scholarly journals The Missing Tailed Phages: Prediction of Small Capsid Candidates

2020 ◽  
Vol 8 (12) ◽  
pp. 1944
Author(s):  
Antoni Luque ◽  
Sean Benler ◽  
Diana Y. Lee ◽  
Colin Brown ◽  
Simon White
Keyword(s):  
Phage Therapy ◽  
Viral Evolution ◽  
Diverse Group ◽  
Genome Length ◽  
Geometrical Features ◽  
Phage Capsid ◽  
The Common ◽  
Icosahedral Capsid ◽  
Gut Metagenome ◽  
Physical Principles

Tailed phages are the most abundant and diverse group of viruses on the planet. Yet, the smallest tailed phages display relatively complex capsids and large genomes compared to other viruses. The lack of tailed phages forming the common icosahedral capsid architectures T = 1 and T = 3 is puzzling. Here, we extracted geometrical features from high-resolution tailed phage capsid reconstructions and built a statistical model based on physical principles to predict the capsid diameter and genome length of the missing small-tailed phage capsids. We applied the model to 3348 isolated tailed phage genomes and 1496 gut metagenome-assembled tailed phage genomes. Four isolated tailed phages were predicted to form T = 3 icosahedral capsids, and twenty-one metagenome-assembled tailed phages were predicted to form T < 3 capsids. The smallest capsid predicted was a T = 4/3 ≈ 1.33 architecture. No tailed phages were predicted to form the smallest icosahedral architecture, T = 1. We discuss the feasibility of the missing T = 1 tailed phage capsids and the implications of isolating and characterizing small-tailed phages for viral evolution and phage therapy.

scholarly journals The Missing Tailed Phages: Prediction of Small Capsid Candidates

2020 ◽  
Author(s):  
Antoni Luque ◽  
Sean Benler ◽  
Diana Lee ◽  
Colin Brown ◽  
Simon White
Keyword(s):  
Phage Therapy ◽  
Viral Evolution ◽  
Diverse Group ◽  
Genome Length ◽  
Geometrical Features ◽  
Phage Capsid ◽  
The Common ◽  
Icosahedral Capsid ◽  
Gut Metagenome ◽  
Physical Principles

Tailed phages are the most abundant and diverse group of viruses on the planet. Yet, the smallest tailed phages display relatively complex capsids and large genomes compared to other viruses. The lack of tailed phages forming the common icosahedral capsid architectures T = 1 and T = 3 is puzzling. Here, we extracted geometrical features from high-resolution tailed phage capsid reconstructions and built a statistical model based on physical principles to predict the capsid diameter and genome length of the missing small tailed phage capsids. We applied the model to 3,348 isolated tailed phage genomes and 1,496 gut metagenome-assembled tailed phage genomes. Four isolated tailed phages were predicted to form T = 3 icosahedral capsids, and twenty-one metagenome-assembled tailed phages were predicted to form T &lt; 3 capsids. The smallest capsid predicted was a T = 4/3 ≈ 1.33 architecture. No tailed phages were predicted to form the smallest icosahedral architecture, T = 1. We discuss the feasibility of the missing T = 1 tailed phage capsids and the implications of isolating and characterizing small tailed phages for viral evolution and phage therapy.

scholarly journals How rhizobia adapt to the nodule environment

2021 ◽  
Author(s):  
Raphael Ledermann ◽  
Carolin C. M. Schulte ◽  
Philip S. Poole
Keyword(s):  
Nitrogen Fixation ◽  
Soil Bacteria ◽  
Root Nodule ◽  
Computational Modelling ◽  
Diverse Group ◽  
Nitrogen Fixing ◽  
The Core ◽  
Physiological Processes ◽  
Mutualistic Relationship ◽  
The Common

Rhizobia are a phylogenetically diverse group of soil bacteria that engage in mutualistic interactions with legume plants. Although specifics of the symbioses differ between strains and plants, all symbioses ultimately result in the formation of specialized root nodule organs which host the nitrogen-fixing microsymbionts called bacteroids. Inside nodules, bacteroids encounter unique conditions that necessitate global reprogramming of physiological processes and rerouting of their metabolism. Decades of research have addressed these questions using genetics, omics approaches, and more recently computational modelling. Here we discuss the common adaptations of rhizobia to the nodule environment that define the core principles of bacteroid functioning. All bacteroids are growth-arrested and perform energy-intensive nitrogen fixation fueled by plant-provided C4-dicarboxylates at nanomolar oxygen levels. At the same time, bacteroids are subject to host control and sanctioning that ultimately determine their fitness and have fundamental importance for the evolution of a stable mutualistic relationship.

