gebhart/patrepeval huggingface dataset:
Genes involved in the copper-dependent regulation of soluble methane monooxygenase of Methylococcus capsulatus (Bath): cloning, sequencing and mutational analysis (2003)

The key enzyme in methane metabolism is methane monooxygenase (MMO), which catalyses the oxidation of methane to methanol. Some methanotrophs, including Methylococcus capsulatus (Bath), possess two distinct MMOs. The level of copper in the environment regulates the biosynthesis of the MMO enzymes in these methanotrophs. Under low-copper conditions, soluble MMO (sMMO) is expressed and regulation takes place at the level of transcription. The structural genes of sMMO were previously identified as mmoXYBZ , mmoD and mmoC . Putative transcriptional start sites, containing a σ 70 - and a σ N -dependent motif, were identified in the 5′ region of mmoX . The promoter region of mmoX was mapped using truncated 5′ end regions fused to a promoterless green fluorescent protein gene. A 9·5 kb region, adjacent to the sMMO structural gene cluster, was analysed. Downstream (3′) from the last gene of the operon, mmoC , four ORFs were found, mmoG , mmoQ , mmoS and mmoR . mmoG shows significant identity to the large subunit of the bacterial chaperonin gene, groEL . In the opposite orientation, two genes, mmoQ and mmoS , showed significant identity to two-component sensor–regulator system genes. Next to mmoS , a gene encoding a putative σ N -dependent transcriptional activator, mmoR was identified. The mmoG and mmoR genes were mutated by marker-exchange mutagenesis and the effects of these mutations on the expression of sMMO was investigated. sMMO transcription was impaired in both mutants. These results indicate that mmoG and mmoR are essential for the expression of sMMO in Mc. capsulatus (Bath).
Synthesis and Biological Evaluation of Dideoxunucleosides Containing A Difluoromethylene Unit (1989)

Abstract 2′-difluoro and 3′-difluoro dideoxynucleosides containing thymine and cytosine as the base were synthesized. These compounds inhibited HeLa cell growth and Moloney leukemia virus to a modest degree.
IL-17 can promote tumor growth through an IL-6–Stat3 signaling pathway (2009)

Although the Th17 subset and its signature cytokine, interleukin (IL)-17A (IL-17), are implicated in certain autoimmune diseases, their role in cancer remains to be further explored. IL-17 has been shown to be elevated in several types of cancer, but how it might contribute to tumor growth is still unclear. We show that growth of B16 melanoma and MB49 bladder carcinoma is reduced in IL-17(-/-) mice but drastically accelerated in IFN-gamma(-/-) mice, contributed to by elevated intratumoral IL-17, indicating a role of IL-17 in promoting tumor growth. Adoptive transfer studies and analysis of the tumor microenvironment suggest that CD4(+) T cells are the predominant source of IL-17. Enhancement of tumor growth by IL-17 involves direct effects on tumor cells and tumor-associated stromal cells, which bear IL-17 receptors. IL-17 induces IL-6 production, which in turn activates oncogenic signal transducer and activator of transcription (Stat) 3, up-regulating prosurvival and proangiogenic genes. The Th17 response can thus promote tumor growth, in part via an IL-6-Stat3 pathway.
Droplet-based single cell RNAseq tools: a practical guide (2019)

Droplet based scRNA-seq systems such as Drop-seq, inDrop and Chromium 10X have been the catalyst for the wide adoption of high-throughput scRNA-seq technologies in the research laboratory. In order to understand the capabilities of these systems to deeply interrogate biology; here we provide a practical guide through all the steps involved in a typical scRNA-seq experiment. Through comparing and contrasting these three main droplet based systems (and their derivatives), we provide an overview of all critical considerations in obtaining high quality and biologically relevant data. We also discuss the limitations of these systems and how they fit into the emerging field of Genomic Cytometry.
Molecular characterization of bovine brain P75, a high affinity binding protein for the regulatory subunit of cAMP-dependent protein kinase II beta. (1991)

