gebhart/patrepeval huggingface dataset:
Petroleum-Degrading Enzymes: Bioremediation and New Prospects (2011)

Anthropogenic forces, such as petroleum spills and the incomplete combustion of fossil fuels, have caused an accumulation of petroleum hydrocarbons in the environment. The accumulation of petroleum and its derivatives now constitutes an important environmental problem. Biocatalysis introduces new ways to improve the development of bioremediation strategies. The recent application of molecular tools to biocatalysis may improve bioprospecting research, enzyme yield recovery, and enzyme specificity, thus increasing cost-benefit ratios. Enzymatic remediation is a valuable alternative as it can be easier to work with than whole organisms, especially in extreme environments. Furthermore, the use of free enzymes avoids the release of exotic or genetically modified organisms (GMO) in the environment.
Copper chelates as possible active forms of the antiarthritic agents (1976)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCopper chelates as possible active forms of the antiarthritic agentsJohn R. J. SorensonCite this: J. Med. Chem. 1976, 19, 1, 135–148Publication Date (Print):January 1, 1976Publication History Published online1 May 2002Published inissue 1 January 1976https://doi.org/10.1021/jm00223a024RIGHTS & PERMISSIONSArticle Views707Altmetric-Citations426LEARN 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 InReddit PDF (2 MB) Get e-Alertsclose Get e-Alerts
Murine models of acute neuronopathic Gaucher disease (2007)

Gaucher disease (GD) is an autosomal recessive lysosomal storage disorder caused by mutations in the glucosidase, beta, acid (GBA) gene that encodes the lysosomal enzyme glucosylceramidase (GCase). GCase deficiency leads to characteristic visceral pathology and, in some patients, lethal neurological manifestations. Here, we report the generation of mouse models with the severe neuronopathic form of GD. To circumvent the lethal skin phenotype observed in several of the previous GCase-deficient animals, we genetically engineered a mouse model with strong reduction in GCase activity in all tissues except the skin. These mice exhibit rapid motor dysfunction associated with severe neurodegeneration and apoptotic cell death within the brain, reminiscent of neuronopathic GD. In addition, we have created a second mouse model, in which GCase deficiency is restricted to neural and glial cell progenitors and progeny. These mice develop similar pathology as the first mouse model, but with a delayed onset and slower disease progression, which indicates that GCase deficiency within microglial cells that are of hematopoietic origin is not the primary determinant of the CNS pathology. These findings also demonstrate that normal microglial cells cannot rescue this neurodegenerative disease. These mouse models have significant implications for the development of therapy for patients with neuronopathic GD.
Selectivity in the Post-Translational, Transglutaminase-Dependent Acylation of Lysine Residues (2009)

Transglutaminases (TGs) are known to exhibit remarkable specificities not only for the Q (or Gln) sites but also for the K (or Lys) sites of proteins with which they react. To gain further insight into K-site specificity, we examined the reactions of dansyl-epsilon-aminocaproyl-GlnGlnIleVal with three chemically and structurally well-characterized proteins (bovine pancreatic ribonuclease A, bovine pancreatic trypsin inhibitor, and chicken egg white lysozyme), as catalyzed by TG2, a biologically important post-translational enzyme. The substrates represent a total of 20 potential surface sites for acylation by the fluorescent Gln probe, yet only two of the lysine side chains reacted with TG2. While the K1 site of ribonuclease and the K15 site of the trypsin inhibitor could be readily acylated by the enzyme, none of the lysines in lysozyme were modified. The findings lead us to suggest that the selection of lysine residues by TG2 is not encoded in the primary amino acid sequence surrounding the target side chain but depends primarily on its being positioned in an accessible segment of the protein structure.
Enhancement of Antiproliferative Activity of Gamma Interferon by the Specific Inhibition of Tyrosine Dephosphorylation of Stat1 (1996)

