gebhart/patrepeval huggingface dataset:
An active-site mutation in the human immunodeficiency virus type 1 proteinase (PR) causes reduced PR activity and loss of PR-mediated cytotoxicity without apparent effect on virus maturation and infectivity (1995)

Infectious retrovirus particles are derived from structural polyproteins which are cleaved by the viral proteinase (PR) during virion morphogenesis. Besides cleaving viral polyproteins, which is essential for infectivity, PR of human immunodeficiency virus (HIV) also cleaves cellular proteins and PR expression causes a pronounced cytotoxic effect. Retroviral PRs are aspartic proteases and contain two copies of the triplet Asp-Thr-Gly in the active center with the threonine adjacent to the catalytic aspartic acid presumed to have an important structural role. We have changed this threonine in HIV type 1 PR to a serine. The purified mutant enzyme had an approximately 5- to 10-fold lower activity against HIV type 1 polyprotein and peptide substrates compared with the wild-type enzyme. It did not induce toxicity on bacterial expression and yielded significantly reduced cleavage of cytoskeletal proteins in vitro. Cleavage of vimentin in mutant-infected T-cell lines was also markedly reduced. Mutant virus did, however, elicit productive infection of several T-cell lines and of primary human lymphocytes with no significant difference in polyprotein cleavage and with similar infection kinetics and titer compared with wild-type virus. The discrepancy between reduced processing in vitro and normal virion maturation can be explained by the observation that reduced activity was due to an increase in Km which may not be relevant at the high substrate concentration in the virus particle. This mutation enables us therefore to dissociate the essential function of PR in viral maturation from its cytotoxic effect.
Chemical modifications of adenine base editor mRNA and guide RNA expand its application scope (2020)

CRISPR-Cas9-associated base editing is a promising tool to correct pathogenic single nucleotide mutations in research or therapeutic settings. Efficient base editing requires cellular exposure to levels of base editors that can be difficult to attain in hard-to-transfect cells or in vivo. Here we engineer a chemically modified mRNA-encoded adenine base editor that mediates robust editing at various cellular genomic sites together with moderately modified guide RNA, and show its therapeutic potential in correcting pathogenic single nucleotide mutations in cell and animal models of diseases. The optimized chemical modifications of adenine base editor mRNA and guide RNA expand the applicability of CRISPR-associated gene editing tools in vitro and in vivo.
Immunosuppressive Factors: Role in Cancer Development and Progression (1998)

The concept of the immunological surveillance against neoplastic cells was initially proposed by Erlich in 1909 and later elaborated by Burnet. This hypothesis states that the normal function of the immune system, in particular the cell-mediated immunity, is to recognize and destroy the transformed and proliferating tumor cells. The role of cell-mediated immunity during the first steps of tumorigenesis remains controversial. However, there is certain evidence about its importance in the progression and dissemination of cancer. The frequent immunosuppressed condition of cancer patients at tumor relapse or recurrence of secondary tumors is a clinical sign supporting this hypothesis, and many studies have demonstrated a defective immune response in patients diagnosed with advanced cancer. Several mechanisms of escape from the immune surveillance have been described, including the immunoselection of tumor antigen-negative variants, the downregulation of MHC class I expression, suppressive T cells, and the elaboration of immunosuppressive cytokines and other factors. Because of the technical difficulty of isolating the very small amounts from culture supernatants or body fluids, only a few of these substances have been characterized and studied with respect to their biological activity: transforming growth factor-beta (TGF-beta), the protein p15E, interleukin 10 (IL-10), prostaglandin E2 (PGE2), mucins, suppressive E-receptor (SER), immunosuppressive acidic protein (IAP), and adhesion molecules. The possibility of monitoring cancer patients by testing biochemical factors related to cancer growth led to a proposal to measure a number of these factors as tumor markers. Some of them, e.g. mucins, enjoy the consensus of the oncologic community, as for some indications they can help the clinician in the management of cancer patients. Except for the class of mucins, the other above-mentioned immunosuppressive factors have not found any clinical application in the laboratory routine because the information deriving from their measurement, although of speculative and scientific interest, has limited clinical value at present. Nevertheless, even if they have no impact on patient management, these substances do have a potential role to play in the study of cancer patients, and should be taken into account when developing new therapeutic strategies.
Brassinosteroid functions to protect the translational machinery and heat‐shock protein synthesis following thermal stress (2002)

