Browsing by Subject "MAP"

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  • Vanhatalo, Jarno; Li, Zitong; Sillanpää, Mikko J. (2019)
    Motivation: Recent advances in high dimensional phenotyping bring time as an extra dimension into the phenotypes. This promotes the quantitative trait locus (QTL) studies of function-valued traits such as those related to growth and development. Existing approaches for analyzing functional traits utilize either parametric methods or semi-parametric approaches based on splines and wavelets. However, very limited choices of software tools are currently available for practical implementation of functional QTL mapping and variable selection. Results: We propose a Bayesian Gaussian process (GP) approach for functional QTL mapping. We use GPs to model the continuously varying coefficients which describe how the effects of molecular markers on the quantitative trait are changing over time. We use an efficient gradient based algorithm to estimate the tuning parameters of GPs. Notably, the GP approach is directly applicable to the incomplete datasets having even larger than 50% missing data rate (among phenotypes). We further develop a stepwise algorithm to search through the model space in terms of genetic variants, and use a minimal increase of Bayesian posterior probability as a stopping rule to focus on only a small set of putative QTL. We also discuss the connection between GP and penalized B-splines and wavelets. On two simulated and three real datasets, our GP approach demonstrates great flexibility for modeling different types of phenotypic trajectories with low computational cost. The proposed model selection approach finds the most likely QTL reliably in tested datasets.
  • Mascher, Martin; Muehlbauer, Gary J.; Rokhsar, Daniel S.; Chapman, Jarrod; Schmutz, Jeremy; Barry, Kerrie; Munoz-Amatriain, Maria; Close, Timothy J.; Wise, Roger P.; Schulman, Alan H.; Himmelbach, Axel; Mayer, Klaus F. X.; Scholz, Uwe; Poland, Jesse A.; Stein, Nils; Waugh, Robbie (2013)
  • Kivikoski, Mikko; Rastas, Pasi; Löytynoja, Ari; Merila, Juha (2021)
    We describe an integrative approach to improve contiguity and haploidy of a reference genome assembly and demonstrate its impact with practical examples. With two novel features of Lep-Anchor software and a combination of dense linkage maps, overlap detection and bridging long reads, we generated an improved assembly of the nine-spined stickleback (Pungitius pungitius) reference genome. We were able to remove a significant number of haplotypic contigs, detect more genetic variation and improve the contiguity of the genome, especially that of X chromosome. However, improved scaffolding cannot correct for mosaicism of erroneously assembled contigs, demonstrated by a de novo assembly of a 1.6-Mbp inversion. Qualitatively similar gains were obtained with the genome of three-spined stickleback (Gasterosteus aculeatus). Since the utility of genome-wide sequencing data in biological research depends heavily on the quality of the reference genome, the improved and fully automated approach described here should be helpful in refining reference genome assemblies.
  • Chen, Linxiao; Turunen, Joonas (2020)
    We consider Boltzmann random triangulations coupled to the Ising model on their faces, under Dobrushin boundary conditions and at the critical point of the model. The first part of this paper computes explicitly the partition function of this model by solving its Tutte's equation, extending a previous result by Bernardi and Bousquet-Melou (J Combin Theory Ser B 101(5):315-377, 2011) to the model with Dobrushin boundary conditions. We show that the perimeter exponent of the model is 7/3 in contrast to the exponent 5/2 for uniform triangulations. In the second part, we show that the model has a local limit in distribution when the two components of the Dobrushin boundary tend to infinity one after the other. The local limit is constructed explicitly using the peeling process along an Ising interface. Moreover, we show that the main interface in the local limit touches the (infinite) boundary almost surely only finitely many times, a behavior opposite to that of the Bernoulli percolation on uniform maps. Some scaling limits closely related to the perimeters of finite clusters are also obtained.
