Earthworm communities in organic and conventional coffee cultivation.

The objective of this work was to evaluate the effect of organic and conventional coffee crops on biomass, population density and diversity of earthworms, in Lerroville, district of Londrina County, Paraná state, Brazil. Earthworm communities were sampled in three areas with organic coffee cultivation (CO1, CO2 and CO3), two with conventional coffee (CC1 and CC2), and a native forest fragment (MT). The soil of the areas CO1, CC1, and MT was classifi ed as Nitossolo Vermelho (Rhodic Kandiudox), while CO2, CO3, and CC2 were on Latossolo Vermelho (Rhodic Hapludox). Eight samples were taken in each area on two occasions, winter and summer, using the Tropical Soil Biology and Fertility (TSBF) method in the 0–20 cm soil layer. The earthworms were handsorted and preserved in 4% formaldehyde, and were later weighed, counted and identifi ed. The highest earthworm biomass, both in winter and summer, occurred in the CO3 area. For population density, the higher numbers of individuals were found in CO1 and CO3. The highest number of species was identifi ed in the organic cultivation. The adoption of organic practices in coffee cultivation favored the diversity, density and biomass of earthworm communities

Structure of the Janus Protein Human CLIC2

Chloride intracellular channel (CLIC) proteins possess the remarkable property of being able to convert from a water-soluble state to a membrane channel state. We determined the three-dimensional structure of human CLIC2 in its water-soluble form by X-ray crystallography at 1.8-Å resolution from two crystal forms. In contrast to the previously characterized CLIC1 protein, which forms a possibly functionally important disulfide-induced dimer under oxidizing conditions, we show that CLIC2 possesses an intramolecular disulfide and that the protein remains monomeric irrespective of redox conditions. Site-directed mutagenesis studies show that removal of the intramolecular disulfide or introduction of cysteine residues in CLIC2, equivalent to those that form the intramolecular disulfide in CLIC1, does not cause dimer formation under oxidizing conditions.We also show that CLIC2 forms pH-dependent chloride channels in vitro with higher channel activity at low pH levels and that the channels are subject to redox regulation. In both crystal forms, we observed an extended loop region from the C-terminal domain, called the foot loop, inserting itself into an interdomain crevice of a neighboring molecule. The equivalent region in the structurally related glutathione transferase superfamily corresponds to the active site. This so-called foot-in-mouth interaction suggests that CLIC2 might recognize other proteins such as the ryanodine receptor through a similar interaction

Polyamine Sharing between Tubulin Dimers Favours Microtubule Nucleation and Elongation via Facilitated Diffusion

We suggest for the first time that the action of multivalent cations on microtubule dynamics can result from facilitated diffusion of GTP-tubulin to the microtubule ends. Facilitated diffusion can promote microtubule assembly, because, upon encountering a growing nucleus or the microtubule wall, random GTP-tubulin sliding on their surfaces will increase the probability of association to the target sites (nucleation sites or MT ends). This is an original explanation for understanding the apparent discrepancy between the high rate of microtubule elongation and the low rate of tubulin association at the microtubule ends in the viscous cytoplasm. The mechanism of facilitated diffusion requires an attraction force between two tubulins, which can result from the sharing of multivalent counterions. Natural polyamines (putrescine, spermidine, and spermine) are present in all living cells and are potent agents to trigger tubulin self-attraction. By using an analytical model, we analyze the implication of facilitated diffusion mediated by polyamines on nucleation and elongation of microtubules. In vitro experiments using pure tubulin indicate that the promotion of microtubule assembly by polyamines is typical of facilitated diffusion. The results presented here show that polyamines can be of particular importance for the regulation of the microtubule network in vivo and provide the basis for further investigations into the effects of facilitated diffusion on cytoskeleton dynamics

Crystal Structure of an Integron Gene Cassette-Associated Protein from Vibrio cholerae Identifies a Cationic Drug-Binding Module

Background The direct isolation of integron gene cassettes from cultivated and environmental microbial sources allows an assessment of the impact of the integron/gene cassette system on the emergence of new phenotypes, such as drug resistance or virulence. A structural approach is being exploited to investigate the modularity and function of novel integron gene cassettes. Methodology/Principal Findings We report the 1.8 A crystal structure of Cass2, an integron-associated protein derived from an environmental V. cholerae. The structure defines a monomeric beta-barrel protein with a fold related to the effector-binding portion of AraC/XylS transcription activators. The closest homologs of Cass2 are multi-drug binding proteins, such as BmrR. Consistent with this, a binding pocket made up of hydrophobic residues and a single glutamate side chain is evident in Cass2, occupied in the crystal form by polyethylene glycol. Fluorescence assays demonstrate that Cass2 is capable of binding cationic drug compounds with submicromolar affinity. The Cass2 module possesses a protein interaction surface proximal to its drug-binding cavity with features homologous to those seen in multi-domain transcriptional regulators. Conclusions/Significance Genetic analysis identifies Cass2 to be representative of a larger family of independent effector-binding proteins associated with lateral gene transfer within Vibrio and closely-related species. We propose that the Cass2 family not only has capacity to form functional transcription regulator complexes, but represents possible evolutionary precursors to multi-domain regulators associated with cationic drug compounds.National Health and Medical Research Council (Australia) (NHMRC grant 488502)National Institutes of Health (U.S.) (Grant GM62414-0 )Ontario. Ministry of Revenue (Challenge Fund

