gebhart/patrepeval huggingface dataset:
Synthesis and Characterization of a Peptide Nucleic Acid Conjugated to a d-Peptide Analog of Insulin-like Growth Factor 1 for Increased Cellular Uptake (1997)

DNA therapeutics show great potential for gene-specific, nontoxic therapy of a wide variety of diseases. The deoxyribose phosphate backbone of DNA has been modified in a number of ways to improve nuclease stability and cell membrane permeability. Recently, a new DNA derivative with an amide backbone instead of a deoxyribose phosphate backbone, peptide nucleic acid (PNA), has shown tremendous potential as an antisense agent. Although PNAs hybridize very strongly and specifically to RNA and DNA, they are taken up by cells very poorly, limiting their potential as nucleic acid binding agents. To improve cellular uptake of a PNA sequence, it was conjugated to a D-amino acid analog of insulin-like growth factor 1 (IGF1), which binds selectively to the cell surface receptor for insulin-like growth factor 1 (IGF1R). The IGF1 D-peptide analog was assembled on (4-methylbenzhydryl)amine resin, and then the PNA was extended as a continuation of the peptide. The conjugate and control sequences were radiolabeled with 14C or fluorescently labeled with fluorescein isothiocyanate. Cellular uptake of the PNA-peptide conjugate, a control with two alanines in the peptide, and a control PNA without the peptide segment were studied in murine BALB/c 3T3 cells, which express low levels of murine IGF1R, in p6 cells, which are BALB/c 3T3 cells which overexpress a transfected human IGF1R gene, and in human Jurkat cells, which do not express IGF1R, as a negative control. The specific PNA-peptide conjugate displayed much higher uptake than the control PNA, but only in cells expressing IGF1R. This approach may allow cell-specific and tissue-specific application of PNAs as gene-regulating agents in vivo.
Polymer-Supported Tetrafluorophenol:  A New Activated Resin for Chemical Library Synthesis (2000)

A new tetrafluorophenol activated resin that facilitates the use of 19F NMR to quantitate loading is presented. This new resin provides a useful tool for acylation, and a novel activated polymeric sulfonate ester to generate sulfonamides. This activated resin reacts with a wide scope of N-nucleophiles including primary and secondary amines, and anilines. This new activated resin methodology provides a powerful tool for pure single-compound library synthesis.
In vitrostability and metabolism of salvinorin A in rat plasma (2009)

Salvinorin A is the main active psychoactive ingredient in Salvia divinorum, a Mexican plant that has been widely available as a hallucinogen in recent years. The aims of this study were to investigate the stability of salvinorin A in rat plasma, esterases responsible for its degradation, and estimation of the degradation products. The apparent first-order rate constants of salvinorin A at 37 degrees C, 25 degrees C, and 4 degrees C were 3.8 x 10(-1), 1.1 x 10(-1), and < 6.0 x 10(-3) h(-1), respectively. Salvinorin A degradation was markedly inhibited by the addition of sodium fluoride, an esterase inhibitor. Moreover, phenylmethylsulfonyl fluoride (serine esterase inhibitor) and bis-p-nitrophenylphosphate (carboxylesterase inhibitor) also inhibited salvinorin A degradation. In contrast, little or no suppression of the degradation was seen with 5,5'-dithiobis-2-nitrobenzoic acid (arylesterase inhibitor),ethopropazine (butyrylcholinesterase inhibitor), and BW284c51 (acetylcholineseterase inhibitor). These findings indicated that carboxylesterase was mainly involved in the salvinorin A hydrolysis in rat plasma.4. The degradation products of salvinorin A estimated by liquid chromatography-mass spectrometry included the deacetylated form (salvinorin B) and the lactone-ring-open forms of salvinorin A and salvinorin B. This lactone-ring-opening reactions were involved in calcium-dependent lactonase.
Role of alpha and beta carboxyl-terminal residues in the kinetics of human oxyhemoglobin dimer assembly. (1994)

