gebhart/patrepeval huggingface dataset:
Specific amino acids in the BAR domain allow homodimerization and prevent heterodimerization of sorting nexin 33 (2010)

SNX33 (sorting nexin 33) is a homologue of the endocytic protein SNX9 and has been implicated in actin polymerization and the endocytosis of the amyloid precursor protein. SNX33 belongs to the large family of BAR (Bin/amphiphysin/Rvs) domain-containing proteins, which alter cellular protein trafficking by modulating cellular membranes and the cytoskeleton. Some BAR domains engage in homodimerization, whereas other BAR domains also mediate heterodimerization between different BAR domain-containing proteins. The molecular basis for this difference is not yet understood. Using co-immunoprecipitations we report that SNX33 forms homodimers, but not heterodimers, with other BAR domain-containing proteins, such as SNX9. Domain deletion analysis revealed that the BAR domain, but not the SH3 (Src homology 3) domain, was required for homodimerization of SNX33. Additionally, the BAR domain prevented the heterodimerization between SNX9 and SNX33, as determined by domain swap experiments. Molecular modelling of the SNX33 BAR domain structure revealed that key amino acids located at the BAR domain dimer interface of the SNX9 homodimer are not conserved in SNX33. Replacing these amino acids in SNX9 with the corresponding amino acids of SNX33 allowed the mutant SNX9 to heterodimerize with SNX33. Taken together, the present study identifies critical amino acids within the BAR domains of SNX9 and SNX33 as determinants for the specificity of BAR domain-mediated interactions and suggests that SNX9 and SNX33 have distinct molecular functions.
Point-by-point fabrication of micro-Bragg gratings in photosensitive fibre using single excimer pulse refractive index modification techniques (1993)

Optical fibre Bragg reflectors have been fabricated using a single pulse of high power 249 nm excimer laser light to photoinduce point-by-point each individual index element forming the grating. Bragg reflectors with a length of 360 μm and reflectivity of 70% have been made.
A PD‐1 polymorphism is associated with disease progression in multiple sclerosis (2005)

T cells are considered to play a pivotal role in orchestrating the self-reactive immune responses in multiple sclerosis (MS). Programmed death 1 (PD-1) is a member of the B7/CD28 superfamily of costimulatory molecules exerting inhibitory functions on T cells. Recently, an intronic 7146G/A polymorphism within the PD-1 gene was described and suggested to be associated with autoimmunity. We investigated whether this genetic polymorphism is a genetic modifier for risk and progression of MS. Blood samples from 939 German MS patients (mean age, 39 years; range, 13-71; 566 patients [60%] with relapsing-remitting MS, 279 (30%) with secondary, and 94 (10%) with primary progressive MS) and 272 healthy white controls were tested. Genotyping was performed by polymerase chain reaction and restriction enzyme digestion; results were confirmed by automatic sequencing. A significant association of the mutated allele with a progressive disease course was detected (44% 7146G vs 56% 7146A, chi(2) p = 0.002). Consequences of the PD-1 mutation for T-cell function were assessed ex vivo in some patients using microsphere-stimulated peripheral blood lymphocytes and purified CD4 cells. Importantly, PD-1-mediated inhibition of T-cell cytokine secretion (interferon-gamma) is impaired in patients carrying the PD-1 polymorphism. In conclusion, our data suggest that PD-1 polymorphism is a genetic modifier of the progression of MS, possibly through inducing a partial defect in PD-1-mediated inhibition of T-cell activation.
Studies on antibacterial properties of gentian violet impregnated silastic. (1993)

The antibacterial activity of gentian violet (GV) impregnated silastic discs was studied by measuring the zone of inhibition (ZOI), (in mm) produced by the discs planted on Staphylococcus epidermidis seeded agar plates. The effect of varying concentration of GV, the duration of antibacterial activity and effect of autoclaving were studied. The mean ZOI for 1 per cent GV was 19.28 +/- 0.89 mm and for 2 per cent GV it was 22.55 +/- 0.71 mm (P < 0.001). There was no significant difference between GV concentrations of 2-5 per cent. Over a period of 1-5 wk, no significant difference was found in the antibacterial activity of GV for any of the concentrations. In each of the concentrations there was a significant reduction in the ZOI after multiple autoclavings. The study thus indicates that it is possible to impart antibacterial properties to silastic implants so that their colonization with Staph. epidermidis can be prevented and this finding has obvious clinical implications.
Mechanism of the Hydrosilylation Reaction of Alkenes at Porous Silicon:  Experimental and Computational Deuterium Labeling Studies (2005)

