gebhart/patrepeval huggingface dataset:
Amino Acid Sequence of Porcine Neurophysin-I (1971)

Abstract Tryptic and chymotryptic peptide fragments obtained from performic acid-oxidized porcine neurophysin-I were isolated and purified by gel filtration, ion exchange chromatography, paper electrophoresis, and paper chromatography. The larger tryptic peptides were further hydrolyzed by papain, chymotrypsin, pepsin, or HCl to yield shorter fragments amenable to Edman degradation. The sum of the compositions of the tryptic peptides, however, exceeded the total number of amino acid residues of porcine neurophysin-I reported earlier. Re-examination of the amino acid composition and further investigation of COOH-terminal peptides showed that the porcine neurophysin-I preparation was not homogeneous with respect to the COOH terminus. The preparation contained two species of neurophysin molecules, in approximately equal amounts, differing in length only by 1 amino acid residue at the COOH terminus. The complete amino acid sequence of both species of porcine neurophysin-I, containing 92 and 91 residues, was determined by conventional methods. The larger molecule contains the entire sequence of the shorter molecule plus an extra leucyl residue at its COOH terminus. Alanine is the NH2-terminal residue of both molecules. Phenylalanine is the COOH terminus of the shorter molecule. Single methionine and tyrosine residues occupy positions 2 and 49, respectively. The location of the seven disulfide linkages of porcine neurophysin-I remains to be determined.
Monoclonal antibodies against surface determinants on gametes of Plasmodium gallinaceum block transmission of malaria parasites to mosquitoes. (1983)

Monoclonal antibodies (MAb) against gametes of the chicken malaria Plasmodium gallinaceum have been derived. All reacted with the surface of extracellular gametes of the parasite in immunofluorescent antibody reactions and all agglutinated both male and female gametes. In the absence of active complement one mu isotype MAb, la 1-D5, mediated at least 95% suppression of infectivity of the parasites to Aedes aegypti mosquitoes. Individually, MAb of the gamma 1 or gamma 2a isotypes mediated only slight suppression in the absence of active complement. Certain combinations of these MAb, however, suppressed parasite infectivity by 90 to 95%. Suppression of infectivity by the MAb was shown to be mainly due to their effects on the events leading up to or including fertilization. Certain gamma 2a isotype MAb, which otherwise mediated minimal or no suppressive effect, completely abolished infectivity of the parasites if complement was present. No target antigen could be identified by immunoprecipitation of Triton X-100 extracts of surface radioiodinated zygotes or gametes of P. gallinaceum for the mu isotype MAb. All gamma isotype MAb precipitated the same three proteins of 240,000, 56,000, and 54,000 daltons under reducing conditions on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, from extracts of radioiodinated male and female gametes. These surface proteins on gametes of both sexes of P. gallinaceum thus appear to include target antigens of anti-gamete transmission blocking immunity.
Synthesis of well‐defined naphthalene and photo‐labile group‐labeled polystyrene via ATRP (2005)

Abstract The atom transfer radical polymerizations of styrene were successfully carried out in bulk and solution, respectively, at 115 °C, with a novel photoiniferter reagent, (1‐naphthyl)methyl N,N ‐diethyldithiocarbamate (NMDC), as an initiator in the presence of copper (I) bromide and N,N,N′,N″,N″ ‐pentamethyldiethylenetriamine. The results showed that NMDC was an effective initiator with high initiation efficiency for ATRP of St. The polymerization rate was first‐order with respect to the monomer concentration and the molecular weights of the obtained polystyrene (PS) increased linearly with the monomer conversion, with very narrow molecular weight distributions ( M w / M n = 1.07–1.29). The functionalized naphthalene‐labeled PS bearing N , N ‐(diethylamino)dithiocarbamoyl group which was confirmed by 1 H NMR analysis, and chain extension of the PS exhibited fluorescence and ultraviolet absorption in chloroform (CHCl 3 ). © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 510–518, 2006
Inherited thrombotic thrombocytopenic purpura (2009)

Thrombotic thrombocytopenic purpura is due to germline mutations of the ADAMTS13 gene in about one fifth of patients. In this perspective article Dr. Galbusera and colleagues examine the pathophysiology of this inherited condition. See related article on page 289.
The Natively Unfolded Character of Tau and Its Aggregation to Alzheimer-like Paired Helical Filaments (2008)

