gebhart/patrepeval huggingface dataset:
Optimization of acid hydrolysis of bagasse from Agave tequilana Weber (2010)

The bagasse of Agave tequilana Weber is a lignocellulosic residue resulting from the production of tequila. At present, the bagasse is not industrialized, and poses a serious contamination problem. Thus, an ongoing research eort is to explore the possibility to obtain added value chemicals from it. The aim of the present work was to determine the eect of temperature, concentration of H2SO4 and reaction time on the hydrolysis of agave bagasse to produce fermentable sugars. The hydrolysis was performed in two sequential batch stages: (a) in the rst stage the optimal conditions were 151oC, 2% of sulfuric acid and 10 min of reaction, yielding 236 g/Kg dry matter and concentration of 26.9g/L of fermentable sugars, and (b) in second stage the optimal experimental conditions for the depolimerization of the biomass resulting from the rst stage were 175o C, 2% of sulfuric acid and 30 min of reaction, yielding 90 g/kg dry matter and concentration of 15 g/L of fermentable sugars. Total fermentable sugars yield from the sequential batch stages was 326 g/kg dry matter (48.50% of the theoretical value).
p53 Translocation to Mitochondria Precedes Its Nuclear Translocation and Targets Mitochondrial Oxidative Defense Protein-Manganese Superoxide Dismutase (2005)

The tumor suppressor gene p53 is activated by reactive oxygen species-generating agents. After activation, p53 migrates to mitochondria and nucleus, a response that eventually leads to apoptosis, but how the two events are related is unknown. Herein, we show that p53 translocation to mitochondria precedes its translocation to nucleus in JB6 skin epidermal cells treated with the tumor promoter 12-O-tetradecanoylphorbol-13-acetate (TPA). Translocation of p53 to mitochondria occurs within 10 minutes after TPA application. In the mitochondria, p53 interacts with the primary antioxidant enzyme, manganese superoxide dismutase (MnSOD), consistent with the reduction of its superoxide scavenging activity, and a subsequent decrease of mitochondrial membrane potential. In contrast to the immediate action on mitochondria, p53 transcriptional activity in the nucleus increases at 1 hour following TPA application, accompanied by an increase in the levels of its target gene bax at 15 hours following TPA treatment. Activation of p53 transcriptional activity is preventable by application of a SOD mimetic (MnTE-2-PyP5+). Thus, p53 translocation to mitochondria and subsequent inactivation of MnSOD explains the observed mitochondrial dysfunction, which leads to transcription-dependent mechanisms of p53-induced apoptosis.
Uptake and processing of glycoproteins by rat hepatic mannose receptor (1987)

A linear compartmental model has been developed for the in vivo metabolism of glycoproteins. The model is applied to the interpretation of dynamic data from the rat on agalactoorosomucoid (AGOR), an N-acetylglucosamine (GlcNAc-)-terminated glycoprotein, and three neoglycoproteins terminating in mannose [mannose36-bovine serum albumin (Man-BSA)] or glucose [maltose29-BSA (Mal29-BSA) and maltose8-BSA (Mal8-BSA)]. All of these proteins are taken up by the Man/GlcNAc receptor on hepatic sinusoidal cells. The rate of uptake was found to be determined by sugar type (Man-BSA, 0.78 min-1 greater than Mal29-BSA, 0.13 min-1), sugar density (Mal29-BSA greater than Mal8-BSA), and the geometry of the sugar display (AGOR, 0.51 min-1 greater than Mal29-BSA). Intracellular transport from the cell membrane to the lysosomes was slower for Man-BSA (approximately 3 min) than for the other ligands (approximately 0 min), suggesting that receptor-ligand uncoupling was slower for Man-BSA for which the receptor had the highest affinity or that extralysosomal catabolism of the other ligands occurred. Catabolism was also determined by the carbohydrate moiety of the ligand; it was greater for Mal29-BSA and Mal8-BSA (greater than or equal to 0.8 min-1) than for Man-BSA (0.27 min-1), and AGOR, with a complex oligosaccharide, was most resistant to degradation (0.14 min-1). An understanding of these structural features of glycoproteins that influence hepatic uptake, transport, and catabolism will be of value in drug targeting and for enzyme replacement in lysosomal storage disorders.(ABSTRACT TRUNCATED AT 250 WORDS)
Kinetics and mechanism of isocyanate reactions. II. Reactions of Aryl Isocyanates with Alcohols in the presence ob tertiary amines (1988)

