Co-designing a Canadian adaptation of a lifestyle-oriented intervention aimed to improve daily functioning of individuals living with chronic pain: a multi-method study protocol of REVEAL(OT) Canada.

Background: Living with chronic pain (CP) often implies major lifestyle changes, including modifications of daily routines and work. Surprisingly, few validated and effective interventions specifically target functional outcomes in this population. Redesign your Everyday Activities and Lifestyle with Occupational Therapy [REVEAL(OT)] is a lifestyle-oriented intervention led by occupational therapists that directly targets the daily functional challenges of living with CP. The intervention was initially developed and studied as an add-on to standard treatment delivered by Danish multidisciplinary specialized pain clinics. Adapting, implementing, and evaluating REVEAL(OT) within the Canadian healthcare system will contribute to broadening the scope of treatments offered in specialized pain clinics that do not yet include occupational therapy. Objective: The proposed study aims to define and refine REVEAL(OT)/CA with partners (authors of original intervention, people with lived experience, clinicians, managers). Methods: This participatory action research will use a multi-method design and follow the ORBIT model for developing behavioral treatments for chronic diseases. A process of co-construction with partners and an advisory committee will take place in two Montreal specialized pain clinics. It consists of two related work packages (WPs). In WP1, a first series of focus groups with partners (n = 86) and workshops with the advisory committee will be conducted to co-develop the hypothetical pathway describing intervention components and their potential mechanisms of action on targeted outcomes, as well as the first version of the adapted intervention manual. WP2 will co-refine REVEAL(OT)/CA by exploring its acceptability, feasibility and mechanisms of action through intervention deliveries (at least twice in each of two specialized pain clinics; n ≥ 60 patients) and focus groups and/or individual interviews with participating patients and partners. At the end of this study, the intervention manual will be generated both in French and English. Discussion: This study will set the stage for subsequent implementation and effectiveness assessment projects and be an important step towards the deployment of interventions aiming to improve engagement in meaningful daily activities among adults living with CP. Registration: OSF Registries, osf.io/8gksa. Registered 3 August 2023, https://osf.io/8gksa.

Real-world EGFR testing practices for non-small-cell lung cancer by thoracic pathology laboratories across Europe.

BACKGROUND: Testing for epidermal growth factor receptor (EGFR) mutations is an essential recommendation in guidelines for metastatic non-squamous non-small-cell lung cancer, and is considered mandatory in European countries. However, in practice, challenges are often faced when carrying out routine biomarker testing, including access to testing, inadequate tissue samples and long turnaround times (TATs). MATERIALS AND METHODS: To evaluate the real-world EGFR testing practices of European pathology laboratories, an online survey was set up and validated by the Pulmonary Pathology Working Group of the European Society of Pathology and distributed to 64 expert testing laboratories. The retrospective survey focussed on laboratory organisation and daily EGFR testing practice of pathologists and molecular biologists between 2018 and 2021. RESULTS: TATs varied greatly both between and within countries. These discrepancies may be partly due to reflex testing practices, as 20.8% of laboratories carried out EGFR testing only at the request of the clinician. Many laboratories across Europe still favour single-test sequencing as a primary method of EGFR mutation identification; 32.7% indicated that they only used targeted techniques and 45.1% used single-gene testing followed by next-generation sequencing (NGS), depending on the case. Reported testing rates were consistent over time with no significant decrease in the number of EGFR tests carried out in 2020, despite the increased pressure faced by testing facilities during the COVID-19 pandemic. ISO 15189 accreditation was reported by 42.0% of molecular biology laboratories for single-test sequencing, and by 42.3% for NGS. 92.5% of laboratories indicated they regularly participate in an external quality assessment scheme. CONCLUSIONS: These results highlight the strong heterogeneity of EGFR testing that still occurs within thoracic pathology and molecular biology laboratories across Europe. Even among expert testing facilities there is variability in testing capabilities, TAT, reflex testing practice and laboratory accreditation, stressing the need to harmonise reimbursement technologies and decision-making algorithms in Europe.

Contacts posing risks of disease introduction in swine breeding herds in Quebec, Canada: Is the frequency of contacts associated with biosecurity measures?

