gebhart/patrepeval huggingface dataset:
Investigating the Sensitivity of NAD+-dependent Sirtuin Deacylation Activities to NADH (2016)

Protein lysine posttranslational modification by an increasing number of different acyl groups is becoming appreciated as a regulatory mechanism in cellular biology. Sirtuins are class III histone deacylases that use NAD(+)as a co-substrate during amide bond hydrolysis. Several studies have described the sirtuins as sensors of the NAD(+)/NADH ratio, but it has not been formally tested for all the mammalian sirtuinsin vitro To address this problem, we first synthesized a wide variety of peptide-based probes, which were used to identify the range of hydrolytic activities of human sirtuins. These probes included aliphatic ϵ-N-acyllysine modifications with hydrocarbon lengths ranging from formyl (C1) to palmitoyl (C16) as well as negatively charged dicarboxyl-derived modifications. In addition to the well established activities of the sirtuins, "long chain" acyllysine modifications were also shown to be prone to hydrolytic cleavage by SIRT1-3 and SIRT6, supporting recent findings. We then tested the ability of NADH, ADP-ribose, and nicotinamide to inhibit these NAD(+)-dependent deacylase activities of the sirtuins. In the commonly used 7-amino-4-methylcoumarin-coupled fluorescence-based assay, the fluorophore has significant spectral overlap with NADH and therefore cannot be used to measure inhibition by NADH. Therefore, we turned to an HPLC-MS-based assay to directly monitor the conversion of acylated peptides to their deacylated forms. All tested sirtuin deacylase activities showed sensitivity to NADH in this assay. However, the inhibitory concentrations of NADH in these assays are far greater than the predicted concentrations of NADH in cells; therefore, our data indicate that NADH is unlikely to inhibit sirtuinsin vivo These data suggest a re-evaluation of the sirtuins as direct sensors of the NAD(+)/NADH ratio.
MyD88-Dependent and -Independent Murine Cytomegalovirus Sensing for IFN-α Release and Initiation of Immune Responses In Vivo (2005)

Antiviral immunity requires early and late mechanisms in which IFN-alpha and IL-12 play major roles. However, the initial events leading to their production remain largely unclear. Given the crucial role of TLR in innate recognition, we investigated their role in antiviral immunity in vivo. Upon murine CMV (MCMV) infection, both MyD88-/- and TLR9-/- mice were more susceptible and presented increased viral loads compared with C57BL/6, TLR2-/-, TLR3-/-, or TLR4-/- mice. However, in terms of resistance to infection, IFN-alpha production and in many other parameters of early inflammatory responses, the MyD88-/- mice showed a more defective response than TLR9-/- mice. In the absence of the TLR9/MyD88 signaling pathway, cytokine production was dramatically impaired with a complete abolition of bioactive IL-12p70 serum release contrasting with a high flexibility for IFN-alpha release, which is initially (36 h) plasmacytoid dendritic cell- and MyD88-dependent, and subsequently (44 h) PDC-, MyD88-independent and, most likely, TLR-independent. NK cells from MCMV-infected MyD88-/- and TLR9-/- mice displayed a severely impaired IFN-gamma production, yet retained enhanced cytotoxic activity. In addition, dendritic cell activation and critical inflammatory cell trafficking toward the liver were still effective. In the long term, except for isotype switching to MCMV-specific IgG1, the establishment of Ab responses was not significantly altered. Thus, our results demonstrate a critical requirement of TLR9 in the process of MCMV sensing to assure rapid antiviral responses, coordinated with other TLR-dependent and -independent events that are sufficient to establish adaptive immunity.
Flexibility between the Protease and Helicase Domains of the Dengue Virus NS3 Protein Conferred by the Linker Region and Its Functional Implications (2010)

