Browsing by Subject "QUANTITATIVE-ANALYSIS"

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  • Itokazu, Yutaka; Tajima, Nobuyoshi; Kerosuo, Laura; Somerharju, Pentti; Sariola, Hannu; Yu, Robert K.; Kakela, Reijo (2016)
    The central nervous system (CNS) harbors multiple glial fibrillary acidic protein (GFAP) expressing cell types. In addition to the most abundant cell type of the CNS, the astrocytes, various stem cells and progenitor cells also contain GFAP+ populations. Here, in order to distinguish between two types of GFAP expressing cells with or without the expression of the A2B5 antigens, we performed lipidomic analyses on A2B5+/GFAP+ and A2B5-/GFAP+ cells from rat spinal cord. First, A2B5+/GFAP- progenitors were exposed to the leukemia inhibitory factor (LIF) or bone morphogenetic protein (BMP) to induce their differentiation to A2B5+/GFAP+ cells or A2B5-/GFAP+ astrocytes, respectively. The cells were then analyzed for changes in their phospholipid, sphingolipid or acyl chain profiles by mass spectrometry and gas chromatography. Compared to A2B5+/GFAP- progenitors, A2B5-/GFAP+ astrocytes contained higher amounts of ether phospholipids (especially the species containing arachidonic acid) and sphingomyelin, which may indicate characteristics of cellular differentiation and inability for multipotency. In comparison, principal component analyses revealed that the lipid composition of A2B5+/GFAP+ cells retained many of the characteristics of A2B5+/GFAP- progenitors, but their lipid profile was different from that of A2B5-/GFAP+ astrocytes. Thus, our study demonstrated that two GFAP+ cell populations have distinct lipid profiles with the A2B5+/GFAP+ cells sharing a phospholipid profile with progenitors rather than astrocytes. The progenitor cells may require regulated low levels of lipids known to mediate signaling functions in differentiated cells, and the precursor lipid profiles may serve as one measure of the differentiation capacity of a cell population.
  • Kilpinen, Lotta; Tigistu-Sahle, Feven; Oja, Sofia; Greco, Dario; Parmar, Amarjit; Saavalainen, Päivi Marjaana; Nikkilä, Janne Tapio; Korhonen, Matti; Lehenkari, Petri; Käkelä, Reijo; Laitinen, Saara (2013)
  • Ruiz-Jimenez, Jose; Lan, Hangzhen; Leleev, Yevgeny; Hartonen, Kari; Riekkola, Marja-Liisa (2020)
    Several calibration approaches were evaluated for the quantitation of volatile organic compounds in air using miniaturized exhaustive and non-exhaustive sampling techniques, such as in-tube extraction (ITEX) and solid phase microextraction (SPME) Arrow. Eleven compounds, 2-ethyl-hexanol, hexanal, nonanal, toluene, ethyl-benzene, methyl isobutyl ketone, acetophenone, p-cymene, alpha-pinene, trimethylamine and triethylamine, all them found in the natural air samples, were selected as model analytes. Liquid injection, liquid standard addition to the sorbent bed and gas phase standards provided by an automatic permeation system, were evaluated in the case of ITEX packed with laboratory-made 10% polyacrylonitrile (PAN) material. Two different approaches, based on sampling of gas phase compounds from the permeation system and from sample vial containing gas phase standards, were evaluated for SPME Arrow with two different coatings, commercial divinylbenzene-poly(dimethylsiloxane) (DVB-PDMS) and laboratory-made mesoporous Mobil Composition of Matter No. 41 (MCM-41). In addition, interface model approach was used for the calculation of the real concentration of the target analytes in the sample from the total amount of analytes injected into the GC-MS in the case of SPME Arrow. Similar results were obtained with the different approaches used for the quantitation by ITEX and SPME Arrow. However, the use of gas phase standards with sample matrix similar to the natural samples, allowed the permeation system to provide the most reliable results for the quantitation of the target analytes. For this approach, linearity (expressed as r(2) values) ranged between 0.991 and 0.999. The limit of detection ranged from 0.5 mu g/m(3) (trimethylamine, MCM-41) to 2.2 x 10(-4) mu g/m(3) (methyl isobutyl ketone, MCM-41). In addition, the use of the fully automated permeation system provided good reproducibility values that were between 1.4% (acetophenone, MCM-41) and 7.8% (methyl isobutyl ketone, 10% PAN). The linear ranges were at least 3 order of magnitude for all the studied analytes with the exception of the calibration curve developed for trimethylamine with SPME Arrow (linear ranges between LOQ and 4.9 mu g/m(3) (DVB-PDMS) and LOQ and 9.8 mu g/m(3) (MCM-41)). (C) 2019 Elsevier B.V. All rights reserved.