Abstract The reaction of phenyl isocyanate with n‐butanol in the presence of tertiary amines has been kinetically studied as a model process for the polyurethane formation under conditions similar to those of industrial scale production. The rate‐determining step is believed to be the nucleophilic attack of tertiary amine on an associate of isocyanate with alcohol which is then converted into a very reactive uronium salt. This salt reacts fast with alcohol giving the final product, the urethane.
Assessment of the proportion of transgene-bearing sperm by fluorescence in situ hybridization: A novel approach for the detection of germline mosaicism in transgenic male founders (2000)

Genetic mosaicism is frequent among transgenic animals produced by pronuclear microinjection. A successful method for the screening of founder animals for germline mosaicism prior to mating would greatly reduce the costs associated with the propagation of the transgenic lines, and improve the efficiency of transgenic livestock production. With this aim, we have devised a simple method to detect integrated transgenes in individual spermatozoa using fluorescence in situ hybridization (FISH). The experiments reported here were undertaken to investigate the efficiency of this FISH-based approach to accurately evaluate the proportion of transgene-bearing sperm and to be applied for the detection of potential germline mosaics. Sperm samples from mice homozygous and hemizygous for a beta-lactoglobulin transgene were analyzed in a first set of experiments. A high hybridization efficiency was achieved, and the proportions of transgene-positive sperm cells in both homozygous (94.8-98.2%) and hemizygous (49.8-51.9%) animals were close to the expected frequencies (100 and 50%, respectively). To evaluate the sensitivity of the assay more directly, simulated mosaic samples with 5, 10, 15, 20 and 40% of transgene-bearing spermatozoa were then prepared and analyzed by FISH. Significant differences in the frequency of transgene-positive sperm were observed between all mosaic samples, indicating that even small deviations (5%) from the expected 50% transgene transmission rate in a founder animal could be reliably detected with our assay. Therefore, the method proposed represents a novel approach for the identification of germline mosaic founder males in livestock transgenic projects and a much more economic and faster alternative to breeding.
Macrocyclic Cell Penetrating Peptides: A Study of Structure-Penetration Properties (2015)

Arginine-rich cell penetrating peptides are short cationic peptides able to cross biological membranes despite their peptidic character. In order to optimize their penetration properties and further elucidate their mechanisms of cellular entry, these peptides have been intensively studied for the last two decades. Although several parameters are simultaneously involved in the internalization mechanism, recent studies suggest that structural modifications influence cellular internalization. Particularly, backbone rigidification, including macrocyclization, was found to enhance proteolytic stability and cellular uptake. In the present work, we describe the synthesis of macrocyclic arginine-rich cell penetrating peptides and study their cellular uptake properties using a combination of flow cytometry and confocal microscopy. By varying ring size, site of cyclization, and stereochemistry of the arginine residues, we studied their structure-uptake relationship and showed that the mode and site of cyclization as well as the stereochemistry influence cellular uptake. This study led to the identification of a hepta-arginine macrocycle as efficient as its linear nona-arginine congener to enter cells.
Templated Spherical High Density Lipoprotein Nanoparticles (2009)

We report the synthesis of high density lipoprotein (HDL) biomimetic nanoparticles capable of binding cholesterol. These structures use a gold nanoparticle core to template the assembly of a mixed phospholipid layer and the adsorption of apolipoprotein A-I. These synthesized structures have the general size and surface composition of natural HDL and, importantly, bind free cholesterol (K(d) = 4 nM). The determination of the K(d) for these particles, with respect to cholesterol complexation, provides a key starting and comparison point for measuring and evaluating the properties of subsequently developed synthetic versions of HDL.
Complex Nature of Enterococcal Pheromone-Responsive Plasmids (2010)

