gebhart/patrepeval huggingface dataset:
Chimeric Restriction Enzymes: What Is Next? (1999)

Chimeric restriction enzymes are a novel class of engineered nucleases in which the non-specific DNA cleavage domain of Fokl (a type IIS restriction endonuclease) is fused to other DNA-binding motifs. The latter include the three common eukaryotic DNA-binding motifs, namely the helix-turn-helix motif, the zinc finger motif and the basic helix-loop-helix protein containing a leucine zipper motif. Such chimeric nucleases have been shown to make specific cuts in vitro very close to the expected recognition sequences. The most important chimeric nucleases are those based on zinc finger DNA-binding proteins because of their modular structure. Recently, one such chimeric nuclease, Zif-QQR-F(N) was shown to find and cleave its target in vivo. This was tested by microinjection of DNA substrates and the enzyme into frog oocytes (Carroll et al., 1999). The injected enzyme made site-specific double-strand breaks in the targets even after assembly of the DNA into chromatin. In addition, this cleavage activated the target molecules for efficient homologous recombination. Since the recognition specificity of zinc fingers can be manipulated experimentally, chimeric nucleases could be engineered so as to target a specific site within a genome. The availability of such engineered chimeric restriction enzymes should make it feasible to do genome engineering, also commonly referred to as gene therapy.
Site-Specific, Thiol-Mediated Conjugation of Fluorescent Probes to Cysteine-Modified Diabodies Targeting CD20 or HER2 (2008)

Small, engineered antibody fragments such as diabodies (50 kDa noncovalent dimers of single-chain Fv fragments) are useful alternatives to their larger antibody counterparts. However, due to their size, they are more susceptible to disruption of their antigen binding sites when modified using random conjugation techniques. Previous work has demonstrated the utility of a C-terminal cysteine modification for site-specific radiolabeling of an anti-CEA diabody, resulting in the creation of a cys-diabody (CysDb). In the present work, the adaptability of the CysDb system was explored by creating two additional CysDbs: one specific for CD20 and one for HER2. Purified CysDbs of both specificities demonstrated behavior consistent with stable, covalent dimers harboring a readily reducible disulfide bond. Each CysDb was site-specifically conjugated to three different fluorophores for optical detection: the large fluorescent proteins phycoerythrin (PE) and allophycocyanin (APC), and the small fluorescent molecule Alexa Fluor488. Fluorophore-conjugated CysDbs bound specifically to their targets in both antigen systems and with each different fluorescent tag as determined by flow cytometry. In vitro specific antigen binding was observed in the presence of a mixture of specific and nonspecifically conjugated CysDbs. Conjugates retained both specificity and fluorescence, demonstrating the successful expansion of the CysDb repertoire to new targets and to new site-specific conjugation possibilities.
Matrix metalloproteinase-9 (MMP-9) is synthesized in neurons of the human hippocampus and is capable of degrading the amyloid-beta peptide (1-40). (1996)

We reported earlier that the levels of Ca2+-dependent metalloproteinases are increased in Alzheimer's disease (AD) specimens, relative to control specimens. Here we show that these enzymes are forms of the matrix metalloproteinase MMP-9 (EC3.4.24. 35) and are expressed in the human hippocampus. Affinity-purified antibodies to MMP-9 labeled pyramidal neurons, but not granular neurons or glial cells. MMP-9 mRNA is expressed in pyramidal neurons, as determined with digoxigenin-labeled MMP-9 riboprobes, and the presence of this mRNA is confirmed with reverse transcriptase PCR. The cellular distribution of MMP-9 is altered in AD because 76% of the total 100 kDa enzyme activity is found in the soluble fraction of control specimens, whereas only 51% is detectable in the same fraction from AD specimens. The accumulated 100 kDa enzyme from AD brain is latent and can be converted to an active form with aminophenylmercuric acetate. MMP-9 also is detected in close proximity to extracellular amyloid plaques. Because a major constituent of plaques is the 4 kDa beta-amyloid peptide, synthetic Abeta1-40 was incubated with activated MMP-9. The enzyme cleaves the peptide at several sites, predominantly at Leu34-Met35 within the membrane-spanning domain. These results establish that neurons have the capacity to synthesize MMP-9, which, on activation, may degrade extracellular substrates such as beta-amyloid. Because the latent form of MMP-9 accumulates in AD brain, it is hypothesized that the lack of enzyme activation contributes to the accumulation of insoluble beta-amyloid peptides in plaques.
In Vivo and In Vitro Antiarrhythmic Effects of SSR149744C in Animal Models of Atrial Fibrillation and Ventricular Arrhythmias (2005)

