Alginate production and <Emphasis Type="Italic">alg8</Emphasis> gene expression by <Emphasis Type="Italic">Azotobacter vinelandii</Emphasis> in continuous cultures

Alginates are polysaccharides that are used as thickening agents, stabilizers, and emulsifiers in various industries. These biopolymers are produced by fermentation with a limited understanding of the processes occurring at the cellular level. The objective of this study was to evaluate the effects of agitation rate and inlet sucrose concentrations (ISC) on alginate production and the expression of the genes encoding for alginate-lyases (algL) and the catalytic subunit of the alginate polymerase complex (alg8) in chemostat cultures of Azotobacter vinelandii ATCC 9046. Increased alginate production (2.4 g l⁻¹) and a higher specific alginate production rate (0.1 g g⁻¹ h⁻¹) were obtained at an ISC of 15 g l⁻¹. Carbon recovery of about 100% was obtained at an ISC of 10 g l⁻¹, whereas it was close to 50% at higher ISCs, suggesting that cells growing at lower sucrose feed rates utilize the carbon source more efficiently. In each of the steady states evaluated, an increase in algL gene expression was not related to a decrease in alginate molecular weight, whereas an increase in the molecular weight of alginate was linked to higher alg8 gene expression, demonstrating a relationship between the alg8 gene and alginate polymerization in A. vinelandii for the first time. The results obtained provide a possible explanation for changes observed in the molecular weight of alginate synthesized and this knowledge can be used to build a recombinant strain able to overexpress alg8 in order to produce alginates with higher molecular weights.     

Climate-driven changes in pollinator assemblages during the last 60?years in an Arctic mountain region in Northern Scandinavia

Climate change is occurring more rapidly in the Arctic than elsewhere, and is predicted to have a large impact on biodiversity, since entire cold-adapted ecosystems are likely to disappear. Here, we highlight changes in the insect species richness and community composition of wild bees, butterflies and moths over 60 years in an area situated above the tree limit (Padjelanta National Park) in northern Sweden. Although there were changes in habitat availability, indicated by a significant decrease in the area of a glacier (from 22 km² in 1898 to 7.5 km² in 2009), and an increase in the area of birch forest in the National Park, we nevertheless found relatively moderate changes in the insect communities. Indeed, the observed number of species increased from 52 in 1944 to 64 in 2008. Remarkably, the mean number of butterflies and moths per site, but not wild bee species, increased significantly. Among the species that were recorded in both periods, the average altitude of 17 species had shifted downhill, 12 shifted uphill, and the altitude of the remaining 17 had not changed. While alterations in community composition were greater at the highest altitudes, changes in the insect community were smaller than expected, indeed much smaller than those reported from agricultural landscapes in North-West Europe. Interestingly, our results suggest that lower alpine altitudes (600–800 m a.s.l.) have become colonized by southern species, but also that high alpine areas (above 1,000 m a.s.l.) have recently become colonized by high alpine species previously absent from these sites, likely as a result of increasing habitat availability. We conclude that wild bee, butterfly, and moth communities in Arctic areas in northern Sweden are in flux, as a result of climate change and suggest that increased attention must be given to conservation planning in cold areas. In addition, we propose that monitoring programs should be established, because more pronounced climate-driven changes can be expected in the future.     

Linaria dalmatica invades south-facing slopes and less grazed areas in grazing-tolerant mixed-grass prairie

Identifying environments where invasive plants are most invasive is key to understanding causes of invasion and developing effective management strategies. In mixed-grass prairie, invasive plants are often successful in relatively wet, nitrogen-rich areas, and areas protected from grazing. Dalmatian toadflax, a common invader of mixed-grass prairie, can also be favored by high water and nitrogen availability, but is thought to be relatively unpalatable to cattle, and therefore favored by grazing. We used spatially-adjusted model selection techniques to quantify relationships between toadflax cover (measured using very high-resolution aerial imagery), and relative snow deposition (estimated with a blowing snow model), slope, aspect, soil texture, and grazing intensity (estimated by proximity to water tanks). Toadflax was common throughout the 400 ha study site, occurring in 742 of 1,861 images. Toadflax cover was high on steeper slopes, particularly those with southern aspects. These two topographic variables were more effective in explaining toadflax distribution than modeled snow deposition, suggesting that factors other than snow deposition cause toadflax invasion on south-facing slopes. Toadflax cover was also high in areas further from water tanks, indicating that grazing may inhibit toadflax invasion. More broadly, this result suggests that grazing can reduce invasion of even relatively unpalatable species in ecosystems with long evolutionary histories of grazing.     

