A three-dimensional model of the U1 small nuclear ribonucleoprotein particle

Most of the pre-mRNAs in the eukaryotic cell are comprised of protein-coding exons and non-protein-coding introns. The introns are removed and the exons are ligated together, or spliced, by a large, macromolecular complex known as the spliceosome. This RNA-protein assembly is made up of five uridine-rich small nuclear RNAs (U1-, U2-, U4-, U5- and U6-snRNA) as well over 300 proteins, which form small nuclear ribonucleoprotein particles (snRNPs). Initial recognition of the 5′ exon/intron splice site is mediated by the U1 snRNP, which is composed of the U1 snRNA as well as at least ten proteins. By combining structural informatics tools with the available biochemical and crystallographic data, we attempted to simulate a complete, three dimensional U1 snRNP from the silk moth, Bombyx mori. Comparison of our model with empirically derived crystal structures and electron micrographs pinpoints both the strengths and weaknesses in the in silico determination of macromolecular complexes. One of the most striking differences between our model and experimentally generated structures is in the positioning of the U1 snRNA stem-loops. This highlights the continuing difficulties in generating reliable, complex RNA structures; however, three-dimensional modeling of individual protein subunits by threading provided models of biological significance and the use of both automated and manual docking strategies generated a complex that closely reflects the assembly found in nature. Yet, without utilizing experimentally-derived contacts to select the most likely docking scenario, ab initio docking would fall short of providing a reliable model. Our work shows that the combination of experimental data with structural informatics tools can result in generation of near-native macromolecular complexes.     

Glycosyl conjugates of biotinylated diaminopyridine applied for study of carbohydrate-to-carbohydrate interaction

Previous studies by us and others established that cell-cell adhesion is mediated by specific carbohydrate-to-carbohydrate interaction (CCI). Those previous studies were based on various biochemical and biophysical approaches, including the use of labeled glycosyl epitopes with fluorescent tag. However, these methods ideally require that the glycosyl epitope must be fixed to a solid phase molecule, preferably with multivalency. The purpose of the present study is to establish a CCI process using specific glycosyl residues conjugated to biotinylated diaminopyridine (BAP), and to observe: (i) clear occurrence of homotypic CCI between “Os Fr.B” having 5–6 GlcNAc termini, vs. absence of such homotypic CCI between “Os Fr.1” having 2 GlcNAc termini; (ii) occurrence of heterotypic CCI between GM3 ganglioside and Os Fr.B, vs. absence of such heterotypic CCI between GM3 and Os Fr.1. Interaction between Os Fr.B-BAP conjugate and Os Fr.B-ceramide mimetic (Os Fr.B-mCer) was demonstrated based on two experiments: (i) dose-dependent binding of Os Fr.B-BAP conjugate to polystyrene plates coated with Os Fr.B-mCer was observed in the presence of bivalent cation, a prerequisite for all CCI processes, and such binding was abolished by EDTA; (ii) binding between equal nanomolar Os Fr.B-BAP and Os Fr.B-mCer was inhibited by mM concentration Os Fr.B without conjugate, in dose-dependent manner. Thus, cell adhesion processes based on homotypic CCI between N-linked glycans having multiple GlcNAc termini, and heterotypic CCI between GM3 and such glycans, were clearly observed using BAP conjugates of glycosyl epitopes.     

Using diffusion distances for flexible molecular shape comparison

Background  

Many molecules are flexible and undergo significant shape deformation as part of their function, and yet most existing molecular shape comparison (MSC) methods treat them as rigid bodies, which may lead to incorrect shape recognition.     

Factors associated with whole carcass condemnation rates in provincially-inspected abattoirs in Ontario 2001-2007: implications for food animal syndromic surveillance

Background  

Ontario provincial abattoirs have the potential to be important sources of syndromic surveillance data for emerging diseases of concern to animal health, public health and food safety. The objectives of this study were to: (1) describe provincially inspected abattoirs processing cattle in Ontario in terms of the number of abattoirs, the number of weeks abattoirs process cattle, geographical distribution, types of whole carcass condemnations reported, and the distance animals are shipped for slaughter; and (2) identify various seasonal, secular, disease and non-disease factors that might bias the results of quantitative methods, such as cluster detection methods, used for food animal syndromic surveillance.     