The mechanism of the formation of Si-C bonded monolayers on silicon by reaction of 1-alkenes with hydrogen-terminated porous silicon surfaces has been studied by both experimental and computational means. We propose that monolayer formation occurs via the same radical chain process as at single-crystal surfaces: a silyl radical attacks the 1-alkene to form both the Si-C bond and a radical center on the beta-carbon atom. This carbon radical may then abstract a hydrogen atom from a neighboring Si-H bond to propagate the chain. Highly deuterated porous silicon and FTIR spectroscopy were used to provide evidence for this mechanism by identifying the IR bands associated with the C-D bond formed in the proposed propagation step. Deuterated porous silicon surfaces formed by galvanostatic etching in 48% DF/D2O:EtOD (1:1) electrolytes showed a 30% greater density of Si-D sites on the surface than Si-H sites on hydrogen-terminated porous silicon surfaces prepared in the equivalent H-electrolyte. The thermal reaction of undec-1-ene and the Lewis acid catalyzed reaction of styrene on a deuterated surface both resulted in alkylated surfaces with the same C-C and C-H vibrational features as formed in the corresponding reactions at a hydrogen-terminated surface. However, a broad band around 2100 cm(-1) was observed upon alkylating the deuterated surfaces. Ab initio and density functional theory calculations on small molecule models showed that the integrated absorbance of this band was comparable to the intensity expected for the C-D stretches predicted by the chain mechanism. The calculations also indicate that there is substantial interaction between the hydrogen atoms on the beta-carbons and the hydrogen atoms on the Si(111)-H surface. These broad 2100 cm(-1) features are therefore assigned to C-D bands arising from the involvement of surface D atoms in the hydrosilylation reactions, while the line broadening can be explained partly by interaction with neighboring surface atoms/groups.
Regioselective α- and β-metallations of thiophene derivatives bearing the 4,4-dimethyloxazolin-2-yl group. Application of the method to syntheses of 2,3- and 2,5-disubstituted thiophene derivatives (1985)

The effects of change of solvent, metallating agent, reaction time and temperature, and of the presence or absence of agents capable of complex formation with either the lithium cation or the oxazoline moiety, on the lithiation of 4,4-dimethyl-2-(2-thienyl)oxazoline are explored. Conditions are thereby estab-lished for high-yielding syntheses of the 3- and 5-lithio-intermediates and for control of regioselectivity of metallation. The nucleophilicity of the 3-lithio-intermediate is profoundly solvent dependent, and appropriate conditions for reaction of both 3- and 5-lithiated species with a wide variety of electrophiles are presented. Syntheses of a range of 2,3- and 2,5-disubstituted thiophene derivatives have thereby been achieved, utilising, in addition, a new method for the transformation of oxazolino into carboxy functionality.The balance between basicity and nucleophilicity of the 3-lithio-intermediate in its reaction with [1H6]- and [2H6]-acetone is shown to be sensitive to isotope effects.
Stromelysin-1 (MMP-3) in synovial fluid of patients with rheumatoid arthritis has potential to cleave membrane bound Fas ligand. (2001)

There was significant correlation between the concentration of sFasL and MMP-3 in SF of patients with RA. In addition, our data indicate that the shedding of FasL may be regulated by MMP-3 in the joint of patients with RA.
Icosahedral Virus Particles as Polyvalent Carbohydrate Display Platforms (2003)

