Optimization of cellulase production by Penicillium occitanis

The mutant Pol6 of Penicillium occitanis is an interesting strain for producing cellulases and hemicellulases. The nitrogen source and substrate that regulate cellulase production were evaluated in shake-flask and fermentor (batch and fed-batch) culture. The nature of the nitrogen source and the C/N ratio markedly affected cellulase production by P. occitanis. When nitrate was used in Mandels and Weber's basal growth medium with a C/N ratio below 20.2, it resulted in more cellulase production than from urea or ammonium sulphate. Crude substrates such as wheat bran and wheat flour residues, used in combination with a local cellulose esparto grass paper pulp as an alternative nitrogen source and cellulose substrates, also gave high cellulase yields. Greatest cellulase yields and productivity were obtained by fed-batch cultivation [23 filter-paper activity units (FPU)/ml and 168 FPUI^–1h^–1].     

Expression of heat shock and cold shock proteins in the gorgonian Leptogorgia virgulata

In this study, we analyzed the response of the temperate, shallow-water gorgonian, Leptogorgia virgulata, to temperature stress. Proteins were pulse labeled with (35)S-methionine/cysteine for 1 h to 2 h at 22 degrees C (control), or 38 degrees C, or for 4 h at 12.5 degrees C. Heat shock induced synthesis of unique proteins of 112, 89, and 74 kDa, with 102, 98 and 56 kDa proteins present in the control as well. Cold shock from 22 degrees C-12.5 degrees C induced the synthesis of a 25 kDa protein, with a 44 kDa protein present in the control as well. Control samples expressed unique proteins of 38, and 33 kDa. Non-radioactive proteins expressed under the same conditions as above, as well as natural field conditions, were tested for reactivity with antibodies to heat shock proteins (HSPs). HSP60 was the major protein found in L. virgulata. Although HSP47, HSP60, and HSP104 were present in all samples, the expression of HSP60 was enhanced in heat stressed colonies, while HSP47 and HSP104 expression were greatest in cold shocked samples. Inducible HSP70 was expressed in cold-shocked, heat-shocked, and field samples. Constitutively expressed HSP70 was absent from all samples. The expression of HSP90 was limited to heat shocked colonies. The expression of both HSP70 and HSP104 suggests that the organism may also develop a stress tolerance response.     

Spatio-temporal Genetic Structuring of Leishmania major in Tunisia by Microsatellite Analysis

In Tunisia, cases of zoonotic cutaneous leishmaniasis caused by Leishmania major are increasing and spreading from the south-west to new areas in the center. To improve the current knowledge on L. major evolution and population dynamics, we performed multi-locus microsatellite typing of human isolates from Tunisian governorates where the disease is endemic (Gafsa, Kairouan and Sidi Bouzid governorates) and collected during two periods: 1991–1992 and 2008–2012. Analysis (F-statistics and Bayesian model-based approach) of the genotyping results of isolates collected in Sidi Bouzid in 1991–1992 and 2008–2012 shows that, over two decades, in the same area, Leishmania parasites evolved by generating genetically differentiated populations. The genetic patterns of 2008–2012 isolates from the three governorates indicate that L. major populations did not spread gradually from the south to the center of Tunisia, according to a geographical gradient, suggesting that human activities might be the source of the disease expansion. The genotype analysis also suggests previous (Bayesian model-based approach) and current (F-statistics) flows of genotypes between governorates and districts. Human activities as well as reservoir dynamics and the effects of environmental changes could explain how the disease progresses. This study provides new insights into the evolution and spread of L. major in Tunisia that might improve our understanding of the parasite flow between geographically and temporally distinct populations.     

Mutational analysis of an archaeal minichromosome maintenance protein exterior hairpin reveals critical residues for helicase activity and DNA binding

Background

The mini-chromosome maintenance protein (MCM) complex is an essential replicative helicase for DNA replication in Archaea and Eukaryotes. While the eukaryotic complex consists of six homologous proteins (MCM2-7), the archaeon Sulfolobus solfataricus has only one MCM protein (ssoMCM), six subunits of which form a homohexamer. We have recently reported a 4.35Å crystal structure of the near full-length ssoMCM. The structure reveals a total of four β-hairpins per subunit, three of which are located within the main channel or side channels of the ssoMCM hexamer model generated based on the symmetry of the N-terminal Methanothermobacter thermautotrophicus (mtMCM) structure. The fourth β-hairpin, however, is located on the exterior of the hexamer, near the exit of the putative side channels and next to the ATP binding pocket.