Biophysical Aspects of EEG and MEG Generation

2017 ◽  
Author(s):  
Wytse J. Wadman ◽  
Fernando H. Lopes da Silva
Keyword(s):  
Electromagnetic Fields ◽  
Maxwell Equations ◽  
Brain Activity ◽  
Electrical Field ◽  
The Third ◽  
Scalp Eeg ◽  
External Electromagnetic Fields ◽  
The Common ◽  
The Brain ◽  
Physical Principles

This chapter reviews the essential physical principles involved in the generation of electroencephalographic (EEG) and magnetoencephalographic (MEG) signals. The general laws governing the electrophysiology of neuronal activity are analyzed within the formalism of the Maxwell equations that constitute the basis for understanding electromagnetic fields in general. Three main topics are discussed. The first is the forward problem: How can one calculate the electrical field that results from a known configuration of neuronal sources? The second is the inverse problem: Given an electrical field as a function of space and time mostly recorded at the scalp (EEG/MEG), how can one reconstruct the underlying generators at the brain level? The third is the reverse problem: How can brain activity be modulated by external electromagnetic fields with diagnostic and/or therapeutic objectives? The chapter emphasizes the importance of understanding the common biophysical framework concerning these three main topics of brain electrical and magnetic activities.

scholarly journals Poorly differentiated XX/XY sex chromosomes are widely shared across skink radiation

2021 ◽  
Vol 288 (1943) ◽  
pp. 20202139
Author(s):  
Alexander Kostmann ◽  
Lukáš Kratochvíl ◽  
Michail Rovatsos
Keyword(s):  
Species Diversity ◽  
Sex Determination ◽  
Sex Chromosomes ◽  
Morphological Variability ◽  
Molecular Sexing ◽  
Diverse Group ◽  
Reptile Species ◽  
Poorly Differentiated ◽  
The Common ◽  
Evolutionarily Stable

Differentiated sex chromosomes are believed to be evolutionarily stable, while poorly differentiated sex chromosomes are considered to be prone to turnovers. With around 1700 currently known species forming ca 15% of reptile species diversity, skinks (family Scincidae) are a very diverse group of squamates known for their large ecological and morphological variability. Skinks generally have poorly differentiated and cytogenetically indistinguishable sex chromosomes, and their sex determination was suggested to be highly variable. Here, we determined X-linked genes in the common sandfish ( Scincus scincus ) and demonstrate that skinks have shared the same homologous XX/XY sex chromosomes across their wide phylogenetic spectrum for at least 85 million years, approaching the age of the highly differentiated ZZ/ZW sex chromosomes of birds and advanced snakes. Skinks thus demonstrate that even poorly differentiated sex chromosomes can be evolutionarily stable. The conservation of sex chromosomes across skinks allows us to introduce the first molecular sexing method widely applicable in this group.

Capsid Structure of Anabaena Cyanophage A-1(L)

2021 ◽  
Author(s):  
Ning Cui ◽  
Feng Yang ◽  
Jun-Tao Zhang ◽  
Hui Sun ◽  
Yu Chen ◽  
...  
Keyword(s):  
Aquatic Ecosystems ◽  
Photosynthetic Bacteria ◽  
Atomic Resolution ◽  
Fold Axis ◽  
Contractile Tail ◽  
Phage Capsid ◽  
Mortise And Tenon ◽  
Pcc 7120 ◽  
Icosahedral Capsid ◽  
Resolution Structure

