bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of the complement and molecular evolution of tRNA genes in cow
Authors: Tang Dave TP , Glazov Evgeny A , McWilliam Sean M , Barris Wesley C , Dalrymple Brian P 
Published: April 2009

Abstract

Background
Detailed information regarding the number and organization of transfer RNA (tRNA) genes at the genome level is becoming readily available with the increase of DNA sequencing of whole genomes. However the identification of functional tRNA genes is challenging for species that have large numbers of repetitive elements containing tRNA derived sequences, such as Bos taurus. Reliable identification and annotation of entire sets of tRNA genes allows the evolution of tRNA genes to be understood on a genomic scale.

Results
In this study, we explored the B. taurus genome using bioinformatics and comparative genomics approaches to catalogue and analyze cow tRNA genes. The initial analysis of the cow genome using tRNAscan-SE identified 31,868 putative tRNA genes and 189,183 pseudogenes, where 28,830 of the 31,868 predicted tRNA genes were classified as repetitive elements by the RepeatMasker program. We then used comparative genomics to further discriminate between functional tRNA genes and tRNA-derived sequences for the remaining set of 3,038 putative tRNA genes. For our analysis, we used the human, chimpanzee, mouse, rat, horse, dog, chicken and fugu genomes to predict that the number of active tRNA genes in cow lies in the vicinity of 439. Of this set, 150 tRNA genes were 100% identical in their sequences across all nine vertebrate genomes studied. Using clustering analyses, we identified a new tRNA-GlyCCC subfamily present in all analyzed mammalian genomes. We suggest that this subfamily originated from an ancestral tRNA-GlyGCC gene via a point mutation prior to the radiation of the mammalian lineages. Lastly, in a separate analysis we created phylogenetic profiles for each putative cow tRNA gene using a representative set of genomes to gain an overview of common evolutionary histories of tRNA genes.

Conclusion
The use of a combination of bioinformatics and comparative genomics approaches has allowed the confident identification of a set of cow tRNA genes that will facilitate further studies in understanding the molecular evolution of cow tRNA genes.
Lack of association between polymorphisms of MASP2and susceptibility to SARS coronavirus infection
Authors: Wang Yan , Yan Jiangwei , Shi Yuling , Li Ping , Liu Chuanxuan , Ma Qingjun , Yang Ruifu , Wang Xiaoyi , zhu Lina , Yang Xiao , Cao Cheng 
Published: May 2009

AbstractBackgroundThe pathogenesis of severe acute respiratory disease syndrome (SARS) is not fully understood. One case-control study has reported an association between susceptibility to SARS andmannan-binding lectin(MBL) in China. As the downstream protein ofMBL, variants of theMBL-associated serine protease-2 (MASP2) gene may be associated with SARS coronavirus (SARS-CoV) infection in the same population.MethodsThirty individuals with SARS were chosen for analysis ofMASP2polymorphisms by means of PCR direct sequencing. Tag single nucleotide polymorphisms (tagSNPs) were chosen using pairwise tagging algorithms. The frequencies of four tag SNPs (rs12711521, rs2261695, rs2273346 and rs7548659) were ascertained in 376 SARS patients and 523 control subjects, using the Beckman SNPstream Ultra High Throughput genotyping platform.ResultsThere is no significant association between alleles or genotypes of theMASP2tagSNP and susceptibility to SARS-CoV in both Beijing and Guangzhou populations. Diplotype (rs2273346 and rs12711521)were analyzed for association with susceptibility to SARS, no statistically significant evidence of association was observed. The Beijing and Guangzhou sample groups were homogeneous regarding demographic and genetic parameters, a joined analysis also showed no statistically significant evidence of association.ConclusionOur data do not suggest a role forMASP2polymorphisms in SARS susceptibility in northern and southern China.
Glycogen synthase kinase-3 inhibition disrupts nuclear factor-kappaB activity in pancreatic cancer, but fails to sensitize to gemcitabine chemotherapy
Authors: Mamaghani Shadi , Patel Satish , Hedley David W 
Published: May 2009

Abstract

Background
Aberrant activation NF-kappaB has been proposed as a mechanism of drug resistance in pancreatic cancer. Recently, inhibition of glycogen synthase kinase-3 has been shown to exert anti-tumor effects on pancreatic cancer cells by suppressing NF-kappaB. Consequently, we investigated whether inhibition of GSK-3 sensitizes pancreatic cancer cells to the chemotherapeutic agent gemcitabine.

