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  • Kainulainen, Veera; Tang, Yurui; Spillmann, Thomas; Kilpinen, Susanne; Reunanen, Justus; Saris, Per E; Satokari, Reetta (BioMed Central, 2015)
    Abstract Background For a good probiotic candidate, the abilities to adhere to intestinal epithelium and to fortify barrier function are considered to be crucial for colonization and functionality of the strain. The strain Lactobacillus acidophilus LAB20 was isolated from the jejunum of a healthy dog, where it was found to be the most pre-dominant lactobacilli. In this study, the adhesion ability of LAB20 to intestinal epithelial cell (IECs) lines, IECs isolated from canine intestinal biopsies, and to canine, porcine and human intestinal mucus was investigated. Further, we studied the ability of LAB20 to fortify the epithelial cell monolayer and to reduce LPS-induced interleukin (IL-8) release from enterocytes. Results We found that LAB20 presented higher adhesion to canine colonic mucus as compared to mucus isolated from porcine colon. LAB20 showed adhesion to HT-29 and Caco-2 cell lines, and importantly also to canine IECs isolated from canine intestinal biopsies. In addition, LAB20 increased the transepithelial electrical resistance (TER) of enterocyte monolayers and thus strengthened the intestinal barrier function. The strain showed also anti-inflammatory capacity in being able to attenuate the LPS-induced IL-8 production of HT-29 cells. Conclusion In conclusion, canine indigenous strain LAB20 is a potential probiotic candidate for dogs adhering to the host epithelium and showing intestinal barrier fortifying and anti-inflammatory effects.
  • Kainulainen, Veera; Tang, Yurui; Spillmann, Thomas; Kilpinen, Susanne; Reunanen, Justus; Saris, Per EJ; Satokari, Reetta (BioMed Central Ltd, 2015)
    Abstract Background For a good probiotic candidate, the abilities to adhere to intestinal epithelium and to fortify barrier function are considered to be crucial for colonization and functionality of the strain. The strain Lactobacillus acidophilus LAB20 was isolated from the jejunum of a healthy dog, where it was found to be the most pre-dominant lactobacilli. In this study, the adhesion ability of LAB20 to intestinal epithelial cell (IECs) lines, IECs isolated from canine intestinal biopsies, and to canine, porcine and human intestinal mucus was investigated. Further, we studied the ability of LAB20 to fortify the epithelial cell monolayer and to reduce LPS-induced interleukin (IL-8) release from enterocytes. Results We found that LAB20 presented higher adhesion to canine colonic mucus as compared to mucus isolated from porcine colon. LAB20 showed adhesion to HT-29 and Caco-2 cell lines, and importantly also to canine IECs isolated from canine intestinal biopsies. In addition, LAB20 increased the transepithelial electrical resistance (TER) of enterocyte monolayers and thus strengthened the intestinal barrier function. The strain showed also anti-inflammatory capacity in being able to attenuate the LPS-induced IL-8 production of HT-29 cells. Conclusion In conclusion, canine indigenous strain LAB20 is a potential probiotic candidate for dogs adhering to the host epithelium and showing intestinal barrier fortifying and anti-inflammatory effects.
  • van Raalte, Alyson A; Kunst, Anton E; Lundberg, Olle; Leinsalu, Mall; Martikainen, Pekka; Artnik, Barbara; Deboosere, Patrick; Stirbu, Irina; Wojtyniak, Bogdan; Mackenbach, Johan P (BioMed Central Ltd, 2012)
    Abstract Background Studies of socioeconomic inequalities in mortality consistently point to higher death rates in lower socioeconomic groups. Yet how these between-group differences relate to the total variation in mortality risk between individuals is unknown. Methods We used data assembled and harmonized as part of the Eurothine project, which includes census-based mortality data from 11 European countries. We matched this to national data from the Human Mortality Database and constructed life tables by gender and educational level. We measured variation in age at death using Theil's entropy index, and decomposed this measure into its between- and within-group components. Results The least-educated groups lived between three and 15 years fewer than the highest-educated groups, the latter having a more similar age at death in all countries. Differences between educational groups contributed between 0.6% and 2.7% to total variation in age at death between individuals in Western European countries and between 1.2% and 10.9% in Central and Eastern European countries. Variation in age at death is larger and differs more between countries among the least-educated groups. Conclusions At the individual level, many known and unknown factors are causing enormous variation in age at death, socioeconomic position being only one of them. Reducing variations in age at death among less-educated people by providing protection to the vulnerable may help to reduce inequalities in mortality between socioeconomic groups.