  • 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.
  • Tsai, Feng-Ching; Bertin, Aurelie; Bousquet, Hugo; Manzi, John; Senju, Yosuke; Tsai, Meng-Chen; Picas, Laura; Miserey-Lenkei, Stephanie; Lappalainen, Pekka; Lemichez, Emmanuel; Coudrier, Evelyne; Bassereau, Patricia (2018)
    One challenge in cell biology is to decipher the biophysical mechanisms governing protein enrichment on curved membranes and the resulting membrane deformation. The ERM protein ezrin is abundant and associated with cellular membranes that are flat, positively or negatively curved. Using in vitro and cell biology approaches, we assess mechanisms of ezrin's enrichment on curved membranes. We evidence that wild-type ezrin (ezrinWT) and its phosphomimetic mutant T567D (ezrinTD) do not deform membranes but self-assemble antiparallelly, zipping adjacent membranes. EzrinTD's specific conformation reduces intermolecular interactions, allows binding to actin filaments, which reduces membrane tethering, and promotes ezrin binding to positively-curved membranes. While neither ezrinTD nor ezrinWT senses negative curvature alone, we demonstrate that interacting with curvature-sensing I-BAR-domain proteins facilitates ezrin enrichment in negatively-curved membrane protrusions. Overall, our work demonstrates that ezrin can tether membranes, or be targeted to curved membranes, depending on conformations and interactions with actin and curvature-sensing binding partners.
  • Feijo Barreira, Luis Miguel; Duporte, Geoffroy; Rönkkö, Tuukka; Parshintsev, Jevgeni; Hartonen, Kari; Schulman, Lydia; Heikkinen, Enna; Jussila, Matti; Kulmala, Markku; Riekkola, Marja-Liisa (2018)
    Biogenic volatile organic compounds (BVOCs) emitted by terrestrial vegetation participate in a diversity of natural processes. These compounds impact both on short-range processes, such as on plant protection and communication, and on high-range processes, by e.g. participation on aerosol particle formation and growth. The biodiversity of plant species around the Earth, the vast assortment of emitted BVOCs, and their trace atmospheric concentrations contribute to the high remaining uncertainties about the effects of these compounds on atmospheric chemistry and physics, and call for the development of novel collection devices that can offer portability with improved selectivity and capacity. In this study, a novel solid-phase microextraction (SPME) Arrow sampling system was used for the static and dynamic collection of BVOCs from the boreal forest, and samples were subsequently analysed on-site by gas chromatography-mass spectrometry (GC-MS). This system offers higher sampling capacity and improved robustness than the traditional equilibrium-based SPME techniques, such as SPME fibers. Field measurements were performed in summer 2017 at the Station for Measuring Ecosystem-Atmosphere Relations (SMEAR II) in Hyytiälä, Finland. Complementary laboratory tests were also performed to compare the SPME-based techniques under controlled experimental conditions and to evaluate the effect of temperature and relative humidity on their extraction performance. The most abundant monoterpenes and aldehydes were successfully collected. A significant improvement on sampling capacity was observed with the new SPME Arrow system when compared to SPME fibers, with collected amounts being approximately 2 times higher for monoterpenes and 7-8 times higher for aldehydes. BVOC species exhibited different affinities for the type of sorbent materials used (PDMS/Carbon WR vs. PDMS/DVB). Higher extraction efficiencies were obtained with dynamic collection prior to equilibrium regime, but this benefit during the field measurements was small probably due to the natural agitation provided by the wind. An increase in temperature and relative humidity caused a decrease in the amounts of analytes extracted under controlled experimental conditions, even though the effect was more significant for PDMS/Carbon WR than for PDMS/DVB. Overall, results demonstrated the benefits and challenges of using SPME Arrow for the sampling of BVOCs in the atmosphere.
