Browsing by Subject "ESTABLISHMENT"

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  • Kostopoulos, Ioannis; Elzinga, Janneke; Ottman, Noora; Klievink, Jay T.; Blijenberg, Bernadet; Aalvink, Steven; Boeren, Sjef; Mank, Marko; Knol, Jan; de Vos, Willem M.; Belzer, Clara (2020)
    Akkermansia muciniphila is a well-studied anaerobic bacterium specialized in mucus degradation and associated with human health. Because of the structural resemblance of mucus glycans and free human milk oligosaccharides (HMOs), we studied the ability of A. muciniphila to utilize human milk oligosaccharides. We found that A. muciniphila was able to grow on human milk and degrade HMOs. Analyses of the proteome of A. muciniphila indicated that key-glycan degrading enzymes were expressed when the bacterium was grown on human milk. Our results display the functionality of the key-glycan degrading enzymes (alpha -l-fucosidases, beta -galactosidases, exo-alpha -sialidases and beta -acetylhexosaminidases) to degrade the HMO-structures 2 ' -FL, LNT, lactose, and LNT2. The hydrolysation of the host-derived glycan structures allows A. muciniphila to promote syntrophy with other beneficial bacteria, contributing in that way to a microbial ecological network in the gut. Thus, the capacity of A. muciniphila to utilize human milk will enable its survival in the early life intestine and colonization of the mucosal layer in early life, warranting later life mucosal and metabolic health.
  • Eshriqui, Ilana; Viljakainen, Heli T.; Ferreira, Sandra; Raju, Sajan C.; Weiderpass, Elisabete; Figueiredo, Rejane A. O. (2020)
    Background Breastfeeding contributes to gastrointestinal microbiota colonization in early life, but its long-term impact is inconclusive. We aimed to evaluate whether the type of feeding during the first six months of life was associated with oral microbiota in adolescence. Methods This is a cross-sectional sub-study using baseline information of 423 adolescents from the Finnish Health in Teens (Fin-HIT) cohort. Type of feeding was recalled by parents and dichotomized as (i) No infant formula; (ii) Infant formula (breastmilk + formula or only formula). Saliva microbiota was analysed using 16S rRNA (V3-V4) sequencing. Alpha diversity and beta diversity were compared between feeding type groups using ANCOVA and PERMANOVA, respectively. Differential bacteria abundance was tested using appropriate general linear models. Results Mean age and body mass index were 11.7 years and 18.0 kg/m(2), respectively. The No formula group contained 41% of the participants. Firmicutes (51.0%), Bacteroidetes (19.1%), and Proteobacteria (16.3%) were the most abundant phyla among all participants. Alpha and beta diversity indices did not differ between the two feeding groups. Three Operational Taxonomic Units (OTUs) belonging to Eubacteria and Veillonella genera (phylum Firmicutes) were more abundant in the No formula than in the Infant formula group (log2fold changes/ p - values - 0.920/ <0.001, - 0.328/ 0.001, - 0.577/ 0.004). Conclusion Differences exist in abundances of some OTUs in adolescence according to feeding type during the first six months of life, but our findings do not support diversity and overall oral microbiota composition in adolescents being affected by early feeding type.
  • Mazina, Olga; Allikalt, Anni; Tapanainen, Juha S.; Salumets, Andres; Rinken, Ago (2017)
    Determination of biological activity of gonadotropin hormones is essential in reproductive medicine and pharmaceutical manufacturing of the hormonal preparations. The aim of the study was to adopt a G-protein coupled receptor (GPCR)-mediated signal transduction pathway based assay for quantification of biological activity of gonadotropins. We focussed on studying human chorionic gonadotropin (hCG) and follicle-stimulating hormone (FSH), as these hormones are widely used in clinical practice. Receptor-specific changes in cellular cyclic adenosine monophosphate (cAMP, second messenger in GPCR signalling) were monitored by a Forster resonance energy transfer (FRET) biosensor protein (T)Epac(VV) in living cells upon activation of the relevant gonadotropin receptor. The BacMam gene delivery system was used for biosensor protein expression in target cells. In the developed assay only biologically active hormones initiated GPCR-mediated cellular signalling. High assay sensitivities were achieved for detection of hCG (limit of detection, LOD: 5 pM) and FSH (LOD: 100 pM). Even the smallscale conformational changes caused by thermal inactivation and reducing the biological activity of the hormones were registered. In conclusion, the proposed assay is suitable for quantification of biological activity of gonadotropins and is a good alternative to antibody- and animal-testing-based assays used in pharmaceutical industry and clinical research.