In mammalian brain, physiological signals carried by cAMP seem to be targeted to intraneuronal sites by the association of cAMP-dependent protein kinase II beta with anchoring proteins that bind the regulatory subunit (RII beta) of the enzyme. Previously, an RII beta-binding domain was characterized in a large (Mr approximately 150,000) candidate anchor protein, rat brain P150 (Bregman, D. B., Bhattacharyya, N., and Rubin, C. S. (1989) J. Biol. Chem. 264, 4648-4656). RII beta-binding proteins with Mr values of 65,000-80,000 were detected in the brains of other species. Since little was known about the structural features of these lower Mr proteins, we undertook the characterization of bovine brain P75 as a prototype. A cDNA encoding 258 amino acid residues at the C terminus of P75 was cloned by probing a lambda gt11 expression library with 32P-RII beta. The cDNA insert was ligated into the pET-3b expression plasmid, and large amounts of the partial P75 polypeptide (designated P47) were produced in Escherichia coli. A purification scheme that yielded 9 mg of soluble P47 from a 1-liter bacterial culture was devised. Antibodies directed against the P47 polypeptide revealed that P75 is expressed almost exclusively in brain. The sequence of 117 amino acid residues at the C terminus of P75 contains the RII beta-binding site and is 80% identical to the corresponding region of P150. In contrast, a lower level of identity (36%) between P75 and P150 at a more N-terminal region indicates that the two RII beta-binding proteins are related, but distinct proteins. P75 is not homologous to microtubule-associated protein 2, an RII alpha-selective binding protein, or any other previously studied proteins. C-terminal truncation analysis disclosed that the final 26 residues in P75 are essential for binding RII beta.
What goes on behind closed doors: physiological versus pharmacological steroid hormone actions (2008)

Steroid-hormone-activated receptor proteins are among the best-understood class of factors for altering gene transcription in cells. Steroid receptors are of major importance in maintaining normal human physiology by responding to circulating concentrations of steroid in the nM range. Nonetheless, most studies of steroid receptor action have been conducted using the supra-physiological conditions of saturating concentrations (> or =100 nM) of potent synthetic steroid agonists. Here we summarize the recent developments arising from experiments using two clinically relevant conditions: subsaturating concentrations of agonist (to mimic the circulating concentrations in mammals) and saturating concentrations of antagonists (which are employed in endocrine therapies to block the actions of endogenous steroids). These studies have revealed new facets of steroid hormone action that could not be uncovered by conventional experiments with saturating concentrations of agonist steroids, such as a plethora of factors/conditions for the differential control of gene expression by physiological levels of steroid, a rational approach for examining the gene-specific variations in partial agonist activity of antisteroids, and a dissociation of steroid potency and efficacy that implies the existence of separate, and possibly novel, mechanistic steps and cofactors.
Monolithic Fourier-transform imaging spectrometer (1995)

The design of a monolithic imaging Fourier-transform spectrometer based on a Sagnac interferometer is discussed.
Quality of Life and Satisfaction with Outcome among Prostate-Cancer Survivors (2008)

Each prostate-cancer treatment was associated with a distinct pattern of change in quality-of-life domains related to urinary, sexual, bowel, and hormonal function. These changes influenced satisfaction with treatment outcomes among patients and their spouses or partners.
Macrocyclic and other novel trichothecenes: their structure, synthesis, and biological significance (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMacrocyclic and other novel trichothecenes: their structure, synthesis, and biological significanceBruce B. Jarvis and Eugene P. MazzolaCite this: Acc. Chem. Res. 1982, 15, 12, 388–395Publication Date (Print):December 1, 1982Publication History Published online1 May 2002Published inissue 1 December 1982https://pubs.acs.org/doi/10.1021/ar00084a002https://doi.org/10.1021/ar00084a002research-articleACS PublicationsRequest reuse permissionsArticle Views281Altmetric-Citations56LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Genetically engineered Bifidobacterium longum for tumor‐targeting enzyme‐prodrug therapy of autochthonous mammary tumors in rats (2006)

