In silico screening and biological evaluation of inhibitors of Src-SH3 domain interaction with a proline-rich ligand

Src signalling and transduction are directly involved in cell growth, cell cycle, malignant transformation and cell migration, providing therapeutic opportunities through inhibition of Src. Here we report virtual screening for novel compounds that inhibit the Src-SH3 protein-protein interaction with a proline-rich peptide ligand. Computational docking of the ZINC compound database was performed using GOLD. Top-scoring compounds were assayed using a fluorescence polarization-based assay. A benzoquinoline derivative showed micromolar inhibition of binding between Src-SH3 and the proline-rich peptide. Several analogues were subsequently assayed showing the requirement of a linker between the benzoquinoline and phenyl rings, and electron donating substituents on the phenyl ring.     

Ceramicines B–D,new antiplasmodial limonoids from Chisocheton ceramicus

Three new limonoids, ceramicines B–D (1–3), have been isolated from the bark of Chisocheton ceramicus. Structures and stereochemistry of 1–3 were fully elucidated and characterized by 2D NMR analysis. Ceramicines exhibited a moderate antiplasmodial activity.     

A predominant β-CGTase G1 engineered to elucidate the relationship between protein structure and product specificity

Low reaction yields and the high cost of obtaining a single type of pure CD make γ-CD costly. Using rational design and with the aid of 3D modeling structures, recombinant CGTase from Bacillus sp. G1 was molecularly engineered with the aim of producing a higher percentage of γ-CD. A single mutation at subsite −3, denoted H43T, was found to increase γ-CD production from 10% to approximately 39% using tapioca starch. This novel increment was probably the result of reduced steric hindrance to the formation of γ-CD because of the shortened side chain together with the shortened loop at positions 86–89, at substrate-binding subsite −3. A mutation (Tyr188 → Trp) and a deletion at loop 139–144 showed little effect on product specificity; however, mutagenesis at these sites affected cyclization, coupling and hydrolysis activities as well as the kinetic properties of the mutant CGTase. Based on rational design, three further mutations of the mutant H43T (denoted H43T/Δ(139–144)/S134T/A137V/L138D/V139I, H43T/S85G and H43T/Y87F) were constructed and produced γ-CD with yields of 20%, 20% and 39%, respectively. The mutant H43T/Δ(139–144)/S134T/A137V/L138D/V139I had very low cyclization and coupling activities, however their hydrolysis activity was retained. Double mutation (H43T/S85G) caused the enzyme to exhibit higher starch hydrolysis activity, approximately 26 times higher than the native CGTase G1. Although the mutants H43T and H43T/Y87F could produce the same percentage (39%) of γ-CD, the latter was more efficient as the total amount of CD produced was higher based on the V_max and k_cat values.     

Mutations in a BTB-Kelch Protein, KLHL7, Cause Autosomal-Dominant Retinitis Pigmentosa

Retinitis pigmentosa (RP) refers to a genetically heterogeneous group of progressive neurodegenerative diseases that result in dysfunction and/or death of rod and cone photoreceptors in the retina. So far, 18 genes have been identified for autosomal-dominant (ad) RP. Here, we describe an adRP locus (RP42) at chromosome 7p15 through linkage analysis in a six-generation Scandinavian family and identify a disease-causing mutation, c.449G→A (p.S150N), in exon 6 of the KLHL7 gene. Mutation screening of KLHL7 in 502 retinopathy probands has revealed three different missense mutations in six independent families. KLHL7 is widely expressed, including expression in rod photoreceptors, and encodes a 75 kDa protein of the BTB-Kelch subfamily within the BTB superfamily. BTB-Kelch proteins have been implicated in ubiquitination through Cullin E3 ligases. Notably, all three putative disease-causing KLHL7 mutations are within a conserved BACK domain; homology modeling suggests that mutant amino acid side chains can potentially fill the cleft between two helices, thereby affecting the ubiquitination complexes. Mutations in an identical region of another BTB-Kelch protein, gigaxonin, have previously been associated with giant axonal neuropathy. Our studies suggest an additional role of the ubiquitin-proteasome protein-degradation pathway in maintaining neuronal health and in disease.     

The Genomics of Speciation in Drosophila: Diversity, Divergence, and Introgression Estimated Using Low-Coverage Genome Sequencing

