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  • 1
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    Capturing Key Attributes of Fine-Grained Sedimentary Rocks In Outcrops, Cores, and Thin Sections: Nomenclature and Description Guidelines (2015)
    Society for Sedimentary Geology (SEPM)
    Details
    Publication Date: 2015-03-14
    Description: A bstract :  An integrated nomenclature scheme is proposed to capture the inherent heterogeneity of fine-grained sedimentary rocks at the 10 2 to 10 –3  mm scale and to assist the evaluation of these rocks as sinks of organic carbon, barriers to fluid flows, and reservoirs of oil and gas. This scheme incorporates previous knowledge and the latest field, petrographic, and laboratory observations. We propose to name fine-grained sedimentary rocks using a root term based on their texture (grain size), which is modified by description of bedding, composition, and grain origin. Regarding texture, we suggest the use of "mudstone" as a class name for the entire spectrum of fine-grained sedimentary rocks. We define mudstone as a rock in which more than fifty percent of its grains are mud (clay and silt) size (〈 62.5 µm). Similar to the approach used for the description of sandstone texture, mudstone texture can be refined by a "coarse," "medium," or "fine" size-range term. Regarding bedding, we follow Campbell's (1967) genetic approach to define laminae, laminasets, and beds, and describe lamina geometry, continuity, and shape. Regarding composition, we propose terms such as "siliceous," "calcareous," "argillaceous," and "carbonaceous" to capture differences in rock composition. The name of a mudstone can be further modified by additional attributes that detail the form and origin of the rock components. Application of this approach to the Cretaceous Eagle Ford Shale illustrates the variability typically present in mudstone successions and demonstrates how our detailed characterization can be used to decipher and predict rock properties of economic interest.
    Print ISSN: 1527-1404
    Topics: Geosciences
    Published by Society for Sedimentary Geology (SEPM)
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  • 2
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    Late Proterozoic and Paleozoic Tides, Retreat of the Moon, and Rotation of the Earth (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-07-05
    Description: The tidal rhythmites in the Proterozoic Big Cottonwood Formation (Utah, United States), the Neoproterozoic Elatina Formation of the Flinders Range (southern Australia), and the Lower Pennsylvanian Pottsville Formation (Alabama, United States) and Mansfield Formation (Indiana, United States) indicate that the rate of retreat of the lunar orbit is dxi/dt approximately k2 sin(2delta) (where xi is the Earth-moon radius vector, k2 is the tidal Love number, and delta is the tidal lag angle) and that this rate has been approximately constant since the late Precambrian. When the contribution to tidal friction from the sun is taken into account, these data imply that the length of the terrestrial day 900 million years ago was approximately18 hours.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sonett -- Kvale -- Zakharian -- Chan -- Demko -- New York, N.Y. -- Science. 1996 Jul 5;273(5271):100-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉C. P. Sonett, Department of Planetary Sciences and Lunar and Planetary Laboratory, University of Arizona, Tucson, AZ 85721, USA. E. P. Kvale, Indiana Geological Survey, Indiana University, Bloomington, IN 47405, USA. A. Zakharian, Lunar and Planetary Laboratory, University of Arizona, Tucson, AZ 85721, USA. M. A. Chan, Department of Geology and Geophysics, University of Utah, Salt Lake City, UT 84112, USA. T. M. Demko, Department of Earth Resources, Colorado State University, Fort Collins, CO 80523, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8688061" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Common variants spanning PLK4 are associated with mitotic-origin aneuploidy in human embryos (2015)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2015-04-11
    Description: Aneuploidy, the inheritance of an atypical chromosome complement, is common in early human development and is the primary cause of pregnancy loss. By screening day-3 embryos during in vitro fertilization cycles, we identified an association between aneuploidy of putative mitotic origin and linked genetic variants on chromosome 4 of maternal genomes. This associated region contains a candidate gene, Polo-like kinase 4 (PLK4), that plays a well-characterized role in centriole duplication and has the ability to alter mitotic fidelity upon minor dysregulation. Mothers with the high-risk genotypes contributed fewer embryos for testing at day 5, suggesting that their embryos are less likely to survive to blastocyst formation. The associated region coincides with a signature of a selective sweep in ancient humans, suggesting that the causal variant was either the target of selection or hitchhiked to substantial frequency.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McCoy, Rajiv C -- Demko, Zachary -- Ryan, Allison -- Banjevic, Milena -- Hill, Matthew -- Sigurjonsson, Styrmir -- Rabinowitz, Matthew -- Fraser, Hunter B -- Petrov, Dmitri A -- R01 GM089926/GM/NIGMS NIH HHS/ -- R01 GM097415/GM/NIGMS NIH HHS/ -- R01 GM100366/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2015 Apr 10;348(6231):235-8. doi: 10.1126/science.aaa3337.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Stanford University, Stanford, CA, USA. ; Natera, Inc., San Carlos, CA, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25859044" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; *Aneuploidy ; Blastomeres ; Embryo, Mammalian/*physiology ; Embryonic Development ; Fathers ; Female ; Fertilization in Vitro ; Genetic Association Studies ; Genetic Testing ; Haplotypes ; Humans ; Male ; *Mitosis ; Mothers ; Phenotype ; *Polymorphism, Single Nucleotide ; Protein-Serine-Threonine Kinases/*genetics/physiology ; Selection, Genetic ; Trophoblasts
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    Massive expansion of the calpain gene family in unicellular eukaryotes (2012)
    BioMed Central
    Details
    Publication Date: 2012-09-30
