gebhart/patrepeval huggingface dataset:
The Effect of Metabolite Analogues on Growth of Bacillus anthracis in the Guinea pig and on the Formation of Virulence-determining Factors (1957)

SUMMARY: Several metabolite analogues have been tested for their effect on the growth of Bacillus anthracis and its ability to synthesize toxin and capsular material during the terminal bacteraemic stage of anthrax in the guinea pig. 8-Azaguanine, 8-azaxanthine and to a lesser degree, ethionine, α-amino-n-butyric acid andp-fluoro-phenylalanine inhibited the in vivo growth of B. anthracis, whilst 2-thiouracil and pyridine 3-sulphonic acid selectively inhibited toxin production. Inhibition of capsule formation was at no time convincingly demonstrated. The annulment of these inhibitions by mixture of the analogues with appropriate metabolites gives evidence that hypoxanthine, adenine, methionine, alanine, phenylalanine and tryptophan are involved in growth in vivo and pyrimidines and nicotinamide in toxin synthesis.
Interaction of Human C1q with IgG and IgM: Revisited (2008)

The first step of activation of the classical complement pathway involves the binding of the globular C1q domain (gC1q) to the antigen-bound IgG or IgM. To improve our understanding of the mechanism of interaction of gC1q with IgG and IgM, we compared the immunoglobulin binding properties of single-residue mutants of individual globular modules of A and C chains. We found that Lys(A200) and Lys(C170) are significant for binding with both immunoglobulins. In addition, two C1q-specific scFv antibodies known as potent inhibitors of C1q-IgG and -IgM interactions were used in the epitope mapping analysis. A set of important residues, which participate in the C1q epitopes for scFv, were identified: Lys(C170) for the scFv3(V) epitope and Arg(B108) and Arg(B109) for the scFv10(V) epitope. The ability of scFv3(V) and scFv10(V) to bind preformed C1q-IgG or C1q-IgM complexes differed: scFv3(V) retained its ability to bind C1q, while scFv10(V) lost it. Given the different locations of the epitopes and the varying abilities of both antibodies to bind C1q-IgG and C1q-IgM complexes, we found that residues from the apical surface of C1q [where the scFv3(V) epitope was located] were involved in the initial recognition of IgG and IgM, while Arg(B108) and Arg(B109) are able to interact during the initial recognition as well as during the final binding of immunoglobulins. The reported results provide the first experimental evidence supporting the notion that apical and equatorial surfaces of gC1q have consecutive involvement following the gC1q reorientation during the interaction with specific C1q ligands.
TheBacillus subtilisSignaling Protein SpoIVB Defines a New Family of Serine Peptidases (2002)

The protein SpoIVB plays a key role in signaling in the final sigma(K) checkpoint of Bacillus subtilis. This regulatory mechanism coordinates late gene expression during development in this organism and we have recently shown SpoIVB to be a serine peptidase. SpoIVB signals by transiting a membrane, undergoing self-cleavage, and then by an unknown mechanism activating a zinc metalloprotease, SpoIVFB, which cleaves pro-final sigma(K) to its active form, final sigma(K), in the outer mother cell chamber of the developing cell. In this work we have characterized the serine peptidase domain of SpoIVB. Alignment of SpoIVB with homologues from other spore formers has allowed site-specific mutagenesis of all potential active site residues within the peptidase domain. We have defined the putative catalytic domain of the SpoIVB serine peptidase as a 160-amino-acid residue segment at the carboxyl terminus of the protein. His236 and Ser378 are the most important residues for proteolysis, with Asp363 being the most probable third member of the catalytic triad. In addition, we have shown that mutations at residues Asn290 and His394 lead to delayed signaling in the final sigma(K) checkpoint. The active site residues suggest that SpoIVB and its homologues from other spore formers are members of a new family of serine peptidases of the trypsin superfamily.
SMAP‐29 has two LPS‐binding sites and a central hinge (2002)

