gebhart/patrepeval huggingface dataset:
A novel activity of HMG domains: promotion of the triple-stranded complex formation between DNA containing (GGA/TCC)11 and d(GGA)11 oligonucleotides (1996)

The high mobility group protein (HMG)-box is a DNA-binding domain found in many proteins that bind preferentially to DNA of irregular structures in a sequence-independent manner and can bend the DNA. We show here that GST-fusion proteins of HMG domains from HMG1 and HMG2 promote a triple-stranded complex formation between DNA containing the (GGA/TCC)11 repeat and oligonucleotides of d(GGA)11 probably due to G:G base pairing. The activity is to reduce association time and requirements of Mg2+ and oligonucleotide concentrations. The HMG box of SRY, the protein determining male-sex differentiation, also has the activity, suggesting that it is not restricted to the HMG-box domains derived from HMG1/2 but is common to those from other members of the HMG-box family of proteins. Interestingly, the box-AB and box-B of HMG1 bend DNA containing the repeat, but SRY fails to bend in a circularization assay. The difference suggests that the two activities of association-promotion and DNA bending are distinct. These results suggest that the HMG-box domain has a novel activity of promoting the association between GGA repeats which might be involved in higher-order architecture of chromatin.
Murine endothelioma cell lines transformed by polyoma middle T oncogene as target for and producers of cytokines (1991)

We studied cytokine-related functional properties of four mouse endotheliomas from different anatomical sites obtained by transformation with middle T oncogene. We examined mRNA expression of IL-6, IL-1 alpha, macrophage-CSF, granulocyte/macrophage-CSF, and two members of an emerging super-family of chemotactic cytokines (JE/monocyte chemoattractant protein-1 (MCP-1) and KC). Exposure to IL-1 augmented or induced cytokine gene transcripts in three endothelioma lines (eEnd.1, sEnd.1, and tEnd) with maximal expression in tEnd.1 cells. Endothelioma cells also responded to TNF-alpha and LPS. Levels of IL-6 and monocyte chemotactic activity (a JE/MCP activity) correlated with mRNA expression. IL-1 also induced production of procoagulant activity and platelet-activating factor in endothelioma cells, with heterogeneity in the levels of response among individuals lines. Murine melanoma B16-F1, human colon carcinoma HT29 cells, CB33MT lymphoblastoid cells, and monocytes adhered to endothelioma monolayers and the adhesive properties of these cell lines were modulated by IL-1 beta, with marked differences among themselves. Murine EC derived from brain capillaries, used as control, shared several properties with bEnd.4 line. Endothelioma lines cause tumors by recruiting host cells. The capacity to produce cytokines that directly or indirectly attract host vascular cells, may play an important role in hemangioma induction in vivo. Murine endothelioma lines, generated by transformation with the polyoma middle T oncogene, retain functional properties of normal endothelium, and may represent an invaluable tool for analysis of the immunobiology and heterogeneity of EC in different tissues.
A comparison of the ADC and T2 mapping in an assessment of blood‐clot lysability (2009)

The structural characteristics of blood clots are associated with their susceptibility to thrombolysis. As their morphology can be characterized by MRI, several attempts have been made to link the lysability of blood clots with their MRI properties; however, so far no study has associated a clot's lysability with the diffusion properties of the water in the clot. The apparent diffusion coefficient (ADC) is highly sensitive to changes in serum mobility and may be used to distinguish between the non-retracted and the fully retracted regions of the blood clot. Therefore, the ADC may be a suitable, or even a better, marker for an assessment of the clot's retraction and consequently for its lysability than the relaxation time T(2). The purpose of this study was to evaluate whether it is possible to predict the outcome of clot thrombolysis by ADC mapping prior to treatment. After two hours of thrombolysis using a recombinant tissue plasminogen activator in plasma, whole-blood clots were efficiently dissolved in regions with ADC >or= 0.8 x 10(-9) m(2)/s or T(2) >or= 130 ms, whereas dissolution was poor and prolonged in regions with ADC < 0.8 x 10(-9) m(2)/s or T(2) < 130 ms. An analysis based on a comparison between the initial and final ADC and T(2) maps after two hours of thrombolysis showed that the ADC can more accurately detect the different grades of clot retraction than T(2) and predict the regions of a clot that are resistant to thrombolysis. Therefore, the ADC could be used as an efficient prognostic marker for the outcome of thrombolysis. However, in vivo studies are needed to test this idea.
Crosslinking of streptomycin to the 30S subunit of Escherichia coli with phenyldiglyoxal (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCrosslinking of streptomycin to the 30S subunit of Escherichia coli with phenyldiglyoxalPierre Melancon, Guy Boileau, and Lea Brakier-GingrasCite this: Biochemistry 1984, 23, 26, 6697–6703Publication Date (Print):December 18, 1984Publication History Published online1 May 2002Published inissue 18 December 1984https://pubs.acs.org/doi/10.1021/bi00321a064https://doi.org/10.1021/bi00321a064research-articleACS PublicationsRequest reuse permissionsArticle Views48Altmetric-Citations9LEARN 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
Subunit Structure of Chondroitinase ABC fromProteus vulgaris (1986)