Human oxyhemoglobin assembly was evaluated in the Soret region by rapidly mixing normal and carboxypeptidase-digested chains (1-10 x 10(-6) M, heme basis) in 0.1 M Tris-HCl, 0.1 M NaCl, 1 mM EDTA, pH 7.4, at 21.5 degrees C. Rate constants of 1.14 (+/- 0.09) and 2.11 (+/- 0.06) x 10(5) M-1 S-1 were measured for the association of Des(Arg-141) alpha with beta A and alpha A with beta A chains, respectively. The slower combination rate of Des(Arg-141) alpha with beta A chains is in agreement with that predicted solely on the basis of electrostatic considerations, as are the measured rate constants of 0.75 (+/- 0.12) and 1.86 (+/- 0.08) x 10(5) M-1 S-1 obtained for the combination of Des(Arg-141) alpha with variant beta S (Glu-6-->Val) and beta N Baltimore (Lys-95-->Glu) chains, respectively. However, the combination rates of alpha A and Des(Arg-141) alpha with beta A chains measured in the pH range from 7.0 to 9.0 demonstrated that the altered overall surface charge was not the only determinant of the assembly rates observed for Des(Arg-141) alpha chains. Furthermore, a rate constant of 11.3 (+/- 0.05) x 10(5) M-1 S-1 (which is 5.4-fold faster than the rate of alpha A beta A dimer assembly) was observed for Des(His-146,Tyr-145) beta chains. These kinetic studies suggest a critical role for the carboxyl-terminal domain in the assembly of human hemoglobin in vitro and perhaps in vivo.
Submicrosecond speed optical coherence tomography system design and analysis by use of acousto-optics (2003)

A novel high-speed no-moving-parts optical coherence tomography (OCT) system is introduced that acquires sample data at less than a microsecond per data point sampling rate. The basic principle of the proposed OCT system relies on use of an acousto-optic deflector. This OCT system has the attractive features of an acousto-optic scanning heterodyne interferometer coupled with an acousto-optic (AO) variable optical delay line operating in a reflective mode. Fundamentally, OCT systems use a broadband light source for high axial resolution inside the sample or living tissue under examination. Inherently, AO devices are Bragg-mode wavelength-sensitive elements. We identify that two beams generated by a Bragg cell naturally have unbalanced and inverse spectrums with respect to each other. This mismatch in spectrums in turn violates the ideal autocorrelation condition for a high signal-to-noise ratio broadband interferometric sensor such as OCT. We solve this fundamental limitation of Bragg cell use for OCT by deploying a new interferometric architecture where the two interfering beams have the same power spectral profile over the bandwidth of the broadband source. With the proposed AO based system, high (e.g., megahertz) intermediate frequency can be generated for low 1/f noise heterodyne detection. System issues such as resolution, number of axial scans, and delay-path selection time are addressed. Experiments described demonstrate our high-speed acousto-optically tuned OCT system where optical delay lines can be selected at submicrosecond speeds.
Lymphadenopathy-Associated Virus: From Molecular Biology to Pathogenicity (1985)

Recent data indicate that the lymphadenopathy-associated virus (LAV) is morphologically similar to animal lentiviruses, such as equine infectious anemia and visna viruses. This finding, together with the cross-reactivity of the core proteins of LAV with those of the equine infectious anemia virus and a similarity in genome structure and biological properties, allows LAV to be placed in the retroviral subfamily of Lentivirinae. Molecular data indicate a high degree of genetic variation of the virus, especially in the envelope gene, which have important implications for the origin of the virus (the T4 lymphotropism may be a recently acquired property) and for future immunization. Another problem is the role of viral infection in the induction of irreversible immunodeficiency. This syndrome occurs in a minority of infected persons, who generally have in common a past of antigenic stimulation and of immune depression before LAV infection.
Differentially expressed genes between drought-tolerant and drought-sensitive barley genotypes in response to drought stress during the reproductive stage (2009)