The CD spectra of SMAP-29, an antimicrobial peptide from sheep, showed disordered structure in aqueous buffers, and significant helicity in membrane-like environments, including SDS micelles, lipopolysaccharide (LPS) dispersions, and trifluoroethanol buffer systems. A structure determined by NMR in 40% perdeuterated trifluoroethanol indicated that residues 8-17 were helical, residues 18-19 formed a hinge, and residues 20-28 formed an ordered, hydrophobic segment. SMAP-29 was flexible in 40% trifluoroethanol, forming two sets of conformers that differed in the relative orientation of the N-terminal domain. We used a chromogenic Limulus assay to determine the EC50 of the peptide (the concentration that bound 50% of the added LPS). Studies with full-length and truncated SMAP-29 molecules revealed that each end of the holopeptide contained an LPS-binding domain. The higher affinity LPS-binding domain was situated in the flexible N-terminal portion. LPS binding to full-length SMAP-29 showed positive cooperativity, so the EC50 of the peptide (2.6 microm) was considerably lower than that of the individual LPS-binding domains. LPS-binding studies with a mixture of truncated peptides revealed that this cooperativity was primarily intramolecular (i.e. involving the N- and C-terminal LPS-binding sites of the same peptide molecule). CAP-18[106 -142], an antimicrobial cathelicidin peptide of rabbits, resembled SMAP-29 in that it contained N- and C-terminal LPS-binding domains, had an EC50 of 2.5 microm, and bound LPS with positive cooperativity. We conclude that the presence of multiple binding sites that function cooperatively allow peptides such as SMAP-29 and CAP-18 to bind LPS with high affinity.
Volatile Components in Stored Rice [Oryza sativa (L.)] of Varieties with and without Lipoxygenase-3 in Seeds (1999)

Lipoxygenase (LOX) is thought to play an important role in the formation of desirable or undesirable flavor and aroma in many plant products. In rice seeds, LOX activity is localized in the bran fraction and LOX-3 is the major isozyme component. We used gas chromatography-mass spectrometry to determine whether the degree of staleness in the flavor of stored brown rice was related to the presence of LOX-3. We found that the amount of hexanal, pentanal, and pentanol in normal raw LOX-3 rice markedly increased during storage at 35 degrees C. That in LOX-3-less rice increased slightly but was a third to a fifth that of normal LOX-3 rice. In cooked rice, the amount of these components from glutinous rice exceeded that in nonglutinous rice, and that in normal LOX-3 rice exceeded that in LOX-3-less rice. These results indicate that the stale flavor production in LOX-3-less rice during storage is less than that in normal LOX-3 rice.
Decrease in Coronary Blood Flow Reserve During Hyperlipidemia Is Secondary to an Increase in Blood Viscosity (2001)

Increasing lipid levels in a fully dilated normal coronary bed causes no change in large or small vessel dimensions. Instead, the increase in blood viscosity causes capillary resistance to rise, which attenuates hyperemic CBF. Therefore, the abnormal CBF reserve associated with hyperlipidemia is due to increase blood viscosity and not abnormal vascular function.
Friedreich's ataxia: Point mutations and clinical presentation of compound heterozygotes (1999)

Friedreich's ataxia is the most common inherited ataxia. Ninety-six percent of patients are homozygous for GAA trinucleotide repeat expansions in the first intron of the frataxin gene. The remaining cases are compound heterozygotes for a GAA expansion and a frataxin point mutation. We report here the identification of 10 novel frataxin point mutations, and the detection of a previously described mutation (G130V) in two additional families. Most truncating mutations were in exon 1. All missense mutations were in the last three exons coding for the mature frataxin protein. The clinical features of 25 patients with identified frataxin point mutations were compared with those of 196 patients homozygous for the GAA expansion. A similar phenotype resulted from truncating mutations and from missense mutations in the carboxy-terminal half of mature frataxin, suggesting that they cause a comparable loss of function. In contrast, the only two missense mutations located in the amino-terminal half of mature frataxin (D122Y and G130V) cause an atypical and milder clinical presentation (early-onset spastic gait with slow disease progression, absence of dysarthria, retained or brisk tendon reflexes, and mild or no cerebellar ataxia), suggesting that they only partially affect frataxin function. The incidence of optic disk pallor was higher in compound heterozygotes than in expansion homozygotes, which might correlate with a very low residual level of normal frataxin produced from the expanded allele.
Expression of carbonic anhydrase IX in breast is associated with malignant tissues and is related to overexpression of c‐erbB2 (2002)

