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.     

Population heterogeneity in clinical cohorts affects the predictive accuracy of brain imaging

Brain imaging research enjoys increasing adoption of supervised machine learning for single-participant disease classification. Yet, the success of these algorithms likely depends on population diversity, including demographic differences and other factors that may be outside of primary scientific interest. Here, we capitalize on propensity scores as a composite confound index to quantify diversity due to major sources of population variation. We delineate the impact of population heterogeneity on the predictive accuracy and pattern stability in 2 separate clinical cohorts: the Autism Brain Imaging Data Exchange (ABIDE, n = 297) and the Healthy Brain Network (HBN, n = 551). Across various analysis scenarios, our results uncover the extent to which cross-validated prediction performances are interlocked with diversity. The instability of extracted brain patterns attributable to diversity is located preferentially in regions part of the default mode network. Collectively, our findings highlight the limitations of prevailing deconfounding practices in mitigating the full consequences of population diversity.

Brain-imaging research enjoys increasing adoption of supervised machine learning for single-subject disease classification. This study explores the contribution of diversity-aware machine learning models to tracking, unpacking and understanding out-of-distribution generalization in large-scale neuroimaging datasets, and shows that population diversity is a key factor contributing to generalization performance.     

Restoration of ER proteostasis attenuates remote apoptotic cell death after spinal cord injury by reducing autophagosome overload

The pathogenic mechanisms that underlie the progression of remote degeneration after spinal cord injury (SCI) are not fully understood. In this study, we examined the relationship between endoplasmic reticulum (ER) stress and macroautophagy, hereafter autophagy, and its contribution to the secondary damage and outcomes that are associated with remote degeneration after SCI. Using a rat model of spinal cord hemisection at the cervical level, we measured ER stress and autophagy markers in the axotomized neurons of the red nucleus (RN). In SCI animals, mRNA and protein levels of markers of ER stress, such as GRP78, CHOP, and GADD34, increased 1 day after the injury, peaking on Day 5. Notably, in SCI animals, the increase of ER stress markers correlated with a blockade in autophagic flux, as evidenced by the increase in microtubule-associated protein 2 light chain 3 (LC3-II) and p62/SQSTM1 (p62) and the decline in LAMP1 and LAMP2 levels. After injury, treatment with guanabenz protected neurons from UPR failure and increased lysosomes biogenesis, unblocking autophagic flux. These effects correlated with greater activation of TFEB and improved neuronal survival and functional recovery—effects that persisted after suspension of the treatment. Collectively, our results demonstrate that in remote secondary damage, impairments in autophagic flux are intertwined with ER stress, an association that contributes to the apoptotic cell death and functional damage that are observed after SCI.Subject terms: Cell death in the nervous system, Neurodegeneration, Molecular neuroscience