A fundamental obstacle in systemic therapy for cancer patients is the specific targeting of therapy directly to solid tumors. A strain of the domestic bacterium Bifidobacterium longum, which is non-pathogenic and anaerobic, showed selective localization to and proliferation within solid tumors after systemic application. Here, we propose a novel approach to cancer gene therapy in which anaerobic and non-pathogenic bacteria of the genus B. longum are used to achieve tumor-specific gene delivery and enzyme-prodrug therapy. We constructed a plasmid, pBLES100-S-eCD, which included eCD. Transfected B. longum produced CD in hypoxic tumors and achieved tumor site-specific conversion of 5-FC to 5-FU. Furthermore, we demonstrated antitumor efficacy in rat bearing autochthonous mammary tumors injected with the transfected B. longum directly or intravenously. This method was confirmed to be effective for enzyme-prodrug therapy not only by intratumoral injection but also by systemic administration. To estimate the toxicity of this bacterial vector, the systemic immunogenicity was evaluated by ASA reaction and the anaphylactic activity of IgG was evaluated by PCA reaction in guinea pigs. In the ASA reaction, no anaphylaxis symptoms were observed in any immunized guinea pigs injected with transfected B. longum. In the PCA reaction, B. longum/S-eCD specific-PCA-induced antibody was not detected. Thus, we proposed that anaerobic bacteria of the genus B. longum were an attractive and safe tumor-targeting vector and transfected B. longum was a potential anticancer agent that could effectively and specifically treat solid tumors.
Immunization with soluble hepatitis B virus surface protein elicits murine H-2 class I-restricted CD8+ cytotoxic T lymphocyte responses in vivo. (1994)

Immunization with soluble proteins only rarely induces a specific response of CD8+ CTL. We describe experiments that demonstrate the efficient and specific in vivo priming of CTL in BALB/c mice immunized with soluble hepatitis B virus (HBV)-derived surface (S) protein. A single (s.c., i.p. or i.v.) injection of a low dose (30 ng to 3 micrograms per mouse) of recombinant S protein particles without adjuvants induced a CTL response. This specific cytotoxic response was read out against a panel of different S protein-expressing transfected mouse cell lines. Effector cells of this response were Ld-restricted, CD3+ CD4- CD8+ CTL. H-2d/Ld+ (BALB/c, C.B-17) mice were responders; H-2d/Ld- (dm2) mutant mice and H-2b (C57BL/6) mice were nonresponders. Injections of various dosages of a S protein-derived, immunogenic, synthetic peptide into BALB/c mice by various routes did not prime CTL. After incorporation of S protein particles into IFA or aluminum hydroxide, these protein Ag lost their ability to specifically stimulate CTL in vivo. After priming of mice with S protein emulsified in IFA or adsorbed to aluminum hydroxide boost injections with native S protein particles were inefficient in stimulating a specific CTL response. These findings are of relevance for the design of synthetic subunit vaccines for which specific stimulation of CD8+ T effector functions is desired.
Epidural Electrical Stimulation for Stroke Rehabilitation (2015)

The primary analysis pertaining to efficacy of EECS during upper limb motor rehabilitation in chronic stroke patients was negative at 4 weeks postrehabilitation. A better treatment response was observed in a subset of patients eliciting stimulation induced upper limb movements during motor threshold assessments performed prior to each rehabilitation session. Post hoc comparisons indicated treatment effect differences at 24 weeks, with the control group showing significant decline in the combined primary outcome measure relative to the investigational group. These results have the potential to inform future chronic stroke rehabilitation trial design.
Elastic Coupling Between RNA Degradation and Unwinding by an Exoribonuclease (2012)

Rrp44 (Dis3) is a key catalytic subunit of the yeast exosome complex and can processively digest structured RNA one nucleotide at a time in the 3' to 5' direction. Its motor function is powered by the energy released from the hydrolytic nuclease reaction instead of adenosine triphosphate hydrolysis as in conventional helicases. Single-molecule fluorescence analysis revealed that instead of unwinding RNA in single base pair steps, Rrp44 accumulates the energy released by multiple single nucleotide step hydrolysis reactions until about four base pairs are unwound in a burst. Kinetic analyses showed that RNA unwinding, not cleavage or strand release, determines the overall RNA degradation rate and that the unwinding step size is determined by the nonlinear elasticity of the Rrp44/RNA complex, but not by duplex stability.
Arterial smooth muscle cells express platelet-derived growth factor (PDGF) A chain mRNA, secrete a PDGF-like mitogen, and bind exogenous PDGF in a phenotype- and growth state-dependent manner (1988)

