Temporal orchestration of glycogen synthase (GlgA) gene expression and glycogen accumulation in the oceanic picoplanktonic cyanobacterium Synechococcus sp. strain WH8103

Glycogen is accumulated during the latter half of the diel cycle in Synechococcus sp. strain WH8103 following a midday maximum in glgA (encoding glycogen synthase) mRNA abundance. This temporal pattern is quite distinct from that of Prochlorococcus and may highlight divergent regulatory control of carbon/nitrogen metabolism in these closely related picocyanobacteria.     

Niche-based prediction of establishment of biocontrol agents: an example with Gratiana boliviana and tropical soda apple

Successful establishment of a biological control agent is a prerequisite for effective reduction of an invasive weed. Niche-based species distribution models can generate valuable information about the potential spread of a biological control agent and help to predict its distribution. The Maximum Entropy Species Distribution Model was used in our study to predict distributions of the leaf beetle Gratiana boliviana Spaeth (Coleoptera: Chrysomelidae) and its target weed, tropical soda apple (TSA), Solanum viarum Dunal (Solanaceae). The specific objectives of this study were to (1) assess the climatic suitability for establishment of this insect across the invasive range of the weed by overlapping predicted current distributions and, (2) examine the niche-related restriction in distribution of the insect by visualising the predictive niche in multivariate space. Accuracy of predicted distributions was tested using binomial tests and area under the curve scores. The results of statistical tests confirmed that the predictions were significantly better than random. The predictions indicated that the potential distribution of G. boliviana in the USA will be more restricted than that of its host plant. Consequently, the beetle's ability to inflict damage to TSA will be geographically limited. Niche visualisation, using a PCA-based analysis, provided evidence of the niche imposed restriction on the distribution of G. boliviana. Overall, this study proposes a new approach for understanding the spatial limitations in establishment of biological control agents, allowing researchers to establish more realistic expectations of success.     

Apoptosis, cell proliferation and vitellogenesis during the folliculogenesis and follicular growth in teleost fish

Aiming to better understand folliculogenesis, this study evaluated cell death and proliferation of ovarian cells, besides cathepsin-D expression in Prochilodus argenteus captured in two sites of the São Francisco River downstream from the Três Marias Dam, Brazil. In the site immediately following the Dam (S1), low levels of dissolved oxygen were registered in the rainy period. The water temperature was higher in the São Francisco River immediately after the confluence with the Abaeté River (S2), regardless of the period. In S1, the ovaries showed smaller oocytes, high caspase-3 enzymatic activity and apoptosis, lower cells in proliferation and GSI, as well as a lesser quantity of cathepsin-D when compared to females captured from S2. Regarding relative frequency of ovarian structures, in the dry period, only oogonia and perinucleolar oocytes were found in fish ovaries from both sites. On the other hand, in the rainy period, the relative frequency of oogonia and perinucleolar oocytes decreased and the vitellogenic oocytes increased in S2. Postovulatory follicles were observed only in S2, whereas atretic follicles occurred at a higher frequency in S1. Our results showed that apoptosis, cell proliferation and cathepsina-D evaluation can be used as biomarkers of environmental impact.     

Differential changes of fat-soluble vitamins and pollutants during lactation in northern elephant seal mother-pup pairs

We investigated the changes of vitamins A and E as well as PCBs and DDTs during lactation in northern elephant seal (Mirounga angustirostris) mother-pup pairs. On average, milk vitamin A concentrations were 6 times higher during late lactation than during early lactation, a pattern that differs dramatically from terrestrial mammals. Vitamin A concentrations also significantly increased in the inner blubber throughout lactation, whereas they remained constant in the outer blubber. Similar dynamics were observed for PCBs and DDTs in maternal blubber and milk. Blubber appears to be an important storage site for vitamin A and organochlorines in seals and a direct transfer of those molecules to the mammary gland may occur. The dynamics of vitamin A, PCBs and DDTs differed from those of vitamin E. There was a significant drop in milk vitamin E concentrations between early and late lactation, which is the usual pattern observed in terrestrial mammals. The dynamics of vitamin E in the blubber layers also differed from those of vitamin A, suggesting different mechanisms of mobilization and transfer into the milk.     

An accounting of C‐based trace gas release during abiotic plant litter degradation

Recent studies showed that photochemical breakdown (photodegradation) of plant material accounts for a substantial portion of litter decomposition and subsequent trace gas release in ecosystems under high radiative load and low precipitation. In the absence of solar radiation, thermal degradation may also cause trace gas release at temperatures below the ignition point. These observations suggest that the abiotic processes of photodegradation and thermal degradation of plant litter may be important in understanding global trace gas budgets. In a laboratory incubation study, we performed a simultaneous carbon (C) accounting of CO₂, CO, and CH₄ produced as a byproduct of photodegradation and thermal degradation of six different plant litter types that varied in chemical composition. The patterns of trace gas release during photodegradation and thermal degradation differed considerably across the six plant materials, suggesting that chemical composition of litter may influence the rates of abiotic degradation. There was a strong positive correlation between the rates of trace gas release during photodegradation and temperature. A significant portion of trace gases were produced during low temperature (< 100 °C) thermal degradation of litter in the absence of solar radiation, which was also positively correlated to temperature. In addition, both thermal degradation and photodegradation occurred in the absence of O₂. This indicates that the mechanism formerly accepted as photo‐oxidation may only be one of several photodegradation processes. We speculate that the direct breakdown of chemical groups such as carboxyl, carbonyl, and methoxyl groups may result in CO₂, CO, and CH₄ release. We suggest that the combined processes of thermal and photodegradation of litter may be a previously under accounted source of C‐based trace gases from terrestrial systems.     

