first polyadenylation signal which it uses. Both mRNAs therefore have the same coding capacity and are probably transcribed from a single gene. Translation in vitro of the 1.9-kb mRNA selected by hybridization with a 3'-end subfragment of pHC12 demonstrated that it by itself can direct the synthesis of both C1 and C2. The difference between the C1 and C2 proteins which results in their electrophoretic separation is not known, but most likely one of them is generated from the other posttranslationally. Since several hnRNP proteins appeared by sodium dodecyl sulfate-polyacrylamide gel electrophoresis as multiple antigenically related polypeptides, this raises the possibility that some of these other groups of hnRNP proteins are also each produced from a single mRNA. The predicted amino acid sequence of the protein indicates that it is composed of two distinct domains: an amino terminus that contains what we have recently described as a RNP consensus sequence, which is the putative RNA-binding site, and a carboxy terminus that is very negatively charged, contains no aromatic amino acids or prolines, and contains a putative nucleoside triphosphate-binding fold, as well as a phosphorylation site for casein kinase type II. The RNP consensus sequence was also found in the yeast poly(A)-binding protein (PABP), the heterogeneous nuclear RNA-binding proteins A1 and A2, and the pre-rRNA binding protein C23. All of these proteins are also composed of at least two distinct domains: an amino terminus, which possesses one or more RNP consensus sequences, and a carboxy terminus, which is unique to each protein, being very acidic in the C proteins and rich in glycine in A1, and C23 and rich in proline in the poly(A)-binding protein. These findings suggest that the amino terminus of these proteins possesses a highly conserved RNA-binding domain, whereas the carboxy terminus contains a region essential to the unique function and interactions of each of the RNA-binding proteins.
Tissue Microarray Sampling Strategy for Prostate Cancer Biomarker Analysis (2002)

High-density tissue microarrays (TMA) are useful for profiling protein expression in a large number of samples but their use for clinical biomarker studies may be limited in heterogeneous tumors like prostate cancer. In this study, the optimization and validation of a tumor sampling strategy for a prostate cancer outcomes TMA is performed. Prostate cancer proliferation determined by Ki-67 immunohistochemistry was tested. Ten replicate measurements of proliferation using digital image analysis (CAS200, Bacus Labs, Lombard, IL, USA) were made on 10 regions of prostate cancer from a standard glass slide. Five matching tissue microarray sample cores (0.6 mm diameter) were sampled from each of the 10 regions in the parallel study. A bootstrap resampling analysis was used to statistically simulate all possible permutations of TMA sample number per region or sample. Statistical analysis compared TMA samples with Ki-67 expression in standard pathology immunohistochemistry slides. The optimal sampling for TMA cores was reached at 3 as fewer TMA samples significantly increased Ki-67 variability and a larger number did not significantly improve accuracy. To validate these results, a prostate cancer outcomes tissue microarray containing 10 replicate tumor samples from 88 cases was constructed. Similar to the initial study, 1 to 10 randomly selected cores were used to evaluate the Ki-67 expression for each case, computing the 90th percentile of the expression from all samples used in each model. Using this value, a Cox proportional hazards analysis was performed to determine predictors of time until prostate-specific antigen (PSA) recurrence after radical prostatectomy for clinically localized prostate cancer. Examination of multiple models demonstrated that 4 cores was optimal. Using a model with 4 cores, a Cox regression model demonstrated that Ki-67 expression, preoperative PSA, and surgical margin status predicted time to PSA recurrence with hazard ratios of 1.49 (95% confidence interval [CI] 1.01-2.20, p = 0.047), 2.36 (95% CI 1.15-4.85, p = 0.020), and 9.04 (95% CI 2.42-33.81, p = 0.001), respectively. Models with 3 cores to determine Ki-67 expression were also found to predict outcome. In summary, 3 cores were required to optimally represent Ki-67 expression with respect to the standard tumor slide. Three to 4 cores gave the optimal predictive value in a prostate cancer outcomes array. Sampling strategies with fewer than 3 cores may not accurately represent tumor protein expression. Conversely, more than 4 cores will not add significant information. This prostate cancer outcomes array should be useful in evaluating other putative prostate cancer biomarkers.
Identification and Characterization of the Major Lysophosphatidylethanolamine Acyltransferase in Saccharomyces cerevisiae (2007)

