gebhart/patrepeval huggingface dataset:
Abnormal recombination products result from aberrant DNA rearrangement of the human T-cell antigen receptor beta-chain gene. (1986)

Two unusual rearrangements of the T-cell antigen receptor beta-chain gene have occurred in the human T-cell tumor line CEM. The beta chain of the T-cell antigen receptor is encoded in germ-line DNA by immunoglobulin-like gene segments that rearrange during the somatic development of T cells to form active genes. Structural analysis of rearranged immunoglobulin genes has already revealed a great deal about the mechanisms by which these genes rearrange. To further characterize the mechanism by which beta-chain genes rearrange, we have determined the organization of the rearranged beta-chain gene segments in the human T-cell tumor line CEM. Three rearranged joining (J) or diversity (D) segments of the beta-chain gene are found in CEM. One of these segments rearranged during the formation of a normal rearranged beta-chain gene that comprises a variable (V beta), D beta, and J beta gene segment associated with a constant region gene segment. Two abnormal recombination products are found at the other rearranged beta-chain locus. One product has the structure, J beta-D beta-J beta, with the J beta gene segments joined in a head-to-head fashion, while the other one consists of a V beta-D beta recombined segment not associated with a J beta gene segment. We propose that the J beta-D beta-J beta structure was formed by an inversion of 6 kilobases of DNA and subsequently, a V beta-D beta rearrangement occurred. The presence of these products in CEM has important implications for our understanding of the mechanism by which somatic rearrangements of beta-chain gene segments occur.
Polarization-dependent optical second-harmonic imaging of a rat-tail tendon (2002)

Using scanning confocal microscopy, we measure the backscattered second harmonic signal generated by a 100 fs laser in rat-tail tendon collagen. Damage to the sample is avoided by using a continuous scanning technique, rather than measuring the signal at discrete points. The second harmonic signal varies by about a factor of 2 across a single cross section of the rat-tail tendon fascicle. The signal intensity depends both on the collagen organization and the backscattering efficiency. This implies that we cannot use intensity measurements alone to characterize collagen structure. However, we can infer structural information from the polarization dependence of the second harmonic signal. Axial and transverse scans for different linear polarization angles of the input beam show that second harmonic generation (SHG) in the rat-tail tendon depends strongly on the polarization of the input laser beam. We develop an analytical model for the SHG as a function of the polarization angle in the rat-tail tendon. We apply this model in determining the orientation of collagen fibrils in the fascicle and the ratio gamma between the two independent elements of the second-order nonlinear susceptibility tensor. There is a good fit between our model and the measured data.
Investigating the MESA (Multipoint Electrotactile Speech Aid): The transmission of segmental features of speech (1978)

Four normal-hearing young adults have been extensively trained in the use of a tactile speech-transmission system. Subjects were tested in the recognition of various phonetic elements including vowels, and stop, nasal, and fricative consonants under three receiving conditions; visual reception alone (lipreading), tactile reception alone, and tactile plus visual reception. Subjects were artificially deafened using earplugs and white noise and all speech tokens were presented live voice. Analysis of the data demonstrates that the tactile transform enables receivers to achieve excellent recognition of vowels in CVC context and the consonantal features of voicing and nasality. This, in combination with high recognition of vowels and the consonantal feature place of articulation through visual receptors, leads to recognition performance in the combined condition (visual plus tactual) which far exceeds either reception condition in isolation.
Modification by oral doxycycline administration of articular cartilage breakdown in osteoarthritis. (1995)

Oral administration of doxycycline has been shown to reduce the severity of articular cartilage breakdown in various animal models of osteoarthritis (OA). This disease modifying effect is associated with reductions in the levels of active and total collagenase and gelatinase in extracts of articular cartilage from the involved joint. These observations appear to justify a clinical trial of doxycycline, a readily available, inexpensive antimicrobial that has been used therapeutically in humans with OA for years with an excellent safety record.
Tuning the Sensitivity of a Foldamer-Based Mercury Sensor by Its Folding Energy (2006)

