Protein-complex structure completion using IPCAS (Iterative Protein Crystal structure Automatic Solution)

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The further study on the accuracy of DEM terrain representation

2003-2004 > Academic research: refereed > Publication in refereed journalVersion of RecordPublishe

Kinetic frustration and the nature of the magnetic and paramagnetic states in iron pnictides and iron chalcogenides

The iron pnictide and chalcogenide compounds are a subject of intensive investigations due to their high temperature superconductivity.\cite{a-LaFeAsO} They all share the same structure, but there is significant variation in their physical properties, such as magnetic ordered moments, effective masses, superconducting gaps and T$_c$. Many theoretical techniques have been applied to individual compounds but no consistent description of the trends is available \cite{np-review}. We carry out a comparative theoretical study of a large number of iron-based compounds in both their magnetic and paramagnetic states. We show that the nature of both states is well described by our method and the trends in all the calculated physical properties such as the ordered moments, effective masses and Fermi surfaces are in good agreement with experiments across the compounds. The variation of these properties can be traced to variations in the key structural parameters, rather than changes in the screening of the Coulomb interactions. Our results provide a natural explanation of the strongly Fermi surface dependent superconducting gaps observed in experiments\cite{Ding}. We propose a specific optimization of the crystal structure to look for higher T$_c$ superconductors.Comment: 5 pages, 3 figures with a 5-page supplementary materia

Cassiterite oxygen isotopes in magmatic-hydrothermal systems: in situ microanalysis, fractionation factor, and applications

Tin and tungsten are important metals for the industrializing society. Deciphering the origin and evolution of hydrothermal fluids responsible for their formation is critical to underpin genetic models of ore formation. Traditional approaches obtain isotopic information mainly from bulk analysis of both ore and gangue minerals, or less frequently from in situ analysis of gangue minerals, which either bear inherited complexities and uncertainties or are indirect constraints. Hence, directly obtaining isotopic information from ore minerals such as cassiterite by in situ techniques is warranted. However, this has been hampered by challenges from both analytical and applicational aspects. In this study, we first demonstrate a lack of crystallographic orientation effects during cassiterite ion microprobe oxygen isotope analysis. Along with our newly developed matrix-matched reference material, the Yongde-Cst, which has a recommended δ18O value of 1.36 ± 0.16‰ (VSMOW) as defined by gas source isotope ratio mass spectrometry, in situ oxygen isotope analysis of cassiterite now is possible. We further refine the oxygen isotope fractionation (1000 ln α) for quartz-cassiterite by first-principles calculations, which is given by the equation of 1.259 × 106/T2 + 8.15 × 103/T − 4.72 (T is temperature in Kelvin). The 1000 ln α for quartz-cassiterite has a sensitive response to temperature, and makes cassiterite-quartz an excellent mineral pair in oxygen isotope thermometry, as described by the equation of T (℃) = 2427 × (δ18Oqtz − δ18Ocst)−0.4326 − 492.4. Using the well-established 1000 ln α of quartz-water, 1000 ln α of cassiterite-water is derived as 2.941 × 106/T2 − 11.45 × 103/T + 4.72 (T in Kelvin), which shows a weak response to temperature. This makes cassiterite an ideal mineral from which to derive δ18O of fluids as robust temperature estimates are no longer a prerequisite. We have applied oxygen isotope analysis to cassiterite samples from six Sn(-W) deposits in China. The results show considerable variability in δ18O values both within a single deposit and among studied deposits. Combining the δ18O of cassiterite samples and the equilibrium oxygen isotope fractionation, we find that the δ18O values of ore-forming fluids show a strong magmatic affinity with variable but mostly no to low degree involvements (~0-10%) of meteoric water, hence our results invite a reassessment on the extent and role of meteoric water in Sn-W mineralization. This study demonstrates that in situ oxygen isotope analysis of cassiterite is a promising tool to refine sources of ore-forming fluids, and to decode hydrothermal dynamics controlling tin and tungsten mineralization

Correlation between expression of DcR3 on tumor cells and sensitivity to FasL

To investigate the correlation between sensitivity to Fas ligand (FasL) and expression level of decoy receptor 3 (DcR3) on tumor cell surface, Fas/DcR3 mRNA expression was detected by RT-PCR. Anti-DcR3 mAb was used to detect expression level of DcR3 on surface of tumor cells by flow cytometry. Caspase-8, caspase-9, caspase-3, Bcl-2 expressions were analyzed by Western blot, respectively. Sensitivity to apoptosis induced by FasL was determined by Annexin V apoptosis kit. The expressions of DcR3 on the surface of tumor cells from high to low were approximately 35.3% in BGC823 cells, and 21.6% in MCF-7 cells, respectively. The apoptotic rates induced by FasL from low to high were 15.6% in BGC823 cells, and 58.2% in MCF-7 cells, respectively. There was a significant correlation between the expression levels of DcR3 with FasL-inducing apoptosis

Postnatal expression of myostain (MSTN) and myogenin (MYoG) genes in Hu sheep of China

The study of candidate genes is an important tool to identify genes associated with economic traits. Skeletal muscle development is an important physiological process in meat animals, and it directly affects meat production. The expression of myostain (MSTN) and myogenin (MYoG) genes in longissimus dorsi, during the early growth stage of Hu sheep, was studied by semi-quantitative Reverse transcription polymerase chain reaction (RT-PCR). The results demonstrate that age and gender were playing a very important role in the expression of sheep muscle. MSTN and MYOG genes showed similar variation pattern for the male and female. The expression level of the MSTN and MYoG genes all showed a positive correlation with live weight, carcass weight and meat percentage, but only showed a significant relationship with meat percentage. MSTN gene showed an extreme significant positive relationship with MYoG.Key words: Sheep, myostain (MSTN), myogenin (MYoG), gene expression, muscle trait

