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1
Authors: Martin Segesdi, Attila Ősi
Published: Mar 2021
Authors: Martin Segesdi, Attila Ősi
Published: Mar 2021
Abstract Sauropterygia was a diverse clade of secondary aquatic reptiles, which represented one of the most important vertebrate groups in the shallow marine communities during the Triassic. However, despite the long history of collection and examination of sauropterygian remains, previous studies have indicated that the fossil record of this group is incomplete, making the understanding of their palaeobiogeographic relations difficult. Here we describe new sauropterygian remains from the Middle Triassic (Ladinian) Templomhegy Dolomite Member (Villány, southern Hungary), which were unearthed during systematic fieldwork of previous years. Among several non-diagnostic sauropterygian remains, this material contains isolated bones belonging to Nothosaurus sp., Simosauridae indet. and a small-sized nothosaurid. The known faunal composition from Villány is similar to what was described from the Middle Triassic of the Germanic Basin and Bihor Mountains (northwestern Romania). Besides isolated elements, a probably associated skeleton of a small-sized eosauropterygian specimen of unknown affinities is also reported here. This locality widens our knowledge on Triassic sauropterygian distribution and provides new information about the previously not well-known Middle Triassic vertebrate fauna of the one-time southern Eurasian shelf region.
1
Authors: Maria Cristina Bonci, Davide Dagnino, Andrea Mandarino, Aaron Mazzini, Michele Piazza
Published: Feb 2021
Authors: Maria Cristina Bonci, Davide Dagnino, Andrea Mandarino, Aaron Mazzini, Michele Piazza
Published: Feb 2021
The aim of this paper is the revision and redocumentation of Ostrea (Gigantostrea) gigantica Solander var. oligoplana Sacco, 1897, Ostrea (Ostrea) isseli n. denom. Rovereto, 1897, and Ostrea (Ostrea) isseli n. denom. var. elongata Rovereto, 1897. These taxa are from the Oligocene strata of the Molare Formation (Tertiary Piedmont Basin, southern Piedmont - central Liguria, NW Italy). The syntypes of O. (G.) gigantica var. oligoplana are in the "Collezione Bellardi e Sacco", at the Museo Regionale di Scienze Naturali di Torino; the syntypes of O. (O.) isseli and O. (O.) isseli var. elongata are in the "Collezione BTP" (BTP Collection, at the Dipartimento di Scienze della Terra, dell'Ambiente e della Vita - DISTAV - of the Università di Genova). The var. oligoplana is here moved to the species rank and allocated to the genus Pycnodonte Fischer von Waldheim, 1835. O. (O.) isseli and O. (O.) isseli var. elongata are recognized as junior synonyms of the Sacco's taxon. Rovereto (1897) compared his new species with Ostrea subgigantea Raulin & Delbos, 1855, a poorly known taxon, that is here figured for the first time and shown to represent a species different from P. oligoplana (Sacco, 1897).
1
Authors: Camilo Broc, Therese Truong, Benoit Liquet
Published: Feb 2021
Authors: Camilo Broc, Therese Truong, Benoit Liquet
Published: Feb 2021
Abstract Background The increasing number of genome-wide association studies (GWAS) has revealed several loci that are associated to multiple distinct phenotypes, suggesting the existence of pleiotropic effects. Highlighting these cross-phenotype genetic associations could help to identify and understand common biological mechanisms underlying some diseases. Common approaches test the association between genetic variants and multiple traits at the SNP level. In this paper, we propose a novel gene- and a pathway-level approach in the case where several independent GWAS on independent traits are available. The method is based on a generalization of the sparse group Partial Least Squares (sgPLS) to take into account groups of variables, and a Lasso penalization that links all independent data sets. This method, called joint-sgPLS, is able to convincingly detect signal at the variable level and at the group level. Results Our method has the advantage to propose a global readable model while coping with the architecture of data. It can outperform traditional methods and provides a wider insight in terms of a priori information. We compared the performance of the proposed method to other benchmark methods on simulated data and gave an example of application on real data with the aim to highlight common susceptibility variants to breast and thyroid cancers. Conclusion The joint-sgPLS shows interesting properties for detecting a signal. As an extension of the PLS, the method is suited for data with a large number of variables. The choice of Lasso penalization copes with architectures of groups of variables and observations sets. Furthermore, although the method has been applied to a genetic study, its formulation is adapted to any data with high number of variables and an exposed a priori architecture in other application fields.