Gamma interferon (IFN-gamma) signals to the nucleus through the activation, by tyrosine phosphorylation, of the latent cytoplasmic transcription factor Stat1 (signal transducer and activator of transcription). It has been demonstrated that the activity of Stat1 is dependent on tyrosine phosphorylation which is regulated by Jak tyrosine kinases as well as by the as-yet-unidentified protein tyrosine phosphatase. We report that the N-terminal domain of Stat1, which is highly conserved among all STAT family members, is required for its tyrosine dephosphorylation. A single amino acid substitution (Arg-31 to Ala) in the Stat1 N-terminal domain inhibited Stat1 tyrosine dephosphorylation. The deletion of the Stat1 N-terminal domain resulted in a mutant Stat1 protein which was constitutively phosphorylated on Tyr-701. Upon IFN-gamma stimulation, the tyrosine phosphorylation of this mutant protein was further enhanced but was not down-regulated by protein tyrosine phosphatase in vivo. When expressed in NIH 3T3 cells, this mutant protein greatly enhanced the antiproliferative activity of IFN-gamma. We suggest that the N-terminal domains of STATs are crucial for modulating STAT activities through regulating the tyrosine dephosphorylation of STATs.
Rationally engineered Cas9 nucleases with improved specificity (2015)

The RNA-guided endonuclease Cas9 is a versatile genome-editing tool with a broad range of applications from therapeutics to functional annotation of genes. Cas9 creates double-strand breaks (DSBs) at targeted genomic loci complementary to a short RNA guide. However, Cas9 can cleave off-target sites that are not fully complementary to the guide, which poses a major challenge for genome editing. Here, we use structure-guided protein engineering to improve the specificity of Streptococcus pyogenes Cas9 (SpCas9). Using targeted deep sequencing and unbiased whole-genome off-target analysis to assess Cas9-mediated DNA cleavage in human cells, we demonstrate that "enhanced specificity" SpCas9 (eSpCas9) variants reduce off-target effects and maintain robust on-target cleavage. Thus, eSpCas9 could be broadly useful for genome-editing applications requiring a high level of specificity.
Retinal Incorporation and Differentiation of Neural Precursors Derived from Human Embryonic Stem Cells (2005)

Retinal and macular degenerations are a major cause of blindness. Cell transplantation is a possible therapeutic approach for the replacement of degenerating retinal cells. Here, we studied the potential of human embryonic stem cells (hESCs) to survive, integrate, and differentiate into retinal cells after intraocular transplantation. Highly enriched cultures of neural precursors (NPs) expressing transcripts of key regulatory genes of retinal development were developed from the hESCs. After spontaneous differentiation in vitro, the NPs gave rise to progeny expressing markers of retinal progenitors and photoreceptor development, though this was uncommon and cells expressing markers of mature photoreceptors were not observed. After transplantation into rat eyes, the NPs survived for 16 weeks, migrated large distances, and integrated in the host retina. Teratoma tumors were not observed. Human cells expressing rhodopsin, blue cone opsin, and neural retina leucine zipper transcription factor were observed in subretinal grafts, but not within vitreal and inner retinal grafts. The results suggest that hESCs have the potential to differentiate into retinal cells and that the subretinal microenvironment supports their differentiation toward a photoreceptor fate. This may be the first step toward further developments that eventually may allow the use of hESCs for transplantation in retinal degenerations.
ChemInform Abstract: COULD CIS‐STILBENE BE PREPARED FROM A BENZYLIC PHOSPHONATE BY A WITTIG‐HORNER REACTION? (1984)

Abstract Das durch Reaktion des Benzylphosphonats (I) mit Benzaldehyd (II) erhaltene Hydroxyphosphonat (III) zersetzt sich im basischen Milieu erwartungsgemäß unter Bildung von trans‐Stilben (IV).
Interrelations between body weight, cigarette smoking and spine mineral density in osteoporotic Czech women. (1993)

This study was designed to assess the influence of body weight and cigarette smoking on vertebral bone mineral density in 241 osteoporotic and age matched 98 normal Czech women. The present study demonstrated that bone density and the frequency of atraumatic vertebral fractures was not related to the body weight. High body weight was not found to show any protective action on bone. However, among a group with vertebral fractures, bone mineral density in cigarette smokers was significantly lower than in nonsmokers, but this effect was not associated with low body weight. The osteoporotic women with and without vertebral fractures had high serum cholesterol concentration which is unequivocally associated with peripheral vascular disease. Thus, our results are suggesting the relationship between atherosclerosis and osteoporosis.
Effect of rapidly resorbable calcium phosphates and a calcium phosphate bone cement on the expression of bone‐related genes and proteins in vitro (2004)