Pheromone-responsive plasmids constitute a unique group of approximately 20 plasmids identified, as yet, only among enterococcal species. Several of their representatives, e.g. pAD1, pCF10, pPD1 and pAM373 have been extensively studied. These plasmids possess a sophisticated conjugation mechanism based on response to sex pheromones--small peptides produced by plasmid-free recipient cells. Detailed analysis of regulation and function of the pheromone response process revealed its great complexity and dual role--in plasmid conjugation and modulation of enterococcal virulence. Among other functional modules identified in pheromone plasmids, the stabilization/partition systems play a crucial role in stable maintenance of the plasmid molecule in host bacteria. Among them, the par locus of pAD1 is one of the exceptional RNA addiction systems. Pheromone-responsive plasmids contribute also to enterococcal phenotype being an important vehicle of antibiotic resistance in this genus. Both types of acquired vancomycin resistance determinants, vanA and vanB, as well many other resistant phenotypes, were found to be located on these plasmids. They also encode two basic agents of enterococcal virulence, i.e. aggregation substance (AS) and cytolysin. AS participates in mating-pair formation during conjugation but can also facilitate the adherence ofenterococci to human tissues during infection. The second protein, cytolysin, displays hemolytic activity and helps to invade eukaryotic cells. There are still many aspects of the nature of pheromone plasmids that remain unclear and more detailed studies are needed to understand their uniqueness and complexity.
Proteomic profiling of heat shock protein 70 family members as biomarkers for hepatitis C virus‐related hepatocellular carcinoma (2003)

To identify proteins linked to the pathogenesis of hepatocellular carcinoma (HCC) associated with hepatitis C virus (HCV), we profiled protein expression levels in samples of HCC. To identify essential proteins, ten samples of HCV-related HCC were analyzed by two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization-time of flight mass spectrometry. These experiments revealed increased levels of nine proteins in cancerous tissues compared to levels in corresponding noncancerous liver tissues. We focused on four members of the heat shock protein 70 family: 78 kDa glucose-regulated protein (GRP78), heat shock cognate 71 kDa protein (HSC70), 75 kDa glucose-regulated protein (GRP75), and heat shock 70 kDa protein 1 (HSP70.1). These results were confirmed by immunoblot analysis. In an additional 11 samples, the same expression patterns of these four proteins were observed. In total, 21 samples showed statistically significant up-regulation of GRP78, GRP75 and HSP70.1 in cancerous tissues. HSC70 showed a tendency toward overexpression. There has been no report describing overexpression of these four proteins simultaneously in HBV-related HCC as well as nonviral HCC. Our results suggest that these four proteins play important roles in the pathogenesis of HCV-related HCC and could be molecular targets for diagnosis and treatment of this disease.
Activation of NF-κB by R5 and X4 Human Immunodeficiency Virus Type 1 Induces Macrophage Inflammatory Protein 1α and Tumor Necrosis Factor Alpha in Macrophages (2002)

NF-kappaB is a transcriptional activator that often regulates inflammatory responses. We demonstrate that human immunodeficiency virus type 1 activates nuclear localization of NF-kappaB in macrophages in a manner dependent upon virus strain but independent of virus replication. Through the use of an inhibitor, NF-kappaB activation was found to be responsible for the cytokine and chemokine induction that we recently reported.
Cerebrospinal Fluid Monoamine Metabolite Levels in Male Arsonists (1987)

Cerebrospinal fluid (CSF) monoamine metabolite levels were studied in 20 arsonists, 20 habitually violent offenders, and ten healthy inpatient volunteers. The arsonists and violent offenders had been in prison an average of six months before the study. Both the raw data and data adjusted by analysis of covariance for group differences in age, height, sex, and season of the lumbar puncture showed significantly lower concentrations of 3-methoxy-4-hydroxyphenylglycol (MHPG) and 5-hydroxyindoleacetic acid (5-HIAA) in the arsonists than in the other groups. The finding remained the same when arsonists with violent suicide attempts were excluded from the analysis. Although CSF concentrations of MHPG or 5-HIAA did not correlate with the severity of repeated fire-setting behavior, low blood glucose nadir in the oral glucose tolerance test (a measure of the tendency toward hypoglycemia) did. These results support the hypothesis that poor impulse control in criminal offenders is associated with low levels of certain CSF monoamine metabolites and with a hypoglycemic tendency.
Activation of soluble guanylate cyclase from rat lung by incubation or by hydrogen peroxide. (1976)

