Coexpression gene network analysis of cold-tolerant Solanum commersonii reveals new insights in response to low temperatures

AbstractAmong abiotic stressors, cold is one of the most harmful for the cultivated potato (Solanum tuberosum L.), a frost‐sensitive crop. RNA sequencing (RNA‐seq) profiling of two different clones of wild potato (S. commersonii Dun.) contrasting in their capacity to withstand low temperatures revealed a higher number of differentially expressed genes (DEGs) under nonacclimated conditions (NAC) in tolerant clone cmm1T vs. the susceptible cmm6‐6 (1,002 and 8,055 DEGs, respectively). By contrast, the number of DEGs was much more comparable when both genotypes were under acclimated conditions (AC). Indeed, a total of 5,650 and 8,936 DEGs were detected in the tolerant genotype vs. the susceptible. Gene ontology (GO) classification under NAC showed a significant role for transcription regulation, lignin catabolic genes, and regulation of plant type secondary cell wall in the cold‐tolerant genotypes, suggesting an important role in conferring tolerance response. By contrast, response to stress and response to stimuli were enriched GO categories in both clones under AC. Unsigned weighted correlation networks analysis (WGCNA) allowed identification of coexpressed hub genes with possible main regulatory functions and major impacts on the phenotype. Among those identified, we clarified the role of CBF4. This gene showed contrasting expression profiles in the two clones under NAC, being induced in cold‐tolerant cmm1T but suppressed in susceptible cmm6‐6. By contrast, under AC, CBF4 was upregulated in both clones. Our study provides a global understanding of mechanisms involved following exposure to NAC and AC in S. commersonii. The mechanisms described here will inform future investigations for detailed validation in studies regarding cold tolerance in plants

DNA-based technologies for grapevine biodiversity exploitation: state of the art and future perspectives

The cultivated grapevine, Vitis vinifera subsp. vinifera L., is represented by an enormous population of varieties and clones. They arise from the accumulation of gametic and somatic mutations during centuries of sexual and asexual propagation. These varieties represent a vast reservoir of traits/alleles that could be useful in improving the berry quality as well as against environmental stresses. However, most of them are still unexploited. For this reason, an efficient characterization system is essential to define the varietal identity, avoid cases of synonymy (identical genotypes but different names) and homonymy (same names but different genotypes) and deepen our understanding of the existing diversity within the grape germplasm. The plethora of DNA-based high-throughput technologies currently available provides promising tools for the analysis of diversity, overcoming many of the limitations of phenotypic-based diversity analyses. However, the analysis of intra-varietal diversity remains challenging. In this scenario, after summarizing the causes and consequences of grapevine genetic inter- and intra-varietal diversity, we review the DNA-based technologies used for varietal genotyping, emphasizing those able to distinguish clones within a variety. This review provides an update on the technologies used to explore grapevine diversity, the knowledge of which is necessary for an efficient exploitation and conservation of the grapevine germplasm

SerpinB3 promotes pro-fibrogenic responses in activated hepatic stellate cells

SerpinB3 is a hypoxia- and hypoxia-inducible factor-2\u3b1-dependent cystein protease inhibitor that is up-regulated in hepatocellular carcinoma and in parenchymal cells during chronic liver diseases (CLD). SerpinB3 up-regulation in CLD patients has been reported to correlate with the extent of liver fibrosis and the production of transforming growth factor-\u3b21, but the actual role of SerpinB3 in hepatic fibrogenesis is still poorly characterized. In the present study we analyzed the pro-fibrogenic action of SerpinB3 in cell cultures and in two different murine models of liver fibrosis. "In vitro" experiments revealed that SerpinB3 addition to either primary cultures of human activated myofibroblast-like hepatic stellate cells (HSC/MFs) or human stellate cell line (LX2 cells) strongly up-regulated the expression of genes involved in fibrogenesis and promoted oriented migration, but not cell proliferation. Chronic liver injury by CCl4 administration or by feeding a methionine/choline deficient diet to transgenic mice over-expressing human SerpinB3 in hepatocytes confirmed that SerpinB3 over-expression significantly increased the mRNA levels of pro-fibrogenic genes, collagen deposition and \u3b1SMA-positive HSC/MFs as compared to wild-type mice, without affecting parenchymal damage. The present study provides for the first time evidence that hepatocyte release of SerpinB3 during CLD can contribute to liver fibrogenesis by acting on HSC/MFs

Hepatocyte-specific deletion of HIF2α prevents NASH-related liver carcinogenesis by decreasing cancer cell proliferation

