cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1313000.v1
title: Jaw mechanics and evolutionary paleoecology of the megaherbivorous dinosaurs from the Dinosaur Park Formation (upper Campanian) of Alberta, Canada

description: ABSTRACTThe question of what role differential jaw mechanics may have played in facilitating dietary niche partitioning among Late Cretaceous megaherbivorous dinosaurs from Laramidia is examined, using the fossil assemblage of the Dinosaur Park Formation as a test case. We use phylogenetic inference to reconstruct the mandibular adductor musculature of these animals, which we then apply to the construction of biomechanical lever models of the mandible to estimate relative bite forces. Our findings reveal predictably weak bite forces in ankylosaurs, and comparatively high bite forces in ceratopsids and hadrosaurids, both of which possessed a mechanical advantage that produced bite forces 2–3 times higher than those forces exerted by the adductor musculature. The impressive jaw mechanism shared by the last two taxa evolved in a stepwise fashion, independently in each lineage. There is tentative evidence to suggest that nodosaurids had more powerful bites than ankylosaurids, but the overall mechanical diversity among megaherbivores from the Dinosaur Park Formation is low, suggesting that differential jaw mechanics could have played only a subsidiary role in niche partitioning. Such mechanical conservatism may have may have been selected for, or it may simply reflect the limits imposed by evolutionary constraints. Regardless, mechanical disparity patterns remained stable throughout the ∼1.5 Ma evolution of the Dinosaur Park Formation megaherbivore chronofauna.SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
DOI: 10.6084/m9.figshare.1313001.v1
title: A new metriorhynchoid (Crocodylomorpha, Thalattosuchia) from the Middle Jurassic of Oregon and the evolutionary timing of marine adaptations in thalattosuchian crocodylomorphs

description: ABSTRACTMetriorhynchid thalattosuchians represent the most extreme archosaurian adaptation to the marine realm. Metriorhynchids possess aquatic adaptations throughout the skeleton. These adaptations were so extensive that some have suggested that they lost the ability to move on land, yet their evolutionary timing remains unresolved. The closest relatives of the metriorhynchoids, the teleosauroids, lack these aquatic adaptations, and the earliest metriorhynchoids are known exclusively from cranial material. Here I describe a partial skull with associated forelimb elements of a new marine crocodylomorph, <i>Zoneait nargorum</i>, gen. et sp. nov., of Aalenian–Bajocian age from the Snowshoe Formation of east-central Oregon. Phylogenetic analysis identifies <i>Zoneait</i> as the sister taxon to Metriorhynchidae. It possesses a derived skull with orbits that are more laterally directed and prefrontals that are more expanded than in other basal metriorhynchoids. The preserved forelimb elements are less derived. The humerus is elongate in comparison with that of other metriorhynchoids. The ulna is slightly reduced in length and flattened but resembles the teleosauroid condition more so than the plate-like element of metriorhynchids. This suggests that marine adaptations in metriorhynchoids were acquired in mosaic fashion, with modifications of the skull preceding forelimb reduction, with this forelimb reduction occurring first in the zeugopodial elements, prior to reduction of the humerus. This evolutionary timing has important implications for the transition from nearshore ambush predation to pelagic open-marine predation in Thalattosuchia, suggesting that adaptations related to prey detection and capture preceded the locomotor adaptations that allowed these organisms to fully invade the oceans.http://zoobank.org/urn:lsid:zoobank.org:pub:407671AC-E785-4831-9FB3-560965F15A2ESUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
DOI: 10.6084/m9.figshare.1313000.v3
title: Jaw mechanics and evolutionary paleoecology of the megaherbivorous dinosaurs from the Dinosaur Park Formation (upper Campanian) of Alberta, Canada