The dengue virus (DENV) NS3 protein is essential for viral polyprotein processing and RNA replication. It contains an N-terminal serine protease region (residues 1-168) joined to an RNA helicase (residues 180-618) by an 11-amino acid linker (169-179). The structure at 3.15 A of the soluble NS3 protein from DENV4 covalently attached to 18 residues of the NS2B cofactor region (NS2B(18)NS3) revealed an elongated molecule with the protease domain abutting subdomains I and II of the helicase (Luo, D., Xu, T., Hunke, C., Grüber, G., Vasudevan, S. G., and Lescar, J. (2008) J. Virol. 82, 173-183). Unexpectedly, using similar crystal growth conditions, we observed an alternative conformation where the protease domain has rotated by approximately 161 degrees with respect to the helicase domain. We report this new crystal structure bound to ADP-Mn(2+) refined to a resolution of 2.2 A. The biological significance for interdomain flexibility conferred by the linker region was probed by either inserting a Gly residue between Glu(173) and Pro(174) or replacing Pro(174) with a Gly residue. Both mutations resulted in significantly lower ATPase and helicase activities. We next increased flexibility in the linker by introducing a Pro(176) to Gly mutation in a DENV2 replicon system. A 70% reduction in luciferase reporter signal and a similar reduction in the level of viral RNA synthesis were observed. Our results indicate that the linker region has evolved to an optimum length to confer flexibility to the NS3 protein that is required both for polyprotein processing and RNA replication.
Oligocarbamate Molecular Transporters:  Design, Synthesis, and Biological Evaluation of a New Class of Transporters for Drug Delivery (2002)

Molecular transporters have the ability to deliver drugs and probe molecules into cells and tissues irrespective of their physical properties. We now report the design, synthesis, and biological evaluation of a new family of molecular transporters, guanidinylated oligocarbamates that enable exceptionally efficient uptake into cells and tissues. The synthesis features a solid-phase stepwise oligomerization to obtain the oligocarbamates and a single step perguanidinylation for the facile introduction of up to nine guanidinium groups. The oligocarbamate 9-mer is found to be among the most efficient transporters known, entering cells faster than even d-Arg9 and HIV-1 Tat49-57. Significantly, this new family of transporters also enables uptake into the formidable skin barrier of a probe molecule that by itself does not penetrate skin.
Cell Death During Development of the Nervous System (1991)

The brain's default mode network consists of discrete, bilateral and symmetrical cortical areas, in the medial and lateral parietal, medial prefrontal, and medial and lateral temporal cortices of the human, nonhuman primate, cat, and rodent brains. Its ...Read More
Effect of Arbutin on Melanogenic Proteins in Human Melanocytes (1998)

The inhibitory effect of arbutin, a naturally occurring beta-D-glucopyranoside derivative of hydroquinone, on melanogenesis was studied biochemically by using human melanocytes in culture. Cells were cultured in the presence of different concentrations of arbutin. The maximum concentration of arbutin that was not inhibitory to growth of the cells was 100 micrograms/ml. At that concentration, melanin synthesis was inhibited significantly by approximately 20% after 5 days, compared with untreated cells. This phenotypic change was associated with the inhibition of tyrosinase and DHICA polymerase activities, and the degree of inhibition was dose dependent. No significant difference in DOPAchrome tautomerase (DT) activity was observed before or after arbutin treatment. Western blotting experiments revealed there were no changes in protein content or in molecular size of tyrosinase, TRP-1 or TRP-2, indicating that inhibition of tyrosinase activity by arbutin might be due to effects at the post-translational level.
Expanding generality of surface-enhanced Raman spectroscopy with borrowing SERS activity strategy (2007)

Surface-enhanced Raman scattering (SERS) was discovered three decades ago and has gone through a tortuous pathway to develop into a powerful diagnostic technique. Recently, the lack of substrate, surface and molecular generalities of SERS has been circumvented to a large extent by devising and utilizing various nanostructures by many groups including ours. This article aims to present our recent approaches of utilizing the borrowing SERS activity strategy mainly through constructing two types of nanostructures. The first nanostructure is chemically synthesized Au nanoparticles coated with ultra-thin shells (ca. one to ten atomic layers) of various transition metals, e.g., Pt, Pd, Ni and Co, respectively. Boosted by the long-range effect of the enhanced electromagnetic (EM) field generated by the highly SERS-active Au core, the originally low surface enhancement of the transition metal can be substantially improved giving total enhancement factors up to 10(4)-10(5). It allows us to obtain the Raman spectra of surface water, having small Raman cross-section, on several transition metals for the first time. To expand the surface generality of SERS, tip-enhanced Raman spectroscopy (TERS) has been employed. With TERS, a nanogap can be formed controllably between an atomically flat metal surface and the tip with an optimized shape, within which the enhanced EM field from the tip can be coupled (borrowed) effectively. Therefore, one can obtain surface Raman signals (TERS signals) from adsorbed species at Au(110), Au(111) and, more importantly, Pt(l10) surfaces. The enhancement factor achieved on these single crystal surfaces can be up to 106, especially with a very high spatial resolution down to about 14 nm. To fully accomplish the borrowing strategy from different nanostructures and to explain the experimental observations, a three-dimensional finite-difference time-domain method was used to calculate and evaluate the local EM field on the core-shell nanoparticle surfaces and the TERS tips. Finally, prospects and further developments of this valuable strategy are briefly discussed with emphasis on the emerging experimental methodologies.
Bucillamine, a thiol antioxidant, prevents transplantation-associated reperfusion injury (2002)

