gebhart/patrepeval huggingface dataset:
JAK3: a novel JAK kinase associated with terminal differentiation of hematopoietic cells. (1994)

The Janus Kinases (JAK) JAK1, JAK2, and TYK2 are protein tyrosine kinases which play a pivotal role in the signal transduction process mediated by cytokines. These kinases appear to transduce signals via their substrates which modulate programs of gene expression specific to the respective signals. It is becoming increasingly evident that certain cytokines such as Granulocyte Colony Stimulating Factor (GCSF) can transmit signals for both cellular proliferation and differentiation. It is at present unclear whether both of these signals are transmitted by the same JAK kinase or whether an entire family of such kinases are involved in this process. To determine if additional members of JAK kinase family exist, we designed a polymerase chain reaction based strategy which resulted in the identification of a new member of the JAK kinase family. This new kinase, which we have named JAK3 is encoded by a 4.3 kb mRNA transcript. Nucleotide sequence analysis of a full length cDNA derived from this mRNA revealed that it encodes an open reading frame of 3897 bp. The protein encoded by this mRNA contains the double catalytic domain characteristic of the JAK family kinases. The most striking difference between JAK3 and the other JAK kinases is the presence of two stretches of additional amino acid sequence of 147 and 28 residues which span between amino acid positions 322 to 469 and 632 to 660 respectively. Expression studies indicate that JAK3 is expressed at very low levels in immature hematopoietic cells, but its expression is dramatically up-regulated during terminal differentiation of these cells. These results suggest that JAK3 plays an important role in the differentiation of hematopoietic cells.
Targeting Hepatitis B Virus With CRISPR/Cas9 (2014)

Hepatitis B virus persistence in infected hepatocytes is due to the presence of covalently closed circular DNA (cccDNA), the template for the transcription of viral RNAs. Antiviral therapies with nucleoside analogues inhibit replication of HBV DNA in capsids present in the cytoplasm of infected cells, but do not reduce or destroy nuclear cccDNA. To investigate whether cccDNA derived from infectious HBV could be directly targeted for destruction, we used the CRISPR/Cas9 system in HepG2 cells expressing the HBV receptor sodium taurocholate cotransporting polypeptide (NTCP). We tested different HBV-specific guide RNAs and demonstrated that they could inhibit HBV infections up to eightfold. Inhibition was due to mutations and deletions in cccDNA similar to those observed with chromosomal DNA cleaved by Cas9 and repaired by nonhomologous end joining (NHEJ). Interferon alpha (IFN-α) did not have a measurable effect on the antiviral activity of the CRISPR/Cas9 system, suggesting that Cas9 and NHEJ activities are not affected by induction of an innate immune response with the cytokine. Taken together, our results demonstrated that Cas9 can be recruited to cccDNA, opening the possibility for the development of future antiviral strategies aimed at targeting cccDNA for endonucleolytic cleavage with small molecules.
Dextran sulfate-Mg2+ precipitation procedure for quantitation of high-density-lipoprotein cholesterol. (1982)

Journal Article Dextran sulfate-Mg2+ precipitation procedure for quantitation of high-density-lipoprotein cholesterol. Get access G R Warnick, G R Warnick Search for other works by this author on: Oxford Academic Google Scholar J Benderson, J Benderson Search for other works by this author on: Oxford Academic Google Scholar J J Albers J J Albers Search for other works by this author on: Oxford Academic Google Scholar Clinical Chemistry, Volume 28, Issue 6, 1 June 1982, Pages 1379–1388, https://doi.org/10.1093/clinchem/28.6.1379 Published: 01 June 1982
Mouse Models of Diabetic Nephropathy (2009)

Diabetic nephropathy is a major cause of ESRD worldwide. Despite its prevalence, a lack of reliable animal models that mimic human disease has delayed the identification of specific factors that cause or predict diabetic nephropathy. The Animal Models of Diabetic Complications Consortium (AMDCC) was created in 2001 by the National Institutes of Health to develop and characterize models of diabetic nephropathy and other complications. This interim report and our online supplement detail the progress made toward that goal, specifically in the development and testing of murine models. Updates are provided on validation criteria for early and advanced diabetic nephropathy, phenotyping methods, the effect of background strain on nephropathy, current best models of diabetic nephropathy, negative models, and views of future directions. AMDCC investigators and other investigators in the field have yet to validate a complete murine model of human diabetic kidney disease. Nonetheless, the critical analysis of existing murine models substantially enhances our understanding of this disease process.
Mapping of the 5′-2-Deoxyribose-5-phosphate Lyase Active Site in DNA Polymerase β by Mass Spectrometry (2000)