A 37,000 x g supernatant fraction prepared from rat lung homogenate demonstrated a 2-to 3-fold increase in guanylate cyclase activity after incubation at 30" for 30 min (preincubation).
Remarkable Phenytoin Sensitivity in 4 Children with SCN8A-related Epilepsy: A Molecular Neuropharmacological Approach (2015)

Mutations in SCN8A are associated with epilepsy and intellectual disability. SCN8A encodes for sodium channel Nav1.6, which is located in the brain. Gain-of-function missense mutations in SCN8A are thought to lead to increased firing of excitatory neurons containing Nav1.6, and therefore to lead to increased seizure susceptibility. We hypothesized that sodium channel blockers could have a beneficial effect in patients with SCN8A-related epilepsy by blocking the overactive Nav1.6 and thereby counteracting the effect of the mutation. Herein, we describe 4 patients with a missense SCN8A mutation and epilepsy who all show a remarkably good response on high doses of phenytoin and loss of seizure control when phenytoin medication was reduced, while side effects were relatively mild. In 2 patients, repeated withdrawal of phenytoin led to the reoccurrence of seizures. Based on the findings in these patients and the underlying molecular mechanism we consider treatment with (high-dose) phenytoin as a possible treatment option in patients with difficult-to-control seizures due to an SCN8A mutation.
Function of IRE1 alpha in the placenta is essential for placental development and embryonic viability (2009)

Inositol requiring enzyme-1 (IRE1), a protein located on the endoplasmic reticulum (ER) membrane, is highly conserved from yeast to humans. This protein is activated during ER stress and induces cellular adaptive responses to the stress. In mice, IRE1alpha inactivation results in widespread developmental defects, leading to embryonic death after 12.5 days of gestation. However, the cause of this embryonic lethality is not fully understood. Here, by using in vivo imaging analysis and conventional knockout mice, respectively, we showed that IRE1alpha was activated predominantly in the placenta and that loss of IRE1alpha led to reduction in vascular endothelial growth factor-A and severe dysfunction of the labyrinth in the placenta, a highly developed tissue of blood vessels. We also used a conditional knockout strategy to demonstrate that IRE1alpha-deficient embryos supplied with functionally normal placentas can be born alive. Fetal liver hypoplasia thought to be responsible for the embryonic lethality of IRE1alpha-null mice was virtually absent in rescued IRE1alpha-null pups. These findings reveal that IRE1alpha plays an essential function in extraembryonic tissues and highlight the relationship of physiological ER stress and angiogenesis in the placenta during pregnancy in mammals.
Molecular weight determination program (1984)

A computer program is described that will determine the molecular weight of DNA, RNA or protein molecules separated according to size by gel electrophoresis. It uses the sizes and migration distances of known molecules in a reference lane to compute a second or third order equation whose curve best fits the data points. It then computes the sizes of all molecules from this equation. Migration distances are measured and entered using an analog tablet. The program is written in Apple Pascal and designed to run on an Apple II Plus computer.
The cloning and overexpression of E coli acyl carrier protein (ACP) (1993)

