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  • Hankonen, Nelli; Heino, Matti T J; Hynynen, Sini-Tuuli; Laine, Hanna; Araújo-Soares, Vera; Sniehotta, Falko F; Vasankari, Tommi; Sund, Reijo; Haukkala, Ari (BioMed Central, 2017)
    Abstract Background No school-based physical activity (PA) interventions among older adolescents have demonstrated long-term effectiveness, and few of them so far have addressed sedentary behaviour (SB). Based on behavioural theories and evidence, we designed a multi-level intervention to increase PA and decrease SB among vocational school students. This study investigates feasibility and acceptability of two main intervention components and research procedures. We also examine uptake of behaviour change techniques (BCTs) by the participants. Methods Design was an outcome assessor blinded, cluster-randomised controlled trial. Four classes of students (matched pairs) were randomised into one intervention and one control arm. The intervention consisted of (1) a 6-h group-based intervention for students, (2) two 2-h training workshops to reduce their students’ sitting in class for teachers, and (3) provision of light PA equipment in classrooms. At baseline (T1), mid-intervention (T2) at 3 weeks, post-intervention (T3) and 6 months after baseline (T4) we measured hypothesised psychosocial mediators and self-reported PA and sitting. Objective assessment of PA and SB (7-day accelerometry) was conducted at T1, T3 and T4. Body composition (bioimpedance) was measured at T1 and T4. Students and teachers in the intervention arm filled in acceptability questionnaires at T3. Results Recruitment rate was 64% (students) and 88.9% (teachers), and at T3, all post-intervention measurements were completed by 33 students (retention 76.7%) and 15 teachers (retention 93.8%). Acceptability ratings of sessions were high (students M = 6.29, scale 1–7), and data collection procedures were feasible. Intervention arm students reported increased use of BCTs, but uptake of some key BCTs was suboptimal. BCT use correlated highly with objective measures of PA. Based on both self-report and student evaluation, teachers in the intervention arm increased the use of sitting reduction strategies at post-intervention and T4 follow-up (p < .05). Conclusions We detected willingness of the target groups to participate, good response rates to questionnaires, adequate retention, as well as acceptability of the trial protocol. Investigation of BCT use among students helped further enhance intervention procedures to promote BCT use. After making necessary modifications identified, intervention effectiveness can next be tested in a definitive trial. Trial registration ISRCTN34534846 . Registered 23 May 2014. Retrospectively registered.
  • Heikkilä, Helka M; Hielm-Björkman, Anna K; Innes, John F; Laitinen-Vapaavuori, Outi M (BioMed Central, 2017)
    Abstract Background Recently, intra-articular botulinum toxin A (IA BoNT A) has been shown to reduce joint pain in osteoarthritic dogs. Similar results have been reported in human patients with arthritis. However, the mechanism of the antinociceptive action of IA BoNT A is currently not known. The aim of this study was to explore this mechanism of action by investigating the effect of IA BoNT A on synovial fluid (SF) and serum substance P (SP), prostaglandin E2 (PGE2), and tumor necrosis factor alpha (TNF-α) in osteoarthritic dogs. Additionally, the aim was to compare SF SP and PGE2 between osteoarthritic and non-osteoarthritic joints, and investigate associations between SP, PGE2, osteoarthritic pain, and the signalment of dogs. Thirty-five dogs with chronic naturally occurring osteoarthritis and 13 non-osteoarthritic control dogs were included in the study. Osteoarthritic dogs received either IA BoNT A (n = 19) or IA placebo (n = 16). Serum and SF samples were collected and osteoarthritic pain was evaluated before (baseline) and 2 and 8 weeks after treatment. Osteoarthritic pain was assessed with force platform, Helsinki Chronic Pain Index, and joint palpation. Synovial fluid samples were obtained from control dogs after euthanasia. The change from baseline in SP and PGE2 concentration was compared between the IA BoNT A and placebo groups. The synovial fluid SP and PGE2 concentration was compared between osteoarthritic and control joints. Associations between SP, PGE2, osteoarthritic pain, and the signalment of dogs were evaluated. Results There was no significant change from baseline in SP or PGE2 after IA BoNT A. Synovial fluid PGE2 was significantly higher in osteoarthritic compared to control joints. Synovial fluid PGE2 correlated with osteoarthritic pain. No associations were found between SP or PGE2 and the signalment of dogs. The concentration of TNF-α remained under the detection limit of the assay in all samples. Conclusions The results suggest that the antinociceptive effect of IA BoNT A in the joint might not be related to the inhibition of SP nor PGE2. Synovial fluid PGE2, but not SP, could be a marker for chronic osteoarthritis and pain in dogs.
