The relationships of major arthropod clades have long been contentious, but refinements in molecular phylogenetics underpin an emerging consensus. Nevertheless, molecular phylogenies have recovered ...topologies that morphological phylogenies have not, including the placement of hexapods within a paraphyletic Crustacea, and an alliance between myriapods and chelicerates. Here we show enhanced congruence between molecular and morphological phylogenies based on 753 morphological characters for 309 fossil and Recent panarthropods. We resolve hexapods within Crustacea, with remipedes as their closest extant relatives, and show that the traditionally close relationship between myriapods and hexapods is an artefact of convergent character acquisition during terrestrialisation. The inclusion of fossil morphology mitigates long-branch artefacts as exemplified by pycnogonids: when fossils are included, they resolve with euchelicerates rather than as a sister taxon to all other euarthropods.
Three-dimensional fossils, especially those preserving soft-part anatomy, are a rich source of palaeontological information; they can, however, be difficult to work with. Imaging of serial planes ...through an object (tomography) allows study of both the inside and outside of three-dimensional fossils. Tomography may be performed using physical grinding or sawing coupled with photography, through optical techniques of serial focusing, or using a variety of scanning technologies such as neutron tomography, magnetic resonance imaging and most usefully X-ray computed tomography. This latter technique is applicable at a variety of scales, and when combined with a synchrotron X-ray source can produce very high-quality data that may be augmented by phase-contrast information to enhance contrast. Tomographic data can be visualized in several ways, the most effective of which is the production of isosurface-based 'virtual fossils' that can be manipulated and dissected interactively.
Zinc inhibits the virulence of diarrheagenic E. coli by inducing the envelope stress response and inhibiting the SOS response. The SOS response is triggered by damage to bacterial DNA. In ...Shiga-toxigenic E. coli, the SOS response strongly induces the production of Shiga toxins (Stx) and of the bacteriophages that encode the Stx genes. In E. coli, induction of the SOS response is accompanied by a higher mutation rate, called the mutator response, caused by a shift to error-prone DNA polymerases when DNA damage is too severe to be repaired by canonical DNA polymerases. Since zinc inhibited the other aspects of the SOS response, we hypothesized that zinc would also inhibit the mutator response, also known as hypermutation. We explored various different experimental paradigms to induce hypermutation triggered by the SOS response, and found that hypermutation was induced not just by classical inducers such as mitomycin C and the quinolone antibiotics, but also by antiviral drugs such as zidovudine and anti-cancer drugs such as 5-fluorouracil, 6-mercaptopurine, and azacytidine. Zinc salts inhibited the SOS response and the hypermutator phenomenon in E. coli as well as in Klebsiella pneumoniae, and was more effective in inhibiting the SOS response than other metals. We then attempted to determine the mechanism by which zinc, applied externally in the medium, inhibits hypermutation. Our results show that zinc interferes with the actions of RecA, and protects LexA from RecA-mediated cleavage, an early step in initiation of the SOS response. The SOS response may play a role in the development of antibiotic resistance and the effect of zinc suggests ways to prevent it.
ABSTRACT
The Late Jurassic to Early Cretaceous interval represents a time of environmental upheaval and cataclysmic events, combined with disruptions to terrestrial and marine ecosystems. ...Historically, the Jurassic/Cretaceous (J/K) boundary was classified as one of eight mass extinctions. However, more recent research has largely overturned this view, revealing a much more complex pattern of biotic and abiotic dynamics than has previously been appreciated. Here, we present a synthesis of our current knowledge of Late Jurassic–Early Cretaceous events, focusing particularly on events closest to the J/K boundary. We find evidence for a combination of short‐term catastrophic events, large‐scale tectonic processes and environmental perturbations, and major clade interactions that led to a seemingly dramatic faunal and ecological turnover in both the marine and terrestrial realms. This is coupled with a great reduction in global biodiversity which might in part be explained by poor sampling. Very few groups appear to have been entirely resilient to this J/K boundary ‘event’, which hints at a ‘cascade model’ of ecosystem changes driving faunal dynamics. Within terrestrial ecosystems, larger, more‐specialised organisms, such as saurischian dinosaurs, appear to have suffered the most. Medium‐sized tetanuran theropods declined, and were replaced by larger‐bodied groups, and basal eusauropods were replaced by neosauropod faunas. The ascent of paravian theropods is emphasised by escalated competition with contemporary pterosaur groups, culminating in the explosive radiation of birds, although the timing of this is obfuscated by biases in sampling. Smaller, more ecologically diverse terrestrial non‐archosaurs, such as lissamphibians and mammaliaforms, were comparatively resilient to extinctions, instead documenting the origination of many extant groups around the J/K boundary. In the marine realm, extinctions were focused on low‐latitude, shallow marine shelf‐dwelling faunas, corresponding to a significant eustatic sea‐level fall in the latest Jurassic. More mobile and ecologically plastic marine groups, such as ichthyosaurs, survived the boundary relatively unscathed. High rates of extinction and turnover in other macropredaceous marine groups, including plesiosaurs, are accompanied by the origin of most major lineages of extant sharks. Groups which occupied both marine and terrestrial ecosystems, including crocodylomorphs, document a selective extinction in shallow marine forms, whereas turtles appear to have diversified. These patterns suggest that different extinction selectivity and ecological processes were operating between marine and terrestrial ecosystems, which were ultimately important in determining the fates of many key groups, as well as the origins of many major extant lineages. We identify a series of potential abiotic candidates for driving these patterns, including multiple bolide impacts, several episodes of flood basalt eruptions, dramatic climate change, and major disruptions to oceanic systems. The J/K transition therefore, although not a mass extinction, represents an important transitional period in the co‐evolutionary history of life on Earth.
