Detecting intergene correlation changes in microarray analysis: a new approach to gene selection

Background  

Microarray technology is commonly used as a simple screening tool with a focus on selecting genes that exhibit extremely large differential expressions between different phenotypes. It lacks the ability to select genes that change their relationships with other genes in different biological conditions (differentially correlated genes). We intend to enrich the above procedure by proposing a nonparametric selection procedure that selects differentially correlated genes.     

Cellular senescence and organismal ageing in the absence of p21CIP1/WAF1 in ku80−/− mice

Ku80 is important in the repair of DNA double-strand breaks by its essential function in non-homologous end-joining. The absence of Ku80 causes the accumulation of DNA damage and leads to premature ageing in mice. We showed that mouse embryonic fibroblasts (MEFs) from ku80^−/− mice senesced rapidly with elevated levels of p53 and p21. Deletion of p21 delayed the early senescence phenotype in ku80^−/− MEFs, despite an otherwise intact response of p53. In contrast to ku80^−/−p53^−/− mice, which die rapidly primarily from lymphomas, there was no significant increase in tumorigenesis in ku80^−/−p21^−/− mice. However, ku80^−/−p21^−/− mice showed no improvement with respect to rough fur coat or osteopaenia, and even showed a shortened lifespan compared with ku80^−/− mice. These results show that the increased lifespan of ku80^−/− MEFs owing to the loss of p21 is not associated with an improvement of the premature ageing phenotypes of ku80^−/− mice observed at the organismal level.     

The proline-rich domain of tau plays a role in interactions with actin

Background  

The microtubule-associated protein tau is able to interact with actin and serves as a cross-linker between the microtubule and actin networks. The microtubule-binding domain of tau is known to be involved in its interaction with actin. Here, we address the question of whether the other domains of tau also interact with actin.     

Phylogeny and evolutionary history of Leymus (Triticeae; Poaceae) based on a single-copy nuclear gene encoding plastid acetyl-CoA carboxylase

Background  

Single- and low- copy genes are less likely subject to concerted evolution, thus making themselves ideal tools for studying the origin and evolution of polyploid taxa. Leymus is a polyploid genus with a diverse array of morphology, ecology and distribution in Triticeae. The genomic constitution of Leymus was assigned as NsXm, where Ns was presumed to be originated from Psathyrostachys, while Xm represented a genome of unknown origin. In addition, little is known about the evolutionary history of Leymus. Here, we investigate the phylogenetic relationship, genome donor, and evolutionary history of Leymus based on a single-copy nuclear Acc1 gene.     

Negative regulating factors of notch signaling may be a key factor for the teeth root formation

It is still an open question that how the teeth root development is initiated at the molecular level. But what we know is that the teeth root development begins after the crown part is completely formed, and then the terminal cervical loop structure faces two developmental fate options when the crown development is quite advanced: it can remain as a ‘crown’ pattern, and continue enamel production, or it can adopt the ‘root’ fate, and begins teeth root development. Epithelial notch and mesenchymal fgf10 signaling are thought to be the key switches of root or crown development pattern. But, for a rodent's molars and incisors, it is very interesting that after a similar teeth crown developmental process, the late development for the molars and incisors is quite different: the molar germ forms a multi-rooted pattern, while the incisor germ forms a single-rooted analogue and without a really root development process. In a recent study, one of the negative regulating factors for notch signaling, sel1l was found strongly related to the molar root development. So we hypotheses that the negative regulating factors of notch signaling, may be the key signals to determine the tooth root developmental onset, and the quantity or function's abnormal of that factors, may lead to hypoplasia of the teeth root.     