  • Keinänen, Marja; Käkelä, Reijo; Ritvanen, Tiina; Myllylä, Timo; Pönni, Jukka; Vuorinen, Pekka J (BioMed Central, 2017)
    Abstract Sprat (Sprattus sprattus) and small herring (Clupea harengus) are the dominant prey fish of Atlantic salmon (Salmo salar) in the Baltic Sea. If the fatty acid (FA) proportions of sprat and herring differ, the dietary history of ascending salmon could be determined from their FA profiles. Therefore, we investigated the FA composition of several age groups of whole sprat and small herring, caught from the three main feeding areas of salmon in autumn and spring. Oleic acid (18:1n-9) was the most prevalent FA in sprat and characteristic of this species. In herring, palmitic acid (16:0) was the most common FA, but herring lipid was characterized by n-6 polyunsaturated FAs, and moreover, by palmitoleic acid (16:1n-7) and vaccenic acid (18:1n-7). Due to the higher lipid content of sprat, the concentrations of all other FAs, excluding these, were higher in sprat than in herring. The concentration of docosahexaenoic acid (DHA, 22:6n-3) increased with an increase in the lipid content and was consequently highest in the youngest specimens, being in young sprat almost double that of young herring, and 2.6 times higher in the sprat biomass than in that of herring. As a result of a decrease in the DHA concentration with age, the ratio thiamine/DHA increased with respect to age in both species, and was lower in sprat than in herring. It is concluded that an abundance of DHA in the diet of salmon most likely increases oxidative stress because of the susceptibility of DHA to peroxidation, and thus decreases thiamine resources of fasting, prespawning salmon. Because the FA composition of sprat and herring differs, and the relative abundancies of prey fish differ between the feeding areas of salmon, the feeding area of ascending salmon can most probably be derived by comparing their FA profiles.
  • Laaksonen, Sauli; Jokelainen, Pikka; Pusenius, Jyrki; Oksanen, Antti (BioMed Central, 2017)
    Abstract Background Slaughter reindeer are exposed to stress caused by gathering, handling, loading and unloading, and by conditions in vehicles during transport. These stress factors can lead to compromised welfare and trauma such as bruises or fractures, aspiration of rumen content, and abnormal odour in carcasses, and causing condemnations in meat inspection and lower meat quality. We investigated the statistical association of slaughter transport distance with these indices using meat inspection data from years 2004–2016, including inspection of 669,738 reindeer originating from Finnish reindeer herding areas. Results Increased stress and decreased welfare of reindeer, as indicated by higher incidence of carcass condemnation due to bruises or fractures, aspiration of rumen content, or abnormal odour, were positively associated with systems involving shorter transport distances to abattoirs. Significant differences in incidence of condemnations were also detected between abattoirs and reindeer herding cooperatives. Conclusions This study indicates that in particular the short-distance transports of reindeer merit more attention. While the results suggest that factors associated with long distance transport, such as driver education, truck design, veterinary supervision, and specialist equipment, may be favourable to reducing pre-slaughter stress in reindeer when compared with short distance transport systems, which occur in a variety of vehicle types and may be done by untrained handlers. Further work is required to elucidate the causal factors to the current results.
