Disease-driven detection of differential inherited SNP modules from SNP network

Detection of the synergetic effects between variants, such as single-nucleotide polymorphisms (SNPs), is crucial for understanding the genetic characters of complex diseases. Here, we proposed a two-step approach to detect differentially inherited SNP modules (synergetic SNP units) from a SNP network. First, SNP-SNP interactions are identified based on prior biological knowledge, such as their adjacency on the chromosome or degree of relatedness between the functional relationships of their genes. These interactions form SNP networks. Second, disease-risk SNP modules (or sub-networks) are prioritised by their differentially inherited properties in IBD (Identity by Descent) profiles of affected and unaffected sibpairs. The search process is driven by the disease information and follows the structure of a SNP network. Simulation studies have indicated that this approach achieves high accuracy and a low false-positive rate in the identification of known disease-susceptible SNPs. Applying this method to an alcoholism dataset, we found that flexible patterns of susceptible SNP combinations do play a role in complex diseases, and some known genes were detected through these risk SNP modules. One example is GRM7, a known alcoholism gene successfully detected by a SNP module comprised of two SNPs, but neither of the two SNPs was significantly associated with the disease in single-locus analysis. These identified genes are also enriched in some pathways associated with alcoholism, including the calcium signalling pathway, axon guidance and neuroactive ligand-receptor interaction. The integration of network biology and genetic analysis provides putative functional bridges between genetic variants and candidate genes or pathways, thereby providing new insight into the aetiology of complex diseases.     

Effects of Aluminum Exposure on the Adherence, Chemotaxis, and Phagocytosis Capacity of Peritoneal Macrophages in Rats

To investigate the effects of aluminum (Al) exposure on peritoneal macrophages of Wistar rats, four groups of ten rats each were orally exposed to 0, 13, 26, and 52?mg?kg(-1) Al(3+) in form of aluminum trichloride (AlCl(3)) in drinking water for 120?days. At the end of the experimental period, the Al concentration in serum, the adherence, chemotaxis, and phagocytosis capacity of peritoneal macrophages were determined. The results showed that the Al concentration in serum significantly increased in a dose-dependent manner; the adherence, chemotaxis, and phagocytosis capacity of peritoneal macrophages decreased with the increase of Al dose, and present a dose-effective relationship. Further, they were significantly lower in the high-dose groups (P?相似文献   

Length–weight relationships for 39 species of moray eel from the waters around Taiwan

Length–weight relationships were determined in 39 muraenid species belonging to seven genera collected during 2003–2008 from the waters around Taiwan. Various fishing methods were used to collect both the adult and pre‐adult moray eel specimens. Length–weight relationship records of 28 species are provided for the first time. New maximum size records of six species were also established: 61.2 cm for Gymnothorax monostigma, 88.2 cm for G. niphostigmus, 68.6 cm for G. shaoi, 53.9 cm for G. taiwanensis, 73.2 cm for G. thyrsoideus, and 37.3 cm for U. micropterus.     

Impaired wound healing with defective expression of chemokines and recruitment of myeloid cells in TLR3-deficient mice

Skin injury evokes both innate and adaptive immune responses to restore tissue integrity. TLRs play a critical role in host responses to injurious insults. Previous studies demonstrated that RNAs released from damaged tissues served as endogenous ligands for TLR3. In this study, we investigated the involvement of TLR3 in skin restoration after injury. Full excisional wounds were created on the skin of mice with TLR3 deficiency. We found that skin wound closure in TLR3(-/-) mice was significantly delayed compared with control littermates. Wound healing parameters, including re-epithelialization, granulation formation, and neovascularization, were decreased in TLR3(-/-) mice. Further studies revealed that the absence of TLR3 led to defective recruitment of neutrophils and macrophages, in association with decreased expression of the chemokines, MIP-2/CXCL2, MIP-1α/CCL3, and MCP-1/CCL2, in the wound. Moreover, in wild type mice, the mRNA level and protein content of TLR3 was significantly upregulated in wounded skins and silencing of TLR3 signal adaptor Toll/IL-1R domain-containing adapter inducing IFN-β with small interfering RNA retarded wound closure. These results indicate an essential role for TLR3 and Toll/IL-1R domain-containing adapter inducing IFN-β in wound healing by regulating chemokine production and recruitment of myeloid cells to wound for tissue repair.     

