bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional Differentiation of Bundle Sheath and Mesophyll Maize Chloroplasts Determined by Comparative Proteomics
Authors: Majeran Wojciech , Cai Yang , Sun Qi , van Wijk Klaas J. 
Published: October 2005

AbstractChloroplasts of maize (Zea mays) leaves differentiate into specific bundle sheath (BS) and mesophyll (M) types to accommodate C4 photosynthesis. Consequences for other plastid functions are not well understood but are addressed here through a quantitative comparative proteome analysis of purified M and BS chloroplast stroma. Three independent techniques were used, including cleavable stable isotope coded affinity tags. Enzymes involved in lipid biosynthesis, nitrogen import, and tetrapyrrole and isoprenoid biosynthesis are preferentially located in the M chloroplasts. By contrast, enzymes involved in starch synthesis and sulfur import preferentially accumulate in BS chloroplasts. The different soluble antioxidative systems, in particular peroxiredoxins, accumulate at higher levels in M chloroplasts. We also observed differential accumulation of proteins involved in expression of plastid-encoded proteins (e.g., EF-Tu, EF-G, and mRNA binding proteins) and thylakoid formation (VIPP1), whereas others were equally distributed. Enzymes related to the C4 shuttle, the carboxylation and regeneration phase of the Calvin cycle, and several regulators (e.g., CP12) distributed as expected. However, enzymes involved in triose phosphate reduction and triose phosphate isomerase are primarily located in the M chloroplasts, indicating that the M-localized triose phosphate shuttle should be viewed as part of the BS-localized Calvin cycle, rather than a parallel pathway.
PGP4, an ATP Binding Cassette P-Glycoprotein, Catalyzes Auxin Transport in Arabidopsis thaliana Roots
Authors: Terasaka Kazuyoshi , Blakeslee Joshua J. , Titapiwatanakun Boosaree , Peer Wendy A. , Bandyopadhyay Anindita , Makam Srinivas N. , Lee Ok Ran , Richards Elizabeth L. , Murphy Angus S. , Sato Fumihiko , Yazaki Kazufumi 
Published: October 2005

Abstract
Members of the ABC (for ATP binding cassette) superfamily of integral membrane transporters function in cellular detoxification, cell-to-cell signaling, and channel regulation. More recently, members of the multidrug resistance P-glycoprotein (MDR/PGP) subfamily of ABC transporters have been shown to function in the transport of the phytohormone auxin in both monocots and dicots. Here, we report that the Arabidopsis thaliana MDR/PGP PGP4 functions in the basipetal redirection of auxin from the root tip. Reporter gene studies showed that PGP4 was strongly expressed in root cap and epidermal cells. PGP4 exhibits apolar plasma membrane localization in the root cap and polar localization in tissues above. Root gravitropic bending and elongation as well as lateral root formation were reduced in pgp4 mutants compared with the wild type. pgp4 exhibited reduced basipetal auxin transport in roots and a small decrease in shoot-to-root transport consistent with a partial loss of the redirective auxin sink in the root. Seedlings overexpressing PGP4 exhibited increased shoot-to-root auxin transport. Heterologous expression of PGP4 in mammalian cells resulted in 1-N-naphthylthalamic acid–reversible net uptake of [3H]indole-3-acetic acid. These results indicate that PGP4 functions primarily in the uptake of redirected or newly synthesized auxin in epidermal root cells.
Transcriptome and Selected Metabolite Analyses Reveal Multiple Points of Ethylene Control during Tomato Fruit Development
Authors: Alba Rob , Payton Paxton , Fei Zhanjun , McQuinn Ryan , Debbie Paul , Martin Gregory B. , Tanksley Steven D. , Giovannoni James J. 
Published: October 2005

AbstractTranscriptome profiling via cDNA microarray analysis identified 869 genes that are differentially expressed in developing tomato (Solanum lycopersicum) pericarp. Parallel phenotypic and targeted metabolite comparisons were employed to inform the expression analysis. Transcript accumulation in tomato fruit was observed to be extensively coordinated and often completely dependent on ethylene. Mutation of an ethylene receptor (Never-ripe [Nr]), which reduces ethylene sensitivity and inhibits ripening, alters the expression of 37% of these 869 genes. Nr also influences fruit morphology, seed number, ascorbate accumulation, carotenoid biosynthesis, ethylene evolution, and the expression of many genes during fruit maturation, indicating that ethylene governs multiple aspects of development both prior to and during fruit ripening in tomato. Of the 869 genes identified, 628 share homology (E-value ≤1 × 10−10) with known gene products or known protein domains. Of these 628 loci, 72 share homology with previously described signal transduction or transcription factors, suggesting complex regulatory control. These results demonstrate multiple points of ethylene regulatory control during tomato fruit development and provide new insights into the molecular basis of ethylene-mediated ripening.
A novel representation of protein sequences for prediction of subcellular location using support vector machines
Authors: Matsuda Setsuro , Vert Jean‐Philippe , Saigo Hiroto , Ueda Nobuhisa , Toh Hiroyuki , Akutsu Tatsuya 
Published: October 2005

