gebhart/patrepeval huggingface dataset:
Genetic Requirements of Phage λ Red-Mediated Gene Replacement in Escherichia coli K-12 (2000)

Recombination between short linear double-stranded DNA molecules and Escherichia coli chromosomes bearing the red genes of bacteriophage lambda in place of recBCD was tested in strains bearing mutations in genes known to affect recombination in other cellular pathways. The linear DNA was a 4-kb fragment containing the cat gene, with flanking lac sequences, released from an infecting phage chromosome by restriction enzyme cleavage in the cell; formation of Lac(-) chloramphenicol-resistant bacterial progeny was measured. Recombinant formation was found to be reduced in ruvAB and recQ strains. In this genetic background, mutations in recF, recO, and recR had large effects on both cell viability and on recombination. In these cases, deletion of the sulA gene improved viability and strain stability, without improving recombination ability. Expression of a gene(s) from the nin region of phage lambda partially complemented both the viability and recombination defects of the recF, recO, and recR mutants and the recombination defect of ruvC but not of ruvAB or recQ mutants.
Temporal Expression of the Transforming Growth Factor-Beta Pathway in the Rabbit Ear Model of Wound Healing and Scarring (2007)

BACKGROUND: Despite numerous studies that have investigated the cellular and molecular mechanisms underlying scar formation, this process still remains poorly understood. The importance of transforming growth factor-β (TGF-β) in these processes has been well recognized, and this study sought to define the temporal expression of the key members in this pathway in a well-established, clinically relevant, rabbit ear model of hypertrophic scarring. STUDY DESIGN: Seven-millimeter (hypertrophic) and 5-mm (nonhypertrophic) punch wounds were made on the ears of 12 rabbits. Wounds were harvested at days 0, 7, 15, 28, and 40. RESULTS: There were no appreciable histologic differences between the 5- and 7-mm wounds at days 7 and 15. At day 28, however, the 7-mm scars were considerably more hypertrophic compared with the 5-mm control scars (p < 0.001). The mRNA levels of TGF-β1 and collagen Iα2 were notably higher in the hypertrophic 7-mm scars at day 28 than in the nonhypertrophic 5-mm scars (p < 0.03). Although not pronounced, levels of TGF-β2 were higher in the hypertrophic scars. There were no other statistically significant differences between the 7- and 5-mm scars. CONCLUSIONS: Elevated levels of TGF-β1, and possibly TGF-β2, are associated with hypertrophic scar formation. Abbreviations and Acronyms: PCR: polymerase chain reaction; SEI: scar elevation index; TBR-I: transforming growth factor-β receptor I; TBR-II: transforming growth factor-β receptor II; TGF-β: transforming growth factor-β.
Tungsten in biological systems (1996)

Tungsten (atomic number 74) and the chemically analogous and very similar metal molybdenum (atomic number 42) are minor yet equally abundant elements on this planet. The essential role of molybdenum in biology has been known for decades and molybdoenzymes are ubiquitous. Yet, it is only recently that a biological role for tungsten has been established in prokaryotes, although not as yet in eukaryotes. The best characterized organisms with regard to their metabolism of tungsten are certain species of hyperthermophilic archaea (Pyrococcus furiosus and Thermococcus litoralis), methanogens (Methanobacterium thermoautotrophicum and Mb. wolfei), Gram-positive bacteria (Clostridium thermoaceticum, C. formicoaceticum and Eubacterium acidaminophilum), Gram-negative anaerobes (Desulfovibrio gigas and Pelobacter acetylenicus) and Gram-negative aerobes (Methylobacterium sp. RXM). Of these, only the hyperthermophilic archaea appear to be obligately tungsten-dependent. Four different types of tungstoenzyme have been purified: formate dehydrogenase, formyl methanofuran dehydrogenase, acetylene hydratase, and a class of phylogenetically related oxidoreductases that catalyze the reversible oxidation of aldehydes. These are carboxylic reductase, and three ferredoxin-dependent oxidoreductases which oxidize various aldehydes, formaldehyde and glyceraldehyde 3-phosphate. All tungstoenzymes catalyze redox reactions of very low potential (≤−420 mV) except one (acetylene hydratase) which catalyzes a hydration reaction. The tungsten in these enzymes is bound by a pterin moiety similar to that found in molybdoenzymes. The first crystal structure of a tungsten- or pterin-containing enzyme, that of aldehyde ferredoxin oxidoreductase from P. furiosus, has revealed a catalytic site with one W atom coordinated to two pterin molecules which are themselves bridged by a magnesium ion. The geochemical, ecological, biochemical and phylogenetic basis for W- vs. Mo-dependent organisms is discussed.
Abstract 5766: Multifunctional biologics for targeted T-cell therapy based on in vivo matured fully human VH domains (2018)