The abnormal aggregation of the microtubule-associated protein Tau into paired helical filaments (PHFs) is one of the hallmarks of Alzheimer disease (AD). Tau in solution behaves as a natively unfolded or intrinsically disordered protein while its aggregation is based on the partial structural transition from random coil to beta-structure. Our aim is to understand in more detail the unfolded nature of Tau, to investigate the aggregation of Tau under different conditions and the molecular interactions of Tau in filaments. We show that soluble Tau remains natively unfolded even when its net charge is minimized, in contrast to other unfolded proteins. The CD signature of the random-coil character of Tau shows no major change over wide variations in charge (pH), ionic strength, solvent polarity, and denaturation. Thus there is no indication of a hydrophobicity-driven collapse, neither in the microtubule-binding repeat domain constructs nor in full-length Tau. This argues that the lack of hydrophobic residues but not the net charge accounts for unfolded nature of soluble Tau. The aggregation of the Tau repeat domain (that forms the core of PHFs) in the presence of nucleating polyanionic cofactors (heparin) is efficient in a range of buffers and pH values between approximately 5 and 10 but breaks down beyond that range, presumably because the pattern of charged interactions disappears. Similarly, elevated ionic strength attenuates aggregation, and the temperature dependence is bell-shaped with an optimum around 50 degrees C. Reporter dyes ThS and ANS record the aggregation process but sense different states (cross-beta-structure vs hydrophobic pockets) with different kinetics. Preformed PHFs are surprisingly labile and can be disrupted by denaturants at rather low concentration ( approximately 1.0 M GdnHCl), much less than required to denature globular proteins. Partial disaggregation of Tau filaments at extreme pH values monitored by CD and EM indicate the importance of salt bridges in filament formation. In contrast, Tau filaments are remarkably resistant to high temperature and high ionic strength. Overall, the stability of PHFs appears to depend mainly on directed salt bridges with contributions from hydrophobic interactions as well, consistent with a recent structural model of the PHF core derived from solid state NMR (Andronesi, O. C., von Bergen, M., Biernat, J., Seidel, K., Griesinger, C., Mandelkow, E., and Baldus, M. (2008) Characterization of Alzheimer's-like paired helical filaments from the core domain of tau protein using solid-state NMR spectroscopy.
Single-molecule protein sequencing through fingerprinting: computational assessment (2015)

Proteins are vital in all biological systems as they constitute the main structural and functional components of cells. Recent advances in mass spectrometry have brought the promise of complete proteomics by helping draft the human proteome. Yet, this commonly used protein sequencing technique has fundamental limitations in sensitivity. Here we propose a method for single-molecule (SM) protein sequencing. A major challenge lies in the fact that proteins are composed of 20 different amino acids, which demands 20 molecular reporters. We computationally demonstrate that it suffices to measure only two types of amino acids to identify proteins and suggest an experimental scheme using SM fluorescence. When achieved, this highly sensitive approach will result in a paradigm shift in proteomics, with major impact in the biological and medical sciences.
USER Cloning and USER Fusion: The Ideal Cloning Techniques for Small and Big Laboratories (2010)

The explosive development of the field of molecular biology has led to the need for simpler and more efficient cloning techniques. These requirements are elegantly met by the ligation-free cloning technique called USER cloning. USER cloning is suitable not only for everyday and high-throughput cloning but also for the one-step construction of complex DNA constructs, which can be achieved in a variant called USER fusion. In this chapter, we present a general protocol for converting any vector into a USER-compatible vector, together with protocols for both USER cloning and USER fusion.
Analysis of Epstein-Barr virus-binding sites on complement receptor 2 (CR2/CD21) using human-mouse chimeras and peptides. At least two distinct sites are necessary for ligand-receptor interaction (1991)

