bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Pentatricopeptide Repeat GeneOTP43Is Required fortrans-Splicing of the Mitochondrialnad1Intron 1 inArabidopsis thaliana
Authors: de Longevialle Andéol Falcon , Meyer Etienne H. , Andrés Charles , Taylor Nicolas L. , Lurin Claire , Millar A. Harvey , Small Ian D. 
Published: October 2007

AbstractThe mitochondrial NADH:ubiquinone oxidoreductase complex (Complex I) is a large protein complex formed from both nuclearly and mitochondrially encoded subunits. Subunit ND1 is encoded by a mitochondrial gene comprising five exons, and the mature transcript requires four RNA splicing events, two of which involve trans-splicing independently transcribed RNAs. We have identified a nuclear gene (OTP43) absolutely required for trans-splicing of intron 1 (and only intron 1) of Arabidopsis thaliana nad1 transcripts. This gene encodes a previously uncharacterized pentatricopeptide repeat protein. Mutant Arabidopsis plants with a disrupted OTP43 gene do not present detectable mitochondrial Complex I activity and show severe defects in seed development, germination, and to a lesser extent in plant growth. The alternative respiratory pathway involving alternative oxidase is significantly induced in the mutant.
Thiamine diphosphate binds to intermediates in the assembly of adenovirus fiber knob trimers in Escherichia coli
Authors: Schulz Ryan , Zhang Yian‐Biao , Liu Chang‐Jun , Freimuth Paul 
Published: October 2007

AbstractAssembly of the adenovirus (Ad) homotrimeric fiber protein is nucleated by its C‐terminal knob domain, which itself can trimerize when expressed as a recombinant protein fragment. The non‐interlocked, globular structure of subunits in the knob trimer implies that trimers assemble from prefolded monomers through a dimer intermediate, but these intermediates have not been observed and the mechanism of assembly therefore remains uncharacterized. Here we report that expression of the Ad serotype 2 (Ad2) knob was toxic for thi− strains of Escherichia coli, which are defective in de novo synthesis of thiamine (vitamin B1). Ad2 knob trimers isolated from a thi+ strain copurified through multiple chromatography steps with a small molecule of mass equivalent to that of thiamine diphosphate (ThDP). Mutant analysis did not implicate any specific site for ThDP binding. Our results suggest that ThDP may associate with assembly intermediates and become trapped in assembled trimers, possibly within one of several large cavities that are partially solvent‐accessible or buried completely within the trimer interior.
Monte Carlo refinement of rigid‐body protein docking structures with backbone displacement and side‐chain optimization
Authors: Lorenzen Stephan , Zhang Yang 
Published: October 2007

AbstractStructures of hitherto unknown protein complexes can be predicted by docking the solved protein monomers. Here, we present a method to refine initial docking estimates of protein complex structures by a Monte Carlo approach including rigid‐body moves and side‐chain optimization. The energy function used is comprised of van der Waals, Coulomb, and atomic contact energy terms. During the simulation, we gradually shift from a novel smoothed van der Waals potential, which prevents trapping in local energy minima, to the standard Lennard‐Jones potential. Following the simulation, the conformations are clustered to obtain the final predictions. Using only the first 100 decoys generated by a fast Fourier transform (FFT)‐based rigid‐body docking method, our refinement procedure is able to generate near‐native structures (interface RMSD <2.5 Å) as first model in 14 of 59 cases in a benchmark set. In most cases, clear binding funnels around the native structure can be observed. The results show the potential of Monte Carlo refinement methods and emphasize their applicability for protein–protein docking.
Protein kinase C delta is phosphorylated on five novel Ser/Thr sites following inducible overexpression in human colorectal cancer cells
Authors: Welman Arkadiusz , Griffiths John R. , Whetton Anthony D. , Dive Caroline 
Published: October 2007

