gebhart/patrepeval huggingface dataset:
The Bioactive Conformation of Neuropeptide Y Analogues at the Human Y2‐Receptor (1997)

Several attempts to investigate the bioactive conformation of neuropeptide Y have been made so far. As cyclic peptides are much more rigid than linear ones, we decided to synthesise cyclic analogues of the C-terminal dodekapeptide amide neuropeptide Y Ac-25-36. Cyclisation was performed by side chain lactamisation of ornithine or lysine and glutamic or aspartic acid. The affinity of the 19 peptides ranged from Ki 0.6 nM to greater than 10,000 nM. We found that the size, position, orientation, configuration. and the location of the cycle plays an important role for receptor recognition. Circular dichroic studies have been performed to characterise the secondary structure of each peptide. Receptor binding studies were carried out on human neuroblastoma cell lines SK-N-MC (Y1) and SMS-KAN (Y2), and on rabbit kidney membranes (Y2). The pharmacological and spectral data showed that the alpha-helix content was not the predominant factor for high Y2-receptor affinity. Instead, the location and the size of the hydrophobic lactam bridge, and the conserved C-terminal tetrapeptide (Arg-Glu-Arg-Tyr) seemed to be the main parameters. Using molecular dynamics, the structures of four cyclic peptides (i,i+4) have been investigated and compared with the previously published NMR structure of one of the cyclic peptide analogues. Significant differences have been found in the overall three-dimensional fold of the peptides. The distances between the N- and the C-terminus allow discrimination between peptides with high binding affinity and those with low binding affinity, because of the correlation that was found with the measured affinity. Thus, this study suggests that a turn-like structure and the orientation of the C-terminus towards the N-terminus play major roles for high affinity binding of cyclic dodecapeptides to the Y2-receptor. None of the cyclic segments exhibits significant affinity to the Y1-receptor. Thus, these results support the hypothesis of a discontinuous binding site of neuropeptide Y at the Y1-receptor.
DUAL-GLO™ LUCIFERASE ASSAY SYSTEM: A HOMOGENEOUS DUAL-REPORTER SYSTEM (2002)

Promega has developed a new, homogeneous reporter assay, the Dual-Glo™ Luciferase Assay System, for monitoring both firefly and Renilla luciferases expressed in mammalian cells in 96- and 384-well plates. The new assay system integrates cell lysis and luminescence chemistry, and the luminescence kinetics have been extended over several hours. The homogeneous assay format allows dual-reporter assays to be more easily and rapidly performed by reducing sample processing requirements and eliminating the need for reagent injectors in luminometers.
Nanomedicine based approaches for the delivery of siRNA in cancer (2009)

Small interfering RNA (siRNA) technology holds great promise as a therapeutic intervention for targeted gene silencing in cancer and other diseases. However, in vivo systemic delivery of siRNA-based therapeutics to tumour tissues/cells remains a challenge. The major limitations against the use of siRNA as a therapeutic tool are its degradation by serum nucleases, poor cellular uptake and rapid renal clearance following systemic administration. Several siRNA-based loco-regional therapeutics are already in clinical trials. Further development of siRNAs for anti-cancer therapy depends on the development of safe and effective nanocarriers for systemic administration. To overcome these hurdles, nuclease-resistant chemically modified siRNAs and variety of synthetic and natural biodegradable lipids and polymers have been developed to systemically deliver siRNA with different efficacy and safety profiles. Cationic liposomes have emerged as one of the most attractive carriers because of their ability to form complexes with negatively charged siRNA and high in vitro transfection efficiency. However, their effectiveness as potential therapeutic carriers is limited by potential for pulmonary toxicity. Recently, our laboratories described the use of neutral 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine based nanoliposomes in murine tumour models. We found this approach to be safe and 10- and 30-fold more effective than cationic liposomes and naked siRNA, respectively, for systemic delivery of siRNA into tumour tissues. Here, we review potential approaches for systemic delivery of siRNA for cancer therapy.
Biochemical and antigenic properties of the Campylobacter flagellar hook protein (1992)

