Comparing FRACHEM and TOUGHREACT for reactive transport modelingof brine-rock interactions in enhanced geothermal systems (EGS)

Coupled modelling of fluid flow and reactive transport ingeothermal systems is challenging because of reservoir conditions such ashigh temperatures, elevated pressures and sometimes high salinities ofthe formation fluids. Thermal hydrological-chemical (THC) codes, such asFRACHEM and TOUGHREACT, have been developed to evaluate the long-termhydrothermal and chemical evolution of exploited reservoirs. In thisstudy, the two codes were applied to model the same geothermal reservoir,to forecast reservoir evolution using respective thermodynamic andkinetic input data. A recent (unreleased) TOUGHREACT version allows theuse of either an extended Debye-Hu?ckel or Pitzer activity model forcalculating activity coefficients, while FRACHEM was designed to use thePitzer formalism. Comparison of models results indicate that differencesin thermodynamic equilibrium constants, activity coefficients andkinetics models can result in significant differences in predictedmineral precipitation behaviour and reservoir-porosity evolution.Differences in the calculation schemes typically produce less differencein model outputs than differences in input thermodynamic and kineticdata, with model results being particularly sensitive to differences inion-interaction parameters for highsalinity systems

The UniProt-GO Annotation database in 2011

The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from the Gene Ontology resource and UniProtKB proteins. Currently supplying over 100 million annotations to 11 million proteins in more than 360 000 taxa, this resource has increased 2-fold over the last 2 years and has benefited from a wealth of checks to improve annotation correctness and consistency as well as now supplying a greater information content enabled by GO Consortium annotation format developments. Detailed, manual GO annotations obtained from the curation of peer-reviewed papers are directly contributed by all UniProt curators and supplemented with manual and electronic annotations from 36 model organism and domain-focused scientific resources. The inclusion of high-quality, automatic annotation predictions ensures the UniProt GO annotation dataset supplies functional information to a wide range of proteins, including those from poorly characterized, non-model organism species. UniProt GO annotations are freely available in a range of formats accessible by both file downloads and web-based views. In addition, the introduction of a new, normalized file format in 2010 has made for easier handling of the complete UniProt-GOA data set

Basic Research Needs for Geosciences: Facilitating 21st Century Energy Systems

To identify research areas in geosciences, such as behavior of multiphase fluid-solid systems on a variety of scales, chemical migration processes in geologic media, characterization of geologic systems, and modeling and simulation of geologic systems, needed for improved energy systems

Re-Annotation Is an Essential Step in Systems Biology Modeling of Functional Genomics Data

One motivation of systems biology research is to understand gene functions and interactions from functional genomics data such as that derived from microarrays. Up-to-date structural and functional annotations of genes are an essential foundation of systems biology modeling. We propose that the first essential step in any systems biology modeling of functional genomics data, especially for species with recently sequenced genomes, is gene structural and functional re-annotation. To demonstrate the impact of such re-annotation, we structurally and functionally re-annotated a microarray developed, and previously used, as a tool for disease research. We quantified the impact of this re-annotation on the array based on the total numbers of structural- and functional-annotations, the Gene Annotation Quality (GAQ) score, and canonical pathway coverage. We next quantified the impact of re-annotation on systems biology modeling using a previously published experiment that used this microarray. We show that re-annotation improves the quantity and quality of structural- and functional-annotations, allows a more comprehensive Gene Ontology based modeling, and improves pathway coverage for both the whole array and a differentially expressed mRNA subset. Our results also demonstrate that re-annotation can result in a different knowledge outcome derived from previous published research findings. We propose that, because of this, re-annotation should be considered to be an essential first step for deriving value from functional genomics data

Perspectives on tracking data reuse across biodata resources

c The Author(s) 2024. Published by Oxford University Press.Motivation: Data reuse is a common and vital practice in molecular biology and enables the knowledge gathered over recent decades to drive discovery and innovation in the life sciences. Much of this knowledge has been collated into molecular biology databases, such as UniProtKB, and these resources derive enormous value from sharing data among themselves. However, quantifying and documenting this kind of data reuse remains a challenge. Results: The article reports on a one-day virtual workshop hosted by the UniProt Consortium in March 2023, attended by representatives from biodata resources, experts in data management, and NIH program managers. Workshop discussions focused on strategies for tracking data reuse, best practices for reusing data, and the challenges associated with data reuse and tracking. Surveys and discussions showed that data reuse is widespread, but critical information for reproducibility is sometimes lacking. Challenges include costs of tracking data reuse, tensions between tracking data and open sharing, restrictive licenses, and difficulties in tracking commercial data use. Recommendations that emerged from the discussion include: development of standardized formats for documenting data reuse, education about the obstacles posed by restrictive licenses, and continued recognition by funding agencies that data management is a critical activity that requires dedicated resources

