gebhart/patrepeval huggingface dataset:
Exceptional and Selective Stabilization of A-T Rich DNA.cntdot.DNA Duplexes by N-Methylpyrrole Carboxamide Peptides Conjugated to Oligodeoxynucleotides (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTExceptional and Selective Stabilization of A-T Rich DNA.cntdot.DNA Duplexes by N-Methylpyrrole Carboxamide Peptides Conjugated to OligodeoxynucleotidesAlexander N. Sinyakov, Sergey G. Lokhov, Igor V. Kutyavin, Howard B. Gamper, and Rich B. Meyer Jr.Cite this: J. Am. Chem. Soc. 1995, 117, 17, 4995–4996Publication Date (Print):May 1, 1995Publication History Published online1 May 2002Published inissue 1 May 1995https://pubs.acs.org/doi/10.1021/ja00122a031https://doi.org/10.1021/ja00122a031research-articleACS PublicationsRequest reuse permissionsArticle Views115Altmetric-Citations32LEARN 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 Get e-Alerts
Dehydroepiandrosterone (DHEA) such as 17β‐estradiol prevents MPTP‐induced dopamine depletion in mice (2002)

Previous work from our laboratory has shown prevention of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced striatal dopamine (DA) depletion in mice by 17beta-estradiol, progesterone, and raloxifene. Dehydroepiandrosterone (DHEA), a neurosteroid, was shown to have neuroprotective activities in various paradigms of neuronal death but its effect in vivo in mice on MPTP toxicity has not been reported. We investigated the effects of 17beta-estradiol (2 microg/day) and DHEA (3 mg/day) for 5 days before and after an acute treatment of four MPTP (10 mg/kg) injections in male C57Bl/6 mice. Striatal DA concentrations and its metabolites dihydroxyphenylacetic acid (DOPAC) and homovanillic acid (HVA) were measured by HPLC. MPTP mice that received 17beta-estradiol or DHEA had striatal DA, DOPAC, and HVA concentrations comparable to intact animals and higher than striatal DA, DOPAC, and HVA levels in saline-MPTP-treated mice. MPTP treatment led to an increase of striatal DA turnover (assessed with the HVA/DA ratio); DHEA and 17beta-estradiol prevented this increase. 17beta-Estradiol did not affect striatal DA and metabolites concentrations in intact mice in this paradigm. Furthermore, in the substantia nigra DHEA and 17beta-estradiol prevented the MPTP-induced dopamine transporter and tyrosine hydroxylase mRNA decreases measured by in situ hybridization. Therefore, DHEA such as 17beta-estradiol is active in preventing the catecholamine-depleting effect of MPTP and our results suggest that this involves neuroprotection of DA neurons.
Identification of β‐amyrin and sophoradiol 24‐hydroxylase by expressed sequence tag mining and functional expression assay (2006)

Triterpenes exhibit a wide range of structural diversity produced by a sequence of biosynthetic reactions. Cyclization of oxidosqualene is the initial origin of structural diversity of skeletons in their biosynthesis, and subsequent regio- and stereospecific hydroxylation of the triterpene skeleton produces further structural diversity. The enzymes responsible for this hydroxylation were thought to be cytochrome P450-dependent monooxygenase, although their cloning has not been reported. To mine these hydroxylases from cytochrome P450 genes, five genes (CYP71D8, CYP82A2, CYP82A3, CYP82A4 and CYP93E1) reported to be elicitor-inducible genes in Glycine max expressed sequence tags (EST), were amplified by PCR, and screened for their ability to hydroxylate triterpenes (beta-amyrin or sophoradiol) by heterologous expression in the yeast Saccharomyces cerevisiae. Among them, CYP93E1 transformant showed hydroxylating activity on both substrates. The products were identified as olean-12-ene-3beta,24-diol and soyasapogenol B, respectively, by GC-MS. Co-expression of CYP93E1 and beta-amyrin synthase in S. cerevisiae yielded olean-12-ene-3beta,24-diol. This is the first identification of triterpene hydroxylase cDNA from any plant species. Successful identification of a beta-amyrin and sophoradiol 24-hydroxylase from the inducible family of cytochrome P450 genes suggests that other triterpene hydroxylases belong to this family. In addition, substrate specificity with the obtained P450 hydroxylase indicates the two possible biosynthetic routes from triterpene-monool to triterpene-triol.
The Effect of Celecoxib, a Cyclooxygenase-2 Inhibitor, in Familial Adenomatous Polyposis (2000)