The introduction of pathogens into swine breeding herds can occur through a variety of contacts involving people, animals, vehicle or various supplies. Appropriate biosecurity is critical to mitigate these risks. A retrospective study was conducted to describe contacts with swine breeding sites over a one-month period and to evaluate their association with biosecurity measures and site characteristics. As part of a larger project, sites which had a recent porcine reproductive and respiratory syndrome virus introduction were selected. A questionnaire, logbooks and pig traceability system were used for collecting data relative to persons or supplies entering the breeding unit, live pig transportation, service vehicles, other animal species, neighboring pig sites and manure spreading around the site. The 84 sites investigated had a median sow inventory of 675. A median of 4 farm staff and 2 visitors entered the breeding unit at least once over the one-month period. A total of 73 sites (87%) received visitor(s), mostly from maintenance and technical services. All sites received at least 3 supply deliveries (median of 8) including semen (99% of sites), small material and/or drugs (98% of sites), bags (87% of sites), and/or equipment (61% of sites). Live pig movements were observed in all sites, with a median number of 5 truck entries on the site or exits from the site. For feed mill, rendering and propane trucks, at least one entry was noted in ≥ 61% of sites. For all service vehicle categories except feed mill and manure vacuum trucks, a single service provider was involved in each site. Dogs and cats were banned from all sites, but wild birds were observed in 8% of sites. Manure spreading within a 100 m radius of pig units was noted in 10% of the sites. With a few exceptions, biosecurity measures were not associated with the frequency of contacts. A 100-sow increase in sow inventory was associated with an increase of 0.34 in the cumulated number of staff entering the breeding unit, of 0.30 in the number of visitors and of 0.19 in the number of live pig movements. Live pig movements were also positively associated with vertically integrated farrow-to-wean (vs. independent farrow-to-wean) production and time interval of 4 weeks or more between farrowing (vs. less than 4). Considering the variety and frequency of contacts observed, biosecurity should be meticulously applied in all breeding herds to prevent endemic and exotic disease introduction.

Prevalence of Coxiella burnetii seropositivity and shedding in farm, pet and feral cats and associated risk factors in farm cats in Quebec, Canada.

Cats represent a potential source of Coxiella burnetii, the aetiological agent of Q fever in humans. The prevalence and risk factors of C. burnetii infection in farm, pet and feral cats were studied in Quebec, Canada, using a cross-sectional study. Serum samples were tested using a specific enzyme-linked immunosorbent assay (ELISA) for the presence of antibodies against C. burnetii, whereas rectal swabs were assayed using real-time quantitative polymerase chain reaction (qPCR) for the molecular detection of the bacteria. Potential risk factors for farm cats were investigated using clinical examinations, questionnaires and results from a concurrent study on C. burnetii farm status. A total of 184 cats were tested: 59 from ruminant farms, 73 pets and 52 feral cats. Among farm cats, 2/59 (3.4%) were ELISA-positive, 3/59 (5.1%) were ELISA-doubtful and 1/59 (1.7%) was qPCR-positive. All pets and feral cats were negative to C. burnetii ELISA and qPCR. Farm cat positivity was associated with a positive C. burnetii status on the ruminant farm (prevalence ratio = 7.6, P = 0.03). Our results suggest that although pet and feral cats do not seem to pose a great C. burnetii risk to public health, more active care should be taken when in contact with cats from ruminant farms.

Clinical and molecular practice of European thoracic pathology laboratories during the COVID-19 pandemic. The past and the near future.

BACKGROUND: This study evaluated the consequences in Europe of the COVID-19 outbreak on pathology laboratories orientated toward the diagnosis of thoracic diseases. MATERIALS AND METHODS: A survey was sent to 71 pathology laboratories from 21 European countries. The questionnaire requested information concerning the organization of biosafety, the clinical and molecular pathology, the biobanking, the workload, the associated research into COVID-19, and the organization of education and training during the COVID-19 crisis, from 15 March to 31 May 2020, compared with the same period in 2019. RESULTS: Questionnaires were returned from 53/71 (75%) laboratories from 18 European countries. The biosafety procedures were heterogeneous. The workload in clinical and molecular pathology decreased dramatically by 31% (range, 3%-55%) and 26% (range, 7%-62%), respectively. According to the professional category, between 28% and 41% of the staff members were not present in the laboratories but did teleworking. A total of 70% of the laboratories developed virtual meetings for the training of residents and junior pathologists. During the period of study, none of the staff members with confirmed COVID-19 became infected as a result of handling samples. CONCLUSIONS: The COVID-19 pandemic has had a strong impact on most of the European pathology laboratories included in this study. Urgent implementation of several changes to the organization of most of these laboratories, notably to better harmonize biosafety procedures, was noted at the onset of the pandemic and maintained in the event of a new wave of infection occurring in Europe.