Conference Article| May 01 1993 The cloning and overexpression of E coli acyl carrier protein (ACP) A. Lesley Jones; A. Lesley Jones 1Dept. of Biochemistry, UWCC, PO Box 903, Cardiff CF1 1STM and Schering Agrochemicals Ltd, Chesterford Park Research Station, Saffron Walden, Essex CB10 1XL Search for other works by this author on: This Site PubMed Google Scholar Peter Kille; Peter Kille 1Dept. of Biochemistry, UWCC, PO Box 903, Cardiff CF1 1STM and Schering Agrochemicals Ltd, Chesterford Park Research Station, Saffron Walden, Essex CB10 1XL Search for other works by this author on: This Site PubMed Google Scholar Jane E. Dancer; Jane E. Dancer 1Dept. of Biochemistry, UWCC, PO Box 903, Cardiff CF1 1STM and Schering Agrochemicals Ltd, Chesterford Park Research Station, Saffron Walden, Essex CB10 1XL Search for other works by this author on: This Site PubMed Google Scholar John L. Harwood John L. Harwood 1Dept. of Biochemistry, UWCC, PO Box 903, Cardiff CF1 1STM and Schering Agrochemicals Ltd, Chesterford Park Research Station, Saffron Walden, Essex CB10 1XL Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1993) 21 (2): 202S. https://doi.org/10.1042/bst021202s Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter LinkedIn Cite Icon Cite Get Permissions Citation A. Lesley Jones, Peter Kille, Jane E. Dancer, John L. Harwood; The cloning and overexpression of E coli acyl carrier protein (ACP). Biochem Soc Trans 1 May 1993; 21 (2): 202S. doi: https://doi.org/10.1042/bst021202s Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search This content is only available as a PDF. © 1993 Biochemical Society1993 Article PDF first page preview Close Modal You do not currently have access to this content.
Equilibrium structure and lateral stress distribution of amphiphilic bilayers from dissipative particle dynamics simulations (2002)

The equilibrium structure and lateral stress profile of fluid bilayer membrane patches are investigated using the Dissipative Particle Dynamics simulation technique. Although there are no attractive forces between the model amphiphiles, they spontaneously aggregate into planar bilayers under suitable conditions of concentration and amphiphile architecture. Pure bilayers of single-chain and double-chain amphiphiles are simulated, and the amphiphile architecture and interaction parameters varied. We find that a strong chain stiffness potential is essential to create the lamellar order typical in natural lipid membranes. Single-chain amphiphiles form bilayers whose lamellar phase is destabilized by reductions in the tail stiffness. Double-chain amphiphiles form bilayers whose rigidity is sensitive to their architecture, and that remain well-ordered for smaller values of their tail stiffness than bilayers of single-chain linear amphiphiles with the same hydrophobic tail length. The lateral stress profile across the bilayers contains a detailed structure reflecting contributions from all the interaction potentials, as well as the amphiphile architecture. We measure the surface tension of the bilayers, and extract estimates of the membrane area stretch modulus and bending rigidity that are comparable to experimental values for typical lipid bilayers. The stress profile is similar to that found in coarse-grained Molecular Dynamics simulations, but requires a fraction of the computational cost. Dissipative Particle Dynamics therefore allows the study of the equilibrium behavior of fluid amphiphilic membranes hundreds of times larger than can be achieved using Molecular Dynamics simulations, and opens the way to the investigation of complex mesoscopic cellular phenomena.
Role of the Colorless Polypeptides in Phycobilisome Reconstitution from Separated Phycobiliproteins (1982)

A phycoerythrin (PE) and phycocyanin (PC) mixture was separated from allophycocyanin on calcium phosphate chromatography from completely dissociated phycobilisomes of the blue-green alga, Nostoc sp. After dialysis of the PE-PC mixture in 0.75 m potassium phosphate, pH 7, which allows reassociation of the dissociated pigment-proteins, complexes of PE and PC in a 2:1 m ratio (PE/PC complex) as well as complexes predominantly of PC (PC/PE complex) were then separated by sedimentation on linear sucrose gradients. These complexes resemble the rods of intact phycobilisomes and transfer energy efficiently from PE to PC. They contain the Group II colorless polypeptides described by Tandeau de Marsac and Cohen-Bazire (1977 Proc Natl Acad Sci USA 74: 1635 61639). Phycobilisomes can be reconstituted by combining the allophycocyanin pool with (a) the PE-PC mixture, (b) the PE/PC complex, or (c) the PC/PE complex. Successful reconstitution is measured by absorption, fluorescence, circular dichroism, and electron microscopy. The major requirement for reconstitution is the 29-kilodalton colorless polypeptide. In its absence, no phycobilisomes are formed. It is the only colorless polypeptide common to both the PE/PC complex and the PC/PE complex, and appears to be the polypeptide responsible for rod attachment to the allophycocyanin. In addition, high phosphate concentrations and 20 degrees C temperatures are needed for reconstitution.