Drought tolerance is a key trait for increasing and stabilizing barley productivity in dry areas worldwide. Identification of the genes responsible for drought tolerance in barley (Hordeum vulgare L.) will facilitate understanding of the molecular mechanisms of drought tolerance, and also facilitate the genetic improvement of barley through marker-assisted selection or gene transformation. To monitor the changes in gene expression at the transcriptional level in barley leaves during the reproductive stage under drought conditions, the 22K Affymetrix Barley 1 microarray was used to screen two drought-tolerant barley genotypes, Martin and Hordeum spontaneum 41-1 (HS41-1), and one drought-sensitive genotype Moroc9-75. Seventeen genes were expressed exclusively in the two drought-tolerant genotypes under drought stress, and their encoded proteins may play significant roles in enhancing drought tolerance through controlling stomatal closure via carbon metabolism (NADP malic enzyme, NADP-ME, and pyruvate dehydrogenase, PDH), synthesizing the osmoprotectant glycine-betaine (C-4 sterol methyl oxidase, CSMO), generating protectants against reactive-oxygen-species scavenging (aldehyde dehydrogenase,ALDH, ascorbate-dependent oxidoreductase, ADOR), and stabilizing membranes and proteins (heat-shock protein 17.8, HSP17.8, and dehydrin 3, DHN3). Moreover, 17 genes were abundantly expressed in Martin and HS41-1 compared with Moroc9-75 under both drought and control conditions. These genes were possibly constitutively expressed in drought-tolerant genotypes. Among them, seven known annotated genes might enhance drought tolerance through signalling [such as calcium-dependent protein kinase (CDPK) and membrane steroid binding protein (MSBP)], anti-senescence (G2 pea dark accumulated protein, GDA2), and detoxification (glutathione S-transferase, GST) pathways. In addition, 18 genes, including those encoding Delta(l)-pyrroline-5-carboxylate synthetase (P5CS), protein phosphatase 2C-like protein (PP2C), and several chaperones, were differentially expressed in all genotypes under drought; thus they were more likely to be general drought-responsive genes in barley. These results could provide new insights into further understanding of drought-tolerance mechanisms in barley.
Selective blockade of tumor angiogenesis (2012)

Blocking tumor angiogenesis is an important goal of cancer therapy, but clinically approved anti-angiogenic agents suffer from limited efficacy and adverse side effects, fueling the need to identify alternative angiogenesis regulators. Tumor endothelial marker 8 (TEM8) is a highly conserved cell surface receptor overexpressed on human tumor vasculature. Genetic disruption of Tem8 in mice revealed that TEM8 is important for promoting tumor angiogenesis and tumor growth but dispensable for normal development and wound healing. The induction of TEM8 in cultured endothelial cells by nutrient or growth factor deprivation suggests that TEM8 may be part of a survival response pathway that is activated by tumor microenvironmental stress. In preclinical studies, antibodies targeted against the extracellular domain of TEM8 inhibited tumor angiogenesis and blocked the growth of multiple human tumor xenografts. Anti-TEM8 antibodies augmented the activity of other anti-angiogenic agents, vascular targeting agents and conventional chemotherapeutic agents and displayed no detectable toxicity. Thus, anti-TEM8 antibodies provide a promising new tool for selective blockade of neovascularization associated with cancer and possibly other angiogenesis-dependent diseases.
Synthesis of Arylthio-Substituted 3,8-Diphenyl-1,2-diazacycloocta-2,4,6,8-tetraenes and Their Thermolysis (1987)

Abstract Nucleophilic substitution of 4,7-dichloro-3,8-diphenyl-1,2-diazocine with arenethiols gave stable 4-arylthio-7-chloro- and/or 4,7-bis(arylthio)-1,2-diazocines. Unsymmetrical 4,7-bis(arylthio)- and 4-acetoxy-7-phenylthio-1,2-diazocines were also prepared from 4-chloro-7-phenylthio-1,2-diazocine. Thermolysis of all the diazocines afforded only arylthio-substituted pyridines with extrusion of benzonitrile.
Plasma Thrombospondin Levels in Sheep With Allergic Asthma (1996)

These results suggest that the two groups of allergic sheep may have two distinct induction processes leading to airway obstruction. The dual peak rise in TSP level that coincided with the airway response also suggests that an early priming effect exists in the DR group, which might have led to the late response. We conclude that intravascular platelet activation often occurs in mast cell-mediated allergic disorders. Therefore, plasma TSP may be useful for monitoring the course of allergic disorders.
The partial purification of properties of a thiaminase from bracken [Pteridium aquilinum (L.) Kuhn] (1957)