The flagellar filament-hook complex was removed from Campylobacter cells by shearing and was purified by differential solubilization and ultracentrifugation at pH 11 followed by cesium chloride buoyant density ultracentrifugation. Flagellar filaments were then dissociated in 0.2 M glycine-HCl (pH 2.2), and purified hooks were collected by ultracentrifugation. The hooks (105 by 24 nm) each displayed a conical protrusion at the proximal end, a concave cavity at the distal end, and helically arranged subunits. The apparent subunit molecular weight of the hook protein of seven of the eight Campylobacter strains studied was 92,500, while that of the other was 94,000. N-terminal amino acid analysis of the hook protein of two strains of Campylobacter coli and one strain of Campylobacter jejuni demonstrated that the first 15 residues were identical. Amino acid composition analysis showed that the Campylobacter hook protein contained 35.7% hydrophobic and 9.5% basic residues. Isoelectric focusing determined that the hook protein was acidic, with a pI of 4.9. Comparisons with the Salmonella and Caulobacter hook protein compositions and N-terminal amino acid sequences indicated that the Campylobacter protein was related, but more distantly than these two proteins were to each other. Immunochemical analysis with four different antisera and a panel of eight strains showed that serospecific epitopes were immunodominant. The Campylobacter hook proteins carried both cross-reactive and specific non-surface-exposed epitopes, as well as serospecific epitopes which were exposed on the surface of the assembled hook. One class of these surface-exposed hook epitopes was shared with serospecific flagellin epitopes and may involve posttranslational modification, while the second class of epitopes was hook specific and not shared with flagellin.
Prostaglandin E2 Promotes Tumor Progression by Inducing Myeloid-Derived Suppressor Cells (2007)

A causative relationship between chronic inflammation and cancer has been postulated for many years, and clinical observations and laboratory experiments support the hypothesis that inflammation contributes to tumor onset and progression. However, the precise mechanisms underlying the relationship are not known. We recently reported that the proinflammatory cytokine, interleukin-1beta, induces the accumulation and retention of myeloid-derived suppressor cells (MDSC), which are commonly found in many patients and experimental animals with cancer and are potent suppressors of adaptive and innate immunity. This finding led us to hypothesize that inflammation leads to cancer through the induction of MDSC, which inhibit immunosurveillance and thereby allow the unchecked persistence and proliferation of premalignant and malignant cells. We now report that host MDSC have receptors for prostaglandin E2 (PGE2) and that E-prostanoid receptor agonists, including PGE2, induce the differentiation of Gr1(+)CD11b(+) MDSC from bone marrow stem cells, whereas receptor antagonists block differentiation. BALB/c EP2 knockout mice inoculated with the spontaneously metastatic BALB/c-derived 4T1 mammary carcinoma have delayed tumor growth and reduced numbers of MDSC relative to wild-type mice, suggesting that PGE2 partially mediates MDSC induction through the EP2 receptor. Treatment of 4T1-tumor-bearing wild-type mice with the cyclooxygenase 2 inhibitor, SC58236, delays primary tumor growth and reduces MDSC accumulation, further showing that PGE2 induces MDSC and providing a therapeutic approach for reducing this tumor-promoting cell population.
Trefoil Factor Peptides and Gastrointestinal Function (2016)

