Mechanism for Burgess Shale-type preservation Gaines, Robert R; Hammarlund, Emma U; Hou, Xianguang ...
Proceedings of the National Academy of Sciences - PNAS,
04/2012, Letnik:
109, Številka:
14
Journal Article
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Exceptionally preserved fossil biotas of the Burgess Shale and a handful of other similar Cambrian deposits provide rare but critical insights into the early diversification of animals. The ...extraordinary preservation of labile tissues in these geographically widespread but temporally restricted soft-bodied fossil assemblages has remained enigmatic since Walcott’s initial discovery in 1909. Here, we demonstrate the mechanism of Burgess Shale-type preservation using sedimentologic and geochemical data from the Chengjiang, Burgess Shale, and five other principal Burgess Shale-type deposits. Sulfur isotope evidence from sedimentary pyrites reveals that the exquisite fossilization of organic remains as carbonaceous compressions resulted from early inhibition of microbial activity in the sediments by means of oxidant deprivation. Low sulfate concentrations in the global ocean and low-oxygen bottom water conditions at the sites of deposition resulted in reduced oxidant availability. Subsequently, rapid entombment of fossils in fine-grained sediments and early sealing of sediments by pervasive carbonate cements at bed tops restricted oxidant flux into the sediments. A permeability barrier, provided by bed-capping cements that were emplaced at the seafloor, is a feature that is shared among Burgess Shale-type deposits, and resulted from the unusually high alkalinity of Cambrian oceans. Thus, Burgess Shale-type preservation of soft-bodied fossil assemblages worldwide was promoted by unique aspects of early Paleozoic seawater chemistry that strongly impacted sediment diagenesis, providing a fundamentally unique record of the immediate aftermath of the "Cambrian explosion."
The evolution of Earth’s biota is intimately linked to the oxygenation of the oceans and atmosphere. We use the isotopic composition and concentration of molybdenum (Mo) in sedimentary rocks to ...explore this relationship. Our results indicate two episodes of global ocean oxygenation. The first coincides with the emergence of the Ediacaran fauna, including large, motile bilaterian animals, ca. 550–560 million year ago (Ma), reinforcing previous geochemical indications that Earth surface oxygenation facilitated this radiation. The second, perhaps larger, oxygenation took place around 400 Ma, well after the initial rise of animals and, therefore, suggesting that early metazoans evolved in a relatively low oxygen environment. This later oxygenation correlates with the diversification of vascular plants, which likely contributed to increased oxygenation through the enhanced burial of organic carbon in sediments. It also correlates with a pronounced radiation of large predatory fish, animals with high oxygen demand. We thereby couple the redox history of the atmosphere and oceans to major events in animal evolution.
Hair can record chemical information reflecting our living conditions, and, therefore, strands of hair have become a potent analytical target within the biological and forensic sciences. While early ...efforts focused on analyzing complete hair strands in bulk, high spatial resolution mass spectrometry imaging (MSI) has recently come to the forefront of chemical hair-strand analysis. MSI techniques offer a localized analysis, requiring fewer de-contamination procedures per default and making it possible to map the distribution of analytes on and within individual hair strands. Applying the techniques to hair samples has proven particularly useful in investigations quantifying the exposure to, and uptake of, toxins or drugs. Overall, MSI, combined with optimized sample preparation protocols, has improved precision and accuracy for identifying several elemental and molecular species in single strands of hair. Here, we review different sample preparation protocols and use cases with a view to make the methodology more accessible to researchers outside of the field of forensic science. We conclude that-although some challenges remain, including contamination issues and matrix effects-MSI offers unique opportunities for obtaining highly resolved spatial information of several compounds simultaneously across hair surfaces.
