scholarly journals Long identical sequences found in multiple bacterial genomes reveal frequent and widespread exchange of genetic material between distant species

2020 ◽  
Author(s):  
Michael Sheinman ◽  
Ksenia Arkhipova ◽  
Peter F. Arndt ◽  
Bas E. Dutilh ◽  
Rutger Hermsen ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Horizontal Transfer ◽  
Transfer Rate ◽  
Genetic Material ◽  
Coarse Grained ◽  
Bacterial Genomes ◽  
Long Distance ◽  
Microbial World ◽  
Order Of Magnitude ◽  
Magnitude Variation

AbstractHorizontal transfer of genomic elements is an essential force that shapes microbial genome evolution. Horizontal Gene Transfer (HGT) occurs via various mechanisms and has been studied in detail for a variety of systems. However, a coarse-grained, global picture of HGT in the microbial world is still missing. One reason is the difficulty to process large amounts of genomic microbial data to find and characterise HGT events, especially for highly distant organisms. Here, we exploit the fact that HGT between distant species creates long identical DNA sequences in genomes of distant species, which can be found efficiently using alignment-free methods. We analysed over 90 000 bacterial genomes and thus identified over 100 000 events of HGT. We further developed a mathematical model to analyse the statistical properties of those long exact matches and thus estimate the transfer rate between any pair of taxa. Our results demonstrate that long-distance gene exchange (across phyla) is very frequent, as more than 8% of the bacterial genomes analysed have been involved in at least one such event. Finally, we confirm that the function of the transferred sequences strongly impact the transfer rate, as we observe a 3.5 order of magnitude variation between the most and the least transferred categories. Overall, we provide a unique view of horizontal transfer across the bacterial tree of life, illuminating a fundamental process driving bacterial evolution.

scholarly journals Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Michael Sheinman ◽  
Ksenia Arkhipova ◽  
Peter F Arndt ◽  
Bas Dutilh ◽  
Rutger Hermsen ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Transfer Rate ◽  
Microbial Evolution ◽  
Functional Categories ◽  
Bacterial Genomes ◽  
Long Distance ◽  
Microbial World ◽  
Alignment Free ◽  
Fundamental Process ◽  
Bacterial Domain

Horizontal Gene Transfer (HGT) is an essential force in microbial evolution. Despite detailed studies on a variety of systems, a global picture of HGT in the microbial world is still missing. Here, we exploit that HGT creates long identical DNA sequences in the genomes of distant species, which can be found efficiently using alignment-free methods. Our pairwise analysis of 93 481 bacterial genomes identified 138 273 HGT events. We developed a model to explain their statistical properties as well as estimate the transfer rate between pairs of taxa. This reveals that long-distance HGT is frequent: our results indicate that HGT between species from different phyla has occurred in at least 8% of the species. Finally, our results confirm that the function of sequences strongly impacts their transfer rate, which varies by more than 3 orders of magnitude between different functional categories. Overall, we provide a comprehensive view of HGT, illuminating a fundamental process driving bacterial evolution.

Quaternary influx of proximal coarse-grained dust altered circum-Mediterranean soil productivity and impacted early human culture

Geology ◽  
2020 ◽  
Vol 49 (1) ◽  
pp. 61-65
Author(s):  
Rivka Amit ◽  
Yehouda Enzel ◽  
Onn Crouvi
Keyword(s):  
Alternative Hypothesis ◽  
Coarse Grained ◽  
Soil Productivity ◽  
Silty Clay ◽  
Coarse Silt ◽  
Long Distance ◽  
Long Distance Transport ◽  
Order Of Magnitude ◽  
The Mediterranean ◽  
Early Human

