Browsing by Subject "QUALITY-CONTROL"

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  • Kyostila, Kaisa; Syrja, Pernilla; Jagannathan, Vidhya; Chandrasekar, Gayathri; Jokinen, Tarja S; Seppala, Eija H.; Becker, Doreen; Drogemuller, Michaela; Dietschi, Elisabeth; Drogemuller, Cord; Lang, Johann; Steffen, Frank; Rohdin, Cecilia; Jaderlund, Karin H.; Lappalainen, Anu K.; Hahn, Kerstin; Wohlsein, Peter; Baumgartner, Wolfgang; Henke, Diana; Oevermann, Anna; Kere, Juha; Lohi, Hannes; Leeb, Tosso (2015)
    Inherited neurodegenerative disorders are debilitating diseases that occur across different species. We have performed clinical, pathological and genetic studies to characterize a novel canine neurodegenerative disease present in the Lagotto Romagnolo dog breed. Affected dogs suffer from progressive cerebellar ataxia, sometimes accompanied by episodic nystagmus and behavioral changes. Histological examination revealed unique pathological changes, including profound neuronal cytoplasmic vacuolization in the nervous system, as well as spheroid formation and cytoplasmic aggregation of vacuoles in secretory epithelial tissues and mesenchymal cells. Genetic analyses uncovered a missense change, c.1288G>A; p.A430T, in the autophagy-related ATG4D gene on canine chromosome 20 with a highly significant disease association (p = 3.8 x 10(-136)) in a cohort of more than 2300 Lagotto Romagnolo dogs. ATG4D encodes a poorly characterized cysteine protease belonging to themacroautophagy pathway. Accordingly, our histological analyses indicated altered autophagic flux in affected tissues. The knockdown of the zebrafish homologue atg4da resulted in a widespread developmental disturbance and neurodegeneration in the central nervous system. Our study describes a previously unknown canine neurological disease with particular pathological features and implicates the ATG4D protein as an important autophagy mediator in neuronal homeostasis. The canine phenotype serves as a model to delineate the disease-causing pathological mechanism(s) and ATG4D function, and can also be used to explore treatment options. Furthermore, our results reveal a novel candidate gene for human neurodegeneration and enable the development of a genetic test for veterinary diagnostic and breeding purposes.
  • Jones, W; Gong, BS; Novoradovskaya, N; Li, D; Kusko, R; Richmond, TA; Johann, DJ; Bisgin, H; Sahraeian, SME; Bushel, PR; Pirooznia, M; Wilkins, K; Chierici, M; Bao, WJ; Basehore, LS; Lucas, AB; Burgess, D; Butler, DJ; Cawley, S; Chang, CJ; Chen, GC; Chen, T; Chen, YC; Craig, DJ; Del Pozo, A; Foox, J; Francescatto, M; Fu, YT; Furlanello, C; Giorda, K; Grist, KP; Guan, MJ; Hao, YY; Happe, S; Hariani, G; Haseley, N; Jasper, J; Jurman, G; Kreil, DP; Labaj, P; Lai, K; Li, JY; Li, QZ; Li, YL; Li, ZG; Liu, ZC; Lopez, MS; Miclaus, K; Miller, R; Mittal, VK; Mohiyuddin, M; Pabon-Pena, C; Parsons, BL; Qiu, FJ; Scherer, A; Shi, TL; Stiegelmeyer, S; Suo, C; Tom, N; Wang, D; Wen, ZN; Wu, LH; Xiao, WZ; Xu, C; Yu, Y; Zhang, JY; Zhang, YF; Zhang, ZH; Zheng, YT; Mason, CE; Willey, JC; Tong, WD; Shi, LM; Xu, J (2021)
    BackgroundOncopanel genomic testing, which identifies important somatic variants, is increasingly common in medical practice and especially in clinical trials. Currently, there is a paucity of reliable genomic reference samples having a suitably large number of pre-identified variants for properly assessing oncopanel assay analytical quality and performance. The FDA-led Sequencing and Quality Control Phase 2 (SEQC2) consortium analyze ten diverse cancer cell lines individually and their pool, termed Sample A, to develop a reference sample with suitably large numbers of coding positions with known (variant) positives and negatives for properly evaluating oncopanel analytical performance.ResultsIn reference Sample A, we identify more than 40,000 variants down to 1% allele frequency with more than 25,000 variants having less than 20% allele frequency with 1653 variants in COSMIC-related genes. This is 5-100x more than existing commercially available samples. We also identify an unprecedented number of negative positions in coding regions, allowing statistical rigor in assessing limit-of-detection, sensitivity, and precision. Over 300 loci are randomly selected and independently verified via droplet digital PCR with 100% concordance. Agilent normal reference Sample B can be admixed with Sample A to create new samples with a similar number of known variants at much lower allele frequency than what exists in Sample A natively, including known variants having allele frequency of 0.02%, a range suitable for assessing liquid biopsy panels.ConclusionThese new reference samples and their admixtures provide superior capability for performing oncopanel quality control, analytical accuracy, and validation for small to large oncopanels and liquid biopsy assays.
