ecospat: an R package to support spatial analyses and modeling of species niches and distributions

The aim of the ecospat package is to make available novel tools and methods to support spatial analyses and modeling of species niches and distributions in a coherent workflow. The package is written in the R language (R Development Core Team) and contains several features, unique in their implementation, that are complementary to other existing R packages. Pre‐modeling analyses include species niche quantifications and comparisons between distinct ranges or time periods, measures of phylogenetic diversity, and other data exploration functionalities (e.g. extrapolation detection, ExDet). Core modeling brings together the new approach of ensemble of small models (ESM) and various implementations of the spatially‐explicit modeling of species assemblages (SESAM) framework. Post‐modeling analyses include evaluation of species predictions based on presence‐only data (Boyce index) and of community predictions, phylogenetic diversity and environmentally‐constrained species co‐occurrences analyses. The ecospat package also provides some functions to supplement the ‘biomod2’ package (e.g. data preparation, permutation tests and cross‐validation of model predictive power). With this novel package, we intend to stimulate the use of comprehensive approaches in spatial modelling of species and community distributions.     

Ca2+ binding to F‐ATP synthase β subunit triggers the mitochondrial permeability transition

F‐ATP synthases convert the electrochemical energy of the H⁺ gradient into the chemical energy of ATP with remarkable efficiency. Mitochondrial F‐ATP synthases can also undergo a Ca²⁺‐dependent transformation to form channels with properties matching those of the permeability transition pore (PTP), a key player in cell death. The Ca²⁺ binding site and the mechanism(s) through which Ca²⁺ can transform the energy‐conserving enzyme into a dissipative structure promoting cell death remain unknown. Through in vitro, in vivo and in silico studies we (i) pinpoint the “Ca²⁺‐trigger site” of the PTP to the catalytic site of the F‐ATP synthase β subunit and (ii) define a conformational change that propagates from the catalytic site through OSCP and the lateral stalk to the inner membrane. T163S mutants of the β subunit, which show a selective decrease in Ca²⁺‐ATP hydrolysis, confer resistance to Ca²⁺‐induced, PTP‐dependent death in cells and developing zebrafish embryos. These findings are a major advance in the molecular definition of the transition of F‐ATP synthase to a channel and of its role in cell death.     

Microbial diversity in degraded and non-degraded petroleum samples and comparison across oil reservoirs at local and global scales

Microorganisms have shown their ability to colonize extreme environments including deep subsurface petroleum reservoirs. Physicochemical parameters may vary greatly among petroleum reservoirs worldwide and so do the microbial communities inhabiting these different environments. The present work aimed at the characterization of the microbiota in biodegraded and non-degraded petroleum samples from three Brazilian reservoirs and the comparison of microbial community diversity across oil reservoirs at local and global scales using 16S rRNA clone libraries. The analysis of 620 16S rRNA bacterial and archaeal sequences obtained from Brazilian oil samples revealed 42 bacterial OTUs and 21 archaeal OTUs. The bacterial community from the degraded oil was more diverse than the non-degraded samples. Non-degraded oil samples were overwhelmingly dominated by gammaproteobacterial sequences with a predominance of the genera Marinobacter and Marinobacterium. Comparisons of microbial diversity among oil reservoirs worldwide suggested an apparent correlation of prokaryotic communities with reservoir temperature and depth and no influence of geographic distance among reservoirs. The detailed analysis of the phylogenetic diversity across reservoirs allowed us to define a core microbiome encompassing three bacterial classes (Gammaproteobacteria, Clostridia, and Bacteroidia) and one archaeal class (Methanomicrobia) ubiquitous in petroleum reservoirs and presumably owning the abilities to sustain life in these environments.