In patients with familial adenomatous polyposis, six months of twice-daily treatment with 400 mg of celecoxib, a cyclooxygenase-2 inhibitor, leads to a significant reduction in the number of colorectal polyps.
Rs12218 In SAA1 gene was associated with serum lipid levels (2013)

Our results indicated that the rs12218 in the SAA1gene was associated with lipid levels in a Chinese population.
MALDI Mass Spectrometry for Direct Tissue Analysis:  A New Tool for Biomarker Discovery (2005)

The direct analysis of tissue sections by MALDI mass spectrometry holds tremendous potential for biomarker discovery. This technology routinely allows many hundreds of proteins to be detected over a mass range of approximately 2000-70 000 Da while maintaining the spatial localization of the proteins detected. This technology has been applied to a wide range of tissue samples, including human glioma tissue and human lung tumor tissue. In many cases, biostatistical analyses of the resulting protein profiles revealed patterns that correlated with disease state and/or clinical endpoints. This work serves as a review of recent applications and summarizes the current state of technology.
A2AR Antagonism with CPI-444 Induces Antitumor Responses and Augments Efficacy to Anti–PD-(L)1 and Anti–CTLA-4 in Preclinical Models (2018)

Adenosine signaling through A2A receptors (A2AR) expressed on immune cells suppresses antitumor immunity. CPI-444 is a potent, selective, oral A2AR antagonist. Blockade of A2AR with CPI-444 restored T-cell signaling, IL2, and IFNγ production that were suppressed by adenosine analogues <i>in vitro</i> CPI-444 treatment led to dose-dependent inhibition of tumor growth in multiple syngeneic mouse tumor models. Concentrations of extracellular adenosine in the tumor microenvironment, measured using microdialysis, were approximately 100-150 nmol/L and were higher than corresponding subcutaneous tissue. Combining CPI-444 with anti-PD-L1 or anti-CTLA-4 treatment eliminated tumors in up to 90% of treated mice, including restoration of immune responses in models that incompletely responded to anti-PD-L1 or anti-CTLA-4 monotherapy. Tumor growth was fully inhibited when mice with cleared tumors were later rechallenged, indicating that CPI-444 induced systemic antitumor immune memory. CD8<sup>+</sup> T-cell depletion abrogated the efficacy of CPI-444 with and without anti-PD-L1 treatment, demonstrating a role for CD8<sup>+</sup> T cells in mediating primary and secondary immune responses. The antitumor efficacy of CPI-444 with and without anti-PD-L1 was associated with increased T-cell activation, a compensatory increase in CD73 expression, and induction of a Th1 gene expression signature consistent with immune activation. These results suggest a broad role for adenosine-mediated immunosuppression in tumors and justify the further evaluation of CPI-444 as a therapeutic agent in patients with solid tumors. <i>Cancer Immunol Res; 6(10); 1136-49. ©2018 AACR</i>.
Novel synthetic oleanane triterpenoids: A series of highly active inhibitors of nitric oxide production in mouse macrophages (1999)

Novel oleanane triterpenoids with modified rings A and C were designed and synthesized. Among them, methyl 2-carboxy-3,12-dioxooleana-1,9-dien-28-oate showed similar high inhibitory activity (IC50 = 0.8 nM) to 2-cyano-3,12-dioxooleana-1,9-dien-28-oic acid (CDDO), which we have synthesized previously, against production of nitric oxide induced by interferon-gamma in mouse macrophages.
Mitogenic signalling and substrate specificity of the Flk2/Flt3 receptor tyrosine kinase in fibroblasts and interleukin 3-dependent hematopoietic cells. (1993)

