The scaling of genetic diversity in a changing and fragmented world

Most species do not live in a constant environment over space or time. Their environment is often heterogeneous with a huge variability in resource availability and exposure to pathogens or predators, which may affect the local densities of the species. Moreover, the habitat might be fragmented, preventing free and isotropic migrations between local sub-populations (demes) of a species, making some demes more isolated than others. For example, during the last ice age populations of many species migrated towards refuge areas from which re-colonization originated when conditions improved. However, populations that could not move fast enough or could not adapt to the new environmental conditions faced extinctions. Populations living in these types of dynamic environments are often referred to as metapopulations and modeled as an array of subdivisions (or demes) that exchange migrants with their neighbors. Several studies have focused on the description of their demography, probability of extinction and expected patterns of diversity at different scales. Importantly, all these evolutionary processes may affect genetic diversity, which can affect the chance of populations to persist. In this chapter we provide an overview on the consequences of fragmentation, long-distance dispersal, range contractions and range shifts on genetic diversity. In addition, we describe new methods to detect and quantify underlying evolutionary processes from sampled genetic data.Laboratoire d’Excellence (LABEX) entitled TULIP: (ANR-10-LABX-41)

Impact of gut hormone FGF-19 on type-2 diabetes and mitochondrial recovery in a prospective study of obese diabetic women undergoing bariatric surgery

Background: The ileal-derived hormone, fibroblast growth factor 19 (FGF-19), may promote weight loss and facilitate type-2 diabetes mellitus remission in bariatric surgical patients. We investigated the effect of different bariatric procedures on circulating FGF-19 levels and the resulting impact on mitochondrial health in white adipose tissue (AT). Methods: Obese and type-2 diabetic women (n = 39, BMI > 35 kg/m2) undergoing either biliopancreatic diversion (BPD), laparoscopic greater curvature plication (LGCP), or laparoscopic adjustable gastric banding (LAGB) participated in this ethics approved study. Anthropometry, biochemical, clinical data, serum, and AT biopsies were collected before and 6 months after surgery. Mitochondrial gene expression in adipose biopsies and serum FGF-19 levels were then assessed. Results: All surgeries led to metabolic improvements with BPD producing the greatest benefits on weight loss (↓30%), HbA1c (↓28%), and cholesterol (↓25%) reduction, whilst LGCP resulted in similar HbA1c improvements (adjusted for BMI). Circulating FGF-19 increased in both BPD and LGCP (χ2(2) = 8.088; P = 0.018), whilst, in LAGB, FGF-19 serum levels decreased (P = 0.028). Interestingly, circulating FGF-19 was inversely correlated with mitochondrial number in AT across all surgeries (n = 39). In contrast to LGCP and LAGB, mitochondrial number in BPD patients corresponded directly with changes in 12 of 14 mitochondrial genes assayed (P < 0.01). Conclusions: Elevated serum FGF-19 levels post-surgery were associated with improved mitochondrial health in AT and overall diabetic remission. Changes in circulating FGF-19 levels were surgery-specific, with BPD producing the best metabolic outcomes among the study procedures (BPD > LGCP > LAGB), and highlighting mitochondria in AT as a potential target of FGF-19 during diabetes remission

Characteristics and outcome in patients with central nervous system involvement treated in European pediatric acute myeloid leukemia study groups

Background: There is no consensus on the treatment for pediatric patients with acute myeloid leukemia and initial central nervous system (CNS) involvement. Methods: To evaluate different CNS-directed treatment options (intrathecal [IT] therapy, CNS irradiation, hematopoietic stem cell transplantation [HSCT]), 261 patients (excluding acute promyelocytic leukemia) with initial CNS involvement treated in trials with similar intensive chemotherapy by four cooperative European study groups (1998–2013) were studied and compared with CNS-negative patients from the Berlin–Frankfurt–Münster group. Results: Patient characteristics in the different study groups were comparable. Young age, high white blood cell count, extramedullary involvement other than the CNS, monoblastic morphology, and inv(16) were associated with CNS involvement (each P &lt; 0.0001). There were no major differences in outcome between the study groups. The cumulative incidence of relapse (CIR) regarding the CNS was higher in initially CNS-positive versus initially CNS-negative patients (all: 8 ± 2% vs. 3 ± 1%, P(Gray) = 0.001; isolated: 4 ± 1% vs. 1 ± 0%, P(Gray) = 0.03). However, global outcome of the CNS-positive cohort (overall survival, 64 ± 3%; event-free survival 48 ± 3%; and CIR 33% ± 3%) did not differ significantly from CNS-negative patients. Risk groups defined by cytogenetics were of likewise prognostic significance in CNS-positive and -negative patients. CNS treatment with cranial irradiation was not superior compared to IT therapy and systemic chemotherapy (± HSCT). Conclusion: Although CNS relapses occurred more frequently in initially CNS-positive patients, their global outcome was similar as in CNS-negative patients. Intensified IT therapy was heterogeneous; however, at least eight applications, preferably with triple IT chemotherapy, seem to be appropriate to accompany dose-intensive systemic chemotherapy

