bluuebunny/crossref_metadata_2025_split huggingface dataset:
Light dependency of nitrogen fixation in a coastal cyanobacterial mat
Authors: Severin Ina , Stal Lucas J 
Published: June 2008

Abstract
The fixation of nitrogen in cyanobacterial mats situated along the littoral gradient on a Dutch barrier island was investigated by using a high-resolution online, near-real-time acetylene reduction assay. Light-response curves of nitrogenase activity yielded a variety of physiological parameters that changed during a day–night cycle. The fitted parameters were used to calculate nitrogen fixation from the incident natural irradiance over several days in two different mat types. Mats occurring in the higher regions of the littoral were composed of a diverse community of cyanobacteria, consisting of both heterocystous and non-heterocystous filamentous species, whereas closer to the low water mark the mats contained mainly non-heterocystous filamentous cyanobacteria. Although the daily cycles of nitrogenase activity differed considerably between the two types of mats, the daily integrated rates of nitrogen fixation were the same. Moreover, the daily integrated nitrogen fixation seemed to be independent from the daily incident photon flux. The measurements further suggest that different types of diazotrophic cyanobacteria become active at different times of the day and that the composition of the mat community affects maximal and daily patterns of nitrogenase activity. Notwithstanding the apparent light independence of nitrogen fixation, the light-response curves as well as light action spectra unequivocally showed that cyanobacteria were the predominant nitrogen-fixing organisms in these mats. It is concluded that the diversity of nitrogen-fixing cyanobacteria leads to an optimization of this process.
Factors Associated With Diagnostic Evaluation for Tuberculosis Among Adults Hospitalized for Clinical Pneumonia in Thailand
Authors: Weber Ann M. , Areerat Peera , Fischer Julie E. , Thamthitiwat Somsak , Olsen Sonja J. , Varma Jay K. 
Published: June 2008

Objective.Thailand is one of 22 countries designated by the World Health Organization as “high burden” with regard to tuberculosis. Preventing nosocomial tuberculosis transmission remains an important, unmet need. We investigated the adequacy of current practices to evaluate hospitalized patients for tuberculosis, which is critical in preventing delayed diagnosis and nosocomial tuberculosis transmission.Methods.Thailand conducts active, population-based surveillance for pneumonia in 2 rural provinces. Case report forms are completed for all persons who are hospitalized and meet a case definition of having clinical pneumonia. We analyzed how frequently patients had an adequate diagnostic evaluation for infectious pulmonary tuberculosis, in accordance with national guidelines. We conducted multivariate analyses to determine patient and health-system factors associated with an inadequate diagnostic evaluation for tuberculosis and with tuberculosis disease.Results.Of 8,853 cases of clinical pneumonia between September 2003 and March 2006,73% were in patients not adequately evaluated for tuberculosis. Acid-fast bacilli (AFB)–positive tuberculosis was diagnosed in 188 cases, which was 2% of all pneumonia cases and 12% of pneumonia cases in patients adequately evaluated for tuberculosis. Diagnostic evaluations for tuberculosis were less commonly performed among those who were younger than 25 years of age, were female, and lacked cough, sputum production, hemoptysis, and dyspnea. Among patients adequately evaluated, a clinical syndrome of no cough, no hemoptysis, and normal chest radiography findings had a 95% negative predictive value.Conclusions.The prevalence of AFB-positive, pulmonary tuberculosis was high among adults hospitalized with clinical pneumonia in Thailand. Most patients were not adequately evaluated for tuberculosis. Efforts are needed to improve identification and diagnosis of infectious tuberculosis cases in hospitalized patients.
Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models
Authors: Poon Art F. Y. , Lewis Fraser I. , Frost Simon D. W. , Kosakovsky Pond Sergei L. 
Published: June 2008

Abstract
Spidermonkey is a new component of the Datamonkey suite of phylogenetic tools that provides methods for detecting coevolving sites from a multiple alignment of homologous nucleotide or amino acid sequences. It reconstructs the substitution history of the alignment by maximum likelihood-based phylogenetic methods, and then analyzes the joint distribution of substitution events using Bayesian graphical models to identify significant associations among sites.
Availability: Spidermonkey is publicly available both as a web application at http://www.data-monkey.org and as a stand-alone component of the phylogenetic software package HyPhy, which is freely distributed on the web (http://www.hyphy.org) as precompiled binaries and open source.
Contact: afpoon@ucsd.edu
Development and validation of a mismatch amplification mutation PCR assay to monitor the dissemination of an emerging variant of Vibrio cholerae O1 biotype El Tor
Authors: Morita Masatomo , Ohnishi Makoto , Arakawa Eiji , Bhuiyan N.A. , Nusrin Suraia , Alam Munirul , Siddique A.K. , Qadri Firdausi , Izumiya Hidemasa , Nair G. Balakrish , Watanabe Haruo 
Published: June 2008