A prevalent alpha-proteobacterium Paracoccus sp. in a population of the Cayenne ticks (Amblyomma cajennense) from Rio de Janeiro,Brazil

As Rocky Mountain Spotted Fever is the most common tick-borne disease in South America, the presence of Rickettsia sp. in Amblyomma ticks is a possible indication of its endemicity in certain geographic regions. In the present work, bacterial DNA sequences related to Rickettsia amblyommii genes in A. dubitatum ticks, collected in the Brazilian state of Mato Grosso, were discovered. Simultaneously, Paracoccus sp. was detected in aproximately 77% of A. cajennense specimens collected in Rio de Janeiro, Brazil. This is the first report of Paracoccus sp. infection in a specific tick population, and raises the possibility of these bacteria being maintained and/or transmitted by ticks. Whether Paracoccus sp. represents another group of pathogenic Rhodobacteraceae or simply plays a role in A. cajennense physiology, is unknown. The data also demonstrate that the rickettsial 16S rRNA specific primers used forRickettsia spp. screening can also detect Paracoccus alpha-proteobacteria infection in biological samples. Hence, a PCR-RFLP strategy is presented to distinguish between these two groups of bacteria.     

Multiplexing and multivariate analysis in neurodegeneration

Limited sample volume is often an obstacle in clinical research and one way to circumvent this is to use multiplex techniques where several different analytes are simultaneously measured. There is a multitude of different platforms that can be used for multiplexing and their uniqueness and similarities will be described. Multivariate analysis is a powerful tool for extracting information from multiplex data. An introduction to one such algorithm is presented followed by examples from the literature, in the field of neurodegeneration, where multiplex and multivariate methods have been used.     

A Genotypic Test for HIV-1 Tropism Combining Sanger Sequencing with Ultradeep Sequencing Predicts Virologic Response in Treatment-Experienced Patients

A tropism test is required prior to initiation of CCR5 antagonist therapy in HIV-1 infected individuals, as these agents are not effective in patients harboring CXCR4 (X4) coreceptor-using viral variants. We developed a clinical laboratory-based genotypic tropism test for detection of CCR5-using (R5) or X4 variants that utilizes triplicate population sequencing (TPS) followed by ultradeep sequencing (UDS) for samples classified as R5. Tropism was inferred using the bioinformatic algorithms geno2pheno_[coreceptor] and PSSM_x4r5. Virologic response as a function of tropism readout was retrospectively assessed using blinded samples from treatment-experienced subjects who received maraviroc (N = 327) in the MOTIVATE and A4001029 clinical trials. MOTIVATE patients were classified as R5 and A4001029 patients were classified as non-R5 by the original Trofile test. Virologic response was compared between the R5 and non-R5 groups determined by TPS, UDS alone, the reflex strategy and the Trofile Enhanced Sensitivity (TF-ES) test. UDS had greater sensitivity than TPS to detect minority non-R5 variants. The median log₁₀ viral load change at week 8 was −2.4 for R5 subjects, regardless of the method used for classification; for subjects with non-R5 virus, median changes were −1.2 for TF-ES or the Reflex Test and −1.0 for UDS. The differences between R5 and non-R5 groups were highly significant in all 3 cases (p<0.0001). At week 8, the positive predictive value was 66% for TF-ES and 65% for both the Reflex test and UDS. Negative predictive values were 59% for TF-ES, 58% for the Reflex Test and 61% for UDS. In conclusion, genotypic tropism testing using UDS alone or a reflex strategy separated maraviroc responders and non-responders as well as a sensitive phenotypic test, and both assays showed improved performance compared to TPS alone. Genotypic tropism tests may provide an alternative to phenotypic testing with similar discriminating ability.     

Automated whole animal bio-imaging assay for human cancer dissemination

A quantitative bio-imaging platform is developed for analysis of human cancer dissemination in a short-term vertebrate xenotransplantation assay. Six days after implantation of cancer cells in zebrafish embryos, automated imaging in 96 well plates coupled to image analysis algorithms quantifies spreading throughout the host. Findings in this model correlate with behavior in long-term rodent xenograft models for panels of poorly- versus highly malignant cell lines derived from breast, colorectal, and prostate cancer. In addition, cancer cells with scattered mesenchymal characteristics show higher dissemination capacity than cell types with epithelial appearance. Moreover, RNA interference establishes the metastasis-suppressor role for E-cadherin in this model. This automated quantitative whole animal bio-imaging assay can serve as a first-line in vivo screening step in the anti-cancer drug target discovery pipeline.