bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of ischaemic exercise training of a normal limb on angiogenesis of a pathological ischaemic limb in rabbits
Authors: Shen Mei , Gao Jing , Li Jianan , Su Juan 
Published: January 2009

The present study was designed to test the hypothesis that local exercise of a normal limb can promote angiogenesis in a pathological ischaemic limb. New Zealand White rabbits underwent left femoral artery ligation (Lig) and electrode implantation on the right sciatic nerve. The rabbits were randomly assigned to four groups: (i) Lig-N group, which did not receive ES (electrical stimulation); (ii) Lig-High group, which received high-intensity ES (2.5 mA, 40Hz for 1 ms) on the right hindlimb; (iii) Lig-Low group, which received low-intensity ES (0.3 mA, 40Hz for 1 ms) on the right hindlimb; (iv) Double-Lig-High group, which underwent femoral artery ligation on both hindlimbs and received high-intensity ES (2.5 mA, 40Hz for 1 ms) on the right hindlimb. The ES procedure included 5 min of stimulation, followed by 5 min of rest, and was repeated eight times a day for 4 weeks. Collateral circulation was examined grossly by angiography, resting blood flow was measured using the microspheres technique, and capillary supply was evaluated by immunohistochemistry. VEGF (vascular endothelial growth factor) mRNA and protein were analysed by real-time RT (reverse transcription)–PCR and Western blotting respectively. Collateral blood flow in all of the major muscles of the left hindlimb in the Lig-High group was highest among the four groups (P&lt;0.01). Capillary supply (P&lt;0.001), VEGF mRNA (P&lt;0.01) and VEGF protein (P&lt;0.01) in the gastrocnemius muscle increased remarkably in the Lig-High group; no statistically significant difference was observed among the other three groups. In conclusion, angiogenesis associated with an up-regulation of VEGF expression in pathological ischaemic limb may be facilitated by 4 weeks of physiological ischaemic exercise training in a normal limb.
Prenatal programming of renal sodium handling in the rat
Authors: Alwasel Saleh H. , Ashton Nick 
Published: January 2009

Prenatally programmed hypertension induced by maternal protein restriction is associated with increased expression of the renal tubular Na+/K+/2Cl− co-transporter (NKCC2) and the Na+/Cl− co-transporter (NCC). This has led to the suggestion that renal Na+ retention contributes to the development of hypertension in the LP rat (offspring exposed to a maternal low-protein diet in utero). However, this hypothesis has not been tested in vivo. Renal clearance measurements in hypertensive 4-week-old male and female LP rats showed that, although the glomerular filtration rate remained unaltered, urine flow (P&lt;0.01) and urinary Na+ excretion rates (1.6±0.3 and 3.0±0.4 μmol·min−1·100 g−1 of body weight in control male and LP male respectively; P&lt;0.001) were increased. Na+ excretion was positively correlated with mean arterial pressure in both males (P&lt;0.01) and females (P&lt;0.05), but neither the slope nor the intercept differed between control and LP rats. Fractional excretion of Na+ was increased in male (1.5±0.2 and 3.0±0.5% in control and LP rats respectively; P&lt;0.001) and female LP rats, implying reduced tubular reabsorption of Na+. Western blotting and quantitative PCR showed that NKCC2 expression was increased, whereas NCC mRNA was not up-regulated. Na+/K+ ATPase α1 subunit expression did not differ from controls; however, there was a significant reduction in whole kidney pump activity (23.4±1.8 and 17.7±1.2 nmol of phosphate·μg−1 of protein·h−1 in control male and male LP rats respectively; P&lt;0.001); immunohistochemistry showed that the α1 subunit was virtually absent from the inner medulla. The greater Na+ excretion of LP rats can be explained, in part, by a pressure–natriuresis mechanism; however, the loss of the Na+/K+ ATPase α1 subunit from the inner medulla and up-regulation of NKCC2 suggests that altered renal Na+ handling is also programmed prenatally.
Effects of HCV co-infection on apoptosis of CD4+ T-cells in HIV-positive patients
Authors: Körner Christian , Krämer Benjamin , Schulte Daniela , Coenen Martin , Mauss Stefan , Fätkenheuer Gerd , Oldenburg Johannes , Nattermann Jacob , Rockstroh Jürgen K. , Spengler Ulrich 
Published: January 2009