The predicted amino acid sequence of human complement receptor 2 (CR2, CD21, C3d,g/Epstein-Barr virus receptor) and its genetic murine homologue are approximately 70% identical. The sequence of each consists of a linear array of 60-70 amino acid repeats designated short consensus repeats (SCRs). Although they share significant sequence identity, a major difference in the activities of these two proteins has been believed to be the ability of human, but not mouse, CR2 to mediate Epstein-Barr virus (EBV) infection of B lymphocytes. In order to formally address this question and to directly compare the activities of the CR2 protein of each species, we have expressed recombinant mouse CR2 (rMCR2) in a human K562 erythroleukemia cell line background. We have found that rMCR2 reacts with two previously described rat anti-MCR2 monoclonal antibodies (mAbs), 7G6 and 7E9, but not mAb 8C12, which recognizes only mouse complement receptor 1. rMCR2 rosettes with erythrocytes bearing mouse and human C3d,g and binds glutaraldehyde cross-linked human C3d,g with a similar Kd as human CR2 (HCR2). rMCR2 does not bind EBV. By using this observation and constructing chimeras bearing portions of MCR2 on a HCR2 background, we have been able to define unique sequences in HCR2 SCRs 1 and 2 important in the interaction with both mAb OKB7, which blocks EBV binding and infection, and with EBV. In addition, by using blocking peptides derived from HCR2 sequence, we have identified a second distinct region in SCR2 important in EBV binding. Therefore, within the first two SCRs of HCR2 are multiple distinct sites of interaction with EBV and with mAb OKB7.
Ribonuclease inhibitor as an intracellular sentry (2003)

Onconase (ONC) is a homolog of RNase A that is in clinical trials as a cancer chemotherapeutic agent. The toxicity of ONC and RNase A variants relies on their ability to evade the cytosolic ribonuclease inhibitor protein (RI) and degrade cellular RNA. We find that these ribonucleases are more toxic for more rapidly growing cells. The enhanced cytotoxicity does not arise from variation in the endogenous level of RI, which is virtually constant. Overproduction of RI diminishes the potency of toxic RNase A variants, but has no effect on the cytotoxicity of ONC. Thus, RI constrains the cytotoxicity of RNase A. These data provide new insights for the development of an optimal ribonuclease-based cancer chemotherapy.
Purification of lutropin and follitropin in high yield from horse pituitary glands. (1984)

A method has been developed for the purification of equine lutropin (eLH) and equine follitropin (eFSH) from horse pituitary glands which attains high yields of both hormones in contrast to previous methods that were devoted to one or the other with inferior recovery of the hormones. Two-pass chromatography over CM-Sephadex was used to separate eLH from eFSH. Subsequent steps employing QAE (quaternary amino-ethyl)-Sephadex chromatography and gel filtration on Sephacryl S-200 produced highly purified hormone preparations. Yields of purified eLH and eFSH were 110 and 60 mg/kg of frozen pituitaries, respectively. Subunits were prepared by dissociation in 8 M guanidine HCl followed by either gel filtration (eLH) or gel filtration followed by QAE-Sephadex chromatography (eFSH). The hormones and their subunits were characterized by sodium dodecyl sulfate-gel electrophoresis, amino acid analysis, NH2-terminal analysis, and by LH and FSH radioligand receptor assays.
Activation of Enteroendocrine Cells via TLRs Induces Hormone, Chemokine, and Defensin Secretion (2007)

Enteroendocrine cells are known primarily for their production of hormones that affect digestion, but they might also be implicated in sensing and neutralizing or expelling pathogens. We evaluate the expression of TLRs and the response to specific agonists in terms of cytokines, defensins, and hormones in enteroendocrine cells. The mouse enteroendocrine cell line STC-1 and C57BL/6 mice are used for in vitro and in vivo studies, respectively. The presence of TLR4, 5, and 9 is investigated by RT-PCR, Western blot, and immunofluorescence analyses. Activation of these receptors is studied evaluating keratinocyte-derived chemokine, defensins, and cholecystokinin production in response to their specific agonists. In this study, we show that the intestinal enteroendocrine cell line STC-1 expresses TLR4, 5, and 9 and releases cholecystokinin upon stimulation with the respective receptor agonists LPS, flagellin, and CpG-containing oligodeoxynucleotides. Release of keratinocyte-derived chemokine and beta-defensin 2 was also observed after stimulation of STC-1 cells with the three TLR agonists, but not with fatty acids. Consistent with these in vitro data, mice showed increased serum cholecystokinin levels after oral challenge with LPS, flagellin, or CpG oligodeoxynucleotides. In addition to their response to food stimuli, enteroendocrine cells sense the presence of bacterial Ags through TLRs and are involved in neutralizing intestinal bacteria by releasing chemokines and defensins, and maybe in removing them by releasing hormones such as cholecystokinin, which induces contraction of the muscular tunica, favoring the emptying of the distal small intestine.
Diphtheria toxin fused to variant human interleukin-3 induces cytotoxicity of blasts from patients with acute myeloid leukemia according to the level of interleukin-3 receptor expression (2005)

