gebhart/patrepeval huggingface dataset:
Design and synthesis of compounds that extend yeast replicative lifespan (2006)

This past decade has seen the identification of numerous conserved genes that extend lifespan in diverse species, yet the number of compounds that extend lifespan is relatively small. A class of compounds called STACs, which were identified as activators of Sir2/SIRT1 NAD+-dependent deacetylases, extend the lifespans of multiple species in a Sir2-dependent manner and can delay the onset of age-related diseases such as cancer, diabetes and neurodegeneration in model organisms. Plant-derived STACs such as fisetin and resveratrol have several liabilities, including poor stability and relatively low potency as SIRT1 activators. To develop improved STACs, stilbene derivatives with modifications at the 4' position of the B ring were synthesized using a Horner-Emmons-based synthetic route or by hydrolyzing deoxyrhapontin. Here, we describe synthetic STACs with lower toxicity toward human cells, and higher potency with respect to SIRT1 activation and lifespan extension in Saccharomyces cerevisiae. These studies show that it is possible to improve upon naturally occurring STACs based on a number of criteria including lifespan extension.
Endothelial Cell Apoptosis Induced by the Peroxisome Proliferator-activated Receptor (PPAR) Ligand 15-Deoxy-Δ12,14-prostaglandin J2 (1999)

15-Deoxy-Delta12,14-prostaglandin J2 (15d-PGJ2) is a bioactive prostanoid produced by dehydration and isomerization of PGD2, a cyclooxygenase product. It was recently shown to activate the nuclear peroxisome proliferator-activated receptor gamma (PPARgamma), a critical transcription factor involved in adipocyte and monocyte differentiation. In this report, we show that 15d-PGJ2 is a potent inducer of caspase-mediated endothelial cell apoptosis. PPARalpha, -delta, and -gamma were expressed by endothelial cells, which, when treated with 15d-PGJ2, induced receptor translocation into the nucleus, and an increase in PPAR response element-driven reporter gene expression. Ciglitizone, a selective activator of PPARgamma, also induced transcriptional activation and endothelial cell apoptosis. Endothelial apoptosis induced by 15d-PGJ2 was inhibited by treatment of cells with an oligonucleotide decoy to a consensus PPAR response element sequence. Furthermore, overexpression of the PPARgamma isotype induced endothelial cell apoptosis, which was further potentiated by 15d-PGJ2 treatment. We conclude that 15d-PGJ2 induces endothelial cell apoptosis via a PPAR-dependent pathway. The PPAR pathway may be a therapeutic target for numerous pathologies in which excessive angiogenesis is implicated.
Primary structure of the neutralization antigen of simian rotavirus SA11 as deduced from cDNA sequence (1984)

DNA sequences complementary to the double-stranded RNA coding for the neutralization antigen (glycoprotein VP7) of simian rotavirus SA11 have been cloned. The VP7 gene consists of 1,062 nucleotides, containing an uninterrupted coding sequence of 978 nucleotides which specifies a glycoprotein of 326 amino acids. The significance of a second possible initiation site 30 nucleotides downstream from the first is discussed. Partial amino acid sequence of this glycoprotein showed unequivocally that the cloned segment (segment 9) codes for glycoprotein VP7 of SA11. The resulting amino acid sequence contained only one carbohydrate acceptor site. Possible sites of membrane interaction and antigenic determinants are discussed based on the analysis of the hydrophobicity and hydrophilicity profiles of VP7.
In vitro cytostatic activity of some amino acid 4-N-substituted cytosines. (1992)

Cytotoxicity of 22 amino acid 4-N-substituted cytosine derivatives was studied on KB and HeLa human tissue cultures. A 4-N-(1H-2-oxo-4 pyrimidyl)-tryptamine with ED50 activity values of 0.145 x 10(-3) mole/l and ED0 = 0.4 x 10(-5) mole/l showed the highest cytotoxic activity and was qualified for further in vivo investigation. The secondary modification of tryptamine substituent seems to be a determining factor of the cytotoxic activity of 4-N-pyrimidinyl amino acids. The activity of the investigated compounds was inversely dependent on their solubility limited by the results of the solubility-activity relationship analysis.
ONCONASE® and Its Therapeutic Potential (2003)

