Efficient large-scale protein sequence comparison and gene matching to identify orthologs and co-orthologs

Broadly, computational approaches for ortholog assignment is a three steps process: (i) identify all putative homologs between the genomes, (ii) identify gene anchors and (iii) link anchors to identify best gene matches given their order and context. In this article, we engineer two methods to improve two important aspects of this pipeline [specifically steps (ii) and (iii)]. First, computing sequence similarity data [step (i)] is a computationally intensive task for large sequence sets, creating a bottleneck in the ortholog assignment pipeline. We have designed a fast and highly scalable sort-join method (afree) based on k-mer counts to rapidly compare all pairs of sequences in a large protein sequence set to identify putative homologs. Second, availability of complex genomes containing large gene families with prevalence of complex evolutionary events, such as duplications, has made the task of assigning orthologs and co-orthologs difficult. Here, we have developed an iterative graph matching strategy where at each iteration the best gene assignments are identified resulting in a set of orthologs and co-orthologs. We find that the afree algorithm is faster than existing methods and maintains high accuracy in identifying similar genes. The iterative graph matching strategy also showed high accuracy in identifying complex gene relationships. Standalone afree available from http://vbc.med.monash.edu.au/～kmahmood/afree. EGM2, complete ortholog assignment pipeline (including afree and the iterative graph matching method) available from http://vbc.med.monash.edu.au/～kmahmood/EGM2.     

Lake sturgeon population attributes and reproductive structure in the Namakan Reservoir,Minnesota and Ontario

Quantified were the age, growth, mortality and reproductive structure of lake sturgeon (Acipenser fulvescens) collected in the US and Canadian waters of the Namakan Reservoir. The hypotheses were tested that (i) age and growth of lake sturgeon in the Namakan Reservoir would differ by sex and reproductive stage of maturity, and (ii) that the relative strength of year‐classes of lake sturgeon in the reservoir would be affected by environmental variables. To quantify age, growth and mortality of the population, existing data was used from a multi‐agency database containing information on all lake sturgeon sampled in the reservoir from 2004 to 2009. Lake sturgeon were sampled in the Minnesota and Ontario waters of the Namakan Reservoir using multi‐filament gillnets 1.8 m high and 30–100 m long and varying in mesh size from 178 to 356 mm stretch. Reproductive structure of the lake sturgeon was assessed only during spring 2008 and 2009 using plasma testosterone and estradiol‐17β concentrations. Ages of lake sturgeon >75 cm ranged from 9 to 86 years (n = 533, mean = 36 years). A catch‐curve analysis using the 1981–1953 year classes estimated total annual mortality of adults to be 4.8% and annual survival as 95.2%. Using logistic regression analysis, it was found that total annual precipitation was positively associated with lake sturgeon year‐class strength in the Namakan Reservoir. A 10 cm increase in total annual precipitation was associated with at least a 39% increase in the odds of occurrence of a strong year class of lake sturgeon in the reservoir. Plasma steroid analysis revealed a sex ratio of 2.4 females: 1 male and, on average, 10% of female and 30% of male lake sturgeon were reproductively mature each year (i.e. potential spawners). Moreover, there was evidence based on re‐captured male fish of both periodic and annual spawning, as well as the ability of males to rapidly undergo gonadal maturation prior to spawning. Knowledge of lake sturgeon reproductive structure and factors influencing recruitment success contribute to the widespread conservation efforts for this threatened species.     

Local people value environmental services provided by forested parks

Garnering support from local people is critical for maintaining ecologically viable and functional protected areas. However, empirical data illustrating local people’s awareness of the importance of nature’s services is limited; hence possibly impeding effective ecosystem (environmental)-services based conservation efforts. Using data from five protected forests in four developing Southeast Asian countries, we provide evidence that local people living near parks value a wide range of environmental services, including cultural, provisioning, and regulating services, provided by the forests. Local people with longer residency valued environmental services more. Educated as well as poor people valued forest ecosystem services more. Conservation education has some influence on people’s environmental awareness. For conservation endeavors to be successful, large-scale transmigration programs should be avoided and local people must be provided with alternative sustenance opportunities and basic education in addition to environmental outreach to reduce their reliance on protected forests and to enhance conservation support.     

Effect of physiological concentrations of insulin and antidiabetic drugs on RNA release from isolated liver nuclei

The addition of 10(-11) M insulin to a cell-free system from rat liver promotes the release of messengerlike RNA from isolated prelabeled nuclei. The stimulation was similar whether the nuclei were preincubated with insulin, or if insulin was added directly to the cell-free system with or without a protease inhibitor. Dot blot hybridization using cloned cDNA for alpha 2u-globulin mRNA showed that this was one of the messages whose release was enhanced by insulin. Nuclei isolated from rats treated with either of the antidiabetics tolbutamide or tolazamide showed no increase in RNA release in the presence of insulin over the concentration range 10(-5) - 10(-14) M. Furthermore, these nuclei did not release detectable levels of alpha 2u-globulin mRNA.     

Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules

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Phylogeny and historical biogeography of the cave-adapted shrimp genus Typhlatya (Atyidae) in the Caribbean Sea and western Atlantic

Aim To infer phylogenetic relationships among five species of the cave‐adapted shrimp genus Typhlatya in order to test competing hypotheses of dispersal and colonization of the disjunct cave localities occupied by these five species. Location Typhlatya species are found in caves and anchialine ponds across the northern margin of the Caribbean Sea, along the Mediterranean and Adriatic coasts and on oceanic islands in the Atlantic and eastern Pacific oceans. This study focuses on five species, one from Bermuda, one from the Caicos Islands and three from the Yucatan Peninsula of Mexico. Methods Partial sequences (c. 1400 bp) from the mitochondrial cytochrome b, 16S rDNA and COI genes were obtained from representative samples of the five species. Phylogenetic inference was carried out with maximum parsimony and maximum likelihood analyses. Parsimony networks were constructed for the Bermudian species Typhlatya iliffei and one Yucatan species Typhlatya mitchelli, to determine the degree of connectivity among populations inhabiting different cave systems. Results All three land masses were recovered as monophyletic. The two insular marine species from Bermuda and the Caicos Islands formed a clade, while the three continental freshwater species from the Yucatan Peninsula formed another. Within both Bermuda and the Yucatan, shared haplotypes were found in different cave systems, suggesting recent or ongoing gene flow among populations in both locales. Main conclusions The two insular marine Typhlatya species originated from an ancestral marine population, possibly already cave‐adapted, that is suggested to have colonized the Caicos Islands and subsequently dispersed to Bermuda via the Gulf Stream. Divergence estimates suggest that colonization occurred before the formation of present‐day anchialine cave habitat, which did not form on either island until the late Pliocene to early Pleistocene. Divergence estimates also indicate that the Yucatan freshwater species split before the formation of freshwater cave habitat in the Yucatan. These species could have inhabited crevicular marine habitats before the late Pliocene/early Pleistocene in the Yucatan or elsewhere in the Caribbean, and subsequently migrated to freshwater caves once they formed.     

Cereal rust fungi genomics and the pursuit of virulence and avirulence factors

Rust diseases cause significant reductions annually in yield of cereal crops worldwide. Traditional monoculture cropping systems apply significant selection pressure on the pathogen to cause rapid shifts in pathotypes. Plant breeders strive to stay ahead of the evolving pathogens by releasing new crop genotypes with new rust resistance genes or gene combinations. Owing to the limited number of known resistance genes and the lack of molecular understanding of the plant-pathogen interaction, rusts remain challenging organisms to study, both at organismal and molecular levels. This review discusses recent progress by a number of laboratories towards better understanding the molecular component of rust disease resistance.     

Last glacial maximum biomes reconstructed from pollen and plant macrofossil data from northern Eurasia

Pollen and plant macrofossil data from northern Eurasia were used to reconstruct the vegetation of the last glacial maximum (LGM: 18,000 ± 2000 ¹⁴C yr bp ) using an objective quantitative method for interpreting pollen data in terms of the biomes they represent ( Prentice et al., 1996 ). The results confirm previous qualitative vegetation reconstructions at the LGM but provide a more comprehensive analysis of the data. Tundra dominated a large area of northern Eurasia (north of 57°N) to the west, south and east of the Scandinavian ice sheet at the LGM. Steppe‐like vegetation was reconstructed in the latitudinal band from western Ukraine, where temperate deciduous forests grow today, to western Siberia, where taiga and cold deciduous forests grow today. The reconstruction shows that steppe graded into tundra in Siberia, which is not the case today. Taiga grew on the northern coast of the Sea of Azov, about 1500 km south of its present limit in European Russia. In contrast, taiga was reconstructed only slightly south of its southern limit today in south‐western Siberia. Broadleaved trees were confined to small refuges, e.g. on the eastern coast of the Black Sea, where cool mixed forest was reconstructed from the LGM data. Cool conifer forests in western Georgia were reconstructed as growing more than 1000 m lower than they grow today. The few scattered sites with LGM data from the Tien‐Shan Mountains and from northern Mongolia yielded biome reconstructions of steppe and taiga, which are the biomes growing there today.     

Succinic acid production from wheat using a biorefining strategy

The biosynthesis of succinic acid from wheat flour was investigated in a two-stage bio-process. In the first stage, wheat flour was converted into a generic microbial feedstock either by fungal fermentation alone or by combining fungal fermentation for enzyme and fungal bio-mass production with subsequent flour hydrolysis and fungal autolysis. In the second stage, the generic feedstock was converted into succinic acid by bacterial fermentation by Actinobacillus succinogenes. Direct fermentation of the generic feedstock produced by fungal fermentation alone resulted in a lower succinic acid production, probably due to the low glucose and nitrogen concentrations in the fungal broth filtrate. In the second feedstock production strategy, flour hydrolysis conducted by mixing fungal broth filtrate with wheat flour generated a glucose-rich stream, while the fungal bio-mass was subjected to autolysis for the production of a nutrient-rich stream. The possibility of replacing a commercial semi-defined medium by these two streams was investigated sequentially. A. succinogenes fermentation using only the wheat-derived feedstock resulted in a succinic acid concentration of almost 16 g l^–1 with an overall yield of 0.19 g succinic acid per g wheat flour. These results show that a wheat-based bio-refinery employing coupled fungal fermentation and subsequent flour hydrolysis and fungal autolysis can lead to a bacterial feedstock for the efficient production of succinic acid.