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  • Obst, Matthias; Exter, Katrina; Allcock, A. Louise; Arvanitidis, Christos; Axberg, Alizz; Bustamante, Maria; Cancio, Ibon; Carreira-Flores, Diego; Chatzinikolaou, Eva; Chatzigeorgiou, Giorgos; Chrismas, Nathan; Clark, Melody S.; Comtet, Thierry; Dailianis, Thanos; Davies, Neil; Deneudt, Klaas; de Cerio, Oihane Diaz; Fortic, Ana; Gerovasileiou, Vasilis; Hablutzel, Pascal; Keklikoglou, Kleoniki; Kotoulas, Georgios; Lasota, Rafal; Leite, Barbara R.; Loisel, Stephane; Leveque, Laurent; Levy, Liraz; Malachowicz, Magdalena; Mavria, Borut; Meyer, Christopher; Mortelmans, Jonas; Norkko, Joanna; Pade, Nicolas; Power, Anne Marie; Ramsak, Andreja; Reiss, Henning; Solbakken, Jostein; Stoehr, Peter A.; Sundberg, Per; Thyrring, Jakob; Troncoso, Jesus S.; Viard, Frederique; Wenne, Roman; Yperifanou, Eleni Loanna; Zbawicka, Malgorzata; Pavloudi, Christina (2020)
    Marine hard-bottom communities are undergoing severe change under the influence of multiple drivers, notably climate change, extraction of natural resources, pollution and eutrophication, habitat degradation, and invasive species. Monitoring marine biodiversity in such habitats is, however, challenging as it typically involves expensive, non-standardized, and often destructive sampling methods that limit its scalability. Differences in monitoring approaches furthermore hinders inter-comparison among monitoring programs. Here, we announce a Marine Biodiversity Observation Network (MBON) consisting of Autonomous Reef Monitoring Structures (ARMS) with the aim to assess the status and changes in benthic fauna with genomic-based methods, notably DNA metabarcoding, in combination with image-based identifications. This article presents the results of a 30-month pilot phase in which we established an operational and geographically expansive ARMS-MBON. The network currently consists of 20 observatories distributed across European coastal waters and the polar regions, in which 134 ARMS have been deployed to date. Sampling takes place annually, either as short-term deployments during the summer or as long-term deployments starting in spring. The pilot phase was used to establish a common set of standards for field sampling, genetic analysis, data management, and legal compliance, which are presented here. We also tested the potential of ARMS for combining genetic and image-based identification methods in comparative studies of benthic diversity, as well as for detecting non-indigenous species. Results show that ARMS are suitable for monitoring hard-bottom environments as they provide genetic data that can be continuously enriched, re-analyzed, and integrated with conventional data to document benthic community composition and detect non-indigenous species. Finally, we provide guidelines to expand the network and present a sustainability plan as part of the European Marine Biological Resource Centre (www.embrc.eu).
  • Li, Xiaodong; Meng, Shuo; Puhakka, Eini; Ikonen, Jussi; Liu, Longcheng; Siitari-Kauppi, Marja (2020)
    To determine the diffusion and sorption properties of radionuclides in intact crystalline rocks, a new electromigration device was built and tested by running with I- and Se(IV) ions. By introducing a potentiostat to impose a constant voltage over the studied rock sample, the electromigration device can give more stable and accurate experimental results than those from the traditional electromigration devices. In addition, the variation in the pH of the background electrolytes was minimised by adding a small amount of NaHCO3 as buffers. To interpret the experimental results with more confidence, an advection-dispersion model was also developed in this study, which accounts for the most important mechanisms governing ionic transport in the electromigration experiments. Data analysis of the breakthrough curves by the advection-dispersion model, instead of the traditional ideal plug-flow model, suggest that the effective diffusivities of I- and Se(IV) are (1.15 +/- 0.06) x 10(-13) m(2)/s and (3.50 +/- 0.86) x 10(-14) m(2)/s, respectively. The results also show that I- is more mobile than Se(IV) ions when migrating through the same intact rock sample and that their sorption properties are almost identical.