Sugar-coated viruses behave as large dendrimeric poly(carbohydrates). Readily prepared from the icosahedral cowpea mosaic virus (one-twelfth of the structure of this scaffold is shown here, with attachment points in yellow) and electrophilic sugar derivatives, the resulting particles bind strongly to the lectin concanavalin-A, forming cross-linked networks. Measurements of binding strength demonstrate effective polyvalencies comparable to the most potent dendrimer- and polymer-based systems reported to date, with the added advantage of near atomic-resolution control over structure.
Four waveplate dual tuner for birefringent filters and multiplexers (1987)

A Solc-type birefringent filter with five crystal elements in a wavelength multiplexer configuration is tuned with a minimum number of waveplates by means of a new four waveplate dual tuner that adds equal retardations to two elements simultaneously.
A Combination of Anti-CD15 Monoclonal Antibody PM-81 and 4-Hydroperoxycyclophosphamide Augments Tumor Cytotoxicity While Sparing Normal Progenitor Cells (1994)

A cyclophosphamide congener, 4-hydroperoxycyclophosphamide (4HC), has been used to purge bone marrow (BM) of residual leukemia cells ex vivo for use in support of high-dose chemotherapy for patients with acute myeloid leukemia (AML) undergoing autologous BM transplantation (ABMT). The efficacy and toxicity of 4HC are dose-related. The maximally tolerated concentration, 60-100 micrograms/ml, is toxic to tumor cells but also to normal committed hematopoietic progenitor cells. The anti-CD15 monoclonal antibody (mAb) PM-81 has also been employed for purging BM in patients with AML. In some patients, all tumor cells may not be lysed due to antigenic heterogeneity. Because the two agents used individually are associated with potential limitations in terms of toxicity to normal cells and efficacy of tumor cell purging, using these agents together might have advantages. In fact, in this study the use of these two agents together in subtherapeutic concentration ranges as single agents revealed killing of cells from the HL60 and NB4 promyelocytic leukemia cell lines in addition to cells from patients with AML while sparing normal progenitor cells. Surprisingly, not only did the combination enhance killing of tumor cells, but the order of addition of the two agents was important in maximizing toxicity to tumor cells. Adding mAb+complement (C') first or simultaneously to 4HC was less effective than adding 4HC first followed by mAb + C'. This combination regimen was toxic to HL60 and NB4 leukemia cells that may not be killed by the mAb alone due to antigen-negative tumor cells or by low concentrations of 4HC.(ABSTRACT TRUNCATED AT 250 WORDS)
Stable SNARE Complex Prior to Evoked Synaptic Vesicle Fusion Revealed by Fluorescence Resonance Energy Transfer (2001)

Although it is clear that soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein receptor (SNARE) complex plays an essential role in synaptic vesicle fusion, the dynamics of SNARE assembly during vesicle fusion remain to be determined. In this report, we employ fluorescence resonance energy transfer technique to study the formation of SNARE complexes. Donor/acceptor pair variants of green fluorescent protein (GFP), cyan fluorescent protein (CFP), and yellow fluorescent protein (YFP) are fused with the N termini of SNAP-25 and synaptobrevin, respectively. In vitro assembly of SNARE core complex in the presence of syntaxin shows strong fluorescence resonance energy transfer (FRET) between the CFP-SNAP-25 and YFP-synaptobrevin. Under the same conditions, CFP fused to the C terminus of SNAP-25, and YFP- synaptobrevin have no FRET. Adenovirus-mediated gene transfer is used to express the fusion proteins in PC12 cells and cultured rat cerebellar granule cells. Strong FRET is associated with neurite membranes and vesicular structures in PC12 cells co-expressing CFP-SNAP-25 and YFP-synaptobrevin. In cultured rat cerebellar granule cells, FRET between CFP-SNAP-25 and YFP-synaptobrevin is mostly associated with sites presumed to be synaptic junctions. Neurosecretion in PC12 cells initiated by KCl depolarization leads to an increase in the extent of FRET. These results demonstrate that significant amounts of stable SNARE complex exist prior to evoked synaptic vesicle fusion and that the assembly of SNARE complex occurs during vesicle docking/priming stage. Moreover, it demonstrates that FRET can be used as an effective tool for investigating dynamic SNARE interactions during synaptic vesicle fusion.
Salmonella-based vaccines for infectious diseases (2007)