  • Macrì, Simone; Di-Poï, Nicolas (2020)
    Despite a remarkable conservation of architecture and function, the cerebellum of vertebrates shows extensive variation in morphology, size, and foliation pattern. These features make this brain subdivision a powerful model to investigate the evolutionary developmental mechanisms underlying neuroanatomical complexity both within and between anamniote and amniote species. Here, we fill a major evolutionary gap by characterizing the developing cerebellum in two non-avian reptile species—bearded dragon lizard and African house snake—representative of extreme cerebellar morphologies and neuronal arrangement patterns found in squamates. Our data suggest that developmental strategies regarded as exclusive hallmark of birds and mammals, including transit amplification in an external granule layer (EGL) and Sonic hedgehog expression by underlying Purkinje cells (PCs), contribute to squamate cerebellogenesis independently from foliation pattern. Furthermore, direct comparison of our models suggests the key importance of spatiotemporal patterning and dynamic interaction between granule cells and PCs in defining cortical organization. Especially, the observed heterochronic shifts in early cerebellogenesis events, including upper rhombic lip progenitor activity and EGL maintenance, are strongly expected to affect the dynamics of molecular interaction between neuronal cell types in snakes. Altogether, these findings help clarifying some of the morphogenetic and molecular underpinnings of amniote cerebellar corticogenesis, but also suggest new potential molecular mechanisms underlying cerebellar complexity in squamates. Furthermore, squamate models analyzed here are revealed as key animal models to further understand mechanisms of brain organization.
  • Parviainen, Tuuli; Goerlandt, Floris; Helle, Inari; Haapasaari, Päivi; Kuikka, Sakari (2021)
    The risk of a large-scale oil spill remains significant in marine environments as international maritime transport continues to grow. The environmental as well as the socio-economic impacts of a large-scale oil spill could be substantial. Oil spill models and modeling tools for Pollution Preparedness and Response (PPR) can support effective risk management. However, there is a lack of integrated approaches that consider oil spill risks comprehensively, learn from all information sources, and treat the system uncertainties in an explicit manner. Recently, the use of the international ISO 31000:2018 risk management framework has been suggested as a suitable basis for supporting oil spill PPR risk management. Bayesian networks (BNs) are graphical models that express uncertainty in a probabilistic form and can thus support decision-making processes when risks are complex and data are scarce. While BNs have increasingly been used for oil spill risk assessment (OSRA) for PPR, no link between the BNs literature and the ISO 31000:2018 framework has previously been made. This study explores how Bayesian risk models can be aligned with the ISO 31000:2018 framework by offering a flexible approach to integrate various sources of probabilistic knowledge. In order to gain insight in the current utilization of BNs for oil spill risk assessment and management (OSRA-BNs) for maritime oil spill preparedness and response, a literature review was performed. The review focused on articles presenting BN models that analyze the occurrence of oil spills, consequence mitigation in terms of offshore and shoreline oil spill response, and impacts of spills on the variables of interest. Based on the results, the study discusses the benefits of applying BNs to the ISO 31000:2018 framework as well as the challenges and further research needs.
  • Parviainen, Ville I.; Joenväärä, Sakari; Tohmola, Niina; Renkonen, Risto (2013)
  • Erkkilä, Arja T.; Manninen, Suvi; Fredrikson, Linda; Bhalke, Monika; Holopainen, Minna; Ruuth, Maija; Lankinen, Maria; Käkelä, Reijo; Öörni, Katariina; Schwab, Ursula S. (2021)
    Background: There is little knowledge on the effects of alpha-linolenic acid (ALA) and n-3 long chain polyunsaturated fatty acids (n-3 LCPUFA) on the LDL lipidome and aggregation of LDL particles. Objective: We examined if consumption of Camelina sativa oil (CSO) as a source of ALA, fatty fish (FF) as a source of n-3 LCPUFA and lean fish (LF) as a source of fish protein affect the lipidome of LDL as compared to a control diet. Methods: Participants with impaired glucose tolerance (39 women and 40 men) were randomized to 4 study groups (CSO providing 10 g/d ALA, FF and LF [both 4 fish meals/wk] and control limiting their fish and ALA intake) in a 12-week, parallel trial. Diets were instructed and dietary fats were provided to the participants. The lipidome of LDL particles isolated from samples collected at baseline and after intervention was analyzed with electrospray ionization-tandem mass spectrometry. Results: In the CSO group, the relative concentrations of saturated and monounsaturated cholesteryl ester species in LDL decreased and the species with ALA increased. In the FF group, LDL phosphatidylcholine (PC) species containing n-3 LCPUFA increased. There was a significant positive correlation between the change in total sphingomyelin and change in LDL aggregation, while total PC and triunsaturated PC species were inversely associated with LDL aggregation when all the study participants were included in the analysis. Conclusion: Dietary intake of CSO and FF modifies the LDL lipidome to contain more polyunsaturated and less saturated lipid species. The LDL surface lipids are associated with LDL aggregation. (c) 2021 National Lipid Association. Published by Elsevier Inc. This is an open access article under the CC BY license ( http://creativecommons.org/licenses/by/4.0/ )