A fluorescent sensor for Hg2+ was obtained by incorporation of two methionine units into a cholate hexamer and by attaching a Dansyl group at the chain end. Folding could be made highly favorable or unfavorable in different solvents. Because folding was required to bring the sulfur groups together to chelate the mercury ion, binding affinity of the foldamer and, thus, its sensitivity as a sensor, could be tuned over broad ranges (at least 5 orders of magnitude) by solvent changes.
Effect of naturally occurring active site mutations on hepatitis C virus NS3 protease specificity (2001)

A comparison of the DNA sequences from all available genotypes of HCV indicate that the active site residues of the NS3 protease are strictly conserved with the exception of positions 123 and 168, which border the S(4) subsite. In genotype 3, the canonic arginine and aspartic acid have been replaced with threonine and glutamine, respectively. To determine if these differences contribute to an altered specificity, we characterized single-chain NS3 proteases from strains 1a, 1b, and 3a with peptide substrates and product inhibitors on the basis of the natural cleavage junction sequences, in addition to polyprotein substrates derived from the 1a strain. No statistically significant differences in specificity were observed. To demonstrate that the active sites were actually different, we generated and evaluated peptide substrates with unnatural extended side-chains. These studies confirmed that there are measurable differences between the NS3 proteases of genotypes 1 and 3. Specifically, a 5-fold difference in K(i) was observed between the proteases from genotypes 1 and 3 when a D-Glu occupied P(5), and a 30-fold difference was seen when this position contained a D-homoglutamate. The contribution of residues 123 and 168 toward the altered specificity was then evaluated individually by site-directed mutagenesis. These mutants showed that potency differences within this series could be attributed to the residue that occupied position 123 of the protease. Modeling these unnatural substrate/mutant protease interactions, on the basis of cocrystal structures of enzyme-substrate complexes, provides a structural basis for these observations. Proteins 2001;43:82-88.
Site‐Specific and Stoichiometric Modification of Antibodies by Bacterial Transglutaminase (2010)

Spot on: Bacterial transglutaminase enables the site-specific modification of Gln side chains of tumor-targeting antibodies with various probes containing lysine or lysine surrogates. The method yields completely homogeneous immunoconjugates with a defined stoichiometry. In comparative in vivo studies with xenografted mice the pharmacological profiles for enzymatically conjugated antibodies were better than those of chemically modified analogues. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Adenylate Kinases 1 and 2 Are Part of the Accessory Structures in the Mouse Sperm Flagellum1 (2006)

Proper sperm function depends on adequate ATP levels. In the mammalian flagellum, ATP is generated in the midpiece by oxidative respiration and in the principal piece by glycolysis. In locations where ATP is rapidly utilized or produced, adenylate kinases (AKs) maintain a constant adenylate energy charge by interconverting stoichiometric amounts of ATP and AMP with two ADP molecules. We previously identified adenylate kinase 1 and 2 (AK1 and AK2) by mass spectrometry as part of a mouse SDS-insoluble flagellar preparation containing the accessory structures (fibrous sheath, outer dense fibers, and mitochondrial sheath). A germ cell-specific cDNA encoding AK1 was characterized and found to contain a truncated 3' UTR and a different 5' UTR compared to the somatic Ak1 mRNA; however, it encoded an identical protein. Ak1 mRNA was upregulated during late spermiogenesis, a time when the flagellum is being assembled. AK1 was first seen in condensing spermatids and was associated with the outer microtubular doublets and outer dense fibers of sperm. This localization would allow the interconversion of ATP and ADP between the fibrous sheath where ATP is produced by glycolysis and the axonemal dynein ATPases where ATP is consumed. Ak2 mRNA was expressed at relatively low levels throughout spermatogenesis, and the protein was localized to the mitochondrial sheath in the sperm midpiece. AK1 and AK2 in the flagellar accessory structures provide a mechanism to buffer the adenylate energy charge for sperm motility.
Detection of Molecular Determinants in Complex Biological Systems Using MALDI-TOF Affinity Mass Spectrometry (2003)