Early work by Shogen and Yoon1 demonstrated an anti-tumor activity in extracts of Northern leopard frog (Rana pipiens) embryos. More than a decade later, in 1987, the main active component of those extracts was isolated and purified by Alfacell M. It turned out to be a small (approximately 12 Kd) basic protein of maternal origin (present also in large amounts in unfertilized oocytes). Its complete amino acid sequence was determined in our laboratory and was found to be unique.2 Surprisingly, the sequence was similar to those of pancreatic ribonuclease A (RNase A, EC 3.1.27.5) and other members of the RNase A superfamily. All 3 catalytic residues of RNase A were conserved as were some of the other residues forming the active site and/or the hydrophobic core.2,3 Thus, the protein seemed to be fully equipped to exert ribonucleolytic activity, and indeed was found capable of degrading highly polymerized RNA from yeast and wheat germ, although the reaction rates were distinctly lower that those of other pancreatic-type ribonucleases.2 It was also cytostatic and cytotoxic to several cancer cell lines in vitro including human submaxillary carcinoma A-253,2,4 and significantly increased the survival of mice bearing M109 Madison Carcinoma5. As we discuss later in this article, the protein also posses strong anti viral activity. We provisionally named the molecule P-30 Protein and later changed the name to Onconase (ONC). In addition to ONC, extracts of Rana pipiens oocytes, contain its natural variant, different by 3 amino acid residues6 and at least 4 variants of a novel cytotoxic ribonuclease, amphinase, recently discovered and sequenced in our laboratory.7 In this article, we discuss the structure and function of ONC as well as therapeutic potential of this enzyme with particular emphasis on its anti viral activity.
Differentiation of embryonic stem cells to a neural fate: A route to re‐building the nervous system? (2004)

The many and varied proposed applications of cell replacement therapies in the treatment of human disease states, particularly those arising from cell loss or dysfunction, have been discussed widely in both the scientific and popular press. Although an attractive concept, cell therapies require the development of a readily available source of donor cells suitable for transplantation. Embryonic stem (ES) cells, with proven ability to differentiate to all cell populations of the embryo and adult in vitro, provide a potential source of therapeutic cells. The differentiation capability of mouse ES cells in vitro has been studied extensively over the last 20 years and the formation of neural precursors and neural cell lineages from mouse ES cells is well established. Cell populations highly enriched/homogenous in neural precursors have been achieved using a variety of chemical or biological inducing agents coupled with selective growth conditions. Preliminary reports suggest that similar neural enrichment is seen when these methodologies are applied to primate and human ES cells. ES cell-derived neural precursors have been analyzed in vitro and in vivo and found to be functionally normal and, after introduction into rodent models of human neurodegenerative diseases, capable of effecting measurable disease recovery. We review progress in the formation of neural precursors from mouse ES cells, particularly the recent reports of directed differentiation of ES in response to biological inductive factors, and assess the transfer of these approaches to human ES cells.
Targeting of amacrine cell neurites to appropriate synaptic laminae in the developing zebrafish retina (2005)

Cellular mechanisms underlying the precision by which neurons target their synaptic partners have largely been determined based on the study of projection neurons. By contrast, little is known about how interneurons establish their local connections in vivo. Here, we investigated how developing amacrine interneurons selectively innervate the appropriate region of the synaptic neuropil in the inner retina, the inner plexiform layer (IPL). Increases (ON) and decreases (OFF) in light intensity are processed by circuits that are structurally confined to separate ON and OFF synaptic sublaminae within the IPL. Using transgenic zebrafish in which the majority of amacrine cells express fluorescent protein, we determined that the earliest amacrine-derived neuritic plexus formed between two cell populations whose somata, at maturity, resided on opposite sides of this plexus. When we followed the behavior of individual amacrine cells over time, we discovered that they exhibited distinct patterns of structural dynamics at different stages of development. During cellular migration, amacrine cells exhibited an exuberant outgrowth of neurites that was undirected. Upon reaching the forming IPL, neurites extending towards the ganglion cell layer were relatively more stable. Importantly, when an arbor first formed, it preferentially ramified in either the inner or outer IPL corresponding to the future ON and OFF sublaminae, and maintained this stratification pattern. The specificity by which ON and OFF amacrine interneurons innervate their respective sublaminae in the IPL contrasts with that observed for projection neurons in the retina and elsewhere in the central nervous system.
Multidomain Synthetic Peptide B2A2 Synergistically Enhances BMP-2 In Vitro (2005)