Flk2/Flt3 is a recently identified receptor tyrosine kinase expressed in brain, placenta, testis, and primitive hematopoietic cells. The mitogenic signalling potential and biochemical properties of Flk2/Flt3 have been analyzed by using a chimeric receptor composed of the extracellular domain of the human colony-stimulating factor 1 receptor and the transmembrane and cytoplasmic domains of murine Flk2/Flt3. We demonstrate that colony-stimulating factor 1 stimulation of the Flk2/Flt3 kinase in transfected NIH 3T3 fibroblasts leads to a transformed phenotype and generates a full proliferative response in the absence of other growth factors. In transfected interleukin 3 (IL-3)-dependent Ba/F3 lymphoid cells, activation of the chimeric receptor can abrogate IL-3 requirement and sustain long-term proliferation. We show that phospholipase C-gamma 1, Ras GTPase-activating protein, the p85 subunit of phosphatidylinositol 3'-kinase, Shc, Grb2, Vav, Fyn, and Src are components of the Flk2/Flt3 signal transduction pathway. In addition, we demonstrate that phospholipase C-gamma 1, the p85 subunit of phosphatidylinositol 3'-kinase, Shc, Grb2, and Src family tyrosine kinases, but not Ras GTPase-activating protein, Vav, or Nck, physically associate with the Flk2/Flt3 cytoplasmic domain. Cell-type-specific differences in tyrosine phosphorylation of p85 and Shc are observed. A comparative analysis of the Flk2/Flt3 signal cascade with those of the endogenous platelet-derived growth factor and IL-3 receptors indicates that Flk2/Flt3 displays specific substrate preferences. Furthermore, tyrosine phosphorylation of p85 and Shc is similarly affected by totally different growth factors in the same cellular background.
Equalizers for multiple input/multiple output channels and PAM systems with cyclostationary input sequences (1992)

The author studies minimum mean square error (MMSE) linear and decision feedback (DF) equalisers for multiple input/multiple output (MIMO) communication systems with intersymbol interference (ISI) and wide-sense stationary (WSS) inputs. To derive these equalizers, one works in the D-transform domain and uses prediction theory results. Partial-response MMSE equalizers are also found. As an application, the author considers a pulse amplitude modulation (PAM) communication system with ISI and cyclostationary inputs. The MMSE linear and DF equalizers are determined by studying an equivalent MIMO system. The resulting filters are expressed in compact matrix notation and are time-invariant, whereas the corresponding single input/single output filters are periodically time-invariant. The author also considers MMSE equalizers for a wide-sense stationary process by introducing a 'random phase'. To aid in the performance evaluation of various equalizers, the author derives their mean square errors.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Structure of the complex polysaccharide C-substance from Streptococcus pneumoniae type 1 (1980)

The complex cell-wall polysaccharide, C-substance, was isolated from Streptococcus pneumoniae type 1 and purified by DEAE-cellulose (HCO3(-) form) and Sephadex column chromatography. The complete structure of this antigen was obtained by the application of methylation and 1H NMR and 13C NMR spectroscopic techniques to a series of oligosaccharide fragments obtained by the selective degradation of the N-acetylated antigen. Native C-substance is composed of the following repeating unit: beta-D-Glup-1 leads to 3-alpha-AAT-Galp-1 leads to 4-alpha-D-GalNAcp-1 leads to 3-beta-D-GalNH2p-1 leads to 1'-ribitol-5-phosphate where AATGal is 2-acetamido-4-amino-2,4,6-trideoxygalactose. Phosphocholine substituents are situated at O(6) of the unacetylated galactosamine residues, and the repeating units are linked through a diphosphate ester from ribitol to O(6) of the beta-D-glucopyranose residue. This structure has also been shown to be common to C-substances prepared from a number of other pneumococcal types based on the criterion of their identical 13C NMR spectra.
Androgens Stimulate Lipogenic Gene Expression in Prostate Cancer Cells by Activation of the Sterol Regulatory Element-Binding Protein Cleavage Activating Protein/Sterol Regulatory Element-Binding Protein Pathway (2001)

Using two independent prostate cancer cell lines (LNCaP and MDA-PCa-2a), we demonstrate that coordinated stimulation of lipogenic gene expression by androgens is a common phenomenon in androgen-responsive prostate tumor lines and involves activation of the sterol regulatory element-binding protein (SREBP) pathway. We show 1) that in both cell lines, androgens stimulate the expression of fatty acid synthase and hydroxymethylglutaryl-coenzyme A synthase, two key lipogenic genes representative for the fatty acid and the cholesterol synthesis pathway, respectively; 2) that treatment with androgens results in increased nuclear levels of active SREBP; 3) that the effects of androgens on promoter-reporter constructs derived from both lipogenic genes (fatty acid synthase and hydroxymethylglutaryl-coenzyme A synthase) depend on the presence of intact SREBP-binding sites; and 4) that cotransfection with dominant-negative forms of SREBPs abolishes the effects of androgens. Related to the mechanism underlying androgen activation of the SREBP pathway, we show that in addition to minor effects on SREBP precursor levels, androgens induce a major increase in the expression of sterol regulatory element-binding protein cleavage-activating protein (SCAP), an escort protein that transports SREBPs from their site of synthesis in the endoplasmic reticulum to their site of proteolytical activation in the Golgi. Both time course studies and overexpression experiments showing that increasing levels of SCAP enhance the production of mature SREBP and stimulate lipogenic gene expression support the contention that SCAP plays a pivotal role in the lipogenic effects of androgens in tumor cells.
Amyloid-β and tau synergistically impair the oxidative phosphorylation system in triple transgenic Alzheimer's disease mice (2009)