We recently demonstrated that yeast actively import lysophosphatidylethanolamine (lyso-PtdEtn) through the action of plasma membrane P-type ATPases and rapidly acylate it to form PtdEtn. The predominant lyso-PtdEtn acyltransferase (LPEAT) activity present in cellular extracts is acyl-CoA dependent, but the identity of the gene encoding this activity was unknown. We now demonstrate that a previously uncharacterized open reading frame, YOR175C, encodes the major acyl-CoA-dependent LPEAT activity in yeast and henceforth refer to it as ALE1 (acyltransferase for lyso-PtdEtn). Ale1p is an integral membrane protein and is highly enriched in the mitochondria-associated endoplasmic reticulum membrane. It is a member of the membrane-bound O-acyltransferase family and possesses a dibasic motif at its C terminus that is likely responsible for Golgi retrieval and retention in the endoplasmic reticulum. An ale1Delta strain retains only trace amounts of acyl-CoA-dependent LPEAT activity, and strains lacking the capacity for PtdEtn synthesis via the phosphatidylserine decarboxylase and Kennedy pathways show a stringent requirement for both exogenous lyso-PtdEtn and a functional ALE1 gene for viability. Ale1p catalytic activity has a pH optimum between pH 7 and 7.5 and a strong preference for unsaturated acyl-CoA substrates.
Ultrathinlayer SDS-polyacrylamide gradient gel electrophoresis of cerebrospinal fluid proteins (1987)

Conference Article| December 01 1987 Ultrathinlayer SDS-polyacrylamide gradient gel electrophoresis of cerebrospinal fluid proteins ANWAR A. SIDDIQUI; ANWAR A. SIDDIQUI 1Department of Biochemistry and Department of Pathology, The Aga Khan University Medical College, P.O. Box 3500, Stadium Road, Karachi-5, Pakistan Search for other works by this author on: This Site PubMed Google Scholar NASEEMA M. ALI; NASEEMA M. ALI 1Department of Biochemistry and Department of Pathology, The Aga Khan University Medical College, P.O. Box 3500, Stadium Road, Karachi-5, Pakistan Search for other works by this author on: This Site PubMed Google Scholar TAJBIBI Z. ALI; TAJBIBI Z. ALI 1Department of Biochemistry and Department of Pathology, The Aga Khan University Medical College, P.O. Box 3500, Stadium Road, Karachi-5, Pakistan Search for other works by this author on: This Site PubMed Google Scholar M. KHURSHID; M. KHURSHID *Department of Medicine, The Aga Khan University Medical College, P.O. Box 3500, Stadium Road, Karachi-5, Pakistan Search for other works by this author on: This Site PubMed Google Scholar MOHAMMAD A. WAQAR MOHAMMAD A. WAQAR 1Department of Biochemistry and Department of Pathology, The Aga Khan University Medical College, P.O. Box 3500, Stadium Road, Karachi-5, Pakistan Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1987) 15 (6): 1111–1113. https://doi.org/10.1042/bst0151111a Article history Received: June 18 1987 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter LinkedIn Cite Icon Cite Get Permissions Citation ANWAR A. SIDDIQUI, NASEEMA M. ALI, TAJBIBI Z. ALI, M. KHURSHID, MOHAMMAD A. WAQAR; Ultrathinlayer SDS-polyacrylamide gradient gel electrophoresis of cerebrospinal fluid proteins. Biochem Soc Trans 1 December 1987; 15 (6): 1111–1113. doi: https://doi.org/10.1042/bst0151111a Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search nav search search input Search input auto suggest search filter All ContentAll JournalsBiochemical Society Transactions Search Advanced Search Keywords: CSF, cerebrospinal fluid This content is only available as a PDF. © 1987 Biochemical Society1987 Article PDF first page preview Close Modal You do not currently have access to this content.
In situ formation of silver nanoparticles in photocrosslinking polymers (2011)

