Redox effects on the excited-state lifetime in chlorosomes and bacteriochlorophyll c oligomers.

Oligomers of [E,E] BChl CF (8, 12-diethyl bacteriochlorophyll c esterified with farnesol (F)) and [Pr,E] BChl CF (analogously, M methyl, Pr propyl) in hexane and aqueous detergent or lipid micelles were studied by means of steady-state absorption, time-resolved fluorescence, and electron spin resonance spectroscopy. The maximum absorption wavelength, excited-state dynamics, and electron spin resonance (EPR) linewidths are similar to those of native and reconstituted chlorosomes of Chlorobium tepidum. The maximum absorption wavelength of oligomers of [E,E] BChl CF was consistently blue-shifted as compared to that of [Pr,E] BChl CF oligomers, which is ascribed to the formation of smaller oligomers with [E,E] BChl CF than [Pr,E] BChl CF. Time-resolved fluorescence measurements show an excited-state lifetime of 10 ps or less in nonreduced samples of native and reconstituted chlorosomes of Chlorobium tepidum. Under reduced conditions the excited-state lifetime increased to tens of picoseconds, and energy transfer to BChl a or long-wavelength absorbing BChl c was observed. Oligomers of [E,E] BChl CF and [Pr,E] BChl CF in aqueous detergent or lipid micelles show a similar short excited-state lifetime under nonreduced conditions and an increase up to several tens of picoseconds upon reduction. These results indicate rapid quenching of excitation energy in nonreduced samples of chlorosomes and aqueous BChl c oligomers. EPR spectroscopy shows that traces of oxidized BChl c radicals are present in nonreduced and absent in reduced samples of chlorosomes and BChl c oligomers. This suggests that the observed short excited-state lifetimes in nonreduced samples of chlorosomes and BChl c oligomers may be ascribed to excited-state quenching by BChl c radicals. The narrow EPR linewidth suggests that the BChl c are arranged in clusters of 16 and 6 molecules in chlorosomes of Chlorobium tepidum and Chloroflexus aurantiacus, respectively.     

Afrotropical Cynipoidea (Hymenoptera)

The Afrotropical Cynipoidea are represented by 306 described species and 54 genera in four families: Cynipidae, Figitidae, Liopteridae and Ibaliidae, the latter represented by a single introduced species. Seven of these genera are only represented by undescribed species in the region. Seven new genus-level synonymies, one genus resurrected from synonymy, 54 new combinations, one combination reinstated, and one new replacement name are presented. We provide identification keys to the families, subfamilies and genera of cynipoid wasps occurring in the Afrotropical region (Africa south of the Sahara, including Madagascar and southern Arabian Peninsula). Online interactive Lucid Phoenix and Lucid matrix keys are available at: http://www.waspweb.org/Cynipoidea/Keys/index.htm. An overview of the biology and checklists of species for each genus are provided. This paper constitutes the first contributory chapter to the book on Afrotropical Hymenoptera.     

Torque-limited RecA polymerization on dsDNA

The assembly of RecA onto a torsionally constrained double-stranded DNA molecule was followed in real time using magnetic tweezers. Formation of a RecA–DNA filament on the DNA tether was stalled owing to different physical processes depending on the applied stretching force. For forces up to 3.6 pN, the reaction stalled owing to the formation of positive plectonemes in the remaining DNA molecule. Release of these plectonemes by rotation of the magnets led to full coverage of the DNA molecule by RecA. At stretching forces larger than 3.6 pN, the twist induced during filament formation caused the reaction to stall before positive supercoils were generated. We deduce a maximum built-up torsion of 10.1 ± 0.7 k_bT. In vivo this built-up torsion may be used to favor regression of a stalled replication fork or to free the chromosomal DNA in E.coli from its condensing proteins.     

A family-based approach reveals the function of residues in the nuclear receptor ligand-binding domain

Literature studies, 3D structure data, and a series of sequence analysis techniques were combined to reveal important residues in the structure and function of the ligand-binding domain of nuclear hormone receptors. A structure-based multiple sequence alignment allowed for the seamless combination of data from many different studies on different receptors into one single functional model. It was recently shown that a combined analysis of sequence entropy and variability can divide residues in five classes; (1) the main function or active site, (2) support for the main function, (3) signal transduction, (4) modulator or ligand binding and (5) the rest. Mutation data extracted from the literature and intermolecular contacts observed in nuclear receptor structures were analyzed in view of this classification and showed that the main function or active site residues of the nuclear receptor ligand-binding domain are involved in cofactor recruitment. Furthermore, the sequence entropy-variability analysis identified the presence of signal transduction residues that are located between the ligand, cofactor and dimer sites, suggesting communication between these regulatory binding sites. Experimental and computational results agreed well for most residues for which mutation data and intermolecular contact data were available. This allows us to predict the role of the residues for which no functional data is available yet. This study illustrates the power of family-based approaches towards the analysis of protein function, and it points out the problems and possibilities presented by the massive amounts of data that are becoming available in the "omics era". The results shed light on the nuclear receptor family that is involved in processes ranging from cancer to infertility, and that is one of the more important targets in the pharmaceutical industry.     

Effect of irradiance and plant age on the dimensions of the growing shoot of poplar

Populus euramericana (Dode) Guinier cv. Robusta plants were cultivated at irradiances of 7.5, 15 and 30 W m⁻² (32.5, 65 and 130 μmol m² s⁻¹), 400–700 nm at 22°C and a relative humidity between 40 and 60% on a gravel culture subirrigated with Hoagland's nutrient solution. The basal diameter of the growing shoot, a measure of the number of apical cells participating in growth, increased proportionally to irradiance and was correlated with mature leaf length. The development of the length of the growing shoot (L_gs) depended also on the nutritional status of the (young) shoot. L_gs was strongly correlated with the rate of height growth.     