Severe steroid-related neuropsychiatric symptoms during paediatric acute lymphoblastic leukaemia therapy—An observational Ponte di Legno Toxicity Working Group Study

\ua9 2024 The Author(s). British Journal of Haematology published by British Society for Haematology and John Wiley &amp; Sons Ltd.Steroids are a mainstay in the treatment of acute lymphoblastic leukaemia (ALL) in children and adolescents; however, their use can cause clinically significant steroid-related neuropsychiatric symptoms (SRNS). As current knowledge on SRNS during ALL treatment is limited, we mapped the phenotypes, occurrence and treatment strategies using a database created by the international Ponte di Legno Neurotoxicity Working Group including data on toxicity in the central nervous system (CNS) in patients treated with frontline ALL protocols between 2000 and 2017. Ninety-four of 1813 patients in the CNS toxicity database (5.2%) experienced clinically significant SRNS with two peaks: one during induction and one during intensification phase. Dexamethasone was implicated in 86% of SRNS episodes. The most common symptoms were psychosis (52%), agitation (44%) and aggression (31%). Pharmacological treatment, mainly antipsychotics and benzodiazepines, was given to 87% of patients while 38% were hospitalised due to their symptoms. Recurrence of symptoms was reported in 29% of patients and two previously healthy patients required ongoing pharmacological treatment at the last follow up. Awareness of SRNS during ALL treatment and recommendation on treatment strategies merit further studies and consensus

Rapid identification of in vitro cell toxicity using an electrochemical membrane screening platform

This study compares the performance and output of an electrochemical phospholipid membrane platform against respective in vitro cell-based toxicity testing methods using three toxicants of different biological action (chlorpromazine (CPZ), colchicine (COL) and methyl methanesulphonate (MMS)). Human cell lines from seven different tissues (lung, liver, kidney, placenta, intestine, immune system) were used to validate this physicochemical testing system. For the cell-based systems, the effective concentration at 50 % cell death (EC₅₀) values are calculated. For the membrane sensor, a limit of detection (LoD) value was extracted as a quantitative parameter describing the minimum concentration of toxicant which significantly affects the structure of the phospholipid sensor membrane layer. LoD values were found to align well with the EC₅₀ values when acute cell viability was used as an end-point and showed a similar toxicity ranking of the tested toxicants. Using the colony forming efficiency (CFE) or DNA damage as end-point, a different order of toxicity ranking was observed. The results of this study showed that the electrochemical membrane sensor generates a parameter relating to biomembrane damage, which is the predominant factor in decreasing cell viability when in vitro models are acutely exposed to toxicants. These results lead the way to using electrochemical membrane-based sensors for rapid relevant preliminary toxicity screens

Constitutively active Lyn kinase causes a cutaneous small vessel vasculitis and liver fibrosis syndrome

Neutrophilic inflammation is a hallmark of many monogenic autoinflammatory diseases; pathomechanisms that regulate extravasation of damaging immune cells into surrounding tissues are poorly understood. Here we identified three unrelated boys with perinatal-onset of neutrophilic cutaneous small vessel vasculitis and systemic inflammation. Two patients developed liver fibrosis in their first year of life. Next-generation sequencing identified two de novo truncating variants in the Src-family tyrosine kinase, LYN, p.Y508*, p.Q507* and a de novo missense variant, p.Y508F, that result in constitutive activation of Lyn kinase. Functional studies revealed increased expression of ICAM-1 on induced patient-derived endothelial cells (iECs) and of β2-integrins on patient neutrophils that increase neutrophil adhesion and vascular transendothelial migration (TEM). Treatment with TNF inhibition improved systemic inflammation; and liver fibrosis resolved on treatment with the Src kinase inhibitor dasatinib. Our findings reveal a critical role for Lyn kinase in modulating inflammatory signals, regulating microvascular permeability and neutrophil recruitment, and in promoting hepatic fibrosis

Relationships of dietary patterns with body composition in older adults differ by gender and PPAR-γ Pro12Ala genotype

