The Spatial and Temporal Variation Characteristics of CH₄and CO₂Emission Flux under Different Land Use Types in the Yellow River Delta Wetland

The Yellow River Delta Wetland is one of the youngest wetlands, and also the most complete, extensive wetlands in China. The wetland in this delta is ecologically important due to their hydrologic attributes and their roles as ecotones between terrestrial and aquatic ecosystems. In the study, the spatial and temporal variation characteristics of CH4 and CO2 emission flux under five kinds of land use types in the wetland were investigated. The results indicated that the greenhouse gas emission flux, especially the CO2 and CH4, showed distinctly spatial and temporal variation under different land use types in the wetland. In the spring, the emission flux of CO2 was higher than that of CO2 in the autumn, and appeared negative in HW3 and HW4 in the autumn. CH4 emission flux of HW4 and HW5 was negative in the spring and autumn, which indicated that the CH4 emission process was net absorption. Among the five kinds of land use types, the CO2 emission flux of HW4 discharged the largest emission flux reaching 29.3 mg.m-2.h-1, but the CH4 emission flux of HW2 discharged the largest emission flux reaching 0.15 mg.m-2.h-1. From the estuary to the inland, the emission flux of CO2 was decreased at first and then appeared increasing trend, but the emission flux of CH4 was contrary to CO2.

Real-Time Air Monitoring of Trichloroethylene and Tetrachloroethylene Using Mobile TAGA Mass Spectrometry

Trichloroethylene (TCE) is a chlorinated liquid that is commonly used for metal degreasing, household and industrial dry cleaning, and in paints and glues. Tetrachloroethylene, also known as perchloroethylene (PCE), is an excellent solvent for organic materials. PCE is volatile, highly stable, non-flammable and widely used in dry cleaning. A new method has been developed for measuring TCE and PCE in ambient air in real-time. Based upon the chemical fingerprinting and concentration levels, the method was able to isolate the source of the emissions to the responsible facility. Real-time monitoring was accomplished by utilizing a low pressure chemical ionization source (LPCI) interfaced to a tandem mass spectrometer (TAGA). Monitoring the response of specific parent/daughter ion pairs, the TAGA was used to measure concentrations of TCE and PCE. By optimizing various TAGA parameters, detection limits (DL) as low as 0.5 μg/m3 was achieved for TCE and PCE. Unlike methods using cartridge sampling and GC/MS analysis, this new method provides a real time measurement for a wide range of TCE and PCE concentrations. This unique method was applied in 2000 and 2002 to measure TCE emitted from a manufacturer of stainless steel tubing in Eastern Ontario. The maximum half-hour average concentration of TCE measured downwind of the facility was 1300 μg/m3 and the maximum instantaneous level was measured at 115,000 μg/m3. The information collected by the TAGA unit was used by the Standard Development Branch of Ontario Ministry of the Environment to adopt the half-hour Point of Impingement (POI) standard of TCE to be 36 μg/m3 in 2010. This method successfully identified and simultaneously measured TCE and PCE during a 2011 air monitoring survey of a hazardous waste disposal and treatment facility in Southern Ontario.

A structural view of the conserved domain of rice stress-responsive NAC1

The importance of NAC(named as NAM,ATAF1,2,and CUC2)proteins in plant development,transcription regulation and regulatory pathways involving proteinprotein interactions has been increasingly recognized.We report here the high resolution crystal structure of SNAC1(stress-responsive NAC)NAC domain at 2.5Å.Although the structure of the SNAC1 NAC domain shares a structural similarity with the reported structure of the ANAC NAC1 domain,some key features,especially relating to two loop regions which potentially take the responsibility for DNA-binding,distinguish the SNAC1 NAC domain from other reported NAC structures.Moreover,the dimerization of the SNAC1 NAC domain is demonstrated by both soluble and crystalline conditions,suggesting this dimeric state should be conserved in this type of NAC family.Additionally,we discuss the possible NAC-DNA binding model according to the structure and reported biological evidences.