CA IX is a tumour-associated carbonic anhydrase with proposed roles in pH modulation and intercellular communication. Its distribution was examined in normal, benign and malignant breast tissues and compared with expression of breast tumour markers including oestrogen receptor, c-erbB2, c-erbB3 and CD44. Tissue specimens were analysed using immunohistochemistry and/or reverse transcriptase-polymerase chain reaction (RT-PCR). CA IX was detected by IHC in 12/26 (46%) malignant tissues, 4/36 (11%) benign lesions, but not in 10 normal breasts. Staining was mostly confined to plasma membranes of abnormal epithelial cells, but in five cases was found in adjacent stroma. Semi-quantitative RT-PCR detected CA9 mRNA in 25/39 (64%) malignant tumours, 11/33 (33%) benign lesions, but in none of three normal breasts. Comparative RT-PCR analysis of malignant tissues revealed a relationship between CA9 positivity and c-erbB2 overexpression (p=0.05). Moreover, CA9-positive specimens displayed a significantly higher median level of c-erbB2 than CA9-negative ones (p=0.02). No significant association was found with the other markers. The results of this study support the possible importance of CA IX for breast carcinogenesis and suggest its potential use as a breast tumour marker.
Beyond the Canonical 20 Amino Acids: Expanding the Genetic Lexicon (2010)

The ability to genetically encode unnatural amino acids beyond the common 20 has allowed unprecedented control over the chemical structures of recombinantly expressed proteins. Orthogonal aminoacyl-tRNA synthetase/tRNA pairs have been used together with nonsense, rare, or 4-bp codons to incorporate >50 unnatural amino acids into proteins in Escherichia coli, Saccharomyces cerevisiae, Pichia pastoris, and mammalian cell lines. This has allowed the expression of proteins containing amino acids with novel side chains, including fluorophores, post-translational modifications, metal ion chelators, photocaged and photocross-linking moieties, uniquely reactive functional groups, and NMR, IR, and x-ray crystallographic probes.
6-Chloropyridazin-3-yl Derivatives Active as Nicotinic Agents:  Synthesis, Binding, and Modeling Studies (2002)

3,8-Diazabicyclo[3.2.1]octane (1), 2,5-diazabicyclo[2.2.1]heptane (2), piperazine (3), and homopiperazine (4) derivatives, substituted at one nitrogen atom with the 6-chloro-3-pyridazinyl group while the other nitrogen atom was either unsubstituted or mono- or dimethylated, were synthesized and tested for their affinity toward the neuronal nicotinic acetylcholine receptors (nAChRs). All of the compounds had K(i) values in the nanomolar range. A molecular modeling study allowed location of their preferred conformations, the energies of which were recalculated in water with a continuum solvent model. Some of the compounds showed, in their populated conformations, only pharmacophoric distances longer than the values taken into consideration by the Sheridan model for nAChRs receptors. Thus, this SAR study gives support to the hypothesis that these longer distances are still compatible with affinity for alpha4beta2 receptors in the nanomolar range.
An unusual guanyl oligonucleotide regulates cellulose synthesis in Acetobacter xylinum (1985)

The mechanism of GTP-specific activation of the membrane-bound cellulose synthase system of Acetobacter xylinum has been further elucidated. The supernatant fraction derived from washed membranes of this organism contains an enzyme which reacts with GTP to form a low molecular mass, heat-stable compound,tentatively characterized as a cyclic oligonuleotide composed of GMP residues, which is the immediate activator of the cellulose synthase. This activation is reversed by a membrane-bound enzyme that degrades the activator; the latter enzyme is inhibited by Ca (2+). It is suggested that the interaction between these enzymes and nucleotide derivatives, mediated by Ca (2+), may regulate cellulose synthesis in VIVO.
Long-Term Treatment of Girls with Ornithine Transcarbamylase Deficiency (1996)

Girls with symptomatic ornithine transcarbamylase deficiency who are treated with drugs that activate new pathways of waste-nitrogen excretion have fewer hyperammonemic episodes and a reduced risk of further cognitive decline.
Solid-State and Solution Properties of the Lanthanide Complexes of a New Heptadentate Tripodal Ligand:  A Route to Gadolinium Complexes with an Improved Relaxation Efficiency (2001)