The use of Salmonella spp. as a delivery system for foreign antigens represents a unique opportunity for the development of ideal vaccines with unparalleled merits. Increased understanding of the mechanisms underlying Salmonella virulence and host immune response will continuously create novel strategies for more effective Salmonella-based vaccines. However, limitations in our capability to manipulate the genome of a vector strain efficiently have delayed the realization of vaccination ideas. Owing to the development of new technologies in recent years, it has now become feasible to rapidly construct Salmonella vaccine strains that carry precise modifications on the chromosomal DNA. This technical advancement will open a new avenue for the effective development of Salmonella-based vaccines for infectious diseases of both human and animal health importance.
Glucuronides in Anti-Cancer Therapy (2003)

Glucuronide prodrugs have shown promising efficacy in anti-cancer therapy due to their increased specificity and reduced systemic toxicity. The prodrugs can be used in prodrug monotherapy (PMT), which is based on elevated tumor beta-glucuronidase activity. beta-Glucuronidase activates the low-toxic prodrugs into highly cytotoxic agents specifically in the tumor site. The specificity of the prodrugs can be further improved by combined use with monoclonal antibodies against tumor-specific antigens, namely antibody-directed enzyme prodrug therapy (ADEPT); and the potency of the prodrugs can be greatly enhanced with the incorporation of an appropriate radionuclide in the combined chemo- and radio-therapy of cancer (CCRTC) strategy. The prodrugs can also be utilized to modify liposomes for efficient delivery of anti-cancer drugs.
High Frequency of Herpesvirus-Specific Clonotypes in the Human T Cell Repertoire Can Remain Stable over Decades with Minimal Turnover (2012)

High-throughput T cell receptor sequencing on sequentially banked blood samples from healthy individuals has shown that high-frequency clonotypes can remain relatively stable for up to 18 years, with minimal inflation, deflation, or turnover. These populations included T cell expansions specific for Epstein-Barr virus. Thus, in spite of exposure to a barrage of microorganisms over the course of life, the dominant clonotypes in the mature peripheral T cell repertoire can alter surprisingly little.
Loss of epithelial differentiation and gain of invasiveness correlates with tyrosine phosphorylation of the E-cadherin/beta-catenin complex in cells transformed with a temperature-sensitive v-SRC gene. (1993)

Loss of histotypic organization of epithelial cells is a common feature in normal development as well as in the invasion of carcinomas. Here we show that the v-src oncogene is a potent effector of epithelial differentiation and invasiveness. MDCK epithelial cells transformed with a temperature-sensitive mutant of v-src exhibit a strictly epithelial phenotype at the nonpermissive temperature for pp60v-src activity (40.5 degrees C) but rapidly loose cell-to-cell contacts and acquire a fibroblast-like morphology after culture at the permissive temperature (35 degrees C). Furthermore, the invasiveness of the cells into collagen gels or into chick heart fragments was increased at the permissive temperature. The profound effects of v-src on intercellular adhesion were not linked to changes in the levels of expression of the epithelial cell adhesion molecule E-cadherin. Rather, we observed an increase in tyrosine phosphorylation of E-cadherin and, in particular, of the associated protein beta-catenin. These results suggest a mechanism by which v-src counteracts junctional assembly and thereby promotes invasiveness and dedifferentiation of epithelial cells through phosphorylation of the E-cadherin/catenin complex.
Biomarker discovery in human SLE nephritis. (2007)

The treatment of systemic lupus erythematosus (SLE) nephritis, while effective, is associated with significant morbidity and mortality. These side effects could be mitigated if the onset, severity, and response of renal flare could be predicted, and therapy modified accordingly. In this review, an approach to derive prediction equations of SLE nephritis flare is discussed. Integral to generating such prediction equations is the identification of biomarkers of lupus nephritis that can serve as input variables for modeling flare. The use of urine as a source of SLE nephritis biomarkers is described, and the results of urine biomarker discovery studies using candidate and proteomic approaches are presented.
Site-Specific Incorporation of Tryptophan Analogues into Recombinant Proteins in Bacterial Cells (2007)