Apoptosis importantly contributes to loss of CD4+ T-cells in HIV infection, and modification of their apoptosis may explain why HIV/HCV (hepatitis C virus)-co-infected patients are more likely to die from liver-related causes, although the effects of HCV on HIV infection remain unclear. In the present study, we studied in a cross-sectional and serial analysis spontaneous ex vivo CD4+ T-cell apoptosis in HIV/HCV-co-infected and HIV-mono-infected patients before and after HAART (highly active antiretroviral therapy). Apoptosis of peripheral blood CD4+ T-cells was measured by both a PARP [poly(ADP-ribose) polymerase] and TUNEL (terminal deoxynucleotidyl transferase-mediated dUTP nick-end labelling) assay to detect cells with irreversible apoptosis. Although hepatitis C alone did not increase CD4+ T-cell apoptosis, HCV co-infection disproportionately increased elevated rates of apoptosis in CD4+ T-cells from untreated HIV-positive patients. Increased CD4+ T-cell apoptosis was closely correlated with HIV, but not HCV, viral loads. Under HAART, increased rates of CD4+ T-cell apoptosis rapidly decreased both in HIV-mono-infected and HIV/HCV-co-infected patients, without any significant difference in apoptosis rates between the two patient groups after 4 weeks of therapy. Nevertheless residual CD4+ T-cell apoptosis did not reach the normal levels seen in healthy controls and remained higher in HIV patients receiving protease inhibitors than in patients with other antiretroviral regimens. The results of the present study suggest that HCV co-infection sensitizes CD4+ T-cells towards apoptosis in untreated HIV-positive patients. However, this effect is rapidly lost under effective antiretroviral therapy.
bioDBnet: the biological database network
Authors: Mudunuri Uma , Che Anney , Yi Ming , Stephens Robert M. 
Published: January 2009

Abstract
Summary: bioDBnet is an online web resource that provides interconnected access to many types of biological databases. It has integrated many of the most commonly used biological databases and in its current state has 153 database identifiers (nodes) covering all aspects of biology including genes, proteins, pathways and other biological concepts. bioDBnet offers various ways to work with these databases including conversions, extensive database reports, custom navigation and has various tools to enhance the quality of the results. Importantly, the access to bioDBnet is updated regularly, providing access to the most recent releases of each individual database.
Availability: http://biodbnet.abcc.ncifcrf.gov
Contact: stephensr@mail.nih.gov
Supplementary information: Supplementary data are available at Bioinformatics online
A novel method for large tree visualization
Authors: Heard Jeff , Kaufmann William , Guan Xiaojun 
Published: January 2009

Abstract
Summary: Many genomic and proteomic analyses generate as a result a tree of genes or proteins. These trees are often large (containing tens of thousands of nodes and edges), and need a visualization tool to fully display all the information contained in the tree. Clustering analysis can be performed on these trees to obtain clusters of proteins, and we need an efficient way to visualize the clustering results. We present a novel tree visualization tool to help with such analyses.
Availability: http://www2.renci.org/~jeff/software/bin/win32/ProteinVis-2.1.6-win32.zip
Contact: jeff@renci.org; xguan@renci.org
Biodiversity informatics: automated approaches for documenting global biodiversity patterns and processes
Authors: Guralnick Robert , Hill Andrew 
Published: January 2009

Abstract
Motivation: Data about biodiversity have been scattered in different formats in natural history collections, survey reports and the literature. A central challenge for the biodiversity informatics community is to provide the means to share and rapidly synthesize these data and the knowledge they provide us to build an easily accessible, unified global map of biodiversity. Such a map would provide raw and summary data and information on biodiversity and its change across the world at multiple scales.
Results: We discuss a series of steps required to create a unified global map of biodiversity. These steps include: building biodiversity repositories; creating scalable species distribution maps; creating flexible, user-programmable pipelines which enable biodiversity assessment; and integrating phylogenetic approaches into biodiversity assessment. We show two case studies that combine phyloinformatic and biodiversity informatic approaches to document large scale biodiversity patterns. The first case study uses data available from the Barcode of Life initiative in order to make species conservation assessment of North American birds taking into account evolutionary uniqueness. The second case study uses full genomes of influenza A available from Genbank to provide an auto-updating documentation of the evolution and geographic spread of these viruses.
Availability: Both the website for tracking evolution and spread of influenza A and the website for applying phyloinformatics analysis to Barcode of Life data are available as outcomes of case studies (http://biodiversity.colorado.edu).
Contact: robert.guralnick@colorado.edu
Steeper biomass spectra of demersal fish communities after trawler exclusion in Sicily
Authors: Sweeting Christopher J. , Badalamenti Fabio , D'Anna Giovanni , Pipitone Carlo , Polunin N. V. C. 
Published: January 2009

