bluuebunny/crossref_metadata_2025_split huggingface dataset:
Update On The Zebrafish Genome Project
Authors: Almeida-King J P , Donaldson S , Laird G K , Lloyd D M , Sehra H K , Collins J E , Howe K , Reimholz B , Torrance J , Trevanion S , Stemple D , Barroso I , Gilbert J G R , Griffiths E , Loveland J E , Storey R , Harrow J L , Hubbard T 
Published: April 2009

AbstractThe zebrafish genome, which consists of 25 linkage groups and is ~1.4Gb in size, is being sequenced, finished and analysed in its entirety at the Wellcome Trust Sanger Institute. The manual annotation is provided by the Human and Vertebrate Analysis and Annotation (HAVANA) group and is released at regular intervals onto the Vertebrate Genome Annotation (Vega) database ("http://vega.sanger.ac.uk":http://vega.sanger.ac.uk) and may be viewed as a DAS source in Ensembl ("http://www.ensembl.org/Danio_rerio":http://www.ensembl.org/Danio_rerio). Our annotation is compiled in close collaboration with the Zebrafish Information Network (ZFIN) ("http://zfin.org/":http://zfin.org/), which has enabled us to provide an accurate, dynamic and distinct resource for the zebrafish community as a whole.Annotation is based on the reference genome sequence, which is derived from a minimal tile path assembly composed of clones that have been mapped, sequenced and meticulously finished to a sequence accuracy of over 99.9% per 100Kb. We expect to have 90% of the zebrafish genome to a finished standard by the end of 2009. Our approach to annotation uses two strategies. Firstly, the generation and annotation of gene lists comprising of cDNA (8995 in total) found in ZFIN that maps to our current reference assembly. And, secondly, by using clone by clone annotation, where we have annotated over 3200 genes, 1100 transcripts and 130 pseudogenes across 11 linkage groups and 3530 clones. As well as our on-going genome annotation we also welcome external annotation requests for specific genes and regions, which already include the annotation of 93 genes associated with human obesity and the scheduled annotation of the Major Histocompatability Complex, which will utilise reference sequence taken from libraries of a double haploid fish and complement our previous work on the human and mouse MHC already published. External requests and any feedback, questions or requests can be sent to zfish-help [at] sanger.ac.uk.
Insulin Resistance Impairs Endothelial Function but not Adrenergic Reactivity or Vascular Structure in Fructose‐fed Rats
Authors: ROMANKO OLGA P. , ALI M. IRFAN , MINTZ JAMES D. , STEPP DAVID W. 
Published: April 2009

ABSTRACTObesity and diabetes are major risk factors for the development of vascular disease in the lower limbs. Previous studies have demonstrated reduced nitric oxide (NO)‐mediated vasodilation, increased adrenergic constriction, and inward, atrophic remodeling in the limb circulation of obese Zucker rats, but the component of the “metabolic syndrome” driving these changes is unclear. Because insulin resistance precedes the state of frank diabetes, the current study hypothesized that insulin resistance independent of obesity induced by fructose feeding would impair microvascular function in the skeletal muscle circulation in lean Zucker rats (LZR). A 66% fructose diet impaired glucose tolerance and induced moderate insulin resistance with no changes in whole‐body hemodynamics of anesthetized rats (FF‐LZR), compared to control LZR. NO‐mediated vasodilation of isolated gracilis arteries, assessed in vitro with acetylcholine and sodium nitroprusside, was reduced ∼20% in FF‐LZR vs. LZR. NO‐independent cGMP‐mediated vasodilation was unimpaired. Pretreatment of isolated vessels with the superoxide scavenger, tempol, improved responses to both vasodilators. Reactivity to adrenergic stimulation was unaltered in FF‐LZR vs. LZR, although constriction to endothelin was increased. Structural and passive mechanical characteristics of isolated gracilis arteries were similar in both LZR and FF‐LZR. Taken together, these findings indicate that moderate insulin resistance is sufficient to impair endothelial function in an oxidant‐dependent manner in the rat hindlimb circulation. Other aspects of skeletal muscle vascular function documented in obese models, specifically adrenergic tone and inward remodeling, must reflect either severe insulin resistance or other aspects of obesity. The factors accounting for nonendothelial vasculopathies remain unknown.
Association between aerobic fitness, body composition, and physical activity in 9‐ and 15‐year‐olds
Authors: Sveinsson Thorarinn , Arngrimsson Sigurbjorn A. , Johannsson Erlingur 
Published: April 2009

