Crystal structure of the MukB hinge domain with coiled‐coil stretches and its functional implications

The structural maintenance of chromosomes (SMC) family proteins are commonly found in the multiprotein complexes involved in chromosome organization, including chromosome condensation and sister chromatid cohesion. These proteins are characterized by forming a V‐shaped homo‐ or heterodimeric structure with two long coiled‐coil arms having two ATPase head domains at the distal ends. The hinge domain, located in the middle of the coiled coil, forms the dimer interface. In addition to being the dimerization module, SMC hinges appear to play other roles, including the gateway function for DNA entry into the cohesin complex. Herein, we report the homodimeric structure of the hinge domain of Escherichia coli MukB, which forms a prokaryotic condensin complex with two non‐SMC subunits, MukE and MukF. In contrast with SMC hinge of Thermotoga maritima which has a sizable central hole at the dimer interface, MukB hinge forms a constricted dimer interface lacking a hole. Under our assay conditions, MukB hinge does not interact with DNA in accordance with the absence of a notable positively charged surface patch. The function of MukB hinge appears to be limited to dimerization of two copies of MukB molecules. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

Wabusk of the Omushkegouk: Cree-Polar Bear (Ursus maritimus) Interactions in Northern Ontario

In order to understand wabusk (polar bear, Ursus maritimus) behaviours and interactions with people in the Hudson Bay lowlands of northern Ontario we conducted this collaborative study of Cree kiskayndamowin/knowledge. Our findings reveal that Cree knowledge supports previously published information on polar bears, while adding further contextual findings: that male polar bears travel greater distances into the muskeg than previously recorded; that wabusk prey on amisk (beaver, Castor canadensis); that wabusk interact with muskwa (black bears, Ursus americanus); and that human-polar bear interactions occur in this region of northern Canada. Bearing in mind that Cree knowledge has been recognized in wildlife management strategies (i.e., for beaver, caribou and moose) elsewhere in Canada, this particular body of information is timely, especially since polar bears are considered threatened under the Ontario Endangered Species Act, and the province is developing a recovery strategy for the Southern Hudson Bay polar bear population. The federal government is also contemplating listing polar bears in Canada as a “species of special concern” under the Species at Risk Act (SARA). While it is unclear as to how these decisions will impact the Cree-polar interactions, the listing of polar bears by both governments, but especially the provincial government of Ontario, must recognize treaty and Aboriginal rights, acknowledge its duties to consult and properly accommodate Aboriginal people’s views, incorporate Cree kiskayndamowin/knowledge of wabusk, and re-examine the proposed Wabusk Co-Management Agreement draft developed by the Ontario Ministry of Natural Resources (OMNR) and Coastal Cree First Nations of Northern Ontario in 1994. The article provides recommendations that highlight how the Northern Cree First Nations, through the development of the Recovery Strategy for Polar Bear in Ontario, can become engaged in the management of wabusk in Ontario and throughout Canada.     

Partial area of cholesterol in monounsaturated diacylphosphatidylcholine bilayers

The influence of cholesterol on the structural parameters of phosphatidylcholine bilayers is studied by small-angle neutron scattering on unilamellar liposomes. Monounsaturated diacylphosphatidylcholines diCn:1PC with the length of acyl chains n = 14, 18 and 22 carbons are used. We confirm that the bilayer thickness increases with increasing concentration of cholesterol for all studied diCn:1PCs. However, partial areas per diCn:1PC and cholesterol molecule on lipid–water interface are found not to depend of cholesterol concentration. The partial area per cholesterol molecule is 0.24 nm². In addition, the partial area per diC18:1PC is larger than that for diC14:1PC and diC22:1PC.     

Extremely low frequency magnetic field and the hatching rate of Fasciola hepatica eggs, the fecundity and survival of liver fluke-infected snail, Lymnaea truncatula

Eggs of Fasciola hepatica were exposed for 10 days to extremely low frequency magnetic field (ELFMF) at the frequency of 50 Hz and density of 2 mT (rms). The results show an accelerated hatching of F. hepatica eggs in relation to control (non-exposed) group. The host snails, Lymnaea truncatula, were divided into three groups; those of groups I and II were infected with the miracidia of F. hepatica hatched from control egg culture, whereas those of group III were infected with miracidia hatched from eggs affected by ELFMF. Thereafter, snails of groups II and III were exposed to ELFMF for 53 days, whereas those of group I were not exposed. At day 14 post infection, a significant decrease was observed in the number of cocoons laid by snails of group III, compared with control. Also, significant mortality in group III snails was observed 42 days post infection. The increased mortality and a lower number of cocoons laid by group III snails have probably resulted from enhanced stimulation of metacercarial parthenogenetic reproduction in consequence of infecting the molluscs with miracidia reared under ELFMF.     

Comparing Membrane Simulations to Scattering Experiments: Introducing the SIMtoEXP Software

SIMtoEXP is a software package designed to facilitate the comparison of biomembrane simulations with experimental X-ray and neutron scattering data. It has the following features: (1) Accepts number density profiles from simulations in a standard but flexible format. (2) Calculates the electron density ε(z) and neutron scattering length density ν(z) profiles along the z direction (i.e., normal to the membrane) and their respective Fourier transforms (i.e., F _ε [q _z ] and F _ν [q _z ]). The resultant four functions are then displayed graphically. (3) Accepts experimental F _ε (q _z ) and F _ν (q _z ) data for graphical comparison with simulations. (4) Allows for lipids and other large molecules to be parsed into component groups by the user and calculates the component volumes following Petrache et al. (Biophys J 72:2237–2242, 1997). The software then calculates and displays the contributions of each component group as volume probability profiles, ρ(z), as well as the contributions of each component to ε(z) and ν(z).     

