gebhart/patrepeval huggingface dataset:
Super-resolution imaging and tracking of protein–protein interactions in sub-diffraction cellular space (2014)

Imaging the location and dynamics of individual interacting protein pairs is essential but often difficult because of the fluorescent background from other paired and non-paired molecules, particularly in the sub-diffraction cellular space. Here we develop a new method combining bimolecular fluorescence complementation and photoactivated localization microscopy for super-resolution imaging and single-molecule tracking of specific protein-protein interactions. The method is used to study the interaction of two abundant proteins, MreB and EF-Tu, in Escherichia coli cells. The super-resolution imaging shows interesting distribution and domain sizes of interacting MreB-EF-Tu pairs as a subpopulation of total EF-Tu. The single-molecule tracking of MreB, EF-Tu and MreB-EF-Tu pairs reveals intriguing localization-dependent heterogonous dynamics and provides valuable insights to understanding the roles of MreB-EF-Tu interactions.
Cellular Uptake of Clostridium botulinum C2 Toxin:  Membrane Translocation of a Fusion Toxin Requires Unfolding of Its Dihydrofolate Reductase Domain (2003)

The Clostridium botulinum C2 toxin is the prototype of the family of binary actin-ADP-ribosylating toxins. C2 toxin is composed of two separated nonlinked proteins. The enzyme component C2I ADP-ribosylates actin in the cytosol of target cells. The binding/translocation component C2II mediates cell binding of the enzyme component and its translocation from acidic endosomes into the cytosol. After proteolytic activation, C2II forms heptameric pores in endosomal membranes, and most likely, C2I translocates through these pores into the cytosol. For this step, the cellular heat shock protein Hsp90 is essential. We analyzed the effect of methotrexate on the cellular uptake of a fusion toxin in which the enzyme dihydrofolate reductase (DHFR) was fused to the C-terminus of C2I. Here, we report that unfolding of C2I-DHFR is required for cellular uptake of the toxin via the C2IIa component. The C2I-DHFR fusion toxin catalyzed ADP-ribosylation of actin in vitro and was able to intoxicate cultured cells when applied together with C2IIa. Binding of the folate analogue methotrexate favors a stable three-dimensional structure of the dihydrofolate reductase domain. Pretreatment of C2I-DHFR with methotrexate prevented cleavage of C2I-DHFR by trypsin. In the presence of methotrexate, intoxication of cells with C2I-DHFR/C2II was inhibited. The presence of methotrexate diminished the translocation of the C2I-DHFR fusion toxin from endosomal compartments into the cytosol and the direct C2IIa-mediated translocation of C2I-DHFR across cell membranes. Methotrexate had no influence on the intoxication of cells with C2I/C2IIa and did not alter the C2IIa-mediated binding of C2I-DHFR to cells. The data indicate that methotrexate prevented unfolding of the C2I-DHFR fusion toxin, and thereby the translocation of methotrexate-bound C2I-DHFR from endosomes into the cytosol of target cells is inhibited.
Novel investigational biologics for the treatment of cancer cachexia (2014)

A critical look of the study protocols and two key challenges limiting the successful evaluation of these agents include: i) lack of a clinically meaningful cachexia definition; and ii) identification and treatment of cachexia in late stage. We describe our observations and clinical experience in an effort to redirect and promote successful strategies to evaluate these novel investigational biologics.
Genomic Testing and Method R Variance Components Theory of Dairy Cattle (2012)

