Phylogeny of fungal hemoglobins and expression analysis of the Aspergillus oryzae flavohemoglobin gene fhbA during hyphal growth.

The fhbA genes encoding putative flavohemoglobins (FHb) from Aspergillus niger and Aspergillus oryzae were isolated. Comparison of the deduced amino acid sequence of the A. niger fhbA gene and other putative filamentous fungal FHb-encoding genes to that of Ralstonia eutropha shows an overall conserved gene structure and completely conserved catalytic amino acids.

Exploring laccase-like multicopper oxidase genes from the ascomycete Trichoderma reesei: a functional, phylogenetic and evolutionary study.

Background: The diversity and function of ligninolytic genes in soil-inhabiting ascomycetes has not yet been elucidated, despite their possible role in plant litter decay processes. Among ascomycetes, Trichoderma reesei is a model organism of cellulose and hemicellulose degradation, used for its unique secretion ability especially for cellulase production. T.

Genome sequence of the model mushroom Schizophyllum commune.

Much remains to be learned about the biology of mushroom-forming fungi, which are an important source of food, secondary metabolites and industrial enzymes. The wood-degrading fungus Schizophyllum commune is both a genetically tractable model for studying mushroom development and a likely source of enzymes capable of efficient degradation of lignocellulosic biomass. Comparative analyses of its 38.

Considering time in LCA: dynamic LCA and its application to global warming impact assessments.

The lack of temporal information is an important limitation of life cycle assessment (LCA). A dynamic LCA approach is proposed to improve the accuracy of LCA by addressing the inconsistency of temporal assessment. This approach consists of first computing a dynamic life cycle inventory (LCI), considering the temporal profile of emissions.

Heterologous production of the Piromyces equi cinnamoyl esterase in Trichoderma reesei for biotechnological applications.

Aims: The objective of the study was to produce and characterize the cinnamoyl esterase EstA from the anaerobic fungus Piromyces equi for potential industrial applications.

Methods And Results: The catalytic domain EstA was produced in Trichoderma reesei. Because the two fungi displayed different genome features, including different codon usage and GC content, a synthetic gene was designed and expressed, leading to the production of the corresponding protein at around 33 mg per litre in the T.

A low-cost thermoelectrically cooled tissue clamp for in vitro cyclic loading and load-to-failure testing of muscles and tendons.

In vitro cyclic loading and load-to-failure testing of muscles and tendons require a reliable linking device between tissues and the actuator that can transmit high loads without slippage or tissue damage. This article describes a simple custom-made thermoelectrically cooled freeze clamp. The effectiveness of the clamp to transmit loads without tissue slippage was evaluated on 10 canine quadriceps femoris myo-tendinous junctions in both load-to-failure and cyclic loading settings.

Strategies for reliable exploitation of evolutionary concepts in high throughput biology.

The recent availability of the complete genome sequences of a large number of model organisms, together with the immense amount of data being produced by the new high-throughput technologies, means that we can now begin comparative analyses to understand the mechanisms involved in the evolution of the genome and their consequences in the study of biological systems. Phylogenetic approaches provide a unique conceptual framework for performing comparative analyses of all this data, for propagating information between different systems and for predicting or inferring new knowledge. As a result, phylogeny-based inference systems are now playing an increasingly important role in most areas of high throughput genomics, including studies of promoters (phylogenetic footprinting), interactomes (based on the presence and degree of conservation of interacting proteins), and in comparisons of transcriptomes or proteomes (phylogenetic proximity and co-regulation/co-expression).

GPR50 is the mammalian ortholog of Mel1c: evidence of rapid evolution in mammals.

Background: The melatonin receptor subfamily contains three members Mel1a, Mel1b and Mel1c, found in all vertebrates except for Mel1c which is found only in fish, Xenopus species and the chicken. Another receptor, the melatonin related receptor known as GPR50, found exclusively in mammals and later identified as a member of the melatonin receptor subfamily because of its identity to the three melatonin receptors despite its absence of affinity for melatonin. The aim of this study was to describe the evolutionary relationships between GPR50 and the three other members of the melatonin receptor subfamily.

