gebhart/patrepeval huggingface dataset:
Transcription of Rhizobium meliloti nodulation genes. Identification of a nodD transcription initiation site in vitro and in vivo. (1987)

Nodulation genes in Rhizobium are required for invasion of the host plant. The nodABC operon is induced by plant activator molecules; this activation requires the gene product of the constitutively expressed nodD locus, which is transcribed divergently from nodABC. We are employing in vitro transcription to elucidate the molecular mechanism of nod gene activation. We used a micropurification technique to obtain RNA polymerase from Rhizobium meliloti, and here demonstrate that it initiated and terminated accurately at the Escherichia coli trp promoter-leader region. E. coli RNA polymerase, however, apparently fails to recognize R. meliloti promoters. We used the R. meliloti RNA polymerase in a minimal transcription system to attempt to localize the divergent start sites for nodD and nodABC. Transcript sizing and fingerprinting, together with synchronized single-round transcription experiments permit us to designate an in vitro transcription initiation site for nodD. Primer extension analysis of in vivo mRNA demonstrates that the initiation site which is utilized in vitro is the same site used in vivo. While nodABC is not transcribed in our minimal in vitro transcription system, this system should prove useful for the study of factors in induced cells which promote expression of this inducible promoter.
Growth Inhibition of Murine Melanoma and Human Colon Carcinoma by Recombinant Human Platelet Factor 4 (1990)

Although it is well established that angiogenesis is essential to tumor development, no human protein with high specificity and efficacy for prevention of angiogenesis has been characterized. In a previous study, we demonstrated that recombinant platelet factor 4 (rPF 4) inhibited angiogenesis in the chicken chorioallantoic membrane. In the present study, we have extended that finding to the use of recombinant human platelet factor 4 (rHuPF 4) to inhibit solid tumor growth in the mouse. rHuPF 4 effectively suppressed the growth of the B16-F10 murine melanoma in syngeneic C57BL/6J hosts and prevented the growth of primary tumors of both B16-F10 murine melanoma and HCT 116 human colon carcinoma in semisyngeneic CByB6F1/J female athymic nude mice. These two transformed cell lines were completely insensitive to rHuPF 4 in vitro at levels (50 micrograms/mL) that extensively inhibit normal endothelial cell proliferation. The migration of human endothelial cells was also inhibited at these concentrations of rHuPF 4, suggesting a second mechanism by which rHuPF 4 may modulate capillary development. The observed antitumor effects of rHuPF 4 might be due to the inhibition of angiogenesis. This finding could have implications for the development of novel therapeutic approaches to angiogenic diseases. Alternative, and possibly concurrent, mechanisms of the rHuPF 4 antitumor effect include lymphokine-activated killer cell activation and the induction of other cytokines.
Effect of nitrogen on the growth, yield and grain protein content of barley (Hordeum vulgare) (1990)

Barley (Hordeurn vulgare) cvv. Grimmett, Galleon and Corvette were grown under irrigated conditions at The University of Queensland, Gatton College. to determine the effects of nitrogen (N) rates (0-200 kg N/ha) on plant growth, yield and grain protein content. Nitrogen delayed maturity in all cultivars, especially in Galleon. Total tiller number and fertile tiller number were increased by N and there was a significant cultivar x N rate interaction. Similar trends were evident in total dry matter at maturity and grain yield, with Galleon producing the highest yields. Fertile tiller percentage was reduced by increasing N rate. Grain protein content increased with the increasing N rate, with differences in the nature of the response between cultivars (i.e. linear in Corvette, quadratic in the other 2 cultivars). Total and fertile tiller numbers were explained by quadratic regressions, with maximum values at 150 kg N/ha (except fertile tillers in Grimmett, maximum value at 100 kg N/ha). The declines in fertile tiller percentage were explained by quadratic equations except in Grimmett, which showed a negatively linear response to increasing N rate. Dry matter yield and grain yield showed quadratic responses to N in Grimmett and Galleon (predicted maximum values near 200 kg N/ha) and linear responses in Corvette, over the experimental range of N rates. The response in grain protein content was explained by quadratic equations for Grimmett and Galleon, with minimum grain protein content occurring at close to 0 and 55 kg N/ha respectively. Corvette showed a linear increase in protein content in response to increasing N rate. It is concluded that plant breeding programs should consider variation in grain yield and protein content in response to N supply and select for efficiency of utilisation of N. Recommended N rates for irrigated barley could be 150-200 kg N/ha. Lower rates will promote strong yield responses, but protein content would remain low.
How Type I Interferons Work in Multiple Sclerosis and Other Diseases: Some Unexpected Mechanisms (2014)