description: ABSTRACTThe question of what role differential jaw mechanics may have played in facilitating dietary niche partitioning among Late Cretaceous megaherbivorous dinosaurs from Laramidia is examined, using the fossil assemblage of the Dinosaur Park Formation as a test case. We use phylogenetic inference to reconstruct the mandibular adductor musculature of these animals, which we then apply to the construction of biomechanical lever models of the mandible to estimate relative bite forces. Our findings reveal predictably weak bite forces in ankylosaurs, and comparatively high bite forces in ceratopsids and hadrosaurids, both of which possessed a mechanical advantage that produced bite forces 2–3 times higher than those forces exerted by the adductor musculature. The impressive jaw mechanism shared by the last two taxa evolved in a stepwise fashion, independently in each lineage. There is tentative evidence to suggest that nodosaurids had more powerful bites than ankylosaurids, but the overall mechanical diversity among megaherbivores from the Dinosaur Park Formation is low, suggesting that differential jaw mechanics could have played only a subsidiary role in niche partitioning. Such mechanical conservatism may have may have been selected for, or it may simply reflect the limits imposed by evolutionary constraints. Regardless, mechanical disparity patterns remained stable throughout the ∼1.5 Ma evolution of the Dinosaur Park Formation megaherbivore chronofauna.SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
DOI: 10.6084/m9.figshare.1313001.v2
title: A new metriorhynchoid (Crocodylomorpha, Thalattosuchia) from the Middle Jurassic of Oregon and the evolutionary timing of marine adaptations in thalattosuchian crocodylomorphs

description: ABSTRACTMetriorhynchid thalattosuchians represent the most extreme archosaurian adaptation to the marine realm. Metriorhynchids possess aquatic adaptations throughout the skeleton. These adaptations were so extensive that some have suggested that they lost the ability to move on land, yet their evolutionary timing remains unresolved. The closest relatives of the metriorhynchoids, the teleosauroids, lack these aquatic adaptations, and the earliest metriorhynchoids are known exclusively from cranial material. Here I describe a partial skull with associated forelimb elements of a new marine crocodylomorph, <i>Zoneait nargorum</i>, gen. et sp. nov., of Aalenian–Bajocian age from the Snowshoe Formation of east-central Oregon. Phylogenetic analysis identifies <i>Zoneait</i> as the sister taxon to Metriorhynchidae. It possesses a derived skull with orbits that are more laterally directed and prefrontals that are more expanded than in other basal metriorhynchoids. The preserved forelimb elements are less derived. The humerus is elongate in comparison with that of other metriorhynchoids. The ulna is slightly reduced in length and flattened but resembles the teleosauroid condition more so than the plate-like element of metriorhynchids. This suggests that marine adaptations in metriorhynchoids were acquired in mosaic fashion, with modifications of the skull preceding forelimb reduction, with this forelimb reduction occurring first in the zeugopodial elements, prior to reduction of the humerus. This evolutionary timing has important implications for the transition from nearshore ambush predation to pelagic open-marine predation in Thalattosuchia, suggesting that adaptations related to prey detection and capture preceded the locomotor adaptations that allowed these organisms to fully invade the oceans.http://zoobank.org/urn:lsid:zoobank.org:pub:407671AC-E785-4831-9FB3-560965F15A2ESUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
DOI: 10.6084/m9.figshare.1312994
title: A novel electronic assessment strategy to support applied Drosophila genetics training on university courses

description: These are the support files for an article which just appeared in the G3 journal (first link below). Abstract: The advent of "omic" technologies has revolutionised Genetics and created a demand to focus classical genetics on its present-day applications (Redfield, 2012, PLoS Biol 10, e1001356ff.). This demand can be met by training students in <em>Drosophila</em> mating scheme design, which is an important problem solving skill routinely applied in many modern research laboratories. It requires thorough understanding and application of classical genetics rules, whilst also introducing to transgenic technologies and the use of model organisms. As we show here, such training can be implemented as a flexible and concise module (~1 day home study, ~8 hours course time) on university courses by using our previously published training package designed for fly researchers (Roote & Prokop, 2013, G3/Bethesda 3, 353ff.). However, assessing this training to make it an accredited course element, is difficult especially on large courses. Here, we present a powerful assessment strategy based on a novel hybrid concept where students solve crossing tasks initially on paper and then answer automatically marked questions on the computer (1.5 hours in total). This procedure can examine student performance on more complex tasks than conventional e-assessments and is more versatile, time-saving and fairer than standard paper-based assignments. Our evaluation shows that the hybrid assessment is effective and reliably detects varying degrees of understanding amongst students. It may be applicable also in other disciplines requiring complex problem solving, such as mathematics, chemistry, physics or informatics. Here, we describe our strategies in detail and provide all resources needed for their implementation.To take the test exam do the following: • go to: www.coursesites.com (link below)<br>• log on: username "flyfacility", password "prokop"<br>• click "Fly Facility" in the "My courses" box<br>• read the texts carefully, then click on "Drosophila Genetics Assessment" and start<br>
DOI: 10.6084/m9.figshare.1312963
title: Mycoplasma CG- and GATC-specific DNA methyltransferases selectively and efficiently methylate the host genome and alter the epigenetic landscape in human cells