AbstractAs the number of complete genomes rapidly increases, accurate methods to automatically predict the subcellular location of proteins are increasingly useful to help their functional annotation. In order to improve the predictive accuracy of the many prediction methods developed to date, a novel representation of protein sequences is proposed. This representation involves local compositions of amino acids and twin amino acids, and local frequencies of distance between successive (basic, hydrophobic, and other) amino acids. For calculating the local features, each sequence is split into three parts: N‐terminal, middle, and C‐terminal. The N‐terminal part is further divided into four regions to consider ambiguity in the length and position of signal sequences. We tested this representation with support vector machines on two data sets extracted from the SWISS‐PROT database. Through fivefold cross‐validation tests, overall accuracies of more than 87% and 91% were obtained for eukaryotic and prokaryotic proteins, respectively. It is concluded that considering the respective features in the N‐terminal, middle, and C‐terminal parts is helpful to predict the subcellular location.
Hydrogen‐bonded turns in proteins: The case for a recount
Authors: Panasik Nick , Fleming Patrick J. , Rose George D. 
Published: October 2005

Abstractβ‐Turns are sites at which proteins change their overall chain direction, and they occur with high frequency in globular proteins. The Protein Data Bank has many instances of conformations that resemble β‐turns but lack the characteristic N–H(i) → O=C(i − 3) hydrogen bond of an authentic β‐turn. Here, we identify potential hydrogen‐bonded β‐turns in the coil library, a Web‐accessible database utility comprised of all residues not in repetitive secondary structure, neither α‐helix nor β‐sheet (http://www.roselab.jhu.edu/coil). In particular, candidate turns were identified as four‐residue segments satisfying highly relaxed geometric criteria but lacking a strictly defined hydrogen bond. Such candidates were then subjected to a minimization protocol to determine whether slight changes in torsion angles are sufficient to shift the conformation into reference‐quality geometry without deviating significantly from the original structure. This approach of applying constrained minimization to known structures reveals a substantial population of previously unidentified, stringently defined, hydrogen‐bonded β‐turns. In particular, 33% of coil library residues were classified as β‐turns prior to minimization. After minimization, 45% of such residues could be classified as β‐turns, with another 8% in 310 helixes (which closely resemble type III β‐turns). Of the remaining coil library residues, 37% have backbone dihedral angles in left‐handed polyproline II structure.
Undistorted structural analysis of soluble proteins by attenuated total reflectance infrared spectroscopy
Authors: Goldberg Michel E. , Chaffotte Alain F. 
Published: October 2005

AbstractWater from the solvent very strongly absorbs light in the frequency range of interest for studying protein structure by infrared (IR) spectroscopy. This renders handling of the observation cells painstaking and time consuming, and limits the reproducibility of the measurements when IR spectroscopy is applied to proteins in aqueous solutions. These difficulties are circumvented by the use of an Attenuated Total Reflectance (ATR) accessory. However, when protein solutions are studied, ATR spectroscopy suffers from several drawbacks, the most severe being nonproportionality of the observed absorbance with the protein concentration and spectral distortions that vary from protein to protein and from sample to sample. In this study, we show (1) that the nonproportionality is due to adsorption of the protein on the ATR crystal surface; (2) that the contribution of the crystal‐adsorbed protein can easily be taken into account, rendering the corrected absorbance proportional to the protein concentration; (3) that the observed variable base line distortions, likely due to changes in the penetration depth of the light beam in solutions with the refractive index that depends on the protein concentration, can be easily eliminated; and (4) that ATR IR spectra thus corrected for protein adsorption and light penetration can be used to properly analyze the secondary structure of proteins in solution.
Insights into the role of the metal binding site in methionine‐R‐sulfoxide reductases B
Authors: Olry Alexandre , Boschi‐Muller Sandrine , Yu Hong , Burnel Daniel , Branlant Guy 
Published: October 2005

