MIND-BEST: Web server for drugs and target discovery; design, synthesis, and assay of MAO-B inhibitors and theoretical-experimental study of G3PDH protein from Trichomonas gallinae

Many drugs with very different affinity to a large number of receptors are described. Thus, in this work, we selected drug-target pairs (DTPs/nDTPs) of drugs with high affinity/nonaffinity for different targets. Quantitative structure-activity relationship (QSAR) models become a very useful tool in this context because they substantially reduce time and resource-consuming experiments. Unfortunately, most QSAR models predict activity against only one protein target and/or they have not been implemented on a public Web server yet, freely available online to the scientific community. To solve this problem, we developed a multitarget QSAR (mt-QSAR) classifier combining the MARCH-INSIDE software for the calculation of the structural parameters of drug and target with the linear discriminant analysis (LDA) method in order to seek the best model. The accuracy of the best LDA model was 94.4% (3,859/4,086 cases) for training and 94.9% (1,909/2,012 cases) for the external validation series. In addition, we implemented the model into the Web portal Bio-AIMS as an online server entitled MARCH-INSIDE Nested Drug-Bank Exploration & Screening Tool (MIND-BEST), located at http://miaja.tic.udc.es/Bio-AIMS/MIND-BEST.php . This online tool is based on PHP/HTML/Python and MARCH-INSIDE routines. Finally, we illustrated two practical uses of this server with two different experiments. In experiment 1, we report for the first time a MIND-BEST prediction, synthesis, characterization, and MAO-A and MAO-B pharmacological assay of eight rasagiline derivatives, promising for anti-Parkinson drug design. In experiment 2, we report sampling, parasite culture, sample preparation, 2-DE, MALDI-TOF and -TOF/TOF MS, MASCOT search, 3D structure modeling with LOMETS, and MIND-BEST prediction for different peptides as new protein of the found in the proteome of the bird parasite Trichomonas gallinae, which is promising for antiparasite drug targets discovery.     

SMN requirement for synaptic vesicle, active zone and microtubule postnatal organization in motor nerve terminals

Low levels of the Survival Motor Neuron (SMN) protein produce Spinal Muscular Atrophy (SMA), a severe monogenetic disease in infants characterized by muscle weakness and impaired synaptic transmission. We report here severe structural and functional alterations in the organization of the organelles and the cytoskeleton of motor nerve terminals in a mouse model of SMA. The decrease in SMN levels resulted in the clustering of synaptic vesicles (SVs) and Active Zones (AZs), reduction in the size of the readily releasable pool (RRP), and the recycling pool (RP) of synaptic vesicles, a decrease in active mitochondria and limiting of neurofilament and microtubule maturation. We propose that SMN is essential for the normal postnatal maturation of motor nerve terminals and that SMN deficiency disrupts the presynaptic organization leading to neurodegeneration.     

Microbial fuel cells meet with external resistance

The influence of external load on the composition of the anodic biofilm microbial community and biomass yield was investigated in a microbial fuel cell fed with glucose and domestic wastewater was used as source of electrogens. Denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR) amplified 16S rRNA gene fragments revealed distinct differences in anodic bacterial communities formed at the anode of each MFC operated under a different external load. These results implied that in an MFC, electrogenic bacteria were enriched under higher current densities, i.e., low external load, and were able to sustain better current and effluent quality. The influence of the external resistance applied to the MFCs during formation of the bacterial communities from sewage wastewater was shown to have no significant effect on power performance of the MFCs nor to have a significant influence on their anodic activity with both glucose and brewery wastewater as fuel. As expected, current generation, COD removal and the biomass yield were all directly influenced by the external load. Significantly, when operated under lower external load, the biomass yield in the MFC was less than that in conventional anaerobic digestion (i.e., control).     

Biomass production and fatty acid accumulation in Chlorella sp. (strain DEC1B) isolated from a petrol refinery in Huelva (Spain)

A microalgal strain was established from Cepsa's refinery wastewater treatment plant in Huelva (southwest of Spain). Genetic analysis of the chloroplastic rbcL gene encoding for the large subunit of the ribulose bisphosphate carboxylase enzyme (Rubisco) showed the strain had high homology with other known rbcL sequences of the genus Chlorella. The strain grows well autotrophically in minimum mineral medium, with a growth rate of 0.28 ± 0.012 day^?1 and a biomass productivity of 138.9 ± 6.7 mg L^?1 day^?1. N‐starvation and/or over illumination with 650 µmol photons m^?2 s^?1 of PAR light on the cultures induced a significant increase in the intracellular content of lipids in this microalga. Total lipids were extracted from the strain biomass with 2:1 chloroform‐methanol, and they accounted for approximately 50% of the dry biomass. Polyunsaturated fatty acids (PUFAs) represented 60.4% of the total fatty acids found in the strain, thus making this biomass attractive as a high added‐value product source. The strain was able to grow efficiently in the refinery treated wastewater from which it was isolated, providing an attractive advantage for further development of more sustainable algal biomass production processes at reduced costs close to a petrol refinery area.     