AbstractSweeting, C. J., Badalamenti, F., D'Anna, G., Pipitone, C., and Polunin, N. V. C. 2009. Steeper biomass spectra of demersal fish communities after trawler exclusion in Sicily. – ICES Journal of Marine Science, 66: 195–202. The effects of trawling on Mediterranean demersal fish communities were assessed by comparing them with the normalized biomass spectra among three gulfs on the north Sicilian coast, one of which had been subject to 15 years of trawler exclusion. Comparisons were conducted across seasons and among depth strata. Biomass-spectra slopes were significantly steeper in the gulf that was closed to trawling than in the unprotected gulfs. This was attributed to the exclusion of trawlers, which lacked catch-size selectivity, and to the continued fishing by artisanal gears that are more size selective. The biomass of all size classes was higher in the protected gulf than in unprotected areas, and increases were greatest in smaller size classes. Community mean individual fish mass was similar among all areas with a wider range of body masses present in the trawl exclusion area, compensating for the greater abundance of small fish. Size-spectra slopes were generally shallower and midpoint heights lower with increasing depth and were greater in autumn than spring; the effect of these seasonal and depth factors was as great as that of protection. Depth patterns are explainable by bathymetric trends in within- and among-species fish size. Seasonal differences were attributed to variation in spawning behaviour and fishery recruitment, with seasonal differences being greater in unprotected locations as a result of recruitment overfishing.
Using MPAs to address regional-scale ecological objectives in the North Sea: modelling the effects of fishing effort displacement
Authors: Greenstreet Simon P. R. , Fraser Helen M. , Piet Gerjan J. 
Published: January 2009

Abstract
Greenstreet, S. P. R., Fraser, H. M., and Piet, G. J. 2009. Using MPAs to address regional-scale ecological objectives in the North Sea: modelling the effects of fishing effort displacement. – ICES Journal of Marine Science, 66: 90–100. The use of Marine Protected Areas (MPAs) to address regional-scale objectives as part of an ecosystem approach to management in the North Sea is examined. Ensuring that displacement of fishing activity does not negate the ecological benefits gained from MPAs is a major concern. Two scenarios are considered: using MPAs to safeguard important areas for groundfish species diversity and using them to reduce fishing impacts on benthic invertebrates. Appropriate MPAs were identified using benthic invertebrate and fish abundance data. Fishing effort redistribution was modelled using international landings and fishing effort data. Closing 7.7% of the North Sea to protect groundfish species diversity increased the fishing impact on benthic invertebrates. Closing 7.3% of the North Sea specifically to protect benthic invertebrates reduced fishing mortality by just 1.7–3.8%, but when combined with appropriate reductions in total allowable catch (TAC), 16.2–17.4% reductions in fishing mortality were achieved. MPAs on their own are unlikely to achieve significant regional-scale ecosystem benefits, because local gains are largely negated by fishing effort displacement into the remainder of the North Sea. However, in combination with appropriate TAC reductions, the effectiveness of MPAs may be enhanced.
First Report of a 16SrI-C Group Phytoplasma Associated With a Yellows-Type Disease Affecting Willow Plants in China
Authors: Wei T. , Wu Y. F. , Wu K. K. , Hou W. , Li Y. R. 
Published: January 2009

In May of 2008, a phytoplasma-like disease was observed on willows (Salix babylonica Linn) grown in the Shaanxi Province. Affected plants showed yellowed leaves with green veins and dieback. Incidence of the disease was less than 10%. Samples were collected from 10 symptomatic and five asymptomatic willow plants from five different areas in Shaanxi Province. Total DNA was extracted from 0.5 g of leaf midrib and stem phloem tissue with a modified cetyltrimethylammoniumbromide (CTAB) method (3). Resulting DNA extracts were analyzed by a nested PCR assay using phytoplasma 16S rRNA gene primer pairs R16mF2/R16mR1 followed by R16F2n/R16R2 (1), which amplified a 1,452- and a 1,246-bp product, respectively. Sequences of amplicons were almost the same. Restriction fragment length polymorphism (RFLP) analysis of the nested 1.2-kb 16S rDNA products with AluI, MseI, HhaI, HpaI, RsaI, HinfI, and TaqI endonucleases (2) indicated that all symptomatic plants were infected by a phytoplasma belonging to aster yellows group (16SrI) subgroup C (16SrI-C) ‘Candidatus Phytoplasma asteris’. None of the symptomless plants tested positive. Nucleotide sequence analysis of cloned 16S rDNA (GenBank Accession No. FJ179166) confirmed the results on the basis of RFLP analyses. Subsequently, the presence of the phytoplasmas in symptomatic plants was also confirmed by transmission electron microscopy. To our knowledge, this is the first molecular evidence of the presence of a phytoplasma associated with a yellows-type disease of willows in northern China and its association with aster yellow group 16SrI, subgroup 16SrI-C. References: (1) D. E. Gundersen and I.-M. Lee. Phytopathol. Mediterr. 35:144, 1996. (2) I.-M. Lee et al. Inst. J. Syst. Bacteriol. 48:1153, 1998. (3) Y. Qi et al. Biotechnol. Bull. 4:44, 2004.
First Report of Laurel Wilt Disease Caused by Raffaelea lauricola on Camphor in Florida and Georgia
Authors: Smith J. A. , Mount L. , Mayfield A. E. , Bates C. A. , Lamborn W. A. , Fraedrich S. W. 
Published: January 2009

