Analysis of the composition of bacterial communities in oil reservoirs from a southern offshore Brazilian basin

The aim of this study was to characterize and compare the bacterial community structure of two distinct oil samples from a petroleum field in Brazil by using both molecular, based on the construction of 16S rRNA gene libraries, and cultivation methods. Statistical comparisons of libraries based on Amplified Ribosomal DNA Restriction Analysis (ARDRA) data revealed no significant differences between the communities recovered in the non-biodegraded (NBD) and highly biodegraded oils (HBD). BlastN analysis of the 16S rRNA gene sequences representative of distinct ribotypes from both oils showed the presence of nine different bacterial genera in these samples, encompassing members of the genera Arcobacter, Halanaerobium, Marinobacter, Propionibacterium, Streptomyces, Leuconostoc, Acinetobacter, Bacillus and Streptococcus. Enrichments obtained using oil as inoculum and sole carbon source yielded bacterial isolates showing high 16S rRNA gene sequence similarity with Achromobacter xylosoxidans, Bacillus subtilis, Brevibacillus sp., Dietzia sp. and Methylobacterium sp. Comparison between the data obtained using cultivation-independent and enrichment cultures suggests that different selection of community members may occur when using distinct approaches. All the organisms found, except for Leuconostoc sp. and Streptococus sp., have been previously reported in the literature as hydrocarbon degraders and/or associated to oil field environments.     

Restrictive flamenco alleles are maintained in Drosophila melanogaster population cages, despite the absence of their endogenous gypsy retroviral targets

The flamenco (flam) locus, located at 20A1-3 in the centromeric heterochromatin of the Drosophila melanogaster X chromosome, is a major regulator of the gypsy/mdg4 endogenous retrovirus. In restrictive strains, functional flam alleles maintain gypsy proviruses in a repressed state. By contrast, in permissive strains, proviral amplification results from infection of the female germ line and subsequent insertions into the chromosomes of the progeny. A restrictive/permissive polymorphism prevails in natural and laboratory populations. This polymorphism was assumed to be maintained by the interplay of opposite selective forces; on one hand, the increase of genetic load caused by proviral insertions would favor restrictive flam alleles because they make flies resistant to these gypsy replicative transpositions and, on the other, a hypothetical resistance cost would select against such alleles in the absence of the retrovirus. However, the population cage data presented in this paper do not fit with this simple resistance cost hypothesis because restrictive alleles were not eliminated in the absence of functional gypsy proviruses; on the contrary, using 2 independent flam allelic pairs, the restrictive frequency rose to about 90% in every experimental population, whatever the pair of alleles and the allelic proportions in the initial inoculum. These data suggest that the flam polymorphism is maintained by some strong balancing selection, which would act either on flam itself, independently of the deleterious effect of gypsy, or on a hypothetical flanking gene, in linkage disequilibrium with flam. Alternatively, restrictive flam alleles might also be resistant to some other retroelements that would be still present in the cage populations, causing a positive selection for these alleles. Whatever selective forces that maintain high levels of restrictive alleles independently of gypsy, this unknown mechanism can set up an interesting kind of antiviral innate immunity, at the population level.     

Bis-semiquinone (bi-radical) formation by photoinduced proton coupled electron transfer in covalently linked catechol-quinone systems: Aviram's hemiquinones revisited

The structure and reactivity of a covalently linked catechol-ortho-benzoquinone (hemiquinone) is studied by UV-Vis and IR absorption spectroscopy. Nanosecond transient absorption spectroscopy of the hemiquinone reveals the formation of bi-radical state consisting of two semiquinone units. It is a long-lived state resulting from proton coupled electron transfer (PCET).     

LIPOFUSCIN (AGING) PIGMENT GRANULES OF THE NEWBORN HUMAN LIVER

We have observed pigmented cytoplasmic granules, with the characteristic staining properties of lipofuscin (ceroid, "wear-and-tear") pigment, in newborn human liver. The pigment is found at the periphery of the lobule in hepatocytes and some bile ductular cells. It is acid-fast, PAS-positive after diastase digestion, slightly argyophilic and sudanophilic, and markedly Schmorl's- and peroxidase positive in paraffin sections. Difficult to see in sections stained with hematoxylin and eosin, the pigment can be detected in unstained sections. The granules also resemble lipofuscin found in adult tissues, in their ultra-structural and enzymatic properties. They are polymorphic, contain granular material of moderate and high electron opacity, and are delimited by a single membrane. Acid phosphatase and β-glucuronidase activities are visualized in the newborn granules, identifying them as lysosomes. The granules also contain copper and, to a much lesser extent, iron. The accumulation of lipofuscin pigment in lysosomes in many tissues correlates well with aging, and this process has been interpreted as a reflection of cellular degeneration or wear-and-tear. However, the presence of lipofuscin granules as a constant component of neonatal liver suggests that they are not a measure of cellular senescence.     

