ORCID Profile
0000-0003-0135-4022
Current Organisations
Universidad de La laguna
,
University of California Davis
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Publisher: Springer Science and Business Media LLC
Date: 16-07-2018
Publisher: Springer Science and Business Media LLC
Date: 26-10-2023
Publisher: Springer Science and Business Media LLC
Date: 11-10-2022
DOI: 10.1038/S41579-021-00636-2
Abstract: Fossilized lipids preserved in sedimentary rocks offer singular insights into the Earth's palaeobiology. These 'biomarkers' encode information pertaining to the oxygenation of the atmosphere and oceans, transitions in ocean plankton, the greening of continents, mass extinctions and climate change. Historically, biomarker interpretations relied on inventories of lipids present in extant microorganisms and counterparts in natural environments. However, progress has been impeded because only a small fraction of the Earth's microorganisms can be cultured, many environmentally significant microorganisms from the past no longer exist and there are gaping holes in knowledge concerning lipid biosynthesis. The revolution in genomics and bioinformatics has provided new tools to expand our understanding of lipid biomarkers, their biosynthetic pathways and distributions in nature. In this Review, we explore how preserved organic molecules provide a unique perspective on the history of the Earth's microbial life. We discuss how advances in molecular biology have helped elucidate biomarker origins and afforded more robust interpretations of fossil lipids and how the rock record provides vital calibration points for molecular clocks. Such studies are open to further exploitation with the expansion of sequenced microbial genomes in accessible databases.
Publisher: Springer Science and Business Media LLC
Date: 16-08-2018
DOI: 10.1038/S41588-018-0197-6
Abstract: In the version of this article initially published, in Fig. 3, the y-axis numbering did not match the log scale indicated in the axis label. The error has been corrected in the HTML and PDF version of the article.
Publisher: Elsevier BV
Date: 02-2014
Publisher: Springer Science and Business Media LLC
Date: 02-08-2014
Publisher: Wiley
Date: 28-08-2017
DOI: 10.1111/GBI.12253
Abstract: Demosponges are a rich natural source of unusual lipids, some of which are of interest as geochemical biomarkers. Although demosponges are animals, they often host dense communities of microbial symbionts, and it is therefore unclear which lipids can be synthesized by the animal de novo, and which require input from the microbial community. To address this uncertainty, we analyzed the lipids of Amphimdeon queenslandica, the only demosponge with a published genome. We correlated the genetic and lipid repertoires of A. queenslandica to identify which biomarkers could potentially be synthesized and/or modified by the sponge. The fatty acid profile of A. queenslandica is dominated by an unusual Δ
Publisher: Wiley
Date: 17-03-2021
DOI: 10.1002/ECE3.7280
Publisher: Research Square Platform LLC
Date: 06-2022
DOI: 10.21203/RS.3.RS-1686449/V1
Abstract: Molecular fossils have been used to augment the physical fossil record, charting the expansion of complex life through the Neoproterozoic Era (~1000-541 Ma). This work relies on the hypothesis that C27 steranes preserved in sedimentary rocks originated from cholesterol, the predominant sterol produced by red algae and animals. Following the same logic, C28 and C29 carbon steranes are widely considered to be derived from the sterols of fungi, green algae and some protists. In this study, we demonstrate that the gene 24-C sterol methyltransferase (smt), which is necessary to produce C28 and C29 sterols, is present in segmented worms, an advanced group of animals. Phylogenetic analysis of the relevant gene suggests it was present in the first animals and lost independently in at least seven major lineages. A molecular clock demonstrates that the SMT specific to animals and their closest ancestors was present through the Neoproterozoic. Based on these results, C27 steranes cannot be considered indicative of Neoproterozoic animals, and C28+ steranes are not solely indicative of fungi or green algae. While our results do not necessarily contradict the emerging picture of Neoproterozoic life informed by molecular fossils, they refute the underlying hypothesis that drives the interpretive paradigm.
