Oxygen-sensing mechanisms of eukaryotic multicellular organisms coordinate hypoxic cellular responses in a spatiotemporal manner. Although this capacity partly allows animals and plants to acutely ...adapt to oxygen deprivation, its functional and historical roots in hypoxia emphasize a broader evolutionary role. For multicellular life-forms that persist in settings with variable oxygen concentrations, the capacity to perceive and modulate responses in and between cells is pivotal. Animals and higher plants represent the most complex life-forms that ever diversified on Earth, and their oxygen-sensing mechanisms demonstrate convergent evolution from a functional perspective. Exploring oxygen-sensing mechanisms across eukaryotic kingdoms can inform us on biological innovations to harness ever-changing oxygen availability at the dawn of complex life and its utilization for their organismal development.
Developments in sequencing technologies and the sequencing of an ever-increasing number of genomes have revolutionised studies of biodiversity and organismal evolution. This accumulation of data has ...been paralleled by the creation of numerous public biological databases through which the scientific community can mine the sequences and annotations of genomes, transcriptomes, and proteomes of multiple species. However, to find the appropriate databases and bioinformatic tools for respective inquiries and aims can be challenging. Here, we present a compilation of DNA and protein databases, as well as bioinformatic tools for phylogenetic reconstruction and a wide range of studies on molecular evolution. We provide a protocol for information extraction from biological databases and simple phylogenetic reconstruction using probabilistic and distance methods, facilitating the study of biodiversity and evolution at the molecular level for the broad scientific community.
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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
3.
Orbital forcing of climate 1.4 billion years ago Zhang, Shuichang; Wang, Xiaomei; Hammarlund, Emma U. ...
Proceedings of the National Academy of Sciences - PNAS,
03/2015, Letnik:
112, Številka:
12
Journal Article
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Fluctuating climate is a hallmark of Earth. As one transcends deep into Earth time, however, both the evidence for and the causes of climate change become difficult to establish. We report ...geochemical and sedimentological evidence for repeated, short-term climate fluctuations from the exceptionally well-preserved ∼1.4-billion-year-old Xiamaling Formation of the North China Craton. We observe two patterns of climate fluctuations: On long time scales, over what amounts to tens of millions of years, sediments of the Xiamaling Formation record changes in geochemistry consistent with long-term changes in the location of the Xiamaling relative to the position of the Intertropical Convergence Zone. On shorter time scales, and within a precisely calibrated stratigraphic framework, cyclicity in sediment geochemical dynamics is consistent with orbital control. In particular, sediment geochemical fluctuations reflect what appear to be orbitally forced changes in wind patterns and ocean circulation as they influenced rates of organic carbon flux, trace metal accumulation, and the source of detrital particles to the sediment.
Significance There is a wealth of evidence pointing to dramatic short-term climate change on Earth over the last few million years. Much of this climate change is driven by variations of Earth’s orbit around the Sun with characteristic frequencies known as Milankovitch cycles. Robust evidence for orbitally driven climate change, however, becomes rare as one descends deep into Earth time. We studied an exceptional record of climate change as recorded in 1.4-billion-year-old marine sediments from North China. This record documents regular changes in subtropical/tropical Hadley Cell dynamics. These changes in dynamics controlled wind strength, rainfall, and ocean circulation, translated into cyclic variations in sediment geochemistry, much like the orbital control on climate today and in the recent past.
Animal tissue requires low-oxygen conditions for its maintenance. The need for low-oxygen conditions contrasts with the idea of an evolutionary leap in animal diversity as a result of expanding oxic ...conditions. To accommodate tissue renewal at oxic conditions, however, vertebrate animals and vascular plants demonstrate abilities to access hypoxia. Here, I argue that multicellular organisms sustain oxic conditions first after internalizing hypoxic conditions. The ‘harnessing’ of hypoxia has allowed multicellular evolution to leave niches that were stable in terms of oxygen concentrations for those where oxygen fluctuates. Since oxygen fluctuates in most settings on Earth's surface, the ancestral niche would have been a deep marine setting. The hypothesis that ‘large life’ depends on harnessing hypoxia is illustrated in the context of conditions that promote the immature cell phenotype (stemness) in animal physiology and tumour biology and offers one explanation for the general rarity of diverse multicellularity over most of Earth's history.
The oxygen content of Earth’s atmosphere has varied greatly through time, progressing from exceptionally low levels before about 2.3 billion years ago, to much higher levels afterward. In the absence ...of better information, we usually view the progress in Earth’s oxygenation as a series of steps followed by periods of relative stasis. In contrast to this view, and as reported here, a dynamic evolution of Earth’s oxygenation is recorded in ancient sediments from the Republic of Gabon from between about 2,150 and 2,080 million years ago. The oldest sediments in this sequence were deposited in well-oxygenated deep waters whereas the youngest were deposited in euxinic waters, which were globally extensive. These fluctuations in oxygenation were likely driven by the comings and goings of the Lomagundi carbon isotope excursion, the longest–lived positive δ ¹³C excursion in Earth history, generating a huge oxygen source to the atmosphere. As the Lomagundi event waned, the oxygen source became a net oxygen sink as Lomagundi organic matter became oxidized, driving oxygen to low levels; this state may have persisted for 200 million years.