Journal Article Subunit Structure of Chondroitinase ABC from Proteus vulgaris Get access Nobuyuki Sato, Nobuyuki Sato Institute for Research and Development, Taiyo Fisheries Co., Ltd., 3–2–9 Tsukishima, Chuo-ku, Tokyo 106, Japan Search for other works by this author on: Oxford Academic Google Scholar Kousaku Murata, Kousaku Murata Research Institute for Food Science, Kyoto University, Uji, Kyoto 611, Japan Search for other works by this author on: Oxford Academic Google Scholar Akira Kimura Akira Kimura Research Institute for Food Science, Kyoto University, Uji, Kyoto 611, Japan Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 50, Issue 4, 1 April 1986, Pages 1057–1059, https://doi.org/10.1080/00021369.1986.10867516 Published: 01 April 1986 Article history Received: 04 October 1985 Published: 01 April 1986
Aspergillus Bibliography - 1993 (1993)

This bibliography attempts to cover genetical and biochemical publications on Aspergillus nidulans and also includes some references to related species.
Isothermal in vitro amplification of DNA by a restriction enzyme/DNA polymerase system. (1992)

An isothermal in vitro DNA amplification method was developed based upon the following sequence of reaction events. Restriction enzyme cleavage and subsequent heat denaturation of a DNA sample generates two single-stranded target DNA fragments (T1 and T2). Present in excess are two DNA amplification primers (P1 and P2). The 3' end of P1 binds to the 3' end of T1, forming a duplex with 5' overhangs. Likewise, P2 binds to T2. The 5' overhangs of P1 and P2 contain a recognition sequence (5'-GTTGAC-3') for the restriction enzyme HincII. An exonuclease-deficient form of the large fragment of Escherichia coli DNA polymerase I (exo- Klenow polymerase) [Derbyshire, V., Freemont, P. S., Sanderson, M. R., Beese, L., Friedman, J. M., Joyce, C. M. & Steitz, T. A. (1988) Science 240, 199-201] extends the 3' ends of the duplexes using dGTP, dCTP, TTP, and deoxyadenosine 5'-[alpha-thio]triphosphate, which produces hemiphosphorothioate recognition sites on P1.T1 and P2.T2. HincII nicks the unprotected primer strands of the hemiphosphorothioate recognition sites, leaving intact the modified complementary strands. The exo- Klenow polymerase extends the 3' end at the nick on P1.T1 and displaces the downstream strand that is functionally equivalent to T2. Likewise, extension at the nick on P2.T2 results in displacement of a downstream strand functionally equivalent to T1. Nicking and polymerization/displacement steps cycle continuously on P1.T1 and P2.T2 because extension at a nick regenerates a nickable HincII recognition site. Target amplification is exponential because strands displaced from P1.T1 serve as targets for P2 and strands displaced from P2.T2 serve as targets for P1. A 10(6)-fold amplification of a genomic sequence from Mycobacterium tuberculosis or Mycobacterium bovis was achieved in 4 h at 37 degrees C.
Can One Derive the Conformational Preference of a β-Peptide from Its CD Spectrum? (2002)