Estimation of transport distance of fine particulate organic matter in relation to channel morphology in tailwaters of the Lake Biwa and reservoir dams

Knowledge on transport and deposition of fine particulate organic matter (FPOM) from reservoir dams is increasingly required for habitat management and restoration of dam tailwater ecosystems. Variations in the transport distance of FPOM, however, have never been studied well, particularly in relation to channel morphology, due to channel size restrictions of artificial tracers such as corn pollen when applied to larger river channels. This study aims to show the relations between FPOM retention efficiency and channel morphology in dam tailwaters using lentic plankters as tracers. We estimated the mean transport distance, S _p, by calculating downstream reduction ratios of lentic tracer plankters and calculated the deposition velocity, v _dep. Suspended FPOM samples were collected in tailwaters of two river channels below reservoir dams and two artificial canals below Lake Biwa in the Yodo River system. The longest S _p (19.2 km) and the shortest one (2.2 km) were recorded in the deep canal and shallow canal, respectively, showing a positive correlation with channel hydraulic radius. The values of v _dep were 4.7–6.4 times higher in river channels than in artificial canals. These results indicate that increasing complexity of bed morphology can minimize S _p, whereas bed degradation and armored bed materials may lead to increased S _p. Advantages of lentic plankters as tracers for estimating distance ranges of reservoir dam impact on river ecosystems are also discussed.     

Viral and Bacterial Pathogens in Bovine Respiratory Disease in Finland

Pathogens causing bovine respiratory tract disease in Finland were investigated. Eighteen cattle herds with bovine respiratory disease were included. Five diseased calves from each farm were chosen for closer examination and tracheobronchial lavage. Blood samples were taken from the calves at the time of the investigation and from 86 calves 3–4 weeks later. In addition, 6–10 blood samples from animals of different ages were collected from each herd, resulting in 169 samples. Serum samples were tested for antibodies to bovine parainfluenza virus-3 (PIV-3), bovine respiratory syncytial virus (BRSV), bovine coronavirus (BCV), bovine adenovirus-3 (BAV-3) and bovine adenovirus-7 (BAV-7). About one third of the samples were also tested for antibodies to bovine virus diarrhoea virus (BVDV) with negative results. Bacteria were cultured from lavage fluid and in vitro susceptibility to selected antimicrobials was tested. According to serological findings, PIV-3, BAV-7, BAV-3, BCV and BRSV are common pathogens in Finnish cattle with respiratory problems. A titre rise especially for BAV-7 and BAV-3, the dual growth of Mycoplasma dispar and Pasteurella multocida, were typical findings in diseased calves. Pasteurella sp. strains showed no resistance to tested antimicrobials. Mycoplasma bovis and Mannheimia haemolytica were not found.     

Selecting high-dimensional mixed graphical models using minimal AIC or BIC forests

Background  

Chow and Liu showed that the maximum likelihood tree for multivariate discrete distributions may be found using a maximum weight spanning tree algorithm, for example Kruskal's algorithm. The efficiency of the algorithm makes it tractable for high-dimensional problems.     

Habitat characteristics contributing to local occupancy and habitat use in rock pool <Emphasis Type="Italic">Daphnia</Emphasis> metapopulations

The effects of invasive macrophytes, water level fluctuations and predation on freshwater unionids Pyganodon grandis and Utterbackia imbecillis were studied in three small impoundments in Northeastern Texas in 2003–2005. Mussel density was sampled with quadrats. Mortality, associated with the water level fluctuations and predation, was estimated by collecting dead shells on the shore at about two month intervals. In two ponds, horizontal distribution of unionids was limited by dense beds of invasive and noxious macrophytes (mainly Eurasian watermilfoil Myriophyllum spicatum and American lotus Nelumbo lutea): mussel densities were significantly lower in these macrophyte beds (P < 0.001). In the third pond with the lowest density of macrophytes (stonewort Chara sp.), unionids were distributed more evenly, and the average unionid biomass was the highest among all ponds studied. Vertical distribution of unionids in all ponds was likely limited by low oxygen at depth >2 m. The total amount of shells found on the shore per year varied from 0.1% to 28% of the total population in the pond and was negatively correlated with water level (r = −0.72 to −0.81, P < 0.005). Mammalian predators consumed up to 19% of the total unionid population and predation was facilitated by water level fluctuations. Handling editor: K. Martens