gebhart/patrepeval huggingface dataset:
Catalytic Activity of Enzymes Altered at Their Active Sites (1988)

Abstract Protein engineering has as its goals the design and construction of new peptides and proteins with novel binding and catalytic properties. In one approach to protein engineering, new active sites have been introduced into naturally occurring proteins either by site‐directed mutagenesis or by chemical modification. Providing that important changes in the tertiary structures do not result from such alterations, at least a portion of the binding site of the original protein should be available for the formation of complexes between the altered enzyme and its substrates. Many examples of active‐site mutations have been described, including the generation by us of a cysteine mutant of alkaline phosphatase. A fundamental limitation of the site‐directed mutagenesis methodology is that replacements of residues are restricted to the twenty naturally occurring amino acids. The alternative, chemical modification, is difficult to carry out for the specific replacement of one amino acid by another. However, we have shown that through such modification coenzyme analogues can be introduced covalently into appropriate positions in proteins, allowing us to produce semisynthetic enzymes with catalytic activities radically altered from those of their precursor proteins. In another approach to protein engineering efforts have focused on the construction of systems where, as a first approximation, folding can be neglected and the preparation of secondary structural units is the target. Examples of the successful design of biologically active peptides and proteins along such lines, taken from our own work, include molecules mimicking apolipoproteins, toxins, and many hormones. In recent studies we have progressed to the stage where we are starting to combine the two general approaches to protein engineering we have described and are able to construct small enzymes like ribonuclease T 1 and its structural analogues.
Antitumoral Effects of Lipid A: Preclinical and Clinical Studies (2002)

Chronic graft-versus-host disease (cGVHD) remains the leading cause of non-relapse mortality after allogeneic stem cell transplantation (SCT) for haematological malignancies. Manifestations of GVHD in the central nervous system (CNS) present as neurocognitive dysfunction in a significant proportion of patients. Neuroinflammation in the cortex of mice and humans in acute GVHD is dependent on host resident microglia-derived TNF. However, the mechanisms driving cGVHD in the CNS are yet to be elucidated. Here, our studies of murine cGVHD revealed a hippocampal-dependent spatial learning and memory deficit associated with inflammation and persistent IFN-γ upregulation. Hippocampal RNA sequencing identified perturbations to structural and functional synapse-related gene expression, in the context of upregulated genes associated with antigen presentation and IFN-γ responses. Brain T cell infiltration was initially dominated by CD8 T cells with an eventual expansion in CD4 T cells, in parallel with a marked infiltration of MHC Class II-expressing bone marrow-derived macrophages (BMDM). After day 70, BMDM constituted 50% of the brain macrophage pool and exhibited a transcriptional signature distinct from host resident microglia. Transfer of MHC class II–deficient BM grafts resulted in attenuated neuroinflammation, implicating donor BMDM as critical mediators of CNS cGVHD. Our identification of the hippocampus as a cGVHD target, and disease mediators distinct from those in the acute phase, highlights the necessity to pursue alternative therapeutic targets for late-stage neurological manifestations post-SCT.
EVALUATION OF STATISTICAL MODELS FOR CLEAR‐AIR SCINTILLATION PREDICTION USING OLYMPUS SATELLITE MEASUREMENTS (1997)

The objective of this study is to evaluate and to compare some of the statistical models for the monthly prediction of clear-air scintillation variance and amplitude from ground meteorological measurements. Two new statistical methods, namely the direct and the modelled physical-statistical prediction models, are also introduced and discussed. They are both based on simulated data of received scintillation power derived from a large historical radiosounding set, acquired in a mid-latitudue site. The long-term predictions derived from each model are compared with measurements from the Olympus satellite beacons at the Louvain-la-Neuve site at 12·5 and 29·7 GHz and at the Milan site at 19·77 GHz during 1992. The model intercomparison is carried out by checking the assumed best-fitting probability density function for the variance and log-amplitude fluctuations and analysing the proposed relationships between scintillation parameters and ground meteorological measurements. Results are discussed in order to understand the potentials and the limits of each prediction model within this case study. The agreement with Olympus measurements is found to be mainly dependent on the proper parametrization of prediction models to the radiometeorological variables along the earth–satellite path. ©1997 by John Wiley & Sons, Ltd.
Purification and biochemical characterization of recombinant hirudin produced by Saccharomyces cerevisiae (1989)