  • Jääskeläinen, Tiina; Kärkkäinen, Olli; Jokkala, Jenna; Klåvus, Anton; Heinonen, Seppo; Auriola, Seppo; Lehtonen, Marko; FINNPEC Core Invest Grp; Hanhineva, Kati; Laivuori, Hannele (2021)
    IntroductionMaternal metabolism changes substantially during pregnancy. However, few studies have used metabolomics technologies to characterize changes across gestation.Objectives and methodsWe applied liquid chromatography-mass spectrometry (LC-MS) based non-targeted metabolomics to determine whether the metabolic profile of serum differs throughout the pregnancy between pre-eclamptic and healthy women in the FINNPEC (Finnish Genetics of Preeclampsia Consortium) Study. Serum samples were available from early and late pregnancy.ResultsProgression of pregnancy had large-scale effects to the serum metabolite profile. Altogether 50 identified metabolites increased and 49 metabolites decreased when samples of early pregnancy were compared to samples of late pregnancy. The metabolic signatures of pregnancy were largely shared in pre-eclamptic and healthy women, only urea, monoacylglyceride 18:1 and glycerophosphocholine were identified to be increased in the pre-eclamptic women when compared to healthy controls.ConclusionsOur study highlights the need of large-scale longitudinal metabolomic studies in non-complicated pregnancies before more detailed understanding of metabolism in adverse outcomes could be provided. Our findings are one of the first steps for a broader metabolic understanding of the physiological changes caused by pregnancy per se.
  • El-Khoury, Riyad; Dufour, Eric; Rak, Malgorzata; Ramanantsoa, Nelina; Grandchamp, Nicolas; Csaba, Zsolt; Duvillie, Bertrand; Benit, Paule; Gallego, Jorge; Gressens, Pierre; Sarkis, Chamsy; Jacobs, Howard T.; Rustin, Pierre (2013)
  • Smura, Teemu; Blomqvist, Soile; Kolehmainen, Pekka; Schuffenecker, Isabelle; Lina, Bruno; Boettcher, Sindy; Diedrich, Sabine; Love, Arthur; Brytting, Mia; Hauzenberger, Elenor; Dudman, Susanne; Ivanova, Olga; Lukasev, Alexander; Fischer, Thea Kolsen; Midgley, Sofie; Susi, Petri; Savolainen-Kopra, Carita; Lappalainen, Maija; Jääskeläinen, Anne J. (2020)
    Picornaviruses (family Picornaviridae) are small, nonenveloped, positive-sense, single-stranded RNA viruses. The members of this family are currently classified into 47 genera and 110 species. Of picornaviruses, entero-and parechoviruses are associated with aseptic meningitis. They are transmitted via fecal-oral and respiratory routes, and occasionally, these viruses may cause a brief viremia and gain access to central nervous system (CNS). During the diagnostic screening of entero-and parechovirus types in Finland in year 2013-14, we detected a cluster of echovirus 4 (E4) infections in young adults and adolescents. As E4 is infrequently detected in Finland, we contacted several Northern and Central European laboratories that conduct routine surveillance for enteroviruses and, for those who have had E4 cases, we send a query for E4 sequences and data. Here we report CNS infections caused by E4 in Finland, Sweden, Norway, Denmark, Iceland and Germany in 2013 and 2014, and show that the E4 detected in these countries form a single lineage. In contrast, E4 strains circulating in these countries preceding the year 2013, and those circulating elsewhere in Europe during 2013-2014, formed several independent clusters.