Nanocomposites of cross-linked methacrylate polymers with silver nanoparticles have been synthesized by coupling photoinitiated free radical polymerization of dimethacrylates with in situ silver ion reduction. A polymerizable methacrylate bearing a secondary amino functional group was used to increase the solubility of the silver salt in the hydrophobic resin system. Fourier transform infrared spectroscopy (FTIR) revealed that the silver ion reduction had no significant effect on the degree of vinyl conversion of the methacrylate. X-ray photoelectron spectroscopy (XPS) measurements showed an increased silver concentration at the composite surface compared to the expected concentration based on the total amount of silver salt added. Furthermore, the surface silver concentration leveled off when the silver salt mass fractions were 0.08% or greater. Composites with low concentrations of silver salt (< 0.08% by mass) exhibited comparable mechanical properties to those containing no silver. Transmission electron microscopy (TEM) confirmed that the silver nanoparticles formed within the polymer matrix were nanocrystalline in nature and primarily ≈ 3 nm in diameter, with some large particle aggregates. Composites containing silver nanoparticles were shown to reduce bacterial colonization with as little as 0.03% (by mass) silver salt, while additional amounts of silver salt did not further decrease their surface colonization. With a substantial effect on bacterial growth and minimal effects on mechanical properties, the in situ formation of silver nanoparticles within methacrylate materials is a promising technique for synthesizing antibacterial nanocomposites for biomedical applications.
Cell death mediated by Fas‐FasL interaction between glial cells and MBP‐reactive T cells (1998)

Apoptosis in T cells that have penetrated into the central nervous system (CNS) may be important for the physiological control of T cells with potentially dangerous reactivities to CNS antigens; such control may be dysfunctional in animals suffering from experimental autoimmune encephalomyelitis (EAE). In this study we examined the expression of Fas and FasL genes both in myelin basic protein (MBP)-reactive T cells and in glial cells and the susceptibility of these cells to death induced by Fas/FasL interaction. Both Fas and FasL gene expression is detectable in glial cells and MBP-reactive T cells. Cell death is not unidirectional: when T cells interact with glial cells death can be induced in the former or in the latter population. The ability to induce death of Fas-expressing cells varies greatly among different lines of MBP-reactive T cells, as does resistance to death induction by cells expressing FasL. Moreover, the ability of T cells both to deliver and to resist death signals is a function of their activation status: T cells freshly activated transmit a stronger apoptotic signal to Fas-positive target cells and are also more resistant to FasL-induced suicide. Soluble form of FasL provides a convenient titratable means of delivering death signals via Fas. However, comparison of the susceptibility of different targets to soluble FasL and to FasL expressed on the surface of a transfected glial line revealed differences, suggesting that signals arising from Fas/FasL interaction may be modulated by additional cell-surface molecules. J. Neurosci. Res. 52:458–467, 1998. © 1998 Wiley-Liss, Inc.
Botnets: big and bigger (2003)

Researchers design honeynet computer networks specifically to be attacked. The hosts that comprise a honeynet and serve as attack targets are called honeypots. Researchers configure them to capture a variety of useful data about computer attacks without compromising other computers. Moreover, honeynet researchers strive to implement data capture and control in such a way that intruders are unaware that their actions are being monitored. Although honeynet technology is relatively new, it is developing rapidly. Honeynets have already proven themselves to be useful sources of information. In this article, I'll describe an attack on a honeypot that occurred in March 2003 during the onset and peak activity of several worms that targeted vulnerable hosts running Windows file sharing. We incorporated the compromised honeypot into a large botnet that attackers used to initiate distributed denial-of-service (DDOS) attacks against several Internet sites. I explain the structure of such botnets, their use by computer attackers, and the threat they pose to Internet sites.
Plasma Prekallikrein (2003)