  • Verbeeren, Jens; Verma, Bhupendra; Niemela, Elina H.; Yap, Karen; Makeyev, Eugene V.; Frilander, Mikko J. (2017)
    Cellular homeostasis of the minor spliceosome is regulated by a negative feed-back loop that targets U11-48K and U11/U12-65K mRNAs encoding essential components of the U12-type intron-specific U11/U12 di-snRNP. This involves interaction of the U11 snRNP with an evolutionarily conserved splicing enhancer giving rise to unproductive mRNA isoforms. In the case of U11/U12-65K, this mechanism controls the length of the 3' untranslated region (3'UTR). We show that this process is dynamically regulated in developing neurons and some other cell types, and involves a binary switch between translation-competent mRNAs with a short 3'UTR to non-productive isoforms with a long 3'UTR that are retained in the nucleus or/and spliced to the downstream amylase locus. Importantly, the choice between these alternatives is determined by alternative terminal exon definition events regulated by conserved U12-and U2-type 50 splice sites as well as sequence signals used for pre-mRNA cleavage and polyadenylation. We additionally show that U11 snRNP binding to the U11/U12-65K mRNA species with a long 3'UTR is required for their nuclear retention. Together, our studies uncover an intricate molecular circuitry regulating the abundance of a key spliceosomal protein and shed new light on the mechanisms limiting the export of non-productively spliced mRNAs from the nucleus to the cytoplasm.
  • Kangas, Salla M.; Teppo, Jaakko; Lahtinen, Maija J.; Suoranta, Anu; Ghimire, Bishwa; Mattila, Pirkko; Uusimaa, Johanna; Varjosalo, Markku; Katisko, Jani; Hinttala, Reetta (2022)
    Background: Transcriptomic and proteomic profiling of human brain tissue is hindered by the availability of fresh samples from living patients. Postmortem samples usually represent the advanced disease stage of the patient. Furthermore, the postmortem interval can affect the transcriptomic and proteomic profiles. Therefore, fresh brain tissue samples from living patients represent a valuable resource of metabolically intact tissue. Implantation of deep brain stimulation (DBS) electrodes into the human brain is a neurosurgical treatment for, e.g., movement disorders. Here, we describe an improved approach to collecting brain tissues from surgical instruments used in implantation of DBS device for transcriptomics and proteomics analyses. Methods: Samples were extracted from guide tubes and recording electrodes used in routine DBS implantation procedure to treat patients with Parkinson's disease, genetic dystonia and tremor. RNA sequencing was performed in tissues extracted from the recording microelectrodes and liquid chromatography-mass spectrometry (LC-MS) performed in tissues from guide tubes. To assess the performance of the current approach, the obtained datasets were compared with previously published datasets representing brain tissues. Results: Altogether, 32,034 RNA transcripts representing the unique Ensembl gene identifiers were detected from eight samples representing both hemispheres of four patients. By using LC-MS, we identified 734 unique proteins from 31 samples collected from 14 patients. The datasets are available in the BioStudies database (accession number S-BSST667). Our results indicate that surgical instruments used in DBS installation retain brain material sufficient for protein and gene expression studies. Comparison with previously published datasets obtained with similar approach proved the robustness and reproducibility of the protocol. Conclusions: The instruments used during routine DBS surgery are a useful source for obtaining fresh brain tissues from living patients. This approach overcomes the issues that arise from using postmortem tissues, such as the effect of postmortem interval on transcriptomic and proteomic landscape of the brain, and can be used for studying molecular aspects of DBS-treatable diseases.
  • Katajisto, Pekka; Doehla, Julia; Chaffer, Christine L.; Pentinmikko, Nalle; Marjanovic, Nemanja; Iqbal, Md Sharif; Zoncu, Roberto; Chen, Walter; Weinberg, Robert A.; Sabatini, David M. (2015)
    By dividing asymmetrically, stem cells can generate two daughter cells with distinct fates. However, evidence is limited in mammalian systems for the selective apportioning of subcellular contents between daughters. We followed the fates of old and young organelles during the division of human mammary stemlike cells and found that such cells apportion aged mitochondria asymmetrically between daughter cells. Daughter cells that received fewer old mitochondria maintained stem cell traits. Inhibition of mitochondrial fission disrupted both the age-dependent subcellular localization and segregation of mitochondria and caused loss of stem cell properties in the progeny cells. Hence, mechanisms exist for mammalian stemlike cells to asymmetrically sort aged and young mitochondria, and these are important for maintaining stemness properties.