  • Hjort, Jan; Karjalainen, Olli; Aalto, Juha Antero; Westermann, Sebastian; Romanovsky, Vladimir; Nelson, Frederick; Etzelmüller, Bernd; Luoto, Miska (2018)
    Degradation of near-surface permafrost can pose a serious threat to the utilization of natural resources, and to the sustainable development of Arctic communities. Here we identify at unprecedentedly high spatial resolution infrastructure hazard areas in the Northern Hemisphere's permafrost regions under projected climatic changes and quantify fundamental engineering structures at risk by 2050. We show that nearly four million people and 70% of current infrastructure in the permafrost domain are in areas with high potential for thaw of near-surface permafrost. Our results demonstrate that one-third of pan-Arctic infrastructure and 45% of the hydrocarbon extraction fields in the Russian Arctic are in regions where thaw-related ground instability can cause severe damage to the built environment. Alarmingly, these figures are not reduced substantially even if the climate change targets of the Paris Agreement are reached.
  • Miettinen, Jukka; Carlier, Simon; Häme, Lauri; Mäkelä, Annikki; Minunno, Francesco; Penttilä, Juho; Pisl, Jan; Rasinmäki, Jussi; Rauste, Yrjo; Seitsonen, Lauri; Tian, Xianglin; Häme, Tuomas (2021)
    Forest biomass and carbon monitoring play a key role in climate change mitigation. Operational large area monitoring approaches are needed to enable forestry stakeholders to meet the increasing monitoring and reporting requirements. Here, we demonstrate the functionality of a cloud-based approach utilizing Sentinel-2 composite imagery and process-based ecosystem model to produce large area forest volume and primary production estimates. We describe the main components of the approach and implementation of the processing pipeline into the Forestry TEP cloud processing platform and produce four large area output maps: (1) Growing stock volume (GSV), (2) Gross primary productivity (GPP), (3) Net primary productivity (NPP) and (4) Stem volume increment (SVI), covering Finland and the Russian boreal forests until the Ural Mountains in 10 m spatial resolution. The accuracy of the forest structural variables evaluated in Finland reach pixel level relative Root Mean Square Error (RMSE) values comparable to earlier studies (basal area 39.4%, growing stock volume 58.5%, diameter 35.5% and height 33.5%), although most of the earlier studies have concentrated on smaller study areas. This can be considered a positive sign for the feasibility of the approach for large area primary production modelling, since forest structural variables are the main input for the process-based ecosystem model used in the study. The full coverage output maps show consistent quality throughout the target area, with major regional variations clearly visible, and with noticeable fine details when zoomed into full resolution. The demonstration conducted in this study lays foundation for further development of an operational large area forest monitoring system that allows annual reporting of forest biomass and carbon balance from forest stand level to regional analyses. The system is seamlessly aligned with process based ecosystem modelling, enabling forecasting and future scenario simulation.
  • Özkan, Güller; Haliloglu, Kamil; Turkoglu, Aras; Öztürk, Halil Ibrahim; Elkoca, Erdal; Poczai, Peter (2022)
    Assessment of genetic diversity among different varieties helps to improve desired characteristics of crops, including disease resistance, early maturity, high yield, and resistance to drought. Molecular markers are one of the most effective tools for discovering genetic diversity that can increase reproductive efficiency. Simple sequence repeats (SSRs), which are codominant markers, are preferred for the determination of genetic diversity because they are highly polymorphic, multi-allelic, highly reproducible, and have good genome coverage. This study aimed to determine the genetic diversity of 40 common bean (Phaseolus vulgaris L.) landraces collected from the Ispir district located in the Northeast Anatolia region of Turkiye and five commercial varieties using SSR markers. The Twenty-seven SSR markers produced a total of 142 polymorphic bands, ranging from 2 (GATS91 and PVTT001) to 12 (BM153) alleles per marker, with an average number of 5.26 alleles. The gene diversity per marker varied between 0.37 and 0.87 for BM053 and BM153 markers, respectively. When heterozygous individuals are calculated proportional to the population, the heterozygosity ranged from 0.00 to 1.00, with an average of 0.30. The expected heterozygosity of the SSR locus ranged from 0.37 (BM053) to 0.88 (BM153), with an average of 0.69. Nei's gene diversity scored an average of 0.69. The polymorphic information content (PIC) values of SSR markers varied from 0.33 (BM053) to 0.86 (BM153), with an average of 0.63 per locus. The greatest genetic distance (0.83) was between lines 49, 50, 53, and cultivar Karacasehir-90, while the shortest (0.08) was between lines 6 and 26. In cluster analysis using Nei's genetic distance, 45 common bean genotypes were divided into three groups and very little relationship was found between the genotypes and the geographical distances. In genetic structure analysis, three subgroups were formed, including local landraces and commercial varieties. The result confirmed that the rich diversity existing in Ispir bean landraces could be used as a genetic resource in designing breeding programs and may also contribute to Turkiye bean breeding programs.
