Electron microscopy of Xrcc4 and the DNA ligase IV–Xrcc4 DNA repair complex

The DNA ligase IV–Xrcc4 complex is responsible for the ligation of broken DNA ends in the non-homologous end-joining (NHEJ) pathway of DNA double strand break repair in mammals. Mutations in DNA ligase IV (Lig4) lead to immunodeficiency and radiosensitivity in humans. Only partial structural information for Lig4 and Xrcc4 is available, while the structure of the full-length proteins and their arrangement within the Lig4–Xrcc4 complex is unknown. The C-terminal domain of Xrcc4, whose structure has not been solved, contains phosphorylation sites for DNA-PKcs and is phylogenetically conserved, indicative of a regulatory role in NHEJ. Here, we have purified full length Xrcc4 and the Lig4–Xrcc4 complex, and analysed their structure by single-particle electron microscopy. The three-dimensional structure of Xrcc4 at a resolution of ～37 Å reveals that the C-terminus of Xrcc4 forms a dimeric globular domain connected to the N-terminus by a coiled-coil. The N- and C-terminal domains of Xrcc4 locate at opposite ends of an elongated molecule. The electron microscopy images of the Lig4–Xrcc4 complex were examined by two-dimensional image processing and a double-labelling strategy, identifying the site of the C-terminus of Xrcc4 and the catalytic core of Lig4 within the complex. The catalytic domains of Lig4 were found to be in the vicinity of the N-terminus of Xrcc4. We provide a first sight of the structural organization of the Lig4–Xrcc4 complex, which suggests that the BRCT domains could provide the link of the ligase to Xrcc4 while permitting some movements of the catalytic domains of Lig4. This arrangement may facilitate the ligation of diverse configurations of damaged DNA.     

Quantitative and qualitative analysis of cellular prion protein (PrPC) expression in bovine somatic tissues

The host encoded cellular prion protein (PrP^C) is an N-linked glycoprotein tethered to the cell membrane by a glycophosphatidylinositol (GPI) anchor. Under certain conditions, PrP^C can undergo conversion into a conformationally-altered isoform (PrP^Sc) widely believed to be the pathogenic agent of transmissible spongiform encephalopathies (TSEs). Understanding the tissue-specific expression of PrP^C is crucial considering that cells expressing high levels of PrP^C bear a risk for conversion and accumulation of PrP^Sc. In the present study, fifteen bovine somatic tissues were analyzed for PrP^C expression by quantitative western blot and immunohistochemistry. Quantitative western blot analysis revealed highest expression of PrP^C in cerebellum, obex and spinal cord. Intermediate levels were detected in thymus, intestine, nerve, heart and spleen, and lower levels in lung, muscle, kidney, lymph node, skin, pancreas and liver. Immunohistochemical analysis detected intense cellular-specific PrP^C staining in neurons, thymocytes and lymphocytes. PrP^C was also detected in the enteric wall, pancreatic islets of langerhans, myocardium, pulmonary alveolar sacs, renal glomeruli and dermal epithelial cells. This study demonstrated the quantitatively varied, wide-spread, tissue- and cell-specific expression pattern of PrP^C in bovine somatic tissues. The importance of this study is to lay the foundation for understanding the tissue-specific expression of PrP^C and to consider the potential participation of more bovine tissues in the transmission of BSE infection.Key words: cellular prion protein (PrP^C), protein expression, bovine somatic tissues, BSE, western blot, immunohistochemistry     

Spatio-Temporal Tracking and Phylodynamics of an Urban Dengue 3 Outbreak in S?o Paulo,Brazil

