Selective isolation of mouse glial nuclei optimized for reliable downstream omics analyses

Background: Isolation of cell types of interest from the brain for molecular applications presents several challenges, including cellular damage during tissue dissociation or enrichment procedures, and low cell number in the tissue in some cases. Techniques have been developed to enrich distinct cell populations using immunopanning or fluorescence activated cell/nuclei sorting. However, these techniques often involve fixation, immunolabeling and DNA staining steps, which could potentially influence downstream omics applications. New method: Taking advantage of readily available genetically modified mice with fluorescent-tagged nuclei, we describe a technique for the purification of cell-type specific brain nuclei, optimized to decrease sample preparation time and to limit potential artefacts for downstream omics applications. We demonstrate the applicability of this approach for the purification of glial cell nuclei and show that the resulting cell-type specific nuclei obtained can be used effectively for omics applications, including ATAC-seq and RNA-seq. Results: We demonstrate excellent enrichment of fluorescently-tagged glial nuclei, yielding high quality RNA and chromatin. We identify several critical steps during nuclei isolation that help limit nuclei rupture and clumping, including quick homogenization, dilution before filtration and loosening of the pellet before resuspension, thus improving yield. Sorting of fluorescent nuclei can be achieved without fixation, antibody labelling, or DAPI staining, reducing potential artifactual results in RNA-seq and ATAC-seq analyses. We show that reproducible glial cell type-specific profiles can be obtained in transcriptomic and chromatin accessibility assays using this rapid protocol. Comparison with existing methods: Our method allows for rapid enrichment of glial nuclei populations from the mouse brain with minimal processing steps, while still providing high quality RNA and chromatin required for reliable omics analyses. Conclusions: We provide a reproducible method to obtain nucleic material from glial cells in the mouse brain with a quick and limited sample preparation

Effects of a healthy meal course on spontaneous energy intake, satiety and palatability

Many food components can influence satiety or energy intake. Combined together, these food components could represent an interesting dietary strategy in the prevention and treatment of obesity. The aims of this study were: 1) to determine the effect of a functional food in the form of a healthy meal course on subsequent energy intake and satiety; 2) to verify if it is possible to maintain palatability while preserving the satiating effects of the test meal. Thirteen subjects were invited to eat two lunch sessions: healthy and control meal courses (2090 kJ/meal). Anthropometric and ad libitum food intake measurements, and visual analogue scales (VAS) were performed during the two lunch sessions. The healthy main course acutely decreased energy intake during the rest of the meal ( − 744 kJ, P ≤ 0·0001) and lipid ( − 6 %, P ≤ 0·0001) compared with the control meal. VAS ratings during the course of the testing showed a meal effect for hunger, desire to eat and prospective food consumption (P ≤ 0·05) and a time effect for all appetite sensations (P ≤ 0·0001). VAS scores on hunger ratings were lower for the healthy meal (P ≤ 0·05), whereas fullness ratings were higher shortly after the healthy main course (P ≤ 0·05). The healthy meal produced a slightly higher palatability rating but this effect was not statistically significant. These results suggest that it is possible to design a healthy meal that decreases spontaneous energy intake and hunger without compromising palatability

CTCF Governs the Identity and Migration of MGE-Derived Cortical Interneurons.

The CCCTC-binding factor (CTCF) is a central regulator of chromatin topology recently linked to neurodevelopmental disorders such as intellectual disability, autism, and schizophrenia. The aim of this study was to identify novel roles of CTCF in the developing mouse brain. We provide evidence that CTCF is required for the expression of the LIM homeodomain factor LHX6 involved in fate determination of cortical interneurons (CINs) that originate in the medial ganglionic eminence (MGE). Conditiona

The population genomic structure of green turtles (<i>Chelonia mydas</i>) suggests a warm-water corridor for tropical marine fauna between the Atlantic and Indian oceans during the last interglacial

The occasional westward transport of warm water of the Agulhas Current, “Agulhas leakage”, around southern Africa has been suggested to facilitate tropical marine connectivity between the Atlantic and Indian oceans, but the “Agulhas leakage” hypothesis does not explain the signatures of eastward gene flow observed in many tropical marine fauna. We investigated an alternative hypothesis: the establishment of a warm-water corridor during comparatively warm interglacial periods. The “warm-water corridor” hypothesis was investigated by studying the population genomic structure of Atlantic and Southwest Indian Ocean green turtles (N = 27) using 12,035 genome-wide single nucleotide polymorphisms (SNPs) obtained via ddRAD sequencing. Model-based and multivariate clustering suggested a hierarchical population structure with two main Atlantic and Southwest Indian Ocean clusters, and a Caribbean and East Atlantic sub-cluster nested within the Atlantic cluster. Coalescent-based model selection supported a model where Southwest Indian Ocean and Caribbean populations diverged from the East Atlantic population during the transition from the last interglacial period (130–115 thousand years ago; kya) to the last glacial period (115–90 kya). The onset of the last glaciation appeared to isolate Atlantic and Southwest Indian Ocean green turtles into three refugia, which subsequently came into secondary contact in the Caribbean and Southwest Indian Ocean when global temperatures increased after the Last Glacial Maximum. Our findings support the establishment of a warm-water corridor facilitating tropical marine connectivity between the Atlantic and Southwest Indian Ocean during warm interglacials

Invariant vector fields and the prolongation method for supersymmetric quantum systems