Fargeted elimination of mutant mitochondria DNA in MELAS-iPSCs by mitoTALENs

Mitochondrial diseases are maternally inherited hetero- geneous disorders that are primarily caused by mitochondrial DNA （mtDNA） mutations. Depending on the ratio of mutant to wild-type mtDNA, known as heteroplasmy, mitochondrial defects can result in a wide spectrum of clinical manifestations. Mitochondria-targeted endonucleases provide an alternative avenue for treating mitochondrial disorders via targeted destruc- tion of the mutant mtDNA and induction of heteroplasmic shifting. Here, we generated mitochondrial disease patient-specific induced pluripotent stem cells （MiPSCs） that harbored a high proportion of m.3243A〉G mtDNA mutations and caused mitochondrial encephalomyopathy and stroke-like episodes （MELAS）. We engineered mitochondrial-targeted transcription activator-like effector nucleases （mitoTALENs） and successfully eliminated the m.3243A〉G mutation in MiPSCs. Off-target mutagenesis was not detected in the targeted MiPSC clones. Utilizing a dual fluorescence iPSC reporter cell line expressing a 3243G mutant mtDNA sequence in the nuclear genome, mitoTALENs displayed a significantly limited ability to target the nuclear genome compared with nuclear-localized TALENs. Moreover, genetically rescued MiPSCs displayed normal mitochondrial respiration and energy production. Moreover, neuronal progenitor cells differentiated from the rescued MiPSCs also demonstrated normal metabolic profiles. Further- more, we successfully achieved reduction in the human m.3243A〉G mtDNA mutation in porcine oocytes via injection of mitoTALEN mRNA. Our study shows the great potential for using mitoTALENs for specific targeting of mutant mtDNA both in iPSCs and mammalian oocytes, which not only provides a new avenue for studying mitochondrial biology and disease but also suggests a potential therapeutic approach for the treatment of mitochondrial disease, as well as the prevention of germline transmission of mutant mtDNA.

Human CD34loCD133lo fetal liver cells support the expansion of human CD34hiCD133hi hematopoietic stem cells

We have recently discovered a unique CD34loCD133lo cell population in the human fetal liver （FL） that gives rise to cells in the hepatic lineage. In this study, we further characterized the biological functions of FL CD341~CD133~~ cells. Our findings show that these CD341~CD133I~ cells express markers of both endodermal and mesodermal lineages and have the capability to differentiate into hepatocyte and mesenchymal lineage cells by ex vivo differentiation assays. Furthermore, we show that CD34~~CD 133I~ cel Is express growth factors that are important for human hematopoietic stem cell （HSC） expansion： stem cell factor （SCF）, insulin-like growth factor 2 （IGF2）, C-X-C motif chemokine 12 （CXCL12）, and factors in the angiopoietin-like protein family. Co-culture of autologous FL HSCs and allogenic HSCs derived from cord blood with CD34loCD133lo cells supports and expands both types of HSCs.These findings are not only essential for extending our understanding of the HSC niche during the development of embryonic and fetal hematopoiesis but will also potentially benefit adult stem cell transplantations in clinics because expanded HSCs demonstrate the same capacity as primary cells to reconstitute the human immune system and mediate long-term hematopoiesis in vivo. Together,CD34loCD133lo cells not only serve as stem/progenitor cells for liver development but are also an essential component of the HSC niche in the human FL.

Engineering humanized mice for improved hematopoietic reconstitution

Humanized mice are immunodeficient animals engrafted with human hematopoietic stem cells that give rise to various lineages of human blood cells throughout the life of the mouse. This article reviews recent advances in the generation of humanized mice, focusing on practical considerations. We discuss features of different immunodeficient recipient mouse strains, sources of human hematopoietic stem cells, advances in expansion and genetic modification of hematopoietic stem cells, and techniques to modulate the cytokine environment of recipient mice, in order to enhance reconstitution of specific human blood lineage cells. We highlight the opportunities created by new technologies and discuss practical considerations on how to make best use of the widening array of basic models for specific research applications.