A Combined Study of Headspace Volatiles using Human Sensory, Mass Spectrometry and Chemometrics.

Smokeless tobacco products (STPs) are widely used in certain parts of the world, yet there is limited understanding of how they are consumed, particularly the impact of chemosensory characteristics on their use. In order to develop an understanding of the drivers of STP use and product acceptability we conducted both human sensory panel testing and chemical analyses on a range of STPs. Free-sorting paired odour testing using sensory panellists identified similarities and clear differences between eleven different STPs. Headspace volatiles, analysed by headspace solid-phase microextraction gas chromatography mass spectrometry (HS-SPME-GC-MS), identified 20 to 70 components depending upon the STP. Key differences in headspace volatiles were found between STPs. For example, the headspace of Skoal Bandits Wintergreen was dominated by methyl salicylate, while Marlboro Spice consists of a more complex profile including pinene, nicotine, eugenol and cymene. Chemometric Target Factor Analysis (TFA) and Hierarchical Cluster Analysis (HCA) of chemistry and sensory data was used to deduce chemical drivers of sensory perceptions. The chemometric strategy used showed that headspace analysis is a complementary screening tool to sensory analysis in classification studies. This study is generic with applications across various product sectors that require routine human sensory panel evaluation.

Micromachined phase-shifted array-type Mirau interferometer for swept-source OCT imaging: design, microfabrication and experimental validation.

OCT instruments permit fast and non-invasive 3D optical biopsies of biological tissues. However, they are bulky and expensive, making them only affordable at the hospital and thus, not sufficiently used as an early diagnostic tool. Significant reduction of system cost and size is achieved by implementation of MOEMS technologies. We propose an active array of 4x4 Mirau microinterferometers where the reference micro-mirrors are carried by a vertical comb-drive microactuator, enabling the implementation of the phase-shifting technique that improves the sensitivity and eliminates unwanted interferometric terms. We focus on the design of the imaging system, the microfabrication and the assembly of the Mirau microinterferometer, and the swept-source OCT imaging.

Feasibility of a Hybrid Web-Based and In-Person Self-management Intervention Aimed at Preventing Acute to Chronic Pain Transition After Major Lower Extremity Trauma (iPACT-E-Trauma): A Pilot Randomized Controlled Trial.

Objective 1) To assess the feasibility of research methods to test a self-management intervention aimed at preventing acute to chronic pain transition in patients with major lower extremity trauma (iPACT-E-Trauma) and 2) to evaluate its potential effects at three and six months postinjury. Design A pilot randomized controlled trial (RCT) with two parallel groups. Setting A supraregional level 1 trauma center. Methods Fifty-six adult patients were randomized. Participants received the intervention or an educational pamphlet. Several parameters were evaluated to determine the feasibility of the research methods. The potential efficacy of iPACT-E-Trauma was evaluated with measures of pain intensity and pain interference with activities. Results More than 80% of eligible patients agreed to participate, and an attrition rate of ≤18% was found. Less than 40% of screened patients were eligible, and obtaining baseline data took 48 hours postadmission on average. Mean scores of mild pain intensity and pain interference with daily activities (<4/10) on average were obtained in both groups at three and six months postinjury. Between 20% and 30% of participants reported moderate to high mean scores (≥4/10) on these outcomes at the two follow-up time measures. The experimental group perceived greater considerable improvement in pain (60% in the experimental group vs 46% in the control group) at three months postinjury. Low mean scores of pain catastrophizing (Pain Catastrophizing Scale score < 30) and anxiety and depression (Hospital Anxiety and Depression Scale scores ≤ 10) were obtained through the end of the study. Conclusions Some challenges that need to be addressed in a future RCT include the small proportion of screened patients who were eligible and the selection of appropriate tools to measure the development of chronic pain. Studies will need to be conducted with patients presenting more serious injuries and psychological vulnerability or using a stepped screening approach.

