Demography and speciation history of the homoploid hybrid pine Pinus densata on the Tibetan Plateau

Pinus densata is an ecologically successful homoploid hybrid that inhabits vast areas of heterogeneous terrain on the south‐eastern Tibetan Plateau as a result of multiple waves of colonization. Its region of origin, route of colonization onto the plateau and the directions of introgression with its parental species have previously been defined, but little is known about the isolation and divergence history of its populations. In this study, we surveyed nucleotide polymorphism over eight nuclear loci in 19 representative populations of P. densata and its parental species. Using this information and coalescence simulations, we assessed the historical changes in its population size, gene flow and divergence in time and space. The results indicate a late Miocene origin for P. densata associated with the recent uplift of south‐eastern Tibet. The subsequent differentiation between geographical regions of this species began in the late Pliocene and was induced by regional topographical changes and Pleistocene glaciations. The ancestral P. densata population had a large effective population size but the central and western populations were established by limited founders, suggesting that there were severe bottlenecks during the westward migration out of the ancestral hybrid zone. After separating from their ancestral populations, population expansion occurred in all geographical regions especially in the western range. Gene flow in P. densata was restricted to geographically neighbouring populations, resulting in significant differentiation between regional groups. The new information on the divergence and demographic history of P. densata reported herein enhances our understanding of its speciation process on the Tibetan Plateau.     

Sharp genetic discontinuity across a unimodal Heliconius hybrid zone

Hybrid zones are powerful natural systems to study evolutionary processes to gain an understanding of adaptation and speciation. In the Cauca Valley (Colombia), two butterfly races, Heliconius cydno cydnides and Heliconius cydno weymeri, meet and hybridize. We characterized this hybrid zone using a combination of mitochondrial DNA (mtDNA) sequences, amplified fragment length polymorphisms (AFLPs), microsatellites and sequences for nuclear loci within and outside of the genomic regions that cause differences in wing colour pattern. The hybrid zone is largely composed of individuals of mixed ancestry. However, there is strong genetic discontinuity between the hybridizing races in mtDNA and, to a lesser extent, in all nuclear markers surveyed. The mtDNA clustering of H. c. cydnides with the H. cydno race from the Magdalena Valley and H. c. weymeri with the H. cydno race from the pacific coast suggests that H. c. cydnides colonized the Cauca Valley from the north, whereas H. c. weymeri did so by crossing the Andes in the southern part, implying a secondary contact origin. Colonization of the valley by H. cydno was accompanied by mimicry shift. Strong ecological isolation, driven by locally adaptive differences in mimetic wing patterns, is playing an important role in maintaining the hybrid zone. However, selection on wing pattern alone is not sufficient to explain the genetic discontinuity observed. There is evidence for differences in male mating preference, but the contribution of additional barriers needs further investigation. Overall, our results support the idea that speciation is a cumulative process, where the combination of multiple isolation barriers, combined with major phenotypic differences, facilitates population divergence in face of gene flow.     

Temperature stress increases hybrid incompatibilities in the parasitic wasp genus Nasonia

Hybrid incompatibilities, measured as mortality and sterility, are caused by the disruption of gene interactions. They are important post-zygotic isolation barriers to species hybridization, and much effort is put into the discovery of the genes underlying these incompatibilities. In hybridization studies of the haplodiploid parasitic wasp genus Nasonia, genic incompatibilities have been shown to affect mortality and sterility. The genomic regions associated with mortality have been found to depend on the cytotype of the hybrids and thus suggest cytonuclear incompatibilities. As environmental conditions can affect gene expression and gene interaction, we here investigate the effect of developmental temperature on sterility and mortality in Nasonia hybrids. Results show that extreme temperatures strongly affect both hybrid sterility (mainly spermatogenic failure) and mortality. Molecular mapping revealed that extreme temperatures increase transmission ratio distortion of parental alleles at incompatible loci, and thus, cryptic incompatible loci surface under temperature stress that remain undiscovered under standard temperatures. Our results underline the sensitivity of hybrid incompatibilities to environmental factors and the effects of unstable epistasis.     