  • Skytthe, Axel; Harris, Jennifer R.; Czene, Kamila; Mucci, Lorelei; Adami, Hans-Olov; Christensen, Kaare; Hjelmborg, Jacob; Holm, Niels V.; Nilsen, Thomas S.; Kaprio, Jaakko; Pukkala, Eero (2019)
    The Nordic countries have comprehensive, population-based health and medical registries linkable on individually unique personal identity codes, enabling complete long-term follow-up. The aims of this study were to describe the NorTwinCan cohort established in 2010 and assess whether the cancer mortality and incidence rates among Nordic twins are similar to those in the general population. We analyzed approximately 260,000 same-sexed twins in the nationwide twin registers in Denmark, Finland, Norway and Sweden. Cancer incidence was determined using follow-up through the national cancer registries. We estimated standardized incidence (SIR) and mortality (SMR) ratios with 95% confidence intervals (CI) across country, age, period, follow-up time, sex and zygosity. More than 30,000 malignant neoplasms have occurred among the twins through 2010. Mortality rates among twins were slightly lower than in the general population (SMR 0.96; CI 95% [0.95, 0.97]), but this depends on information about zygosity. Twins have slightly lower cancer incidence rates than the general population, with SIRs of 0.97 (95% CI [0.96, 0.99]) in men and 0.96 (95% CI [0.94, 0.97]) in women. Testicular cancer occurs more often among male twins than singletons (SIR 1.15; 95% CI [1.02, 1.30]), while cancers of the kidney (SIR 0.82; 95% CI [0.76, 0.89]), lung (SIR 0.89; 95% CI [0.85, 0.92]) and colon (SIR 0.90; 95% CI [0.87, 0.94]) occur less often in twins than in the background population. Our findings indicate that the risk of cancer among twins is so similar to the general population that cancer risk factors and estimates of heritability derived from the Nordic twin registers are generalizable to the background populations.
  • Kooijmans, Linda M. J.; Maseyk, Kadmiel; Seibt, Ulli; Sun, Wu; Vesala, Timo; Mammarella, Ivan; Kolari, Pasi; Aalto, Juho; Franchin, Alessandro; Vecchi, Roberta; Valli, Gianluigi; Chen, Huilin (2017)
    Nighttime vegetative uptake of carbonyl sulfide (COS) can exist due to the incomplete closure of stomata and the light independence of the enzyme carbonic anhydrase, which complicates the use of COS as a tracer for gross primary productivity (GPP). In this study we derived night-time COS fluxes in a boreal forest (the SMEAR II station in Hyytiala, Finland; 61 degrees 51 ' N, 24 degrees 17 ' E; 181ma.s.l.) from June to November 2015 using two different methods: eddy-covariance (EC) measurements (FCOS-EC) and the radon-tracer method (FCOS-Rn). The total night-time COS fluxes averaged over the whole measurement period were -6.8 +/- 2.2 and -7.9 +/- 3.8 pmolm (-2) s (-1) for FCOS-Rn and FCOS-EC, respectively, which is 33-38% of the average daytime fluxes and 21% of the total daily COS uptake. The correlation of Rn-222 (of which the source is the soil) with COS (average R-2 = 0.58) was lower than with CO2 (0.70), suggesting that the main sink of COS is not located at the ground. These observations are supported by soil chamber measurements that show that soil contributes to only 34-40% of the total night-time COS uptake. We found a decrease in COS uptake with decreasing nighttime stomatal conductance and increasing vapor-pressure deficit and air temperature, driven by stomatal closure in response to a warm and dry period in August. We also discuss the effect that canopy layer mixing can have on the radon-tracer method and the sensitivity of (FCOS-EC) to atmospheric turbulence. Our results suggest that the nighttime uptake of COS is mainly driven by the tree foliage and is significant in a boreal forest, such that it needs to be taken into account when using COS as a tracer for GPP.