AbstractMethionine sulfoxide reductases B (MsrBs) catalyze the reduction of methionine‐R‐sulfoxide via a three‐step chemical mechanism including a reductase step, formation of an intradisulfide bond followed by a thioredoxin recycling process. Fifty percent of the MsrBs, including the Escherichia coli enzyme, possess a metal binding site composed of two CXXC motifs of unknown function. It is located on the opposite side of the active site. The overexpressed E. coli MsrB tightly binds one atom of zinc/iron. Substitution of the cysteines of E. coli MsrB results in complete loss of bound metal and reductase activity, and leads to a low‐structured conformation of the protein as shown by CD, fluorescence, and DSC experiments. Introduction of the two CXXC motifs in Neisseria meningitidis MsrB domain leads to a MsrB that tightly binds one atom of zinc/iron, shows a strongly increased thermal stability and displays a reductase activity similar to that of the wild‐type but lacking thioredoxin recycling activity. These results demonstrate the stabilizing effect of the metal and the existence of a preformed metal binding site in the nonbound metal MsrB. The data also indicate that metal binding to N. meningitidis MsrB induces subtle structural modifications, which prevent formation of a competent binary complex between oxidized MsrB and reduced thioredoxin but not between reduced MsrB and substrate. The fact that the E. coli and the N. meningitidis MsrBs exhibit a similar thermal stability suggests the existence of other structural factors in the nonbound metal MsrBs that compensate the metal bound stabilizing effect.
Serum biomarkers for cardiovascular inflammation in subclinical hypothyroidism
Authors: Hueston William J. , King Dana E. , Geesey Mark E. 
Published: October 2005

SummaryObjective Cardiovascular disease has been reported to be more common in patients with elevated levels of TSH and with normal thyroxine levels, termed subclinical hypothyroidism (SCH). The aim of this study was to determine whether individuals with SCH were more likely than euthyroid controls to have elevations in inflammatory biomarkers that are associated with cardiac disease.Methods From the National Health and Nutrition Examination Survey (NHANES) 1999–2002 data we identified respondents aged ≥ 40 who met the laboratory criteria for SCH. We compared the average values and frequencies of elevated C‐reactive protein (CRP) and homocysteine in the SCH individuals to those in euthyroid individuals.Results A total of 1608 individuals were included in the analysis of whom 45 (2·8%) met the criteria for SCH, with seven (15·6%) having TSH levels between 10 and 15 IU/l. We found no differences in median, mean or the percentage of elevated CRP or homocysteine in individuals with SCH compared to euthyroid controls. Linear regression models adjusting for age, gender, the presence of other cardiac risk factors, and whether the individual was using a cholesterol‐lowering drug also failed to show any association between SCH and either high‐sensitivity CRP (hsCRP) (P = 0·62) or homocysteine (P = 0·63) levels. When we examined the subset of people with TSH levels between 10 and 15 IU/l, we again found no difference in mean hsCRP or homocysteine compared to control.Conclusions In this large population‐based sample, hsCRP and homocysteine levels do not differ for individuals with SCH compared to euthyroid individuals. This suggests that cardiac inflammation is not greater in individuals with SCH.
Viability assessment of lactic acid bacteria in commercial dairy products stored at 4 °C using LIVE/DEAD® BacLightTM staining and conventional plate counts
Authors: Moreno Yolanda , Collado M. Carmen , Ferrús M. Antonia , Cobo José M. , Hernández Enrique , Hernández Manuel 
Published: October 2005

SummaryThe viability of lactic acid bacteria (LAB) from commercial fermented milks was studied during storage at 4 °C. The enumeration of total viable bacteria was assessed using fluorescence microscopy. Plate counting on selective media was used to enumerate LAB. Using LIVE/DEAD® BacLightTM viability staining, it was observed that bacterial counts decreased gradually after expiry dates, the number of viable bacteria remaining above 106 bacteria g−1 for all of the products. Viable cell counts estimated by plating onto selective media were lower than those obtained by direct microscopic counting. The viability of LAB contained in acid products decreased during their storage period at 4 °C. All products contain viable LAB ranging from 108 to 109 bacteria g−1 and could be considered as probiotic, given that the recommended minimum number of probiotic bacteria in such food products is approximately 107 bacteria mL−1 product. The number of bifidobacteria in commercial fermented milks declared to contain bifidobacteria varied from 104 to 107 bacteria mL−1. This study confirms the usefulness of fluorescent techniques for a rapid and accurate evaluation of bacterial viability in probiotic products.
Chemical and microbiological quality of Garris, Sudanese fermented camel's milk product
Authors: Sulieman Abdel Moneim El‐Hadi , Ilayan Abdalla Adam , Faki Ahmed El‐Awad El 
Published: October 2005