  • Kyro, M. J.; Hallikainen, Helena K.; Valkonen, Sauli; Hypponen, M.; Puttonen, Pasi; Bergsten, Urban; Winsa, H.; Rautio, P. (2022)
    Natural regeneration is a commonly used forest regeneration method in northern Finland. It is not known, however, what would be the optimal overstory density and ground vegetation composition for seedling emergence and survival, and if site preparation is needed to accompany overstory density manipulation. We studied the effects of overstory density (unthinned control and thinning to 50,150, and 250 trees.ha(-1)) and ground vegetation removal (mechanical site preparation with disc trenching) on the number of naturally germinated pine seedlings and survival of individual seedlings over a period of 8 to 11 years. Bare mineral soil was a superior seedbed compared to intact vegetation cover, even though the mortality rate was high on mineral soil. Greater cover of lingonberry, crowberry, and slash had a negative effect on seedling number. Seedling mortality was initially high (60% died during the first 2 years) but decreased throughout the first 5 years. The survival rate of seedlings located in the mineral soil of the upper part of the disc trencher track was twice as high as that of seedlings located in the lower part of the track. High coverage of hair mosses (Polytrichum spp.) was associated with poorer seedling survival. An overstory density of 50-150 trees.ha(-1) with site preparation seems to be an efficient treatment to promote regeneration under these circumstances.
  • Anttonen, Mikko; Pihlajoki, Marjut; Andersson, Noora; Georges, Adrien; L'Hote, David; Vattulainen, Sanna; Farkkila, Anniina; Unkila-Kallio, Leila; Veitia, Reiner A.; Heikinheimo, Markku (2014)
  • Kasurinen, Aaro; Gramolelli, Silvia; Hagström, Jaana; Laitinen, Alli; Kokkola, Arto; Miki, Yuichiro; Lehti, Kaisa; Yashiro, Masakazu; Ojala, Päivi M.; Böckelman, Camilla; Haglund, Caj (2019)
    Matrix metalloproteinase 14 (MMP14), a membrane-associated matrix metalloproteinase, has been shown to influence the invasion and metastasis of several solid tumors. Prospero homeobox protein 1 (PROX1), involved in the development and cell fate determination, is also expressed in malignant diseases functioning either as a tumor-suppressing or oncogenic factor. In certain cancers PROX1 appears to transcriptionally suppress MMP14 expression. This study, therefore, aimed to explore the association between MMP14 and PROX1 and understand their potential as prognostic biomarkers in gastric cancer. The cohort consisted of 313 individuals operated for gastric adenocarcinoma between 2000 and 2009 in the Department of Surgery, Helsinki University Hospital. MMP14 and PROX1 expressions were studied using immunohistochemistry in the patient sample and using immunoblotting and immunofluorescence in gastric cancer cell lines. We generated survival curves using the Kaplan-Meier method, determining significance via the log-rank test. A high MMP14 expression associated with being >= 67 years (P = .041), while a positive nuclear PROX1 expression associated with tumors of a diffuse histological type (P = .041) and a high cytoplasmic PROX1 expression (P <.001). Five-year disease-specific survival among patients with a high MMP14 expression was 35.9% (95% confidence interval [CI] 24.9-46.9), compared to 45.3% (95% CI 38.0-52.6) for patients with a low MMP14 (P = .030). Survival was worse specifically among those with a high MMP14 and absent nuclear PROX1 expression (hazard ratio [HR] 1.65; 95% CI 1.09-2.51; P = .019). Thus, this study confirms that a high MMP14 expression predicts a worse survival in gastric cancer, revealing for the first time that survival is particularly worse when PROX1 is low.