Treatment of cells with B2A2 alone marginally increased ALP activity. However, B2A2 plus BMP-2 resulted in 5- to 40-fold augmentation of ALP compared with BMP-2 alone in C3H10T1/2 or C2C12 cells, respectively. This synergistic enhancement was observed over a broad concentration range (4-1000 ng/ml BMP-2). B2A2 interacted directly with BMP receptor isoforms (preferentially to BMPR-Ib and ActivinR-II). In cells, B2A2 + BMP-2 led to a repression of MAP kinase and an increase of Smad activation, consistent with known activation pathways of BMP-2. B2A2 was ineffective when paired with other cytokine/growth factors (basic fibroblast growth factor [FGF-2], TGF-beta1, vascular endothelial growth factor [VEGF]). Simultaneous co-administration was not strictly required. Pulse-chase experiments revealed that temporal separations up to 1 h were still effective. B2A2 was also effective when delivered in a polystyrene- or stainless steel-coated surface through a heparin platform (silyl-heparin) while BMP-2 was added exogenously in solution. These results suggest that B2A2 might promote aggregation of receptor subunits, enabling BMP-2 to activate signaling pathways at effectively lower concentrations. Synthetic multidomain constructs like B2A2 may be useful to accelerate bone repair/deposition through augmentation of endogenous levels of BMP-2 or through local BMP-2 contained in artificial or engineered matrices.
Toll-Like Receptor 2 (TLR2)-Dependent-Positive and TLR2-Independent-Negative Regulation of Proinflammatory Cytokines by Mycobacterial Lipomannans (2004)

Lipoarabinomannans (LAM) and lipomannans (LM) are integral parts of the mycobacterial cell wall recognized by cells involved in the innate immune response and have been found to modulate the cytokine response. Typically, mannosylated LAM from pathogenic mycobacteria have been reported to be anti-inflammatory, whereas phosphoinositol-substituted LAM from nonpathogenic species are proinflammatory molecules. In this study, we show that LM from several mycobacterial species, including Mycobacterium chelonae, Mycobacterium kansasii, and Mycobacterium bovis bacillus Calmette-Guérin, display a dual function by stimulating or inhibiting proinflammatory cytokine synthesis through different pathways in murine primary macrophages. LM, but none of the corresponding LAM, induce macrophage activation characterized by cell surface expression of CD40 and CD86 and by TNF and NO secretion. This activation is dependent on the presence of Toll-like receptor (TLR) 2 and mediated through the adaptor protein myeloid differentiation factor 88 (MyD88), but independent of either TLR4 or TLR6 recognition. Surprisingly, LM exerted also a potent inhibitory effect on TNF, IL-12p40, and NO production by LPS-activated macrophages. This TLR2-, TLR6-, and MyD88-independent inhibitory effect is also mediated by LAM from M. bovis bacillus Calmette-Guérin but not by LAM derived from M. chelonae and M. kansasii. This study provides evidence that mycobacterial LM bear structural motifs susceptible to interact with different pattern recognition receptors with pro- or anti-inflammatory effects. Thus, the ultimate response of the host may therefore depend on the prevailing LM or LAM in the mycobacterial envelope and the local host cell receptor availability.
Lipid raft-associated protein sorting in exosomes (2003)