  • Flechard, Chris R.; Ibrom, Andreas; Skiba, Ute M.; de Vries, Wim; van Oijen, Marcel; Cameron, David R.; Dise, Nancy B.; Korhonen, Janne F. J.; Buchmann, Nina; Legout, Arnaud; Simpson, David; Sanz, Maria J.; Aubinet, Marc; Loustau, Denis; Montagnani, Leonardo; Neirynck, Johan; Janssens, Ivan A.; Pihlatie, Mari; Kiese, Ralf; Siemens, Jan; Francez, Andre-Jean; Augustin, Juergen; Varlagin, Andrej; Olejnik, Janusz; Juszczak, Radoslaw; Aurela, Mika; Berveiller, Daniel; Chojnicki, Bogdan H.; Dammgen, Ulrich; Delpierre, Nicolas; Djuricic, Vesna; Drewer, Julia; Dufrene, Eric; Eugster, Werner; Fauvel, Yannick; Fowler, David; Frumau, Arnoud; Granier, Andre; Gross, Patrick; Hamon, Yannick; Helfter, Carole; Hensen, Arjan; Horvath, Laszlo; Kitzler, Barbara; Kruijt, Bart; Kutsch, Werner L.; Lobo-do-Vale, Raquel; Lohila, Annalea; Longdoz, Bernard; Marek, Michal; Matteucci, Giorgio; Mitosinkova, Marta; Moreaux, Virginie; Neftel, Albrecht; Ourcival, Jean-Marc; Pilegaard, Kim; Pita, Gabriel; Sanz, Francisco; Schjoerring, Jan K.; Sebastia, Maria-Teresa; Tang, Y. Sim; Uggerud, Hilde; Urbaniak, Marek; van Dijk, Netty; Vesala, Timo; Vidic, Sonja; Vincke, Caroline; Weidinger, Tamas; Zechmeister-Boltenstern, Sophie; Butterbach-Bah, Klaus; Nemitz, Eiko; Sutton, Mark A. (2020)
    The impact of atmospheric reactive nitrogen (N-r) deposition on carbon (C) sequestration in soils and biomass of unfertilized, natural, semi-natural and forest ecosystems has been much debated. Many previous results of this dC/dN response were based on changes in carbon stocks from periodical soil and ecosystem inventories, associated with estimates of N-r deposition obtained from large-scale chemical transport models. This study and a companion paper (Flechard et al., 2020) strive to reduce uncertainties of N effects on C sequestration by linking multi-annual gross and net ecosystem productivity estimates from 40 eddy covariance flux towers across Europe to local measurement-based estimates of dry and wet N-r deposition from a dedicated collocated monitoring network. To identify possible ecological drivers and processes affecting the interplay between C and N-r inputs and losses, these data were also combined with in situ flux measurements of NO, N2O and CH4 fluxes; soil NO3- leaching sampling; and results of soil incubation experiments for N and greenhouse gas (GHG) emissions, as well as surveys of available data from online databases and from the literature, together with forest ecosystem (BAS-FOR) modelling. Multi-year averages of net ecosystem productivity (NEP) in forests ranged from -70 to 826 gCm(-2) yr(-1) at total wet + dry inorganic N-r deposition rates (N-dep) of 0.3 to 4.3 gNm(-2) yr(-1) and from -4 to 361 g Cm-2 yr(-1) at N-dep rates of 0.1 to 3.1 gNm(-2) yr(-1) in short semi-natural vegetation (moorlands, wetlands and unfertilized extensively managed grasslands). The GHG budgets of the forests were strongly dominated by CO2 exchange, while CH4 and N2O exchange comprised a larger proportion of the GHG balance in short semi-natural vegetation. Uncertainties in elemental budgets were much larger for nitrogen than carbon, especially at sites with elevated N-dep where N-r leaching losses were also very large, and compounded by the lack of reliable data on organic nitrogen and N-2 losses by denitrification. Nitrogen losses in the form of NO, N2O and especially NO3- were on average 27%(range 6 %-54 %) of N-dep at sites with N-dep <1 gNm(-2) yr(-1) versus 65% (range 35 %-85 %) for N-dep > 3 gNm(-2) yr(-1). Such large levels of N-r loss likely indicate that different stages of N saturation occurred at a number of sites. The joint analysis of the C and N budgets provided further hints that N saturation could be detected in altered patterns of forest growth. Net ecosystem productivity increased with N-r deposition up to 2-2.5 gNm(-2) yr(-1), with large scatter associated with a wide range in carbon sequestration efficiency (CSE, defined as the NEP/GPP ratio). At elevated N-dep levels (> 2.5 gNm(-2) yr(-1)), where inorganic N-r losses were also increasingly large, NEP levelled off and then decreased. The apparent increase in NEP at low to intermediate N-dep levels was partly the result of geographical cross-correlations between N-dep and climate, indicating that the actual mean dC/dN response at individual sites was significantly lower than would be suggested by a simple, straightforward regression of NEP vs. N-dep.
  • Wang, Kai; Zheng, Xunhua; Pihlatie, Mari; Vesala, Timo; Liu, Chunyan; Haapanala, Sami; Mammarella, Ivan; Rannik, Ullar; Liu, Huizhi (2013)
    Nitrous oxide (N2O) fluxes from a cotton field in northern China were measured for a year using the static chamber method based on a gas chromatograph (GC) and the eddy covariance (EC) technique based on a tunable diode laser (TDL). The aims were to compare the N2O fluxes obtained from both techniques, assess the uncertainties in the fluxes and evaluate the annual direct emission factors (EFds, i.e. the loss rate of fertilizer nitrogen via N2O emission) using the year-round datasets. During the experimental period, the hourly and daily mean chamber fluxes ranged from 0.6 to 781.8 and from 1.2 to 468.8 g N m−2 h−1, respectively. The simultaneously measured daily mean EC fluxes varied between −10.8 and 912.0 g N m−2 h−1. The EC measurements only provided trustworthy 30-min fluxes during high-emission period (a 20-day period immediately after the irrigation that followed the nitrogen fertilization event). A reliable comparison was confined to the high-emission period and showed that the chamber fluxes were 17–20% lower than the EC fluxes. This difference may implicate the magnitude of systematic underestimation in the fluxes from chamber measurements. The annual emission from the fertilized cotton field was estimated at 1.43 kg N ha−1 yr−1 by the chamber observations and 3.15 kg N ha−1 yr−1 by the EC measurements. The EFds calculated from the chamber and EC data were 1.04% and 1.65%, respectively. The chamber-based estimate was very close to the default value (1.0%) recommended by the Intergovernmental Panel on Climate Change. However, the difference in the EFds based on the two measurement techniques may vary greatly with changing environmental conditions and management practices. Further comparison studies are still needed to elucidate this issue.