A genetic contribution from the Far East into Ashkenazi Jews via the ancient Silk Road

Contemporary Jews retain a genetic imprint from their Near Eastern ancestry, but obtained substantial genetic components from their neighboring populations during their history. Whether they received any genetic contribution from the Far East remains unknown, but frequent communication with the Chinese has been observed since the Silk Road period. To address this issue, mitochondrial DNA (mtDNA) variation from 55,595 Eurasians are analyzed. The existence of some eastern Eurasian haplotypes in eastern Ashkenazi Jews supports an East Asian genetic contribution, likely from Chinese. Further evidence indicates that this connection can be attributed to a gene flow event that occurred less than 1.4 kilo-years ago (kya), which falls within the time frame of the Silk Road scenario and fits well with historical records and archaeological discoveries. This observed genetic contribution from Chinese to Ashkenazi Jews demonstrates that the historical exchange between Ashkenazim and the Far East was not confined to the cultural sphere but also extended to an exchange of genes

Genome structure of cotton revealed by a genome-wide SSR genetic map constructed from a BC1 population between gossypium hirsutum and G. barbadense

<p>Abstract</p> <p>Background</p> <p>Cotton, with a large genome, is an important crop throughout the world. A high-density genetic linkage map is the prerequisite for cotton genetics and breeding. A genetic map based on simple polymerase chain reaction markers will be efficient for marker-assisted breeding in cotton, and markers from transcribed sequences have more chance to target genes related to traits. To construct a genome-wide, functional marker-based genetic linkage map in cotton, we isolated and mapped expressed sequence tag-simple sequence repeats (EST-SSRs) from cotton ESTs derived from the A₁, D₅, (AD)₁, and (AD)₂genome.</p> <p>Results</p> <p>A total of 3177 new EST-SSRs developed in our laboratory and other newly released SSRs were used to enrich our interspecific BC₁genetic linkage map. A total of 547 loci and 911 loci were obtained from our EST-SSRs and the newly released SSRs, respectively. The 1458 loci together with our previously published data were used to construct an updated genetic linkage map. The final map included 2316 loci on the 26 cotton chromosomes, 4418.9 cM in total length and 1.91 cM in average distance between adjacent markers. To our knowledge, this map is one of the three most dense linkage maps in cotton. Twenty-one segregation distortion regions (SDRs) were found in this map; three segregation distorted chromosomes, Chr02, Chr16, and Chr18, were identified with 99.9% of distorted markers segregating toward the heterozygous allele. Functional analysis of SSR sequences showed that 1633 loci of this map (70.6%) were transcribed loci and 1332 loci (57.5%) were translated loci.</p> <p>Conclusions</p> <p>This map lays groundwork for further genetic analyses of important quantitative traits, marker-assisted selection, and genome organization architecture in cotton as well as for comparative genomics between cotton and other species. The segregation distorted chromosomes can be a guide to identify segregation distortion loci in cotton. The annotation of SSR sequences identified frequent and rare gene ontology items on each chromosome, which is helpful to discover functions of cotton chromosomes.</p

Acute effects of remote ischemic preconditioning on cutaneous microcirculation - a controlled prospective cohort study

<p>Abstract</p> <p>Background</p> <p>Therapeutic strategies aiming to reduce ischemia/reperfusion injury by conditioning tissue tolerance against ischemia appear attractive not only from a scientific perspective, but also in clinics. Although previous studies indicate that remote ischemic intermittent preconditioning (RIPC) is a systemic phenomenon, only a few studies have focused on the elucidation of its mechanisms of action especially in the clinical setting. Therefore, the aim of this study is to evaluate the acute microcirculatory effects of remote ischemic preconditioning on a distinct cutaneous location at the lower extremity which is typically used as a harvesting site for free flap reconstructive surgery in a human in-vivo setting.</p> <p>Methods</p> <p>Microcirculatory data of 27 healthy subjects (25 males, age 24 ± 4 years, BMI 23.3) were evaluated continuously at the anterolateral aspect of the left thigh during RIPC using combined Laser-Doppler and photospectrometry (Oxygen-to-see, Lea Medizintechnik, Germany). After baseline microcirculatory measurement, remote ischemia was induced using a tourniquet on the contralateral upper arm for three cycles of 5 min.</p> <p>Results</p> <p>After RIPC, tissue oxygen saturation and capillary blood flow increased up to 29% and 35% during the third reperfusion phase versus baseline measurement, respectively (both p = 0.001). Postcapillary venous filling pressure decreased statistically significant by 16% during second reperfusion phase (p = 0.028).</p> <p>Conclusion</p> <p>Remote intermittent ischemic preconditioning affects cutaneous tissue oxygen saturation, arterial capillary blood flow and postcapillary venous filling pressure at a remote cutaneous location of the lower extremity. To what extent remote preconditioning might ameliorate reperfusion injury in soft tissue trauma or free flap transplantation further clinical trials have to evaluate.</p> <p>Trial registration</p> <p>ClinicalTrials.gov: <a href="http://www.clinicaltrials.gov/ct2/show/NCT01235286">NCT01235286</a></p

Dynamic structure of Mo-O species in Ag-Mo-P-O catalyst for oxidative dehydrogenation of propane

The dynamic structure of Mo-O species in Ag-Mo-P-O catalyst was studied by in situ confocal microprobe laser Raman spectroscopy (LRS) and catalytic test. The results indicate Mo-O species of MoO3 transformed to Mo-O species of AgMoO2PO4 in C3H8/O-2/N, (3/1/4) flow at 773 K. This behavior is closely relative to oxidative dehydrogenation of propane and intrinsic properties of Mo-O species. The Mo-O species of AgMoO2PO4 may be active species for oxidative dehydrogenation of propane