Background & aims: Hypoxia and hypoxia-inducible factors (HIFs) are involved in chronic liver disease progression. We previously showed that hepatocyte HIF-2\u3b1 activation contributed significantly to nonalcoholic fatty liver disease progression in experimental animals and human patients. In this study, using an appropriate genetic murine model, we mechanistically investigated the involvement of hepatocyte HIF-2\u3b1 in experimental nonalcoholic steatohepatitis (NASH)-related carcinogenesis. Methods: The role of HIF-2\u3b1 was investigated by morphologic, cellular, and molecular biology approaches in the following: (1) mice carrying hepatocyte-specific deletion of HIF-2\u3b1 (HIF-2\u3b1-/- mice) undergoing a NASH-related protocol of hepatocarcinogenesis; (2) HepG2 cells stably transfected to overexpress HIF-2\u3b1; and (3) liver specimens from NASH patients with hepatocellular carcinoma. Results: Mice carrying hepatocyte-specific deletion of HIF-2\u3b1 (hHIF-2\u3b1-/-) showed a significant decrease in the volume and number of liver tumors compared with wild-type littermates. These effects did not involve HIF-1\u3b1 changes and were associated with a decrease of cell proliferation markers proliferating cell nuclear antigen and Ki67. In both human and rodent nonalcoholic fatty liver disease-related tumors, HIF-2\u3b1 levels were strictly associated with hepatocyte production of SerpinB3, a mediator previously shown to stimulate liver cancer cell proliferation through the Hippo/Yes-associated protein (YAP)/c-Myc pathway. Consistently, we observed positive correlations between the transcripts of HIF-2\u3b1, YAP, and c-Myc in individual hepatocellular carcinoma tumor masses, while HIF-2\u3b1 deletion down-modulated c-Myc and YAP expression without affecting extracellular signal-regulated kinase 1/2, c-Jun N-terminal kinase, and AKT-dependent signaling. In\ua0vitro data confirmed that HIF-2\u3b1 overexpression induced HepG2 cell proliferation through YAP-mediated mechanisms. Conclusions: These results indicate that the activation of HIF-2\u3b1 in hepatocytes has a critical role in liver carcinogenesis during NASH progression, suggesting that HIF-2\u3b1-blocking agents may serve as novel putative therapeutic tools

Enhancing an Autonomic Cloud Architecture with Mobile Agents

"\"In cloud environments application scheduling, i.e., the matching of applications with the resources they need to be executed, is a hot research topic. Autonomic computing provides viable solutions to implement robust architectures that are enough flexible to tackle scheduling problems. CHASE is a framework based on an autonomic engine, designed to optimize resource management in clouds, grids or hybrid cloud-grid environments. Its optimizations are based on real-time knowledge of the status of managed resources. This requires continuous monitoring, which is difficult to be carried out in distributed and rapidly-changing environments as clouds. This paper presents a monitoring system to support autonomicity based on the mobile agents computing paradigm.\"

Mobile Agents Self-Optimization with MAWeS

The mobile agents programming paradigm is an emerging approach for distributed programming. Agents-based platforms are considered good solutions in many fields, such as GRID [1–3] or SOA (Service Oriented Architecture) [4, 5]. In mobile agents systems, classical techniques for system optimization (such as ad-hoc tuning, performance engineered software development,...) are not applicable. This is essentially due to continuous changes of the execution contexts, as an agent is able to suspend its own execution, to transfer itself to another agent-enabled host and to resume its execution at that destination. As a result, the platform usually does not have complete control over the execution node state. So, even if the mobile agents approach may help to develop performance-oriented applications, in practice the only solution to guarantee critical requirements seems to be the use of an architecture able to auto-configure and to auto-tune until the given requirements are met. Moreover, when an agent moves itself, it impacts the state of the new system. A prediction of the modifie

Performance prediction through simulation of a hybrid MPI/OpenMP application

This paper deals with the performance prediction of hybrid MPI/OpenMP code. The use of HeSSE (Heterogeneous System Simulation Environment), along with an XML-based prototype language, MetaPL, makes it possible to predict hybrid application performance in many different working conditions, e.g., without the fully developed code or in an unavailable system. After a review of hybrid programming techniques and a brief overview of the HeSSE simulation environment, the problems related to the simulation of hybrid code and to its description through trace files are dealt with. The whole application modeling and analysis cycle is presented and validated, predicting the performance of a parallel N-body code on a SMP cluster and comparing it to the timings measured on the real system

The wild side of potato: insights into the genome sequence of the stress-tolerant S. commersonii Dun

Solanum commersonii is a potato species native to Central and South America. Despite being genetically isolated from cultivated potato, in the past few years it has garnered significant research interest because it exhibits high tolerance to both biotic and abiotic stresses. Among the abiotic stresses, particularly interesting are its freezing tolerance and capacity to cold acclimatize. Little is understood of the genetic determi- nants and mechanisms beyond its resistance traits. This is partially due to the lack of genomic resources for potato germplasm. The group at the University of Naples has recently decoded, for the first time, the genome of S. commersonii, ushering in a new era of whole-genome sequencing of wild potato relatives. After illustrating the genome structure and organization of this species and its intrigffuing evolutionary roots, this chapter describes findings relative to the identification of the candidate genes for cold stress tolerance. The genome sequence of S. commersonii will pave the way to an understanding of the molecular dynamics that have given this species so many adaptive characteristics