gebhart/patrepeval huggingface dataset:
Carbon Nanotubes Protect DNA Strands during Cellular Delivery (2008)

To protect against nuclease digestion, or single-strand binding protein interactions, oligonucleotides for targeted delivery into intracellular systems must be stable. To accomplish this, we have developed single-walled carbon nanotubes as a carrier for single-stranded DNA probe delivery. This has resulted in superior biostability for intracellular application and, hence, has achieved the desired protective attributes, which are particularly important when DNA probes are used for intracellular measurements. Specifically, when bound to single-walled carbon nanotubes, DNA probes are protected from enzymatic cleavage and interference from nucleic acid binding proteins. Moreover, and equally important, our study shows that a single-walled carbon nanotube-modified DNA probe, which targets a specific mRNA inside living cells, has increased self-delivery capability and intracellular biostability when compared to free DNA probes. Therefore, this new conjugate provides significant advantages for basic genomic studies in which DNA probes are used to monitor intracellular levels of molecules.
Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis (2009)

Differentiation of mouse embryonic stem cells (mESCs) is accompanied by changes in replication timing. To explore the relationship between replication timing and cell fate transitions, we constructed genome-wide replication-timing profiles of 22 independent mouse cell lines representing 10 stages of early mouse development, and transcription profiles for seven of these stages. Replication profiles were cell-type specific, with 45% of the genome exhibiting significant changes at some point during development that were generally coordinated with changes in transcription. Comparison of early and late epiblast cell culture models revealed a set of early-to-late replication switches completed at a stage equivalent to the post-implantation epiblast, prior to germ layer specification and down-regulation of key pluripotency transcription factors [POU5F1 (also known as OCT4)/NANOG/SOX2] and coinciding with the emergence of compact chromatin near the nuclear periphery. These changes were maintained in all subsequent lineages (lineage-independent) and involved a group of irreversibly down-regulated genes, at least some of which were repositioned closer to the nuclear periphery. Importantly, many genomic regions of partially reprogrammed induced pluripotent stem cells (piPSCs) failed to re-establish ESC-specific replication-timing and transcription programs. These regions were enriched for lineage-independent early-to-late changes, which in female cells included the inactive X chromosome. Together, these results constitute a comprehensive "fate map" of replication-timing changes during early mouse development. Moreover, they support a model in which a distinct set of replication domains undergoes a form of "autosomal Lyonization" in the epiblast that is difficult to reprogram and coincides with an epigenetic commitment to differentiation prior to germ layer specification.
cAMP‐induced differentiation of human neuronal progenitor cells is mediated by nuclear fibroblast growth factor receptor‐1 (FGFR1) (2003)

Activation of cAMP signaling pathway and its transcriptional factor cyclic AMP response element binding protein (CREB) and coactivator are key determinants of neuronal differentiation and plasticity. We show that nuclear fibroblast growth factor receptor-1 (FGFR1) mediates cAMP-induced neuronal differentiation and regulates CREB and CREB binding protein (CBP) function in alpha-internexin-expressing human neuronal progenitor cells (HNPC). In proliferating HNPC, FGFR1 was associated with the cytoplasm and plasma membrane. Treatment with dB-cAMP induced nuclear accumulation of FGFR1 and caused neuronal differentiation, accompanied by outgrowth of neurites expressing MAP2 and neuron-specific neurofilament-L protein and enolase. HNPC transfected with nuclear/cytoplasmic FGFR1 or non-membrane FGFR1(SP-/NLS), engineered to accumulate exclusively in the cell nucleus, underwent neuronal differentiation in the absence of cAMP stimulation. In contrast, FGFR1/R4, with highly hydrophobic transmembrane domain of FGFR4, was membrane associated, did not enter the nucleus and failed to induce neuronal differentiation. Transfection of tyrosine kinase-deleted dominant negative receptor mutants, cytoplasmic/nuclear FGFR1(TK-) or nuclear FGFR1(SP-/NLS)(TK-), prevented cAMP-induced neurite outgrowth. Nuclear FGFR1 localized in speckle-like domains rich in phosphorylated histone 3 and splicing factors, regions known for active RNA transcription and processing, and activated the neurofilament-L gene promoter. FGFR1(SP-/NLS) transactivated CRE, up-regulated phosphorylation and transcriptional activity of CREB and stimulated the activity of CBP several-fold. Thus, cAMP-induced nuclear accumulation of FGFR1 provides a signal that triggers molecular events leading to neuronal differentiation.
Localization of vitronectin binding domain in plasminogen activator inhibitor-1. (1994)