The use of biodegradable bone substitutes is advantageous for alveolar ridge augmentation because it avoids second-site surgery for autograft harvesting. This study examines the effect of novel, rapidly resorbable calcium phosphates and a calcium phosphate bone cement on the expression of bone-related genes and proteins by human bone-derived cells (HBDCs) and compares this behavior to that of tricalciumphosphate (TCP). Test materials were alpha-TCP, two materials with a crystalline phase Ca(2)KNa(PO(4))(2) and with a small amorphous portion containing either magnesium potassium phosphate (material denominated GB14) or silica phosphate (material denominated GB9), and a calcium phosphate bone cement (material denominated Biocement D). HBDCs were grown on the substrata for 3, 7, 14, and 21 days, counted, and probed for various mRNAs and proteins (type I collagen, osteocalcin, osteopontin, osteonectin, alkaline phosphatase, and bone sialoprotein). All substrates supported continuous cellular growth for 21 days. In the presence of GB14 and Biocement D specimens cell proliferation was reduced and cell differentiation increased. At day 21, the greatest number of cells was found on GB9 expressing significantly higher levels of bone-related proteins than cells grown on all other surfaces. Because all novel materials facilitated the expression of the osteoblastic phenotype at least as much as TCP and the polystyrene control, these biomaterials can be regarded as excellent candidate bone substitute materials. GB9 induced the highest proliferation and cellular differentiation after 21 days of incubation, suggesting that this material may possess a higher potency for enhancing osteogenesis than TCP.
Glycosylation at specific sites of erythropoietin is essential for biosynthesis, secretion, and biological function. (1988)

The glycoprotein hormone erythropoietin (Ep), the primary regulator of erythropoiesis, is synthesized by the kidney and secreted as the mature protein with three N-linked and one O-linked oligosaccharide chains. To investigate the role(s) of each carbohydrate moiety in the biosynthesis and function of Ep, we have used oligonucleotide-directed mutagenesis of a cDNA for human Ep to alter the amino acids at each of the carbohydrate attachment sites. Each mutated cDNA construct was expressed in stably transfected sublines of a kidney cell line, baby hamster kidney. We show, by preventing attachment of N-linked carbohydrate at asparagines 38 or 83, or preventing O-linked glycosylation at serine 126, that glycosylation of each of these specific sites is critical for proper biosynthesis and secretion of Ep. Fractionation of cellular extracts demonstrated that the mutant proteins lacking glycosylation at each of these three sites, (38, 83, and 126) were associated mainly with membrane components or were degraded rapidly. Less than 10% of these three mutant proteins were processed properly and secreted from the cells. The Ep protein lacking N-linked glycosylation at asparagine 24 is synthesized and secreted as efficiently as native Ep. The carbohydrates at positions 24 and 38 may be involved in the biological activity of Ep, since the absence of either of the oligosaccharide side chains at these positions reduced the hormone's biological activity.
IRISHS: the infrared imaging spatial heterodyne spectrometer: a new pushbroom Fourier transform ultraspectral imager with no moving parts (1999)

Imaging spatial heterodyne spectroscopy (ISHS) was invented by Roesler and Harlander and applied to the far UV. It also has advantages for remote sensing applications in the visible and IR bands. We have designed, assembled, and ground-tested a new instrument designed for eventual airborne or spaceborne deployment for imaging spectroscopy at ultraspectral resolution. IRISHS is a true, imaging, Fourier transform spectrometer (FTS) with a fully open square field of view, where the third dimension required to assemble data cubes is acquired by scanning the FOV linearly over the scene. Spatially displayed fringes are difference with a spatial frequency determined by a pair of diffraction gratings, giving easily sampled fringe patterns. The current system operates between 8 and 12.5 microns in six sub-bands and employs a 256 X 256 pixel focal plane array. In comparison to dispersive imaging spectrometers with equivalent resolution, ISHS has: 1) much larger etendue in a small package; 2) full-field imaging for ease in image reconstruction; 3) approximately the same signal-to-noise ratio in equivalent observing scenarios, expect in the case where the entire dispersive spectrometer is cryogenically cooled. In comparison to conventional FTS, ISHS has: 1) no moving parts during data collection; 2) pushbroom imaging, 3) approximately the same S/N for equivalent conditions, 4) much lower data rate.
Sodium channels as molecular targets in multiple sclerosis. (2002)