  • Gong, BS; Li, D; Kusko, R; Novoradovskaya, N; Zhang, YF; Wang, SZ; Pabon-Pena, C; Zhang, ZH; Lai, K; Cai, WS; LoCoco, JS; Lader, E; Richmond, TA; Mittal, VK; Liu, LC; Johann, DJ; Willey, JC; Bushel, PR; Yu, Y; Xu, C; Chen, GC; Burgess, D; Cawley, S; Giorda, K; Haseley, N; Qiu, FJ; Wilkins, K; Arib, H; Attwooll, C; Babson, K; Bao, LL; Bao, WJ; Lucas, AB; Best, H; Bhandari, A; Bisgin, H; Blackburn, J; Blomquist, TM; Boardman, L; Burgher, B; Butler, DJ; Chang, CJ; Chaubey, A; Chen, T; Chierici, M; Chin, CR; Close, D; Conroy, J; Coleman, JC; Craig, DJ; Crawford, E; del Pozo, A; Deveson, IW; Duncan, D; Eterovic, AK; Fan, XH; Foox, J; Furlanello, C; Ghosal, A; Glenn, S; Guan, MJ; Haag, C; Hang, XY; Happe, S; Hennigan, B; Hipp, J; Hong, HX; Horvath, K; Hu, JH; Hung, LY; Jarosz, M; Kerkhof, J; Kipp, B; Kreil, DP; Lapunzina, P; Li, P; Li, QZ; Li, WH; Li, ZG; Liang, Y; Liu, SQ; Liu, ZC; Ma, C; Marella, N; Martin-Arenas, R; Megherbi, DB; Meng, QC; Mieczkowski, PA; Morrison, T; Muzny, D; Ning, BT; Parsons, BL; Paweletz, CP; Pirooznia, M; Qu, WB; Raymond, A; Rindler, P; Ringler, R; Sadikovic, B; Scherer, A; Schulze, E; Sebra, R; Shaknovich, R; Shi, Q; Shi, TL; Silla-Castro, JC; Smith, M; Lopez, MS; Song, P; Stetson, D; Strahl, M; Stuart, A; Supplee, J; Szankasi, P; Tan, HW; Tang, LY; Tao, YH; Thakkar, S; Thierry-Mieg, D; Thierry-Mieg, J; Thodima, VJ; Thomas, D; Tichy, B; Tom, N; Garcia, EV; Verma, S; Walker, K; Wang, C; Wang, JW; Wang, YX; Wen, ZN; Wirta, V; Wu, LH; Xiao, CL; Xiao, WZ; Xu, SB; Yang, M; Ying, JM; Yip, SH; Zhang, GL; Zhang, S; Zhao, MR; Zheng, YT; Zhou, XY; Mason, CE; Mercer, T; Tong, WD; Shi, LM; Jones, W; Xu, JS (2021)
    BackgroundTargeted sequencing using oncopanels requires comprehensive assessments of accuracy and detection sensitivity to ensure analytical validity. By employing reference materials characterized by the U.S. Food and Drug Administration-led SEquence Quality Control project phase2 (SEQC2) effort, we perform a cross-platform multi-lab evaluation of eight Pan-Cancer panels to assess best practices for oncopanel sequencing.ResultsAll panels demonstrate high sensitivity across targeted high-confidence coding regions and variant types for the variants previously verified to have variant allele frequency (VAF) in the 5-20% range. Sensitivity is reduced by utilizing VAF thresholds due to inherent variability in VAF measurements. Enforcing a VAF threshold for reporting has a positive impact on reducing false positive calls. Importantly, the false positive rate is found to be significantly higher outside the high-confidence coding regions, resulting in lower reproducibility. Thus, region restriction and VAF thresholds lead to low relative technical variability in estimating promising biomarkers and tumor mutational burden.ConclusionThis comprehensive study provides actionable guidelines for oncopanel sequencing and clear evidence that supports a simplified approach to assess the analytical performance of oncopanels. It will facilitate the rapid implementation, validation, and quality control of oncopanels in clinical use.