The relevance and significance of the plasma kallikrein/kinin system as a risk factor for the development of vascular complications in diabetic patients was explored in a cross-sectional study. We measured the circulating levels of plasma prekallikrein (PK) activity, factor XII, and high-molecular weight kininogen in the plasma of 636 type 1 diabetic patients from the Diabetes Control and Complications Trial/Epidemiology and Diabetes Intervention and Complications Study cohort. The findings demonstrated that type 1 diabetic patients with blood pressure > or =140/90 mmHg have increased PK levels compared with type 1 diabetic patients with blood pressure <140/90 (1.53 +/- 0.07 vs. 1.27 +/- 0.02 units/ml; P < 0.0001). Regression analysis also determined that plasma PK levels positively and significantly correlated with diastolic (DBP) and systolic blood pressures (SBP) as continuous variables (r = 0.17 and 0.18, respectively; P < 0.0001). In multivariate regression analysis, the semipartial r(2) value for PK was 2.93% for SBP and 2.92% for DBP (P < 0.0001). A positive correlation between plasma PK levels and the urinary albumin excretion rate (AER) was also observed (r = 0.16, P < 0.0001). In categorical analysis, patients with macroalbuminuria had a significantly higher level of plasma PK than normoalbuminuric patients (1.45 +/- 0.08 vs. 1.27 +/- 0.02 units/ml; P < 0.01), whereas microalbuminuric patients had an intermediate PK value (1.38 +/- 0.05 units/ml; P = NS). Among patients in the microalbuminuric subgroup, we observed a positive and independent correlation between PK and AER in univariate and multivariate regression analysis (r = 0.27, P < 0.03; n = 63). We concluded that in type 1 diabetes, 1) PK levels are elevated in association with increased blood pressure; 2) PK levels are independently correlated with AER and are categorically elevated in patients with macroalbuminuria; and 3) although the positive correlation between PK and AER within the subgroups of patients with microalbuminuria suggest that PK could be a marker for progressive nephropathy, longitudinal studies will be necessary to address this issue.
Polymersomes: Tough Vesicles Made from Diblock Copolymers (1999)

Vesicles were made from amphiphilic diblock copolymers and characterized by micromanipulation. The average molecular weight of the specific polymer studied, polyethyleneoxide-polyethylethylene (EO40-EE37), is several times greater than that of typical phospholipids in natural membranes. Both the membrane bending and area expansion moduli of electroformed polymersomes (polymer-based liposomes) fell within the range of lipid membrane measurements, but the giant polymersomes proved to be almost an order of magnitude tougher and sustained far greater areal strain before rupture. The polymersome membrane was also at least 10 times less permeable to water than common phospholipid bilayers. The results suggest a new class of synthetic thin-shelled capsules based on block copolymer chemistry.
Role of Tyrosine Kinase Activity of Epidermal Growth Factor Receptor in the Lysophosphatidic Acid-stimulated Mitogen-activated Protein Kinase Pathway (1998)

Recent evidence indicates that the epidermal growth factor (EGF) receptor mediates a branch of lysophosphatidic acid (LPA)-induced signal transduction pathways that activate mitogen-activated protein (MAP) kinase. However, it is unclear whether the intrinsic tyrosine kinase activity of EGF receptor is involved. We previously showed that reactive oxygen species (ROS) were involved in the LPA-stimulated MAP kinase pathway. Here, we identify tyrosine phosphorylation of EGF receptor as an LPA signaling step that requires ROS. To evaluate the role of the tyrosine kinase activity of EGF receptor in the LPA-stimulated MAP kinase pathway, we examined the effects of an EGF receptor-specific tyrosine kinase inhibitor, PD158780. PD158780 potently inhibited the LPA-stimulated MAP kinase kinase 1/2 (MKK1/2) activation and EGF receptor tyrosine phosphorylation in HeLa cells, while it had no detectable effect on c-Src kinase activity. PD158780 also inhibited LPA-induced MKK1/2 activation and DNA synthesis in NIH 3T3 cells. Furthermore, we compared LPA-stimulated MKK1/2 and MAP kinase activation, transcriptional activity of the c-fos promoter, and DNA synthesis in B82L cells, which lack endogenous EGF receptor, and B82L cells expressing kinase-defective or wild-type human EGF receptor. Results obtained from analysis of these cell lines suggest that the EGF receptor tyrosine kinase contributes to the LPA-stimulated MAP kinase activation, c-fos transcription, and mitogenesis.
A Fragment of Paxillin Binds the α4Integrin Cytoplasmic Domain (Tail) and Selectively Inhibits α4-Mediated Cell Migration (2002)