With the discovery that organisms possess multiple DNA polymerases (Pols) displaying different fidelities, processivities, and activities came the realization that mechanisms must exist to manage the ...actions of these diverse enzymes to prevent gratuitous mutations. Although many of the Pols encoded by most organisms are largely accurate, and participate in DNA replication and DNA repair, a sizeable fraction display a reduced fidelity, and act to catalyze potentially error-prone translesion DNA synthesis (TLS) past lesions that persist in the DNA. Striking the proper balance between use of these different enzymes during DNA replication, DNA repair, and TLS is essential for ensuring accurate duplication of the cell's genome. This review highlights mechanisms that organisms utilize to manage the actions of their different Pols. A particular emphasis is placed on discussion of current models for how different Pols switch places with each other at the replication fork during high fidelity replication and potentially error-pone TLS.
The SOS response to DNA damage is a conserved stress response in Gram-negative and Gram-positive bacteria. Although this pathway has been studied for years, its relevance is still not familiar to ...many working in the fields of clinical antibiotic resistance and stewardship. Under some conditions, the SOS response favors DNA repair and preserves the genetic integrity of the organism. On the other hand, the SOS response also includes induction of error-prone DNA polymerases, which can increase the rate of mutation, called the mutator phenotype or "hypermutation." As a result, mutations can occur in genes conferring antibiotic resistance, increasing the acquisition of resistance to antibiotics. Almost all of the work on the SOS response has been on bacteria exposed to stressors
. In this study, we sought to quantitate the effects of SOS-inducing drugs
, in comparison with the same drugs
. We used a rabbit model of intestinal infection with enteropathogenic Escherichia coli strain E22. SOS-inducing drugs triggered the mutator phenotype response
as well as
. Exposure of E. coli strain E22 to ciprofloxacin or zidovudine, both of which induce the SOS response
, resulted in increased antibiotic resistance to 3 antibiotics: rifampin, minocycline, and fosfomycin. Zinc was able to inhibit the SOS-induced emergence of antibiotic resistance
, as previously observed
. Our findings may have relevance in reducing the emergence of resistance to new antimicrobial drugs.
Abstract
The Msh2–Msh3 mismatch repair (MMR) complex in Saccharomyces cerevisiae recognizes and directs repair of insertion/deletion loops (IDLs) up to ∼17 nucleotides. Msh2–Msh3 also recognizes and ...binds distinct looped and branched DNA structures with varying affinities, thereby contributing to genome stability outside post-replicative MMR through homologous recombination, double-strand break repair (DSBR) and the DNA damage response. In contrast, Msh2–Msh3 promotes genome instability through trinucleotide repeat (TNR) expansions, presumably by binding structures that form from single-stranded (ss) TNR sequences. We previously demonstrated that Msh2–Msh3 binding to 5′ ssDNA flap structures interfered with Rad27 (Fen1 in humans)-mediated Okazaki fragment maturation (OFM) in vitro. Here we demonstrate that elevated Msh2–Msh3 levels interfere with DNA replication and base excision repair in vivo. Elevated Msh2–Msh3 also induced a cell cycle arrest that was dependent on RAD9 and ELG1 and led to PCNA modification. These phenotypes also required Msh2–Msh3 ATPase activity and downstream MMR proteins, indicating an active mechanism that is not simply a result of Msh2–Msh3 DNA-binding activity. This study provides new mechanistic details regarding how excess Msh2–Msh3 can disrupt DNA replication and repair and highlights the role of Msh2–Msh3 protein abundance in Msh2–Msh3-mediated genomic instability.