A-1(L) is a freshwater cyanophage with a contractile tail that specifically infects Anabaena sp. PCC 7120, one of the model strains for molecular studies of cyanobacteria. Although isolated for half a century, its structure remains unknown, which limits our understanding on the interplay between A-1(L) and its host. Here we report the 3.35 Å cryo-EM structure of A-1(L) capsid, representing the first near-atomic resolution structure of a phage capsid with a T number of 9. The major capsid gp4 proteins assemble into 91 capsomers, including 80 hexons: 20 at the center of the facet and 60 at the facet edge, in addition to 11 identical pentons. These capsomers further assemble into the icosahedral capsid, via gradually increasing curvatures. Different from the previously reported capsids of known-structure, A-1(L) adopts a non-covalent chainmail structure of capsid stabilized by two kinds of mortise-and-tenon inter-capsomer interactions: a three-layered interface at the pseudo three-fold axis combined with the complementarity in shape and electrostatic potential around the two-fold axis. This unique capsomer construction enables A-1(L) to possess a rigid capsid, which is solely composed of the major capsid proteins with an HK97 fold. IMPORTANCE Cyanobacteria are the most abundant photosynthetic bacteria, contributing significantly to the biomass production, O 2 generation, and CO 2 consumption on our planet. Their community structure and homeostasis in natural aquatic ecosystems are largely regulated by the corresponding cyanophages. In this study, we solved the structure of cyanophage A-1(L) capsid at near-atomic resolution and revealed a unique capsid construction. This capsid structure provides the molecular details for better understanding the assembly of A-1(L), and a structural platform for future investigation and application of A-1(L) in combination with its host Anabaena sp. PCC 7120. As the first isolated freshwater cyanophage that infects the genetically tractable model cyanobacterium, A-1(L) should become an ideal template for the genetic engineering and synthetic biology studies.

scholarly journals Gut metagenome associations with extensive digital health data in a volunteer-based Estonian microbiome cohort

2021 ◽  
Author(s):  
Oliver Aasmets ◽  
Kertu Krigul ◽  
Kreete Lüll ◽  
Andres Metspalu ◽  
Elin Org
Keyword(s):  
Digital Health ◽  
Health Data ◽  
Metagenomic Sequencing ◽  
Health Records ◽  
Microbiome Composition ◽  
Host Interactions ◽  
Microbiome Research ◽  
The Common ◽  
Gut Metagenome

Abstract Microbiome research is starting to move beyond the exploratory phase towards interventional trials and therefore well-characterized cohorts will be instrumental for generating hypothesis and providing new knowledge. As part of the Estonian Biobank (EstBB), we established the Estonian Microbiome Cohort (EstMB) which includes stool, oral and plasma samples from 2,509 participants and is supplemented with multi-omic measurements, questionnaires, and regular linkages to national electronic health records (EHRs). In this study, we analyzed stool data from deep metagenomic sequencing together with rich phenotyping, including 71 diseases, 136 medications, 21 dietary questions, 5 procedures, and 19 other factors. The data revealed numerous relationships (n = 3262) with different microbiome features. Additionally, we present that long-term antibiotic usage, independent from recent administration, has a significant impact on the microbiome composition, partly explaining the common associations between diseases. Overall, this study extends the understanding of microbiome–host interactions and facilitates the development of microbiome-related studies.

scholarly journals Overlapping Genes and Size Constraints in Viruses - An Evolutionary Perspective

2015 ◽  
Author(s):  
Nadav Brandes ◽  
Michal Linial
Keyword(s):  
Viral Evolution ◽  
High Rate ◽  
Evolutionary Constraints ◽  
Absolute Amount ◽  
Evolutionary Perspective ◽  
Overlapping Genes ◽  
Viral Capsids ◽  
Size Constraints ◽  
Gene Overlapping ◽  
The Common

Viruses are the simplest replicating units, characterized by a limited number of coding genes and an exceptionally high rate of overlapping genes. We sought a unified explanation for the evolutionary constraints that govern genome sizes, gene overlapping and capsid properties. We performed an unbiased statistical analysis over the ~100 known viral families, and came to refute widespread assumptions regarding viral evolution. We found that the volume utilization of viral capsids is often low, and greatly varies among families. Most notably, we show that the total amount of gene overlapping is tightly bounded. Although viruses expand three orders of magnitude in genome length, their absolute amount of gene overlapping almost never exceeds 1500 nucleotides, and mostly confined to <4 significant overlapping instances. Our results argue against the common theory by which gene overlapping is driven by a necessity of viruses to compress their genome. Instead, we support the notion that overlapping has a role in gene novelty and evolution exploration.

scholarly journals In that vein: inflated wing veins contribute to butterfly hearing

2018 ◽  
Vol 14 (10) ◽  
pp. 20180496 ◽  
Author(s):  
Penghui Sun ◽  
Natasha Mhatre ◽  
Andrew C. Mason ◽  
Jayne E. Yack
Keyword(s):  
Functional Significance ◽  
Impedance Matching ◽  
Low Frequency ◽  
Diverse Group ◽  
Wing Vein ◽  
Butterfly Wings ◽  
The World ◽  
The Common ◽  
Wing Veins ◽  
Distinguishing Features

