Structural Basis of Rap Phosphatase Inhibition by Phr Peptides

Two-component systems, composed of a sensor histidine kinase and an effector response regulator (RR), are the main signal transduction devices in bacteria. In Bacillus, the Rap protein family modulates complex signaling processes mediated by two-component systems, such as competence, sporulation, or biofilm formation, by inhibiting the RR components involved in these pathways. Despite the high degree of sequence homology, Rap proteins exert their activity by two completely different mechanisms of action: inducing RR dephosphorylation or blocking RR binding to its target promoter. However the regulatory mechanism involving Rap proteins is even more complex since Rap activity is antagonized by specific signaling peptides (Phr) through a mechanism that remains unknown at the molecular level. Using X-ray analyses, we determined the structure of RapF, the anti-activator of competence RR ComA, alone and in complex with its regulatory peptide PhrF. The structural and functional data presented herein reveal that peptide PhrF blocks the RapF-ComA interaction through an allosteric mechanism. PhrF accommodates in the C-terminal tetratricopeptide repeat domain of RapF by inducing its constriction, a conformational change propagated by a pronounced rotation to the N-terminal ComA-binding domain. This movement partially disrupts the ComA binding site by triggering the ComA disassociation, whose interaction with RapF is also sterically impaired in the PhrF-induced conformation of RapF. Sequence analyses of the Rap proteins, guided by the RapF-PhrF structure, unveil the molecular basis of Phr recognition and discrimination, allowing us to relax the Phr specificity of RapF by a single residue change.     

Financial Risk Assessment and Optimal Planning of Biofuels Supply Chains under Uncertainty

Biofuels provide an attractive alternative for satisfying energy demands in a more sustainable way than fossil fuels. To establish a biorefinery, an optimal plan must be implemented for the entire associated supply chain, covering such aspects as selection of feedstocks, location, and capacity of biorefineries, selection of processing technologies, production amounts and transportation flows. In this context, there are several parameters, including the availability of biomass, product demand, and product prices, which are difficult to predict because they might change drastically over the different seasons of the year as well as across years. To address this challenge, this work presents a mathematical programming model for the optimal planning of a distributed system of biorefineries that considers explicitly the uncertainty associated with the supply chain operation as well as the associated risk. The potential of the proposed approach is demonstrated through its application to the production of biofuels in Mexico, considering multiple raw materials and products.     

Environmental DNA metabarcoding reveals winners and losers of global change in coastal waters

Studies of the ecological effects of global change often focus on one or a few species at a time. Consequently, we know relatively little about the changes underway at real-world scales of biological communities, which typically have hundreds or thousands of interacting species. Here, we use COI mtDNA amplicons from monthly samples of environmental DNA to survey 221 planktonic taxa along a gradient of temperature, salinity, dissolved oxygen and carbonate chemistry in nearshore marine habitat. The result is a high-resolution picture of changes in ecological communities using a technique replicable across a wide variety of ecosystems. We estimate community-level differences associated with time, space and environmental variables, and use these results to forecast near-term community changes due to warming and ocean acidification. We find distinct communities in warmer and more acidified conditions, with overall reduced richness in diatom assemblages and increased richness in dinoflagellates. Individual taxa finding more suitable habitat in near-future waters are more taxonomically varied and include the ubiquitous coccolithophore Emiliania huxleyi and the harmful dinoflagellate Alexandrium sp. These results suggest foundational changes for nearshore food webs under near-future conditions.     

Neural control of breathing: insights from genetic mouse models.

Recent studies described the in vivo ventilatory phenotype of mutant newborn mice with targeted deletions of genes involved in the organization and development of the respiratory-neuron network. Whole body flow barometric plethysmography is the noninvasive method of choice for studying unrestrained newborn mice. Breathing-pattern abnormalities with apneas occur in mutant newborn mice that lack genes involved in the development and modulation of rhythmogenesis. Studies of deficits in ventilatory responses to hypercapnia and/or hypoxia helped to identify genes involved in chemosensitivity to oxygen and carbon dioxide. Combined studies in mutant newborn mice and in humans have shed light on the pathogenesis of genetically determined respiratory-control abnormalities such as congenital central hypoventilation syndrome, Rett syndrome, and Prader-Willi syndrome. The development of mouse models has opened up the field of research into new treatments for respiratory-control disorders in humans.     

Sperm motility parameters and spermatozoa morphometric characterization in marine species: A study of swimmer and sessile species

The biodiversity of marine ecosystems is diverse and a high number of species coexist side by side. However, despite the fact that most of these species share a common fertilization strategy, a high variability in terms of the size, shape, and motion of spermatozoa can be found. In this study, we have analyzed both the sperm motion parameters and the spermatozoa morphometric features of two swimmer (pufferfish and European eel) and two sessile (sea urchin and ascidian) marine species. The most important differences in the sperm motion parameters were registered in the swimming period. Sessile species sperm displayed notably higher values than swimmer species sperm. In addition, the sperm motilities and velocities of the swimmer species decreased sharply once the sperm was activated, whereas the sessile species were able to maintain their initial values for a long time. These results are linked directly to the species-specific lifestyles. Although sessile organisms, which show limited or no movement, need sperm with a capacity to swim for long distances to find the oocytes, swimmer organisms can move toward the female and release gametes near it, and therefore the spermatozoa does not need to swim for such a long time. At the same time, sperm morphology is related to sperm motion parameters, and in this study an in-depth morphometric analysis of ascidian, sea urchin, and pufferfish spermatozoa, using computer-assisted sperm analysis software, has been carried out for the first time. A huge variability in shapes, sizes, and structures of the studied species was found using electron microscopy.     

Chronological implications of the nothrotheriid ‘Xyophorus’ (Mammalia,Xenarthra) from the Collón Curá Formation (Miocene of Patagonia,Argentina)

The specimen described herein and assigned to ‘Xyophorus’ sp. (Mammalia, Xenarthra, Tardigrada) was collected in the locality Cerro Zeballos, northwestern Chubut Province, Argentina. The fossiliferous sediments bearing the specimen are correlated with Collón Curá Formation. The specimen has the features described for other members of ‘Xyophorus’ (e.g. shape and size of the molariforms, relationship between diastema length, m1 and m2 length) and has a Diastema Length/Tooth Row Length index (DL/TRL index) of ca. 14, between that of ‘X.’ villarroeli (12.07) from the Mauri Formation, Bolivia (ca. 10.3 Ma) and that of ‘X.’ bondesioi (16.45) from Arroyo Chasicó Formation, Argentina (ca. 10–8.7 Ma). The relationship between DL/TRL index and age of the bearing sediments, would suggest a Tortonian age (late Miocene) for the deposits of Collón Curá Formation at Cerro Zeballos, which results in a ‘younger age’ compared to the middle Miocene age traditionally accepted for the Collón Curá Formation bearing the Colloncuran fauna sensu stricto. Although no absolute ages for Cerro Zeballos are available yet, the geographic proximity of Cerro Zeballos to Cushamen River (with levels dated at ca. 11.2 Ma) supports the tentative Tortonian age indicated by the presence of ‘Xyophorus’ sp.