Complete genome sequence of the marine methyl-halide oxidizing Leisingera methylohalidivorans type strain (DSM 14336T), a representative of the Roseobacter clade

Leisingera methylohalidivorans Schaefer et al. 2002 emend. Vandecandelaere et al. 2008 is the type species of the genus Leisingera. The genus belongs to the Roseobacter clade (Rhodobacteraceae, Alphaproteobacteria), a widely distributed lineage in marine environments. Leisingera and particularly L. methylohalidivorans strain MB2^T is of special interest due to its methylotrophy. Here we describe the complete genome sequence and annotation of this bacterium together with previously unreported aspects of its phenotype. The 4,650,996 bp long genome with its 4,515 protein-coding and 81 RNA genes consists of three replicons, a single chromosome and two extrachromosomal elements with sizes of 221 kb and 285 kb.     

Overexpression and loss-of-function at <Emphasis Type="Italic">TIME FOR COFFEE</Emphasis> results in similar phenotypes in diverse growth and physiological responses

Plant experience diurnal changes in their environment that can be anticipated and responded to via the circadian clock. Integration of external signals by this clock ensures metabolic homeostasis and ultimately enhances fitness. TIME FOR COFFEE (TIC) is known to be associated to the circadian clock, being required to maintain rhythmic period and amplitude, and to regulate clock-driven physiological responses. The molecular function of TIC has so far only been studied with loss-of-function mutants. The biochemical activity of TIC remains elusive. To learn more about TIC in diverse physiological processes, here we generated TIC overexpressing plants (TICox) and characterized their impact on plant growth, development, and circadianclock activity. TICox plants displayed phenotypic similarity with tic mutants. This included defects in leaf morphology, the developmental transition from the vegetative to reproductive phase, and circadian-clock function. These observations allowed us to hypothesize that TIC is an element of protein complexes that are involved in global biological processes.     

New enzymes,new pathways and an alternative view on starch biosynthesis in both photosynthetic and heterotrophic tissues of plants

Since the initial discovery showing that ADPglucose (ADPG) serves as the universal glucosyl donor in the reaction catalyzed by starch synthase, the mechanism of starch biosynthesis in both leaves and heterotrophic organs has generally been considered to be an unidirectional process wherein ADPG pyrophosphorylase (AGPase) exclusively catalyzes the synthesis of ADPG and acts as the major limiting step of the gluconeogenic process. There is however mounting evidence that ADPG linked to starch biosynthesis is produced de novo in the cytosol by means of sucrose synthase (SuSy). In this review we show and discuss the numerous pitfalls of the ‘classic’ view of starch biosynthesis. In addition, we describe many overlooked aspects of both ADPG and starch metabolism. With the overall data we propose an ‘alternative’ model of starch biosynthesis, applicable to both photosynthetic and heterotrophic tissues, according to which both sucrose and starch biosynthetic processes are tightly interconnected by means of an ADPG synthesizing SuSy activity. According to this new view, starch metabolism embodies catabolic and anabolic reactions taking place simultaneously in which AGPase plays a vital role in the scavenging of starch breakdown products.     

Population structure of North African honey bees is influenced by both biological and anthropogenic factors

Honey bee diversity is under threat due to anthropogenic factors as the use of pesticides and the replacement of local colonies to recover from colony losses. To assess the effect of these activities on the genetic diversity and structure of North African honey bee colonies, we studied colonies from the north (Tellian) and the south (Saharan) regions in Algeria, by determining their mitochondrial haplotype and the variation of ten microsatellite loci. Particular haplotypes have been found with a high frequency in each region that may constitute subspecies-specific markers for Apis mellifera intermissa (haplotype A8 at the north) and A. m. sahariensis (haplotype A9 at the south). Moreover, the presence of the haplotype A8 in some Saharan colonies may reflect recent introductions of A. m. intermissa. Structure analysis suggests that a natural differentiation between honey bee populations from Saharan and Tellian regions still exists despite increased colony movements (migration, queen purchases, etc.) during the last decades. One apiary established for the conservation of A. m. sahariensis showed no indication of maternal introgression since all the colonies bear the same haplotype A9. Furthermore, Hardy–Weinberg equilibrium observed in this population indicates that this apiary is appropriate for conservation programs of A. m. sahariensis.     

