Whole-Genome Sequences of DA and F344 Rats with Different Susceptibilities to Arthritis,Autoimmunity, Inflammation and Cancer

DA (D-blood group of Palm and Agouti, also known as Dark Agouti) and F344 (Fischer) are two inbred rat strains with differences in several phenotypes, including susceptibility to autoimmune disease models and inflammatory responses. While these strains have been extensively studied, little information is available about the DA and F344 genomes, as only the Brown Norway (BN) and spontaneously hypertensive rat strains have been sequenced to date. Here we report the sequencing of the DA and F344 genomes using next-generation Illumina paired-end read technology and the first de novo assembly of a rat genome. DA and F344 were sequenced with an average depth of 32-fold, covered 98.9% of the BN reference genome, and included 97.97% of known rat ESTs. New sequences could be assigned to 59 million positions with previously unknown data in the BN reference genome. Differences between DA, F344, and BN included 19 million positions in novel scaffolds, 4.09 million single nucleotide polymorphisms (SNPs) (including 1.37 million new SNPs), 458,224 short insertions and deletions, and 58,174 structural variants. Genetic differences between DA, F344, and BN, including high-impact SNPs and short insertions and deletions affecting >2500 genes, are likely to account for most of the phenotypic variation between these strains. The new DA and F344 genome sequencing data should facilitate gene discovery efforts in rat models of human disease.     

C:N:P stoichiometry in Australian soils with respect to vegetation and environmental factors

Aims

We estimate organic carbon (C): total nitrogen (N): total phosphorus (P) ratios in soils under Australia’s major native vegetation groups.

Methods

We use digital datasets for climate, soils, and vegetation created for the National Land and Water Resources Audit in 2001. Analysis-of-variance is used to investigate differences in nutrient ratios between ecosystems. Linear discriminant analysis and logistic regression are used to investigate the relative importance of climatic variables and soil nutrients in vegetation patterns.

Results

We find that the N:P and C:P ratios have a greater range of values than the C:N ratio, although major vegetation groups tend to show similar trends across all three ratios. Some apparently homeostatic groupings emerge: those with very low, low, medium, or high N:P and C:P. Tussock grasslands have very low soil N, N:P, and C:P, probably due to frequent burning. Eucalypt woodlands have low soil N:P and C:P ratios, although their total P level varies. Rainforests and Melaleuca forests have medium soil N:P and C:P ratios, although their total P level is different. Heathlands, tall open eucalypt forests, and shrublands occur on soils with low levels of total P, and high N:P and C:P ratios that reflect foliar nutrient ratios and recalcitrant litter.

Conclusions

Certain plant communities have typical soil nutrient stoichiometries but there is no single Redfield-like ratio. Vegetation patterns largely reflect soil moisture but for several plant communities, eucalypt communities in particular, soil N and P (or N:P) also play a significant role. Soil N:P and the presence of Proteaceae appear indicative of nutrient constraints in ecosystems.     

A homogeneous and nonisotopic assay for phosphatidylinositol 4-kinases

Phosphatidylinositol 4-kinases (PI 4-kinases) catalyze the conversion of phosphatidylinositol to phosphatidylinositol 4-phosphate (PtdIns4P). The four known mammalian PI 4-kinases, PI4KA, PI4KB, PI4K2A, and PI4K2B have roles in intracellular lipid and protein trafficking. PI4KA and PI4KB also assist in the replication of several positive-sense RNA viruses. The identification of selective inhibitors of these kinases would be facilitated by assays suitable for high-throughput screening. We describe a homogeneous and nonisotopic assay for PI 4-kinase activity based on the bioluminescent detection of the ADP produced by kinase reactions. We have evaluated this assay with known nonselective inhibitors of PI 4-kinases and show that it performs similar to radiometric assay formats previously described in the literature. In addition, this assay generates Z-factor values of >0.7 for PI4KA in a 384-well format, demonstrating its suitability for high-throughput screening applications.     

Enzymatic and molecular characterization of an endo-1,3-β-d-glucanase from the crystalline styles of the mussel Perna viridis

The retaining endo-1,3-β-d-glucanase (EC 3.2.1.39) was isolated from the crystalline styles of the commercially available Vietnamese edible mussel Perna viridis. It catalyzes hydrolysis of β-1,3-bonds in glucans and enables to catalyze a transglycosylation reaction. Resources of mass-spectrometry for analysis of enzymatic products were studied. cDNA sequence of endo-1,3-β-d-glucanase was determined by RT-PCR in conjunction with the rapid amplification of cDNA ends (RACE) methods. The cDNA of 1380 bp contains an open reading frame of 1332 bp encoding a mature protein of 328 amino acids. On basis of amino acid sequence analysis endo-1,3-β-d-glucanase was classified as a glycoside hydrolase of family 16.     