Type I interferons (IFNs) are important in innate and adaptive immunity. They are used to treat virus infections, cancer, and multiple sclerosis (MS). There are 5 type I IFN families in humans-IFN-α with 13 subtypes, plus IFN-β, ɛ, κ, and ω. Because their receptor binding affinities vary, these IFNs have different gene induction profiles and quite variable therapeutic effects. IFN-α subtypes may each be specific for certain viruses, but can be neurotoxic. IFN-β induces IFN-α, plus has additional direct effects on target cells. IFN-β was the first therapy approved that could change the course of MS. It has broader specificity than IFN-α, enhances cognition in MS, and may be neuroprotective and can potentially enhance fertility in women. Priming the IFN signaling system with an injection of IFN-β can enhance subnormal type I IFN signals in MS. Many other commonly used drugs and vitamins may potentiate clinical benefits of IFN-β.
Toponome Mapping in Prostate Cancer: Detection of 2000 Cell Surface Protein Clusters in a Single Tissue Section and Cell Type Specific Annotation by Using a Three Symbol Code (2009)

The toponome imaging technology MELC/TIS was applied to analyze prostate cancer tissue. By cyclical imaging procedures, we detected 2100 cell surface protein clusters in a single tissue section. This study provides the whole data set, a new kind of high dimensional data space, solely based on the structure-bound architecture of an in situ protein network, a putative fraction of the tissue code of prostate cancer. It is visualized as a colored mosaic composed of distinct protein clusters, together forming a motif expressed exclusively on the cell surface of neoplastic cells in prostate acini. Cell type specific expression of this motif, found in this preliminary study, suggests that high-throughput toponome analyses of a larger number of cases will provide insight into disease specific protein networks.
Characterization of Five Abscisic Acid-Responsive cDNA Clones Isolated from the Desiccation-Tolerant Plant Craterostigma plantagineum and Their Relationship to Other Water-Stress Genes (1990)

Leaves of resurrection plants tolerate desiccation as do embryos of many higher plants. From the resurrection plant Craterostigma plantagineum a number of desiccation-related transcripts have recently been cloned; they are abundantly expressed in dried leaves and abscisic acid-treated dried callus (D Bartels, K Schneider, G Terstappen, D Piatkowski, F Salamini [1990] Planta 18: 27-34). Five distinct cDNA clones representing low copy number genes were selected for further characterization. Their nucleotide sequences were determined and proteins were predicted with a molecular mass between 16 and 34 kilodaltons. Three of these proteins have unusual amino acid compositions and extreme hydrophilic characters. Two of them contain a cluster of contiguous serine residues and lysine-rich repeats. These sequence motifs display homologies to desiccation-related genes expressed in embryos or dehydrated seedlings of several plants. A third cDNA clone contains tracts of sequences which are related to a cotton Lea (late embryogenesis abundant) gene (JC Baker, C Steele, L Dure III [1988] Plant Mol Biol II: 277-291). Secondary structure predictions are discussed and suggest that the deduced proteins could play a role in protecting core cell structures in a dehydrated cell. It is concluded that at least in part the gene products involved in the desiccation-induced pathways are common to leaves of resurrection plants and embryos. Two cDNA clones appear to code for Craterostigma-specific mRNAs. The expression patterns of all five transcripts were studied in comparison to desiccated leaves in dehydrated roots, in wound-stressed leaves and in salt-stressed callus. The data obtained point to the possibility that not only specificity of induction but also the expression level of specific gene products may be of importance for osmoprotection.
GADD34 induces cell death through inactivation of Akt following traumatic brain injury (2013)