  • Koort, Joanna; Coenye, Tom; Vandamme, Peter; Sukura, Antti; Björkroth, Johanna (Society for General Microbiology, 2004)
    Isolates 302, 334, 356, 377 and 379, detected in modified atmosphere packaged (MAP) broiler meat, together with LMG 12317T and LMG 13617, detected in dog tonsils, were analysed in a polyphasic taxonomy study including numerical analysis of ribopatterns and whole cell protein patterns, 16S rDNA sequence analysis, DNA-DNA hybridisation and determination of some phenotypic properties. The results indicated that these isolates represent a new species in the genus Enterococcus. The isolates showed classical phenotypic reactions for the genus Enterococcus with the exception of not possessing the Lancefield group D antigen. Isolates 334, LMG 12317T, and LMG 13617 showed the highest 16S rDNA sequence similarity (98.3-99.0%) with the Enterococcus pallens type strain. In the distance matrix tree based on 16S rDNA sequences, the three isolates were located in the Enterococcus avium –group with E. pallens as their closest phylogenic neighbour. Numerical analyses of whole cell protein patterns and HindIII/EcoRI ribotypes placed all seven isolates together in a single cluster separated from the E. avium group reference strains. The DNA-DNA hybridisation level between strains 334 and LMG 12317T was 93.5% confirming that they represent the same species. Low hybridisation levels (12-30%) were, on the other hand, obtained with the E. pallens and Enterococcus raffinosus type strains. The name Enterococcus hermanniensis sp. nov. is proposed, with strain LMG 12317T (=CCUG 48100 T) as the type strain.
  • Björkroth, Johanna; Ristiniemi, Minna; Vandamme, Peter; Korkeala, Hannu (Elsevier, 2005)
    In order to show which of the initial lactic acid bacteria (LAB) contaminants are also causing spoilage of a modified-atmosphere-packaged (MAP), marinated broiler leg product at 6ºC, LAB were enumerated and identified on the 2nd and 17th day following manufacture. A total of 8 fresh and 13 spoiled packages were studied for LAB levels. In addition, aerobic mesophilic bacteria and Enterobacteriaceae were determined. The average CFU/g values in the 8 fresh packages were 1.3 × 103, 9.8 × 103 and 2.6 × 102 on de Man Rogosa Sharpe agar (MRS), Plate Count Agar (PCA) and Violet Red Bile Glucose agar (VRBG), respectively. The commercial shelf life for the product had been set as 12 days and all packages analyzed on the 17th day were deemed unfit for human consumption by the sensory analysis. The corresponding CFU/g averages in the spoiled product were 1.4 × 109, 1.1 × 109 and 3.9 × 107 on MRS, PCA and VRBG agar, respectively. For characterization of LAB population, 104 colonies originating from the fresh and 144 colonies from the spoiled packages were randomly picked, cultured pure and identified to species level using a 16 and 23S rDNA HindIII RFLP (ribotyping) database. The results showed that enterococci (35.7% of the LAB population) were dominating in the fresh product whereas carnobacteria (59.7%) dominated among the spoilage LAB. Enterococcus faecalis, Carnobacterium piscicola and Carnobacterium divergens were the main species detected. In general, when the initial LAB population is compared to the spoilage LAB, a shift from homofermentative cocci towards carnobacteria, Lactobacillus sakei/curvatus and heterofermentative rods is seen in this marinated product.