Abstract The objective of this study is to determine the change in reliability from non genomic evaluations or Parent Averages to genomic evaluations. Due to recent industry popularity of genomic evaluations the California Polytechnic University, San Luis Obispo, decided to participate in the genetic movement of the dairy cattle industry. Genomic evaluations of both Holstein and Jersey cows at the Cal Poly dairy were chosen based on genetic superiority in order to possibly generate more income for the dairy and increase the herd’s popularity. Leading genomic companies such as Pfizer Animal Health, and GenSeek made genomic evaluation of the Cal Poly herd affordable by donating genomic sampling kits. Using the BovineSNP50 Bead Chip and BovineSNP6 Bead Chip, hair and blood samples were taken from the Cal Poly cows and heifers and were sent to the respected companies to generate official genomic evaluations. The data that this project focused on was the change in reliability of health traits such as Productive Life, as well as type and production traits including Net Merit Dollars, Cheese Merit Dollars, Genomic Total Performance Index, and Predicted Transmitting Ability for Type. Increases from traditional parent averages reliabilities to genomic evaluations reliabilities were obtained for all 6 core traits that were evaluated from the tested animals. In 59 Jersey’s that were tested, average reliabilities scores increased from an average of 45% to 69.61%. In addition the 51 tested Holstein females reliabilities raised from 43% to 74%. The genomic evaluations also suggest that the Cal Poly herd is genetically superior, they have two cows in the California top 100 GTPI cow and heifer lists for their respected breed. The gain in reliability of core industry traits and development of genetically superior animals of the Cal Poly herd has in turn increased their popularity of their herd, as well as potentially generating more income from its superior cows and heifers. A genomic based breeding program that Cal Poly has installed will speed up genetic progress of its herd by two years for each generation. The genomic evaluations of the Cal Poly herd will be used as a breeding tool to generate superior genomic bulls and heifers for potential future income. The algorithm that is used for estimating the variance of genetic components is called Method R, and it will be used to analyze the correlation between Traditional Total Performance Index (TPI) to the Genomic Total Performance Index (GTPI/GJPI). The algorithm Method R, must equal 1 regardless of the sample size in order for the theory to be true (Reverter, 1994). If the computed R is greater than 1, then the variance component ration or slope is underestimated, but if it is less than 1 it is overstated (Reverter, 1994). Moreover the Method R algorithm will essentially prove that if the newly designed, chromosome based, genomic predictions are correlated with the traditional parent averages.
Chaperoning of Insertion of Membrane Proteins into Lipid Bilayers by Hemifluorinated Surfactants:  Application to Diphtheria Toxin (2006)

Hemifluorinated compounds, such as HF-TAC, make up a novel class of nondetergent surfactants designed to keep membrane proteins soluble under nondissociating conditions [Breyton, C., et al. (2004) FEBS Lett. 564, 312]. Because fluorinated and hydrogenated chains do not mix well, supramicellar concentrations of these surfactants can coexist with intact lipid vesicles. To test the ability of HF-TAC to assist proper membrane insertion of proteins, we examined its effect on the pH-triggered insertion of the diphtheria toxin T-domain. The function of the T-domain is to translocate the catalytic domain across the lipid bilayer in response to acidification of the endosome. This translocation is accompanied by the formation of a pore, which we used as a measure of activity in a vesicle leakage assay. We have also used Förster resonance energy transfer to follow the effect of HF-TAC on aggregation of aqueous and membrane-bound T-domain. Our data indicate that the pore-forming activity of the T-domain is affected by the dynamic interplay of two principal processes: productive pH-triggered membrane insertion and nonproductive aggregation of the aqueous T-domain at low pH. The presence of HF-TAC in the buffer is demonstrated to suppress aggregation in solution and ensure correct insertion and folding of the T-domain into the lipid vesicles, without solubilizing the latter. Thus, hemifluorinated surfactants stabilize the low-pH conformation of the T-domain as a water-soluble monomer while acting as low-molecular weight chaperones for its insertion into preformed lipid bilayers.
Pulmonary microvascular injury after intestinal ischemia-reperfusion: role of P-selectin (1993)

The objective of this study was to determine whether pulmonary endothelial expression of the adhesive glycoprotein P-selectin contributes to the lung injury and leukostasis observed after intestinal ischemia-reperfusion (I/R). The pulmonary capillary filtration coefficient and lung myeloperoxidase activity were determined in rat lungs isolated after 120 min of superior mesenteric artery occlusion and 90 min of reperfusion. Intestinal I/R resulted in a marked increase in the pulmonary capillary filtration coefficient compared with control and sham-operated rats. The increase in pulmonary microvascular permeability elicited by intestinal I/R was effectively prevented by pretreatment with a P-selectin monoclonal antibody (MAb; MAb PB1.3) but was unaffected by a control MAb. The intestinal I/R-induced increase in pulmonary microvascular permeability was accompanied by a dramatic sequestration of granulocytes in the lung compared with control and sham-operated rats; however, neither the P-selectin nor the control MAbs affected this event. These results indicate that P-selectin contributes to the pulmonary microvascular dysfunction observed after intestinal I/R. The inhibition of intestinal I/R-induced lung injury by immunoneutralization of P-selectin appears to be unrelated to the accompanying lung leukosequestration.
Expression and characterization of a functional rat liver Na+ bile acid cotransport system in COS-7 cells (1994)

