Browsing by Issue Date

Sort by: Order: Results:

Now showing items 1-20 of 263
  • Puurunen, Jenni; Tiira, Katriina; Lehtonen, Marko; Hanhineva, Kati; Lohi, Hannes (BioMed Central, 2016)
    Abstract Background Anxieties, such as shyness, noise phobia and separation anxiety, are common but poorly understood behavioural problems in domestic dogs, Canis familiaris. Although studies have demonstrated genetic and environmental contributions to anxiety pathogenesis, better understanding of the molecular underpinnings is needed to improve diagnostics, management and treatment plans. As a part of our ongoing canine anxiety genetics efforts, this study aimed to pilot a metabolomics approach in fearful and non-fearful dogs to identify candidate biomarkers for more objective phenotyping purposes and to refer to potential underlying biological problem. Methods We collected whole blood samples from 10 fearful and 10 non-fearful Great Danes and performed a liquid chromatography combined with mass spectrometry (LC–MS)-based non-targeted metabolite profiling. Results Non-targeted metabolomics analysis detected six 932 metabolite entities in four analytical modes [RP and HILIC; ESI(−) and ESI(+)], of which 239 differed statistically between the test groups. We identified changes in 13 metabolites (fold change ranging from 1.28 to 2.85) between fearful and non-fearful dogs, including hypoxanthine, indoxylsulfate and several phospholipids. These molecules are involved in oxidative stress, tryptophan and lipid metabolisms. Conclusions We identified significant alterations in the metabolism of fearful dogs, and some of these changes appear relevant to anxiety also in other species. This pilot study demonstrates the feasibility of the non-targeted metabolomics and warrants a larger replication study to confirm the role of the identified biomarkers and pathways in canine anxiety.
  • Taponen, Suvi; Nykäsenoja, Suvi; Pohjanvirta, Tarja; Pitkälä, Anna; Pyörälä, Satu (BioMed Central, 2016)
    Abstract Background Coagulase-negative staphylococci (CoNS) are the most common bovine mastitis causing bacteria in many countries. It is known that resistance for antimicrobials is in general more common in CoNS than in Staphylococcus aureus but little is known about the antimicrobial resistance of specific CoNS species. In this study, 400 CoNS isolates from bovine mastitic milk samples were identified to species level using ribotyping and MALDI-TOF MS, and their antimicrobial susceptibility was determined using a commercially available microdilution system. The results were interpreted according to the epidemiological cut-off values by the European Committee on Antimicrobial Susceptibility testing. Results The most common CoNS species were S. simulans, S. epidermidis, S. chromogenes and S. haemolyticus. Penicillin resistance was the most common type of antimicrobial resistance. Staphylococcus epidermidis was the most resistant among the four major species. Almost one-third of our S. epidermidis isolates were resistant to >2 antimicrobials and close to 7 % were multidrug resistant. The majority of S. epidermidis isolates were resistant to benzylpenicillin. On the contrary, only few S. simulans isolates were penicillin-resistant. Phenotypic oxacillin resistance was found in all four main species, and 34 % of the isolates were oxacillin resistant. However, only 21 isolates (5 %) were positive for the mecA gene. Of these, 20 were S. epidermidis and one S. sciuri. mecC positive isolates were not found. Conclusion Staphylococcus epidermidis differed from the three other major CoNS species as resistance to the tested antimicrobials was common, several isolates were multidrug resistant, and 19 % of the isolates carried the mecA gene encoding methicillin resistance.
  • Valros, Anna; Munsterhjelm, Camilla; Hänninen, Laura; Kauppinen, Tiina; Heinonen, Mari (BioMed Central, 2016)
    Abstract Background Tail biting is a common and serious welfare problem in pig production, causing large economical losses. Tail docking is performed routinely in most EU countries to reduce the tail biting risk. However, tail docking is painful, and does not prevent tail biting totally. The risk factors behind tail docking are multifactorial and most analyses are based on studies using biological or epidemiological approaches. There is very little information available on how producers deal with tail biting on-farm. There are also no studies on the attitude of producers towards tail docking and tail biting in systems with long-tailed pigs. We aimed to study how farmers rate the efficiency of different measures for preventing and intervening with tail biting, when tail docking is not allowed. Furthermore, we investigated the attitudes of Finnish farmers to tail docking and tail biting. Results Respondents scored feeding-related issues to be most important for prevention of tail biting, identifying and removing the biting pig as most important intervention measures, and straw as the most important manipulable material when preventing tail biting. Tail biting was not perceived as a very serious problem by over 70 % of the respondents, even though docking is not allowed, and was reported to occur close to a level which was also considered acceptable by the respondents. Most respondents did not think it is probable they would raise tail docked pigs if it were possible, but about 21 % probably would. Conclusions In comparison with other authors’ findings, the ranking of importance of risk factors for tail biting differs between scientists and farmers, and between farmers in different cultures of pig production. In addition, the attitude towards tail biting and tail docking appears to be very different in producers with different experiences of tail docking. These results indicate that a scientist-farmer dialogue, as well as international communication is important when trying to reduce the risk of tail biting, and subsequently the need for tail docking.
