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  • Seo, Seung B; Zeng, Xiangpei; King, Jonathan L; Larue, Bobby L; Assidi, Mourad; Al-Qahtani, Mohamed H; Sajantila, Antti; Budowle, Bruce (BioMed Central, 2015)
    Abstract Background Massively parallel sequencing (MPS) technologies have the capacity to sequence targeted regions or whole genomes of multiple nucleic acid samples with high coverage by sequencing millions of DNA fragments simultaneously. Compared with Sanger sequencing, MPS also can reduce labor and cost on a per nucleotide basis and indeed on a per sample basis. In this study, whole genomes of human mitochondria (mtGenome) were sequenced on the Personal Genome Machine (PGMTM) (Life Technologies, San Francisco, CA), the out data were assessed, and the results were compared with data previously generated on the MiSeqTM (Illumina, San Diego, CA). The objectives of this paper were to determine the feasibility, accuracy, and reliability of sequence data obtained from the PGM. Results 24 samples were multiplexed (in groups of six) and sequenced on the at least 10 megabase throughput 314 chip. The depth of coverage pattern was similar among all 24 samples; however the coverage across the genome varied. For strand bias, the average ratio of coverage between the forward and reverse strands at each nucleotide position indicated that two-thirds of the positions of the genome had ratios that were greater than 0.5. A few sites had more extreme strand bias. Another observation was that 156 positions had a false deletion rate greater than 0.15 in one or more individuals. There were 31-98 (SNP) mtGenome variants observed per sample for the 24 samples analyzed. The total 1237 (SNP) variants were concordant between the results from the PGM and MiSeq. The quality scores for haplogroup assignment for all 24 samples ranged between 88.8%-100%. Conclusions In this study, mtDNA sequence data generated from the PGM were analyzed and the output evaluated. Depth of coverage variation and strand bias were identified but generally were infrequent and did not impact reliability of variant calls. Multiplexing of samples was demonstrated which can improve throughput and reduce cost per sample analyzed. Overall, the results of this study, based on orthogonal concordance testing and phylogenetic scrutiny, supported that whole mtGenome sequence data with high accuracy can be obtained using the PGM platform.
  • Seo, Seung Bum; Zeng, Xiangpei; King, Jonathan L; Larue, Bobby L; Assidi, Mourad; Al-Qahtani, Mohamed H; Sajantila, Antti; Budowle, Bruce (BioMed Central Ltd, 2015)
    Abstract Background Massively parallel sequencing (MPS) technologies have the capacity to sequence targeted regions or whole genomes of multiple nucleic acid samples with high coverage by sequencing millions of DNA fragments simultaneously. Compared with Sanger sequencing, MPS also can reduce labor and cost on a per nucleotide basis and indeed on a per sample basis. In this study, whole genomes of human mitochondria (mtGenome) were sequenced on the Personal Genome Machine (PGMTM) (Life Technologies, San Francisco, CA), the out data were assessed, and the results were compared with data previously generated on the MiSeqTM (Illumina, San Diego, CA). The objectives of this paper were to determine the feasibility, accuracy, and reliability of sequence data obtained from the PGM. Results 24 samples were multiplexed (in groups of six) and sequenced on the at least 10 megabase throughput 314 chip. The depth of coverage pattern was similar among all 24 samples; however the coverage across the genome varied. For strand bias, the average ratio of coverage between the forward and reverse strands at each nucleotide position indicated that two-thirds of the positions of the genome had ratios that were greater than 0.5. A few sites had more extreme strand bias. Another observation was that 156 positions had a false deletion rate greater than 0.15 in one or more individuals. There were 31-98 (SNP) mtGenome variants observed per sample for the 24 samples analyzed. The total 1237 (SNP) variants were concordant between the results from the PGM and MiSeq. The quality scores for haplogroup assignment for all 24 samples ranged between 88.8%-100%. Conclusions In this study, mtDNA sequence data generated from the PGM were analyzed and the output evaluated. Depth of coverage variation and strand bias were identified but generally were infrequent and did not impact reliability of variant calls. Multiplexing of samples was demonstrated which can improve throughput and reduce cost per sample analyzed. Overall, the results of this study, based on orthogonal concordance testing and phylogenetic scrutiny, supported that whole mtGenome sequence data with high accuracy can be obtained using the PGM platform.