AbstractPhosphorylation plays an important role in regulation of protein kinase C delta (PKCδ). To date, three Ser/Thr residues (Thr 505, Ser 643, and Ser 662) and nine tyrosine residues (Tyr 52, Tyr 64, Tyr 155, Tyr 187, Tyr 311, Tyr 332, Tyr 512, Tyr 523, and Tyr 565) have been defined as regulatory phosphorylation sites for this protein (rat PKCδ numbering). We combined doxycycline‐regulated inducible gene expression technology with a hypothesis‐driven mass spectrometry approach to study PKCδ phosphorylation pattern in colorectal cancer cells. We report identification of five novel Ser/Thr phosphorylation sites: Thr 50, Thr 141, Ser 304, Thr 451, and Ser 506 (human PKCδ numbering) following overexpression of PKCδ in HCT116 human colon carcinoma cells grown in standard tissue culture conditions. Identification of potential novel phosphorylation sites will affect further functional studies of this protein, and may introduce additional complexity to PKCδ signaling.
A rapid and universal tandem‐purification strategy for recombinant proteins
Authors: McCluskey Andrew J. , Poon Gregory M.K. , Gariépy Jean 
Published: October 2007

AbstractA major goal in the production of therapeutic proteins, subunit vaccines, as well as recombinant proteins needed for structure determination and structural proteomics is their recovery in a pure and functional state using the simplest purification procedures. Here, we report the design and use of a novel tandem (His)6‐calmodulin (HiCaM) fusion tag that combines two distinct purification strategies, namely, immobilized metal affinity (IMAC) and hydrophobic interaction chromatography (HIC), in a simple two‐step procedure. Two model constructs were generated by fusing the HiCaM purification tag to the N terminus of either the enhanced green fluorescent protein (eGFP) or the human tumor suppressor protein p53. These fusion constructs were abundantly expressed in Escherichia coli and rapidly purified from cleared lysates by tandem IMAC/HIC to near homogeneity under native conditions. Cleavage at a thrombin recognition site between the HiCaM‐tag and the constructs readily produced untagged, functional versions of eGFP and human p53 that were >97% pure. The HiCaM purification strategy is rapid, makes use of widely available, high‐capacity, and inexpensive matrices, and therefore represents an excellent approach for large‐scale purification of recombinant proteins as well as small‐scale protein array designs.
Expression screening of integral membrane proteins fromHelicobacter pylori26695
Authors: Psakis Georgios , Nitschkowski Sandra , Holz Caterina , Kreß Daniel , Maestre‐Reyna Manuel , Polaczek Julia , Illing Gerd , Essen Lars‐Oliver 
Published: October 2007

AbstractThe efficiency ofHelicobacter pylorias a mucosal pathogen is caused by unique soluble and integral membrane proteins, which allow its survival at acidic pH and successful colonization of the gastric environment. With about one‐fourth of theH. pylori's proteome comprising integral membrane proteins, the need for solution of their three‐dimensional (3D) structures becomes persistent as it can potentially drive the generation of more effective drugs. This study presents a medium‐throughput approach for cloning and expression screening of integral membrane proteins fromH. pylori(26695) usingEscherichia colias the expression host. One‐hundred sixteenH. pyloritargets were cloned into two different vector systems and heterologously expressed inE. coli. Eighty‐four percent of these proteins displayed medium to high expression. No clear‐cut correlation was found between expression levels and number of putative transmembrane spans, predicted functionality, and molecular mass. Nonetheless, expression of transporters and hypothetical proteins ≤40 kDa with two to four transmembrane spans displayed generally high expression levels. To statistically strengthen the quality of the data from the medium‐throughput approach, a comparison with data derived from robotic‐based methodologies was conducted. Optimization of expression and solubilization conditions for selected targets was also performed. Seventeen targets have been purified and subjected to crystallization so far. Eighteen percent of these targets (2/17) produced crystals under specific sets of crystallization conditions.
Phosphoinositide binding regulates α‐actinin CH2 domain structure: Analysis by hydrogen/deuterium exchange mass spectrometry
Authors: Full Stephen J. , Deinzer Max L. , Ho P. Shing , Greenwood Jeffrey A. 
Published: October 2007