The dengue virus has a single-stranded positive-sense RNA genome of ∼10.700 nucleotides with a single open reading frame that encodes three structural (C, prM, and E) and seven nonstructural (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5) proteins. It possesses four antigenically distinct serotypes (DENV 1–4). Many phylogenetic studies address particularities of the different serotypes using convenience samples that are not conducive to a spatio-temporal analysis in a single urban setting. We describe the pattern of spread of distinct lineages of DENV-3 circulating in São José do Rio Preto, Brazil, during 2006. Blood samples from patients presenting dengue-like symptoms were collected for DENV testing. We performed M-N-PCR using primers based on NS5 for virus detection and identification. The fragments were purified from PCR mixtures and sequenced. The positive dengue cases were geo-coded. To type the sequenced samples, 52 reference sequences were aligned. The dataset generated was used for iterative phylogenetic reconstruction with the maximum likelihood criterion. The best demographic model, the rate of growth, rate of evolutionary change, and Time to Most Recent Common Ancestor (TMRCA) were estimated. The basic reproductive rate during the epidemics was estimated. We obtained sequences from 82 patients among 174 blood samples. We were able to geo-code 46 sequences. The alignment generated a 399-nucleotide-long dataset with 134 taxa. The phylogenetic analysis indicated that all samples were of DENV-3 and related to strains circulating on the isle of Martinique in 2000–2001. Sixty DENV-3 from São José do Rio Preto formed a monophyletic group (lineage 1), closely related to the remaining 22 isolates (lineage 2). We assumed that these lineages appeared before 2006 in different occasions. By transforming the inferred exponential growth rates into the basic reproductive rate, we obtained values for lineage 1 of R₀ = 1.53 and values for lineage 2 of R₀ = 1.13. Under the exponential model, TMRCA of lineage 1 dated 1 year and lineage 2 dated 3.4 years before the last sampling. The possibility of inferring the spatio-temporal dynamics from genetic data has been generally little explored, and it may shed light on DENV circulation. The use of both geographic and temporally structured phylogenetic data provided a detailed view on the spread of at least two dengue viral strains in a populated urban area.     

Impacts of the emerald ash borer (EAB) eradication and tree mortality: potential for a secondary spread of invasive plant species

Since the discovery of the emerald ash borer in 2002, eradication efforts have been implemented in an attempt to eliminate or contain the spread of this invasive beetle. The eradication protocol called for the removal of every ash tree within a 0.8 km radius around an infested tree. In 2005 this study was established to identify environmental changes attributed to the eradication program and measure subsequent shifts in forest community composition and structure. We conducted this study in Ohio and compared areas that received the eradication treatment (ash trees cut down), to areas that were left uncut, (ash still standing). The goal of this project was to identify how the plant community is responding in these two areas. The eradication protocol accelerated the formation and size of gaps within the forest and thus increased the duration and intensity of light penetrating through to the forest floor. In addition, the use of track vehicles for removal of cut trees resulted in significant soil compaction. The resultant plant community had greater species diversity (H′). When specific species composition differences were compared, an increase in the establishment of invasive plant species was detected in areas that received eradication efforts compared to those that did not. Invasive species accounted for 18.7% of the total herbaceous cover in this highly disturbed environment which included Cirsium arvense, Rhamnus cathartica and 2 species of Lonicera. In contrast, invasive species accounted for <1% of the total herbaceous cover in the undisturbed uncut areas.     

Interactive Effects of Three Ecosystem Engineers on Infiltration in a Semi-Arid Mediterranean Grassland

The redistribution of water in semi-arid environments is critical for the maintenance and survival of vegetation patches. We used a systems approach to examine the interactive effects of three engineers—Stipa tenacissima, biological soil crusts, and the European rabbit (Oryctolagus cuniculus)—on infiltration processes in a model gypseous semi-arid Mediterranean grassland. We measured the early (sorptivity) and later (steady-state infiltration) stages of infiltration at two supply potentials using disk permeameters, which allowed us to determine the relative effects of different engineers and soil micropores on water flow through large macropores. We detected few effects under tension when flow was restricted to matrix pores, but under ponding, sorptivity and steady-state infiltration adjacent to Stipa tussocks were 2–3 times higher than in intact or rabbit-disturbed biological soil crusts. Structural Equation Modeling (SEM) showed that both Stipa and biological soil crust cover exerted substantial and equal positive effects on infiltration under ponding, whereas indirectly, rabbit disturbance negatively affected infiltration by reducing crust cover. Under tension, when macropores were prevented from conducting water, Stipa had a direct negative effect and biological soil crust cover was relatively unimportant. More complex SEM models demonstrated that (1) Stipa primarily influenced biological soil crusts by reducing their richness, (2) rabbits exerted a small negative effect on crust richness, and (3) lichens were negatively, and mosses positively, correlated with a derived “infiltration” axis. Our results highlight the importance of biological soil crusts as key players in the maintenance of infiltration processes in Stipa grasslands, and demonstrate the modulating role played by rabbits through their surface disturbances.     