  • Tonteri, Elina; Jokelainen, Pikka; Matala, Juho; Pusenius, Jyrki; Vapalahti, Olli (BioMed Central, 2016)
    Abstract Background The incidence of tick-borne encephalitis (TBE) in humans has increased in Finland, and the disease has emerged in new foci. These foci have been investigated to determine the circulating virus subtype, the tick host species and the ecological parameters, but countrywide epidemiological information on the distribution of TBEV has been limited. Methods In this study, we screened sera from hunter-harvested wild cervids for the presence of antibodies against tick-borne encephalitis virus (TBEV) with a hemagglutination inhibition test. The positive results were confirmed by a neutralisation assay. Results Nine (0.74 %) of 1213 moose, one (0.74 %) of 135 white-tailed deer, and none of the 17 roe deer were found seropositive for TBEV. A close geographical congruence between seropositive cervids and recently reported human TBE cases was observed: nine of the ten seropositive animals were from known endemic areas. Conclusions Our results confirm the local circulation of TBEV in several known endemic areas. One seropositive moose had been shot in an area where human TBE cases have not been reported, suggesting a possible new focus. Moose appear to be a useful sentinel animal for the presence of TBEV in the taiga region.
  • Massinen, Satu; Wang, Jingwen; Laivuori, Krista; Bieder, Andrea; Tapia Paez, Isabel; Jiao, Hong; Kere, Juha (BioMed Central, 2016)
    Abstract Background The DYX5 locus for developmental dyslexia was mapped to chromosome 3 by linkage study of a large Finnish family, and later, roundabout guidance receptor 1 (ROBO1) was implicated as a candidate gene at DYX5 with suppressed expression from the segregating rare haplotype. A functional magnetoencephalographic study of several family members revealed abnormal auditory processing of interaural interaction, supporting a defect in midline crossing of auditory pathways. In the current study, we have characterized genetic variation in the broad ROBO1 gene region in the DYX5-linked family, aiming to identify variants that would increase our understanding of the altered expression of ROBO1. Methods We have used a whole genome sequencing strategy on a pooled sample of 19 individuals in combination with two individually sequenced genomes. The discovered genetic variants were annotated and filtered. Subsequently, the most interesting variants were functionally tested using relevant methods, including electrophoretic mobility shift assay (EMSA), luciferase assay, and gene knockdown by lentiviral small hairpin RNA (shRNA) in lymphoblasts. Results We found one novel intronic single nucleotide variant (SNV) and three novel intergenic SNVs in the broad region of ROBO1 that were specific to the dyslexia susceptibility haplotype. Functional testing by EMSA did not support the binding of transcription factors to three of the SNVs, but one of the SNVs was bound by the LIM homeobox 2 (LHX2) protein, with increased binding affinity for the non-reference allele. Knockdown of LHX2 in lymphoblast cell lines extracted from subjects from the DYX5-linked family showed decreasing expression of ROBO1, supporting the idea that LHX2 regulates ROBO1 also in human. Conclusions The discovered variants may explain the segregation of dyslexia in this family, but the effect appears subtle in the experimental settings. Their impact on the developing human brain remains suggestive based on the association and subtle experimental support.
  • Tiškina, Valentina; Capligina, Valentina; Must, Külli; Berzina, Inese; Ranka, Renate; Jokelainen, Pikka (BioMed Central, 2016)
    Abstract A previously splenectomized dog from Estonia was presented with a sudden lack of appetite and discoloration of the urine. Despite supportive therapy, its condition deteriorated dramatically during 1 day. Severe thrombocytopenia and high numbers of protozoan hemoparasites were evident in blood smears, and the hematocrit dropped from 46 to 33 %. The dog was euthanized before specific antibabesial treatment was initiated. Blood samples from the dog and from two other dogs in the same household tested positive for Babesia using molecular methods, and the sequences of partial 18S rRNA gene confirmed the causative species as Babesia canis canis. The risk of severe, rapidly progressing babesiosis in splenectomized dogs merits awareness.