The mechanism of the 5'-2-deoxyribose-5-phosphate lyase reaction catalyzed by mammalian DNA beta-polymerase (beta-pol) was investigated using a cross-linking methodology in combination with mass spectrometric analyses. The approach included proteolysis of the covalently cross-linked protein-DNA complex with trypsin, followed by isolation, peptide mapping, and mass spectrometric and tandem mass spectrometric analyses. The 8-kDa domain of beta-pol was covalently cross-linked to a 5'-2-deoxyribose-5-phosphate-containing DNA substrate by sodium borohydride reduction. Using tandem mass spectrometry, the location of the DNA adduct on the 8-kDa domain was unequivocally determined to be at the Lys(72) residue. No additional amino acid residues were found as minor cross-linked species. These data allow assignment of Lys(72) as the sole Schiff base nucleophile in the 8-kDa domain of beta-pol. These results provide the first direct evidence in support of a catalytic mechanism involving nucleophilic attack by Lys(72) at the abasic site.
Sequence variation and evolution of nuclear DNA in man and the primates (1981)

Recent advances in nucleic acid technology have facilitated the detection and detailed structural analysis of a wide variety of genes in higher organisms, including those in man. This in turn has opened the way to an examination of the evolution of structural genes and their surrounding and intervening sequences. In a study of the evolution of haemoglobin genes and neighbouring sequences in man and the primates, we have investigated gene arrangement and DNA sequence divergence both within and between species ranging from Old World monkeys to man. This analysis is beginning to reveal the evolutionary constraints that have acted on this region of the genome during primate evolution. Furthermore, DNA sequence variation, both within and between species, provides, in principle, a novel and powerful method for determining interspecific phylogenetic distances and also for analysing the structure of present-day human populations. Application of this new branch of molecular biology to other areas of the human genome should prove important in unravelling the history of genetic changes that have occurred during the evolution of man.
Purification of Bispecific F(ab′) 2 from Murine Trinoma OC/TR with Specificity for CD3 and Ovarian Cancer (1994)

A study was made of the stability of the murine bispecific trinoma OC/TR with respect to secretion of both types of parental heavy and light chains. OC/TR is a cell line producing bispecific antibody that reacts with the CD3 antigen on T cells and the folate-binding receptor--frequently found to be overexpressed on ovarian carcinoma cells. Of the 10 different IgG combinations theoretically possible with 2 heavy and 2 light chains, 6 combinations were secreted. Subclones varied considerably in relative production of the two parental heavy and light chains. A detailed analysis was made of the binding characteristics and retargeting activity of each of the IgGs produced. From a clone producing a relatively high quantity of bispecific IgG, a large-scale production was initiated. The purification of clinical grade bispecific F(ab')2 from harvest fluids is described. The yield from this purification process was found to be comparable to the yield of bispecific F(ab')2 after chemical cross-linking of two different Fab'.
Expression of antibody Fab domains on bacteriophage surfaces. Potential use for antibody selection (1991)

We describe a method for expressing an antibody Fab fragment on the surface of M13 filamentous bacteriophage. The L chain gene, preceded by an Escherichia coli signal sequence, is linked to the 5' end of the gene for the M13 major coat protein. A partial H chain gene, preceded by an E. coli signal sequence and truncated at the end of the CH1 region, is inserted on a plasmid adjacent to the fused L chain gene, so both genes are under the transcriptional control of an inducible promoter. The plasmid also contains the M13 origin of replication. When the promoter is induced, functional antibody Fab fragment appears on the surface of the E. coli inner membrane, as shown by specific binding to an Ag-affinity matrix. When the E. coli are further infected with a helper phage, allowing replication and packaging of the plasmid into phage particles, the resulting phage specifically bind to an Ag-coated plate, indicating they have antibody Fab fragment on their surface. The antibody-expressing phage can also be specifically bound to and eluted from an Ag-affinity column. These observations support the possibility of a new way of generating antibodies, in which amplified Ig cDNA from an appropriate B cell population is cloned into a suitable M13 vector, and phage containing the genes for desired antibodies are selected directly by binding to an Ag-affinity matrix.
Significance of Cross-Linking of α2-Plasmin Inhibitor to Fibrin in Inhibition of Fibrinolysis and in Hemostasis (1982)