Methods
GSK-3 inhibition was achieved using the pharmacological agent AR-A014418 or siRNA against GSK-3 alpha and beta isoforms. Cytotoxicity was measured using a Sulphorhodamine B assay and clonogenic survival following exposure of six different pancreatic cancer cell lines to a range of doses of either gemcitabine, AR-A014418 or both for 24, 48 and 72 h. We measured protein expression levels by immunoblotting. Basal and TNF-alpha induced activity of NF-kappaB was assessed using a luciferase reporter assay in the presence or absence of GSK-3 inhibition.

Results
GSK-3 inhibition reduced both basal and TNF-alpha induced NF-kappaB luciferase activity. Knockdown of GSK-3 beta reduced nuclear factor kappa B luciferase activity to a greater extent than GSK-3 alpha, and the greatest effect was seen with dual knockdown of both GSK-3 isoforms. GSK-3 inhibition also resulted in reduction of the NF-kappaB target proteins XIAP, Bcl-XL, and cyclin D1, associated with growth inhibition and decreased clonogenic survival. In all cell lines, treatment with either AR-A014418, or gemcitabine led to growth inhibition in a dose- and time-dependent manner. However, with the exception of PANC-1 where drug synergy occurred with some dose schedules, the inhibitory effect of combined drug treatment was additive, sub-additive, or even antagonistic.

Conclusion
GSK-3 inhibition has anticancer effects against pancreatic cancer cells with a range of genetic backgrounds associated with disruption of NF-kappaB, but does not significantly sensitize these cells to the standard chemotherapy agent gemcitabine. This lack of synergy might be context or cell line dependent, but could also be explained on the basis that although NF-kappaB is an important mediator of pancreatic cancer cell survival, it plays a minor role in gemcitabine resistance. Further work is needed to understand the mechanisms of this effect, including the potential for rational combination of GSK3 inhibitors with other targeted agents for the treatment of pancreatic cancer.
Pivotal Advance: Eosinophilia in the MES rat strain is caused by a loss–of–function mutation in the gene for cytochrome b(–245), alpha polypeptide (Cyba)
Authors: Mori Masayuki , Li Guixin , Hashimoto Maiko , Nishio Ayako , Tomozawa Hiroshi , Suzuki Nobuyoshi , Usami Shin–ichi , Higuchi Keiichi , Matsumoto Kiyoshi 
Published: May 2009

Abstract
NADPH oxidase plays a role in homeostatic regulation of innate immunity beyond conventional microbicidial functions.
MES is a rat strain that spontaneously develops severe blood eosinophilia as a hereditary trait. Herein, we report that eosinophilia in MES rats is caused by a loss–of–function mutation in the gene for cytochrome b(–245), α polypeptide (Cyba; also known as p22phox), which is an essential component of the superoxide–generating NADPH oxidase complex. The MES rat has a deletion of four nucleotides, including the 5′ splice donor GpT of intron 4 of the Cyba gene. As a consequence of the deletion, a 51–nucleotide sequence of intron 4 is incorporated into the Cyba transcripts. Leukocytes from the MES strain lack both CYBA protein and NADPH oxidase activity. Nevertheless, unlike patients with chronic granulomatous disease, who suffer from infections with pathogens due to similar genetic defects in NADPH oxidase, MES rats retain normal innate immune defense against Staphylococcus aureus infection. This is due to large quantities of peritoneal eosinophils in MES rats, which phagocytose and kill the bacteria. MES rat has a balance defect due to impaired formation of otoconia in the utricles and saccules. Eosinophilia of the MES rat was normalized by introduction of a normal Cyba transgene. The mechanisms by which impairment of NADPH oxidase leads to eosinophilia in the MES rat are elusive. However, our study highlights the essential role of NADPH oxidase in homeostatic regulation of innate immunity beyond conventional microbicidial functions.
Electroreception in the euryhaline stingray, Dasyatis sabina
Authors: McGowan D. W. , Kajiura S. M. 
Published: May 2009

