gebhart/patrepeval huggingface dataset:
Expression of Aureobasidium pullulans xynA in, and secretion of the xylanase from, Saccharomyces cerevisiae (1996)

A previous report dealt with the cloning in Escherichia coli and sequencing of both the cDNA and genomic DNA encoding a highly active xylanase (XynA) of Aureobasidium pullulans (X.-L. Li and L. G. Ljungdahl, Appl. Environ. Microbiol. 60:3160-3166, 1994). Now we show that the gene was expressed in Saccharomyces cerevisiae under the GAL1 promoter in pYES2 and that its product was secreted into the culture medium. S. cerevisiae clone pCE4 with the whole open reading frame of xynA, including the part coding for the signal peptide, had xylanase activity levels of 6.7 U ml-1 in the cell-associated fraction and 26.2 U ml-1 in the culture medium 4 h after galactose induction. Two protein bands with sizes of 25 and 27 kDa and N-terminal amino acid sequences identical to that of APX-II accounted for 82% of the total proteins in the culture medium of pCE4. These proteins were recognized by anti-APX-II antibody. The results suggest that the XynA signal peptide supported the posttranslational processing of xynA product and the efficient secretion of the active xylanase from S. cerevisiae. Clones pCE3 and pGE3 with inserts of cDNA and genomic DNA, respectively, containing only the mature enzyme region attached by a Met codon had low levels of xylanase activity in the cell-associated fractions (1.6 U ml-1) but no activity in the culture media. No xylanase activity was detected in clone pGE4, which was the same as pCE4, except that pGE4 had a 59-bp intron in the signal peptide region. A comparison of the A. pullulans and S. cerevisiae signal peptides demonstrated that the XynA signal peptide was at least three times more efficient than those of S. cerevisiae invertase or mating alpha-factor pheromone in secreting the heterologous xylanase from S. cerevisiae cells.
Natural Variations and Genome-Wide Association Studies in Crop Plants (2013)

Natural variants of crops are generated from wild progenitor plants under both natural and human selection. Diverse crops that are able to adapt to various environmental conditions are valuable resources for crop improvements to meet the food demands of the increasing human population. With the completion of reference genome sequences, the advent of high-throughput sequencing technology now enables rapid and accurate resequencing of a large number of crop genomes to detect the genetic basis of phenotypic variations in crops. Comprehensive maps of genome variations facilitate genome-wide association studies of complex traits and functional investigations of evolutionary changes in crops. These advances will greatly accelerate studies on crop designs via genomics-assisted breeding. Here, we first discuss crop genome studies and describe the development of sequencing-based genotyping and genome-wide association studies in crops. We then review sequencing-based crop domestication studies and offer a perspective on genomics-driven crop designs.
Assembly and secretion of pentameric IgM in a fusion between a nonsecreting B cell lymphoma and an IgG-secreting plasmacytoma. (1979)

A new immunoglobulin product has been obtained by hybridization of mouse cell lines arrested at different stages in B lymphocyte development. One line was shown to have the characteristics of an undifferentiated B cell that synthesizes monomeric IgM as a membrane receptor but does not express J chain. The second line was represent of a fully differentiated plasma cell synthesizing large amounts of IgG and J chain, but no IgM. Fusion of the two cell types yielded independent hybrid clones that secreted pentameric IgM, normally the first product of antigen-driven B cell differentiation. Analyses of the hybrid cells indicated that the IgM was expressed as a result of complementation between the synthetic capacities of the parental lines. The hybrid cells synthesized both monomeric IgM and J chain and assembled these components into a pentameric molecule with the expected stoichiometry of one J chain per five monomeric units. These findings provided further evidence that the induction of B cell differentiation includes a signal for de novo synthesis of the J chain. Moreover, the complementation achieved by this hybridization provides a system for identifying other intracellular events in B cell differentiation to IgM secretion.
Gene expression of periostin in the early stage of fracture healing detected by cDNA microarray analysis (2003)