Exosomes are small membrane vesicles secreted by cells upon fusion of multivesicular endosomes with the cell surface. The mechanisms underlying the specific sorting of proteins in exosomal membranes are far from being unraveled. We demonstrate here, using different cells, that some molecules are released in the extracellular medium via their association with lipid raft domains of the exosomal membrane. Various typical raft-associated molecules could be detected by immunoblot in exosomes and Triton X-100-insoluble fractions isolated from exosomes of different origins. Partial localization of major histocompatibility complex (MHC) class II molecules with detergent-resistant fractions isolated from Daudi-secreted exosomes was demonstrated by immunoblot and confirmed by electron microscopy colocalization of MHC class II molecules and ganglioside GM1. Moreover, we found that exosome-associated Lyn (1) had a lower molecular weight compared with Lyn detected in cell-isolated detergent-resistant domains, (2) was absent from the Triton X-100-insoluble fraction isolated from exosomes, and (3) had lost its partitioning capacity in Triton X-114. Exosomal Lyn is probably cleaved by a caspase-3-like activity contained in secreted vesicles. All together, the data highlight the presence of lipid microdomains in exosomal membranes and suggest their participation in vesicle formation and structure, as well as the direct implication of exosomes in regulatory mechanisms.
Reorientation of a liquid crystalline side-chain polymer in electric and magnetic fields investigated by solid-state1H-NMR (1998)

With a capacitor placed in the radio frequency coil of an nuclear magnetic resonance spectrometer it is possible to investigate reorientational processes in liquid crystalline polymers induced by the static magnetic field of the spectrometer and a dynamic electric field between the capacitor plates. In the nematic phase, the alignment of the director is a result of the interplay between two competing fields. The director can be rotated in every desired angle by the simultaneous application of the electric field. The dynamics of the process depends strongly on the strength of the electric field and on the temperature. The arrangement allows the in situ measurement of switching times, of the rotational vicosity γ1, etc. © 1998 John Wiley & Sons, Ltd.
Carbon nanotube forests as top electrodes for AlN-based electroacoustic resonators (2014)

High sensitive sensors are one of the goals of the modern society due to an increasing necessity for real-time monitoring. To achieve this, new devices and materials are being developed nowadays. In particular, electroacoustic resonators have gained importance in the chemical and biological sensors field owing to their promising performances. Although important advances have been made in the electroacoustic field, additional work is still required to improve the quality factor of the acoustic resonators and their sensing layer. Carbon nanotubes (CNTs) are good candidate materials to act as sensing layers but they can also be used as electrodes. Here we use CNT forests as top electrodes for solidly mounted resonators (SMR) based in AlN thin films and we study their influence on the latters. We prove that, under specific conditions, SMRs do not degrade during the high-temperature CNTs growth process. Also, CNT forests have a weak influence on the SMRs acoustic characteristics. The main drawback regarding their use is a large parasitic resistance presented by the devices. However, this can be solved by depositing denser CNT forests or by growing them on metallic top electrodes layers. SMRs with CNT top electrode can be used as high sensitive and high selective gas sensors due to their high performance and increased functionalized area that CNTs offer.
Prodrugs of Anthracyclines for Use in Antibody-Directed Enzyme Prodrug Therapy (1998)

A series of new prodrugs of daunorubicin and doxorubicin which are candidates for antibody-directed enzyme prodrug therapy (ADEPT) is reported. These compounds (25a,b,c and 32a,b,c) have been designed to generate cytotoxic drugs after activation with beta-glucuronidase. As expected, recovery of the active drug was observed after enzymatic cleavage by Escherichia coli beta-glucuronidase as well as by a fusion protein which has been obtained from human beta-glucuronidase and humanized CEA-specific binding region. The six prodrugs are highly stable and are more than 100-fold less cytotoxic than doxorubicin against murine L1210 cell lines. The ortho-substituted phenyl carbamates 25a,b,c are better substrates for beta-glucuronidase than the corresponding para-substituted analogues. After taking into account additional factors such as stability in plasma and kinetics of enzymatic cleavage, we selected the o-nitro prodrug 25c for clinical trials.
Regulation of the Inflammatory Response in Cardiac Repair (2012)