Leukemic blasts from patients with acute myeloid leukemia (AML) frequently express high levels of the interleukin-3 receptor alpha chain (IL-3Ralpha). In the present study, we have explored the sensitivity of primary leukemic blasts obtained from 34 patients with AML to a diphtheria toxin (DT) composed of the catalytic and translocation domains of DT (DT388) fused to IL-3 (DT388IL-3) and to DT388 fused to a variant IL-3 with increased binding affinity (DT388IL-3[K116W]). On a molar basis, DT388IL-3[K116W] was significantly more active than DT388IL-3 in mediating leukemic cell killing. The rate of cell killing induced by the 2 DT/IL-3 fusion proteins was significantly correlated with the level of IL-3Ralpha/IL-3Rbeta expressed on leukemic blasts. These observations support a potential use of DT388IL-3[K116W] in the treatment of refractory AMLs and provide a simple biochemical parameter for the selection of eligible patients.
A new class of hybrid mesoporous materials with functionalized organic monolayers for selective adsorption of heavy metal ions (2000)

Thiol- and amino-functionalized SBA-15 silicas with uniform mesoporosities were prepared and employed for removing heavy metal ions from waste water; the thiolated SBA-15 adsorbent exhibited a higher complexation affinity for Hg2+, while the other metal ions (Cu2+, Zn2+, Cr3+ and Ni2+) showed exceptional binding ability with its aminated analogue.
Mismatch repair and the fidelity of genetic recombination (1989)

Two modes of mismatch repair are known to operate in bacteria: long-patch mismatch repair and very short patch mismatch repair. Very short patch mismatch repair systems act on a specific mismatch by conserving only one base pair. Therefore, when very short patch mismatch repair acts on heteroduplex recombination intermediates, it hyper-recombines specific markers by creating patchwork sequences, i.e., apparent multiple exchange events, on the repaired strand. Long-patch mismatch repair is antirecombinagenic, apparently by decomposing heteroduplex DNA or aborting its formation whenever well-recognized mismatches are formed by strand exchange between nonidentical parental sequences. It is postulated here that mismatch-stimulated antirecombination by long-patch mismatch repair is a "proofreading" system assuring high fidelity of homologous recombination. This accounts for chromosomal stability in eucaryotes (i.e., the rare occurrence of chromosomal aberrations and mitotic recombination versus the high frequency of precise sister chromatid exchange), suggests a role for diverged repetitive and other noncoding sequences as chromosomal antirecombination elements, and provides a molecular mechanism for speciation without the necessity of geographical separation.
Solution Structure of a Novel Tryptophan-Rich Peptide with Bidirectional Antimicrobial Activity (2005)

Trp-rich antimicrobial peptides play important roles in the host innate defense mechanisms of many plants, insects, and mammals. A new type of Trp-rich peptide, Ac-KWRRWVRWI-NH(2), designated Pac-525, was found to possess improved activity against both gram-positive and -negative bacteria. We have determined that the solution structures of Pac-525 bound to membrane-mimetic sodium dodecyl sulfate (SDS) micelles. The SDS micelle-bound structure of Pac-525 adopts an alpha-helical segment at residues Trp2, Arg3, and Arg4. The positively charged residues are clustered together to form a hydrophilic patch. The three hydrophobic residues Trp2, Val6, and Ile9 form a hydrophobic core. The surface electrostatic potential map indicates the three tryptophan indole rings are packed against the peptide backbone and form an amphipathic structure. Moreover, the reverse sequence of Pac-525, Ac-IWRVWRRWK-NH(2), designated Pac-525(rev), also demonstrates similar antimicrobial activity and structure in membrane-mimetic micelles and vesicles. A variety of biophysical and biochemical methods, including circular dichroism, fluorescence spectroscopy, and microcalorimetry, were used to show that Pac-525 interacted strongly with negatively charged phospholipid vesicles and induced efficient dye release from these vesicles, suggesting that the antimicrobial activity of Pac-525 may be due to interactions with bacterial membranes.
Portable CE system with contactless conductivity detection in an injection molded polymer chip for on-site food analysis (2008)