The tripodal ligand (alpha,alpha',alpha' 'nitrilotri(6-methyl-2-pyridinecarboxylic acid)) (H(3)tpaa) forms a Gd(III) complex which has a relaxivity (r(1p) = 13.3 mM(-1) s(-1) at 25 degrees C and at 60 MHz) remarkably higher than those of the currently clinically used contrast agents based on octacoordinate polyaminocarboxylate complexes (3.5-4.7 mM(-1) s(-1)) and a reasonably good thermodynamic stability. The crystal structure of the ligand and of its La, Nd, Eu, Gd, Tb, Ho, Tm, Yb, and Lu complexes have been determined by X-ray crystallography. The neutral H(3)tpaa molecule adopts, in the solid state, a preorganized tripodal conformation in which the three H(3)tpaa arms are located on the same side of the molecule, ready to bind a metal ion in a heptadentate coordination mode. The structures of the Ln(III) complexes vary along the series for their nuclearity and number of water molecules coordinated to the metal, and a tetrameric structure is observed for the La(3+) ion (9- and 10-coordinate metal centers), dimeric structures are formed from the Nd(3+) ion through the Yb(3+) ion (9-coordinate), and a monomeric structure results for Lu(3+) (8-coordinate). The relaxivity studies presented here suggest that the high relaxivity of the Gd(tpaa) complex is mainly the consequence of a shorter bound water proton-Gd(III) distance associated with a probable water coordination equilibrium between tris(aqua) and bis(aqua) complexes, giving raise to a mean number of coordinated water molecules q > 2. Both effects are strongly related to the ligand flexibility, which allows for a large volume available for water binding. The observed rapid water exchange rate is probably due to the presence of a low-energy barrier between 10-, 9-, and 8- coordinate geometries. Although the low solubility of the Gd complex of tpaa prevents its practical application as an MRI contrast agent, the straightforward introduction of substituents on the pyridine rings allows us to envisage ligands with a higher water solubility, containing functional groups leading to macromolecular systems with very high relaxivity.
Efficient Blue‐ and White‐Emitting Electrophosphorescent Devices Based on Platinum(II) [1,3‐Difluoro‐4,6‐di(2‐pyridinyl)benzene] Chloride (2008)

Efficient blue and white single-doped organic light-emitting devices based a novel platinum complex – platinum(II) [1,3-difluoro-4,6-di(2-pyridinyl)benzene] chloride – are reported (see figure). The blue and white devices show peak efficiencies of 16% and 9% and CIE chromaticity coordinates of (0.15, 0.26) and (0.33, 0.36), respectively. These results demonstrate that the utilization of platinum complexes is a viable approach for the development of blue electrophosphorescent devices.
Yield, Yield Components, and Fiber Properties of Insect‐Resistant Cotton Lines Containing a Bacillus thuringiensis Toxin Gene (1994)

Crop yield and quality could be affected in transgenic crop plants carrying foreign genes which confer resistance to plant pests. Scientists at Monsanto Company produced nine transgenic cotton ( Gossypium hirsutum L.) lines, each containing one of the two Bacillus thuringiensis var. kurstaki (Berliner) constructs, cryIA(b) or cryIA(c) , that encode a protein toxic to lepidopteran insects. We undertook this study to determine whether these transgenic lines exhibit any undesirable agronomic or fiber properties. At Maricopa, AZ, we grew five, four, and three transgenic lines in field plots in 1990, 1991, and 1992, respectively; the parental ‘Coker 312’ and the locally adapted, nectariless, high fiber‐strength ‘Md 51 ne’ were included each year. Somaclonal variation, insertion of the insect‐control protein genes, and the expression of the insecticidal protein caused no general reduction in lint yield, primary or secondary yield components, or fiber properties. The transgenic lines varied significantly in every trait measured. Mean lint yields over the 3 yr were as follows: transgenic lines, 135.4 ± 4.5 g m −2 ; Coker 312, 115.1 ± 7.7 g m −2 , MD 51 ne, 141.2 ± 11.4 g m −2 . Six of the nine transgenic lines yielded significantly more lint (13–30%) than did Coker 312. Lint yields of the same six lines (10% less to 7% more) were not significantly different than that of MD 51 ne. Compared with Coker 312, four of nine transgenic lines had longer fiber, eight had stronger fiber, two had higher fiber elongation, and two did not differ significantly in micronaire. Compared with MD 51 ne, five of the nine transgenic lines did not differ significantly in fiber length, two did not differ in strength, three did not differ in elongation, and six did not differ in micronaire. These transgenic lines are valuable sources of germplasm, not only for insect resistance but also for agronomic and fiber properties.
Planar chip device for PCR and hybridization with surface acoustic wave pump (2004)