A cDNA for the rat liver sodium-dependent bile acid cotransporter was expressed in COS-7 cells to study the functional properties of the translated protein in a mammalian cell line. A 1.2-kb insert was ligated into a pMAMneo vector and transiently transfected using electroporation. After optimal conditions were established, the transiently transfected COS cells were screened with fluorescent-conjugated labeled bile acids for evidence of expression of the cotransporter after 48 h. The uptake of [3H]taurocholate ([3H]TC) was then determined in cells transfected with or without the bile acid insert. Progressive uptake of [3H]TC (0.45 microM) was observed for 30 min in the presence of sodium. In contrast, no uptake of [3H]TC was observed in the absence of sodium, in nontransfected COS cells, or in COS cells transfected with the empty plasmid. Kinetic studies revealed a Michaelis constant (Km) of 29 microM, essentially identical to the Km of this cotransporter described in intact rat hepatocytes and membrane vesicles. Uptake of [3H]TC (5.0 microM) at 5 min (n = 3-6) was inhibited by 100 microM taurochenodeoxycholic acid (81%), tauroursodeoxycholic acid (77%), cholic acid (55%), chenodeoxycholic acid (74%), and ursodeoxycholic acid (56%) but not by 100 microM taurodehydrocholate, 1 mM probenecid, or 100 microM bilirubin. In contrast, bumetanide (500 microM) inhibited [3H]TC uptake by 52%. These studies indicate that the isolated cDNA codes for a physiological bile acid transporter present in rat hepatocytes and that posttranslational factors present in mammalian cells may not be as important in defining properties of this cotransport system.
Directed Differentiation into Neural Lineages and Therapeutic Potential of Porcine Embryonic Stem Cells in Rat Parkinson's Disease Model (2010)

This study was conducted to direct porcine embryonic stem (pES) cells differentiating into neural lineages and to investigate therapeutic potential of GFP-expressing pES (pES/GFP(+)) in the rat model of Parkinson's disease (PD). Directed differentiation of pES into neural lineages was induced by suspension culture in medium containing RA, SHH, and FGF combinations without going through embryoid body formation. A high yield of nestin-expressing neural precursors was found in all treatments on day 2 after the 12-day induction. On day 6 after replating, more than 86.2 and 83.4% of the differentiated cells stained positively for NFL and MAP2, respectively. The expression of TH, ChAT, and GABA specific markers were also observed in these NFL-positive neural cells. The undifferentiated pES/GFP(+) cells and their neuronal differentiation derivatives were transplanted into the Sprague-Dawley (SD) rat's brain, and their survival and development was determined by using live animal fluorescence optical imaging system every 15 days. The results showed that fluorescent signals from the injection site of SD rats' brain could be detected through the experimental period of 3 months. The level of fluorescent signal detected in the treatment group was twofold that of the control group. The results of behavior analysis showed that PD rats exhibited stably decreased asymmetric rotations after transplantation with pES/GFP(+)-derived D18 neuronal progenitors. The dopaminergic differentiation of grafted cells in the brain was further confirmed by immunohistochemical staining with anti-TH, anti-DA, and anti-DAT antibodies. These results suggested that the differentiation approach we developed would direct pES cells to differentiate into neural lineages and benefit the development of novel therapeutics involving stem cell transplantation.
ChemInform Abstract: Synthesis of Axially Dissymmetric Chiral Ammonium Salts by Quaternization of Secondary Amines with (R)‐(+)‐2,2′‐Bis(bromomethyl)‐ 6,6′‐dinitrobiphenyl and (R)‐(+)‐2,2′‐Bis(bromomethyl)‐1,1′‐binaphthyl and an Examination of Their Abilities as Chiral Phase‐Transfer Catalysts. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
World Health Organization/HIVResNet Drug Resistance Laboratory Strategy (2008)