Alzheimer's disease (AD) is characterized by amyloid-beta (Abeta)-containing plaques, neurofibrillary tangles, and neuron and synapse loss. Tangle formation has been reproduced in P301L tau transgenic pR5 mice, whereas APP(sw)PS2(N141I) double-transgenic APP152 mice develop Abeta plaques. Cross-breeding generates triple transgenic ((triple)AD) mice that combine both pathologies in one model. To determine functional consequences of the combined Abeta and tau pathologies, we performed a proteomic analysis followed by functional validation. Specifically, we obtained vesicular preparations from (triple)AD mice, the parental strains, and nontransgenic mice, followed by the quantitative mass-tag labeling proteomic technique iTRAQ and mass spectrometry. Within 1,275 quantified proteins, we found a massive deregulation of 24 proteins, of which one-third were mitochondrial proteins mainly related to complexes I and IV of the oxidative phosphorylation system (OXPHOS). Notably, deregulation of complex I was tau dependent, whereas deregulation of complex IV was Abeta dependent, both at the protein and activity levels. Synergistic effects of Abeta and tau were evident in 8-month-old (triple)AD mice as only they showed a reduction of the mitochondrial membrane potential at this early age. At the age of 12 months, the strongest defects on OXPHOS, synthesis of ATP, and reactive oxygen species were exhibited in the (triple)AD mice, again emphasizing synergistic, age-associated effects of Abeta and tau in perishing mitochondria. Our study establishes a molecular link between Abeta and tau protein in AD pathology in vivo, illustrating the potential of quantitative proteomics.
Frequency modulated lasers for interferometric optical gyroscopes (2016)

We study the use of frequency modulated lasers in interferometric optical gyroscopes and show that by exploiting various frequency modulation signals, the laser coherence can be controlled. We show that both angle random walk and bias stability of an interferometric optical gyroscope based on laser sources can be improved with this technique.
TrkA Immunoglobulin-Like Ligand Binding Domains Inhibit Spontaneous Activation of the Receptor (2000)

The extracellular region of the nerve growth factor (NGF) receptor, TrkA, contains two immunoglobulin (Ig)-like domains that are required for specific ligand binding. We have investigated the possible role of these two Ig-like domains in receptor dimerization and activation by using different mutants of the TrkA extracellular region. Deletions of each Ig-like domain, of both, and of the entire extracellular region were made. To probe the structural constraints on ligand-independent receptor dimerization, chimeric receptors were generated by swapping the Ig-like domains of the TrkA receptor for the third or fourth Ig-like domain of c-Kit. We also introduced single-amino-acid changes in conserved residues within the Ig-like domains of TrkA. Most of these TrkA variants did not bind NGF, and their expression in PC12nnr5 cells, which lack endogenous TrkA, promoted ligand-independent neurite outgrowth. Some TrkA mutant receptors induced malignant transformation of Rat-1 cells, as assessed by measuring proliferation in the absence of serum, anchorage-independent growth, and tumorigenesis in nude mice. These mutants exhibited constitutive phosphorylation and spontaneous dimerization consistent with their biological activities. Our data suggest that spontaneous dimerization of TrkA occurs when the structure of the Ig-like domains is altered, implying that the intact domains inhibit receptor dimerization in the absence of NGF.
Simplified RNA secondary structure mapping by automation of SHAPE data analysis (2011)

