gebhart/patrepeval huggingface dataset:
Biotechnological applications for surface-engineered bacteria (2004)

Display of heterologous proteins on the surface of micro-organisms, enabled by means of recombinant DNA technology, has become an increasingly popular strategy in microbiology, biotechnology and vaccinology. Both Gram-negative and Gram-positive bacteria have been investigated for potential applications. The present review will describe the most commonly used systems for bacterial display, with a focus on the biotechnology applications. Live bacterial vaccine-delivery vehicles have long been investigated through the surface display of foreign antigens and, recently, 'second-generation' vaccine-delivery vehicles have been generated by the addition of mucosal targeting signals, as a means to increase immune responses. Engineered bacteria have also the potential to act as novel microbial biocatalysts with heterologous enzymes immobilized as surface exposed on the bacterial cell surface. They provide the potential for new types of whole-cell diagnostic devices, since single-chain antibodies and other type of tailor-made binding proteins can be displayed on bacteria. Bacteria with increased binding capacity for certain metal ions can be created, and potential environmental or biosensor applications for such recombinant bacteria as biosorbents are being explored. Certain bacteria have also been employed to display various polypeptide libraries for use as devices in in vitro selection applications. Part of the present review has been devoted to a more in-depth description of a promising Gram-positive display system, i.e. Staphylococcus carnosus, and its applications. The review describes the basic principles of the different bacterial display systems and discusses current uses and possible future trends of these emerging technologies.
ABE production from corn: a recent economic evaluation (2001)

This article details an economic assessment of butanol production from corn using the newly developed hyper-butanol-producing strain of Clostridium beijerinckii BA101. Butanol is produced in batch reactors and recovered by distillation. For a plant with 153,000 metric tons of acetone, butanol, and ethanol (ABE) production capacity, the production equipment cost and total working capital cost is US$33.47x10(6) and US$110.46x10(6), respectively. Based on a corn price (C(p)) of US$79.23 x ton(-1) (US$2.01 x bushel(-1)), an ABE yield of 0.42 (g ABE/g glucose) butanol price is projected to be US$0.34 x kg(-1). An improved yield of 0.50 will reduce this price to US$0.29 x kg(-1). Assumptions, such as by-product credit for gases and complete conversion of corn steep liquor (CSL) to fermentation by-products, have been taken into consideration. An increased price of corn to US$197.10 x ton(-1) would result in a butanol price of US$0.47 x kg(-1). A grass-rooted plant would result in a butanol price of US$0.73 x kg(-1) (C(p) US$79.23 x ton(-1)). In a worst case scenario, the price of butanol would increase to US$1.07 x kg(-1) (C(p) 197.10 x ton(-1) for a grass-rooted plant and assuming no credit for gases). This is based on the assumption that corn price would not increase to more than US$197.10 x ton(-1).
Dual-gate AlGaN/GaN modulation-doped field-effect transistors with cut-off frequencies f/sub T/>60 GHz (2000)

We demonstrate dual-gate AlGaN/GaN modulation-doped field-effect transistors (MODFETs) with gate-lengths of 0.16 μm and 0.35 μm for the first and second gates, respectively. The dual-gate device exhibits a current-gain cut-off frequency f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> >60 GHz, and can simultaneously achieve a high breakdown voltage of >+100 V. In comparison to single-gate devices with the same gate length 0.16 μm, dual-gate FETs can significantly increase breakdown voltages, largely increasing the maximum allowable drain bias for high power application. The continuous wave (CW) output power is in excess of 3.5 W/mm at 8.2 GHz. The corresponding large-signal gain is 12 dB and the power added efficiency is 45%. The dual-gate device with different gate lengths shows the capability of providing simultaneous high cut-off frequencies, and high breakdown voltages for broadband power amplifiers.
Accessibility of receptor-bound urokinase to type-1 plasminogen activator inhibitor. (1989)