With rapidly increasing access to antiretroviral drugs globally, HIV drug resistance (HIVDR) has become a significant public health issue. This requires a coordinated and collaborative response from country level to international level to assess the extent of HIVDR and the establishment of efficient and evidence-based strategies to minimize its appearance and onward transmission. In parallel with the rollout of universal access to HIV treatment, countries are developing protocols based on the recommendations of the World Health Organization (WHO) to measure, at a population level, both transmitted HIVDR and HIVDR emerging during treatment. The WHO in collaboration with international experts (HIVResNet Laboratory Working Group), has developed a laboratory strategy, which has the overall goal of delivering quality-assured HIV genotypic results on specimens derived from the HIVDR surveys. The results will be used to help control the emergence and spread of drug resistance and to guide decision makers on antiretroviral therapy policy at national, regional and global level. The HIVDR Laboratory Strategy developed by the WHO includes several key aspects: the formation of a global network of national, regional and specialized laboratories accredited to perform HIVDR testing using a common set of WHO standard and performance indicators; recommendations of acceptable methods for collection, handling, shipment and storage of specimens in field conditions; and the provision of laboratory technical support, capacity building and quality assurance for network laboratories. The WHO/HIVResNet HIVDR Laboratory Network has been developed along the lines of other successful laboratory networks coordinated by the WHO. As of August 2007, assessment for accreditation has been conducted in 30 laboratories, covering the WHO's African, South-East Asia, Western Pacific, and the Caribbean Regions.
Inhibitor of Apoptosis Proteins Physically Interact with and Block Apoptosis Induced by Drosophila Proteins HID and GRIM (1998)

Reaper (RPR), HID, and GRIM activate apoptosis in cells programmed to die during Drosophila development. We have previously shown that transient overexpression of RPR in the lepidopteran SF-21 cell line induces apoptosis and that members of the inhibitor of apoptosis (IAP) family of antiapoptotic proteins can inhibit RPR-induced apoptosis and physically interact with RPR through their BIR motifs (D. Vucic, W. J. Kaiser, A. J. Harvey, and L. K. Miller, Proc. Natl. Acad. Sci. USA 94:10183-10188, 1997). In this study, we found that transient overexpression of HID and GRIM also induced apoptosis in the SF-21 cell line. Baculovirus and Drosophila IAPs blocked HID- and GRIM-induced apoptosis and also physically interacted with them through the BIR motifs of the IAPs. The region of sequence similarity shared by RPR, HID, and GRIM, the N-terminal 14 amino acids of each protein, was required for the induction of apoptosis by HID and its binding to IAPs. When stably overexpressed by fusion to an unrelated, nonapoptotic polypeptide, the N-terminal 37 amino acids of HID and GRIM were sufficient to induce apoptosis and confer IAP binding activity. However, GRIM was more complex than HID since the C-terminal 124 amino acids of GRIM retained apoptosis-inducing and IAP binding activity, suggesting the presence of two independent apoptotic motifs within GRIM. Coexpression of IAPs with HID stabilized HID levels and resulted in the accumulation of HID in punctate perinuclear locations which coincided with IAP localization. The physical interaction of IAPs with RPR, HID, and GRIM provides a common molecular mechanism for IAP inhibition of these Drosophila proapoptotic proteins.
A Compatible Stereophonic System for the AM Broadcast Band (1960)

Stereophonic broadcasting presents a variety of problems, including compatibility, out-of-band radiation, stereo performance, distortion, signal-to-noise, receiver tuning, and receiver cost. Possible system solutions can be classified as either ``multiplicative'' or ``additive,'' depending upon whether the quadrature sidebands representative of the stereo information (L-R) are modulated by the envelope information (L+R), or are essentially independent of the envelope information, respectively. The preferred AM-FM system uses a pre-emphasized (L-R) signal to frequency modulate the carrier which is then amplitude modulated with (L+R). Stereophonic field test transmissions over Radio Station WNBC have demonstrated compatibility with existing monophonic receivers and excellent reception on stereophonic receivers of simple design.
Nicotine administration and withdrawal affect survival in systemic inflammation models (2008)

