ADAPTIVE RESPONSES TO AQUATIC POLLUTION: DISPERSAL, PHYSIOLOGICAL ACCLIMATION, GENETIC ADAPTATION IN THE BROWN BULLHEAD (AMEIURUS NEBULOSUS)

Organisms are likely to display adaptive responses to their local environment, it may be local adaptation or physiological acclimation, and both improve performance (increase fitness) in stressful habitats. In this dissertation, I explore adaptive responses to pollution stress in the brown bullhead ( Ameiurus nebulosus ) from the Detroit River, as a model for integration of evolutionary and ecotoxicologial analyses. I develop a systematic hierarchical scheme to investigate the role of adaptive processes in response to stressful environments. My literature-based review suggests initial investigation of dispersal as confounding adaptive response to degraded local environment. If there is low dispersal I suggest variation in gene transcription as a biomarker for accurate and repeatable measures of the response to pollution stress, as gene transcription is a very early response to contaminant stress. Following my proposed approach, I examined dispersal and molecular adaptive responses in brown bullhead and developed tools for the analyses: population genetic markers, a custom microarray and transcriptome libraries. The population genetic study demonstrates high population structure F ST = 0.095 indicating limited long-term gene flow but contemporary dispersal associated with high contaminant levels (37% dispersals within each region). My initial transcriptome characterisation was done with next generation sequencing (NGS) on challenged and control individuals from two sites (degraded and clean). The NGS transcriptome characterisation was resulted in 3.4 million assembled reads and identified 5515 transcribed genes across clean and polluted background populations. Many gene transcription patterns were as expected as part of an adaptive response; however, some expected transcription induction was not observed. Thus I used a 128 gene custom ecotoxicology response microarray to quantify dose and temporal response of selected genes in brown bullhead exposed to B[a]P. This identified 5 up-regulated and 5 downregulated gene responses: up-regulation included a variety of response profiles, while down-regulation was simple gene repression. All forms of adaptive responses in contaminant indicator species have the potential to confound our interpretation of toxicity in natural and lab environments. This may have important management and legislative implications. Of equal interest, my thesis research highlights some behavioural and molecular mechanisms for adaptive responses in Detroit River bullhead

Genetisk analys av avelsfisk, Lax och havsöring 2017-2018 från svenska kompensationsodlingar

I flera av Sveriges stora älvar sker odling och utsättning av lax och havsöring som kompensation för minskad naturlig reproduktion orsakad av vattenkraften. All kompensationsodlad utsatt fisk ska vara fenklippt, och en mindre andel ska enligt vattendom även vara märkt på annat sätt. Länge har så kallade Carlin-märken använts för storskalig s.k. ”driftsmärkning” av laxungar (smolt). Av olika skäl har dock återrapporteringen av märkt fisk sjunkit, och Carlin-märkena har även visat sig kunna påverka fisken negativt. Som alternativ till yttre märken kan man dra nytta av att all fisk är ”genetiskt märkta” från födseln. Genom DNA-prov från avelsfisk kan man göra diverse uppföljningar av odlingsverksamheten som att identifiera felvandrare och familjegrupper, samt avgöra om avelspar är helsyskon. Med tiden går det även att identifiera den återvändande lekfiskens föräldrar från tidigare års avel. I denna rapport presenteras resultat efter DNA-analys av lax och havsöring från sex respektive fem kompensationsodlingar i Sverige. Målsättningen har varit att lägga grunden för ett ”genetiskt märkningsprogram” för dessa arter. Samtliga odlade stammar uppvisade jämförelsevis hög genetisk variation, vilket kan förklaras av att nya avelsfiskar fångas in till aveln varje år och att ”felvandring” mellan älvar förekommer (dvs. fisken simmar upp i annan älv än där den är född). Inom aveln 2017 och 2018 var det mest älvseget material som användes, men det förekom även en andel felvandrare. Den genetiska likheten var högre mellan fisk från olika år inom samma älv jämfört med andra älvar. Generellt var de odlade stammarna från närliggande älvar mer genetiskt lika, vilket är samma mönster som förekommer bland vilda bestånd av lax och havsöring. Havsöringen från Luleälven var dock genetiskt mest lik den från Dalälven och Ljusnan, trots det geografiska avståndet, vilket sannolikt återspeglar äldre omflyttningar av fisk (och därmed genetiskt material). Ett flertal helsyskongrupper av varierande storlek kunde identifieras bland lekfisken, och i några fall hade helsyskon av slumpen också parats med varandra. Skellefteälven har låtit DNA-analysera sina avelslaxar under flera år; bland avelsfisken 2018 från denna älv gick det därför att identifiera 89 (utav 100) laxar som avkomma till tidigare analyserade föräldrar från aveln 2014