Urokinase plasminogen activator (uPA) interacts with a surface receptor and with specific inhibitors, such as plasminogen activator inhibitor type 1 (PAI-1). These interactions are mediated by two functionally independent domains of the molecule: the catalytic domain (at the carboxyl terminus) and the growth factor domain (at the amino terminus). We have now investigated whether PAI-1 can bind and inhibit receptor-bound uPA. Binding of 125I-labeled ATF (amino-terminal fragment of uPA) to human U937 monocyte-like cells can be competed for by uPA-PAI-1 complexes, but not by PAI-1 alone. Performed 125I-labeled uPA-PAI-1 complexes can bind to uPA receptor with the same binding specificity as uPA. PAI-1 also binds to, and inhibits the activity of, receptor-bound uPA in U937 cells, as shown in U937 cells by a caseinolytic plaque assay. Plasminogen activator activity of these cells is dependent on exogenous uPA, is competed for by receptor-binding diisopropyl fluorophosphate-treated uPA, and is inhibited by the addition of PAI-1. In conclusion, in U937 cells the binding to the receptor does not shield uPA from the action of PAI-1. The possibility that in adherent cells a different localization of PAI-1 and uPA leads to protection of uPA from PAI-1 is to be considered.
Conversion of recombinant hirudin to the natural form by in vitro tyrosine sulfation. Differential substrate specificities of leech and bovine tyrosylprotein sulfotransferases. (1990)

Hirudin, a tyrosine-sulfated protein secreted by the leech Hirudo medicinalis, is one of the most potent anticoagulants known. The hirudin cDNA has previously been cloned and has been expressed in yeast, but the resulting recombinant protein was found to be produced in the unsulfated form, which is known to have an at least 10 times lower affinity for thrombin than the naturally occurring tyrosine-sulfated hirudin. Here we describe the in vitro tyrosine sulfation of recombinant hirudin by leech and bovine tyrosylprotein sulfotransferase (TPST). With both enzymes, in vitro sulfation of recombinant hirudin occurred at the physiological site (Tyr-63) and rendered the protein biochemically and biologically indistinguishable from natural hirudin. However, leech TPST had an over 20-fold lower apparent Km value for recombinant hirudin than bovine TPST. Further differences in the catalytic properties of leech and bovine TPSTs were observed when synthetic peptides were tested as substrates. Moreover, a synthetic peptide corresponding to the 9 carboxyl-terminal residues of hirudin (which include Tyr-63) was sulfated by leech TPST with a similar apparent Km value as full length hirudin, indicating that structural determinants residing in the immediate vicinity of Tyr-63 are sufficient for sulfation to occur.
Proteolytic activity of an antibody light chain. (1994)

The light chain (L chain) of a mAb raised against unactivated vasoactive intestinal peptide (VIP) hydrolyzed this peptide, whereas the heavy chain (H chain) and an irrelevant L chain were without activity. The reaction kinetics were consistent with efficient substrate recognition by the anti-VIP L chain compared with conventional proteases. The L chain cleaved four peptide bonds clustered between residues 16 and 21 in VIP. Mixtures of the L chain with its H chain partner displayed reduced hydrolytic activity compared with the free L chain, suggesting that the H chain is a modulator of the catalytic activity. These observations suggest: 1) the immune system can generate catalytic sites in the L chain subunit of Abs found in response to polypeptide Ags, and 2) free L chains found in vivo could display an Ag-specific catalytic function.
Vinylogous polypeptides: an alternative peptide backbone (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTVinylogous polypeptides: an alternative peptide backboneMasahiko Hagihara, Neville J. Anthony, Thomas J. Stout, Jon Clardy, and Stuart L. SchreiberCite this: J. Am. Chem. Soc. 1992, 114, 16, 6568–6570Publication Date (Print):July 1, 1992Publication History Published online1 May 2002Published inissue 1 July 1992https://pubs.acs.org/doi/10.1021/ja00042a052https://doi.org/10.1021/ja00042a052research-articleACS PublicationsRequest reuse permissionsArticle Views1103Altmetric-Citations235LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Analysis of factors affecting the periplasmic production of recombinant proteins in Escherichia coli. (2007)