     

Aedes albopictus bionomics data collection by citizen participation on Procida Island,a promising Mediterranean site for the assessment of innovative and community-based integrated pest management methods

In the last decades, the colonization of Mediterranean Europe and of other temperate regions by Aedes albopictus created an unprecedented nuisance problem in highly infested areas and new public health threats due to the vector competence of the species. The Sterile Insect Technique (SIT) and the Incompatible Insect Technique (IIT) are insecticide-free mosquito-control methods, relying on mass release of irradiated/manipulated males, able to complement existing and only partially effective control tools. The validation of these approaches in the field requires appropriate experimental settings, possibly isolated to avoid mosquito immigration from other infested areas, and preliminary ecological and entomological data. We carried out a 4-year study in the island of Procida (Gulf of Naples, Italy) in strict collaboration with local administrators and citizens to estimate the temporal dynamics, spatial distribution, and population size of Ae. albopictus and the dispersal and survival of irradiated males. We applied ovitrap monitoring, geo-spatial analyses, mark-release-recapture technique, and a citizen-science approach. Results allow to predict the seasonal (from April to October, with peaks of 928–9,757 males/ha) and spatial distribution of the species, highlighting the capacity of Ae. albopictus population of Procida to colonize and maintain high frequencies in urban as well as in sylvatic inhabited environments. Irradiated males shown limited ability to disperse (mean daily distance travelled <60m) and daily survival estimates ranging between 0.80 and 0.95. Overall, the ecological characteristics of the island, the acquired knowledge on Ae. albopictus spatial and temporal distribution, the high human and Ae. albopictus densities and the positive attitude of the resident population in being active parts in innovative mosquito control projects provide the ground for evidence-based planning of the interventions and for the assessment of their effectiveness. In addition, the results highlight the value of creating synergies between research groups, local administrators, and citizens for affordable monitoring (and, in the future, control) of mosquito populations.     

Hsp70 as a stress marker of sea urchin coelomocytes in short term cultures.

Coelomocytes are the immune effectors of the sea urchin and have shown to respond to environmental and experimental challenge by the activation of stress markers. We extended our in vivo studies to in vitro short term cultures of sea urchin coelomocytes by analysing their response to temperature being stress, acid pH and heavy metals, using the hsp70 protein as a stress marker. We found that the in vitro time course of temperature stress recapitulates results obtained in vivo where the highest overexpression was observed after 1 hour. Coelomocytes overexpress hsp70 in a time-dependent manner when cultured for 1 to 6 hr at pH 4.7 +/- 0.2 in isotonic buffer, supplemented with EDTA as anticoagulant. A peak in the level of hsp70 expression was observed at 2 hr of culture, corresponding to a 10-fold increase over the levels of control coelomocytes cultured at pH 7.3 +/- 0.2. The effect of different concentrations of CdCl2 in the culture over a period of 4 hr was also tested. We found that CdCl2 greatly increases the hsp70 expression, with 10(-3) M the dose at which the highest overexpression is observed.     

Increasing the Carbon Flux toward Synthesis of Short-Chain-Length-Medium-Chain-Length Polyhydroxyalkanoate in the Peroxisome of Saccharomyces cerevisiae through Modification of the β-Oxidation Cycle

Short-chain-length-medium-chain-length polyhydroxyalkanoates were synthesized in Saccharomyces cerevisiae from intermediates of the β-oxidation cycle by expressing the polyhydroxyalkanoate synthases from Aeromonas caviae and Ralstonia eutropha in the peroxisomes. The quantity of polymer produced was increased by using a mutant of the β-oxidation-associated multifunctional enzyme with low dehydrogenase activity toward R-3-hydroxybutyryl coenzyme A.     

Adapted Changes in Left Ventricular Structure and Function in Severe Uncomplicated Obesity

Objective: A massive amount of fat tissue, as that observed in obese subjects with BMI over 50 kg/m², could affect cardiac morphology and performance, but few data on this issue are available. We sought to evaluate cardiac structure and function in uncomplicated severely obese subjects. Research Methods and Procedures: We studied 55 uncomplicated severely obese patients, 40 women, 15 men, mean age 35.5 ± 10.2 years, BMI 51.2 ± 8.8 kg/m², range 43 to 81 kg/m², with a history of fat excess of at least 10 years, and 55 age‐matched normal‐weight subjects (40 women, 15 men, mean BMI 23.8 ± 1.2 kg/m²) as a control group. Each subject underwent an echocardiogram to evaluate left ventricular (LV) mass and geometry and systolic and diastolic function. Results: Severely obese subjects showed greater LV mass and indexed LV mass than normal‐weight subjects (p < 0.01 for all parameters). Nevertheless, LV mass was appropriate for sex, height^2.7, and stroke work in most (77%) uncomplicated severely obese subjects. In addition, no significant difference in LV mass indices and LV mass appropriateness between obese subjects with BMI ≥ 50 kg/m² and those with BMI ≤ 50 kg/m² was found. Obese subjects also showed higher ejection fraction and midwall shortening than normal‐weight subjects (p = 0.05 and p < 0.01, respectively), suggesting a hyperdynamic systolic function. No significant difference in systolic performance between obese subjects with BMI ≥ 50 kg/m² and those with BMI ≤ 50 kg/m² was seen. Discussion: Our data show that uncomplicated severe obesity, despite the massive fat tissue amount, is associated largely with adapted and appropriate changes in cardiac structure and function.     