FOLy: an integrated database for the classification and functional annotation of fungal oxidoreductases potentially involved in the degradation of lignin and related aromatic compounds.

The breakdown of lignin by fungi is a key step during carbon recycling in terrestrial ecosystems. This process is of great interest for green and white biotechnological applications. Given the importance of these enzymatic processes, we have classified the enzymes potentially involved in lignin catabolism into sequence-based families and integrated them in a newly developed database, designated Fungal Oxidative Lignin enzymes (FOLy).

Conceptual bases for quantifying the role of the environment on gene evolution: the participation of positive selection and neutral evolution.

To demonstrate that a given change in the environment has contributed to the emergence of a given genotypic and phenotypic shift during the course of evolution, one should ask to what extent such shifts would have occurred without environmental change. Of course, such tests are rarely practical but phenotypic novelties can still be correlated to genomic shifts in response to environmental changes if enough information is available. We surveyed and re-evaluated the published data in order to estimate the role of environmental changes on the course of species and genomic evolution.

Molecular evolution of the human SRPX2 gene that causes brain disorders of the Rolandic and Sylvian speech areas.

Background: The X-linked SRPX2 gene encodes a Sushi Repeat-containing Protein of unknown function and is mutated in two disorders of the Rolandic/Sylvian speech areas. Since it is linked to defects in the functioning and the development of brain areas for speech production, SRPX2 may thus have participated in the adaptive organization of such brain regions. To address this issue, we have examined the recent molecular evolution of the SRPX2 gene.

Ancestral animal genomes reconstruction.

Reconstructing the evolutionary history of all species is an essential objective for evolutionary biologists. Much effort has been devoted to ancestral genome reconstruction. Numbered genome sequencing of current and extinct organisms enables evolutionary biologists to compare genomic data and reconstruct ancestral genomes.

The effect of axis alignment on shoulder joint kinematics analysis during arm abduction.

Background: A joint coordinate system allows coherence between the performed movement, its mathematical representation and the clinical interpretation of the kinematics of joint motion. In 2005, the International Society of Biomechanics (ISB) defined a joint coordinate system for the shoulder. To improve kinematics interpretation, the ISB suggested aligning the coordinate systems of the humerus and the scapula.

In vitro integration of an ichnovirus genome segment into the genomic DNA of lepidopteran cells.

Polydnaviruses (PDVs) are dsDNA viruses transmitted by ichneumonid and braconid endoparasitoids to their lepidopteran hosts during oviposition. Wasp carriers are asymptomatic and transmit the virus to their progeny through the germ line; replication is confined to the calyx region of the wasp ovary, where the virus accumulates in the fluid bathing the eggs. In the lepidopteran host, however, no virus replication takes place, but PDV gene expression is essential for successful parasitism.

Tracking the connection between evolutionary and functional shifts using the fungal lipase/feruloyl esterase A family.

Background: There have been many claims of adaptive molecular evolution, but what role does positive selection play in functional divergence? The aim of this study was to test the relationship between evolutionary and functional shifts with special emphasis on the role of the environment. For this purpose, we studied the fungal lipase/feruloyl esterase A family, whose functional diversification makes it a very promising candidate.

Results: The results suggested functional shift following a duplication event where neofunctionalisation of feruloyl esterase A had occurred with conservation of the ancestral lipase function.

Bromodomain testis-specific protein is expressed in mouse oocyte and evolves faster than its ubiquitously expressed paralogs BRD2, -3, and -4.

By using in silico methods in a previous study, we identified 100 oocyte-specific genes and 150 genes, enriched in the mouse oocyte. Interestingly, approximately half of the oocyte-specific genes tend to cluster on mouse chromosomes as if they have recently duplicated during evolution. In this study, we focused our attention on mouse BRDT, which belongs to a family of four structurally related proteins characterized by two N-terminal bromodomains and one C-terminal extraterminal domain (ET domain), defining the BET family.

The use of evolutionary biology concepts for genome annotation.