Melanin-based coloration and host-parasite interactions under global change.

The role of parasites in shaping melanin-based colour polymorphism, and the consequences of colour polymorphism for disease resistance, remain debated. Here we review recent evidence of the links between melanin-based coloration and the behavioural and immunological defences of vertebrates against their parasites. First we propose that (1) differences between colour morphs can result in variable exposure to parasites, either directly (certain colours might be more or less attractive to parasites) or indirectly (variations in behaviour and encounter probability). Once infected, we propose that (2) immune variation between differently coloured individuals might result in different abilities to cope with parasite infection. We then discuss (3) how these different abilities could translate into variable sexual and natural selection in environments varying in parasite pressure. Finally, we address (4) the potential role of parasites in the maintenance of melanin-based colour polymorphism, especially in the context of global change and multiple stressors in human-altered environments. Because global change will probably affect both coloration and the spread of parasitic diseases in the decades to come, future studies should take into account melanin-based coloration to better predict the evolutionary responses of animals to changing disease risk in human-altered environments.

Challenges in the diagnosis of acute cyanide poisoning.

OBJECTIVE: The aim of this systematic review was to identify isolated acute cyanide poison cases and to identify reported signs, symptoms, and laboratory findings. METHODS: We searched MEDLINE, Cochrane Reviews, and Web of Science case reports and series using a number of MeSH descriptors pertaining to cyanide, toxicity, and poisonings. We excluded studies on plants, laboratory analyses, smoke inhalation poisonings, animals as well as non-English language articles and those in which data were not available. Data extracted included demographics, exposure characteristics, acute signs/symptoms, and medical management and outcome. RESULTS: From the initial 2976 articles retrieved, 65 articles (52 case reports, 13 case series) met inclusion criteria and described 102 patients. Most patients were unresponsive (78%), hypotensive (54%), or had respiratory failure (73%); other signs and symptoms included cardiac arrest (20%), seizures (20%), cyanosis (15%), cherry red skin (11%), and had an odor present (15%). Medical management included cyanide antidote kit (20%), sodium thiosulfate (40%), and hydroxocobalamin (29%). The majority of cases (66%) required intubation with mechanical ventilation and a substantial number (39%) developed refractory hypotension requiring vasopressor support. CONCLUSIONS: Contrary to general reviews published on cyanide toxicity, reports of cherry red skin and bitter almond odor were rare among published cyanide cases. Consistent with other studies, metabolic acidosis with significant lactic acidosis were the laboratory values consistently associated with cyanide toxicity. Healthcare providers may overlook cyanide toxicity in the differential diagnosis, if certain expected characteristics, such as the odor of almonds or a cherry red color of the skin are absent on physical examination.

The impact of repeated mismatches in kidney transplantations performed after nonrenal solid organ transplantation.

The aim of this study was to determine whether kidney transplantations performed after previous nonrenal solid organ transplants are associated with worse graft survival when there are repeated HLA mismatches (RMM) with the previous donor(s). We performed a retrospective cohort study using data from the Scientific Registry of Transplant Recipients. Our cohort comprised 6624 kidney transplantations performed between January 1, 1990 and January 1, 2015. All patients had previously received 1 or more nonrenal solid organ transplants. RMM were observed in 35.3% of kidney transplantations and 3012 grafts were lost over a median follow-up of 5.4 years. In multivariate Cox regression analyses, we found no association between overall graft survival and either RMM in class 1 (hazard ratio [HR]: 0.97, 95% confidence interval [CI] 0.89-1.07) or class 2 (HR: 0.95, 95% CI 0.85-1.06). Results were similar for the associations between RMM, death-censored graft survival, and patient survival. Our results suggest that the presence of RMM with previous donor(s) does not have an important impact on allograft survival in kidney transplant recipients who have previously received a nonrenal solid organ transplant.

Influence of population size, density, and proximity to talent clubs on the likelihood of becoming elite youth athlete.