Tree regeneration responses in a lowland Nothofagus-dominated forest after bamboo dieback in South-Central Chile

The bamboo Chusquea quila (Poaceae:Bambuseae) is the most abundant understory species ofNothofagus-dominated forests at low elevations inthe Chilean Lake District. Species of this genus strongly inhibit theestablishment and growth of tree species, especially those of the genusNothofagus. At intervals of many years, this bambooflowerssynchronously and dies, creating large-scale disturbances. The mainobjective of this study was to determine the influence of bamboo dieback ontreeregeneration, especially of shade-intolerant species. The forest studiedis a remnant stand of old-growth forest dominated by emergent individualsof N. obliqua and Eucryphiacordifoliawhich project about 10 m above a main canopy formed byAextoxicon punctatum, Laureliaphilippiana, and Podocarpus saligna. Treeseedlings that established prior to bamboo dieback were recorded in six gapsdensely covered by bamboo. After the dieback event in the early 1990's,recruitment, height growth and survivorship were monitored in four gaps duringtwo growing seasons. After the synchronous mass flowering and death ofChusqueaquila, both reorganization of advance regeneration and new seedlingrecruitment were observed in gaps. The advance regeneration consisted mainly ofthe shade-tolerant species A. punctatum,L. philippiana, and Amomyrtus luma.These species together with E. cordifolia accounted forover 90% of the total individuals in gaps. During the following twoseasons, c. 40% of the advance regeneration either died or was damaged.Root suckers of E. cordifolia and L.philippiana were taller and grew faster than the seedlings of otherspecies. Nothofagus obliqua was unable to establishadvanceregeneration in gaps formerly dominated by bamboo. New recruitment resulted inthe synchronized establishment of treeseedlings, especially less shade-tolerant species such as N.obliqua, Aristotelia chilensis,Rhaphithamnus spinosus, and E.cordifolia. These species recruited into the gaps almost entirelyduring the first season right after the bamboo dieback. However, by the end ofthe second season, these species had a lower density due to a combination oflower recruitment rate, shortened recruitment period, and greater mortalityratecompared to the shade-tolerant species. New bamboo seedlings grew fasterand were more abundant than tree seedlings, except for root suckers (bothnew establishment and advance regeneration) of E.cordifolia which is more likely to successfully recruit into thecanopy. Seedlings of N. obliqua compete poorly with bambooseedlings; its successful recruitment may require bamboo flowering coincidentwith a mast seed year for the tree species.     

Amino acids are compatible osmolytes for volume recovery after hypertonic shrinkage in vascular endothelial cells

The response to chronic hypertonic stress has been studied inhuman endothelial cells derived from saphenous veins. In complete growth medium the full recovery of cell volume requires several hoursand is neither associated with an increase in cellK⁺ nor hindered by bumetanide butdepends on an increased intracellular pool of amino acids. The highestincrease is exhibited by neutral amino acid substrates of transportsystem A, such as glutamine and proline, and by the anionic amino acidglutamate. Transport system A is markedly stimulated on hypertonicstress, with an increase in activity roughly proportional to the extentand the duration of the osmotic shrinkage. Cycloheximide prevents the increase in transport activity of system A and the recovery of cellvolume. It is concluded that human endothelial cells counteract hypertonic stress through the stimulation of transport system A and theconsequent expansion of the intracellular amino acid pool.