  • Piiroinen, Rami; Fassnacht, Fabian Ewald; Heiskanen, Janne; Maeda, Eduardo; Mack, Benjamin; Pellikka, Petri (2018)
    Eucalyptus spp. and Acacia mearnsii are common exotic tree species in eastern Africa that have shown (strong) invasive behavior in some regions. Acacia mearnsii is considered a highly invasive species that is replacing native species and Eucalyptus spp. are known to consume high amounts of groundwater with suspected effects on native flora. Mapping the occurrence of these species in the Taita Hills, Kenya (part of the Eastern Arc Mountains Biodiversity Hotspot) is important as there is lack of knowledge on their occurrence and ecological impact in the area. Mapping methods that require a lot of fieldwork are impractical in areas like the Taita Hills, where the terrain is rugged and the infrastructure is poor. Our aim was hence to map the occurrence of these tree species in a 100 km(2) area using airborne imaging spectroscopy and laser scanning. We used a one class biased support vector machine (BSVM) classifier as it needs labeled training data only for the positive classes (A. mearnsii and Eucalyptus spp.), which potentially reduces the amount of required fieldwork. We also introduce a new approach for parameterizing and setting the threshold level simultaneously for the BSVM classifier. The second aim was to link the occurrence of these species to selected environmental variables. The results showed that the BSVM classifier is suitable for mapping Acacia mearnsii and Eucalyptus spp., holding the potential to improve the efficiency of field data collection. The introduced parametrization/threshold selection method performed better than other commonly used approaches. The crown level Fl-score was 0.76 for Eucalyptus spp. and 0.78 for A. mearnsii. We show that Eucalyptus spp. and A. mearnsii trees cover 0.8% and 1.6% of the study area, respectively. Both species are particularly located on steeper slopes and higher altitudes. Both species have significant occurrences in areas close to the biggest remaining native forest patch (Ngangao) in the study area. Nonetheless, follow-up studies are needed to evaluate their impact on the native flora and fauna, as well as their impact on the water resources. The maps created in this study in combination with such follow-up studies could serve as base data to generate guidelines that authorities can use to take action in handling the problems these species are causing.
  • Lundgren, Sara N.; Madan, Juliette C.; Karagas, Margaret R.; Morrison, Hilary G.; Hoen, Anne G.; Christensen, Brock C. (2019)
    The process of breastfeeding exposes infants to bioactive substances including a diversity of bacteria from breast milk as well as maternal skin. Knowledge of the character of and variation in these microbial communities, as well as the factors that influence them, is limited. We aimed to identify profiles of breastfeeding-associated microbial communities and their association with maternal and infant factors. Bilateral milk samples were collected from women in the New Hampshire Birth Cohort Study at approximately 6 weeks postpartum without sterilization of the skin in order to capture the infant-relevant exposure. We sequenced the V4-V5 hypervariable region of the bacterial 16S rRNA gene in 155 human milk samples. We used unsupervised clustering (partitioning around medoids) to identify microbial profiles in milk samples, and multinomial logistic regression to test their relation with maternal and infant variables. Associations between alpha diversity and maternal and infant factors were tested with linear models. Four breastfeeding microbiome types (BMTs) were identified, which differed in alpha diversity and in Streptococcus, Staphylococcus, Acinetobacter, and Pseudomonas abundances. Higher maternal pre-pregnancy BMI was associated with increased odds of belonging to BMT1 [OR (95% CI) = 1.13 (1.02, 1.24)] or BMT3 [OR (95% CI) = 1.12 (1.01, 1.25)] compared to BMT2. Independently, increased gestational weight gain was related to reduced odds of membership in BMT1 [OR (95% CI) = 0.66 (0.44, 1.00) per 10 pounds]. Alpha diversity was positively associated with gestational weight gain and negatively associated with postpartum sample collection week. There were no statistically significant associations of breastfeeding microbiota with delivery mode. Our results indicate that the breastfeeding microbiome partitions into four profiles and that its composition and diversity is associated with measures of maternal weight.