ABSTRACTA mismatch amplification mutation PCR assay was developed and validated for rapid detection of the biotype specific cholera toxin B subunit of V. cholerae O1. This assay will enable easy monitoring of the spread of a new emerging variant of the El Tor biotype of V. cholerae O1.
Microsatellite analysis reveals high genetic diversity but low genetic structure in Ethiopian indigenous cattle populations
Authors: Dadi H. , Tibbo M. , Takahashi Y. , Nomura K. , Hanada H. , Amano T. 
Published: June 2008

SummaryEthiopian cattle are under threat from uncontrolled mating practices and are at high risk of becoming genetically homogeneous. Therefore, to evaluate genetic diversity, population structure and degree of admixture, 30 microsatellite markers were genotyped using 351 DNA samples from 10 Ethiopian cattle populations and the Holstein breed. The mean number of alleles per cattle population ranged from 6.93 ± 2.12 in Sheko to 7.50 ± 2.35 in Adwa. The mean observed and expected heterozygosities were 0.674 ± 0.015 and 0.726 ± 0.019 respectively. Ethiopian cattle populations have maintained a high level of within‐population genetic differentiation (98.7%), the remainder being accounted for by differentiation among populations (1.3%). A highly significant deficiency in heterozygotes was detected within populations (FIS = 0.071; P < 0.001) and total inbreeding (FIT = 0.083; P < 0.001). The study populations were highly admixed but distinct from pure Bos taurus and Bos indicus breeds. The various levels of admixture and high genetic diversity make Ethiopian cattle populations suitable for future genetic improvement and utilization under a wide range of agro‐ecologies in Ethiopia.
A high‐resolution comparative radiation hybrid map of ovine chromosomal regions that are homologous to human chromosome 6 (HSA6)
Authors: Wu C. H. , Nomura K. , Goldammer T. , Hadfield T. , Dalrymple B. P. , McWilliam S. , Maddox J. F. , Womack J. E. , Cockett N. E. 
Published: June 2008

SummaryIn this study, we constructed high‐resolution radiation hybrid (RH) and comparative maps of ovine chromosomes or chromosomal segments that are homologous to human chromosome 6 (HSA6). A total of 251 markers were successfully genotyped across the recently developed USUoRH5000 whole‐genome panel; 208 of these markers were assigned to five RH linkage groups distributed on three ovine chromosomes (OAR8, 9 and 20). The RH maps have good correspondence with previous chromosome painting data, although a small centromeric region on OAR9 that is homologous to HSA6 had not been previously detected using human chromosome paints on ovine chromosomal spreads. High percentages of the ovine markers were identified as orthologues in the bovine (86.3%), dog (85.8%), horse (69.3%) and human (88.7%) genomes. These maps contribute to investigations in mammalian chromosome evolution and the search for economic trait loci in sheep.
Early season herbivore differentially affects plant defence responses to subsequently colonizing herbivores and their abundance in the field
Authors: POELMAN ERIK H. , BROEKGAARDEN COLETTE , VAN LOON JOOP J. A. , DICKE MARCEL 
Published: June 2008