Abstract Crescendo Biologics has created a proprietary transgenic mouse devoid of any antibody light chains from which it generates highly diverse fully human VH domain (‘Humabody') building blocks. In vivo maturation optimizes Humabody potency and develops superior biophysical properties. Their small size (13kDa) and high stability permits Humabody assembly into an almost limitless array of multifunctional formats optimally configured for therapeutic efficacy. These small versatile single VH domain building blocks permit the rapid exploration of a vast range of 3D format space to identify optimal therapeutic solutions. This fully modular plug &amp; play approach lacks the constraints of traditional mAbs and enables a radical rethink of how a multifunctional molecule can be designed and assembled to deliver enhanced therapeutic benefit. Such molecules are capable of target engagement that is unachievable using regular mAbs. Using Humabody VH addressing key targets in the immune-oncology space, Crescendo has exemplified the potential for optimally configured molecules to deliver enhanced efficacy both in vitro and in vivo. Examples include: CB307, a unique T-cell engaging format with a novel mode of action. CB201, a biparatopic antagonist which ‘handcuffs' PD1: one domain binding and blocking PD1 from engaging with its ligands, the other binding a nonblocking epitope. With a binding affinity of 175pM and a unique ability to localise rapidly to PD-1 positive T-cells, CB201 demonstrates significantly enhanced in vivo efficacy over IgG-based PD-1 antagonists in a PDX tumour model in NSG mice. CB108, a half-life extended paratopic Humabody binding PSMA has demonstrated superior tumour targeting with enhanced internalisation and highly efficient accumulation in target-positive tumours with up to 18 percent ID per g recorded in a 24hr imaging study. These data support the progression of highly differentiated therapeutics into the clinic. Citation Format: Brian Mcguinness, James Legg, Phil Bland-Ward, Peter Pack. Multifunctional biologics for targeted T-cell therapy based on in vivo matured fully human VH domains [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5766.
Efficient generation of 2'-deoxyuridin-5-yl at 5'-(G/C)AAXUXU-3' (X = Br, I) sequences in duplex DNA under UV-irradiation (2004)

A highly sequence-specific photoreaction of 5'-(G/C)AA(X)U(X)U-3' was found by using 450-base pair DNA fragments containing (X)U under UV-irradiation (X = Br, I). The molecular basis of this high photoreactivity was investigated in detail using synthetic octanucleotides. Based on the experimental data, the mechanism for the efficient photoreaction was proposed.
Effect of carbohydrate source on alpha-amylase and glucoamylase formation byClostridium acetobutylicum SA-1 (1986)

An examination into the effect of different carbohydrate sources indicated that the production of extracellular alpha-amylase and glucoamylase was under similar biosynthetic control in Clostridium acetobutylicum SA-1. Cell-associated starch-hydrolytic enzymes may be more important than extracellular enzymes in the processing of the starch molecule.
Stereochemistry of base-catalyzed ring opening of 1,3,2-oxathiaphospholanes. Absolute configuration of 2-{N-[(Rc)-1-(.alpha.-naphthyl)ethyl]amino}-2-thiono-1,3,2-oxathiaphospholanes and O,S-dimethyl N-[(Rc)-1-(.alpha.-naphthyl)ethyl]phosphoramidothioates (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStereochemistry of base-catalyzed ring opening of 1,3,2-oxathiaphospholanes. Absolute configuration of 2-{N-[(Rc)-1-(.alpha.-naphthyl)ethyl]amino}-2-thiono-1,3,2-oxathiaphospholanes and O,S-dimethyl N-[(Rc)-1-(.alpha.-naphthyl)ethyl]phosphoramidothioatesB. Uznanski, A. Grajkowski, B. Krzyzanowska, A. Kazmierkowska, W. J. Stec, M. W. Wieczorek, and J. BlaszczykCite this: J. Am. Chem. Soc. 1992, 114, 26, 10197–10202Publication Date (Print):December 1, 1992Publication History Published online1 May 2002Published inissue 1 December 1992https://pubs.acs.org/doi/10.1021/ja00052a017https://doi.org/10.1021/ja00052a017research-articleACS PublicationsRequest reuse permissionsArticle Views247Altmetric-Citations37LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
The tumor necrosis factor receptor 2 signal transducers TRAF2 and c-IAP1 are components of the tumor necrosis factor receptor 1 signaling complex (1996)

