bluuebunny/crossref_metadata_2025_split huggingface dataset:
LinkinPath: from sequence to interconnected pathway
Authors: Ingsriswang Supawadee , Yokwai Sunai , Wichadakul Duangdao 
Published: June 2011

Abstract
Summary: LinkinPath is a pathway mapping and analysis tool that enables users to explore and visualize the list of gene/protein sequences through various Flash-driven interactive web interfaces including KEGG pathway maps, functional composition maps (TreeMaps), molecular interaction/reaction networks and pathway-to-pathway networks. Users can submit single or multiple datasets of gene/protein sequences to LinkinPath to (i) determine the co-occurrence and co-absence of genes/proteins on animated KEGG pathway maps; (ii) compare functional compositions within and among the datasets using TreeMaps; (iii) analyze the statistically enriched pathways across the datasets; (iv) build the pathway-to-pathway networks for each dataset; (v) explore potential interaction/reaction paths between pathways; and (vi) identify common pathway-to-pathway networks across the datasets.
Availability: LinkinPath is freely available to all interested users at http://www.biotec.or.th/isl/linkinpath/.
Contact: supawadee@biotec.or.th
Supplementary information: Supplementary data are available at Bioinformatics online.
First Report of Pepino mosaic virus Infecting Tomato in Mexico
Authors: Ling K.-S. , Zhang W. 
Published: June 2011

Pepino mosaic virus (PepMV) (genus Potexvirus) was first reported in Europe to be infecting greenhouse tomatoes (Solanum lycopersicum) in 2000 (3). Subsequently, it has also been identified in Canada and the United States (1) and has become widespread on greenhouse tomatoes in many countries. In early spring of 2010, symptoms including chlorotic mosaic or chlorotic patches on leaves, necrotic stems, and fruit deformation or marbling were noted. Approximately 50% of plants in a greenhouse in Jocotitlan, Mexico exhibited symptoms. Twenty-three symptomatic samples in four separate collections between April 2010 and January 2011 all tested positive for the presence of PepMV by ELISA and/or Agristrips (BioReba, Switzerland). Two symptomless samples were negative for PepMV. Biological inoculation with the isolate MX10-05 to three Nicotiana benthamiana and three tomato cv. Horizon plants all resulted in chlorotic mosaic symptoms on the systemic leaves and PepMV on the inoculated plants was confirmed by ELISA. To determine the genotype of PepMV in MX10-05, two primer sets targeting different part of the virus genome (separated by 2,744 nt) were selected for reverse transcription (RT)-PCR using total plant RNA extracted with the RNeasy Plant Mini Kit (Qiagen, Valencia, CA). A RT-PCR product (840 bp) was obtained using the first primer set (PepMV-Ch2.F541: 5′CATGGAACCAGCTGATGTGA and PepMV-Ch2.R1380: 5′TCTTTGTATATGGTCGCAGC) targeting the 5′ portion of the RNA-dependent RNA polymerase (RdRp) gene. The PCR product was cloned in pCR2.1 using the TOPO TA cloning system (Invitrogen, Carlsbad, CA) and a single clone was sequenced in both directions (Functional Biosciences, Madison, WI). After primer trimming, the 800-bp sequence (GenBank Accession No. JF811600) was shown in BLASTn to have its highest nucleotide sequence identity (99.4%) to the type PepMV-CH2 (DQ000985), 98% to other CH2/US2 isolates, 85% to US1, and 84% to EU. Another RT-PCR product (also 840 bp) was generated using the second primer set (PepMV-Ch2.F4081: 5′AAAAACGCTGTACCCAAAAC and PepMV-Ch2.R4920: 5′CAGAAATGTGTTCAGAGGGG) targeting the 3′ portion of RdRp and TGB1 genes. This second genome segment enables the differentiation of the CH2 and US2 genotypes. The resulting 800 bp (JF811600) had the highest nucleotide sequence identity (99.5%) to the type PepMV CH2, 97% to other CH2 isolates, 83% to US2, and only 81% to the EU genotype. Taken together, these sequence analyses support the identification of MX10-05 as a PepMV-CH2 isolate (2). However, the presence of other PepMV genotypes cannot be excluded once sequences from other isolates are obtained and analyzed. To our knowledge, this is the first report of PepMV on greenhouse tomatoes in Mexico. References: (1). C. J. French et al. Plant Dis. 85:1121, 2001. (2). K.-S. Ling. Virus Genes 34:1, 2007. (3). R. A. A. van der Vlugt et al. Plant Dis. 84:103, 2000.
Extracellular Nucleotides and Apyrases Regulate Stomatal Aperture in Arabidopsis
Authors: Clark Greg , Fraley Devin , Steinebrunner Iris , Cervantes Andrew , Onyirimba James , Liu Angela , Torres Jonathan , Tang Wenqiang , Kim Joshua , Roux Stanley J. 
Published: June 2011