    Description: Background: Calpains are Ca2+-dependent cysteine proteases that participate in a range of crucial cellular processes. Dysfunction of these enzymes may cause, for instance, life-threatening diseases in humans, the loss of sex determination in nematodes and embryo lethality in plants. Although the calpain family is well characterized in animal and plant model organisms, there is a great lack of knowledge about these genes in unicellular eukaryote species (i.e. protists). Here, we study the distribution and evolution of calpain genes in a wide range of eukaryote genomes from major branches in the tree of life. Results: Our investigations reveal 24 types of protein domains that are combined with the calpain-specific catalytic domain CysPc. In total we identify 41 different calpain domain architectures, 28 of these domain combinations have not been previously described. Based on our phylogenetic inferences, we propose that at least four calpain variants were established in the early evolution of eukaryotes, most likely before the radiation of all the major supergroups of eukaryotes. Many domains associated with eukaryotic calpain genes can be found among bacteria or archaebacteria but never in combination with the CysPc domain. Conclusions: The analyses presented here show that ancient modules present in prokaryotes, and a few de novo eukaryote domains, have been assembled into many novel domain combinations along the evolutionary history of eukaryotes. Some of the new calpain genes show a narrow distribution in a few branches in the tree of life, likely representing lineage-specific innovations. Hence, the functionally important classical calpain genes found among humans and vertebrates make up only a tiny fraction of the calpain family. In fact, a massive expansion of the calpain family occurred by domain shuffling among unicellular eukaryotes and contributed to a wealth of functionally different genes.
    Electronic ISSN: 1471-2148
    Topics: Biology
    Published by BioMed Central
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  • 5
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    WALTER: an easy way to online evaluate telomere lengths from terminal restriction fragment analysis (2021)
    BioMed Central
    Details
    Publication Date: 2021-03-22
    Description: Background Telomeres, nucleoprotein structures comprising short tandem repeats and delimiting the ends of linear eukaryotic chromosomes, play an important role in the maintenance of genome stability. Therefore, the determination of the length of telomeres is of high importance for many studies. Over the last years, new methods for the analysis of the length of telomeres have been developed, including those based on PCR or analysis of NGS data. Despite that, terminal restriction fragment (TRF) method remains the gold standard to this day. However, this method lacks universally accepted and precise tool capable to analyse and statistically evaluate TRF results. Results To standardize the processing of TRF results, we have developed WALTER, an online toolset allowing rapid, reproducible, and user-friendly analysis including statistical evaluation of the data. Given its web-based nature, it provides an easily accessible way to analyse TRF data without any need to install additional software. Conclusions WALTER represents a major upgrade from currently available tools for the image processing of TRF scans. This toolset enables a rapid, highly reproducible, and user-friendly evaluation of almost any TRF scan including in-house statistical evaluation of the data. WALTER platform together with user manual describing the evaluation of TRF scans in detail and presenting tips and troubleshooting, as well as test data to demo the software are available at https://www.ceitec.eu/chromatin-molecular-complexes-jiri-fajkus/rg51/tab?tabId=125#WALTER and the source code at https://github.com/mlyc93/WALTER.
    Electronic ISSN: 1471-2105
    Topics: Biology , Computer Science
    Published by BioMed Central
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  • 6
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    Massive expansion of the calpain gene family in unicellular eukaryotes (2012)
    BioMed Central
    Details
    Publication Date: 2012-09-29
    Description: Background Calpains are Ca2+-dependent cysteine proteases that participate in a range of crucial cellular processes. Dysfunction of these enzymes may cause, for instance, life-threatening diseases in humans, the loss of sex determination in nematodes and embryo lethality in plants. Although the calpain family is well characterized in animal and plant model organisms, there is a great lack of knowledge about these genes in unicellular eukaryote species (i.e. protists). Here, we study the distribution and evolution of calpain genes in a wide range of eukaryote genomes from major branches in the tree of life. Results Our investigations reveal 24 types of protein domains that are combined with the calpain-specific catalytic domain CysPc. In total we identify 41 different calpain domain architectures, 28 of these domain combinations have not been previously described. Based on our phylogenetic inferences, we propose that at least four calpain variants were established in the early evolution of eukaryotes, most likely before the radiation of all the major supergroups of eukaryotes. Many domains associated with eukaryotic calpain genes can be found among eubacteria or archaebacteria but never in combination with the CysPc domain. Conclusions The analyses presented here show that ancient modules present in prokaryotes, and a few de novo eukaryote domains, have been assembled into many novel domain combinations along the evolutionary history of eukaryotes. Some of the new calpain genes show a narrow distribution in a few branches in the tree of life, likely representing lineage-specific innovations. Hence, the functionally important classical calpain genes found among humans and vertebrates make up only a tiny fraction of the calpain family. In fact, a massive expansion of the calpain family occurred by domain shuffling among unicellular eukaryotes and contributed to a wealth of functionally different genes.
    Electronic ISSN: 1471-2148
    Topics: Biology
    Published by BioMed Central
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