Hydrogen sulfide is involved in the chilling stress response in Vitis vinifera L.

Hydrogen sulfide (H2S) is an important signaling molecule involved in several stress-resistance processes in plants, such as drought and heavy metal stresses. However, little is known about the roles of H2S in responses to chilling stress. In this paper, we demonstrated that chilling stress enhance the H2S levels, the H2S synthetase (L-/D-cysteine desulfhydrase, L/DCD) activities, and the expression of L/DCD gene in Vitis vinifera L. ‘F-242’. Furthermore, the seedlings were treated with sodium hydrosulfide (NaHS, a H2S donor) and hypotaurine (HT, a H2S scavenger) at 4°C to examine the effects of exogenous H2S on grape. The results revealed that the high activity of superoxide dismutase and enhanced expression of VvICE1 and VvCBF3 genes, but low level of super oxide anion radical, malondialdehyde content and cell membrane permeability were detected after addition of NaHS. In contrast, HT treatment displayed contrary effect under the chilling temperature. Taken together, these data suggested that H2S might be directly involved in the cold signal transduction pathway of grape

Detecting copy number status and uncovering subclonal markers in heterogeneous tumor biopsies

<p>Abstract</p> <p>Background</p> <p>Genomic aberrations can be used to determine cancer diagnosis and prognosis. Clinically relevant novel aberrations can be discovered using high-throughput assays such as Single Nucleotide Polymorphism (SNP) arrays and next-generation sequencing, which typically provide aggregate signals of many cells at once. However, heterogeneity of tumor subclones dramatically complicates the task of detecting aberrations.</p> <p>Results</p> <p>The aggregate signal of a population of subclones can be described as a linear system of equations. We employed a measure of allelic imbalance and total amount of DNA to characterize each locus by the copy number status (gain, loss or neither) of the strongest subclonal component. We designed simulated data to compare our measure to existing approaches and we analyzed SNP-arrays from 30 melanoma samples and transcriptome sequencing (RNA-Seq) from one melanoma sample.</p> <p>We showed that any system describing aggregate subclonal signals is underdetermined, leading to non-unique solutions for the exact copy number profile of subclones. For this reason, our illustrative measure was more robust than existing Hidden Markov Model (HMM) based tools in inferring the aberration status, as indicated by tests on simulated data. This higher robustness contributed in identifying numerous aberrations in several loci of melanoma samples. We validated the heterogeneity and aberration status within single biopsies by fluorescent <it>in situ </it>hybridization of four affected and transcriptionally up-regulated genes E2F8, ETV4, EZH2 and FAM84B in 11 melanoma cell lines. Heterogeneity was further demonstrated in the analysis of allelic imbalance changes along single exons from melanoma RNA-Seq.</p> <p>Conclusions</p> <p>These studies demonstrate how subclonal heterogeneity, prevalent in tumor samples, is reflected in aggregate signals measured by high-throughput techniques. Our proposed approach yields high robustness in detecting copy number alterations using high-throughput technologies and has the potential to identify specific subclonal markers from next-generation sequencing data.</p

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. RESULTS: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. CONCLUSIONS: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups

STUDY ON TOUGHNESS OF DOMESTIC PRESSURE VESSEL STEEL Q345R AT LOW TEMPERATURE

In the present paper,the relevant provision in the ASME Code Case about"Applicability of the ASME exemption curve for Chinese pressure vessel steel Q345R"has been analyzed by using failure assessment procedure on the basis of true material testing data. For the normalized Q345 R investigated in this paper,the results indicated that both Charpy impact toughness and fracture toughness at low temperature are better than the requirements in ASME Code,the provision in ASME Code classifying Q345 R in Exemption curve A excessively underestimated the toughness of the material

Oxygen-Carrier-Aided Combustion in a Bench-Scale Fluidized Bed

In a circulating fluidized bed (CFB) boiler, one of the basic functions of the bed materials is to transport heat between different parts of the boiler to clecrease heat gradients and, thereby, smoothen the operation. A novel concept, oxygen Carrier-aided combustion (OCAC), replaces some or all of the bed materials with an oxygen carrier, which is a metal oxide that, through chemical redox reaction, not only transports heat but also transports oxygen between oxygen-lean and oxygen-rich areas of the boiler. The oxygen carrier also acts as internal oxygen storage, which increases the total amount of available oxygen in the boiler. The concept of OCAC was demonstrated by Thunman et al. at Chalmers University of Technology, where the bed material (sand) in a 12 MW boiler was replaced with iron titanium mineral (ilmenite). In this work, a small fluidized bed reactor is used to mimic the condition in OCAC with regard to fuel conversion as well as NO formation and to test other oxygen carrier, materials. Four oxygen carriers were tested, two ores (ilmenite and manganese ore), and two Oxide scales (denoted as AQS and LDst), which were byproducts from the steel production of the Swedish company SSAB. Sand was also used as a reference. Wood char was used as the fuel, and concentrations of CO2, CO, CH4, O-2, and NO in the exhaust gases were monitored. The effect of oxygen carriers on combustion efficiency and NO emission was investigated at different air/fuel ratios. The results Show that, utilization of an oxygen carrier reduces the level of CO emission, thereby increasing the efficiency of combustion. It is also Shown that the increase In combustion efficiency can be largely attributed to the reactivity of the oxygen carriers with CO. With OCAC, it was possible to reduce the level of excess air and, thereby, lower the level of NO emissions while maintaining the same level of CO emission

De novo paternal origin duplication of chromosome 11p15.5: report of two Chinese cases with Beckwith-Wiedemann syndrome

Abstract Background The molecular etiology of Beckwith-Wiedemann syndrome (BWS) is complex and heterogeneous. Several subtypes of epigenetic-genetic alterations including aberrant methylation patterns, segmental uniparental disomy, single gene mutations, and copy number changes have been described. An integrated molecular approach to analyze the epigenetic-genetic alterations is required for accurate diagnosis of BWS. Case presentation We reported two Chinese cases with BWS detected by genome-wide copy number analysis and locus-specific methylation profiling. Prenatal analysis on cord blood of patient 1 showed a de novo paternal origin duplication spanning 896Kb at 11p15.5. Patient 2 was referred at 2-month old and the genetic analysis showed a de novo 228.8Kb deletion at 11p15.5 telomeric end and a de novo duplication of 2.5 Mb at 11p15.5–15.4. Both the duplications are of paternal origin with gain of methylation at the imprinting center 1 and thus belong to the subgroup of a low tumor risk. Conclusion Results from these two cases and other reported cases from literature indicated that paternally derived duplications at 11p15.5 region cause BWS. Combined chromosome microarray analysis and methylation profiling provided reliable diagnosis for this subtype of BWS. Characterization of genetic defects in BWS patients could lead to better understanding the genetic mechanisms of this clinically and genetically heterogeneous disorder