AbstractThe aim of this study was to examine the interrelationship between aerobic fitness, body composition, and physical activity in 9‐ and 15‐year‐olds. The 270 participants were randomly selected from 18 primary and secondary schools in Iceland. Aerobic fitness was assessed by a graded exercise test on a bicycle ergometer. Body composition was estimated via: logarithm of sum of four skinfolds (loge skinfolds), waist adjusted for height, and body mass index (BMI). Physical activity was measured with Actigraph activity monitors using total activity each day as the physical activity variable. Aerobic fitness was chosen as the primary outcome variable, body composition as the secondary variable, and physical activity as the tertiary variable. All the full models explained a similar proportion of fitness variance for both age groups (45–65%). Among the 15‐year‐olds, loge skinfolds explained a significantly larger proportion of the fitness variance (54%) than waist adjusted for height (29%) and BMI (15%), but all the body composition variables explained a similar proportion of the fitness variance (35–42%) among the 9‐year‐olds. Physical activity explained a smaller proportion (0%) of the unadjusted variance in fitness for the 9‐year‐olds than for the 15‐year‐olds (19%). This group difference became non‐significant (0% vs. 4%) when adjusting for loge skinfolds but remained significant when controlling for waist adjusted for height (0% vs. 15%) and BMI (0% vs. 18%). Gender differences in aerobic fitness after puberty can largely be explained by gender differences in loge skinfolds and physical activity. In conclusion, the interrelationship between fitness, body composition, physical activity, and gender is not the same among 9‐ and 15‐year‐olds.
Development of a performance assessment tool for rock climbers
Authors: Brent Simon , Draper Nick , Hodgson Christopher , Blackwell Gavin 
Published: April 2009

AbstractRock climbing is a popular adventure sport for which there is a growing body of scientific knowledge. There is, however, a lack of sport‐specific assessment tools to monitor performance. The aim of this study was to examine the potential of the rock‐over climbing test (ROCT) as a measure of climbing performance. The ROCT was conducted on a climbaflex board and involved the climber making a rock‐over move for which the height gained from lower to upper handhold was measured. Results indicated there was a significant relationship between scaled (to the height of the climber) ROCT scores and climbing ability (r=0.67, P<0.0005). Regression modelling revealed that the ROCT explained 45% of the variance in scores between climbers. The ROCT differentiated between climber ability levels. Mean ROCT scores for novice, intermediate, advanced, and elite climbers were 59.5%, 71%, 82%, and 90% of participant height respectively. Results of analysis of variance revealed that these differences were significant (F 3,42=13.38, P<0.0005). Limits of agreement and intra‐class correlation indicated that the ROCT is a reliable performance measure. Our findings suggest that the ROCT is a useful measure of climbing performance.
Evaluation of body composition using three different methods compared to dual‐energy X‐ray absorptiometry
Authors: Duz Serkan , Kocak Mehmet , Korkusuz Feza 
Published: April 2009

