A proboscidean from the late Oligocene of Eritrea, a "missing link" between early Elephantiformes and Elephantimorpha, and biogeographic implications.
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ABSTRACT:
SUBMITTER: Shoshani J
PROVIDER: S-EPMC1859925 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:As the world's second largest sand sea and one of the most important dust sources to the global aerosol system, the formation of the Taklimakan Desert marks a major environmental event in central Asia during the Cenozoic. Determining when and how the desert formed holds the key to better understanding the tectonic-climatic linkage in this critical region. However, the age of the Taklimakan remains controversial, with the dominant view being from ∼ 3.4 Ma to ∼ 7 Ma based on magnetostratigraphy of sedimentary sequences within and along the margins of the desert. In this study, we applied radioisotopic methods to precisely date a volcanic tuff preserved in the stratigraphy. We constrained the initial desertification to be late Oligocene to early Miocene, between ∼ 26.7 Ma and 22.6 Ma. We suggest that the Taklimakan Desert was formed as a response to a combination of widespread regional aridification and increased erosion in the surrounding mountain fronts, both of which are closely linked to the tectonic uplift of the Tibetan-Pamir Plateau and Tian Shan, which had reached a climatically sensitive threshold at this time.
| S-EPMC4485093 | biostudies-literature
Project description:The origin and deep evolution of retroviruses remain largely unclear. It has been proposed that retroviruses might have originated from a Ty3/Gypsy retrotransposon, but all known Ty3/Gypsy retrotransposons are only distantly related to retroviruses. Retroviruses and some plant Athila/Tat elements (within Ty3/Gypsy retrotransposons) independently evolved a dual RNase H domain and an env/env-like gene. Here, we reported the discovery of a novel lineage of retrotransposons, designated Odin retrotransposons, in the genomes of eight sea anemones (order Actinaria) within the Cnidaria phylum. Odin retrotransposons exhibited unique genome features, encoding a dual RNase H domain (like retroviruses) but no env gene (like most Ty3/Gypsy retrotransposons). Phylogenetic analyses based on reverse transcriptase showed that Odin retrotransposons formed a sister group to lokiretroviruses, and lokiretroviruses and Odin retrotransposons together were sister to canonical retroviruses. Moreover, phylogenetic analyses based on RNase H and integrase also supported the hypothesis that Odin retrotransposons were sisters to lokiretroviruses. Lokiretroviruses and canonical retroviruses did not form a monophyletic group, indicating that lokiretroviruses and canonical retroviruses might represent two distinct virus families. Taken together, the discovery of Odin retrotransposons narrowed down the evolutionary gaps between retrotransposons and canonical retroviruses and lokiretroviruses. IMPORTANCE The origin of retroviruses remains largely unclear. In this study, we discovered a novel retrotransposon lineage, Odin retrotransposons, within the genomes of sea anemones (order Actinaria). In contrast to retroviruses and most retrotransposons, Odin retrotransposons encode a dual RNase H domain but no env gene. Phylogenetic analyses showed that Odin retrotransposons were sisters to lokiretroviruses, and lokiretroviruses and Odin retrotransposons were sisters to retroviruses, establishing an evolutionary framework to decipher the origin of retroviruses (canonical retroviruses and lokiretroviruses). Our results provided insights into the diversity and deep evolution of LTR retrotransposons closely related to retroviruses.
| S-EPMC9040795 | biostudies-literature
Project description:Reinforcement learning systems usually assume that a value function is defined over all states (or state-action pairs) that can immediately give the value of a particular state or action. These values are used by a selection mechanism to decide which action to take. In contrast, when humans and animals make decisions, they collect evidence for different alternatives over time and take action only when sufficient evidence has been accumulated. We have previously developed a model of memory processing that includes semantic, episodic and working memory in a comprehensive architecture. Here, we describe how this memory mechanism can support decision making when the alternatives cannot be evaluated based on immediate sensory information alone. Instead we first imagine, and then evaluate a possible future that will result from choosing one of the alternatives. Here we present an extended model that can be used as a model for decision making that depends on accumulating evidence over time, whether that information comes from the sequential attention to different sensory properties or from internal simulation of the consequences of making a particular choice. We show how the new model explains both simple immediate choices, choices that depend on multiple sensory factors and complicated selections between alternatives that require forward looking simulations based on episodic and semantic memory structures. In this framework, vicarious trial and error is explained as an internal simulation that accumulates evidence for a particular choice. We argue that a system like this forms the "missing link" between more traditional ideas of semantic and episodic memory, and the associative nature of reinforcement learning.