Fem års DNA-analys av avelsfisk - kompensationsodlad lax och havsöring från åtta älvar

För att kompensera för kraftigt minskad naturlig reproduktion orsakad av vattenkraftsutbyggnad sker odling och utsättning av betydande mängder lax och havsöring i ett flertal av våra större vattendrag. Varje år tas nya avelsfiskar in för kramning (sea ranching). I Sverige ska all kompensationsodlad utsatt fisk vara fettfeneklippt. Tidigare märktes även en andel av lax- och havsöringsungarna (smolten) med yttre så kallade Carlinmärken, där inrapporterade återfynd har använts för olika studier och uppföljningar. Av flera olika anledningar har dock dessa märkningar i princip upphört. Som ett alternativ till yttre märkning har molekylärgenetiska analyser av återvändande avelsfisk börjat användas för att samla in information om de kompensationsodlade lax- och havsöringsstammarna. Genom att dra nytta av det faktum att samtliga individer bär på en unik genuppsättning, går det att baserat på data från återkommande DNA-analyser av avelsfisk göra diverse uppföljningar av odlingsverksamheten. De första DNA-analyserna genomfördes 2014. Därefter har antalet stammar som omfattas av analyserna gradvis ökat. Resultat från DNA-analyser av lax och havsöring erhållna till och med aveln 2018 har presenterats tidigare (Söderberg m.fl. 2019). I denna rapport ges en uppdaterad sammanställning av slutsatser och erfarenheter baserad på fortsatta analyser (t.o.m. aveln 2022) av totalt sju lax- och sex havsöringsstammar.Samtliga de undersökta lax- och havsöringsstammarna uppvisade jämförelsevis hög genetisk variationsgrad, vilket kan förklaras av att det genom åren ingått inslag av älvsfrämmande individer bland de kramade avelsfiskarna. För lax i Skellefteälven observerades dock en signifikant minskad variationsgrad (färre anlagsvarianter) från 2014 till 2022 vilken kan återspegla en relativt hög förekomst av sterila hanar i kombination med att man relativt nyligen övergått till att para en hona med endast en hane. Under samma tidsperiod uppvisade laxen i Ljusnan tecken på ökad genetisk variationsgrad, vilket sammanfaller med en kraftigt ökad andel identifierad älvsfrämmande avelsfisk (från 3-4 % 2014-2015 till drygt 50 % 2022, en extremt hög nivå). Med undantag för Ljusnan varierade den genomsnittliga andelen älvsfrämmande lax mellan 0,3 och 3,3 %. Även för havsöring var andelen älvsfrämmande avelsfisk identifierad via DNA låg och utan något exempel på en större förändring över tid. Hos båda arterna härstammade de flesta älvsfrämmande avelsfiskarna från geografiskt mer närliggande älvar.Hittills (t.o.m. 2022) har ca 25 % av de DNA-analyserade avelslaxarna identifierade föräldrar från tidigare år, där Skellefteälven och Lagan dominerar tack vare längst tidsserier. Inom några år förväntas föräldrar till samtliga odlade individer från de sju laxstammar som ingår i projektet att kunna identifieras. För havsöring, som analyserats under kortare tid, är andelen med identifierade föräldrar hittills endast 8 %. Även för denna art förväntas en snabbt ökande andel avelsfisk med identifierade föräldrar under de kommande åren. Andelen identifierade helsyskon som råkat bli parade med varandra varierade mellan noll och några få procent per år och stam, med tendens till något högre andelar hos havsöring jämfört med lax.Avslutningsvis ges några exempel där DNA-baserade föräldraskapsbestämningar (för lax) använts som utgångspunkt för storleksjämförelser av hanar och honor med olika antal år i havet, ursprungsidentifieringar av kustfångade odlade individer, konstruktion av stamträd (pedigree) samt beräkningar av genetiskt effektiv populationsstorlek (Ne). Baserat på antal återvändande avkommor per kramad förälder beräknades Ne för lax i Skellefteälven och Lagan till omkring 200 respektive 320 (per generation), vilket understiger det långsiktiga mål om Ne ≥ 500 som ofta refereras till i genetiska bevarandesammanhang. För att erhålla ökade effektiva populationsstorlekar krävs sannolikt fler avelslaxar i kombination med åtgärder som syftar till att ge en minskad variation i antalet avkommor per förälder

Thiamin dynamics during the adult life cycle of Atlantic salmon (Salmo salar)