How different regimens of nicotine administration and withdrawal affect systemic inflammation is largely unknown. We studied the effects of chronic and acute nicotine administration and of nicotine withdrawal on the outcome of aseptic and septic systemic inflammation. Male C57BL/6 mice were implanted with subcutaneous osmotic pumps (to deliver nicotine) and intrabrain telemetry probes (to measure temperature). Aseptic inflammation was induced by lipopolysaccharide (40 mg/kg ip); sepsis was induced by cecal ligation and puncture. The chronic nicotine administration group received nicotine (28 mg.kg(-1).day(-1)) for 2 wk before the induction of inflammation and continued receiving nicotine until the end of the experiment; the acute nicotine administration group received saline for 2 wk and nicotine thereafter; the nicotine withdrawal group received nicotine for 2 wk and saline thereafter; and the no-nicotine group was infused with saline throughout the experiment. Compared with no nicotine, the chronic nicotine administration did not affect survival in either model of inflammation, possibly due to the development of nicotine tolerance. The acute nicotine administration increased the survival rate in aseptic inflammation from 11 to 33% (possibly by suppressing inflammation) but worsened the outcome of sepsis (possibly because the suppression of inflammation promoted microbial proliferation). Oppositely to acute nicotine, nicotine withdrawal increased the survival rate in sepsis from 18 to 40%. The effects on survival were not due to changes in body temperature. We conclude that acute nicotine administration and nicotine withdrawal affect survival in systemic inflammation and that these effects strongly depend on whether inflammation is aseptic or septic.
Lifetime and 12-Month Prevalence of DSM-III-R Psychiatric Disorders in the United States (1994)

The prevalence of psychiatric disorders is greater than previously thought to be the case. Furthermore, this morbidity is more highly concentrated than previously recognized in roughly one sixth of the population who have a history of three or more comorbid disorders. This suggests that the causes and consequences of high comorbidity should be the focus of research attention. The majority of people with psychiatric disorders fail to obtain professional treatment. Even among people with a lifetime history of three or more comorbid disorders, the proportion who ever obtain specialty sector mental health treatment is less than 50%. These results argue for the importance of more outreach and more research on barriers to professional help-seeking.
Mechanism of the reaction catalyzed by dihydrofolate reductase from Escherichia coli: pH and deuterium isotope effects with NADPH as the variable substrate (1988)

The variations with pH of the kinetic parameters and primary deuterium isotope effects for the reaction of NADPH with dihydrofolate reductase from Escherichia coli have been determined. The aims of the investigations were to elucidate the chemical mechanism of the reaction and to obtain information about the location of the rate-limiting steps. The V and V/KNADPH profiles indicate that a single ionizing group at the active center of the enzyme must be protonated for catalysis, whereas the Ki profiles show that the binding of NADPH to the free enzyme and of ATP-ribose to the enzyme-dihydrofolate complex is pH independent. From the results of deuterium isotope effects on V/KNADPH, it is concluded that NADPH behaves as a sticky substrate. It is this stickiness that raises artificially the intrinsic pK value of 6.4 for the Asp-27 residue of the enzyme-dihydrofolate complex [Howell, E. E., Villafranca, J. E., Warren, M. S., Oatley, S. J., & Kraut, J. (1986) Science (Washington, D.C.) 231, 1123] to an observed value of 8.9. Thus, the binary enzyme complex is largely protonated at neutral pH. The elevation of the intrinsic pK value of 6.4 for the ternary enzyme-NADPH-dihydrofolate complex to 8.5 is not due to the kinetic effects of substrates. Rather, it is the consequence of the lower, pH-independent rate of product release and the faster pH-dependent catalytic step. At neutral pH, the proportion of enzyme present as a protonated ternary enzyme-substrate complex is sufficient to keep catalysis faster than product release.(ABSTRACT TRUNCATED AT 250 WORDS)