Abstractα‐Actinin is an actin bundling protein that regulates cell adhesion by directly linking actin filaments to integrin adhesion receptors. Phosphatidylinositol (4,5)‐diphosphate (PtdIns (4,5)‐P2) and phosphatidylinositol (3,4,5)‐triphosphate (PtdIns (3,4,5)‐P3) bind to the calponin homology 2 domain of α‐actinin, regulating its interactions with actin filaments and integrin receptors. In this study, we examine the mechanism by which phosphoinositide binding regulates α‐actinin function using mass spectrometry to monitor hydrogen–deuterium (H/D) exchange within the calponin homology 2 domain. The overall level of H/D exchange for the entire protein showed that PtdIns (3,4,5)‐P3 binding alters the structure of the calponin homology 2 domain increasing deuterium incorporation, whereas PtdIns (4,5)‐P2 induces changes in the structure decreasing deuterium incorporation. Analysis of peptic fragments from the calponin homology 2 domain showed decreased local H/D exchange within the loop region preceding helix F with both phosphoinositides. However, the binding of PtdIns (3,4,5)‐P3 also induced increased exchange within helix E. This suggests that the phosphate groups on the fourth and fifth position of the inositol head group of the phosphoinositides constrict the calponin homology 2 domain, thereby altering the orientation of actin binding sequence 3 and decreasing the affinity of α‐actinin for filamentous actin. In contrast, the phosphate group on the third position of the inositol head group of PtdIns (3,4,5)‐P3 perturbs the calponin homology 2 domain, altering the interaction between the N and C terminus of the full‐length α‐actinin antiparallel homodimer, thereby disrupting bundling activity and interaction with integrin receptors.
Host–pathogen protein interactions predicted by comparative modeling
Authors: Davis Fred P. , Barkan David T. , Eswar Narayanan , McKerrow James H. , Sali Andrej 
Published: October 2007

AbstractPathogens have evolved numerous strategies to infect their hosts, while hosts have evolved immune responses and other defenses to these foreign challenges. The vast majority of host–pathogen interactions involve protein–protein recognition, yet our current understanding of these interactions is limited. Here, we present and apply a computational whole‐genome protocol that generates testable predictions of host–pathogen protein interactions. The protocol first scans the host and pathogen genomes for proteins with similarity to known protein complexes, then assesses these putative interactions, using structure if available, and, finally, filters the remaining interactions using biological context, such as the stage‐specific expression of pathogen proteins and tissue expression of host proteins. The technique was applied to 10 pathogens, including species of Mycobacterium, apicomplexa, and kinetoplastida, responsible for “neglected” human diseases. The method was assessed by (1) comparison to a set of known host–pathogen interactions, (2) comparison to gene expression and essentiality data describing host and pathogen genes involved in infection, and (3) analysis of the functional properties of the human proteins predicted to interact with pathogen proteins, demonstrating an enrichment for functionally relevant host–pathogen interactions. We present several specific predictions that warrant experimental follow‐up, including interactions from previously characterized mechanisms, such as cytoadhesion and protease inhibition, as well as suspected interactions in hypothesized networks, such as apoptotic pathways. Our computational method provides a means to mine whole‐genome data and is complementary to experimental efforts in elucidating networks of host–pathogen protein interactions.
Nutrition in catering
Authors: Lawson J. M. , Hunt C. , Glew G. 
Published: October 2007

SummaryFor the purposes of this paper, catering activities are classified into three parts: If or profit, 2 at breakeven, 3 subsidised. The second group are mainly canteens and the health service and the third group includes the armed forces and some educational authorities. However, the industry has a poor statistical base and quantitive data are only available for broad characteristics. In 1978 the industry in the UK employed 2.14 million and the industry is labour intensive. Also in 1978 the National Health Service provided 600 million meals and some 3.5 million school meals were prepared a day during school term. Overall, it is estimated that, in 1976, eating out accounted for 12 per cent of expenditure on foods.The newer systems of catering, cook freeze and cook‐chill, are described and the significance of the separation of production from service which these systems make possible are assessed with particular reference to nutrient value at the time of consumption. The most labile nutrients are vitamins C, thiamin and folic acid.The advantages of Fast Foods in encouraging the consumption of nutritious foods are discussed and particular attention is drawn to the potential risk of over consumption of salt, energy and fat and under consumption of folic acid and iron if total diets consist exclusively of specific fast foods.The potential use of institutional catering in an educational role is discussed with particular reference to a trial organised with the Mersey Docks and Harbour Company as part of the Port of Liverpool Heart Health Campaign, where an attempt will be made to decrease the intake of fat and salt and to increase the intake of fibre.
Intense sweeteners in the UK
Authors: HENNESSY TESSA J. 
Published: October 2007