A complete enzymatic recovery of ferulic acid from corn residues with extracellular enzymes from Neosartorya spinosa NRRL185

An economic ferulic acid recovery from biomass via biological methods is of interest for a number of reasons. Ferulic acid is a precursor to vanillin synthesis. It is also a known antioxidant with potential food and medical applications. Despite its universal presence in all plant cell wall material, the complex structure of the plant cell wall makes ferulic acid recovery from biomass a challenging bioprocess. Previously, without pretreatment, very low (3-13%) recovery of ferulic acid from corn residues was achieved. We report here the discovery of a filamentous fungus Neosartorya spinosa NRRL185 capable of producing a full complement of enzymes to release ferulic acid and the development of an enzymatic process for a complete recovery of ferulic acid from corn bran and corn fibers. A partial characterization of the extracellular proteome of the microbe revealed the presence of at least seven cellulases and hemicellulases activities, including multiple iso-forms of xylanase and ferulic acid esterase. The recovered ferulic acid was bio-converted to vanillin, demonstrating its potential application in natural vanillin synthesis. The enzymatic ferulic acid recovery accompanied a significant release of reducing sugars (76-100%), suggesting much broader applications of the enzymes and enzyme mixtures from this organism.     

Structural characteristics and physicochemical properties of oxidized corn starches varying in amylose content

The effects of amylose content on the extent of oxidation and the distribution of carboxyl groups in hypochlorite-oxidized corn starches were investigated. Corn starches including waxy corn starch (WC), common corn starch (CC), and 50% and 70% high-amylose corn starches (AMC) were oxidized with NaOCl at three concentrations (0.8%, 2%, and 5%). Carboxyl and carbonyl content of oxidized starches increased with increasing NaOCl concentration. High-AMC (70%) had slightly higher carboxyl and carbonyl contents at 0.8% NaOCl, whereas WC had significantly higher carboxyl and carbonyl contents at 2% and 5% NaOCl levels. Carbohydrate profiles by high-performance size-exclusion chromatography indicate that amylose was more susceptible to depolymerization than amylopectin. Degradation of amylopectin long chains (DP >24) was more pronounced in WC and CC than in AMCs. The crystalline lamellae of WC started to degrade at 2% NaOCl, but those of the other corn starches remained intact even at 5% NaOCl level according to X-ray crystallinity. By using anion-exchange chromatography for separation and size-exclusion chromatography for characterization, carboxyl groups were found to be more concentrated on amylopectin than on amylose, particularly in AMCs. Oxidation decreased gelatinization temperature and enthalpy with WC showing the most decrease and 70% AMC showing the least. The gelatinization enthalpy of 50% AMC decreased significantly faster than those of CC and 70% AMC after 0.8% oxidation. Retrogradation of amylopectin slightly increased after oxidation with increasing oxidation level. The peak viscosities of oxidized WC and CC were higher than those of their native counterparts at 0.8% NaOCl, but this increase was not observed in AMCs. The setback viscosities of 2% NaOCl-oxidized 50% and 70% AMCs were much higher than those of the unmodified counterparts. The extent of oxidation and physicochemical properties of oxidized starches varied greatly with the amylase:amylopectin ratio of corn starches. Amylose was suggested to play an important role in controlling the oxidation efficiency.     

Topological and dynamical properties of Azurin anchored to a gold substrate as investigated by molecular dynamics simulation

A classical molecular dynamics study of the electron transfer protein azurin, covalently bound to a gold substrate through its native disulphide group, is carried out at full hydration. With the aim of investigating the effects on the protein structure and dynamics as induced by the presence of an electric field, simulations are performed on neutral, positively and negatively charged substrates. A number of parameters, such as the average structure, the root mean square deviations and fluctuations, the intraprotein hydrogen bonds and solvent accessible surface of the protein, are monitored during 10 ns of run. The orientation, the height and the lateral size of the protein, with respect to the substrate are evaluated and compared with the experimental data obtained by scanning probe nanoscopies. The electron transfer properties between the copper redox center and the disulphide bridge bound to the substrate are investigated and briefly discussed.     

