Comparative metagenomics and functional profiling of crude oil-polluted soils in Bodo West Community,Ogoni, with other sites of varying pollution history

The impact of long-term crude oil pollution on soil microbial community structure in Bodo West Community, Ogoniland, Nigeria, was investigated to determine the amenability of the soil to microbial mediated remediation. Crude oil-polluted and pristine soil samples were collected approximately from 0 to 30 cm depth for both chemical and microbiological analyses. Total petroleum hydrocarbons (TPH) and polycyclic aromatic hydrocarbons (PAH) were determined using gas chromatograph–mass spectrophotometer (GC-MS). The soil microbiome was determined using the Illumina MiSeq platform. Results from this study were then compared with publicly available data from other oil-polluted sites. Taxonomic biomarkers and pathways associated with oil-polluted soils were detected using bioinformatics pipelines. TPH in the polluted and pristine soils were 7591 mg/kg and 199.70 mg/kg respectively, while the values of PAHs were significantly higher (p < 0.05) in the oil-polluted soil. Predictive functional and biomarker analysis demonstrated that microbes detected in the oil-polluted environment were involved in different metabolic pathways for degradation of a broad set of xenobiotic aromatic compounds. Established hydrocarbon degraders belonging to the families Alcanivoracaceae and Oceanospirillaceae were mostly detected in the oil-polluted soils. Sneathiella, Parvibaculum, Sphingobium, and Oceanicaulis were among biomarker taxa. The bacterial families Acidithiobacillaceae and Desulfobacteraceae were differentially more abundant in Bodo West spill site than any other site used for comparison. Furthermore, differentially represented species in our study site and other oil-polluted sites ranged from 21 to 42 bacterial families. The findings from this study revealed the bacterial community had a strong dependence on hydrocarbons and that acid-tolerant bacterial families can as well contribute significantly to biodegradation in the site and other polluted sites in Ogoniland usually known to have an acidic pH. Further research on Bodo West spill site will reveal the novel enzymes and pathways for enhanced microbial mediated eco-restoration.

     

Nucleus of the boar spermatozoon: structure and modifications in frozen, frozen-thawed, or sodium dodecyl sulfate-treated cells

After cryosubstitution and Epon embedding, or after Nanoplast embedding and very thin sectioning, the chromatin of ejaculated or diluted boar spermatozoa appears to be formed of DNA fibers embedded in a quite homogeneous matrix. After sodium dodecyl sulfate (SDS) treatment, and to a lesser extent after freeze-thawing, the DNA fibers are present mostly between cords, probably proteinaceous in nature. The quantity of free sulfhydryl (SH) groups, as calculated from staining by DACM and flow fluorometry, is increased in thawed or SDS-treated cells. The quantity of NH2 groups, calculated from electron microscopy image analysis of alcoholic phosphotungstic acid-stained cells, is decreased in thawed nuclei. The DNA is more accessible to the fluorochrome ethidium bromide after freeze-thawing, and its sensitivity to HCl hydrolysis is modified, during the Feulgen-like staining procedure using acriflavine. The X-ray energy dispersive analysis of cryosections of nuclei indicates that the slight separation of DNA and nucleoproteins in freeze-thawed spermatozoa could result from a dramatic modification of the nuclear ionic environment during thawing.     

La métabolomique: un nouvel outil pour la recherche translationnelle en cancérologie

Development and validation of novel diagnostic and prognostic tools for cancer patients are a clinically unmet need, especially to help predicting survival or treatment response and toxicity. Metabolomics provides a dynamic portrait of the metabolic state of a tumour in response to pathophysiological stimuli (such as tumour growth or tumour shrinkage) and helps us understand the molecular mechanism sustaining these phenomena. Recent literature presented encouraging data on potential applications of metabolomics in translational research. Analysis of alterations of the metabolic network may lead to identify novel biomarkers and/or therapeutic target.     

Forest refugia and riverine barriers promote diversification in the West African pygmy shrew (Crocidura obscurior complex,Soricomorpha)

The Crocidura obscurior or West African pygmy shrew complex is endemic to West African forests from south‐eastern Guinea, eastern Liberia, southern Côte d'Ivoire and south‐western Ghana. We explore the genetic and morphometric diversity of 239 individuals of the C. obscurior complex from 17 localities across its geographical range. Using genetic data from three mitochondrial (16S, cytochrome b and COI) and four nuclear markers (BRCA1, STAT5A, HDAC2 and RIOK3) and skull geometric morphometrics, we show that this complex is composed of two cryptic and sympatric species, C. obscurior and C. eburnea. We then test several hypotheses to infer their evolutionary history. The observed phylogeographical pattern based on cytochrome b and COI sequences fits the forest refuge theory: during arid phases of the Plio‐Pleistocene, around 3.5, 2.1, 1 and 0.5 Mya, a small number of populations survived in isolated forest patches and diverged allopatrically. During wetter climatic periods, forests expanded, leading to secondary contacts between previously isolated populations. Our results also suggest the possible contribution of episodes of isolation in subrefuges. Historical variation of the West African hydrographic network could also have contributed to the observed patterns of genetic differentiation. Rivers such as the Volta and Sassandra may act as past and/or current barriers to gene flow. Although these two species have sympatric distributions, their phylogeographical histories are somewhat dissimilar due to small differences in their dispersal abilities and ecological requirements.     