BMC Womens Health

BACKGROUND: The French national cancer institute (INCa) conducted a series of studies to assist decision-making in view of the implementation of organised cervical cancer screening that will be launched in 2018. The programme will concern all women aged 25-65 and targeted interventions will be developed for underscreened populations. This is an evolution from an equality-based approach to a step-by-step strategy of equity aiming to tackle health cancer inequalities that are avoidable and represents unfair differences. Here we present the work of the expert-group in ethics drafted by INCa to review the ethical issues prior to the programme implementation. DISCUSSION: We discuss the value of such a strategy and presents reflections with regard to issues of stigmatization, respect for individual freedom and autonomy. Indeed, the balance has to be found between the search for beneficence and the potential occurrence of perverse effects, which should be considered with particular attention. CONCLUSION: Moving toward an equity-oriented policy under a strategy of proportionate universalism faces a number of challenges, thus an overview of ethics and social sciences must be an integral part of the process

An online database for the detection of novel archaeal sequences in human ESTs

We have developed a rapid, automated screening system and online database to detect foreign sequences of archaeal origin in human expressed sequence tags. The aim of the screening is to detect transcripts that may be derived from novel, putative archaeal pathogens or symbionts

6's, 7's, and 8's : protein organization and recruitment in RNA-binding LSM complexes

Sm and Sm-like (Lsm) proteins are core components of the ribonucleoprotein complexes essential to key nucleic acid processing events within the eukaryotic cell nucleus (e.g. pre-mRNA splicing, mRNA degradation and histone processing). They assemble as poly-protein ring scaffolds that have the capacity to bind RNA substrates and other necessary protein factors. In viro, seven Lsm or Sm proteins form hetro-complexes, the exact components of which dictate the ultimate biological function. Thus, a heptameric assembly of Lsm [2+3+4+5+6+7+8] engages with and stabilises U6 snRNPs in the nucleus. Our group provided some of the first Lsm and Sm homo-heptameric ring structures of archaeal and eukaryotic origin (1,2). Here we report the first definition of a new organization of this family of proteins, found for a momomeric assembly of yeast Lsm3. The crystal structure revels a β-propeller ring of octomers organised via “head-to-head” stacking. Most importantly, the C-termini of some subunits are organised in additional beta sheet interactions with loop elements of neighbouring octomers. This provides some of the first understanding of the way in which Lsm proteins organise and recruit proteins to the ring scaffold. In an ongoing study to investigate inter-subunit interactions of Lsm assemblies, we have employed site-directed mutagenesis to identify key residues for thermal and folding stability. Chimaeras that introduce native-like interfaces into the Lsm3 homomeric assembly have enhanced thermal stability. The definition provided by our crystal structure of (Lsm3)₈ allows rationalisation of the key interfacial regions involved.1 page(s

Coherent vibronic coupling in light-harvesting complexes from photosynthetic marine algae

Observations of long-lived coherences in photosynthetic light-harvesting complexes utilize short pulses with broad spectral bandwidths to coherently excite multiple transitions and coherent superpositions. In order to identify the role that such quantum effects might play in efficient energy transfer, however, an alternative approach is required. We have developed a technique for two-color photon echo spectroscopy to selectively excite the pathway of interest and measure its evolution in the absence of any other excitation. We use this technique to excite a coherence pathway in phycocyanin-645 from cryptophyte algae and measure the dynamics of this coherence. A decoherence time of 500 fs was measured, and clear signatures for strong coupling between the electronic states and phonon modes were observed, allowing coherent coupling between otherwise nonresonant transitions. This provides detailed experimental evidence of the long-lived coherences and the nature of the quantum mechanical interactions between electronic states and phonon modes in phycocyanin-645 from cryptophyte marine algae

And now we are 8 : protein recruitment by LSM rings within RNPS

Sm and Sm-like (Lsm) proteins are core components of ribonucleoprotein complexes essential to key nucleic acid processing events such as pre-mRNA splicing, mRNA degradation and histone processing. The proteins assemble as multi-unit ring scaffolds that bind RNA substrates and other necessary protein factors. Our recent crystal structure of the octameric yeast Lsm3 ring, alongside solution NMR studies, reveals a new organization for these proteins, as well as a mechanism for recruitment of other protein components to the RNP scaffold. In vivo, seven Lsm proteins form hetero-complexes, the exact components of which dictate their specific biological function. By engineering appropriate polyproteins, we have now begun to probe the structural and functional features of both mRNA-degrading Lsm[1-7] complex, as well as the U6 component Lsm[2-8].1 page(s