Cancer cells utilize the forces of natural selection to evolve evolvability allowing a constant supply of heritable variation that permits a cancer species to evolutionary track changing hazards and ...opportunities. Over time, the dynamic tumor ecosystem is exposed to extreme, catastrophic changes in the conditions of the tumor—natural (e.g., loss of blood supply) or imposed (therapeutic). While the nature of these catastrophes may be varied or unique, their common property may be to doom the current cancer phenotype unless it evolves rapidly. Poly‐aneuploid cancer cells (PACCs) may serve as efficient sources of heritable variation that allows cancer cells to evolve rapidly, speciate, evolutionarily track their environment, and most critically for patient outcome and survival, permit evolutionary rescue, therapy resistance, and metastasis. As a conditional evolutionary strategy, they permit the cancer cells to accelerate evolution under stress and slow down the generation of heritable variation when conditions are more favorable or when the cancer cells are closer to an evolutionary optimum. We hypothesize that they play a critical and outsized role in lethality by their increased capacity for invasion and motility, for enduring novel and stressful environments, and for generating heritable variation that can be dispensed to their 2N+ aneuploid progeny that make up the bulk of cancer cells within a tumor, providing population rescue in response to therapeutic stress. Targeting PACCs is essential to cancer therapy and patient cure—without the eradication of the resilient PACCs, cancer will recur in treated patients.
The end Ordovician (Hirnantian) extinction was the first of the five big Phanerozoic extinction events, and the first that involved metazoan-based communities. It comprised two discrete pulses, both ...linked in different ways to an intense but short-lived glaciation at the South Pole. The first, occurring at, or just below, the Normalograptus extraordinarius graptolite Biozone, mainly affected nektonic and planktonic species together with those living on the shallow shelf and in deeper water whereas the second, within the N. persculptus graptolite Biozone, was less focused, eradicating faunas across a range of water depths. In all about 85% of marine species were removed. Proposed kill mechanisms for the first phase have included glacially-induced cooling, falling sea level and chemical recycling in the oceans, but a general consensus is lacking. The second phase is more clearly linked to near-global anoxia associated with a marked transgression during the Late Hirnantian. Most recently, however, new drivers for the extinctions have been proposed, including widespread euxinia together with habitat destruction caused by plate tectonic movements, suggesting that the end Ordovician mass extinctions were a product of the coincidence of a number of contributing factors. Moreover, when the deteriorating climate intensified, causing widespread glaciation, a tipping point was reached resulting in catastrophe.
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► End Ordovician extinction event, the first of the five big extinctions. ► Linking the catastrophe for the first time to a tipping point. ► Short-lived ice age corresponded with a unique continental configuration.
A Mesoproterozoic iron formation Canfield, Donald E.; Zhang, Shuichang; Wang, Huajian ...
Proceedings of the National Academy of Sciences - PNAS,
04/2018, Letnik:
115, Številka:
17
Journal Article
Recenzirano
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We describe a 1,400 million-year old (Ma) iron formation (IF) from the Xiamaling Formation of the North China Craton. We estimate this IF to have contained at least 520 gigatons of authigenic Fe, ...comparable in size to many IFs of the Paleoproterozoic Era (2,500–1,600 Ma). Therefore, substantial IFs formed in the time window between 1,800 and 800 Ma, where they are generally believed to have been absent. The Xiamaling IF is of exceptionally low thermal maturity, allowing the preservation of organic biomarkers and an unprecedented view of iron-cycle dynamics during IF emplacement. We identify tetramethyl aryl isoprenoid (TMAI) biomarkers linked to anoxygenic photosynthetic bacteria and thus phototrophic Fe oxidation. Although we cannot rule out other pathways of Fe oxidation, iron and organic matter likely deposited to the sediment in a ratio similar to that expected for anoxygenic photosynthesis. Fe reduction was likely a dominant and efficient pathway of organic matter mineralization, as indicated by organic matter maturation by Rock Eval pyrolysis combined with carbon isotope analyses: Indeed, Fe reduction was seemingly as efficient as oxic respiration. Overall, this Mesoproterozoic-aged IF shows many similarities to Archean-aged (>2,500 Ma) banded IFs (BIFs), but with an exceptional state of preservation, allowing an unprecedented exploration of Fe-cycle dynamics in IF deposition.
Advances in curative treatment to remove the primary tumor have increased survival of localized cancers for most solid tumor types, yet cancers that have spread are typically incurable and account ...for >90% of cancer-related deaths. Metastatic disease remains incurable because, somehow, tumors evolve resistance to all known compounds, including therapies. In all of these incurable patients,
lethal cancer evolves capacities for both metastasis and resistance. Therefore, cancers in different patients appear to follow the same eco-evolutionary path that independently manifests in affected patients. This convergent outcome, that always includes the ability to metastasize and exhibit resistance, demands an explanation beyond the slow and steady accrual of stochastic mutations. The common denominator may be that cancer starts as a speciation event when a unicellular protist breaks away from its multicellular host and initiates a cancer clade within the patient. As the cancer cells speciate and diversify further, some evolve the capacity to evolve: evolvability. Evolvability becomes a heritable trait that influences the available variation of other phenotypes that can then be acted upon by natural selection. Evolving evolvability may be an adaptation for cancer cells. By generating and maintaining considerable heritable variation, the cancer clade can, with high certainty, serendipitously produce cells resistant to therapy and cells capable of metastasizing. Understanding that cancer cells can swiftly evolve responses to novel and varied stressors create opportunities for adaptive therapy, double-bind therapies, and extinction therapies; all involving strategic decision making that steers and anticipates the convergent coevolutionary responses of the cancers.
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."
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