  • Fabritius, Henna; Rönkä, Katja; Ovaskainen, Otso (BioMed Central, 2015)
    Abstract Background Species movement responses to landscape structures have been studied using a variety of methods, but movement research is still in need of simple methods that help predicting and comparing movements across structurally different landscapes. We demonstrate how habitat-specific movement models can be used to disentangle causes of differentiated movement patterns in structurally different landscapes and to predict movement patterns in altered and artificial landscapes. In our case study, we studied the role of riparian landscapes to the persistence of the endangered false heath fritillary butterfly (Melitaea diamina) in its newly discovered coastal distribution region in Finland. We compared the movement parameters of the riparian population to two reference populations by using capture-recapture data and habitat-specific diffusion modelling, and analysed the role of the river and riverbank buffer zones in facilitating or hindering false heath fritillary movement with movement simulations. Results The riparian population of the false heath fritillary did not show major differences to reference populations in terms of movement parameters within breeding habitat, high-quality matrix and low-quality matrix. However, movement simulations showed that the habitat-specific movement parameters estimated for the false heath fritillary can lead into markedly different movement patterns in structurally different landscapes. An artificial riparian landscape mimicking those of the coastal distribution resulted into more directional, longitudinal movements both parallel and perpendicular to the river than a more mosaic-like landscape, but the existence of the river in the landscape reduced movements across the river. Conclusions Our study demonstrates how habitat-specific movement models enable comparisons of movement patterns across structurally different real, altered and artificial landscapes. As such, they can be used to compare movement parameters across populations, to study the effects of management interventions to endangered species and to identify areas that have high sensitivity to individual movement. In our case study, the river is shown to perform a dual role for the movements of the riparian false heath fritillary population. Whereas the river acts as a moderate movement barrier for the false heath fritillary, the longitudinal configuration of riverbank habitats provides a means especially for the male false heath fritillaries to move across the landscape.
  • Hemilä, Harri; Chalker, Elizabeth (BioMed Central, 2015)
    Abstract Background A previous meta-analysis found that high dose zinc acetate lozenges reduced the duration of common colds by 42%, whereas low zinc doses had no effect. Lozenges are dissolved in the pharyngeal region, thus there might be some difference in the effect of zinc lozenges on the duration of respiratory symptoms in the pharyngeal region compared with the nasal region. The objective of this study was to determine whether zinc acetate lozenges have different effects on the duration of common cold symptoms originating from different anatomical regions. Methods We analyzed three randomized trials on zinc acetate lozenges for the common cold administering zinc in doses of 80–92 mg/day. All three trials reported the effect of zinc on seven respiratory symptoms, and three systemic symptoms. We pooled the effects of zinc lozenges for each symptom and calculated point estimates and 95% confidence intervals (95% CI). Results Zinc acetate lozenges shortened the duration of nasal discharge by 34% (95% CI: 17% to 51%), nasal congestion by 37% (15% to 58%), sneezing by 22% (−1% to 45%), scratchy throat by 33% (8% to 59%), sore throat by 18% (−10% to 46%), hoarseness by 43% (3% to 83%), and cough by 46% (28% to 64%). Zinc lozenges shortened the duration of muscle ache by 54% (18% to 89%), but there was no difference in the duration of headache and fever. Conclusions The effect of zinc acetate lozenges on cold symptoms may be associated with the local availability of zinc from the lozenges, with the levels being highest in the pharyngeal region. However our findings indicate that the effects of zinc ions are not limited to the pharyngeal region. There is no indication that the effect of zinc lozenges on nasal symptoms is less than the effect on the symptoms of the pharyngeal region, which is more exposed to released zinc ions. Given that the adverse effects of zinc in the three trials were minor, zinc acetate lozenges releasing zinc ions at doses of about 80 mg/day may be a useful treatment for the common cold, started within 24 hours, for a time period of less than two weeks.