description: Aberrant DNA methylation is frequently observed in disease, including many cancer types, yet the underlying mechanisms remain unclear. Because germline and somatic mutations in the genes that are responsible for DNA methylation are infrequent in malignancies, additional mechanisms must be considered. <i>Mycoplasmas spp</i>., including <i>Mycoplasma hyorhinis,</i> efficiently colonize human cells and may serve as a vehicle for delivery of enzymatically active microbial proteins into the intracellular milieu. Here, we performed, for the first time, genome-wide and individual gene mapping of methylation marks generated by the <i>M. hyorhinis</i> CG- and GATC-specific DNA cytosine methyltransferases (MTases) in human cells. Our results demonstrated that, upon expression in human cells, MTases readily translocated to the cell nucleus. In the nucleus, MTases selectively and efficiently methylated the host genome at the DNA sequence sites free from pre-existing endogenous methylation, including those in a variety of cancer-associated genes. We also established that mycoplasma is widespread in colorectal cancers, suggesting that either the infection contributed to malignancy onset or, alternatively, that tumors provide a favorable environment for mycoplasma growth. In the human genome, ∼11% of GATC sites overlap with CGs (e.g., CGAT<sup>m</sup>CG); therefore, the methylated status of these sites can be perpetuated by human DNMT1. Based on these results, we now suggest that the GATC-specific methylation represents a novel type of infection-specific epigenetic mark that originates in human cells with a previous exposure to infection. Overall, our findings unveil an entirely new panorama of interactions between the human microbiome and epigenome with a potential impact in disease etiology.
DOI: 10.6084/m9.figshare.1312986
title: Alteration of <i>Arabidopsis SLAC1</i> promoter and its association with natural variation in drought tolerance

description: Natural variation for drought tolerance is a major issue in adaptation and geographic distribution of terrestrial plants. Despite the importance, little is known about the genes and molecular mechanisms that determine its naturally occurring diversity. We analyzed the intraspecific drought tolerance variation between 2 accessions of <i>Arabidopsis thaliana</i>, Columbia (Col)-0 and Wassilewskija (Ws)-2. Measurement of weight loss in detached seedlings demonstrated a clear difference between drought-tolerant Col-0 and drought-sensitive Ws-2. They also differed in their stomatal response under drought condition. Using a quantitative genetic approach, we found a significant quantitative locus on chromosome 1. Surveying in the locus, we extrapolated that the <i>SLAC1</i> gene, which is associated with stomatal closure, was likely responsible for the difference of drought tolerance. Comparison of their nucleotide and amino acid sequences revealed that there were few differences in regions encoding <i>SLAC1</i> protein but was a large deletion in <i>SLAC1</i> promoter of Ws-2. Histochemical GUS staining showed that the <i>SLAC1</i> expressed dominantly in guard cells of Col-0, but did less in guard cells of Ws-2. Quantitative PCR analysis also showed that transcript level of <i>SLAC1</i> in guard cells was higher in Col-0 than in Ws-2. The <i>SLAC1</i> transcription analyses indicate low accumulation of <i>SLAC1</i> in guard cells of Ws-2. When taken together, our results suggest that the low drought tolerance of Ws-2 was associated with the deletion of the promoter region of Ws-2 <i>SLAC1</i>.
DOI: 10.6084/m9.figshare.1313000.v2
title: Jaw mechanics and evolutionary paleoecology of the megaherbivorous dinosaurs from the Dinosaur Park Formation (upper Campanian) of Alberta, Canada