CD spectroscopy is often used to elucidate the secondary structure of peptides built from non-natural amino acids such as beta-amino acids. The interpretation of such CD spectra is not always unambiguous. Here, we present a case where two beta-hexapeptides, a dimethyl-beta-hexapeptide indicated as DM-BHP (A) and its nonmethylated analogue indicated as BHP (B), exhibit similar CD spectra, whereas they are expected to differ in secondary structure. The structural properties of both peptides were studied by molecular dynamics simulation, and from the resulting trajectories, the corresponding CD spectra were calculated. Starting from a fully extended conformation, BHP is observed to form a 3(14)-helix, while DM-BHP remains unfolded. However, even though these two peptides hardly share any conformations, their calculated CD spectra are alike and show the same features as the experimentally measured ones. Our results imply that a particular CD pattern can be induced by spatially different structures, which makes it difficult to derive the conformational preference of a peptide from its CD spectrum alone. To gain more insight into the relationship between the preferred conformation of a peptide and its CD spectrum, more accurate methods to calculate the CD spectrum for a given conformation are required.
Selective Somatostatin 5 (SST5) and Somatostatin 2 (SST2) Nonpeptide Agonists Potently Suppress Glucose- and Tolbutamide-Stimulated Dynamic Insulin Secretion From Isolated Human Islets (2021)

Abstract Congenital hyperinsulinism (HI) is the most common cause of persistent hypoglycemia in newborns and infants and arises from dysregulated insulin secretion. Rapid recognition and treatment are vital to prevent seizures, permanent developmental delays, coma, or even death. Very few medical options exist to treat congenital HI patients: the KATP channel activator diazoxide, the injectable somatostatin receptor peptide agonists octreotide and lanreotide, or chronic glucose infusions. However, side effects and/or limited efficacy render these therapies inadequate for many patients. Somatostatin is a 14-amino acid peptide hormone with a broad spectrum of biological actions, which are regulated through five somatostatin receptor subtypes (SST1-SST5). Somatostatin’s common physiological role is to down-regulate secretion of other hormones in various tissues. Its role in the maintenance of euglycemia is to regulate insulin and glucagon secretion from pancreatic β- and α-cells, respectively. Somatostatin regulates insulin secretion by decreasing the intracellular levels of cAMP, inhibition of voltage-gated calcium channels (VGCC), activation of the G protein-activated inward rectifier K+ channel (GIRK), and direct inhibition of insulin exocytosis. Several studies have evaluated the effect of somatostatin, somatostatin peptide analogs, and a limited number of nonpeptide somatostatin receptor agonists on insulin secretion in static assays using isolated human islets. However, the lack of highly selective agonists has made the interpretation of the contribution of SST receptor sub-types difficult to discern. Our programs for the treatment of hyperinsulinism, acromegaly, and other indications have led to the development of selective nonpeptide SST2, SST3, SST4, and SST5 agonists, possessing EC50s &amp;lt; 1 nM in cell-based assays of receptor activation and selectivity &amp;gt; 130 times over the other members of the family. The ability of these selective nonpeptide agonists to regulate glucose- and tolbutamide-stimulated dynamic insulin secretion from human islets was evaluated using a perifusion system (Biorep, FL). We found that selective SST2 and SST5 agonists potently suppressed dynamic insulin secretion in contrast to SST3 or SST4 selective agonists. Importantly, SST5 agonists were shown to have a greater effect than selective SST2 agonists or diazoxide, demonstrating their potential utility in human conditions such as congenital HI. In addition, SST5 activation is also known to have a smaller effect on glucagon secretion and is also less prone to agonist-driven desensitization than SST2 activation. Taken together, these studies support our program to identify, characterize, and develop potent, nonpeptide, orally-bioavailable, selective SST5 agonists with appropriate pharmaceutical and safety characteristics for the treatment of congenital HI.
Voltage-gated Na+ channel beta 1 subunit mRNA expressed in adult human skeletal muscle, heart, and brain is encoded by a single gene. (1994)

