Disentangling the effects of global climate and regional land-use change on the current and future distribution of mangroves in South Africa

The mangrove distribution in South Africa is fragmented and restricted to small forest patches occupying only 16 % of the estuaries within the current range. In this study we used species distribution models to test (1) whether the absence of mangrove forest and its species (Avicennia marina, Bruguiera gymnorrhiza and Rhizophora mucronata) within their current range is driven by climate or by climate combined with human or geomorphic perturbation and (2) how climate change may potentially affect the latitudinal limit of the mangrove forests and its species in South Africa. We used three modelling techniques (generalized linear models, generalized additive models and gradient boosting machines) and a set of three climate-based predictive variables (minimum air temperature of the coldest month, waterbalance and growing-degree days) combined separately with an index of human or geomorphic perturbation. Climate variables for the future projections were derived from two general circulation models driven by two socio-economic scenarios (A2a and B2a). Within the range of the mangrove forest, the fragmented distribution of the mangroves in South Africa was not explained by our set of climate variables alone. The index of human perturbations slightly improved the predictions but the index of geomorphic perturbation did not. Climate change will create climatically suitable sites for the mangrove forest and the two species A. marina and B. gymnorrhiza beyond their current limits, but model outcomes did not agree on the future potential distribution of R. mucronata. We were able to successfully predict range limits and to detect future climatically suitable sites beyond the current limits. Factors controlling mangrove distribution within its range are still to be identified although absences were partly explained by human perturbations.     

Flaxseed (Linum usitatissimum L.) extract as well as (+)-secoisolariciresinol diglucoside and its mammalian derivatives are potent inhibitors of α-amylase activity

Type 2 diabetes mellitus (T2DM) is one of the common global diseases. Flaxseed is by far the richest source of the dietary lignans (i.e., secoisolariciresinol diglucoside) which have been shown to delay the development of T2DM in animal models. Herein, we propose the first evidences for a mechanism of action involving the inhibition of the pancreatic α-amylase (EC 3.2.1.1) by flaxseed-derived lignans that could therefore constitute a promising nutraceutical for the prevention and the treatment of T2DM.     

Test-Retest Reliability of Innovated Strength Tests for Hip Muscles

The burden of hip muscles weakness and its relation to other impairments has been well documented. It is therefore a pre-requisite to have a reliable method for clinical assessment of hip muscles function allowing the design and implementation of a proper strengthening program. Motor-driven dynamometry has been widely accepted as the gold-standard for lower limb muscle strength assessment but is mainly related to the knee joint. Studies focusing on the hip joint are less exhaustive and somewhat discrepant with regard to optimal participants position, consequently influencing outcome measures. Thus, we aimed to develop a standardized test setup for the assessment of hip muscles strength, i.e. flexors/extensors and abductors/adductors, with improved participant stability and to define its psychometric characteristics. Eighteen participants performed unilateral isokinetic and isometric contractions of the hip muscles in the sagittal and coronal plane at two separate occasions. Peak torque and normalized peak torque were measured for each contraction. Relative and absolute measures of reliability were calculated using the intraclass correlation coefficient and standard error of measurement, respectively. Results from this study revealed higher levels of between-day reliability of isokinetic/isometric hip abduction/flexion peak torque compared to existing literature. The least reliable measures were found for hip extension and adduction, which could be explained by a less efficient stabilization technique. Our study additionally provided a first set of reference normalized data which can be used in future research.     

First Evidence of Simultaneous Circulation of Three Different Dengue Virus Serotypes in Africa

Gabon, in Central Africa, was affected for the first time in 2007 and then in 2010 by simultaneous outbreaks of chikungunya and Dengue serotype 2 (DENV-2) viruses. Through the national surveillance of dengue-like syndromes between 2007 and 2010, we observed continuous circulation of DENV-2 in a southward movement. This rapid spread of DENV-2 was associated with the emergence of DENV-1 in 2007 and DENV-3 in 2010. Interestingly, we detected six DENV-2 infected patients with hemorrhagic signs during the second outbreak in 2010. Although these cases do not meet all standard WHO criteria for severe Dengue with hemorrhage (formerly DHF), this is the first report of several dengue fever cases associated with hemorrhagic signs during a simultaneous circulation of different DENV serotypes in Africa. Together, these findings suggest that DENV is becoming more widely established on this continent and that DHF will likely become a serious public-health problem in the near future.     

