RNF8 ubiquitylates histones at DNA double-strand breaks and promotes assembly of repair proteins

Accumulation of repair proteins on damaged chromosomes is required to restore genomic integrity. However, the mechanisms of protein retention at the most destructive chromosomal lesions, the DNA double-strand breaks (DSBs), are poorly understood. We show that RNF8, a RING-finger ubiquitin ligase, rapidly assembles at DSBs via interaction of its FHA domain with the phosphorylated adaptor protein MDC1. This is accompanied by an increase in DSB-associated ubiquitylations and followed by accumulation of 53BP1 and BRCA1 repair proteins. Knockdown of RNF8 or disruption of its FHA or RING domains impaired DSB-associated ubiquitylation and inhibited retention of 53BP1 and BRCA1 at the DSB sites. In addition, we show that RNF8 can ubiquitylate histone H2A and H2AX, and that its depletion sensitizes cells to ionizing radiation. These data suggest that MDC1-mediated and RNF8-executed histone ubiquitylation protects genome integrity by licensing the DSB-flanking chromatin to concentrate repair factors near the DNA lesions.     

Spatial distribution of the Daphnia longispina species complex and other planktonic crustaceans in the heterogeneous environment of canyon-shaped reservoirs

Canyon-shaped reservoirs are often characterised by longitudinalgradients of environmental factors (including trophic level,phytoplankton and zooplankton biomass and abundance of planktivorousfish) affecting the taxonomic composition of the pelagic community.We tested the hypothesis that the spatial distribution of differentspecies and interspecific hybrids of the Daphnia longispinaspecies complex is non-random under such conditions. Duringthe summer stratification, we sampled crustacean zooplanktonfrom 11 reservoirs, covering both longitudinal (upstream, middle,dam) and vertical (epi-, meta- and hypolimnion) environmentalgradients. Allozyme electrophoresis was used to discriminateamong different Daphnia taxa. All three frequently hybridizingEuropean species of the complex (galeata, cucullata, longispina= hyalina) and hybrids with Daphnia galeata were commonly recorded.Smaller-bodied Daphnia cucullata and its hybrids, when present,preferred mostly the nutrient- and food-rich upstream regions;D. longispina and its hybrids were more commonly found in thedownstream part, and often dominated in the meta- or hypolimnion.Redundancy analyses confirmed significant differences in theDaphnia taxon composition, as well as in spatial distributionof other crustacean species, along both gradients. For the firsttime, we demonstrate regular patterns in the horizontal distributionof Daphnia species and hybrids within a water body, thus acceptingour hypothesis. Such spatial distributional patterns may stronglyimpact local hybridization processes.     

Proteomic analysis of hepatic iron overload in mice suggests dysregulation of urea cycle, impairment of fatty acid oxidation, and changes in the methylation cycle

Liver iron overload can be found in hereditary hemochromatosis, chronic liver diseases such as alcoholic liver disease, and chronic viral hepatitis or secondary to repeated blood transfusions. The excess iron promotes liver damage, including fibrosis, cirrhosis, and hepatocellular carcinoma. Despite significant research effort, we remain largely ignorant of the cellular consequences of liver iron overload and the cellular processes that result in the observed pathological changes. In addition, the variability in outcome and the compensatory response that likely modulates the effect of increased iron levels are not understood. To provide insight into these critical questions, we undertook a study to determine the consequences of iron overload on protein levels in liver using a proteomic approach. Using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) combined with matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS), we studied hepatic iron overload induced by carbonyl iron-rich diet in mice and identified 30 liver proteins whose quantity changes in condition of excess liver iron. Among the identified proteins were enzymes involved in several important metabolic pathways, namely the urea cycle, fatty acid oxidation, and the methylation cycle. This pattern of changes likely reflects compensatory and pathological changes associated with liver iron overload and provides a window into these processes.     

Heterosubtypic immunity to influenza A virus infection requires a properly diversified antibody repertoire

Heterosubtypic immunity (HSI) is defined as cross-protection to infection with an influenza A virus serotype other than the one used for primary infection. Although HSI has been thought to be mediated by serotype cross-reactive cytotoxic T lymphocytes (CTL) that recognize conserved epitopes of structural proteins, recent studies suggest that antibodies (Abs) may make a significant contribution. In this study, we provide further evidence for the role of Abs in HSI using transgenic mice lacking terminal deoxyribonucleotidyltransferase (TdT), which adds N nucleotides to V-D and D-J junctions of the complementary determining region 3 (CDR3) (TdT(-/-)) and mice with altered Ab repertoires due to replacement of the complete locus of heavy chain diversity segments (D(H)) with an altered D(H) segment (namely, Delta D-iD). Both types of mice failed to generate complete HSI, although they were able to mount protective immunity to a homologous challenge. Lower levels of virus-specific antibodies along with more severely impaired HSI were observed in TdT(-/-) mice compared to those in Delta D-iD mice, while CTL activity remained unchanged in both types of mice. These findings indicate that a properly diversified antibody repertoire is required for HSI and that N addition by TdT is a more effective mechanism in the induction of a properly diversified antibody repertoire and, therefore, complete HSI. The results suggest that the diversity of the antibody repertoire as determined by the composition of the D region of HCDR3 and by N addition are among the mechanisms selected for in evolution to create a favorable environment to resolve infections with mutated viruses.     