  • Myllärniemi, Marjukka; Tikkanen, Jussi; Hulmi, Juha J; Pasternack, Arja; Sutinen, Eva; Rönty, Mikko; Leppäranta, Outi; Ma, Hongqiang; Ritvos, Olli; Koli, Katri (BioMed Central Ltd, 2014)
    Abstract Background Activins are members of the TGF-ß superfamily of growth factors. First, we identified by expression array screening that activin-B and follistatin are upregulated in human idiopathic pulmonary fibrosis (IPF). Next, we wanted to clarify their specific role in lung fibrosis formation. Methods We used specific antibodies for activin-A and -B subunits and follistatin to measure and localize their levels in idiopathic pulmonary fibrosis and control lung biopsies. To inhibit activin signaling, we used soluble activin type IIB receptor fused to the Fc portion of human IgG1 (sActRIIB-Fc) in two different mouse models of pulmonary fibrosis. Results Activin-B and follistatin mRNA levels were elevated in the human IPF lung. Immunoreactivity to activin-A, -B and follistatin localized predominantly to the hyperplastic, activated alveolar epithelium, but was also seen in inflammatory cells. Mice treated with sActRIIB-Fc showed increased skeletal muscle mass and a clear reduction in alveolar cell counts in bronchoalveolar lavage fluid, but no significant antifibrotic effect in the lung was observed. Conclusions The upregulation of activin-B and follistatin in IPF is a novel finding. Our results indicate that activin inhibition is not an efficient tool for antifibrotic therapy, but could be useful in reducing alveolar cellular response to injury. Activin-B and follistatin levels may be useful as biomarkers of IPF.
  • van de Bunt, Bert; Bron, Peter A; Sijtsma, Lolke; de Vos, Willem M; Hugenholtz, Jeroen (BioMed Central Ltd, 2014)
    Abstract Background Lactococcus lactis is a lactic acid bacterium that has been used for centuries in the production of a variety of cheeses, as these bacteria rapidly acidify milk and greatly contribute to the flavour of the fermentation end-products. After a short growth phase during cheese ripening L. lactis enters an extended non-growing state whilst still strongly contributing to amino acid-derived flavour formation. Here, a research approach is presented that allows investigation of strain- and amino acid-specific flavour formation during the non-growing state. Results Non-growing cells of five selected L. lactis strains were demonstrated to degrade amino acids into flavour compounds that are relevant in food fermentations and differs greatly from production of flavour compounds using growing cells. As observed earlier in other research set-ups and with other microorganisms, addition of NADH, α-ketoglutarate and pyridoxal-5-phosphate was demonstrated to be essential for optimal flavour formation, suggesting that intracellular pools of these substrates are too low for the significant production of the flavour compounds. Production of flavours during the non-growing phase strongly depends on the individual amino acids that were supplied, on the presence of other amino acids (mixtures versus single compounds), and on the strain used. Moreover, we observed that the plasmid-free model strains L. lactis MG1363 and IL1403 produce relatively low amounts of flavour components under the various conditions tested. Conclusions By using this simplified and rapid approach to study flavour formation by non-growing lactic acid bacteria, lengthy ripening periods are no longer required to assess the capacity of strains to produce flavours in the long, non-growing state of dairy fermentation. In addition, this method also provides insight into the conversion of single amino acids versus the conversion of a mixture of amino acids as produced during protein degradation. The generated results are complementary to earlier generated datasets using growing cells, allowing assessment of the full flavour forming potential of strains used as starter cultures in industrial food fermentation processes.
  • Presseau, Justin; Ivers, Noah M; Newham, James J; Knittle, Keegan; Danko, Kristin J; Grimshaw, Jeremy M (BioMed Central, 2015)
    Abstract Background Methodological guidelines for intervention reporting emphasise describing intervention content in detail. Despite this, systematic reviews of quality improvement (QI) implementation interventions continue to be limited by a lack of clarity and detail regarding the intervention content being evaluated. We aimed to apply the recently developed Behaviour Change Techniques Taxonomy version 1 (BCTTv1) to trials of implementation interventions for managing diabetes to assess the capacity and utility of this taxonomy for characterising active ingredients. Methods Three psychologists independently coded a random sample of 23 trials of healthcare system, provider- and/or patient-focused implementation interventions from a systematic review that included 142 such studies. Intervention content was coded using the BCTTv1, which describes 93 behaviour change techniques (BCTs) grouped within 16 categories. We supplemented the generic coding instructions within the BCTTv1 with decision rules and examples from this literature. Results Less than a quarter of possible BCTs within the BCTTv1 were identified. For implementation interventions targeting providers, the most commonly identified BCTs included the following: adding objects to the environment, prompts/cues, instruction on how to perform the behaviour, credible source, goal setting (outcome), feedback on outcome of behaviour, and social support (practical). For implementation interventions also targeting patients, the most commonly identified BCTs included the following: prompts/cues, instruction on how to perform the behaviour, information about health consequences, restructuring the social environment, adding objects to the environment, social support (practical), and goal setting (behaviour). The BCTTv1 mapped well onto implementation interventions directly targeting clinicians and patients and could also be used to examine the impact of system-level interventions on clinician and patient behaviour. Conclusions The BCTTv1 can be used to characterise the active ingredients in trials of implementation interventions and provides specificity of content beyond what is given by broader intervention labels. Identification of BCTs may provide a more helpful means of accumulating knowledge on the content used in trials of implementation interventions, which may help to better inform replication efforts. In addition, prospective use of a behaviour change techniques taxonomy for developing and reporting intervention content would further aid in building a cumulative science of effective implementation interventions.