Previous studies have found significant differences in the likelihood of becoming an elite athlete depending on community population sizes and densities, an effect known as the place of early development, or birthplace effect. However, the results have not been consistent between sports or European countries. As both professional and voluntary clubs are vital to the talent development systems in Europe, the proximity of an athlete's place of early development to the location of talent clubs may be an important predictor of the likelihood of becoming an elite athlete. Therefore, the primary purpose of this study was to investigate the place of early development effect and the effect of proximity to talent clubs. The samples included elite youth league athletes (579 football and 311 handball) and national youth athletes (85 football and 80 handball) and a comparison group of 147 221 football and 26 290 handball youth athletes. Odds ratios showed variations in the optimal community size and density across sports. Geospatial analyses of proximity to talent clubs highlighted a trend indicating that most national and elite youth league athletes in both sports had their place of early development in their sport near a talent club. The results suggest that proximity is an important predictor in the development of expertise across sports, but future studies need to clarify if proximity is important in other countries and sports.

Leveraging a Clinical Phase Ib Proof-of-Concept Study for the GPR40 Agonist MK-8666 in Patients With Type 2 Diabetes for Model-Informed Phase II Dose Selection.

GPR40 mediates free fatty acid-induced insulin secretion in beta cells. We investigated the safety, pharmacokinetics, and glucose response of MK-8666, a partial GPR40 agonist, after once-daily multiple dosing in type 2 diabetes patients. This double-blind, multisite, parallel-group study randomized 63 patients (placebo, n = 18; 50 mg, n = 9; 150 mg, n = 18; 500 mg, n = 18) for 14-day treatment. The results showed no serious adverse effects or treatment-related hypoglycemia. One patient (150-mg group) showed mild-to-moderate transaminitis at the end of dosing. Median MK-8666 Tmax was 2.0-2.5 h and mean apparent terminal half-life was 22-32 h. On Day 15, MK-8666 reduced fasting plasma glucose by 54.1 mg/dL (500 mg), 36.0 mg/dL (150 mg), and 30.8 mg/dL (50 mg) more than placebo, consistent with translational pharmacokinetic/pharmacodynamic model predictions. Maximal efficacy for longer-term assessment is projected at 500 mg based on exposure-response analysis. In conclusion, MK-8666 was generally well tolerated with robust glucose-lowering efficacy.

Identification of the ectoenzyme CD38 as a marker of committed preadipocytes.

BACKGROUND/OBJECTIVES: Characterisation of the adipocyte cellular lineage is required for a better understanding of white adipose tissue homoeostasis and expansion. Although several studies have focused on the phenotype of the most immature adipocyte progenitors, very few tools exist to identify committed cells. In haematopoiesis, the CD38 ectoenzyme is largely used to delineate various stages of stem cell lineage commitment. We hypothesise that this marker could be used to identify committed preadipocytes. METHODS: Complementary strategies including flow cytometry, cell-sorting approaches, immunohistochemistry and primary cultures of murine adipose progenitors isolated from different fat pads of control or high-fat diet exposed C57BL/6 J mice were used to determine the molecular expression profile, proliferative and differentiation potentials of adipose progenitors expressing the CD38 molecule. RESULTS: We demonstrate here that a subpopulation of CD45- CD31- CD34+ adipose progenitors express the cell surface protein CD38. Using a cell-sorting approach, we found that native CD45- CD31- CD34+ CD38+ (CD38+) adipose cells expressed lower CD34 mRNA and protein levels and higher levels of adipogenic genes such as Pparg, aP2, Lpl and Cd36 than did the CD45- CD31- CD34+ CD38- (CD38-) population. When cultivated, CD38+ cells displayed reduced proliferative potential, assessed by BrdU incorporation and colony-forming unit assays, and greater adipogenic potential. In vitro, both CD38 mRNA and protein levels were increased during adipogenesis and CD38- cells converted into CD38+ cells when committed to the adipogenic differentiation programme. We also found that obesity development was associated with an increase in the number of CD38+ adipose progenitors, this effect being more pronounced in intra-abdominal than in subcutaneous fat, suggesting a higher rate of adipocyte commitment in visceral depots. CONCLUSIONS: Together, these data demonstrate that CD38 represents a new marker that identifies committed preadipocytes as CD45- CD31- CD34low CD38+ cells.

