Phylogenetic analysis of the Tc1/mariner superfamily reveals the unexplored diversity of pogo-like elements

This is the final version. Available from BMC via the DOI in this record. Background: Tc1/mariner transposons are widespread DNA transposable elements (TEs) that have made important contributions to the evolution of host genomic complexity in metazoans. However, the evolution and diversity of the Tc1/mariner superfamily remains poorly understood. Following recent developments in genome sequencing and the availability of a wealth of new genomes, Tc1/mariner TEs have been identified in many new taxa across the eukaryotic tree of life. To date, the majority of studies focussing on Tc1/mariner elements have considered only a single host lineage or just a small number of host lineages. Thus, much remains to be learnt about the evolution of Tc1/mariner TEs by performing analyses that consider elements that originate from across host diversity. Results: We mined the non-redundant database of NCBI using BLASTp searches, with transposase sequences from a diverse set of reference Tc1/mariner elements as queries. A total of 5158 Tc1/mariner elements were retrieved and used to reconstruct evolutionary relationships within the superfamily. The resulting phylogeny is well resolved and includes several new groups of Tc1/mariner elements. In particular, we identify a new family of plant-genome restricted Tc1/mariner elements, which we call PlantMar. We also show that the pogo family is much larger and more diverse than previously appreciated, and we review evidence for a potential revision of its status to become a separate superfamily. Conclusions: Our study provides an overview of Tc1-mariner phylogeny and summarises the impressive diversity of Tc1-mariner TEs among sequenced eukaryotes. Tc1/mariner TEs are successful in a wide range of eukaryotes, especially unikonts (the taxonomic supergroup containing Amoebozoa, Opisthokonta, Breviatea, and Apusomonadida). In particular, ecdysozoa, and especially arthropods, emerge as important hosts for Tc1/mariner elements (except the PlantMar family). Meanwhile, the pogo family, which is by far the largest Tc1/mariner family, also includes many elements from fungal and chordate genomes. Moreover, there is evidence of the repeated exaptation of pogo elements in vertebrates, including humans, in addition to the well-known example of CENP-B. Collectively, our findings provide a considerable advancement in understanding of Tc1/mariner elements, and more generally they suggest that much work remains to improve understanding of the diversity and evolution of DNA TEs.Biotechnology & Biological Sciences Research Council (BBSRC)European Research Council (ERC

Evolution of Mutator transposable elements across eukaryotic diversity

This is the final version. Available on open access from BMC via the DOI in this recordBackground: Mutator-like elements (MULEs) are a significant superfamily of DNA transposons on account of their: (i) great transpositional activity and propensity for insertion in or near gene sequences, (ii) their consequent high mutagenic capacity, and, (iii) their tendency to acquire host gene fragments. Consequently, MULEs are important genetic tools and represent a key study system for research into host-transposon interactions. Yet, while several studies have focused on the impacts of MULEs on crop and fungus genomes, their evolution remains comparatively poorly explored. Results: We perform comprehensive bioinformatic and phylogenetic analyses to address currently available MULE diversity and reconstruct evolution for the group. For this, we mine MULEs from online databases, and combine these search results with available transposase sequences retrieved from online databases andpreviously published studies. Our analyses uncover two entirely new MULE invertebrate-specific clades that contain elements almost entirely restricted to arthropod hosts, considerably expanding the set of MULEs known from this host group, and suggesting that many additional MULEs may await discovery from further arthropod genomes. In several cases, close relationships occur between MULEs recovered from distantly related host organisms, suggesting that horizontal transfer events may have played an important role in the evolution of the group. However, it is apparent that MULEs from plants remain relatively separate from MULEs identified from other host groups. MULE structure varies considerably across phylogeny, and TIR length is shown to vary greatly both within and between MULE groups. Our phylogeny suggests that MULE diversity is clustered in well-supported groups, typically according to host taxonomy. With reference to this, we make suggestions on how MULE diversity can be partitioned to provide a robust taxonomic framework. Conclusions: Our study represents a considerable move forwardadvance in the understanding of MULE diversity, host range and evolution, and providesing a taxonomic framework for the classification of additional further MULE elements that await discovery. Our findingsIt also raises a number of questions in relating to MULE biology, suggesting that this group will provide a rich avenue for future study.Biotechnology & Biological Sciences Research Council (BBSRC)USDA-NIF