An α‐amylase is a novel receptor for Bacillus thuringiensis ssp. israelensis Cry4Ba and Cry11Aa toxins in the malaria vector mosquito Anopheles albimanus (Diptera: Culicidae)

Bacillus thuringiensis ssp. israelensis (Bti) produces four Cry toxins (Cry4Aa, Cry4Ba, Cry10Aa and Cry11Aa), and two Cyt proteins (Cyt1Aa and Cyt2Ba), toxic to mosquito‐larvae of the genus Aedes, Anopheles and Culex, important human disease vectors that transmit dengue virus, malaria and filarial parasites respectively. Previous work showed that Bti is highly toxic to Anopheles albimanus, the main vector for transmission of malaria in Mexico. In this work, we analysed the toxicity of isolated Cry proteins of Bti and identified an An. albimanus midgut protein as a putative Cry4Ba and Cry11Aa receptor molecule. Biossays showed that Cry4Ba and Cry11Aa of Bti are toxic to An. albimanus larvae. Ligand blot assays indicated that a 70 kDa glycosylphosphatidylinositol‐anchored protein present in midgut brush border membrane vesicles of An. albimanus interacts with Cry4Ba and Cry11Aa toxins. This protein was identified as an α‐amylase by mass spectrometry and enzymatic activity assays. The cDNA that codes for the α‐amylase was cloned by means of 5′‐ and 3′‐RACE experiments. Recombinant α‐amylase expressed in Escherichia coli specifically binds Cry4Ba and Cry11Aa toxins.     

A new herrerasaurid (Dinosauria, Saurischia) from the Upper Triassic Ischigualasto Formation of northwestern Argentina

Herrerasauridae comprises a basal clade of dinosaurs best known from the Upper Triassic of Argentina and Brazil, which have yielded remains of Herrerasaurus ischigualastensis and Staurikosaurus pricei, respectively. Systematic opinion regarding the position of Herrerasauridae at the base of Dinosauria has varied. Here we describe a new herrerasaurid, Sanjuansaurus gordilloi gen. n., sp. n., based on a partial skeleton from Carnian-age strata of the the Upper Triassic Ischigualasto Formation of northwestern Argentina. The new taxon is diagnosed by numerous features, including long, band-shaped and posterolaterally oriented transverse process on the posterior cervical vertebrae; neural spines of the sixth to eighth dorsal vertebrae, at least, bearing acute anterior and posterior processes; scapula and coracoid with everted lateral margins of the glenoid; and short pubis (63% of the femoral length). Phylogenetic analysis placed Sanjuansaurus within a monophyletic Herrerasauridae, at the base of Theropoda and including Herrerasaurus and Staurikosaurus. The presence of Sanjuansaurus at the base of the Ischigualasto Formation, along with other dinosaurs such as Herrerasaurus, Eoraptor, Panphagia, and Chromogisaurus suggests that saurischian dinosaurs in southwestern Pangea were already widely diversified by the late Carnian rather than increasing in diversity across the Carnian-Norian boundary.     

Use of microbial activity parameters for determination of a biosolid stability index

Variations in microbial activity during the aerobic digestion of sludge generated at wastewater treatment plants were studied. Results obtained by the measurement of enzymatic activity and microbiological parameters were compared with those determined by traditional methods (COD, suspended solids, etc.). Their variation with digestion time was monitored for batch digestion over a period of 135 days. The relationship between these measurements and control parameters of the sludge was also investigated. It was found that the traditional physicochemical and microbiological parameters present a series of problems which detract from their usefulness. The enzymatic parameters dehydrogenase activity (primary metabolism) and esterase activity (secondary metabolism) are better able to characterise the process, and the ratio of these two variables may be used to estimate the degree of endogenesis and, consequently, the degree of stability of the aerobic sludge digestion. In addition, these techniques are swift and simple to employ.     

Integron-sequestered dihydrofolate reductase: a recently redeployed enzyme

The introduction and wide use of antibacterial drugs has resulted in the emergence of resistant organisms. DfrB dihydrofolate reductase (DHFR) is a bacterial enzyme that is uniquely associated with mobile gene cassettes within integrons, and confers resistance to the drug trimethoprim. This enzyme has intrigued microbiologists since it was discovered more than thirty years ago because of its simple structure, enzymatic inefficiency and its virtual insensitivity to trimethoprim. Here, for the first time, a comprehensive discussion of genetic, evolutionary, structural and functional studies of this enzyme is presented together. This information supports the ideas that DfrB DHFR is a poorly adapted catalyst and has recently been recruited to perform a novel enzymatic activity in response to selective pressure.