Chronic Administration of Anacetrapib Is Associated With Accumulation in Adipose and Slow Elimination.

Anacetrapib is a novel cholesteryl-ester transfer protein (CETP) inhibitor in late-stage clinical development, shown in preceding clinical trials to have residual pharmacological activity after prolonged washout after chronic dosing. Preclinical findings suggest that white adipose tissue is a potential depot and that accumulation into adipose tissue governs the long-term kinetics of anacetrapib in mice. A phase I study performed to test this hypothesis in humans revealed that plasma exposure was correlated with fat content in food administered with the drug. Plasma concentrations of anacetrapib seemed to reach plateau faster than adipose concentrations. Anacetrapib continued to accumulate in adipose during the treatment period despite apparent plateau in plasma with only minimal decline in adipose levels up to 1 year postdose. Because of its high lipophilicity, anacetrapib partitions into adipose tissue, this likely forms a drug reservoir that, in turn, contributes to the long residence time of the drug in plasma.

Comparison of semi-automated and manual methods to measure the volume of prostate cancer on magnetic resonance imaging.

PURPOSE: The purpose of this study was to determine the accuracy of manual semi-automated and volumetric measurements to assess prostate cancer volume on multiparametric magnetic resonance imaging (MP-MRI) using whole-mount histopathology for validation. MATERIALS AND METHODS: We evaluated 30 consecutive men (median age, 65.7 years; interquartile range [IQR], 61.5-70.9 years) with a median prostatic specific antigen of 8.5ng/dL (IQR, 5.5-10.5ng/dL), who underwent MP-MRI before radical prostatectomy. Index tumor volume was determined prospectively and independently on the basis of MRI and whole-mount section volumetric assessment using the maximum histologic diameter (MHD) and the histologic volume (HV). The MRI index tumor volume was determined by two independent radiologists using a single measurement of the maximum tumor dimension (MTD), a simplified MR ellipsoid volume (MREV) calculation and a MR region of interest volume (MROV) segmentation displayed by a commercially available OsiriX®. MTD was compared to MHD, whereas MREV and MROV were compared to HV. RESULTS: Thirty index lesions (median HV, 1.514 cm3; IQR, 0.05-3.780 cm3) were analyzed. The MREV, MROV and HD were significantly correlated with each other (r>0.5). Inter-observer agreement for measurements was good for each method (r>0.780). The MTD was the best predictor of maximum histologic diameter (r=0.980 and 0.791) and had an excellent inter-variability correlation (P<0.0001). CONCLUSION: Prostate cancer histologic volume can be assessed using MREV or MROV with a good accuracy and low inter-observer variability. MTD has the lowest inter-observer variability and provides best degrees of correlation with MHD. MTD should be used on MRI for selecting and following patients for active surveillance and staging before focal treatment of prostate cancer.

The Cdc42/Rac1 regulator CdGAP is a novel E-cadherin transcriptional co-repressor with Zeb2 in breast cancer.

The loss of E-cadherin causes dysfunction of the cell-cell junction machinery, which is an initial step in epithelial-to-mesenchymal transition (EMT), facilitating cancer cell invasion and the formation of metastases. A set of transcriptional repressors of E-cadherin (CDH1) gene expression, including Snail1, Snail2 and Zeb2 mediate E-cadherin downregulation in breast cancer. However, the molecular mechanisms underlying the control of E-cadherin expression in breast cancer progression remain largely unknown. Here, by using global gene expression approaches, we uncover a novel function for Cdc42 GTPase-activating protein (CdGAP) in the regulation of expression of genes involved in EMT. We found that CdGAP used its proline-rich domain to form a functional complex with Zeb2 to mediate the repression of E-cadherin expression in ErbB2-transformed breast cancer cells. Conversely, knockdown of CdGAP expression led to a decrease of the transcriptional repressors Snail1 and Zeb2, and this correlated with an increase in E-cadherin levels, restoration of cell-cell junctions, and epithelial-like morphological changes. In vivo, loss of CdGAP in ErbB2-transformed breast cancer cells impaired tumor growth and suppressed metastasis to lungs. Finally, CdGAP was highly expressed in basal-type breast cancer cells, and its strong expression correlated with poor prognosis in breast cancer patients. Together, these data support a previously unknown nuclear function for CdGAP where it cooperates in a GAP-independent manner with transcriptional repressors to function as a critical modulator of breast cancer through repression of E-cadherin transcription. Targeting Zeb2-CdGAP interactions may represent novel therapeutic opportunities for breast cancer treatment.

