bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Family of MicroRNAs Present in Plants and Animals
Authors: Arteaga-Vázquez Mario , Caballero-Pérez Juan , Vielle-Calzada Jean-Philippe 
Published: December 2006

AbstractAlthough many miRNAs are deeply conserved within each kingdom, none are known to be conserved between plants and animals. We identified Arabidopsis thaliana miR854 and miR855, two microRNAs (miRNAs) with multiple binding sites in the 3′ untranslated region (3′UTR) of OLIGOURIDYLATE binding PROTEIN1b (At UBP1b), forming miRNA:mRNA interactions similar to those that cause translational repression/mRNA cleavage in animals. At UBP1b encodes a member of a heterogeneous nuclear RNA binding protein (hnRNP) family. The 3′UTR of At UBP1b is sufficient to repress reporter protein expression in tissues expressing miR854 or miR855 (rosette leaves and flowers, respectively) but not where both miRNAs are absent (cauline leaves). Intergenic regions containing sequences closely resembling miR854 are predicted to fold into stable miRNA precursors in animals, and members of the miR854 family are expressed in Caenorhabditis elegans, Mus musculus, and Homo sapiens, all with imperfect binding sites in the 3′UTR of genes encoding the T cell Intracellular Antigen-Related protein, an hnRNP of the UBP1 family. Potential binding sites for miR854 are absent from UBP1-like genes in fungi lacking the miRNA biogenetic machinery. Our results indicate that plants and animals share miRNAs of the miR854 family, suggesting a common origin of these miRNAs as regulators of basal transcriptional mechanisms.
Identification of Important Regions for Ethylene Binding and Signaling in the Transmembrane Domain of the ETR1 Ethylene Receptor of Arabidopsis
Authors: Wang Wuyi , Esch Jeff J. , Shiu Shin-Han , Agula Hasi , Binder Brad M. , Chang Caren , Patterson Sara E. , Bleecker Anthony B. 
Published: December 2006

Abstract
The ethylene binding domain (EBD) of the Arabidopsis thaliana ETR1 receptor is modeled as three membrane-spanning helices. We surveyed ethylene binding activity in different kingdoms and performed a bioinformatic analysis of the EBD. Ethylene binding is confined to land plants, Chara, and a group of cyanobacteria but is largely absent in other organisms, consistent with our finding that EBD-like sequences are overrepresented among plant and cyanobacterial species. We made amino acid substitutions in 37 partially or completely conserved residues of the EBD and assayed their effects on ethylene binding and signaling. Mutations primarily in residues in Helices I and II midregions eliminated ethylene binding and conferred constitutive signaling, consistent with the inverse-agonist model of ethylene receptor signaling and indicating that these residues define the ethylene binding pocket. The largest class of mutations, clustered near the cytoplasmic ends of Helices I and III, gave normal ethylene binding activity yet still conferred constitutive signaling. Therefore, these residues may play a role in turning off the signal transmitter domain of the receptor. By contrast, only two mutations were loss of function with respect to signaling. These findings yield insight into the structure and function of the EBD and suggest a conserved role of the EBD as a negative regulator of the signal transmitter domain.
The SH3 domain of a M7 interacts with its C‐terminal proline‐rich region
Authors: Wang Qinghua , Deloia Matthew A. , Kang Yang , Litchke Casey , Zhang Naixia , Titus Margaret A. , Walters Kylie J. 
Published: December 2006