Trefoil factor (TFF) peptides, with a 40-amino acid motif and including six conserved cysteine residues that form intramolecular disulfide bonds, are a family of mucin-associated secretory molecules mediating many physiological roles that maintain and restore gastrointestinal (GI) mucosal homeostasis. TFF peptides play important roles in response to GI mucosal injury and inflammation. In response to acute GI mucosal injury, TFF peptides accelerate cell migration to seal the damaged area from luminal contents, whereas chronic inflammation leads to increased TFF expression to prevent further progression of disease. Although much evidence supports the physiological significance of TFF peptides in mucosal defenses, the molecular and cellular mechanisms of TFF peptides in the GI epithelium remain largely unknown. In this review, we summarize the functional roles of TFF1, 2, and 3 and illustrate their action mechanisms, focusing on defense mechanisms in the GI tract.
Temperature and phase behavior of infrared intensities: the poly(methylene) chain (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTemperature and phase behavior of infrared intensities: the poly(methylene) chainR. G. Snyder, M. Maroncelli, H. L. Strauss, and V. M. HallmarkCite this: J. Phys. Chem. 1986, 90, 22, 5623–5630Publication Date (Print):October 1, 1986Publication History Published online1 May 2002Published inissue 1 October 1986https://pubs.acs.org/doi/10.1021/j100280a030https://doi.org/10.1021/j100280a030research-articleACS PublicationsRequest reuse permissionsArticle Views587Altmetric-Citations191LEARN 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 options Get e-Alerts
Transcription syndromes and the role of RNA polymerase II general transcription factors in human disease. (1996)

Messenger RNA synthesis is a major site for the regulation of gene expression. Eukaryotic messenger RNA synthesis is catalyzed by multisubunit RNA polymerase II (1–3) and proceeds via multiple stages, which are designated preinitiation, initiation, elongation, and termination and which have come to be referred to collectively as the transcription cycle (Fig. 1). The past decade was a watershed for biochemical studies of eukaryotic messenger RNA synthesis. A diverse collection of transcription factors and other nuclear proteins that govern the activity of RNA polymerase II during messenger RNA synthesis was identified and characterized, and unprecedented progress in several key research areas has provided a deeper understanding of the biochemical mechanisms underlying many aspects of eukaryotic transcriptional regulation. First, major breakthroughs in investigations of the structures of eukaryotic protein-coding genes and the role of chromatin in the regulation of their expression were achieved. Chromatin proteins, such as histones and HMG proteins, were found to play crucial roles in gene regulation by packaging genes into inactive or transcriptionally repressed configurations (4–9). Second, many DNA binding transactivators that interact specifically with upstream promoter elements and enhancer sequences located in the promoter-regulatory regions of genes were isolated, classified according to their structures, and found to regulate the expression of specific genes or gene families by controlling the rate of initiation (10) and, as shown more recently, the efficiency of elongation by RNA polymerase II (11–13). Third, chromatin remodeling proteins, such as the multisubunit SWI/SNF (14, 15) and NURF (16, 17) complexes, were discovered and found to play key roles in transcriptional activation by promoting conversion of regions of inactive chromatin into transcriptionally active, open chromatin, thereby allowing DNA binding transactivators and RNA polymerase II access to the promoter-regulatory regions of genes (4, 18–23). Fourth, coactivators, such as the SRB-containing mediator complex (2, 3, 24, 25), CREB binding protein (CBP) 1
Mutations affecting mRNA splicing are the most common molecular defects in patients with neurofibromatosis type 1 (2000)

Neurofibromatosis type 1 (NF1) is one of the most common inherited disorders in humans and is caused by mutations in the NF1 gene. To date, the majority of the reported NF1 mutations are predicted to result in protein truncation, but very few studies have correlated the causative NF1 mutation with its effect at the mRNA level. We have applied a whole NF1 cDNA screening methodology to the study of 80 unrelated NF1 patients and have identified 44 different mutations, 32 being novel, in 52 of these patients. Mutations were detected in 87% of the familial cases, but in 51% of the sporadic ones. At least 15 of the 80 NF1 patients (19%) had recurrent mutations. The study shows that in 50% of the patients in whom the mutations were identified, these resulted in splicing alterations. Most of the splicing mutations did not involve the conserved AG/GT dinucleotides of the splice sites. One frameshift, two nonsense and two missense mutations were also responsible for alterations in mRNA splicing. The location and type of mutation within the NF1 gene, and its putative effect at the protein level, do not indicate any relationship to any specific clinical feature of NF1. The high proportion of aberrant spliced transcripts detected in NF1 patients stresses the importance of studying mutations at both the genomic and RNA level. It is possible that part of the clinical variability in NF1 could be due to mutations affecting mRNA splicing, which is the most common molecular defect in NF1.
Rapid Identification of Potent Nonpeptidic Serine Protease Inhibitors (2006)