Myocardial necrosis triggers an inflammatory reaction that clears the wound from dead cells and matrix debris, while activating reparative pathways necessary for scar formation. A growing body of evidence suggests that accentuation, prolongation, or expansion of the postinfarction inflammatory response results in worse remodeling and dysfunction following myocardial infarction. This review manuscript discusses the cellular effectors and endogenous molecular signals implicated in suppression and containment of the inflammatory response in the infarcted heart. Clearance of apoptotic neutrophils, recruitment of inhibitory monocyte subsets and regulatory T cells, macrophage differentiation and pericyte/endothelial interactions may play an active role in restraining postinfarction inflammation. Multiple molecular signals may be involved in suppressing the inflammatory cascade. Negative regulation of toll-like receptor signaling, downmodulation of cytokine responses, and termination of chemokine signals may be mediated through the concerted action of multiple suppressive pathways that prevent extension of injury and protect from adverse remodeling. Expression of soluble endogenous antagonists, decoy receptors, and posttranslational processing of bioactive molecules may limit cytokine and chemokine actions. Interleukin-10, members of the transforming growth factor-β family, and proresolving lipid mediators (such as lipoxins, resolvins, and protectins) may suppress proinflammatory signaling. In human patients with myocardial infarction, defective suppression, and impaired resolution of inflammation may be important mechanisms in the pathogenesis of remodeling and in progression to heart failure. Understanding of inhibitory and proresolving signals in the infarcted heart and identification of patients with uncontrolled postinfarction inflammation and defective cardiac repair is needed to design novel therapeutic strategies.
Zinc interactions and conserved motifs of the cGMP-binding cGMP-specific phosphodiesterase suggest that it is a zinc hydrolase. (1994)

cGMP-binding cGMP-specific phosphodiesterase (cG-BPDE) binds tightly to a Zn(2+)-chelate column (Francis, S. H., and Corbin, J. D. (1988) Methods Enzymol. 159, 722-729). Using three different approaches, Zn2+ is now shown to bind to cG-BPDE, and the Kd is determined to be approximately 0.5 microM, with a binding stoichiometry of approximately 3 mol of Zn2+/mol of monomer. A similar concentration range of Zn2+ (0.05-1 microM Zn2+) also supports phosphodiesterase (PDE) catalytic activity. The Zn2+ binding to cG-BPDE is not diminished by, nor is catalysis supported by, relatively high concentrations of Cu2+, Cd2+, Ca2+, or Fe2+. Neither cGMP nor 3-isobutyl-1-methylxanthine affects Zn2+ binding under the conditions used. Mn2+, Co2+, or Mg2+ supports catalysis, but only at significantly higher concentrations (4-, 15-, and 250-fold, respectively) than that required for Zn2+. Two tandem amino acid sequences, which are conserved in the catalytic domains of all characterized mammalian PDEs, resemble the single sequence motif that has been shown to coordinate Zn2+ in the catalytic sites of Zn2+ hydrolases such as thermolysin.
Astrocyte Control of Synaptic Transmission and Neurovascular Coupling (2006)

From a structural perspective, the predominant glial cell of the central nervous system, the astrocyte, is positioned to regulate synaptic transmission and neurovascular coupling: the processes of one astrocyte contact tens of thousands of synapses, while other processes of the same cell form endfeet on capillaries and arterioles. The application of subcellular imaging of Ca2+ signaling to astrocytes now provides functional data to support this structural notion. Astrocytes express receptors for many neurotransmitters, and their activation leads to oscillations in internal Ca2+. These oscillations induce the accumulation of arachidonic acid and the release of the chemical transmitters glutamate, d-serine, and ATP. Ca2+ oscillations in astrocytic endfeet can control cerebral microcirculation through the arachidonic acid metabolites prostaglandin E2 and epoxyeicosatrienoic acids that induce arteriole dilation, and 20-HETE that induces arteriole constriction. In addition to actions on the vasculature, the release of chemical transmitters from astrocytes regulates neuronal function. Astrocyte-derived glutamate, which preferentially acts on extrasynaptic receptors, can promote neuronal synchrony, enhance neuronal excitability, and modulate synaptic transmission. Astrocyte-derived d-serine, by acting on the glycine-binding site of the N-methyl-d-aspartate receptor, can modulate synaptic plasticity. Astrocyte-derived ATP, which is hydrolyzed to adenosine in the extracellular space, has inhibitory actions and mediates synaptic cross-talk underlying heterosynaptic depression. Now that we appreciate this range of actions of astrocytic signaling, some of the immediate challenges are to determine how the astrocyte regulates neuronal integration and how both excitatory (glutamate) and inhibitory signals (adenosine) provided by the same glial cell act in concert to regulate neuronal function.