A heterogeneous computing environment to solve the 768-bit RSA challenge

In December 2009 the 768-bit, 232-digit number RSA-768 was factored using the number field sieve. Overall, the computational challenge would take more than 1700 years on a single, standard core. In the article we present the heterogeneous computing approach, involving different compute clusters and Grid computing environments, used to solve this problem.     

The crystal structure of the dimeric colicin M immunity protein displays a 3D domain swap

Bacteriocins are proteins secreted by many bacterial cells to kill related bacteria of the same niche. To avoid their own suicide through reuptake of secreted bacteriocins, these bacteria protect themselves by co-expression of immunity proteins in the compartment of colicin destination. In Escherichia coli the colicin M (Cma) is inactivated by the interaction with the Cma immunity protein (Cmi). We have crystallized and solved the structure of Cmi at a resolution of 1.95? by the recently developed ab initio phasing program ARCIMBOLDO. The monomeric structure of the mature 10kDa protein comprises a long N-terminal α-helix and a four-stranded C-terminal β-sheet. Dimerization of this fold is mediated by an extended interface of hydrogen bond interactions between the α-helix and the four-stranded β-sheet of the symmetry related molecule. Two intermolecular disulfide bridges covalently connect this dimer to further lock this complex. The Cmi protein resembles an example of a 3D domain swapping being stalled through physical linkage. The dimer is a highly charged complex with a significant surplus of negative charges presumably responsible for interactions with Cma. Dimerization of Cmi was also demonstrated to occur in vivo. Although the Cmi-Cma complex is unique among bacteria, the general fold of Cmi is representative for a class of YebF-like proteins which are known to be secreted into the external medium by some Gram-negative bacteria.     

Dermal application of nitric oxide releasing acidified nitrite-containing liniments significantly reduces blood pressure in humans

Vascular ischemic diseases, hypertension, and other systemic hemodynamic and vascular disorders may be the result of impaired bioavailability of nitric oxide (NO). NO but also its active derivates like nitrite or nitroso compounds are important effector and signal molecules with vasodilating properties. Our previous findings point to a therapeutical potential of cutaneous administration of NO in the treatment of systemic hemodynamic disorders. Unfortunately, no reliable data are available on the mechanisms, kinetics and biological responses of dermal application of nitric oxide in humans in vivo. The aim of the study was to close this gap and to explore the therapeutical potential of dermal nitric oxide application. We characterized with human skin in vitro and in vivo the capacity of NO, applied in a NO-releasing acidified form of nitrite-containing liniments, to penetrate the epidermis and to influence local as well as systemic hemodynamic parameters. We found that dermal application of NO led to a very rapid and significant transepidermal translocation of NO into the underlying tissue. Depending on the size of treated skin area, this translocation manifests itself through a significant systemic increase of the NO derivates nitrite and nitroso compounds, respectively. In parallel, this translocation was accompanied by an increased systemic vasodilatation and blood flow as well as reduced blood pressure. We here give evidence that in humans dermal application of NO has a therapeutic potential for systemic hemodynamic disorders that might arise from local or systemic insufficient availability of NO or its bio-active NO derivates, respectively.     

Exclusive conservation of mitochondrial group II intron nad4i548 among liverworts and its use for phylogenetic studies in this ancient plant clade

Liverworts occupy a pivotal position in land plant (embryophyte) phylogeny as the presumed earliest-branching major clade, sister to all other land plants, including the mosses, hornworts, lycophytes, monilophytes and seed plants. Molecular support for this earliest dichotomy in land plant phylogeny comes from strikingly different occurrences of introns in mitochondrial genes distinguishing liverworts from all other embryophytes. Exceptionally, however, the nad5 gene--the mitochondrial locus hitherto used most widely to elucidate early land plant phylogeny--carries a group I type intron that is shared between liverworts and mosses. We here explored whether a group II intron, the other major type of organellar intron, would similarly be conserved in position across the entire diversity of extant liverworts and could be of use for phylogenetic analyses in this supposedly most ancient embryophyte clade. To this end, we investigated the nad4 gene as a candidate locus possibly featuring different introns in liverworts as opposed to the non-liverwort embryophyte (NLE) lineage. We indeed found group II intron nad4i548 universally conserved in a wide phylogenetic sampling of 55 liverwort taxa, confirming clade specificity and surprising evolutionary stability of plant mitochondrial introns. As expected, intron nad4i548g2 carries phylogenetic information in its variable sequences, which confirms and extends previous cladistic insights on liverwort evolution. We integrate the new nad4 data with those of the previously established mitochondrial nad5 and the chloroplast rbcL and rps4 genes and present a phylogeny based on the fused datasets. Notably, the phylogenetic analyses suggest a reconsideration of previous phylogenetic and taxonomic assignments for the genera Calycularia and Mylia and resolve a sister group relationship of Ptilidiales and Porellales.     

Genome sequence of Wickerhamomyces anomalus DSM 6766 reveals genetic basis of biotechnologically important antimicrobial activities

The ascomycetous yeast Wickerhamomyces anomalus (formerly Pichia anomala and Hansenula anomala) exhibits antimicrobial activities and flavoring features that are responsible for its frequent association with food, beverage and feed products. However, limited information on the genetic background of this yeast and its multiple capabilities are currently available. Here, we present the draft genome sequence of the neotype strain W.?anomalus DSM 6766. On the basis of pyrosequencing, a de novo assembly of this strain resulted in a draft genome sequence with a total size of 25.47?Mbp. An automatic annotation using RAPYD generated 11?512 protein-coding sequences. This annotation provided the basis to analyse metabolic capabilities, phylogenetic relationships, as well as biotechnologically important features and yielded novel candidate genes of W.?anomalus DSM 6766 coding for proteins participating in antimicrobial activities.