  • Alanko, Jarno; Cunial, Fabio; Belazzougui, Djamal; Mäkinen, Veli (BioMed Central, 2017)
    Abstract Background A metagenomic sample is a set of DNA fragments, randomly extracted from multiple cells in an environment, belonging to distinct, often unknown species. Unsupervised metagenomic clustering aims at partitioning a metagenomic sample into sets that approximate taxonomic units, without using reference genomes. Since samples are large and steadily growing, space-efficient clustering algorithms are strongly needed. Results We design and implement a space-efficient algorithmic framework that solves a number of core primitives in unsupervised metagenomic clustering using just the bidirectional Burrows-Wheeler index and a union-find data structure on the set of reads. When run on a sample of total length n, with m reads of maximum length ℓ each, on an alphabet of total size σ, our algorithms take O(n(t+logσ)) time and just 2n+o(n)+O(max{ℓ σlogn,K logm}) bits of space in addition to the index and to the union-find data structure, where K is a measure of the redundancy of the sample and t is the query time of the union-find data structure. Conclusions Our experimental results show that our algorithms are practical, they can exploit multiple cores by a parallel traversal of the suffix-link tree, and they are competitive both in space and in time with the state of the art.
  • Sweeney, Patrick; Park, Hyunsun; Baumann, Marc; Dunlop, John; Frydman, Judith; Kopito, Ron; McCampbell, Alexander; Leblanc, Gabrielle; Venkateswaran, Anjli; Nurmi, Antti; Hodgson, Robert (BioMed Central, 2017)
    Abstract A hallmark of neurodegenerative proteinopathies is the formation of misfolded protein aggregates that cause cellular toxicity and contribute to cellular proteostatic collapse. Therapeutic options are currently being explored that target different steps in the production and processing of proteins implicated in neurodegenerative disease, including synthesis, chaperone-assisted folding and trafficking, and degradation via the proteasome and autophagy pathways. Other therapies, like mTOR inhibitors and activators of the heat shock response, can rebalance the entire proteostatic network. However, there are major challenges that impact the development of novel therapies, including incomplete knowledge of druggable disease targets and their mechanism of action as well as a lack of biomarkers to monitor disease progression and therapeutic response. A notable development is the creation of collaborative ecosystems that include patients, clinicians, basic and translational researchers, foundations and regulatory agencies to promote scientific rigor and clinical data to accelerate the development of therapies that prevent, reverse or delay the progression of neurodegenerative proteinopathies.
  • Hewetson, Michael; Sykes, Ben W; Hallowell, Gayle D; Tulamo, Riitta-Mari (BioMed Central, 2017)
    Abstract Background Equine gastric ulcer syndrome (EGUS) is common in adult horses, particularly those involved in performance disciplines. Currently, detection of EGUS by gastroscopy is the only reliable ante mortem method for definitive diagnosis; however it is unsuitable as a screening test because it is expensive, time consuming, and is not readily available to most veterinarians. Sucrose permeability testing represents a simple, economical alternative to gastroscopy for screening purposes, and the feasibility of this approach in the horse has been previously reported. The aim of this study was to determine the diagnostic accuracy of blood sucrose as a screening test for EGUS in a large group of adult horses with and without naturally occurring gastric disease. Results One hundred and one adult horses with or without naturally occurring gastric ulceration were studied. The diagnostic accuracy of blood sucrose for diagnosis of gastric lesions (GL), glandular lesions (GDL), squamous lesions (SQL), and clinically significant lesions (CSL) at 45 and 90 min after administration of 1 g/kg of sucrose via nasogastric intubation was assessed using receiver operator characteristics (ROC) curves and calculating the area under the curve (AUC). For each lesion type, sucrose concentration in blood was compared to gastroscopy, as the gold standard, and sensitivities (Se) and specificities (Sp) were calculated across a range of sucrose concentrations. Ulcer grading was performed blindly by one observer; and the results were validated by comparing them with that of two other observers, and calculating the level of agreement. Cut-off values were selected manually to optimize Se. The prevalence of GL, GDL, SQL, and CSL was 83, 70, 53 and 58% respectively. At the selected cut-offs, Se ranged from 51 to 79% and Sp ranged from 43 to 72%, depending upon the lesion type and time of sampling. Conclusions Blood sucrose is neither a sensitive or specific test for detecting EGUS in this population of adult horses with naturally occurring gastric ulceration. Further studies aimed at evaluating the performance characteristics of the test in different study populations are warranted. Given the limitations of endoscopy, due consideration should also be given to alternative methods for comparison of blood sucrose with a gold standard.