Attempts to characterize antigens present in low concentration or with small amounts of available tissue can be difficult using standard methodology. For example, the molecule in question may be too small to resolve on a standard sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) gel or may not be detectable by immunoblotting due to loss of antigenicity following gel electrophoresis. Clearly, this type of analysis would be aided by enabling new technologies or by the implementation of alternative strategies. Hutchens et al. () have previously outlined new strategies for the enhanced detection and structural characterization of biopolymers by laser desorption/ionization time-of-flight mass spectrometry, an approach that has been termed affinity mass spectrometry (AMS). This technique can be used with enzyme-linked signal amplification to determine the relative amount of a particular antigen present in a complex mixture. We have used AMS with enzyme-linked signal amplification to search for small amounts of autoantigens in a complex mixture of liver homogenate or in bile duct epithelial cell homogenate (). In addition, we have used standard immunoprecipitation of crude liver homogenates coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) to analyze diseased vs. control liver for both known and unknown molecules. Although the following methods are somewhat specific with regard to the particular disease, primary biliary cirrhosis (PBC), studied by our laboratory, this technology provides a level of sensitivity in the femtomole range using crude cell lysates that we believe will be of wide application in the study of a number of disease states.
Glucagon-Like Peptide-1-(7–36) Amide and Peptide YY Mediate Intraduodenal Fat-Induced Inhibition of Acid Secretion in Dogs* (1998)

Intraduodenal fat inhibits gastric acid secretion via the release of one or more hormonal enterogastrones thought to arise from ileocolonic mucosa. This study determined whether glucagon-like peptide-1 (GLP-1)-(7-36) amide and peptide YY (PYY), colocalized in L cells found in the ileum, mediate intraduodenal fat-induced inhibition of stimulated gastric acid, and evaluated the influence of cholecystokinin-A (CCK-A) receptor activation. Gastric acid secretion in response to duodenal perfusions of 8% peptone was measured in conscious dogs with gastric and duodenal cannulas. Intraduodenal administration of a 10% fat emulsion suppressed gastric acid secretion by 72 +/- 4% (P < 0.001) and increased plasma levels of GLP-1 and PYY by 44 +/- 5 and 46 +/- 4 fmol/ml, respectively (both P < 0.01). Pretreatment with the CCK-A receptor antagonist MK-329 completely reversed the inhibition of gastric acid by fat, suppressed rises of plasma GLP-1 (maximum change, 23 +/- 4 fmol/ml), and reduced plasma PYY responses to baseline. Intravenous infusions of 50 pmol/kg x h GLP-1 or PYY, which reproduced plasma elevations after intraduodenal fat, inhibited gastric acid secretion by 66 +/- 5% and 51 +/- 6%, respectively (both P < 0.01); coinfusions of GLP-1 and PYY abolished gastric acid secretion (P < 0.001) without influencing plasma gastrin or somatostatin. Pretreatment with 1500 pmol/kg x h of the GLP-1 antagonist exendin-(9-39) amide did not alter the magnitude of inhibition of gastric acid caused by exogenous GLP-1. These results indicate that GLP-1 and PYY released by intraduodenal fat, in part through CCK-dependent pathways, are major enterogastrones in dogs. This inhibitory action occurs independent of circulating concentrations of somatostatin and gastrin and appears to involve a GLP-1 receptor distinct from that mediating incretin effects.
Human transferrin receptor internalization is partially dependent upon an aromatic amino acid on the cytoplasmic domain. (1990)