Voltage-gated Na+ channels are heteromeric proteins consisting of alpha and beta subunits. Although alpha subunits alone are sufficient to encode functional channels, beta 1 subunits appear to modulate the kinetics of inactivation. We have used a cross-species reverse transcriptase polymerase chain reaction approach to isolate cDNAs encoding a Na+ channel beta 1 subunit from human heart and skeletal muscle. The deduced amino acid sequence of the human beta 1 subunit exhibits 96% identity with the rat brain beta 1 subunit. Human beta 1 mRNA transcripts are abundantly expressed in skeletal muscle, heart, and brain. Genomic Southern blot hybridization experiments suggest that a single gene located on chromosome 19 encodes the human beta 1 subunit that is expressed in all three of these tissues. Co-expression of the human beta 1 subunit with the recombinant human skeletal muscle alpha subunit (hSkM1) in Xenopus oocytes results in Na+ currents that inactivate rapidly. In contrast, the human beta 1 subunit has no effect on the function of the tetrodotoxin-insensitive human heart Na+ channel (hH1). These findings indicate that the human beta 1 subunit is widely expressed but does not functionally modify all Na+ channel isoforms.
The potential of hybrid antibodies secreted by hybrid-hybridomas in tumour therapy (1988)

Using a simple method for the selection of hybrid cell growth from the cell fusion of pairs of existing hybridoma cell lines, 2 different hybrid-hybridoma cell lines were produced. Both hybrid-hybridomas secreted bi-specific antibody with similar specificity for human CD3 and for mouse Thy-l but in one case the parental antibody isotypes were both IgG2b and in the other case the CD3 antibody was IgG2b and the anti-Thy-l antibody was IgG2c. In a model in vitro system both bi-specific antibodies were able to elicit potent cell killing of a Thy-l expressing mouse tumour cell line by human effector cell blasts. The cell blasts were generated from resting peripheral blood mononuclear cells using a mitogenic monoclonal antibody (MAb) (YTH361). The parental anti-Thy-l IgG2b but not the IgG2c antibody was also able to mediate cell killing by ADCC. This ADCC killing was inhibited by a MAb to the CD16 Fc receptor but the killing elicited by the bi-specific antibodies was not. Both mechanisms of tumour cell killing may be of great potential in human tumour therapy with MAbs.
63 Effect of inhalational anesthesia on cerebral blood flow in Moyamoya Disease (1999)

1Department of Anesthesiology, Kohnan Hospital 2Department of Neurosurgery, Anesthesiology, Tohoku University School of Medicine, Sendai, Japan
Theory of trapped polaritons in patterned microcavities (2006)

Abstract We consider the system of a quantum well embedded in a planar semiconductor microcavity with a shallow circular mesa patterned on top of the cavity spacer. For this system we develop the linear coupling theory of polaritons. We then compute polariton eigenstates and the corresponding optical spectrum. The theory predicts the existence of laterally confined polariton states with a discrete energy spectrum, as well as continuum states above the finite mesa potential barrier. (© 2006 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Ternary and Multivariate Quality Control Charts of Aggregate Gradation for Hot Mix Asphalt (2004)

Several statistical methods for controlling the quality of aggregate gradation are proposed, based on a multivariate model that describes compositional data. First, ternary quality control charts are developed to control a three-part gradation such as that given by the restricted zone method, with both hexagonal and elliptical acceptance regions. Second, multivariate quality control charts are developed with multiple category and T2 acceptance regions. Hexagonal and multiple category regions use fixed lower and upper control limits for each category and are easier to interpret by a visual plot, whereas elliptical and T2 regions account for the correlations among the categories and are more accurate and efficient. The control charts may be used to show the dynamic status of consecutive average values and can easily be applied with spreadsheet software such as Microsoft Excel.
Kinetics of Biosynthesis of Iron-Regulated Membrane Proteins in Escherichia coli (1982)