Five fusion proteins between Z domains derived from Staphylococcal Protein A and Green Fluorescent Protein or Human Proinsulin were produced on the periplasm of Escherichia coli. The effects of the molecular weight and amino acid composition of the translocated peptide, culture medium composition, and growth phase of the bacterial culture were analyzed regarding the expression and periplasmic secretion of the recombinant proteins. It was found that secretion was not affected by the size of the translocated peptide (17-42 kDa) and that the highest periplasmic production values were obtained on the exponential phase of growth. Moreover, the highest periplasmic values were obtained in minimal medium, showing the relevance of the culture medium composition on secretion. In silico prediction analysis suggested that with respect to the five proteins used in this study, those that are prone to form alpha-helix structures are more translocated to the periplasm.
Spatiotemporal Depletion of Connexins Using Antisense Oligonucleotides (2003)

Antisense oligodeoxynucleotides have considerable potential as agents for the manipulation of specific gene expression (2–3). They function by entering the cell and binding to the messenger RNA (mRNA), thereby blocking protein translation (See Note 1). The short half-life of oligonucleotides can be overcome, sustained delivery can be achieved, and specific tissue targeting can be obtained using a Pluronic gel delivery system. It is therefore possible to gain an understanding of the roles of connexins, which are expressed in dynamic and spatially controlled patterns, through transient reduction in the expression of specific connexin proteins. This leads to dramatic but precisely defined aberrations in embryonic development, for example (3). The major advantage of the approach is the ability to achieve spatiotemporal regulation of connexin gene expression while reducing some of the problems associated with gene knockout approaches (see Tables 1 and 2 ).
Piezophysiology of yeast: occurrence and significance. (2004)

Hydrostatic pressure is a thermodynamic parameter that has recently received further consideration in various experimental fields. Although the physicochemical basis of pressure effects is well established, the effects of high pressure on in vivo biological processes have not been systematically investigated due to its presumed complexity. The word "piezophysiology" was proposed to describe the unique cellular responses to high pressure in living cells. The yeast Saccharomyces cerevisiae is one of the best-characterized organisms in many fields in bioscience. Here I review the accumulated literature on cellular responses to increasing hydrostatic pressure in yeast, focusing on survival, growth, gene expression and metabolism.
High‐Speed Modulator Based on Electro‐Optic Polymer Infiltrated Subwavelength Grating Waveguide Ring Resonator (2018)

Abstract Silicon‐organic hybrid integrated devices show great potential in high‐speed optical interconnects and sensors. In this paper, a high‐speed modulator based on an electro‐optic (EO) polymer (SEO125) infiltrated sub‐wavelength grating (SWG) waveguide ring resonator is presented. The core of the SWG waveguide consists of periodically arranged silicon pillars along the light propagation direction, which provides large mode volume overlap with EO polymer. The optimized SWG shows a mode volume overlap of 36.2% with a silicon duty cycle of 0.7. The 3‐dB modulation bandwidth of the fabricated modulator is measured to be larger than 40 GHz occupying an area of 70 μm x 29 μm, which is the largest bandwidth and the most compact footprint that has been demonstrated for ring resonators on the silicon‐organic hybrid platform.
Identification of a very long chain polyunsaturated fatty acid Δ4‐desaturase from the microalga Pavlova lutheri1 (2003)

Pavlova lutheri, a marine microalga, is rich in the very long chain polyunsaturated fatty acids (VLCPUFAs) eicosapentaenoic (20:5n-3) and docosahexaenoic (22:6n-3) acids. Using an expressed sequence tag approach, we isolated a cDNA designated Pldes1, and encoding an amino acid sequence showing high similarity with polyunsaturated fatty acid front-end desaturases. Heterologous expression in yeast demonstrated that PlDES1 desaturated 22:5n-3 and 22:4n-6 into 22:6n-3 and 22:5n-6 respectively, and was equally active on both substrates. Thus, PlDES1 is a novel VLCPUFA Delta4-desaturase. Pldes1 expression is four-fold higher during the mid-exponential phase of growth compared to late exponential and stationary phases.
Early Induction of Moderate Hypothermia Suppresses Systemic Inflammatory Cytokines and Intracellular Adhesion Molecule-1 in Rats With Caerulein-Induced Pancreatitis and Endotoxemia (2008)

Early induction of MH might be protective against pancreatic injury and systemic inflammation in AP and endotoxemia.
Synthesis and Characterization of Monolayer-Capped PtVFe Nanoparticles with Controllable Sizes and Composition (2005)