  • Markkula, Ritva A; Kalso, Eija A; Kaprio, Jaakko A (BioMed Central, 2016)
    Abstract Background Fibromyalgia (FM) is a pain syndrome, the mechanisms and predictors of which are still unclear. We have earlier validated a set of FM-symptom questions for detecting possible FM in an epidemiological survey and thereby identified a cluster with “possible FM”. This study explores prospectively predictors for membership of that FM-symptom cluster. Methods A population-based sample of 8343 subjects of the older Finnish Twin Cohort replied to health questionnaires in 1975, 1981, and 1990. Their answers to the set of FM-symptom questions in 1990 classified them in three latent classes (LC): LC1 with no or few symptoms, LC2 with some symptoms, and LC3 with many FM symptoms. We analysed putative predictors for these symptom classes using baseline (1975 and 1981) data on regional pain, headache, migraine, sleeping, body mass index (BMI), physical activity, smoking, and zygosity, adjusted for age, gender, and education. Those with a high likelihood of having fibromyalgia at baseline were excluded from the analysis. In the final multivariate regression model, regional pain, sleeping problems, and overweight were all predictors for membership in the class with many FM symptoms. Results The strongest non-genetic predictor was frequent headache (OR 8.6, CI 95 % 3.8–19.2), followed by persistent back pain (OR 4.7, CI 95 % 3.3–6.7) and persistent neck pain (OR 3.3, CI 95 % 1.8–6.0). Conclusions Regional pain, frequent headache, and persistent back or neck pain, sleeping problems, and overweight are predictors for having a cluster of symptoms consistent with fibromyalgia.
  • Huttunen, Sanna; Toivanen, Marko; Liu, Chenghai; Tikkanen-Kaukanen, Carina (BioMed Central, 2016)
    Abstract Background Epidemics of meningococcal meningitis cause significant health problems especially in Sub-Saharan Africa. Novel anti-infective candidates are needed. In modern anti-adhesion therapy initial attachment of bacteria to host cells is prevented. Our unique studies have revealed anti-adhesive candidates from natural products, namely milk and berries, against Neisseria meningitidis adhesion. In the present study against N. meningitidis adhesion, a novel binding inhibitor was found; salvianolic acid B (SA-B), a polyphenol from the radix Salviae miltiorrhizae, an important part of Chinese folk medicine. Methods In order to test inhibition of meningococcal pili binding and anti-adhesion activity of SA-B, bovine thyroglobulin, a reference glycoprotein for meningococcal receptor was used in a microtiter plate assay. Inhibitory activity was tested by using serial dilutions of SA-B extracts of 98 and 70 % purity. Results were confirmed in a HEC-1B cell dot assay and antimicrobial activity was measured by using a microbroth dilution assay. Results Almost total (93 %) inhibition of pili binding, anti-adhesion, was achieved with the 70 % extract of SA-B at the concentration of 0.3 mg/mL in the bovine thyroglobulin reference model. 50 % binding inhibition activity was achieved with 0.6 µg/mL of the SA-B extract. Total inhibition of the pili binding to HEC-1B cells was found at the tested concentration of 0.5 mg/mL. The 98 % pure SA-B resulted in weaker inhibition. At the concentration of 0.3 mg/mL 78 % inhibition was achieved in the thyroglobulin model. For 50 % inhibition 2.4 μg/mL of pure SA-B was needed. The difference between the binding inhibition activities (70 and 98 % pure SA-B) was statistically significant (P = 0.03). Antimicrobial activity of 70 % SA-B, when investigated against N. meningitidis, was detected only in relatively high concentrations. Conclusions Our results indicate that plant SA-B may prevent meningococcal infections by inhibiting meningococcal binding and may thus have an impact on the amount of nasopharyngeal carriers of N. meningitidis. This may prevent the spreading of meningococcal infections between humans. One could conclude that SA-B and its source dried radix S. miltiorrhizae, which is an important part of Chinese folk medicine, could be valuable candidates for further research in meningococcal disease prevention.