The human phylome

The human phylome, which includes evolutionary relationships of all human proteins and their homologs among thirty-nine fully sequenced eukaryotes, is reconstructed

Current approaches to gene regulatory network modelling

Many different approaches have been developed to model and simulate gene regulatory networks. We proposed the following categories for gene regulatory network models: network parts lists, network topology models, network control logic models, and dynamic models. Here we will describe some examples for each of these categories. We will study the topology of gene regulatory networks in yeast in more detail, comparing a direct network derived from transcription factor binding data and an indirect network derived from genome-wide expression data in mutants. Regarding the network dynamics we briefly describe discrete and continuous approaches to network modelling, then describe a hybrid model called Finite State Linear Model and demonstrate that some simple network dynamics can be simulated in this model

A SARS-CoV-2 neutralizing antibody protects from lung pathology in a COVID-19 hamster model

The emergence of SARS-CoV-2 led to pandemic spread of coronavirus disease 2019 (COVID-19), manifesting with respiratory symptoms and multi-organ dysfunction. Detailed characterization of virus-neutralizing antibodies and target epitopes is needed to understand COVID-19 pathophysiology and guide immunization strategies. Among 598 human monoclonal antibodies (mAbs) from ten COVID-19 patients, we identified 40 strongly neutralizing mAbs. The most potent mAb CV07-209 neutralized authentic SARS-CoV-2 with IC(50) of 3.1 ng/ml. Crystal structures of two mAbs in complex with the SARS-CoV-2 receptor-binding domain at 2.55 and 2.70 A revealed a direct block of ACE2 attachment. Interestingly, some of the near-germline SARS-CoV-2 neutralizing mAbs reacted with mammalian self-antigens. Prophylactic and therapeutic application of CV07-209 protected hamsters from SARS-CoV-2 infection, weight loss and lung pathology. Our results show that non-self-reactive virus-neutralizing mAbs elicited during SARS-CoV-2 infection are a promising therapeutic strategy

Buoyancy Effects on Upward Brine Displacement Caused by CO2 Injection

Upward displacement of brine from deep reservoirs driven by pressure increases resulting from CO{sub 2} injection for geologic carbon sequestration may occur through improperly sealed abandoned wells, through permeable faults, or through permeable channels between pinch-outs of shale formations. The concern about upward brine flow is that, upon intrusion into aquifers containing groundwater resources, the brine may degrade groundwater. Because both salinity and temperature increase with depth in sedimentary basins, upward displacement of brine involves lifting fluid that is saline but also warm into shallower regions that contain fresher, cooler water. We have carried out dynamic simulations using TOUGH2/EOS7 of upward displacement of warm, salty water into cooler, fresher aquifers in a highly idealized two-dimensional model consisting of a vertical conduit (representing a well or permeable fault) connecting a deep and a shallow reservoir. Our simulations show that for small pressure increases and/or high-salinity-gradient cases, brine is pushed up the conduit to a new static steady-state equilibrium. On the other hand, if the pressure rise is large enough that brine is pushed up the conduit and into the overlying upper aquifer, flow may be sustained if the dense brine is allowed to spread laterally. In this scenario, dense brine only contacts the lower-most region of the upper aquifer. In a hypothetical case in which strong cooling of the dense brine occurs in the upper reservoir, the brine becomes sufficiently dense that it flows back down into the deeper reservoir from where it came. The brine then heats again in the lower aquifer and moves back up the conduit to repeat the cycle. Parameter studies delineate steady-state (static) and oscillatory solutions and reveal the character and period of oscillatory solutions. Such oscillatory solutions are mostly a curiosity rather than an expected natural phenomenon because in nature the geothermal gradient prevents the cooling in the upper aquifer that occurs in the model. The expected effect of upward brine displacement is either establishment of a new hydrostatic equilibrium or sustained upward flux into the bottom-most region of the upper aquifer