Research Article| September 01 1957 The partial purification of properties of a thiaminase from bracken [Pteridium aquilinum (L.) Kuhn] R. H. Kenten R. H. Kenten 1Biochemistry Department, Rothamsted Experimental Station, Harpenden, Herts Search for other works by this author on: This Site PubMed Google Scholar Biochem J (1957) 67 (1): 25–33. https://doi.org/10.1042/bj0670025 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation R. H. Kenten; The partial purification of properties of a thiaminase from bracken [Pteridium aquilinum (L.) Kuhn]. Biochem J 1 September 1957; 67 (1): 25–33. doi: https://doi.org/10.1042/bj0670025 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 Journal Search Advanced Search This content is only available as a PDF. © 1957 CAMBRIDGE UNIVERSITY PRESS1957 Article PDF first page preview Close Modal You do not currently have access to this content.
Anthocyanin regulatory gene expression in transgenic white clover can result in an altered pattern of pigmentation (2000)

This study presents the first evidence of heterologous anthocyanin regulatory genes altering anthocyanin expression in stably transformed leguminous plants. Two families of anthocyanin regulatory genes, myc ( delila , B-Peru ) and myb ( myb.Ph2 , C1 ), are involved in the activation of the phenylpropanoid pathway. White clover ( Trifolium repens cv. Haifa) plants were transformed with dicotyledonous and monocotyledonous myb or myc genes. Some of these transformed plants exhibited enhanced anthocyanin accumulation in a range of tissues. One plant, transformed with the B-Peru gene driven by the Cauliflower Mosaic Virus 35S promoter, displayed a unique pattern of anthocyanin accumulation in the leaf. The accumulation of anthocyanin in this plant was closely associated with the crescent of leaves, which is normally white. The red pigmentation declined in intensity in the oldest leaf stage. The B-Peru message was detected in all leaf stages of this white clover plant. This anthocyanin pattern was shown to be heritable.
Modification of the coding sequence enhances plant expression of insect control protein genes. (1991)

Increased expression of the insect control protein genes of Bacillus thuringiensis in plants has been critical to the development of genetically improved plants with agronomically acceptable levels of insect resistance. The expression of the cryIA(b) gene was compared to partially modified (3% nucleotide difference) and to fully modified (21% nucleotide difference) cryIA(b) and cryIA(c) genes in tobacco and tomato. The modified genes increased the frequency of plants that produced the proteins at quantities sufficient to control insects and dramatically increased the levels of these proteins. Among the most highly expressing transformed plants for each gene, the plants with the partially modified cryIA(b) gene had a 10-fold higher level of insect control protein and plants with the fully modified cryIA(b) had a 100-fold higher level of CryIA(b) protein compared with the wild-type gene. Similar results were obtained with the fully modified cryIA(c) gene in plants. Specific sequences of the partially modified cryIA(b) gene were analyzed for their ability to affect cryIA(b) gene expression in tobacco. The DNA sequence of a single region was identified as important to the improvement of plant expression of the cryIA(b) gene. The increased levels of cryIA(b) mRNA were not directly proportional to the increased levels of CryIA(b) protein in plants transformed with the modified cryIA(b) genes, indicating that the nucleotide sequence of these genes had an effect in improving their translational efficiency in plants.
Mantle cell lymphoma in relapse: the role of emerging new drugs (2010)

Understanding these targeted therapies in the context of the biology of MCL, has the potential to develop novel therapeutic platforms for the treatment of relapsed MCL, and will hopefully change the outcome for patients with this challenging clinical condition.
Measurement of the Airway Surface Liquid Volume with Simple Light Refraction Microscopy (2011)

In the cystic fibrosis (CF) lung, the airway surface liquid (ASL) volume is depleted, impairing mucus clearance from the lung and leading to chronic airway infection and obstruction. Several therapeutics have been developed that aim to restore normal airway surface hydration to the CF airway, yet preclinical evaluation of these agents is hindered by the paucity of methods available to directly measure the ASL. Therefore, we sought to develop a straightforward approach to measure the ASL volume that would serve as the basis for a standardized method to assess mucosal hydration using readily available resources. Primary human bronchial epithelial (HBE) cells cultured at an air-liquid interface develop a liquid meniscus at the edge of the culture. We hypothesized that the size of the fluid meniscus is determined by the ASL volume, and could be measured as an index of the epithelial surface hydration status. A simple method was developed to measure the volume of fluid present in meniscus by imaging the refraction of light at the ASL interface with the culture wall using low-magnification microscopy. Using this method, we found that primary CF HBE cells had a reduced ASL volume compared with non-CF HBE cells, and that known modulators of ASL volume caused the predicted responses. Thus, we have demonstrated that this method can detect physiologically relevant changes in the ASL volume, and propose that this novel approach may be used to rapidly assess the effects of airway hydration therapies in high-throughput screening assays.
Intercellular Communication in MarineVibrioSpecies: Density-Dependent Regulation of the Expression of Bioluminescence (2014)