  • Wang, Yilin; Hedman, Lea; Perdomo, Maria F; Elfaitouri, Amal; Bölin-Wiener, Agnes; Kumar, Arun; Lappalainen, Maija; Söderlund-Venermo, Maria; Blomberg, Jonas; Hedman, Klaus (BioMed Central, 2016)
    Abstract Background Human parvovirus B19 (B19V), cytomegalovirus (CMV) and Toxoplasma gondii (T. gondii) may cause intrauterine infections with potentially severe consequences to the fetus. Current serodiagnosis of these infections is based on detection of antibodies most often by EIA and individually for each pathogen. We developed singleplex and multiplex microsphere-based Suspension Immuno Assays (SIAs) for the simultaneous detection of IgG antibodies against B19V, CMV and T. gondii. Methods We tested the performances of SIAs as compared to in-house and commercial reference assays using serum samples from well-characterized cohorts. Results The IgG SIAs for CMV and T. gondii showed good concordance with the corresponding Vidas serodiagnostics. The B19V IgG SIA detected IgG in all samples collected >10 days after onset of symptoms and showed high concordance with EIAs (in-house and Biotrin). The serodiagnostics for these three pathogens performed well in multiplex format. Conclusions We developed singleplex and multiplex IgG SIAs for the detection of anti-B19V,-CMV and -T. gondii antibodies. The SIAs were highly sensitive and specific, and had a wide dynamic range. These components thus should be suitable for construction of a multiplex test for antibody screening during pregnancy.
  • Haapala, Sini; Niemitalo-Haapola, Elina; Raappana, Antti; Kujala, Tiia; Suominen, Kalervo; Jansson-Verkasalo, Eira; Kujala, Teija (BioMed Central, 2016)
    Abstract Background A large group of young children are exposed to repetitive middle ear infections but the effects of the fluctuating hearing sensations on immature central auditory system are not fully understood. The present study investigated the consequences of early childhood recurrent acute otitis media (RAOM) on involuntary auditory attention switching. Methods By utilizing auditory event-related potentials, neural mechanisms of involuntary attention were studied in 22–26 month-old children (N = 18) who had had an early childhood RAOM and healthy controls (N = 19). The earlier and later phase of the P3a (eP3a and lP3a) and the late negativity (LN) were measured for embedded novel sounds in the passive multi-feature paradigm with repeating standard and deviant syllable stimuli. The children with RAOM had tympanostomy tubes inserted and all the children in both study groups had to have clinically healthy ears at the time of the measurement assessed by an otolaryngologist. Results The results showed that lP3a amplitude diminished less from frontal to central and parietal areas in the children with RAOM than the controls. This might reflect an immature control of involuntary attention switch. Furthermore, the LN latency was longer in children with RAOM than in the controls, which suggests delayed reorientation of attention in RAOM. Conclusions The lP3a and LN responses are affected in toddlers who have had a RAOM even when their ears are healthy. This suggests detrimental long-term effects of RAOM on the neural mechanisms of involuntary attention.
  • Häggman, Johanna; Junni, Reijo; Simojoki, Heli; Juga, Jarmo; Soveri, Timo (BioMed Central, 2015)
    Abstract Background The aim of the study was to provide detailed herd level cost information about an outbreak of interdigital phlegmon (IP), which has been an emerging problem with enlarged loose house barns in Finland in recent years. During enlargement, the farmer’s financial situation is sensitive because of the large investments to the farm business and unexpected costs can risk the farm’s survival. Results The University of Helsinki research herd and three commercial herds having outbreaks of IP in 2012 or 2013 were visited to collect detailed information about the costs and economic impact of the outbreaks. The majority of the costs came from the discarded milk due to the antibiotic treatments. In Finland IP is usually treated with parental benzylpenicillin for 5 days which result in discarded milk for a total of 11 days. Third generation cephalosporins, widely used in other countries, have no milk withdrawal time. However, the use of these antibiotics is not recommended in Finland since these antimicrobials are critically important for human health. Herd-level costs varied between 4560 and 28,386 € depending on the herd size, the frequency of the infected cows, the antibiotics used and other costs involved. The average cost per infected cow was 489 €. Conclusions The outbreaks of IP cause severe economic losses to dairy farms and the costs are lower if cows are treated with antibiotics with no withdrawal time. However, other costs, such as involuntary culling, reduced production and fertility also produce substantial costs to the farms. Early detection of sick animals, rapid treatment and control measures to limit the outbreak of IP can lower the costs. Because of the high costs farms should concentrate on preventing the disease.