Abstract
This study investigates the role of extracellular nucleotides and apyrase enzymes in regulating stomatal aperture. Prior data indicate that the expression of two apyrases in Arabidopsis (Arabidopsis thaliana), APY1 and APY2, is strongly correlated with cell growth and secretory activity. Both are expressed strongly in guard cell protoplasts, as determined by reverse transcription-polymerase chain reaction and immunoblot analyses. Promoter activity assays for APY1 and APY2 show that expression of both apyrases correlates with conditions that favor stomatal opening. Correspondingly, immunoblot data indicate that APY expression in guard cell protoplasts rises quickly when these cells are moved from darkness into light. Both short-term inhibition of ectoapyrase activity by polyclonal antibodies and long-term suppression of APY1 and APY2 transcript levels significantly disrupt normal stomatal behavior in light. Stomatal aperture shows a biphasic response to applied adenosine 5′-[γ-thio]triphosphate (ATPγS) or adenosine 5′-[β-thio] diphosphate, with lower concentrations inducing stomatal opening and higher concentrations inducing closure. Equivalent concentrations of adenosine 5′-O-thiomonophosphate have no effect on aperture. Two mammalian purinoceptor inhibitors block ATPγS- and adenosine 5′-[β-thio] diphosphate-induced opening and closing and also partially block the ability of abscisic acid to induce stomatal closure and of light to induce stomatal opening. Treatment of epidermal peels with ATPγS induces increased levels of nitric oxide and reactive oxygen species, and genetically suppressing the synthesis of these agents blocks the effects of nucleotides on stomatal aperture. A luciferase assay indicates that treatments that induce either the closing or opening of stomates also induce the release of ATP from guard cells. These data favor the novel conclusion that ectoapyrases and extracellular nucleotides play key roles in regulating stomatal functions.
Abnormal liver tests in people aged 75 and above: prevalence and association with mortality
Authors: Fleming K. M. , West J. , Aithal G. P. , Fletcher A. E. 
Published: June 2011

Aliment Pharmacol Ther 2011; 34: 324–334SummaryBackground  Despite their common use the occurrence and consequences of abnormal liver tests remain unclear.Aims  To estimate the prevalence and mortality associated with abnormal liver tests in people aged 75 years and above.Methods  A cohort study on 13 276 people aged 75 years and above, registered with general practices, with a valid measurement of one or more liver test, calculating the prevalence of abnormal aspartate transaminase (AST), alkaline phosphatase (ALP) or bilirubin. Hazard ratios (HRs) were calculated for all‐cause and cause‐specific mortality comparing elderly patients with abnormal liver tests to elderly patients with normal liver tests.Results  At least one abnormal liver test was found in 2175 subjects (16.1%, 95% CI [15.4%, 16.7%]). The prevalence of a single abnormal liver test was 3.3% (95% CI [3.0%, 3.7%]) for AST, 9.2% (95% CI [8.8%, 9.7%]) for ALP and 5.4% (95% CI [5.1%, 5.9%]) for bilirubin. Abnormal AST, ALP and bilirubin were associated with increased risks of all‐cause mortality; adjusted HRs, 1.27(95% CI [1.09, 1.47]), 1.47(95% CI [1.35, 1.61]) and 1.15(95% CI [1.02, 1.30]), respectively. Abnormal AST and ALP were associated with sevenfold and sixfold increased risk of death from liver disease, respectively. Two or more abnormal liver tests were associated with 2‐fold and 17‐fold increased risk of death from cancer and liver disease, respectively. Of the causes examined, absolute mortality rates were highest for cardiovascular disease in subjects with and without abnormal liver tests.Conclusions  Abnormal liver tests occur commonly in elderly people and are associated with a modest increase in all‐cause mortality. There was a strong association with liver disease; however, the majority of deaths were not due to this cause.
Growth Rate Hypothesis does not apply across colimiting conditions: cholesterol limitation affects phosphorus homoeostasis of an aquatic herbivore
Authors: Lukas Marcus , Sperfeld Erik , Wacker Alexander 
Published: June 2011

