Modeling the climatic drivers of spatial patterns in vegetation composition since the Last Glacial Maximum

Projecting the future composition and function of communities is a major challenge, and there is an urgent need to develop, improve, and test the predictive capacity of ecological models under different climate states. We tested the effect of climate on spatial patterns of plant community composition over the past 21 000 yr, focusing on whether the spatial relationships between environmental distance and compositional dissimilarity are stable over time. We used a network of fossil‐pollen sites in eastern North America, combined with paleoclimate simulations from the Last Glacial Maximum (LGM; 21 000 calibrated years before present, 21 kyr BP) to the present. We modeled relationships between climate, geography, and compositional dissimilarity at 1 kyr periods using generalized dissimilarity modeling (GDM) and determined the strongest predictors of compositional dissimilarity. We assessed the performance of models calibrated for one time period (e.g. 14 kyr BP) in predicting patterns in the same period as well as at other times (e.g. 12 kyr BP), and tested whether predictive performance was related to the magnitude of climate change between the calibration and prediction time periods. Finally, we examined whether pooling data from multiple time periods improved predictive performance. Models explained 32 to 51% of compositional dissimilarity between locations within any single time period. The best set of predictors changed across time, with summer temperature and geographic distance the strongest predictors of compositional dissimilarity for most time periods. Models built for one time period explained turnover during nearby time periods relatively well, but performance decayed across time and with increasing climate change. Results were similar regardless of whether models were projected forward or backward through time, and did not improve when data were pooled across time. GDM predicts well the spatial patterns of past compositional dissimilarity and holds promise for modeling the drivers of compositional dissimilarity across space and time. However, the modeled relationships between compositional turnover and environmental distance are non‐stationary, so caution is needed when predicting across periods of significant climatic change.     

Human immunodeficiency virus viremia induces plasmacytoid dendritic cell activation in vivo and diminished alpha interferon production in vitro

Human immunodeficiency virus type 1 (HIV-1) infection has been associated with perturbations of plasmacytoid dendritic cells (PDC), including diminished frequencies in the peripheral blood and reduced production of type I interferons (IFNs) in response to in vitro stimulation. However, recent data suggest a paradoxical increase in production of type 1 interferons in vivo in HIV-infected patients compared to uninfected controls. Using a flow cytometric assay to detect IFN-alpha-producing cells within unseparated peripheral blood mononuclear cells, we observed that short-term interruptions of antiretroviral therapy are sufficient to result in significantly reduced IFN-alpha production by PDC in vitro in response to CpG A ligands or inactivated HIV particles. The primary cause of diminished IFN-alpha production was reduced responsiveness of PDC to de novo stimulation, not diminished per cell IFN-alpha production or migration of cells to lymphoid organs. Real-time PCR analysis of purified PDC from patients prior to and during treatment interruptions revealed that active HIV-1 replication is associated with upregulation of type I IFN-stimulated gene expression. Treatment of hepatitis C virus-infected patients with IFN-alpha2b and ribavirin for hepatitis C virus infection resulted in a profound suppression of de novo IFN-alpha production in response to CpG A or inactivated HIV particles, similar to the response observed in HIV-infected patients. Together, these results suggest that diminished production of type I interferons in vitro by PDC from HIV-1-infected patients may not represent diminished interferon production in vivo. Rather, diminished function in vitro is likely a consequence of prior activation via type I interferons or HIV virions in vivo.     

BeoBLAST: distributed BLAST and PSI-BLAST on a Beowulf cluster

BeoBLAST is an integrated software package that handles user requests and distributes BLAST and PSI-BLAST searches to nodes of a Beowulf cluster, thus providing a simple way to implement a scalable BLAST system on top of relatively inexpensive computer clusters. Additionally, BeoBLAST offers a number of novel search features through its web interface, including the ability to perform simultaneous searches of multiple databases with multiple queries, and the ability to start a search using the PSSM generated from a previous PSI-BLAST search on a different database. The underlying system can also handle automated querying for high throughput work. AVAILABILITY: Source code is available under the GNU public license at http://bioinformatics.fccc.edu/     