Ischemia/reperfusion (I/R) injury is a serious potential threat to outcomes in organ transplantation and other clinical arenas in which there is temporary interruption of blood flow. I/R is a frequent cause of primary failure in organ transplantation. We hypothesized that the antioxidant bucillamine, a potent sulfhydryl donor, would protect against I/R injury in high-risk organ transplants. Because livers subjected to prolonged ischemia and very fatty livers are highly susceptible to severe I/R injury, we studied the effect of bucillamine in three animal models of liver transplantation: two ex vivo models of isolated perfused livers, either normal or fatty rat livers, and an in vivo model of syngenic orthotopic liver transplants in rats. In all models, livers were deprived of oxygen for 24 h before either ex vivo reperfusion or transplantation. In the ex vivo models, bucillamine treatment significantly improved portal vein blood flow and bile production, preserved normal liver architecture, and significantly reduced liver enzyme release and indices of oxidative stress. Moreover, bucillamine treatment significantly increased levels of reduced glutathione in the liver and lowered levels of oxidized glutathione in both liver and blood. In rats subjected to liver transplants, bucillamine significantly enhanced survival and protected against hepatic injury. Possible mechanisms of this protection include prevention of excessive accumulation of toxic oxygen species, interruption of redox signaling in hepatocytes, and inhibition of macrophage activation. This study demonstrates the potential utility of bucillamine or other cysteine-derived thiol donors for improving outcomes in organ transplantation and other clinical settings involving I/R injury.
Temporal Profiles and Cellular Sources of Three Nitric Oxide Synthase Isoforms in the Brain after Experimental Contusion (2000)

In this model, the most striking finding regarding NO-producing enzymes was the expression of iNOS in polymorphonuclear cells and macrophages, cells that invade injured brain tissue. iNOS is thus implicated as a therapeutic target in contusional injuries. This pattern of NOS expression cannot be generalized to all types of brain injuries. The different compartments and cells that can produce NO are differentially regulated; therefore, compartmentalization can explain why NO is beneficial or detrimental, depending on the circumstances. A knowledge of different potential sites and sources of NO is required for any attempts to interfere with the pathophysiological properties of NO.
CD4+ CD25+ Regulatory T Cell Selection (2004)

Accumulating evidence indicates that regulatory T cells play a crucial role in preventing autoimmunity. To examine the processes by which regulatory CD4(+) T cells are produced during immune repertoire formation, we have developed transgenic mice that express the influenza virus hemagglutinin (HA) and coexpress major histocompatibility complex class II-restricted T cell receptors (TCRs) with varying affinities for the HA-derived CD4(+) T cell determinant S1. We show that interactions with a single self-peptide can induce thymocytes bearing an autoreactive TCR to undergo selection to become CD4(+) CD25(+) regulatory T cells, and that thymocytes bearing TCRs with low affinity for S1 do not undergo selection into this pathway. We show that CD4(+) thymocytes with identical specificity for the S1 self-peptide can undergo overt deletion versus abundant selection to become CD4(+) CD25(+) regulatory T cells in response to variations in expression of the S1 self-peptide in different lineages of HA transgenic mice. We also show that CD4(+) CD25(+) T cells proliferate in response to their selecting self-peptide in the periphery. Moreover, they do not proliferate in response to lymphopenia in the absence of the selecting self-peptide, reflecting a low level of expression of the high-affinity receptor for IL-7 (CD127) relative to conventional CD4(+) T cells. These studies are determining how specificity for self-peptides directs the thymic selection and peripheral expansion of CD4(+) CD25(+) regulatory T cells. Moreover, the differing responsiveness of CD4(+) CD25(+) regulatory T cells to cytokine- versus self-peptide-mediated signals may direct their accumulation to sites where the self-peptide is expressed.
Recent research in marine natural products: the puupehenones (1979)