A B S T R A C T When blood is clotted, a2-plasmin in- hibitor (a2PI) is cross-linked to fibrin by activated fi- brin-stabilizing factor (activated coagulation Factor XIII, plasma transglutaminase). The amount of cross- linked a2-PI is proportional to the amount of a2PI pres- ent at the time of clotting. Plasma from a patient with congenital deficiency of a2PI was supplemented with various amounts of purified a2PI. Clots were prepared from these plasmas and were suspended in plasma con- taining a normal concentration of a2PI, and sponta- neous clot lysis was observed. When the clot was formed in the presence of calcium ions and thereby allowing cross-linking to occur, the rate and extent of fibrinolysis were found to be inversely proportional to the concentrations of a2PI present in the clot at the time of clotting. When the clot was formed in the absence of calcium ions so that no cross-linking oc- curred, the clot underwent fibrinolysis at similar rates, regardless of the concentrations of a2PI in the clot. When the clot formed in the presence of calcium ions was squeezed and washed to remove unbound proteins before being suspended in plasma, the extent of fi- brinolysis was also inversely proportional to the amount of a2PI cross-linked to fibrin. Similar results were ob- tained when the clot was suspended in buffered saline instead of plasma. These observations suggest that spontaneous fibrinolysis is mainly carried out by plas- minogen/plasminogen activator bound to fibrin, and this fibrinolysis caused by fibrin-associated activation of plasminogen was mainly inhibited by a2PI cross- linked to fibrin. To further support this concept, a2PI treated with activated fibrin-stabilizing factor and that had lost most of its cross-linking capacity was used in similar experiments. This modified a2PI had the same inhibitory activity on plasmin as the native inhibitor, but gave significantly less inhibition of fibrinolysis in
4-Hydroxy-2-Nonenal Levels Increase in the Plasma of Patients with Adult Respiratory Distress Syndrome as Linoleic Acid Appears to Fall (1994)

Gas chromatograph-mass spectrometry has been applied to the analysis of plasma linoleic acid and one of its oxidation products, 4-hydroxy-2-nonenal (HNE), in adult patients with the acute respiratory distress syndrome (ARDS). Peak areas of total ion chromatograms showed there to be negative correlations between loss of linoleic acid and formation of HNE (measured by selective ion monitoring) in 7 out 10 patients studied. When HNE was quantitated by selective ion monitoring, with reference to a pure standard of HNE and an internal standard of nonanoic acid, ARDS patients showed significantly increased levels of HNE (0.412 +/- 0.023 nmol/ml) compared with normal healthy controls (0.205 +/- 0.018 nmol/ml).
Effects of phenylalanine amonia-lyase and phenylalanine deprivation on murine leukemic lymphoblasts in vitro. (1973)

Treatment of murine leukemic (L5178Y) lymphoblasts in vitro with phenylalanine ammonia-lyase resulted in a decrease in protein synthesis, followed by decreases in RNA and DNA synthesis, inhibition of cell division, and a loss of cell viability. Compared with enzyme treatment, phenylalanine deprivation resulted in similar decreases in cell viability. These results confirm earlier studies and further support the concept that phenylalanine ammonia-lyase exerts its inhibitory effect by depriving rapidly dividing cells of the essential amino acid phenylalanine.
Risk Stratification With Coccidioidal Skin Test to Prevent Valley Fever Among Inmates, California, 2015 (2018)

Two California state prisons (A and B) have very high rates of coccidioidomycosis (Valley Fever). The prison health care service sought to improve their prevention strategy by risk stratification with a newly available spherulin-based Coccidioides delayed-type hypersensitivity test. Of the 36,789 voluntarily screened inmates, 4.7% experienced adverse reactions. A positive test (8.6% of those tested) was independently associated with (1) incarceration at prisons A and B, (2) admission to prison from a Coccidioides-endemic county, (3) length of stay at prisons A and B, and (4) increasing age. These findings suggest that the test is safe and performing well at risk stratification; the prison system now restricts inmates with negative tests from prisons A and B. This novel use of the test might benefit other coccidioidomycosis prevention programs.
Enhanced responsiveness to nuclear factor kappa B contributes to the unique phenotype of simian immunodeficiency virus variant SIVsmmPBj14 (1994)