Neuronal cell death contributes significantly to the pathology of traumatic brain injury (TBI) irrespective of the mode or severity of the injury. Activation of a pro-survival protein, Akt, is known to be regulated by an E3 ligase TRAF6 through a process of ubiquitination-coupled phosphorylation at its T308 residue. Here we show that upregulation of a pro-apototic protein, GADD34, attenuates TRAF6-mediated Akt activation in a controlled cortical impact model of TBI in mice. TBI induces the expression of GADD34 by stimulating binding of a stress inducible transcription factor, ATF4, to the GADD34 promoter. GADD34 then binds with TRAF6 and prevents its interaction with Akt. This event leads to retention of Akt in the cytosol and prevents phosphorylation at the T308 position. Finally, in vivo depletion of GADD34 using a lentiviral knockdown approach leads to a rescue of Akt activation and markedly attenuates TBI-induced cell death.
Oral Grape Seed Extract Inhibits Prostate Tumor Growth and Progression in TRAMP Mice (2007)

Prostate cancer chemoprevention is an alternative and potential strategy to control this malignancy. Herein, we evaluated the chemopreventive efficacy of grape seed extract (GSE) against prostate cancer in transgenic adenocarcinoma of the mouse prostate (TRAMP) mice where animals were fed with GSE by oral gavage at 200 mg/kg body weight dose during 4 to 28 weeks of age. Our results showed a significant reduction (46%, P < 0.01) in the weight of genitourinary tract organs in the GSE-fed mice. The GSE-fed group of mice had a higher incidence of prostatic intraepithelial neoplasia but showed strong reduction in the incidence of adenocarcinoma compared with mice in control group. Prostate tissue from the GSE group showed approximately 50% (P < 0.001) decrease in proliferating cell nuclear antigen (PCNA)-positive cells and 64% (P < 0.01) reduction in total PCNA protein level compared with the control group; however, GSE increased apoptotic cells by 8-fold. Furthermore, GSE strongly decreased the protein levels of cyclin B1, cyclin A, and cyclin E by 84% (P < 0.05), 96% (P < 0.05), and 89% (P < 0.001), respectively. The protein expression of cyclin-dependent kinases 2 and 6 and Cdc2 was also decreased by more than 90% (P < 0.05) in the prostate from the GSE-fed group. Together, for the first time, we identified that oral GSE inhibits prostate cancer growth and progression in TRAMP mice, which could be mediated via a strong suppression of cell cycle progression and cell proliferation and an increase in apoptosis.
Fault-tolerant stream processing using a distributed, replicated file system (2008)

We present SGuard, a new fault-tolerance technique for distributed stream processing engines (SPEs) running in clusters of commodity servers. SGuard is less disruptive to normal stream processing and leaves more resources available for normal stream processing than previous proposals. Like several previous schemes, SGuard is based on rollback recovery [18]: it checkpoints the state of stream processing nodes periodically and restarts failed nodes from their most recent checkpoints. In contrast to previous proposals, however, SGuard performs checkpoints asynchronously: i.e. , operators continue processing streams during the checkpoint thus reducing the potential disruption due to the checkpointing activity. Additionally, SGuard saves the checkpointed state into a new type of distributed and replicated file system (DFS) such as GFS [22] or HDFS [9], leaving more memory resources available for normal stream processing. To manage resource contention due to simultaneous checkpoints by different SPE nodes, SGuard adds a scheduler to the DFS. This scheduler coordinates large batches of write requests in a manner that reduces individual checkpoint times while maintaining good overall resource utilization. We demonstrate the effectiveness of the approach through measurements of a prototype implementation in the Borealis [2] open-source SPE using HDFS [9] as the DFS.
Nuclear localization of PAPS synthetase 1: a sulfate activation pathway in the nucleus of eukaryotic cells (2000)

Sulfation is a major modification of many molecules in eukaryotes that is dependent on the enzymatic synthesis of an activated sulfate donor, 3'-phosphoadenosine 5'-phosphosulfate (PAPS). While sulfate activation has long been assumed to occur in the cytosol, we show in this study that human PAPS synthetase 1 (PAPSS1), a bifunctional ATP sulfurylase/adenosine 5'-phosphosulfate (APS) kinase enzyme sufficient for PAPS synthesis, accumulates in the nucleus of mammalian cells. Nuclear targeting of the enzyme is mediated by its APS kinase domain and requires a catalytically dispensable 21 amino acid sequence at the amino terminus. Human PAPSS1 and Drosophila melanogaster PAPSS localize to the nucleus in yeast and relieve the methionine auxotrophy of ATP sulfurylase- or APS kinase-deficient strains, suggesting that PAPSS1 is fully functional in vivo when targeted to the nucleus. A second PAPS synthetase gene, designated PAPSS2, has recently been described, mutations of which are responsible for abnormal skeletal development in human spondyloepimetaphyseal dysplasia and murine brachymorphism. We found that PAPSS2, which localizes to the cytoplasm when ectopically expressed in mammalian cells, is relocated to the nucleus when coexpressed with PAPSS1. Taken together, these results indicate that a sulfation pathway might exist in the nucleus of eukaryotic cells. -Besset, S., Vincourt, J.-B., Amalric, F., Girard, J.-P. Nuclear localization of PAPS synthetase 1: a sulfate activation pathway in the nucleus of eukaryotic cells.
Using Tablet for visual exploration of second-generation sequencing data (2012)