Abstract The carbonate mountainous landscape around most of the Mediterranean is karstic, is almost barren, and has thin soils. Erosion of preexisting thicker soils is a common hypothesis used to explain this bare terrain. An alternative hypothesis is that in the Mediterranean region, thin soils are attributed to long-distance transport of very fine, silty clay dust, resulting in low mass accumulation rates. Even if accreted over millennia, such dust cannot produce thick, highly productive soils. A pronounced anomaly in the Mediterranean is the thick, more productive soil of the semiarid southern Levant (SL). These soils contain order-of-magnitude coarser grains than the characteristic thin soils in the Mediterranean and a high proportion (>70%) of coarse silt quartz sourced from the nearby Sinai-Negev erg, the primary contributor of the Negev loess. This proximal intense dust supply produced greatly thicker soils. However, influx of coarse silt quartz loess is a geologically recent phenomenon in the SL. Pre-loess (i.e., older than 200 ka, pre-coarse-silt influx) SL soils are much finer and were generated by long-distance dust from the Sahara and Arabia like most other Mediterranean soils. Thus, we hypothesize that the geologically recent Negev Desert loess interval caused a drastic change in mountainous soil properties within the SL, enriching the Levant’s ecology and affecting early human development. The high amounts of coarse silt deposited on the landscape have contributed to the unique sustainable agriculture in the SL, which assisted in transforming the Levant into “the land of milk and honey” and a cradle of civilizations.

Systematics, Biogeography, and Morphological Character Evolution of the Hemiepiphytic Subfamily Monsteroideae (Araceae)

2019 ◽  
Vol 104 (1) ◽  
pp. 33-48 ◽  
Author(s):  
Alejandro Zuluaga ◽  
Martin Llano ◽  
Ken Cameron
Keyword(s):  
Dna Sequences ◽  
Pacific Islands ◽  
R Package ◽  
Morphological Characters ◽  
Ancestral State ◽  
Seed Shape ◽  
Long Distance ◽  
The Pacific ◽  
And Migration ◽  
The Tropics

The subfamily Monsteroideae (Araceae) is the third richest clade in the family, with ca. 369 described species and ca. 700 estimated. It comprises mostly hemiepiphytic or epiphytic plants restricted to the tropics, with three intercontinental disjunctions. Using a dataset representing all 12 genera in Monsteroideae (126 taxa), and five plastid and two nuclear markers, we studied the systematics and historical biogeography of the group. We found high support for the monophyly of the three major clades (Spathiphylleae sister to Heteropsis Kunth and Rhaphidophora Hassk. clades), and for six of the genera within Monsteroideae. However, we found low rates of variation in the DNA sequences used and a lack of molecular markers suitable for species-level phylogenies in the group. We also performed ancestral state reconstruction of some morphological characters traditionally used for genera delimitation. Only seed shape and size, number of seeds, number of locules, and presence of endosperm showed utility in the classification of genera in Monsteroideae. We estimated ancestral ranges using a dispersal-extinction-cladogenesis model as implemented in the R package BioGeoBEARS and found evidence for a Gondwanan origin of the clade. One tropical disjunction (Monstera Adans. sister to Amydrium Schott–Epipremnum Schott) was found to be the product of a previous Boreotropical distribution. Two other disjunctions are more recent and likely due to long-distance dispersal: Spathiphyllum Schott (with Holochlamys Engl. nested within) represents a dispersal from South America to the Pacific Islands in Southeast Asia, and Rhaphidophora represents a dispersal from Asia to Africa. Future studies based on stronger phylogenetic reconstructions and complete morphological datasets are needed to explore the details of speciation and migration within and among areas in Asia.

scholarly journals Mineralogical, numerical and analytical studies of the coupled oxidation of pyrite and coal

2003 ◽  
Vol 67 (2) ◽  
pp. 381-398 ◽  
Author(s):  
K. A. Evans ◽  
C. J. Gandy ◽  
S. A. Banwart
Keyword(s):  
Reactive Transport ◽  
Transport Model ◽  
Pyrite Oxidation ◽  
Spoil Heap ◽  
Reaction Fronts ◽  
Order Of Magnitude ◽  
Magnitude Variation ◽  
Discharge Chemistry ◽  
Analytical Expressions

Mineralogical, bulk and field leachate compositions are used to identify important processes governing the evolution of discharges from a coal spoil heap in County Durham. These processes are incorporated into a numerical one-dimensional advective-kinetic reactive transport model which reproduces field results, including gas compositions, to within an order of magnitude. Variation of input parameters allows the effects of incorrect initial assumptions on elemental profiles and discharge chemistry to be assessed. Analytical expressions for widths and speeds of kinetic reaction fronts are developed and used to predict long-term development of mineralogical distribution within the heap. Results are consistent with observations from the field site. Pyrite oxidation is expected to dominate O2 consumption in spoil heaps on the decadal timescale, although C oxidation may stabilize contaminants in effluents on the centennial scale.