  • Kovalchuk, Andriy; Kohler, Annegret; Martin, Francis; Asiegbu, Fred O (BioMed Central, 2015)
    Abstract Background Transporter proteins are predicted to have an important role in the mycorrhizal symbiosis, due to the fact that this type of an interaction between plants and fungi requires a continuous nutrient and signalling exchange. ABC transporters are one of the large groups of transporter proteins found both in plants and in fungi. The crucial role of plant ABC transporters in the formation of the mycorrhizal symbiosis has been demonstrated recently. Some of the fungal ABC transporter-encoding genes are also induced during the mycorrhiza formation. However, no experimental evidences of the direct involvement of fungal ABC transporters in this process are available so far. To facilitate the identification of fungal ABC proteins with a potential role in the establishment of the mycorrhizal symbiosis, we have performed an inventory of the ABC protein-encoding genes in the genomes of 25 species of mycorrhiza-forming fungi. Results We have identified, manually annotated and curated more than 1300 gene models of putative ABC protein-encoding genes. Out of those, more than 1000 models are predicted to encode functional proteins, whereas about 300 models represent gene fragments or putative pseudogenes. We have also performed the phylogenetic analysis of the identified sequences. The sets of ABC proteins in the mycorrhiza-forming species were compared to the related saprotrophic or plant-pathogenic fungal species. Our results demonstrate the high diversity of ABC genes in the genomes of mycorrhiza-forming fungi. Via comparison of transcriptomics data from different species, we have identified candidate groups of ABC transporters that might have a role in the process of the mycorrhiza formation. Conclusions Results of our inventory will facilitate the identification of fungal transporters with a role in the mycorrhiza formation. We also provide the first data on ABC protein-coding genes for the phylum Glomeromycota and for orders Pezizales, Atheliales, Cantharellales and Sebacinales, contributing to the better knowledge of the diversity of this protein family within the fungal kingdom.
  • Herczeg, Gábor; Gonda, Abigél; Balázs, Gergely; Noreikiene, Kristina; Merilä, Juha (BioMed Central, 2015)
    Abstract Background Plasticity in brain size and the size of different brain regions during early ontogeny is known from many vertebrate taxa, but less is known about plasticity in the brains of adults. In contrast to mammals and birds, most parts of a fish’s brain continue to undergo neurogenesis throughout adulthood, making lifelong plasticity in brain size possible. We tested whether maturing adult three-spined sticklebacks (Gasterosteus aculeatus) reared in a stimulus-poor environment exhibited brain plasticity in response to environmental enrichment, and whether these responses were sex-specific, thus altering the degree of sexual size dimorphism in the brain. Results Relative sizes of total brain and bulbus olfactorius showed sex-specific responses to treatment: males developed larger brains but smaller bulbi olfactorii than females in the enriched treatment. Hence, the degree of sexual size dimorphism (SSD) in relative brain size and the relative size of the bulbus olfactorius was found to be environment-dependent. Furthermore, the enriched treatment induced development of smaller tecta optica in both sexes. Conclusions These results demonstrate that adult fish can alter the size of their brain (or brain regions) in response to environmental stimuli, and these responses can be sex-specific. Hence, the degree of SSD in brain size can be environment-dependent, and our results hint at the possibility of a large plastic component to SSD in stickleback brains. Apart from contributing to our understanding of the processes shaping and explaining variation in brain size and the size of different brain regions in the wild, the results show that provision of structural complexity in captive environments can influence brain development. Assuming that the observed plasticity influences fish behaviour, these findings may also have relevance for fish stocking, both for economical and conservational purposes.