  • Hemilä, Harri (BioMed Central Ltd, 2014)
    Abstract Physical activity increases oxidative stress and therefore the antioxidant effects of vitamin C administration might become evident in people undertaking vigorous exercise. Vitamin C is involved in the metabolism of histamine, prostaglandins, and cysteinyl leukotrienes, all of which appear to be mediators in the pathogenesis of exercise-induced bronchoconstriction (EIB). Three studies assessing the effect of vitamin C on patients with EIB were subjected to a meta-analysis and revealed that vitamin C reduced postexercise FEV1 decline by 48% (95% CI: 33% to 64%). The correlation between postexercise FEV1 decline and respiratory symptoms associated with exercise is poor, yet symptoms are the most relevant to patients. Five other studies examined subjects who were under short-term, heavy physical stress and revealed that vitamin C reduced the incidence of respiratory symptoms by 52% (95% CI: 36% to 65%). Another trial reported that vitamin C halved the duration of the respiratory symptoms in male adolescent competitive swimmers. Although FEV1 is the standard outcome for assessing EIB, other outcomes may provide additional information. In particular, the mean postexercise decline of FEF50 is twice the decline of FEV1. Schachter and Schlesinger (1982) reported the effect of vitamin C on exercise-induced FEF60 levels in 12 patients suffering from EIB and their data are analyzed in this paper. The postexercise FEF60 decline was greater than 60% for five participants and such a dramatic decline indicates that the absolute postexercise FEF60 level becomes an important outcome in its own right. Vitamin C increased postexercise FEF60 levels by 50% to 150% in those five participants, but had no significant effect in the other seven participants. Thus, future research on the effects of vitamin C on EIB should not be restricted to measuring only FEV1. Vitamin C is inexpensive and safe, and further study on those people who have EIB or respiratory symptoms associated with exercise is warranted.
  • Hemilä, Harri (BioMed Central, 2014)
    Abstract Physical activity increases oxidative stress and therefore the antioxidant effects of vitamin C administration might become evident in people undertaking vigorous exercise. Vitamin C is involved in the metabolism of histamine, prostaglandins, and cysteinyl leukotrienes, all of which appear to be mediators in the pathogenesis of exercise-induced bronchoconstriction (EIB). Three studies assessing the effect of vitamin C on patients with EIB were subjected to a meta-analysis and revealed that vitamin C reduced postexercise FEV1 decline by 48% (95% CI: 33% to 64%). The correlation between postexercise FEV1 decline and respiratory symptoms associated with exercise is poor, yet symptoms are the most relevant to patients. Five other studies examined subjects who were under short-term, heavy physical stress and revealed that vitamin C reduced the incidence of respiratory symptoms by 52% (95% CI: 36% to 65%). Another trial reported that vitamin C halved the duration of the respiratory symptoms in male adolescent competitive swimmers. Although FEV1 is the standard outcome for assessing EIB, other outcomes may provide additional information. In particular, the mean postexercise decline of FEF50 is twice the decline of FEV1. Schachter and Schlesinger (1982) reported the effect of vitamin C on exercise-induced FEF60 levels in 12 patients suffering from EIB and their data are analyzed in this paper. The postexercise FEF60 decline was greater than 60% for five participants and such a dramatic decline indicates that the absolute postexercise FEF60 level becomes an important outcome in its own right. Vitamin C increased postexercise FEF60 levels by 50% to 150% in those five participants, but had no significant effect in the other seven participants. Thus, future research on the effects of vitamin C on EIB should not be restricted to measuring only FEV1. Vitamin C is inexpensive and safe, and further study on those people who have EIB or respiratory symptoms associated with exercise is warranted.