SummaryIn the present study, some of the chemical and microbiological characteristics of garris, a Sudanese traditionally fermented camel's milk product, were investigated. The chemical analyses included, pH, titrable acidity and ethanol contents. A total of 100 strains of lactic acid bacteria (LAB) were isolated from twenty samples of traditionally fermented household garris. The selected isolates were phenotypically characterized by their ability to ferment 49 carbohydrates using API 50 CHL kits and additional biochemical tests. LAB dominated the microflora of garris samples, and the major genera were Lactobacillus (74%), followed by Lactococcus (12%), Enterococcus (10%) and Leuconostocs (4%). The most predominant Lactobacillus species were identified as Lactobacillus paracasei ssp. paracasei (64 strains), L. fermentum (seven strains) and only three strains as L. plantarum. Most strains produced the enzymes that are relevant to cultured dairy product processing. The Lactococcus species were identified as Lactococcus lactis. The average pH value of the samples was 4.42 ± 0.21. The pH values were accompanied with increasing of titrable acidity which averaged 1.72 ± 0.04%. The relatively high amounts of ethanol detected in all samples (average 1.40 ± 0.03%) together with the high yeasts counts (6.0 ± 0.53 log10 cfu mL−1), indicated that the fermentation process of garris is a yeast‐lactic fermentation.
Composition of dishes consumed in Cameroon
Authors: Ponka Roger , Fokou Elie , Fotso Martin , Tchouanguep Félicité Mbiapo , Leke Rose , Souopgui Jacob , Bih Mercy Achu 
Published: October 2005

SummaryThis study deals with determination of some of the mineral salts and phytate contents in the food consumed by inhabitants of Cameroon known as Ngali II, a rural area, which is a malaria endemic zone. The food consumed by the people of this area are light and thick sauces prepared from several green leafy vegetables, leguminous seeds and cucurbit seeds (egusi seeds), pastes prepared from leguminous seeds or egusi seeds complemented with different tubers and plantains. The mineral salt contents were determined by atomic absorption spectrophotometry and phytate by spectrophotometric methods. The results are expressed in mg (100 g)−1 dry weight. Iron: 1.32–28.46, zinc: 2.0–7.28, copper: 0.13–1.09, magnesium: 24.5–369.8 and phytate: 9.08–1988.2. This study reveals that a high consumption of food rich in zinc will greatly reduce the high prevalence of malaria in Ngali II.
Efficacy of repeated high‐dose hepatitis B vaccine (80 μg) in patients with chronic liver disease
Authors: Aziz A. , Aziz S. , Li D. S. , Murphy L. , Leone N. , Kennedy M. , Dhillon S. , Van Thiel D. H. 
Published: October 2005

Summary.  Patients with chronic liver disease (CLD) respond poorly to standard hepatitis B (HBV) vaccine given as sequential 20 μg IM shots because of an overall impaired immune response. Many of these patients go on to liver transplantation and are at risk of acquiring recurrent or de novo HBV infection.To evaluate the efficacy and safety of high‐dose (80 μg) IM HBV vaccination in patients with CLD who had previously failed to respond to a standard three‐dose schedule of 40 μg IM vaccine given monthly.A retrospective review was undertaken at our institution of 79 patients with CLD who were treated with high‐dose (80 μg) HBV vaccinations. All had previously failed a three‐dose course of 40 μg HBV vaccine. An HBV vaccine response was defined as an anti‐HBs titer greater than 100 mIU/ml. Liver enzymes, creatinine, age, prothrombin time, total vaccine dose, and MELD score were recorded.No adverse events were reported. Seventy‐two per cent (57/79) of the subjects had an adequate response after receiving a mean total dose of 220 μg vaccine (range 80–800 μg). Twenty‐eight per cent (22/79) of the subjects did not respond after receiving a mean total dose of 420 μg vaccine (range 240–720 μg). Non‐responders had more severe hepatic disease defined as a higher mean total bilirubin level (p = 0.003) and a lower mean albumin level (p < 0.05). Age, prothrombin time, MELD score, and creatinine were not statistically significant between the responders and non‐responders.Repeated high‐dose (80 μg) HBV vaccination, in patients who do not respond to standard HBV vaccine doses, is safe and effective in the majority of patients with CLD.
Treatment of lymph node tuberculosis – a randomized clinical trial of two 6‐month regimens
Authors: Jawahar M. S. , Rajaram K. , Sivasubramanian S. , Paramasivan C. N. , Chandrasekar K. , Kamaludeen M. N. , Thirithuvathas A. J. , Ananthalakshmi V. , Prabhakar R. 
Published: October 2005