SummaryThe article reviews the background to the FA CC report on sweeteners in food, and the recommendations made by the committee, regarding a permitted list of intense and bulk sweeteners.With the introduction of several new sweeteners onto the UK market imminent, the article describes the properties, applications and nutritional/dietetic implications resulting from the use of the intense sweeteners that have been approved for food use in the UK.
Enzymes in food processing
Authors: COWAN W. D. 
Published: October 2007

SummaryThe purpose of the article is to review the use of food grade industrial enzymes in food processing. Only those enzymes directly added or deliberately used by the food manufacturer are considered. Areas of application covered include the baking industry, the dairy industry, the starch processing industry, the protein processing industry, and the fruit juice industry. The brewing and distilling industries are not included here as part of the food processing area.In addition, enzymes applied to cleaning of food processing plant and in food analysis are mentioned.Finally, the future developments of these products are briefly reviewed.
Flavour perception
Authors: THOMSON D. M. H. 
Published: October 2007

SummaryFlavour is a product of perception and is, thus, a sensory rather than a physical or chemical phenomenon. It is largely the combination of taste (salt, sweet, bitter, acid), perceived when the gustatory receptor cells located on the tongue are stimulated, and odour, perceived when any of 17,000different volatile chemicals enter the nasal cavity and interact with the olfactory receptor cells. However, pain, heat, cold, tactile and other sensations also contribute to flavour.One manifestation of appetite is change in the perceived pleasantness of flavour during food consumption, and this may influence the amount eaten. Appetite is flavour‐specific to some extent, which encourages variety in food intake and hence the acquisition of a range of nutrients. Flavour pleasantness may also be important in the regulation of weight control. For these reasons, flavour must be taken into account when considering nutritional aspects of diets.
Determination of contaminants in food
Authors: FOLKES D. J. 
Published: October 2007

SummaryAtomic absorption spectroscopy, chromatography methods and mass spectrometry have had a major impact on the determination of contaminants and the limits of determination are reported. Specific examples of contaminants discussed are arsenic, lead, mercury, cadmium, organochlorine pesticides, polynuclear aromatic hydrocarbons, polychlorinated biphenyls, vinyl chloride monomer, styrene and nitrosamines.
Human metabolic response to exercise
Authors: WILLIAMS C. 
Published: October 2007

SummaryThe energy necessary to support prolonged submaximal exercise is provided by the aerobic metabolism of carbohydrate and fatty acids. Carbohydrate is stored as glycogen, a polymer of glucose, in the liver and in the skeletal muscles, whereas the fatty acids used by working muscles are mainly derived from triglycerides stored in white adipose tissue cells. The relative contributions of carbohydrate and fatty acids to muscle metabolism depend on the relative exercise intensity. The relative exercise intensity is defined as the oxygen cost of the exercise (V02) expressed as a percentage of the individual's maximum oxygen uptake (% V02 max). At exercise intensities which represent a large % V02 max for an individual, muscle glycogen is the main contributor to muscle metabolism. Fatigue is associated with the depletion of the limited intramuscular glycogen stores. When a carbohydrate‐rich diet is consumed during recovery after exercise, the muscle glycogen stores are increased above theirpre‐exercise concentrations. Thus an exercise and diet regime has been developed to exploit the glycogen supercompensa‐tion phenomenon and so increase endurance capacity.
Fluid and electrolyte balance in prolonged exercise
Authors: MAUGHAN R. J. 
Published: October 2007