SSR149744C (2-butyl-3-{4-[3-(dibutylamino)propyl]benzoyl}-1-benzofuran-5-carboxylate isopropyl fumarate) is a new noniodinated benzofuran derivative structurally related to amiodarone and dronedarone that is currently undergoing clinical trials as an antiarrhythmic agent. As SSR149744C exhibits electrophysiological and hemodynamic properties of class I, II, III, and IV antiarrhythmic agents, the aim of this study was to evaluate its acute intravenous (IV) or oral (PO) antiarrhythmic activities in in vitro and in vivo animal models of atrial and ventricular arrhythmias. In vagally induced atrial fibrillation (AF) in anesthetized dogs, SSR149744C (3 and 10 mg/kg IV) terminated AF in all 7 dogs and prevented reinduction in 4 out of 7 dogs; effective refractory periods of right atrium were dose-dependently and frequency-independently lengthened. In low-K+ medium-induced AF models, SSR149744C (0.1 to 1 microM) prevented AF in isolated guinea pig hearts in a concentration-dependent manner. At the ventricular level, SSR149744C (0.1 to 10 mg/kg IV and 3 to 90 mg/kg PO) prevented reperfusion-induced arrhythmias in anesthetized rats with a dose-effect relationship, and, at doses of 30 to 90 mg/kg PO, it reduced early (0-24 hours) mortality following permanent left coronary artery ligature in conscious rats. The present results show that SSR149744C is an effective antiarrhythmic agent in atrial fibrillation and in ventricular arrhythmias. Like amiodarone and dronedarone, its efficiency in these animal models of arrhythmias is likely be related to its multifactorial mechanism of action.
An analysis of the temperature dependence of force, during steady shortening at different velocities, in (mammalian) fast muscle fibres (2008)

We examined, over a wide range of temperatures (10–35°C), the isometric tension and tension during ramp shortening at different velocities (0.2–4 L 0/s) in tetanized intact fibre bundles from a rat fast (flexor hallucis brevis) muscle; fibre length (L 0) was 2.2 mm and sarcomere length ~2.5 μm. During a ramp shortening, the tension change showed an initial inflection of small amplitude (P 1), followed by a larger exponential decline towards an approximate steady level; the tension continued to decline slowly afterwards and the approximate steady tension at a given velocity was estimated as the tension (P 2) at the point of intersection between two linear slopes, as previously described (Roots et al. 2007). At a given temperature, the tension P 2 declined to a lower level and at a faster rate (from an exponential curve fit) as the shortening velocity was increased; the temperature sensitivity of the rate of tension decline during ramp shortening at different velocities was low (Q 10 0.9–1.5). The isometric tension and the P 2 tension at a given shortening velocity increased with warming so that the relation between tension and (reciprocal) temperature was sigmoidal in both. In isometric muscle, the temperature T 0.5 for half-maximal tension was ~10°C, activation enthalpy change (∆H) was ~100 kJ mol−1 and entropy change (∆S) ~350 J mol−1 K−1. In shortening, these were increased with increase of velocity so that at a shortening velocity (~4 L 0/s) producing maximal power at 35°C, T 0.5 was ~28°C, ∆H was ~200 kJ mol−1 and ∆S ~ 700 J mol−1 K−1; the same trends were seen in the tension data from isotonic release experiments on intact muscle and in ramp shortening experiments on maximally Ca-activated skinned fibres. In general, our findings show that the sigmoidal relation between force and temperature can be extended from isometric to shortening muscle; the implications of the findings are discussed in relation to the crossbridge cycle. The data indicate that the endothermic, entropy driven process that underlies crossbridge force generation in isometric muscle (Zhao and Kawai 1994; Davis, 1998) is even more pronounced in shortening muscle, i.e. when doing external work.
Histone hyperacetylation can induce unfolding of the nucleosome core particle (1990)

