Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes

Genome-wide experimental methods to identify disease genes, such as linkage analysis and association studies, generate increasingly large candidate gene sets for which comprehensive empirical analysis is impractical. Computational methods employ data from a variety of sources to identify the most likely candidate disease genes from these gene sets. Here, we review seven independent computational disease gene prioritization methods, and then apply them in concert to the analysis of 9556 positional candidate genes for type 2 diabetes (T2D) and the related trait obesity. We generate and analyse a list of nine primary candidate genes for T2D genes and five for obesity. Two genes, LPL and BCKDHA, are common to these two sets. We also present a set of secondary candidates for T2D (94 genes) and for obesity (116 genes) with 58 genes in common to both diseases.     

Identification and Characterization of the Cassava Core-Clock Gene EARLY FLOWERING 4

The angiosperm circadian clock has been well established from molecular-genetic studies in a temperate plant model. Conservation of clock function is less explored in plants from the tropics. Cassava (Manihot esculenta) is a staple crop grown in the tropics that has been of limited research interest, and more generally, research on photoperiod and clock genes has been sparse. EARLY FLOWERING 4 (AtELF4) of the temperate plant Arabidopsis thaliana (Arabidopsis) has been reported to be required for photoperiod perception and circadian function. Here, we describe our start to identify circadian and photoperiod genes in cassava with an account on the characterization of its ELF4 gene (MeELF4). After isolating MeELF4, a phylogenetic study was conducted and it was found to cluster within the ELF4 subclade of the ELF4/EFL super-family. Similar to studies in temperate plants, MeELF4 was shown to be an evening-expressed gene in cassava. This collectively suggested to us that MeELF4 could be a functional ortholog of AtELF4. To test this, complementation studies of MeELF4 were performed in the Arabidopsis elf4 mutant. Hypocotyl-length measurements and flowering-time analysis were performed. MeELF4-complementation transgenics in the elf4 background were restored to the wild-type growth habit, suggesting a total rescue of photoperiodic perception. To expand on the molecular role of MeELF4 in the resulting transgenic-complementation lines, the CCA1 and CCR2 promoter-luciferase markers where respectively introduced and bioluminescence-imaging experiments revealed a restoration of circadian-regulated gene expression. The collective results showed that the cassava gene MeELF4 is a functional clock ortholog of AtELF4.     

Interactions between thiamine and large anions. Crystal structures of (H-thiamine)[Pt(SCN)4] · 3H2O and (H-thiamine)[Pt(SCN)6] · H2O

The reaction of thiamine with K₂Pt^IICl₄ and with Pt^IVCl₄ in the presence of excess NaSCN in aqueous solution gave thiamine salts, (H-thiamine)[Pt(SCN)₄] · 3H₂O (1) and (H-thiamine)[Pt(SCN)₆] · H₂O (2), respectively, structures of which have been determined by X-ray diffraction. The thiamine molecule adopts the usual F conformation in each salt. In 1, [Pt(SCN)₄]²⁻ ions act as large planar spacers in the crystal lattice and interact scarcely with thiamine, except for a hydrogen bonding with the terminal hydroxy O(5γ). Instead, water molecules form two types of host–guest-like interactions with the pyrimidine and the thiazolium moieties of a thiamine molecule, one being a C(2)–Hwaterpyrimidine bridge and the other being an N(4′)–Hwaterthiazolium bridge. In 2, despite the much larger ion size, octahedral [Pt(SCN)₆]²⁻ ions form a C(2)–Hanionpyrimidine bridge and an N(4′)–Hanionthiazolium bridge. An additional hydrogen bonding between the anion and the terminal O(5γ) of thiamine creates a hydrogen-bonded macrocyclic ring {thiaminium–[Pt(SCN)₆]²⁻}₂, a supramolecule.     

Monoclonal antibodies against the presynaptic calcium channel antagonist omega-conotoxin GVI A from cone snail poison

Monoclonal antibodies have been prepared against omega-conotoxin GVI A, a peptide isolated from marine snails of the genus Conus (Conus geographus and Conus magus). This toxin is a blocker of select presynaptic Ca2+ channels in the central nervous system. Antigenic omega-conotoxin GVI A was synthesized as a covalent conjugate with bovine serum albumin and injected s.c. An ELISA assay combined with a competitive inhibition assay was used to select and characterize monoclonal antibodies able to recognize and bind the free toxin. Several of the antibodies were found to block omega-conotoxin GVI A inhibition of 45Ca transport into rat brain synaptosomes and to block omega-conotoxin GVI A binding to membranes from the same preparation. The antibodies recognize native, synthetic toxin, and are useful for analysis of toxin in biological fluids.     

A genome-wide scan of loci linked to serum adiponectin in two populations of African descent

Objective: The objectives were to identify quantitative trait loci linked to serum adiponectin concentration and to estimate heritability in two populations of African descent. Research Methods and Procedures: We conducted a genome scan for serum adiponectin concentration in two populations of African descent. Genome‐wide microsatelitte markers were typed in an African‐American population consisting of 203 families from the Chicago area and in a Nigerian Yoruba population consisting of 146 families. Linkage analysis was performed to identify loci. Variance component model was used to estimate heritability. Results: Estimates of heritability adjusted for age, gender, and BMI were 0.45 and 0.70 for the African‐American and Nigerian families, respectively. In both populations, adiponectin was significantly negatively correlated with BMI, height, and weight. After adjusting for age, gender, and BMI, we found evidence of genetic linkage to adiponectin on chromosomes 11 [limit of detection (LOD) score = 2.89] and 17 (LOD score = 1.35) in the Nigerian sample. Among the African‐Americans, we found genetic linkage on chromosomes 2 (LOD score = 1.82), 4 (LOD score = 2.12), and 11 (LOD score = 2.33). Analysis based on combined data yielded a maximum LOD score of 3.21 on chromosome 11. Discussion: Consistency of the finding on chromosome 11 suggests that this region is likely to be involved in regulation of adiponectin, either through a primary influence on hormone levels or through pathways influencing body composition. These results suggest that adiponectin could be a potential therapeutic target for obesity.     

