Home About us Contact
|
Home About us Contact | ||
|
|
||
Analysis Alone (analysis + alone)
Selected AbstractsCarbon source accounting for fish using combined DNA and stable isotope analyses in a regulated lowland river weir poolMOLECULAR ECOLOGY, Issue 1 2010CHRISTOPHER M. HARDY Abstract Determining the source and flow of carbon, energy and nutrients through food webs is essential for understanding ecological connectivity and thus determining the impact of management practices on biodiversity. We combined DNA sequencing, microarrays and stable isotope analyses to test whether this approach would allow us to resolve the carbon flows through food webs in a weir pool on the lower Murray River, a highly impacted, complex and regulated ecosystem in southern Australia. We demonstrate that small fish in the Murray River consume a wide range of food items, but that a significant component of carbon and nitrogen entering the food web during dry periods in summer, but not spring, is derived from nonconventional sources other than in-channel primary producers. This study also showed that isotopic analyses alone cannot distinguish food sources and that a combined approach is better able to elucidate food-consumer dynamics. Our results highlight that a major river ecosystem, stressed by reduced environmental flows, can rapidly undergo significant and previously undetected changes that impact on the ecology of the system as a whole. [source] Myotonic dystrophy type 2EUROPEAN JOURNAL OF NEUROLOGY, Issue 5 2002J. Finsterer Myotonic dystrophy type 2 (DM2) is a clinically but not genetically heterogeneous, multisystem disorder, that is clinically similar to, but distinct from myotonic dystrophy type 1 (DM1). Initially, different phenotypes of DM2 were described by Ricker (proximal myotonic myopathy, PROMM), Ranum (myotonic dystrophy 2, DM2) and Udd (proximal myotonic dystrophy, PDM). Clinical features these three phenotypes had in common were diffuse, proximal or distal weakness, wasting, myotonia, cataract, cerebral, endocrine and cardiac abnormalities. Initially, the clinical differences between DM1 and PROMM seemed unmistakable, but meanwhile it has become apparent that the clinical differences between these entities are blurring. In 1999, Day et al., Meola et al. and Ricker et al. mapped the mutated gene of all three phenotypes to chromosome 3q. In 2001, the three different phenotypes were found to rely on the same mutation in the ZNF9 gene on chromosome 3q21.3. Although DM2 may be clinically heterogeneous, it is by result of a mutation in a single gene. The mutation responsible for DM2 is a CCTG-repeat expansion of 75,11 000 repeats in intron 1 of the ZNF9 gene on chromosome 3q21.3. Because of the clinical heterogeneity, the diagnosis of DM2 should rely on DNA analysis alone. [source] Influence of fault map resolution on pore pressure distribution and secondary hydrocarbon migration; Tune area, North SeaGEOFLUIDS (ELECTRONIC), Issue 2 2006A. E. LOTHE Abstract Pressure and hydrocarbon migration modelling was carried out in the Tune Field area, Viking Graben, offshore Norway. The pressures are considered to be controlled by compartments bounded by mapped faults. Two different interpreted fault maps at the top reservoir level (Brent Group) are used as input to the modelling. First, a low-resolution fault map is used, with only the large faults interpreted, and next, both large and small faults are included. The simulations show high overpressures generated in the western area, in the deeper part of the Viking Graben, and hydrostatic in the eastern areas. A sharp transition zone results from using the low-resolution fault map in the simulations. Small N,S striking faults situated in between the wells have to have higher sealing capacity than expected from juxtaposition analysis alone, to be able to match the overpressures measured in well 30/5-2 and 30/8-1S in the Tune Field, and well 30/8-3 east of Tune. The intermediate pressure in the western part is probably related to flow in the deeper parts of the sedimentary column in the compartment, where well 30/8-3 is situated. The secondary oil migration models show that overpressures have major effects on the migration pathways of hydrocarbons. The level of detail in the fault interpretation is important for simulation results, both for pressure distribution and for hydrocarbon migration. [source] Identification of forty-five novel and twenty-three