Sodium channels are expressed at high density in myelinated axons and play an obligatory role in conducting action potentials along axons within the mammalian brain and spinal cord. It is not surprising, therefore, that they are involved in several aspects of the pathophysiology of multiple sclerosis (MS). First, the deployment of additional sodium channels to demyelinated parts of the axon (which had expressed low densities of sodium channels when covered by the myelin) provides a molecular substrate for the restoration of action potential conduction, a process that contributes to remissions in patients with MS. Second, there is evidence for changes in the expression pattern of sodium channels within Purkinje cells, both in animal models of MS and in human MS. It has been hypothesized that dysregulated sodium channel expression may contribute to symptom production in MS. If this hypothesis is correct, subtype-specific channel blockade may be therapeutically effective as a symptomatic treatment for ataxia and other cerebellar symptoms in MS. Finally, a noninactivating sodium conductance can trigger calcium-mediated axonal injury via reverse sodium-calcium exchange. Identifying the underlying channel may permit the development of therapeutic strategies that will prevent or retard axonal degeneration in MS.
Characterization of Novel Histidine-Tagged Tat-Peptide Complexes Dual-Labeled with 99mTc-Tricarbonyl and Fluorescein for Scintigraphy and Fluorescence Microscopy (2002)

To enable concurrent whole body scintigraphy and direct imaging of subcellular localization of permeation peptides, dual-labeled Tat-peptides useful for both radiometric analysis and fluorescence microscopy are desired for molecular imaging applications. Thus, novel dual-labeled D-Tat-peptides comprising Tat-basic domain (hgrkkrrqrrrgc), C-terminus conjugated with fluorescein-5-maleimide (FM) and N-terminus chelated with [(99m)Tc(CO)(3)] via histidine coordination, were synthesized and characterized. In human Jurkat cells, radiotracer uptake and washout studies revealed concentration-dependent accumulation of the dual-labeled Tat-peptide within cells. Subcellular localization of Tat-peptide was confirmed by fluorescence microscopy using an analogous [Re(CO)(3)] dual-labeled Tat-peptide. As seen with C-terminus single-labeled Tat-peptides, localization to the nucleoli was observed with the dual-labeled Tat-peptide, suggesting that the mechanism of Tat-peptide uptake and localization was not dependent on free peptide termini at either end. In Balb/c mice, biodistribution studies performed with the dual-labeled Tat-peptide showed fluorescence intensity by microscopic analysis that visually confirmed and correlated directly with scintigraphic and radiometric data. Of note, following intravenous administration, little brain penetration of these permeation sequences was observed in vivo. His[(99m)Tc(CO)(3)]-, DTPA[(99m)Tc(CO)(3)]-, and epsilon-lys-gly-cys[(99m)Tc(O)]-labeled Tat-peptides showed significant pharmacokinetic differences in liver and kidney depending on labeling strategy, indicating that Tat-peptide biodistribution can be impacted by the chelation moiety coordinated with (99m)Tc. Thus, we have shown that dual-labeled (99m)Tc-tricarbonyl Tat-peptide-FM conjugates can be conveniently synthesized and enable direct comparison of quantitative radiometric and qualitative fluorescence data both in vitro as well as in vivo.
Structure of the Methanococcus jannaschii Mevalonate Kinase, a Member of the GHMP Kinase Superfamily (2002)