Out of Australia and back again: the world‐wide historical biogeography of non‐pollinating fig wasps (Hymenoptera: Sycophaginae)

Aim Figs (Ficus, Moraceae) are exploited by rich communities of often host‐specific phytophagous wasps. Among them, gall‐inducing Sycophaginae (Hymenoptera, Chalcidoidea) may share a common history with Ficus and their mutualistic pollinators (Agaonidae). We investigate here, for the first time, the phylogeny and biogeographical history of Sycophaginae and compare the timing of radiation and dispersion of major clades with available data on Ficus and fig pollinators. Reconstructing the history of their host colonization and association over space and time is central to understanding how fig wasp communities were assembled. Location World‐wide. Methods Maximum likelihood and Bayesian analyses were conducted on 4267 bp of mitochondrial and nuclear DNA to produce a phylogeny of all genera of Sycophaginae. Two relaxed clock methods with or without rate autocorrelation were used for date estimation. Analyses of ancestral area were also conducted to investigate the geographical origin of the Sycophaginae. Results The phylogeny is well resolved and supported. Our data suggest a post‐Gondwanan origin for the Sycophaginae (50–40 Ma) and two independent out‐of‐Australia dispersal events to continental Asia. Given palaeoclimatic and palaeogeographic records, the following scenario appears the most likely. The ancestor of Idarnes+Apocryptophagus migrated to Greater India through the Ninetyeast Ridge (40–30 Ma). The ancestor of Anidarnes+Conidarnes dispersed later via Sundaland (25–20 Ma). Idarnes and Anidarnes subsequently reached the New World via the North Atlantic land bridges during the Late Oligocene Warming Event. Apocryptophagus reached Africa c. 20 Ma via the Arabic corridors and returned to Australasia following the expansion of Sundaland tropical forests (20–10 Ma). Main conclusions Sycophaginae probably invaded the fig microcosm in Australia c. 50–40 Ma after the origin of their host plant. Once associated with figs, they dispersed out of Australia and radiated together with their host fig and associated pollinator through the tropics. We recorded a good coincidence of timing between dispersal events of Sycophaginae and continental connections. Furthermore, fruit pigeons that disperse figs probably spread out of Australasia through the Indian Ocean via the Ninetyeast Ridge c. 38 Ma. Therefore, our study highlights the potential for combining molecular phylogenetics with multiple methods of dating of interacting groups to reconstruct the historical biogeography of plant–herbivore associations.     

Spike‐in SILAC proteomic approach reveals the vitronectin as an early molecular signature of liver fibrosis in hepatitis C infections with hepatic iron overload

Hepatitis C virus (HCV)‐induced iron overload has been shown to promote liver fibrosis, steatosis, and hepatocellular carcinoma. The zonal‐restricted histological distribution of pathological iron deposits has hampered the attempt to perform large‐scale in vivo molecular investigations on the comorbidity between iron and HCV. Diagnostic and prognostic markers are not yet available to assess iron overload‐induced liver fibrogenesis and progression in HCV infections. Here, by means of Spike‐in SILAC proteomic approach, we first unveiled a specific membrane protein expression signature of HCV cell cultures in the presence of iron overload. Computational analysis of proteomic dataset highlighted the hepatocytic vitronectin expression as the most promising specific biomarker for iron‐associated fibrogenesis in HCV infections. Next, the robustness of our in vitro findings was challenged in human liver biopsies by immunohistochemistry and yielded two major results: (i) hepatocytic vitronectin expression is associated to liver fibrogenesis in HCV‐infected patients with iron overload; (ii) hepatic vitronectin expression was found to discriminate also the transition between mild to moderate fibrosis in HCV‐infected patients without iron overload.     

The link between small heat shock proteins and the immune system

There is now compelling evidence that members of the family of small heat shock proteins (HSP) can be secreted by a variety of different types of cells. Secretion of small HSP may at times represent altruistic delivery of supporting and stabilizing factors from one cell to another. A probably more general effect of extracellular small HSP, however, is exerted by their ability to activate macrophages and macrophage-like cells. When doing so, small HSP induce an immune-regulatory state of activation, stimulating macrophages to suppress inflammation. For this reason, small HSP deserve consideration as broadly applicable therapeutic agents for inflammatory disorders. In one particular case, however, adaptive immune responses to the small HSP itself may subvert the protective quality of the innate immune response it triggers. This situation only applies to alpha B-crystallin, and is unique for humans as well. In this special case, local concentrations of alpha B-crystallin determine the balance between protective innate responses and destructive adaptive responses, the latter of which are held responsible for the development of multiple sclerosis lesions. This article is part of a Directed Issue entitled: Small HSPs in physiology and pathology.     

Review of Afrotropical Figitinae (Figitidae,Cynipoidea, Hymenoptera) with the first records of Neralsia and Lonchidia for the region

The cynipoid subfamily Figitinae is poorly represented in the Afrotropical region with two genera (Figites Latreille and Xyalophora Kieffer) and six species currently known. Here we record an additional two genera (Neralsia Cameron and Lonchidia Thomson) for the region and describe three new species: Neralsia haddocki sp. n.; Xyalophora tedjoansi sp. n.; Xyalophora tintini sp. n. Benoit’s species described in 1956 are synonymized under Figites aciculatus (Benoit, 1956): Figites effossus syn. n.; Figites favonius syn. n.; Figites furvus syn. n.; Figites fraudator syn. n. Identification keys to the figitine genera and species occurring in the Afrotropical region are provided. Online interactive Lucid Phoenix and Lucid matrix keys are available at: http://www.waspweb.org/Cynipoidea/Keys/index.htm