The advent of second-generation sequencing (2GS) has provided a range of significant new challenges for the visualization of sequence assemblies. These include the large volume of data being generated, short-read lengths and different data types and data formats associated with the diversity of new sequencing technologies. This article illustrates how Tablet-a high-performance graphical viewer for visualization of 2GS assemblies and read mappings-plays an important role in the analysis of these data. We present Tablet, and through a selection of use cases, demonstrate its value in quality assurance and scientific discovery, through features such as whole-reference coverage overviews, variant highlighting, paired-end read mark-up, GFF3-based feature tracks and protein translations. We discuss the computing and visualization techniques utilized to provide a rich and responsive graphical environment that enables users to view a range of file formats with ease. Tablet installers can be freely downloaded from http://bioinf.hutton.ac.uk/tablet in 32 or 64-bit versions for Windows, OS X, Linux or Solaris. For further details on the Tablet, contact tablet@hutton.ac.uk.
Identification and characterization of capsaicin-hydrolyzing enzymes purified from rat liver microsomes. (1994)

To elucidate the metabolic pathway of capsaicin (CAP), CAP-hydrolyzing enzymes, involved in the initial step of hydrolysis, were purified from rat liver microsomes and were characterized. CAP-hydrolyzing enzymes, whose activity was assayed by HPLC, were found to be located in the lumen of endoplasmic reticulum (ER). The enzymes were extracted from microsomes with Triton X-100 and purified by DEAE-cellulose, Sephadex G-200 (superfine), and isoelectrofocusing (IEF) chromatography. The enzymes were eluted from a gel filtration column as peaks with relative molecular mass of 60,000 and 180,000; IEF using Rotofor Cell showed that pIs of these enzymes are around 5.6 and 6.1, respectively. Total CAP-hydrolyzing activity of enzyme pI 5.6 was much greater than that of enzyme pI 6.1. With several lines of criteria, these fully characterized enzymes were identified as previously known hydrolase pI 5.6 and hydrolase pI 6.1.
Synthesis and Evaluation of Surface and Biological Properties of Some Lactic Acid‐Based Anionic Surfactants (2016)

Abstract In the present study, 11 lactic acid‐based anionic surfactants were synthesized and evaluated for their surface and biological activities. The synthesis involved the esterification of lactic acid with a range of fatty alcohols differing in chain length as well as in branching and unsaturation. The resultant ester was sulfonated by treatment with chlorosulfonic acid followed by salt formation with aqueous NaOH solution. The surface properties of all the synthesized surfactants were determined using surface tensiometry. Synthesized surfactants showed low critical micelle concentration (CMC) values and a decreasing trend with an increase in the alkyl chain length. Alkyl branching also led to a mild change in CMC values when compared with linear counterparts having the same number of carbon atoms, though such decreases or increases were observed to be dependent on the position and number of the branching. Some of the synthesized surfactants exhibited good antimicrobial and anti‐cancer activities against the tested microbial strains and cell lines.
Ricin-like plant toxins are evolutionarily related to single-chain ribosome-inhibiting proteins from Phytolacca. (1984)