AbstractInduction of plant defences by early season herbivores can mediate interspecific herbivore competition. We have investigated plant‐mediated competition between three herbivorous insects through studies at different levels of biological integration. We have addressed (i) gene expression; (ii) insect behaviour and performance under laboratory conditions; and (iii) population dynamics under field conditions. We studied the expression of genes encoding a trypsin inhibitor and genes that are involved in glucosinolate biosynthesis in response to early season herbivory by Pieris rapae caterpillars in Brassica oleracea plants. Furthermore, we studied the interaction of these transcriptional responses with responses to secondary herbivory by the two specialist herbivores, P. rapae and Plutella xylostella, and the generalist Mamestra brassicae. P. rapae‐induced responses strongly interacted with plant responses to secondary herbivory. Sequential feeding by specialist herbivores resulted in enhanced or similar expression levels of defence‐related genes compared to primary herbivory by specialists. Secondary herbivory by the generalist M. brassicae resulted in lower gene expression levels than in response to primary herbivory by this generalist. Larval performance of both specialist and generalist herbivores was negatively affected by P. rapae‐induced plant responses. However, in the field the specialist P. xylostella was more abundant on P. rapae‐induced plants and preferred these plants over undamaged plants in oviposition experiments. In contrast, the generalist M. brassicae was more abundant on control plants and preferred undamaged plants for oviposition. P. rapae did not discriminate between plants damaged by conspecifics or undamaged plants. Our study shows that early season herbivory differentially affects transcriptional responses involved in plant defence to secondary herbivores and their population development dependent upon their degree of host plant specialization.
A comparison of grain‐size analysis methods for sand‐dominated fluvial sediments
Authors: CHEETHAM MICHAEL D. , KEENE ANNABELLE F. , BUSH RICHARD T. , SULLIVAN LEIGH A. , ERSKINE WAYNE D. 
Published: June 2008

AbstractGrain‐size distribution is a fundamental tool for interpreting sedimentary units within depositional systems. The techniques assessed in this study are commonly used to determine grain‐size distributions for sand‐dominated sediments. However, the degree of consistency and differences in interpretation when using a combination of grain‐size methods have not yet been assessed systematically for sand‐dominated fluvial sediments. Results obtained from laser diffraction, X‐ray attenuation and scanning electron microscopy grain‐size analysis techniques were compared with those obtained from the traditional sieve/hydrometer method. Scanning electron microscopy was shown to provide an inaccurate quantitative analysis of grain‐size distributions because of difficulties in obtaining representative samples for examination. The X‐ray attenuation method is unsuitable for sand‐dominated sediments because of its upper size range of only 300 μm. The consistently strong correlation between the laser diffraction results and the sieve/hydrometer results shows that these methods are comparable for sand‐dominated fluvial sediments. Provided that sample preparation is consistent, the latter two methods can be used together within a study of such sediments while maintaining a high degree of accuracy. These results indicate that data for sand‐dominated fluvial sediments gained from the long‐established sieve/hydrometer method can be compared with confidence to those obtained by modern studies using laser diffraction techniques.
The interaction between Cistaceae and a highly specific seed‐harvester ant in a Mediterranean scrubland
Authors: Bastida F. , Talavera S. , Ortiz P. L. , Arista M. 
Published: June 2008

AbstractWe studied the interaction between the ant Goniomma kugleri and Cistaceae in a Cistus ladanifer‐dominated scrubland, in southwestern Spain. We monitored seed harvesting, and studied ant preferences among Cistaceae seeds and their capture efficiencies for preferred seeds. For the stand of C. ladanifer, we estimated seed losses due to the ants. Harvesting was restricted to two seasons: mid‐autumn to late winter, and late spring. Ant diet relied on Cistaceae seeds: during autumn and winter 90% of seeds returned to nests were of C. ladanifer, and the remaining fraction also comprised Cistaceae seeds. At this time, the ants harvested seeds directly from the plants. In late spring, the ant diet consisted of Tuberaria guttata s.l. seeds. Goniomma kugleri selectively collected Cistaceae seeds. For preferred species, seed removal rates at the colony level and seed capture times invested by individual workers were correlated with seed size. Because of shorter capture time and higher success frequency, capture efficiency in terms of number of seeds captured per unit time was higher for small‐seeded species. Although each ant colony collected large numbers (up to 105) of C. ladanifer seeds over the autumn–winter season, the impact of ant removal on the annual seed output was moderate, at around 20%. It is likely that, in C. ladanifer, the staggered seed release period, and the pulsed exposure of seed clumps in capsules through progressive locule dehiscence, effectively minimise seed losses to the ants.
VASCULAR DYSFUNCTION IN THE α‐GALACTOSIDASE A‐KNOCKOUT MOUSE IS AN ENDOTHELIAL CELL‐, PLASMA MEMBRANE‐BASED DEFECT
Authors: Park James L , Whitesall Steven E , D’Alecy Louis G , Shu Liming , Shayman James A 
Published: June 2008