  • Akmal, Jan Sher; Salmi, Mika; Hemming, Björn; Teir, Linus; Suomalainen, Anni; Kortesniemi, Mika; Partanen, Jouni; Lassila, Antti (2020)
    Featured Application Accuracy of additively manufactured implants for clinical surgery. Abstract In craniomaxillofacial surgical procedures, an emerging practice adopts the preoperative virtual planning that uses medical imaging (computed tomography), 3D thresholding (segmentation), 3D modeling (digital design), and additive manufacturing (3D printing) for the procurement of an end-use implant. The objective of this case study was to evaluate the cumulative spatial inaccuracies arising from each step of the process chain when various computed tomography protocols and thresholding values were independently changed. A custom-made quality assurance instrument (Phantom) was used to evaluate the medical imaging error. A sus domesticus (domestic pig) head was analyzed to determine the 3D thresholding error. The 3D modeling error was estimated from the computer-aided design software. Finally, the end-use implant was used to evaluate the additive manufacturing error. The results were verified using accurate measurement instruments and techniques. A worst-case cumulative error of 1.7 mm (3.0%) was estimated for one boundary condition and 2.3 mm (4.1%) for two boundary conditions considering the maximum length (56.9 mm) of the end-use implant. Uncertainty from the clinical imaging to the end-use implant was 0.8 mm (1.4%). This study helps practitioners establish and corroborate surgical practices that are within the bounds of an appropriate accuracy for clinical treatment and restoration.
  • Hilander, Taru; Zhou, Xiao-Long; Konovalova, Svetlana; Zhang, Fu-Ping; Euro, Liliya; Shilov, Dmitri; Poutanen, Matti; Chihade, Joseph; Wang, En-Duo; Tyynismaa, Henna (2018)
    Accuracy of protein synthesis is enabled by the selection of amino acids for tRNA charging by aminoacyl-tRNA synthetases (ARSs), and further enhanced by the proofreading functions of some of these enzymes for eliminating tRNAs mischarged with noncognate amino acids. Mouse models of editing-defective cytoplasmic alanyl-tRNA synthetase (AlaRS) have previously demonstrated the importance of proofreading for cytoplasmic protein synthesis, with embryonic lethal and progressive neurodegeneration phenotypes. Mammalian mitochondria import their own set of nuclear-encoded ARSs for translating critical polypeptides of the oxidative phosphorylation system, but the importance of editing by the mitochondrial ARSs for mitochondrial proteostasis has not been known. We demonstrate here that the human mitochondrial AlaRS is capable of editing mischarged tRNAs in vitro, and that loss of the proofreading activity causes embryonic lethality in mice. These results indicate that tRNA proofreading is essential in mammalian mitochondria, and cannot be overcome by other quality control mechanisms.
  • Hänninen, Ulrika A.; Katainen, Riku; Tanskanen, Tomas; Plaketti, Roosa-Maria; Laine, Riku; Hamberg, Jiri; Ristimäki, Ari; Pukkala, Eero; Taipale, Minna; Mecklin, Jukka-Pekka; Forsström, Linda M.; Pitkänen, Esa; Palin, Kimmo; Välimäki, Niko; Mäkinen, Netta; Aaltonen, Lauri A. (2018)
    Small bowel adenocarcinoma (SBA) is an aggressive disease with limited treatment options. Despite previous studies, its molecular genetic background has remained somewhat elusive. To comprehensively characterize the mutational landscape of this tumor type, and to identify possible targets of treatment, we conducted the first large exome sequencing study on a population-based set of SBA samples from all three small bowel segments. Archival tissue from 106 primary tumors with appropriate clinical information were available for exome sequencing from a patient series consisting of a majority of confirmed SBA cases diagnosed in Finland between the years 2003-2011. Paired-end exome sequencing was performed using Illumina HiSeq 4000, and OncodriveFML was used to identify driver genes from the exome data. We also defined frequently affected cancer signalling pathways and performed the first extensive allelic imbalance (Al) analysis in SBA. Exome data analysis revealed significantly mutated genes previously linked to SBA (TP53, KRAS, APC, SMAD4, and BRAF), recently reported potential driver genes (SOX9, ATM, and ARID2), as well as novel candidate driver genes, such as ACVR2A, ACVR1B, BRCA2, and SMARCA4. We also identified clear mutation hotspot patterns in ERBB2 and BRAF. No BRAF V600E mutations were observed. Additionally, we present a comprehensive mutation signature analysis of SBA, highlighting established signatures 1A, 6, and 17, as well as U2 which is a previously unvalidated signature. Finally, comparison of the three small bowel segments revealed differences in tumor characteristics. This comprehensive work unveils the mutational landscape and most frequently affected genes and pathways in SBA, providing potential therapeutic targets, and novel and more thorough insights into the genetic background of this tumor type.