De novo design of peptides targeted to the EF hands of calmodulin

This report describes the use of the concept of inversion of hydropathy patterns to the de novo design of peptides targeted to a predetermined site on a protein. Eight- and 12-residue peptides were constructed with the EF hands or Ca(2+)-coordinating sites of calmodulin as their anticipated points of interaction. These peptides, but not unrelated peptides nor those with the same amino acid composition but a scrambled sequence, interacted with the two carboxyl-terminal Ca(2+)-binding sites of calmodulin as well as the EF hands of troponin C. The interactions resulted in a conformational change whereby the 8-mer peptide-calmodulin complex could activate phosphodiesterase in the absence of Ca(2+). In contrast, the 12-mer peptide-calmodulin complex did not activate phosphodiesterase but rather inhibited activation by Ca(2+). This inhibition could be overcome by high levels of Ca(2+). Thus, it would appear that the aforementioned concept can be used to make peptide agonists and antagonists that are targeted to predetermined sites on proteins such as calmodulin.     

Characterisation of <Emphasis Type="Italic">mycobacteria</Emphasis> isolated from slaughter cattle in pastoral regions of Uganda

Background  

Bovine tuberculosis is a zoonotic problem in pastoral cattle and communities in Uganda. Tuberculin tests in pastoral cattle had shown a high herd but low animal prevalence, with a high proportion of avian reactors. No work had been done to identify the mycobacterial species involved. The objective of the study was to isolate and characterise Mycobacterial species causing tuberculous lesions in slaughtered animals. Lesioned organs compatible with bovine tuberculosis in slaughtered cattle from pastoral areas in Uganda were collected and cultured to isolate mycobacteria. AccuProbe culture identification kits for the Mycobacterium tuberculosis complex, M. avium complex and M. avium were used to identify the isolates. Spoligotyping and Insertion Sequence (IS) 1311 and IS1245 Restriction Fragment Length Polymorphism analysis (RFLP) were used to further characterise the isolates.     

A new type of Ca(2+) channel blocker that targets Ca(2+) sensors and prevents Ca(2+)-mediated apoptosis.

Calmodulin (CaM), as well as other Ca(2+) binding motifs (i.e., EF hands), have been demonstrated to be Ca(2+) sensors for several ion channel types, usually resulting in an inactivation in a negative feedback manner. This provides a novel target for the regulation of such channels. We have designed peptides that interact with EF hands of CaM in a specific and productive manner. Here we have examined whether these peptides block certain Ca(2+)-permeant channels and inhibit biological activity that is dependent on the influx of Ca(2+). We found that these peptides are able to enter the cell and directly, as well as indirectly (through CaM), block the activity of glutamate receptor channels in cultured neocortical neurons and a nonselective cation channel in Jurkat T cells that is activated by HIV-1 gp120. As a consequence, apoptosis mediated by an influx of Ca(2+) through these channels was also dose-dependently inhibited by these novel peptides. Thus, this new type of Ca(2+) channel blocker may have utility in controlling apoptosis due to HIV infection or neuronal loss due to ischemia.     

Using generalized dissimilarity modelling to analyse and predict patterns of beta diversity in regional biodiversity assessment

Generalized dissimilarity modelling (GDM) is a statistical technique for analysing and predicting spatial patterns of turnover in community composition (beta diversity) across large regions. The approach is an extension of matrix regression, designed specifically to accommodate two types of nonlinearity commonly encountered in large-scaled ecological data sets: (1) the curvilinear relationship between increasing ecological distance, and observed compositional dissimilarity, between sites; and (2) the variation in the rate of compositional turnover at different positions along environmental gradients. GDM can be further adapted to accommodate special types of biological and environmental data including, for example, information on phylogenetic relationships between species and information on barriers to dispersal between geographical locations. The approach can be applied to a wide range of assessment activities including visualization of spatial patterns in community composition, constrained environmental classification, distributional modelling of species or community types, survey gap analysis, conservation assessment, and climate-change impact assessment.