  • Hemminki, Elina; Virtanen, Jorma I; Veerus, Piret (BioMed Central Ltd, 2014)
    Abstract Background To present empirical data on how the variation in regulating clinical research and patient care was perceived in Finland between 2009 and 2012. Methods Notes of interviews with 22 research ethics committee (REC) chairpersons were analyzed to identify whether differences in the regulation of clinical research and patient care were addressed. REC chairpersons’ opinions on three imaginary cases of clinical research projects challenging current research ethics rules (vignettes) were requested with a questionnaire; 18 of the 22 interviewed chairpersons responded. Results Based on REC chairpersons’ interviews, the differences between care and research regulation were not considered important issues in Finland. In the vignettes, REC chairpersons’ assumptions on how their REC would decide varied in regard to allowing research without informed consent, while solutions that are not allowed by current law were even anticipated. Mostly, but not always, the chairpersons’ own personal view agreed with their REC. Conclusions The distinction between care and research regulation has not been publicly challenged by Finnish RECs, even though it is a challenge when research relevant to health care is carried out. There is a need for debate and changes in laws and practices.
  • Hemilä, Harri; Al-Biltagi, Mohammed; Baset, Ahmed A (BioMed Central Ltd, 2011)
    Abstract Background We previously found a significant benefit of vitamin C supplementation in asthmatic children. Purpose To test whether the effect of vitamin C on asthma is heterogeneous over the participant population. Methods Egyptian asthmatic children between 7 and 10 years of age (n = 60) were included in the cross-over trial. They were administered 0.2 grams per day of vitamin C and placebo for separate 6-week periods. The variation in the vitamin C effect on two clinically relevant outcomes was analyzed: the childhood asthma control test (C-ACT), which measures the severity of asthma symptoms (the scale ranges from 0 to 27 points, < 20 points indicating unsatisfactory asthma control), and FEV1. We used linear modeling to examine the variation of the vitamin C effect in the subgroups. Results The effect of vitamin C on the C-ACT was significantly modified by age and baseline C-ACT levels. In the children aged 7.0-8.2 years with a baseline C-ACT of 18 to 19 points, vitamin C increased the C-ACT score by 4.2 points (95% CI: 3.3-5.3); whereas in the children aged 8.3-10 years who had a baseline C-ACT of 14 to 15 points, vitamin C increased the C-ACT score by only 1.3 points (95% CI: 0.1-2.5). The effect of vitamin C on the FEV1 levels was significantly modified by age and exposure to dampness. In the children aged 7.0-8.2 years with no exposure to dampness, vitamin C increased the FEV1 level by 37% (95% CI: 34-40%), whereas in the children aged 8.3-10 years with exposure to dampness or mold in their bedroom more than one year prior to the study, vitamin C increased the FEV1 level by only 21% (95% CI: 18-25%). Conclusions We found strong evidence that the effect of vitamin C on asthmatic children is heterogeneous. Further research is needed to confirm our findings and identify the groups of children who would receive the greatest benefit from vitamin C supplementation.
  • Mikonranta, Lauri; Mappes, Johanna; Laakso, Jouni; Ketola, Tarmo (BioMed Central, 2015)
    Abstract Background Pathogens evolve in a close antagonistic relationship with their hosts. The conventional theory proposes that evolution of virulence is highly dependent on the efficiency of direct host-to-host transmission. Many opportunistic pathogens, however, are not strictly dependent on the hosts due to their ability to reproduce in the free-living environment. Therefore it is likely that conflicting selection pressures for growth and survival outside versus within the host, rather than transmission potential, shape the evolution of virulence in opportunists. We tested the role of within-host selection in evolution of virulence by letting a pathogen Serratia marcescens db11 sequentially infect Drosophila melanogaster hosts and then compared the virulence to strains that evolved only in the outside-host environment. Results We found that the pathogen adapted to both Drosophila melanogaster host and novel outside-host environment, leading to rapid evolutionary changes in the bacterial life-history traits including motility, in vitro growth rate, biomass yield, and secretion of extracellular proteases. Most significantly, selection within the host led to decreased virulence without decreased bacterial load while the selection lines in the outside-host environment maintained the same level of virulence with ancestral bacteria. Conclusions This experimental evidence supports the idea that increased virulence is not an inevitable consequence of within-host adaptation even when the epidemiological restrictions are removed. Evolution of attenuated virulence could occur because of immune evasion within the host. Alternatively, rapid fluctuation between outside-host and within-host environments, which is typical for the life cycle of opportunistic bacterial pathogens, could lead to trade-offs that lower pathogen virulence.
