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We assessed the effect of redox conditions on the mobility of lead (Pb), copper (Cu), and iron (Fe) from sediments affected by acid mine drainage (AMD). This was accomplished by integrating laboratory microcosm experiments, aqueous chemistry, diffraction, and electron microscopy. Microcosm experiments underwent 3 consecutive 5 day redox phases: oxic-anoxicoxic. The sediments contained Fe (51,000 mg/kg), Pb (307 mg/kg), and Cu (30 mg/kg), and minerals such as Illite, albite, and goethite. Microscopy analyses revealed that Pb and Cu are associated with Al-silicates and jarosite. Iron release peaked under anoxic conditions (∼250 mg/L), then decreased in the second oxic phase (<70 mg/L). Extraction experiments confirmed that Pb and Cu are water-labile at pH 3.4 (Pb: 27 μg/L exceeding the United States Environmental Protection Agency drinking water action level of 15 μg/L, Cu: 75 μg/L), but less labile at pH 6.4 (Pb: 7 μg/L, Cu: 3 μg/L). DNA sequencing detected metal-tolerant fungal genera (Trichoderma, Fusarium, Penicillium, and Aspergillus) in the sediments. This study provides insights into the biogeochemical processes influencing the lability of metals in AMD-affected sites, which have relevant implications for risk assessment, remediation strategies, and recovery of critical minerals. 

Abstract Arabidopsis thaliana is currently the most-studied plant species on earth, with an unprecedented number of genetic, genomic, and molecular resources having been generated in this plant model. In the era of translating foundational discoveries to crops and beyond, we aimed to highlight the utility and challenges of using Arabidopsis as a reference for applied plant biology research, agricultural innovation, biotechnology, and medicine. We hope that this review will inspire the next generation of plant biologists to continue leveraging Arabidopsis as a robust and convenient experimental system to address fundamental and applied questions in biology. We aim to encourage laboratory and field scientists alike to take advantage of the vast Arabidopsis datasets, annotations, germplasm, constructs, methods, and molecular and computational tools in our pursuit to advance understanding of plant biology and help feed the world's growing population. We envision that the power of Arabidopsis-inspired biotechnologies and foundational discoveries will continue to fuel the development of resilient, high-yielding, nutritious plants for the betterment of plant and animal health and greater environmental sustainability. 

Previous studies have demonstrated that privacy issues in mobile apps often stem from the integration of third-party libraries (TPLs). To shed light on factors that contribute to these issues, we investigate the privacy-related configuration choices available to and made by Android app developers who incorporate the Facebook Android SDK and Facebook Audience Network SDK in their apps. We compile these Facebook SDKs' privacy-related settings and their defaults. Employing a multi-method approach that integrates static and dynamic analysis, we analyze more than 6,000 popular apps to determine whether the apps incorporate Facebook SDKs and, if so, whether and how developers modify settings. Finally, we assess how these settings align with the privacy practices that developers disclose in the apps’ privacy labels and policies. We observe widespread inconsistencies between practices and disclosures in popular apps. These inconsistencies often stem from privacy settings, including a substantial number of cases in which apps retain default settings over alternatives that offer greater privacy. We observe fewer possible compliance issues in potentially child-directed apps, but issues persist even in these apps. We discuss remediation strategies that SDK and TPL providers could employ to help developers, particularly developers with fewer resources who rely heavily on SDKs. Our recommendations include aligning default privacy settings with data minimization principles and other conservative practices and making privacy-related SDK information both easier to find and harder to miss. 

The underlying factors that lead to specific strains within a species to emerge as human pathogens remain mostly enigmatic. The diarrheal disease cholera is caused by strains from a phylogenetically confined group within theVibrio choleraespecies, the pandemic cholera group (PCG), making it an ideal model system to tackle this puzzling phenomenon. Comprehensive analyses of over 1,840V. choleraegenomes, including environmental isolates from this study, reveal that the species consists of eleven groups, with the PCG belonging to the largest and located within a lineage shared with environmental strains. This hierarchical classification provided us with a framework to unravel the ecoevolutionary dynamics of the genetic determinants associated with the emergence of toxigenicV. cholerae. Our analyses indicate that this phenomenon is largely dependent on the acquisition of unique modular gene clusters and allelic variations that confer a competitive advantage during intestinal colonization. We determined that certain PCG-associated alleles are essential for successful colonization whereas others provide a nonlinear competitive advantage, acting as a critical bottleneck that clarifies the isolated emergence of PCG. For instance, toxigenic strains encoding non-PCG alleles of a)tcpFor b) a sextuple allelic exchange mutant for genestcpA,toxT,VC0176,VC1791,rfbT,andompU, lose their ability to colonize the intestine. Interestingly, these alleles do not play a role in the colonization of newly established model environmental reservoirs. Our study uncovers the evolutionary roots of toxigenicV. choleraeoffering a tractable approach for investigating the emergence of pathogenic clones within an environmental population. 

Abstract Epigenetic modifications directly regulate the patterns of gene expression by altering DNA accessibility and chromatin structure. A knowledge gap is presented by the need to directly measure these modifications, especially for unannotated organisms with unknown primary histone sequences. In the present work, we developed and applied a novel workflow for identifying and annotating histone proteoforms directly from mass spectrometry-based measurements for the endangered Caribbean coral Acropora cervicornis. Combining high-accuracy de novo top-down and bottom-up analysis based on tandem liquid chromatography, trapped ion mobility spectrometry, non-ergodic electron-based fragmentation, and high-resolution mass spectrometry, near complete primary sequence (up to 99%) and over 86 post-translational modification annotations were obtained from pull-down histone fractions. In the absence of reliable genome annotations, H2A, H2B, and H4 histone sequences and the annotation of the post-translational modifications of the stressed A. cervicornis coral allow for a better understanding of chromatin remodeling and new strategies for targeting intervention and restoration of endangered reef corals.