Substrate activity screening was used to rapidly identify a novel and potent (kinact/Ki=59 000 M−1 s−1) nonpeptidic chymotrypsin inhibitor with MW<500. The inhibitor is more potent than the best reported tetrapeptidyl phosphonate chymotrypsin inhibitor and demonstrated selectivity over a panel of other serine proteases, including the closely related enzyme cathepsin G. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2268/2006/z600081_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Healthy and diseased corticospinal motor neurons are selectively transduced upon direct AAV2-2 injection into the motor cortex (2015)

Direct gene delivery to the neurons of interest, without affecting other neuron populations in the cerebral cortex, represent a challenge owing to the heterogeneity and cellular complexity of the brain. Genetic modulation of corticospinal motor neurons (CSMN) is required for developing effective and long-term treatment strategies for motor neuron diseases, in which voluntary movement is impaired. Adeno-associated viruses (AAV) have been widely used for neuronal transduction studies owing to long-term and stable gene expression as well as low immunoreactivity in humans. Here we report that AAV2-2 transduces CSMN with high efficiency upon direct cortex injection and that transduction efficiencies are similar during presymptomatic and symptomatic stages in hSOD1(G93A) transgenic amyotrophic lateral sclerosis (ALS) mice. Our findings reveal that choice of promoter improves selectivity as AAV2-2 chicken β-actin promoter injection results in about 70% CSMN transduction, the highest percentage reported to date. CSMN transduction in both wild-type and transgenic ALS mice allows detailed analysis of single axon fibers within the corticospinal tract in both cervical and lumbar spinal cord and reveals circuitry defects, which mainly occur between CSMN and spinal motor neurons in hSOD1(G93A) transgenic ALS mice. Our findings set the stage for CSMN gene therapy in ALS and related motor neuron diseases.
The CLAVATA1‐related BAM1, BAM2 and BAM3 receptor kinase‐like proteins are required for meristem function in Arabidopsis (2005)

Organ formation at shoot and flower meristems in plants requires the maintenance of a population of centrally located stem cells and the differentiation of peripherally located daughter cells. The CLAVATA (CLV) gene products in Arabidopsis, including the CLV1 receptor-kinase, regulate this process by promoting the differentiation of stem cells on the meristem flanks. Here, we have analyzed the developmental roles of the CLV1-related BAM1 (derived from barely any meristem 1), BAM2 and BAM3 receptor-like kinases. Loss-of-function alleles of these receptors lead to phenotypes consistent with the loss of stem cells at the shoot and flower meristem, suggesting that their developmental role is opposite to that of CLV1. These closely related receptors are further distinguished from CLV1, whose expression and function is highly specific, by having broad expression patterns and multiple developmental roles. These include a requirement for BAM1, BAM2 and BAM3 in the development of high-ordered vascular strands within the leaf and a correlated control of leaf shape, size and symmetry. In addition, BAM1, BAM2 and BAM3 are required for male gametophyte development, as well as ovule specification and function. Significantly, the differing roles of CLV1 and BAM receptors in meristem and organ development are largely driven by differences in expression patterns.
The three-photon spectrum of the 1B2u←1A1g transition in benzene: Analysis of vibronic and rotational structure (1984)

A vibrational and rotational analysis of the three-photon fluorescence excitation spectrum of the 1B2u←1A1g transition in gas-phase benzene is presented. The group theoretically allowed origin and any associated vibrational structure are absent. In addition, there is no evidence for any rotational structure based on a rank-three transition tensor. Coherent loss mechanisms are carefully considered and then rejected as possible interferences in the three-photon fluorescence spectrum. Polarization measurements and observed vibronic structure indicate a dominant rank one (vibronic) contribution to the three-photon cross section. The lack of three-photon allowed structure in this 1B2u←1A1g transition of benzene is consistent with the pseudoparity selection rules of alternant hydrocarbon theory, yet such strict adherence to them would seem surprising. The appearance of the e2g mode ν8 in the three-photon spectrum marks the first experimental determination of its frequency in the 1B2u state.
General method for cloning amplified DNA by differential screening with genomic probes. (1982)