known NF1 mutations in Chinese patients with neurofibromatosis type 1,,HUMAN MUTATION, Issue 8 2006Ming-Jen Lee Abstract Neurofibromatosis type 1 (NF1), characterized by skin neurofibromas and an excess of café-au-lait spots, is due to mutations in the neurofibromin (NF1) gene. Identifying the genetic defect in individuals with the disease represents a significant challenge because the gene is extremely large with a high incidence of sporadic mutations across the entire gene ranging from single nucleotide substitutes to large deletions. In the present study, we have used a combination of techniques (heteroduplex analysis, sequencing, loss of heterozygosity and quantification of gene dosage) to define the genetic defect in 68 individuals from a cohort of 107 NF1 Taiwanese patients of Chinese origin. Fifty-eight were initially identified using heteroduplex analytical techniques and confirmed by sequence analysis. A further five were identified by direct sequence analysis alone. The reminders were shown to carry large deletions in the NF1 gene by demonstrating loss of heterozygosity that was confirmed by gene dosage measurements using quantitative-PCR techniques. Mis-sense, non-sense, frame-shift or splice-site mutations were identified across the entire gene of which the majority (45/68) were novel in nature. The detection rate with the various analytical techniques and the types of mutation detected are consistent with published data involving both individuals and large cohort studies from other ethnic backgrounds. © 2006 Wiley-Liss, Inc. [source] Visual Analysis or Semi-Automated Gray-Scale-Based Color Mapping of the Carotid Plaque: Which Method Correlates the Best with the Presence of Cerebrovascular Symptoms and/or Lesions on MRI?JOURNAL OF NEUROIMAGING, Issue 2 2009Isabelle Momjian MD ABSTRACT BACKGROUND AND PURPOSE To determine the correlation between carotid plaque morphology, assessed by two different ultrasonographic methods, and presence of cerebrovascular events and/or lesions on magnetic resonance imaging (MRI). PATIENTS AND METHODS Visual analysis of plaque echogenicity using a five-type classification was performed. Further, a semi-automated gray-scale-based color mapping of the whole plaque and of its surface was achieved. RESULTS There were 31 (35%) symptomatic (23 strokes and 8 transitory ischemic attacks [TIAs]) and 58 (65%) asymptomatic carotid stenoses. MRI lesions related to the carotid stenosis if located in the ipsilateral cortical, subcortical, or watershed area, were present in 27 cases (30%). In a multivariate logistic regression model, degree of stenosis (P= .03) and a predominant red color on the surface (P= .04) were independent factors associated with the presence of cerebrovascular events and/or lesions on MRI. Sensitivity and specificity were, respectively, 80% and 63% by combining degree of stenosis and color mapping of plaque surface. CONCLUSION Degree of stenosis and a predominant red color on plaque surface were independent factors associated with the presence of cerebrovascular events and/or lesions on MRI. No correlation was observed with any particular type of plaque based on visual analysis alone. [source] A NEW LYNGBYA SPECIES FROM AQUARENA SPRINGS, SAN MARCOS, TEXASJOURNAL OF PHYCOLOGY, Issue 2001Article first published online: 24 SEP 200 Mills, J. T.1 & Johansen, J. R.2 1Department of Biology, St. Edwards University, Austin, TX 78704.USA; 2Department of Biology, John Carroll University, University Heights, OH 44118 USA A large Lyngbya species was isolated from Aquarena Springs, a series of freshwater, nonmineral springs flowing from the Edwards Aquifer that are impounded to form Spring Lake. The species grows in rather large, loosely formed clumps at a depth of 2-3 meters, and consists of sheathed filaments from 55 to 60 um in thickness containing a single trichome that ranges from 45-50 um in thickness in each sheath. The sheath is 5-6um thick. Our isolate is similar to Plectonema wollei Farlow ex Gomont, a large, thick sheathed morphospecies which has recently been placed in Lyngbya wollei (Farlow ex Gomont) Onodera et al. It is also similar to Blennothrix species, another large-trichomed genus with a distinctive form of false branching. However, the Lyngbya from Aquarena Springs shows no evidence of false branching of any type, forms loose clusters rather than mats, and is larger than any of the species currently described in