  • Piisilä, Maria; Keceli, Mehmet A; Brader, Günter; Jakobson, Liina; Jõesaar, Indrek; Sipari, Nina; Kollist, Hannes; Palva, E T; Kariola, Tarja (BioMed Central, 2015)
    Abstract Background The Arabidopsis thaliana F-box protein MORE AXILLARY GROWTH2 (MAX2) has previously been characterized for its role in plant development. MAX2 appears essential for the perception of the newly characterized phytohormone strigolactone, a negative regulator of polar auxin transport in Arabidopsis. Results A reverse genetic screen for F-box protein mutants altered in their stress responses identified MAX2 as a component of plant defense. Here we show that MAX2 contributes to plant resistance against pathogenic bacteria. Interestingly, max2 mutant plants showed increased susceptibility to the bacterial necrotroph Pectobacterium carotovorum as well as to the hemi-biotroph Pseudomonas syringae but not to the fungal necrotroph Botrytis cinerea. max2 mutant phenotype was associated with constitutively increased stomatal conductance and decreased tolerance to apoplastic ROS but also with alterations in hormonal balance. Conclusions Our results suggest that MAX2 previously characterized for its role in regulation of polar auxin transport in Arabidopsis, and thus plant development also significantly influences plant disease resistance. We conclude that the increased susceptibility to P. syringae and P. carotovorum is due to increased stomatal conductance in max2 mutants promoting pathogen entry into the plant apoplast. Additional factors contributing to pathogen susceptibility in max2 plants include decreased tolerance to pathogen-triggered apoplastic ROS and alterations in hormonal signaling.
  • Karkamo, Veera; Kaistinen, Anu; Näreaho, Anu; Dillard, Kati; Vainio-Siukola, Katri; Vidgrén, Gabriele; Tuoresmäki, Niina; Anttila, Marjukka (BioMed Central Ltd, 2014)
    Abstract Background Leishmania spp. are zoonotic protozoans that infect humans and other mammals such as dogs. The most significant causative species in dogs is L. infantum. In dogs, leishmaniosis is a potentially progressive, chronic disease with varying clinical outcomes. Autochthonous cases of canine leishmaniosis have not previously been reported in the Nordic countries. Results In this report we describe the first diagnosed autochthonous cases of canine leishmaniosis in Finland, in which transmission via a suitable arthropod vector was absent. Two Finnish boxers that had never been in endemic areas of Leishmania spp., had never received blood transfusions, nor were infested by ectoparasites were diagnosed with leishmaniosis. Another dog was found with elevated Leishmania antibodies. A fourth boxer dog that had been in Spain was considered to be the source of these infections. Transmission occurred through biting wounds and semen, however, transplacental infection in one of the dogs could not be ruled out. Two of the infected dogs developed a serious disease and were euthanized and sent for necropsy. The first one suffered from membranoproliferative glomerulonephritis and the second one had a chronic systemic disease. Leishmania sp. was detected from tissues by PCR and/or IHC in both dogs. The third infected dog was serologically positive for Leishmania sp. but remained free of clinical signs. Conclusions This case report shows that imported Leishmania-infected dogs may pose a risk for domestic dogs, even without suitable local arthropod vectors.
  • Tripathi, Sushil; Flobak, Åsmund; Chawla, Konika; Baudot, Anaïs; Bruland, Torunn; Thommesen, Liv; Kuiper, Martin; Lægreid, Astrid (BioMed Central, 2015)
    Abstract Background The gastrointestinal peptide hormones cholecystokinin and gastrin exert their biological functions via cholecystokinin receptors CCK1R and CCK2R respectively. Gastrin, a central regulator of gastric acid secretion, is involved in growth and differentiation of gastric and colonic mucosa, and there is evidence that it is pro-carcinogenic. Cholecystokinin is implicated in digestion, appetite control and body weight regulation, and may play a role in several digestive disorders. Results We performed a detailed analysis of the literature reporting experimental evidence on signaling pathways triggered by CCK1R and CCK2R, in order to create a comprehensive map of gastrin and cholecystokinin-mediated intracellular signaling cascades. The resulting signaling map captures 413 reactions involving 530 molecular species, and incorporates the currently available knowledge into one integrated signaling network. The decomposition of the signaling map into sub-networks revealed 18 modules that represent higher-level structures of the signaling map. These modules allow a more compact mapping of intracellular signaling reactions to known cell behavioral outcomes such as proliferation, migration and apoptosis. The integration of large-scale protein-protein interaction data to this literature-based signaling map in combination with topological analyses allowed us to identify 70 proteins able to increase the compactness of the map. These proteins represent experimentally testable hypotheses for gaining new knowledge on gastrin- and cholecystokinin receptor signaling. The CCKR map is freely available both in a downloadable, machine-readable SBML-compatible format and as a web resource through PAYAO ( http://sblab.celldesigner.org:18080/Payao11/bin/ ). Conclusion We have demonstrated how a literature-based CCKR signaling map together with its protein interaction extensions can be analyzed to generate new hypotheses on molecular mechanisms involved in gastrin- and cholecystokinin-mediated regulation of cellular processes.