Recombinant hirudin was produced by the yeast Saccharomyces cerevisiae using the alpha-pheromone prepro sequence to direct its secretion into the culture medium. The secreted hirudin was isolated to greater than or equal to 95% purity as measured by 205-nm absorbance integration from a reverse-phase chromatogram. One major activity peak corresponding to the complete, correctly processed molecule and two minor activity peaks corresponding to C-terminally truncated forms were identified. The primary structure of the major peak, determined by N-terminal sequencing of tryptic peptides, was that predicted from the cDNA sequence, and the molecular mass analyzed by fast atom bombardment mass spectrometry (FAB-MS) was 6892.6 (calculated 6892.5). UV spectral analysis suggested that, in contrast to the natural molecule, recombinant hirudin produced by S. cerevisiae is not sulfated.
Clades of Adeno-Associated Viruses Are Widely Disseminated in Human Tissues (2004)

The potential for using Adeno-associated virus (AAV) as a vector for human gene therapy has stimulated interest in the Dependovirus genus. Serologic data suggest that AAV infections are prevalent in humans, although analyses of viruses and viral sequences from clinical samples are extremely limited. Molecular techniques were used in this study to successfully detect endogenous AAV sequences in 18% of all human tissues screened, with the liver and bone marrow being the most predominant sites. Sequence characterization of rescued AAV DNAs indicated a diverse array of molecular forms which segregate into clades whose members share functional and serologic similarities. One of the most predominant human clades is a hybrid of two previously described AAV serotypes, while another clade was found in humans and several species of nonhuman primates, suggesting a cross-species transmission of this virus. These data provide important information regarding the biology of parvoviruses in humans and their use as gene therapy vectors.
Gene Expression Profiling Separates Chromophobe Renal Cell Carcinoma from Oncocytoma and Identifies Vesicular Transport and Cell Junction Proteins as Differentially Expressed Genes (2006)

We showed that chromophobe RCC and oncocytoma are distinguishable by mRNA expression profiles and a panel of gene products potentially useful as diagnostic markers were identified.
Wideband characterization of scattering channels (1997)

A statistical approach using a parametric spectral conversion of singular value decomposition Prony (SVD-P) is introduced to provide better resolution in channel characterization. The approach has been applied to analysing the transfer function of a transhorizon channel captured using a wideband channel sounder. The procedure is presented for the estimation of delay power spectrum, delay spread and coherence bandwidth of the experimental channel.
A new paradigm for profiling testicular gene expression during normal and disturbed human spermatogenesis (2006)

The aim of this study was to identify gene expression patterns of the testis that correlate with the appearance of distinct stages of male germ cells. We avoided the pitfalls of mixed pathological phenotypes of the testis and circumvented the inapplicability of using the first spermatogenic wave as done previously on rodents. This was accomplished by using 28 samples showing defined and highly homogeneous pathologies selected from 578 testicular biopsies obtained from 289 men with azoospermia (two biopsies each). The molecular signature of the different developmental stages correlated with the morphological preclassification of the testicular biopsies, as shown by resampling-based hierarchical clustering using different measures of variability. By using analysis of variance (ANOVA) and extensive permutation analysis, we filtered 1181 genes that exhibit exceptional statistical significance in testicular expression and grouped subsets with transcriptional changes within the pre-meiotic (348 genes), post-meiotic (81 genes) and terminal differentiation (38 genes) phase. Several distinct molecular classes, metabolic pathways and transcription factor binding sites are involved, depending on the transcriptional profile of the gene clusters that were built using a novel clustering procedure based on not only similarity but also statistical significance.
Tumor necrosis factor primes neutrophils for hypochlorous acid production (1989)