  • Sartelli, Massimo; Viale, Pierluigi; Koike, Kaoru; Pea, Federico; Tumietto, Fabio; van Goor, Harry; Guercioni, Gianluca; Nespoli, Angelo; Tranà, Cristian; Catena, Fausto; Ansaloni, Luca; Leppaniemi, Ari; Biffl, Walter; Moore, Frederick A; Poggetti, Renato; Pinna, Antonio D; Moore, Ernest E (BioMed Central Ltd, 2011)
    Abstract Intra-abdominal infections are still associated with high rate of morbidity and mortality. A multidisciplinary approach to the management of patients with intra-abdominal infections may be an important factor in the quality of care. The presence of a team of health professionals from various disciplines, working in concert, may improve efficiency, outcome, and the cost of care. A World Society of Emergency Surgery (WSES) Consensus Conference was held in Bologna on July 2010, during the 1st congress of the WSES, involving surgeons, infectious disease specialists, pharmacologists, radiologists and intensivists with the goal of defining recommendations for the early management of intra-abdominal infections. This document represents the executive summary of the final guidelines approved by the consensus conference.
  • Remes, Hanna; Martikainen, Pekka (BioMed Central, 2015)
    Abstract Background Sociodemographic differences in injury mortality are well-established, but population-level studies on social patterns of injury morbidity remain few in numbers, particularly among young adults. Yet injuries are the leading cause of mortality, morbidity and disability among young people. Studies among children have shown steep social gradients in severe injuries, but less is known on the social patterning of injuries in late adolescence and early adulthood, when young people are in the process of becoming independent adults. This study examines how young adults’ current living arrangements, education, main economic activity, and parental social background are associated with hospital-treated injuries in late adolescence and early adulthood. Methods The study uses prospective, individual-level data gathered from several administrative sources. From a representative 11% sample of the total Finnish population, we included young people between ages 17–29 years during the follow-up (N = 134 938). We used incidence rates and Cox proportional hazards models to study hospital-treated injuries and poisonings in 1998–2008. Results Higher rates of injury were found among young adults living alone, single mothers, the lower educated and the non-employed, as well as those with lower parental social background, experience of childhood family changes or living with a single parent, and those who had left the parental home at a young age. Injury risks were consistently higher among young adults with lower education, but current living arrangements and main economic activity showed some age-related nuances in the associations: both earlier and later than average transitions in education, employment, and family formation associated with increased injury risks. The social differentials were strongest in poisonings, intentional self-harm, and assaults, but social patterns were also found in falls, traffic-related injuries and other unintentional injuries, underlining the existence of multiple distinct mechanisms and pathways behind the differentials. Conclusions The transition to adulthood is a life period of heightened risk of injury, during which both parental social background and the young people’s own social position are important determinants of serious injuries that require inpatient care.
  • Syrjänen, Leo; Valanne, Susanna; Kuuslahti, Marianne; Tuomela, Tea; Sriram, Ashwin; Sanz, Alberto; Jacobs, Howard T; Rämet, Mika; Parkkila, Seppo (BioMed Central, 2015)
    Abstract Background Carbonic anhydrases (CAs, EC 4.2.1.1) are ubiquitous enzymes that catalyze the reversible hydration reaction of carbon dioxide. CAs are present as six structurally divergent enzyme families: α, β, γ, δ, ζ and η. β-CAs have a wide distribution across different species including invertebrates. Previously, we showed that Drosophila melanogaster β-CA is a highly active mitochondrial enzyme. In this study, we investigated the function of Drosophila β-CA by silencing the expression of the β-CA gene using UAS/GAL4-based RNA interference (RNAi) in Drosophila in vivo. Results Crossing β-CA RNAi lines over ubiquitous Actin driver flies did not produce any viable progeny, indicating that β-CA expression is required for fly development. RNAi silencing of β-CA ubiquitously in adult flies did not affect their survival rate or function of mitochondrial electron transport chain. Importantly, β-CA RNAi led to impaired reproduction. All β-CA knockdown females were sterile, and produced few or no eggs. Whole ovaries of knockdown females looked normal but upon cadherin staining, there was an apparent functional defect in migration of border cells, which are considered essential for normal fertilization. Conclusions These results indicate that although Drosophila β-CA is dispensable for survival of adult flies, it is essential for female fertility.