The kinematical and dynamical symmetries of equations describing the time evolution of quantum systems like the supersymmetric harmonic oscillator in one space dimension and the interaction of a non-relativistic spin one-half particle in a constant magnetic field are reviewed from the point of view of the vector field prolongation method. Generators of supersymmetries are then introduced so that we get Lie superalgebras of symmetries and supersymmetries. This approach does not require the introduction of Grassmann valued differential equations but a specific matrix realization and the concept of dynamical symmetry. The Jaynes-Cummings model and supersymmetric generalizations are then studied. We show how it is closely related to the preceding models. Lie algebras of symmetries and supersymmetries are also obtained.Comment: 37 pages, 7 table

Loss of ATRX in Chondrocytes Has Minimal Effects on Skeletal Development

BACKGROUND:Mutations in the human ATRX gene cause developmental defects, including skeletal deformities and dwarfism. ATRX encodes a chromatin remodeling protein, however the role of ATRX in skeletal development is currently unknown. METHODOLOGY/PRINCIPAL FINDINGS:We induced Atrx deletion in mouse cartilage using the Cre-loxP system, with Cre expression driven by the collagen II (Col2a1) promoter. Growth rate, body size and weight, and long bone length did not differ in Atrx(Col2cre) mice compared to control littermates. Histological analyses of the growth plate did not reveal any differences between control and mutant mice. Expression patterns of Sox9, a transcription factor required for cartilage morphogenesis, and p57, a marker of cell cycle arrest and hypertrophic chondrocyte differentiation, was unaffected. However, loss of ATRX in cartilage led to a delay in the ossification of the hips in some mice. We also observed hindlimb polydactily in one out of 61 mutants. CONCLUSIONS/SIGNIFICANCE:These findings indicate that ATRX is not directly required for development or growth of cartilage in the mouse, suggesting that the short stature in ATR-X patients is caused by defects in cartilage-extrinsic mechanisms

Demographic changes in Pleistocene sea turtles were driven by past sea level fluctuations affecting feeding habitat availability

Pleistocene environmental changes are generally assumed to have dramatically affected species’ demography via changes in habitat availability, but this is challenging to investigate due to our limited knowledge of how Pleistocene ecosystems changed through time. Here, we tracked changes in shallow marine habitat availability resulting from Pleistocene sea level fluctuations throughout the last glacial cycle (120–14 thousand years ago; kya) and assessed correlations with past changes in genetic diversity inferred from genome-wide SNPs, obtained via ddRAD sequencing, in Caribbean hawksbill turtles, which feed in coral reefs commonly found in shallow tropical waters. We found sea level regression resulted in an average 75% reduction in shallow marine habitat availability during the last glacial cycle. Changes in shallow marine habitat availability correlated strongly with past changes in hawksbill turtle genetic diversity, which gradually declined to ~1/4th of present-day levels during the Last Glacial Maximum (LGM; 26–19 kya). Shallow marine habitat availability and genetic diversity rapidly increased after the LGM, signifying a population expansion in response to warming environmental conditions. Our results suggest a positive correlation between Pleistocene environmental changes, habitat availability and species’ demography, and that demographic changes in hawksbill turtles were potentially driven by feeding habitat availability. However, we also identified challenges associated with disentangling the potential environmental drivers of past demographic changes, which highlights the need for integrative approaches. Our conclusions underline the role of habitat availability on species’ demography and biodiversity, and that the consequences of ongoing habitat loss should not be underestimated

Direct estimation of genome mutation rates from pedigrees in free-ranging baleen whales

Current low germline mutation rate (&#x1d707;) estimates in baleen whales have greatly influenced research ranging from assessments of whaling impacts to evolutionary cancer biology. However, the reported rates were subject to methodological errors and uncertainty. We estimated &#x1d707; directly from pedigrees in natural populations of four baleen whale species and the results were similar to primates. The implications of revised &#x1d707; values include pre-exploitation population sizes at 14% of previous genetic diversity-based estimates and the conclusion that &#x1d707; in itself is insufficient to explain low cancer rates in gigantic mammals (i.e., Peto’s Paradox). We demonstrate the feasibility of estimating &#x1d707; from whole genome pedigree data in natural populations, which has wide-ranging implications for the many ecological and evolutionary inferences that rely on &#x1d707;

Prenatal stress and risk of behavioral morbidity from age 2 to 14 years: The influence of the number, type, and timing of stressful life events

The maternal experience of stressful events during pregnancy has been associated with a number of adverse consequences for behavioral development in offspring, but the measurement and interpretation of prenatal stress varies among reported studies. The Raine Study recruited 2900 pregnancies and recorded life stress events experienced by 18 and 34 weeks’ gestation along with numerous sociodemographic data. The mother’s exposure to life stress events was further documented when the children were followed-up in conjunction with behavioral assessments at ages 2, 5, 8, 10, and 14 years using the Child Behavior Checklist. The maternal experience of multiple stressful events during pregnancy was associated with subsequent behavioral problems for offspring. Independent (e.g., death of a relative, job loss) and dependent stress events (e.g., financial problems, marital problems) were both significantly associated with a greater incidence of mental health morbidity between age 2 and 14 years. Exposure to stressful events in the first 18 weeks of pregnancy showed similar associations with subsequent total and externalizing morbidity to events reported at 34 weeks of gestation. These results were independent of postnatal stress exposure. Improved support for women with chronic stress exposure during pregnancy may improve the mental health of their offspring in later life