Graphical Abstract
Graphical Abstract
The underlying microscopic response of filler networks in reinforced rubber to dynamic strain is not well understood due to the experimental difficulty of directly measuring filler network behavior ...in samples undergoing dynamic strain. This difficulty can be overcome with in situ X-ray photon correlation spectroscopy (XPCS) measurements. The contrast between the silica filler and the rubber matrix for X-ray scattering allows us to isolate the filler network behavior from the overall response of the rubber. This in situ XPCS technique probes the microscopic breakdown and reforming of the filler network structure, which are responsible for the nonlinear dependence of modulus on strain, known in the rubber science community as the Payne effect. These microscopic changes in the filler network structure have consequences for the macroscopic material performance, especially for the fuel efficiency of tire tread compounds. Here, we elucidate the behavior with in situ dynamic strain XPCS experiments on industrially relevant, vulcanized rubbers filled (13 vol %) with novel air-milled silica of ultrahigh-surface area (UHSA) (250 m2/g). The addition of a silane coupling agent to rubber containing this silica causes an unexpected and counterintuitive increase in the Payne effect and decrease in energy dissipation. For this rubber, we observe a nearly two-fold enhancement of the storage modulus and virtually equivalent loss tangent compared to a rubber containing a coupling agent and conventional silica. Interpretation of our in situ XPCS results simultaneously with interpretation of traditional dynamic mechanical analysis (DMA) strain sweep experiments reveals that the debonding or yielding of bridged bound rubber layers is key to understanding the behavior of rubber formulations containing the silane coupling agent and high-surface area silica. These results demonstrate that the combination of XPCS and DMA is a powerful method for unraveling the microscale filler response to strain which dictates the dynamic mechanical properties of reinforced soft matter composites. With this combination of techniques, we have elucidated the great promise of UHSA silica when used in concert with a silane coupling agent in filled rubber. Such composites simultaneously exhibit large moduli and low hysteresis under dynamic strain.
Cambrian bivalved arthropod reveals origin of arthrodization Legg, David A.; Sutton, Mark D.; Edgecombe, Gregory D. ...
Proceedings - Royal Society. Biological sciences/Proceedings - Royal Society. Biological Sciences,
12/2012, Volume:
279, Issue:
1748
Journal Article
Peer reviewed
Open access
Extant arthropods are diverse and ubiquitous, forming a major constituent of most modern ecosystems. Evidence from early Palaeozoic Konservat Lagerstätten indicates that this has been the case since ...the Cambrian. Despite this, the details of arthropod origins remain obscure, although most hypotheses regard the first arthropods as benthic predators or scavengers such as the fuxianhuiids or megacheirans (‘great-appendage’ arthropods). Here, we describe a new arthropod from the Tulip Beds locality of the Burgess Shale Formation (Cambrian, series 3, stage 5) that possesses a weakly sclerotized thorax with filamentous appendages, encased in a bivalved carapace, and a strongly sclerotized, elongate abdomen and telson. A cladistic analysis resolved this taxon as the basal-most member of a paraphyletic grade of nekto-benthic forms with bivalved carapaces. This grade occurs at the base of Arthropoda (panarthropods with arthropodized trunk limbs) and suggests that arthrodization (sclerotization and jointing of the exoskeleton) evolved to facilitate swimming. Predatory and fully benthic habits evolved later in the euarthropod stem-lineage and are plesiomorphically retained in pycnogonids (sea spiders) and euchelicerates (horseshoe crabs and arachnids).
Translesion synthesis (TLS) by specialized DNA polymerases (Pols) is an evolutionarily conserved mechanism for tolerating replication-blocking DNA lesions. Using the Escherichia coli
-encoded Pol IV ...as a model to understand how TLS is coordinated with the actions of the high-fidelity Pol III replicase, we previously described a novel Pol IV mutant containing a threonine 120-to-proline mutation (Pol IV-T120P) that failed to exchange places with Pol III at the replication fork
as part of a Pol III-Pol IV switch. This
defect correlated with the inability of Pol IV-T120P to support TLS
, suggesting Pol IV gains access to the DNA, at least in part, via a Pol III-Pol IV switch. Interaction of Pol IV with the β sliding clamp and the single-stranded DNA binding protein (SSB) significantly stimulates Pol IV replication and facilitates its access to the DNA. In this work, we demonstrate that Pol IV interacts physically with Pol III. We further show that Pol IV-T120P interacts normally with the β clamp, but is impaired in interactions with the α catalytic and εθ proofreading subunits of Pol III, as well as SSB. Taken together with published work, these results provide strong support for the model in which Pol IV-Pol III and Pol IV-SSB interactions help to regulate the access of Pol IV to the DNA. Finally, we describe several additional E. coli Pol-Pol interactions, suggesting Pol-Pol interactions play fundamental roles in coordinating bacterial DNA replication, DNA repair, and TLS.
Specialized DNA polymerases (Pols) capable of catalyzing translesion synthesis (TLS) generate mutations that contribute to bacterial virulence, pathoadaptation, and antimicrobial resistance. One mechanism by which the bacterial TLS Pol IV gains access to the DNA to generate mutations is by exchanging places with the bacterial Pol III replicase via a Pol III-Pol IV switch. Here, we describe multiple Pol III-Pol IV interactions and discuss evidence that these interactions are required for the Pol III-Pol IV switch. Furthermore, we describe several additional E. coli Pol-Pol interactions that may play fundamental roles in managing the actions of the different bacterial Pols in DNA replication, DNA repair, and TLS.
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