The ability to control the size and composition of metal nanoparticles is essential in preparing binary or ternary catalysts. This paper reports the results of an investigation of a core−shell synthesis protocol for the preparation of monolayer-capped ternary platinum−vanadium−iron (PtVFe) nanoparticles with a few nanometers in core sizes. Our approach involves the use of metal precursors, capping agents, and reducing agents in controllable ratios for the reaction in a single organic phase. By manipulating the relative concentration ratios of the metal precursors such as platinum acetylacetonate, vanadyl acetylacetonate, and iron pentacarbonyl, and capping agents such as oleic amine and oleic acids, the core−shell type nanoparticles in which the nanocrystal PtVFe cores are encapsulated with a shell of mixed amine/acid monolayer have been successfully synthesized. The average diameters of the nanocrystalline cores are well controlled between 1.4 and 3.5 nm with high monodispersity (±0.3−0.5 nm). The chemical composition of the nanocrystalline cores is shown to be effectively controllable in the range of Pt (20−40%), V (10−40%), and Fe (40−70%) by manipulating the feeding ratios of the metal precursors. The results of characterizations using TEM, DCP-AES, XRD, FTIR, and TGA techniques are discussed, along with their implications to the exploration of the nanoparticles as fuel cell catalysts.
The E4 transcilpilonal unit of Ad2: far upstream sequences are required for its transactivation by E1A (1984)

We have investigated the effect of the E1A polypeptides of adenovirus 2 on the transcription of the viral E4 region. For this purpose, we have fused the promoter region of the E4 gene to the bacterial gene coding for chloramphenicol acetyl transferase. We have found that transcription from the E4 promoter is increased at least 20 fold in the presence of the E1A region. We have also found that the largest E1A polypeptide is the regulating factor, whereas the shortest has no apparent effect. Deletion of sequences upstream from position -158, as measured from the cap site, reduces the efficiency of the transcription in the presence of E1A by more than 15 fold. An important regulatory domain lies between positions -158 and -179. This domain contains the sequence 5' GGGAAGTGAC 3' which is homologous to the E1A enhancer core sequence. Another similar sequence is also present at position -149.
Nucleotide sequence encoding the major glycoprotein (GP2) of rat pancreatic secretory (zymogen) granule membranes (1990)

Journal Article Nucleotide sequence encoding the major glycoprotein (GP2) of rat pancreatic secretory (zymogen) granule membranes Get access Shin-lchi Fukuoka, Shin-lchi Fukuoka Laboratory of Cell and Molecular Biology, Dana Research Institute, Harvard Medical School and Beth Israel HospitalBoston, MA 02215, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar George Scheele George Scheele * Laboratory of Cell and Molecular Biology, Dana Research Institute, Harvard Medical School and Beth Israel HospitalBoston, MA 02215, USA *To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 18, Issue 19, 11 October 1990, Page 5900, https://doi.org/10.1093/nar/18.19.5900 Published: 11 October 1990 Article history Received: 20 July 1990 Published: 11 October 1990
Preclinical Evaluation of Gadolinium (III) Texaphyrin Complex (1994)

Gadolinium (III) texaphyrin complex appears to be an effective and safe MRI contrast agent.
Development of criteria for the classification and reporting of osteoarthritis: Classification of osteoarthritis of the knee (1986)

For the purposes of classification, it should be specified whether osteoarthritis (OA) of the knee is of unknown origin (idiopathic, primary) or is related to a known medical condition or event (secondary). Clinical criteria for the classification of idiopathic OA of the knee were developed through a multicenter study group. Comparison diagnoses included rheumatoid arthritis and other painful conditions of the knee, exclusive of referred or para-articular pain. Variables from the medical history, physical examination, laboratory tests, and radiographs were used to develop sets of criteria that serve different investigative purposes. In contrast to prior criteria, these proposed criteria utilize classification trees, or algorithms.
Expression, cloning, and characterization of a Candida albicans gene, ALA1, that confers adherence properties upon Saccharomyces cerevisiae for extracellular matrix proteins (1997)