AbstractIn this study, we compared the simple methods of skinfolds, ultrasound, and bioelectrical impedance analysis (BIA) against the standard of dual‐energy X‐ray absorptiometry (DEXA) in the assessment of body fat in normoactive Turkish male and female university students. We wished to develop new regression equations to more accurately predict percent body fat from skinfolds and ultrasound for this group of individuals. One hundred and four male (age 22.2±2.5 years; height 1.77±0.06 m; mass 74.9±10.4 kg) and one hundred and four female (age 21.9±1.9 years; height 1.65±0.06 m; mass 55.6±7.9 kg) students aged 18–26 years participated in the study. Analysis of variance and confidence intervals were used to compare mean percent body fat derived from skinfolds, ultrasound, BIA, and DEXA measurements, while intra‐class correlation coefficients and Pearson correlation coefficients were used to evaluate the strength of the relationship between the methods. Bland and Altman plot analysis was used to evaluate the strength of agreement of the three methods with DEXA. Moreover, multiple regression analyses were conducted to develop new regression equations to predict percent body fat from subcutaneous fat thickness measured at three sites. The accuracy of the predictive equations was assessed by a cross‐validation test. Mean percent body fat derived from DEXA (18.5±6.2% for males, 28.4±1.3% for females) was found to be significantly (p<0.01) greater than that derived from skinfolds (12.4±5.5% for males, 20.8±1.0% for females), ultrasound (12.0±7.8% for males, 25.0±1.4% for females), and BIA (13.7±4.9% for males, 19.2±1.0% for females) in both males and females. According to the Bland and Altman plot analysis, ultrasound gave the closest results to DEXA for females and males and females combined, whereas BIA gave the closest results to DEXA for males. Skinfolds were the second closest measure to DEXA for all groups. Results of the regression analysis showed that measurement of subcutaneous fat thickness at three sites by skinfolds and ultrasound best predicted percent body fat for males and females respectively. Multiple correlations using three sites simultaneously in the skinfold measurements were r=0.92 ( =2.4) and r=0.91 ( =2.8), and in the ultrasound measurements were r=0.93 ( =2.3) and r=0.90 ( =3.0), for males and females respectively. In conclusion, comparison of the methods revealed that the three techniques could not be used interchangeably in this population. However, with these new regression equations, ultrasound and skinfolds are confirmed to be accurate, portable, and non‐invasive tools for use in field studies. As a result, ultrasound can be used accurately on all individuals, regardless of whether they are obese or thin.
FDR made easy in differential feature discovery and correlation analyses
Authors: Ling Xuefeng Bruce , Cohen Harvey , Jin Joseph , Lau Irwin , Schilling James 
Published: April 2009

AbstractSummary: Rapid progress in technology, particularly in high-throughput biology, allows the analysis of thousands of genes or proteins simultaneously, where the multiple comparison problems occurs. Global false discovery rate (gFDR) analysis statistically controls this error, computing the ratio of the number of false positives over the total number of rejections. Local FDR (lFDR) method can associate the corrected significance measure with each hypothesis testing for its feature-by-feature interpretation. Given the large feature number and sample size in any genomics or proteomics analysis, FDR computation, albeit critical, is both beyond the regular biologists' specialty and computationally expensive, easily exceeding the capacity of desktop computers. To overcome this digital divide, a web portal has been developed that provides bench-side biologists easy access to the server-side computing capabilities to analyze for FDR, differential expressed genes or proteins, and for the correlation between molecular data and clinical measurements.Availability: http://translationalmedicine.stanford.edu/Mass-Conductor/FDR.htmlContacts: xuefeng_ling@yahoo.com; jschill@stanford.eduSupplementary information: Supplementary data are available at Bioinformatics online.
A local multiple alignment method for detection of non-coding RNA sequences
Authors: Tabei Yasuo , Asai Kiyoshi 
Published: April 2009

AbstractMotivation: Non-coding RNAs (ncRNAs) show a unique evolutionary process in which the substitutions of distant bases are correlated in order to conserve the secondary structure of the ncRNA molecule. Therefore, the multiple alignment method for the detection of ncRNAs should take into account both the primary sequence and the secondary structure. Recently, there has been intense focus on multiple alignment investigations for the detection of ncRNAs; however, most of the proposed methods are designed for global multiple alignments. For this reason, these methods are not appropriate to identify locally conserved ncRNAs among genomic sequences. A more efficient local multiple alignment method for the detection of ncRNAs is required.Results: We propose a new local multiple alignment method for the detection of ncRNAs. This method uses a local multiple alignment construction procedure inspired by ProDA, which is a local multiple aligner program for protein sequences with repeated and shuffled elements. To align sequences based on secondary structure information, we propose a new alignment model which incorporates secondary structure features. We define the conditional probability of an alignment via a conditional random field and use a γ-centroid estimator to align sequences. The locally aligned subsequences are clustered into blocks of approximately globally alignable subsequences between pairwise alignments. Finally, these blocks are multiply aligned via MXSCARNA. In benchmark experiments, we demonstrate the high ability of the implemented software, SCARNA_LM, for local multiple alignment for the detection of ncRNAs.Availability: The C++ source code for SCARNA_LM and its experimental datasets are available at http://www.ncrna.org/software/scarna_lm/download.Contact: scarna@m.aist.go.jpSupplementary information: Supplementary data are available at Bioinformatics online.
CATMAID: collaborative annotation toolkit for massive amounts of image data
Authors: Saalfeld Stephan , Cardona Albert , Hartenstein Volker , Tomančák Pavel 
Published: April 2009

