EPR studies on a Hipip type iron-sulfur center in the succinate dehydrogenase segment of the respiratory chain

In addition to the two species of ferredoxin-type iron-sulfur centers (Centers S-1 and S-2), a Hipip-type iron-sulfur center (Center S-3) has been detected in the reconstitutively active soluble succinate dehydrogenases. E_m7,4 determined in a particulate, antimycin A sensitive succinate-cytochrome $\text{c}$ reductase is +60 ± 15 mV. This center is extremely labile towards oxygen in a manner similar to the reconstitutive activity of the dehydrogenase. Even freshly prepared reconstitutively active enzyme shows a considerably diminished content of Center S-3 relative to flavin and displays a partly modified spectra. All reconstitutively inactive dehydrogenases give rise to a highly modified or no Center S-3 spectra at all. These observations indicate that Center S-3 is a constituent of succinate dehydrogenase and plays a role in the physiological function of the enzyme, $\text{i.e.}$ transferring electrons most probably to ubiquinone.     

Crystal structure of HEL4, a soluble, refoldable human V(H) single domain with a germ-line scaffold

The antigen binding site of antibodies usually comprises associated heavy (V(H)) and light (V(L)) chain variable domains, but in camels and llamas, the binding site frequently comprises the heavy chain variable domain only (referred to as V(HH)). In contrast to reported human V(H) domains, V(HH) domains are well expressed from bacteria and yeast, are readily purified in soluble form and refold reversibly after heat-denaturation. These desirable properties have been attributed to highly conserved substitutions of the hydrophobic residues of V(H) domains, which normally interact with complementary V(L) domains. Here, we describe the discovery and characterisation of an isolated human V(H) domain (HEL4) with properties similar to those of V(HH) domains. HEL4 is highly soluble at concentrations of > or =3 mM, essentially monomeric and resistant to aggregation upon thermodenaturation at concentrations as high as 56 microM. However, in contrast to V(HH) domains, the hydrophobic framework residues of the V(H):V(L) interface are maintained and the only sequence changes from the corresponding human germ-line segment (V3-23/DP-47) are located in the loops comprising the complementarity determining regions (CDRs). The crystallographic structure of HEL4 reveals an unusual feature; the side-chain of a framework residue (Trp47) is flipped into a cavity formed by Gly35 of CDR1, thereby increasing the hydrophilicity of the V(H):V(L) interface. To evaluate the specific contribution of Gly35 to domain properties, Gly35 was introduced into a V(H) domain with poor solution properties. This greatly enhanced the recovery of the mutant from a gel filtration matrix, but had little effect on its ability to refold reversibly after heat denaturation. Our results confirm the importance of a hydrophilic V(H):V(L) interface for purification of isolated V(H) domains, and constitute a step towards the design of isolated human V(H) domains with practical properties for immunotherapy.     

Fourier transform infrared spectroscopy provides a fingerprint for the tetramer and for the aggregates of transthyretin

Transthyretin (TTR) is an amyloidogenic protein whose aggregation is responsible for several familial amyloid diseases. Here, we use FTIR to describe the secondary structural changes that take place when wt TTR undergoes heat- or high-pressure-induced denaturation, as well as fibril formation. Upon thermal denaturation, TTR loses part of its intramolecular beta-sheet structure followed by an increase in nonnative, probably antiparallel beta-sheet contacts (bands at 1,616 and 1,686 cm(-1)) and in the light scattering, suggesting its aggregation. Pressure-induced denaturation studies show that even at very elevated pressures (12 kbar), TTR loses only part of its beta-sheet structure, suggesting that pressure leads to a partially unfolded species. On comparing the FTIR spectrum of the TTR amyloid fibril produced at atmospheric pressure upon acidification (pH 4.4) with the one presented by the native tetramer, we find that the content of beta-sheets does not change much upon fibrillization; however, the alignment of beta-sheets is altered, resulting in the formation of distinct beta-sheet contacts (band at 1,625 cm(-1)). The random-coil content also decreases in going from tetramers to fibrils. This means that, although part of the tertiary- and secondary-structure content of the TTR monomers has to be lost before fibril formation, as previously suggested, there must be a subsequent reorganization of part of the random-coil structure into a well-organized structure compatible with the amyloid fibril, as well as a readjustment of the alignment of the beta-sheets. Interestingly, the infrared spectrum of the protein recovered from a cycle of compression-decompression at pD 5, 37 degrees C, is quite similar to that of fibrils produced at atmospheric pressure (pH 4.4), which suggests that high hydrostatic pressure converts the tetramers of TTR into an amyloidogenic conformation.     

3''End labelling of RNA with 32P suitable for rapid gel sequencing.