1
Authors: Duan, Aiping, et al
Published: Feb 2021
Authors: Duan, Aiping, et al
Published: Feb 2021
Abstract Background Cell type-specific transcriptional programming results from the combinatorial interplay between the repertoire of active regulatory elements. Disease-associated variants disrupt such programming, leading to altered expression of downstream regulated genes and the onset of pathological states. However, due to the non-linear regulatory properties of non-coding elements such as enhancers, which can activate transcription at long distances and in a non-directional way, the identification of causal variants and their target genes remains challenging. Here, we provide a multi-omics analysis to identify regulatory elements associated with functional kidney disease variants, and downstream regulated genes. Results In order to understand the genetic risk of kidney diseases, we generated a comprehensive dataset of the chromatin landscape of human kidney tubule cells, including transcription-centered 3D chromatin organization, histone modifications distribution and transcriptome with HiChIP, ChIP-seq and RNA-seq. We identified genome-wide functional elements and thousands of interactions between the distal elements and target genes. The results revealed that risk variants for renal tumor and chronic kidney disease were enriched in kidney tubule cells. We further pinpointed the target genes for the variants and validated two target genes by CRISPR/Cas9 genome editing techniques in zebrafish, demonstrating that SLC34A1 and MTX1 were indispensable genes to maintain kidney function. Conclusions Our results provide a valuable multi-omics resource on the chromatin landscape of human kidney tubule cells and establish a bioinformatic pipeline in dissecting functions of kidney disease-associated variants based on cell type-specific epigenome.
1
Authors: Hof, Lotta, et al
Published: Feb 2021
Authors: Hof, Lotta, et al
Published: Feb 2021
Abstract Background Organoids are morphologically heterogeneous three-dimensional cell culture systems and serve as an ideal model for understanding the principles of collective cell behaviour in mammalian organs during development, homeostasis, regeneration, and pathogenesis. To investigate the underlying cell organisation principles of organoids, we imaged hundreds of pancreas and cholangiocarcinoma organoids in parallel using light sheet and bright-field microscopy for up to 7 days. Results We quantified organoid behaviour at single-cell (microscale), individual-organoid (mesoscale), and entire-culture (macroscale) levels. At single-cell resolution, we monitored formation, monolayer polarisation, and degeneration and identified diverse behaviours, including lumen expansion and decline (size oscillation), migration, rotation, and multi-organoid fusion. Detailed individual organoid quantifications lead to a mechanical 3D agent-based model. A derived scaling law and simulations support the hypotheses that size oscillations depend on organoid properties and cell division dynamics, which is confirmed by bright-field microscopy analysis of entire cultures. Conclusion Our multiscale analysis provides a systematic picture of the diversity of cell organisation in organoids by identifying and quantifying the core regulatory principles of organoid morphogenesis.
1
Authors: Malehmir, Alireza, et al
Published: Feb 2021
Authors: Malehmir, Alireza, et al
Published: Feb 2021
Abstract. Many metallic mineral deposits have sufficient physical property contrasts, particularly density,to be detectable using seismic methods. These deposits are sometimes significant for our society andeconomic growth and can help to accelerate the energy transition towards decarbonization. However,their exploration at depth requires high-resolution and sensitive methods. Following a series of2D seismic trials, a sparse, narrow source–receiver azimuth, 3D seismic survey was conducted inthe Blötberget mine, in central Sweden, covering an area of approximately 6 km2 fordeep-targeting iron oxide deposits and their host rock structures. The survey benefited from acollaborative work by putting together 1266 seismic recorders and a 32 t vibrator,generating 1056 shot points in a fixed geometry setup. Shots were fired at every 10 mwhere possible, and receivers were placed at every 10–20 m. Notable quality data were acquireddespite the area being dominated by swampy places as well as by built-up roads and historicaltailings. The data processing had to overcome these challenges for the staticcorrections and strong surface waves in particular. A tailored for hardrock setting and processing workflow wasdeveloped for handling such a dataset, where the use of mixed 2D and 3D refraction staticcorrections was relevant. The resulting seismic volume is rich in terms of reflectivity, with clearsoutheast-dipping reflections originating from the iron oxide deposits extending vertically andlaterally at least 300 m beyond what was known from available boreholes. As a result, weestimate potential additional resources from the 3D reflection seismic experiment on the order of10 Mt to be worth drilling for detailed assessments. The mineralization is crosscut by at leasttwo major sets of northwest-dipping reflections interpreted to dominantly be normal faults and to beresponsible for much of the lowland in the Blötberget area. Moreover, thesepost-mineralization faults likely control the current 3D geometry of the deposits. Curved andsubmerged reflections interpreted from folds or later intrusions are also observed, showing thegeological complexity of the study area. The seismic survey also delineates the near-surfaceexpression of a historical tailing as a by-product of refraction static corrections, demonstratingwhy 3D seismic data are so valuable for both mineral exploration and mine planning applications.