any of the genera in question. When we sequenced the 16SrRNA and associated 16S-23S internal transcribed spacer (ITS), phylogenetic analysis indicated the taxon was most similar to Oscillatoria sanctae. However, there are so few taxa in the Oscillatoriaceae sensu stricto that have been sequenced, phylogenetic placement of the taxon by molecular analysis alone is not possible at present. Two different ITS configurations were obtained, one with both the tRNA "Ile" gene and the tRNA "Ala" gene, the other with no tRNA genes. Our work represents the first molecular analysis of any form in the large-trichomed Lyngbya clade. [source] Mass spectrometric genomic data mining: Novel insights into bioenergetic pathways in Chlamydomonas reinhardtiiPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 23 2006Jens Allmer Abstract A new high-throughput computational strategy was established that improves genomic data mining from MS experiments. The MS/MS data were analyzed by the SEQUEST search algorithm and a combination of de novo amino acid sequencing in conjunction with an error-tolerant database search tool, operating on a 256 processor computer cluster. The error-tolerant search tool, previously established as GenomicPeptideFinder (GPF), enables detection of intron-split and/or alternatively spliced peptides from MS/MS data when deduced from genomic DNA. Isolated thylakoid membranes from the eukaryotic green alga Chlamydomonas reinhardtii were separated by 1-D SDS gel electrophoresis, protein bands were excised from the gel, digested in-gel with trypsin and analyzed by coupling nano-flow LC with MS/MS. The concerted action of SEQUEST and GPF allowed identification of 2622 distinct peptides. In total 448 peptides were identified by GPF analysis alone, including 98 intron-split peptides, resulting in the identification of novel proteins, improved annotation of gene models, and evidence of alternative splicing. [source] Array-based proteomics: mapping of protein circuitries for diagnostics, prognostics, and therapy guidance in cancerTHE JOURNAL OF PATHOLOGY, Issue 5 2006C Gulmann Abstract The human proteome, due to the enormity of post-translational permutations that result in large numbers of isoforms, is much more complex than the genome and alterations in cancer can occur in ways that are not predictable by translational analysis alone. Proteomic analysis therefore represents a more direct way of investigating disease at the individual patient level. Furthermore, since most novel therapeutic targets are proteins, proteomic analysis potentially has a central role in patient care. At the same time, it is becoming clear that mapping entire networks rather than individual markers may be necessary for robust diagnostics as well as tailoring of therapy. Consequently, there is a need for high-throughput multiplexed proteomic techniques, with the capability of scanning multiple cases and analysing large numbers of endpoints. New types of protein arrays combined with advanced bioinformatics are currently being used to identify molecular signatures of individual tumours based on protein pathways and signalling cascades. It is envisaged that analysing the cellular ,circuitry' of ongoing molecular networks will become a powerful clinical tool in patient management. Copyright © 2006 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. [source] Founder Effects for ATM Gene Mutations in Italian Ataxia Telangiectasia FamiliesANNALS OF HUMAN GENETICS, Issue 5 2009Luciana Chessa Summary We screened ATM gene mutations in 104 Italian Ataxia-Telangiectasia patients from 91 unrelated families (detection rate 90%) and found 21 recurrent mutations in 63 families. The majority (67%) of patients were compound heterozygotes, while 33% were homozygotes. To determine the existence of common haplotypes and potential founder effects, we analyzed five microsatellite markers within and flanking the ATM gene. Haplotype analysis was carried out in 48/63 families harbouring 16 of the 21 recurrent mutations. Forty different haplotypes were detected in the 48 A-T families studied. We found that the majority of patients with the same recurrent mutation originated from the same geographical area. All but one recurrent mutation analyzed displayed a common haplotype suggesting a single origin that then spread to different geographical areas. The high number of different haplotypes does not allow the screening of ATM mutations