gebhart/patrepeval huggingface dataset:
Soluble protein oligomers as emerging toxins in alzheimer's and other amyloid diseases (2007)

Amyloid diseases are a group of degenerative disorders characterized by cell/tissue damage caused by toxic protein aggregates. Abnormal production, processing and/or clearance of misfolded proteins or peptides may lead to their accumulation and to the formation of amyloid aggregates. Early histopathological investigation of affected organs in different amyloid diseases revealed the ubiquitous presence of fibrillar protein aggregates forming large deposits known as amyloid plaques. Further in vitro biochemical and cell biology studies, as well as studies using transgenic animal models, provided strong support to what initially seemed to be a solid concept, namely that amyloid fibrils played crucial roles in amyloid pathogenesis. However, recent studies describing tissue-specific accumulation of soluble protein oligomers and their strong impact on cell function have challenged the fibril hypothesis and led to the emergence of a new view: Fibrils are not the only toxins derived from amyloidogenic proteins and, quite possibly, not the most important ones with respect to disease etiology. Here, we review some of the recent findings and concepts in this rapidly developing field, with emphasis on the involvement of soluble oligomers of the amyloid-beta peptide in the pathogenesis of Alzheimer's disease. Recent studies suggesting that soluble oligomers from different proteins may share common mechanisms of cytotoxicity are also discussed. Increased understanding of the cellular toxic mechanisms triggered by protein oligomers may lead to the development of rational, effective treatments for amyloid disorders.
DNA repair synthesis in human fibroblasts requires DNA polymerase delta. (1988)

When UV-irradiated cultured diploid human fibroblasts were permeabilized with Brij-58 then separated from soluble material by centrifugation, conservative DNA repair synthesis could be restored by a soluble factor obtained from the supernatant of similarly treated HeLa cells. Extensive purification of this factor yielded a 10.2 S, 220,000-dalton polypeptide with the DNA polymerase and 3'- to 5'-exonuclease activities reported for DNA polymerase delta II (Crute, J. J., Wahl, A. F., and Bambara, R. A. (1986) Biochemistry 25, 26-36). Monoclonal antibody to KB cell DNA polymerase alpha, while binding to HeLa DNA polymerase alpha, did not bind to the HeLa DNA polymerase delta. Moreover, at micromolar concentrations N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate (BuPdGTP) and 2-(p-n-butylanilino)-2'-deoxyadenosine 5'-triphosphate (BuAdATP) were potent inhibitors of DNA polymerase alpha, but did not inhibit the DNA polymerase delta. Neither purified DNA polymerase alpha nor beta could promote repair DNA synthesis in the permeabilized cells. Furthermore, under conditions which inhibited purified DNA polymerase alpha by greater than 90%, neither monoclonal antibodies to DNA polymerase alpha, BuPdGTP, nor BuAdATP was able to inhibit significantly the DNA repair synthesis mediated by the DNA polymerase delta. Thus, it appears that a major portion of DNA repair synthesis induced by UV irradiation might be catalyzed by DNA polymerase delta. When xeroderma pigmentosum human diploid fibroblasts were utilized, DNA repair synthesis dependent upon ultraviolet light could be restored by addition of both T4 endonuclease V and DNA polymerase delta, but not by addition of either one alone. This result suggests that cytosol-depleted permeabilized DNA repair-defective human fibroblasts and HeLa DNA polymerase delta might be exploited to provide a functional assay for purifying active DNA repair factors from DNA repair-proficient cells without a preknowledge of their function.
The design and applications of superomniphobic surfaces (2014)