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Authors: Krishnan, Vandhana, et al
Published: Feb 2021
Authors: Krishnan, Vandhana, et al
Published: Feb 2021
Abstract Background Benchmarking the performance of complex analytical pipelines is an essential part of developing Lab Developed Tests (LDT). Reference samples and benchmark calls published by Genome in a Bottle (GIAB) consortium have enabled the evaluation of analytical methods. The performance of such methods is not uniform across the different genomic regions of interest and variant types. Several benchmarking methods such as hap.py, vcfeval, and vcflib are available to assess the analytical performance characteristics of variant calling algorithms. However, assessing the performance characteristics of an overall LDT assay still requires stringing together several such methods and experienced bioinformaticians to interpret the results. In addition, these methods are dependent on the hardware, operating system and other software libraries, making it impossible to reliably repeat the analytical assessment, when any of the underlying dependencies change in the assay. Here we present a scalable and reproducible, cloud-based benchmarking workflow that is independent of the laboratory and the technician executing the workflow, or the underlying compute hardware used to rapidly and continually assess the performance of LDT assays, across their regions of interest and reportable range, using a broad set of benchmarking samples. Results The benchmarking workflow was used to evaluate the performance characteristics for secondary analysis pipelines commonly used by Clinical Genomics laboratories in their LDT assays such as the GATK HaplotypeCaller v3.7 and the SpeedSeq workflow based on FreeBayes v0.9.10. Five reference sample truth sets generated by Genome in a Bottle (GIAB) consortium, six samples from the Personal Genome Project (PGP) and several samples with validated clinically relevant variants from the Centers for Disease Control were used in this work. The performance characteristics were evaluated and compared for multiple reportable ranges, such as whole exome and the clinical exome. Conclusions We have implemented a benchmarking workflow for clinical diagnostic laboratories that generates metrics such as specificity, precision and sensitivity for germline SNPs and InDels within a reportable range using whole exome or genome sequencing data. Combining these benchmarking results with validation using known variants of clinical significance in publicly available cell lines, we were able to establish the performance of variant calling pipelines in a clinical setting.
1
Authors: Bücker, Matthias, et al
Published: Feb 2021
Authors: Bücker, Matthias, et al
Published: Feb 2021
Abstract. Karst water resources play an important role in drinking water supply but arehighly vulnerable to even slight changes in climate. Thus, solid andspatially dense geological information is needed to model the response ofkarst hydrological systems to such changes. Additionally, environmentalinformation archived in lake sediments can be used to understand past climateeffects on karst water systems. In the present study, we carry out amulti-methodological geophysical survey to investigate the geologicalsituation and sedimentary infill of two karst lakes (Metzabok and Tzibaná)of the Lacandon Forest in Chiapas, southern Mexico. Both lakes present largeseasonal lake-level fluctuations and experienced an unusually sudden andstrong lake-level decline in the first half of 2019, leaving Lake Metzabok(maximum depth ∼25 m) completely dry and Lake Tzibaná (depth∼70 m) with a water level decreased byapprox. 15 m. Before this event, during a lake-level high stand inMarch 2018, we collected water-borne seismic data with a sub-bottom profiler(SBP) and transient electromagnetic (TEM) data with a newly developed floatingsingle-loop configuration. In October 2019, after the sudden drainage event,we took advantage of this unique situation and carried out complementarymeasurements directly on the exposed lake floor of Lakes Metzabok andTzibaná. During this second campaign, we collected time-domain inducedpolarization (TDIP) and seismic refraction tomography (SRT) data. Byintegrating the multi-methodological data set, we (1) identify 5–6 mthick, likely undisturbed sediment sequences on the bottom of both lakes,which are suitable for future paleoenvironmental drilling campaigns, (2)develop a comprehensive geological model implying a strong interconnectivitybetween surface water and karst aquifer, and (3) evaluate the potential of theapplied geophysical approach for the reconnaissance of the geologicalsituation of karst lakes. This methodological evaluation reveals that underthe given circumstances, (i) SBP and TDIP phase images consistently resolvethe thickness of the fine-grained lacustrine sediments covering the lakefloor, (ii) TEM and TDIP resistivity images consistently detect the upperlimit of the limestone bedrock and the geometry of fluvial deposits of a riverdelta, and (iii) TDIP and SRT images suggest the existence of a layer thatseparates the lacustrine sediments from the limestone bedrock and consists ofcollapse debris mixed with lacustrine sediments. Our results show that thecombination of seismic methods, which are most widely used for lake-bottomreconnaissance, with resistivity-based methods such as TEM and TDIP cansignificantly improve the interpretation by resolving geological units orbedrock heterogeneities, which are not visible from seismic data. Only the useof complementary methods provides sufficient information to developcomprehensive geological models of such complex karst environments
