Massively parallel sequencing of the polyadenylated RNAs has played a key role in delineating transcriptome complexity, including alternative use of an exon, promoter, 5' or 3' splice site or ...polyadenylation site, and RNA modification. However, reads derived from the current RNA-seq technologies are usually short and deprived of information on modification, compromising their potential in defining transcriptome complexity. Here, we applied a direct RNA sequencing method with ultralong reads using Oxford Nanopore Technologies to study the transcriptome complexity in
We generated approximately six million reads using native poly(A)-tailed mRNAs from three developmental stages, with average read lengths ranging from 900 to 1100 nt. Around half of the reads represent full-length transcripts. To utilize the full-length transcripts in defining transcriptome complexity, we devised a method to classify the long reads as the same as existing transcripts or as a novel transcript using sequence mapping tracks rather than existing intron/exon structures, which allowed us to identify roughly 57,000 novel isoforms and recover at least 26,000 out of the 33,500 existing isoforms. The sets of genes with differential expression versus differential isoform usage over development are largely different, implying a fine-tuned regulation at isoform level. We also observed an unexpected increase in putative RNA modification in all bases in the coding region relative to the UTR, suggesting their possible roles in translation. The RNA reads and the method for read classification are expected to deliver new insights into RNA processing and modification and their underlying biology in the future.
The shale of the Permian Lucaogou Formation in the Jimusar sag, Junggar Basin (abbreviated as the Lucaogou shale) is a typical lacustrine type-II source rock, and is among the most representative ...target zones for shale oil exploration in China. However, little attention has been paid to the dynamic changes of the shale decomposition; hydrocarbon generation, retention, and expulsion; physico-chemical properties; and producibility of shale oil at different stages of maturation in this shale. Semi-open pyrolysis experiments were performed on the Lucaogou shale; products including expelled gas, oil (expelled oil), bitumen (retained oil), and residual rock were obtained, and their quantities and chemical and physical compositions were comprehensively characterized. The results show that the density and molecular weight of the oil are lower than those of the bitumen, whereas the API gravity of the oil is higher than that of the bitumen, indicating the preferential expulsion of light hydrocarbons and short chains. The saturate, aromatic, resin and asphaltene (SARA) percentages of oils under the current semi-open pyrolysis experiments were similar to those of natural oils recovered from the Lucaogou Formation, suggesting that semi-open pyrolysis can achieve the same purpose as hydrous pyrolysis to simulate natural oil composition. The measured vitrinite reflectance (Ro) of the pyrolyzed shale was lower than the calculated Easy%Ro, which is in accord with findings from the Chang 7 shale (another typical lacustrine type-II shale in China) but distinct from previously reported type-III coals and marine type-II shales. Similar to the Chang 7 shale, the decomposition process of the Lucaogou shale did not follow the sequential reaction model described as kerogen → bitumen → oil or kerogen → NSOs → HCs. The generation of HCs (oil) and NSOs (bitumen) was independent and followed the “alternate pathway” mechanism under semi-open pyrolysis conditions. In the early oil window (Ro ˂ 1.0%), the hydrocarbon expulsion efficiency was relatively low, meaning that the shale simultaneously retained considerable amounts of oil during peak oil generation. The producibility of shale oil reached its maximum at the end of the oil window (1.0–1.2 %Ro), and this interval is considered the most suitable for fracturing technology.
•Hydrocarbon generation, retention, and expulsion process of lacustrine type-II shale was systematically explored.•Semi-open pyrolysis system was applied to simulate natural maturation of shale.•Both chemical and physical properties of oil and bitumen were analyzed.
The invariant development and transparent body of the nematode Caenorhabditis elegans enables complete delineation of cell lineages throughout development. Despite extensive studies of cell division, ...cell migration and cell fate differentiation, cell morphology during development has not yet been systematically characterized in any metazoan, including C. elegans. This knowledge gap substantially hampers many studies in both developmental and cell biology. Here we report an automatic pipeline, CShaper, which combines automated segmentation of fluorescently labeled membranes with automated cell lineage tracing. We apply this pipeline to quantify morphological parameters of densely packed cells in 17 developing C. elegans embryos. Consequently, we generate a time-lapse 3D atlas of cell morphology for the C. elegans embryo from the 4- to 350-cell stages, including cell shape, volume, surface area, migration, nucleus position and cell-cell contact with resolved cell identities. We anticipate that CShaper and the morphological atlas will stimulate and enhance further studies in the fields of developmental biology, cell biology and biomechanics.