The objective of this work is to identify the elements of the human transferrin receptor that are involved in receptor internalization, intracellular sorting, and recycling. We have found that an aromatic side chain at position 20 on the cytoplasmic portion of the human transferrin receptor is required for efficient internalization. The wild-type human transferrin receptor has a tyrosine at this position. Replacement of the Tyr-20 with an aromatic amino acid does not alter the rate constant of internalization, whereas substitution with the nonaromatic amino acids serine, leucine, or cysteine reduces the internalization rate constant approximately three-fold. These results are consistent with similar studies of other receptor systems that have also documented the requirement for a tyrosine in rapid internalization. The amino terminus of the transferrin receptor is cytoplasmic, with the tyrosine 41 amino acids from the membrane. These two features distinguish the transferrin receptor from the other membrane proteins for which the role of tyrosine in internalization has been examined, because these proteins have the opposite polarity with respect to the membrane and because the tyrosines are located closer to the membrane (within 25 amino acids). The externalization rate for the recycling of the transferrin receptor is not altered by any of these substitutions, demonstrating that the aromatic amino acid internalization signal is not required for the efficient exocytosis of internalized receptor.
Androgens act synergistically to enhance estrogen‐induced upregulation of human tissue kallikreins 10, 11, and 14 in breast cancer cells via a membrane bound androgen receptor (2008)

The regulation of gene expression by steroid hormones plays an important role in the normal development and function of many organs, as well as in the pathogenesis of endocrine-related cancers, especially breast cancer. However, clinical data suggest that combined testosterone and estrogen treatments on post-menopausal women increase the risk of breast cancer. Experiments have shown that many, if not all kallikreins are under steroid hormone regulation in breast cancer cell lines. Their implication as prognostic and diagnostic markers has also been well-documented. Thus, we investigated the effect of combined hormone stimulation with androgens and 17beta-estradiol on the ductal caricinoma cell line BT474. This cell line has been shown to be sensitive to both, androgens (secreting PSA) and estrogens (secreting a number of kallikreins including KLK10, 11, and KLK14). We found that PSA expression was downregulated upon combined hormone stimulation, confirming reports that estrogen can antagonize and block the activity of the androgen receptor. Upon analysis of estrogen-sensitive kallikreins 10, 11, and 14, all showed to be synergistically enhanced in their expression three- to fourfold, upon joint hormone treatment versus individual hormone stimulation. The enhancement is dependent upon the action of androgens as treatment with the androgen receptor antagonist cyproterone actetate normalized the expression of KLK10, 11, and KLK14 to estrogen-stimulation levels. The synergistic effects between estrogens and androgens on estrogen-sensitive genes may have implications on the role of the kallikreins in associated risk of breast cancer and progression.
Nested PCR optimized for detection of Bordetella pertussis in clinical nasopharyngeal samples (1994)

Several genes and sequences in Bordetella pertussis have been used as targets in diagnostic PCR assays. A previously developed single-step PCR assay for the detection of B. pertussis was based on an insertion sequence, IS480, that is present in about 70 to 80 copies in each genome. The diagnostic sensitivity, specificity, and reliability of this assay with aspirated and heat-treated samples from the nasopharynx of patients and their contacts was improved by the use of a nested PCR configuration. The nested PCR assay produced a 205-bp fragment with all of the 115 B. pertussis strains tested and was negative with all strains belonging to other Bordetella species (n = 44) as well as other bacteria commonly found in the upper respiratory tract (n = 115). The diagnostic value of the assay was verified by giving positive results for B. pertussis in all the 51 nasopharyngeal aspirates from culture-positive patients. The assay also detected 18 positive aspirates from a total of 196 culture-negative patients. A confirmatory cleavage of the 205-bp nested PCR product by MvaI gave in all cases two bands of 88 and 117 bp. In conclusion, this newly developed nested PCR assay was shown to be reasonably fast and uncomplicated, with an optimal sensitivity and a high degree of specificity for the diagnosis of B. pertussis in aspirated nasopharyngeal samples processed simply by heat treatment. The detection level in the nested PCR was about 10 bacteria per ml, or seven to eight insertion sequence copies per 10 microliters of boiled sample.
Evidence for the reversibility of the acyl-CoA:lysophosphatidylcholine acyltransferase in microsomal preparations from developing safflower (Carthamus tinctorius L.) cotyledons and rat liver (1984)

