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991.
FM You KR Deal J Wang MT Britton JN Fass D Lin A Dandekar CA Leslie M Aradhya MC Luo J Dvorak 《BMC genomics》2012,13(1):354
ABSTRACT: BACKGROUND: A genome-wide set of single nucleotide polymorphisms (SNPs) is a valuable resource in genetic research and breeding and is usually developed by re-sequencing a genome. If a genome sequence is not available, an alternative strategy must be used. We previously reported the development of a pipeline (AGSNP) for genome-wide SNP discovery in coding sequences and other single-copy DNA without a complete genome sequence in self-pollinating (autogamous) plants. Here we updated this pipeline for SNP discovery in outcrossing (allogamous) species and demonstrated its efficacy in SNP discovery in walnut (Juglans regia L.). RESULTS: The first step in the original implementation of the AGSNP pipeline was the construction of a reference sequence and the identification of single-copy sequences in it. To identify single-copy sequences, multiple genome equivalents of short SOLiD reads of another individual were mapped to shallow genome coverage of long Sanger or Roche 454 reads making up the reference sequence. The relative depth of SOLiD reads was used to filter out repeated sequences from single-copy sequences in the reference sequence. The second step was a search for SNPs between SOLiD reads and the reference sequence. Polymorphism within the mapped SOLiD reads would have precluded SNP discovery; hence both individuals had to be homozygous. The AGSNP pipeline was updated here for using SOLiD or other type of short reads of a heterozygous individual for these two principal steps. A total of 32.6X walnut genome equivalents of SOLiD reads of vegetatively propagated walnut scion cultivar 'Chandler' were mapped to 48,661 'Chandler' bacterial artificial chromosome (BAC) end sequences (BESs) produced by Sanger sequencing during the construction of a walnut physical map. A total of 22,799 putative SNPs were initially identified. A total of 6,000 Infinium II type SNPs evenly distributed along the walnut physical map were selected for the construction of an Infinium BeadChip, which was used to genotype a walnut mapping population having 'Chandler' as one of the parents. Genotyping results were used to adjust the filtering parameters of the updated AGSNP pipeline. With the adjusted filtering criteria, 69.6% of SNPs discovered with the updated pipeline were real and could be mapped on the walnut genetic map. A total of 13,439 SNPs were discovered by BES re-sequencing. BESs harboring SNPs were in 677 FPC contigs covering 98% of the physical map of the walnut genome. CONCLUSION: The updated AGSNP pipeline is a versatile SNP discovery tool for a high-throughput, genome-wide SNP discovery in both autogamous and allogamous species. With this pipeline, a large set of SNPs were identified in a single walnut cultivar. 相似文献
992.
Katrin Knittel Andreas Lemke Heike Eilers Karin Lochte Olaf Pfannkuche 《Geomicrobiology journal》2013,30(4):269-294
Cold seep environments such as sediments above outcropping hydrate at Hydrate Ridge (Cascadia margin off Oregon) are characterized by methane venting, high sulfide fluxes caused by the anaerobic oxidation of methane, and the presence of chemosynthetic communities. Recent investigations showed that another characteristic feature of cold seeps is the occurrence of methanotrophic archaea, which can be identified by specific biomarker lipids and 16S rDNA analysis. This investigation deals with the diversity and distribution of sulfate-reducing bacteria, some of which are directly involved in the anaerobic oxidation of methane as syntrophic partners of the methanotrophic archaea. The composition and activity of the microbial communities at methane vented and nonvented sediments are compared by quantitative methods including total cell counts, fluorescence in situ hybridization (FISH), bacterial production, enzyme activity, and sulfate reduction rates. Bacteria involved in the degradation of particulate organic carbon (POC) are as active and diverse as at other productive margin sites of similar water depths. The availability of methane supports a two orders of magnitude higher microbial biomass (up to 9.6 2 10 10 cells cm m 3 ) and sulfate reduction rates (up to 8 w mol cm m 3 d m 1 ) in hydrate-bearing sediments, as well as a high bacterial diversity, especially in the group of i -proteobacteria including members of the branches Desulfosarcina/Desulfococcus , Desulforhopalus , Desulfobulbus , and Desulfocapsa . Most of the diversity of sulfate-reducing bacteria in hydrate-bearing sediments comprises seep-endemic clades, which share only low similarities with previously cultured bacteria. 相似文献
993.
