bluuebunny/crossref_metadata_2025_split huggingface dataset:
Purdue Ionomics Information Management System. An Integrated Functional Genomics Platform
Authors: Baxter Ivan , Ouzzani Mourad , Orcun Seza , Kennedy Brad , Jandhyala Shrinivas S. , Salt David E. 
Published: December 2006

Abstract
The advent of high-throughput phenotyping technologies has created a deluge of information that is difficult to deal with without the appropriate data management tools. These data management tools should integrate defined workflow controls for genomic-scale data acquisition and validation, data storage and retrieval, and data analysis, indexed around the genomic information of the organism of interest. To maximize the impact of these large datasets, it is critical that they are rapidly disseminated to the broader research community, allowing open access for data mining and discovery. We describe here a system that incorporates such functionalities developed around the Purdue University high-throughput ionomics phenotyping platform. The Purdue Ionomics Information Management System (PiiMS) provides integrated workflow control, data storage, and analysis to facilitate high-throughput data acquisition, along with integrated tools for data search, retrieval, and visualization for hypothesis development. PiiMS is deployed as a World Wide Web-enabled system, allowing for integration of distributed workflow processes and open access to raw data for analysis by numerous laboratories. PiiMS currently contains data on shoot concentrations of P, Ca, K, Mg, Cu, Fe, Zn, Mn, Co, Ni, B, Se, Mo, Na, As, and Cd in over 60,000 shoot tissue samples of Arabidopsis (Arabidopsis thaliana), including ethyl methanesulfonate, fast-neutron and defined T-DNA mutants, and natural accession and populations of recombinant inbred lines from over 800 separate experiments, representing over 1,000,000 fully quantitative elemental concentrations. PiiMS is accessible at www.purdue.edu/dp/ionomics.
Modulation of Ethylene Responses Affects Plant Salt-Stress Responses
Authors: Cao Wan-Hong , Liu Jun , He Xin-Jian , Mu Rui-Ling , Zhou Hua-Lin , Chen Shou-Yi , Zhang Jin-Song 
Published: December 2006

Abstract
Ethylene signaling plays important roles in multiple aspects of plant growth and development. Its functions in abiotic stress responses remain largely unknown. Here, we report that alteration of ethylene signaling affected plant salt-stress responses. A type II ethylene receptor homolog gene NTHK1 (Nicotiana tabacum histidine kinase 1) from tobacco (N. tabacum) conferred salt sensitivity in NTHK1-transgenic Arabidopsis (Arabidopsis thaliana) plants as judged from the phenotypic change, the relative electrolyte leakage, and the relative root growth under salt stress. Ethylene precursor 1-aminocyclopropane-1-carboxylic acid suppressed the salt-sensitive phenotype. Analysis of Arabidopsis ethylene receptor gain-of-function mutants further suggests that receptor function may lead to salt-sensitive responses. Mutation of EIN2, a central component in ethylene signaling, also results in salt sensitivity, suggesting that EIN2-mediated signaling is beneficial for plant salt tolerance. Overexpression of the NTHK1 gene or the receptor gain-of-function activated expression of salt-responsive genes AtERF4 and Cor6.6. In addition, the transgene NTHK1 mRNA was accumulated under salt stress, suggesting a posttranscriptional regulatory mechanism. These findings imply that ethylene signaling may be required for plant salt tolerance.
Somatic Cytokinesis and Pollen Maturation inArabidopsisDepend on TPLATE, Which Has Domains Similar to Coat Proteins
Authors: Van Damme Daniël , Coutuer Silvie , De Rycke Riet , Bouget Francois-Yves , Inzé Dirk , Geelen Danny 
Published: December 2006