Publisher: Proceedings of the National Academy of Sciences
Date: 22-02-2016
Abstract: An unusual molecule is found in rocks ∼650–540 million y old, and its likely precursor, 24-isopropylcholesterol (24-ipc), is produced by some modern sea sponges. The sterane hydrocarbon analog of 24-ipc offers a potential “molecular fossil” for early animals, but certain algae also produce traces of this molecule, so it is unclear when and how frequently the ability to synthesize 24-ipc evolved. In this study, we connect 24-ipc production to a gene and conclude that algae and sponges independently evolved 24-ipc synthesis through unique gene duplication events. Although the timing of the sponge gene duplication overlaps with the geological record of the molecular fossil, the algal gene duplication occurs significantly later, supporting the connection of 24-ipc to sponges and providing the oldest evidence for animal life.
Publisher: MDPI AG
Date: 23-02-2023
DOI: 10.3390/BIOMEDICINES11030676
Abstract: Asthma is the most prevalent pediatric chronic disease. Bronchodilator drug response (BDR) and fractional exhaled nitric oxide (FeNO) are clinical biomarkers of asthma. Although DNA methylation (DNAm) contributes to asthma pathogenesis, the influence of DNAm on BDR and FeNO is scarcely investigated. This study aims to identify DNAm markers in whole blood associated either with BDR or FeNO in pediatric asthma. We analyzed 121 s les from children with moderate-to-severe asthma. The association of genome-wide DNAm with BDR and FeNO has been assessed using regression models, adjusting for age, sex, ancestry, and tissue heterogeneity. Cross-tissue validation was assessed in 50 nasal s les. Differentially methylated regions (DMRs) and enrichment in traits and biological pathways were assessed. A false discovery rate (FDR) 0.1 and a genome-wide significance threshold of p 9 × 10−8 were used to control for false-positive results. The CpG cg12835256 (PLA2G12A) was genome-wide associated with FeNO in blood s les (coefficient= −0.015, p = 2.53 × 10−9) and nominally associated in nasal s les (coefficient = −0.015, p = 0.045). Additionally, three CpGs were suggestively associated with BDR (FDR 0.1). We identified 12 and four DMRs associated with FeNO and BDR (FDR 0.05), respectively. An enrichment in allergic and inflammatory processes, smoking, and aging was observed. We reported novel associations of DNAm markers associated with BDR and FeNO enriched in asthma-related processes.
Publisher: Research Square Platform LLC
Date: 07-11-2022
DOI: 10.21203/RS.3.RS-2202848/V1
Abstract: Fossilized lipids offer one of only few windows into ancient ecosystems. The utility of such biomarkers is determined by the phylogenetic distribution of lipid biosynthetic capabilities in extant organisms and extrapolation of this information into the past. 2-Methylhopanes in sedimentary rocks were once used to infer the importance of Cyanobacteria as primary producers in the geological past. However, the discovery of the hopanoid C-2 methyltransferase (HpnP) in Alphaproteobacteria led to the downfall of this molecular proxy. In the present study, we re-examined the distribution of HpnP in a new phylogenetic framework including novel candidate phyla, and re-interpreted a revised geological record of 2-methylhopanes based on contamination-free s les. We show that HpnP was likely present in the last common ancestor of Cyanobacteria, while the gene appeared in Alphaproteobacteria only around 750 million years ago. A subsequent rise of sedimentary 2-methylhopanes around 600 Ma likely reflects the expansion of Alphaproteobacteria that coincided with the rise of eukaryotic algae — possibly connected by algal dependency on microbially-produced vitamin B12. Our findings re-establish 2-methylhopanes as cyanobacterial biomarkers prior to 750 Ma and thus as a potential tool to measure the importance of oxygenic Cyanobacteria as primary producers on the early Earth. Our study illustrates how genetics can improve the diagnostic value of biomarkers and refine the reconstruction of early ecosystems.
Location: United States of America
Location: United States of America
Location: United States of America
Location: United States of America
No related grants have been discovered for David Gold.