Plasminogen activator inhibitor type 1 (PAI-1) is the rapid physiologic inhibitor of tissue-type plasminogen activator and urokinase-type plasminogen activator (uPA). In plasma and the extracellular matrix, PAI-1 is associated with the adhesive glycoprotein vitronectin. In order to characterize the PAI-1 structural domain responsible for binding to vitronectin, the segment of the PAI-1 cDNA encoding amino acids 13-147 (nucleotides 248-650) was randomly mutagenized and subcloned into a bacterial expression vector containing the mature PAI-1 coding sequence. Recombinant PAI-1 mutants were expressed in Escherichia coli and bacterial lysates assayed in duplicate for uPA inhibitory activity and vitronectin binding. Of 190 clones screened, six consistently demonstrated decreased vitronectin binding relative to uPA inhibitory activity. DNA sequence analysis of four of these clones identified 10 unique missense mutations, all located between base pairs 298 and 641, with each clone containing between one and four substitutions. Each substitution was expressed independently by site-directed mutagenesis and again analyzed for uPA inhibitory activity and vitronectin binding. Five point mutations that selectively disrupt vitronectin binding were identified. All 5 residues are located on the exterior of the PAI-1 structure. These findings appear to define a complex binding surface that bridges alpha-helices C and E to beta-strand 1A and includes amino acids 55, 109, 110, 116, and 123. These results suggest that vitronectin binding may stabilize the active conformation of PAI-1 by restricting the movement of beta-sheet A and thereby preventing insertion of the reactive center loop.
Chemical Synthesis of Oligonucleotides (2005)

It can fairly be said that synthetic oligonucleotides are the fuel that drives the engine of molecular biology. Nearly every technique in use today in molecular biology employs chemically synthesized DNAs or RNAs. This includes PCR, Real-Time PCR, DNA sequencing, site directed mutagenesis, single-nucleotide polymorphism (SNP) assays, microarrays, and the rapidly expanding world of small RNAs. Unlike other reagents, however, oligonucleotides are not stock items that can be stored, warehouse fashion, until needed. Each oligonucleotide is custom made according to the specific needs of the individual researcher and purified according to the application for which it is intended.
Probe-based electrochemical fabrication of freestanding Cu nanowire array (2006)

We demonstrate the fabrication of individual Cu nanowires with a probe-based electrochemical deposition method. The electrolyte used for the electrochemical deposition was carried within a pipette probe, which eliminated the need for a plating bath and created a clean environment for the continuous fabrication of nanostructures. The fabrication of vertically aligned, solid, polycrystalline Cu nanowire arrays was realized, with the Cu nanowires having diameters down to 200nm and lengths up to 10μm.
Multicomponent DNA Carrier with a Vesicular Stomatitis Virus G-Peptide Greatly Enhances Liver-Targeted Gene Expression in Mice (1999)

Genes can be targeted to hepatocytes in vitro and in vivo by the use of asialoorosomucoid-polylysine conjugates. After systemic application, this nonviral vector is recognized by highly selective asialoglycoprotein (AsGP) receptors on the sinusoidal liver cell membrane and is taken up via receptor-mediated endocytosis. As most of the DNA is rapidly transferred to lysosomes where it is degraded, transfection efficiency is low and gene expression transient. To address this problem, we incorporated a pH-dependent synthetic hemolytic peptide derived of the G-protein of Vesicular Stomatitis Virus (VSV) into the gene transfer system, to increase endosomal escape of internalized DNA. The multicomponent carrier binds DNA in a nondamaging way, is still recognized by the AsGP receptor, and is targeted to the liver in vivo. Injection of DNA complexes containing a luciferase marker gene resulted in luciferase expression of 29 000 pg/g liver which corresponded to an increase of a factor of 10(3) overexpression after injection of DNA complexes without endosomolytic peptide. Furthermore, the amount of intact transgene within isolated liver cell nuclei was increased by a factor of 10(1)-10(2) by the use of the multicomponent carriers. These results demonstrate that incorporation of a hemolytic peptide into a nonviral vector can greatly increase gene expression while retaining cell type targetability in vivo.
A Gas-phase Electrochemical Reactor for Carbon Dioxide Reduction back to Liquid Fuels (2013)