The two cell surface receptors for tumor necrosis factor (TNF) interact with a number of intracellular signal transducing proteins. The association of TRADD, a 34-kDa cytoplasmic protein containing a C-terminal death domain, with aggregated TNF receptor 1 (TNF-R1) through their respective death domains leads to NF-kappa B activation and programmed cell death. In contrast, TNF receptor 2 (TNF-R2) interacts with the TNF receptor associated factors 2/1 (TRAF2/TRAF1) heterocomplex, which mediates the recruitment of two cellular inhibitor of apoptosis proteins (c-IAP1 and c-IAP2) to TNF-R2. Here we show that the TNF-R2 signal transducers TRAF2 and c-IAP1 are a part of the TNF-R1 signaling complex. The recruitment of TRAF2 and c-IAP1 to TNF-R1 is TNF-dependent, is mediated by TRADD, and is independent of TNF-R2. These data establish the physiological involvement of TRAF2 and c-IAP1 in TNF-R1 signaling and help provide a molecular explanation for both the overlapping and distinct signals generated by the two TNF receptors.
Octa(thymidine methanephosphonates) of partially defined stereochemistry: synthesis and effect of chirality at phosphorus on binding to pentadecadeoxyriboadenylic acid (1990)

Block condensation of MePOCI2 or MeP(NEt2)2 with appropriately protected tetra(thymidine methanephosphonates) of predetermined sense of chirality at asymmetric phosphonate centres gave two pairs of diastereomeric mixtures, namely (SpSpSpSpSpSpSp + SpSpSpRpSpSpSp) 5a and (RpRpRpRpRpRpRp + RpRpRpSpRpRpRp) 5b. A comparison of the CD spectra of 5a and 5b with those of octathymidylic acid (7) and a random mixture of diastereomers of octa(thymidine methanephosphonate) (6), and also a comparison of the Tm of complexes formed between 5a, 5b, 6 or 7, and pentadecadeoxyriboadenylic acid (8), indicates that octamer 5b and its complex with its complementary oligonucleotide has a well-ordered structure due to the 'outward' or 'pseudoequatorial' orientation of the methyl group of each internucleotide methanephosphonate function of Rp configuration. Results presented in this report clearly indicate that the stability of hybrids formed between octa(thymidine methanephosphonate) and pentadecadeoxyriboadenylic acid depends on the stereochemistry of each internucleotide methanephosphonate function and strongly suggests that stereoselective synthesis of P-chiral oligonucleotide analogues is an important goal.
A 10‐year survey, 1980–1990, of prenatally diagnosed small supernumerary marker chromosomes, identified by fish analysis. Outcome and follow‐up of 14 cases diagnosed in a series of 12 699 prenatal samples (1995)

A cytogenetic survey and follow-up studies were made of 14 cases with supernumerary marker chromosomes, identified among 12,699 prenatal samples, investigated at our institution over a 10-year period from 1980 to 1990. FISH (fluorescence in situ hybridization) techniques were employed to identify the chromosomal origin of the marker chromosomes. Five cases were familial, all derived from acrocentric chromosomes, and all without apparent phenotypic effects in the children. Nine cases represented de novo aberrations. In two cases (one with a marker from chromosome 14 or 22, the other with a ring-like marker derived from chromosome 17), the pregnancies continued and apparently normal babies were delivered at term, but the child with a marker derived from chromosome 17 showed slight psychomotor retardation at 2 years of age. All other pregnancies with de novo markers were terminated. In three cases, significant abnormalities were found at autopsy. One of these had an isochromosome 12p and the phenotype was consistent with Pallister-Killian syndrome. In conclusion, marker chromosome identification, as well as clinical follow-up, is essential for the purpose of improving genetic counselling.
The silencing protein SIR2 and its homologs are NAD-dependent protein deacetylases (2000)

