A D-cysteine desulfhydrase, SlDCD2, participates in tomato fruit ripening by modulating ROS homoeostasis and ethylene biosynthesis

Hydrogen sulfide(H_(2)S)is involved in multiple processes during plant growth and development.D-cysteine desulfhydrase(DCD)can produce H_(2)S with D-cysteine as the substrate;however,the potential developmental roles of DCD have not been explored during the tomato lifecycle.In the present study,SlDCD2 showed increasing expression during fruit ripening.Compared with the control fruits,the silencing of SlDCD2 by pTRV2-SlDCD2 accelerated fruit ripening.A SlDCD2 gene-edited mutant was constructed by CRISPR/Cas9 transformation,and the mutant exhibited accelerated fruit ripening,decreased H_(2)S release,higher total cysteine and ethylene contents,enhanced chlorophyll degradation and increased carotenoid accumulation.Additionally,the expression of multiple ripening-related genes,including NYC1,PAO,SGR1,PDS,PSY1,ACO1,ACS2,E4,CEL2,and EXP was enhanced during the dcd2 mutant tomato fruit ripening.Compared with the wild-type fruits,SlDCD2 mutation induced H_(2)O_(2) and malondialdehyde(MDA)accumulation in fruits,which led to an imbalance in reactive oxygen species(ROS)metabolism.A correlation analysis indicated that H_(2)O_(2) content was strongly positively correlated with carotenoids content,ethylene content and ripening-related gene expression and negatively correlated with the chlorophyll content.Additionally,the dcd2 mutant showed earlier leaf senescence,which may be due to disturbed ROS homeostasis.In short,our findings show that SlDCD2 is involved in H_(2)S generation and that the reduction in endogenous H_(2)S production in the dcd2 mutant causes accelerated fruit ripening and premature leaf senescence.Additionally,decreased H_(2)S in the dcd2 mutant causes excessive H_(2)O_(2) accumulation and increased ethylene release,suggesting a role of H_(2)S and SlDCD2 in modulating ROS homeostasis and ethylene biosynthesis.

Comparative systems biology between human and animal models based on next-generation sequencing methods

Animal models provide myriad benefits to both experimental and clinical research. Unfortunately, in many situations, they fall short of expected results or provide contradictory results. In part, this can be the result of traditional molecular biological approaches that are relatively inefficient in elucidating underlying molecular mechanism. To improve the efficacy of animal models, a technological breakthrough is required. The growing availability and application of the high-throughput methods make systematic comparisons between human and animal models easier to perform. In the present study, we introduce the concept of the comparative systems biology, which we define as "comparisons of biological systems in different states or species used to achieve an integrated understanding of life forms with all their characteristic complexity of interactions at multiple levels". Furthermore, we discuss the applications of RNA-seq and ChIP-seq technologies to comparative systems biology between human and animal models and assess the potential applications for this approach in the future studies.

Comparative systems biology between human and animal models based on next-generation sequencing methods

Animal models provide myriad benefits to both experimental and clinical research.Unfortunately,in many situations,they fall short of expected results or provide contradictory results.In part,this can be the result of traditional molecular biological approaches that are relatively inefficient in elucidating underlying molecular mechanism.To improve the efficacy of animal models,a technological breakthrough is required.The growing availability and application of the high-throughput methods make systematic comparisons between human and animal models easier to perform.In the present study,we introduce the concept of the comparative systems biology,which we define as“comparisons of biological systems in different states or species used to achieve an integrated understanding of life forms with all their characteristic complexity of interactions at multiple levels”.Furthermore,we discuss the applications of RNA-seq and ChIP-seq technologies to comparative systems biology between human and animal models and assess the potential applications for this approach in the future studies.

Developer Role Evolution in Open Source Software Ecosystem： An Explanatory Study on GNOME

An open source software （OSS） ecosystem refers to an OSS development community composed of many software projects and developers contributing to these projects. The projects and developers co-evolve in an ecosystem. To keep healthy evolution of such OSS ecosystems, there is a need of attracting and retaining developers, particularly project leaders and core developers who have major impact on the project and the whole team. Therefore, it is important to figure out the factors that influence developers＇ chance to evolve into project leaders and core developers. To identify such factors, we conducted a case study on the GNOME ecosystem. First, we collected indicators reflecting developers＇ subjective willingness to contribute to the project and the project environment that they stay in. Second, we calculated such indicators based on the GNOME dataset. Then, we fitted logistic regression models by taking as independent variables the resulting indicators after eliminating the most collinear ones, and taking as a dependent variable the future developer role （the core developer or project leader）. The results showed that part of such indicators （e.g., the total number of projects that a developer joined） of subjective willingness and project environment significantly influenced the developers＇ chance to evolve into core developers and project leaders. With different validation methods, our obtained model performs well on predicting developmental core developers, resulting in stable prediction performance （0.770, F-value）.