In addition to their essential role in plant development, brassinosteroids have the ability to protect plants from various environmental stresses. Currently it is not understood how brassinosteroids control plant stress responses at the molecular level. We have begun an investigation into the molecular mechanisms underlying 24-epibrassinolide (EBR)-mediated stress resistance. Earlier we found that treatment of Brassica napus seedlings with EBR leads to a significant increase in their basic thermotolerance, and results in higher accumulation of four major classes of heat-shock proteins (hsps) as compared to untreated seedlings. Surprisingly, previous studies have shown that while hsp levels were significantly higher in treated seedlings during the recovery period, transcripts corresponding to these hsps were present at higher levels in untreated seedlings. To understand mechanisms controlling hsp synthesis in EBR-treated and untreated seedlings, we studied protein synthesis in vivo as well as in vitro, and assessed the levels of components of the translational machinery in these seedlings. We report here that increased accumulation of hsps in EBR-treated seedlings results from higher hsp synthesis, even when the mRNA levels are lower than in untreated seedlings, and that several translation initiation and elongation factors are present at significantly higher levels in EBR-treated seedlings as compared to untreated seedlings. These results suggest that EBR treatment limits the loss of some of the components of the translational apparatus during prolonged heat stress, and increases the level of expression of some of the components of the translational machinery during recovery, which correlates with a more rapid resumption of cellular protein synthesis following heat stress and a higher survival rate.
Galactosyl ceramide or a derivative is an essential component of the neural receptor for human immunodeficiency virus type 1 envelope glycoprotein gp120. (1991)

This report demonstrates that galactosyl ceramide (GalCer) or a molecule derived from it may serve as an alternative receptor for human immunodeficiency virus in the nervous system. Recombinant gp120, an envelope glycoprotein of human immunodeficiency virus type 1, specifically binds to GalCer and its derivatives. This specificity was studied by inhibiting binding of radioiodinated gp120 to GalCer with antibodies to GalCer, antibodies to gp120, and an excess of unlabeled gp120. Binding activity was also removed by absorbing gp120 with liposomes containing GalCer. In addition, studies using natural and semisynthetic lipids indicate that the linkage between galactose and ceramide is essential for binding. The significance of an alternative receptor for human immunodeficiency virus in the nervous system is discussed.
Harnessing Nature’s Insight: Design of Aspartyl Protease Inhibitors from Treatment of Drug-Resistant HIV to Alzheimer’s Disease (2009)

ADVERTISEMENT RETURN TO ISSUEPerspectiveNEXTHarnessing Nature's Insight: Design of Aspartyl Protease Inhibitors from Treatment of Drug-Resistant HIV to Alzheimer's Disease†Arun K. Ghosh‡View Author Information Departments of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907†Adapted from a lecture presented at the Robert Scarborough Award Symposium, 236th National Meeting of the American Chemical Society, Philadelphia, PA, August 17−21, 2008; Abstract MEDI-211.‡ Contact information: phone, (765) 494-5323; fax, (765) 496-1612; e-mail, [email protected]Cite this: J. Med. Chem. 2009, 52, 8, 2163–2176Publication Date (Web):March 26, 2009Publication History Received16 January 2009Published online26 March 2009Published inissue 23 April 2009https://pubs.acs.org/doi/10.1021/jm900064chttps://doi.org/10.1021/jm900064creview-articleACS PublicationsCopyright © 2009 American Chemical SocietyRequest reuse permissionsArticle Views5277Altmetric-Citations41LEARN 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-Alertsclose SUBJECTS:Inhibitors,Ligands,Peptides and proteins,Pharmaceuticals,X-rays Get e-Alerts
cAMP-specific phosphodiesterase HSPDE4D3 mutants which mimic activation and changes in rolipram inhibition triggered by protein kinase A phosphorylation of Ser-54: generation of a molecular model (1998)