  • Aho, Velma T E; Pereira, Pedro A B; Haahtela, Tari; Pawankar, Ruby; Auvinen, Petri; Koskinen, Kaisa (BioMed Central, 2015)
    Abstract For a long time, the human lower airways were considered a sterile environment where the presence of microorganisms, typically revealed by culturing, was interpreted as an abnormal health state. More recently, high-throughput sequencing-based studies have led to a shift in this perception towards the notion that even in healthy conditions the lower airways show either transient presence or even permanent colonization by microorganisms. However, challenges related to low biomass and contamination in samples still remain, and the composition, structure and dynamics of such putative microbial communities are unclear. Here, we review the evidence for the presence of microbial communities in the human lower airways, in healthy subjects and within the context of medical conditions of interest. We also provide an overview of the methodology pertinent to high-throughput sequencing studies, specifically those based on amplicon sequencing, including a discussion of good practices and common pitfalls.
  • Borgquist, Signe; Zhou, Wenjing; Jirström, Karin; Amini, Rose-Marie; Sollie, Thomas; Sørlie, Therese; Blomqvist, Carl; Butt, Salma; Wärnberg, Fredrik (BioMed Central, 2015)
    Abstract Background HER2 is a well-established prognostic and predictive factor in invasive breast cancer. The role of HER2 in ductal breast carcinoma in situ (DCIS) is debated and recent data have suggested that HER2 is mainly related to in situ recurrences. Our aim was to study HER2 as a prognostic factor in a large population based cohort of DCIS with long-term follow-up. Methods All 458 patients diagnosed with a primary DCIS 1986–2004 in two Swedish counties were included. Silver-enhanced in situ hybridisation (SISH) was used for detection of HER2 gene amplification and protein expression was assessed by immunohistochemistry (IHC) in tissue microarrays. HER2 positivity was defined as amplified HER2 gene and/or HER2 3+ by IHC. HER2 status in relation to new ipsilateral events (IBE) and Invasive Breast Cancer Recurrences, local or distant (IBCR) was assessed by Kaplan-Meier survival analyses and Cox proportional hazards regression models. Results Primary DCIS was screening-detected in 75.5 % of cases. Breast conserving surgery (BCS) was performed in 78.6 % of whom 44.0 % received postoperative radiotherapy. No patients received adjuvant endocrine- or chemotherapy. The majority of DCIS could be HER2 classified (N = 420 (91.7 %)); 132 HER2 positive (31 %) and 288 HER2 negative (69 %)). HER2 positivity was related to large tumor size (P = 0.002), high grade (P < 0.001) and ER- and PR negativity (P < 0.001 for both). During follow-up (mean 184 months), 106 IBCRs and 105 IBEs were identified among all 458 cases corresponding to 54 in situ and 51 invasive recurrences. Eighteen women died from breast cancer and another 114 had died from other causes. The risk of IBCR was statistically significantly lower subsequent to a HER2 positive DCIS compared to a HER2 negative DCIS, (Log-Rank P = 0.03, (HR) 0.60 (95 % CI 0.38–0.94)). Remarkably, the curves did not separate until after 10 years. In ER-stratified analyses, HER2 positive DCIS was associated with lower risk of IBCR among women with ER negative DCIS (Log-Rank P = 0.003), but not for women with ER positive DCIS. Conclusions Improved prognostic tools for DCIS patients are warranted to tailor adjuvant therapy. Here, we demonstrate that HER2 positive disease in the primary DCIS is associated with lower risk of recurrent invasive breast cancer.