Abstract
Summary: High-resolution, three-dimensional (3D) imaging of large biological specimens generates massive image datasets that are difficult to navigate, annotate and share effectively. Inspired by online mapping applications like GoogleMaps™, we developed a decentralized web interface that allows seamless navigation of arbitrarily large image stacks. Our interface provides means for online, collaborative annotation of the biological image data and seamless sharing of regions of interest by bookmarking. The CATMAID interface enables synchronized navigation through multiple registered datasets even at vastly different scales such as in comparisons between optical and electron microscopy.
Availability: http://fly.mpi-cbg.de/catmaid
Contact: tomancak@mpi-cbg.de
Disruption ofOsYSL15Leads to Iron Inefficiency in Rice Plants
Authors: Lee Sichul , Chiecko Jeff C. , Kim Sun A. , Walker Elsbeth L. , Lee Youngsook , Guerinot Mary Lou , An Gynheung 
Published: April 2009

AbstractUptake and translocation of metal nutrients are essential processes for plant growth. Graminaceous species release phytosiderophores that bind to Fe3+; these complexes are then transported across the plasma membrane. We have characterized OsYSL15, one of the rice (Oryza sativa) YS1-like (YSL) genes that are strongly induced by iron (Fe) deficiency. The OsYSL15 promoter fusion to β-glucuronidase showed that it was expressed in all root tissues when Fe was limited. In low-Fe leaves, the promoter became active in all tissues except epidermal cells. This activity was also detected in flowers and seeds. The OsYSL15:green fluorescent protein fusion was localized to the plasma membrane. OsYSL15 functionally complemented yeast strains defective in Fe uptake on media containing Fe3+-deoxymugineic acid and Fe2+-nicotianamine. Two insertional osysl15 mutants exhibited chlorotic phenotypes under Fe deficiency and had reduced Fe concentrations in their shoots, roots, and seeds. Nitric oxide treatment reversed this chlorosis under Fe-limiting conditions. Overexpression of OsYSL15 increased the Fe concentration in leaves and seeds from transgenic plants. Altogether, these results demonstrate roles for OsYSL15 in Fe uptake and distribution in rice plants.
A Mobile Secretory Vesicle Cluster Involved in Mass Transport from the Golgi to the Plant Cell Exterior
Authors: Toyooka Kiminori , Goto Yumi , Asatsuma Satoru , Koizumi Masato , Mitsui Toshiaki , Matsuoka Ken 
Published: April 2009

AbstractSecretory proteins and extracellular glycans are transported to the extracellular space during cell growth. These materials are carried in secretory vesicles generated at the trans-Golgi network (TGN). Analysis of the mammalian post-Golgi secretory pathway demonstrated the movement of separated secretory vesicles in the cell. Using secretory carrier membrane protein 2 (SCAMP2) as a marker for secretory vesicles and tobacco (Nicotiana tabacum) BY-2 cell as a model cell, we characterized the transport machinery in plant cells. A combination of analyses, including electron microscopy of quick-frozen cells and four-dimensional analysis of cells expressing fluorescent-tagged SCAMP2, enabled the identification of a clustered structure of secretory vesicles generated from TGN that moves in the cell and eventually fuses with plasma membrane. This structure was termed the secretory vesicle cluster (SVC). The SVC was also found in Arabidopsis thaliana and rice (Oryza sativa) cells and moved to the cell plate in dividing tobacco cells. Thus, the SVC is a motile structure involved in mass transport from the Golgi to the plasma membrane and cell plate in plant cells.
The RNA Binding Protein ELF9 Directly ReducesSUPPRESSOR OF OVEREXPRESSION OF CO1Transcript Levels inArabidopsis, Possibly via Nonsense-Mediated mRNA Decay
Authors: Song Hae-Ryong , Song Ju-Dong , Cho Jung-Nam , Amasino Richard M. , Noh Bosl , Noh Yoo-Sun 
Published: April 2009