SummaryDue to the low efficiency of the metabolic process, large amounts of heat are produced when the demand for energy is high. Since body temperature must be maintained within narrow limits, the excess heat must be dissipated and the only heat loss mechanism which can cope with high rates of heat production is evaporation of sweat from the skin; during exercise in the heat, sweat rates may exceed 2 litres/hour. Total losses in events such as marathon races may be as much as 8 per cent of body weight. In addition to water loss, some depletion of electroytes will occur, though this is generally of lesser importance. The fluid loss is distributed among plasma extracellular and. intracellular water compartments in varying proportions. From the point of view of the ability to continue working, maintenance of plasma volume is the major consideration; even small decreases in plasma volume impair exercise tolerance. The ability to replace fluid losses during exercise is limited by the rates of gastric emptying and intestinal absorption, which fall far short of the rate of loss during severe exercise. Replacement of electrolyte losses can normally wait until the post‐exercise period.
Dietary intake and smoking, social class and season
Authors: FEHILY ANN M. 
Published: October 2007

SummaryAssociations between nutrient intakes and each of the following are discussed: season, social class and smoking habit. Examination of recent data suggests that seasonal variation in nutrient intakes is minimal. Social class has some effect on intakes of energy and carbohydrate, manual workers tending to have greater intakes than non‐manual workers. Smoking habit has the greatest effect on nutrient intakes, smokers tending to have lower intakes of several vitamins and minerals compared with non‐smokers, although total energy intakes are similar.
Potato ‐ a gift from the Andes
Authors: WOOLFE JENNIFER A. 
Published: October 2007

SummaryThe potato is a source of high‐quality protein, having a particularly favourable lysine content, which makes it a useful supplement to lysine‐deficient staples. It contains significant quantities of dietary fibre and is the most important source of ascorbic acid in the British diet, as well as supplementing thiamin, niacin, folic acid, vitamin B6 and pantothenic acid, and the minerals iron, copper, zinc and phosphorus.
Immunoassays in food analysis
Authors: ALLEN J. C. 
Published: October 2007

SummaryImmunoassays have found considerable application in clinical diagnosis, but have so far had surprisingly little impact on food analysis. This situation should now change, with the advent of the first commercially‐produced immunoassay kits specifically for food analysis. Immunoassays differ from other modern methods of analysis in that the high technology resides in the molecules rather than the apparatus. They are thus easy to perform, sensitive, specific and relatively inexpensive. Since they may be adapted for the determination of food toxins, antinutritional factors, additives, vitamins, etc., they offer considerable potential to the nutritional analyst.
Diet and pregnancy
Authors: PASSMORE R. 
Published: October 2007

SummaryIn the past 50years the number of babies who are stillborn or die in the first few weeks of life has fallen dramatically. This is attributed largely to improvements in social conditions and to improved nutrition during childhood and adolescence.The majority of women who normally eat a varied diet can enjoy their normal foods during pregnancy and require no specific dietary advice other than that which applies to the population as a whole.The causes of low birth weight (a known risk factor for survival and normal development) and congenital defects remain a challenge to medical science.
Schools, nutrition and the wind of change
Authors: TURNER SHEILA A. 
Published: October 2007

SummaryCurrent thinking in education emphasizes the need to make teaching relevant to everyday life and to integrate studies. Nutrition education is an area which can contribute to and benefit from this approach. Snack provision, planned and prepared by 4 to 7year olds; the development of school gardens; the involvement of parents in the selection of items for schools meals; the provision of food related teaching materials by the Association of Science Education and the development of nutrition education guidelines incorporating in‐service training for teachers, are some of the activities which can be seen in schools today.
Fat in baked products
Authors: HODGE D. G. 
Published: October 2007

SummaryThe fat content of biscuits ranges from 5‐20 per cent and from 9‐20per cent for cakes. Cream fillings may be significant additional contributors. Fat has a major functional role to play since it is able to occlude air. Additionally, fat improves eating quality by contributing to “mouthfeel” and carrying flavour. This paper, in the light of the COMA (1984) report “Diet and Cardiovascular Disease”, considers the possibilities for altering the composition of the fat to reduce the proportion of saturated fat and the reduction of the fat content of recipes.