Laurel wilt is a recently described (1) vascular disease of redbay (Persea borbonia (L.) Spreng) and other plants in the family Lauraceae. The wilt is caused by Raffaelea lauricola, a fungus vectored by the nonnative redbay ambrosia beetle (Xyleborus glabratus Eichhoff) (1,2). Since 2003, laurel wilt has caused widespread mortality of redbay in Georgia, South Carolina, and Florida (1) and has recently been found on avocado in Florida (4). Since June of 2007, wilted shoots and branch dieback have been observed in several camphor trees (Cinnamomum camphora (L.) Sieb.) in residential areas of McIntosh and Glynn counties in Georgia and Baker County in Florida. Symptomatic camphor trees ranged from 4.5 to 12 m high and occurred in areas where redbay mortality due to laurel wilt has been frequently observed during the last 2 to 3 years. In some camphor trees, only the smaller branches (<2 cm in diameter) were wilting or dead, whereas in other trees (e.g., Baker County, Florida), the larger branches and substantial portions of the crown were also symptomatic. Rapid wilt that affects entire trees that is usually observed in redbay, has not been observed in camphor. Some camphor trees in residential areas of Jekyll Island, Georgia (Glynn County), where extensive wilt of redbay has occurred, have exhibited only localized wilt of some shoots or branches and other camphors remain asymptomatic. Removal of bark from wilted branch sections revealed black-to-brownish staining in the sapwood, characteristic of laurel wilt. Although no evidence of ambrosia beetles was observed on these samples, more extensive surveys are needed to determine the role of this vector in laurel wilt of camphor. Wood chips from symptomatic areas of branches were surface sterilized and plated on cycloheximide-streptomycin malt agar as previously described (1,4) and R. lauricola was routinely isolated. Small subunit (18S) sequences from rDNA were amplified by PCR and sequenced using primers NS1 and NS4 (3). BLASTn searches revealed homology to R. lauricola C2203 (GenBank Accession No. EU123076, 100% similarity, e-value of 0.0, and a total score of 1,886). The small subunit rDNA sequence for this isolate has been deposited into GenBank ( http://www.ncbi.nlm.nih.gov/Genbank/index.html ) and has been assigned Accession No. EU 853303. The presence of laurel wilt in camphor provides an opportunity to understand the pathogen distribution and possible resistance mechanisms in this host, which could have implications for efforts to remediate the impacts of the disease in redbay and other species in the Lauraceae in the southeastern United States. References: (1) S. W Fraedrich et al. Plant Dis. 92:215, 2008. (2) T. C. Harrington et al. Mycotaxon 104:399, 2008. (3) M. A. Innis et al. PCR Protocols, A Guide to Methods and Applications. Academic Press. San Diego, CA, 1990. (4) A. E. Mayfield, III et al. Plant Dis. 92:976, 2008.
First Report of Downy Mildew Caused by a Peronospora sp. on Basil in Florida and the United States
Authors: Roberts P. D. , Raid R. N. , Harmon P. F. , Jordan S. A. , Palmateer A. J. 
Published: January 2009