Ser-13 and Ser-54 were shown to provide the sole sites for the protein kinase A (PKA)-mediated phosphorylation of the human cAMP-specific phosphodiesterase isoform HSPDE4D3. The ability of PKA to phosphorylate and activate HSPDE4D3 was mimicked by replacing Ser-54 with either of the negatively charged amino acids, aspartate or glutamate, within the consensus motif of RRES54. The PDE4 selective inhibitor rolipram ¿4-[3-(cyclopentoxy)-4-methoxyphenyl]-2-pyrrolidone¿ inhibited both PKA-phosphorylated HSPDE4D3 and the Ser-54-->Asp mutant, with an IC50 value that was approximately 8-fold lower than that seen for the non-PKA-phosphorylated enzyme. Lower IC50 values for inhibition by rolipram were seen for a wide range of non-activated residue 54 mutants, except for those which had side-chains able to serve as hydrogen-bond donors, namely the Ser-54-->Thr, Ser-54-->Tyr and Ser-54-->Cys mutants. The Glu-53-->Ala mutant exhibited an activity comparable with that of the PKA phosphorylated native enzyme and the Ser-54-->Asp mutant but, in contrast to the native enzyme, was insensitive to activation by PKA, despite being more rapidly phosphorylated by this protein kinase. The activated Glu-53-->Ala mutant exhibited a sensitivity to inhibition by rolipram which was unchanged from that of the native enzyme. The double mutant, Arg-51-->Ala/Arg-52-->Ala, showed no change in either enzyme activity or rolipram inhibition from the native enzyme and was incapable of providing a substrate for PKA phosphorylation at Ser-54. No difference in inhibition by dipyridamole was seen for the native enzyme and the Ser-54-->Asp and Ser-54-->Ala mutants. A model is proposed which envisages that phosphorylation by PKA triggers at least two distinct conformational changes in HSPDE4D3; one of these gives rise to enzyme activation and another enhances sensitivity to inhibition by rolipram. Activation of HSPDE4D3 by PKA-mediated phosphorylation is suggested to involve disruption of an ion-pair interaction involving the negatively charged Glu-53. The increase in susceptibility to inhibition by rolipram upon PKA-mediated phosphorylation is suggested to involve the disruption of a hydrogen-bond involving the side-chain hydroxy group of Ser-54.
Influence of the Perfusate Temperature on Lung Preservation: Is There an Optimum? (1997)

The optimal temperature of the pulmonary flush perfusate is still a matter of controversy. At present, a temperature of 10 degrees C is favored. This study deals with the structural and functional impact of different perfusate temperatures on lung preservation. In an extracorporeal rat heart-lung model lungs were preserved with Perfadex solution of 4, 15 and 25 degrees C and submitted to 2 h ischemia. Heart-lung blocks harvested from male rats were perfused with Krebs-Henseleit solution and ventilated with room air. Lungs were perfused with deoxygenated perfusate via the working right ventricle while the coronary arteries were retrogradely perfused with oxygenated perfusate. Oxygenation capacity (dPO2), peak inspiratory pressure (PIP) and pulmonary vascular resistance were measured. After establishment of baseline functional parameters hearts were arrested with 10 ml St. Thomas cardioplegia and lungs were flushed with 20 ml Perfadex solution. The heart-lung block was then stored for 2 h at 10 degrees C. Reperfusion was performed thereafter under the same conditions. At the end of the trial the lung tissue water was measured by the wet/dry ratio. The perfusion time of the groups flushed with 15 or 25 degrees C perfusate was significantly lower than that of the 4 degrees C group. After 20 min reperfusion dPO2 of the groups flushed with 15 or 25 degrees C was superior to those submitted to a 4 degrees C flush perfusion. PIP was significantly lower in the 15 degrees C group than in the 4 and 25 degrees C groups. The wet/dry ratio revealed the smallest water content in the 15 degrees C group. We conclude that the post-ischemic lung function is dependent on the temperature of the flush perfusate. Among the tested temperatures, perfusion at 15 degrees C showed the best results. The optimum may therefore lie in this range.
Cleavage of intracellular hepatitis C RNA in the virus core protein coding region by deoxyribozymes (2005)