Roles of SCaBP8 in salt stress response

The tissue-preferential distributed calcium sensors, SOS3 and SCaBP8, play important roles in SOS pathway to cope with saline conditions. Both SOS3 and SCaBP8 interact with and activate SOS2. However the regulatory mechanism for SOS2 activation and membrane recruitment by SCaBP8 differs from SOS3. SCaBP8 is phosphorylated by SOS2 at plasma membrane (PM) under salt stress. This phosphorylation anchors the SCaBP8-SOS2 complex on plasma membrane and activates PM Na⁺/H⁺ anti-porter, such as SOS1. Here, we describe that SOS2 has high binding affinity and catalytic efficiency to SCaBP8, suggesting that phosphorylation of SCaBP8 by SOS2 perhaps occurs rapidly in salt condition. SCaBP8 is also phosphorylated by PKS5 (SOS2-like Protein Kinase5) which negatively regulates PM H⁺-ATPase activity and functions in plant alkaline tolerance, providing a clue to roles of SCaBP8 in both salt and alkaline tolerance. SOS2 interacts with SOS3 and SCaBP8 with its FISL motif at C-terminus. However, luciferase activity complement assay indicates that SOS2 N-terminal is also essential for interacting with these proteins in plant.Key words: calcium signal, kinase activity, luciferase complementDue to their sessile nature, plants have developed elaborate strategies to deal with a number of environmental challenges. One overwhelming constraint is high salinity in the soil, which inhibits plant growth and decreases the agricultural productivity. Efflux and/or sequestering of sodium ion to apoplastic space/vacuolar are well-known cellular mechanisms that plants protect them from saline stress.¹ Recently identified SOS (salt overly sensitive) pathway plays critical roles in maintaining ion homeostasis in response to high salinity.² Two calcium sensors, SOS3 and SCaBP8 (SOS3-like calcium binding protein8), perceive cytosolic calcium signature triggered by salt, interact with and activate a Thr/Ser protein kinase, SOS2 and recruit it to the plasma membrane. Then, the formed SOS3-SOS2 or SCaBP8-SOS2 complex activates a PM Na⁺/H⁺ anti-porter, SOS1.^2–4 Moreover, SOS2 also regulates vascular Na⁺/H⁺ antiporter activity.⁵ Previously, we reported that SCaBP8 and SOS3 function distinctly in activation of SOS2.³ For instance, N-terminal myristoylation of SOS3 plays an important role in salt tolerance.⁶ However, there is no consensus myristoylated motif in SCaBP8. Instead, an N-terminal hydrophobic domain is sufficient to facilitate the association of SCaBP8 to plasma membrane.³ In addition, SCaBP8 is phosphorylated by SOS2 under salt stress and this phosphorylation stabilizes the interaction of SOS2 and SCaBP8.⁴ In this report, we describe that SCaBP8 possibly is rapidly phosphorylated by SOS2 under salt stress and also phosphorylated by another stress responsible protein kinase, implying additional roles of SCaBP8 in stress responses.     

Isolation and characterization of 12 polymorphic microsatellite markers from ladyfish (Elops saurus Linnaeus)

Ladyfish (Elops saurus Linnaeus) is an economically important marine fish species. 76 microsatellite loci were isolated from an enriched genomic library of Elops saurus. Twelve of these markers were polymorphic in a test population with alleles per locus ranging from three to nine. The number of observed, expected heterozygosity and polymorphism information content (PIC) per locus in 20 individuals ranged from 0.2000 to 1.0000, 0.1897–0.8846, 0.1769–0.8476, respectively. One markers significantly deviated from Hardy-Weinberg equilibrium after Bonferroni correction analysis and there was no significant linkage disequilibrium found between pairs of markers. As a result, 12 microsatellite markers probably should provide sufficient level of genetic diversity to investigate the fine-scale population structure, stock management and enhancement, genetic linkage map construction and molecular marker-assisted breeding in Elops saurus Linnaeus.     

Mitochondria: One of the origins for autophagosomal membranes?

Macroautophagy is a transport pathway to the lysosome/vacuole that contributes to the degradation of numerous intracellular components. Despite the recent advances achieved in the understanding of the molecular mechanism underlying macroautophagy, the membrane origin of autophagosomes, the hallmark of this process is still a mystery. It has been suggested that mitochondria may be one of the lipid sources for autophagosome formation and that possibly this organelle provides the phosphatidylethanolamine (PE) that covalently links to the members of the ubiquitin-like Atg8/microtubule-associated protein 1 light chain 3 (LC3) protein family. These lipidated proteins are inserted into the outer and inner surface of autophagosomes and are essential for the biogenesis of these large double-membrane vesicles. However, because PE is an integral component of all cellular membranes, designing appropriate experiments to determine the origin of the autophagosomal PE is not easy. In this review, we discuss the idea that mitochondria provide the pool of PE necessary for the autophagosome biogenesis and we propose some possible experimental approaches aimed to explore this possibility.     

Recurrent hepatocellular carcinoma cells with stem cell-like properties: possible targets for immunotherapy

Background aimsHepatocellular carcinoma (HCC) recurs with high frequency. Characterization of recurrent HCC cells will facilitate the design of future therapeutic strategies for recurrent HCC.MethodsTwo cell lines, Hep-11 and Hep-12, were established from the same HCC patient's primary and recurrent tumor tissues, respectively, and then analyzed for stem cell-like properties, immune evasion strategies and immunogenicity.ResultsCompared with Hep-11 cells, Hep-12 cells expressed higher levels of liver progenitor cell makers and displayed persistent tumorigenic potential in the serial transplantation assay. Although Hep-12 cells down-regulated human leukocyte antigen (HLA) class I expression, they could still be recognized and killed by autologous-activated tumor-infiltrating lymphocytes (TIL) in vitro. Pre-treatment with cytokines such as tumor necrosis factor-α (TNF-α) and interferon-γ (IFN-γ) increased the expression of HLA class I molecules on Hep-12 cells, and rendered them more susceptible to CD8⁺ T-cell-mediated recognition and TIL-mediated cytotoxicity in vitro.ConclusionsOur results indicate that Hep-12 cells possess stem cell-like properties, are susceptible to autologous-activated TIL-mediated recognition and cytotoxicity, and pre-treatment with TNF-α and IFN-γ enhances their immunogenicity. This is the first evidence to support the hypothesis that immunotherapy can be used to target recurrent HCC cells with stem cell-like properties. This strategy may be an effective therapeutic approach to prevent HCC recurrence and control recurrent HCC growth.