Tumor necrosis factor (TNF) has a weak direct effect on neutrophil oxidative metabolism and primes neutrophils for oxidant release in response to other stimuli. We examined the effect of recombinant human TNF alpha (rTNF alpha) on production of hypochlorous acid (HOCl) by human neutrophils. TNF alone, even at concentrations of 1,000 U/ml, did not stimulate HOCl production. In contrast, rTNF alpha, in a dose-dependent manner, primed neutrophils for HOCl production in response to the weak agent unopsonized zymosan. rTNF alpha concentrations as low as 10 U/ml resulted in a fivefold increase in HOCl in this system. rTNF alpha-primed cells also exhibited increased phagocytosis. Priming in this model system occurred regardless of whether cells were preincubated with rTNF alpha before addition of zymosan or coincubated with both rTNF alpha and zymosan. rTNF alpha priming for HOCl production could not be washed away and required a lag period of approximately 10 min. rTNF alpha priming was not dependent on extracellular Ca2+ and Mg2+. Preincubation experiments demonstrated that rTNF alpha priming was not inhibited by the microfilament blocker cytochalasin B. Although the mechanism remains unclear, these findings demonstrate that rTNF alpha has an important priming effect on the neutrophil myeloperoxidase pathway.
Enantioselective Synthesis of Cyclohexenylalkenes by Asymmetric Deprotonation of 4-tert-Butylcyclohexanone Followed by O-Nonaflation and Heck Couplings (2001)

Formation of (S)-4-tert-butylcyclohex-1-enyl nonaflate 4 by reaction with nonafluorobutanesulfonyl fluoride was found to be highly enantioselective both from (S)-4-tert-butyl-1-(trimethyl-siloxy)cyclohexene 3 and from the corresponding lithium enolate 2. The latter was generated by kinetic deprotonation of 4-tert-butylcyclohexanone 1 with lithium (R,R′)-bis(1-phenylethyl)amide as enantiopure base. A number of functionalized 2-(4-tert-butylcyclohex-1-enyl)alkenes 6 were prepared with roughly 90% enantiomeric excess from trimethylsilyl enol ether 3 using a one-pot nonaflation/Heck reaction sequence.
Identification of the structural proteins of an ATP-driven potassium transport system in Escherichia coli. (1978)

The three structural proteins of the ATP-driven Kdp potassium transport system of Escherichia coli [Rhoads, D. B., Waters, F. B. & Epstein, W. (1976) J. Gen. Physiol. 67, 325-341] have been identified and found to be located in the inner membrane. The high-affinity repressible Kdp system in one of four potassium transport systems in E. coli. The Kdp proteins were identified both in growing cells as well as in heavily UV-irradiated cells infected with transducing phages carrying the kdp operon. Although all previously identified ATP-driven transport systems of Gram-negative bacteria have been shown to contain a periplasmic protein component, no evidence was found for such a component or for an outer membrane component of the Kdp system. The molecular weights of the three inner membrane proteins, KdpA, KdpB, and KdpC, were determined to be 47,000, 90,000 and 22,000, respectively.
Therapy with cultured T cells: principles revisited (1997)

In animals and in humans, T-cell therapy can cure advanced disseminated leukemia that would otherwise be fatal. The therapeutic effect of immune T cells is quantitative. As the dose of effector T cells is increased, survival is proportionately increased. Therefore, effective T-cell therapy is predicated on the ability to procure large numbers of immune effector T cells. By using cultured T cells, the number of immune T cells can be increased in vivo substantially above the level achievable by vaccination. The survival of cultured T cells in vivo is dependent upon both the culture conditions used and the therapeutic regimens employed. Under appropriate conditions, cultured T cells can proliferate in vivo in response to stimulation by antigen, distribute widely and survive long term to provide effector function and immunologic memory. Given that T cells recognize peptides, the need for immunization with tumor can be circumvented by immunization with peptide. Peptide-specific T cells and the progeny of single T-cell clones can provide the necessary cellular functions to eradicate disseminated murine leukemia. The ability of cloned T cells to similarly provide substantial measurable immunity in humans has been validated in clinical trials. By priming with peptides and by using established culture conditions, T-cell therapy can now be directed against virtually any antigen within the host T-cell repertoire. The major remaining question to be answered is which proteins and which peptides are the most suitable targets for T-cell therapy trials.
Induction of breast cancer resistance protein by the camptothecin derivative DX-8951f is associated with minor reduction of antitumour activity (2002)