description: ABSTRACTThe question of what role differential jaw mechanics may have played in facilitating dietary niche partitioning among Late Cretaceous megaherbivorous dinosaurs from Laramidia is examined, using the fossil assemblage of the Dinosaur Park Formation as a test case. We use phylogenetic inference to reconstruct the mandibular adductor musculature of these animals, which we then apply to the construction of biomechanical lever models of the mandible to estimate relative bite forces. Our findings reveal predictably weak bite forces in ankylosaurs, and comparatively high bite forces in ceratopsids and hadrosaurids, both of which possessed a mechanical advantage that produced bite forces 2–3 times higher than those forces exerted by the adductor musculature. The impressive jaw mechanism shared by the last two taxa evolved in a stepwise fashion, independently in each lineage. There is tentative evidence to suggest that nodosaurids had more powerful bites than ankylosaurids, but the overall mechanical diversity among megaherbivores from the Dinosaur Park Formation is low, suggesting that differential jaw mechanics could have played only a subsidiary role in niche partitioning. Such mechanical conservatism may have may have been selected for, or it may simply reflect the limits imposed by evolutionary constraints. Regardless, mechanical disparity patterns remained stable throughout the ∼1.5 Ma evolution of the Dinosaur Park Formation megaherbivore chronofauna.SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
DOI: 10.6084/m9.figshare.1312963.v1
title: Mycoplasma CG- and GATC-specific DNA methyltransferases selectively and efficiently methylate the host genome and alter the epigenetic landscape in human cells

description: ABSTRACTAberrant DNA methylation is frequently observed in disease, including many cancer types, yet the underlying mechanisms remain unclear. Because germline and somatic mutations in the genes that are responsible for DNA methylation are infrequent in malignancies, additional mechanisms must be considered. <i>Mycoplasmas spp</i>., including <i>Mycoplasma hyorhinis</i>, efficiently colonize human cells and may serve as a vehicle for delivery of enzymatically active microbial proteins into the intracellular milieu. Here, we performed, for the first time, genome-wide and individual gene mapping of methylation marks generated by the <i>M. hyorhinis</i> CG- and GATC-specific DNA cytosine methyltransferases (MTases) in human cells. Our results demonstrated that, upon expression in human cells, MTases readily translocated to the cell nucleus. In the nucleus, MTases selectively and efficiently methylated the host genome at the DNA sequence sites free from pre-existing endogenous methylation, including those in a variety of cancer-associated genes. We also established that mycoplasma is widespread in colorectal cancers, suggesting that either the infection contributed to malignancy onset or, alternatively, that tumors provide a favorable environment for mycoplasma growth. In the human genome, ˜11% of GATC sites overlap with CGs (e.g., CGAT<sup>m</sup>CG); therefore, the methylated status of these sites can be perpetuated by human DNMT1. Based on these results, we now suggest that the GATC-specific methylation represents a novel type of infection-specific epigenetic mark that originates in human cells with a previous exposure to infection. Overall, our findings unveil an entirely new panorama of interactions between the human microbiome and epigenome with a potential impact in disease etiology.
DOI: 10.6084/m9.figshare.1312986.v1
title: Alteration of <i>Arabidopsis SLAC1</i> promoter and its association with natural variation in drought tolerance

description: Natural variation for drought tolerance is a major issue in adaptation and geographic distribution of terrestrial plants. Despite the importance, little is known about the genes and molecular mechanisms that determine its naturally occurring diversity. We analyzed the intraspecific drought tolerance variation between two accessions of <i>Arabidopsis thaliana</i>, Columbia (Col)-0 and Wassilewskija (Ws)-2. Measurement of weight loss in detached seedlings demonstrated a clear difference between drought-tolerant Col-0 and drought-sensitive Ws-2. They also differed in their stomatal response under drought condition. Using a quantitative genetic approach, we found a significant quantitative locus on chromosome 1. Surveying in the locus, we extrapolated that the <i>SLAC1</i> gene, which is associated with stomatal closure, was likely responsible for the difference of drought tolerance. Comparison of their nucleotide and amino acid sequences revealed that there were few differences in regions encoding SLAC1 protein but was a large deletion in <i>SLAC1</i> promoter of Ws-2. Histochemical GUS staining showed that the <i>SLAC1</i> expressed dominantly in guard cells of Col-0, but did less in guard cells of Ws-2. Quantitative PCR analysis also showed that transcript level of <i>SLAC1</i> in guard cells was higher in Col-0 than in Ws-2. The <i>SLAC1</i> transcription analyses indicate low accumulation of SLAC1 in guard cells of Ws-2. When taken together, our results suggest that the low drought tolerance of Ws-2 was associated with the deletion of the promoter region of Ws-2 <i>SLAC1</i>.
DOI: 10.6084/m9.figshare.1312986.v2
title: Alteration of <i>Arabidopsis SLAC1</i> promoter and its association with natural variation in drought tolerance