SUMMARY

Fabry disease results from an X‐linked mutation in the lysosomal α‐galactosidase A (Gla) gene. Defective Gla results in multi‐organ accumulation of neutral glycosphingolipids (GSLs), especially in the vascular endothelium, with the major GSL accumulated being globotriaosylceramide (Gb3). Excessive endothelial Gb3 accumulation is associated with increased thrombosis, atherogenesis and endothelial dysfunction. However, the mechanism(s) by which endothelial dysfunction occurs is unclear. The purpose of the present study was to further characterize the vasculopathy associated with a murine model of Fabry disease.
Vascular reactivity was performed in vessels from wild‐type (Gla+/0) and Gla‐knockout (Gla−/0) mice. Conscious blood pressure and heart rate were measured in Gla+/0 and Gla−/0 mice by telemetry.
The present study demonstrates that vascular smooth muscle (VSM) contractions to phenylephrine and serotonin, but not to U46619, were blunted in Gla−/0 mice. Endothelium‐dependent contraction and receptor‐mediated endothelium‐dependent relaxation to acetylcholine were significantly attenuated in vessels from Gla−/0 mice. However, receptor‐independent endothelium‐dependent relaxation to the calcium ionophore ionomycin remained intact in vessels from Gla−/0 mice. Furthermore, VSM reactivity was normal in aortas from Gla−/0 mice in the absence of endothelium. These changes in vascular function were observed without changes in whole‐animal blood pressure or heart rate.
These results suggest that the vasculopathy associated with Fabry disease is localized to the endothelium, despite the accumulation of GSLs throughout the vasculature.
ASSOCIATION BETWEEN PPARGC1A GENE POLYMORPHISMS AND CORONARY ARTERY DISEASE IN A CHINESE POPULATION
Authors: Zhang Yan , Xu Weiwei , Li Xiaoyu , Tang Yibo , Xie Peng , Ji Yong , Fan Leming , Chen Qi 
Published: June 2008

SUMMARY

Peroxisome proliferrator‐activated receptor γ coactivator‐1α (PGC‐1α; PPARGC1A) is a coactivator of the nuclear hormone receptor family that participates in the transcriptional programme of lipid metabolism and oxidative stress implicated in atherogenesis. Therefore, in the present study, we investigated PPARGC1A polymorphisms in the prevalence of coronary artery disease (CAD).
A case‐control study comprising 342 patients with CAD and 334 controls was performed in a Chinese population. Two single nucleotide polymorphisms (Gly482Ser and Thr394Thr) in the PPARGC1A gene were genotyped and compared using the polymerase chain reaction–restriction fragment length polymorphism method.
The XA (GA + AA) genotype of Gly482Ser displayed a higher frequency in CAD patients than that in control subjects (P = 0.019; adjusted odds ratio = 1.53; 95% confidence interval 1.06–2.20). No significant difference in Thr394Thr genotype distribution or in Gly482Ser–Thr394Thr haplotype combinations was found between CAD patients and controls. Furthermore, we found that the significantly increased risk of CAD associated with the XA genotypes of Gly482Ser was more evident among subjects who were younger than 64 years of age, female, overweight and with hypertension.
The results indicate that the PPARGC1A Gly482Ser polymorphism may contribute to the risk of CAD in the Chinese population investigated.
A NOVEL HIGH‐THROUGHPUT ASSAY FOR THE QUANTITATIVE ASSESSMENT OF RECEPTOR TRAFFICKING
Authors: Grimsey Natasha L , Narayan Pritika J , Dragunow Mike , Glass Michelle 
Published: June 2008

SUMMARYReceptor transport between intracellular compartments has important consequences for receptor function and is an exciting area of current study. Existing methods for studying receptor trafficking often require labour‐intensive techniques or are difficult to quantify reliably. We report a novel high‐throughput method that uses automated imaging and analysis tools to accurately quantify cannabinoid CB1 receptor trafficking.Haemagglutinin (HA)‐tagged CB1 was stably expressed in HEK‐293 cells and cell surface or total receptors were detected immunocytochemically. Images of receptor and nuclear staining were acquired with an automated fluorescent microscope (Discovery‐1; Molecular Devices, Sunnyvale, CA, USA) and quantified at high throughput with MetaMorph (Molecular Devices) software. The ‘Granularity’ assay measured internalization by counting receptor clusters that appear during receptor endocytosis, a well‐established approach. Our assay, referred to as ‘Total Grey Value per Cell’ (TGVC), measures the total fluorescence above background, normalized to cell count.Incubation with the cannabinoid agonist HU‐210 (100 nmol/L) resulted in rapid CB1 internalization, reaching a maximum within 20 min. Whether quantified by Granularity or TGVC, the time‐course of endocytosis could be modelled with exponentially derived curves and with similar half‐lives. We demonstrate the sensitivity of our TGVC method by measuring the concentration dependence of CB1 internalization and its versatility by measuring downregulation following chronic agonist exposure, whereby total CB1 was reduced to approximately 55% of basal after 3 h.The TGVC quantification method described is efficient, accurate and versatile and is likely to provide a valuable tool in receptor trafficking studies.
Lessons from a review of thyroglobulin assays in the management of thyroid cancer
Authors: Wong J. , Lu Z. , Doery J. , Fuller P. 
Published: June 2008