AbstractMyosins play essential roles in migration, cytokinesis, endocytosis, and adhesion. They are composed of a large N‐terminal motor domain with ATPase and actin binding sites and C‐terminal neck and tail regions, whose functional roles and structural context in the protein are less well characterized. The tail regions of myosins I, IV, VII, XII, and XV each contain a putative SH3 domain that may be involved in protein–protein interactions. SH3 domains are reported to bind proline‐rich motifs, especially “PxxP” sequences, and such interactions serve regulatory functions. The activity of Src, PI3, and Itk kinases, for example, is regulated by intramolecular interactions between their SH3 domain and internal proline‐rich sequences. Here, we use NMR spectroscopy to reveal the structure of a protein construct from Dictyostelium myosin VII (DdM7) spanning A1620–T1706, which contains its SH3 domain and adjacent proline‐rich region. The SH3 domain forms the signature β‐barrel architecture found in other SH3 domains, with conserved tryptophan and tyrosine residues forming a hydrophobic pocket known to bind “PxxP” motifs. In addition, acidic residues in the RT or n–Src loops are available to interact with the basic anchoring residues that are typically found in ligands or proteins that bind SH3 domains. The DdM7 SH3 differs in the hydrophobicity of the second pocket formed by the 310 helix and following β‐strand, which contains polar rather than hydrophobic side chains. Most unusual, however, is that this domain binds its adjacent proline‐rich region at a surface remote from the region previously identified to bind “PxxP” motifs. The interaction may affect the orientation of the tail without sacrificing the availability of the canonical “PxxP”‐binding surface.
Is glycine a surrogate for a d‐amino acid in the collagen triple helix?
Authors: Horng Jia‐Cherng , Kotch Frank W. , Raines Ronald T. 
Published: December 2006

AbstractCollagen is the most abundant protein in animals. Every third residue in a collagen strand is a glycine with φ, ψ = −70°, 175°. A recent computational study suggested that replacing these glycine residues with d‐alanine or d‐serine would stabilize the collagen triple helix. This hypothesis is of substantial importance, as the glycine residues in collagen constitute nearly 10% of the amino acid residues in humans. To test this hypothesis, we synthesized a series of collagen mimic peptides that contain one or more d‐alanine or d‐serine residues replacing the canonical glycine residues. Circular dichroism spectroscopy and thermal denaturation experiments indicated clearly that the substitution of glycine with d‐alanine or d‐serine greatly disfavors the formation of a triple helix. Host–guest studies also revealed that replacing a single glycine residue with d‐alanine is more destabilizing than is its replacement with l‐alanine, a substitution that results from a common mutation in patients with collagen‐related diseases. These data indicate that the glycine residues in collagen are not a surrogate for a d‐amino acid and support the notion that the main‐chain torsion angles of a glycine residue in the native structure (especially, φ > 0°) are critical determinants for its beneficial substitution with a d‐amino acid in a protein.
Self‐assembly of coiled‐coil tetramers in the 1.40 Å structure of a leucine‐zipper mutant
Authors: Deng Yiqun , Zheng Qi , Liu Jie , Cheng Chao‐Sheng , Kallenbach Neville R. , Lu Min 
Published: December 2006

AbstractThe hydrophobic core of the GCN4 leucine‐zipper dimerization domain is formed by a parallel helical association between nonpolar side chains at the a and d positions of the heptad repeat. Here we report a self‐assembling coiled‐coil array formed by the GCN4‐pAe peptide that differs from the wild‐type GCN4 leucine zipper by alanine substitutions at three charged e positions. GCN4‐pAe is incompletely folded in normal solution conditions yet self‐assembles into an antiparallel tetraplex in crystals by formation of unanticipated hydrophobic seams linking the last two heptads of two parallel double‐stranded coiled coils. The GCN4‐pAe tetramers in the lattice associate laterally through the identical interactions to those in the intramolecular dimer–dimer interface. The van der Waals packing interaction in the solid state controls extended supramolecular assembly of the protein, providing an unusual atomic scale view of a mesostructure.
Mixed osmolytes: The degree to which one osmolyte affects the protein stabilizing ability of another
Authors: Holthauzen Luis Marcelo F. , Bolen D. Wayne 
Published: December 2006