  • Thomson, Katariina; Eskola, Katarina; Eklund, Marjut; Suominen, Kristiina; Maatta, Merita; Junnila, Jouni; Nykasenoja, Suvi; Niinisto, Kati; Gronthal, Thomas; Rantala, Merja (2022)
    Background Extended-spectrum beta-lactamase producing Enterobacterales (ESBL-E) are important causative agents for infections in humans and animals. At the Equine Veterinary Teaching Hospital of the University of Helsinki, the first infections caused by ESBL-E were observed at the end of 2011 leading to enhanced infection surveillance. Contact patients were screened for ESBL-E by culturing infection sites and rectal screening. This study was focused on describing the epidemiology and microbiological characteristics of ESBL-E from equine patients of the EVTH during 2011-2014, and analysing putative risk factors for being positive for ESBL-E during an outbreak of Klebsiella pneumoniae ST307. Results The number of ESBL-E isolations increased through 2012-2013 culminating in an outbreak of multi-drug resistant K. pneumoniae ST307:bla(CTX-M-1):bla(TEM):bla(SHV) during 04-08/2013. During 10/2011-05/2014, altogether 139 ESBL-E isolates were found from 96 horses. Of these, 26 were from infection-site specimens and 113 from rectal-screening swabs. A total of 118 ESBL-E isolates from horses were available for further study, the most numerous being K. pneumoniae (n = 44), Escherichia coli (n = 31) and Enterobacter cloacae (n = 31). Hospital environmental specimens (N = 47) yielded six isolates of ESBL-E. Two identical E. cloacae isolates originating from an operating theatre and a recovery room had identical or highly similar PFGE fingerprint profiles as five horse isolates. In the multivariable analysis, mare-foal pairs (OR 4.71, 95% CI 1.57-14.19, P = 0.006), length of hospitalisation (OR 1.62, 95% CI 1.28-2.06, P < 0.001) and passing of a nasogastric tube (OR 2.86, 95% CI 1.03-7.95, P = 0.044) were associated with being positive for ESBL-E during the K. pneumoniae outbreak. Conclusions The occurrence of an outbreak caused by a pathogenic ESBL-producing K. pneumoniae ST307 strain highlights the importance of epidemiological surveillance of ESBL-E in veterinary hospitals. Limiting the length of hospitalisation for equine patients may reduce the risk of spread of ESBL-E. It is also important to acknowledge the importance of nasogastric tubing as a potential source of acquiring ESBL-E. As ESBL-E were also found in stomach drench pumps used with nasogastric tubes, veterinary practices should pay close attention to appropriate equipment cleaning procedures and disinfection practices.
  • Fischer, Daniel; Mosler, Karl; Mottonen, Jyrki; Nordhausen, Klaus; Pokotylo, Oleksii; Vogel, Daniel (2020)
    The Oja median is one of several extensions of the univariate median to the multivariate case. It has many desirable properties, but is computationally demanding. In this paper, we first review the properties of the Oja median and compare it to other multivariate medians. Then, we discuss four algorithms to compute the Oja median, which are implemented in our R package OjaNP. Besides these algorithms, the package contains also functions to compute Oja signs, Oja signed ranks, Oja ranks, and the related scatter concepts. To illustrate their use, the corresponding multivariate one- and C-sample location tests are implemented.
  • Petersen, Anders Ø.; Julienne, Hanna; Hyötyläinen, Tuulia; Sen, Partho; Fan, Yong; Pedersen, Helle Krogh; Jäntti, Sirkku; Hansen, Tue H.; Nielsen, Trine; Jørgensen, Torben; Hansen, Torben; Myers, Pernille Neve; Nielsen, H. Bjørn; Ehrlich, S. Dusko; Orešič, Matej; Pedersen, Oluf (2021)
    Knowledge about in vivo effects of human circulating C-6 hydroxylated bile acids (BAs), also called muricholic acids, is sparse. It is unsettled if the gut microbiome might contribute to their biosynthesis. Here, we measured a range of serum BAs and related them to markers of human metabolic health and the gut microbiome. We examined 283 non-obese and obese Danish adults from the MetaHit study. Fasting concentrations of serum BAs were quantified using ultra-performance liquid chromatography-tandem mass-spectrometry. The gut microbiome was characterized with shotgun metagenomic sequencing and genome-scale metabolic modeling. We find that tauro- and glycohyocholic acid correlated inversely with body mass index (P = 4.1e-03, P = 1.9e-05, respectively), waist circumference (P = 0.017, P = 1.1e-04, respectively), body fat percentage (P = 2.5e-03, P = 2.3e-06, respectively), insulin resistance (P = 0.051, P = 4.6e-4, respectively), fasting concentrations of triglycerides (P = 0.06, P = 9.2e-4, respectively) and leptin (P = 0.067, P = 9.2e-4). Tauro- and glycohyocholic acids, and tauro-a-muricholic acid were directly linked with a distinct gut microbial community primarily composed of Clostridia species (P = 0.037, P = 0.013, P = 0.027, respectively). We conclude that serum conjugated C-6-hydroxylated BAs associate with measures of human metabolic health and gut communities of Clostridia species. The findings merit preclinical interventions and human feasibility studies to explore the therapeutic potential of these BAs in obesity and type 2 diabetes.