  • Idehen, Esther E; Korhonen, Tellervo; Castaneda, Anu; Juntunen, Teppo; Kangasniemi, Mari; Pietilä, Anna-Maija; Koponen, Päivikki (BioMed Central, 2017)
    Abstract Background Previous studies revealed low participation in cervical cancer screening among immigrants compared with non-immigrants. Only a few studies about factors associated with immigrants’ lower participation rates have been conducted in European countries that have universal access for all eligible women. Our study aimed to explore factors associated with cervical screening participation among women of Russian, Somali, and Kurdish origin in Finland. Methods We used data from the Migrant Health and Well-being Survey, 2010-2012. Structured face-to-face interviews of groups of immigrants aged 25-60 yielded 620 responses concerning screening participation in the previous five years. Statistical analysis employed logistic regression. Results The age-adjusted participation rates were as follows: among women of Russian origin 73.9% (95% CI 68.1-79.7), for Somalis 34.7% (95% CI 26.4-43.0), and for Kurds 61.3% (95% CI 55.0-67.7). Multiple logistic regressions showed that the most significant factor increasing the likelihood of screening participation among all groups was having had at least one gynecological check-up in the previous five years (Odds ratio [OR] = 6.54-26.2; p < 0.001). Other factors were higher education (OR = 2.63; p = 0.014), being employed (OR = 4.31; p = 0.007), and having given birth (OR = 9.34; p = 0.014), among Kurds; and literacy in Finnish/Swedish (OR = 3.63; p = 0.003) among Russians. Conclusions Our results demonstrate that women who refrain from using reproductive health services, those who are unemployed and less educated, as well as those with poor language proficiency, might need more information on the importance of screening participation. Primary and occupational healthcare services may have a significant role in informing immigrant women about this importance.
  • Vilander, Laura M; Kaunisto, Mari A; Vaara, Suvi T; Pettilä, Ville (BioMed Central, 2017)
    Abstract Background Acute kidney injury (AKI) is a multifactorial syndrome, but knowledge about its pathophysiology and possible genetic background is limited. Recently the first hypothesis-free genetic association studies have been published to explore individual susceptibility to AKI. We aimed to replicate the previously identified associations between five candidate single nucleotide polymorphisms (SNP) in apoptosis-related genes BCL2, SERPINA4, SERPINA5, and SIK3 and the development of AKI, using a prospective cohort of critically ill patients with sepsis/septic shock, in Finland. Methods This is a prospective, observational multicenter study. Of 2567 patients without chronic kidney disease and with genetic samples included in the Finnish Acute Kidney Injury (FINNAKI) study, 837 patients had sepsis and 627 patients had septic shock. AKI was defined according to the Kidney Disease: Improving Global Outcomes (KDIGO) criteria, considering stages 2 and 3 affected (severe AKI), stage 0 unaffected, and stage 1 indecisive. Genotyping was done using iPLEXTM Assay (Agena Bioscience). The genotyped SNPs were rs8094315 and rs12457893 in the intron of the BCL2 gene, rs2093266 in the SERPINA4 gene, rs1955656 in the SERPINA5 gene and rs625145 in the SIK3 gene. Association analyses were performed using logistic regression with PLINK software. Results We found no significant associations between the SNPs and severe AKI in patients with sepsis/septic shock, even after adjustment for confounders. Among patients with septic shock (252 with severe AKI and 226 without AKI (149 with KDIGO stage 1 excluded)), the SNPs rs2093266 and rs1955656 were significantly (odds ratio 0.63, p = 0.04276) associated with stage 2–3 AKI after adjusting for clinical and demographic variables. Conclusions The SNPs rs2093266 in the SERPINA4 and rs1955656 in the SERPINA5 were associated with the development of severe AKI (KDIGO stage 2–3) in critically ill patients with septic shock. For the other SNPs, we did not confirm the previously reported associations.