A direct correlation exists between the level of histone H4 hyperacetylation induced by sodium butyrate and the extent to which nucleosomes lose their compact shape and become elongated (62.0% of the particles have a length/width ratio over 1.6; overall mean in the length/width ratio = 1.83 +/- 0.48) when bound to electron microscope specimen grids at low ionic strength (1mM EDTA, 10mM Tris, pH 8.0). A marked proportion of elongated core particles is also observed in the naturally occurring hyperacetylated chicken testis chromatin undergoing spermatogenesis when analyzed at low ionic strength (36.8% of the particles have a length/width ratio over 1.6). Core particles of elongated shape (length/width ratio over 1.6) generated under low ionic strength conditions are absent in the hypoacetylated chicken erythrocyte chromatin and represent only 2.3% of the untreated Hela S3 cell core particles containing a low proportion of hyperacetylated histones. The marked differences between control and hyperacetylated core particles are absent if the particles are bound to the carbon support film in the presence of 0.2 M NaCl, 6mM MgCl2 and 10mM Tris pH 8.0, conditions known to stabilize nucleosomes. A survey of the published work on histone hyperacetylation together with the present results indicate that histone hyperacetylation does not produce any marked disruption of the core particle 'per se', but that it decreases intranucleosomal stabilizing forces as judged by the lowered stability of the hyperacetylated core particle under conditions of shearing stress such as cationic competition by the carbon support film of the EM grid for DNA binding.
Adult skeletal muscle stem cells differentiate into endothelial lineage and ameliorate renal dysfunction after acute ischemia (2004)

We previously demonstrated that endothelial cells are severely damaged during renal ischemia-reperfusion and that transplantation of adult human endothelial cells into athymic nude rats subjected to renal ischemia resulted in a dramatic protection of the kidney against injury and dysfunction. Morphological studies demonstrated the engraftment of transplanted cells into renal microvasculature. The goal of the present study was to determine the potential efficacy of in vitro expanded skeletal muscle-derived stem cells (MDSC) differentiated along the endothelial lineage in ameliorating acute renal injury. MDSC obtained from the Tie-2-green fluorescent protein (GFP) mice were used as donors of differentiated and nondifferentiated stem cells. FVB mice, used as recipients, were subjected to renal ischemia and transplanted with the above MDSC. The differentiation of MDSC along the endothelial lineage was monitored by the appearance of Tie-2 promotor-driven expression of GFP. These mouse endothelial cell antigen-, endothelial nitric oxide synthase (eNOS)-, Flk-1-, Flt-1-, and CD31-positive cells engrafted into renal microvasculature and significantly protected short-term renal function after ischemia. Transplantation of nondifferentiated MDSC characterized by the expression of Sca-1 (low levels of CD34, Flk-1, and cKit, and negative for GFP, eNOS, and CD31) did not improve short-term renal dysfunction. In conclusion, the data 1) provide a rich source of MDSC, 2) delineate protocols for their in vitro expansion and differentiation along the endothelial lineage, and 3) demonstrate their efficacy in preserving renal function immediately after ischemic insult.
Das gottförmige Vakuum (2011)

Im Allgemeinen wird der französische Philosoph Blaise Pascal als Urheber der Idee von einem „gottförmigen Vakuum“ genannt. In seinen im 17. Jahrhundert erschienenen Pensées beschreibt er einen im Inneren jedes Menschen vorhandenen grenzenlosen Abgrund, eine Leere, die danach strebt, gefüllt zu werden. Das Konzept reicht aber viel weiter in die Vergangenheit, nämlich bis zu den Ursprüngen des Lebens auf der Erde. Nach Ansicht vieler Menschen ging die Entstehung des religiösen Impulses — jenes mächtigen Bedürfnisses, im Dasein einen tieferen Sinn zu finden — Hand in Hand mit der Entstehung der Menschheit.
Characterization of the allosteric modulatory protein associated with non-NMDA receptors (1993)