AbstractSUPPRESSOR OF OVEREXPRESSION OF CO1 (SOC1) is regulated by a complex transcriptional regulatory network that allows for the integration of multiple floral regulatory inputs from photoperiods, gibberellin, and FLOWERING LOCUS C. However, the posttranscriptional regulation of SOC1 has not been explored. Here, we report that EARLY FLOWERING9 (ELF9), an Arabidopsis thaliana RNA binding protein, directly targets the SOC1 transcript and reduces SOC1 mRNA levels, possibly through a nonsense-mediated mRNA decay (NMD) mechanism, which leads to the degradation of abnormal transcripts with premature translation termination codons (PTCs). The fully spliced SOC1 transcript is upregulated in elf9 mutants as well as in mutants of NMD core components. Furthermore, a partially spliced SOC1 transcript containing a PTC is upregulated more significantly than the fully spliced transcript in elf9 in an ecotype-dependent manner. A Myc-tagged ELF9 protein (MycELF9) directly binds to the partially spliced SOC1 transcript. Previously known NMD target transcripts of Arabidopsis are also upregulated in elf9 and recognized directly by MycELF9. SOC1 transcript levels are also increased by the inhibition of translational activity of the ribosome. Thus, the SOC1 transcript is one of the direct targets of ELF9, which appears to be involved in NMD-dependent mRNA quality control in Arabidopsis.
Pausing of Golgi Bodies on Microtubules Regulates Secretion of Cellulose Synthase Complexes in Arabidopsis
Authors: Crowell Elizabeth Faris , Bischoff Volker , Desprez Thierry , Rolland Aurélia , Stierhof York-Dieter , Schumacher Karin , Gonneau Martine , Höfte Herman , Vernhettes Samantha 
Published: April 2009

Abstract
Plant growth and organ formation depend on the oriented deposition of load-bearing cellulose microfibrils in the cell wall. Cellulose is synthesized by plasma membrane–bound complexes containing cellulose synthase proteins (CESAs). Here, we establish a role for the cytoskeleton in intracellular trafficking of cellulose synthase complexes (CSCs) through the in vivo study of the green fluorescent protein (GFP)-CESA3 fusion protein in Arabidopsis thaliana hypocotyls. GFP-CESA3 localizes to the plasma membrane, Golgi apparatus, a compartment identified by the VHA-a1 marker, and, surprisingly, a novel microtubule-associated cellulose synthase compartment (MASC) whose formation and movement depend on the dynamic cortical microtubule array. Osmotic stress or treatment with the cellulose synthesis inhibitor CGA 325'615 induces internalization of CSCs in MASCs, mimicking the intracellular distribution of CSCs in nongrowing cells. Our results indicate that cellulose synthesis is coordinated with growth status and regulated in part through CSC internalization. We find that CSC insertion in the plasma membrane is regulated by pauses of the Golgi apparatus along cortical microtubules. Our data support a model in which cortical microtubules not only guide the trajectories of CSCs in the plasma membrane, but also regulate the insertion and internalization of CSCs, thus allowing dynamic remodeling of CSC secretion during cell expansion and differentiation.
Misexpression of FATTY ACID ELONGATION1 in theArabidopsisEpidermis Induces Cell Death and Suggests a Critical Role for Phospholipase A2 in This Process
Authors: Reina-Pinto José J. , Voisin Derry , Kurdyukov Sergey , Faust Andrea , Haslam Richard P. , Michaelson Louise V. , Efremova Nadia , Franke Benni , Schreiber Lukas , Napier Johnathan A. , Yephremov Alexander 
Published: April 2009

AbstractVery-long-chain fatty acids (VLCFAs) are important functional components of various lipid classes, including cuticular lipids in the higher plant epidermis and lipid-derived second messengers. Here, we report the characterization of transgenic Arabidopsis thaliana plants that epidermally express FATTY ACID ELONGATION1 (FAE1), the seed-specific β-ketoacyl-CoA synthase (KCS) catalyzing the first rate-limiting step in VLCFA biosynthesis. Misexpression of FAE1 changes the VLCFAs in different classes of lipids but surprisingly does not complement the KCS fiddlehead mutant. FAE1 misexpression plants are similar to the wild type but display an essentially glabrous phenotype, owing to the selective death of trichome cells. This cell death is accompanied by membrane damage, generation of reactive oxygen species, and callose deposition. We found that nuclei of arrested trichome cells in FAE1 misexpression plants cell-autonomously accumulate high levels of DNA damage, including double-strand breaks characteristic of lipoapoptosis. A chemical genetic screen revealed that inhibitors of KCS and phospholipase A2 (PLA2), but not inhibitors of de novo ceramide biosynthesis, rescue trichome cells from death. These results support the functional role of acyl chain length of fatty acids and PLA2 as determinants for programmed cell death, likely involving the exchange of VLCFAs between phospholipids and the acyl-CoA pool.