  • Khanshour, Anas M.; Kou, Ikuyo; Fan, Yanhui; Einarsdottir, Elisabet; Makki, Nadja; Kidane, Yared H.; Kere, Juha; Grauers, Anna; Johnson, Todd A.; Paria, Nandina; Patel, Chandreshkumar; Singhania, Richa; Kamiya, Nobuhiro; Takeda, Kazuki; Otomo, Nao; Watanabe, Kota; Luk, Keith D. K.; Cheung, Kenneth M. C.; Herring, John A.; Rios, Jonathan J.; Ahituv, Nadav; Gerdhem, Paul; Gurnett, Christina A.; Song, You-Qiang; Ikegawa, Shiro; Wise, Carol A. (2018)
    Adolescent idiopathic scoliosis (AIS) is the most common musculoskeletal disorder of childhood development. The genetic architecture of AIS is complex, and the great majority of risk factors are undiscovered. To identify new AIS susceptibility loci, we conducted the first genome-wide meta-analysis of AIS genome-wide association studies, including 7956 cases and 88 459 controls from 3 ancestral groups. Three novel loci that surpassed genome-wide significance were uncovered in intragenic regions of the CDH13 (P-value_rs4513093 = 1.7E-15), ABO (P-value_ rs687621 = 7.3E-10) and SOX6 (P-value_ rs1455114 = 2.98E-08) genes. Restricting the analysis to females improved the associations at multiple loci, most notably with variants within CDH13 despite the reduction in sample size. Genome-wide gene-functional enrichment analysis identified significant perturbation of pathways involving cartilage and connective tissue development. Expression of both SOX6 and CDH13 was detected in cartilage chondrocytes and chromatin immunoprecipitation sequencing experiments in that tissue revealed multiple HeK27ac-positive peaks overlapping associated loci. Our results further define the genetic architecture of AIS and highlight the importance of vertebral cartilage development in its pathogenesis.
  • Hancock, D. B.; Reginsson, G. W.; Gaddis, N. C.; Chen, X.; Saccone, N. L.; Lutz, S. M.; Qaiser, Beenish; Sherva, R.; Steinberg, S.; Zink, F.; Stacey, S. N.; Glasheen, C.; Chen, J.; Gu, F.; Frederiksen, B. N.; Loukola, A.; Gudbjartsson, D. F.; Brueske, I.; Landi, M. T.; Bickeboeller, H.; Madden, P.; Farrer, L.; Kaprio, J.; Kranzler, H. R.; Gelernter, J.; Baker, T. B.; Kraft, P.; Amos, C. I.; Caporaso, N. E.; Hokanson, J. E.; Bierut, L. J.; Thorgeirsson, T. E.; Johnson, E. O.; Stefansson, K. (2015)
    We conducted a 1000 Genomes-imputed genome-wide association study (GWAS) meta-analysis for nicotine dependence, defined by the Fagerstrom Test for Nicotine Dependence in 17 074 ever smokers from five European-ancestry samples. We followed up novel variants in 7469 ever smokers from five independent European-ancestry samples. We identified genome-wide significant association in the alpha-4 nicotinic receptor subunit (CHRNA4) gene on chromosome 20q13: lowest P = 8.0 x 10(-9) across all the samples for rs2273500-C (frequency = 0.15; odds ratio = 1.12 and 95% confidence interval = 1.08-1.17 for severe vs mild dependence). rs2273500-C, a splice site acceptor variant resulting in an alternate CHRNA4 transcript predicted to be targeted for nonsense-mediated decay, was associated with decreased CHRNA4 expression in physiologically normal human brains (lowest P = 7.3 x 10(-4)). Importantly, rs2273500-C was associated with increased lung cancer risk (N = 28 998, odds ratio = 1.06 and 95% confidence interval = 1.00-1.12), likely through its effect on smoking, as rs2273500-C was no longer associated with lung cancer after adjustment for smoking. Using criteria for smoking behavior that encompass more than the single 'cigarettes per day' item, we identified a common CHRNA4 variant with important regulatory properties that contributes to nicotine dependence and smoking-related consequences.
  • Niemelä, Elina H.; Oghabian, Ali; Staals, Raymond H. J.; Greco, Dario; Pruijn, Ger J. M.; Frilander, Mikko J. (2014)
  • Rannik, U.; Haapanala, S.; Shurpali, Narasinha; Mammarella, I.; Lind, Saara; Hyvönen, Niina; Peltola, O.; Zahniser, Mark; Martikainen, Pertti; Vesala, T. (2015)
    Four gas analysers capable of measuring nitrous oxide (N2O) concentration at a response time necessary for eddy covariance flux measurements were operated from spring until winter 2011 over a field cultivated with reed canary grass (RCG, Phalaris arundinacea, L.), a perennial bioenergy crop in eastern Finland. The instruments were TGA100A (Campbell Scientific Inc.), CW-TILDAS-CS (Aerodyne Research Inc.), N2O / CO-23d (Los Gatos Research Inc.) and QC-TILDAS-76-CS (Aerodyne Research Inc.). The period with high emissions, lasting for about 2 weeks after fertilization in late May, was characterized by an up to 2 orders of magnitude higher emission, whereas during the rest of the campaign the N2O fluxes were small, from 0.01 to 1 nmol m−2 s−1. Two instruments, CW-TILDAS-CS and N2O / CO-23d, determined the N2O exchange with minor systematic difference throughout the campaign, when operated simultaneously. TGA100A produced the cumulatively highest N2O estimates (with 29% higher values during the period when all instruments were operational). QC-TILDAS-76-CS obtained 36% lower fluxes than CW-TILDAS-CS during the first period, including the emission episode, whereas the correspondence with other instruments during the rest of the campaign was good. The reasons for systematic differences were not identified, suggesting further need for detailed evaluation of instrument performance under field conditions with emphasis on stability, calibration and any other factors that can systematically affect the accuracy of flux measurements. The instrument CW-TILDAS-CS was characterized by the lowest noise level (with a standard deviation of around 0.12 ppb at 10 Hz sampling rate) as compared to N2O / CO-23d and QC-TILDAS-76-CS (around 0.50 ppb) and TGA100A (around 2 ppb). We identified that for all instruments except CW-TILDAS-CS the random error due to instrumental noise was an important source of uncertainty at the 30 min averaging level and the total stochastic error was frequently of the same magnitude as the fluxes when N2O exchange was small at the measurement site. Both instruments based on continuous-wave quantum cascade laser, CW-TILDAS-CS and N2O / CO-23d, were able to determine the same sample of low N2O fluxes with a high mutual coefficient of determination at the 30 min averaging level and with minor systematic difference over the observation period of several months. This enables us to conclude that the new-generation instrumentation is capable of measuring small N2O exchange with high precision and accuracy at sites with low fluxes.