Atypical squamous cells as a diagnostic pitfall in pulmonary Wegener's granulomatosis. A case report

BACKGROUND: Wegener's granulomatosis (WG) is characterized by systemic, necrotizing, granulomatous inflammation accompanied by vasculitis. It classically involves the triad of the upper respiratory tract, lungs and kidneys. Isolated pulmonary lesions of WG may present in some patients as pulmonary masses, simulating neoplasms. The features of WG can be suggested by cytologic study. Atypical epithelial cells associated with WG have previously been reported as a cause of a false positive diagnosis of bronchoalveolar carcinoma. CASE: In this case the cytologic findings included atypical squamous cells in a background of acute, chronic and granulomatous inflammation. In several respiratory specimens the atypical squamous cells were incorrectly interpreted as diagnostic of squamous cell carcinoma. The correct diagnosis of WG was confirmed with open lung biopsy, which demonstrated necrotizing granulomatous inflammation with geographic necrosis and associated vasculitis. CONCLUSION: Markedly atypical squamous cells mimicking squamous cell carcinoma can be found accompanying the inflammatory process associated with WG and are a possible diagnostic pitfall. The possibility of WG as well as other inflammatory processes should always be considered in the differential diagnosis of squamous cell carcinoma of the lung. This case is the only reported case of WG in which atypical squamous cells were a diagnostic pitfall, initially suggesting a diagnosis of squamous cell carcinoma.     

The cost of growing large: costs of post‐weaning growth on body mass senescence in a wild mammal

Individual body mass often positively correlates with survival and reproductive success, whereas fitness costs of growing large are rarely detected in vertebrates in the wild. Evidence that adult body mass progressively declines with increasing age is accumulating across mammalian populations. Growing fast to a large body can increase the cellular damage accumulated throughout life, leading body growth in early life to be negatively associated with the rate of body mass senescence. Moreover, the onset of mass senescence may strongly depend on both sex‐specific reproductive tactics and environmental conditions. Assessing the timing and the rate of body mass decline with increasing age thus offers an opportunity to look for costs of having grown fast, especially after a poor start during early life, in both sexes and in different environments. Using a unique dataset including 30 years of longitudinal data on age‐specific body mass collected in two roe deer Capreolus capreolus populations subjected to contrasted environmental conditions, we looked for potential costs of high post‐weaning growth rate in terms of steeper rate of body mass senescence. Our analyses of body mass senescence accounted for the potential variation in the onset of senescence and allowed explicit comparisons of this variable between sexes and populations. Higher growth rates late in the growing period (after weaning) were associated with a steeper rate of body mass senescence, regardless of early mass (gained before weaning), but at different extents depending on sex and environmental conditions. Body mass senescence occurred earlier in males than in females, especially in the population facing limiting resources. In the wild, although heavy individuals generally survive better than small ones, the costs of growing large late in the growing period only became apparent late in life through mass senescence.     

Assessing the effects of management on forest growth across France: insights from a new functional–structural model

Background and Aims

The structure of a forest stand, i.e. the distribution of tree size features, has strong effects on its functioning. The management of the structure is therefore an important tool in mitigating the impact of predicted changes in climate on forests, especially with respect to drought. Here, a new functional–structural model is presented and is used to assess the effects of management on forest functioning at a national scale.

Methods

The stand process-based model (PBM) Castanea was coupled to a stand structure module (SSM) based on empirical tree-to-tree competition rules. The calibration of the SSM was based on a thorough analysis of intersite and interannual variability of competition asymmetry. The coupled Castanea–SSM model was evaluated across France using forest inventory data, and used to compare the effect of contrasted silvicultural practices on simulated stand carbon fluxes and growth.

Key Results

The asymmetry of competition varied consistently with stand productivity at both spatial and temporal scales. The modelling of the competition rules enabled efficient prediction of changes in stand structure within the Castanea PBM. The coupled model predicted an increase in net primary productivity (NPP) with management intensity, resulting in higher growth. This positive effect of management was found to vary at a national scale across France: the highest increases in NPP were attained in forests facing moderate to high water stress; however, the absolute effect of management on simulated stand growth remained moderate to low because stand thinning involved changes in carbon allocation at the tree scale.

Conclusions

This modelling approach helps to identify the areas where management efforts should be concentrated in order to mitigate near-future drought impact on national forest productivity. Around a quarter of the French temperate oak and beech forests are currently in zones of high vulnerability, where management could thus mitigate the influence of climate change on forest yield     

Nck-1 antagonizes the endoplasmic reticulum stress-induced inhibition of translation

Eukaryotic cells have developed specific mechanisms to overcome environmental stress. Here we show that the Src homology 2/3 (SH2/SH3) domain-containing protein Nck-1 prevents the unfolded protein response normally induced by pharmacological endoplasmic reticulum (ER) stress agents. Overexpression of Nck-1 enhances protein translation, whereas it abrogates eukaryotic initiation factor 2alpha (eIF2alpha) phosphorylation and inhibition of translation in response to tunicamycin or thapsigargin treatment. Nck-1 overexpression also attenuates induction of the ER chaperone, the immunoglobulin heavy chain-binding protein (BiP), and impairs cell survival in response to thapsigargin. We provided evidence that in these conditions, the effects of Nck on the unfolded protein response (UPR) involve its second SH3 domain and a calyculin A-sensitive phosphatase activity. In addition, we demonstrated that protein translation is reduced in mouse embryonic fibroblasts lacking both Nck isoforms and is enhanced in similar cells expressing high levels of Nck-1. In these various mouse embryonic fibroblasts, we also provided evidence that Nck modulates the activation of the ER resident eIF2alpha kinase PERK and consequently the phosphorylation of eIF2alpha on Ser-51 in response to stress. Our study establishes that Nck is required for optimal protein translation and demonstrates that, in addition to its adaptor function in mediating signaling from the plasma membrane, Nck also mediates signaling from the ER membrane compartment.