  • Kauhanen, Dimple; Sysi-Aho, Marko; Koistinen, Kaisa M.; Laaksonen, Reijo; Sinisalo, Juha; Ekroos, Kim (2016)
    Monitoring the levels of the ceramides (Cer) d18:1/16:0, Cer d18:1/18:0, Cer d18:1/24:0, and Cer d18:1/24:1 and ratios thereof in human plasma empowers the prediction of fatal outcome of coronary artery disease (CAD). We describe a validated liquid chromatography-tandem mass spectrometry (LC-MS/MS) methodology for clinical-scaled measurement of the four distinct ceramides. Rapid plasma precipitation was accomplished in 96-well format. Excellent extraction recoveries in the range of 98-109 % were achieved for each ceramide. Addition of corresponding D-7-labeled ceramide standards facilitated precise quantification of each plasma ceramide species utilizing a novel short 5-min LC-MS/MS method. Neither matrix interference nor carryover was observed. Robust intra- and inter-assay accuracy and precision <15 % at five different concentrations were obtained. Linear calibration lines with regressions, R (2) > 0.99, were achieved for all analytes. Short-term bench top, long-term plasma, and extract stability demonstrated that the distinct ceramides were stable in the conditions evaluated. The validity of the methodology was demonstrated by determining the precise ceramide concentrations in a small CAD case-control study. Thus, our LC-MS/MS methodology features simple sample preparation and short analysis time for accurate quantification of Cer d18:1/16:0, Cer d18:1/18:0, Cer d18:1/24:0, and Cer d18:1/24:1, designed for routine analysis.
  • COST Action GENIEURI BM1106 Microb; Vork, Lisa; Penders, John; Jalanka, Jonna; Salonen, Anne; de Vos, Willem M.; Jonkers, Daisy M. A. E. (2021)
    Introduction Stool consistency has been associated with fecal microbial composition. Stool consistency often varies over time, in subjects with and without gastrointestinal disorders, raising the question whether variability in the microbial composition should be considered in microbiota studies. We evaluated within-subject day-to-day variability in stool consistency and the association with the fecal microbiota in irritable bowel syndrome (IBS) and healthy subjects, over seven days. Methods Twelve IBS patients and 12 healthy subjects collected fecal samples during seven consecutive days. Stool consistency was determined by the patient-reported Bristol Stool Scale (BSS) and fecal dry weight percentage. 16S rRNA V4 gene sequencing was performed and microbial richness (alpha diversity; Chao1 index, observed number of species, effective Shannon index) and microbial community structure (beta diversity; Bray-Curtis distance, generalized UniFrac, and taxa abundance on family level) were determined. Results Linear mixed-effects models showed significant associations between stool consistency and microbial richness, but no time effect. This implies that between-subject but not within-subject variation in microbiota over time can partially be explained by variation in stool consistency. Redundancy analysis showed a significant association between stool consistency and microbial community structure, but additional linear mixed-effects models did not demonstrate a time effect on this. Conclusion This study supports an association between stool consistency and fecal microbiota, but no effect of day-to-day fluctuations in stool consistency within seven days. This consolidates the importance of considering stool consistency in gut microbiota research, though confirms the validity of single fecal sampling to represent an individual's microbiota at a given time point. NCT00775060.
  • Witjes, Julia J.; Smits, Loek P.; Pekmez, Ceyda T.; Prodan, Andrei; Meijnikman, Abraham S.; Troelstra, Marian A.; Bouter, Kristien E. C.; Herrema, Hilde; Levin, Evgeni; Holleboom, Adriaan G.; Winkelmeijer, Maaike; Beuers, Ulrich H.; van Lienden, Krijn; Aron-Wisnewky, Judith; Mannisto, Ville; Bergman, Jacques J.; Runge, Jurgen H.; Nederveen, Aart J.; Dragsted, Lars O.; Konstanti, Prokopis; Zoetendal, Erwin G.; de Vos, Willem; Verheij, Joanne; Groen, Albert K.; Nieuwdorp, Max (2020)
    The intestinal microbiota has been linked to the development and prevalence of steatohepatitis in humans. Interestingly, steatohepatitis is significantly lower in individuals taking a plant-based, low-animal-protein diet, which is thought to be mediated by gut microbiota. However, data on causality between these observations in humans is scarce. In this regard, fecal microbiota transplantation (FMT) using healthy donors is safe and is capable of changing microbial composition in human disease. We therefore performed a double-blind randomized controlled proof-of-principle study in which individuals with hepatic steatosis on ultrasound were randomized to two study arms: lean vegan donor (allogenic n = 10) or own (autologous n = 11) FMT. Both were performed three times at 8-week intervals. A liver biopsy was performed at baseline and after 24 weeks in every subject to determine histopathology (Nonalcoholic Steatohepatitis Clinical Research Network) classification and changes in hepatic gene expression based on RNA sequencing. Secondary outcome parameters were changes in intestinal microbiota composition and fasting plasma metabolomics. We observed a trend toward improved necro-inflammatory histology, and found significant changes in expression of hepatic genes involved in inflammation and lipid metabolism following allogenic FMT. Intestinal microbial community structure changed following allogenic FMT, which was associated with changes in plasma metabolites as well as markers of .Conclusion:Allogenic FMT using lean vegan donors in individuals with hepatic steatosis shows an effect on intestinal microbiota composition, which is associated with beneficial changes in plasma metabolites and markers of steatohepatitis.