  • Oksanen, Antti; Åsbakk, Kjetil; Raekallio, Marja; Nieminen, Mauri (BioMed Central Ltd, 2014)
    Abstract Background Overwintering (breeding) reindeer (Rangifer tarandus tarandus) are commonly treated with ivermectin against parasitic infestations once yearly in autumn-winter roundups. The only preparations registered to reindeer are those for subcutaneous injection. However, also oral extra-label ivermectin administration is used. Twenty-six, 8-month-old reindeer calves were randomly allocated into three groups. Group 1 (n&#8201;=&#8201;9) received oral ivermectin mixture (Ivomec&#174; vet mixt. 0.8&#160;mg/ml, oral ovine liquid drench formulation), Group 2 (n&#8201;=&#8201;9) oral ivermectin paste (Ivomec&#174; vet 18.7&#160;mg/g equine paste), and Group 3 (n&#8201;=&#8201;8) subcutaneous injection of ivermectin (Ivomec&#174; 10&#160;mg/ml vet inj.), each group at a dose of 200&#160;&#956;g/kg body weight. Blood samples were collected at treatment and at days 1, 2, 3, 6, 9 and 16 post treatment. Plasma concentrations of ivermectin were determined by high-pressure liquid chromatography (HPLC) with fluorescence detection. Results The peak plasma concentration (Cmax) was reached by 2&#160;days after each treatment. The Cmax and Area Under Curve (AUC) differed significantly between the groups: Cmax was 30.2&#8201;&#177;&#8201;3.9, 14.9&#8201;&#177;&#8201;5.7 and 63.1&#8201;&#177;&#8201;13.1&#160;ng/ml, and AUC&#8734; was 2881&#8201;&#177;&#8201;462, 1299&#8201;&#177;&#8201;342 and 6718&#8201;&#177;&#8201;1620&#160;ng*h/ml for groups 1, 2 and 3, respectively (mean&#8201;&#177;&#8201;standard deviation). Conclusions The differences in plasma concentrations of ivermectin are concomitant with earlier observed differences in antiparasitic efficacy, which discounts the use of the equine paste in reindeer in favour of the oral ovine liquid drench formulation, or preferably, the reindeer-registered subcutaneous injection formulation.
  • Piirilä, Päivi L; Hodgson, Ulla; Wuorimaa, Tomi; Smith, Hans-Jürgen; Sovijärvi, Anssi RA (BioMed Central Ltd, 2014)
    Abstract Background Dynamic gas compression during forced expiration has an influence on conventional flow-volume spirometry results. The extent of gas compression in different pulmonary disorders remains obscure. Utilizing a flow plethysmograph we determined the difference between thoracic and mouth flows during forced expiration as an indication of thoracic gas compression in subjects with different pulmonary diseases characterized by limitations in pulmonary mechanics. Methods Patients with emphysema (N = 16), interstitial lung disease (ILD) (N = 15), obesity (N = 15) and healthy controls (N = 16) were included. Compressed expiratory flow-volume curves (at mouth) and corresponding compression-free curves (thoracic) were recorded. Peak flow (PEF) and maximal flows at 75%, 50% and 25% of remaining forced vital capacity (MEF75, MEF50 and MEF25) were derived from both recordings. Their respective difference was assessed as an indicator of gas compression. Results In all groups, significant differences between thoracic and mouth flows were found at MEF50 (p &lt; 0.01). In controls, a significant difference was also measured at MEF75 (p &lt;0.005), in emphysema subjects, at PEF and MEF75 (p &lt; 0.05, p &lt; 0.005) and in obese subjects at MEF75 (p &lt;0.005) and MEF25 (p &lt; 0.01). ILD patients showed the lowest difference between thoracic and mouth flows at MEF75 relative to controls and emphysema patients (p &lt; 0.005, p &lt; 0.001). Obese subjects did not differ from controls, however, the difference between thoracic and mouth flows was significantly higher than in patients with emphysema at MEF50 (p &lt; 0.001) and MEF25 (p &lt; 0.005). Conclusions Alveolar gas compression distorts the forced expiratory flow volume curve in all studied groups at the middle fraction of forced expiratory flow. Consequently, mouth flows are underestimated and the reduction of flow measured at 75% and 50% of vital capacity is often considerable. However, gas compression profiles in stiff lungs, in patients with decreased elastic recoil in emphysema and in obesity differ; the difference between thoracic and mouth flows in forced expiration was minimal in ILD at the first part of forced expiration and was higher in obesity than in emphysema at the middle and last parts of forced expiration.