  • Barreto, Goncalo; Soininen, Antti; Ylinen, Pekka; Sandelin, Jerker; Konttinen, Yrjö T; Nordström, Dan C; Eklund, Kari K (BioMed Central, 2015)
    Abstract Background Soluble biglycan (sBGN) and soluble decorin (sDCN), are two closely related essential components of extracellular matrix which both have been shown to possess proinflammatory properties. We studied whether sBGN or sDCN were present in synovial fluid (SF) of osteoarthritis (OA) or rheumatoid arthritis (RA) patients and studied sBGN or sDCN potential role in the degradation of OA cartilage. Methods SF obtained from meniscus tear, OA, and RA patients were analysed for sBGN and sDCN using enzyme-linked immunosorbent assays. OA chondrocytes and cartilage explants were stimulated for 48 h with 5 μg/ml sBGN or 1 μg/ml lipopolysaccharide. Messenger RNA (mRNA) levels of Toll-like receptors (TLRs), proteinases and cartilage matrix molecules were determined using quantitative real-time polymerase chain reaction. Protein levels of matrix metalloproteinases (MMPs) and cytokines were measured using Luminex xMap technology. Production of nitric oxide (NO), release of proteoglycans and soluble collagen were measured from conditioned culture media using biochemical assays. OA cartilage explant proteoglycans were stained for Safranin O and quantified using image analysis. TLR4 activation by sBGN and sDCN was studied in engineered HEK-293 cells with TLR4 signalling genes inserted together with a reporter gene. Results sBGN was found in meniscus tear SF (14 ± 2 ng/ml), OA SF (582 ± 307 ng/ml) and RA SF (1191 ± 482 ng/ml). Low levels of sDCN could also be detected in SF of meniscus tear (51 ± 4) ng/ml, OA (52 ± 3 ng/ml), and RA (49 ± 4 ng/ml). Stimulation of chondrocytes with sBGN increased significantly the mRNA and protein expression of catabolic MMPs, including MMP1, MMP9 and MMP13, and of inflammatory cytokines interleukin (IL)-6 and IL-8, whereas the expression of anabolic markers aggrecan and collagen type II was decreased. sBGN induced release of proteoglycans, collagen and NO from chondrocytes and cartilage explants. The catabolic response in explants was dependent of OA cartilage degradation stage. The mechanism of action of sBGN was mainly mediated through the TLR4-nuclear factor-κB pathway. Conclusions High levels of sBGN was found in advanced OA and RA SF. sBGN activates chondrocytes mainly via TLR4, which results in net loss of cartilage. Thus, sBGN can be a mediator of OA cartilage degradation and also a potential biomarker for arthritis.
  • Eeva, Tapio; Andersson, Tommi; Berglund, Åsa M M; Brommer, Jon E; Hyvönen, Raimo; Klemola, Tero; Laaksonen, Toni; Loukola, Olli; Morosinotto, Chiara; Rainio, Kalle; Sirkiä, Päivi M; Vesterinen, Eero J (BioMed Central, 2015)
    Abstract Background Birds host several ectoparasitic fly species with negative effects on nestling health and reproductive output, and with the capability of transmitting avian blood parasites. Information on the abundance and distribution of the ectoparasitic fly genera Ornithomya (Hippoboscidae) and Protocalliphora (Calliphoridae) in northern Europe is still generally poor, and we thus explored their geographic range and occurrence of these flies in the nests of a common avian model species, the pied flycatcher Ficedula hypoleuca. Methods Nests of F. hypoleuca were collected from 21 locations across Fennoscandia in summer 2013, across a latitudinal gradient (between 56 °N – 70 °N) and examined for the presence of fly puparia. Adult specimens of Ornithomya spp. were also collected for species identification. Fly species were identified morphologically and identifications confirmed with DNA barcoding. Results We found three species: two louse-flies − Ornithomya chloropus and O. avicularia − and one blow-fly, Protocalliphora azurea. The prevalence of O. avicularia was higher in southern latitudes and this species was not encountered beyond 62 °N whereas O. chloropus and P. azurea occurred across the whole range of latitudes. The prevalence of O. chloropus further increased with increasing distance from the coast – a pattern not documented before. The three fly species showed no interspecific associations in their prevalence. Conclusions Our study revealed relatively high prevalence for all the species (O. chloropus 59 %, O. avicularia 20 %, P. azurea 32 %), and an interesting spatial pattern in the prevalence of the two louse fly species. Our sample did not indicate any major range shifts towards the north for the southern species as compared to the information from the past. Morphological identification of O. chloropus did not match with the corresponding sequences published in the GenBank and taxonomy of this group calls for further studies.
  • Bofah, Emmanuel A; Hannula, Markku S (Springer US, 2015)
    Abstract Relationships among motivational constructs from the 2011 Trends in International Mathematics and Science Study (TIMSS 2011) were investigated for eight-graders in all the five participating African countries, representing 38,806 (49 % girls). First, we investigated the psychometric properties (factor structure, reliabilities, method effect, and measurement invariance—country and gender) of the mathematics motivational constructs across the five educational systems. There was empirical support for the multidimensionality of the construct and the TIMSS 2011 motivational construct was largely invariant across cultures. Furthermore, a series of confirmatory factor analyses revealed that there is a need to control method effects associated with negatively worded items in the measurement model. There was support suggesting that in many cultures responses to negatively worded items are systematically different. The factor structures and reliabilities (i.e., confidence and the like mathematics scales) were affected by negatively worded items. Second, the relationships between the constructs, achievements and background variables such as parental education, gender and students’ educational aspirations were investigated. We identified several significant relationships between self-belief and mathematics achievement. Differences in the latent mean achievement and the motivational construct were similar to those that have been described in the literature as “paradoxical” and “perplexing”. Nations with high mathematics achievement seem to have students with more negative mathematics self-belief. Some results extend, whereas others refute the findings of previous research. For instance, the relationship between students’ mathematics confidence and mathematics achievement was lower than the relationship between the value of mathematics and achievement in some countries and it was the reverse in others. However, consistent with cultural stereotypes, boys rated their mathematics competence higher than girls. The findings are discussed with reference to implications for cross-cultural research and practice.