SUMMARY
This study quantified the electrosensitivity of a euryhaline elasmobranch,the Atlantic stingray (Dasyatis sabina) across a range of salinities. Specimens from a permanent freshwater (FW) population in the St Johns River system, FL, USA, were compared with stingrays from the tidally dynamic Indian River Lagoon in east Florida, USA. Behavioral responses of stingrays to prey-simulating electric stimuli were quantified in FW (0 p.p.t., ρ=2026Ω cm), brackish (15 p.p.t., ρ=41 Ω cm) and full strength seawater (35 p.p.t., ρ=19 Ω cm). This study demonstrated that the electrosensitivity of D. sabina is significantly reduced in FW. In order to elicit a feeding response, stingrays tested in FW required an electric field 200–300× greater than stingrays tested in brackish and saltwater (median FW treatments=1.4 μV cm–1, median brackish–saltwater treatments=6 nV cm–1), and the maximum orientation distance was reduced by 35.2%, from 44.0 cm in the brackish and saltwater treatments to 28.5 cm in FW. The St Johns River stingrays did not demonstrate an enhanced electrosensitivity in FW, nor did they exhibit reduced sensitivity when introduced to higher salinities. Stingrays from both populations responded similarly to the prey-simulating stimulus when tested at similar salinities, regardless of their native environment. The reduction in electrosensitivity and detection range in FW is attributed to both an environmental factor (electrical resistivity of the water) and the physiological function of the ampullary canals. The plasticity of this sensory system to function across such a wide environmental range demonstrates its adaptive significance.
Biomechanics of byssal threads outside the Mytilidae: Atrina rigida and Ctenoides mitis
Authors: Pearce Trevor , LaBarbera Michael 
Published: May 2009

SUMMARY
The byssus is the set of proteinaceous threads widely used by bivalves to attach themselves to the substrate. Previous researchers have focused on a single byssate family, the Mytilidae. However, the properties of byssal threads from species outside this family are of interest – first,because evolutionary patterns are only detectable if species from a range of taxa are examined, and second, because recent biomimetic research efforts would benefit from a wider range of `mussel glue' exemplars. In the present study, we measured the mechanical properties of the byssal threads of two species outside the Mytilidae, the pen shell Atrina rigida Lightfoot and the flame `scallop' Ctenoides mitis Lamarck. The mechanical properties of their byssal threads were significantly different from those of mytilids. For instance, the byssal threads of both species were significantly weaker than mytilid threads. Atrina rigida threads were significantly less extensible than mytilid threads, while C. mitis threads exhibited the highest extensibility ever recorded for the distal region of byssal threads. However, there were also interesting similarities in material properties across taxonomic groups. For instance, the threads of A. rigida and Modiolus modiolus Linnaeus both exhibited a prominent double-yield behavior, high stiffness combined with low extensibility, and similar correlations between stiffness and other thread properties. These similarities suggest that the thread properties of some semi-infaunal species may have evolved convergently. Further research on these patterns, along with biochemical analysis of threads which exhibit unusual properties like double-yield behavior, promises to contribute to both evolutionary biology and materials engineering.
Kinematics of horizontal and vertical caterpillar crawling
Authors: van Griethuijsen Linnea I. , Trimmer Barry A. 
Published: May 2009

SUMMARYUnlike horizontal crawling, vertical crawling involves two counteracting forces: torque rotating the body around its center of mass and gravity resisting forward movement. The influence of these forces on kinematics has been examined in the soft-bodied larval stage of Manduca sexta. We found that crawling and climbing are accomplished using the same movements,with both segment timing and proleg lift indistinguishable in horizontal and vertical locomotion. Minor differences were detected in stride length and in the delay between crawls, which led to a lower crawling speed in the vertical orientation. Although these differences were statistically significant, they were much smaller than the variation in kinematic parameters between animals. The ability of Manduca to crawl and climb using the same movements is best explained by Manduca's relatively small size, slow speed and strong, controlled, passive grip made possible by its proleg/crochets.
Evaluation of changes in serum lipoprotein and apolipoprotein patterns in cows with ketosis
Authors: İleri-Büyükoğlu Tülay , Şahinduran Şima , Sezer Kenan , Güldür Tayfun 
Published: May 2009