The interplay between increased tooth crown‐height and chewing efficiency,and implications for Cervidae evolution

Mammals of numerous lineages have evolved high‐crowned (hypsodont) teeth particularly during the last 20 million years. This major phenotypic change is one of the most widely studied evolutionary phenomena in a broad range of disciplines, though the mechanisms underlying its transformation remain unresolved. Here, we present the first Finite Element Analysis (FEA) to investigate the alternative hypothesis that there is a biomechanical link between increased hypsodonty and a more effective mastication in deer. Our FE experiments compared patterns of stress and strain within and between different fossil and living species under different loading conditions, and found that more hypsodont teeth are suited for restricting stresses to those areas where chewing loading occurs. This mechanical improvement is consequence of specific and pronounced variations in tooth geometry and morphology of the occlusal surface that are strongly related to crown growth in the vertical plane. We demonstrate that hypsodonty enables selenodont‐teeth to adopt a mechanically improved design that increases the pressure whilst shearing foods. As ruminants are physiologically limited by both the quantity of food consumed and the time spent in the mastication and digestion, hypsodonty is highly advantageous when feeding on mechanically resistant, tough and fibrous foods. Consequently, it allows grass‐eaters to spend less time chewing, thereby increasing the volume of food ingested and/or providing more time for digestion. This study provides a promising line of evidences in support of biomechanical effectiveness, in addition to or instead of increased wear resistance, as a factor in explaining the evolutionary origins of the hypsodont phenotype.     

The active microbial diversity drives ecosystem multifunctionality and is physiologically related to carbon availability in Mediterranean semi‐arid soils

Biogeochemical processes and ecosystemic functions are mostly driven by soil microbial communities. However, most methods focus on evaluating the total microbial community and fail to discriminate its active fraction which is linked to soil functionality. Precisely, the activity of the microbial community is strongly limited by the availability of organic carbon (C) in soils under arid and semi‐arid climate. Here, we provide a complementary genomic and metaproteomic approach to investigate the relationships between the diversity of the total community, the active diversity and ecosystem functionality across a dissolved organic carbon (DOC) gradient in southeast Spain. DOC correlated with the ecosystem multifunctionality index composed by soil respiration, enzyme activities (urease, alkaline phosphatase and β‐glucosidase) and microbial biomass (phospholipid fatty acids, PLFA). This study highlights that the active diversity (determined by metaprotoemics) but not the diversity of the whole microbial community (evaluated by amplicon gene sequencing) is related to the availability of organic C and it is also connected to the ecosystem multifunctionality index. We reveal that DOC shapes the activities of bacterial and fungal populations in Mediterranean semi‐arid soils and determines the compartmentalization of functional niches. For instance, Rhizobales thrived at high‐DOC sites probably fuelled by metabolism of one‐C compounds. Moreover, the analysis of proteins involved in the transport and metabolism of carbohydrates revealed that Ascomycota and Basidiomycota occupied different nutritional niches. The functional mechanisms for niche specialization were not constant across the DOC gradient.     

Dry and wet periods drive rapid shifts in community assembly in an estuarine ecosystem

The impacts of changing climate regimes on emergent processes controlling the assembly of ecological communities remain poorly understood. Human alterations to the water cycle in the western United States have resulted in greater interannual variability and more frequent and severe extremes in freshwater flow. The specific mechanisms through which such extremes and climate regime shifts may alter ecological communities have rarely been demonstrated, and baseline information on current impacts of environmental variation is widely lacking for many habitats and communities. Here, we used observations and experiments to show that interannual variation in winter salinity levels in San Francisco Bay controls the mechanisms determining sessile invertebrate community composition during the following summer. We found consistent community changes in response to decadal‐scale dry and wet extremes during a 13‐year period, producing strikingly different communities. Our results match theoretical predictions of major shifts in species composition in response to environmental forcing up to a threshold, beyond which we observed mass mortality and wholesale replacement of the former community. These results provide a window into potential future community changes, with environmental forcing altering communities by shifting the relative influences of the mechanisms controlling species distributions and abundances. We place these results in the context of historical and projected future environmental variation in the San Francisco Bay Estuary.     

Length‐weight relationship for sea catfishes (Siluriformes: Ariidae) from the southeastern Gulf of California with new records on maximum length

The parameters of length‐weight relationship (LWR) are presented for seven species of catfish from the southeastern Gulf of California. Samples were obtained every three months, in Bahia de Matanchen (using bottom trawl nets consistent of 72 hauls, with mesh sizes of 3.2 cm in the wings and 2.54 cm in the cod‐end) from February to November, 2016 and in the San Blas estuarine system (using gill nets consistent of 32 hauls, with mesh sizes of 5 cm) from August, 2015 to May, 2016 respectively. The allometric coefficient (b) of LWR varied from 2.797 for the Cominate Sea Catfish (Occidentarius platypogon (Günther, 1864)) to 3.373 for the Tete Sea Catfish (Ariopsis gilberti (Jordan & Williams, 1895)). Four species reached new records on maximum total length (Tete Sea Catfish, A. gilberti; Widehead Sea Catfish, A. guatemalensis (Günther, 1864); Conguito Sea Catfish, Cathorops liropus (Bristol, 1897); and Curator Sea Catfish, C. raredonae Marceniuk, Betancur‐R, & Acero, 2009). For six of these species this accounts for the first report on estimations of LWR parameters.