  • Seibold, Petra; Schmezer, Peter; Behrens, Sabine; Michailidou, Kyriaki; Bolla, Manjeet K; Wang, Qin; Flesch-Janys, Dieter; Nevanlinna, Heli; Fagerholm, Rainer; Aittomäki, Kristiina; Blomqvist, Carl; Margolin, Sara; Mannermaa, Arto; Kataja, Vesa; Kosma, Veli-Matti; Hartikainen, Jaana M; Lambrechts, Diether; Wildiers, Hans; Kristensen, Vessela; Alnæs, Grethe G; Nord, Silje; Borresen-Dale, Anne-Lise; Hooning, Maartje J; Hollestelle, Antoinette; Jager, Agnes; Seynaeve, Caroline; Li, Jingmei; Liu, Jianjun; Humphreys, Keith; Dunning, Alison M; Rhenius, Valerie; Shah, Mitul; Kabisch, Maria; Torres, Diana; Ulmer, Hans-Ulrich; Hamann, Ute; Schildkraut, Joellen M; Purrington, Kristen S; Couch, Fergus J; Hall, Per; Pharoah, Paul; Easton, Doug F; Schmidt, Marjanka K; Chang-Claude, Jenny; Popanda, Odilia (BioMed Central, 2015)
    Abstract Background Personalized therapy considering clinical and genetic patient characteristics will further improve breast cancer survival. Two widely used treatments, chemotherapy and radiotherapy, can induce oxidative DNA damage and, if not repaired, cell death. Since base excision repair (BER) activity is specific for oxidative DNA damage, we hypothesized that germline genetic variation in this pathway will affect breast cancer-specific survival depending on treatment. Methods We assessed in 1,408 postmenopausal breast cancer patients from the German MARIE study whether cancer specific survival after adjuvant chemotherapy, anthracycline chemotherapy, and radiotherapy is modulated by 127 Single Nucleotide Polymorphisms (SNPs) in 21 BER genes. For SNPs with interaction terms showing p < 0.1 (likelihood ratio test) using multivariable Cox proportional hazard analyses, replication in 6,392 patients from nine studies of the Breast Cancer Association Consortium (BCAC) was performed. Results rs878156 in PARP2 showed a differential effect by chemotherapy (p = 0.093) and was replicated in BCAC studies (p = 0.009; combined analysis p = 0.002). Compared to non-carriers, carriers of the variant G allele (minor allele frequency = 0.07) showed better survival after chemotherapy (combined allelic hazard ratio (HR) = 0.75, 95 % 0.53–1.07) and poorer survival when not treated with chemotherapy (HR = 1.42, 95 % 1.08–1.85). A similar effect modification by rs878156 was observed for anthracycline-based chemotherapy in both MARIE and BCAC, with improved survival in carriers (combined allelic HR = 0.73, 95 % CI 0.40–1.32). None of the SNPs showed significant differential effects by radiotherapy. Conclusions Our data suggest for the first time that a SNP in PARP2, rs878156, may together with other genetic variants modulate cancer specific survival in breast cancer patients depending on chemotherapy. These germline SNPs could contribute towards the design of predictive tests for breast cancer patients.
  • Roine, Ulrika; Roine, Timo; Salmi, Juha; Nieminen-von Wendt, Taina; Tani, Pekka; Leppämäki, Sami; Rintahaka, Pertti; Caeyenberghs, Karen; Leemans, Alexander; Sams, Mikko (BioMed Central, 2015)
    Abstract Background Recent brain imaging findings suggest that there are widely distributed abnormalities affecting the brain connectivity in individuals with autism spectrum disorder (ASD). Using graph theoretical analysis, it is possible to investigate both global and local properties of brain’s wiring diagram, i.e., the connectome. Methods We acquired diffusion-weighted magnetic resonance imaging data from 14 adult males with high-functioning ASD and 19 age-, gender-, and IQ-matched controls. As with diffusion tensor imaging-based tractography, it is not possible to detect complex (e.g., crossing) fiber configurations, present in 60–90 % of white matter voxels; we performed constrained spherical deconvolution-based whole brain tractography. Unweighted and weighted structural brain networks were then reconstructed from these tractography data and analyzed with graph theoretical measures. Results In subjects with ASD, global efficiency was significantly decreased both in the unweighted and the weighted networks, normalized characteristic path length was significantly increased in the unweighted networks, and strength was significantly decreased in the weighted networks. In the local analyses, betweenness centrality of the right caudate was significantly increased in the weighted networks, and the strength of the right superior temporal pole was significantly decreased in the unweighted networks in subjects with ASD. Conclusions Our findings provide new insights into understanding ASD by showing that the integration of structural brain networks is decreased and that there are abnormalities in the connectivity of the right caudate and right superior temporal pole in subjects with ASD.