AbstractMixtures of organic osmolytes occur in cells of many organisms, raising the question of whether their actions on protein stability are independent or synergistic. To investigate this question it is desirable to develop a system that permits evaluation of the effect of one osmolyte on the efficacy of another to either force‐fold or denature a protein. A means of evaluating the efficacy of an osmolyte is provided by itsm‐value, an experimental quantity that measures the ability of the osmolyte to force a protein to unfold or fold. An experimental system is presented that enables evaluations of them‐values of osmolytes in the presence and absence of a second osmolyte. The experimental system involves use of a marginally stable protein in 10 mM buffer (pH 7, 200 mM salt, and 34°C) that is at the midpoint of its native to denatured transition. These conditions enable determination ofm‐values for protecting and denaturing osmolytes in the presence and absence of a second osmolyte, permitting assessment of the extent to which the two osmolytes affect each other's efficacy. The two osmolytes investigated in this work are the denaturing osmolyte, urea, and the protecting osmolyte, sarcosine. Results show unequivocally that neither osmolyte alters the efficacy of the other in forcing the protein to fold or unfold—the osmolytes act independently on the protein despite their combined concentrations being in the multi‐molar range. These osmolytes avoid altering one another's efficacy at these high concentrations because the number of osmolyte interaction sites on the protein is large and the binding constants are quite small. Consequently, the site occupancies are low enough in number that the two osmolytes neither compete nor cooperate in interacting with the protein.
Thermal Destruction of Streptococcus faecalis in Prepared Frozen Foods a
Authors: OTT THOMAS M. , EL‐BISI HAMED M. , ESSELEN WILLIAM B. 
Published: December 2006

SUMMARYThe thermal destruction rates of Streptococcus faecalis, ATCC 7080, were determined in a selected group of meat and fish precooked frozen products. Data on heat transfer through these products in a hot air household electric oven, were also obtained. Accordingly, the theoretical thermal treatments required to render such products commercially sterile were computed following the procedure of the General method of process calculation for canned foods with some modification. Inoculated product tests were also made to confirm the adequacy of the computed thermal treatments.It is concluded that the procedure adopted for establishing the thermal treatment was accurate and proved feasible for this type of product. Based on the thermal resistance of our test strain, the heat treatments recommended on the commercial packages seem to be adequate, provided the heating and cooling procedures are similar to those followed in the present experiments. In the case of one product out of the five tested, however, the minimum recommended heating period fell short of the computed thermal requirement for that product.
Loss of Ascorbic Acid During Estimation by the Roe‐Kuether Method
Authors: TEWARI C. P. , KRISHNAN P. S. 
Published: December 2006

SUMMARYApplication of the 2,4‐dinitrophenylhydrazine method of Roe and co‐workers to plant extracts, wherein ascorbic acid was present largely or completely in the form of DHA and DKA, resulted in abnormal data, in the sense that the value of AA + DHA + DKA was significantly lower than that of DHA + DKA. Such a discrepancy, though not to the same degree, was observed also when the analyses were carried out on solutions of DHA. The loss is believed to take place during H2S treatment, there being a correlation between the extent of loss and the duration of H2S treatment, in the majority of the experiments.
Effect of Different Temperatures on Various Bacteria Isolated from Frozen Meat Piesa
Authors: KERELUK K. , PETERSON A. C. , GUNDERSON M. F. 
Published: December 2006

SUMMARYThe effect of temperature, particularly storage temperature, is one of the most important factors in controlling microbial populations of frozen foods. Adequate temperature control of frozen foods should limit the growth of microorganisms and insure maintenance of original quality and wholesomeness. This investigation was undertaken to show that correct storage temperature; do inhibit the growth of bacteria which might be considered as the source of potential public health hazard, while certain saprophytic species are able to survive and grow well at the same low temperatures. The cultures were all isolated from chicken pies.Bacterial counts were determined by plating techniques on Brain Heart Infusion (BHI) agar after various time intervals up to 30 days at ‐13°, 0°, 5°, 10°, 20° and 37° C, using both BHI broth and chicken gravy as media. Very similar results were obtained in the two media. Escherichia coli and Streptococcus faecalis had a minimum growth temperature between 5° and 10° C for active reproduction. A minimum growth temperature between 5° and 10° C was observed for the culture of Staphylococcus aureus. Of two cultures representing variants of Pseudomonas fluorescens, one culture followed the growth‐temperature pattern shown by the previously mentioned organisms and failed to grow at or below 5° C. The other P. fluorescens culture grew rapidly at 5° C. Ability to grow at low temperatures is a constitutive characteristic of the organism and is not common to all types of bacteria. At refrigerator temperatures, the growth of the psychrophilic saprophytic species tested completely outstripped the growth of several bacteria of public health significance. This indicates the great likelihood that a frozen food on defrosting, particularly in a refrigerator, would become completely unacceptable, due to the development of off flavors and odors and deteriorated physical appearance before it became a health hazard.
Rheology of Cocoa Butter. IV. Further Studies of “Omega” Crystallinity
Authors: STERLING CLARENCE 
Published: December 2006