  • Korpela, K.; Zijlmans, M. A C; Kuitunen, M.; Kukkonen, K.; Savilahti, E.; Salonen, A.; de Weerth, C.; de Vos, W. M (BioMed Central, 2017)
    Abstract Background Children with high body mass index (BMI) at preschool age are at risk of developing obesity. Early identification of factors that increase the risk of excessive weight gain could help direct preventive actions. The intestinal microbiota and antibiotic use have been identified as potential modulators of early metabolic programming and weight development. To test if the early microbiota composition is associated with later BMI, and if antibiotic use modifies this association, we analysed the faecal microbiota composition at 3 months and the BMI at 5–6 years in two cohorts of healthy children born vaginally at term in the Netherlands (N = 87) and Finland (N = 75). We obtained lifetime antibiotic use records and measured weight and height of all children. Results The relative abundance of streptococci was positively and the relative abundance of bifidobacteria negatively associated with the BMI outcome. The association was especially strong among children with a history of antibiotic use. Bacteroides relative abundance was associated with BMI only in the children with minimal lifetime antibiotic exposure. Conclusions The intestinal microbiota of infants are predictive of later BMI and may serve as an early indicator of obesity risk. Bifidobacteria and streptococci, which are indicators of microbiota maturation in infants, are likely candidates for metabolic programming of infants, and their influence on BMI appears to depend on later antibiotic use.
  • Kaimio, Mirja; Saijonmaa-Koulumies, Leena; Laitinen-Vapaavuori, Outi (BioMed Central, 2017)
    Abstract Background American Cocker Spaniels are overrepresented among breeds that require surgery as a treatment of end-stage otitis externa. However, the prevalence of otitis externa (OE) in this breed remains unknown. We reviewed the year 2010 medical records of 55 private veterinary clinics in Finland to determine the prevalence of OE in American Cocker Spaniels compared with English Cocker and English and Welsh Springer Spaniels. An American Cocker Spaniel owner questionnaire was designed to identify potential risk factors for end-stage OE. Results From the medical records of 98,736 dogs, the prevalence of OE was highest in Welsh Springer Spaniels (149 out of 468, 31.8%, [95% confidence interval 27.6–36.0]), followed by American Cocker (89/329, 27.0%, [22.2–31.7]), English Springer (96/491, 19.6%, [16.1–23.1]) and English Cocker Spaniels (231/1467, 15.7%, [13.8–17.6]). The mean number of OE episodes in ear-diseased dogs and the number of ear surgeries were highest in American Cocker Spaniels. Owner questionnaires were received for 151 American Cocker Spaniels, 85 (56%) of which had suffered from OE. In 47% (40/85) of these dogs, OE occurred without concurrent skin lesions, 46% (33/72) displayed the first signs of OE before 1 year of age. In 24% (20/85) of the dogs, the signs of OE recurred within 1 month or continued despite treatment, 16% (14/85) required surgery (n = 11) or were euthanized (n = 5; 2 of the operated dogs and 3 others) due to severe OE. The onset of OE before the age of 1 year significantly increased the risk (OR 3.8, 95% CI 1.1–13.6) of end-stage OE. Conclusions The prevalence of OE in American Cocker Spaniels in Finland was higher than previously reported in Cocker Spaniels, but the highest prevalence of OE was found in Welsh Springer Spaniels. Compared to the other Spaniels, OE was more often recurrent and more frequently surgically managed in American Cocker Spaniels. Based on the questionnaire, early onset (<1 year) of OE increased the risk of end-stage OE. In American Cocker Spaniels, OE requires an intensive approach from the first treatment, and prevention of recurrence should be emphasised. The causes and treatment of OE in this breed warrant further study.