The Xiamaling Formation in the North China Block contains a well-preserved 1400 Ma sedimentary sequence with a low degree of thermal maturity. Previous studies have confirmed the dynamic and complex ...nature of this evolving marine setting, including the existence of an oxygen-minimum zone, using multi-proxy approaches, including iron speciation, trace metal dynamics, and organic geochemistry. Here, we investigate the prevailing redox conditions during diagenesis via the biomarkers of rearranged hopanes from the finely laminated sediments of the organic-rich black shales in Units 2 and 3 of the Xiamaling Formation. We find that rearranged hopanes are prominent in the biomarker composition of the oxygen-minimum zone sediment, which is completely different from that of the sediment in the overlying anoxic strata. Since the transition process from hopanes to rearranged hopanes requires oxygen via oxidation at the C-l6 alkyl position of 17α(H)-hopanes, we infer that dissolved oxygen led to the transformation of hopane precursors into rearranged hopanes during the early stages of diagenesis. The use of hopanoid hydrocarbons as biomarkers of marine redox conditions has rarely been previously reported, and the hydrocarbon signatures point towards oxic bottom waters during the deposition of Unit 3 of the Xiamaling Formation, which is consistent with the earlier oxygen-minimum zone environmental interpretation of this Unit.
Abstract
Therapeutic resistance is one of the main reasons for treatment failure in cancer patients. The polyaneuploid cancer cell (PACC) state has been shown to promote resistance by providing a ...refuge for cancer cells from the effects of therapy and by helping them adapt to a variety of environmental stressors. This state is the result of aneuploid cancer cells undergoing whole genome doubling and skipping mitosis, cytokinesis, or both. In this paper, we create a novel mathematical framework for modeling the eco-evolutionary dynamics of state-structured populations and use this framework to construct a model of cancer populations with an aneuploid and a PACC state. Using in silico simulations, we explore how the PACC state allows cancer cells to (1) survive extreme environmental conditions by exiting the cell cycle after S phase and protecting genomic material and (2) aid in adaptation to environmental stressors by increasing the cancer cell’s ability to generate heritable variation (evolvability) through the increase in genomic content that accompanies polyploidization. In doing so, we demonstrate the ability of the PACC state to allow cancer cells to persist under therapy and evolve therapeutic resistance. By eliminating cells in the PACC state through appropriately-timed PACC-targeted therapies, we show how we can prevent the emergence of resistance and promote cancer eradication.
Updating the Definition of Cancer Brown, Joel S; Amend, Sarah R; Austin, Robert H ...
Molecular cancer research,
11/2023, Letnik:
21, Številka:
11
Journal Article
Recenzirano
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Most definitions of cancer broadly conform to the current NCI definition: "Cancer is a disease in which some of the body's cells grow uncontrollably and spread to other parts of the body." These ...definitions tend to describe what cancer "looks like" or "does" but do not describe what cancer "is" or "has become." While reflecting past insights, current definitions have not kept pace with the understanding that the cancer cell is itself transformed and evolving. We propose a revised definition of cancer: Cancer is a disease of uncontrolled proliferation by transformed cells subject to evolution by natural selection. We believe this definition captures the essence of the majority of previous and current definitions. To the simplest definition of cancer as a disease of uncontrolled proliferation of cells, our definition adds in the adjective "transformed" to capture the many tumorigenic processes that cancer cells adopt to metastasize. To the concept of uncontrolled proliferation of transformed cells, our proposed definition then adds "subject to evolution by natural selection." The subject to evolution by natural selection modernizes the definition to include the genetic and epigenetic changes that accumulate within a population of cancer cells that lead to the lethal phenotype. Cancer is a disease of uncontrolled proliferation by transformed cells subject to evolution by natural selection.