Conference Article| February 01 1993 Characterization of the allosteric modulatory protein associated with non-NMDA receptors Jeremy M. Henley Jeremy M. Henley 1Department of Pharmacology, Medical School, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K. Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1993) 21 (1): 89–93. https://doi.org/10.1042/bst0210089 Article history Received: July 27 1992 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 Jeremy M. Henley; Characterization of the allosteric modulatory protein associated with non-NMDA receptors. Biochem Soc Trans 1 February 1993; 21 (1): 89–93. doi: https://doi.org/10.1042/bst0210089 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 Society Transactions Search Advanced Search Keywords: AMPA, α-amino-3-hydroxy-5-methylisoxazolepropionate, CaM, Ca2+/calmodulin-dependent kinase, CNS, central nervous system, GluR, glutamate receptor, GluR-MP, glutamate receptor modulatory protein, LTP, long-term potentiation, NMDA, N-methyl-D-aspartate, OG, n-octyl-β-glucopyranoside, PKC, protein kinase C This content is only available as a PDF. © 1993 Biochemical Society1993 Article PDF first page preview Close Modal You do not currently have access to this content.
Raman imaging as a probe of chemical and biomechanical properties of bone tissue (2000)

Raman microspectroscopy and imaging can be used to probe the chemical properties of newly mineralized bone tissue. In this study, our early mineralization models are neonatal murine cranial suture tissue and prostate cancer cell cultures. The murine cranial tissue was harvested from animals three weeks postnatal. On this time scale, remodeling does not corrupt the temporal record inherent in the spatial distribution of mineral species. When analyzing transects, line images, of the cranial tissue, multivariate data processing is required to generate chemical state plots from the hundreds of Raman spectra acquired during a single transect experiment. In most cranial tissue specimens more than one phosphate mineral environment is observed, allowing inferences on the relation between chemical structure and physiologically important properties. The prostate cancer cell cultures were cultured for up to nine days. Point microspectroscopy reveals the ratios of mineral species present and the amount of protein species in the cell cultures changes dramatically over the course of 9 days. Very low carbonation, typical of early-mineralized tissue, is observed in both of these models.
The Drosophila Polycomb Group proteins ESC and E(Z) are present in a complex containing the histone-binding protein p55 and the histone deacetylase RPD3 (2001)

The Drosophila Polycomb Group (PcG) proteins are required for stable long term transcriptional silencing of the homeotic genes. Among PcG genes, esc is unique in being critically required for establishment of PcG-mediated silencing during early embryogenesis, but not for its subsequent maintenance throughout development. We previously showed that ESC is physically associated in vivo with the PcG protein E(Z). We report here that ESC, together with E(Z), is present in a 600 kDa complex that is distinct from complexes containing other PcG proteins. We have purified this ESC complex and show that it also contains the histone deacetylase RPD3 and the histone-binding protein p55, which is also a component of the chromatin remodeling complex NURF and the chromatin assembly complex CAF-1. The association of ESC and E(Z) with p55 and RPD3 is conserved in mammals. We show that RPD3 is required for silencing mediated by a Polycomb response element (PRE) in vivo and that E(Z) and RPD3 are bound to the Ubx PRE in vivo, suggesting that they act directly at the PRE. We propose that histone deacetylation by this complex is a prerequisite for establishment of stable long-term silencing by other continuously required PcG complexes.
Hypoxia and Serum Deprivation-Induced Apoptosis in Mesenchymal Stem Cells (2005)

In recent years, the understanding that regeneration progresses at the level of the myocardium has placed stem cell research at the center stage in cardiology. Despite an increasing interest in cell transplant research, relatively little is known about the biochemical regulation of the stem cell itself after transplantation into an ischemic heart. We demonstrated here, using rat mesenchymal stem cells (MSCs), that cells undergo caspase-dependent apoptosis in response to hypoxia and serum deprivation (SD), which are both components of ischemia in vivo. In particular, the treated cells exhibited mitochondrial dysfunction, including cytochrome C release, loss in DeltaPsim, and Bax accumulation, but in a p53-independent manner. Although the cells treated by hypoxia/SD possess the activity of caspase-8, zIEDT-fmk, a specific caspase-8 inhibitor, failed to inhibit cell apoptosis induced in our system. Taken together, our findings indicate that MSCs are sensitive to hypoxia/SD stimuli that involve changes in mitochondrial integrity and function but are potentially independent of caspase-8.
Targeted homologous recombination at the endogenous adenine phosphoribosyltransferase locus in Chinese hamster cells. (1989)