  • Juntheikki, Joni (Helsingfors universitet, 2014)
    Purpose of this thesis is to estimate the carbon sequestration potential in eucalyptus plantations in Uruguay. This study also aims to show how beneficial these plantations are for carbon sinks. The aim of this research is calculate total carbon balance in eucalyptus plantations and compare the results to degraded lands. This study is first-of-its-kind study in Uruguay, but not unique globally. The objective was to use a modeling approach to formulate the results. The methodology of this study is based to the dynamic growth model (CO2fix V3.1). Model is developed to calculate and estimate forest carbon fluxes and stocks. In this study the model was utilized for estimating how much carbon is sequestered in eucalyptus plantations and soils. In this thesis the model was used to simulate eucalyptus forest plantations that stem from numerous studies and different data. Ad hoc Excel model was generated to form calculated results from the simulated data. A separate sensitivity analysis is also formulated to reveal a possible different outcome. The framework is based on a stand-level inventory data of forestry plantations provided by the Ministry of Uruguay (MGAP) and companies. Also multiple scientific reports and previous studies were used as guidelines for simulations and results. The forest stand, yield, soil and weather data used for this study are from three different departments. There are over 700 000 hectares of different species of eucalyptus plantations in Uruguay. The theoretical framework was tested computationally with eleven simulations. CO2fix was parameterized for fast-growing eucalyptus species used in different parts of Uruguay. The model gave outputs per hectare and then this result was scaled up to the national level. This study will also estimate how much grassland (Pampa) and former pasture land could sequester carbon. Situation prior to plantation is a baseline scenario and it is compared to the expected carbon sequestration of plantations. The model is also used to calculate the effect of changing rotation length on carbon stocks of forest ecosystem (forest vegetation and soil) and wood products. The results of this study show that currently the 707,674 hectares of eucalyptus plantations in Uruguay have the potential to sequester 65 million tonnes of carbon and reduce 238 million tonnes of CO2. The calculated carbon storage is 38 and simulated 25 million tonnes of C, products are deducted from the equation. During 22 years (1990–2012) the annual carbon sequestration benefit (afforestation-baseline) without products is 1 757 847 Mg C. The results suggest that it is reasonable to establish eucalyptus plantations on degraded, grassland (Pampa) and abandoned pasture land. The implications of the results are that eucalyptus plantations in Uruguay actually enhance carbon sequestration, are carbon sinks and store more carbon than grassland and abandoned pasture land. Plantations have a vast sequestration potential and are important in mitigating of CO2 emission and effects of the climate change. The findings endorse the significance of plantations to increase carbon sinks and this role will broaden in the future. The most relevant findings of this study are that afforestation increases the soil carbon in 10-year rotation plantations by 34% (101.1>75.6) and in 12-year rotation 38% (104.4>75.6 Mg Cha-1) in a 60-year simulation. The net (afforestation-baseline) average carbon stock benefit in the soil is 25.5 Mg C ha?1 in a 60-year simulation. The (CO2Fix) model indicate that the total average carbon sequestration for eucalyptus plantations is 92.3 Mg Cha?1. The average total carbon storage ranges from 25.8–138.5 Mg Cha?1 during a 60-year simulation. The simulations show that the net annual carbon storage in the living biomass is 29.1, 25.5 (soil) and 37.6 Mg C (products) on the average scenario. There is some fluctuation in the sequestration results in other 10 simulations. Previous studies have showed that the average carbon stock for eucalyptus plantations varies from 30–60 Mg C ha-1, when soil and products are deducted. The capacity of forest ecosystems to sequester carbon in the long run could be even more strengthened if a rotation length increases. Extending rotation from 10 to 12 years increased the average soil carbon stock from 25.5 to 28.8 Mg C (by 13%) in 60 year simulation. The results also indicate that mean annual precipitation (MAP) alters the carbon sinks of the forest ecosystem. There are some limitations in this study and they are clearly explained and analyzed. Hence, most of the results are estimations. Ministry and companies need to prolong planting of trees and even intensify annual programs in order to achieve carbon sequestration targets. Further research is needed to get an estimate of the total forest ecosystem carbon storages and fluxes.