Records of anglerfishes (Lophiiformes: Lophiidae) from the western South Pacific Ocean, with descriptions of two new species

Species of Lophiidae collected from the western South Pacific Ocean are examined. Nine nominal species are recognized, all but one species with their distributions extended eastwards and southwards from the western Pacific Ocean. Two new species are described from Polynesia. Lophiodes iwamotoi n. sp. is described from five specimens collected from Savannah Seamount. It is characterized by a relatively long third dorsal-fin spine (56.9-70.8% standard length, L(S)) that extends (when retracted) to between the end of the soft dorsal fin and caudal-fin base; a relatively short fifth dorsal-fin spine (10.5-13.1% L(S)); a relatively short and narrow head; 19-20 pectoral-fin rays. Lophiodes maculatus n. sp. is described from 20 specimens collected from Marquesas Islands. It is characterized by an extremely long third dorsal-fin spine (71.9-87.2% L(S)), extending well beyond the caudal-fin base; a relatively short fifth dorsal-fin spine (11.4-16.5% L(S)); 17-18 pectoral-fin rays. A key to the lophiids in the western South Pacific Ocean is provided.     

A functional role for TorsinA in herpes simplex virus 1 nuclear egress

Herpes simplex virus 1 (HSV-1) capsids leave the nucleus by a process of envelopment and de-envelopment at the nuclear envelope (NE) that is accompanied by structural alterations of the NE. As capsids translocate across the NE, transient primary enveloped virions form in the perinuclear space. Here, we provide evidence that torsinA (TA), a ubiquitously expressed ATPase, has a role in HSV-1 nuclear egress. TA resides within the lumen of the endoplasmic reticulum (ER)/NE and functions in maintaining normal NE architecture. We show that perturbation of TA normal function by overexpressing torsinA wild type (TAwt) inhibits HSV-1 production. Ultrastructural analysis of infected cells overexpressing TAwt revealed reduced levels of surface virions in addition to accumulation of novel, double-membrane structures called virus-like vesicles (VLVs). Although mainly found in the cytoplasm, VLVs resemble primary virions in their size, by the appearance of the inner membrane, and by the presence of pUL34, a structural component of primary virions. Collectively, our data suggest a model in which interference of TA normal function by overexpression impairs de-envelopment of the primary virions leading to their accumulation in a cytoplasmic membrane compartment. This implies novel functions for TA at the NE.     

Potent and broad anti-HIV-1 activity exhibited by a glycosyl-phosphatidylinositol-anchored peptide derived from the CDR H3 of broadly neutralizing antibody PG16

PG9 and PG16 are two recently isolated quaternary-specific human monoclonal antibodies that neutralize 70 to 80% of circulating HIV-1 isolates. The crystal structure of PG16 shows that it contains an exceptionally long CDR H3 that forms a unique stable subdomain that towers above the antibody surface to confer fine specificity. To determine whether this unique architecture of CDR H3 itself is sufficient for epitope recognition and neutralization, we cloned CDR H3 subdomains derived from human monoclonal antibodies PG16, PG9, b12, E51, and AVF and genetically linked them to a glycosyl-phosphatidylinositol (GPI) attachment signal. Each fusion gene construct is expressed and targeted to lipid rafts of plasma membranes through a GPI anchor. Moreover, GPI-CDR H3(PG16, PG9, and E51), but not GPI-CDR H3(b12 and AVF), specifically neutralized multiple clades of HIV-1 isolates with a great degree of potency when expressed on the surface of transduced TZM-bl cells. Furthermore, GPI-anchored CDR H3(PG16), but not GPI-anchored CDR H3(AVF), specifically confers resistance to HIV-1 infection when expressed on the surface of transduced human CD4(+) T cells. Finally, the CDR H3 mutations (Y100HF, D100IA, and G7) that were previously shown to compromise the neutralization activity of antibody PG16 also abolished the neutralization activity of GPI-CDR H3(PG16). Thus, we conclude that the CDR H3 subdomain of PG16 neutralizes HIV-1 when targeted to the lipid raft of the plasma membrane of HIV-1-susceptible cells and that GPI-CDR H3 can be an alternative approach for determining whether the CDR H3 of certain antibodies alone can exert epitope recognition and neutralization.