  • Kaseva, Tuomas; Omidali, Bahareh; Hippeläinen, Eero; Mäkelä, Teemu; Wilppu, Ulla; Sofiev, Alexey; Merivaara, Arto; Yliperttula, Marjo; Savolainen, Sauli; Salli, Eero (2022)
    Background The segmentation of 3D cell nuclei is essential in many tasks, such as targeted molecular radiotherapies (MRT) for metastatic tumours, toxicity screening, and the observation of proliferating cells. In recent years, one popular method for automatic segmentation of nuclei has been deep learning enhanced marker-controlled watershed transform. In this method, convolutional neural networks (CNNs) have been used to create nuclei masks and markers, and the watershed algorithm for the instance segmentation. We studied whether this method could be improved for the segmentation of densely cultivated 3D nuclei via developing multiple system configurations in which we studied the effect of edge emphasizing CNNs, and optimized H-minima transform for mask and marker generation, respectively. Results The dataset used for training and evaluation consisted of twelve in vitro cultivated densely packed 3D human carcinoma cell spheroids imaged using a confocal microscope. With this dataset, the evaluation was performed using a cross-validation scheme. In addition, four independent datasets were used for evaluation. The datasets were resampled near isotropic for our experiments. The baseline deep learning enhanced marker-controlled watershed obtained an average of 0.69 Panoptic Quality (PQ) and 0.66 Aggregated Jaccard Index (AJI) over the twelve spheroids. Using a system configuration, which was otherwise the same but used 3D-based edge emphasizing CNNs and optimized H-minima transform, the scores increased to 0.76 and 0.77, respectively. When using the independent datasets for evaluation, the best performing system configuration was shown to outperform or equal the baseline and a set of well-known cell segmentation approaches. Conclusions The use of edge emphasizing U-Nets and optimized H-minima transform can improve the marker-controlled watershed transform for segmentation of densely cultivated 3D cell nuclei. A novel dataset of twelve spheroids was introduced to the public.
  • Hallamaa, Raija; Batchu, Krishna (2016)
    Background: Lipids have become an important target for searching new biomarkers typical of different autoimmune and allergic diseases. The most common allergic dermatitis of the horse is related to stings of insects and is known as insect bite hypersensitivity (IBH) or summer eczema, referring to its recurrence during the summer months. This intense pruritus has certain similarities with atopic dermatitis of humans. The treatment of IBH is difficult and therefore new strategies for therapy are needed. Autoserum therapy based on the use of serum phospholipids has recently been introduced for horses. So far, serum lipids relating to these allergic disorders have been poorly determined. The main aim of this study was to analyse phospholipid profiles in the sera of horses with allergic dermatitis and in their healthy controls and to further assess whether these lipid profiles change according to the clinical status after therapy. Methods: Sera were collected from 10 horses with allergic dermatitis and from 10 matched healthy controls both before and 4 weeks after the therapy of the affected horses. Eczema horses were treated with an autogenous preparation made from a horse's own serum and used for oral medication. Samples were analysed for their phospholipid content by liquid chromatography coupled to a triple-quadrupole mass spectrometer (LC-MS). Data of phospholipid concentrations between the groups and over the time were analysed by using the Friedman test. Correlations between the change of concentrations and the clinical status were assessed by Spearman's rank correlation test. Results: The major phospholipid classes detected were phosphatidylcholine (PC), sphingomyelin (SM), phosphatidylinositol (PI) and phosphatidylethanolamine (PE). Eczema horses had significantly lower total concentrations of PC (p <0.0001) and SM (p = 0.0115) than their healthy controls. After a 4-week therapy, no significant differences were found between the groups. Changes in SM concentrations correlated significantly with alterations in clinical signs (p = 0.0047). Conclusions: Horses with allergic dermatitis have an altered phospholipid profile in their sera as compared with healthy horses and these profiles seem to change according to their clinical status. Sphingomyelin seems to have an active role in the course of equine insect bite hypersensitivity.