description: Natural variation for drought tolerance is a major issue in adaptation and geographic distribution of terrestrial plants. Despite the importance, little is known about the genes and molecular mechanisms that determine its naturally occurring diversity. We analyzed the intraspecific drought tolerance variation between 2 accessions of <i>Arabidopsis thaliana</i>, Columbia (Col)-0 and Wassilewskija (Ws)-2. Measurement of weight loss in detached seedlings demonstrated a clear difference between drought-tolerant Col-0 and drought-sensitive Ws-2. They also differed in their stomatal response under drought condition. Using a quantitative genetic approach, we found a significant quantitative locus on chromosome 1. Surveying in the locus, we extrapolated that the <i>SLAC1</i> gene, which is associated with stomatal closure, was likely responsible for the difference of drought tolerance. Comparison of their nucleotide and amino acid sequences revealed that there were few differences in regions encoding <i>SLAC1</i> protein but was a large deletion in <i>SLAC1</i> promoter of Ws-2. Histochemical GUS staining showed that the <i>SLAC1</i> expressed dominantly in guard cells of Col-0, but did less in guard cells of Ws-2. Quantitative PCR analysis also showed that transcript level of <i>SLAC1</i> in guard cells was higher in Col-0 than in Ws-2. The <i>SLAC1</i> transcription analyses indicate low accumulation of <i>SLAC1</i> in guard cells of Ws-2. When taken together, our results suggest that the low drought tolerance of Ws-2 was associated with the deletion of the promoter region of Ws-2 <i>SLAC1</i>.
DOI: 10.6084/m9.figshare.1312963.v2
title: Mycoplasma CG- and GATC-specific DNA methyltransferases selectively and efficiently methylate the host genome and alter the epigenetic landscape in human cells

description: Aberrant DNA methylation is frequently observed in disease, including many cancer types, yet the underlying mechanisms remain unclear. Because germline and somatic mutations in the genes that are responsible for DNA methylation are infrequent in malignancies, additional mechanisms must be considered. <i>Mycoplasmas spp</i>., including <i>Mycoplasma hyorhinis,</i> efficiently colonize human cells and may serve as a vehicle for delivery of enzymatically active microbial proteins into the intracellular milieu. Here, we performed, for the first time, genome-wide and individual gene mapping of methylation marks generated by the <i>M. hyorhinis</i> CG- and GATC-specific DNA cytosine methyltransferases (MTases) in human cells. Our results demonstrated that, upon expression in human cells, MTases readily translocated to the cell nucleus. In the nucleus, MTases selectively and efficiently methylated the host genome at the DNA sequence sites free from pre-existing endogenous methylation, including those in a variety of cancer-associated genes. We also established that mycoplasma is widespread in colorectal cancers, suggesting that either the infection contributed to malignancy onset or, alternatively, that tumors provide a favorable environment for mycoplasma growth. In the human genome, ∼11% of GATC sites overlap with CGs (e.g., CGAT<sup>m</sup>CG); therefore, the methylated status of these sites can be perpetuated by human DNMT1. Based on these results, we now suggest that the GATC-specific methylation represents a novel type of infection-specific epigenetic mark that originates in human cells with a previous exposure to infection. Overall, our findings unveil an entirely new panorama of interactions between the human microbiome and epigenome with a potential impact in disease etiology.