Irradiated cationic mesoporphyrin induces larger damage to isolated rat liver mitochondria than the anionic form

The action of irradiated cationic Fe(III)TMPyP and anionic Fe(III)TPPS4 forms of mesoporphyrins on mitochondrial functions was investigated using experimental conditions that caused minimal effects on mitochondria in the dark. Treatment of mitochondria with 1 microM Fe(III)TMPyP for 2 min decreased the respiratory control by 3% in the dark and 28% after irradiation. Fe(III)TPPS4 (1 microM) had no significant effect on respiratory control under any of the above conditions. Both porphyrins increased the mitochondrial production of reactive oxygen species in the presence of Ca2+; however, the effect of Fe(III)TMPyP was significantly stronger. In both cases, this overproduction was associated with membrane lipid peroxidation. It was also observed that the association constant of Fe(III)TMPyP with mitochondria was 11 times higher than that of Fe(III)TPPS4. In conclusion, the damage to isolated mitochondria induced by Fe(III)TMPyP under illumination was larger than by Fe(III)TPPS4, probably because its cationic charge favors association with the mitochondrial membrane. This is supported by the decrease in the association constant of Fe(III)TMPyP with mitochondria in higher salt medium.     

Exploring the binding sites of the haloalkane dehalogenase DhlA from Xanthobacter autotrophicus GJ10

The catalytic site of haloalkane dehalogenase DhlA is buried more than 10 A from the protein surface. While potential access channels to this site have been reported, the precise mechanism of substrate import and product export is still unconfirmed. We used computational methods to examine surface pockets and their putative roles in ligand access to and from the catalytic site. Computational solvent mapping moves small organic molecule as probes over the protein surface in order to identify energetically favorable sites, that is, regions that tend to bind a variety of molecules. The mapping of three DhlA structures identifies seven such regions, some of which have been previously suggested to be involved in the binding and the import/export of substrates or products. These sites are the active site, the putative entrance of the channel leading to the active site, two pockets that bind Br- ions, a pocket in the slot region, and two additional sites between the main domain and the cap of DhlA. We also performed mapping and free energy analysis of the DhlA structures using the substrate, 1,2-dichloroethane, and halide ions as probes. The findings were compared to crystallographic data and to results obtained by CAVER, a program developed for finding routes from protein clefts and cavities to the surface. Solvent mapping precisely reproduced all three Br- binding sites identified by protein crystallography and the openings to four channels found by CAVER. The analyses suggest that (i) the active site has the highest affinity for the substrate molecule, (ii) the substrate initially binds at the entrance of the main tunnel, (iii) the site Br2, close to the entrance, is likely to serve as an intermediate binding site in product export, (iv) the site Br3, induced in the structure at high concentrations of Br-, could be part of an auxiliary route for product release, and (v) three of the identified sites are likely to be entrances of water-access channels leading to the active site. For comparison, we also mapped haloalkane dehalogenases DhaA and LinB, both of which contain significantly larger and more solvent accessible binding sites than DhlA. The mapping of DhaA and LinB places the majority of probes in the active site, but most of the other six regions consistently identified in DhlA were not observed, suggesting that the more open active site eliminates the need for intermediate binding sites for the collision complex seen in DhlA.     

<Emphasis Type="Italic">Daphnia galeata</Emphasis> in the deep hypolimnion: spatial differentiation of a “typical epilimnetic” species

One of the most serious threats to tropical mangrove ecosystems caused by shrimp farming activities is the poor management of pond waste materials. We hypothesise that mangroves can tolerate chemical residues discharged from shrimp farms and can be used as biofilters, but the capability of mangroves to cope with solid sediments dredged from shrimp ponds is limited. Our study in Pak Phanang, Thailand, confirmed that the excess sediments discharged from nearby shrimp ponds reduced mangrove growth rates and increased mortality rates. A series of transformed multi-temporal satellite images was used in combination with the field data to support this claim. In addition, a comparison between four dominant mangrove species revealed that Avicennia marina could tolerate sedimentation rates of >6 cm year⁻¹, while Bruguiera cylindrica tolerated sedimentation rates of 5 cm year⁻¹ (total sediment depth = 25 cm) before dying, while Excoecaria agallocha and Lumnitzera racemosa performed intermediate. This outcome implied that in our situation A. marina and to lesser extent E. agallocha and L. racemosa could be more effective as biofilters than B. cylindrica, as they may survive the sedimentation longer in the disposal areas. Further studies on the impact of sedimentation and chemical pollution of shrimp farm wastes on mangrove mortality and growth are required.