  • Mostowy, Rafal; Croucher, Nicholas J.; Andam, Cheryl P.; Corander, Jukka; Hanage, William P.; Marttinen, Pekka (2017)
    Prokaryotic evolution is affected by horizontal transfer of genetic material through recombination. Inference of an evolutionary tree of bacteria thus relies on accurate identification of the population genetic structure and recombination-derived mosaicism. Rapidly growing databases represent a challenge for computational methods to detect recombinations in bacterial genomes. We introduce a novel algorithm called fastGEAR which identifies lineages in diverse microbial alignments, and recombinations between them and from external origins. The algorithm detects both recent recombinations (affecting a few isolates) and ancestral recombinations between detected lineages (affecting entire lineages), thus providing insight into recombinations affecting deep branches of the phylogenetic tree. In simulations, fastGEAR had comparable power to detect recent recombinations and outstanding power to detect the ancestral ones, compared with state-of-the-art methods, often with a fraction of computational cost. We demonstrate the utility of the method by analyzing a collection of 616 whole-genomes of a recombinogenic pathogen Streptococcus pneumoniae, for which the method provided a high-resolution view of recombination across the genome. We examined in detail the penicillin-binding genes across the Streptococcus genus, demonstrating previously undetected genetic exchanges between different species at these three loci. Hence, fastGEAR can be readily applied to investigate mosaicism in bacterial genes across multiple species. Finally, fastGEAR correctly identified many known recombination hotspots and pointed to potential new ones. Matlab code and Linux/Windows executables are available at https://users.ics.aalto.fi/similar to pemartti/fastGEAR/ (last accessed February 6, 2017).
  • Verrinder, Elsi; Wester, Niklas; Leppänen, Elli; Lilius, Tuomas; Kalso, Eija; Mikladal, Bjo̷rn; Varjos, Ilkka; Koskinen, Jari; Laurila, Tomi (2021)
    Disposable single-use electrochemical sensor strips were used for quantitative detection of small concentrations of morphine in untreated capillary whole blood. Single-walled carbon nanotube (SWCNT) networks were fabricated on a polymer substrate to produce flexible, reproducible sensor strips with integrated reference and counter electrodes, compatible with industrial-scale processes. A thin Nafion coating was used on top of the sensors to enable direct electrochemical detection in whole blood. These sensors were shown to detect clinically relevant concentrations of morphine both in buffer and in whole blood samples. Small 38 mu L finger-prick blood samples were spiked with 2 mu L of morphine solution of several concentrations and measured without precipitation of proteins or any other further pretreatment. A linear range of 0.5-10 mu M was achieved in both matrices and a detection limit of 0.48 mu M in buffer. In addition, to demonstrate the applicability of the sensor in a point-of-care device, single-determination measurements were done with capillary samples from three subjects. An average recovery of 60% was found, suggesting that the sensor only measures the free, unbound fraction of the drug. An interference study with other opioids and possible interferents showed the selectivity of the sensor. This study clearly indicates that these Nafion/SWCNT sensor strips show great promise as a point-of-care rapid test for morphine in blood.