SHAPE (Selective 2'-hydroxyl acylation analysed by primer extension) technology has emerged as one of the leading methods of determining RNA secondary structure at the nucleotide level. A significant bottleneck in using SHAPE is the complex and time-consuming data processing that is required. We present here a modified data collection method and a series of algorithms, embodied in a program entitled Fast Analysis of SHAPE traces (FAST), which significantly reduces processing time. We have used this method to resolve the secondary structure of the first ~900 nt of the hepatitis C virus (HCV) genome, including the entire core gene. We have also demonstrated the ability of SHAPE/FAST to detect the binding of a small molecule inhibitor to the HCV internal ribosomal entry site (IRES). In conclusion, FAST allows for high-throughput data processing to match the current high-throughput generation of data possible with SHAPE, reducing the barrier to determining the structure of RNAs of interest.
Lateral Symbiont Acquisition in a Maternally Transmitted Chemosynthetic Clam Endosymbiosis (2008)

Deep-sea clams of the family Vesicomyidae live in symbiosis with intracellular chemosynthetic bacteria. These symbionts are transmitted maternally (vertically) between host generations and should therefore show a pattern of genetic variation paralleling that of the cotransmitted host mitochondrion. However, instances of lateral (nonvertical) symbiont acquisition could still occur, thereby decoupling symbiont and mitochondrial phylogenies. Here, we provide the first evidence against strict maternal cotransmission of symbiont and mitochondrial genomes in vesicomyids. Analysis of Vesicomya sp. mt-II clams from hydrothermal vents on the Juan de Fuca Ridge (northeastern Pacific) revealed a symbiont phylotype (designated symB(VII)) highly divergent from previously described symbionts of the same host lineage. SymB(VII)-hosting clams occurred at low frequency (0.02) relative to individuals hosting the dominant symbiont phylotype. Phylogenetic analysis of 16S rRNA genes from a wide range of symbionts and free-living bacteria clustered symB(VII) within the monophyletic clade of vesicomyid symbionts. Further analysis of 3 symbiont loci (23S, dnaK, and soxA) across 11 vesicomyid taxa unambiguously placed symB(VII) as sister to the symbiont of a distantly related host lineage, Vesicomya sp. from the Mid-Atlantic Ridge (98.9% median nucleotide identity across protein-coding loci). Using likelihood and Bayesian model discrimination methods, we rejected the strict maternal cotransmission hypothesis by showing a significant decoupling of symbiont and host mitochondrial (COI and mt16S genes) phylogenies. Indeed, decoupling occurred even when symB(VII) was excluded from phylogenetic reconstructions, suggesting a history of host switching in this group. Together, the data indicate a history of lateral symbiont transfer in vesicomyids, with symB(VII) being the most conspicuous example. Interpreted alongside previous studies of the vesicomyid symbiosis, these results suggest a mixed mode of symbiont transmission characterized by predominantly vertical transmission punctuated with instances of lateral symbiont acquisition. Lateral acquisition may facilitate the exchange of genetic material (recombination) among divergent symbiont lineages, rendering the evolutionary history of vesicomyid symbiont genomes much more complex than previously thought.
Trans-sialidase activity of Photobacterium damsela 2,6-sialyltransferase and its application in the synthesis of sialosides (2009)

Trans-sialidases catalyze the transfer of a sialic acid from one sialoside to an acceptor to form a new sialoside. alpha2,3-Trans-sialidase activity was initially discovered in the parasitic protozoan Trypanosoma cruzi, and more recently was found in a multifunctional Pasteurella multocida sialyltransferase PmST1. alpha2,8-Trans-sialidase activity was also described for a multifunctional Campylobacter jejuni sialyltransferase CstII. We report here the discovery of the alpha2,6-trans-sialidase activity of a previously reported recombinant truncated bacterial alpha2,6-sialyltransferase from Photobacterium damsela (Delta15Pd2,6ST). This is the first time that the alpha2,6-trans-sialidase activity has ever been identified. Kinetic studies indicate that Delta15Pd2,6ST-catalyzed trans-sialidase reaction follows a ping-pong bi-bi reaction mechanism. Cytidine 5'-monophosphate, the product of sialyltransferase reactions, is not required by the trans-sialidase activity of the enzyme but enhances the trans-sialidase activity modestly as a non-essential activator. Using chemically synthesized Neu5AcalphapNP and LacbetaMU, alpha2,6-linked sialoside Neu5Acalpha2,6LacbetaMU has been obtained in one-step in high yield using the trans-sialidase activity of Delta15Pd2,6ST. In addition to the alpha2,6-trans-sialidase activity, Delta15Pd2,6ST also has alpha2,6-sialidase activity. The multifunctionality is thus a common feature of many bacterial sialyltransferases.