  • Prusinkiewicz, Przemyslaw; Zhang, Teng; Owens, Andrew; Cieslak, Mikolaj; Elomaa, Paula (2022)
    A survey and model of fasciated flower heads separate fundamental and derived characteristics of phyllotactic patterns and highlight open problems in phyllotaxis research. Phyllotaxis is commonly considered in the context of circular meristems or receptacles, yet non-circular (fasciated) structures also give rise to new primordia and organs. Here we investigate phyllotactic patterns in fasciated flower heads in the Asteraceae plant family. We begin by surveying the phenomenon of fasciation. We then show that phyllotactic patterns in fasciated heads can be generated by removing the inessential assumption of circularity from the previously published model of gerbera heads. To characterize these patterns, we revisit the conceptual framework in which phyllotactic patterns are commonly described. We note that some notions, in particular parastichies and parastichy numbers, maintain their significance in non-circular phyllotaxis, whereas others, in particular the divergence angle, need to be extended or lose their role. These observations highlight a number of open problems related to phyllotaxis in general, which may be elucidated by studies of fasciated heads.
  • Solman, Maja; Ligabue, Alessio; Blazevits, Olga; Jaiswal, Alok; Zhou, Yong; Liang, Hong; Lectez, Benoit; Kopra, Kari; Guzman, Camilo; Harma, Harri; Hancock, John F.; Aittokallio, Tero; Abankwa, Daniel (2015)
    Hotspot mutations of Ras drive cell transformation and tumorigenesis. Less frequent mutations in Ras are poorly characterized for their oncogenic potential. Yet insight into their mechanism of action may point to novel opportunities to target Ras. Here, we show that several cancer-associated mutations in the switch III region moderately increase Ras activity in all isoforms. Mutants are biochemically inconspicuous, while their clustering into nanoscale signaling complexes on the plasma membrane, termed nanocluster, is augmented. Nanoclustering dictates downstream effector recruitment, MAPK-activity, and tumorigenic cell proliferation. Our results describe an unprecedented mechanism of signaling protein activation in cancer.
  • Pagliari, Maria Teresa; Rosendaal, Frits R.; Ahmadinejad, Minoo; Badiee, Zahra; Baghaipour, Mohammad-Reza; Baronciani, Luciano; Hidalgo, Olga Benitez; Bodo, Imre; Budde, Ulrich; Castaman, Giancarlo; Eshghi, Peyman; Goudemand, Jenny; Karimi, Mehran; Keikhaei, Bijan; Lassila, Riitta; Leebeek, Frank W. G.; Fernandez, Maria Fernanda Lopez; Mannucci, Pier Mannuccio; Marino, Renato; Oldenburg, Johannes; Peake, Ian; Santoro, Cristina; Schneppenheim, Reinhard; Tiede, Andreas; Toogeh, Gholamreza; Tosetto, Alberto; Trossaert, Marc; Yadegari, Hamideh; Zetterberg, Eva M. K.; Peyvandi, Flora; Federici, Augusto B.; Eikenboom, Jeroen (2022)
    Background Type 3 von Willebrand disease (VWD) is a severe bleeding disorder caused by the virtually complete absence of von Willebrand factor (VWF). Pathophysiological mechanisms of VWD like defective synthesis, secretion, and clearance of VWF have previously been evaluated using ratios of VWF propeptide (VWFpp) over VWF antigen (VWF:Ag) and factor (F)VIII coagulant activity (FVIII:C) over VWF:Ag. Objective To investigate whether the VWFpp/VWF:Ag and FVIII:C/VWF:Ag ratios may also be applied to understand the pathophysiological mechanism underlying type 3 VWD and whether VWFpp is associated with bleeding severity. Methods European and Iranian type 3 patients were enrolled in the 3WINTERS-IPS study. Plasma samples and buffy coats were collected and a bleeding assessment tool was administered at enrolment. VWF:Ag, VWFpp, FVIII:C, and genetic analyses were performed centrally, to confirm patients' diagnoses. VWFpp/VWF:Ag and FVIII:C/VWF:Ag ratios were compared among different variant classes using the Mann-Whitney test. Median differences with 95% confidence intervals (CI) were estimated using the Hodges-Lehmann method. VWFpp association with bleeding symptoms was assessed using Spearman's rank correlation. Results Homozygosity/compound heterozygosity for missense variants showed higher VWFpp level and VWFpp/VWF:Ag ratio than homozygosity/compound heterozygosity for null variants ([VWFpp median difference, 1.4 IU/dl; 95% CI, 0.2-2.7; P = .016]; [VWFpp/VWF:Ag median difference, 1.4; 95% CI, 0-4.2; P = .054]). FVIII:C/VWF:Ag ratio was similarly increased in both. VWFpp level did not correlate with the bleeding symptoms (r = .024; P = .778). Conclusions An increased VWFpp/VWF:Ag ratio is indicative of missense variants, whereas FVIII:C/VWF:Ag ratio does not discriminate missense from null alleles. The VWFpp level was not associated with the severity of bleeding phenotype.