Hybridization capture of Larix candidate adaptive genes from sedimentary ancient DNA.

2021 ◽  
Author(s):  
Stefano Meucci ◽  
Luise Schulte ◽  
Kathleen R. Stoof-Leichsenring ◽  
Stefan Kruse ◽  
Konstantin Krutovsky ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Dna Sequences ◽  
Environmental Changes ◽  
Genetic Material ◽  
Siberian Larch ◽  
Shotgun Sequencing ◽  
Adaptive Genetic Variation ◽  
Hybridization Capture ◽  
Sequencing Method ◽  
Larch Species

<p>Siberian larch forests dominate large areas of northern Russia and contribute important roles for the world´s ecosystem. In order to understand the past dynamics of larches and their adaptive genetic variation, sedimentary ancient DNA (sedaDNA) extracted from lake sediment cores is a crucial source of genetic material. The difficulty of retrieving extremely rare DNA sequences from samples reaching back up to 25000 years in age, is challenging. Previous studies (Schulte et al.) showed that the hybridization capture allowed an enrichment of targeted sequences by several orders of magnitude in comparison to shotgun sequencing method. Therefore, we established for the first time, a hybridization capture method targeting 65 candidate adaptive genes laying on the Larix nuclear genome. Our preliminary results showed the ability of our newly established method to enrich extremely rare DNA sequences of the targeted Larix candidate adaptive genes, which were not retrieved by shotgun sequencing method applied on the same samples. Furthermore, the results allowed to detect and compare specific nucleotide polymorphism of adaptive candidate genes among sedaDNA samples distributed in space and time. The establishment of this new method is laying the basis to investigate possible adaptive variation of larch species acquired across the dry and cold conditions of the Last Glacial Maximum (LGM); as well as their possible advantages or disadvantages in relation to the current environmental changes toward dry and warm conditions.</p>

scholarly journals Genome Sequence of Torulaspora microellipsoides CLIB 830T

2018 ◽  
Vol 6 (26) ◽  
Author(s):  
Virginie Galeote ◽  
Frédéric Bigey ◽  
Hugo Devillers ◽  
Raúl A. Ortiz-Merino ◽  
Sylvie Dequin ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Genome Sequence ◽  
Horizontal Transfer ◽  
Reference Genome ◽  
Genetic Material ◽  
Ascomycetous Yeast ◽  
Content Type ◽  
Transfer Mechanisms

We report here the genome sequence of the ascomycetous yeast Torulaspora microellipsoides CLIB 830T. A reference genome for this species, which has been found as a donor of genetic material in wine strains of Saccharomyces cerevisiae, will undoubtedly give clues to our understanding of horizontal transfer mechanisms between species in the wine environment.

scholarly journals Making of fusion genes in cancer: An in-silico study of mechanism of chromosomal translocations

2018 ◽  
Author(s):  
Kiran Lalwani ◽  
Shivani Sheth ◽  
Inayatullah Sheikh ◽  
Afzal Ansari ◽  
Fulesh Kunwar ◽  
...  
Keyword(s):  
Dna Sequences ◽  
In Silico ◽  
Molecular Mechanisms ◽  
Fusion Gene ◽  
Genetic Material ◽  
Chromosomal Translocations ◽  
In Silico Study ◽  
Clinical Consequences ◽  
The Stability ◽  
Genomic Regions