Summary1. Herbivores show stronger control of element homoeostasis than primary producers, which can lead to constraints in carbon and nutrient transfer efficiencies from plants to animals. Insufficient dietary phosphorus (P) availability can cause reduced body P contents along with lower growth rates of animals, leading to a positive relationship between growth and body P.2. We examined how a second limiting food component in combination with dietary P limitation influences growth and P homoeostasis of a herbivore and how this colimitation influences the hypothesized positive correlation between body P content and growth rates. Therefore, we investigated the responses in somatic growth and P stoichiometry of Daphnia magna raised on a range of diets with different amounts of P and the sterol cholesterol.3. Somatic growth rates of D. magna increased asymptotically with increasing P as well as with increasing cholesterol availability. The body P content increased with increasing dietary P and stabilized at high dietary P availability. The observed plasticity in D. magna’s P stoichiometry became stronger with increasing cholesterol availability, i.e. with decreasing colimitation by cholesterol.4. At P‐limiting conditions, the positive correlation between body P content and growth rate, as predicted by the growth rate hypothesis (GRH) applied to the within‐species level, declined with increasing cholesterol limitation and disappeared entirely when cholesterol was not supplied. Thus, even when Daphnia shows no growth response owing to strong limitation by the colimiting nutrient, the body P content may vary substantially, calling into question the unconditional use of herbivores’ P content as predictor of a potential P limitation in nature.5. The observed interaction between dietary P and cholesterol on Daphnia’s growth and stoichiometry can be used as a conceptual framework of how colimiting essential nutrients affect herbivore homoeostasis, and provide further insights into the applicability of the GRH within a consumer species.
The translational regulatory function of SecM requires the precise timing of membrane targeting
Authors: Yap Mee‐Ngan , Bernstein Harris D. 
Published: June 2011

SummaryIn Escherichia coli, secA expression is regulated at the translational level by an upstream gene (secM) that encodes a presecretory protein. SecM contains a C‐terminal sequence motif that induces a transient translation arrest. Inhibition of SecM membrane targeting prolongs the translation arrest and increases SecA synthesis by concomitantly altering the structure of the secM–secA mRNA. Here we show that the SecM signal peptide plays an essential role in this regulatory process by acting as a molecular timer that co‐ordinates membrane targeting with the synthesis of the arrest motif. We found that signal peptide mutations that alter targeting kinetics and insertions or deletions that change the distance between the SecM signal peptide and the arrest motif perturb the balance between the onset and release of arrest that is required to regulate SecA synthesis. Furthermore, we found that the strength of the interaction between the ribosome and the SecM arrest motif is calibrated to ensure the release of arrest upon membrane targeting. Our results strongly suggest that several distinctive features of the SecM protein evolved as a consequence of constraints imposed by the ribosome and the Sec machinery.
Induction of telomere‐mediated chromosomal truncation and stability of truncated chromosomes in Arabidopsis thaliana
Authors: Teo Chee How , Ma Lu , Kapusi Eszter , Hensel Götz , Kumlehn Jochen , Schubert Ingo , Houben Andreas , Mette Michael Florian 
Published: June 2011