Infection with a variant of simian immunodeficiency virus, SIVsmmPBj14, leads to severe acute disease in macaques. This study was designed to investigate the functional significance of previously described mutations in the viral long terminal repeat (LTR) and to elucidate their contribution to the unique phenotype of SIVsmmPBj14. LTR-directed transcription was measured by using luciferase reporter constructs that were transiently transfected into cultured cells. In a wide range of cell types, the basal transcriptional activity of the LTR from SIVsmmPBj14 was found to be 2- to 4.5-fold higher than that of an LTR from a non-acutely pathogenic strain. These LTRs differ by five point mutations and a 22-bp duplication in SIVsmmPBj14, which includes a nuclear factor kappa B (NF kappa B) site. Transcriptional differences between these LTRs were further enhanced by two- to threefold upon treatment of cells with phorbol ester or tumor necrosis factor alpha or by cotransfection with plasmids expressing NF kappa B subunits. Mutagenesis studies, and the use of a reporter construct containing an enhancerless promoter, indicate that these transcriptional effects are due principally to the 22-bp sequence duplication and the NF kappa B site contained within it. Finally, infectious virus stocks that were isogenic except for the LTR were generated. The LTR from SIVsmmPBj14 was found to confer an increase in the kinetics of virus replication in cultured cells. Inclusion of this LTR in recombinant SIVs also resulted in a two- to threefold rise in the extent of cellular proliferation that was induced in quiescent simian peripheral blood mononuclear cells. These studies are consistent with the hypothesis that LTR mutations assist SIVsmmPBj14 in responding efficiently to cellular stimulation and allow it to replicate to high titers during the acute phase of viral infection.
The t(1;19)(q23;p13) results in consistent fusion of E2A and PBX1 coding sequences in acute lymphoblastic leukemias (1991)

The t(1;19)(q23;p13) chromosomal translocation is observed cytogenetically in 25% of children with pre-B-cell acute lymphoblastic leukemia (ALL) and is associated with an adverse treatment outcome. The t(1;19) juxtaposes the E2A gene from chromosome 19 with the PBX1 gene on chromosome 1, leading to the production of fusion transcripts and resultant chimeric proteins that contain the transcriptional-activating motif of E2A and the DNA-binding homeodomain of PBX1. To investigate the molecular nature of E2A/PBX1 fusion in patients with t(1;19) ALL we used an RNA-based polymerase chain reaction (PCR) procedure to amplify a portion of the chimeric transcript. We detected E2A/PBX1 fusion transcripts in cells from 97% (37 of 38) of cases in which the t(1;19) had been observed cytogenetically. Molecular evidence of E2A/PBX1 fusion transcripts was also observed in a patient in whom a t(1;19) was not detected cytogenetically and in one patient with subclinical levels of minimal residual disease before overt clinical relapse. In all PCR-positive cases the junction of E2A and PBX1 coding sequences occurred at precisely the same location as demonstrated by hybridization of PCR products with a fusion site-specific detection oligonucleotide. These findings demonstrate the consistent fusion of E2A and PBX1 coding sequences resulting from t(1;19) and suggest that site-specific fusion of E2A and PBX1 is an important pathogenic event in t(1;19) ALL.
Preparation of oligonucleotide-peptide conjugates (1991)

A procedure for preparing oligonucleotide-peptide conjugates is presented. It is based on appending a maleimide group to the oligonucleotide for selective coupling to the thiol side chain of a cysteine residue in the peptide. A convenient chromatographic purification procedure, based on Fmoc-on/Fmoc-off, is described.
The Use of Xenopus laevis Oocytes for the Functional Characterization of Heterologously Expressed Membrane Proteins (2000)

The oocytes of the South African clawed frog X. laevis are widely used for the expression of heterologous proteins. The functional characterization of membrane proteins in particular has significantly profited from the use of this expression system. Heterologous cRNA can easily be injected and protein expression and function be studied with several techniques. This review will give a short overview into the variety of methods applicable. They span from different electrophysiological methods such as two electrode voltage clamp, patch clamp and ion-selective electrodes over cytochemistry to protein biochemistry. In spite of the wide usage of Xenopus oocytes, caution should be taken interpreting the results of protein expression. Heterologous proteins may either interact with endogenous proteins, the background of endogenous protein function may be relatively high, or altered protein behaviour may occur due to differences of the ambient temperature or altered cellular environment.
A Systematic Review of the Factors Affecting Accuracy of SUV Measurements (2010)