Using biological iron chelators to control specifically iron availability to Escherichia coli K-12 in conjunction with radioactive pulse-labels, we examined the biosynthesis of six iron-regulated membrane proteins. Iron deprivation induced the synthesis of five proteins, which had molecular weights of 83,000 (83K), 81K (Fep), 78K (TonA), 74K (Cir), and 25K. The kinetics of induction were the same in entA and entA(+) strains, but were affected by the initial iron availability in the media. Iron-poor cells induced rapidly (half-time, 10 min), whereas iron-rich cells began induction after a lag and showed a slower induction half-time (30 min). Within this general pattern of induction after iron deprivation, several different kinetic patterns were apparent. The 83K, 81K, and 74K proteins were coordinately controlled under all of the conditions examined. The 78K and 25K proteins were regulated differently. The synthesis of a previously unrecognized 90K inner membrane protein was inhibited by iron deprivation and stimulated by iron repletion. Both ferrichrome and ferric enterobactin completely repressed 81K and 74K synthesis when the siderophores were supplied at concentrations of 5 muM in vivo (half-time, 2.5 min). At concentrations less than 5 muM, however, both siderophores repressed synthesis only temporarily; the duration of repression was proportional to the amount of ferric siderophore added. The half-lives of the 81K and 74K mRNAs, as measured by rifampin treatment, were 1.2 and 1.6 min, respectively. The results of this study suggest that enteric bacteria are capable of instantaneously detecting and reacting to fluctuations in the extracellular iron concentration and that they store iron during periods of iron repletion for utilization during periods of iron stress. Neither iron storage nor iron regulation of envelope protein synthesis is dependent on the ability of the bacteria to form heme.
Identification and expression of NEU3, a novel human sialidase associated to the plasma membrane (2000)

Several mammalian sialidases have been described so far, suggesting the existence of numerous polypeptides with different tissue distributions, subcellular localizations and substrate specificities. Among these enzymes, plasma-membrane-associated sialidase(s) have a pivotal role in modulating the ganglioside content of the lipid bilayer, suggesting their involvement in the complex mechanisms governing cell-surface biological functions. Here we describe the identification and expression of a human plasma-membrane-associated sialidase, NEU3, isolated starting from an expressed sequence tag (EST) clone. The cDNA for this sialidase encodes a 428-residue protein containing a putative transmembrane helix, a YRIP (single-letter amino acid codes) motif and three Asp boxes characteristic of sialidases. The polypeptide shows high sequence identity (78%) with the membrane-associated sialidase recently purified and cloned from Bos taurus. Northern blot analysis showed a wide pattern of expression of the gene, in both adult and fetal human tissues. Transient expression in COS7 cells permitted the detection of a sialidase activity with high activity towards ganglioside substrates at a pH optimum of 3.8. Immunofluorescence staining of the transfected COS7 cells demonstrated the protein's localization in the plasma membrane.
β-Catenin signaling is required for neural differentiation of embryonic stem cells (2004)

Culture of embryonic stem (ES) cells at high density inhibits both beta-catenin signaling and neural differentiation. ES cell density does not influence beta-catenin expression, but a greater proportion of beta-catenin is targeted for degradation in high-density cultures. Moreover, in high-density cultures, beta-catenin is preferentially localized to the membrane further reducing beta-catenin signaling. Increasing beta-catenin signaling by treatment with Wnt3a-conditioned medium, by overexpression of beta-catenin, or by overexpression of a dominant-negative form of E-cadherin promotes neurogenesis. Furthermore, beta-catenin signaling is sufficient to induce neurogenesis in high-density cultures even in the absence of retinoic acid (RA), although RA potentiates the effects of beta-catenin. By contrast, RA does not induce neurogenesis in high-density cultures in the absence of beta-catenin signaling. Truncation of the armadillo domain of beta-catenin, but not the C terminus or the N terminus, eliminates its proneural effects. The proneural effects of beta-catenin reflect enhanced lineage commitment rather than proliferation of neural progenitor cells. Neurons induced by beta-catenin overexpression either alone or in association with RA express the caudal neuronal marker Hoxc4. However, RA treatment inhibits the beta-catenin-mediated generation of tyrosine hydroxylase-positive neurons, suggesting that not all of the effects of RA are dependent upon beta-catenin signaling. These observations suggest that beta-catenin signaling promotes neural lineage commitment by ES cells, and that beta-catenin signaling may be a necessary co-factor for RA-mediated neuronal differentiation. Further, enhancement of beta-catenin signaling with RA treatment significantly increases the numbers of neurons generated from ES cells, thus suggesting a method for obtaining large numbers of neural species for possible use in for ES cell transplantation.