  • Haltia, Ulla-Maija; Andersson, Noora; Yadav, Bhagwan; Farkkila, Anniina; Kulesskiy, Evgeny; Kankainen, Matti; Tang, Jing; Butzow, Ralf; Riska, Annika; Leminen, Arto; Heikinheimo, Markku; Kallioniemi, Olli; Unkila-Kallio, Leila; Wennerberg, Krister; Aittokallio, Tero; Anttonen, Mikko (2017)
    Objective. Resistance to standard chemotherapy poses a major clinical problem in the treatment of ovarian cancer patients. Adult-type granulosa cell tumor (AGCT) is a unique ovarian cancer subtype for which efficient treatment options are lacking in advanced disease. To this end, systematic drug response and transcriptomics profiling were performed to uncover new therapy options for AGCTs. Methods. The responses of three primary and four recurrent AGCTs to 230 anticancer compounds were screened in vitro using a systematic drug sensitivity and resistance testing (DSRT) platform, coupled with mRNA sequencing. The responses of the AGCTs were compared with those of human granulosa luteal cells and bone marrow mononuclear cells. Results. Patient-derived AGCT cells showed selective sensitivity to the Src family tyrosine kinase inhibitor dasatinib. A combination of either dasatinib or an mTOR-inhibitor everolimus with paclitaxel resulted in synergistic inhibition of AGCT cell viability. The key kinase targets of dasatinib and members of the mTOR pathway were constantly expressed at mRNA and protein levels, indicating multikinase signal addictions in the AGCT cells. Transcriptomic characterization of the tumors revealed no known oncogenic mutations, suggesting that the drug sensitivity of AGCTs was rather conveyed by selective target expression. Conclusions. We used a systematic functional approach to reveal novel treatment options for a unique gynecological cancer. The selective synergy found between taxanes and dasatinib or mTOR inhibitors warrants further clinical investigations of these combinations in relapsed or aggressive AGCTs and demonstrate that high throughput drug screening and molecular profiling can provide an effective approach to uncover new therapy options. (C) 2016 Elsevier Inc. All rights reserved.
  • Kulmuni, Jonna; Butlin, Roger K.; Lucek, Kay; Savolainen, Vincent; Westram, Anja Marie (2020)
    y Speciation, that is, the evolution of reproductive barriers eventually leading to complete isolation, is a crucial process generating biodiversity. Recent work has contributed much to our understanding of how reproductive barriers begin to evolve, and how they are maintained in the face of gene flow. However, little is known about the transition from partial to strong reproductive isolation (RI) and the completion of speciation. We argue that the evolution of strong RI is likely to involve different processes, or new interactions among processes, compared with the evolution of the first reproductive barriers. Transition to strong RI may be brought about by changing external conditions, for example, following secondary contact. However, the increasing levels of RI themselves create opportunities for new barriers to evolve and, and interaction or coupling among barriers. These changing processes may depend on genomic architecture and leave detectable signals in the genome. We outline outstanding questions and suggest more theoretical and empirical work, considering both patterns and processes associated with strong RI, is needed to understand how speciation is completed. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
  • Tannure Faria, Julio Cezar; Ribeiro-Kumara, Caius; da Rocha Costa, Rayssa Silva; Nieri, Erick Martins; de Carvalho, Dulcineia; Brasil Pereira Pinto, Jose Eduardo; de Sena Neto, Alfredo Rodrigues; Brondani, Gilvano Ebling (2022)
    Background: Micropropagation, an in vitro vegetative propagation technique using small propagules is one of the main applications of plant tissue culture. It can be used to clone specific plants with desired traits and reduce the cost of plant propagation. In this study, we developed a protocol for micropropagation of Eucalyptus microcorys F.Muell using a selected mature tree, in which we tested various combinations of different culture media and evaluated the use of biodegradable polyester-based microvessels during the adventitious rooting and acclimatisation phases. Methods: Epicormic shoots were used as an explant source. After the in vitro explant establishment and multiplication, we tested 8 combinations of BAP, NAA and IBA in the elongation phase. Three types of microvessels were tested in the adventitious rooting phase and acclimatisation of the microcuttings. Results: Epicormic shoots had an establishment percentage of 40.6% and a total of 820 explants were generated by the 11th subculture, with an average of 12 buds per explant. Best shoot elongation results were achieved with BAP (0.05 mg L-1) + NAA (1 mg L-1) and BAP (0.05 mg L-1) + NAA (1 mg L-1) + IBA (1 mg L-1) combinations, whereas microvessel types M2 and M3 provided higher rooting and acclimatisation. According to the results of ISSR markers, at the end of 535 days of in vitro cultivation, cloning was successful between acclimatised micro-plantlets and the parent plant. Conclusions: The micropropagation protocol using microvessels was efficient in producing E. microcorys clonal microplantlets and is recommended for further studies with this species, and for testing in the micropropagation of other species.