Mapping of genes expressed in activated porcine Peyer's patch

To determine the chromosomal locations for genes expressed in porcine Peyer's patches, polymerase chain reaction-based mapping of expressed sequence tags (ESTs) isolated from a porcine Peyer's patch-specific cDNA library was performed across a 6500-rad swine radiation hybrid panel. A total of 116 ESTs were mapped with LOD scores >6.0, and another 11 ESTs had LOD scores between 5.0 and 6.0. Of these 127 ESTs, 63% matched known genes (相似文献   

An integrated radiation hybrid map of bovine chromosome 18 that refines a critical region associated with multiple ocular defects in cattle

Congenital multiple ocular defects (MOD) of Japanese black cattle is a hereditary ocular disorder with an autosomal recessive mode of inheritance showing developmental defects of the lens, retina and iris, persistent embryonic eye vascularization and microphthalmia. The MOD locus has been mapped by linkage analysis to a 6.6-cM interval on the proximal end of bovine chromosome 18, which corresponds to human chromosome 16q and mouse chromosome 8. To refine the MOD region in cattle, we constructed an integrated radiation hybrid (RH) map of the proximal region of bovine chromosome 18, which consisted of 17 genes and 10 microsatellite markers, using the SUNbRH7000 panel. Strong conservation of gene order was found among the corresponding chromosomal regions in cattle, human and mouse. The MOD-critical region was fine mapped to a 59.5-cR region that corresponds to a 6.3-Mb segment of human chromosome 16 and a 4.8-Mb segment of mouse chromosome 8. Several positional candidate genes, including FOXC2 and USP10, were identified in this region.     

A high-resolution comparative radiation hybrid map of equine chromosome 4q12-q22

In this study, we present a comprehensive 5000-rad radiation hybrid map of a 40-cM region on equine chromosome 4 (ECA4) that contains quantitative trait loci for equine osteochondrosis. We mapped 29 gene-associated sequence tagged site markers using primers designed from equine expressed sequence tags or BAC clones in the ECA4q12-q22 region. Three blocks of conserved synteny, showing two chromosomal breakpoints, were identified in the segment of ECA4q12-q22. Markers from other segments of HSA7q mapped to ECA13p and ECA4p, and a region of HSA7p was homologous to ECA13p. Therefore, we have improved the resolution of the human-equine comparative map, which allows the identification of candidate genes underlying traits of interest.     

Citric acid production by Aspergillus niger on wet corn distillers grains

AIMS: To determine which citric acid-producing strain of Aspergillus niger utilized wet corn distillers grains most effectively to produce citric acid. METHODS AND RESULTS: Citric acid and biomass production by the fungal strains were analysed on the untreated grains or autoclaved grains using an enzyme assay and a gravimetric method respectively. Fungal citric acid production on the grains was found to occur on the untreated or autoclaved grains. The highest citric acid level on the grains was produced by A. niger ATCC 9142. The autoclaved grains supported less citric acid production by the majority of strains screened. Biomass production by the fungal strains on the untreated or autoclaved grains was quite similar. The highest citric acid yields for A. niger ATCC 9142, ATCC 10577, ATCC 11414, ATCC 12846 and ATCC 26550 were found on the untreated grains. Treatment of the grains had little effect on citric acid yields based on reducing sugars consumed by A. niger ATCC 9029 and ATCC 201122. CONCLUSIONS: It is feasible for citric acid-producing strains of A. niger to excrete citric acid on wet corn distillers grains whether the grains are treated or untreated. The most effective citric acid-producing strain of A. niger was ATCC 9142. SIGNIFICANCE AND IMPACT OF THE STUDY: The study shows that the ethanol processing co-product wet corn distillers grains could be utilized as a substrate for the commercial production of citric acid by A. niger without treatment of the grains.