Homologs of the chromatin-bound yeast silent information regulator 2 (SIR2) protein are found in organisms from all biological kingdoms. SIR2 itself was originally discovered to influence mating-type control in haploid cells by locus-specific transcriptional silencing. Since then, SIR2 and its homologs have been suggested to play additional roles in suppression of recombination, chromosomal stability, metabolic regulation, meiosis, and aging. Considering the far-ranging nature of these functions, a major experimental goal has been to understand the molecular mechanism(s) by which this family of proteins acts. We report here that members of the SIR2 family catalyze an NAD-nicotinamide exchange reaction that requires the presence of acetylated lysines such as those found in the N termini of histones. Significantly, these enzymes also catalyze histone deacetylation in a reaction that absolutely requires NAD, thereby distinguishing them from previously characterized deacetylases. The enzymes are active on histone substrates that have been acetylated by both chromatin assembly-linked and transcription-related acetyltransferases. Contrary to a recent report, we find no evidence that these proteins ADP-ribosylate histones. Discovery of an intrinsic deacetylation activity for the conserved SIR2 family provides a mechanism for modifying histones and other proteins to regulate transcription and diverse biological processes.
Identification and characterization of intracellular proteins that bind oligonucleotides with phosphorothioate linkages (2015)

Although the RNase H-dependent mechanism of inhibition of gene expression by chemically modified antisense oligonucleotides (ASOs) has been well characterized, little is known about the interactions between ASOs and intracellular proteins that may alter cellular localization and/or potency of ASOs. Here, we report the identification of 56 intracellular ASO-binding proteins using multi-step affinity selection approaches. Many of the tested proteins had no significant effect on ASO activity; however, some proteins, including La/SSB, NPM1, ANXA2, VARS and PC4, appeared to enhance ASO activities, likely through mechanisms related to subcellular distribution. VARS and ANXA2 co-localized with ASOs in endocytic organelles, and reduction in the level of VARS altered lysosome/ASO localization patterns, implying that these proteins may facilitate ASO release from the endocytic pathway. Depletion of La and NPM1 reduced nuclear ASO levels, suggesting potential roles in ASO nuclear accumulation. On the other hand, Ku70 and Ku80 proteins inhibited ASO activity, most likely by competition with RNase H1 for ASO/RNA duplex binding. Our results demonstrate that phosphorothioate-modified ASOs bind a set of cellular proteins that affect ASO activity via different mechanisms.
Semaphorin 3A Stimulates Neurite Extension and Regulates Gene Expression in PC12 Cells (2004)

The secreted semaphorin 3A (Sema3A) is a member of a large family of proteins that act as guidance signals for axons and dendrites. While the receptors and signaling pathways that mediate the repulsive effects of semaphorins are beginning to be understood in some detail, the mechanisms that are responsible for the ability of Sema3A to stimulate the extension of dendrites remain to be elucidated. Here we show that PC12 cells, a model widely used to study neuronal differentiation, can be used to dissect this pathway. Sema3A is as effective as nerve growth factor in stimulating the extension of neurites from PC12 cells. We show that Sema3A is able to regulate gene expression and identify mitochondria as a novel target of Sema3A signaling. Pharmacological block of mitochondrial reactive oxygen species production abolishes the extension of neurites in response to Sema3A. These results show that the characterization of transcripts that are regulated by axon guidance signals may help to identify novel components of their signaling pathways.
Spanning Large Workspaces Using Small Haptic Devices (2005)