  • Fortino, Vittorio; Smolander, Olli-Pekka; Auvinen, Petri; Tagliaferri, Roberto; Greco, Dario (BioMed Central, 2014)
    Abstract Background Inferring operon maps is crucial to understanding the regulatory networks of prokaryotic genomes. Recently, RNA-seq based transcriptome studies revealed that in many bacterial species the operon structure vary with the change of environmental conditions. Therefore, new computational solutions that use both static and dynamic data are necessary to create condition specific operon predictions. Results In this work, we propose a novel classification method that integrates RNA-seq based transcriptome profiles with genomic sequence features to accurately identify the operons that are expressed under a measured condition. The classifiers are trained on a small set of confirmed operons and then used to classify the remaining gene pairs of the organism studied. Finally, by linking consecutive gene pairs classified as operons, our computational approach produces condition-dependent operon maps. We evaluated our approach on various RNA-seq expression profiles of the bacteria Haemophilus somni, Porphyromonas gingivalis, Escherichia coli and Salmonella enterica. Our results demonstrate that, using features depending on both transcriptome dynamics and genome sequence characteristics, we can identify operon pairs with high accuracy. Moreover, the combination of DNA sequence and expression data results in more accurate predictions than each one alone. Conclusion We present a computational strategy for the comprehensive analysis of condition-dependent operon maps in prokaryotes. Our method can be used to generate condition specific operon maps of many bacterial organisms for which high-resolution transcriptome data is available.
  • Kasteenpohja, Teija; Marttunen, Mauri; Aalto-Setälä, Terhi; Perälä, Jonna; Saarni, Samuli I; Suvisaari, Jaana (BioMed Central, 2015)
    Abstract Background Under-treated depression may be especially harmful in early adulthood. The aims of this study are to describe treatments received for depressive disorders, to define factors associated with treatment adequacy and dropouts from treatment in a Finnish general population sample of young adults. Methods A nationally representative two-stage cluster sample of 1894 Finns aged 19 to 34 years was sent a questionnaire containing several mental health screens. All screen positives and a random sample of screen negatives were invited to participate in a mental health assessment including a SCID interview. Case records from mental health treatments for the same sample were obtained for the final diagnostic assessment. Based on all available information, receiving antidepressant pharmacotherapy for at least two months with at least four visits with any type of physician or at least eight sessions of psychotherapy within 12 months or at least four days of hospitalization were regarded as minimally adequate treatment. Treatment dropout was rated if the treatment strategy was assessed to be adequate according to the case records but the patient discontinued the visits. Results Of participants with depressive disorders (n = 142), 40.9% received minimally adequate treatment. In multiple logistic regression models, substance use disorder and female gender were associated with at least one visit with a physician, while having major depressive disorder was associated with visits with a physician at least 4 times a year. Women had higher odds of having received any psychotherapy and psychotherapy lasting for at least 8 sessions in a year. Low education and a history of suicide attempt were associated with increased odds of treatment dropout. None of the factors explained the final outcome of minimally adequate treatment. Conclusions Treatment adequacy in the present study was better than previously seen, but more efforts are needed to provide adequate treatment for young adults, especially those with low education and suicidality.
  • 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-&#223; 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, &#945;-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.