The mevalonate-dependent pathway is used by many organisms to synthesize isopentenyl pyrophosphate, the building block for the biosynthesis of many biologically important compounds, including farnesyl pyrophosphate, dolichol, and many sterols. Mevalonate kinase (MVK) catalyzes a critical phosphoryl transfer step, producing mevalonate 5'-phosphate. The crystal structure of thermostable MVK from Methanococcus jannaschii has been determined at 2.4 A, revealing an overall fold similar to the homoserine kinase from M. jannaschii. In addition, the enzyme shows structural similarity with mevalonate 5-diphosphate decarboxylase and domain IV of elongation factor G. The active site of MVK is in the cleft between its N- and C-terminal domains. Several structural motifs conserved among species, including a phosphate-binding loop, have been found in this cavity. Asp(155), an invariant residue among MVK sequences, is located close to the putative phosphate-binding site and has been assumed to play the catalytic role. Analysis of the MVK model in the context of the other members of the GHMP kinase family offers the opportunity to understand both the mechanism of these enzymes and the structural details that may lead to the design of novel drugs.
Cloning and expression of a rat Smad1: Regulation by TGF� and modulation by the ras/MEK pathway (1999)

A new family of signaling intermediates for TGFbeta superfamily members and other growth factors has recently been identified and termed Smads. It has been suggested that the Smad1 subfamily is regulated primarily by the TGFbeta superfamily member bone morphogenetic protein (BMP). Here we demonstrate that TGFbeta induced phosphorylation of endogenous Smad1 in untransformed IECs and that the RI and RII TGFbeta receptors were detectable in Smad1 immunocomplexes. Expression of a dominant-negative mutant of Ras inhibited the ability of TGFbeta to phosphorylate endogenous Smad1. In a separate series of experiments, we have cloned a rat homologue of the drosophila mad gene (termed RSmad1) by screening an intestinal epithelial cell (IEC) cDNA library. By using an in vitro kinase assay with RSmad1 as the substrate, we demonstrate that the TGFbeta receptor complex can directly phosphorylate RSmad1. We show, further, that a dominant-negative mutant of MEK1 inhibited the ability of RSmad1 to induce the TGFbeta-responsive reporter p3TP-Lux in a human breast cancer cell line. Collectively, our data demonstrate that TGFbeta can regulate Smadl and that the Ras and MEK signaling components are partially required for the ability of TGFbeta to regulate Smad1.
Retinoid Signaling Determines Germ Cell Fate in Mice (2006)

Germ cells in the mouse embryo can develop as oocytes or spermatogonia, depending on molecular cues that have not been identified. We found that retinoic acid, produced by mesonephroi of both sexes, causes germ cells in the ovary to enter meiosis and initiate oogenesis. Meiosis is retarded in the fetal testis by the action of the retinoid-degrading enzyme CYP26B1, ultimately leading to spermatogenesis. In testes of Cyp26b1-knockout mouse embryos, germ cells enter meiosis precociously, as if in a normal ovary. Thus, precise regulation of retinoid levels during fetal gonad development provides the molecular control mechanism that specifies germ cell fate.
Biosynthesis of bacterial glycogen. Primary structure of Escherichia coli ADP-glucose:alpha-1,4-glucan, 4-glucosyltransferase as deduced from the nucleotide sequence of the glgA gene. (1986)

The nucleotide sequence of the glgA gene, coding for glycogen synthase (EC 2.4.1.21) was elucidated. It consists of 1431 base pairs specifying a protein of 477 amino acids. The deduced amino acid sequence was consistent with the amino acid analysis obtained with the pure protein as well as with the molecular weight as determined from sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The deduced amino acid sequence was also consistent with the amino-terminal acid sequence and amino acid sequence analysis of various peptides obtained from CNBr degradation of purified glycogen synthase.
Large interactive visualization of density functions on big data infrastructure (2015)

Point set visualization is required in lots of visualization techniques. Scatter plots as well as geographic heat-maps are straightforward examples. Data analysts are now well trained to use such visualization techniques. The availability of larger and larger datasets raises the need to make these techniques scale as fast as the data grows. The Big Data Infrastructure offers the possibility to scale horizontally. Designing point set visualization methods that fit into that new paradigm is thus a crucial challenge. In this paper, we present a complete architecture which fully fits into the Big Data paradigm and so enables interactive visualization of heatmaps at ultra-scale. A new distributed algorithm for multi-scale aggregation of point set is given and an adaptive GPU based method for kernel density estimation is proposed. A complete prototype working with Hadoop, HBase, Spark and WebGL has been implemented. We give a benchmark of our solution on a dataset having more than 2 billion points.