| S-EPMC7758424 | biostudies-literature
Project description:BackgroundFunctional traits are the primary biotic component driving organism influence on ecosystem functions; in consequence, traits are widely used in ecological research. However, most animal trait-based studies use easy-to-measure characteristics of species that are at best only weakly associated with functions. Animal-mediated pollination is a key ecosystem function and is likely to be influenced by pollinator traits, but to date no one has identified functional traits that are simple to measure and have good predictive power.MethodsHere, we show that a simple, easy to measure trait (hairiness) can predict pollinator effectiveness with high accuracy. We used a novel image analysis method to calculate entropy values for insect body surfaces as a measure of hairiness. We evaluated the power of our method for predicting pollinator effectiveness by regressing pollinator hairiness (entropy) against single visit pollen deposition (SVD) and pollen loads on insects. We used linear models and AICC model selection to determine which body regions were the best predictors of SVD and pollen load.ResultsWe found that hairiness can be used as a robust proxy of SVD. The best models for predicting SVD for the flower species Brassica rapa and Actinidia deliciosa were hairiness on the face and thorax as predictors (R2 = 0.98 and 0.91 respectively). The best model for predicting pollen load for B. rapa was hairiness on the face (R2 = 0.81).DiscussionWe suggest that the match between pollinator body region hairiness and plant reproductive structure morphology is a powerful predictor of pollinator effectiveness. We show that pollinator hairiness is strongly linked to pollination-an important ecosystem function, and provide a rigorous and time-efficient method for measuring hairiness. Identifying and accurately measuring key traits that drive ecosystem processes is critical as global change increasingly alters ecological communities, and subsequently, ecosystem functions worldwide.
| S-EPMC5180583 | biostudies-literature
Project description: Not available
| S-EPMC308925 | biostudies-literature
Project description:Living baleen whales, or Mysticeti, lack teeth and instead feed using keratinous baleen plates to sieve prey-laden water. This feeding strategy is profoundly different from that of their toothed ancestors, which processed prey using the differentiated dentition characteristic of mammals. The fossil record of mysticetes reveals stem members that include extinct taxa with dentition, illuminating the morphological states that preceded the loss of teeth and the subsequent origin of baleen. The relationships among stem mysticetes, including putative clades such as Mammalodontidae and Aetiocetidae, remain debatable. Aetiocetids are among the more species-rich clade of stem mysticetes, and known only from fossil localities along the North Pacific coastline. Here, we report a new aetiocetid, Salishicetus meadi gen. et sp. nov, from the late Oligocene of Washington State, USA. Salishicetus preserves a near-complete lower dentition with extensive occlusal wear, indicating that it processed prey using shearing cheek teeth in the same way as its stem cetacean ancestors. Using a matrix with all known species of aetiocetids, we recover a monophyletic Aetiocetidae, crownward of a basal clade of Mammalodontidae. The description of Salishicetus resolves phylogenetic relationships among aetiocetids, which provides a basis for reconstructing ancestral feeding morphology along the stem leading to crown Mysticeti.
| S-EPMC5936946 | biostudies-literature
Project description:A minor electrophoretically fast component was found in ferritin from iron-loaded rat liver in addition to a major electrophoretically slow ferritin similar to that observed in control rats. The electrophoretically fast ferritin showed immunological identity with the slow component, but on electrophoresis in SDS it gave a peptide of 17.3 kDa, in contrast with the electrophoretically slow ferritin, which gave a major band corresponding to the L-subunit (20.7 kDa). Thus the electrophoretically fast ferritin resembles that reported by Massover [(1985) Biochim. Biophys. Acta 829, 377-386] in livers of mice with short-term parenteral iron overload. The electrophoretically fast ferritin had a lower iron content (2000 Fe atoms/molecule) than the electrophoretically slow ferritin (3000 Fe atoms/molecule). Removal and re-incorporation of iron was possible without effect on the electrophoretic mobility of either ferritin species. On subcellular fractionation the electrophoretically fast ferritin was enriched in pellet fractions and was the sole soluble ferritin isolated from iron-laden secondary lysosomes (siderosomes). The amount and relative proportion of the electrophoretically fast species increased with iron loading. Haemosiderin isolated from siderosomes was found to contain a peptide reactive to anti-ferritin serum and corresponding to the 17.3 kDa peptide of the electrophoretically fast ferritin species. Unlike the electrophoretically slow ferritin, the electrophoretically fast ferritin did not become significantly radioactive in a 1 h biosynthetic labelling experiment. We conclude that the minor ferritin is not, as has been suggested for mouse liver ferritin, 'a completely new species of smaller holoferritin that represents a shift in the ferritin phenotype' in response to siderosis, but a precursor of haemosiderin, in agreement with the proposal by Richter [(1984) Lab. Invest. 50, 26-35] concerning siderosomal ferritin.