Unique mating behavior,and reproductive biology of a simultaneous hermaphroditic marine flatworm (Platyhelminthes,Tricladida, Maricola)

Flatworms generally are simultaneous hermaphrodites that exhibit various kinds of mating behavior. Here we report on the mating behavior and reproductive biology of the planarian Paucumara falcata. We recognized three phases in its mating behavior: a courtship, copulation, and postcopulatory phase. During the last‐mentioned phase, the partners showed a unique and very characteristic behavior in which their bodies intertwined, forming a spiral. Histological study of partners in copula revealed that the sclerotic tip of the musculo‐parenchymatic organ pierces the body wall of the partner and then becomes lodged in its parenchyma, suggesting that this organ may act as an anchor, thus stabilizing the worms during copulation. Similar organs in other species of marine triclad may also perform a stabilizing role during copulation. During copulation in individuals of P. falcata, sperm transfer was reciprocal or only unilateral. Copulation duration ranged 13–35 min (average 20 ± 5 min), irrespective of whether the mating was successful (i.e., resulted in the production of fertile cocoons). The spiraling phase lasted on average 10 min; some worms did not show the postcopulatory spiraling phase during their mating behavior. After successful copulation, an individual worm produced 1–12 fertile cocoons over a period of 1–17 days; from a cocoon hatched either one young (in 70% of the cases), or two young worms.     

Ghd7 is a negative regulator of zinc concentration in brown rice

Molecular Breeding - In recent years, rice false smut (RFS) has grown from being a minor to a major disease affecting rice productivity. The genetic basis of the host’s defense against RFS is...     

Unravelling lactate-acetate and sugar conversion into butyrate by intestinal Anaerobutyricum and Anaerostipes species by comparative proteogenomics

The d - and l -forms of lactate are important fermentation metabolites produced by intestinal bacteria but are found to negatively affect mucosal barrier function and human health. Both enantiomers of lactate can be converted with acetate into the presumed beneficial butyrate by a phylogenetically related group of anaerobes, including Anaerobutyricum and Anaerostipes spp. This is a low energy yielding process with a partially unknown pathway in Anaerobutyricum and Anaerostipes spp. and hence, we sought to address this via a comparative genomics, proteomics and physiology approach. We compared growth of Anaerobutyricum soehngenii on lactate with that on sucrose and sorbitol. Comparative proteomics revealed complete pathway of butyrate formation from sucrose, sorbitol and lactate. Notably, a gene cluster, lctABCDEF was abundantly expressed when grown on lactate. This gene cluster encodes a lactate dehydrogenase (lctD), electron transport proteins A and B (lctCB), nickel-dependent racemase (lctE), lactate permease (lctF) and short-chain acyl-CoA dehydrogenase (lctG). Investigation of available genomes of intestinal bacteria revealed this new gene cluster to be highly conserved in only Anaerobutyricum and Anaerostipes spp. Present study demonstrates that A. soehngenii and several related Anaerobutyricum and Anaerostipes spp. are highly adapted for a lifestyle involving lactate plus acetate utilization in the human intestinal tract.     

Bringing the Visible Universe into Focus with Robo-AO

The angular resolution of ground-based optical telescopes is limited by the degrading effects of the turbulent atmosphere. In the absence of an atmosphere, the angular resolution of a typical telescope is limited only by diffraction, i.e., the wavelength of interest, λ, divided by the size of its primary mirror''s aperture, D. For example, the Hubble Space Telescope (HST), with a 2.4-m primary mirror, has an angular resolution at visible wavelengths of ~0.04 arc seconds. The atmosphere is composed of air at slightly different temperatures, and therefore different indices of refraction, constantly mixing. Light waves are bent as they pass through the inhomogeneous atmosphere. When a telescope on the ground focuses these light waves, instantaneous images appear fragmented, changing as a function of time. As a result, long-exposure images acquired using ground-based telescopes - even telescopes with four times the diameter of HST - appear blurry and have an angular resolution of roughly 0.5 to 1.5 arc seconds at best.Astronomical adaptive-optics systems compensate for the effects of atmospheric turbulence. First, the shape of the incoming non-planar wave is determined using measurements of a nearby bright star by a wavefront sensor. Next, an element in the optical system, such as a deformable mirror, is commanded to correct the shape of the incoming light wave. Additional corrections are made at a rate sufficient to keep up with the dynamically changing atmosphere through which the telescope looks, ultimately producing diffraction-limited images.The fidelity of the wavefront sensor measurement is based upon how well the incoming light is spatially and temporally sampled¹. Finer sampling requires brighter reference objects. While the brightest stars can serve as reference objects for imaging targets from several to tens of arc seconds away in the best conditions, most interesting astronomical targets do not have sufficiently bright stars nearby. One solution is to focus a high-power laser beam in the direction of the astronomical target to create an artificial reference of known shape, also known as a ''laser guide star''. The Robo-AO laser adaptive optics system^2,3 employs a 10-W ultraviolet laser focused at a distance of 10 km to generate a laser guide star. Wavefront sensor measurements of the laser guide star drive the adaptive optics correction resulting in diffraction-limited images that have an angular resolution of ~0.1 arc seconds on a 1.5-m telescope.