We discussed here on a novel approach to recycle CO2 back to liquid fuels by using nanostructured carbon-based materials (doped with suitable metal nanoparticles) as electrocatalysts. This approach is based on the development of a new photo-electrocatalytic (PEC) reactor, working in gas phase, which is quite different from the conventional reactors that operate typically in aqueous slurry and/or in batch. Gas phase operation, under solvent-less conditions, has many advantages (easy recovery of the products, no problems of CO2 solubility, etc.) with respect to liquid phase. The reaction mechanism is also quite different and longer chains of products can be obtained. In particular we investigated the competition of the side reaction of H2 formation by water electrolysis (which is unavoidable in such kinds of systems) with the CO2 reduction process. The understanding of this competitive reaction is very significant in order to maximize the process performances. Moreover the capability to develop advanced nanostructured electrodes, by modulating their properties during the synthesis, allowed to improve the efficiency of the CO2 reduction process, enhancing the productivity and tuning the selectivity towards higher chain hydrocarbons and other chemicals. The CO2 reduction to liquid fuels by solar energy represents an attractive solution which may contribute to the alternative use of clean and renewable sources to cope with the depletion of fossil fuels. The target is to develop a sort of “artificial leaf” which may collect the solar energy as the nature does, by capturing directly CO2 and converting it back to fuels.
A microbial factory for lactate-based polyesters using a lactate-polymerizing enzyme (2008)

Polylactate (PLA) is synthesized as a representative bio-based polyester by the chemo-bio process on the basis of metal catalyst-mediated chemical polymerization of lactate (LA) supplied by microbial fermentation. To establish the one-step microbial process for synthesis of LA-based polyesters, we explored whether polyhydroxyalkanoate (PHA) synthase would exhibit polymerizing activity toward a LA-coenzyme A (CoA), based on the fact that PHA monomeric constituents, especially 3-hydroxybutyrate (3HB), are structurally analogous to LA. An engineered PHA synthase was discovered as a candidate by a two-phase in vitro polymerization system previously developed. An LA-CoA producing Escherichia coli strain with a CoA transferase gene was constructed, and the generation of LA-CoA was demonstrated by capillary electrophoresis/MS analysis. Next, when the engineered PHA synthase gene was introduced into the resultant recombinant strain, we confirmed the one-step biosynthesis of the LA-incorporated copolyester, P(6 mol% LA-co-94 mol% 3HB), with a number-average molecular weight of 1.9 x 10(5), as revealed by gel permeation chromatography, gas chromatography/MS, and NMR.
The nerve supply to the human lumbar intervertebral discs. (1981)

The lumbar intervertebral discs are supplied by a variety of nerves. The posterior aspects of the discs and the posterior longitudinal ligament are innervated by the sinuvertebral nerves. The posterolateral aspects of the discs receive branches from adjacent ventral primary rami and from the grey rami communicantes near their junction with the ventral primary rami. The lateral aspects of the discs receive other branches from the rami communicantes. Some rami communicantes cross intervertebral discs and are embedded in the connective tissue of the disc deep to the origin of psoas. Such paradiscal rami are likely to be another source of innervation to the discs. The anterior longitudinal ligament is innervated by recurrent branches of rami communicantes.
Rapid Identification of Staphylococcus aureus and the mecA Gene from BacT/ALERT Blood Culture Bottles by Using the LightCycler System (2002)

One hundred BacT/ALERT blood culture bottles growing gram-positive cocci in clusters were cultured and studied by LightCycler PCR for the sa442 and mecA genes. PCR was 100% sensitive and specific for detecting Staphylococcus aureus and methicillin resistance in S. aureus but was less accurate for methicillin resistance in coagulase-negative staphylococci.
Sulphated Sugar Alpha-Cyclodextrin Sulphate, a Uniquely Potent Anti-HIV Agent, Also Exhibits Marked Synergism with AZT, and Lymphoproliferative Activity (1990)

