Searching for genetic variants with unusual differentiation between subpopulations is an established approach for identifying signals of natural selection. However, existing methods generally require ...discrete subpopulations. We introduce a method that infers selection using principal components (PCs) by identifying variants whose differentiation along top PCs is significantly greater than the null distribution of genetic drift. To enable the application of this method to large datasets, we developed the FastPCA software, which employs recent advances in random matrix theory to accurately approximate top PCs while reducing time and memory cost from quadratic to linear in the number of individuals, a computational improvement of many orders of magnitude. We apply FastPCA to a cohort of 54,734 European Americans, identifying 5 distinct subpopulations spanning the top 4 PCs. Using the PC-based test for natural selection, we replicate previously known selected loci and identify three new genome-wide significant signals of selection, including selection in Europeans at ADH1B. The coding variant rs1229984∗T has previously been associated to a decreased risk of alcoholism and shown to be under selection in East Asians; we show that it is a rare example of independent evolution on two continents. We also detect selection signals at IGFBP3 and IGH, which have also previously been associated to human disease.
The contribution of repetitive elements to quantitative human traits is largely unknown. Here we report a genome-wide survey of the contribution of short tandem repeats (STRs), which constitute one ...of the most polymorphic and abundant repeat classes, to gene expression in humans. Our survey identified 2,060 significant expression STRs (eSTRs). These eSTRs were replicable in orthogonal populations and expression assays. We used variance partitioning to disentangle the contribution of eSTRs from that of linked SNPs and indels and found that eSTRs contribute 10-15% of the cis heritability mediated by all common variants. Further functional genomic analyses showed that eSTRs are enriched in conserved regions, colocalize with regulatory elements and may modulate certain histone modifications. By analyzing known genome-wide association study (GWAS) signals and searching for new associations in 1,685 whole genomes from deeply phenotyped individuals, we found that eSTRs are enriched in various clinically relevant conditions. These results highlight the contribution of STRs to the genetic architecture of quantitative human traits.
Crosslinking and immunoprecipitation (CLIP) protocols have made it possible to identify transcriptome-wide RNA-protein interaction sites. In particular, PAR-CLIP utilizes a photoactivatable ...nucleoside for more efficient crosslinking. We present an approach, centered on the novel PARalyzer tool, for mapping high-confidence sites from PAR-CLIP deep-sequencing data. We show that PARalyzer delineates sites with a high signal-to-noise ratio. Motif finding identifies the sequence preferences of RNA-binding proteins, as well as seed-matches for highly expressed microRNAs when profiling Argonaute proteins. Our study describes tailored analytical methods and provides guidelines for future efforts to utilize high-throughput sequencing in RNA biology. PARalyzer is available at http://www.genome.duke.edu/labs/ohler/research/PARalyzer/.
Palaeozoic (Silurian and Devonian) bedded cherts from the Balkan Terrane in western Bulgaria occur in three tectonic units: Svoge, Lyubash-Golo Bardo, and Morava. The Silurian and Devonian ages of ...the chert-bearing lithostratigraphic successions have been determined by conodonts and graptolite macrofauna. The silica source and depositional settings of the cherts have been interpreted based on the received mineralogical, petrographic, and geochemical (major, trace, and rare earth elements) data. The presence of radiolarian tests, the Si/Si+Al+Fe+Ca ratios, and Al–Fe–Mn diagram plotting at the non-hydrothermal field, testify that the source of silica in the studied rocks is mostly biogenic or both biogenic and terrigenous in origin. Differential thermal analysis results suggest that the Silurian and Devonian siliceous rocks were presumably formed in predominating anoxic oceanic conditions and only sporadically in oxic waters. The MnO/TiO
2
ratio and received Al
2
O
3
, Fe
2
O
3
, TiO
2
, La
n
, and Ce
n
contents indicate that the studied cherts have been deposited in continental margin environments. Most probably, they have been formed in slope and outer-shelf settings on the passive margin of northern peri-Gondwana.