Thiamin is an essential water-soluble B vitamin known for its wide range of metabolic functions and antioxidant properties. Over the past decades, reproductive failures induced by thiamin deficiency have been observed in several salmonid species worldwide, but it is unclear why this micronutrient deficiency arises. Few studies have compared thiamin concentrations in systems of salmonid populations with or without documented thiamin deficiency. Moreover, it is not well known whether and how thiamin concentration changes during the marine feeding phase and the spawning migration. Therefore, samples of Atlantic salmon (Salmo salar) were collected when actively feeding in the open Baltic Sea, after the sea migration to natal rivers, after river migration, and during the spawning period. To compare populations of Baltic salmon with systems without documented thiamin deficiency, a population of landlocked salmon located in Lake Vänern (Sweden) was sampled as well as salmon from Norwegian rivers draining into the North Atlantic Ocean. Results showed the highest mean thiamin concentrations in Lake Vänern salmon, followed by North Atlantic, and the lowest in Baltic populations. Therefore, salmon in the Baltic Sea seem to be consistently more constrained by thiamin than those in other systems. Condition factor and body length had little to no effect on thiamin concentrations in all systems, suggesting that there is no relation between the body condition of salmon and thiamin deficiency. In our large spatiotemporal comparison of salmon populations, thiamin concentrations declined toward spawning in all studied systems, suggesting that the reduction in thiamin concentration arises as a natural consequence of starvation rather than to be related to thiamin deficiency in the system. These results suggest that factors affecting accumulation during the marine feeding phase are key for understanding the thiamin deficiency in salmonids. Atlantic salmon, Baltic Sea, M74 syndrome, Salmon life cycle, Thiamin, Thiamin deficiencypublishedVersio

Functional loss of IKBE leads to NF-KB deregulation in aggressive chronic lymphocytic leukemia

NF-?B is constitutively activated in chronic lymphocytic leukemia (CLL); however, the implicated molecular mechanisms remain largely unknown. Thus, we performed targeted deep sequencing of 18 core complex genes within the NF-?B pathway in a discovery and validation CLL cohort totaling 315 cases. The most frequently mutated gene was NFKBIE (21/315 cases; 7%), which encodes I?B?, a negative regulator of NF-?B in normal B cells. Strikingly, 13 of these cases carried an identical 4-bp frameshift deletion, resulting in a truncated protein. Screening of an additional 377 CLL cases revealed that NFKBIE aberrations predominated in poor-prognostic patients and were associated with inferior outcome. Minor subclones and/or clonal evolution were also observed, thus potentially linking this recurrent event to disease progression. Compared with wild-type patients, NFKBIE-deleted cases showed reduced I?B? protein levels and decreased p65 inhibition, along with increased phosphorylation and nuclear translocation of p65. Considering the central role of B cell receptor (BcR) signaling in CLL pathobiology, it is notable that I?B? loss was enriched in aggressive cases with distinctive stereotyped BcR, likely contributing to their poor prognosis, and leading to an altered response to BcR inhibitors. Because NFKBIE deletions were observed in several other B cell lymphomas, our findings suggest a novel common mechanism of NF-?B deregulation during lymphomagenesis. <br/

Variation in Structure and Process of Care in Traumatic Brain Injury: Provider Profiles of European Neurotrauma Centers Participating in the CENTER-TBI Study.

INTRODUCTION: The strength of evidence underpinning care and treatment recommendations in traumatic brain injury (TBI) is low. Comparative effectiveness research (CER) has been proposed as a framework to provide evidence for optimal care for TBI patients. The first step in CER is to map the existing variation. The aim of current study is to quantify variation in general structural and process characteristics among centers participating in the Collaborative European NeuroTrauma Effectiveness Research in Traumatic Brain Injury (CENTER-TBI) study. METHODS: We designed a set of 11 provider profiling questionnaires with 321 questions about various aspects of TBI care, chosen based on literature and expert opinion. After pilot testing, questionnaires were disseminated to 71 centers from 20 countries participating in the CENTER-TBI study. Reliability of questionnaires was estimated by calculating a concordance rate among 5% duplicate questions. RESULTS: All 71 centers completed the questionnaires. Median concordance rate among duplicate questions was 0.85. The majority of centers were academic hospitals (n = 65, 92%), designated as a level I trauma center (n = 48, 68%) and situated in an urban location (n = 70, 99%). The availability of facilities for neuro-trauma care varied across centers; e.g. 40 (57%) had a dedicated neuro-intensive care unit (ICU), 36 (51%) had an in-hospital rehabilitation unit and the organization of the ICU was closed in 64% (n = 45) of the centers. In addition, we found wide variation in processes of care, such as the ICU admission policy and intracranial pressure monitoring policy among centers. CONCLUSION: Even among high-volume, specialized neurotrauma centers there is substantial variation in structures and processes of TBI care. This variation provides an opportunity to study effectiveness of specific aspects of TBI care and to identify best practices with CER approaches