| S-EPMC1148141 | biostudies-other
Project description:BACKGROUND: The pantropical genus Bauhinia, along with the northern temperate Cercis and several tropical genera, bear bilobate, bifoliolate, or sometimes unifoliolate leaves, which constitute the tribe Cercideae as sister to the rest of the family Leguminosae based on molecular phylogenetics. Hence, the fossil record of Cercideae is pivotal to understand the early evolution and biogeographic history of legumes. RESULTS: Three fossil species of Bauhinia were described from the Oligocene Ningming Formation of Guangxi, South China. Bauhinia ningmingensis sp. nov. is characterized by its bifoliolate, pulvinate leaves bearing basal acrodromous primary veins and brochidodromous secondary veins. B. cheniae sp. nov. bears moderately or deeply bilobate, pulvinate leaves, with basal actinodromous primary veins and eucamptodromous secondary veins. B. larsenii D.X. Zhang et Y.F. Chen emend. possesses shallowly or moderately bilobate, pulvinate leaves bearing basal actinodromous primary veins and brochidodromous secondary veins, as well as elliptic, stipitate, non-winged, and oligo-seeded fruits. Meanwhile, previously reported Bauhinia fossils were reviewed, and those pre-Oligocene foliage across the world are either questionable or have been rejected due to lacking of reliable evidence for their pulvini or/and basal actinodromous or acrodromous venations. Besides Oligocene leaves and fruits presented here, foliage and/or wood of Bauhinia have been documented from the Miocene-Pliocene of Thailand, India, Nepal, Uganda, and Ecuador. CONCLUSIONS: Bauhinia has exhibited a certain diversity with bifoliolate- and bilobate-leafed species in a low-latitude locality-Ningming since at least the Oligocene, implying that the tropical zone of South China may represent one of the centres for early diversification of the genus. The reliable macrofossils of Bauhinia and Cercis have made their debut in the Eocene-Oligocene floras from mid-low latitudes and appeared to lack in the coeval floras at high latitudes, implying a possible Tethys Seaway origin and spread of legumes. However, detailed scenarios for the historical biogeography of Bauhinia and its relatives still need more robust dataset from palaeobotany and molecular phylogeny in future research.
| S-EPMC4101841 | biostudies-other
Project description:F(1)F(o)-ATP synthase is the enzyme responsible for most of the ATP synthesis in living systems. The catalytic domain F(1) of the F(1)F(o) complex, F(1)-ATPase, has the ability to hydrolyze ATP. A fundamental problem in the development of a detailed mechanism for this enzyme is that it has not been possible to determine experimentally the relation between the ligand binding affinities measured in solution and the different conformations of the catalytic beta subunits (beta(TP), beta(DP), beta(E)) observed in the crystal structures of the mitochondrial enzyme, MF(1). Using free energy difference simulations for the hydrolysis reaction ATP+H(2)O --> ADP+P(i) in the beta(TP) and beta(DP) sites and unisite hydrolysis data, we are able to identify beta(TP) as the "tight" (K(D) = 10(-12) M, MF(1)) binding site for ATP and beta(DP) as the "loose" site. An energy decomposition analysis demonstrates how certain residues, some of which have been shown to be important in catalysis, modulate the free energy of the hydrolysis reaction in the beta(TP) and beta(DP) sites, even though their structures are very similar. Combined with the recently published simulations of the rotation cycle of F(1)-ATPase, the present results make possible a consistent description of the binding change mechanism of F(1)-ATPase at an atomic level of detail.
| S-EPMC298694 | biostudies-literature
Project description:There is a growing body of evidence supporting that cancer cells share many similarities with embryonic stem cells (ESCs). For example, aggressive cancers and ESCs share a common gene expression signature that includes hundreds of genes. Since ESC genes are not present in most adult tissues, they could be ideal candidate targets for cancer-specific diagnosis and treatment. This is an exciting cancer-targeting model. The major hurdle to test this model is to identify the key factors/pathway(s) within ESCs that are responsible for the cancer phenotype. SALL4 is one of few genes that can establish this link. The first publication of SALL4 is on its mutation in a human inherited disorder with multiple developmental defects. Since then, over 300 papers have been published on various aspects of this gene in stem cells, development, and cancers. This review aims to summarize our current knowledge of SALL4, including a SALL4-based approach to classify and target cancers. Many questions about this important gene still remain unanswered, specifically, on how this gene regulates cell fates at a molecular level. Understanding SALL4's molecular functions will allow development of specific targeted approaches in the future.
| S-EPMC4823161 | biostudies-literature