Proteomic Biomarkers Associated with Streptococcus agalactiae Invasive Genogroups

Group B streptococcus (GBS, Streptococcus agalactiae) is a leading cause of meningitis and sepsis in newborns and an etiological agent of meningitis, endocarditis, osteoarticular and soft tissue infections in adults. GBS isolates are routinely clustered in serotypes and in genotypes. At present one GBS sequence type (i.e. ST17) is considered to be closely associated with bacterial invasiveness and novel proteomic biomarkers could make a valuable contribution to currently available GBS typing data. For that purpose we analyzed the protein profiles of 170 genotyped GBS isolates by Surface-Enhanced Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (SELDI). Univariate statistical analysis of the SELDI profiles identified four protein biomarkers significantly discriminating ST17 isolates from those of the other sequence types. Two of these biomarkers (MW of 7878 Da and 12200 Da) were overexpressed and the other two (MW of 6258 Da and 10463 Da) were underexpressed in ST17. The four proteins were isolated by mass spectrometry-assisted purification and their tryptic peptides analyzed by LC-MS/MS. They were thereby identified as the small subunit of exodeoxyribonuclease VII, the 50S ribosomal protein L7/L12, a CsbD-like protein and thioredoxin, respectively. In conclusion, we identified four candidate biomarkers of ST17 by SELDI for high-throughput screening. These markers may serve as a basis for further studies on the pathophysiology of GBS infection, and for the development of novel vaccines.     

Evolutionary History of the Plant Pathogenic Bacterium Xanthomonas axonopodis

Deciphering mechanisms shaping bacterial diversity should help to build tools to predict the emergence of infectious diseases. Xanthomonads are plant pathogenic bacteria found worldwide. Xanthomonas axonopodis is a genetically heterogeneous species clustering, into six groups, strains that are collectively pathogenic on a large number of plants. However, each strain displays a narrow host range. We address the question of the nature of the evolutionary processes – geographical and ecological speciation – that shaped this diversity. We assembled a large collection of X. axonopodis strains that were isolated over a long period, over continents, and from various hosts. Based on the sequence analysis of seven housekeeping genes, we found that recombination occurred as frequently as point mutation in the evolutionary history of X. axonopodis. However, the impact of recombination was about three times greater than the impact of mutation on the diversity observed in the whole dataset. We then reconstructed the clonal genealogy of the strains using coalescent and genealogy approaches and we studied the diversification of the pathogen using a model of divergence with migration. The suggested scenario involves a first step of generalist diversification that spanned over the last 25 000 years. A second step of ecology-driven specialization occurred during the past two centuries. Eventually, secondary contacts between host-specialized strains probably occurred as a result of agricultural development and intensification, allowing genetic exchanges of virulence-associated genes. These transfers may have favored the emergence of novel pathotypes. Finally, we argue that the largest ecological entity within X. axonopodis is the pathovar.     

Beta-Actin Is Involved in Modulating Erythropoiesis during Development by Fine-Tuning Gata2 Expression Levels

The functions of actin family members during development are poorly understood. To investigate the role of beta-actin in mammalian development, a beta-actin knockout mouse model was used. Homozygous beta-actin knockout mice are lethal at embryonic day (E)10.5. At E10.25 beta-actin knockout embryos are growth retarded and display a pale yolk sac and embryo proper that is suggestive of altered erythropoiesis. Here we report that lack of beta-actin resulted in a block of primitive and definitive hematopoietic development. Reduced levels of Gata2, were associated to this phenotype. Consistently, ChIP analysis revealed multiple binding sites for beta-actin in the Gata2 promoter. Gata2 mRNA levels were almost completely rescued by expression of an erythroid lineage restricted ROSA26-promotor based GATA2 transgene. As a result, erythroid differentiation was restored and the knockout embryos showed significant improvement in yolk sac and embryo vascularization. These results provide new molecular insights for a novel function of beta-actin in erythropoiesis by modulating the expression levels of Gata2 in vivo.     