  • Sweeney, Patrick; Park, Hyunsun; Baumann, Marc; Dunlop, John; Frydman, Judith; Kopito, Ron; McCampbell, Alexander; Leblanc, Gabrielle; Venkateswaran, Anjli; Nurmi, Antti; Hodgson, Robert (2017)
    A hallmark of neurodegenerative proteinopathies is the formation of misfolded protein aggregates that cause cellular toxicity and contribute to cellular proteostatic collapse. Therapeutic options are currently being explored that target different steps in the production and processing of proteins implicated in neurodegenerative disease, including synthesis, chaperone-assisted folding and trafficking, and degradation via the proteasome and autophagy pathways. Other therapies, like mTOR inhibitors and activators of the heat shock response, can rebalance the entire proteostatic network. However, there are major challenges that impact the development of novel therapies, including incomplete knowledge of druggable disease targets and their mechanism of action as well as a lack of biomarkers to monitor disease progression and therapeutic response. A notable development is the creation of collaborative ecosystems that include patients, clinicians, basic and translational researchers, foundations and regulatory agencies to promote scientific rigor and clinical data to accelerate the development of therapies that prevent, reverse or delay the progression of neurodegenerative proteinopathies.
  • Mammarella, Ivan; Peltola, Olli; Nordbo, Annika; Järvi, Leena; Rannik, Üllar (2016)
    We have carried out an inter-comparison between EddyUH and EddyPro (R), two public software packages for post-field processing of eddy covariance data. Datasets including carbon dioxide, methane and water vapour fluxes measured over 2 months at a wetland in southern Finland and carbon dioxide and water vapour fluxes measured over 3 months at an urban site in Helsinki were processed and analysed. The purpose was to estimate the flux uncertainty due to the use of different software packages and to evaluate the most critical processing steps, determining the largest deviations in the calculated fluxes. Turbulent fluxes calculated with a reference combination of processing steps were in good agreement, the systematic difference between the two software packages being up to 2.0 and 6.7% for half-hour and cumulative sum values, respectively. The raw data preparation and processing steps were consistent between the software packages, and most of the deviations in the estimated fluxes were due to the flux corrections. Among the different calculation procedures analysed, the spectral correction had the biggest impact for closed-path latent heat fluxes, reaching a nocturnal median value of 15% at the wetland site. We found up to a 43% median value of deviation (with respect to the run with all corrections included) if the closed-path carbon dioxide flux is calculated without the dilution correction, while the methane fluxes were up to 10% lower without both dilution and spectroscopic corrections. The Webb-Pearman-Leuning (WPL) and spectroscopic corrections were the most critical steps for open-path systems. However, we found also large spectral correction factors for the open-path methane fluxes, due to the sensor separation effect.
  • Nordbo, Annika; Jarvi, Leena; Vesala, Timo (2012)
    Eddy covariance (EC) measurements of turbulent fluxes of momentum, sensible heat and latent heat—in addition to net radiation measurements—were conducted for three consecutive years in an urban environment: Helsinki, Finland. The aims were to: (i) quantify the detection limit and random uncertainty of turbulent fluxes, (ii) assess the systematic error caused by EC calculation-procedure choices on the energy balance residual, and (iii) report the energy balance of the world’s northernmost urban flux station. The mean detection limits were about 10% of the observed flux, and the random uncertainty was 9–16%. Of all fluxes, the latent heat flux— as measured with a closed-path gas analyzer—was most prone to systematic calculation errors due to water vapor interactions with tube walls: using a lag window that is too small can cause a 15% lack of data (due to the dependency of lag time on relative humidity) and omitting spectral corrections can cause on average a 26% underestimation of the flux. The systematic errors in EC calculation propagate into the energy balance residual and can be larger than the residual itself: for example, omitting spectral corrections overestimates the residual by 13% or 18% on average, depending on the analyzer.