A new general method of labelling the 2',3'-diol end of RNA with 32P has been devised suitable for gel sequencing. Poly(A) polymerase (E. coli) is incubated with the RNA and limiting amounts of alpha-32P-ATP. The mono-addition product is then cleaved with periodate and beta-eliminated with aniline, leaving the RNA terminally labelled with 3' 32P-phosphate. When applied to a model compound, tRNAPhe from E. coli, over 28 residues could be read from the 3' end.     

Linking Flow Regime,Floodplain Lake Connectivity and Fish Catch in a Large River-Floodplain System,the Volga–Akhtuba Floodplain (Russian Federation)

River-floodplain systems are amongst the most productive—but often severely impacted—aquatic systems worldwide. We explored the ecological response of fish to flow regime in a large river-floodplain system by studying the relationships between (1) discharge and inundated floodplain area, with a focus on spatial and temporal patterns in floodplain lake connectivity, and (2) flood volume and fisheries catch. Our results demonstrate a non-linear relationship between discharge and floodplain inundation with considerable hysteresis due to differences in inundation and drainage rate. Inundation extent was mostly determined by flood volume, not peak discharge. We found that the more isolated lakes (that is, lakes with a shorter connection duration to the river) are located at higher local elevation and at larger hydrological distance from the main rivers: geographical distance to the river appears a poor predictor of lake isolation. Although year-to-year fish catches in the floodplain were significantly larger with larger flood volumes in the floodplain, they were not in the main river, suggesting that mechanisms that increase catch, such as increased floodplain access or increased somatic growth, are stimulated by flooding in the floodplain, but not in the river. Fish species that profit from flooding belong to different feeding guilds, suggesting that all trophic levels may benefit from flooding. We found indications that the ecological functioning of floodplains is not limited to its temporary availability as habitat. Refugia can be present within the floodplain itself, which should be considered in the management of large rivers and their floodplain.     

Partial purification and determination of molecular weights of glyoxalases by filtration on dextran gel

Glyoxalase I and glyoxalase II (EC. 4.4.1.5 and EC 3.1.2.6) were separated by gel filtration on Sephadex G-75 and G-100. This simple procedure permitted also the partial purification of glyoxalase II. The purification coefficient in a single run from supernatant from beef liver was about 1 : 30 compared with 1 : 15 after the fifth step of purification with classical methods.     

Modelling viral impact on bacterioplankton in the North Sea using artificial neural networks

The temporal variability of the viral impact on bacterioplankton during the summer-winter transition in the North Sea was determined and artificial neural networks (ANNs) were developed to predict viral production and the frequency of infected bacterial cells (FIC). Viral production and FIC were estimated using a virus-dilution approach during four cruises in the southern North Sea between July and December 2000 and an additional cruise in June 2001. Supplementary data such as bacterial production, and bacterial and viral abundance were collected to relate changes in FIC and viral production to the dynamics of other biotic parameters. Average viral abundance varied between 4.4 x 10(6) ml(-1) in December and 29.8 x 10(6) ml(-1) in July. Over the seasonal cycle, viral abundance correlated best with bacterial production. Average bacterial abundance varied between 0.5 x 10(6) ml(-1) in December and 1.3 x 10(6) ml(-1) in July. Monthly average values of FIC ranged from 9% in September to 39% in June and the average viral production from 11 x 10(4) ml(-1) h(-1) in December to 35 x 10(4) ml(-1) h(-1) in July. The data set was used to develop ANN-based models of viral production and FIC. Viral production was modelled best using sampling time, and bacterial and viral abundance as input parameters to an ANN with two hidden neurons. Modelling of FIC was performed using bacterial production as an additional input parameter for an ANN with three hidden neurons. The models can be used to simulate viral production and FIC based on regularly recorded and easily obtainable parameters such as bacterial production, bacterial and viral abundance.     

Warsaw Breakage Syndrome, a Cohesinopathy Associated with Mutations in the XPD Helicase Family Member DDX11/ChlR1

The iron-sulfur-containing DNA helicases XPD, FANCJ, DDX11, and RTEL represent a small subclass of superfamily 2 helicases. XPD and FANCJ have been connected to the genetic instability syndromes xeroderma pigmentosum and Fanconi anemia. Here, we report a human individual with biallelic mutations in DDX11. Defective DDX11 is associated with a unique cellular phenotype in which features of Fanconi anemia (drug-induced chromosomal breakage) and Roberts syndrome (sister chromatid cohesion defects) coexist. The DDX11-deficient patient represents another cohesinopathy, besides Cornelia de Lange syndrome and Roberts syndrome, and shows that DDX11 functions at the interface between DNA repair and sister chromatid cohesion.