Basil is grown as a specialty crop in greenhouse and field production in Florida and other regions of the United States. Downy mildew on basil (Ocimum basilicum) was detected from four production sites (Collier, Hendry, Miami-Dade, and Palm Beach counties) in south Florida in the fall of 2007, and within months, it was also found in west-central north Florida (Hillsborough County). Incidence reached nearly 100% on some of the affected crops and caused complete yield losses on basil grown both in the field for fresh market and potted herbs market. Symptoms developed during transit on basil that appeared symptomless at harvest. Symptoms initially appeared as yellowing on the lower leaves that was typically delineated by the veins, although in some cases the entire leaf area of the leaf surface was affected. A gray, fuzzy growth was apparent on the abaxial leaf surface. Microscopic observation detected dichotomous branching, hyaline sporangiophores (220 to 750 × 4 to 9 μm) bearing single sporangia. Sporangia were light brown, ovoid to slightly ellipsoid, and measured 14 to 15 × 15 to 18 μm. Oospores were not observed. Leaves of potted basil plants and coleus (Solenostemon scutellarioides) were inoculated with a suspension containing 1 × 105 sporangia/ml and sprayed till runoff (approximately 15 ml per plant) with a hand-held pressurized aerosol canister. Plants were covered with a plastic bag for 24 h and maintained in the greenhouse under ambient conditions. Noninoculated plants served as controls. After 7 days, symptoms typical of downy mildew occurred only on the inoculated basil plants and sporulation was confirmed microscopically. The internal transcribed spacer regions of an isolate collected in Hendry County were sequenced bidirectionally. The consensus sequence was deposited into GenBank (Accession No. FJ346561). Sequence data matched (100% homology) with a Peronospora sp. reported on sweet basil in Switzerland (GenBank Accession No. AY884605) and was similar (99% homology) to an isolate (GenBank Accession No. DQ523586) reported on coleus, although inoculation to coleus failed to confirm pathogenicity on this host. The sequence data also distinguished the isolate from P. lamii (87% homology) previously reported to occur on basil. The pathogen was identified as a Peronospora sp. based on morphological characteristics and sequencing homology (1–3). References: (1) L. Belbahri et al. Mycol. Res. 109:1276, 2005. (2) S. Francis. CMI Descriptions of Pathogenic Fungi and Bacteria. No. 688. CMI, Kew, England, 1981. (3) A. McLeod et al. Plant Dis. 90:1115, 2006.
First Report of Fusarium solani Causing Wilt of Olea europaea in Nepal
Authors: Vettraino A. M. , Shrestha G. P. , Vannini A. 
Published: January 2009

Leaf drop, wilt, and mortality were observed in September of 2007 on approximately 10% of 1- to 2-year-old olive (Olea europaea cv. Leccino) plants shipped from Europe and growing in a nursery in the District of Makwampur, Nepal. Roots of symptomatic and asymptomatic plants were disinfected in 1% NaOCl, cut into 1 cm long pieces, plated on 2% potato dextrose agar, and maintained at 20°C with 14 h of light per day. Colonies with white mycelium developed after 3 days. Microconidia and three-septated macroconidia averaged 11 × 3.9 μm and 38 × 5 μm, respectively. Chlamydospores were produced singly and in pairs. On the basis of culture characteristics, the fungus was identified as Fusarium solani (2). The ITS1-5.8S-ITS2 DNA sequences of 10 monoconidial cultures shared 99% identity with F. solani strains available on the NCBI databases (GenBank Accession Nos. 1115947 and 1115999). Pathogenicity tests were conducted with F. solani isolates NR1 and NR2 obtained from symptomatic plants. Twelve-month-old rooted cuttings of O. europaea cv. Leccino were transferred to pots containing a soilless mix and F. solani-infected oat grains (10:1 vol/vol). Fifteen plants of each F. solani isolate were inoculated. Noninfested sterilized oat grains were used for the control treatment. Symptoms on inoculated plants included leaf abscission followed by wilting and plant death approximately 10 days after inoculation and resembled those observed on the naturally infected plants. Noninoculated control plants remained healthy. The fungus was reisolated from roots of symptomatic tissues and was identical in appearance to the isolates used to inoculate the plants. No colonies of F. solani were isolated from noninoculated plants. F. solani has been reported as weakly pathogenic on olive in Spain (4) and highly aggressive on olive in Argentina (1) and India (3). To our knowledge, this is the first report of F. solani causing wilt and mortality of young olive plants in Nepal. References: (1) S. Babbit et al. Plant Dis. 86:326, 2002. (2) C. Booth. Fusarium Laboratory Guide to the Identification of the Major Species. CMI, Kew, England, 1977. (3) R. L. Munjal et al. Studies on diseases of olive in Himachal Pradesh. Page 437 in: Improvement of Forest Biomass. Symposium Proceedings. Indian Society of Tree Scientists. P. K. Kosla, ed. Sdan, India, 1982. (4) M. E. Sánchez Hernández et al. Eur. J. Plant Pathol. 104:347, 1998.