DX-8951f (exatecan mesylate), a new water-soluble derivative of camptothecin, is currently being evaluated in phase II clinical trials. Resistance may be acquired when treating cancer patients with DX-8951f. Therefore, we selected a subline of the human ovarian cancer cell line A2780 for resistance against DX-8951f to investigate possible mechanisms of resistance. This DX-8951f-resistant subline, designated 2780DX8 (resistance factor=9.3), displayed a typical cross-resistance pattern including compounds, such as topotecan (resistance factor =34), SN-38 (resistance factor =47), mitoxantrone (resistance factor =59) and doxorubicin (resistance factor =2.9), which have previously been associated with the expression of breast cancer resistance protein. 2780DX8 cells did not show changes in the topoisomerase I gene, in topoisomerase I protein levels or catalytic activity. Overexpression of breast cancer resistance protein could be detected, both at the mRNA and protein level, while staining for Pgp, MRP1, or LRP was negative. GF120918, an inhibitor of breast cancer resistance protein, was able to reverse the DX-8951f-induced resistance in 2780DX8 cells. In vivo experiments in well-established 2780DX8 human tumour xenografts demonstrated that the growth inhibition induced by CPT-11 was more affected by breast cancer resistance protein expression than that of DX-8951f. These data indicate for the first time that DX-8951f is able to induce breast cancer resistance protein as a mechanism of resistance. Breast cancer resistance protein, however, results in only minor reduction of antitumour activity of DX-8951f which is an advantage over topotecan and CPT-11/SN-38.
Insulin-Like Growth Factor I-Triggered Cell Migration and Invasion Are Mediated by Matrix Metalloproteinase-91 (1999)

MCF-7 cells migrate through vitronectin-coated filters in response to insulin-like growth factor I (IGF-I); migration is inhibited by the matrix metalloproteinase (MMP) inhibitor BB-94, but not by the serine proteinase inhibitor aprotinin. MMP-9 was identified in the conditioned medium of MCF-7 cells; in addition, fluorescence-activated cell sorting analysis revealed its presence on the cell surface, where MMP-9 activity was also found using a specific fluorogenic peptide. Furthermore, the messenger RNA encoding MMP-9 was detected in MCF-7 cells by PCR. The IGF-I concentration leading to maximal MCF-7 invasion produces an increase in cell surface proteolytic activity after short incubation periods. At 18 h, however, preincubation of MCF-7 cells with IGF-I produces at 18 h a dose-dependent decrease in cell-associated MMP-9 activity and an increase in soluble MMP-9. MCF-7 invasion is dependent on the alpha(v)beta5 integrin, a vitronectin receptor. The levels of alpha(v)- and beta5-subunits expressed in MCF-7 cells depend on the IGF-I concentration, which triggers an increase in both of these subunits. Based on these results, we suggest that IGF-I-induced MCF-7 cell migration is mediated by the MMP-9 activity on the cell surface and by alpha(v)beta5 integrin.
Establishment and Characterization of a Human Primary Prostatic Adenocarcinoma Cell Line (ND-1) (1992)