Adult rat arterial smooth muscle cells are shown to express platelet-derived growth factor (PDGF) A chain mRNA, to secrete a PDGF-like mitogen, and to bind exogenous PDGF in a phenotype- and growth state-dependent manner. In the intact aortic media, where the cells are in a contractile phenotype, only minute amounts of PDGF A chain and no B chain (c-sis) RNA were detected. After cultivation and modulation of the cells into a synthetic phenotype, the A chain gene was distinctly expressed, whereas the B chain gene remained unexpressed. Cells kept in serum-free medium on a substrate of plasma fibronectin showed high levels of A chain RNA and high PDGF receptor activity, but did not secrete detectable amounts of PDGF-like mitogen. After exposure to PDGF, which is itself sufficient to initiate DNA synthesis and mitosis in these cells, a PDGF-like mitogen was released into the extracellular medium. Concomitantly, the amount of A chain transcripts per cell and the ability of the cells to bind radioactive PDGF decreased. Similarly, smooth muscle cells initially grown in the presence of serum released more PDGF-like mitogen, contained fewer A chain transcripts, and bound more radioactive PDGF in proliferating than in stationary cultures. The findings confirm the notion that adult rat arterial smooth muscle cells are able to promote their own growth in an autocrine or paracrine manner. Furthermore, they reveal some basic principles in the control of this process.
The detection in urine specimens of IgG and IgM antibodies to hepatitis A and hepatitis B core antigens (1992)

The use of urine as a noninvasive specimen for the diagnosis of hepatitis A (HAV) and hepatitis B (HBV) virus infections was investigated. Specimens of urine were collected at the same time as blood or saliva specimens, or singly in cases of previously serologically confirmed recent infection. The specimens were tested for IgG and IgM anti-HAV and anti-HBc by immunoglobulin class-specific capture radioimmunoassays (GACRIA and MACRIA). On the basis of assays on urine specimens it was possible to distinguish between individuals who were susceptible or immune to HAV or who had recently been infected with HAV. Using assays on 327 corresponding saliva specimens as reference tests, the observed sensitivity and specificity of tests on urine specimens by anti-HAV GACRIA were 98.9% and 99.1%, respectively, and by anti-HAV MACRIA were 95.8% and 99.6%, respectively. IgM and IgG anti-HBc were detected readily in the urine of 35 acute or recent cases of hepatitis B but were not found in the urine of seronegative individuals. Of the urine specimens from 52 individuals who were HBsAg carriers or who had had long past HBV infections, 49 contained detectable IgG anti-HBc. Of urine specimens from 42 HBsAg carriers, 11 contained raised IgM anti-HBc levels. Urine, which is a convenient specimen to collect, can be used to study outbreaks of hepatitis A, to ascertain the HAV immune status of individuals, to differentiate hepatitis A from hepatitis B, and to identify individuals who have been naturally exposed to HBV.
Protein engineering of the restriction endonuclease EcoRV (1998)

We generated variants of the restriction endonuclease EcoRV that discriminate between recognition sites with different flanking sequences. This was achieved by designing new contacts to the bases in the major groove of the DNA preceding and following the EcoRV recognition site. We selected Ala181 as the starting point for the extension of the site specificity of EcoRV because, according to the structure of the specific EcoRV x DNA complex, this residue is involved in a water mediated contact with the bases flanking the recognition sequence on the 5' side. A substitution of this alanine residue by other amino acid residues changes the protein-DNA interface in this region and potentially creates new contacts, such that EcoRV variants could have an extended specificity, i.e. a greater selectivity for EcoRV sites within a particular sequence context. EcoRV variants with naturally occurring amino acid residues at position 181 were produced and their selectivity analyzed with oligodeoxynucleotide and plasmid substrates that differ only in the base pairs immediately flanking the EcoRV site. Some variants, having amino acid residues with long or bulky side chains at position 181 showed altered preferences for the base pairs flanking the recognition sequence with oligodeoxynucleotide substrates without loosing their catalytic efficiency. One variant, A181K, is able to discriminate between purine and pyrimidine bases on the 5' side of the recognition sequence, probably by means of a new hydrogen bond to the N7 of the purine base. Another variant, A181E, strongly prefers a thymine base on the 5' side of the recognition sequence, presumably due to a hydrogen bond formed between the protonated glutamic acid residue and the O4 of thymine.
Genetic transformation in commercial Tasmanian cultivars of opium poppy, Papaver somniferum, and movement of transgenicpollen in the field (2003)

