Biology subjects

Berg, J. S.

Publications and source records attributed to Berg, J. S..

5 recordsLinked to original sources

bioRxiv2021

Ancient and modern geochemical signatures in the 13,500-year sedimentary record of Lake Cadagno

Although lake sediments are globally important organic carbon sinks and therefore important habitats for deep microbial life, the deep lacustrine biosphere has thus far been little studied compared to its marine counterpart. To investigate the impact of the underexplored deep lacustrine biosphere on the sediment geochemical environment and vice versa, we performed a comprehensive microbiological and geochemical characterization of a sedimentary sequence from Lake Cadagno covering its entire environmental history since formation following glacial retreat. We found that both geochemical gradients and microbial community shifts across the [~]13.5 kyr subsurface sedimentary record reflect redox changes in the lake, going from oxic to anoxic and sulfidic. Most microbial activity occurs within the top 40 cm of sediment, where millimolar sulfate concentrations diffusing in from the bottom water are completely consumed. In deeper sediment layers, organic carbon remineralization is much slower but microorganisms nonetheless subsist on fermentation, sulfur cycling, metal reduction, and methanogenesis. The most surprising finding was the presence of a deep, oxidizing groundwater source. This water source generates an inverse redox gradient at the bottom of the sedimentary sequence and could contribute to the remineralization of organic matter sequestered in the energy-limited deep subsurface.

microbiology↗

bioRxiv2020

A Validated Functional Analysis of PALB2 Missense Variants for Use in Clinical Variant Interpretation

Clinical genetic testing readily detects germline genetic variants. Yet, the evidence available for variant classification as benign or pathogenic is often limited by the rarity of individual variants, leading to many "variant of uncertain significance" (VUS) classifications. VUS cannot guide clinical decisions, complicating counseling and management. Laboratory assays can potentially aid reclassification, but require benchmarking against variants with definitive interpretations to have sufficient predictive power for clinical use. Of all clinically identified germline variants in hereditary breast cancer gene PALB2 (Partner and Localizer of BRCA2), ~50% are VUS and ~90% of VUS are missense. Truncating PALB2 variants have homologous recombination (HR) defects and instead rely on error-prone non-homologous end-joining (NHEJ) for DNA damage repair (DDR). Recent reports show some missense PALB2 variants may also be damaging, but thus far functional studies have lacked benchmarking controls. Using the Traffic Light Reporter (TLR) to quantify cellular HR and NHEJ using fluorescent markers, we assessed variant-level DDR capacity in hereditary breast cancer genes. We first determined the TLRs dynamic range using BRCA2 missense variants of known significance as benchmarks for normal/abnormal HR function. We then tested 37 PALB2 variants, generating functional data for germline PALB2 variants at a moderate level of evidence for a pathogenic interpretation (PS3_moderate) for 8 variants, or a supporting level of evidence in favor of a benign interpretation (BS3_supporting) for 13 variants, based on the ability of the assay to correctly classify PALB2 validation controls. This new data can be applied in subsequent variant interpretations for direct clinical benefit.

genetics↗

bioRxiv2019

Recommendations for application of the functional evidence PS3/BS3 criterion using the ACMG/AMP sequence variant interpretation framework

BackgroundThe American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) clinical variant interpretation guidelines established criteria (PS3/BS3) for functional assays that specified a \"strong\" level of evidence. However, they did not provide detailed guidance on how functional evidence should be evaluated, and differences in the application of the PS3/BS3 codes is a contributor to variant interpretation discordance between laboratories. This recommendation seeks to provide a more structured approach to the assessment of functional assays for variant interpretation and guidance on the use of various levels of strength based on assay validation.\n\nMethodsThe Clinical Genome Resource (ClinGen) Sequence Variant Interpretation (SVI) Working Group used curated functional evidence from ClinGen Variant Curation Expert Panel-developed rule specifications and expert opinions to refine the PS3/BS3 criteria over multiple in-person and virtual meetings. We estimated odds of pathogenicity for assays using various numbers of variant controls to determine the minimum controls required to reach moderate level evidence. Feedback from the ClinGen Steering Committee and outside experts were incorporated into the recommendations at multiple stages of development.\n\nResultsThe SVI Working Group developed recommendations for evaluators regarding the assessment of the clinical validity of functional data and a four-step provisional framework to determine the appropriate strength of evidence that can be applied in clinical variant interpretation. These steps are: 1. Define the disease mechanism; 2. Evaluate applicability of general classes of assays used in the field; 3. Evaluate validity of specific instances of assays; 4. Apply evidence to individual variant interpretation. We found that a minimum of eleven total pathogenic and benign variant controls are required to reach moderate-level evidence in the absence of rigorous statistical analysis.\n\nConclusionsThe recommendations and approach to functional evidence evaluation described here should help clarify the clinical variant interpretation process for functional assays. Further, we hope that these recommendations will help develop productive partnerships with basic scientists who have developed functional assays that are useful for interrogating the function of a variety of genes.