  • Mpindi, John Patrick; Sara, Henri; Haapa-Paananen, Saija; Kilpinen, Sami; Pisto, Tommi; Bucher, Elmar; Ojala, Kalle; Iljin, Kristiina; Vainio, Paula; Bjorkman, Mari; Gupta, Santosh; Kohonen, Pekka; Nees, Matthias; Kallioniemi, Olli (2011)
    Background Meta-analysis of gene expression microarray datasets presents significant challenges for statistical analysis. We developed and validated a new bioinformatic method for the identification of genes upregulated in subsets of samples of a given tumour type (‘outlier genes’), a hallmark of potential oncogenes. Methodology A new statistical method (the gene tissue index, GTI) was developed by modifying and adapting algorithms originally developed for statistical problems in economics. We compared the potential of the GTI to detect outlier genes in meta-datasets with four previously defined statistical methods, COPA, the OS statistic, the t-test and ORT, using simulated data. We demonstrated that the GTI performed equally well to existing methods in a single study simulation. Next, we evaluated the performance of the GTI in the analysis of combined Affymetrix gene expression data from several published studies covering 392 normal samples of tissue from the central nervous system, 74 astrocytomas, and 353 glioblastomas. According to the results, the GTI was better able than most of the previous methods to identify known oncogenic outlier genes. In addition, the GTI identified 29 novel outlier genes in glioblastomas, including TYMS and CDKN2A. The over-expression of these genes was validated in vivo by immunohistochemical staining data from clinical glioblastoma samples. Immunohistochemical data were available for 65% (19 of 29) of these genes, and 17 of these 19 genes (90%) showed a typical outlier staining pattern. Furthermore, raltitrexed, a specific inhibitor of TYMS used in the therapy of tumour types other than glioblastoma, also effectively blocked cell proliferation in glioblastoma cell lines, thus highlighting this outlier gene candidate as a potential therapeutic target. Conclusions/Significance Taken together, these results support the GTI as a novel approach to identify potential oncogene outliers and drug targets. The algorithm is implemented in an R package (Text S1).
  • Cuni-Sanchez, Aida; Sullivan, Martin J. P.; Platts, Philip J.; Lewis, Simon L.; Marchant, Rob; Imani, Gerard; Hubau, Wannes; Abiem, Iveren; Adhikari, Hari; Albrecht, Tomas; Altman, Jan; Amani, Christian; Aneseyee, Abreham B.; Avitabile, Valerio; Banin, Lindsay; Batumike, Rodrigue; Bauters, Marijn; Beeckman, Hans; Begne, Serge K.; Bennett, Amy C.; Bitariho, Robert; Boeckx, Pascal; Bogaert, Jan; Braeuning, Achim; Bulonvu, Franklin; Burgess, Neil D.; Calders, Kim; Chapman, Colin; Chapman, Hazel; Comiskey, James; de Haulleville, Thales; Decuyper, Mathieu; DeVries, Ben; Dolezal, Jiri; Droissart, Vincent; Ewango, Corneille; Feyera, Senbeta; Gebrekirstos, Aster; Gereau, Roy; Gilpin, Martin; Hakizimana, Dismas; Hall, Jefferson; Hamilton, Alan; Hardy, Olivier; Hart, Terese; Heiskanen, Janne; Hemp, Andreas; Herold, Martin; Hiltner, Ulrike; Horak, David; Kamdem, Marie-Noel; Kayijamahe, Charles; Kenfack, David; Kinyanjui, Mwangi J.; Klein, Julia; Lisingo, Janvier; Lovett, Jon; Lung, Mark; Makana, Jean-Remy; Malhi, Yadvinder; Martin, Emanuel H.; Mitchard, Edward T. A.; Morel, Alexandra; Mukendi, John T.; Muller, Tom; Nchu, Felix; Nyirambangutse, Brigitte; Okello, Joseph; Peh, Kelvin S. -H.; Pellikka, Petri; Phillips, Oliver L.; Plumptre, Andrew; Qie, Lan; Rovero, Francesco; Sainge, Moses N.; Schmitt, Christine B.; Sedlacek, Ondrej; Ngute, Alain S. K.; Sheil, Douglas; Sheleme, Demisse; Simegn, Tibebu Y.; Simo-Droissart, Murielle; Sonke, Bonaventure; Soromessa, Teshome; Sunderland, Terry; Svoboda, Miroslav; Taedoumg, Hermann; Taplin, James; Thomas, Sean C.; Timberlake, Jonathan; Tuagben, Darlington; Umunay, Peter; Uzabaho, Eustrate; Verbeeck, Hans; Vleminckx, Jason; Wallin, Goran; Wheeler, Charlotte; Willcock, Simon; Woods, John T.; Zibera, Etienne (2021)