by haplotype analysis alone in the Italian population. The finding of recurrent public mutations without founder effect suggests the existence of ,mild' hot spots of mutation located along the sequence of the ATM gene. [source] Metabonomic profiling of liver metabolites by gas chromatography,mass spectrometry and its application to characterizing hyperlipidemiaBIOMEDICAL CHROMATOGRAPHY, Issue 3 2010Shenghua Gu Abstract The measurement of metabolites in tissues is of great importance in metabonomic research in the biomedical sciences, providing more relevant information than is available from systemic biofluids. The liver is the most important organ/tissue for most biochemical reactions, and the metabolites in the liver are of great interest to scientists. To develop an optimized extraction method and comprehensive profiling technique for liver metabolites, organic solvents of various compositions were designed using design of experiments to extract metabolites from the liver, and the metabolites were profiled by gas chromatography/time-of-flight mass spectrometry (GC/TOF-MS). The resolved peak areas were processed by principle components analysis, partial least-squares projections to latent structures, and discriminant analysis. The results suggest the highest extraction efficiency was for methanol,water, which maximized the majority of GC/TOF-MS responses. The optimal solvent was applied to extract metabolites in liver of hyperlipidemia hamster and the control. The GC/TOF-MS profiles of liver metabolites showed obvious differences between hyperlipidemic hamsters and controls. A comparison of liver and serum data from the same animals identified common biomarkers and presented complementary information. Our results suggest that liver metabonomics is a valuable technique and that the combined analysis of systematic biofluids and local tissues is meaningful and complementary, recovering more comprehensive metabonomic data than either analysis alone. Copyright © 2009 John Wiley & Sons, Ltd. [source] Deep-seated, well differentiated lipomatous tumors of the chest wall and extremitiesCANCER, Issue 2 2005The role of cytogenetics in classification, prognostication Abstract BACKGROUND Intramuscular lipomas and atypical lipomatous tumors (ALT) are common deep-seated lipomatous tumors of the chest wall and extremities. Distinguishing between these two entities can be difficult based on histologic analysis alone. However, the cytogenetic profiles of ALT and intramuscular lipomas are distinct. Correct classification is important, because aggressive local disease recurrence occurs more frequently in patients with ALT than in patients with intramuscular lipoma. The authors examined their single institutional experience and correlated their classification with clinical features and outcome. METHODS In the current study, 106 patients with deep-seated, well differentiated adipose tumors of the chest wall and extremities were classified as having ALT or intramuscular lipoma using a combined approach of histology and cytogenetics, if available. The classification was correlated with clinicopathologic features and follow-up data. RESULTS Fifty-five patients were classified as having intramuscular lipoma and 51 were classified as having ALT. Classification did not correlate with age and gender (P = 0.28 and P = 0.96, respectively). Intramuscular lipomas were smaller than ALTs (P < 0.0001), but there was significant overlap between the 2 groups. ALT occurred preferentially in the lower extremity (P < 0.0009). Four percent of patients with intramuscular lipomas and 27% of patients with ALTs developed local disease recurrence (P = 0.0006). Disease recurrence did not correlate with patient age at diagnosis, patient gender, tumor size, and tumor location (P = 0.45, P = 0.26, P = 0.49, and P = 0.28, respectively). Within the subset of patients with ALTs, disease recurrence did not correlate with patient age at diagnosis, patient gender, or tumor location (P = 0.38, P = 0.54, and P = 0.86, respectively). CONCLUSIONS Classification of deep-seated, well differentiated lipomatous tumors of the extremities and chest wall using a combined approach of histology and cytogenetics correlated well with biologic behavior/disease recurrence. This combined approach is advocated to better stratify patients for treatment purposes and follow-up. Cancer 2005. © 2004 American Cancer Society. [source] | ||||||||||||||||