  • Puukko, Esa; Lehto, Jukka; Lindberg, Antero; Voutilainen, Mikko (2018)
    This study aims to determine upscaling factors for the radionuclides' distribution coefficients (Kd) on crushed rocks to intact rock for the safety analysis of radionuclide migration from spent nuclear fuel in bedrock towards biosphere. Here we report the distribution coefficients for intact rock determined by electromigration sorption experiments and compare the results with those from recently performed batch sorption experiments. In total 34 rock samples, representing three typical rock types from Olkiluoto Finland, were studied in order to determine distribution coefficients, effective diffusion coefficients and porosities using the electromigration sorption experiments, formation factor experiments and porosity measurement. The parameters determined represent the three main parameters of geosphere used in the safety assessment of spent nuclear fuel disposal. The distribution coefficients of cesium and strontium on intact rock varied between (0.12–26.2) × 10−3 m3/kg and (1.4–13.3) × 10−3 m3/kg, respectively, whereas recent results for crushed rock varied between (2–57) × 10−3 m3/kg and (17–40) × 10−3 m3/kg, respectively. This implies that crushing increases the distribution coefficient significantly and upscaling factors from 3 to 33 were determined for scaling the distribution coefficients of crushed rock to ones of intact rock. The determined distribution coefficients of cesium and strontium for intact rock can be directly applied in the safety assessment whereas the upscaling factors can be used to convert distribution coefficients determined for crushed rock into ones for intact rock. Based on the results for porosities and effective diffusion coefficients it was concluded that they do not seem to correlate with sorption parameters. However, an alteration state, heterogeneity and mineral content seem to be important factors affecting the distribution coefficients and upscaling factors.
  • Oskolkov, Nikolay; Santel, Malgorzata; Parikh, Hemang M.; Ekstrom, Ola; Camp, Gray J.; Miyamoto-Mikami, Eri; Strom, Kristoffer; Mir, Bilal Ahmad; Kryvokhyzha, Dmytro; Lehtovirta, Mikko; Kobayashi, Hiroyuki; Kakigi, Ryo; Naito, Hisashi; Eriksson, Karl-Fredrik; Nystedt, Bjorn; Fuku, Noriyuki; Treutlein, Barbara; Paabo, Svante; Hansson, Ola (2022)
    Background: Skeletal muscle fiber type distribution has implications for human health, muscle function, and performance. This knowledge has been gathered using labor-intensive and costly methodology that limited these studies. Here, we present a method based on muscle tissue RNA sequencing data (totRNAseq) to estimate the distribution of skeletal muscle fiber types from frozen human samples, allowing for a larger number of individuals to be tested. Methods: By using single-nuclei RNA sequencing (snRNAseq) data as a reference, cluster expression signatures were produced by averaging gene expression of cluster gene markers and then applying these to totRNAseq data and inferring muscle fiber nuclei type via linear matrix decomposition. This estimate was then compared with fiber type distribution measured by ATPase staining or myosin heavy chain protein isoform distribution of 62 muscle samples in two independent cohorts (n = 39 and 22). Results: The correlation between the sequencing-based method and the other two were r(ATpas) = 0.44 [0.13-0.67], [95% CI], and r(myosin) = 0.83 [0.61-0.93], with p = 5.70 x 10(-3) and 2.00 x 10(-6), respectively. The deconvolution inference of fiber type composition was accurate even for very low totRNAseq sequencing depths, i.e., down to an average of similar to 10,000 paired-end reads. Conclusions: This new method (https://github.com/OlaHanssonLab/PredictFiberType) consequently allows for measurement of fiber type distribution of a larger number of samples using totRNAseq in a cost and labor-efficient way. It is now feasible to study the association between fiber type distribution and e.g. health outcomes in large well-powered studies.
  • Kuitunen, Marja-Leena; Dutoit, Jean-Claude; Siegenthaler, Peter; Rapinoja, Marja-Leena; Vanninen, Paula Sinikka (2022)
    Sensitive and reliable analysis of alkylphosphonic acids (APAs) and 2-(N,N-dialkylamino)ethanesulfonic acids (SAs), the degradation products of chemical warfare agents (CWAs), is one of the most important tasks for verification of the Chemical Weapons Convention (CWC). Unambiguous identification of these chemicals is required in a variety of environmental matrices, including soil and water. These acids with low volatility are very polar, and efficient and reliable methylation methods for their derivatization are needed for analysis with gas chromatography-mass spectrometry (GC-MS). In this study, the derivatization conditions for trimethylsilyldiazomethane (TMSDAM) methylation were optimized for rapid GC-MS screening. Optimized methylation of APAs and SAs with TMSDAM was compared with methylation with diazomethane. The TMSDAM methylation of SAs and benzilic acid was further compared with silylation with N-methyl-N-(tert-butyldimethylsilyl)trifluoroacetamide. The significance and necessity of cation exchange prior to derivatization and analysis were tested on samples with a high inorganic background. A recommendation to use the method for methylation of water samples and aqueous extracts using TMSDAM is given. The robustness of the method was illustrated by the successful identification of APAs and SAs in aqueous samples from proficiency tests organized by the Organisation for the Prohibition of Chemical Weapons.