Surfaces that display contact angles >150° along with low contact angle hysteresis with essentially all high and low surface tension liquids, including water, oils and alcohols, are known as superomniphobic surfaces. Such surfaces have a range of commercial applications, including self-cleaning, non-fouling, stain-free clothing, drag reduction, corrosion prevention and separation of liquids. Such surfaces have thus generated immense academic and industrial interest in recent years. In this review, we discuss the systematic design of superomniphobic surfaces. In particular, we discuss the significance of surface energy, roughness and the critical role of re-entrant texture in obtaining the so-called Cassie–Baxter state with low surface tension liquids. We also discuss how hierarchical scales of texture can yield high contact angles and decrease the contact angle hysteresis of superomniphobic surfaces by reducing the solid–liquid contact area. On the basis of this understanding, we discuss dimensionless design parameters that allow for the systematic design of superomniphobic surfaces. We also review the current literature on superomniphobic surfaces, paying particular attention to surfaces that demonstrate good mechanical, chemical and radiation durability—traits that are essential for any commercial application of superomniphobic surfaces. Finally, we conclude by identifying the unresolved challenges in the fabrication of durable superomniphobic surfaces and highlight the future needs in the field. Surfaces that display contact angles >150° along with a low contact angle hysteresis for both low and high surface tension liquids are known as superomniphobic surfaces. Such surfaces have several applications, including self-cleaning, non-fouling, stain-free clothing, drag reduction, corrosion prevention and separation of liquids. In this review, we discuss the design criteria, recent studies, applications, challenges and potential of superomniphobic surfaces. Surfaces that strongly repel low surface tension liquids (e.g. oils and alcohols) are classified as superoleophobic and those that strongly repel high surface tension liquids (e.g. water) are classified as superhydrophobic. However, if a surface shows both these characteristics, it can be considered superomniphobic. Liquid droplets on superomniphobic surfaces roll off very easily and, as a result, these surfaces are attractive as non-fouling coatings, self-cleaning surfaces and liquid-separation techniques. Anish Tuteja at the University of Michigan, United States, and colleagues review the design principles required to fabricate superomniphobic surfaces. They discuss surface energy, roughness and hierarchical scales of surface texture, and recognize the importance of re-entrant textures (i.e. convex topography) to achieve superomniphobicity. Several examples of superomniphobic surfaces are presented with particular focus on the need to improve chemical and mechanical durability, to realize their full potential in commercial and industrial applications.
Formation of Natamycin:Cyclodextrin Inclusion Complexes and Their Characterization (2003)

Natamycin is a broad spectrum antimycotic with very low water solubility, which is used to extend the shelf life of shredded cheese products. beta-Cyclodextrin (beta-CD), hydroxypropyl beta-cyclodextrin (HP beta-CD), and gamma-cyclodextrin (gamma-CD) were found to form inclusion complexes with natamycin in aqueous solution. The increase in solubility of natamycin with added beta-CD was observed to be linear (type A(L) phase solubility diagram). The 1:1 stability constant of natamycin:beta-CD complex was estimated from its phase solubility diagram to be 1010 M(-1). The phase solubility diagrams of both gamma-CD and HP beta-CD exhibited negative deviation from linearity (type A(N) diagram) and, therefore, did not allow the estimation of binding constants. The water solubility of natamycin was increased 16-fold, 73-fold, and 152-fold with beta-CD, gamma-CD, and HP beta-CD, respectively. The natamycin:CD inclusion complexes resulted in in vitro antifungal activity nearly equivalent to that of natamycin in its free state.
Characterization of Ganglioside Expression in Human Melanoma Cells: Immunological and Biochemical Analysis1 (1993)

The expression of N-glycolylneuraminic acid (NeuGc)-containing gangliosides in human melanoma cells grown both in culture and as xenografts in athymic (nu/nu) mice was analyzed extensively with specific mouse monoclonal antibodies (MAbs). Three MAbs (GMR8, GMR14, and GMR3) specific for GM3(NeuGc), GM2(NeuGc), and GD3(NeuGc-NeuGc-), respectively, were used. Significant differences were observed in the ganglioside compositions between the cultured cells in vitro and the tumors grown in vivo. The major difference was that the cells cultured in serum-free medium did not express any NeuGc-containing gangliosides, whereas those grown in nude mice expressed a number of NeuGc-containing gangliosides, namely GM3(NeuGc), GM2(NeuGc), GD3(NeuAc-NeuGc-), GD3(NeuGc-NeuAc-), and GD3(NeuGc-NeuGc-). The structures of these gangliosides were also determined chemically. No activity of CMP-NeuAc hydroxylase was demonstrated either in the melanoma cells cultured in vitro or in those grown in nude mice, suggesting that these cells incorporated NeuGc-containing glycoconjugates from the mouse sera and converted them to other NeuGc-containing gangliosides. The mouse sera contained only GM2(NeuGc), but not the other NeuGc-containing gangliosides or any NeuAc-containing gangliosides.
Graspables (2009)