A designed yeast phenylalanyl-tRNA synthetase (yPheRS (T415G)) activates four tryptophan (Trp) analogues (6-chlorotryptophan (6ClW), 6-bromotryptophan (6BrW), 5-bromotryptophan (5BrW), and benzothienylalanine (BT)) that are not utilized by the endogenous E. coli translational apparatus. Introduction of yPheRS (T415G) and a mutant yeast phenylalanine amber suppressor tRNA (ytRNAPheCUA_UG) into an E. coli expression host allowed site-specific incorporation of three of these analogues (6ClW, 6BrW, and BT) into recombinant murine dihydrofolate reductase in response to amber stop codons with at least 98% fidelity. All three analogues were introduced at the Trp66 position in the chromophore of a cyan fluorescent protein variant (CFP6) to investigate the attendant changes in spectral properties. Each of the analogues caused blue shifts in the fluorescence emission and absorption maxima. The CFP6 variant bearing BT at position 66 exhibited an unusually large Stokes shift (56 nm). An expanded set of genetically encoded Trp analogues should enable the design of new proteins with novel spectral properties.
Bacterial contaminants of fuel ethanol production (2004)

Bacterial contamination is an ongoing problem for commercial fuel ethanol production facilities. Both chronic and acute infections are of concern, due to the fact that bacteria compete with the ethanol-producing yeast for sugar substrates and micronutrients. Lactic acid levels often rise during bouts of contamination, suggesting that the most common contaminants are lactic acid bacteria. However, quantitative surveys of commercial corn-based fuel ethanol facilities are lacking. For this study, samples were collected from one wet mill and two dry grind fuel ethanol facilities over a 9 month period at strategic time points and locations along the production lines, and bacterial contaminants were isolated and identified. Contamination in the wet mill facility consistently reached 10(6) bacteria/ml. Titers from dry grind facilities were more variable but often reached 10(8)/ml. Antibiotics were not used in the wet mill operation. One dry grind facility added antibiotic to the yeast propagation tank only, while the second facility dosed the fermentation with antibiotic every 4 h. Neither dosing procedure appeared to reliably reduce overall contamination, although the second facility showed less diversity among contaminants. Lactobacillus species were the most abundant isolates from all three plants, averaging 51, 38, and 77% of total isolates from the wet mill and the first and second dry grind facilities, respectively. Although populations varied over time, individual facilities tended to exhibit characteristic bacterial profiles, suggesting the occurrence of persistent endemic infections.
Modulation of the Arabidopsis KAT1 channel by an activator of protein kinase C in Xenopus laevis oocytes (2010)

The Arabidopsis thaliana K(+) channel KAT1 has been suggested to play a key role in the regulation of the aperture of stomatal pores on the surface of plant leaves. Calcium-dependent and calcium-independent signaling pathways are involved in abscisic acid-mediated regulation of guard cell turgidity. Although the activity of the KAT1 channel is thought to be regulated by calcium-dependent protein kinases, the effect of phosphorylation on KAT1 and the phosphorylated target sites remain elusive. Because it has been proposed that the phosphorylation recognition sequence of plant calcium-dependent protein kinases resembles that of animal protein kinases C, in this study, we used the Xenopus laevis oocyte protein kinase C to identify the target sites of calcium-dependent protein kinases. KAT1 expressed in Xenopus oocytes was inhibited by the protein kinase C activator phorbol 12-myristate 13-acetate. On the basis of an in silico search, we selected S/T-X-K/R motifs facing the cytosol, as it has been reported that protein kinase C and calcium-dependent protein kinase share a common consensus sequence. Mutagenesis analyses revealed that six Ser/Thr residues were responsible for the reduction in activity after phorbol 12-myristate 13-acetate application. Simultaneous mutation of the five residues located in the carboxyl-terminus region of KAT1 led to a K(+) channel mutant that was insensitive to protein kinase C. These results indicate that, in plant cells, a kinase analogous to protein kinase C might exist that may modulate KAT1 channel activity through calcium-dependent phosphorylation at some of the pinpointed residues in the cytosolic region of KAT1.