The north-vergent Balkan fold–thrust belt of the Balkanide orogen, extending from northeast Serbia to the Black Sea region, was formed during at least two Alpine compressional events. However, ...remnants of the Variscan orogen are still preserved in its western and central parts. In the central part (Central Stara Planina Mountains), two pre-Permian metamorphic complexes of contrasting metamorphic degrees, the low-grade Stara Planina and high-grade Sredna Gora complexes, are juxtaposed along a major Variscan tectonic zone and intruded by voluminous granitoids of previously unknown age. Here, we present an extensive structural and U–Pb (TIMS and LA-ICP-MS) geochronological analysis, constraining several magmatic and tectonic events in the pre-Alpine evolution of the area. For the first time, early Cambrian magmatism (531.7 ± 1.5 Ma/519.4 ± 2 Ma) is reported from a granite intruding the low-grade Stara Planina complex. The juxtaposition of the metamorphic complexes before 314 Ma was followed by a transpressional stage between 313 and 306 Ma. The last Variscan penetrative ductile deformation was associated with the final emplacement stages of the Ambaritsa sheet-like pluton at about 306 Ma under still ongoing compression. In addition, at least two post-Variscan magmatic pulses of granitoid magmatism (at ca. 306–304 Ma and 250 Ma) have been distinguished in the studied area. Later, Alpine ductile to brittle deformational events led to an additional reworking of the Variscan edifice.
protein expression landscape of the Arabidopsis root Petricka, Jalean J; Schauer, Monica A; Megraw, Molly ...
Proceedings of the National Academy of Sciences - PNAS,
05/2012, Letnik:
109, Številka:
18
Journal Article
Recenzirano
Odprti dostop
Because proteins are the major functional components of cells, knowledge of their cellular localization is crucial to gaining an understanding of the biology of multicellular organisms. We have ...generated a protein expression map of the Arabidopsis root providing the identity and cell type-specific localization of nearly 2,000 proteins. Grouping proteins into functional categories revealed unique cellular functions and identified cell type-specific biomarkers. Cellular colocalization provided support for numerous protein–protein interactions. With a binary comparison, we found that RNA and protein expression profiles are weakly correlated. We then performed peak integration at cell type-specific resolution and found an improved correlation with transcriptome data using continuous values. We performed GeLC-MS/MS (in-gel tryptic digestion followed by liquid chromatography-tandem mass spectrometry) proteomic experiments on mutants with ectopic and no root hairs, providing complementary proteomic data. Finally, among our root hair-specific proteins we identified two unique regulators of root hair development.
The Paleozoic evolution of the Paleo-Tethys (NW Turkey) remains unclear due to lack of sufficient geological and geochronological data from the Strandja Massif. In the present contribution, we ...provide new geological, petrographical, geochemical, and first zircon LA-ICP-MS (U–Pb) and apatite (U-Th)/He age data from the ultramafic and mafic metamorphic rocks, remnants of the Paleo-Tethys in the Strandja Massif. The ultramafic and mafic metamorphic rocks in the Karaçoban area (Lalapaşa, NW Thrace) are the host serpentinite body located in contact with the surrounding gneisses, and hornblend-hornfels, chloritite, and amphibolite bands as the blackwall-rocks of metasomatized mantle peridotite. Of these, the chloritite has unusually high zircon contents, which contrast with the usual lack of this mineral in ultramafic rocks. The LA-ICPMS zircon geochronology of chloritites gives clue for two main age clusters, dated at 360 ± 2.2 Ma and 316.6 ± 2.5 Ma, which most probably correspond to its magmatic crystallization and metamorphism. The application of Ti-in-zircon thermometer (T
ZT
) reveals crystallization temperatures ranging from 696 to 852 °C for the chloritite. Seven apatite crystals of the chloritite yielded (U-Th)/He (AHe) ages from 33.3 ± 2.1 to 56.1 ± 5.6 Ma. The AHe ages are not scattered and tightly clustered with a weighted average of 46.4 ± 2.9 Ma. This age could be interpreted that the ultramafic and mafic metamorphic rocks of the Strandja Massif exhumed and cooled in the Lutetian time at ~ 65 to 70 °C. The studied ultramafic and mafic metamorphic rocks represent igneous protoliths in an oceanic ridge extensional setting associated with the Upper Paleozoic opening of the Paleo-Tethys.