To comprehensively evaluate gene expression in the early stage of fracture healing, we used a cDNA microarray with 2304 cDNA clones derived from an oligo-capped mouse embryo library. Closed mid-diaphyseal fractures were created in mouse tibiae and expression profiles were analyzed 3 days after fracture. Six genes were up-regulated in comparison to those in unfractured bones and these included three genes previously identified but never shown to be present in fractures, periostin, calumenin, and FHL-1. Cloning of these genes has been completed but their expression pattern and function during fracture healing and bone formation remain to be elucidated. Up-regulation of the six genes was reconfirmed by semi-quantitative RT-PCR analysis. Spatial and temporal expression of one of the newly identified fracture-induced genes, periostin, was analyzed using in situ hybridization, because it displayed the highest up-regulation ratio. A signal for periostin was detected in undifferentiated mesenchymal cells and immature preosteoblastic cells in the periosteal tissues between days 3 and 14 after fracture. Northern analysis showed that periostin gene expression rapidly increased by day 3, reached a peak on day 7, and declined by day 14. These findings suggest that periostin is a specific marker for preosteoblasts and may play an important role in periosteal callus formation during the early stage of fracture healing.
Intercuneiform Instability and the “Gap” Sign (1999)

We describe three cases of low-energy injuries to the midfoot resulting in rupture of Lisfranc's ligament without tarsometatarsal injury. Examination of the feet revealed an obvious physical sign only on weightbearing, and all three patients were noted at surgery to have intercuneiform instability in association with a rupture of Lisfranc's ligament.
Engineering Escherichia coli for Biodiesel Production Utilizing a Bacterial Fatty Acid Methyltransferase (2011)

The production of low-cost biofuels in engineered microorganisms is of great interest due to the continual increase in the world's energy demands. Biodiesel is a renewable fuel that can potentially be produced in microbes cost-effectively. Fatty acid methyl esters (FAMEs) are a common component of biodiesel and can be synthesized from either triacylglycerol or free fatty acids (FFAs). Here we report the identification of a novel bacterial fatty acid methyltransferase (FAMT) that catalyzes the formation of FAMEs and 3-hydroxyl fatty acid methyl esters (3-OH-FAMEs) from the respective free acids and S-adenosylmethionine (AdoMet). FAMT exhibits a higher specificity toward 3-hydroxy free fatty acids (3-OH-FFAs) than FFAs, synthesizing 3-hydroxy fatty acid methyl esters (3-OH-FAMEs) in vivo. We have also identified bacterial members of the fatty acyl-acyl carrier protein (ACP) thioesterase (FAT) enzyme family with distinct acyl chain specificities. These bacterial FATs exhibit increased specificity toward 3-hydroxyacyl-ACP, generating 3-OH-FFAs, which can subsequently be utilized by FAMTs to produce 3-OH-FAMEs. PhaG (3-hydroxyacyl ACP:coenzyme A [CoA] transacylase) constitutes an alternative route to 3-OH-FFA synthesis; the coexpression of PhaG with FAMT led to the highest level of accumulation of 3-OH-FAMEs and FAMEs. The availability of AdoMet, the second substrate for FAMT, is an important factor regulating the amount of methyl esters produced by bacterial cells. Our results indicate that the deletion of the global methionine regulator metJ and the overexpression of methionine adenosyltransferase result in increased methyl ester synthesis.
Mechanism of voltage-sensitive fluorescence in a microbial rhodopsin (2013)

Microbial rhodopsins were recently introduced as genetically encoded fluorescent indicators of membrane voltage. An understanding of the mechanism underlying this function would aid in the design of improved voltage indicators. We asked, what states can the protein adopt, and which states are fluorescent? How does membrane voltage affect the photostationary distribution of states? Here, we present a detailed spectroscopic characterization of Archaerhodopsin 3 (Arch). We performed fluorescence spectroscopy on Arch and its photogenerated intermediates in Escherichia coli and in single HEK293 cells under voltage-clamp conditions. These experiments probed the effects of time-dependent illumination and membrane voltage on absorption, fluorescence, membrane current, and membrane capacitance. The fluorescence of Arch arises through a sequential three-photon process. Membrane voltage modulates protonation of the Schiff base in a 13-cis photocycle intermediate (M ⇌ N equilibrium), not in the ground state as previously hypothesized. We present experimental protocols for optimized voltage imaging with Arch, and we discuss strategies for engineering improved rhodopsin-based voltage indicators.
A Trajectory-Based Ball Tracking Framework with Visual Enrichment for Broadcast Baseball Videos * (2008)