SUMMARYAn X‐ray diffraction study was made of several plastic fats, including lard, butterfat, oleomargarine, and hydrogenated vegetable shortenings. Their liquid contents were varied by altering the holding temperature. Separate mixtures were made of cocoa butter or tristearin with corn oil, tributyrin, or trioctanoin, and their diffraction patterns were obtained. The crystal form (omega), previously described for oxidized cocoa butter, was found in the first group of fats and in the corn oil‐tristearin mixture. Omega crystallinity was not related to the solid‐liquid ratio of the fats or to differences in molecular length in the constituent fatty acid radicals. Omega crystallinity seemed to be related to a general difficulty in crystallization, probably due to steric hindrances.
The Chemical Composition of Beef Protein Fractions Before and After Irradiationa
Authors: HEDIN P. A. , KURTZ GEORGE W. , KOCH ROBERT B. 
Published: December 2006

SUMMARYA protein from beef prepared by ammonium sulfate fractionation of a hot‐water extract, gave a “wet dog” odor when irradiated. This protein has an amino acid constitution similar to that of gelatin, is associated with a nitrogen‐containing polysaccharide, and exhibits the solubility properties of a glucoprotein. When irradiated, 15% of the nitrogen becomes dialyzable and 13% of the amino acids are destroyed. The sulfhydryl content decreases markedly, whereas the ammonia, as determined after acid hydrolysis, and the ultraviolet absorption increase. Similar radiation‐induced changes can be observed with proteins that do not produce an odor. Consequently, the odor discussed in this report does not appear to be produced from simple amino acids per se.
Pectic Substances of Valencia Oranges at Different Stages of Maturitya
Authors: SINCLAIR WALTON B. , JOLLIFFE VIRGIL A. 
Published: December 2006

SUMMARYSeasonal changes in concentrations of pectic substances of the peel and pulp were followed by determining the total‐ and water‐soluble pectic substances as an‐hydrogalacturonic acid during growth and development under normal conditions. With the rapid development of fruit growth in the early part of the season, a tremendous initial increase occurred in the total‐ and water‐soluble pectic materials followed‘by a gradual decrease through the remainder of the season. The percentage methylation of the pectic substances of Valencia orange peel rises rapidly to approximately an 80 per cent level and remains relatively constant during the rest of the season.
Carbonyls in Qxidizing Fat. IV. The Role of Various Fatty Acid Components in Carbonyl Generation
Authors: ELLIS REX , GADDIS A. M. , CURRIE GEORGE T. 
Published: December 2006

SUMMARYVolatile monocarbonyls produced by mildly oxidized esters of oleic, linoleic, linolenic acids and fats have been characterized by paper chromatography of 2,4‐dinitrophenylhydrazone derivatives. The unsaturated fatty acid esters yielded a total of 7 n‐alkanals, 8 n‐alk‐2‐enals, and 4 alk‐2,4‐dienals; and similar results were obtained with the fats. Each unsaturated acid produced three major characteristic aldehydes. Comparisons of esters and glycerides showed the presence of keto or aldehyde ester scission products.
The Effect of Methylation Upon the Antioxidant and Chelation Capacity of Quercetin and Dihydroquercetin in a Lard Substratea, b, c
Authors: CRAWFORD DAVID L. , SINNHUBER RUSSELL O. , AFT HARVEY 
Published: December 2006

SUMMARYThe relative importance of the hydroxyl group positions of quercetin and the metal‐complexing sites of the molecule to antioxidant capacity in lard was investigated. The antioxidant action of quercetin seems to be a combination of reaction with free radicals and metal‐ion complexing; with the former being the more important. Selective methylation of the hydroxyl groups of the quercetin molecule generally decreased the antioxidant activity. Ultraviolet absorption spectra of quercetin and copper‐quercetin complexes suggest that quercetin will complex two moles of copper ion by intramolecular complexing and a third by intermolecular complexing. Copper‐quercetin complexes retain some antioxidant ability although it is much less than that of uncomplexed quercetin.
The Carbohydrates in the Peel of Oranges and Grapefruita
Authors: TING S. V. , DESZYCK E. J. 
Published: December 2006