We report a new transformation protocol for the pharmaceutically important opium poppy, Papaver somniferum L.; the protocol allows transformation for the first time of high yielding commercial cultivars. The method involves Agrobacterium tumefaciens infection of hypocotyl explants, followed by the production of antibiotic- or herbicide-resistant embryogenic callus and the subsequent induction of somatic embryos and plants. Key elements of the improvement are the use of buffering agents to stabilise medium pH and bottom-cooling of the cultures. Transformation was verified by PCR and Southern blot hybridisation. Transcription of transgenes was confirmed by RT-PCR and product sequencing. Expression of transgenes was detected by histochemical GUS staining, phosphinothricin acetyltransferase (PAT) enzyme assays for bar and pat genes, and western analysis of transgenic sunflower seed albumin protein. Expression of various transgenes was detected in stem, leaf, seed, capsule and latex. The pat gene was demonstrated to be stably inherited to the T<sub>2</sub> generation and to confer phosphinothricin (PPT) herbicide resistance. Most T<sub>0</sub> plants showed normal morphology, were self-fertile and the transgenes displayed the expected Mendelian segregation. The percentage of explants producing somatic embryos that developed into plantlets able to be transplanted to soil, ranged from 6-11% in two Tasmanian cultivars.A field trial using pat transgenic plants was designed to estimate the frequency of hybridisation at various distances into buffer rows of non-transgenic poppies and to related weed species, P. somniferum spp. setigerum and P. dubium. The frequency of hybridisation to completely compatible poppy fell sharply with distance, being 2.6% at 20 cm, 2.13% at 0.5 m and falling to 0% at 2.5 and 5 m. No hybridisation could be detected to two weed species under open pollination conditions, including the compatible P. somniferum spp. setigerum, when grown as close as 20 cm, despite flowering at the same time as the transgenic plants in the presence of foraging bees.
CXC-chemokines, a new group of cytokines in congestive heart failure — possible role of platelets and monocytes (2000)

This study demonstrates for the first time elevated levels of CXC-chemokines in CHF, which may be of importance for progression of heart failure. Our findings further suggest that activated monocytes and platelets may contribute to enhanced CXC-chemokine levels in CHF.
The C-terminal (BRCT) Domains of BRCA1 Interact in Vivo with CtIP, a Protein Implicated in the CtBP Pathway of Transcriptional Repression (1998)

The BRCA1 tumor suppressor encodes a polypeptide with two recognizable protein motifs: a RING domain near the N terminus and two tandem BRCT domains at the C terminus. Studies of tumor-associated mutations indicate that the RING and BRCT sequences are required for BRCA1-mediated tumor suppression. In addition, recent work has shown that BRCA1 is a potent regulator of RNA transcription and that the BRCT domains are also essential for this activity. Therefore, we used the Sos recruitment system to screen for proteins that bind this critical region of BRCA1. Our results show that the BRCT domains interact in vivo with CtIP, a protein originally identified on the basis of its association with the CtBP transcriptional co-repressor. This finding suggests that BRCA1 regulates gene expression, at least in part, by modulating CtBP-mediated transcriptional repression. Moreover, the in vivo interaction between BRCA1 and CtIP is completely ablated by each of three independent tumor-associated mutations affecting the BRCT motifs of BRCA1. These results indicate that the BRCA1-CtIP interaction may be required for tumor suppression by BRCA1.