CO₂ Modeling in a Deep Saline Aquifer: A Predictive Uncertainty Analysis Using Design of Experiment

When field data are limited, stratigraphic models are used instead of detailed, fully heterogeneous models (FHM) to represent deep saline aquifers in numerical simulations of CO2 storage. This study evaluates parameter sensitivity and prediction uncertainty of three stratigraphic models of decreasing complexity (i.e., facies, layered, formation) against that of a FHM. For select simulation outcomes (i.e., CO2 mass profiles, gas plume shape, brine leakage), parameter sensitivity and associated prediction uncertainty are compared among the models, with the FHM serving as a reference. The analysis is conducted using the computationally efficient design of experiment (DoE) and response surface (RS) methodology. Results suggest that when a competent caprock exists (permeability −4 mD), the facies and layered models are capable of capturing the most important sensitivity parameters of the FHM, that is, residual gas saturation, heterogeneity variance, and salinity. Using the important parameters identified by DoE, RS modeling then suggests that the same two models also capture the ranges of predictions in mobile gas, trapped gas, and brine leakage. The formation model is less accurate in capturing the sensitivity and prediction ranges of the FHM, although it is accurate in predicting brine leakage into the overlying formation

DataSheet1_Nonmuscle Myosin II is Required for Larval Shell Formation in a Patellogastropod.pdf

The molecular mechanisms underlying larval shell development in mollusks remain largely elusive. We previously found evident filamentous actin (F-actin) aggregations in the developing shell field of the patellogastropod Lottia goshimai, indicating roles of actomyosin networks in the process. In the present study, we functionally characterized nonmuscle myosin II (NM II), the key molecule in actomyosin networks, in the larval shell development of L. goshimai. Immunostaining revealed general colocalization of phosphorylated NM II and F-actin in the shell field. When inhibiting the phosphorylation of NM II using the specific inhibitor blebbistatin in one- or 2-h periods during shell field morphogenesis (6–8 h post-fertilization, hpf), the larval shell plate was completely lost in the veliger larva (24 hpf). Scanning electron microscopy revealed that the nascent larval shell plate could not be developed in the manipulated larvae (10 hpf). Further investigations revealed that key events in shell field morphogenesis were inhibited by blebbistatin pulses, including invagination of the shell field and cell shape changes and cell rearrangements during shell field morphogenesis. These factors caused the changed morphology of the shell field, despite the roughly retained “rosette” organization. To explore whether the specification of related cells was affected by blebbistatin treatments, we investigated the expression of four potential shell formation genes (bmp2/4, gata2/3, hox1 and engrailed). The four genes did not show evident changes in expression level, indicating unaffected cell specification in the shell field, while the gene expression patterns showed variations according to the altered morphology of the shell field. Together, our results reveal that NM II contributes to the morphogenesis of the shell field and is crucial for the formation of the larval shell plate in L. goshimai. These results add to the knowledge of the mechanisms of molluskan shell development.</p

A part of differentially expressed genes/proteins between CL and JU.

<p>We present the major differentially expressed proteins of curiosity in this table. An expanded table is available in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135008#pone.0135008.s004" target="_blank">S3 Table</a>. The fold changes (FCs) were calculated using the formula: FC = Log₂ (JU/CL). “↑” and “↓” indicate higher expression in JU and CL, respectively. “–” indicates no significant difference between the two stages (no variation, n.v.).</p><p>^a: The Student’s <i>t</i>-test was used to compare the mRNA expressions between the two stages and the difference was considered significant when <i>p</i> <0.05.</p><p>A part of differentially expressed genes/proteins between CL and JU.</p

A part of differentially expressed genes/proteins between CL and JU.