Hepatitis C virus (HCV) infection represents an important global health problem. Current antiviral therapeutics for HCV have proven inadequate in stemming the disease process. A novel therapeutic strategy involves the use of deoxyribozymes, also known as DNA enzymes or DNAzymes. These catalytic DNA molecules, designed to target and cleave specific RNA sequences, have shown promise in in vitro experimental models for various diseases and may serve as an alternative or adjunct to current HCV drug therapy. We designed and tested several deoxyribozymes that can bind and cleave highly conserved RNA sequences encoding the HCV core protein in in vitro systems. One of these deoxyribozymes reduced the level of our HCV RNA target by 32% and 48% after 24 h of cell exposure when tested in human hepatoma and epithelial cell lines, respectively. As this deoxyribozyme showed significant cleavage activity against HCV core protein target RNA in human cells, it may have potential as a therapeutic candidate for clinical trial in HCV infected patients.
Bargaining under Incomplete Information (1983)

This paper presents and analyzes a bargaining model of bilateral monopoly under uncertainty. Under the bargaining rule proposed, the buyer and the seller each submit sealed offers that determine whether the good in question is sold and the transfer price. The Nash equilibrium solution of this bargaining game implies an offer strategy of each party that is monotonic in its own reservation price and depends on its assessment of the opponent's reservation price. Issues of relative bargaining advantage and efficiency are examined for a number of special cases. Finally, we discuss the appropriateness of the Nash solution concept.
Generation of lipooligosaccharide mutants of Haemophilus influenzae type b (1992)

We previously reported the analysis of recombinant plasmids from Haemophilus influenzae type b (Hib) that lead to modifications of Escherichia coli lipopolysaccharide (LPS) (Y. Abu Kwaik, R. E. McLaughlin, M. A. Apicella, and S. M. Spinola, Mol. Microbiol. 5:2475-2480, 1991). The modified LPS species are recognized by monoclonal antibodies (MAbs) 6E4 and 3F11. MAb 6E4 binds to a stable 2-keto-3-deoxyoctulosonic acid epitope, while MAb 3F11 binds to a Gal beta 1-4GlcNac epitope that phase varies in Hib at a frequency of 2 to 5%. The internal EcoRI fragment containing most of the DNA required for LPS modification in E. coli was used as the target for transposon mutagenesis. Plasmids containing minitransposon m-Tn3(Cm) randomly inserted into the target fragment were transformed into the isogenic Hib strain, and transposon integration into the Hib chromosome was verified by colony hybridization. The lipooligosaccharides of 36 transformants were phenotypically and antigenically characterized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and reactivity with a variety of MAbs that recognize both stable and phase-varying lipooligosaccharide epitopes. The majority of the mutants had altered reactivity with MAb 6E4. With one exception, these mutants retained the ability to express phase-varying epitopes. Analysis of the transformants suggested that the 6E4 epitope was contained on an oligosaccharide chain separate from that of phase-varying epitopes and appeared to be assembled in at least three separate steps.
The effects of bone plug length and screw diameter on the holding strength of bone‐tendon‐bone grafts (1998)

The effect of bone plug length and Kurosaka screw (DePuy, Warsaw, IN) diameter on graft holding strength of the bone-tendon-bone construct was determined. Random length porcine bone plugs were assigned to fixation with 7 or 9 mm Kurosaka screws. Peak load to failure was determined. There was a significant decrease in peak load to failure of the 5-mm long bone plugs compared with longer bone plugs. No difference was found between longer lengths of bone plug in either the 7- or 9-mm screw diameter groups. The 9-mm diameter screws significantly increased peak load to failure for both 1- and 2-cm bone plug lengths.
Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes (2015)