Pitching contents play the key role in the resultant victory or defeat in a baseball game. Utilizing the physical characteristic of ball motion, this paper presents a trajectory-based framework for automatic ball tracking and pitching evaluation in broadcast baseball videos. The task of ball detection and tracking in broadcast baseball videos is very challenging because in video frames, the noises may cause many ball-like objects, the ball size is small, and the ball may deform due to its high speed movement. To overcome these challenges, we first define a set of filters to prune most non-ball objects but retain the ball, even if it is deformed. In ball position prediction and trajectory extraction, we analyze the 2D distribution of ball candidates and exploit the characteristic that the ball trajectory presents in a near parabolic curve in video frames. Most of the non-qualified trajectories are pruned, which greatly improves the computational efficiency. The missed balls can also be recovered in the trajectory by applying the position prediction. The experiments of ball tracking on the testing sequences of JPB, MLB and CPBL captured from different TV channels show promising results. The ball tracking framework is able to extract the ball trajectory, superimposed on the video, and in near real-time provide visual enrichment before the next pitch coming up without specific cameras or equipments set up in the stadiums. It can also be utilized in strategy analysis and intelligence statistics for player training.
Novel and Conserved Micrornas in Dalian Purple Urchin (Strongylocentrotus Nudus) Identified by Next Generation Sequencing (2011)

MicroRNAs are regulators in regulation of broad range of phenotypes. The purple urchin, Strongylocentrotus nudus, is one of the most important marine economic animals that widely distributed in the cold seas along the coasts of eastern pacific area. To date, only 45 microRNAs have been identified in a related species, Strongylocentrotus purpurtus, and there is no report on S. nudus microRNAs. Herein, solexa sequencing technology was used to high throughput sequencing analysis of microRNAs in small RNA library isolated from five tissues of S. nudus. Totally, 8,966,865 reads were yielded, 131,015 of which were related to 415 unique microRNAs including 345 deuterostoma conserved and 70 urchin specific microRNAs, as well as 5 microRNA* sequences. The miRNA features including length distribution, end variations and genomic locations were characterized. Annotation of targets revealed a broad range of biological processes and signal transduction pathways that regulated by urchin miRNAs, of which signal transduction mechanisms was the subgroup containing the maximum targets. In addition, the expression of 100 miRNAs in female gonad was confirmed using microRNA microarray analysis. This study provides a first large scale cloning and characterization of S.nudus miRNAs and their potential targets, providing the foundation for further characterization for their role in the regulation of diversity of physiological processes.
Inhibition of the Interaction of AGE–RAGE Prevents Hyperglycemia-Induced Fibrosis of the Peritoneal Membrane (2003)

The peritoneal membrane of long-term peritoneal dialysis patients is characterized by a loss of ultrafiltration capacity, associated morphologically with submesothelial fibrosis and neoangiogenesis. Exposure to high glucose concentrations in peritoneal dialysate and the resultant advanced glycation end-products (AGE) accumulation have been implicated in the development of these changes, but their exact pathophysiological role is unknown. We examined the effect of the interaction of AGE with one of their receptors (i.e., RAGE) on the function and structure of the peritoneum exposed to high ambient glucose concentrations. Streptozotocin-induced diabetic rats and control rats were treated during 6 wk with either neutralizing monoclonal anti-RAGE antibodies or control antibodies. The expression of RAGE was strongly enhanced in the peritoneal membrane of the diabetic animals. The diabetic peritonea were characterized by an elevated transport of small solutes, lower ultrafiltration rates, a higher vascular density, and an upregulation of endothelial nitric oxide synthase expression. These parameters were unaffected by treatment with anti-RAGE antibodies. In contrast, anti-RAGE but not control antibodies prevented upregulation of TGF-beta, development of submesothelial fibrosis, and fibronectin accumulation in the peritoneum of diabetic animals. In conclusion, binding of AGE to RAGE increases the expression of TGF-beta and contributes to the development of submesothelial fibrosis. Neoangiogenesis and the resultant loss of ultrafiltration capacity are mediated by different pathogenetic pathways.
Fatty acyl chain composition in the determination of renal membrane order. (1986)