Dietary patterns may better capture the multifaceted effects of diet on body composition than individual nutrients or foods. The objective of this study was to investigate the dietary patterns of a cohort of older adults, and examine relationships of dietary patterns with body composition. The influence of a polymorphism in the peroxisome proliferator-activated receptor-γ (PPAR-γ) gene was considered. The Health, Aging and Body Composition (Health ABC) Study is a prospective cohort study of 3,075 older adults. Participants’ body composition and genetic variation were measured in detail. Food intake was assessed with a semi-quantitative food frequency questionnaire (Block Dietary Data Systems, Berkeley, CA), and dietary patterns of 1,809 participants with complete data were derived by cluster analysis. Six clusters were identified, including a ‘Healthy foods’ cluster characterized by higher intake of low-fat dairy products, fruit, whole grains, poultry, fish and vegetables. An interaction was found between dietary patterns and PPAR-γ Pro12Ala genotype in relation to body composition. While Pro/Pro homozygous men and women in the ‘Healthy foods’ cluster did not differ significantly in body composition from those in other clusters, men with the Ala allele in the ‘Healthy foods’ cluster had significantly lower levels of adiposity than those in other clusters. Women with the Ala allele in the ‘Healthy foods’ cluster differed only in right thigh intermuscular fat from those in other clusters. Relationships between diet and body composition in older adults may differ by gender and by genetic factors such as PPAR-γ Pro12Ala genotype

Influência do resfriamento dinâmico na medição da tensão limite de escoamento

Non-Newtonian fluids may present several complex characteristics, such as viscoelasticity, plasticity and thixotropy. Understanding the behaviour of these materials is essential to facilitate its applicability, since many of them are present in daily life, such as gels, chocolate, and mayonnaise. The material studied on the present work was an waxy crude oil. The oil, present in reservoirs located in deep water, when subjected to low temperatures during production shutdowns, precipitates its paraffin, creating a structure which may be very resistant to flow. Thus, the formed material may represent a great difficulty to production restart. The design of pumps and compressors used in these systems depend on a rheological property called yield stress and therefore, it is essential to obtain reliable values of this rheological parameter. However, the complex behaviour, and the dependence of the crude oil characteristics on the shearing and temperature history make this a challenging task. Besides these, other factors may influence the measurement of yield stress, as the effect of wall slip and if the cooling is static or dynamic. This work shows the variation of yield stress for tests with dynamic cooling. The imposition of a stress during cooling caused the reduction in yield stress 0. Increasing the imposed stress, 0 decreased until it reached a minimum. Next, it was noticed an increase in yield stress with increasing imposed stress. The experiments carried out in this work were made in a commercial stress control rheometer. The effect of wall slip was tested by comparing smooth and rough geometries and it was verified signs of its presence, with the reduction of yield stress for smooth geometries. The equation of Weissenberg-Rabinowitsch, used for correction of the inhomogeneity of the shear stress along the radius geometry, seemed to be not necessary for the demonstrated results.Fluidos não newtonianos podem apresentar diversas características complexas, como a viscoelasticidade, plasticidade e tixotropia. Entender o comportamento de materiais tão complexos é fundamental para facilitar sua aplicabilidade, já que muitos estão presentes no cotidiano das pessoas, como géis, chocolate e maionese. O material estudado no presente trabalho foi um petróleo parafínico. O petróleo, presente em bacias localizadas em águas profundas, quando submetido a baixas temperaturas durante paradas de produção, precipita suas parafinas dando origem a uma estrutura que pode ser muito resistente ao escoamento. Dessa forma, o material formado pode representar uma grande dificuldade para o reinício da produção. O dimensionamento das bombas e compressores utilizados para retomada da produção depende de uma propriedade reológica denominada tensão limite de escoamento e, por isso, é fundamental obter valores confiáveis desse parâmetro reológico. No entanto, o comportamento complexo, e a dependência das características do petróleo com o histórico de cisalhamento e temperatura tornam a tarefa desafiadora. Outros fatores podem influenciar na medição da tensão limite de escoamento, como o efeito do escorregamento na parede do sensor da geometria e se o resfriamento é estático ou dinâmico. Este trabalho mostra a variação da tensão limite de escoamento para ensaios com resfriamento dinâmico. A imposição de tensão durante o resfriamento causou a redução da tensão limite de escoamento 0. Elevando-se a tensão imposta, 0 reduziu até atingir um valor mínimo. Em seguida, percebeu-se um aumento da tensão limite de escoamento com o aumento da tensão imposta. Os experimentos realizados neste trabalho foram feitos em um reômetro comercial do tipo tensão controlada (“stress controlled”). O efeito de escorregamento da amostra foi testado comparando geometrias com superfícies lisas e ranhuradas e foi possível verificar sinais de sua presença, com a redução da tensão limite de escoamento para geometrias lisas. A equação de Weissenberg-Rabinowitsch, utilizada para correção da não homogeneidade da tensão de cisalhamento ao longo do raio da geometria, mostrou-se não necessária para os resultados demonstrados