Legionella pneumophila Effector RomA Uniquely Modifies Host Chromatin to Repress Gene Expression and Promote Intracellular Bacterial Replication

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Highlights? Upon infection, L. pneumophila secretes RomA, a SET domain-containing methyltransferase ? RomA triggers H3K14 trimethylation, causing a switch from gene activation to repression ? ChIP-seq identified 4,870 H3K14 methylated promoter regions, including innate immune genes ? RomA SET domain is required for efficient intracellular replication of L. pneumophila     

The Impact of Gene Duplication,Insertion, Deletion,Lateral Gene Transfer and Sequencing Error on Orthology Inference: A Simulation Study

The identification of orthologous genes, a prerequisite for numerous analyses in comparative and functional genomics, is commonly performed computationally from protein sequences. Several previous studies have compared the accuracy of orthology inference methods, but simulated data has not typically been considered in cross-method assessment studies. Yet, while dependent on model assumptions, simulation-based benchmarking offers unique advantages: contrary to empirical data, all aspects of simulated data are known with certainty. Furthermore, the flexibility of simulation makes it possible to investigate performance factors in isolation of one another.Here, we use simulated data to dissect the performance of six methods for orthology inference available as standalone software packages (Inparanoid, OMA, OrthoInspector, OrthoMCL, QuartetS, SPIMAP) as well as two generic approaches (bidirectional best hit and reciprocal smallest distance). We investigate the impact of various evolutionary forces (gene duplication, insertion, deletion, and lateral gene transfer) and technological artefacts (ambiguous sequences) on orthology inference. We show that while gene duplication/loss and insertion/deletion are well handled by most methods (albeit for different trade-offs of precision and recall), lateral gene transfer disrupts all methods. As for ambiguous sequences, which might result from poor sequencing, assembly, or genome annotation, we show that they affect alignment score-based orthology methods more strongly than their distance-based counterparts.     

Seasonal and Geographic Variation of Southern Blue Whale Subspecies in the Indian Ocean

Understanding the seasonal movements and distribution patterns of migratory species over ocean basin scales is vital for appropriate conservation and management measures. However, assessing populations over remote regions is challenging, particularly if they are rare. Blue whales (Balaenoptera musculus spp) are an endangered species found in the Southern and Indian Oceans. Here two recognized subspecies of blue whales and, based on passive acoustic monitoring, four “acoustic populations” occur. Three of these are pygmy blue whale (B.m. brevicauda) populations while the fourth is the Antarctic blue whale (B.m. intermedia). Past whaling catches have dramatically reduced their numbers but recent acoustic recordings show that these oceans are still important habitat for blue whales. Presently little is known about the seasonal movements and degree of overlap of these four populations, particularly in the central Indian Ocean. We examined the geographic and seasonal occurrence of different blue whale acoustic populations using one year of passive acoustic recording from three sites located at different latitudes in the Indian Ocean. The vocalizations of the different blue whale subspecies and acoustic populations were recorded seasonally in different regions. For some call types and locations, there was spatial and temporal overlap, particularly between Antarctic and different pygmy blue whale acoustic populations. Except on the southernmost hydrophone, all three pygmy blue whale acoustic populations were found at different sites or during different seasons, which further suggests that these populations are generally geographically distinct. This unusual blue whale diversity in sub-Antarctic and sub-tropical waters indicates the importance of the area for blue whales in these former whaling grounds.