We have developed a system that permits analysis of targeted homologous recombination at an endogenous, chromosomal gene locus in cultured mammalian cells. Using a hemizygous, adenine phosphoribosyltransferase (APRT)-deficient, Chinese hamster ovary (CHO) cell mutant as a transfection recipient, we have demonstrated correction of a nonrevertible deletion mutation by targeted homologous recombination. Transfection with a plasmid carrying a fragment of the APRT gene yielded APRT+ recombinants at a frequency of approximately 4.1 x 10(-7). The ratio of targeted recombination to nontargeted integrations of plasmid sequences was approximately 1:4000. Analysis of 31 independent APRT+ recombinants revealed conversions of the endogenous APRT gene, targeted integration at the APRT locus, and a third class of events in which the plasmid donor APRT fragment was converted to a full-length, functional gene.
Weighing DNA for Fast Genetic Diagnosis (1998)

BIOTECHNOLOGYA fast new way to analyze gene sequences vaporizes the DNA and accelerates the molecules through a vacuum chamber; tiny differences in the time it takes the DNA fragments to reach the detector reveal small differences in their mass, and hence their sequence. Recent advances in a decade-old mass spectrometry technique called MALDI-TOF are now being used to analyze hundreds of DNA samples of up to 100 base pairs each in a matter of minutes. The technique could one day let doctors determine which disease genes a patient carries as quickly and accurately as they can now perform a cholesterol or blood chemistry test.
Effect of density variation and non-covalent functionalization on the compressive behavior of carbon nanotube arrays (2011)

Arrays of aligned carbon nanotubes (CNTs) have been proposed for different applications, including electrochemical energy storage and shock-absorbing materials. Understanding their mechanical response, in relation to their structural characteristics, is important for tailoring the synthesis method to the different operational conditions of the material. In this paper, we grow vertically aligned CNT arrays using a thermal chemical vapor deposition system, and we study the effects of precursor flow on the structural and mechanical properties of the CNT arrays. We show that the CNT growth process is inhomogeneous along the direction of the precursor flow, resulting in varying bulk density at different points on the growth substrate. We also study the effects of non-covalent functionalization of the CNTs after growth, using surfactant and nanoparticles, to vary the effective bulk density and structural arrangement of the arrays. We find that the stiffness and peak stress of the materials increase approximately linearly with increasing bulk density.
Role of PACAP in migraine headaches (2014)

In the current issue of Brain, Amin and colleagues report their investigation of the incidence of migraine attacks, the changes in diameter of selected extra-and intracranial arteries and the changes in the plasma levels of pituitary adenylate cyclase-activating polypeptide-38 (PACAP-38) and vasoactive intestinal peptide (VIP) after the infusion of VIP and PACAP-38.Such an investigation is essential for migraine research, because it comprises a head-tohead comparison of the vascular and biochemical responses of these peptides with longlasting observations of migraine attacks.The authors reported that 73% (n=16) and 18% (n=4) of their patients developed migraine-like attacks after PACAP-38 and after VIP infusion, respectively.Three of the four patients who developed migraine-like headache after VIP administration also reported attacks after PACAP-38 treatment.This study elegantly demonstrated that PACAP-38 infusion induces more migraine headache attacks than VIP.VIP and PACAP-38 are potent vasodilators of cerebral and dural arteries.All three receptors for VIP/PACAP are present on cranial arteries.Amin et al. observed that both neuropeptides caused pronounced dilations of the extracranial (the superficial temporal artery, the middle
Wnt-11 signalling controls ventricular myocardium development by patterning N-cadherin and β-catenin expression (2009)

We conclude that Wnt-11 signalling serves as a critical cell adhesion cue for the organization of the cardiomyocytes in the developing ventricular wall, which is essential for the establishment of a functional heart.
A low-noise self-calibrating dynamic comparator for high-speed ADCs (2008)

This paper presents a low offset voltage, low noise dynamic latched comparator using a self-calibrating technique. The new calibration technique does not require any amplifiers for the offset voltage cancellation and quiescent current. It achieves low offset voltage of 1.69 mV at 1 sigma in low power consumption, while 13.7 mV is measured without calibration. Furthermore the proposed comparator requires only one phase clock while conventionally two phase clocks were required leading to relaxed clock. Moreover, a low input noise of 0.6 mV at 1 sigma, three times lower than the conventional one, is obtained. Prototype comparators are realized in 90 nm 10M1P CMOS technology. Experimental and simulated results show that the comparator achieves 1.69 mV offset at 250 MHz operating, while dissipating 40 μW/GHz ( 20 fJ/conv. ) from a 1.0 V supply.