The past decade has seen the completion of numerous whole-genome sequencing projects, began with bacterial genomes and continued with eukaryotic species from different phyla: fungi, plants and animals. Besides, more biological information are produced and are shared thanks to information exchange systems, and more biological concepts, as well as more bioinformatics tools, are available. In this article, we will describe how the evolutionary biology concepts, as well as computer science, are useful for a better understanding of biology in general and genome annotation in particular.

Production of a chimeric enzyme tool associating the Trichoderma reesei swollenin with the Aspergillus niger feruloyl esterase A for release of ferulic acid.

The main goals of this work were to produce the fusion protein of the Trichoderma reesei swollenin I (SWOI) and Aspergillus niger feruloyl esterase A (FAEA) and to study the effect of the physical association of the fusion partners on the efficiency of the enzyme. The fusion protein was produced up to 25 mg l(-1) in the T. reesei strains Rut-C30 and CL847.

Effect of substrate temperature on morphology and electrochemical performance of radio frequency magnetron sputtered lithium nickel vanadate films used as negative electrodes for lithium microbatteries.

Lithium nickel vanadate thin films were prepared by radio frequency magnetron sputtering at various substrate temperatures (Ts). These thin films have been investigated as anode electrode material in the use of microbatteries. Films were characterized by Rutherford backscattering spectroscopy, nuclear reaction analysis, Auger electron spectroscopy, glancing-incidence X-ray diffraction analysis, Raman spectroscopy, scanning electron microscopy, atomic force microscopy, and high-resolution transmission electron microscopy techniques.

Construction of engineered bifunctional enzymes and their overproduction in Aspergillus niger for improved enzymatic tools to degrade agricultural by-products.

Two chimeric enzymes, FLX and FLXLC, were designed and successfully overproduced in Aspergillus niger. FLX construct is composed of the sequences encoding the feruloyl esterase A (FAEA) fused to the endoxylanase B (XYNB) of A. niger.

Overproduction and characterization of xylanase B from Aspergillus niger.

The xynB gene, which encodes endo-beta-1,4-xylanase XynB, in Aspergillus niger BRFM281 was amplified by RT-PCR using mRNA isolated from a culture containing sugar beet pulp as an inducer. The cDNA was cloned into an expression cassette under the control of the strong and constitutive glyceraldhehyde-3-phosphate dehydrogenase gene promoter. The expression system was designed to produce the recombinant enzyme XynB with a six-histidine peptide fused to the carboxy end of the protein.

Design and production in Aspergillus niger of a chimeric protein associating a fungal feruloyl esterase and a clostridial dockerin domain.

A chimeric enzyme associating feruloyl esterase A (FAEA) from Aspergillus niger and dockerin from Clostridium thermocellum was produced in A. niger. A completely truncated form was produced when the dockerin domain was located downstream of the FAEA (FAEA-Doc), whereas no chimeric protein was produced when the bacterial dockerin domain was located upstream of the FAEA (Doc-FAEA).

Prevalence and clinical significance of solitary pulmonary sub-segmental microembolism.

Background: Solitary pulmonary microembolism is rarely discussed as a distinct diagnostic entity. The purpose of this investigation was to determine the prevalence and clinical significance of embolism limited to subsegmental branches in a group of patients discharged from hospital on anticoagulants with a diagnosis of pulmonary embolism based on ventilation-perfusion imaging followed by selective angiography.

Material And Methods: Of 29 consecutive patients with classic signs of pulmonary embolism at angiography, we identified a subgroup of 5 patients with sub-segmental embolism, which was solitary in all cases.

Homologous expression of the feruloyl esterase B gene from Aspergillus niger and characterization of the recombinant enzyme.

The faeB gene encoding the feruloyl esterase B (FAEB) was isolated from Aspergillus niger BRFM131 genomic DNA. The faeB gene, with additional sequence coding for a C-terminal histidine tag, was inserted into an expression vector under the control of the gpd promoter and trpC terminator and expressed in a protease deficient A. niger strain.