We present a compact portable chip-based capillary electrophoresis system that employs capacitively coupled contactless conductivity detection (C<sup>4</sup>D) operating at 4 MHz as an alternative detection method compared to the commonly used optical detection employing laser-induced fluorescence. The disposable chip for this system is fabricated out of PMMA using injection molding; the electrodes are screen-printed or thin-film electrodes. The system allows the measurement of small ions like Li, Na, K typically present in foodstuff like milk and mineral water as well as acids in wine.
The C Terminus of the Metabotropic Glutamate Receptor Subtypes 2 and 7 Specifies the Receptor Signaling Pathways (2001)

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Melanoma angiogenesis and metastasis modulated by ribozyme targeting of the secreted growth factor pleiotrophin (1996)

Clinical and experimental evidence suggests that spreading of malignant cells from a localized tumor (metastasis) is directly related to the number of microvessels in the primary tumor. This tumor angiogenesis is thought to be mediated by tumor-cell-derived growth factors. However, most tumor cells express a multitude of candidate angiogenesis factors and it is difficult to decipher which of these are rate-limiting factors in vivo. Herein we use ribozyme targeting of pleiotrophin (PTN) in metastatic human melanoma cells to assess the significance of this secreted growth factor for angiogenesis and metastasis. As a model we used human melanoma cells (1205LU) that express high levels of PTN and metastasize from subcutaneous tumors to the lungs of experimental animals. In these melanoma cells, we reduced PTN mRNA and growth factor activity by transfection with PTN-targeted ribozymes and generated cell lines expressing different levels of PTN. We found that the reduction of PTN does not affect growth of the melanoma cells in vitro. In nude mice, however, tumor growth and angiogenesis were decreased in parallel with the reduced PTN levels and apoptosis in the tumors was increased. Concomitantly, the metastatic spread of the tumors from the subcutaneous site to the lungs was prevented. These studies support a direct link between tumor angiogenesis and metastasis through a secreted growth factor and identify PTN as a candidate factor that may be rate-limiting for human melanoma metastasis.
Synthetic peptide homologous to beta protein from Alzheimer disease forms amyloid-like fibrils in vitro. (1987)

Progressive amyloid deposition in senile plaques and cortical blood vessels may play a central role in the pathogenesis of Alzheimer disease. We have used x-ray diffraction and electron microscopy to study the molecular organization and morphology of macromolecular assemblies formed by three synthetic peptides homologous to beta protein of brain amyloid: beta-(1-28), residues 1-28 of the beta protein; [Ala16]beta-(1-28), beta-(1-28) with alanine substituted for lysine at position 16; and beta-(18-28), residues 18-28 of the beta protein. beta-(1-28) readily formed fibrils in vitro that were similar in ultrastructure to the in vivo amyloid and aggregated into large bundles resembling those of senile plaque cores. X-ray patterns from partially dried, oriented pellets showed a cross-beta-conformation. A series of small-angle, equatorial maxima were consistent with a tubular fibril having a mean diameter of 86 A and a wall composed of pairs of cross-beta-pleated sheets. The data may also be consistent with pairs of cross-beta-sheets that are centered 71-A apart. [Ala16]beta-(1-28) formed beta-pleated sheet assemblies that were dissimilar to in vivo fibrils. The width of the 10-A spacing indicated stacks of about six sheets. Thus, substitution of the uncharged alanine for the positively charged lysine in the beta-strand region enhances the packing of the sheets and dramatically alters the type of macromolecular aggregate formed. beta-(18-28) formed assemblies that had even a greater number of stacked sheets, approximately equal to 24 per diffracting domain as indicated by the sharp intersheet reflection. Our findings on these homologous synthetic assemblies help to define the specific sequence that is required to form Alzheimer-type amyloid fibrils, thus providing an in vitro model of age-related cerebral amyloidogenesis.
Passage through mitosis is required for oncoretroviruses but not for the human immunodeficiency virus (1994)

The human immunodeficiency virus productively infects and integrates into cells that have been arrested in the cell cycle with either gamma irradiation or aphidicolin. Integration by oncoretroviruses such as the murine leukemia virus (MuLV), on the other hand, depends on cell proliferation. Although the entire cell cycle is not necessary for MuLV infection, it is essential that the infected cells pass through mitosis. The long terminal repeat circle junction, a marker for nuclear entry, is first observed in MuLV-infected cells immediately after mitosis. These results suggest that mitosis is necessary for nuclear entry of MuLV, but not human immunodeficiency virus, unintegrated proviral DNA.