  • Ritari, Jarmo; Salojärvi, Jarkko; Lahti, Leo; de Vos, Willem M (BioMed Central, 2015)
    Abstract Background Current sequencing technology enables taxonomic profiling of microbial ecosystems at high resolution and depth by using the 16S rRNA gene as a phylogenetic marker. Taxonomic assignation of newly acquired data is based on sequence comparisons with comprehensive reference databases to find consensus taxonomy for representative sequences. Nevertheless, even with well-characterised ecosystems like the human intestinal microbiota it is challenging to assign genus and species level taxonomy to 16S rRNA amplicon reads. A part of the explanation may lie in the sheer size of the search space where competition from a multitude of highly similar sequences may not allow reliable assignation at low taxonomic levels. However, when studying a particular environment such as the human intestine, it can be argued that a reference database comprising only sequences that are native to the environment would be sufficient, effectively reducing the search space. Results We constructed a 16S rRNA gene database based on high-quality sequences specific for human intestinal microbiota, resulting in curated data set consisting of 2473 unique prokaryotic species-like groups and their taxonomic lineages, and compared its performance against the Greengenes and Silva databases. The results showed that regardless of used assignment algorithm, our database improved taxonomic assignation of 16S rRNA sequencing data by enabling significantly higher species and genus level assignation rate while preserving taxonomic diversity and demanding less computational resources. Conclusion The curated human intestinal 16S rRNA gene taxonomic database of about 2500 species-like groups described here provides a practical solution for significantly improved taxonomic assignment for phylogenetic studies of the human intestinal microbiota.
  • McAneney, Helen; Tully, Mark A; Hunter, Ruth F; Kouvonen, Anne; Veal, Philip; Stevenson, Michael; Kee, Frank (BioMed Central, 2015)
    Abstract Background It has been argued that though correlated with mental health, mental well-being is a distinct entity. Despite the wealth of literature on mental health, less is known about mental well-being. Mental health is something experienced by individuals, whereas mental well-being can be assessed at the population level. Accordingly it is important to differentiate the individual and population level factors (environmental and social) that could be associated with mental health and well-being, and as people living in deprived areas have a higher prevalence of poor mental health, these relationships should be compared across different levels of neighbourhood deprivation. Methods A cross-sectional representative random sample of 1,209 adults from 62 Super Output Areas (SOAs) in Belfast, Northern Ireland (Feb 2010 – Jan 2011) were recruited in the PARC Study. Interview-administered questionnaires recorded data on socio-demographic characteristics, health-related behaviours, individual social capital, self-rated health, mental health (SF-8) and mental well-being (WEMWBS). Multi-variable linear regression analyses, with inclusion of clustering by SOAs, were used to explore the associations between individual and perceived community characteristics and mental health and mental well-being, and to investigate how these associations differed by the level of neighbourhood deprivation. Results Thirty-eight and 30 % of variability in the measures of mental well-being and mental health, respectively, could be explained by individual factors and the perceived community characteristics. In the total sample and stratified by neighbourhood deprivation, age, marital status and self-rated health were associated with both mental health and well-being, with the ‘social connections’ and local area satisfaction elements of social capital also emerging as explanatory variables. An increase of +1 in EQ-5D-3 L was associated with +1SD of the population mean in both mental health and well-being. Similarly, a change from ‘very dissatisfied’ to ‘very satisfied’ for local area satisfaction would result in +8.75 for mental well-being, but only in the more affluent of areas. Conclusions Self-rated health was associated with both mental health and mental well-being. Of the individual social capital explanatory variables, ‘social connections’ was more important for mental well-being. Although similarities in the explanatory variables of mental health and mental well-being exist, socio-ecological interventions designed to improve them may not have equivalent impacts in rich and poor neighbourhoods.