Synchronous Behavior of Two Coupled Electronic Neurons

We report on experimental studies of synchronization phenomena in a pair of analog electronic neurons (ENs). The ENs were designed to reproduce the observed membrane voltage oscillations of isolated biological neurons from the stomatogastric ganglion of the California spiny lobster Panulirus interruptus. The ENs are simple analog circuits which integrate four dimensional differential equations representing fast and slow subcellular mechanisms that produce the characteristic regular/chaotic spiking-bursting behavior of these cells. In this paper we study their dynamical behavior as we couple them in the same configurations as we have done for their counterpart biological neurons. The interconnections we use for these neural oscillators are both direct electrical connections and excitatory and inhibitory chemical connections: each realized by analog circuitry and suggested by biological examples. We provide here quantitative evidence that the ENs and the biological neurons behave similarly when coupled in the same manner. They each display well defined bifurcations in their mutual synchronization and regularization. We report briefly on an experiment on coupled biological neurons and four dimensional ENs which provides further ground for testing the validity of our numerical and electronic models of individual neural behavior. Our experiments as a whole present interesting new examples of regularization and synchronization in coupled nonlinear oscillators.Comment: 26 pages, 10 figure

Re-evaluating the resource potential of lomas fog oasis environments for Preceramic hunter-gatherers under past ENSO modes on the south coast of Peru

Lomas – ephemeral seasonal oases sustained by ocean fogs – were critical to ancient human ecology on the desert Pacific coast of Peru: one of humanity’s few independent hearths of agriculture and “pristine” civilisation. The role of climate change since the Late Pleistocene in determining productivity and extent of past lomas ecosystems has been much debated. Here we reassess the resource potential of the poorly studied lomas of the south coast of Peru during the long Middle Pre-ceramic period (c. 8,000 – 4,500 BP): a period critical in the transition to agriculture, the onset of modern El Niño Southern Oscillation (‘ENSO’) conditions, and eustatic sea-level rise and stabilisation and beach progradation. Our method combines vegetation survey and herbarium collection with archaeological survey and excavation to make inferences about both Preceramic hunter-gatherer ecology and the changed palaeoenvironments in which it took place. Our analysis of newly discovered archaeological sites – and their resource context – show how lomas formations defined human ecology until the end of the Middle Preceramic Period, thereby corroborating recent reconstructions of ENSO history based on other data. Together, these suggest that a five millennia period of significantly colder seas on the south coast induced conditions of abundance and seasonal predictability in lomas and maritime ecosystems, that enabled Middle Preceramic hunter-gatherers to reduce mobility by settling in strategic locations at the confluence of multiple eco-zones at the river estuaries. Here the foundations of agriculture lay in a Broad Spectrum Revolution that unfolded, not through population pressure in deteriorating environments, but rather as an outcome of resource abundance.We thank the Ministerio de Cultural del Perú for granting permission for archaeological fieldwork (Resolución Directoral Nº 933-2012-DGPC-VMPCIC/MC, 19 December 2012 and Nº 386-2014-DGPA-VMPCIC/MC, 22 August 2014) and the export of samples for dating; Don Alberto Benavides Ganoza and the people of Samaca for facilitating fieldwork; the Leverhulme Trust (grant number RPG-117) and the late Don Alberto Benavides de la Quintana (grant number RG69428) and the McDonald Institute for Archaeological Research for funding Cambridge University’s One River Archaeological Project, and the NERC Radiocarbon facility (grant number NF/2013/2/2) for funding radiocarbon dating. We also thank the Servicio Nacional Forestal y de Fauna Silvestre (SERFOR) and the Servicio Nacional de Áreas Naturales Protegidas por el Estado (SERNANP), Peru for permits for the Proyecto Kew Perú to carry out botanical and ecological survey, and Delsy Trujillo, Eric Ramírez, Consuelo Borda and other participants of the Proyecto Kew Perú: Conservación, Restauración de Hábitats y Medios de Vida Útiles, Ica, Peru.This is the final version of the article. It first appeared from Elsevier via http://dx.doi.org/10.1016/j.quascirev.2015.10.02