Karin?Strehlow Jenny?DavisEmail author Lien?Sim Jane?Chambers Stuart?Halse David?Hamilton Pierre?Horwitz Arthur?McComb Ray?Froend 《Hydrobiologia》2005,552(1):17-31
Many rivers and wetlands in south-western Australia are threatened by salinisation due to rising saline watertables, which
have resulted from land clearing and the replacement of deep-rooted perennial species with shallow-rooted annual species.
A four to six weekly sampling program of water quality, submerged macrophytes and macroinvertebrates was undertaken at six
wetlands, from September 2002 to February 2004, to investigate seasonal variation in a range of primary and secondary saline
systems. The wetlands dried and filled at different times in response to local rainfall patterns, and salinities varied accordingly
with evapoconcentration and dilution. Two types of clear-water wetlands were recognised; those dominated by submerged aquatic
macrophytes (Ruppia, Lepilaena and Lamprothamnium) and those dominated by benthic microbial communities. Two types of turbid wetlands were also recognised; those with high
concentrations of phytoplankton and those with high concentrations of suspended sediments. A primary saline lake and two lakes
that have only recently been affected by secondary salinisation persisted in a clear, macrophyte-dominated regime throughout
most of the study period, except during drying and filling. Two lakes with a long history of secondary salinisation (70 years)
moved between regimes over the study period. A clear, benthic microbial community – dominated regime only persisted at the
wetland which contained permanent water throughout the study period. The turbid regimes were only present during drying and
refilling phases. A richer and more abundant macroinvertebrate fauna was associated with the clear, macrophyte- dominated
wetlands. Our results suggest that the development of management guidelines that recognise the presence of different ecological
regimes and that consider the interactions between water regime, salinity, and primary and secondary production will be more
useful in protecting biodiversity and ecological function in these systems than managing salinity as a single factor. 相似文献
994.
Corsin Battaglia Karin S?derstr?m Jordi Escarré Franz-Josef Haug Matthieu Despeisse Christophe Ballif 《Journal of visualized experiments : JoVE》2013,(71)
We describe a nanomoulding technique which allows low-cost nanoscale patterning of functional materials, materials stacks and full devices. Nanomoulding combined with layer transfer enables the replication of arbitrary surface patterns from a master structure onto the functional material. Nanomoulding can be performed on any nanoimprinting setup and can be applied to a wide range of materials and deposition processes. In particular we demonstrate the fabrication of patterned transparent zinc oxide electrodes for light trapping applications in solar cells. 相似文献
995.
996.
Saskia Letz Christine Haag Egbert Schulze Karin Frank-Raue Friedhelm Raue Benjamin Hofner Bernhard Mayr Christof Sch?fl 《PloS one》2014,9(12)
Introduction
Activating calcium sensing receptor (CaSR) mutations cause autosomal dominant hypocalcemia (ADH) characterized by low serum calcium, inappropriately low PTH and relative hypercalciuria. Four activating CaSR mutations cause additional renal wasting of sodium, chloride and other salts, a condition called Bartter syndrome (BS) type 5. Until today there is no specific medical treatment for BS type 5 and ADH. We investigated the effects of different allosteric CaSR antagonists (calcilytics) on activating CaSR mutants.Methods
All 4 known mutations causing BS type 5 and five ADH mutations were expressed in HEK 293T cells and receptor signalling was studied by measurement of intracellular free calcium in response to extracellular calcium ([Ca2+]o). To investigate the effect of calcilytics, cells were stimulated with 3 mM [Ca2+]o in the presence or absence of NPS-2143, ATF936 or AXT914.Results
All BS type 5 and ADH mutants showed enhanced signalling activity to [Ca2+]o with left shifted dose response curves. In contrast to the amino alcohol NPS-2143, which was only partially effective, the quinazolinone calcilytics ATF936 and AXT914 significantly mitigated excessive cytosolic calcium signalling of all BS type 5 and ADH mutants studied. When these mutants were co-expressed with wild-type CaSR to approximate heterozygosity in patients, ATF936 and AXT914 were also effective on all mutants.Conclusion
The calcilytics ATF936 and AXT914 are capable of attenuating enhanced cytosolic calcium signalling activity of CaSR mutations causing BS type 5 and ADH. Quinazolinone calcilytics might therefore offer a novel treatment option for patients with activating CaSR mutations. 相似文献997.