Fluorescence in situ hybridization (FISH) is a powerful single-cell technique for studying nuclear structure and organization. Here we report two advances in FISH-based imaging. We first describe the in situ visualization of single-copy regions of the genome using two single-molecule super-resolution methodologies. We then introduce a robust and reliable system that harnesses single-nucleotide polymorphisms (SNPs) to visually distinguish the maternal and paternal homologous chromosomes in mammalian and insect systems. Both of these new technologies are enabled by renewable, bioinformatically designed, oligonucleotide-based Oligopaint probes, which we augment with a strategy that uses secondary oligonucleotides (oligos) to produce and enhance fluorescent signals. These advances should substantially expand the capability to query parent-of-origin-specific chromosome positioning and gene expression on a cell-by-cell basis.
Neuropilin-1 Is a Placenta Growth Factor-2 Receptor (1998)

Placenta growth factor (PlGF) belongs to the family of vascular endothelial growth factors (VEGFs). It binds to the flt-1 VEGF receptor but not to the KDR/flk-1 receptor which is thought to mediate most of the angiogenic and proliferative effects of VEGF. Three PlGF isoforms are produced by alternative splicing. PlGF-1 and PlGF-3 differ from PlGF-2 since they lack the exon 6 encoded peptide which bestows upon PlGF-2 its heparin binding properties. Cross-linking experiments revealed that 125I-PlGF-2 binds to two endothelial cell surface receptors in a heparin dependent fashion. The binding of 125I-PlGF-2 to these receptors was inhibited by an excess of PlGF-2 and by the 165-amino acid form of VEGF (VEGF165), but not at all by VEGF121 and very marginally if at all by PlGF-1. The apparent molecular weight and the binding characteristics of these receptors correspond to those of the recently identified VEGF165 specific receptor neuropilin-1, and we therefore conclude that neuropilin-1 is a receptor for PlGF-2. The binding of 125I-PlGF-2 as well as the binding of 125I-VEGF165 to these receptors was inhibited by a synthetic peptide derived from exon 6 of PlGF. Furthermore, the binding of 125I-PlGF-2, but not that of 125I-VEGF165, was also inhibited by a synthetic peptide derived from exon 7 of PlGF. These observations indicate that the peptides encoded by these exons probably participate in the formation of the domain which mediates the binding of PlGF-2 to these receptors. We have also determined, using chemically modified heparin species, that the presence of sulfate moieties on the glucosamine-O-6 and on the iduronic acid-O-2 groups of heparin was required for the potentiation of 125I-PlGF-2 binding to these receptors. To determine if PlGF-2 is able to induce biological responses that are not induced by PlGF-1, we compared the effects of PlGF-1 and PlGF-2 on the migration and proliferation of endothelial cells. Both PlGF forms induced migration of endothelial cells. However, there was no quantitative difference between the response to PlGF-2 and the response to PlGF-1. Furthermore, neither PlGF-1 nor PlGF-2 had any effect upon the proliferation of the endothelial cells.
Effects of multiple-passage probabilities on fluorescent signals from biological media (1997)

By applying a random-walk model for photon migration, we find an exact expression for fluorescent signals emitted from a homogeneous, optically turbid medium containing a single fluorescent mass. In contrast to diffusion-theory-based models, our analysis accounts for multiple photon passages through the fluorophore sites and allows for a variable degree of fluorescent absorptivity. We particularly discuss effects on the amplitudes and phase shifts of frequency-domain fluorescent signals.
A Nucleolin-Targeted Multimodal Nanoparticle Imaging Probe for Tracking Cancer Cells Using an Aptamer (2009)

We developed a nanoparticle-based cancer-specific imaging probe using the AS1411 aptamer in vivo and in vitro. This multimodal targeting imaging strategy, using a cancer-specific AS1411 aptamer, can be used as a versatile imaging tool for specific cancer diagnosis.
The different faces of poly(ethylene glycol) (1997)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.