In nature, closely related species may hybridize while still retaining their distinctive identities. Chromosomal regions that experience reduced recombination in hybrids, such as within inversions, have been hypothesized to contribute to the maintenance of species integrity. Here, we examine genomic sequences from closely related fruit fly taxa of the Drosophila pseudoobscura subgroup to reconstruct their evolutionary histories and past patterns of genic exchange. Partial genomic assemblies were generated from two subspecies of Drosophila pseudoobscura (D. ps.) and an outgroup species, D. miranda. These new assemblies were compared to available assemblies of D. ps. pseudoobscura and D. persimilis, two species with overlapping ranges in western North America. Within inverted regions, nucleotide divergence among each pair of the three species is comparable, whereas divergence between D. ps. pseudoobscura and D. persimilis in non-inverted regions is much lower and closer to levels of intraspecific variation. Using molecular markers flanking each of the major chromosomal inversions, we identify strong crossover suppression in F₁ hybrids extending over 2 megabase pairs (Mbp) beyond the inversion breakpoints. These regions of crossover suppression also exhibit the high nucleotide divergence associated with inverted regions. Finally, by comparison to a geographically isolated subspecies, D. ps. bogotana, our results suggest that autosomal gene exchange between the North American species, D. ps. pseudoobscura and D. persimilis, occurred since the split of the subspecies, likely within the last 200,000 years. We conclude that chromosomal rearrangements have been vital to the ongoing persistence of these species despite recent hybridization. Our study serves as a proof-of-principle on how whole genome sequencing can be applied to formulate and test hypotheses about species formation in lesser-known non-model systems.     

Epistasis among Drosophila persimilis factors conferring hybrid male sterility with D. pseudoobscura bogotana

The Bateson-Dobzhansky-Muller model posits that hybrid incompatibilities result from genetic changes that accumulate during population divergence. Indeed, much effort in recent years has been devoted to identifying genes associated with hybrid incompatibilities, often with limited success, suggesting that hybrid sterility and inviability are frequently caused by complex interactions between multiple loci and not by single or a small number of gene pairs. Our previous study showed that the nature of epistasis between sterility-conferring QTL in the Drosophila persimilis-D. pseudoobscura bogotana species pair is highly specific. Here, we further dissect one of the three QTL underlying hybrid male sterility between these species and provide evidence for multiple factors within this QTL. This result indicates that the number of loci thought to contribute to hybrid dysfunction may have been underestimated, and we discuss how linkage and complex epistasis may be characteristic of the genetics of hybrid incompatibilities. We further pinpoint the location of one locus that confers hybrid male sterility when homozygous, dubbed "mule-like", to roughly 250 kilobases.     

Responses of pre‐dispersal seed predators to sequential flowering of Dipterocarps in Malaysia

Many species of Dipterocarpaceae and other plant families reproduce synchronously at irregular, multi‐year intervals in Southeast Asian forests. These community‐wide general flowering events are thought to facilitate seed survival through satiation of generalist seed predators. During a general flowering event, closely related Shorea species (Dipterocarpaceae) stagger their flowering times by several weeks, which may minimize cross pollination and interspecific competition for pollinators. Generalist, pre‐dispersal seed predators might also track flowering hosts and influence predator satiation. We addressed the question of whether pre‐dispersal seed predation differed between early and late flowering Shorea species by monitoring flowering, fruiting and seed predation intensity over two general flowering events at the Pasoh Research Forest, Malaysia. Pre‐dispersal insect seed predators killed up to 63 percent of developing seeds, with Nanophyes shoreae, a weevil that feeds on immature seeds being the most important predator for all Shorea species. This weevil caused significantly greater pre‐dispersal seed predation in earlier flowering species. Long larval development time precluded oviposition by adults that emerged from the earliest flowering Shorea on the final flowering Shorea. In contrast, larvae of weevils that feed on mature seeds before seed dispersal (Alcidodes spp.), appeared in seeds of all Shorea species almost simultaneously. We conclude that general flowering events have the potential to satiate post‐dispersal seed predators and pre‐dispersal seed predators of mature fruit, but are less effective at satiating pre‐dispersal predators of immature fruit attacking early flowering species.     

Density,distribution and population structure of <Emphasis Type="Italic">Opusia indica</Emphasis> (Ocypodoidae: Camptandriidae) in a coastal mangrove creek in Pakistan

The density, distribution and population structure of Opusia indica were studied through transects method. Two transects were delimited in a mangrove area of Korangi creek (24°79′ N/67°20′ E). On each transect, three 0.25 m² quadrats were sampled at three tidal levels on a monthly basis during low tide. A total of 1919 crabs were obtained, of which 775 were males, 945 were non-ovigerous females and 199 were ovigerous females. Density of crabs varied between 198 m⁻² to 798 m⁻². The density and size distribution showed significant difference from low tide level to high tide level and were positively correlated with the percent moisture, percent organic matter and sediment structure. Based on carapace width (CW) males were significantly larger than the females indicating sexual dimorphism. The monthly size frequency distribution of crabs showed recruitment of juvenile crabs (< than 4 mm) nearly throughout the year except in few months. The monthly sex ratio deviated from 1:1 throughout the year, with female bias (χ ² = 31.633, P = 0.001 and df =11). Breeding was seasonal with peaks in SW monsoon. Size at sexual maturity based on smallest ovigerous female was CW = 4.0 mm. The average number of eggs per female were 2066 ± 479 (n = 25). Positive linear relationship was observed between the size of the female crabs and the egg numbers (r ² = 0.554).