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- Librado, P., et al.
(author)
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The origins and spread of domestic horses from the Western Eurasian steppes
- 2021
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 598, s. 634-640
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Journal article (peer-reviewed)abstract
- Analysis of 273 ancient horse genomes reveals that modern domestic horses originated in the Western Eurasian steppes, especially the lower Volga-Don region. Domestication of horses fundamentally transformed long-range mobility and warfare(1). However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling(2-4) at Botai, Central Asia around 3500 bc(3). Other longstanding candidate regions for horse domestication, such as Iberia(5) and Anatolia(6), have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 bc, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association(7) between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 bc(8,9) driving the spread of Indo-European languages(10). This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium bc Sintashta culture(11,12).
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- Ni, S., et al.
(author)
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Early diagenesis of foraminiferal calcite under anoxic conditions : A case study from the Landsort Deep, Baltic Sea (IODP Site M0063)
- 2020
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In: Chemical Geology. - : Elsevier BV. - 0009-2541. ; 558
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Journal article (peer-reviewed)abstract
- The chemical composition of foraminiferal calcite is widely used for studying past environmental conditions and biogeochemistry. However, high rates of microbial organic matter degradation and abundant dissolved metal sources in sediments and pore waters may impede the application of foraminifera-based proxies due to formation of secondary carbonates or other authigenic minerals on and/or inside of foraminiferal tests. Secondary carbonate precipitation severely alters the bulk foraminiferal geochemistry and can be difficult to eliminate through standard foraminiferal trace element cleaning procedures. We present results showing the mineral composition and formation sequence of diagenetic coatings on foraminiferal tests formed under extreme anoxic conditions in the Baltic Sea's deepest basin (the Landsort Deep, IODP Exp. 347, Site M0063). Our study focuses primarily on the diagenetic carbonates present on and in the tests of the low-oxygen tolerant benthic foraminiferal species Elphidium selseyensis and Elphidium clavatum. We applied various geochemical and imaging methods to ascertain the diagenesis processes and the authigenic mineral formation sequence on foraminifera. The authigenic carbonates were enriched in Mn, Mg, Fe and Ba, depending on the environmental redox conditions when the authigenic carbonates were precipitated. Concentrations of redox-sensitive elements such as Mn and Fe were particularly elevated in bottom waters and sedimentary pore waters under oxygen-depleted conditions in the Landsort Deep, resulting in formation of carbonates with highly elevated Mn and Fe contents. In addition to Mn- and Fe carbonates, several other types of authigenic minerals also formed on and in the foraminiferal chambers, including authigenic calcite, and non-carbonate accessory minerals. The formation sequence reveals the redox sensitivities of different elements and the preferential sequence of oxidants used by the microbes during organic matter oxidation and secondary redox reactions. This study provides a case study of extreme early diagenesis of foraminiferal calcite and may serve as a valuable guide when interpreting foraminiferal trace element records from low oxygen environments.
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- Zhang, X P, et al.
(author)
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Mutagenesis and computer modelling approach to study determinants for recognition of signal peptides by the mitochondrial processing peptidase
- 2001
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In: The Plant Journal. - 0960-7412 .- 1365-313X. ; 27:5, s. 427-438
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Journal article (peer-reviewed)abstract
- Determinants for the recognition of a mitochondrial presequence by the mitochondrial processing peptidase (MPP) have been investigated using mutagenesis and bioinformatics approaches. All plant mitochondrial presequences with a cleavage site that was confirmed by experimental studies can be grouped into three classes. Two major classes contain an arginine residue at position -2 or -3, and the third class does not have any conserved arginines. Sequence logos revealed loosely conserved cleavage motifs for the first two classes but no significant amino acid conservation for the third class. Investigation of processing determinants for a class III precursor, Nicotiana plumbaginifolia F(1)beta precursor of ATP synthase (pF(1)beta), was performed using a series of pF(1)beta presequence mutants and mutant presequence peptides derived from the C-terminal portion of the presequence. Replacement of -2 Gln by Arg inhibited processing, whereas replacement of either the most proximally located -5 Arg or -15 Arg by Leu had only a low inhibitory effect. The C-terminal portion of the pF(1)beta presequence forms a helix-turn-helix structure. Mutations disturbing or prolonging the helical element upstream of the cleavage site inhibited processing significantly. Structural models of potato MPP and the C-terminal pF(1)beta presequence peptide were built by homology modelling and empirical conformational energy search methods, respectively. Molecular docking of the pF(1)beta presequence peptide to the MPP model suggested binding of the peptide to the negatively charged binding cleft formed by the alpha -MPP and beta -MPP subunits in close proximity to the H111XXE114H115X(116-190)E191 proteolytic active site on beta -MPP. Our results show for the first time that the amino acid at the -2 position, even if not an arginine, as well as structural properties of the C-terminal portion of the presequence are important determinants for the processing of a class III precursor by MPP.
