Conformational transitions driven by pyridoxal‐5′‐phosphate uptake in the psychrophilic serine hydroxymethyltransferase from Psychromonas ingrahamii

Serine hydroxymethyltransferase (SHMT) is a pyridoxal‐5′‐phosphate (PLP)‐dependent enzyme belonging to the fold type I superfamily, which catalyzes in vivo the reversible conversion of l ‐serine and tetrahydropteroylglutamate (H₄PteGlu) to glycine and 5,10‐methylenetetrahydropteroylglutamate (5,10‐CH₂‐H₄PteGlu). The SHMT from the psychrophilic bacterium Psychromonas ingrahamii (piSHMT) had been recently purified and characterized. This enzyme was shown to display catalytic and stability properties typical of psychrophilic enzymes, namely high catalytic activity at low temperature and thermolability. To gain deeper insights into the structure–function relationship of piSHMT, the three‐dimensional structure of its apo form was determined by X‐ray crystallography. Homology modeling techniques were applied to build a model of the piSHMT holo form. Comparison of the two forms unraveled the conformation modifications that take place when the apo enzyme binds its cofactor. Our results show that the apo form is in an “open” conformation and possesses four (or five, in chain A) disordered loops whose electron density is not visible by X‐ray crystallography. These loops contain residues that interact with the PLP cofactor and three of them are localized in the major domain that, along with the small domain, constitutes the single subunit of the SHMT homodimer. Cofactor binding triggers a rearrangement of the small domain that moves toward the large domain and screens the PLP binding site at the solvent side. Comparison to the mesophilic apo SHMT from Salmonella typhimurium suggests that the backbone conformational changes are wider in psychrophilic SHMT. Proteins 2014; 82:2831–2841. © 2014 Wiley Periodicals, Inc.     

Co-management and Spatial Features Contribute to Secure Fish Abundance and Fishing Yields in Tropical Floodplain Lakes

Empirical data are needed to show the efficacy of co-management, which is regarded as a promising approach to achieve conservation goals. In this study, we addressed the potential influence of fisheries co-management to increase fish abundance and fishing yields in the lower Tocantins River Basin (Brazilian Amazon), downstream from a large dam. We analyzed 590 fish landings (6.7 t of fish) from five fishing villages and 48 fish samples obtained using gillnets (10,378 fish from 101 species) in 12 floodplain lakes in four regions: two with incipient co-management and two unmanaged. The fish species richness did not differ among the regions, but the lakes in the regions that were co-managed had higher fish abundance (biomass and number of individuals) and a higher mean proportion of fish reproducing during the high water season. Fishers had higher catches per unit of effort in the co-managed regions than fishers in the non-managed regions. These results were also influenced by geographic factors (distance and accessibility of lakes), as fish biomass was higher in lakes that were distant from the main river and from the main city in the region. Managers should thus consider strategic selection of the geographic locations of managed sites, even in remote areas. However, the fish biomass sampled in lakes was more related to region than to the lakes’ geographical location. Therefore, co-management has at least partially contributed to increased fish abundance and fishing yields in the studied region, through the protection of an important fish habitat (lakes). We provide empirical evidence that co-management can contribute to the maintenance of fish abundance, sustainability of fisheries, and food security in large tropical rivers impacted by damming.     

Plasticity in the Rat Prefrontal Cortex: Linking Gene Expression and an Operant Learning with a Computational Theory

The plasticity in the medial Prefrontal Cortex (mPFC) of rodents or lateral prefrontal cortex in non human primates (lPFC), plays a key role neural circuits involved in learning and memory. Several genes, like brain-derived neurotrophic factor (BDNF), cAMP response element binding (CREB), Synapsin I, Calcium/calmodulin-dependent protein kinase II (CamKII), activity-regulated cytoskeleton-associated protein (Arc), c-jun and c-fos have been related to plasticity processes. We analysed differential expression of related plasticity genes and immediate early genes in the mPFC of rats during learning an operant conditioning task. Incompletely and completely trained animals were studied because of the distinct events predicted by our computational model at different learning stages. During learning an operant conditioning task, we measured changes in the mRNA levels by Real-Time RT-PCR during learning; expression of these markers associated to plasticity was incremented while learning and such increments began to decline when the task was learned. The plasticity changes in the lPFC during learning predicted by the model matched up with those of the representative gene BDNF. Herein, we showed for the first time that plasticity in the mPFC in rats during learning of an operant conditioning is higher while learning than when the task is learned, using an integrative approach of a computational model and gene expression.     