  • Haiko, Johanna; Savolainen, Laura E.; Hilla, Risto; Patari-Sampo, Anu (2016)
    Complicated urinary tract infections, such as pyelonephritis, may lead to sepsis. Rapid diagnosis is needed to identify the causative urinary pathogen and to verify the appropriate empirical antimicrobial therapy. We describe here a rapid identification method for urinary pathogens: urine is incubated on chocolate agar for 3 h at 35 degrees C with 5%CO2 and subjected to MALDI-TOF MS analysis by VITEK MS. Overall 207 screened clinical urine samples were tested in parallel with conventional urine culture. The method, called U-si-MALDI-TOF (urine short incubation MALDI-TOF), showed correct identification for 86% of Gram-negative urinary tract pathogens (Escherichia coli, Klebsiella pneumoniae, and other Enterobacteriaceae), when present at >10(5) cfu/ml in culture (n = 107), compared with conventional culture method. However, Gram-positive bacteria (n = 28) were not successfully identified by U-si-MALDI-TOF. This method is especially suitable for rapid identification of E. coli, the most common cause of urinary tract infections and urosepsis. Turnaround time for identification using U-si-MALDI-TOF compared with conventional urine culture was improved from 24 h to 4-6 h. (C) 2016 Elsevier B.V. All rights reserved.
  • Mitt, Mario; Kals, Mart; Parn, Kalle; Gabriel, Stacey B.; Lander, Eric S.; Palotie, Aarno; Ripatti, Samuli; Morris, Andrew P.; Metspalu, Andres; Esko, Tonu; Magi, Reedik; Palta, Priit (2017)
    Genetic imputation is a cost-efficient way to improve the power and resolution of genome-wide association (GWA) studies. Current publicly accessible imputation reference panels accurately predict genotypes for common variants with minor allele frequency (MAF) >= 5% and low-frequency variants (0.5
  • Ambers, Angie; Votrubova, Jitka; Vanek, Daniel; Sajantila, Antti; Budowle, Bruce (2018)
    Bones are a valuable source of DNA in forensic, anthropological, and archaeological investigations. There are a number of scenarios in which the only samples available for testing are highly degraded and/or skeletonized. Often it is necessary to perform more than one type of marker analysis on such samples in order to compile sufficient data for identification. Lineage markers, such as Y-STRs and mitochondrial DNA (mtDNA), represent important systems to complement autosomal DNA markers and anthropological metadata in making associations between unidentified remains and living relatives or for characterization of the remains for historical and archaeological studies. In this comparative study, Y-STR typing with both Yfiler and Yfiler Plus (Thermo Fisher Scientific, Waltham, MA, USA) was performed on a variety of human skeletal remains, including samples from the American Civil War (1861-1865), the late nineteenth century gold rush era in Deadwood, SD, USA (1874-1877), the Seven Years' War (1756-1763), a seventeenth-century archaeological site in Raspenava, Bohemia (Czech Republic), and World War II (1939-1945). The skeletal remains used for this study were recovered from a wide range of environmental conditions and were extracted using several common methods. Regardless of the DNA extraction method used and the age/condition of the remains, 22 out of 24 bone samples yielded a greater number of alleles using the Yfiler Plus kit compared to the Yfiler kit using the same quantity of input DNA. There was no discernable correlation with the degradation index values for these samples. Overall, the efficacy of the Yfiler Plus assay was demonstrated on degraded DNA from skeletal remains. Yfiler Plus increases the discriminatory power over the previous generation multiplex due to the larger set of Y-STR markers available for analysis and buffer modifications with the newer version kit. Increased haplotype resolution is provided to infer or refute putative genetic relationships.