Sulphated sugars, alpha-cyclodextrin sulphate (A-CDS), sodium pentosan polysulphate (PPS), and beta-cyclodextrin sulphate (B-CDS) were evaluated for their inhibitory effect on the replication of human immunodeficiency virus (HIV-1) in normal human peripheral blood mononuclear cells (PMNCs). All three drugs had potent anti-HIV activity, A-CDS being the most potent. A-CDS, PPS and B-CDS were also tested for their direct inhibitory effect on reverse transcriptase (RT) in vitro. PPS inhibited the RT reaction at 4.0 μg ml −1 and above whereas B-CDS and A-CDS did not. The drugs were not cytotoxic up to 100 μg ml −1 and also showed significant lymphoproliferative activities. PPS and B-CDS exhibited higher lymphoproliferative activity than A-CDS. A-CDS, B-CDS, and PPS showed profound antiviral synergism with AZT. An additive anti-HIV effect, rather than a synergestic effect, was observed between the sulphated sugars. Thus, these sulphated sugars, because of their nontoxic nature, lymphoproliferative activity and anti-HIV activity at low concentrations, may be valuable chemotherapeutic agents in the treatment of AIDS. In particular, A-CDS, because of its marked anti-HIV synergism with AZT (which would lower the required dose of AZT in vivo), could result in an efficacious and essentially nontoxic combination chemotherapy for AIDS.
Effects of L-carnitine on exercise tolerance in chronic stable angina: a multicenter, double-blind, randomized, placebo controlled crossover study. (1985)

L-carnitine was studied in forty-four men with stable chronic angina in a multicenter, double-blind, randomized, placebo controlled crossover trial. A cycloergometer exercise test was performed after a 10-day wash-out with placebo and at the end of each 4-week treatment period with either L-carnitine (1 g twice daily) or placebo. The mean (+/- SD) exercise work load showed an increase after L-carnitine compared to placebo (102.73 +/- 22.23 and 97.05 +/- 22.77 watts respectively, p = 0.001), as did the watts to onset of angina (95.7 +/- 24.07 and 87.44 +/- 24.67, p = 0.000). On the contrary, the ST segment depression was reduced by L-carnitine compared to placebo both at the maximum work load (1.40 +/- 0.90 and 1.69 +/- 0.82 mm, p = 0.05) and at the maximum work load common to L-carnitine and placebo (1.24 +/- 0.90 and 1.66 +/- 0.79 mm, p = 0.005). 22.7% of the patients became free of angina with L-carnitine and 9.1% with placebo. Resting and exercise blood pressure, heart-rate and double product were unaffected by L-carnitine. 1 patient decided to discontinue the trial because of gastric pyrosis while taking the active drug. The results of this study show that treatment with L-carnitine increases exercise tolerance and reduces ECG indices of ischemia in stable effort-induced angina.
Asymmetric Synthesis of Oxygen Heterocycles via Pd‐Catalyzed Dynamic Kinetic Asymmetric Transformations: Application to Nucleosides (2003)

Racemic butadiene and isoprene monoepoxide react with unsaturated alcohols in the presence of a chiral palladium catalyst and a boron co-catalyst to give 3-alkoxy-4-hydroxy-1-butene and 3-alkoxy-4-hydroxy-3-methyl-1-butene, respectively, with excellent regio- and enantioselectivity in a dynamic kinetic asymmetric transformation whereby both enantiomers of the starting epoxides provide the same enantiomeric product. In the case of 2-phenylbutadiene monoepoxide, easily available from phenacyl chloride and vinylmagnesium bromide, the reaction proceeds by kinetic resolution. A model to rationalize the result is presented. The bis-olefin products are ideal substrates for the Ru catalyzed ring closing metathesis. In this way, five-, six-, and seven-membered oxygen heterocycles are readily available enantiomerically pure. The value of this very simple two step process is demonstrated by the use of the five-membered ring heterocycles to form unnatural and unusual nucleosides that cannot be easily accessed by other means. The sequence involves a Ru catalyzed isomerization of the initial 2,5-dihydrofuran to a 2,3-dihydrofuran followed by a selenium promoted addition of a pyrimidine or purine base. One advantage of this strategy is the easy access to either enantiomeric series, both of which have important biological applications.
Determination of strain state and composition of highly mismatched group-III nitride heterostructures by x-ray diffraction (2002)