The end-Ordovician extinction consisted of two discrete pulses, both linked, in various ways, to glaciation at the South Pole. The first phase, starting just below the Normalograptus extraordinarius ...Zone, particularly affected nektonic and planktonic species, while the second pulse, associated with the Normalograptus persculptus Zone, was less selective. Glacially induced cooling and oxygenation are two of many suggested kill mechanisms for the end-Ordovician extinction, but a general consensus is lacking. We have used geochemical redox indicators, such as iron speciation, molybdenum concentrations, pyrite framboid size distribution and sulfur isotopes to analyze the geochemistry in three key Hirnantian sections. These indicators reveal that reducing conditions were occasionally present at all three sites before the first pulse of the end-Ordovician extinction, and that these conditions expanded towards the second pulse. Even though the N. extraordinarius Zone appears to have been a time of oxygenated deposition, pyrite is significantly enriched in 34S in our sections as well as in sections reported from South China. This suggests a widespread reduction in marine sulfate concentrations, which we attribute to an increase in pyrite burial during the early Hirnantian. The S-isotope excursion coincides with a major positive carbon isotope excursion indicating elevated rates of organic carbon burial as well. We argue that euxinic conditions prevailed and intensified in the early Hirnantian oceans, and that a concomitant global sea level lowering pushed the chemocline deeper than the depositional setting of our sites. In the N. persculptus Zone, an interval associated with a major sea level rise, our redox indicators suggests that euxinic conditions, and ferruginous in some places, encroached onto the continental shelves. In our model, the expansion of euxinic conditions during the N. extraordinarius Zone was generated by a reorganization of nutrient cycling during sea level fall, and we argue, overall, that these dynamics in ocean chemistry played an important role for the end-Ordovician mass extinction. During the first pulse of the extinction, euxinia and a steepened oxygen gradient in the water column caused habitat loss for deep-water benthic and nektonic organisms. During the second pulse, the transgression of anoxic water onto the continental shelves caused extinction in shallower habitats.
► A sulfur isotope excursion shows widespread euxinia in the ‘oxic’ early Hirnantian. ► The nutrient-driven event was forced by sea level fall in a low-oxygen world. ► Euxinic conditions are also observed in the pre- and late Hirnantian. ► Anoxia, not cooling or oxygenation, was a likely kill-mechanism in the end-Ordovician mass extinction particularly in deeper-water faunas.
The Xiamaling Formation is an exceptionally well-preserved sedimentary succession deposited on a marine passive margin about 1400 million years ago. We used a multi-proxy approach, including iron ...speciation, trace metal dynamics, and organic geochemistry, to explore the evolution of ocean chemistry through most of the Xiamaling Formation. This evolution is put in the context of the paleogeography and the sedimentological evolution of the Xiamaling depositional system. Overall, the Xiamaling Formation is informally divided into six units based on both sedimentological and geochemical criteria. Of the six units, we fully explored four of them. Unit 4, the lowest unit we studied, is comprised of deep-water red muds, periodically interrupted by green-colored silt and sandy turbidites. Iron extraction results show that the red muds are enriched in highly reactive iron, indicating a water-column source for the iron. However, the low organic carbon contents, low hydrogen index (HI) values, and the oxidized nature of the reactive iron pool indicate deposition in oxygenated bottom waters. We interpret unit 4 to represent a low-productivity ferruginous oxygen-minimum zone (OMZ) environment, underlain by oxygenated bottom waters. The transition to unit 3 reflects an increase in primary productivity, and the development of a more biologically active OMZ, that supported anoxygenic phototrophic bacteria. Still, in this unit, the bottom waters remained oxygenated. The overlying unit 2 represents the transition to deep-water deoxygenation and anoxic waters at the sediment surface. These waters were ferruginous in the bottom part of the unit and sulfidic (euxinic) towards the top. In the uppermost unit 1, euxinic conditions continued, punctuated by more frequent water-column oxygenation towards the upper part of the unit. We place the evolution of these chemical dynamics in the context of climate and climate change, and in particular, the placement of the Xiamaling Formation in relation to the Intertropical Convergence Zone (ITCZ) and the resulting Hadley Cell dynamics. Also, while our results demonstrate the persistence of anoxic water-column conditions high in the water column during the deposition of the Xiamaling Formation, they also demonstrate bottom water oxygenation near the seafloor during the deposition of three of the four units, and over a time interval extending to 10's of millions of years.