The Graspables project is an exploration of how measuring the way people hold and manipulate objects can be used as a user interface. As computational ability continues to be implemented in more and more objects and devices, new interaction methods need to be developed. The Graspables System is embodied by a physical set of sensors combined with pattern recognition software that can determine how users hold a device. The Graspables System has been implemented in two prototypes, the Bar of Soap and the Ball of Soap. Applications developed for these prototypes demonstrate the effectiveness of grasp-recognition as an interface in multiple scenarios.
Cloning and expression of the major 47-kilodalton surface immunogen of Treponema pallidum in Escherichia coli (1986)

Monoclonal antibodies directed against the 47-kilodalton (kDa) major outer membrane surface immunogen of virulent Treponema pallidum subsp. pallidum were used to select Escherichia coli recombinant clones expressing the 47-kDa immunogen. The phenotype of the clones was dependent on the presence of recombinant plasmid in the host cell. Southern hybridization revealed that the cloned T. pallidum subsp. pallidum DNA sequence was an accurate representation of the T. pallidum subsp. pallidum genomic DNA arrangement. Purified immunoglobulin G from rabbits experimentally infected with T. pallidum subsp. pallidum and human secondary syphilitic sera specifically reacted with the clones, while normal human serum or immunoglobulin G from normal rabbit serum did not. Results of Southern hybridization indicated that a homologous 47-kDa immunogen gene was absent in at least four species of nonpathogenic treponemes tested, as well as from total rabbit genomic DNA. Rabbit anti-T. phagedenis biotype Reiter (treponemal nonpathogen) antiserum and a monoclonal antibody directed against a common treponemal determinant were unreactive with the clones. Western blotting and radioimmunoprecipitation experiments with specific monoclonal antibodies revealed that the recombinant (E. coli) and native (T. pallidum subsp. pallidum) forms of the antigen had identical electrophoretic mobilities. The availability of recombinant 47-kDa immunogen provides a new opportunity for biochemical analysis of the protein, structure-function studies, examination of its role in microbial pathogenesis, and assessment of its diagnostic and vaccinogenic potentials.
Clearance mechanism of a mannosylated antibody–enzyme fusion protein used in experimental cancer therapy (2006)

MFECP1 is a mannosylated antibody-enzyme fusion protein used in antibody-directed enzyme prodrug therapy (ADEPT). The antibody selectively targets tumor cells and the targeted enzyme converts a prodrug into a toxic drug. MFECP1 is obtained from expression in the yeast Pichia pastoris and produced to clinical grade. The P. pastoris-derived mannosylation of the fusion protein aids rapid normal tissue clearance required for successful ADEPT. The work presented provides evidence that MFECP1 is cleared by the endocytic and phagocytic mannose receptor (MR), which is known to bind to mannose-terminating glycans. MR-transfected fibroblast cells internalize MFECP1 as revealed by flow cytometry and confocal microscopy. Immunofluorescence microscopy shows that in vivo clearance in mice occurs predominantly by MR on liver sinusoidal endothelial cells, although MR is also expressed on adjacent Kupffer cells. In the spleen, MFECP1 is taken up by MR-expressing macrophages residing in the red pulp and not by dendritic cells which are found in the marginal zone and white pulp. Clearance can be inhibited in vivo by the MR inhibitor mannan as shown by increased enzyme activities in blood. The work improves understanding of interactions of MFECP1 with normal tissue, shows that glycosylation can be exploited in the design of recombinant anticancer therapeutics and opens the ways for optimizing pharmacokinetics of mannosylated recombinant therapeutics.
MPL515 mutations in myeloproliferative and other myeloid disorders: a study of 1182 patients (2006)