SummaryMinichromosomes possess functional centromeres and telomeres and thus should be stably inherited. They offer an enormous opportunity to plant biotechnology as they have the potential to simultaneously transfer and stably express multiple genes. Segregating independently of host chromosomes, they provide a platform for accelerating plant breeding. Following a top‐down approach, we truncated endogenous chromosomes in Arabidopsis thaliana by Agrobacterium‐mediated transfer of T‐DNA constructs containing telomere sequences. Blocks of A. thaliana telomeric repeats were inserted into a binary vector suitable for stable transformation. After transfer of these constructs into the natural tetraploid A. thaliana accession Wa‐1, chromosome truncation by T‐DNA‐induced de novo formation of telomeres could be confirmed by DNA gel blot analysis, PCR (polymerase chain reaction), and fluorescence in situ hybridisation. The addition of new telomere repeats in this process could start alternatively from within the T‐DNA‐derived telomere repeats or from adjacent sequences close to the right border of the T‐DNA. Truncated chromosomes were transmissible in sexual reproduction, but were inherited at rates lower than expected according to Mendelian rules.
Knockdown of CENH3 in Arabidopsis reduces mitotic divisions and causes sterility by disturbed meiotic chromosome segregation
Authors: Lermontova Inna , Koroleva Olga , Rutten Twan , Fuchs Joerg , Schubert Veit , Moraes Izabel , Koszegi David , Schubert Ingo 
Published: June 2011

SummaryThe histone H3 variant (CENH3) of centromeric nucleosomes is essential for kinetochore assembly and thus for chromosome segregation in eukaryotes. The mechanism(s) that determine centromere identity, assembly and maintenance of kinetochores are still poorly understood. Although the role of CENH3 during mitosis has been studied in several organisms, little is known about its meiotic function. We show that RNAi‐mediated CENH3 knockdown in Arabidopsis thaliana caused dwarfism as the result of a reduced number of mitotic divisions. The remaining mitotic divisions appeared to be error‐free. CENH3 RNAi transformants had reduced fertility because of frequently disturbed meiotic chromosome segregation. N‐terminally truncated EYFP–CENH3(C) is deposited to and functional within Arabidopsis centromeres of mitotic chromosomes, but cannot be loaded onto centromeres of meiotic nuclei. Thus the N‐terminal part is apparently required for CENH3 loading during meiosis. EYFP–CENH3(C) expression reduces the amount of endogenous CENH3, thus mimicking the effect of RNAi. The consequences of reduced endogenous CENH3 and lack of meiotic incorporation of EYFP–CENH3(C) are reduced fertility caused by insufficient CENH3 loading to the centromeres of meiotic chromosomes, subsequent lagging of chromosomes and formation of micronuclei.
Carbohydrate dynamics in roots and rhizomes of Cirsium arvense and Tussilago farfara
Authors: NKURUNZIZA L , STREIBIG J C 
Published: June 2011

Nkurunziza L & Streibig JC (2011). Carbohydrate dynamics in roots and rhizomes of Cirsium arvense and Tussilago farfara. Weed Research51, 461–468.SummaryInformation on the source–sink dynamics of carbohydrates during early plant growth can indicate when perennial weeds are most vulnerable to mechanical control. In this study, carbohydrate contents in the roots or rhizomes of two noxious perennial weeds, Cirsium arvense and Tussilago farfara, and basipetal translocation of photo‐assimilates were measured. We used HPLC for carbohydrate measurements and 14C labelling to follow the translocation of photo‐assimilates during early growth. These measurements were related to leaf number and leaf area. Fructan and fructose changed significantly over the experimental periods. Fructan for both species was greatest within 2 weeks after planting 5‐cm‐long root/rhizome fragments and declined thereafter. After 2 weeks, fructose concentrations, which were at their minimum level at planting time, rose sharply because of fructan depolymerisation. The radioactive carbon applied to the aerial parts translocated rapidly to root or rhizome systems around 500–600 d °C after emergence. We concluded that while the fructan was continuously depleted in the roots or rhizomes and reached their minimum levels 33 days after emergence (DAE), the basipetal translocation of photo‐assimilates started earlier (21–23 DAE). The carbon compensation point occurred at eight or six leaves for C. arvense and T. farfara, with a total leaf area of 200 cm2 for both species.
Effects of diets with different protein and dl‐methionine levels on the growth performance and N‐balance of growing minks
Authors: Zhang H. H. , Li G. Y. , Ren E. J. , Xing X. M. , Wu Q. , Yang F. H. 
Published: June 2011