Predicting seasonal and spatial variations in diet quality of Pyrenean chamois (Rupicapra pyrenaica pyrenaica) using near infrared reflectance spectroscopy

Monitoring nutritional status of wildlife is key to understanding the population response to changes in food availability. Several direct and indirect methods have been proposed for such purposes, but faecal nitrogen (FN) is by far the most commonly used indirect non-invasive indicator of free-ranging ruminant diet quality. In this work, two methods were used to estimate the FN content in 291 pellet samples of Pyrenean chamois (Rupicapra pyrenaica pyrenaica) collected during a 2-year period (May 2009 to May 2011) in two chamois populations from the Catalan Pyrenees, Spain: the Dumas LECO analyzer and near-infrared reflectance spectroscopy (NIRS). In order to optimize further FN estimations we performed three different NIRS calibrations: (1) general, across year, season and populations; (2) population-specific; and (3) season-specific, i.e., different periods of vegetation growth. FN ranged from 1.66 % to 2.85 % (dry matter basis) and was higher in the main vegetation growing season than in winter. Concerning NIRS calibration, our study confirmed that FN of Pyrenean chamois can be accurately determined by NIRS, since the general calibration was accurate enough to predict FN. It is concluded that NIRS represents a non-destructive, emission-free and low-cost analytical technique which may reduce the use of conventional laborious methods for estimating FN in long-term wildlife monitoring.     

Suppressive effect of bacterial polysaccharides on BAFF system is responsible for their poor immunogenicity

Capsular polysaccharides of encapsulated bacteria are weakly immunogenic T cell-independent type 2 (TI-2) Ags. Recent findings suggest that BAFF system molecules have a critical role in the development of Ab responses against TI-2 Ags. In this study, we investigated the effect of bacterial polysaccharides on B cell responses to BAFF and a proliferation-inducing ligand (APRIL). We determined that B cells exposed to meningococcal type C polysaccharide (MCPS) or group B Streptococcus serotype V (GBS-V) were unresponsive to BAFF- and APRIL-induced Ig secretion. Moreover, MCPS and GBS-V strongly downregulated transmembrane activator and calcium-modulator and cyclophilin ligand interactor, the BAFF and APRIL receptor that is responsible for Ab development against TI-2 Ags. Interestingly, (4-hydroxy-3-nitrophenyl)acetyl-Ficoll (NP-Ficoll), a prototype TI-2 Ag, did not manifest a suppressive effect on B cells. Paradoxically, whereas GBS-V and MCPS inhibited IFN-γ-induced BAFF production from dendritic cells, NP-Ficoll strongly increased BAFF secretion. TLR 9 agonist CpG deoxyoligonucleotide (ODN) was able to reverse the MCPS-mediated transmembrane activator and calcium-modulator and cyclophilin ligand interactor suppression but could not rescue the Ig secretion in BAFF- or APRIL-stimulated B cells. In support of these in vitro observations, it was observed that CpG ODN could help augment the Ab response against NP in mice immunized with a CpG ODN-containing NP-Ficoll vaccine but exhibited only marginal adjuvant activity for MCPS vaccine. Collectively, these results suggest a mechanism for the weak immunogenicity of bacterial polysaccharides and explain the previously observed differences between bacterial polysaccharide and NP-Ficoll immunogenicity.     

The fossil record of the Peronosporomycetes (Oomycota)

Evidence of fossil Peronosporomycetes has been slow to accumulate. In this review various fossils historically assigmed to the Peronosporomycets are dicussed briefly and an explanation is provided as to why the fossil record of this grouop has remained inconsistent. In recent year there has been several new reports of fossil peronosporomycetes based on structurally preserved oogonium-antheridium complexes from Derovonian and Carboniferous rocks that demonstrate the existence of these organisms as fossils and refute the long-standing assumption that they are too delicate to be preserved. Among these are serral tyoes characterized by oogonial surface members of the group. To date at last three groups of fossil vascular plants (i.e. lycophytes, ferns and seed ferns) are known to host peronosporomycetes aas endophytes; however only one form has been identified as a parasite.