Chromosomal translocations involve exchange of genetic material between non- homologous chromosomes leading to the formation of a fusion gene with altered function. The clinical consequences of non-random and recurrent chromosomal translocations have been so well understood in carcinogenesis that they serve as diagnostic and prognostic markers and also help in therapy decisions, mainly in leukemia and lymphoma. However, the molecular mechanisms underlying these recurrent genetic exchanges are yet to be understood. Various approaches employed include the extent of the vicinity of the partner chromosomes in the nucleus, DNA sequences at the breakpoints, etc. The present study addresses the stability of DNA sequences at the breakpoint regions using in-silico approach in terms of physicochemical properties such as; AT%, flexibility, melting temperature, enthalpy, entropy, stacking energy and free energy. Changes in these properties may lead to instability of DNA which could affect gene expression in particular and genome organization in general. Our study indicates that the fusion sequences are comparatively more unstable and hence, more prone to breakage. Current study along with others could lead to developing a model for predicting breakage prone genomic regions using this novel in-silico approach.

scholarly journals Strength Tests on Newly Fallen Snow

1969 ◽  
Vol 8 (54) ◽  
pp. 427-440 ◽  
Author(s):  
R. Perla
Keyword(s):  
Cone Penetrometer ◽  
Light Weight ◽  
Large Drop ◽  
Torque Wrench ◽  
Strength Tests ◽  
Order Of Magnitude ◽  
Magnitude Variation ◽  
A New Technique ◽  
Shear Frame

AbstractModified versions ofin situstrength tests previously applied to metamorphosed snow were developed to measure the mechanical properties of newly fallen snow during storm periods. A large drop-cone penetrometer, protected from the wind by an aluminum shell, was used to determine snow “hardness”. A lightweight model of the Haefeli ram penetrometer measured “ram numbers”. Shear strengths were obtained from large, light-weight frames. Some preliminary tests were made with a shear vane driven by a torque wrench. A new technique was devised for measuring tensile strength whereby a cantilever beam of snow is undercut until it fails under its own weight. Comparisons between the cantilever test and the shear-frame test show high ratios for tensile to shear strength. Cantilever strength plotted against density shows an order of magnitude variation in strength at all densities.

scholarly journals FcαRI binding at the IgA1 CH2–CH3 interface induces long-range conformational changes that are transmitted to the hinge region

2018 ◽  
Vol 115 (38) ◽  
pp. E8882-E8891 ◽  
Author(s):  
Monica T. Posgai ◽  
Sam Tonddast-Navaei ◽  
Manori Jayasinghe ◽  
George M. Ibrahim ◽  
George Stan ◽  
...  
Keyword(s):  
Binding Site ◽  
Long Range ◽  
Conformational Changes ◽  
Lectin Binding ◽  
Coarse Grained ◽  
Alanine Scanning Mutagenesis ◽  
Long Distance ◽  
Receptor Binding Site ◽  
Binding Interface ◽  
Functional Dynamics

IgA effector functions include proinflammatory immune responses triggered upon clustering of the IgA-specific receptor, FcαRI, by IgA immune complexes. FcαRI binds to the IgA1–Fc domain (Fcα) at the CH2–CH3 junction and, except for CH2 L257 and L258, all side-chain contacts are contributed by the CH3 domain. In this study, we used experimental and computational approaches to elucidate energetic and conformational aspects of FcαRI binding to IgA. The energetic contribution of each IgA residue in the binding interface was assessed by alanine-scanning mutagenesis and equilibrium surface plasmon resonance (SPR). As expected, hydrophobic residues central to the binding site have strong energetic contributions to the FcαRI:Fcα interaction. Surprisingly, individual mutation of CH2 residues L257 and L258, found at the periphery of the FcαRI binding site, dramatically reduced binding affinity. Comparison of antibody:receptor complexes involving IgA or its precursor IgY revealed a conserved receptor binding site at the CH2–CH3 junction (or its equivalent). Given the importance of residues near the CH2–CH3 junction, we used coarse-grained Langevin dynamics simulations to understand the functional dynamics in Fcα. Our simulations indicate that FcαRI binding, either in an asymmetric (1:1) or symmetric (2:1) complex with Fcα, propagated long-range conformational changes across the Fc domains, potentially impacting the hinge and Fab regions. Subsequent SPR experiments confirmed that FcαRI binding to the Fcα CH2–CH3 junction altered the kinetics of HAA lectin binding at the IgA1 hinge. Receptor-induced long-distance conformational transitions have important implications for the interaction of aberrantly glycosylated IgA1 with anti-glycan autoantibodies in IgA nephropathy.

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