  • de Vries, Ronald P; Riley, Robert; Wiebenga, Ad; Aguilar-Osorio, Guillermo; Amillis, Sotiris; Uchima, Cristiane A; Anderluh, Gregor; Asadollahi, Mojtaba; Askin, Marion; Barry, Kerrie; Battaglia, Evy; Bayram, Özgür; Benocci, Tiziano; Braus-Stromeyer, Susanna A; Caldana, Camila; Cánovas, David; Cerqueira, Gustavo C; Chen, Fusheng; Chen, Wanping; Choi, Cindy; Clum, Alicia; dos Santos, Renato A C; Damásio, André R d L; Diallinas, George; Emri, Tamás; Fekete, Erzsébet; Flipphi, Michel; Freyberg, Susanne; Gallo, Antonia; Gournas, Christos; Habgood, Rob; Hainaut, Matthieu; Harispe, María L; Henrissat, Bernard; Hildén, Kristiina S; Hope, Ryan; Hossain, Abeer; Karabika, Eugenia; Karaffa, Levente; Karányi, Zsolt; Kraševec, Nada; Kuo, Alan; Kusch, Harald; LaButti, Kurt; Lagendijk, Ellen L; Lapidus, Alla; Levasseur, Anthony; Lindquist, Erika; Lipzen, Anna; Logrieco, Antonio F; MacCabe, Andrew; Mäkelä, Miia R; Malavazi, Iran; Melin, Petter; Meyer, Vera; Mielnichuk, Natalia; Miskei, Márton; Molnár, Ákos P; Mulé, Giuseppina; Ngan, Chew Y; Orejas, Margarita; Orosz, Erzsébet; Ouedraogo, Jean P; Overkamp, Karin M; Park, Hee-Soo; Perrone, Giancarlo; Piumi, Francois; Punt, Peter J; Ram, Arthur F J; Ramón, Ana; Rauscher, Stefan; Record, Eric; Riaño-Pachón, Diego M; Robert, Vincent; Röhrig, Julian; Ruller, Roberto; Salamov, Asaf; Salih, Nadhira S; Samson, Rob A; Sándor, Erzsébet; Sanguinetti, Manuel; Schütze, Tabea; Sepčić, Kristina; Shelest, Ekaterina; Sherlock, Gavin; Sophianopoulou, Vicky; Squina, Fabio M; Sun, Hui; Susca, Antonia; Todd, Richard B; Tsang, Adrian; Unkles, Shiela E; van de Wiele, Nathalie; van Rossen-Uffink, Diana; Oliveira, Juliana V d C; Vesth, Tammi C; Visser, Jaap; Yu, Jae-Hyuk; Zhou, Miaomiao; Andersen, Mikael R; Archer, David B; Baker, Scott E; Benoit, Isabelle; Brakhage, Axel A; Braus, Gerhard H; Fischer, Reinhard; Frisvad, Jens C; Goldman, Gustavo H; Houbraken, Jos; Oakley, Berl; Pócsi, István; Scazzocchio, Claudio; Seiboth, Bernhard; vanKuyk, Patricia A; Wortman, Jennifer; Dyer, Paul S; Grigoriev, Igor V (BioMed Central, 2017)
    Abstract Background The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus. Results We have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera. Comparative studies of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. Observed genomic differences were validated with experimental studies. This revealed several highlights, such as the potential for sex in asexual species, organic acid production genes being a key feature of black aspergilli, alternative approaches for degrading plant biomass, and indications for the genetic basis of stress response. A genome-wide phylogenetic analysis demonstrated in detail the relationship of the newly genome sequenced species with other aspergilli. Conclusions Many aspects of biological differences between fungal species cannot be explained by current knowledge obtained from genome sequences. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Insights gained could be exploited for biotechnological and medical applications of fungi.