AbstractThyroglobulin (Tg) measurement has become increasingly an important and integral part of the follow up and management of patients with differentiated thyroid cancer. Clinicians predominantly rely on Tg for decision‐making for surveillance of patients with differentiated thyroid cancer, but despite this new reliance, issues regarding Tg measurement have not been appropriately addressed especially within a local context. In the process of developing an institutional protocol we have identified that there are significant clinical and technical issues regarding Tg measurement, and surprisingly Tg assessment is currently not part of an external quality control programme. We conducted a small pilot study to specifically emphasize some of the assay issues. We aim to inform endocrinologists, pathologists and nuclear medicine physicians, the need and urgency for these issues to be addressed to improve the ongoing surveillance of differentiated thyroid cancer.
Expression of functional Toll‐like receptors and nucleotide‐binding oligomerization domain proteins in murine cementoblasts and their upregulation during cell differentiation
Authors: Nemoto E. , Honda T. , Kanaya S. , Takada H. , Shimauchi H. 
Published: June 2008

Background and Objective:  While the primary role of cementoblasts is to synthesize the components of cementum, we have reported that immortalized murine cementoblasts (OCCM‐30) express functional Toll‐like receptor (TLR)‐2 and ‐4, and these receptors are involved in the alteration of gene expression associated with cementum formation and in the upregulation of osteoclastogenesis‐associated molecules, such as receptor activator of nuclear factor‐κB (NF‐κB) ligand. We hypothesized that cementoblasts express a wide range of pattern recognition receptors in a manner comparable to osteoblasts, which are known to express various functional TLRs and nucleotide‐binding oligomerization domain (NOD) proteins.Material and Methods:  Murine cementoblasts and pre‐osteoblasts were used. The gene and protein levels of TLRs/NODs were analyzed using real‐time polymerase chain reaction and flow cytometry. Interleukin‐6 (IL‐6) and activated NF‐κB were measured using enzyme‐linked immunosorbent assay.Results:  The expressions of TLR‐1, ‐2, ‐4, ‐6 and ‐9, CD14, NOD‐1 and ‐2 were detected in cementoblasts and were upregulated upon differentiation induced by ascorbic acid. Similar patterns were observed in the mouse MC3T3‐E1 osteoblast cell line. Synthetic ligands, Pam3CSK4 (TLR‐1/2 agonist), Pam2CGDPKHPKSF (TLR‐2/6 agonist), lipid A (TLR4 agonist), CpG DNA (TLR‐9 agonist), FK565 (NOD1 agonist) and muramyldipeptide (NOD2 agonist), effectively induced NF‐κB activation in cementoblasts and/or ascorbic acid‐treated cementoblasts. Furthermore, these ligands induced IL‐6 production in a NF‐κB‐dependent manner in cementoblasts and/or ascorbic acid‐treated cementoblasts.Conclusion:  These results indicate that cementoblasts possess functional TLR and NOD signaling systems and have a similar capacity to osteoblasts in responding to a wide variety of pathogens.
Isolation and characterization of microsatellite markers in Oligoryzomys longicaudatus (Muridae, Sigmodontinae, Oryzomini), the natural reservoir of genotype Andes hantavirus
Authors: GONZÁLEZ‐ITTIG RAÚL E. , SALAZAR‐BRAVO JORGE , POLOP JAIME J. , GARDENAL CRISTINA N. 
Published: June 2008

AbstractThe rodent Oligoryzomys longicaudatus or long‐tailed pygmy rice rat is the reservoir of the aetiological agent of the hantavirus pulmonary syndrome in southern Argentina and Chile. We characterize 11 polymorphic microsatellite loci which would be useful for studies on microgeographical population structure in the species. Amplification of these loci in 42 individuals from four natural populations revealed four to 21 alleles per locus, and values of observed heterozygosities ranging from 0.371 to 0.896. Cross‐species amplifications showed that some of the primers designed may be useful for other species of the genus Oligoryzomys.