Insects have evolved a diversity of hearing organs specialized to detect sounds critical for survival. We report on a unique structure on butterfly wings that enhances hearing. The Satyrini are a diverse group of butterflies occurring throughout the world. One of their distinguishing features is a conspicuous swelling of their forewing vein, but the functional significance of this structure is unknown. Here, we show that wing vein inflations function in hearing. Using the common wood nymph, Cercyonis pegala , as a model, we show that (i) these butterflies have ears on their forewings that are most sensitive to low frequency sounds (less than 5 kHz); (ii) inflated wing veins are directly connected to the ears; and (iii) when vein inflations are ablated, sensitivity to low frequency sounds is impaired. We propose that inflated veins contribute to low frequency hearing by impedance matching.

scholarly journals Molecular phylogeny of the tribe Philodryadini Cope, 1886 (Dipsadidae: Xenodontinae): Rediscovering the diversity of the South American Racers

2020 ◽  
Vol 60 ◽  
pp. e20206053
Author(s):  
Juan Camilo Arredondo ◽  
Felipe Gobbi Grazziotin ◽  
Gustavo Jose Scrocchi Manfrini ◽  
Miguel Trefaut Urbano Rodrigues ◽  
Sandro Luís Bonatto ◽  
...  
Keyword(s):  
Sensu Stricto ◽  
Taxon Sampling ◽  
South American ◽  
Diverse Group ◽  
Phylogenetic Hypothesis ◽  
The South ◽  
Clade B ◽  
Molecular Phylogenetic ◽  
The Common ◽  
New Tribe

South American racers of the tribe Philodryadini are a widespread and diverse group of Neotropical snakes with a complex taxonomic and systematic history. Recent studies failed to present a robust phylogenetic hypothesis for the tribe, mainly due to incomplete taxon sampling. Here we provide the most extensive molecular phylogenetic analysis of Philodryadini available so far, including 20 species (83% of the known diversity) from which six were not sampled previously. Our results reveal that Philodryadini is not monophyletic, but instead includes a central Andean clade formed by Philodryas simonsii, P. tachymenoides, and P. amaru, and a southern and cis-Andean clade including all remaining philodryadines. This discovery requires resurrection of two genera as well as erection of a new tribe of Xenodontinae for the central Andean clade. Within the southern and cis-Andean radiation, our analyses resolve a basal dichotomy separating two main lineages: Clade A, containing the Common Green Racers P. laticeps and P. viridissima and the South American Vine snakes P. georgeboulengeri and P. argentea; and Clade B, including the remaining species of Philodryas sensu stricto. We resurrect the genera Chlorosoma and Xenoxybelis to better represent the monophyly of lineages within the southern and cis-Andean clade.

scholarly journals Poorly differentiated XX/XY sex chromosomes are widely shared across skink radiation

2020 ◽  
Author(s):  
Alexander Kostmann ◽  
Lukáš Kratochvíl ◽  
Michail Rovatsos
Keyword(s):  
Species Diversity ◽  
Sex Chromosomes ◽  
Morphological Variability ◽  
The Other ◽  
Molecular Sexing ◽  
Diverse Group ◽  
Reptile Species ◽  
Poorly Differentiated ◽  
The Common ◽  
Evolutionarily Stable

AbstractDifferentiated sex chromosomes are believed to be evolutionarily stable, and their emergence was suggested to lead to a remarkable increase in the diversification rate and in disparity in such groups as birds, mammals and snakes. On the other hand, poorly differentiated sex chromosomes are considered to be prone to turnovers. With around 1.700 currently known species forming c. 15% of reptile species diversity, skinks (family Scincidae) are a very diverse group of squamates known for their large ecological and morphological variability. Skinks generally have poorly differentiated and cytogenetically hardly distinguishable sex chromosomes and their sex determination was suggested to be highly variable. Here, we determined X-linked genes in the common sandfish (Scincus scincus) and demonstrate that skinks have shared the same homologous XX/XY sex chromosomes across their wide phylogenetic spectrum for at least 85 million years, approaching the age of the highly differentiated ZZ/ZW sex chromosomes of birds and advanced snakes. Skinks thus demonstrate that even poorly differentiated sex chromosomes can be evolutionarily stable and that large diversity can emerge even in groups with poorly differentiated sex chromosomes. The conservation of sex chromosomes across skinks allows us to introduce the first molecular sexing method widely applicable in this group.

Sign in / Sign up

Export Citation Format

Share Document