AbstractTPLATE was previously identified as a potential cytokinesis protein targeted to the cell plate. Disruption of TPLATE in Arabidopsis thaliana leads to the production of shriveled pollen unable to germinate. Vesicular compartmentalization of the mature pollen is dramatically altered, and large callose deposits accumulate near the intine cell wall layer. Green fluorescent protein (GFP)–tagged TPLATE expression under the control of the pollen promoter Lat52 complements the phenotype. Downregulation of TPLATE in Arabidopsis seedlings and tobacco (Nicotiana tabacum) BY-2 suspension cells results in crooked cell walls and cell plates that fail to insert into the mother wall. Besides accumulating at the cell plate, GFP-fused TPLATE is temporally targeted to a narrow zone at the cell cortex where the cell plate connects to the mother wall. TPLATE-GFP also localizes to subcellular structures that accumulate at the pollen tube exit site in germinating pollen. Ectopic callose depositions observed in mutant pollen also occur in RNA interference plants, suggesting that TPLATE is implicated in cell wall modification. TPLATE contains domains similar to adaptin and β-COP coat proteins. These data suggest that TPLATE functions in vesicle-trafficking events required for site-specific cell wall modifications during pollen germination and for anchoring of the cell plate to the mother wall at the correct cortical position.
The Plant-Specific ssDNA Binding Protein OSB1 Is Involved in the Stoichiometric Transmission of Mitochondrial DNA inArabidopsis
Authors: Zaegel Vincent , Guermann Benoît , Le Ret Monique , Andrés Charles , Meyer Denise , Erhardt Mathieu , Canaday Jean , Gualberto José M. , Imbault Patrice 
Published: December 2006

AbstractPlant mitochondrial genomes exist in a natural state of heteroplasmy, in which substoichiometric levels of alternative mitochondrial DNA (mtDNA) molecules coexist with the main genome. These subgenomes either replicate autonomously or are created by infrequent recombination events. We found that Arabidopsis thaliana OSB1 (for Organellar Single-stranded DNA Binding protein1) is required for correct stoichiometric mtDNA transmission. OSB1 is part of a family of plant-specific DNA binding proteins that are characterized by a novel motif that is required for single-stranded DNA binding. The OSB1 protein is targeted to mitochondria, and promoter–β-glucuronidase fusion showed that the gene is expressed in budding lateral roots, mature pollen, and the embryo sac of unfertilized ovules. OSB1 T-DNA insertion mutants accumulate mtDNA homologous recombination products and develop phenotypes of leaf variegation and distortion. The mtDNA rearrangements occur in two steps: first, homozygous mutants accumulate subgenomic levels of homologous recombination products; second, in subsequent generations, one of the recombination products becomes predominant. After the second step, the process is no longer reversible by backcrossing. Thus, OSB1 participates in controlling the stoichiometry of alternative mtDNA forms generated by recombination. This regulation could take place in gametophytic tissues to ensure the transmission of a functional mitochondrial genome.
Prediction of structures of multidomain proteins from structures of the individual domains
Authors: Wollacott Andrew M. , Zanghellini Alexandre , Murphy Paul , Baker David 
Published: December 2006

AbstractWe describe the development of a method for assembling structures of multidomain proteins from structures of isolated domains. The method consists of an initial low‐resolution search in which the conformational space of the domain linker is explored using the Rosetta de novo structure prediction method, followed by a high‐resolution search in which all atoms are treated explicitly and backbone and side chain degrees of freedom are simultaneously optimized. The method recapitulates, often with very high accuracy, the structures of existing multidomain proteins.
Thermodynamic stability of a cold‐adapted protein, type III antifreeze protein, and energetic contribution of salt bridges
Authors: García‐Arribas Olga , Mateo Roberto , Tomczak Melanie M. , Davies Peter L. , Mateu Mauricio G. 
Published: December 2006

AbstractA thermodynamic analysis of a cold‐adapted protein, type III anti‐freeze protein (AFP), was carried out. The results indicate that the folding equilibrium of type III AFP is a reversible, unimolecular, two‐state process with no populated intermediates. Compared to most mesophilic proteins whose folding is two‐state, the psychrophilic type III AFP has a much lower thermodynamic stability at 25°C, ∼3 kcal/mol, and presents a remarkably downshifted stability–temperature curve, reaching a maximum of 5 kcal/mol around 0°C. Type III AFPs contain few and non‐optimally distributed surface charges relative to their mesophilic homologs, the C‐terminal domains of sialic acid synthases. We used thermodynamic double mutant cycles to evaluate the energetic role of every surface salt bridge in type III AFP. Two isolated salt bridges provided no contribution to stability, while the Asp36–Arg39 salt bridge, involved in a salt bridge network with the C‐terminal carboxylate, had a substantial contribution (∼1 kcal/mol). However, this contribution was more than counteracted by the destabilizing effect of the Asp36 carboxylate itself, whose removal led to a net 30% increase in stability at 25°C. This study suggests that type III AFPs may have evolved for a minimally acceptable stability at the restricted, low temperature range (around 0°C) at which AFPs must function. In addition, it indicates that salt bridge networks are used in nature also for the stability of psychrophilic proteins, and has led to a type III AFP variant of increased stability that could be used for biotechnological purposes.
The transmembrane homotrimer of ADAM 1 in model lipid bilayers
Authors: Gan Siok Wan , Xin Lin , Torres Jaume 
Published: December 2006