SummaryThis study was performed to evaluate the effects of diets with different protein and dl‐methionine (Met) levels on nitrogen (N) retention, nutrient digestibility, growth performance, and some blood parameters in growing minks. Eighty healthy male minks were selected and randomly divided into five groups with different types of diet. The dietary protein levels, expressed as percentage of dry matter (DM), were 36% (HP) and 28% (LP), corresponding to average 363g and 295g protein/kg DM, respectively. LP was supplemented with Met (0.3%, 0.6% and 0.9% DM); the codes were LP+M1, LP+M2 and LP+M3, respectively. From July to middle of September, the average daily gain and feed: gain ratio (F/G) of the minks that received the diet with 0.6% Met added to the low protein diet was better than feeding HP and other groups. Fecal N and Urinary N of group LP+M2 were the lowest one, in contrast, the daily retention of N was the highest one. Digestibility of DM and CP were not affected by different diets, but digestibility of fat declined with dietary protein level decreasing. Serum urea nitrogen (SUN) was affected by different protein and Met levels. Considering all factors the best performance could be observed offering LP+M2, the prime level of Met was 13.87 g/kg DM in dietary, and 258.5 g digestible protein kg−1 DM was enough for mink in growing period. Furthermore, addition of Met in low protein diets for minks would be beneficial in terms of reduced feed expenses and lower nitrogen emissions to the environment.
Effect of feeding Bacillus subtilis natto fermentation product on milk production and composition, blood metabolites and rumen fermentation in early lactation dairy cows
Authors: Peng H. , Wang J. Q. , Kang H. Y. , Dong S. H. , Sun P. , Bu D. P. , Zhou L. Y. 
Published: June 2011

SummaryThis experiment was conducted to determine the effect of Bacillus subtilis natto fermentation product supplementation on blood metabolites, rumen fermentation and milk production and composition in early lactation dairy cows. Thirty‐six multiparous Holstein cows (DIM = 29 ± 6 days, parity = 2.8 ± 1.1) were blocked by DIM and parity and then randomly assigned to three treatments (12 per treatment) in a 9‐week trial. Cows in control, DFM1 and DFM2 were fed TMR diets supplemented with 0, 6 and 12 g of B. subtilis natto solid‐state fermentation product per day per cow respectively. Plasma non‐esterified fatty acids were lower (p = 0.03) in DFM1 and DFM2 compared with control cows (633 and 639 vs. 685 μm). Ruminal propionate increased (23.9 vs. 26.3 and 26.9/100 mol, control vs. DFM1 and DFM2 respectively) and acetate decreased (64.2 vs. 62.7 and 62.1/100 mol, control vs. DFM1 and DFM2 respectively) with increasing B. subtilis natto fermentation product supplementation. DMI of the cows in three treatments was not affected by B. subtilis natto fermentation product supplementation, but milk yield was 3.1 and 3.2 kg/day higher for DFM1 and DFM2 than that for control cows on average across the 9‐week trial, and significant differences were observed during weeks 5–9 of the trial, which resulted in 9.5% and 11.7% increase in feed efficiency. B. subtilis natto fermentation product supplementation did not affect milk fat percentage and protein yield but increased (p < 0.05) milk fat yield and lactose percentage (p < 0.01) and tended to decrease protein percentage (p = 0.06). The findings show that B. subtilis natto fermentation product was effective in increasing lactation performance of early lactation dairy cows possibly by altering the rumen fermentation pattern without any negative effects on blood metabolites.
Neonatal lactic acidosis with methylmalonic aciduria due to novel mutations in the SUCLG1 gene
Authors: Sakamoto Osamu , Ohura Toshihiro , Murayama Kei , Ohtake Akira , Harashima Hiroko , Abukawa Daiki , Takeyama Junji , Haginoya Kazuhiro , Miyabayashi Shigeaki , Kure Shigeo 
Published: June 2011