Survival and redox activity of Friedmanniomyces endolithicus, an Antarctic endemic black meristematic fungus,after gamma rays exposure

Despite living organisms are not exposed to acute ionizing radiation under natural conditions, some exhibit a high radiation resistance. Understanding this phenomenon is important for assessing the impact of radiation-related accidents, occupational exposures and space missions. In this context, in this study we analyzed the effect of gamma rays on the Antarctic cryptoendolithic melanized fungus Friedmanniomyces endolithicus CCFEE 5208 and demonstrated its resistance to acute doses of gamma radiation (up to 400 Gy), accompanied by increase in metabolic activity.     

Structural Basis of Formation of the Microtubule Minus-End-Regulating CAMSAP-Katanin Complex

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Mapping of recent brachiopod microstructure: A tool for environmental studies

Shells of brachiopods are excellent archives for environmental reconstructions in the recent and distant past as their microstructure and geochemistry respond to climate and environmental forcings. We studied the morphology and size of the basic structural unit, the secondary layer fibre, of the shells of several extant brachiopod taxa to derive a model correlating microstructural patterns to environmental conditions. Twenty-one adult specimens of six recent brachiopod species adapted to different environmental conditions, from Antarctica, to New Zealand, to the Mediterranean Sea, were chosen for microstructural analysis using SEM, TEM and EBSD. We conclude that: 1) there is no significant difference in the shape and size of the fibres between ventral and dorsal valves, 2) there is an ontogenetic trend in the shape and size of the fibres, as they become larger, wider, and flatter with increasing age. This indicates that the fibrous layer produced in the later stages of growth, which is recommended by the literature to be the best material for geochemical analyses, has a different morphostructure and probably a lower organic content than that produced earlier in life.In two species of the same genus living in seawater with different temperature and carbonate saturation state, a relationship emerged between the microstructure and environmental conditions. Fibres of the polar Liothyrella uva tend to be smaller, rounder and less convex than those of the temperate Liothyrella neozelanica, suggesting a relationship between microstructural size, shell organic matter content, ambient seawater temperature and calcite saturation state.     

Enhanced resolution of specific chromosome and nuclear regions by reflectance laser scanning confocal microscopy

 DNA sequences digested by HaeIII and reconstructed by in situ nick translation employing digoxigenin-labelled nucleotides are usually revealed either by horseradish peroxidase or FITC fluorescence. To obtain a significant improvement in terms of resolution, sensitivity and specificity, colloidal gold has been used instead of FITC (as the reporter molecule) to reveal the labelled DNA. Colloidal gold and propidium iodide were visualised by employing the reflectance mode and the 488-nm laser line of a confocal laser scanning microscope. In chromosomes, the fluorescent reaction pattern showed diffuse areas of labelling in which it was impossible to identify any specific kind of banding along the arms. In some chromosomes and, in particular, 1 and 9, a C-negative banding due to the negativity of the centromeric areas was seen. A more accurate localisation on chromosomes, including telomeric regions, often organised in spot pairs that resembled an R-like banding, was detected using 1-nm colloidal gold. A fine labelling was also demonstrated in nuclei, especially at their peripheral heterochromatin. The non-fading properties of colloidal gold combined with visualisation by reflectance confocal laser scanning microscopy demonstrated the possibility of obtaining a higher spatial resolution than when using conventional fluorophores or higher laser wavelength. This improved way to study the localization of HaeIII digestion sites in single chromosomes and in interphase nuclei made the reaction a valuable tool for the detection of antigens or of specific DNA sequences in biological preparations. Accepted: 5 September 1996