AbstractFertilin is a transmembrane protein heterodimer formed by the two subunits fertilin α and fertilin β that plays an important role in sperm–egg fusion. Fertilin α and β are members of the ADAM family, and contain each one transmembrane α‐helix, and are termed ADAM 1 and ADAM 2, respectively. ADAM 1 is the subunit that contains a putative fusion peptide, and we have explored the possibility that the transmembrane α‐helical domain of ADAM 1 forms homotrimers, in common with other viral fusion proteins. Although this peptide was found to form various homooligomers in SDS, the infrared dichroic data obtained with the isotopically labeled peptide at specific positions is consistent with the presence of only one species in DMPC or POPC lipid bilayers. Comparison of the experimental orientational data with molecular dynamics simulations performed with sequence homologues of ADAM 1 show that the species present in lipid bilayers is only consistent with an evolutionarily conserved homotrimeric model for which we provide a backbone structure. These results support a model where ADAM 1 forms homotrimers as a step to create a fusion active intermediate.
Evaluation of features for catalytic residue prediction in novel folds
Authors: Youn Eunseog , Peters Brandon , Radivojac Predrag , Mooney Sean D. 
Published: December 2006

AbstractStructural genomics projects are determining the three‐dimensional structure of proteins without full characterization of their function. A critical part of the annotation process involves appropriate knowledge representation and prediction of functionally important residue environments. We have developed a method to extract features from sequence, sequence alignments, three‐dimensional structure, and structural environment conservation, and used support vector machines to annotate homologous and nonhomologous residue positions based on a specific training set of residue functions. In order to evaluate this pipeline for automated protein annotation, we applied it to the challenging problem of prediction of catalytic residues in enzymes. We also ranked the features based on their ability to discriminate catalytic from noncatalytic residues. When applying our method to a well‐annotated set of protein structures, we found that top‐ranked features were a measure of sequence conservation, a measure of structural conservation, a degree of uniqueness of a residue's structural environment, solvent accessibility, and residue hydrophobicity. We also found that features based on structural conservation were complementary to those based on sequence conservation and that they were capable of increasing predictor performance. Using a family nonredundant version of the ASTRAL 40 v1.65 data set, we estimated that the true catalytic residues were correctly predicted in 57.0% of the cases, with a precision of 18.5%. When testing on proteins containing novel folds not used in training, the best features were highly correlated with the training on families, thus validating the approach to nonhomologous catalytic residue prediction in general. We then applied the method to 2781 coordinate files from the structural genomics target pipeline and identified both highly ranked and highly clustered groups of predicted catalytic residues.
Redesigning protein pKavalues
Authors: Tynan‐Connolly Barbara Mary , Nielsen Jens Erik 
Published: December 2006

AbstractThe ability to re‐engineer enzymatic pH‐activity profiles is of importance for industrial applications of enzymes. We theoretically explore the feasibility of re‐engineering enzymatic pH‐activity profiles by changing active site pKavalues using point mutations. We calculate the maximum achievable ΔpKavalues for 141 target titratable groups in seven enzymes by introducing conservative net‐charge altering point mutations. We examine the importance of the number of mutations introduced, their distance from the target titratable group, and the characteristics of the target group itself. The results show that multiple mutations at 10Å can change pKavalues up to two units, but that the introduction of a requirement to keep other pKavalues constant reduces the magnitude of the achievable ΔpKa. The algorithm presented shows a good correlation with existing experimental data and is available for download and via a web server athttp://enzyme.ucd.ie/pKD.
Atomic model of human Rcd‐1 reveals an armadillo‐like‐repeat protein with in vitro nucleic acid binding properties
Authors: Garces Robert G. , Gillon Wanda , Pai Emil F. 
Published: December 2006

