Integrating genetic and network analysis to characterize genes related to mouse weight

Systems biology approaches that are based on the genetics of gene expression have been fruitful in identifying genetic regulatory loci related to complex traits. We use microarray and genetic marker data from an F2 mouse intercross to examine the large-scale organization of the gene co-expression network in liver, and annotate several gene modules in terms of 22 physiological traits. We identify chromosomal loci (referred to as module quantitative trait loci, mQTL) that perturb the modules and describe a novel approach that integrates network properties with genetic marker information to model gene/trait relationships. Specifically, using the mQTL and the intramodular connectivity of a body weight–related module, we describe which factors determine the relationship between gene expression profiles and weight. Our approach results in the identification of genetic targets that influence gene modules (pathways) that are related to the clinical phenotypes of interest.     

Thy-1 regulates fibroblast focal adhesions, cytoskeletal organization and migration through modulation of p190 RhoGAP and Rho GTPase activity

The precise biological role of Thy-1, a glycophosphatidyl-inositol (GPI)-linked cell surface glycoprotein in non-caveolar lipid raft microdomains, remains enigmatic. Evidence suggests that Thy-1 affects intracellular signaling through src-family protein kinases, and modulates adhesive and migratory events, such as thymocyte adhesion and neurite extension. Primary fibroblasts sorted based on presence or absence of cell surface Thy-1 display strikingly distinct morphologies and differ with respect to production of and response to cytokines and growth factors. It is unclear the extent to which Thy-1 mediates these differences. Findings reported here indicate a novel role for Thy-1 in regulating the activity of Rho GTPase, a critical regulator of cellular adhesion and cytoskeletal organization. Endogenous or heterologous Thy-1 expression promotes focal adhesion and stress fiber formation, characteristic of increased Rho GTPase activity, and inhibits migration. Immunoblotting following transfection of RFL6 fibroblasts with Thy-1 demonstrates that Thy-1 expression inhibits src-family protein tyrosine kinase (SFK) activation, resulting in decreased phosphorylation of p190 Rho GTPase-activating protein (GAP). This results in a net increase in active Rho, and increased stress fibers and focal adhesions. We therefore conclude that Thy-1 surface expression regulates fibroblast focal adhesions, cytoskeletal organization and migration by modulating the activity of p190 RhoGAP and Rho GTPase.     

Influence of maternal environment on the number of transferable embryos obtained in response to superovulatory FSH treatments in ewes

In a first experiment, embryo viability was estimated after recovery in the uterus or the oviduct of 70 Manchega ewes following a treatment of superovulation with decreasing doses of OVAGEN. Fewer viable embryos (5.6 +/- 0.9 vs. 8.3 +/- 0.8, P < 0.05) and more degenerative embryos (31.3% vs. 6.8%, P < 0.005) were obtained from the uterus than from the oviduct respectively. In a second experiment performed on 14 ewes, embryo viability was analyzed in relation to the follicular population estimated by ultrasonography (follicles > or = 2 mm) at the first FSH administration. Progesterone (P4) and oestradiol 17beta (E2) concentrations were also determined from the beginning of the superovulation treatment to the recovery of the embryos. The number of viable embryos (4.3 +/- 1.4) was positively correlated (r = 0.824) with of 2-4 mm diameter follicles (P < 0.05), and with E2 concentrations at -12 h (r = 0.891, P < 0.01) , 0 h (r = 0.943, P < 0.0001) and +24 h (r = 0.948, P < 0.05) from estrus detection. Prolonged high levels of E2 up to 72 h with low levels of P4 on days 3 and 4 after estrus had a negative (P < 0.05) effect on embryo viability. These results indicate that ovarian response to superovulatory protocols is related to the individual variations in the number of follicles of 2-4 mm at the start of FSH treatment, and that embryo viability is conditioned by the steroid patterns during the time spent in the genital tract of the super-ovulated ewes.     

Differentiation of an adult neuron cell line increases susceptibility to rabies infection

A wide variety of in vitro models have been used for studying rabies infection, however, currently, no central nervous system (CNS) adult neuron cultures are available. The current study determined the susceptibility to rabies infection in an adult CNS neuron cell line (CAD-R1). Cultures of CAD-R1 cells were held for 5 days in medium containing serum (undifferentiated CAD-R1 cells) or in serum-free medium (differentiated CAD-R1 cells). They were then infected with highly neurotropic rabies virus (RV) strain (CVS), obtained from fibroblastic cells (CVS-BHK) or from adult mouse brain (CVS-MB). Undifferentiated and differentiated cells were infected with the two RV strains, but the percentage of infected cells in differentiated cultures was significantly greater (83% and 79%, respectively) than in undifferentiated cells (51% and 60%) (Student's t test<0.05). Susceptibility to infection apparently depended on cellular differentiation state, possibly due to acquisition of additional morphological and biochemical characteristics during the differentiation process that made them more susceptible to RV infection. Therefore, CAD R1 cells may represent a good model for RV infection, making them a useful tool for studying RV neurotropism, infection pathogeny, isolation of street virus or producing safer and most potent vaccines.     