This chapter focuses on the different molecular mechanisms two model luminous bacteria, Vibrio fischeri (a symbiont) and V. harveyi (a free-living microbe), use for regulating lux expression. Expression of luminescence in most bacteria is tightly regulated by the density of the population. In V. fischeri, the regulatory genes involved in density-dependent control of luminescence are adjacent to the luxCDABEG operon encoding the luciferase enzymes. The regulatory genes that control luminescence in V. harveyi are different from those of V. fischeri. One complementation group of V. harveyi dim mutants could be restored to full light production by a family of recombinant cosmids containing a subset of common restriction fragments. Initial HAI-1 and HAI-2 signal recognition by LuxN and LuxQ could activate a series of phosphotransfer reactions. Two-component circuits have been characterized in which a single protein contains both a sensor kinase and a response regulator domain (similar to LuxN and LuxQ) and a second protein contains both a response regulator domain and a DNA binding motif (similar to LuxO). The differences between the regulatory circuits controlling density-dependent expression of luminescence in V. fischeri and V. harveyi are striking. Subsequent mutations and gene duplications and rearrangements generated new and multiple autoinducers, receptivities, and regulatory connections, finally resulting in a bacterium with the properties of V. harveyi.
Molecular and developmental biology of the hemangioblast (2008)

The hemangioblast hypothesis was proposed a century ago. The existence of hemangioblasts is now demonstrated in mouse and human embryonic stem cell (ESC)-derived embryoid bodies (EBs), in the mouse and zebrafish gastrula, and in adults. The hemangioblast is believed to derive from mesodermal cells, and is enriched in the Bry+Flk1+ and Flk1+Scl+ cell populations in EBs and in the posterior primitive streak of the mouse gastrula and in the ventral mesoderm of the zebrafish gastrula. However, recent studies suggest that the hemangioblast does not give rise to all endothelial and hematopoietic lineages in mouse and zebrafish embryos. Although several signaling pathways are known to involve the generation of hemangioblasts, it remains largely unknown how the hemangioblast is formed and what are the master genes controlling hemangioblast development. This review will summarize our current knowledge, challenges, and future directions on molecular and developmental aspects of the hemangioblast.
Chemical Biology Investigation of Cell Death Pathways Activated by Endoplasmic Reticulum Stress Reveals Cytoprotective Modulators of ASK1 (2008)

The accumulation of unfolded proteins in the endoplasmic reticulum (ER) is caused by many disease-relevant conditions, inducing conserved signaling events collectively known as the unfolded protein response. When ER stress is excessive or prolonged, cell death (usually occurring by apoptosis) is triggered. We undertook a chemical biology approach for investigating mechanisms of ER stress-induced cell death. Using a cell-based high throughput screening assay to identify compounds that rescued a neuronal cell line from thapsigargin-induced cell death, we identified benzodiazepinones that selectively inhibit cell death caused by inducers of ER stress (thapsigargin and tunicamycin) but not by inducers of extrinsic (tumor necrosis factor) or intrinsic (mitochondrial) cell death pathways. The compounds displayed activity in several cell lines and primary cultured neurons. Mechanism of action studies revealed that these compounds inhibit ER stress-induced activation of p38 MAPK and kinases responsible for c-Jun phosphorylation. Active benzodiazepinones suppressed cell death at the level of apoptotic signal kinase-1 (ASK1) within the IRE1 pathway but without directly inhibiting the kinase activity of ASK1 or >400 other kinases tested. Rather, active compounds enhanced phosphorylation of serine 967 of ASK1, promoting ASK1 binding to 14-3-3, an event associated with suppression of ASK1 function. Reducing ASK1 protein expression using small interfering RNA also protected cells from ER stress-induced apoptosis, confirming the importance of this protein kinase. Taken together, these findings demonstrate an essential role for ASK1 in cell death induced by ER stress. The compounds identified may prove useful for revealing endogenous mechanisms that regulate inhibitory phosphorylation of ASK1.