Recently, a gain-of-function MPL mutation, MPLW515L, was described in patients with JAK2V617F-negative myelofibrosis with myeloid metaplasia (MMM). To gain more information on mutational frequency, disease specificity, and clinical correlates, genomic DNA from 1182 patients with myeloproliferative and other myeloid disorders and 64 healthy controls was screened for MPL515 mutations, regardless of JAK2V617F mutational status: 290 with MMM, 242 with polycythemia vera, 318 with essential thrombocythemia (ET), 88 with myelodysplastic syndrome, 118 with chronic myelomonocytic leukemia, and 126 with acute myeloid leukemia (AML). MPL515 mutations, either MPLW515L (n = 17) or a previously undescribed MPLW515K (n = 5), were detected in 20 patients. The diagnosis of patients with mutant MPL alleles at the time of molecular testing was de novo MMM in 12 patients, ET in 4, post-ET MMM in 1, and MMM in blast crisis in 3. Six patients carried the MPLW515L and JAK2V617F alleles concurrently. We conclude that MPLW515L or MPLW515K mutations are present in patients with MMM or ET at a frequency of approximately 5% and 1%, respectively, but are not observed in patients with polycythemia vera (PV) or other myeloid disorders. Furthermore, MPL mutations may occur concurrently with the JAK2V617F mutation, suggesting that these alleles may have functional complementation in myeloproliferative disease.
The — 16 region, a vital sequence for the utilization of a promoter in Bacillus subtilis and Escherichia coli (1995)

The promoter (amyP) of the Bacillus subtilis alpha-amylase gene, which is recognized by E sigma A, has a three out of six match to the consensus promoter in both the -35 and -10 hexamers. Oligonucleotide-directed mutagenesis was used to identify important bases for promoter utilization in the spacer sequence between the hexamers. Mutations in the sequence TGTG extending from positions -18 to -15 (the -16 region) caused a 5-94-fold decrease in alpha-amylase production. A G-C transversion at position -15 was the most detrimental mutation: it essentially eliminated amyP utilization in B. subtilis and in Escherichia coli. Mutating the -35 and -10 hexamers to the E sigma A consensus promoter increased alpha-amylase production 56-fold in B. subtilis and fivefold in E. coli. Introducing the -15 G to C transversion into the consensus promoter reduced alpha-amylase production threefold, in contrast to the 94-fold reduction for the wild-type promoter in B. subtilis. The -15 G to C transversion did not reduce alpha-amylase synthesis directed by the consensus promoter in E. coli. The alpha-amylase gene is subject to two forms of transcriptional regulation: catabolite repression and temporal regulation. None of the mutants constructed in this study had any effect on either type of regulation. The -16 region, especially the G at position -15, appears to be moderately conserved in B. subtilis and in other Gram-positive organisms and weakly conserved in E. coli. The evidence suggests that the -16 region is an additional region of E sigma A promoters in B. subtilis and E sigma 70 promoters in E. coli, essential in some weak promoters such as the alpha-amylase promoter but, of little benefit to very strong promoters.
Streptococcus pyogenesGlycoprotein-Binding Strepadhesin Activity Is Mediated by a Surface-Associated Carbohydrate-Degrading Enzyme, Pullulanase (2003)

The interactions between pathogenic bacteria and the host need to be resolved at the molecular level in order to develop novel antiadhesive drugs and vaccines. We have previously identified strepadhesin, a novel glycoprotein-binding activity in Streptococcus pyogenes binding to thyroglobulin, submaxillar mucin, fetuin, and asialofetuin. The activity is known to be regulated by Mga, a regulator of streptococcal virulence factors, and is carried by the surface-associated streptococcal cysteine protease, SpeB. In the present study, we focused on the high strepadhesin activity in an S. pyogenes strain (NZ131rgg) lacking SpeB expression. By extracting surface proteins from the bacteria, a new strepadhesin protein was identified, and mass spectrometric analysis and database search identified it as a putative pullulanase. The gene was cloned, and the recombinant pullulanase (PulA) exhibited pullulanase and starch hydrolyzing activity, as well as strepadhesin activity. Sequencing of the pulA gene revealed an open reading frame with 3,498 bp encoding a protein of 1,165 amino acids with a predicted molecular mass of 129 kDa. PulA exhibited properties typical for a gram-positive surface protein with a putative signal sequence and LPKTGE cell wall anchoring motif and contained the four highly conserved regions common to pullulanases. Mutant bacteria deficient in PulA expression showed diminished strepadhesin activity on bacterial dot blot assay and reduced adherence to thyroglobulin immobilized on microtiter plates. Thus, S. pyogenes strepadhesin activity is carried by a surface-bound pullulanase, which combines glycoprotein-binding and carbohydrate-degrading activities in the same molecule.
Mixed valency in rare-earth fullerides (2007)