Isolation and structural elucidation of three sponge metabolites, puupehenone (4) and its monochloro (~) and monobromo (J~) derivatives is descri~ed, The compounds are products of mixed ~{osynthesis and consist of a c 15 unrearranged drimane and a 1,2,4-trihydroxybenzene moiety, Halogen is incorporated in the aromatic part of the molecule and the chlorine isomer predominates over the bromine compound. The structures are based on spectral data and on single crystal x-ray diffraction of a c 1 8 ozonolysis product (~) of puupehenone (~). Puupehenone ~) possesses moderate activity against gram-positive bacteria and against fungi.
Evaluation of Immunoglobulins from Plant Cells (1991)

Expression of cDNA constructs encoding full-length mouse immunoglobulin chains with their native leader sequences or fusion constructs substituting the native leader with a pre-pro sequence derived from Saccharomyces cerevisiae yielded blocked N-termini on the gamma chain or the correct amino terminal sequence on the mature kappa chain. Lectin binding assays revealed that assembled immunoglobulin complexes contained a glycosylated heavy chain. The attached glycan was resistant to digestion by endoglycosidase H and its lectin binding pattern was distinguishable from that of the mammalian glycan. The results indicated processing of the immunoglobulin carbohydrate in the tobacco Golgi to yield a complex oligosaccharide. Secretion of antibody by protoplasts isolated from regenerated transgenic plants or from suspension callus cells was demonstrated by pulse-chase labeling experiments. When purified, the tobacco-produced antibody was found to possess the antigen binding and catalytic properties of the murine monoclonal antibody. Kinetic parameters (Km, Ki, Vmax, and kcat) of the tobacco-derived antibody were comparable to those of the mouse-derived antibody. The results in general show that the endomembrane system of tobacco cells possesses cognate mechanisms for the recognition of diverse leader sequences. These signals can be used to initiate the assembly, processing, and secretion by plant cells of complex foreign proteins.
The TCR/CD3 Complex: Opening the Gate to Successful Vaccination (2009)

The success of vaccination is directly or indirectly based on the specificity of antigen recognition by T lymphocytes, their efficient activation and expansion, and the generation of vaccine-specific effectors and memory cells. These traits are largely dependent on the correct assembly and expression of sufficient number of functional TCR/CD3 complexes in the cell surface. In this review, some of the genetic and epigenetic factors that determine the correct assembly and structure of the TCR/CD3 complex are summarized. Those physiologic or pathologic factors leading to natural variations, or pathologic alterations of the standard that might lead to poor response to vaccination and that could give some possibilities to pharmacological intervention are emphasized.
Adenovirus Serotype 7 Retention in a Late Endosomal Compartment prior to Cytosol Escape Is Modulated by Fiber Protein (2001)

The intracellular trafficking of adenovirus (Ad) subgroup B (e.g., Ad7) differs from that of subgroup C (e.g., Ad5) in that Ad5 rapidly escapes from endocytic compartments following infection whereas Ad7 accumulates in organelles. To assess the hypothesis that Ad7 is targeted to the lysosomal pathway, Ad7 and Ad5 were conjugated with fluorophores and their trafficking in A549 epithelial cells was analyzed by fluorescence microscopy. Within 1 h after infection, Ad7, but not Ad5, accumulated in the cytoplasm of A549 cells. The pH in the environment of Ad5 was nearly neutral (pH 7), while Ad7 occupied acidic compartments (pH 5) over the first 2 h with a gradual shift toward neutrality by 8 h. Ad7 partially colocalized with alpha(2)-macroglobulin and late endosomal and lysosomal marker proteins, including Rab7, mannose-6-phosphate receptor, and LAMP-1. The pH optimum for membrane lysis by Ad7, as well as a chimeric Ad5 capsid that expressed the Ad7 fiber (Ad5fiber7), was pH 5.5, while that for lysis by Ad5 was pH 6.0. Thus, the native trafficking pathway for Ad7 involves residence in late endosomes and lysosomes, with information encoded in the Ad7 fiber acting as a pH-dependent trigger for membrane lysis and escape to the cytosol.
Differential expression of Kir4.1 and aquaporin 4 in the retina from endotoxin-induced uveitis rat. (2007)