AbstractRcd‐1, a protein highly conserved across eukaryotes, was initially identified as a factor essential for nitrogen starvation‐invoked differentiation in fission yeast, and its Saccharomyces cerevisiae homolog, CAF40, has been identified as part of the CCR4–NOT transcription complex, where it interacts with the NOT1 protein. Mammalian homologs are involved in various cellular differentiation processes including retinoic acid‐induced differentiation and hematopoetic cell development. Here, we present the 2.2 Å X‐ray structure of the highly conserved region of human Rcd‐1 and investigate possible functional abilities of this and the full‐length protein. The monomer is made up of six armadillo repeats forming a solvent‐accessible, positively‐charged cleft 21–22 Å wide that, in contrast to other armadillo proteins, stays fully exposed in the dimer. Prompted by this finding, we established that Rcd‐1 can bind to single‐ and double‐stranded oligonucleotides in vitro with the affinity of G/C/T ≫ A. Mutation of an arginine residue within the cleft strongly reduced or abolished oligonucleotide binding. Rcd‐1's ability to bind to nucleic acids, in addition to the previously reported protein–protein interaction with NOT1, suggests a new feature in Rcd‐1's role in regulation of overall cellular differentiation processes.
Modification of the Pad‐plate Method of Determining Chlortetracycline in Egg White
Authors: BOYD JOSEPHINE W. , WEISER H. H. , HAQUE RIAZ UL , WINTER A. R. 
Published: December 2006

SUMMARYThe sensitivity of the pad‐plate method for detecting chlortetracycline in egg white is increased by using pH 4.5 citrate buffer rather than pH 4.5 phosphate buffer as a diluent. It is also increased by allowing about four hours for diffusion of antibiotic prior to incubation of the assay plates. Under these conditions of assay, protein binding of the antibiotic was not an important factor.
Destruction of alpha‐Tocopherol by gamma‐Irradiationa
Authors: ROSE DYSON , LIPS H. J. , CYR R. 
Published: December 2006

SUMMARYIrradiation (Cow source) of solutions of DL‐a‐tocopherol caused extensive destruction of this vitamin and gave rise to products similar to those obtained by autoxidation. Irradiation in saturated solvents (mineral oil, methyl myristate) destroyed more tocopherol than did irradiation in unsaturated solvents (methyl oleate, methyl linoleate). Destruction by 2.0 Mrad of irradiation increased with increasing tocopherol concentration, but the increase became negligible above 0.5% tocopherol in the saturated and 0.1% tocopherol in the unsaturated solvents.
The Volatile Sulfur Components of Cabbagea
Authors: BAILEY S. D. , BAZINET M. L. , DRISCOLL J. L. , McCARTHY A. I. 
Published: December 2006

SUMMARYNaturally occurring volatile sulfur compounds in cabbage have been identified by mass spectrometry and gas chromatography. Twenty sulfur compounds are reported of which five are isothiocyanates, five sulfides, nine disulfides and one tri‐sulfide. Two additional isothiocyanates and one trisulfide are tentatively reported. The method of mass spectral analysis is described for representative members of these sulfur compounds. Gas chromatography of fresh, dehydrated and rehydrated cabbage clearly shows the presence of allyl isothiocyanate in fresh cabbage and its regeneration by enzymatic action in dehydrated‐ cabbage. The identification of five isothiocyanates reveals the presence of corresponding thioglucosides from which the isothiocyanates are released by enzymatic hydrolysis. Similarly corresponding reactions leading to the formation of sulfides are discussed.
A Comparison of Some Taste‐Test Methodsa
Authors: GRIDGEMAN N. T. 
Published: December 2006

SUMMARYA long‐term investigation into the efficacy of different egg preservatives was used to compare different taste‐panel techniques. The main contrast is between rating, according to a specified subjective quality scale, and multiple pair comparison, according to flavor preference. A subsidiary contrast is between pair comparison with degrees of preference, and (on the same data) with straight binary preferences. All results are scored, presented graphically, and subjected to an analysis of variance. Pair comparison, especially with (three) degrees of freedom, proved to be more discriminatory than rating. Some aspects of the logic of the comparison of sensory scales are discussed.
Effects of Gamma Irradiation on the Chemical Properties of Actin and Actomyosin of Meatsa
Authors: FUJIMAKI MASAO , ARAKAWA NOBUHIKO , OGAWA GENGO 
Published: December 2006