Preparation and Analysis of Native Chromatin-Modifying Complexes.

Nucleosomes, the basic units of chromatin, are decorated with a myriad of posttranslational modifications (PTMs) by the action of chromatin modifiers. These enzymes function almost exclusively as part of stable protein complexes that assist their recruitment to specific genomic loci, specify their substrate, and provide allosteric control. By altering the interactions within nucleosomes or with neighboring nucleosomes and serving as a platform to engage effector proteins, PTMs deposited by histone-modifying complexes influence virtually every nuclear process and are at the heart of the epigenetic mechanisms. Hence, it is critical to identify their components, define their structures, and characterize their biochemical activities. Here we describe protocols for tandem affinity purification (TAP) of native histone acetyltransferase (HAT) and methyltransferase (HMT) complexes from human cells engineered to express bait proteins from a genomic safe harbor or their endogenous chromosomal genes, using zinc-finger nucleases (ZFNs), TAL effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 systems. The approaches presented aim to preserve natural transcriptional and posttranscriptional regulation and minimize biochemical artifacts due to ectopic expression. Near homogenous preparations of native complexes are obtained in sufficient amounts to perform biochemical assays and characterize their components.

Adaptive divergence in embryonic thermal plasticity among Atlantic salmon populations.

In the context of global changes, the long-term viability of populations of endangered ectotherms may depend on their adaptive potential and ability to cope with temperature variations. We measured responses of Atlantic salmon embryos from four populations to temperature variations and used a QST -FST approach to study the adaptive divergence among these populations. Embryos were reared under two experimental conditions: a low temperature regime at 4 °C until eyed-stage and 10 °C until the end of embryonic development and a high temperature regime with a constant temperature of 10 °C throughout embryonic development. Significant variations among populations and population × temperature interactions were observed for embryo survival, incubation time and length. QST was higher than FST in all but one comparison suggesting an important effect of divergent selection. QST was also higher under the high-temperature treatment than at low temperature for length and survival due to a higher variance among populations under the stressful warmer treatment. Interestingly, heritability was lower for survival under high temperature in relation to a lower additive genetic variance under that treatment. Overall, these results reveal an adaptive divergence in thermal plasticity in embryonic life stages of Atlantic salmon suggesting that salmon populations may differentially respond to temperature variations induced by climate change. These results also suggest that changes in temperature may alter not only the adaptive potential of natural populations but also the selection regimes among them.

Low reproductive isolation and highly variable levels of gene flow reveal limited progress towards speciation between European river and brook lampreys.

Ecologically based divergent selection is a factor that could drive reproductive isolation even in the presence of gene flow. Population pairs arrayed along a continuum of divergence provide a good opportunity to address this issue. Here, we used a combination of mating trials, experimental crosses and population genetic analyses to investigate the evolution of reproductive isolation between two closely related species of lampreys with distinct life histories. We used microsatellite markers to genotype over 1000 individuals of the migratory parasitic river lamprey (Lampetra fluviatilis) and freshwater-resident nonparasitic brook lamprey (Lampetra planeri) distributed in 10 sympatric and parapatric population pairs in France. Mating trials, parentage analyses and artificial fertilizations demonstrated a low level of reproductive isolation between species even though size-assortative mating may contribute to isolation. Most parapatric population pairs were strongly differentiated due to the joint effects of geographic distance and barriers to migration. In contrast, we found variable levels of gene flow between sympatric populations ranging from panmixia to moderate differentiation, which indicates a gradient of divergence with some population pairs that may correspond to alternative morphs or ecotypes of a single species and others that remain partially isolated. Ecologically based divergent selection may explain these variable levels of divergence among sympatric population pairs, but incomplete genome swamping following secondary contact could have also played a role. Overall, this study illustrates how highly differentiated phenotypes can be maintained despite high levels of gene flow that limit the progress towards speciation.