The alpha(4) integrins play important roles in embryogenesis, hematopoiesis, cardiac development, and the immune responses. The alpha(4) integrin subunit is indispensable for these biological processes, possibly because the alpha(4) subunit regulates cellular functions differently from other integrin alpha subunits. We have previously reported that the alpha(4) cytoplasmic domain directly and tightly binds paxillin, an intracellular signaling adaptor molecule, and this interaction accounts for some of the unusual functional responses to alpha(4) integrin-mediated cell adhesion. We also have identified a conserved 9-amino acid region (Glu(983)-Tyr(991)) in the alpha(4) cytoplasmic domain that is sufficient for paxillin binding, and an alanine substitution at either Glu(983) or Tyr(991) within this region disrupted the alpha(4)-paxillin interaction and reversed the effects of the alpha(4) cytoplasmic domain on cell spreading and migration. In the current study, we have mapped the alpha(4)-binding site within paxillin using mutational analysis, and examined its effects on the alpha(4) tail-mediated functional responses. Here we report that sequences between residues Ala(176) and Asp(275) of paxillin are sufficient for binding to the alpha(4) tail. We found that the alpha(4) tail, paxillin, and FAT, the focal adhesion targeting domain of pp125(FAK), could form a ternary complex and that the alpha(4)-binding paxillin fragment, P(Ala(176)-Asp(275)), specifically blocked paxillin binding to the alpha(4) tail more efficiently than it blocked binding to FAT. Furthermore, when expressed in cells, this alpha(4)-binding paxillin fragment specifically inhibited the alpha(4) tail-stimulated cell migration. Thus, paxillin binding to the alpha(4) tail leads to enhanced cell migration and inhibition of the alpha(4)-paxillin interaction selectively blocks the alpha4-dependent cellular responses.
The azidonitration of tri-O-acetyl-D-galactal (1979)

Reaction of 3,4,6-tri-O-acetyl-D-galactal with excess ceric ammonium nitrate and sodium azide in acetonitrile produced 2-azido-1-nitrate addition products (53% β-galacto, 22% α-galacto, and 8% α-talo) and N-acetyl-3,4,6-tri-O-acetyl-2-azido-2-deoxy-α-D-galactopyranosylamine was formed, on hydrolysis, in 10% yield. The reaction product provides a convenient source of D-galactosamine and 3,4,6-tri-O-acetyl-2-azido-2-deoxy-α-D-galactopyranosylhalides. The crystalline β-chloride is also reported. The use of these glycosyl halides as reactants for the preparation of 2-azido-2-deoxy-α- and -β-D-galactopyranosides under conditions promoted by both mercuric cyanide and silver salts are reported.
Strigolactones: Chemical Signals for Fungal Symbionts and Parasitic Weeds in Plant Roots (2006)

Isolation and identification of plant symbiotic signals open up new ways for studying the molecular basis of plant-AM-fungus interactions. This discovery provides a clear answer to a long-standing question in parasitic plant biology: what is the natural role for germination stimulants? It could also provide a new strategy for the management and control of beneficial fungal symbionts and of devastating parasitic weeds in agriculture and natural ecosystems.
Porphyrins can catalyze the interconversion of DNA quadruplex structural types. (1999)

The binding of porphyrins to quadruplex DNAs provides a model system for the examination of drug binding to telomere, centromere, triplet repeat and other DNAs which may form quadruplex structures in vivo. Porphyrins, and certain other molecules that interact with quadruplex DNAs, have been shown to have significant biological activity. In this investigation the interactions of porphyrins with quadruplex DNAs have been examined by optical and NMR methods. The fluorescence of selected porphyrins can be used to discriminate between duplex and quadruplex DNAs. The fluorescence of the porphyrins can also be used to discriminate partially between the chair, basket and parallel stranded types of quadruplex DNA. At the relatively high DNA concentrations used in NMR, the porphyrins catalyze the conversion of both chair and basket type structures into parallel strand quadruplex DNAs. A DNA-porphyrin system has been found which appears to be a model for an intermediate of the catalytic pathway.