A diverse array of genetic factors contribute to the pathogenesis of Systemic Lupus Erythematosus

Systemic lupus erythematosus (SLE) is a chronic systemic autoimmune disease with variable clinical presentation frequently affecting the skin, joints, haemopoietic system, kidneys, lungs and central nervous system. It can be life threatening when major organs are involved. The full pathological and genetic mechanisms of this complex disease are yet to be elucidated; although roles have been described for environmental triggers such as sunlight, drugs and chemicals, and infectious agents. Cellular processes such as inefficient clearing of apoptotic DNA fragments and generation of autoantibodies have been implicated in disease progression. A diverse array of disease-associated genes and microRNA regulatory molecules that are dysregulated through polymorphism and copy number variation have also been identified; and an effect of ethnicity on susceptibility has been described.     

Identification of an essential molecular contact point on the duck hepatitis B virus reverse transcriptase

The hepadnaviral polymerase (P) functions in a complex with viral nucleic acids and cellular chaperones. To begin to identify contacts between P and its partners, we assessed the exposure of the epitopes of six monoclonal antibodies (MAbs) to the terminal protein domain of the duck hepatitis B virus P protein in a partially denaturing buffer (RIPA) and a physiological buffer (IPP150). All MAbs immunoprecipitated in vitro translated P well in RIPA, but three immunoprecipitated P poorly in IPP150. Therefore, the epitopes for these MAbs were obscured in the native conformation of P but were exposed when P was in RIPA. Epitopes for MAbs that immunoprecipitated P poorly in IPP150 were between amino acids (aa) 138 and 202. Mutation of a highly conserved motif within this region (T3; aa 176 to 183) improved the immunoprecipitation of P by these MAbs and simultaneously inhibited DNA priming by P. Peptides containing the T3 motif inhibited DNA priming in a dose-dependent manner, whereas eight irrelevant peptides did not. T3 function appears to be conserved among the hepadnaviruses because mutating T3 ablated DNA synthesis in both duck hepatitis B virus and hepatitis B virus. These results indicate that (i) the conserved T3 motif is a molecular contact point whose ligand can be competed by soluble T3 peptides, (ii) the occupancy of T3 obscures the epitopes for three MAbs, and (iii) proper occupancy of T3 by its ligand is essential for DNA priming. Therefore, small-molecule ligands that compete for binding to T3 with its natural ligand could form a novel class of antiviral drugs.     

Hybridization and contemporary evolution in an introduced cichlid fish from Lake Malawi National Park

Rapidly evolving systems offer the chance to observe genetic and phenotypic change in real time. We exploit a well-characterized introduction of cichlid fish into Lake Malawi National Park to document a short history of habitat colonization and the evolution of genes and colour pattern. In the early 1960s, a fish exporter introduced individuals of Cynotilapia afra to a single site (Mitande Point) of Thumbi West Island and, as late as 1983, the species was confined to this location. In 2001, C. afra had colonized the entire perimeter of Thumbi West. In July of that year, we sampled C. afra individuals from six sites around the island and scored variation in dorsal fin colour as well as allelic diversity at six microsatellite loci. We found that, in two decades, C. afra had diverged into genetically distinct, phenotypically different northern and southern populations. We observed a high proportion of hybrids between the introduced C. afra and the native Metriaclima zebra on the southern coast of Thumbi West, and speculate that hybridization is facilitated by low water clarity at these windward sites. The short history of C. afra at Thumbi West is a microcosm of contemporary evolutionary divergence and may provide the opportunity to study the process from start to finish in genetic detail.     

Odontogenic tumors in Nigerian children and adolescents- a retrospective study of 92 cases

Background

Tumours arising from odontogenic tissues are rare and constitute a heterogenous group of interesting lesions. The aim of this study was to determine the relative frequency of odontogenic tumors (OT) among Nigerian children and adolescents 19 years or younger.

Patients and methods

The histopathology records were retrospectively reviewed for all the tumors and tumor-like lesions of the oral cavity and the jaws seen in children and adolescents ≤ 19 years seen between January 1980 and December 2003. Hematoxylin and eosin-stained sections were re-evaluated and the diagnosis in each case was confirmed or modified according to World Health Organization (WHO) classification, 1992; and were subjected to analysis of age, sex, site of tumor and histopathologic type.

Results

A total of 477 tumors and tumor-like lesions were seen in patients ≤ 19 years during the period of the study. Of these, 92 (19.3%) were odontogenic tumors. Benign odontogenic tumors constituted 98.9% of the cases seen, while only 1 case (1.1%) of malignant variety was seen during the period. The mean (SD) age of patients was 14.9 (± 3.1) years (range, 4–19 years). Male-to-female ratio was 1:1; and mandible-to-maxilla ratio was 2.7:1. OT's were most frequently seen in patients aged 16–19 years (46.7%) and the least number (2.2%) were found in patients aged 0–5 years. Among nine histologic types of OT seen, ameloblastoma (48.9%), adenomatoid odontogenic tumor (19.6%) and odontogenic myxoma (8.7%) were predominant. Multicystic/solid and unicystic variants of ameloblastoma were diagnosed in 40 (89%) and 5 (11%) cases respectively.

Conclusions

Odontogenic tumors are relatively common in children and adolescents in Nigeria. One out of every 5 children and adolescents with tumors and tumor-like lesions of oral cavity and the jaws seen in this study had a diagnosis of odontogenic tumor.