Adherence of Candida albicans to host tissues is a necessary step for maintenance of its commensal status and is likely a necessary step in the pathogenesis of candidiasis. The extracellular matrix (ECM) proteins are some of the host tissue and plasma proteins to which C. albicans adheres through adhesins located on the fungal cell surface. To isolate genes encoding ECM adhesins, an assay was developed based on the ability of yeast cells to adhere to magnetic beads coated with the ECM protein fibronectin, type IV collagen, or laminin. A C. albicans genomic library was constructed by cloning XbaI-partially-digested and size-selected fragments into pAUR112, an Escherichia coli-yeast low-copy-number shuttle vector. The C. albicans library was transformed into Saccharomyces cerevisiae YPH 499, and clones capable of adherence were selected by using ECM protein-coated magnetic beads. A plasmid containing an approximately 8-kb insert was isolated from 29 adherent clones. These clones exhibited adherence to all ECM protein-coated magnetic beads and to human buccal epithelial cells. The ALA1 gene (for agglutinin-like adhesin) was localized by subcloning it into a 5-kb XbaI fragment which retained the adherence phenotype in both orientations. The complete DNA sequence of the 5-kb insert was determined, and an open reading frame (ORF) encoding 1,419 amino acid residues was identified. Deletions from the 5' and 3' ends extending into the DNA sequence encoding the 1,419-amino-acid ORF product inactivated the adherence phenotype, suggesting that it is the coding region of the ALA1 gene. A database search identified ALA1 to be similar to the C. albicans ALS1 (for agglutinin-like sequence 1) protein and the S. cerevisiae agglutinin protein (AG alpha1), although the homology at the primary amino acid sequence level is limited to the first half of each of these proteins. ALA1 contains a central domain of six tandem repeats of 36 amino acids. We discuss the significance of various predicted ALA1 structural motifs and their relationships to function in the adherence process.
Suppression of complex I gene expression induces optic neuropathy (2003)

Optic nerve degeneration is a feature common to diseases with mutations in genes that encode complex I of the respiratory chain. Vulnerability of this central nervous system tract is a mystery, because of the paucity of animal models used to investigate effects of the mutated DNA in tissues rather than isolated in cultured cells. Using a ribozyme designed to degrade the mRNA encoding a critical nuclear-encoded subunit gene of complex I (NDUFA1), we tested whether oxidative phosphorylation deficiency can recapitulate the optic neuropathy of mitochondrial disease. Injection of adenoassociated virus expressing this ribozyme led to axonal destruction and demyelination, the hallmarks of Leber hereditary optic neuropathy.
Device discovery in short-range wireless ad hoc networks (2003)

The performance of many envisioned applications in short-range wireless ad hoc networking will critically rely on the promptness of the self-configuring network procedures. In that sense, a fundamental problem in ad hoc networks, is device discovery and/or network initialization. We propose a randomized distributed algorithm for rapid device discovery during the deployment of an ad hoc network. The algorithm uses the approach of the non-blocked stack algorithm to resolve collisions, which ensures time-efficient execution when the number of devices in the network is large. The self-starting concepts used may be significant for inferring other self-configuring algorithms for ad hoc networks.
Evidence of a dissociative S N1(P) mechanism of phosphoryl transfer by rabbit muscle pyruvate kinase (1978)

Adenosine 5′-[αβ-18O,β-18O2]triphosphate has been prepared and used to investigate the mechanism of action of rabbit muscle pyruvate kinase. In the presence of pyruvate kinase and pyruvate, randomisation of the β-18O2 labels with the βγ-O bridge occurs as expected. However randomisation also occurs in the presence of the potent inhibitor oxalate, an analogue of enol pyruvate, and also in the absence of pyruvate or a pyruvate analogue. Since there is evidence against the involvement of a phosphoenzyme intermediate in the reaction pathway of pyruvate kinase, the results indicate that phosphoryl transfer in pyruvate kinase occurs by a dissociative SN1(P) mechanism, involving the transient high energy but tightly enzyme bound metaphosphate ion intermediate. The rate constants for the pyruvate kinase catalysed 18O-redistribution in adenosine 5′-[αβ-18O,β-18O2]triphosphate alone and in the presence of oxalate and pyruvate are 1.1 × 102 min–1, 2.0 × 102 min–1, and 2.0 × 103 min–1 respectively.