Isolation and characterization of new proliferating cell nuclear antigen (POL30) mutator mutants that are defective in DNA mismatch repair

A number of studies have suggested a role for proliferating cell nuclear antigen (PCNA) in DNA mismatch repair (MMR). However, the majority of mutations in the POL30 gene encoding PCNA that cause MMR defects also cause replication and other repair defects that contribute to the increased mutation rate caused by these mutations. Here, 20 new pol30 mutants were identified and screened for MMR and other defects, resulting in the identification of two mutations, pol30-201 and pol30-204, that appear to cause MMR defects but little if any other defects. The pol30-204 mutation altered an amino acid (C81R) in the monomer-monomer interface region and resulted in a partial general MMR defect and a defect in MSH2-MSH6 binding in vitro. The pol30-201 mutation altered an amino acid (C22Y) located on the surface of the PCNA trimer that slides over the DNA but did not cause a defect in MSH2-MSH6 binding in vitro. The pol30-201 mutation caused an intermediate mutator phenotype. However, the pol30-201 mutation caused almost a complete defect in the repair of AC and GT mispairs and only a small defect in the repair of a "+T" insertion, an effect similar to that caused by an msh6Delta mutation, indicating that pol30-201 primarily effects MSH6-dependent MMR. The chromosomal double mutant msh3-FF>AA msh6-FF>AA eliminating the conserved FF residues of the PCNA interacting motif of these proteins caused a small (<10%) defect in MMR but showed synergistic interactions with mutations in POL30, indicating that the FF>AA substitution may not eliminate PCNA interactions in vivo. These results indicate that the interaction between PCNA and MMR proteins is more complex than was previously appreciated.     

Population of the black howler monkey (Alouatta pigra) in a fragmented landscape in Palenque,Chiapas, Mexico

Little is known about the population characteristics of Alouatta pigra under conditions of forest fragmentation-information that is important to understanding its tolerance to habitat loss. In this work we present data on forest loss and on troop size, age, and sex composition for a population of black howler monkeys existing in the fragmented landscape surrounding the Mayan site of Palenque, Chiapas, Mexico. Two aerial photos (1:70,000) of the study area (261 km(2)) taken in 1984 and 2001 were examined to assess forest loss. Between June and December 2001 and January and March 2002 we surveyed 44 forest fragments for the presence of howler monkeys. Examination of aerial photos showed that 33% of the forest present in 1984 had disappeared by 2001, and detected an increment in the number of forest fragments present in the landscape. We discovered a total of 115 howler monkeys living in 22 of the 44 forest fragments studied, of which 107 were members of 18 troops. The rest were solitary males or small groups of males living in isolated forest fragments. Troop size ranged from two to 15 individuals (mean 5.9+3.0 ind). 31% and 15% of individuals in the troops were juveniles and infants, respectively, suggesting continued reproductive activity. Howler monkey troops in the forest fragments were on average smaller (5.9+/-3.0 ind) than troops in the nearby protected forest of the Mayan site (7.0+/-2.8 ind). The mean density of howlers in the forest fragments was 119+/-82.9 ind/km(2). The establishment of corridors is suggested as a possible conservation scenario for the fragmented howler population investigated, and as a conservation measure to connect this population with the howler population found in the protected forest of the Mayan site.     

Abundance of Gall Midges on Poulsenia armata (Moraceae): Importance of Host Plant Size and Light Environment in Tropical Rain Forests1

We studied the effects of contrasting light environments on the relationship between the host plant size of Poulsenia armata and the abundance of two gall midges in a tropical rain forest in Veracruz, Mexico. The number and density of two gall morphs (i.e., laminar and vein‐petiole galls) were positively correlated with plant size only in trees found in the forest but not in gaps. The availability of foliar area of P. armata trees was greater in forest gaps than in the forest. The foliar area was positively correlated with the abundance of laminar galls in trees in forest sites, but not with vein‐petiole galls. We concluded that the abundance of two morphs of gall midges on P. armata was associated with host plant size only in the forest trees. Larger plants had more galls than small plants, although this relationship was affected by local light environments.     

Genotypic Characterization of the Common Bean Bacterial Blight Pathogens, Xanthomonas axonopodis pv. phaseoli and Xanthomonas axonopodis pv. phaseoli var. fuscans by rep-PCR and PCR–RFLP of the Ribosomal Genes

Common bacterial blight (CBB), caused by Xanthomonas axonopodis pv. phaseoli and X. axonopodis pv. phaseoli var. fuscans is one of the most destructive diseases of common bean worldwide. The interrelatedness, genetic diversity and geographical distribution of the CBB pathogens was assessed using restriction fragment length polymorphism (RFLP) analysis of polymerase chain reaction amplified 16S ribosomal gene, including the 16S–23S intergenic spacer region and repetitive element PCR (rep‐PCR). RFLP profiles generated by the restriction endonucleases MboI, RsaI and HaeIII differentiated X. axonopodis pv. phaseoli from X. axonopodis pv. phaseoli var. fuscans and non‐pathogenic Xanthomonas species associated with common bean. Cluster analysis of rep‐PCR profiles revealed a high level of genetic differentiation (G_ST = 0.56) between the two CBB pathogens, showing that they are genetically distinct. Significant levels of genetic diversity were observed within each strain, indicating that the two bacteria are not clonal. More genetic diversity was observed in X. axonopodis pv. phaseoli (H = 0.134; I = 0.223) than X. axonopodis pv. phaseoli var. fuscans (H = 0.108; I = 0.184). However, no geographical differentiation was evident for either X. axonopodis pv. phaseoli var. fuscans (GST = 0.013) or X. axonopodis pv. phaseoli (G_ST = 0.017). This lack of geographical differentiation has important practical implications, as available host resistance genes are likely to be effective in controlling the disease in diverse geographical areas.