Xu S Schlüter PM Scopece G Breitkopf H Gross K Cozzolino S Schiestl FP 《Evolution; international journal of organic evolution》2011,65(9):2606-2620
Floral isolation is an important component of pollinator-driven speciation. However, up to now, only a few studies have quantified its strength and relative contribution to total reproductive isolation. In this study, we quantified floral isolation among three closely related, sympatric orchid species of the genus Ophrys by directly tracking pollen flow. Ophrys orchids mimic their pollinators' mating signals, and are pollinated by male insects during mating attempts. This pollination system, called sexual deception, is usually highly specific. However, whether pollinator specialization also conveys floral isolation is currently under debate. In this study, we found strong floral isolation: among 46 tracked pollen transfers in two flowering seasons, all occurred within species. Accounting for observation error rate, we estimated a floral isolation index ≥0.98 among each pair of species. Hand pollination experiments suggested that postpollination barriers were effectively absent among our study species. Genetic analysis based on AFLP markers showed a clear species clustering and very few F(1) hybrids in natural populations, providing independent evidence that strong floral isolation prevents significant interspecies gene flow. Our results provide the first direct evidence that floral isolation acts as the main reproductive barrier among closely related plant species with specialized pollination. 相似文献
998.
Using different independent procedures for assaying soluble auxin-binding in etiolated pea epicotyls, wo could prove the reliability
of the (XH4)2SO4-pelleting assay both for crude cytosols as well as for specific protein fractions obtained after chromatofocusing. Three
distinct genotypes (two parent lines, one tall recombinant) investigated so far exhibit characteristic differences with respect
to soluble auxin-binding kinetics in their cytosols. 相似文献
999.
Neuroglobin (Ngb) is a small globular protein that binds diatomic ligands like oxygen, carbon monoxide (CO) and nitric oxide
at a heme prosthetic group. We have performed FTIR spectroscopy in the infrared stretching bands of CO and flash photolysis
with monitoring in the electronic heme absorption bands to investigate structural heterogeneity at the active site of Ngb
and its effects on CO binding and migration at cryogenic temperatures. Four CO stretching bands were identified; they correspond
to discrete conformations that differ in structural details and CO binding properties. Based on a comparison of bound-state
and photoproduct IR spectra of the wild-type protein, Ngb distal pocket mutants and myoglobin, we have provided structural
interpretations of the conformations associated with the different CO bands. We have also studied ligand migration to the
primary docking site, B. Rebinding from this site is governed by very low enthalpy barriers (∼1 kJ/mol), indicating an extremely
reactive heme iron. Moreover, we have observed ligand migration to a secondary docking site, C, from which CO rebinding involves
higher enthalpy barriers. 相似文献
1000.
Judenhofer MS Wehrl HF Newport DF Catana C Siegel SB Becker M Thielscher A Kneilling M Lichy MP Eichner M Klingel K Reischl G Widmaier S Röcken M Nutt RE Machulla HJ Uludag K Cherry SR Claussen CD Pichler BJ 《Nature medicine》2008,14(4):459-465
Noninvasive imaging at the molecular level is an emerging field in biomedical research. This paper introduces a new technology synergizing two leading imaging methodologies: positron emission tomography (PET) and magnetic resonance imaging (MRI). Although the value of PET lies in its high-sensitivity tracking of biomarkers in vivo, it lacks resolving morphology. MRI has lower sensitivity, but produces high soft-tissue contrast and provides spectroscopic information and functional MRI (fMRI). We have developed a three-dimensional animal PET scanner that is built into a 7-T MRI. Our evaluations show that both modalities preserve their functionality, even when operated isochronously. With this combined imaging system, we simultaneously acquired functional and morphological PET-MRI data from living mice. PET-MRI provides a powerful tool for studying biology and pathology in preclinical research and has great potential for clinical applications. Combining fMRI and spectroscopy with PET paves the way for a new perspective in molecular imaging. 相似文献