Abstract
Objective—To detect changes in serum lipoprotein and apolipoprotein profiles via precipitation and electrophoresis in ketotic cows and in those cows treated with different methods.
Animals—21 cows with clinical and subclinical ketosis, 7 healthy cows in the early lactation period, and 7 healthy cows in the nonlactation period.
Procedures—Ketotic cows were allocated into 3 groups; the first group was treated with dextrose and dexamethasone, the second group with dextrose and prednisolone, and the third group with dextrose and insulin. The β and α lipoproteins were precipitated with dextran sulfate-magnesium chloride in ketotic cows after treatment and healthy cows in the nonlactation and lactation periods. The serum samples, precipitates, and supernatants were examined via agarose gel electrophoresis for detection of alterations in serum lipoproteins. Subsequently, alterations in serum apolipoproteins were detected via SDS-PAGE of precipitates.
Results—Compared with serum β and α lipoprotein concentrations in healthy cows during nonlactation, those in cows during lactation were higher; however, those in cows with ketosis were lower. The SDS-PAGE analysis of serum β lipoproteins revealed that apolipoprotein E (approx 36 and 40 kDa) decreased in ketotic cows, in comparison with healthy cows in the nonlactation and lactation periods, but increased after treatment. Decreases in apolipo-protein B (approx 222 kDa), apolipoprotein A-I (19 and 24 kDa), apolipoprotein A-IV (55 kDa), apolipoprotein C-III (8.8 and 10.2 kDa), and albumin (66 kDa) concentrations were detected in ketotic cows, in comparison with the healthy cows in the lactation period.
Conclusions and Clinical Relevance—Serum lipoprotein and apolipoproteins may routinely be determined via precipitation and electrophoresis in the diagnosis and treatment of ketosis.
Pharmacokinetics and bioavailability of metformin in horses
Authors: Hustace Jaime L. , Firshman Anna M. , Mata John E. 
Published: May 2009

Abstract
Objective—To determine pharmacokinetics and oral bioavailability of metformin in healthy horses.
Animals—4 adult horses.
Procedures—6 g of metformin was administered 3 times IV and PO (fed and unfed) to each horse, by use of a crossover design, with a 1-week washout period between treatments. Plasma metformin concentration was determined via high-pressure liquid chromatography.
Results—Mean ± SD distribution half-life of metformin following IV administration was 24.9 ± 0.4 minutes with a volume of distribution of 0.3 ± 0.1 L/kg. Mean area under the curve was 20.9 ± 2.0 h·μg/mL for IV administration; PO administration resulted in area under the curves of 1.6 ± 0.4 h·μg/mL in unfed horses and 0.8 ± 0.2 h·μg/mL in fed horses. Bioavailability was determined to be approximately 7.1 ± 1.5% in unfed horses and 3.9 ± 1.0% in fed horses. The maximal concentration following PO administration in unfed horses was 0.4 ± 0.1 μg/mL with a time at maximal concentration of 0.9 ± 0.1 hours. In fed horses, maximal concentration was reduced to 0.3 ± 0.04 μg/mL with a time at maximal concentration at 1.3 ± 0.3 hours.
Conclusions and Clinical Relevance—The low bioavailability of metformin may explain the reported lack of clinical success in improving insulin sensitivity with metformin treatment in horses. Dosages and dose intervals previously used may have been insufficient to achieve plasma concentrations of drug comparable to the therapeutic range achieved in humans. Therefore, a larger and more frequently administered dose may be required to fully evaluate efficacy of metformin in horses.
Prognostic indicators for nonambulatory cattle treated by use of a flotation tank system in a referral hospital: 51 cases (1997–2008)
Authors: Burton Alexandra J. , Nydam Daryl V. , Ollivett Theresa L. , Divers Thomas J. 
Published: May 2009

Abstract
Objective—To evaluate clinical variables assessed during the first 24 hours of hospitalization as prognostic indicators for nonambulatory cattle treated by use of a flotation tank.
Design—Retrospective case series.
Animals—51 nonambulatory cattle that underwent flotation treatment.
Procedures—Signalment, history, serum biochemical analyses, patient behavior during flotation, and outcome data were collected from medical records. Outcome was survival to discharge from the hospital or nonsurvival (death or euthanasia). Data were analyzed by use of Wilcoxon rank sum, Fisher exact, and χ2 tests.
Results—19 of 51 cattle survived. Survivors and nonsurvivors did not differ significantly with regard to median weight; age; stage of lactation; duration of recumbency prior to flotation; serum potassium, ionized calcium, or phosphate concentrations at admission to the hospital; or serum creatine kinase activity (value at admission to the hospital, highest value, and last recorded value). Cattle that were able to walk out of the tank after the first flotation treatment were 4.8 times as likely to survive as those that could not. Cattle that did not eat during flotation treatment were 1.9 times as likely to die as those that ate. Cattle that stood apparently normally on all limbs during the first flotation treatment were 2.9 times as likely to survive as those that had an asymmetric stance or were unable to stand.
Conclusions and Clinical Relevance—Results indicated that objective variables evaluated during the first 24 hours of hospitalization and flotation treatment are associated with outcome among nonambulatory cattle; findings might assist in logical decision making with respect to treatment options.
Developing a dedicated cestode life cycle database: lessons from the hymenolepidids
Authors: Lefebvre F. , Georgiev B. , Bray R. , Littlewood D. 
Published: April 2009