Glycine-Rich Loop of Mitochondrial Processing Peptidase α-Subunit Is Responsible for Substrate Recognition by a Mechanism Analogous to Mitochondrial Receptor Tom20

Tryptophan fluorescence measurements were used to characterize the local dynamics of the highly conserved glycine-rich loop (GRL) of the mitochondrial processing peptidase (MPP) α-subunit in the presence of the substrate precursor. Reporter tryptophan residue was introduced into the GRL of the yeast α-MPP (Y299W) or at a proximal site (Y303W). Time-resolved and steady-state fluorescence spectroscopy demonstrated that for Trp299, the primary contact with the yeast malate dehydrogenase precursor evokes a change of the local GRL mobility. Moreover, time-resolved measurements showed that a functionless α-MPP with a single-residue deletion in the loop (Y303W/ΔG292) is defective particularly in the primary contact with substrate. Thus, the GRL was proved to be part of a contact site of the enzyme specifically recognizing the substrate. Regarding the surface exposure and presence of the hydrophobic patches within the GRL, we proposed a functional analogy between the presequence recognition by the hydrophobic binding groove of the Tom20 mitochondrial import receptor and the GRL of the α-MPP. A molecular dynamics (MD) simulation of the MPP-substrate peptide complex model was employed to test this hypothesis. The initial positioning and conformation of the substrate peptide in the model fitting were chosen based on the analogy of its interaction with the Tom20 binding groove. MD simulation confirmed the stability of the proposed interaction and showed also a decrease in GRL flexibility in the presence of substrate, in agreement with fluorescence measurements. Moreover, conserved substrate hydrophobic residues in positions + 1 and − 4 to the cleavage site remain in close contact with the side chains of the GRL during the entire production part of MD simulation as stabilizing points of the hydrophobic interaction. We conclude that the GRL of the MPP α-subunit is the crucial evolutional outcome of the presequence recognition by MPP and represents a functional parallel with Tom20 import receptor.     

Characterization of a legumain/vacuolar processing enzyme and YVADase activity in Papaver pollen

Legumains, also known as Vacuolar Processing Enzymes (VPEs) have received considerable attention recently, as they share structural properties with mammalian caspase-1 and exhibit YVADase/caspase-1-like cleavage activity. Although many legumains have been cloned, knowledge about their detailed characteristics and intracellular localization is relatively limited. We previously identified several caspase-like activities activated by self-incompatibility (SI) in pollen; a DEVDase was required for programmed cell death (PCD), but YVADase was not (Bosch and Franklin-Tong in Proc Natl Acad Sci USA 104:18327–18332, 2007; Thomas and Franklin-Tong in Nature 429:305–309, 2004). Here we report identification of a legumain/VPE from Papaver rhoeas pollen (PrVPE1) that binds to the DEVD tetrapeptide, a signature substrate for caspase-3. A detailed characterization of the recombinant PrVPE1 cleavage activity revealed that, like other VPEs, it has YVADase activity and requires an acidic pH for activity. Unlike other legumain/VPEs, it also exhibits DEVDase and IETDase activities and apparently does not require processing for activity. The pollen-expressed PrVPE1 localizes to a reticulate compartment resembling the vacuole. Examination of YVADase activity using live-cell imaging of pollen tubes revealed YVADase activity in mitochondria of growing pollen tubes. The unexpected features of PrVPE1, together with evidence for YVADase activity in plant mitochondria, indicate that VPEs, YVADases, their localization and functions in plant cells merit further investigation.     

Molecular profiling and identification of methanogenic archaeal species from rabbit caecum

During a comparison of 16S rDNA PCR-denaturant gradient gel electrophoresis (DGGE) profiles of methanogenic archaea from rumen fluid, rabbit caecum and pig feces, a unique band common to all rabbit caecum samples was observed. DGGE profiling also showed that the methanogen community from the New Zealand White adult rabbits is different and less complex than the methanogen communities from the rumen and pig feces. Small subunit ribosomal gene sequences of methanogenic archaea were subsequently retrieved from the constructed rabbit caecum 16S rDNA gene library. Results of the phylogenetic analysis indicated that rabbit caecum is inhabited by members of the genus Methanobrevibacter and is possibly one-species dominated, because all the retrieved sequences exhibited similarity values of 99% or higher. This species may well be a novel species of the genus Methanobrevibacter. It belongs to a distinct phylogenetic group containing Methanobrevibacter woesei, Methanobrevibacter thaueri and Methanobrevibacter gottschalkii strains isolated from animal feces, and Methanobrevibacter smithii from the predominating methanogen population of the human large bowel.     

Biological control of broad mites (<Emphasis Type="Italic">Polyphagotarsonemus latus</Emphasis>) with the generalist predator <Emphasis Type="Italic">Amblyseius swirskii</Emphasis>

The broad mite is a serious pest of a variety of crops worldwide. Several phytoseiid mites have been described to control these mites. However, broad mites are still one of the major pest problems on greenhouse pepper in South-eastern Spain. The generalist predatory mite A. swirskii is widely used against other pests of pepper plants such as thrips and whiteflies, the latter being a vector of broad mites. We assessed the potential of A. swirskii to control broad mites. The oviposition rate of A. swirskii on a diet of broad mites was lower than on a diet of pollen, but higher than oviposition in the absence of food. Population-dynamical experiments with A. swirskii on single sweet pepper plants in a greenhouse compartment showed successful control of broad mites.