Scanner and reconstruction parameters can significantly affect SUV measurements. When using serial SUV measurements to assess early response to therapy, imaging should be performed on the same scanner using the same image acquisition and reconstruction protocols. In addition, attention to detail is required for accurate determination of the administered radiopharmaceutical dose.
Phospholipase Cϵ Suppresses Integrin Activation (2006)

Phospholipase Cepsilon (PLCepsilon) is a newly described effector of the small GTP-binding protein H-Ras. Utilizing H-Ras effector mutants, we show that mutants H-Ras(G12V/E37G) and H-Ras(G12V/D38N) suppressed integrin activation in an ERK-independent manner. H-Ras(G12V/D38N) specifically activated the PLCepsilon effector pathway and suppressed integrin activation. Inhibition of PLCepsilon activation with a kinase-dead PLCepsilon mutant prevented H-Ras(G12V/D38N) from suppressing integrin activation, and low level expression of H-Ras(G12V/D38N) could synergize with wild-type PLCepsilon to suppress integrins. In addition, knockdown of endogenous PLCepsilon with small interfering RNA blocked H-Ras(G12V/D38N)-mediated integrin suppression. Suppressing integrin function with the H-Ras(G12V/D38N) mutant reduced cell adhesion to von Willebrand factor and fibronectin; this reduction in cell adhesion was blocked by coexpression of the kinase-dead PLCepsilon mutant. These results show that H-Ras suppresses integrin affinity via independent Raf and PLCepsilon signaling pathways and demonstrate a new physiological function for PLCepsilon in the regulation of integrin activation.
Eukaryotic methionyl aminopeptidases: two classes of cobalt-dependent enzymes. (1995)

Using partial amino acid sequence data derived from porcine methionyl aminopeptidase (MetAP; methionine aminopeptidase, peptidase M; EC 3.4.11.18), a full-length clone of the homologous human enzyme has been obtained. The cDNA sequence contains 2569 nt with a single open reading frame corresponding to a protein of 478 amino acids. The C-terminal portion representing the catalytic domain shows limited identity with MetAP sequences from various prokaryotes and yeast, while the N terminus is rich in charged amino acids, including extended strings of basic and acidic residues. These highly polar stretches likely result in the spuriously high observed molecular mass (67 kDa). This cDNA sequence is highly similar to a rat protein, termed p67, which was identified as an inhibitor of phosphorylation of initiation factor eIF2 alpha and was previously predicted to be a metallopeptidase based on limited sequence homology. Model building established that human MetAP (p67) could be readily accommodated into the Escherichia coli MetAP structure and that the Co2+ ligands were fully preserved. However, human MetAP was found to be much more similar to a yeast open reading frame that differed markedly from the previously reported yeast MetAP. A similar partial sequence from Methanothermus fervidus suggests that this p67-like sequence is also found in prokaryotes. These findings suggest that there are two cobalt-dependent MetAP families, presently composed of the prokaryote and yeast sequences (and represented by the E. coli structure) (type I), on the one hand, and by human MetAP, the yeast open reading frame, and the partial prokaryotic sequence (type II), on the other.
Nanofiber Assembly by Rotary Jet-Spinning (2010)

High-voltage electrical fields and low production rate limit electrospinning, the electrical charging of polymer liquids, as a means of nanofiber fabrication. Here, we show a facile method of fabrication of aligned three-dimensional nanofiber structures by utilizing high-speed, rotating polymer solution jets to extrude fibers. Termed rotary jet-spinning, fiber morphology, diameter, and web porosity can be controlled by varying nozzle geometry, rotation speed, and polymer solution properties. We demonstrate the utility of this technique for tissue engineering by building anisotropic arrays of biodegradable polymer fibers and seeding the constructs with neonatal rat ventricular cardiomyocytes. The myocytes used the aligned fibers to orient their contractile cytoskeleton and to self-organize into a beating, multicellular tissue that mimics the laminar, anisotropic architecture of the heart muscle. This technique may prove advantageous for building uniaxially aligned nanofiber structures for polymers which are not amenable to fabrication by electrospinning.