Abstract
The Cestode Life Cycle Database (CLCdb) project was initiated in 2005 with the objective to develop a comprehensive and centralised resource to store, retrieve and analyse key information concerning tapeworm life cycles; e.g. morphogenesis, intermediate host identities, transmission patterns, etc. It constitutes the first electronic database to deal with complex life cycle information for any helminth taxon. Here we critically evaluate our experience after exhaustively entering data for our model group, the cyclophyllidean family Hymenolepididae. After providing basic statistics (530 consulted references; ∼ 230 ‘known’ life cycle), we identify future needs in turning the CLCdb into an open access monograph covering all cestode groups. We review the added benefits and potential utilities of the database for cestodologists and other users, including ecologists and veterinarians, and we call for specialist contributions. Since late 2007, a short version of the CLCdb has been available online, with basic functionalities and tools (www.nhm.ac.uk/research-curation/projects/cestode-life-cycle/index.html).
Overview of Research Progress on Peanut (Arachis hypogaea L.) Host Resistance to Aflatoxin Contamination and Genomics at the Guangdong Academy of Agricultural Sciences
Authors: Liang Xuanqiang , Zhou Guiyuan , Hong Yanbin , Chen Xiaopin , Liu Haiyan , Li Shaoxiong 
Published: April 2009

Abstract
Aflatoxin contamination in peanut is a serious and world-wide problem concerning food safety and human health. Plant-host resistance is a highly desirable tactic that can be used to manage this problem. This review summarizes research progress in peanut host resistance mechanisms to aflatoxin contamination at the Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China. Through systematic resistance evaluations, germplasm lines resistant to Aspergillus flavus invasion have been identified and two resistant cultivars were developed and released in South China. The resistance has been associated with testa wax and presence of cutin layer, active oxygen and membrane lipid peroxidation, phytoalexin accumulation, and antifungal proteins in the peanut kernels. Functional genomics will be a valuable tool to understand the comprehensive mechanisms governing the resistance pathways. In this paper we also summarized the advances made by our group in the area of genomic research, especially in mining EST-SSRs, development of a genetic linkage map and QTLs mapping in the cultivated peanut species.
Health-Related Quality of Life, Physical Function, Fatigue, and Disease Activity in Children with Established Polyarticular Juvenile Idiopathic Arthritis
Authors: RINGOLD SARAH , WALLACE CAROL A. , RIVARA FREDERICK P. 
Published: May 2009

Objective.To compare child self-report and parent/proxy report of health-related quality of life (HRQOL), disability, and fatigue in children with active polyarticular juvenile idiopathic arthritis (JIA) to that of children with inactive polyarticular JIA and to previous data from healthy controls.Methods.Cross-sectional survey of children with polyarticular JIA diagnosed and treated between 2000 to 2006 and their parent/proxy. The Childhood Health Assessment Questionnaire, Pediatric Quality of Life Inventory (PedsQL) Generic Core Scales, PedsQL Rheumatology Module, and PedsQL Multidimensional Fatigue Scale were administered. Disease activity data were collected from the physician clinic notes. Comparisons were performed with t tests. Correlations between patient and parent/proxy reports were measured with Pearson correlation coefficients.Results.Sixty children and/or their parents/proxies participated (79% response rate). Disease activity status was available for 52, and 32 met criteria for inactive disease (62%). Participants reported lower scores on the PedsQL Generic Core Scales (range 2.54–9.13 points lower) and the PedsQL Rheumatology Module (range 2.46–6.96 points lower) than those with inactive disease. Participants also reported lower scores on the PedsQL Multidimensional Fatigue Scale than did healthy controls, regardless of disease activity status (range 0.06–9.2 points lower).Conclusion.Although children in this cohort with polyarticular JIA and inactive disease reported HRQOL scores similar to those of healthy controls, children with polyarticular JIA and their parents/proxies tended to report more fatigue than controls, regardless of disease activity. Application of these measures prospectively to larger cohorts of children with JIA is needed to assess these differences.