We have developed a microfluidic device operating at a planar surface instead of a closed channel network. The fluid is transported in single droplets using surface acoustic waves (SAW) on a piezoelectric LiNbO(3) substrate. The surface of the piezo is chemically structured to induce high contact angles of the droplets or enclose areas where the liquid can wet the substrate. Combining the SAW technique with thin film resistance heaters, a biological analysis chip with integrated DNA amplification by PCR and hybridization was designed. To prevent evaporation of the PCR reagents at high temperatures the sample is enclosed in droplets of mineral oil. On this chip the SAW resolves dried primers, shifts the oil capped liquid between the two heaters and mixes during hybridization. The chip is able to perform a highly sensitive, fast and specific PCR with a volume as low as 200 nl. During the temperature cycles an online monitoring of the DNA concentration is feasible with an optical unit, providing a sensitivity of 0.1 ng. After PCR the product is moved to the second heater for the hybridization on a spotted DNA array. With our chip we were able to detect a single nucleotide polymorphism (SNP) responsible for the Leiden Factor V syndrome from human blood.
The PWWP domain: a potential protein–protein interaction domain in nuclear proteins influencing differentiation? (2000)

Upon characterization of WHSC1, a gene mapping to the Wolf-Hirschhorn syndrome critical region and at its C-terminus similar to the Drosophila ASH1/trithorax group proteins, we identified a novel protein domain designated PWWP domain. To gain insight into its structure, evolutionary conservation and its potential functional role, we performed database searches to identify other PWWP domain-containing proteins. We retrieved 39 proteins, and a multiple alignment shows that the domain spans some 70 amino acids. It is present in proteins of nuclear origin and plays a role in cell growth and differentiation. Due to its position, the composition of amino acids close to the PWWP motif and the pattern of other domains present, we hypothesize that the domain is involved in protein-protein interactions.
Abolition of Crypticity of Arthrobacter pyridinolis Toward Glucose and α-Glucosides by Tricarboxylic Acid Cycle Intermediates (1973)

Arthrobacter pyridinolis cannot grow on glucose as sole carbon source, although the cells possess catabolic enzymes of the Embden-Meyerhof and pentose phosphate pathways as well as a complete tricarboxylic acid cycle. Crypticity toward glucose is abolished by a period of growth in a medium containing malate, succinate, citrate, or fumarate in addition to glucose. Other carbon sources, which support as rapid growth as does malate (e.g. asparagine), do not enable the cells to use glucose. Malate, succinate, citrate, and fumarate abolish crypticity toward glucose only in the second phase of diauxic growth after the tricarboxylic acid cycle intermediate has been depleted. This sequence of events, first observed in growth curves, has been verified by experiments in which the incorporation of radioactive substrates into trichloroacetic acid-insoluble cellular material was followed. The tricarboxylic acid cycle intermediates which confer the ability to utilize glucose also enhance the utilization of the alphaglucosides sucrose and maltose. The mechanism whereby growth on certain tricarboxylic acid cycle intermediates confers the subsequent ability to grow on glucose is related to a transport system for glucose and alpha-glucosides. This transport system has been assayed by measuring the uptake of [1-(14)C]-2-deoxyglucose. Cells grown for varying periods of time in asparagine, asparagine plus glucose, or malate do not transport 2-deoxyglucose. Cells from malate-glucose cultures that are in the exponential phase of growth on glucose can transport 2-deoxyglucose. Transport of 2-deoxyglucose shows Michaelis-Menten kinetics with a K(m) of 2.9 x 10(-4) M. It is competitively inhibited by glucose, alpha-methylglucopyranoside, and maltose. The transport of 2-deoxyglucose is inhibited by cyanide, dinitrophenol, azide, and N-ethylmaleimide, but not by malonate or fluoride. No phosphoenolpyruvate: d-glucose phosphotransferase activity has been detected, and the 2-deoxyglucose transported into the cell is not phosphorylated.
Perspectives on tubulin isotype function and evolution based on the observation that Tetrahymena thermophila microtubules contain a single α‐ and β‐tubulin (1993)

We have cloned and sequenced the two beta-tubulin genes of the ciliated protozoan Tetrahymena thermophila. The two genes encode identical 443 amino acid peptides which are 99.7% identical to the beta-tubulin proteins of T. pyriformis and 95% identical to human beta 1 tubulin. T. thermophila contains only one alpha-tubulin gene (Callahan et al., 1984: Cell 36:441-445). Thus, all of the extremely diverse microtubule structures in this unicellular organism can be formed from a single alpha- and a single beta-tubulin peptide. We have also carried out a phylogenetic analysis of 84 complete beta-tubulin peptide sequences. This analysis supports two hypotheses regarding beta-tubulin evolution and function: 1) Multifunctional beta-tubulins are under greater evolutionary constraint than beta-tubulins present in specialized cells or in cells with very few microtubule related functions, which can evolve rapidly; and 2) Cells which form axonemes maintain a homogeneous population of tubulins.