The Elatsite–Chelopech ore field in the northern part of the Panagyurishte district in Central Bulgaria comprises numerous spatially associated porphyry copper and epithermal gold deposits and ...prospects. In addition to the mineralization and alteration features, trace elements, lead and sulfur isotope signatures of sulfide minerals from porphyry copper, base metal and gold-base metal deposits/prospects have been studied. LA-ICP-MS analyses of pyrite, arsenopyrite and sulfosalt minerals validate them as major carriers for Au, Ag, Sb, Se and Co. Pyrite from the three types of mineralization has specific geochemical characteristics. Pyrite from the porphyry copper deposits/prospects has generally lower total trace element content compared to pyrite from the epithermal prospects, except for Se, Co and Ni. Pyrite from the base metal and gold-base metal veins is enriched in As, Au, Ag, Sb and Pb. In pyrite from the base metal deposits, Co and Ni have contents comparable to the pyrite from the porphyry copper deposits, while pyrite from the gold-base metal veins shows lower Co and Ni. Arsenopyrite from these deposits shows similar features. Similarly, sphalerite from the gold-base metal veins also has lower Co content compared to sphalerite from the base metal veins but higher In and Cu contents. In addition to the close spatial relationships between the Elatsite and Gorna Kamenitsa porphyry Cu deposits and Negarstitsa-West and Dolna Kamenitsa base metal prospects, as well as similarities in the mineralization and alteration styles, the lead isotopic (206Pb/204Pb = 18.61–18.68, 207Pb/204Pb = 15.64–15.65 for porphyry and 206Pb/204Pb = 18.55–18.67, 207Pb/204Pb = 15.64–15.68 for base metal) and sulfur isotopic (δ34S values of −3 to +1‰ for porphyry and δ34S values of −1.7 to +3.5‰ for base metal) signatures of sulfides support the idea of a genetic link between these two types of deposits. The porphyry and base-metal mineralization result from a common major ore-forming event during the Late Cretaceous, corresponding to deep/higher-temperature and shallower/distal/lower-temperature environments, respectively. In particular, more radiogenic lead (206Pb/204Pb = 18.41–18.47, 207Pb/204Pb = 15.67–15.76) and slightly different sulfur isotopic compositions (δ34S values of +3.5 to +10.6‰) of sulfides from the distal gold-base metal veins of Kordunsko Dere, Svishti Plaz and Shipkite might be a consequence of the interaction of the ore-forming fluids with an external older crustal and isotopically positive S source. Alternatively, a different fluid source/event for the formation of these gold-base metal veins may be suggested.
The Balkan Vegetation Database (BVD; GIVD ID: EU-00-019) is a regional database, which was established in 2014. It comprises phytosociological relevés covering various vegetation types from nine ...countries of the Balkan Peninsula (Albania – 153 relevés, Bosnia and Herzegovina – 1715, Bulgaria – 12,282, Greece – 465, Croatia – 69, Kosovo – 493, Montenegro – 440, North Macedonia – 13 and Serbia – 2677). Currently, it contains 18,306 relevés (compared to 9.580 in 2016), and most of them (82.8%) are geo-referenced. The database includes both digitized relevés from the literature (65.6%) and unpublished data (34.5%). Plot size is available for 84.7% of all relevés. During the last four years some “header data information” was improved e.g. elevation (now available for 83.4% of all relevés), aspect (67.7%), slope (66%), total cover of vegetation (54.3%), cover of tree, shrub, herb, bryophyte and lichen layers (27.1%, 20.1%, 40.2%, 11.5% and 2.1%), respectively. Data access is either semi-restricted (65.6%) or restricted (34.4%). Most relevés (84.6%) are classified to syntaxa of different levels. The database has been used for numerous studies with various objectives from floristic, vegetation and habitat-related topics, to macroecological studies at the local, regional, national, continental and global levels. During the last four years, BVD data were requested from 111 different projects via the EVA and sPlot databases.
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