EIU differently alters the expression of Kir4.1 and AQP4 in the retina. The differential expression of Kir4.1 and AQP4 during EIU implies a disturbance of water and potassium transport in the retina, which may contribute to the retinal edema during ocular inflammation.
Effect of concentration of compounds containing iron on the growth of Porphyromonas gingivalis (1995)

We examined the effect of the concentration of various types of iron molecules on the regulation of growth of Porphyromonas gingivalis. Bacterial growth was monitored spectrophotometrically. The hemin-depleted cells of P. gingivalis 381 were incubated in the basal medium plus test substrates such as hemoglobin, hemin, transferrin and various inorganic iron compounds. The relationship between the specific growth rate of organisms and the concentration of iron-containing compounds was determined. The value of Ks, a parameter analogous to the Michaelis-Menten constant, was estimated. P. gingivalis 381 showed a Kss value of 3.85, 4.91 and 0.0017 μM for hemin, transferrin and hemoglobin, respectively. However, the inorganic iron compounds tested did not support growth of P. gingivalis. These findings suggest that P. gingivalis utilizes hemoglobin as an iron source much more effectively than other iron-containing compounds under an iron-limited environment.
Dynamics of Cervical Remodeling during Pregnancy and Parturition: Mechanisms and Current Concepts (2007)

The cervix serves as a protective barrier from invading microorganisms and as a structural barrier to delivery of the fetus. Among all biological processes, the phenomenal connective tissue remodeling that occurs in the cervix during and after parturition is unparalleled in scope and magnitude. The process of connective tissue remodeling in the cervix during pregnancy occurs in four stages: softening, ripening, dilation, and repair. Although overlapping in time, each stage is uniquely regulated. Results from studies using serial measurements of cervical length indicate that cervical ripening precedes myometrial contractions of labor by several weeks, suggesting that parturition in women is a process of long duration and that uterine contractions of labor are late events in the parturition process. A clear understanding of the biologic mechanisms that regulate cervical remodeling during pregnancy is needed to influence the preterm birth rate and to develop strategies to prevent preterm dilation of the cervix.
DNA-Minus Temperature-Sensitive Mutants of Adenovirus Type 5 Help Adenovirus-Associated Virus Replication (1976)

Efficient potentiation of adenovirus-associated viruses (AAV) replication occurs in coinfections with either of two DNA-minus temperature-sensitive mutants of adenovirus type 5 (Ad5), ts125 and ts149. The helper activity of these mutants does not result from leakiness. At the nonpermissive termperature (39.5 C) there was little or no detectable adenovirus DNA synthesis, and only a relatively low level of adenovirus transcription was observed. However, the synthesis of AAV DNA and RNA and the yield of infectious AAV were comparable in amounts to those found when wild-type Ad5 was the helper. Furthermore, an apparent lag in the initiation of AAV transcription after the onset of AAV DNA synthesis was seen in coinfections with both wild type or ts125. These findings strongly suggest that the adenovirus factor(s) required for AAV multiplication is produced early in the adenovirus DNA replication, this requirement does not include all factors directly needed for adenovirus DNA synthesis.
Degradation of surfactant protein D by alveolar macrophages (1998)

Surfactant protein (SP) D is a pulmonary surfactant-associated protein that may function in lung host defense. SP-D is produced by alveolar type II cells and nonciliated bronchiolar epithelial (Clara) cells of the airway and is secreted into the air space. Here we investigated whether alveolar macrophages degraded SP-D in vitro. We also examined the effects of SP-A and lipids on SP-D metabolism. The results showed that alveolar macrophages bound and degraded SP-D in a time- and temperature-dependent fashion. After 100 min of incubation, the formation of trichloroacetic acid-soluble degradation products increased 4-fold in the medium and 30-fold in the cells. The degradation of SP-D was via a cell-associated process because SP-D was not degraded when incubated in medium previously conditioned by alveolar macrophages. Gel autoradiography of cell lysate samples after incubation with 125I-labeled SP-D demonstrated an increase in degradation products, further confirming the degradation of SP-D by alveolar macrophages. In addition, the degradation of SP-D was not affected by coincubation with SP-A or surfactant-like liposomes containing either phosphatidylglycerol or phosphatidylinositol. In conclusion, alveolar macrophages rapidly degrade SP-D and may play an important role in SP-D turnover and clearance.