genetics↗

bioRxiv2018

Dark aerobic sulfide oxidation by anoxygenic phototrophs in the anoxic waters of Lake Cadagno

SUMMARYAnoxygenic phototrophic sulfide oxidation by green and purple sulfur bacteria (PSB) plays a key role in sulfide removal from anoxic shallow sediments and stratified waters. Although some PSB can also oxidize sulfide with nitrate and oxygen, little is known about the prevalence of this chemolithotrophic lifestyle in the environment. In this study, we investigated the role of these phototrophs in light-independent sulfide removal in the chemocline of Lake Cadagno. Our temporally resolved, high-resolution chemical profiles indicated that dark sulfide oxidation was coupled to high oxygen consumption rates of ~9 M O2{middle dot}h-1. Single-cell analyses of lake water incubated with 13CO2 in the dark revealed that Chr. okenii was to a large extent responsible for aerobic sulfide oxidation and it accounted for up to 40 % of total dark carbon fixation. The genome of Chr. okenii reconstructed from the Lake Cadagno metagenome confirms its capacity for microaerophilic growth and provides further insights into its metabolic capabilities. Moreover, our genomic and single-cell data indicated that other PSB grow microaerobically in these apparently anoxic waters. Altogether, our observations suggest that aerobic respiration may not only play an underappreciated role in anoxic environments, but also that organisms typically considered strict anaerobes may be involved.\n\nORIGINALITY-SIGNIFICANCE STATEMENTThis study reveals that dark aerobic sulfide oxidation within an anoxic layer dominated by anoxygenic phototrophic bacteria in the stratified water column of Lake Cadagno is to a large extent carried out by the anoxygenic phototrophic bacterium Chromatium okenii. Our findings imply that aerobic metabolisms may be more prevalent in anoxic zones than previously thought. We also present an environmental metagenome-assembled genome of Chr. okenii which is the first genome sequence for the genus Chromatium and reveals new interesting physiological features of this environmentally relevant organism, including its capacity for aerobic respiration.

microbiology↗

bioRxiv2017

Evaluating the clinical validity of gene-disease associations: an evidence-based framework developed by the Clinical Genome Resource

With advances in genomic sequencing technology, the number of reported gene-disease relationships has rapidly expanded. However, the evidence supporting these claims varies widely, confounding accurate evaluation of genomic variation in a clinical setting. Despite the critical need to differentiate clinically valid relationships from less well-substantiated relationships, standard guidelines for such evaluation do not currently exist. The NIH-funded Clinical Genome Resource (ClinGen) has developed a framework to define and evaluate the clinical validity of gene-disease pairs across a variety of Mendelian disorders. In this manuscript we describe a proposed framework to evaluate relevant genetic and experimental evidence supporting or contradicting a gene-disease relationship, and the subsequent validation of this framework using a set of representative gene-disease pairs. The framework provides a semi-quantitative measurement for the strength of evidence of a gene-disease relationship which correlates to a qualitative classification: \"Definitive\", \"Strong\", \"Moderate\", \"Limited\", \"No Reported Evidence\" or \"Conflicting Evidence.\" Within the ClinGen structure, classifications derived using this framework are reviewed and confirmed or adjusted based on clinical expertise of appropriate disease experts. Detailed guidance for utilizing this framework and access to the curation interface is available on our website. This evidence-based, systematic method to assess the strength of gene-disease relationships will facilitate more knowledgeable utilization of genomic variants in clinical and research settings.

genetics↗