Results

In order to better understand this hairpin's role in DNA binding and helicase activity, we performed a detailed mutational and biochemical analysis of nine residues on this exterior β-hairpin (EXT-hp). We examined the activities of the mutants related to their helicase function, including hexamerization, ATPase, DNA binding and helicase activities. The assays showed that some of the residues on this EXT-hp play a role for DNA binding as well as for helicase activity.

Conclusions

These results implicate several current theories regarding helicase activity by this critical hexameric enzyme. As the data suggest that EXT-hp is involved in DNA binding, the results reported here imply that the EXT-hp located near the exterior exit of the side channels may play a role in contacting DNA substrate in a manner that affects DNA unwinding.

     

Organolanthanide constrained geometry complexes modified for catalysis: synthesis, structure, and aminoalkene hydroamination properties of a pyrrolidine-substituted constrained geometry organolutetium complex

The reaction of the organolutetium complex (CGC′)LuCl₃Li₂(THF), (1; CGC′ = [Me₂Si(3-pyrrolidinyl-1-η⁵-indenyl)(^tBuN)]²⁻) with NaN(TMS)₂ provides a straightforward route to the halide-free organolutetium amido complex, (CGC′)LuN(TMS)₂(THF) (2). These new complexes were characterized by standard analytical methodology. The monomeric complex 2 crystallizes in the monoclinic space group P2₁/c with four molecules in a cell of dimensions a = 11.1566(6) Å, b = 14.9805(8) Å, c = 22.18007(12) Å, and β = 90.0620(10)°. Complex 2 is an active precatalyst for the intramolecular hydroamination/cyclization of representative aminoalkenes with turnover frequencies as high as 205 h⁻¹ at room temperature.     

Causal inference in biomolecular pathways using a Bayesian network approach and an Implicit method

We introduce here the concept of Implicit networks which provide, like Bayesian networks, a graphical modelling framework that encodes the joint probability distribution for a set of random variables within a directed acyclic graph. We show that Implicit networks, when used in conjunction with appropriate statistical techniques, are very attractive for their ability to understand and analyze biological data. Particularly, we consider here the use of Implicit networks for causal inference in biomolecular pathways. In such pathways, an Implicit network encodes dependencies among variables (proteins, genes), can be trained to learn causal relationships (regulation, interaction) between them and then used to predict the biological response given the status of some key proteins or genes in the network. We show that Implicit networks offer efficient methodologies for learning from observations without prior knowledge and thus provide a good alternative to classical inference in Bayesian networks when priors are missing. We illustrate our approach by an application to simulated data for a simplified signal transduction pathway of the epidermal growth factor receptor (EGFR) protein.     

Evaluation of a gp63–PCR Based Assay as a Molecular Diagnosis Tool in Canine Leishmaniasis in Tunisia

A gp63PCR method was evaluated for the detection and characterization of Leishmania (Leishmania) (L.) parasites in canine lymph node aspirates. This tool was tested and compared to other PCRs based on the amplification of 18S ribosomal genes, a L. infantum specific repetitive sequence and kinetoplastic DNA minicircles, and to classical parasitological (smear examination and/or culture) or serological (IFAT) techniques on a sample of 40 dogs, originating from different L. infantum endemic regions in Tunisia. Sensitivity and specificity of all the PCR assays were evaluated on parasitologically confirmed dogs within this sample (N = 18) and control dogs (N = 45) originating from non–endemic countries in northern Europe and Australia. The gp63 PCR had 83.5% sensitivity and 100% specificity, a performance comparable to the kinetoplast PCR assay and better than the other assays. These assays had comparable results when the gels were southern transferred and hybridized with a radioactive probe. As different infection rates were found according to the technique, concordance of the results was estimated by (κ) test. Best concordance values were between the gp63PCR and parasitological methods (74.6%, 95% confidence intervals CI: 58.8–95.4%) or serology IFAT technique (47.4%, 95% CI: 23.5–71.3%). However, taken together Gp63 and Rib assays covered most of the samples found positive making of them a good alternative for determination of infection rates. Potential of the gp63PCR-RFLP assay for analysis of parasite genetic diversity within samples was also evaluated using 5 restriction enzymes. RFLP analysis confirmed assignment of the parasites infecting the dogs to L. infantum species and illustrated occurrence of multiple variants in the different endemic foci. Gp63 PCR assay thus constitutes a useful tool in molecular diagnosis of L. infantum infections in dogs in Tunisia.