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Authors: Mohammed Bello, David G. Cornwell, Nicholas Rawlinson, Anya M. Reading, Othaniel K. Likkason
Published: Feb 2021
Authors: Mohammed Bello, David G. Cornwell, Nicholas Rawlinson, Anya M. Reading, Othaniel K. Likkason
Published: Feb 2021
Abstract. In an effort to improve our understanding of the seismiccharacter of the crust beneath southeast Australia and how it relates tothe tectonic evolution of the region, we analyse teleseismic earthquakesrecorded by 24 temporary and 8 permanent broadband stations using thereceiver function method. Due to the proximity of the temporary stations toBass Strait, only 13 of these stations yielded usable receiver functions,whereas seven permanent stations produced receiver functions for subsequentanalysis. Crustal thickness, bulk seismic velocity properties, and internalcrustal structure of the southern Tasmanides – an assemblage of Palaeozoicaccretionary orogens that occupy eastern Australia – are constrained byH–κ stacking and receiver function inversion, which point to the following: a ∼ 39.0 km thick crust; an intermediate–high Vp/Vs ratio(∼ 1.70–1.76), relative to ak135; and a broad (> 10 km) crust–mantle transition beneath the Lachlan Fold Belt. These results areinterpreted to represent magmatic underplating of mafic materials at thebase of the crust. a complex crustal structure beneath VanDieland, aputative Precambrian continental fragment embedded in the southernmostTasmanides, that features strong variability in the crustal thickness (23–37 km) and Vp/Vs ratio (1.65–193), the latter of which likely representscompositional variability and the presence of melt. The complex origins ofVanDieland, which comprises multiple continental ribbons, coupled withrecent failed rifting and intraplate volcanism, likely contributes to theseobservations. stations located in the East Tasmania Terrane andeastern Bass Strait (ETT + EB) collectively indicate a crust of uniformthickness (31–32 km), which clearly distinguishes it from VanDieland to thewest.Moho depths are also compared with the continent-wide AusMoho model insoutheast Australia and are shown to be largely consistent, except inregions where AusMoho has few constraints (e.g. Flinders Island). A jointinterpretation of the new results with ambient noise, teleseismic tomography,and teleseismic shear wave splitting anisotropy helps provide new insightinto the way that the crust has been shaped by recent events, includingfailed rifting during the break-up of Australia and Antarctica and recentintraplate volcanism.
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Authors: Victor A. Shegelski, Erin O. Campbell, Kirsten M. Thompson, Caroline M. Whitehouse, Felix A.H. Sperling
Published: Feb 2021
Authors: Victor A. Shegelski, Erin O. Campbell, Kirsten M. Thompson, Caroline M. Whitehouse, Felix A.H. Sperling
Published: Feb 2021
Abstract The mountain pine beetle ( Dendroctonus ponderosae Hopkins) (Coleoptera: Curculionidae) is a significant destructive force in the pine forests of western Canada and has the capacity to spread east into a novel host tree species, jack pine (Pinaceae). New populations have been documented in central Alberta, Canada, but the source populations for these outbreaks have yet to be identified. In this study, we use genetic data to identify parent populations for recent outbreak sites near Slave Lake, Lac La Biche, and Hinton, Alberta. We found the northern population cluster that entered Alberta near Grande Prairie was the source of the most eastern established population near Lac La Biche, and the range expansion to this leading-edge population has been too rapid to establish evidence of population structure. However, some dispersal from a population in the Jasper and Hinton area has been detected as far north and east as Slave Lake, Alberta. We also identified two potential source populations for the current outbreak in Hinton: most beetles appear to be from Jasper National Park, Alberta, but some also originated from the northern population cluster. These findings demonstrate the dynamic dispersal capabilities of mountain pine beetle across the Alberta landscape and the potential hazard of increased dispersal to newly established leading-edge populations.
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