No AccessJournal of Urology1 Nov 1992Establishment and Characterization of a Human Primary Prostatic Adenocarcinoma Cell Line (ND-1) Perinchery Narayan, and Rajvir Dahiya Perinchery NarayanPerinchery Narayan , and Rajvir DahiyaRajvir Dahiya View All Author Informationhttps://doi.org/10.1016/S0022-5347(17)36978-1AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail A human primary prostatic adenocarcinoma cell line named ND-1 has been established in long term tissue culture. The cultured cells show growth in both monolayers and in soft agar suspension and produce subcutaneous tumors in nude mice. Cytogenetic analysis by G-banding demonstrated an aneuploid karyotype with a modal chromosome number of 62, and multiple marker chromosomes with 25-30% structural abnormalities. Ploidy analysis revealed that the majority of ND-1 cells (67%) had a DNA mass of 10.1 picogram and DNA index of 1.41. Nineteen percent of cells had a DNA mass of 21.3 picogram and DNA index of 3.0. Electron microscopic studies revealed common features of neoplastic epithelial cells such as numerous microvilli, junctional complexes, abnormal nuclei, nucleoli, and mitochondria. Due to the absence of a structurally normal Y chromosome, confirmation of the presence of a derived Y chromosome was achieved through the use of C-banding and through fluorescent in situ hybridization with a Y chromosome repeat probe. Tandem E PSA immunoenzymatic assay revealed that these ND-1 cells secrete small amounts of prostate specific antigen. © 1992 by The American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetailsCited BySOBEL R and SADAR M (2018) CELL LINES USED IN PROSTATE CANCER RESEARCH: A COMPENDIUM OF OLD AND NEW LINES—PART 1Journal of Urology, VOL. 173, NO. 2, (342-359), Online publication date: 1-Feb-2005.DASARI V, DENG D, PERINCHERY G, YEH C and DAHIYA R (2018) DNA METHYLATION REGULATES THE EXPRESSION OF Y CHROMOSOME SPECIFIC GENES IN PROSTATE CANCERJournal of Urology, VOL. 167, NO. 1, (335-338), Online publication date: 1-Jan-2002.LI L, ZHAO H, NAKAJIMA K, OH B, FILHO L, CARROLL P and DAHIYA R (2018) METHYLATION OF THE E-CADHERIN GENE PROMOTER CORRELATES WITH PROGRESSION OF PROSTATE CANCERJournal of Urology, VOL. 166, NO. 2, (705-709), Online publication date: 1-Aug-2001. Volume 148Issue 5 Part 1November 1992Page: 1600-1604 Advertisement Copyright & Permissions© 1992 by The American Urological Association Education and Research, Inc.Keywordsantigenscell lineDNAprostatic neoplasiaMetricsAuthor Information Perinchery Narayan More articles by this author Rajvir Dahiya More articles by this author Expand All Advertisement PDF DownloadLoading ...
Thermochemistry of materials by laser vaporization mass spectrometry, part II - graphite (1987)

In an earlier study (Part I of this series) an experimental approach, which couples laser heating of refractory materials under vacuum with mass spectrometric detection of the vapor plume species for thermochemical determinations, was demonstrated using the BN refractory system at 2900 K.
IP-10 induces dissociation of newly formed blood vessels (2009)

The signals that prune the exuberant vascular growth of tissue repair are still ill defined. We demonstrate that activation of CXC chemokine receptor 3 (CXCR3) mediates the regression of newly formed blood vessels. We present evidence that CXCR3 is expressed on newly formed vessels in vivo and in vitro. CXCR3 is expressed on vessels at days 7-21 post-wounding, and is undetectable in unwounded or healed skin. Treatment of endothelial cords with CXCL10 (IP-10), a CXCR3 ligand present during the resolving phase of wounds, either in vitro or in vivo caused dissociation even in the presence of angiogenic factors. Consistent with this, mice lacking CXCR3 express a greater number of vessels in wound tissue compared to wild-type mice. We then hypothesized that signaling from CXCR3 not only limits angiogenesis, but also compromises vessel integrity to induce regression. We found that activation of CXCR3 triggers micro-calpain activity, causing cleavage of the cytoplasmic tail of beta3 integrins at the calpain cleavage sites c'754 and c'747. IP-10 stimulation also activated caspase 3, blockage of which prevented cell death but not cord dissociation. This is the first direct evidence for an extracellular signaling mechanism through CXCR3 that causes the dissociation of newly formed blood vessels followed by cell death.
Hedgehog signaling: modulation of cancer properies and tumor mircroenvironment (2016)

Cancer poses a serious health problem in society and is increasingly surpassing cardiovascular disease as the leading cause of mortality in the United States. Current therapeutic strategies for cancer are extreme and harsh to patients and often have limited success; the danger of cancer is intensified as it metastasizes to secondary locations such as lung, bone, and liver, posing a dire threat to patient treatment and survival. Hedgehog signaling is an important pathway for normal development. Initially identified in Drosophila, the vertebrate and mammalian equivalent of the pathway has been studied extensively for its role in cancer development and progression. As this pathway regulates key target genes involved in development, its action also allows for the modulation of the microenvironment to prepare a tumor-suitable niche by manipulating tumor cell growth, differentiation, and immune regulation, thus creating an enabling environment for progression and metastasis. In this review, we will summarize recent scientific discoveries reporting the impact of the Hedgehog signaling pathway on the tumor initiation process and metastatic cascade, shedding light on the ability of the tumor to take over a mechanism crucially intended for development and normal function.