Acyl exchange between acyl-CoA and position 2 of sn-phosphatidylcholine occurs in the microsomal preparations of developing safflower cotyledons. Evidence is presented to show that the acyl exchange is catalysed by the combined back and forward reactions of an acyl-CoA:lysophosphatidylcholine acyltransferase (EC 2.3.1.23). The back reaction of the enzyme was demonstrated by the stimulation of the acyl exchange with free CoA and by the observation that the added CoA was acylated with acyl groups from position 2 of sn-phosphatidylcholine. Re-acylation of the, endogenously produced, lysophosphatidylcholine with added acyl-CoA occurred with the same specificity as that observed with added palmitoyl lysophosphatidylcholine. A similar acyl exchange, catalysed by an acyl-CoA:lysophosphatidylcholine acyltransferase, occurred in microsomal preparations of rat liver. The enzyme from safflower had a high specificity for oleate and linoleate, whereas arachidonate was the preferred acyl group in the rat liver microsomal preparations. The rate of the back reaction was 3-5% and 0.2-0.4% of the forward reaction in the microsomal preparations of safflower and rat liver respectively. Previous observations, that the acyl exchange in safflower microsomal preparations was stimulated by bovine serum albumin and sn-glycerol 3-phosphate, can now be explained by the lowered acyl-CoA concentrations in the incubation mixture with albumin and in the increase in free CoA in the presence of sn-glycerol 3-phosphate (by rapid acylation of sn-glycerol 3-phosphate with acyl groups from acyl-CoA to yield phosphatidic acid). Bovine serum albumin and sn-glycerol 3-phosphate, therefore, shift the equilibrium in acyl-CoA:lysophosphatidylcholine acyltransferase-catalysed reactions towards the rate-limiting step in the acyl exchange process, namely the removal of acyl groups from phosphatidylcholine. The possible role of the acyl exchange in the transfer of acyl groups between complex lipids is discussed.
ADAM8 as a Novel Serological and Histochemical Marker for Lung Cancer (2004)

Our data suggest that ADAM8 should be useful as a diagnostic marker and probably as a therapeutic target.
Short gap-filling synthesis by DNA polymerase beta is processive (1993)

Mammalian DNA polymerase beta (beta-pol) is considered to be part of the DNA repair machinery. However, there have been conceptual problems with this idea because beta-pol does not completely fill some gapped substrates, and unlike other DNA polymerases, beta-pol adds just one dNMP for each cycle of binding to the DNA substrate, incorporation, and product release (distributive synthesis). To examine the questions of complete gap filling and gap recognition by beta-pol, we designed template-primer substrates with a range of gap sizes from 1 to 53 template residues between the 3'-OH primer and a downstream polynucleotide. M13mp18(+) single-stranded DNA was used as template, and synthetic deoxyoligonucleotides were used as primers and downstream polynucleotides. We find that beta-pol can completely fill gaps and that the gap-filling activity on substrates with gaps of up to 6 nucleotides is highly processive rather than distributive; processive synthesis to fill a gap strictly required 5'-phosphate on the 5'-moiety of the gap. Similar specificity for filling short gaps was not observed with other DNA polymerases. These results on substrate specificity and the mechanism of beta-pol suggest distinct requirements for the role of beta-pol in vivo.
Analysis of Antibody Response in Humans to the Type A OspC Loop 5 Domain and Assessment of the Potential Utility of the Loop 5 Epitope in Lyme Disease Vaccine Development (2006)

The OspC protein of Borrelia burgdorferi is an immunodominant antigen. Here we demonstrate that the loop 5 domain of type A OspC is surface exposed, elicits bactericidal antibody in mice, and is antigenic in humans. The data suggest that loop 5 may be suitable for inclusion in a polyvalent, chimeric OspC vaccinogen.