Identifying miRNA-disease association based on integrating miRNA topological similarity and functional similarity

Background:MicroRNAs(miRNAs)are a significant type of non-coding RNAs,which usually were encoded by endogenous genes with about?22 nt nucleotides.Accumulating biological experiments have shown that miRNAs have close associations with various human diseases.Although traditional experimental methods achieve great successes in miRNA-disease interaction identification,these methods also have some limitations.Therefore,it is necessary to develop computational method to predict miRNA-disease interactions.Methods:Here,we propose a computational framework(MDVSI)to predict interactions between miRNAs and diseases by integrating miRNA topological similarity and functional similarity.Firstly,the CosRA index is utilized to measure miRNA similarity based on network topological feature.Then,in order to enhance the reliability of miRNA similarity,the functional similarity and CosRA similarity are integrated based on linear weight method.Further,the potential miRNA-disease associations are predicted by using recommendation method.In addition,in order to overcome limitation of recommendation method,for new disease,a new strategy is proposed to predict potential interactions between miRNAs and new disease based on disease functional similarity.Results:To evaluate the performance of different methods,we conduct ten-fold cross validation and de novo test in experiment and compare MDVSI with two the-state-of-art methods.The experimental result shows that MDVSI achieves an AUC of 0.91,which is at least 0.012 higher than other compared methods.Conclusions:In summary,we propose a computational framework(MDSVI)for miRNA-disease interaction prediction.The experiment results demonstrate that it outperforms other the-state-of^the-art methods.Case study shows that it can effectively identify potential miRNA-disease interactions.

The niche for hematopoietic stem cell expansion: a collaboration network

Transplantation of hematopoietic stem/progenitor cells(HSPC)has become one of the most effective treatments for several hematological malignancies,cancers and genetic immune disorders.However,the lack of histocompatible donor sources and the number of stem cells suitable for engraftment are major constraints in the clinic,and these constraints greatly hamper the use of stem cell therapy.In humans,fetal liver and bone marrow are the two major locations of hematopoiesis before and after birth,respectively.Thus,understanding the specialized stem cell microenvironment supporting the self-renewal and expansion of HSPC in fetal liver and bone marrow is not only essential for extending the current knowledge of stem cell biology but is also beneficial to adult regenerative medicine in the clinic.

Privacy-preserving decision tree for epistasis detection

The interaction between gene loci,namely epistasis,is a widespread biological genetic phenomenon.In genome-wide association studies(GWAS),epistasis detection of complex diseases is a major challenge.Although many approaches using statistics,machine learning,and information entropy were proposed for epistasis detection,the privacy preserving for single nucleotide polymorphism(SNP)data has been largely ignored.Thus,this paper proposes a novel two-stage approach.A fusion strategy assists in combining and sorting the SNPs importance scores obtained by the relief and mutual information,thereby obtaining a candidate set of SNPs.This avoids missing some SNPs with strong interaction.Furthermore,differentially private decision tree is applied to search for SNPs.This achieves the efficient epistasis detection of complex diseases on the basis of privacy preserving compared with heuristic methods.The recognition rate on simulation data set is more than 90%.Also,several susceptible loci including rs380390 and rs1329428 are found in the real data set for Age-related Macular Degeneration(AMD).This demonstrates that our method is promising in epistasis detection.

Erratum to:Identifying miRNA-disease association based on integrating miRNA topological similarity and functional similarity

The original version of this article unfortunately contained a mistake in the name of the last author.The corrected name is Yi-Ping Phoebe Chen.

Privacy-preserving decision tree for epistasis detection

The interaction between gene loci,namely epistasis,is a widespread biological genetic phenomenon.In genome-wide association studies(GWAS),epistasis detection of complex diseases is a major challenge.Although many approaches using statistics,machine learning,and information entropy were proposed for epistasis detection,the privacy preserving for single nucleotide polymorphism(SNP)data has been largely ignored.Thus,this paper proposes a novel two-stage approach.A fusion strategy assists in combining and sorting the SNPs importance scores obtained by the relief and mutual information,thereby obtaining a candidate set of SNPs.This avoids missing some SNPs with strong interaction.Furthermore,differentially private decision tree is applied to search for SNPs.This achieves the efficient epistasis detection of complex diseases on the basis of privacy preserving compared with heuristic methods.The recognition rate on simulation data set is more than 90%.Also,several susceptible loci including rs380390 and rs1329428 are found in the real data set for Age-related Macular Degeneration(AMD).This demonstrates that our method is promising in epistasis detection.