Functional analysis of germline <em>VANGL2</em> variants using rescue assays of <em>vangl2</em> knockout zebrafish

\ua9 The Author(s) 2023. Published by Oxford University Press. Developmental studies have shown that the evolutionarily conserved Wnt Planar Cell Polarity (PCP) pathway is essential for the development of a diverse range of tissues and organs including the brain, spinal cord, heart and sensory organs, as well as establishment of the left-right body axis. Germline mutations in the highly conserved PCP gene VANGL2 in humans have only been associated with central nervous system malformations, and functional testing to understand variant impact has not been performed. Here we report three new families with missense variants in VANGL2 associated with heterotaxy and congenital heart disease p.(Arg169His), non-syndromic hearing loss p.(Glu465Ala) and congenital heart disease with brain defects p.(Arg135Trp). To test the in vivo impact of these and previously described variants, we have established clinically-relevant assays using mRNA rescue of the vangl2 mutant zebrafish. We show that all variants disrupt Vangl2 function, although to different extents and depending on the developmental process. We also begin to identify that different VANGL2 missense variants may be haploinsufficient and discuss evidence in support of pathogenicity. Together, this study demonstrates that zebrafish present a suitable pipeline to investigate variants of unknown significance and suggests new avenues for investigation of the different developmental contexts of VANGL2 function that are clinically meaningful

Quantitative historical analysis uncovers a single dimension of complexity that structures global variation in human social organization

Do human societies from around the world exhibit similarities in the way that they are structured, and show commonalities in the ways that they have evolved? These are long-standing questions that have proven difficult to answer. To test between competing hypotheses, we constructed a massive repository of historical and archaeological information known as "Seshat: Global History Databank." We systematically coded data on 414 societies from 30 regions around the world spanning the last 10,000 years. We were able to capture information on 51 variables reflecting nine characteristics of human societies, such as social scale, economy, features of governance, and information systems. Our analyses revealed that these different characteristics show strong relationships with each other and that a single principal component captures around three-quarters of the observed variation. Furthermore, we found that different characteristics of social complexity are highly predictable across different world regions. These results suggest that key aspects of social organization are functionally related and do indeed coevolve in predictable ways. Our findings highlight the power of the sciences and humanities working together to rigorously test hypotheses about general rules that may have shaped human history

MISA [Material gráfico]

Copia digital. Madrid : Ministerio de Educación, Cultura y Deporte, 201

Intestinal carriage of Staphylococcus aureus: How does its frequency compare with that of nasal carriage and what is its clinical impact?

The bacterial species Staphylococcus aureus, including its methicillin-resistant variant (MRSA), finds its primary ecological niche in the human nose, but is also able to colonize the intestines and the perineal region. Intestinal carriage has not been widely investigated despite its potential clinical impact. This review summarizes literature on the topic and sketches the current state of affairs from a microbiological and infectious diseases' perspective. Major findings are that the average reported detection rate of intestinal carriage in healthy individuals and patients is 20% for S. aureus and 9% for MRSA, which is approximately half of that for nasal carriage. Nasal carriage seems to predispose to intestinal carriage, but sole intestinal carriage occurs relatively frequently and is observed in 1 out of 3 intestinal carriers, which provides a rationale to include intestinal screening for surveillance or in outbreak settings. Colonization of the intestinal tract with S. aureus at a young age occurs at a high frequency and may affect the host's immune system. The frequency of intestinal carriage is generally underestimated and may significantly contribute to bacterial dissemination and subsequent risk of infections. Whether intestinal rather than nasal S. aureus carriage is a primary predictor for infections is still ill-defined