  • Verardo, Lucas L; Sevón-Aimonen, Marja-Liisa; Serenius, Timo; Hietakangas, Ville; Uimari, Pekka (BioMed Central, 2017)
    Abstract Background One of the most commonly used quality measurements of pork is pH measured 24 h after slaughter. The most probable mode of inheritance for this trait is oligogenic with several known major genes, such as PRKAG3. In this study, we used whole-genome SNP genotypes of over 700 AI boars; after a quality check, 42,385 SNPs remained for association analysis. All the boars were purebred Finnish Yorkshire. To account for relatedness of the animals, a pedigree-based relationship matrix was used in a mixed linear model to test the effect of SNPs on pH measured from loin. A bioinformatics analysis was performed to identify the most promising genes in the significant regions related to meat quality. Results Genome-wide association study (GWAS) revealed three significant chromosomal regions: one on chromosome 3 (39.9 Mb–40.1 Mb) and two on chromosome 15 (58.5 Mb–60.5 Mb and 132 Mb–135 Mb including PRKAG3). A conditional analysis with a significant SNP in the PRKAG3 region, MARC0083357, as a covariate in the model retained the significant SNPs on chromosome 3. Even though linkage disequilibrium was relatively high over a long distance between MARC0083357 and other significant SNPs on chromosome 15, some SNPs retained their significance in the conditional analysis, even in the vicinity of PRKAG3. The significant regions harbored several genes, including two genes involved in cyclic AMP (cAMP) signaling: ADCY9 and CREBBP. Based on functional and transcription factor-gene networks, the most promising candidate genes for meat pH are ADCY9, CREBBP, TRAP1, NRG1, PRKAG3, VIL1, TNS1, and IGFBP5, and the key transcription factors related to these genes are HNF4A, PPARG, and Nkx2-5. Conclusions Based on SNP association, pathway, and transcription factor analysis, we were able to identify several genes with potential to control muscle cell homeostasis and meat quality. The associated SNPs can be used in selection for better pork. We also showed that post-GWAS analysis reveals important information about the genes’ potential role on meat quality. The gained information can be used in later functional studies.
  • Ludwig, Anastasia; Rivera, Claudio; Uvarov, Pavel (BioMed Central, 2017)
    Abstract Background Cation-chloride cotransporters (CCCs) are indispensable for maintaining chloride homeostasis in multiple cell types, but K–Cl cotransporter KCC2 is the only CCC member with an exclusively neuronal expression in mammals. KCC2 is critical for rendering fast hyperpolarizing responses of ionotropic γ-aminobutyric acid and glycine receptors in adult neurons, for neuronal migration in the developing central nervous system, and for the formation and maintenance of small dendritic protrusions—dendritic spines. Deficit in KCC2 expression and/or activity is associated with epilepsy and neuropathic pain, and effective strategies are required to search for novel drugs augmenting KCC2 function. Results We revised current methods to develop a noninvasive optical approach for assessing KCC2 transport activity using a previously characterized genetically encoded chloride sensor. Our protocol directly assesses dynamics of KCC2-mediated chloride efflux and allows measuring genuine KCC2 activity with good spatial and temporal resolution. As a proof of concept, we used this approach to compare transport activities of the two known KCC2 splice isoforms, KCC2a and KCC2b, in mouse neuronal Neuro-2a cells. Conclusions Our noninvasive optical protocol proved to be efficient for assessment of furosemide-sensitive chloride fluxes. Transport activities of the N-terminal splice isoforms KCC2a and KCC2b obtained by the novel approach matched to those reported previously using standard methods for measuring chloride fluxes.
  • Koskinen, Lotta L E; Seppälä, Eija H; Weissl, Jutta; Jokinen, Tarja S; Viitmaa, Ranno; Hänninen, Reetta L; Quignon, Pascale; Fischer, Andrea; André, Catherine; Lohi, Hannes (BioMed Central, 2017)
    Abstract Background Idiopathic or genetic adult-onset epilepsy is a common neurological disorder in domestic dogs. Genetic association has been reported only with ADAM23 on CFA 37 in few breeds. To identify novel epilepsy genes, we performed genome-wide association (GWA) analyses in four new breeds, and investigated the association of the previously reported ADAM23 haplotype with the epilepsy phenotype in eight breeds. Results GWA analysis did not reveal new epilepsy loci. ADAM23 association (p < 0.05) was identified in five breeds. Combined analysis of all eight breeds showed significant association (p = 4.6e−6, OR 1.9). Conclusions Our results further support the role of ADAM23 in multiple breeds as a common risk gene for epilepsy with low penetrance. The lack of findings in the GWA analyses points towards inefficient capture of genetic variation by the current SNP arrays, causal variant(s) with low penetrance and possible phenocopies. Future work will include studies on ADAM23 function and expression in canine neurons, as well as whole-genome sequencing in order to identify additional IE genes.