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- Brinkmann, Inda, et al.
(author)
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Benthic Foraminiferal Mn/Ca as Low-Oxygen Proxy in Fjord Sediments
- 2023
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In: Global Biogeochemical Cycles. - 0886-6236. ; 37:5
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Journal article (peer-reviewed)abstract
- Fjord systems are typically affected by low-oxygen conditions, which are increasing in extent and severity, forced by ongoing global changes. Fjord sedimentary records can provide high temporal resolution archives to aid our understanding of the underlying mechanisms and impacts of current deoxygenation. However, such archives can only be interpreted with well-calibrated proxies. Bottom-water oxygen conditions determine redox regime and availability of redox-sensitive trace elements such as manganese, which in turn may be recorded by manganese-to-calcium ratios (Mn/Ca) in biogenic calcium carbonates (e.g., benthic foraminifera tests). However, biological influences on Mn incorporation (e.g., species-specific Mn fractionation, ontogeny, living and calcification depths) are still poorly constrained. We analyzed Mn/Ca of living benthic foraminifera (Bulimina marginata, Nonionellina labradorica), sampled at low- to well-oxygenated conditions over a seasonal gradient in Gullmar Fjord, Swedish West coast (71–217 μmol/L oxygen (O2)), by laser-ablation ICP-MS. High pore-water Mn availability in the fjord supported Mn incorporation by foraminifera. B. marginata recorded contrasting Mn redox regimes sensitively and demonstrated potential as proxy for low-oxygen conditions. Synchrotron-based scanning X-ray fluorescence nanoimaging of Mn distributions across B. marginata tests displayed Mn/Ca shifts by chambers, reflecting bottom-water oxygenation history and/or ontogeny-driven life strategy preferences. In contrast, Mn/Ca signals of N. labradorica were extremely high and insensitive to environmental variability. We explore potential biologically controlled mechanisms that could potentially explain this species-specific response. Our data suggest that with the selection of sensitive candidate species, the Mn/Ca proxy has potential to be further developed for quantitative oxygen reconstructions in the low-oxygen range.
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- Brinkmann, I., et al.
(author)
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Foraminiferal Mn/Ca as Bottom-Water Hypoxia Proxy: An Assessment of Nonionella stella in the Santa Barbara Basin, USA
- 2021
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In: Paleoceanography and Paleoclimatology. - 2572-4517. ; 36:11
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Journal article (peer-reviewed)abstract
- Hypoxia is of increasing concern in marine areas, calling for a better understanding of mechanisms leading to decreasing dissolved oxygen concentrations ([O2]). Much can be learned about the processes and implications of deoxygenation for marine ecosystems using proxy records from low-oxygen sites, provided proxies, such as the manganese (Mn) to calcium (Ca) ratio in benthic foraminiferal calcite, are available and well calibrated. Here we report a modern geochemical data set from three hypoxic sites within the Santa Barbara Basin (SBB), USA, where we study the response of Mn/Caforam in the benthic foraminifer Nonionella stella to variations in sedimentary redox conditions (Mn, Fe) and bottom-water dissolved [O2]. We combine molecular species identification by small subunit rDNA sequencing with morphological characterization and assign the SBB N. stella used here to a new phylotype (T6). Synchrotron-based scanning X-ray fluorescence (XRF) imaging and Secondary Ion Mass Spectrometry (SIMS) show low Mn incorporation (partition coefficient DMn < 0.05) and limited proxy sensitivity of N. stella, at least within the range of dissolved [O2] (2.7–9.6 μmol/l) and Mnpore-water gradients (2.12–21.59 μmol/l). Notably, even though intra- and interspecimen Mn/Ca variability (33% and 58%, respectively) was only partially controlled by the environment, Mn/Caforam significantly correlated with both pore-water Mn and bottom-water [O2]. However, the prevalent suboxic bottom-water conditions and limited dissolved [O2] range complicate the interpretation of trace-elemental trends. Additional work involving other oxygenation proxies and samples from a wider oxygen gradient should be pursued to further develop foraminiferal Mn/Ca as an indicator for hypoxic conditions.
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- Desta, Z, et al.
(author)
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PharmVar GeneFocus: CYP2B6
- 2021
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In: Clinical pharmacology and therapeutics. - : Wiley. - 1532-6535 .- 0009-9236. ; 110:1, s. 82-97
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Journal article (peer-reviewed)
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