SUMMARYEffects of gamma irradiation on the chemical properties of actin and actomyosin during aging of meats have been studied. Meats were irradiated with 4 × 106 rad of cobalt‐60 gamma rays at 40° F in three steps, i.e., immediately after slaughter, at maximum rigor, and at “rigor off.” Actin and two kinds of actomyosin (AMS and AML, previously reported by authors) were isolated from irradiated and control meats. The contents of sulfhydryl groups and amino acids, viscosity, the activity of ATPase and ATP sensitivity of actin and actomyosin were determined. From the results, actin is thought to be only slightly sensitive to irradiation as compared with actomyosin, and the latter, especially AML (a long‐time extracted actomyosin) is considered to be very sensitive. In this case, it is inferred that the depolymerization must have taken place in actomyosin molecule by irradiation on meats. The effects of the time of irradiation on the chemical properties of actomyosin in meats seem to be more remarkable at rigor off than at the other two steps.
The Oxidation of Lipids in Thin Filmssa
Authors: TOGASHI H. J. , HENICK A. S. , KOCH ROBERT B. 
Published: December 2006

SUMMARYA model system of thin films of lipid supported on dry gelatin plates was used for studying rates of lipoxidation. Variations in the nature of the gelatins used in the supporting surfaces showed significant differences in protective action against lipid oxidation. It is suggested that the observed differences may be due to differences in the orienting effects of the surfaces. Gamma‐tocopherol was found to be an effective inhibitor of the oxidation of the films. Synthetic phenolic antioxidants were not nearly as effective. Phospholipid in large concentration was also an effective inhibitor.
Isolation, Identification and Comparison of the Volatiles of Peach Fruit as Related to Harvest Maturity and Artificial Ripening
Authors: DO J. Y. , SALUNKHE D. K. , OLSON L. E. 
Published: December 2006

SUMMARY: Volatiles of peach (Prunus persica L., cultivar, Gleason Early Elberta) fruit were studied by gas‐liquid chromatography, thin‐layer chromatography and infrared spectrometry. Chromatograms of the volatiles of hard‐mature, firm‐mature, soft‐mature, tree‐ripe and artificially ripened, hard‐mature fruit were obtained with temperature programing and flame ionization detection. The volatile concentrates of tree‐ripe peaches produced 86 peaks. The major peaks were isolated and the infrared spectra determined and compared with authentic compounds.In general, concentrations of volatile components increased with advancing maturity. The main volatile components were identified as gamma‐ and delta‐lactones, esters, aldehydes, benzyl alcohol and d‐limonene.The highest total lactone concentration occurred in tree‐ripe peaches and was more than four times that of firm‐mature fruit. Gamma‐decalactone predominated among the lactones in tree‐ripe peaches. Artificially ripened peaches had very small amounts of gamma‐decalactone and lacked gamma‐ and delta‐dodecalactone, with a total lactone concentration abouf one‐fifth that of free‐ripe fruit. Concentrations of esters in artificially ripened fruit reached only one‐third to one‐half those of tree‐ripe peaches. Benzaldehyde was the predominant volatile in tree‐ripe peaches and occurred in five times the concentration found in artificially ripened fruit. These may be the determining factors relative to the inferiority of artificially ripened as compared to free‐ripened fruits.
Pacific Cod Muscle 5′‐Nucleotidase
Authors: TARR H. L. A. , GARDNER L. J. , INGRAM P. 
Published: December 2006

SUMMARY: A 5′‐nucleotidase, widely distributed in teleost fish muscles, was purified about 20‐fold from Pacific cod (Gadus macrocephalus) by chromatography of a dialyzed aqueous extract of the muscle on DEAE‐cellulose. The enzyme was unstable and lost 85% of its activity in 1 hr at 37°C 53% in 10 min at 42°C and 40% in 1 hr at 30°C. It was stable for 6 days at 0°C, could be dialyzed for up to 3 days at 0°C against 1 mM tris buffer pH 7.5 and quickly frozen and thawed without loss of activity. However, it was inactivated rapidly when held at −30°C. Brief exposure to pH 4.0 or 5.0 effected marked destruction. Attempts at further purification by means of chromatography on hydroxylapatite, adsorption using alumina Cγ and starch gel electrophoresis failed due to instability.The enzyme was strongly inhibited by EDTA, pyrophosphate, KF and ZnCl2 (1‐10 mM); less markedly inhibited by GSH, 2‐mercaptoethanol, carbonate and CaCl2 (10 to 100 mM). It was strongly activated by Mn++ and weakly activated by Mg++. The optimum pH was 7.6, and the Km was 5 × 10−4M with UMP and 8 −4M with IMP. It hydrolyzed, in order of effectiveness, LJMP, IMP, CMP, d‐AMP, GMP, d‐IMP, d‐GMP, d‐UMP and AMP, but not p‐nitro phenylphosphate, sugar phosphates or a number of other compounds including 2′,3′‐nucleotides.