Exploring large virtual environments using a small haptic device with limited-workspace capabilities is a challenging task because the user very quickly reaches the borders of the physical workspace of the device. In the case of a computer mouse, this problem is solved by lifting the device off the table and repositioning it at a different location. With most ground-based haptic devices such indexing procedure is not possible and requires the use of an additional switch to decouple the device from the cursor and allow the user to relocate the end-effector at the center of the physical workspace. Below certain physical workspace dimensions such indexing methods become cumbersome to the operator and therefore different control paradigms are required. This paper presents a new approach referred to as workspace drift control which progressively relocates the physical workspace of the device mapped inside the virtual environment towards the area of interest of the operator without disturbing his or her perception of the environment. This technique uses the fact that people are greatly influenced by what they perceive visually and often do not notice small deviations of their hand unless that small deviation has a corresponding visual component.
Characterization and Comparison of Disulfide Linkages and Scrambling Patterns in Therapeutic Monoclonal Antibodies: Using LC-MS with Electron Transfer Dissociation (2011)

The disulfides in three monoclonal antibodies (mAb), the anti-HER2, anti-CD11a, and GLP-1 with IgG4-Fc fusion protein, were completely mapped by LC-MS with the combination of electron-transfer dissociation (ETD) and collision induced dissociation (CID) fragmentation. In addition to mapping the 4 inter- and 12 intrachain disulfides (total 16), the identification of scrambled disulfides in degraded samples (heat-stress) was achieved. The scrambling was likely attributed to an initial breakage between the light (Cys 214) and heavy (Cys 223) chains in anti-HER2, with the same observation found in a similar therapeutic mAb, anti-CD11a. On the other hand, the fusion antibody, with no light chain but containing only two heavy chains, generated much less scrambling under the same heat-stressed conditions. The preferred sites of scrambling were identified, such as the intrachain disulfide for CxxC in the heavy chain, and the C194 of the heavy chain pairing with the terminal Cys residue (C214) in the light chain. The interchain disulfides between the light and heavy chains were weaker than the interchain disulfides between the two heavy chains. The relative high abundance ions observed in ETD provided strong evidence for the linked peptide information, which was particularly useful for the identification of the scrambled disulfides. The use of sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) helped the separation of these misfolded proteins for the determination of scrambled disulfide linkages. This methodology is useful for comparison of disulfide stability generated from different structural designs and providing a new way to determine the scrambling patterns, which could be applied for those seeking to determine unknown disulfide linkages.
Measurement of Cell Adhesion and Migration Using Phosphor-Screen Autoradiography (1996)

This study demonstrates the use of phosphor-screen autoradiography as a means of measuring cell adhesion and cell expansion on polymer surfaces. The method has particular merit in cases where a specific substrate may be opaque or biochemically incompatible with colorimetric assay methodologies. With the phosphor-screen autoradiography method, there was a linear relationship between cell number and quantitated radioactivity. The technique has also been validated by comparison with a colorimetric assay of adhesion conducted for attachment to conventional culture substrata. The data supported the view that the use of phosphor-screen autoradiography was a valid method for detecting cell attachment, and it gave equivalent results to the colorimetric assay. Furthermore, a comparison between phosphor-screen autoradiography and a dye-staining method showed that this technique can be used as a means of quantifying cellular expansion over surfaces.
Synaptic Connections and Small Circuits Involving Excitatory and Inhibitory Neurons in Layers 2-5 of Adult Rat and Cat Neocortex: Triple Intracellular Recordings and Biocytin Labelling In Vitro (2002)

Dual and triple intracellular recordings with biocytin labelling in slices of adult neocortex explored small circuits of synaptically connected neurons. 679 paired recordings in rat and 319 in cat yielded 135 and 42 excitatory postsynaptic potentials (EPSPs) and 37 and 26 inhibitory postsynaptic potentials (IPSPs), respectively. Patterns of connectivity and synaptic properties were similar in the two species, although differences of scale and in the range of morphologies were observed. Excitatory 'forward' projections from layer 4 to 3, like those from layer 3 to 5, targeted pyramidal cells and a small proportion of interneurons, while excitatory 'back' projections from layer 3 to 4 selected interneurons, including parvalbumin immuno-positive basket cells. Layer 4 interneurons that inhibited layer 3 pyramidal cells included both basket cells and dendrite-targeting cells. Large interneurons, resembling cells previously described as large basket cells, in layers 4 and 3 (cat), with long myelinated horizontal axon collaterals received frequent excitatory inputs from both layers. A very high rate of connectivity was observed between pairs of interneurons, often with quite different morphologies, and the resultant IPSPs, like the EPSPs recorded in interneurons, were brief compared with those recorded in pyramidal and spiny stellate cells.