Albiglutide and cardiovascular outcomes in patients with type 2 diabetes and cardiovascular disease (Harmony Outcomes): a double-blind, randomised placebo-controlled trial

Background: Glucagon-like peptide 1 receptor agonists differ in chemical structure, duration of action, and in their effects on clinical outcomes. The cardiovascular effects of once-weekly albiglutide in type 2 diabetes are unknown. We aimed to determine the safety and efficacy of albiglutide in preventing cardiovascular death, myocardial infarction, or stroke. Methods: We did a double-blind, randomised, placebo-controlled trial in 610 sites across 28 countries. We randomly assigned patients aged 40 years and older with type 2 diabetes and cardiovascular disease (at a 1:1 ratio) to groups that either received a subcutaneous injection of albiglutide (30–50 mg, based on glycaemic response and tolerability) or of a matched volume of placebo once a week, in addition to their standard care. Investigators used an interactive voice or web response system to obtain treatment assignment, and patients and all study investigators were masked to their treatment allocation. We hypothesised that albiglutide would be non-inferior to placebo for the primary outcome of the first occurrence of cardiovascular death, myocardial infarction, or stroke, which was assessed in the intention-to-treat population. If non-inferiority was confirmed by an upper limit of the 95% CI for a hazard ratio of less than 1·30, closed testing for superiority was prespecified. This study is registered with ClinicalTrials.gov, number NCT02465515. Findings: Patients were screened between July 1, 2015, and Nov 24, 2016. 10 793 patients were screened and 9463 participants were enrolled and randomly assigned to groups: 4731 patients were assigned to receive albiglutide and 4732 patients to receive placebo. On Nov 8, 2017, it was determined that 611 primary endpoints and a median follow-up of at least 1·5 years had accrued, and participants returned for a final visit and discontinuation from study treatment; the last patient visit was on March 12, 2018. These 9463 patients, the intention-to-treat population, were evaluated for a median duration of 1·6 years and were assessed for the primary outcome. The primary composite outcome occurred in 338 (7%) of 4731 patients at an incidence rate of 4·6 events per 100 person-years in the albiglutide group and in 428 (9%) of 4732 patients at an incidence rate of 5·9 events per 100 person-years in the placebo group (hazard ratio 0·78, 95% CI 0·68–0·90), which indicated that albiglutide was superior to placebo (p&lt;0·0001 for non-inferiority; p=0·0006 for superiority). The incidence of acute pancreatitis (ten patients in the albiglutide group and seven patients in the placebo group), pancreatic cancer (six patients in the albiglutide group and five patients in the placebo group), medullary thyroid carcinoma (zero patients in both groups), and other serious adverse events did not differ between the two groups. There were three (&lt;1%) deaths in the placebo group that were assessed by investigators, who were masked to study drug assignment, to be treatment-related and two (&lt;1%) deaths in the albiglutide group. Interpretation: In patients with type 2 diabetes and cardiovascular disease, albiglutide was superior to placebo with respect to major adverse cardiovascular events. Evidence-based glucagon-like peptide 1 receptor agonists should therefore be considered as part of a comprehensive strategy to reduce the risk of cardiovascular events in patients with type 2 diabetes. Funding: GlaxoSmithKline

Functional loss of IκBε leads to NF-κB deregulation in aggressive chronic lymphocytic leukemia

NF-κB is constitutively activated in chronic lymphocytic leukemia (CLL); however, the implicated molecular mechanisms remain largely unknown. Thus, we performed targeted deep sequencing of 18 core complex genes within the NF-κB pathway in a discovery and validation CLL cohort totaling 315 cases. The most frequently mutated gene was NFKBIE (21/315 cases; 7%), which encodes IκBε, a negative regulator of NF-κB in normal B cells. Strikingly, 13 of these cases carried an identical 4-bp frameshift deletion, resulting in a truncated protein. Screening of an additional 377 CLL cases revealed that NFKBIE aberrations predominated in poor-prognostic patients and were associated with inferior outcome. Minor subclones and/or clonal evolution were also observed, thus potentially linking this recurrent event to disease progression. Compared with wild-type patients, NFKBIE-deleted cases showed reduced IκBε protein levels and decreased p65 inhibition, along with increased phosphorylation and nuclear translocation of p65. Considering the central role of B cell receptor (BcR) signaling in CLL pathobiology, it is notable that IκBε loss was enriched in aggressive cases with distinctive stereotyped BcR, likely contributing to their poor prognosis, and leading to an altered response to BcR inhibitors. Because NFKBIE deletions were observed in several other B cell lymphomas, our findings suggest a novel common mechanism of NF-κB deregulation during lymphomagenesis