    Tropical forests store 40-50 per cent of terrestrial vegetation carbon(1). However, spatial variations in aboveground live tree biomass carbon (AGC) stocks remain poorly understood, in particular in tropical montane forests(2). Owing to climatic and soil changes with increasing elevation(3), AGC stocks are lower in tropical montane forests compared with lowland forests(2). Here we assemble and analyse a dataset of structurally intact old-growth forests (AfriMont) spanning 44 montane sites in 12 African countries. We find that montane sites in the AfriMont plot network have a mean AGC stock of 149.4 megagrams of carbon per hectare (95% confidence interval 137.1-164.2), which is comparable to lowland forests in the African Tropical Rainforest Observation Network(4) and about 70 per cent and 32 per cent higher than averages from plot networks in montane(2,5,6) and lowland(7) forests in the Neotropics, respectively. Notably, our results are two-thirds higher than the Intergovernmental Panel on Climate Change default values for these forests in Africa(8). We find that the low stem density and high abundance of large trees of African lowland forests(4) is mirrored in the montane forests sampled. This carbon store is endangered: we estimate that 0.8 million hectares of old-growth African montane forest have been lost since 2000. We provide country-specific montane forest AGC stock estimates modelled from our plot network to help to guide forest conservation and reforestation interventions. Our findings highlight the need for conserving these biodiverse(9,10) and carbon-rich ecosystems. The aboveground carbon stock of a montane African forest network is comparable to that of a lowland African forest network and two-thirds higher than default values for these montane forests.
  • Hassan, Shabbeer; Surakka, Ida; Taskinen, Marja-Riitta; Salomaa, Veikko; Palotie, Aarno; Wessman, Maija; Tukiainen, Taru; Pirinen, Matti; Palta, Priit; Ripatti, Samuli (2021)
    Previous research has shown that using population-specific reference panels has a significant effect on downstream population genomic analyses like haplotype phasing, genotype imputation, and association, especially in the context of population isolates. Here, we developed a high-resolution recombination rate mapping at 10 and 50 kb scale using high-coverage (20-30x) whole-genome sequenced data of 55 family trios from Finland and compared it to recombination rates of non-Finnish Europeans (NFE). We tested the downstream effects of the population-specific recombination rates in statistical phasing and genotype imputation in Finns as compared to the same analyses performed by using the NFE-based recombination rates. We found that Finnish recombination rates have a moderately high correlation (Spearman's rho = 0.67-0.79) with NFE, although on average (across all autosomal chromosomes), Finnish rates (2.268 +/- 0.4209 cM/Mb) are 12-14% lower than NFE (2.641 +/- 0.5032 cM/Mb). Finnish recombination map was found to have no significant effect in haplotype phasing accuracy (switch error rates similar to 2%) and average imputation concordance rates (97-98% for common, 92-96% for low frequency and 78-90% for rare variants). Our results suggest that haplotype phasing and genotype imputation mostly depend on population-specific contexts like appropriate reference panels and their sample size, but not on population-specific recombination maps. Even though recombination rate estimates had some differences between the Finnish and NFE populations, haplotyping and imputation had not been noticeably affected by the recombination map used. Therefore, the currently available HapMap recombination maps seem robust for population-specific phasing and imputation pipelines, even in the context of relatively isolated populations like Finland.