The relative roles of phospholipid fatty acyl chain length and phospholipid fatty acyl chain unsaturation in the determination of rat renal brush border membrane order were examined using multilamellar liposomes. Exposure of brush border membranes to sphingomyelinase resulted in a time- and concentration-dependent decrement in sphingomyelin content. Liposomes prepared from lipid extracts of these membranes were reconstituted to defined phosphatidylcholine (PC)/sphingomyelin (SPH) ratios with pure synthetic PCs of defined chain length and degrees of unsaturation. Mixed-acid PCs from bovine liver, egg, and the rat renal brush border membrane were also examined. The steady state fluorescence anisotropy of 1,6-diphenyl-1,3,5-hexatriene (DPH) at 37 degrees C was used to reflect acyl chain packing. The steady state anisotropy of DPH in liposomes isolated from the rat renal brush border membrane averaged 0.205 +/- 0.001, n = 8. When liposomes were reconstituted to PC/SPH ratios of 1.1, 1.6, and 2.4 with saturated PCs of acyl chain length 16 to 22, differences in anisotropy between groups were not observed. However, when PCs containing unsaturated or mixed-acid fatty acyl chains were introduced, anisotropy decreased in a concentration dependent fashion. These data suggest that phospholipid fatty acyl chain unsaturation, but not acyl chain length, has a powerful influence on renal brush border membrane order and the PC/SPH ratio is an important determinant of renal membrane order by virtue of the unsaturated fatty acids normally present with these phospholipids.
Injection locking of VCSELs (2003)

Injection locking has been actively researched for its possibility to improve laser performance for both digital and analog applications. When a modulated follower laser (also termed "slave" laser) is locked to the master laser, its nonlinear distortion and frequency chirp may be reduced. As well, the resonance frequency can increase to several times higher than its free running case. We show that the frequency response (S21) of an injection-locked laser is similar to a parasitic-limited laser with a high resonance frequency. The S21 was studied experimentally and the condition to achieve a flat, enhanced frequency response was identified. For analog applications, a record 112 dB-Hz <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> 3/, single-tone third harmonic spur-free dynamic range of a 1.55-μm vertical cavity surface emitting lasers (VCSEL) was demonstrated. An improvement was attained for a wide-injection parameter space. In a 50-km 2.5-Gb/s digital link, a 2-dB power penalty reduction at 10/sup -9/ bit error rate was also demonstrated. As a novel application, an injection-locked uncooled tunable VCSEL was shown to have a reasonable modulation performance in a wide abient temperature range. The VCSEL was locked to a designated wavelength and the injection compensated the temperature-induced performance degradation. This concept can be extremely attractive for low-cost dense wavelength division muliplexed transmitters.
A Zebrafish Model of Human Barth Syndrome Reveals the Essential Role of Tafazzin in Cardiac Development and Function (2006)

Barth syndrome is an X-linked disorder characterized by cardiomyopathy, skeletal myopathy, neutropenia, organic aciduria, and growth retardation caused by mutations in tafazzin. The sequence similarity of tafazzin to acyltransferases suggests a role in mitochondrial phospholipid metabolism. To study the role of tafazzin in heart function and development, we created a knockdown zebrafish model. Zebrafish tafazzin mRNA is first evident at 7 hours post-fertilization (hpf). At 10 and 24 hpf, tafazzin mRNA is ubiquitous, with highest levels in the head. By 51 hpf, expression becomes cardiac restricted. The tafazzin knockdown created by antisense morpholino yolk injection resulted in dose-dependent lethality, severe developmental and growth retardation, marked bradycardia and pericardial effusions, and generalized edema, signs that resemble human Barth syndrome heart failure. This knockdown phenotype was rescued by concomitant injection of normal tafazzin mRNA. Abnormal cardiac development, with a linear, nonlooped heart, and hypomorphic tail and eye development proves that tafazzin is essential for overall zebrafish development, especially of the heart. The tafazzin knockdown zebrafish provides an animal model similar to Barth syndrome to analyze the severity of human mutants and to test potential treatments.
Toward Understanding Reactive Adsorption of Ammonia on Cu-MOF/Graphite Oxide Nanocomposites (2011)