Mutant Syrian hamster cell lines resistant to N-(phosphonacetyl)-L-aspartate, a potent and specific inhibitor of aspartate transcarbamylase, have amplified the gene coding for the multifunctional protein (CAD) that includes this activity. The average amount of DNA amplified is approximately 500 kilobases per gene copy, about 20 times the length of the CAD gene itself. A differential screening method which uses genomic DNAs as probes was developed to isolate recombinant phage containing fragments of amplified DNA. One probe was prepared by reassociating fragments of total genomic DNA from 165-28, a mutant cell line with 190 times the wild-type complement of CAD genes, until all of the sequences repeated about 200 times were annealed and then isolating the double-stranded DNA with hydroxyapatite.This DNA was highly enriched in sequences from the entire amplified region, whereas the same sequences were very rare in DNA prepared similarly from wild-type cells. After both DNAs were labeled by nick translation, highly repeated sequences were removed by hybridization to immobilized total genomic DNA from wild-type cells. A library of cloned DNA fragments from mutant 165-28 was screened with both probes, and nine independent fragments containing about 165 kilobases of amplified DNA, including the CAD gene, have been isolated so far. These cloned DNAs can be used to study the structure of the amplified region, to evaluate the nature of the amplification event, and to investigate gene expression from the amplified DNA. For example, one amplified fragment included a gene coding for a 3.8-kilobase, cytoplasmic, polyadenylated RNA which was overproduced greatly in cells resistant to N-(phosphonacetyl)-L-aspartate. The method for cloning amplified DNA is general and can be used to evaluate the possible involvement of gene amplification in phenomena such as drug resistance, transformation, or differentiation. DNA fragments corresponding to any region amplified about 10-fold or more can be cloned, even if no function for the region is known. The method for removing highly repetitive sequences from genomic DNA probes should also be of general use.
Development of a novel mineral based haemostatic agent consisting of a combination of bentonite and zeolite minerals. (2011)

To our knowledge, this is the 1st study to investigate the alterations of bleeding and clotting time following the use of lantern mantle powder as well as bentonite or the mixture of bentonite-zeolite minerals. The results obtained in this study clearly show the significant alterations in the volume of blood loss as well as the bleeding or clotting time following the topical use of the mixture of bentonite-zeolite minerals. Controlling the generation of heat was a great achievement in development of the novel haemostatic agent produced in this study.
Efficiency of Antisense Oligonucleotide Drug Discovery (2002)

The costs for discovering and developing new drugs continue to escalate, with current estimates that the average cost is more than $800 million for each new drug brought to the market. Pharmaceutical companies are under enormous pressure to increase their efficiency for bringing new drugs to the market by third-party payers, shareholders, and their patients, and at the same time regulators are placing increased demands on the industry. To be successful in the future, pharmaceutical companies must change how they discover and develop new drugs. So far, new technologies have done little to increase overall efficiency of the industry and have added additional costs. Platform technologies such as monoclonal antibodies and antisense oligonucleotides have the potential of reducing costs for discovery of new drugs, in that many of the steps required for traditional small molecules can be skipped or streamlined. Additionally the success of identifying a drug candidate is much higher with platform technologies compared to small molecule drugs. This review will highlight some of the efficiencies of antisense oligonucleotide drug discovery compared to traditional drugs and will point out some of the current limitations of the technology.
From the Bioweapons Trenches, New Tools for Battling Microbes (1999)

BIOTECHNOLOGY INDUSTRY ORGANIZATION MEETINGSEATTLE, WASHINGTON-- Some 5700 biotech buffs gathered here from 16 to 20 May for the annual meeting of the Biotechnology Industry Organization. Most sessions focused on business, but one drew big interest from scientists: a showcase of projects funded by the U.S. Defense Advanced Research Projects Agency's antibioterrorism initiative.