<p>We present the major differentially expressed proteins of curiosity in this table. An expanded table is available in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135008#pone.0135008.s004" target="_blank">S3 Table</a>. The fold changes (FCs) were calculated using the formula: FC = Log₂ (JU/CL). “↑” and “↓” indicate higher expression in JU and CL, respectively. “–” indicates no significant difference between the two stages (no variation, n.v.).</p><p>^a: The Student’s <i>t</i>-test was used to compare the mRNA expressions between the two stages and the difference was considered significant when <i>p</i> <0.05.</p><p>A part of differentially expressed genes/proteins between CL and JU.</p

A Label-Free Proteomic Analysis on Competent Larvae and Juveniles of the Pacific Oyster <i>Crassostrea gigas</i>

<div><p>Current understandings on the molecular mechanisms underlying bivalve metamorphosis are still fragmentary, and a comprehensive description is required. In this study, using a large-scale label-free proteomic approach, we described and compared the proteomes of competent larvae (CL) and juveniles (JU) of the Pacific oyster, <i>Crassostrea gigas</i>. A total of 788 proteins were identified: 392 in the CL proteome and 636 in the JU proteome. Gene Ontology analysis of the proteome from each sample revealed active metabolic processes in both stages. Further quantitative analyses revealed 117 proteins that were differentially expressed between the two samples. These proteins were divided into eight groups: cytoskeleton and cell adhesion, protein synthesis and degradation, immunity and stress response, development of particular tissues, signal regulation, metabolism and energy supply, transport, and other proteins. A certification experiment using real-time PCR assay confirmed 20 of 30 examined genes exhibited the same trends at the mRNA and protein levels. The differentially expressed proteins may play roles in tissue remodeling, signal transduction, and organ development during and after metamorphosis. Novel roles were proposed for some differentially expressed proteins, such as chymotrypsin. The results of this work provide an overview of metamorphosis and post-metamorphosis development of <i>C</i>. <i>gigas</i> at the protein level. Future studies on the functions of the differentially expressed proteins will help to obtain a more in-depth understanding of bivalve metamorphosis.</p></div

Quantitative analysis between the two developmental stages.

<p>a. The scatter plot distributions of the FCs of the 240 proteins that were detectable in both stages. The Y axis represent FC and the X axis represents the log₂ transformation of total spectra from the four runs. The range of one SD of the mean is indicated by dashed lines. Those proteins fell out of the range are candidate differentially expressed proteins. b. The distributions of the 117 differentially expressed proteins. All proteins have the H-sc of at least ten.</p

The sperm proteome of the Pacific oyster <i>Crassostrea gigas</i> and immunolocalization of heat shock proteins

<div><p>The Pacific oyster <i>Crassostrea gigas</i> is a potential model organism of bivalve mollusks. Comprehensive studies on the proteome of its sperm are necessary to expand our understanding on its reproduction and development, which however are still poor currently. In this study, to improve the situation, we conducted a proteomic analysis on the sperm based on two-dimensional electrophoresis combined with protein identification through mass spectra data. Fifty-six protein spots with constant and relatively high expression levels were selected for protein identification. Among them, 36 were identified (corresponding to 31 proteins), including cytoskeletal proteins, proteins involved in energy supply, protein modifiers, signal regulators, antioxidant proteins, and others. We proposed that these proteins might play important roles in sperm motility, gamete interaction, and oxidation resistance. In particular, we observed several heat shock proteins that were proved to play essential roles in animal sperms. A further immunofluorescence experiment revealed a mitochondria localization of Hsp60s and wide distributions of Hsp70s, indicating these proteins might function in various processes such as mitochondrial function, gamete interaction, and regulation of receptor activity. Our data will provide fundamental supports for the studies on the mechanisms of fertilization and contribute to expand the understandings on reproduction and development of bivalve mollusks.</p></div

The primers of 30 interested genes and reference genes.

<p>The primers of 30 interested genes and reference genes.</p

Protein identification and GO analysis.

<p>a. A Venn diagram showing the numbers of proteins identified from each sample. The number in the bracket indicates a hit from the decoy database. b. Results of GO analysis (the "biological process" category). More information of GO analysis is provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135008#pone.0135008.s003" target="_blank">S2 Table</a>.</p

Statistics of protein identification.

<p>More details were provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135008#pone.0135008.s002" target="_blank">S1 Table</a>.</p><p>^a: include one hit from the decoy database.</p><p>Statistics of protein identification.</p