AbstractBackground:  Succinyl‐coenzyme A ligase (SUCL) is a mitochondrial enzyme that catalyses the reversible conversion of succinyl‐coenzyme A to succinate. SUCL consists of an α subunit, encoded by SUCLG1, and a β subunit, encoded by either SUCLA2 or SUCLG2. Recently, mutations in SUCLG1 or SUCLA2 have been identified in patients with infantile lactic acidosis showing elevated urinary excretion of methylmalonate, mitochondrial respiratory chain (MRC) deficiency, and mitochondrial DNA depletion.Methods:  Case description of a Japanese female patient who manifested a neonatal‐onset lactic acidosis with urinary excretion of methylmalonic acid. Enzymatic analyses (MRC enzyme assay and Western blotting) and direct sequencing analysis of SUCLA2 and SUCLG1 were performed.Results:  MRC enzyme assay and Western blotting showed that MRC complex I was deficient. SUCLG1 mutation analysis showed that the patient was a compound heterozygote for disease‐causing mutations (p.M14T and p.S200F).Conclusion:  For patients showing neonatal lactic acidosis and prolonged mild methylmalonic aciduria, MRC activities and mutations of SUCLG1 or SUCLA2 should be screened for.
PNEUMATIC DILATION FOR ACHALASIA CARDIA: REDUCTION IN LOWER ESOPHAGEAL SPHINCTER PRESSURE IN ASSESSING RESPONSE AND FACTORS ASSOCIATED WITH RECURRENCE DURING LONG‐TERM FOLLOW UP
Authors: GHOSHAL UDAY C , RANGAN MURALI , MISRA ASHA 
Published: June 2011

Background:  Data on utility of post‐pneumatic dilation (PD) lower esophageal sphincter (LES) pressure measurement in evaluating short and long‐term efficacy of dilation, which tears the non‐relaxing LES in achalasia, are scanty.Methods:  Post‐PD LES pressure was measured in 72/98 patients with achalasia. The best cut‐off pressure classifying responders and non‐responders was determined by receiver operating characteristic (ROC) curve. Factors associated with non‐response and recurrence were evaluated.Results:  Of 98 patients (41.1 ± 13.3 years, 58 male), 75 improved, three had perforation requiring surgery, and 20 did not respond to the first PD session. Of 18/20 patients undergoing a second PD, 11 improved and six non‐responders needed myotomy. 37/58 (71%) male and 17/40 (42.5%) female patients had a first PD with a 35‐mm balloon (P = 0.03). Age and gender of patients did not influence outcome. LES pressure was lower in responders or in those having recurrence than in non‐responders (17 mmHg [6.4–75], 11 mmHg [4.6–31]vs 25 mmHg [13–55]). On the ROC curve, 22.5 mmHg was the best cut‐off value differentiating responders and non‐responders (area under curve [AUC] 0.73). Of the 86 patients responding to PD, 20 had recurrence. Patients who responded to one session of PD or had LES pressure <10 mmHg after the procedure recurred less often, although there was no relationship with age and gender.Conclusion:  Post‐PD LES pressure measurement is useful to assess treatment response. Patients responding to the first session and those with post‐PD LES pressure <10 mmHg tended to recur less. Age and gender did not influence outcome, which might be related to preferential use of a 35‐mm balloon, particularly for male patients, during the first session.