Mixed-valence phenomena associated with the highly correlated narrow-band behaviour of the 4f electrons in rare earths are well documented for a variety of rare-earth chalcogenides, borides and intermetallics (Kondo insulators and heavy fermions). The family of rare-earth fullerides with stoichiometry RE2.75C60 (RE=Sm, Yb, Eu) also displays an analogous phenomenology and a remarkable sensitivity of the rare-earth valency to external stimuli (temperature and pressure) making them the first known molecular-based members of this fascinating class of materials. Using powerful crystallographic and spectroscopic techniques which provide direct indications of what is happening in these materials at the microscopic level, we find a rich variety of temperature- and pressure-driven abrupt or continuous valence transitions-the electronically active fulleride sublattice acts as an electron reservoir that can accept electrons from or donate electrons to the rare-earth 4f/5d bands, thereby sensitively modulating the valence of the rare-earth sublattice.
[Inhibitory activity of monomeric and polymeric selectin ligands]. (2000)

The ability of tetrasaccharides (SiaLex, SiaLea, HSO3Lex), their conjugates with polyacrylamide (40 kDa), and several other monomeric and polymeric substances to block selectins has been compared with that of polysaccaride fucoidan. Two assay systems were used: one was constructed on the base of recombinant E-, P-, and L-selectins; the other was a rat model of peritoneal inflammation. IC50 values for the neoglycoconjugate SiaLea-PAA were 6, 40, and 85 microM with the recombinant E-, P-, and L-selectins, respectively; all monomeric inhibitors were about two orders of magnitude weaker. PAA-conjugates, containing as a ligand tyrosine-o-sulfate in addition to one of the above mentioned oligosaccharides, were the most potent synthetic blockers. Compared with the most potent of the known inhibitors, fucoidan, bi-ligand glycoconjugate HSO3Lea-PAA-sTyr, displayed in vitro similar activity in blocking L-selectin, while its activity towards P-selectin was ten times lower. All the synthetic polymers tested were able to inhibit neutrophil extravasation to inflammation site, acting in concentration about 10 mg/kg. Thus, the effect of SiaLex is considerably more effective in vivo than in vitro, whereas heavily charged fucoidan and bi-ligand neoglycoconjugate acted in converse manner.
In vitro response of Ichthyophthirius multifiliis to sera from immune channel catfish (1987)

Sera from channel catfish rendered immune to the protozoan pathogen Ichthyophthirius multifiliis were screened for activity against live parasites. Cells in the infective stage (tomites) were incubated in doubling dilutions of immune and pre‐immune sera from fish that had been immunized by exposure to sublethal infections. When examined by light microscopy, tomites were found to agglutinate in the presence of immune sera. While the stength of individual sera varied, agglutination of cells occurred at dilutions as high as 1:128. Cells showed little tendency to agglutinate in pre‐immune sera, and virtually no effects were seen with dilutions of pre‐immune sera greater than 1:16. Agglutination was usually accompanied by release of mucus from cells, and while tomites appeared to be immobilized, their cilia continued to beat. Low dilutions of immune sera appeared to be toxic. Similar effects on tomites were seen with rabbit antisera prepared against Ichthyophthirius cilia. The involvement of humoral antibodies in agglutination and protective immunity is discussed.
Selective Detection of Protein Crystals by Second Harmonic Microscopy (2008)

The unique symmetry properties of second harmonic generation (SHG) microscopy enabled sensitive and selective imaging of protein microcrystals with negligible contributions from solvated proteins or amorphous protein aggregates. In studies of microcrystallites of green fluorescent protein (GFP) prepared in 500 pL droplets, the SHG intensities rivaled those of fluorescence, but with superb selectivity for crystalline regions. GFP in amorphous aggregates and in solution produced substantial background fluorescence, but no detectable SHG. The ratio of the forward-to-backward detected SHG provides a measure of the particle size, suggesting detection limits down to crystallites 100 nm in diameter under low magnification (10x). In addition to being sensitive and highly selective, second-order nonlinear optical imaging of chiral crystals (SONICC) is directly compatibility with virtually all common protein crystallization platforms.