Abstract
Recent evidence suggests that a polyaneuploid cancer cell (PACC) state may play a key role in the adaptation of cancer cells to stressful environments and in promoting therapeutic ...resistance. The PACC state allows cancer cells to pause cell division and to avoid DNA damage and programmed cell death. Transition to the PACC state may also lead to an increase in the cancer cell’s ability to generate heritable variation (evolvability). One way this can occur is through evolutionary triage. Under this framework, cells gradually gain resistance by scaling hills on a fitness landscape through a process of mutation and selection. Another way this can happen is through self-genetic modification whereby cells in the PACC state find a viable solution to the stressor and then undergo depolyploidization, passing it on to their heritably resistant progeny. Here, we develop a stochastic model to simulate both of these evolutionary frameworks. We examine the impact of treatment dosage and extent of self-genetic modification on eco-evolutionary dynamics of cancer cells with aneuploid and PACC states. We find that under low doses of therapy, evolutionary triage performs better whereas under high doses of therapy, self-genetic modification is favored. This study generates predictions for teasing apart these biological hypotheses, examines the implications of each in the context of cancer, and provides a modeling framework to compare Mendelian and non-traditional forms of inheritance.
Elevated molybdenum (Mo) contents in organic-rich sediments are indicative of deposition from an anoxic and sulfide-rich (euxinic) water-column. This can be used for tracing past euxinic conditions ...in ancient oceans from sedimentary archives. Conventional analytical detection of elevated molybdenum levels is, however, expensive and cannot be directly performed in the field. Here, we show that handheld x-ray absorption spectroscopy (HHXRF) on both rock-powders and rock surfaces provides a powerful tool for laboratory or field-based, geochemical characterization of Mo content and the tracing of euxinic depositional conditions. We further present a sedimentary Mo database, compiled from over 300 globally distributed modern marine sites, to show that modern euxinic marine basins are characterized by molybdenum enrichment (>25ppm) relative to average crust (~1.5ppm) and river suspended matter (~3ppm). Only Mn-oxide rich deposits from oxygenated deep sea settings match such high Mo enrichments, but these are easily distinguished from Mo-rich sediments from the continental shelves. Hence, past and present organic rich sediments enriched in Mo are indicative of (at least intermittent) water-column euxinia.
We analyzed the molybdenum content of powdered and homogenized samples of Holocene, Miocene, Triassic–Jurassic, Ordovician and Cambrian age by HHXRF and Inductively-Coupled-Plasma-Mass-Spectrometry (ICPMS). We further analyzed 2 certified NIST standard references (NIST-2781 with Mo: 47ppm and NIST-2702 with Mo: 10ppm) for analytical control. Analytical precision (1σ) after 30, 120, and 300seconds of measuring time was 4, 2, and 1ppm, with a respective detection limit of 11, 5, 3ppm (3σ, noise level). The data were accurate to within the given precision (1σ) after a daily calibration to samples covering a range of Mo concentrations from 0 to >30ppm.
Hand-held XRF equipment also allows Mo measurements directly on fresh rock surfaces, both in the field and under laboratory conditions. Rock-samples from a Cambrian drill core closely match ICPMS obtained Mo concentrations from homogenous powders of the same rocks. Collectively, our data show that HHXRF as a quick and reliable method for the precise and accurate quantification of molybdenum concentrations in both rock powders and at fresh rock surfaces. The non-destructive nature of the HHXRF measurements is combined with low (per sample) analytical costs, minor sample preparation and easy applicability in the field.
•Modern organic-rich sediments with >25ppm Mo were deposited from sulfidic waters.•HH-XRF detects >11 and >4ppm Mo in rocks in just 30 and 300seconds, respectively.•HH-XRF can be used to reliably identify euxinic sediments in the field.•HH-XRF records abrupt stratigraphic Mo changes, not recognized with traditional bulk analysis.
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