  • Virtanen, Elina A.; Söderholm, Maria; Moilanen, Atte (2022)
    Conservation planning addresses the development and expansion of protected areas and requires data on for instance species, habitats, and biodiversity. Data on threats is often minimal, although necessary in conservation planning. In principle, threats should guide which conservation actions to take and where, and how to allocate resources. The lack of threat information may also limit the validity of areas to be conserved, if the condition of areas is degraded by threats unknown. The protocol described here outlines the methodology for a systematic review to explore how threats are theoretically and methodologically understood and used in conservation plans across freshwater, marine and terrestrial environments. Our primary research question is: how have threats informed conservation planning? Studies will be categorized according to the types of threats and conservation features used, theoretical and methodological approaches applied, geographical context, and biome. The results are expected to increase our understanding about how threats can and should be addressed in conservation planning.
  • Abera, Temesgen; Heiskanen, Janne; Maeda, Eduardo; Hailu, Binyam Tesfaw; Pellikka, Petri (2022)
    While cropland expansion and demand for woodfuel exert increasing pressure on woody vegetation in East Africa, climate change is inducing woody cover gain. It is however unclear if these contrasting patterns have led to net fractional woody cover loss or gain. Here we used non-parametric fractional woody cover (WC) predictions and breakpoint detection algorithms driven by satellite observations (Landsat and MODIS) and airborne laser scanning to unveil the net fractional WC change during 2001-2019 over Ethiopia and Kenya. Our results show that total WC loss was 4-times higher than total gain, leading to net loss. The contribution of abrupt WC loss (59%) was higher than gradual losses (41%). We estimated an annual WC loss rate of up to 5% locally, with cropland expansion contributing to 57% of the total loss in the region. Major hotspots of WC loss and degradation corridors were identified inside as well as surrounding protected areas, in agricultural lands located close to agropastoral and pastoral livelihood zones, and near highly populated areas. As the dominant vegetation type in the region, Acacia-Commiphora bushlands and thickets ecosystem was the most threatened, accounting 69% of the total WC loss, followed by montane forest (12%). Although highly outweighed by loss, relatively more gain was observed in woody savanna than in other ecosystems. These results reveal the marked impact of human activities on woody vegetation and highlight the importance of protecting endangered ecosystems from increased human activities for mitigating impacts on climate and supporting sustainable ecosystem service provision in East Africa.
  • Huang, Jie; Howie, Bryan; McCarthy, Shane; Memari, Yasin; Walter, Klaudia; Min, Josine L.; Danecek, Petr; Malerba, Giovanni; Trabetti, Elisabetta; Zheng, Hou-Feng; Gambaro, Giovanni; Richards, J. Brent; Durbin, Richard; Timpson, Nicholas J.; Marchini, Jonathan; Soranzo, Nicole; UK10K Consortium; Paunio, Tiina (2015)
    Imputing genotypes from reference panels created by whole-genome sequencing (WGS) provides a cost-effective strategy for augmenting the single-nucleotide polymorphism (SNP) content of genome-wide arrays. The UK10K Cohorts project has generated a data set of 3,781 whole genomes sequenced at low depth (average 7x), aiming to exhaustively characterize genetic variation down to 0.1% minor allele frequency in the British population. Here we demonstrate the value of this resource for improving imputation accuracy at rare and low-frequency variants in both a UK and an Italian population. We show that large increases in imputation accuracy can be achieved by re-phasing WGS reference panels after initial genotype calling. We also present a method for combining WGS panels to improve variant coverage and downstream imputation accuracy, which we illustrate by integrating 7,562WGS haplotypes from the UK10K project with 2,184 haplotypes from the 1000 Genomes Project. Finally, we introduce a novel approximation that maintains speed without sacrificing imputation accuracy for rare variants.