SUMMARYThe carbohydrates of the citrus peel were divided according to their solubility in 80% ethanol. The alcohol‐soluble solids were composed of about 80% total sugars. Free xylose was found in trace amounts. Glucose, fructose, and sucrose were the main sugars present. Sucrose content of the peel was in general lower than the total reducing sugars. The alcohol‐insoluble solids were separated into “pectic substance,”“hemicellulose,” and “cellulose” fractions by extracting with different solvents. The “pectic substance” fraction upon hydrolysis yielded arabinose, galactose, and galacturonic acid. “Hemicellulose” fraction contained xylose, arabinose, galactose, glucose, and some uronic acids in its hydrolysate. In the “cellulose” fraction, glucose was dominant with some xylose and arabinose being also present. Traces of galactose and some uronic acids and in some cases mannose were found. On the average only between 53 and 70 per cent of the alcohol‐insoluble solids were recovered as carbohydrates in the peel of various citrus varieties.
Autoxidation of Fish Oils. I. Identification of Volatile Monocarbonyl Compounds from Autoxidized Salmon Oila, b, c
Authors: YU T. C. , DAY EDGAR A. , SINNHUBER RUSSELL O. 
Published: December 2006

SUMMARYIsolation and identification of a number of volatile monocarbonyls from autoxidized salmon oil were accomplished. The carbonyls, volatile by vacuum steam distillation, were reacted with 2,4‐dinitrophenylhydrazine. The 2,4‐dinitrophenyl‐hydrazones were separated by partition and paper chromatograpy. Spectrophotometric analyses and melting‐point determinations were made. The data show that, in addition to malonaldehyde previously reported, positive identification was made on 15 monocarbonyls: the C2, C3, C5, C6, C7, C8, and C9 alkanals; the C3, C4, C5, C6, C8, C9, and C10 2‐enals; and hept‐2,4‐dienal. Tentative identification of butanal, dec‐2,4‐dienal, and undec‐2‐enal was based upon a comparison of chro‐matographic behavior and absorption spectra of the authentic with the unknown. The isolated ketones, tentatively identified as 2‐hexanone, 2‐octanone, 2‐nonanone, and 2‐decanone, were characterized by the preceding methods and by their behavior in alcoholic potassium hydroxide. Five additional compounds of unknown identity were isolated; three provided sufficient material for melting‐point determinations. Including the forerun, at least 28 carbonyls were found in the volatile portion of rancid salmon oil.
Oxidation of Fat in Model Systems Related to Dehydrated Foods.a II. Composition and Position of Dispersed Lipid Components and Their Effect on Oxidation Rates
Authors: BISHOV S. J. , HENICK A. S. , KOCH ROBERT B. 
Published: December 2006

SUMMARYOxidation rates at elevated temperatures of model dehydrated systems containing dispersed lipids are influenced by concentration of the components, type of dispersing medium, and position of the lipid film with respect to the dispersing medium. Generally, the proteins decreased, and polymeric carbohydrates accelerated, oxidation rates. Arginine and lysine salts of safflower fatty acids were extremely stable. Phospholipids had a stabilizing influence when dispersed with the fat and the dispersing medium prior to freeze‐drying or when applied as a film between the dry medium and the fat film. When the positions of the fat and the phospholipid films were reversed, the protective action of the phospholipids on the stability of the system decreased markedly.
Survival of Bacillus stearothermophilus Spores as a Means of Measuring Effective Electron‐Beam Dosagea,b
Authors: POSTWEILER JUNE E. , CALDWELL ELWOOD F. 
Published: December 2006

SUMMARYBecause of the limited penetrating ability of low‐voltage electrons, depth and density are necessarily major considerations in the experimental irradiation of food by this means. In this study, survival of bacteria dispersed in agar was used to indicate the effective amounts of irradiation resulting at various depths from various electron doses to the surface. The per cent survival at each depth was plotted against the dose received as measured by cobalt glass dosimeters located at the same depth. These had been calibrated in terms of dose response by means of gamma radiation delivered by a source accurately calibrated by ferrous dosimetry. Within the 3‐cm depth studied, a linear relationship was found between dose and log per cent survival.