The adsorption of ammonia on HKUST-1 (a metal-organic framework, MOF) and HKUST-1/graphite oxide (GO) composites was investigated in two different experimental conditions. From the isotherms, the isosteric heats of adsorption were calculated from the Clausius-Clapeyron equation following the virial approach. The results on HKUST-1 were compared with those obtained using molecular simulation studies. All materials exhibit higher ammonia adsorption capacities than those reported in the literature. The ammonia adsorption on the composites is higher than that measured separately on the MOF component and on GO. The strong adsorption of ammonia caused by chemical interactions on different adsorption sites is evidenced by the trends in the isosteric heats of adsorption. The molecular simulations conducted on HKUST-1 support the trends observed experimentally. In particular, the strong chemisorption of ammonia on the metallic centers of HKUST-1 is confirmed. Nevertheless, higher adsorption capacities are predicted compared with the experimental results. This discrepancy is mainly assigned to the partial collapse of the MOF structure upon exposure to ammonia, which is not accounted for in the simulation study.
The LightCycler TM : A Microvolume Multisample Fluorimeter with Rapid Temperature Control (1997)

Experimental and commercial microvolume fluorimeters with rapid temperature control are described. Fluorescence optics adopted from flow cytometry were used to interrogate 1-10-microL samples in glass capillaries. Homogeneous temperature control and rapid change of sample temperatures (10 degrees C/s) were obtained by a circulating air vortex. A prototype 2-color, 32-sample version was constructed with a xenon arc for excitation, separate excitation and emission paths, and photomultiplier tubes for detection. The commercial LightCycler, a 3-color, 24-sample instrument, uses a blue light-emitting diode for excitation, paraxial epi-illumination through the capillary tip and photodiodes for detection. Applications include analyte quantification and nucleic acid melting curves with fluorescent dyes, enzyme assays with fluorescent substrates and techniques that use fluorescence resonance energy transfer. Microvolume capability allows analysis of very small or expensive samples. As an example of one application, rapid cycle DNA amplification was continuously monitored by three different fluorescence techniques, Which included using the double-stranded DNA dye SYBR Green I, a dual-labeled 5'-exonuclease hydrolysis probe, and adjacent fluorescein and Cy5z-labeled hybridization probes. Complete amplification and analysis requires only 10-15 min.
Tiotropium bromide, a new long-acting antimuscarinic bronchodilator: a pharmacodynamic study in patients with chronic obstructive pulmonary disease (COPD). Dutch Study Group (1995)

The objective of the present study was to investigate the dose-dependent bronchodilator efficacy and duration of action of the newly developed antimuscarinic agent tiotropium bromide in patients with chronic obstructive pulmonary disease (COPD). In a randomized, double-blind, placebo-controlled, crossover design, patients inhaled single doses of 10-80 micrograms tiotropium bromide and placebo, formulated in lactose powder capsules. The washout period between test doses was 72 h. Thirty five patients were enrolled in the trial (32 males and 3 females; mean age 64 yrs). Baseline forced expiratory volume in one second (FEV1) (mean 1.34 L) was less than 65% of predicted and was < 70% of forced vital capacity (FVC). All subjects had a smoking history of more than 10 pack-years. The mean reversibility of FEV1 after inhalation of 40 micrograms ipratropium bromide was 28%. Pulmonary function testing was performed before and at regular time intervals for up to 32 h after test drug administration. Compared to placebo, tiotropium bromide produced significant improvements in FEV1, FVC, peak expiratory flow rate (PEFR) and forced mid-expiratory flow (FEF25-75%). The bronchodilator response was almost immediate; peak improvement in FEV1 was reached 1-4 h after test drug inhalation, and the duration of action extended to 32 h after the 20, 40 and 80 micrograms doses. A clear dose-response relationship was seen for peak FEV1 and for the average FEV1 over differing time periods during the 32 h observation period, 80 micrograms of test drug being superior to the 10 micrograms dose. Peak improvement in FEV1 ranged 19-26% of test-day baseline for tiotropium bromide doses compared to 16% for placebo. The large improvement for placebo is probably due to carry-over effect which was significant. After excluding carry-over effect, the peak response to placebo decreased to 11%, whilst for tiotropium bromide doses it ranged 20-25%; standard error for mean difference was about 4%. There was no evidence of systemic anticholinergic effects. In this population of patients with COPD, tiotropium bromide was found to be a safe and long-acting bronchodilator, demonstrating a clear dose-response relationship following single dose administration.