Quercus species divergence is driven by natural selection on evolutionarily less integrated traits

Functional traits are organismal attributes that can respond to environmental cues, thereby providing important ecological functions. In addition, an organism’s potential for adaptation is defined by the patterns of covariation among groups of functionally related traits. Whether an organism is evolutionarily constrained or has the potential for adaptation is based on the phenotypic integration or modularity of these traits. Here, we revisited leaf morphology in two European sympatric white oaks (Quercus petraea (Matt.) Liebl. and Quercus robur L.), sampling 2098 individuals, across much of their geographical distribution ranges. At the phenotypic level, leaf morphology traditionally encompasses discriminant attributes among different oak species. Here, we estimated in situ heritability, genetic correlation, and integration across such attributes. Also, we performed Selection Response Decomposition to test these traits for potential differences in oak species’ evolutionary responses. Based on the uncovered functional units of traits (modules) in our study, the morphological module “leaf size gradient” was highlighted among functionally integrated traits. Equally, this module was defined in both oaks as being under “global regulation” in vegetative bud establishment and development. Lamina basal shape and intercalary veins’ number were not, or, less integrated within the initially defined leaf functional unit, suggesting more than one module within the leaf traits’ ensemble. Since these traits generally show the greatest species discriminatory power, they potentially underwent effective differential response to selection among oaks. Indeed, the selection of these traits could have driven the ecological preferences between the two sympatric oaks growing under different microclimates.Subject terms: Quantitative trait, Evolutionary biology     

"Active" one-carbon generation in Saccharomyces cerevisiae.

A new mutation introducing a one-carbon requirement (e.g., formate) for the glycine-supplemented growth of a serine-glycine auxotroph (ser1) was correlated with a lack of glycine decarboxylase activity. The presence of oxalate decarboxylase activity or glyoxylate decarboxylase activity did not overcome the one-carbon requirement. Another mutation characterized by the absence of oxalate decarboxylase activity did not introduce a one-carbon requirement. The presence and physiological significance of glycine decarboxylase activity in Saccharomyces are thus inferred.     

Cardiopulmonary bypass surgery in swine: a research model

Similarities between humans and swine have been established on the basis of anatomic and physiologic characteristics. Consequently, the use of swine in biomedical research has increased over the last few decades. Most cardiopulmonary bypass (CPB) techniques in swine are only partial CPBs without cardiac arrest or aortic clamping. In addition, the post-operative period is often limited to a few hours. We decided to establish a swine model of total CPB with cardiac arrest and aortic clamping while allowing a post-operative period of 24 h. The purpose of this article is to describe our swine model that closely simulates the human situation in CPB surgery. Cardiac arrest with cardioplegia and aortic clamping was undertaken for 75 min. CPB was well-tolerated, and all pigs were weaned from it. Post-operative care was continued for 24 h. Hemodynamic and respiratory changes, characterized by reduced cardiac function, arrhythmias, and decreased oxygenation associated with ischemia-reperfusion and the inflammatory process under CPB, were recorded and compared to the same parameters in control pigs.     

Formalizing reliability in the taxonomic congruence approach

In the 'total evidence' approach to phylogenetics, the reliability of a clade is implicitly measured by its degree of support, often embodied in a robustness index such as a bootstrap proportion. In the taxonomic congruence approach, the measurement of reliability has been implemented by various consensus or supertree methods, but was seldom explicitly discussed as such. We explore a reliability index for clades using their repetition across independent data sets. All possible combinations of the elementary data sets are used to compose the sets of independent data sets, across which the repetitions are counted. The more a clade occurs across such independent combinations, the higher its index. However, if other repeated clades occur that are incompatible with that clade, its index is decreased to take into account the uncertainty resulting from conflicting hypotheses. Results can be summarized through a greedy consensus tree in which clades appear according to their repetition indices. This index is tested on a 73 acanthomorph taxa data set composed of five independent molecular markers and multiple combinations of them. On this particular application, we confirm that reliability as defined here and robustness (estimated by bootstrap proportions obtained from a 'total evidence' approach) should be clearly distinguished.