A comparison has been made of the amino-terminal sequences of a number of ribosome-inhibiting proteins (RIPs) and cytotoxins. These include the monomeric enzymes PAP, PAP-S, PAP-II, and dodecandrin and the enzymatic A chains from the heterodimeric toxins ricin and modeccin. We show that these proteins have all evolved from a single ancestor. A statistical analysis is used to show the likely evolutionary relationship among the proteins. A similar analysis was performed on the amino-terminal sequences of ricin, Ricinus agglutinin, and modeccin B chains. These are galactoside-binding proteins associated with the A-chain enzymes. From the two comparisons we propose a scheme for the development of two major classes of proteins. The RIP and sugar-binding genes probably evolved independently. In some plant lines the genes never fused, although the RIP gene replicated and developed into several proteins expressed at various stages of plant maturation. In another line the RIP gene fused with a sugar binding (B-chain) gene to form the class of heterodimeric toxins. In some species this fused gene appears to have multiplied, one or more of the toxin genes mutating to code for a self-dimerizing agglutinin molecule.
Efficient filter flow for space-variant multiframe blind deconvolution (2010)

Ultimately being motivated by facilitating space-variant blind deconvolution, we present a class of linear transformations, that are expressive enough for space-variant filters, but at the same time especially designed for efficient matrix-vector-multiplications. Successful results on astronomical imaging through atmospheric turbulences and on noisy magnetic resonance images of constantly moving objects demonstrate the practical significance of our approach.
IL-11 produced by breast cancer cells augments osteoclastogenesis by sustaining the pool of osteoclast progenitor cells (2013)

Our data indicate that a) IL-11 plays an important role in osteoclastogenesis by stimulating the development and/or survival of osteoclast progenitor cells and b) breast cancer may promote osteolysis in part by increasing the pool of osteoclast progenitor cells via tumor cell-derived IL-11. However, given the heterogeneous nature of the bone marrow cells, the precise mechanism by which IL-11 treatment gives rise to a population of osteoclast progenitor cells warrants further investigation.
Isolation of an Egg-Adapted Influenza A(H3N2) Virus without Amino Acid Substitutions at the Antigenic Sites of Its Hemagglutinin (2018)

Antigenic changes in the hemagglutinin protein of recent A(H3N2) viruses often arise when these viruses adapt to their egg host. By serial egg passages of a cell-propagated virus, we successfully isolated an egg-adapted influenza A(H3N2) virus, A/Saitama/103/2014, without amino acid substitutions at the antigenic sites of its hemagglutinin protein but with multiple substitutions in its neuraminidase protein. Antigenic analysis of this egg-adapted A/Saitama/103/2014 virus indicated that its antigenicity did not differ from that of the World Health Organization prototype cell-propagated vaccine virus: A/Hong Kong/4801/2014. Our results suggest that this strategy may facilitate egg-based vaccine production without antigenic alterations in hemagglutinin by egg adaptation.
Thiol–Disulphide Interchange Reactions in the Setting of Single Wool Fibres (1966)

Wool fibres pretreated with fluoro–2, 4–dinitrobenzene, N –ethylmaleimide, peracetic acid, or nitrous acid set less readily than untreated fibres when stretched for 1 h at 100C in water or acetate buffer at pH 5. Incorporation of sodium bisulphite in the setting solution at concentrations greater than 0005 M eliminated these differences, except for fibres that had been treated with nitrous acid. The set retained by both untreated and modified fibres was increased by the addition of bisulphite to the setting solution. The presence of bisulphite in the solution used for releasing (1 h at 100C) the fibres set in the absence of bisulphite decreased the set retained, but had no effect if the fibres were set in the presence of bisulphite. Treatment of the unmodified wool fibres with solutions of bromine, peracetic acid, or methyl mercuric iodide before and during release at 100C greatly increased the set retained in an acetate buffer. Similar aftertreatments of the modified fibres caused a relatively small increase in set. Setting in buffer solutions at pH 9, when followed by release in the same solution, was only slightly decreased in extent by pretreatment of the fibres with N –ethylmaleimide or peracetic acid, whereas setting was prevented by pretreatment with fluoro–2, 4–dinitrobenzene or nitrous acid. The presence of sulphite in the solutions used for setting or releasing the fibres did not affect the result. It is suggested that rearrangement of disulphide bonds by a thiol–disulphide interchange reaction is chiefly responsible for setting of wool fibres at pH 5 in the absence of a reducing agent, but that a second type of interaction, possibly the formation of β–keratin, assumes great importance when the fibres are set in bisulphite solution. Setting at pH 9 probably takes place by the formation of new covalent linkages. Lysine side–chain groups may participate in the formation of these linkages.