We present an accurate model for the dynamical x-ray diffraction analysis of highly mismatched materials systems. Our approach features an exact incidence parameter as well as an exact calculation of the changes of Bragg angle and lattice plane inclination due to strain. We show that the commonly used approximations for these parameters are, in general, unable to describe diffraction profiles of different reflections consistently, and utterly fail for a strain on the order of 1% or more. The model as presented explicitly considers crystals with zincblende and wurtzite structure of arbitrary orientation and the resulting distortions. The validity of our model is demonstrated by various experimental examples, including closely lattice-matched GaAs/AlAs structures on GaAs(001) and GaAs(113), as well as highly mismatched GaN layers, (Al, Ga)N/GaN and GaN/(In, Ga)N heterostructures on 6H-SiC(0001) and γ-LiAlO2(100).
Reliability of real-time reverse-transcription PCR in clinical diagnostics: gold standard or substandard? (2009)

Molecular diagnostics is one of the major growth areas of modern medicine, with real-time PCR established as a qualitative and quantitative technology that is rapid, accurate and sensitive. The sequencing of the human genome, comprehensive genomic, mRNA and miRNA expression profiling of numerous cancer types, the ongoing identification of disease-associated polymorphisms and the expanding availability of genomic sequence information for human pathogens has opened the door to a wide range of translational applications for this technology. Consequently, novel real-time PCR assays have been developed for diagnosis and prognosis, treatment monitoring, transplant biology and pathogen detection, as well as more controversial uses such as lifestyle genotyping. However, this technology is still troubled by significant technical deficiencies. Hence its often-improper use as a clinical tool has important public health implications, most recently demonstrated through its association with the measles, mumps and rubella vaccine/autism controversy. This serves as a timely reminder of the indispensable requirement for careful experimental design, validation and analysis.
Conductance properties of single inwardly rectifying potassium channels in ventricular cells from guinea‐pig heart. (1984)

Single ventricular cells were enzymatically isolated from adult guinea-pig hearts (Isenberg & Klöckner, 1982). The patch-clamp technique (Hamill, Marty, Neher, Sakmann & Sigworth, 1981) was used to examine the conductance properties of an inward-rectifying K+ channel present in their sarcolemmal membrane. When the K+ concentration on the extracellular side of the patch was between 10.8 and 300 mM, inward current steps were observed at potentials more negative than the K+ equilibrium potential (EK). At more positive potentials no current steps were detectable, demonstrating the strong rectification of the channel. The zero-current potential extrapolated from the voltage dependence of the inward currents depends on the external K4 concentration [K+]o in a fashion expected for a predominantly K+-selective ion channel. It is shifted by 49 mV for a tenfold change in [K+]o. The conductance of the channel depends on the square root of [K+]o. In approximately symmetrical transmembrane K+ concentrations (145 mM-external K+), the single-channel conductance is 27 pS (at 19-23 degrees C). In normal Tyrode solution (5.4 mM-external K+) we calculate a single-channel conductance of 3.6 pS. The size of inward current steps at a fixed negative membrane potential V increases with [K+]o. The relation between step size and [K+]o shows saturation. Assuming a Michaelis-Menten scheme for binding of permeating K+ to the channel, an apparent binding constant of 210 mM is calculated for a membrane potential of -100 mV. For this potential the current at saturating [K+]o is estimated as 6.5 pA. The rectification of the single-channel conductance at membrane potentials positive to EK occurs within 1.5 ms of stepping the membrane potential from a potential of high conductance to one of low conductance. In addition to the main conductance state, the channel can adopt several substates of conductance. The main state could be the result of the simultaneous opening of four conducting subunits, each of which has a conductance of about 7 pS in 145 mM-external K+. The density of the inward-rectifying K+ channels in the ventricular sarcolemma is 0-10 channel/10 micron2 of surface membrane; the average of twenty-eight patches was 1 channel/1.8 micron2. It is concluded that the inward-rectifying K+ channels mediate the resting K+ conductance of ventricular heart muscle and the current termed IK1 in conventional voltage-clamp experiments.