  • Susiluoto, Tuija; Korkeala, Hannu; Björkroth, Johanna (Elsevier, 2002)
    Lactic acid bacteria (LAB) in retail, modified-atmosphere-packaged (MAP), marinated broiler meat strips on sell-by day were mainly identified as Leuconostoc gasicomitatum. A total of 32 packages, 3 to 5 packages of 7 differently marinated broiler meat products, were studied at the end of the producer-defined shelf life (at 6ºC, 7 to 9 days depending on the manufacturer). Prior to the microbiological analyses, appearance and smell of the product was checked and pH measured. Bacteria were cultured on MRS and Tomato Juice Agar (TJA), Rogosa SL agar (SLA), Plate Count Agar (PCA) and Streptomycin Thallium Acetate Agar (STAA) for the enumeration of LAB, lactobacilli, total bacterial count and B. thermosphacta, respectively. The average CFU/g of the 32 packages was 2.3 × 108 on PCA. The highest bacterial average, 3.1 × 108, was recovered on TJA, the corresponding CFU/g averages on MRS and SLA being 2.3 × 108 and 1.3 × 108, respectively. Despite the high LAB numbers, radical spoilage changes such as unpleasant odor, slime production and formation of gas were not recognized. B. thermosphacta did not form a significant part of the bacterial population since none of the levels exceeded the spoilage threshold level of 105 CFU/g reported in previous studies. In order to characterize the dominating LAB population, as many as 85, 85 and 88 colonies from MRS, TJA and SLA, respectively, were randomly picked and cultured pure. LAB were identified to species level using a 16 and 23S rDNA HindIII RFLP (ribotyping) database. Fifty-six of the 170 isolates picked from the non-selective LAB media (MRS and TJA) were identified as Leuconostoc gasicomitatum, followed by Carnobacterium divergens (41 isolates), Lactobacillus sakei and Lactobacillus curvatus subsp. melibiosus (31 isolates) and Lactobacillus curvatus subsp. curvatus (20 isolates) species. SLA proved not to be completely selective for lactobacilli because the growth of Leuconostoc spp. was not inhibited, Carnobacterium spp. were the only species not detected on SLA.
  • Estonian Biobank Res Team; Lepamets, Maarja; Auwerx, Chiara; Noukas, Margit; Kals, Mart; Kutalik, Zoltan (2022)
    Copy-number variations (CNV) are believed to play an important role in a wide range of complex traits, but discovering such associations remains challenging. While whole-genome sequencing (WGS) is the gold-standard approach for CNV detection, there are several orders of magnitude more samples with available genotyping microarray data. Such array data can be exploited for CNV detection using dedicated software (e.g., PennCNV); however, these calls suffer from elevated false-positive and -negative rates. In this study, we developed a CNV quality score that weights PennCNV calls (pCNVs) based on their likelihood of being true positive. First, we established a measure of pCNV reliability by leveraging evidence from multiple omics data (WGS, transcriptomics, and methylomics) obtained from the same samples. Next, we built a predictor of omics-confirmed pCNVs, termed omics-informed quality score (OQS), using only PennCNV software output parameters. Promisingly, OQS assigned to pCNVs detected in close family members was up to 35% higher than the OQS of pCNVs not carried by other relatives (p < 3.0 x 10(-90)), outperforming other scores. Finally, in an association study of four anthropometric traits in 89,516 Estonian Biobank samples, the use of OQS led to a relative increase in the trait variance explained by CNVs of up to 56% compared with published quality filtering methods or scores. Overall, we put forward a flexible framework to improve any CNV detection method leveraging multi-omics evidence, applied it to improve PennCNV calls, and demonstrated its utility by improving the statistical power for downstream association analyses.
  • Salokas, Kari; Liu, Xiaonan; Öhman, Tiina; Chowdhury, Iftekhar; Gawriyski, Lisa; Keskitalo, Salla; Varjosalo, Markku (2022)
    Much cell-to-cell communication is facilitated by cell surface receptor tyrosine kinases (RTKs). These proteins phosphorylate their downstream cytoplasmic substrates in response to stimuli such as growth factors. Despite their central roles, the functions of many RTKs are still poorly understood. To resolve the lack of systematic knowledge, we apply three complementary methods to map the molecular context and substrate profiles of RTKs. We use affinity purification coupled to mass spectrometry (AP-MS) to characterize stable binding partners and RTK–protein complexes, proximity-dependent biotin identification (BioID) to identify transient and proximal interactions, and an in vitro kinase assay to identify RTK substrates. To identify how kinase interactions depend on kinase activity, we also use kinase-deficient mutants. Our data represent a comprehensive, systemic mapping of RTK interactions and substrates. This resource adds information regarding well-studied RTKs, offers insights into the functions of less well-studied RTKs, and highlights RTK-RTK interactions and shared signaling pathways.