Morphogenesis is a precise and robust dynamic process during metazoan embryogenesis, consisting of both cell proliferation and cell migration. Despite the fact that much is known about specific ...regulations at molecular level, how cell proliferation and migration together drive the morphogenesis at cellular and organismic levels is not well understood. Using Caenorhabditis elegans as the model animal, we present a phase field model to compute early embryonic morphogenesis within a confined eggshell. With physical information about cell division obtained from three-dimensional time-lapse cellular imaging experiments, the model can precisely reproduce the early morphogenesis process as seen in vivo, including time evolution of location and morphology of each cell. Furthermore, the model can be used to reveal key cell-cell attractions critical to the development of C. elegans embryo. Our work demonstrates how genetic programming and physical forces collaborate to drive morphogenesis and provides a predictive model to decipher the underlying mechanism.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Based on 991 groups of analysis data of shale samples from the Lower Member of the Cretaceous Eagle Ford Formation of 1317 production wells and 72 systematic coring wells in the U.S. Gulf Basin, the ...estimated ultimate recovery (EUR) of shale oil and gas of the wells are predicted by using two classical EUR estimation models, and the average values predicted excluding the effect of engineering factors are taken as the final EUR. Key geological factors controlling EUR of shale oil and gas are fully investigated. The reservoir capacity, resources, flow capacity and fracability are the four key geological parameters controlling EUR. The storage capacity of shale oil and gas is directly controlled by total porosity and hydrocarbon-bearing porosity, and indirectly controlled by total organic carbon (TOC) and vitrinite reflectance (Ro). The resources of shale oil and gas are controlled by hydrocarbon-bearing porosity and effective shale thickness etc. The flow capacity of shale oil and gas is controlled by effective permeability, crude oil density, gas-oil ratio, condensate oil-gas ratio, formation pressure gradient, and Ro. The fracability of shale is directly controlled by brittleness index, and indirectly controlled by clay content in volume. EUR of shale oil and gas is controlled by six geological parameters: it is positively correlated with effective shale thickness, TOC and fracture porosity, negatively correlated with clay content in volume, and increases firstly and then decreases with the rise of Ro and formation pressure gradient. Under the present upper limit of horizontal well fracturing effective thickness of 65 m and the lower limit of EUR of 3×104 m3, when TOC<2.3%, or Ro<0.85%, or clay content in volume larger than 25%, and fractures and micro-fractures aren’t developed, favorable areas of shale oil and gas hardly occur.
The Jimsar Sag is an important shale oil exploration target area in the Junggar Basin, northwestern China. The Permian Lucaogou Formation, with a thickness of 200–300 m, is the primary exploration ...target. High-frequency variation in lithology is a typical feature of the Lucaogou Formation, reflecting the fluctuation of the depositional environment and organic matter enrichment. The evolution of the depositional environment and accumulation mechanism of organic matter still need to be elucidated for the Lucaogou Formation. High-resolution sampling of the entire Lucaogou Formation was applied to a 248 m long core from Well JX in the Jimsar Sag to examine the depositional environment and organic matter enrichment. The findings unveiled that the Lucaogou Formation was deposited under a hot and arid climate, within the confines of a closed saline paleo-lake, where sediments endured an extended period of anoxic conditions, displayed periodic oscillations in paleo-temperature and paleo-salinity values over time, alongside a continuous rise in paleo-water depth. The predominant source lithology of the Lucaogou Formation is felsic igneous rock. Small-scale transgression and hydrothermal sedimentation occurred during the deposition of the Lucaogou Formation. The prevailing hot climate and enduring reducing environment fostered ideal circumstances for the enrichment of organic matter in the Lucaogou Formation. Due to different sedimentary environments and enrichment mechanisms, organic matter is enriched in two modes in the Lucaogou Formation.
Understanding the cellular architecture is a fundamental problem in various biological studies. C. elegans is widely used as a model organism in these studies because of its unique fate ...determinations. In recent years, researchers have worked extensively on C. elegans to excavate the regulations of genes and proteins on cell mobility and communication. Although various algorithms have been proposed to analyze nucleus, cell shape features are not yet well recorded. This paper proposes a method to systematically analyze three-dimensional morphological cellular features.
Three-dimensional Membrane Morphological Segmentation (3DMMS) makes use of several novel techniques, such as statistical intensity normalization, and region filters, to pre-process the cell images. We then segment membrane stacks based on watershed algorithms. 3DMMS achieves high robustness and precision over different time points (development stages). It is compared with two state-of-the-art algorithms, RACE and BCOMS. Quantitative analysis shows 3DMMS performs best with the average Dice ratio of 97.7% at six time points. In addition, 3DMMS also provides time series of internal and external shape features of C. elegans.