SummaryObjective  The currently recommended treatment for lymph node tuberculosis is 6 months of rifampicin and isoniazid plus pyrazinamide for the first 2 months, given either daily or thrice weekly. The objective of this study was to assess the efficacy of a 6‐month twice‐weekly regimen and a daily two‐drug regimen.Methods  Patients with biopsy confirmed superficial lymph node tuberculosis were randomly allocated to receive either a daily self‐administered 6‐month regimen of rifampicin and isoniazid, or a twice‐weekly, directly observed, 6‐month regimen of rifampicin and isoniazid plus pyrazinamide for the first 2 months, in Madurai, South India, Patients were followed up for 36 months after completing treatment.Results  Of 277 enrolled patients, data was available for analysis in 268. At the end of treatment, 116 of 134 [87%; 95% confidence interval (CI) 81–93%] patients in each treatment group had a favourable clinical response; 14 (11%; 95% CI 6–16%) and 17 (13%; 95% CI 7–19%) patients had a doubtful response, and 4 (3%; 95% CI 0–6%) and 1 (1%; 95% CI 0–2%) patients had an unfavourable response among those treated with the daily and twice‐weekly regimen, respectively. During 36 months after completion of treatment, five patients [2 (2%; 95% CI 1–3%) and 3 (2%; 95% CI 1–3%) patients treated with the daily and twice‐weekly regimen, respectively] had relapse of lymph node tuberculosis, of 260 assessed. Adverse reactions probably attributable to the treatment regimens occurred in 1% of the patients treated daily and in 11% of those treated twice‐weekly (P < 0.001). At the end of 36 months after treatment, 126 of 134 (94%; 95% CI 90–98%) and 129 of 134 (96%; 95% CI 94–98%) of the patients treated with the daily and twice‐weekly regimen, respectively, had a successful outcome.Conclusion  Both the self‐administered daily regimen and the fully observed twice‐weekly regimen were highly efficacious for treating patients with lymph node tuberculosis and may be considered as alternative options to the recommended regimens.
Repellent properties of celery, Apium graveolens L., compared with commercial repellents, against mosquitoes under laboratory and field conditions
Authors: Tuetun Benjawan , Choochote Wej , Kanjanapothi Duangta , Rattanachanpichai Eumporn , Chaithong Udom , Chaiwong Prasong , Jitpakdi Atchariya , Tippawangkosol Pongsri , Riyong Duangrat , Pitasawat Benjawan 
Published: October 2005

SummaryIn our search for new bioactive products against mosquito vectors, we reported the slightly larvicidal and adulticidal potency, but remarkable repellency of Apium graveolens both in laboratory and field conditions. Repellency of the ethanolic preparation of hexane‐extracted A. graveolens was, therefore, investigated and compared with those of 15 commercial mosquito repellents including the most widely used, DEET. Hexane‐extracted A. graveolens showed a significant degree of repellency in a dose‐dependent manner with vanillin added. Ethanolic A. graveolens formulations (10–25% with and without vanillin) provided 2–5 h protection against female Aedes aegypti. Repellency that derived from the most effective repellent, 25% of hexane‐extracted A. graveolens with the addition of 5% vanillin, was comparable to the value obtained from 25% of DEET with 5% vanillin added. Moreover, commercial repellents, except formulations of DEET, showed lower repellency than that of A. graveolens extract. When applied on human skin under field conditions, the hexane‐extracted A. graveolens plus 5% vanillin showed a strong repellent action against a wide range of mosquito species belonging to various genera. It had a protective effect against Aedes gardnerii, Aedes lineatopennis, Anopheles barbirostris, Armigeres subalbatus, Culex tritaeniorhynchus, Culex gelidus, Culex vishnui group and Mansonia uniformis. The hexane‐extracted A. graveolens did not cause a burning sensation or dermal irritation when applied to human skin. No adverse effects were observed on the skin or other parts of the human volunteers’ body during 6 months of the study period or in the following 3 months, after which time observations ceased. Therefore, A. graveolens can be a potential candidate for use in the development of commercial repellents that may be an alternative to conventional synthetic chemicals, particularly in community vector control applications.