We have developed the 3DMMS based technique for embryonic shape reconstruction at the single-cell level. With cells accurately segmented, 3DMMS makes it possible to study cellular shapes and bridge morphological features and biological expression in embryo research.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The North Himalaya is a prospective area for Sb, Sb–Au, Au, Pb–Zn(−Ag), and Sb–Pb–Zn–Ag mineralization. Geochemical anomalies for mineralizing elements and element associations were identified using ...concentration–area (C–A) fractal model together with statistical analyses, including the mean±2 standard deviation (Mean+2STD) and the median±2 median absolute deviation (Median+2MAD). The results show that the Mean+2STD for log-transformed data and C–A model could well identify the geochemical anomalies associated with mineralization in the North Himalaya. Sb+Au anomalies show a better spatial association with Sb, Sb–Au, and Sb–Pb–Zn–Ag deposits than those of single Sb element. Au anomalies are associated with all deposits, and Pb+Zn+Ag anomalies are associated with Pb–Zn and Sb–Pb–Zn–Ag deposits. In addition, weak anomalies associated with Sb mineralization can be identified by the singularity method. With the utilization of the Sb+Au, Sb, Au and Pb+Zn+Ag anomalies identified by C–A fractal model and Mean+2STD for log-transformed data, as well as the singularity method, we can facilitate the exploration targeting of various deposits in the North Himalaya. In addition, our results also show that principal component analysis (PCA) of centered logratio (clr) transformed data can accurately recognize three different geochemical assemblage compositions representing three different types of mineralization (i.e., Au, Pb–Zn–Ag and Sb) in the North Himalaya.
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•PCA of clr-transformed data can recognize three types of mineralization in the North Himalaya.•Geochemical anomalies were identified using concentration–area fractal model and statistical analyses.•Approaches for targeting various types of deposits were advanced.•Singularity method can identify weak anomalies and should be combined with other methods.
Homology-based recombination (HR) is the cornerstone of genetic mapping. However, a lack of sufficient sequence homology or the presence of a genomic rearrangement prevents HR through crossing, which ...inhibits genetic mapping in relevant genomic regions. This is particularly true in species hybrids whose genomic sequences are highly divergent along with various genome arrangements, making the mapping of genetic loci, such as hybrid incompatibility (HI) loci, through crossing impractical. We previously mapped tens of HI loci between two nematodes, Caenorhabditis briggsae and C. nigoni, through the repeated backcrossing of GFP-linked C. briggsae fragments into C. nigoni. However, the median introgression size was over 7 Mb, indicating apparent HR suppression and preventing the subsequent cloning of the causative gene underlying a given HI phenotype. Therefore, a robust method that permits recombination independent of sequence homology is desperately desired. Here, we report a method of highly efficient targeted recombination (TR) induced by CRISPR/Cas9 with dual guide RNAs (gRNAs), which circumvents the HR suppression in hybrids between the two species. We demonstrated that a single gRNA was able to induce efficient TR between highly homologous sequences only in the F1 hybrids but not in the hybrids that carry a GFP-linked C. briggsae fragment in an otherwise C. nigoni background. We achieved highly efficient TR, regardless of sequence homology or genetic background, when dual gRNAs were used that each specifically targeted one parental chromosome. We further showed that dual gRNAs were able to induce efficient TR within genomic regions that had undergone inversion, in which HR-based recombination was expected to be suppressed, supporting the idea that dual-gRNA-induced TR can be achieved through nonhomology-based end joining between two parental chromosomes. Recombination suppression can be circumvented through CRISPR/Cas9 with dual gRNAs, regardless of sequence homology or the genetic background of the species hybrid. This method is expected to be applicable to other situations in which recombination is suppressed in interspecies or intrapopulation hybrids.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
During fertility treatment, diminished ovarian reserve (DOR) is a challenge that can seriously affect a patient's reproductive potential. However, the pathogenesis of DOR is still unclear and its ...treatment options are limited. This study aimed to explore DOR's molecular mechanisms.
We used R software to analyze the mRNA microarray dataset E-MTAB-391 downloaded from ArrayExpress, screen for differentially expressed genes (DEGs), and perform functional enrichment analyses. We also constructed the protein-protein interaction (PPI) and miRNA-mRNA networks. Ovarian granulosa cells (GCs) from women with DOR and the control group were collected to perform untargeted metabolomics analyses. Additionally, small molecule drugs were identified using the Connectivity Map database.
We ultimately identified 138 DEGs. Our gene ontology (GO) analysis indicated that DEGs were mainly enriched in cytokine and steroid biosynthetic processes. According to the Kyoto Encyclopedia of Genes and Genomes (KEGG), the DEGs were mainly enriched in the AGE (advanced glycation end-product)-RAGE (receptor for AGE) signaling pathway in diabetic complications and steroid biosynthesis. In the PPI network, we determined that JUN, EGR1, HMGCR, ATF3, and SQLE were hub genes that may be involved in steroid biosynthesis and inflammation. miRNAs also played a role in DOR development by regulating target genes. We validated the differences in steroid metabolism across GCs using liquid chromatography-tandem mass spectrometry (LC-MS/MS). We selected 31 small molecules with potentially positive or negative influences on DOR development.
We found that steroidogenesis and inflammation played critical roles in DOR development, and our results provide promising insights for predicting and treating DOR.
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