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It has often been suggested that the productivity of an ecosystem affects the number of species that it can support. Despite decades of study, the nature, extent, and underlying mechanisms of this relationship are unclear. One suggested mechanism is the “more individuals” hypothesis (MIH). This proposes that productivity controls the number of individuals in the ecosystem, and that more individuals can be divided into a greater number of species before their population size is sufficiently small for each to be at substantial risk of extinction. Here, we test this hypothesis using REvoSim: an individual‐based eco‐evolutionary system that simulates the evolution and speciation of populations over geological time, allowing phenomena occurring over timescales that cannot be easily observed in the real world to be evaluated. The individual‐based nature of this system allows us to remove assumptions about the nature of speciation and extinction that previous models have had to make. Many of the predictions of the MIH are supported in our simulations: Rare species are more likely to undergo extinction than common species, and species richness scales with productivity. However, we also find support for relationships that contradict the predictions of the strict MIH: species population size scales with productivity, and species extinction risk is better predicted by relative than absolute species population size, apparently due to increased competition when total community abundance is higher. Furthermore, we show that the scaling of species richness with productivity depends upon the ability of species to partition niche space. Consequently, we suggest that the MIH is applicable only to ecosystems in which niche partitioning has not been halted by species saturation. Some hypotheses regarding patterns of biodiversity implicitly or explicitly overlook niche theory in favor of neutral explanations, as has historically been the case with the MIH. Our simulations demonstrate that niche theory exerts a control on the applicability of the MIH and thus needs to be accounted for in macroecology., We use simulation experiments to test the predictions of the more‐individuals hypothesis of biodiversity. We find that many of these predictions are supported, but that interspecific competition and limits to niche diversity can provide additional complexity not predicted by the more‐individuals hypothesis.

Expression of the Escherichia coli dnaN-encoded β clamp at ≥10-fold higher than chromosomally expressed levels impedes growth by interfering with DNA replication. We hypothesized that the excess β clamp sequesters the replicative DNA polymerase III (Pol III) to inhibit replication. As a test of this hypothesis, we obtained eight mutant clamps with an inability to impede growth and measured their ability to stimulate Pol III replication in vitro. Compared with the wild-type clamp, seven of the mutants were defective, consistent with their elevated cellular levels failing to sequester Pol III. However, the βE202K mutant that bears a glutamic acid-to-lysine substitution at residue 202 displayed an increased affinity for Pol IIIα and Pol III core (Pol IIIαeθ), suggesting that it could still sequester Pol III effectively. Of interest, βE202K supported in vitro DNA replication by Pol II and Pol IV but was defective with Pol III. Genetic experiments indicated that the dnaNE202K strain remained proficient in DNA damage-induced mutagenesis but was induced modestly for SOS and displayed sensitivity to UV light and methyl methanesulfonate. These results correlate an impaired ability of the mutant βE202K clamp to support Pol III replication in vivo with its in vitro defect in DNA replication. Taken together, our results (i) support the model that sequestration of Pol III contributes to growth inhibition, (ii) argue for the existence of an additional mechanism that contributes to lethality, and (iii) suggest that physical and functional interactions of the β clamp with Pol III are more extensive than appreciated currently. IMPORTANCE The β clamp plays critically important roles in managing the actions of multiple proteins at the replication fork. However, we lack a molecular understanding of both how the clamp interacts with these different partners and the mechanisms by which it manages their respective actions. We previously exploited the finding that an elevated cellular level of the β clamp impedes Escherichia coli growth by interfering with DNA replication. Using a genetic selection method, we obtained novel mutant β clamps that fail to inhibit growth. Their analysis revealed that βE202K is unique among them. Our work offers new insights into how the β clamp interacts with and manages the actions of E. coli DNA polymerases II, III, and IV.

Expression of the Escherichia coli dnaN-encoded β clamp at ≥10-fold higher than chromosomally expressed levels impedes growth by interfering with DNA replication. A mutant clamp (β(E202K) bearing a glutamic acid-to-lysine substitution at residue 202) binds to DNA polymerase III (Pol III) with higher affinity than the wild-type clamp, suggesting that its failure to impede growth is independent of its ability to sequester Pol III away from the replication fork. Our results demonstrate that the dnaN(E202K) strain underinitiates DNA replication due to insufficient levels of DnaA-ATP and expresses several DnaA-regulated genes at altered levels, including nrdAB, that encode the class 1a ribonucleotide reductase (RNR). Elevated expression of nrdAB was dependent on hda function. As the β clamp-Hda complex regulates the activity of DnaA by stimulating its intrinsic ATPase activity, this finding suggests that the dnaN(E202K) allele supports an elevated level of Hda activity in vivo compared with the wild-type strain. In contrast, using an in vitro assay reconstituted with purified components the β(E202K) and wild-type clamp proteins supported comparable levels of Hda activity. Nevertheless, co-overexpression of the nrdAB-encoded RNR relieved the growth defect caused by elevated levels of the β clamp. These results support a model in which increased cellular levels of DNA precursors relieve the ability of elevated β clamp levels to impede growth and suggest either that multiple effects stemming from the dnaN(E202K) mutation contribute to elevated nrdAB levels or that Hda plays a noncatalytic role in regulating DnaA-ATP by sequestering it to reduce its availability. IMPORTANCE DnaA bound to ATP acts in initiation of DNA replication and regulates the expression of several genes whose products act in DNA metabolism. The state of the ATP bound to DnaA is regulated in part by the β clamp-Hda complex. The dnaN(E202K) allele was identified by virtue of its inability to impede growth when expressed ≥10-fold higher than chromosomally expressed levels. While the dnaN(E202K) strain exhibits several phenotypes consistent with heightened Hda activity, the wild-type and β(E202K) clamp proteins support equivalent levels of Hda activity in vitro. Taken together, these results suggest that β(E202K)-Hda plays a noncatalytic role in regulating DnaA-ATP. This, as well as alternative models, is discussed.

Most Palaeozoic brittle stars lack the fused arm ossicles (vertebrae) that facilitate the remarkable mode of walking that characterizes living forms. Here we describe a stem ophiuroid from the Herefordshire Lagerstätte (Silurian, Wenlock Series), which is exceptional in preserving the body cavity uncompacted and the long tube feet. We assign the specimen to the order Oegophiurida. The morphology of the arms and attitude of the specimen suggest that locomotion may have been achieved by arm propulsion combined with podial walking. This ophiuroid increases the diversity of echinoderm higher taxa with preserved soft parts represented in the Herefordshire Lagerstätte.

Evolutionary inferences require reliable phylogenies. Morphological data have traditionally been analyzed using maximum parsimony, but recent simulation studies have suggested that Bayesian analyses yield more accurate trees. This debate is ongoing, in part, because of ambiguity over modes of morphological evolution and a lack of appropriate models. Here, we investigate phylogenetic methods using two novel simulation models—one in which morphological characters evolve stochastically along lineages and another in which individuals undergo selection. Both models generate character data and lineage splitting simultaneously: the resulting trees are an emergent property, rather than a fixed parameter. Standard consensus methods for Bayesian searches (Mki) yield fewer incorrect nodes and quartets than the standard consensus trees recovered using equal weighting and implied weighting parsimony searches. Distances between the pool of derived trees (most parsimonious or posterior distribution) and the true trees—measured using Robinson-Foulds (RF), subtree prune and regraft (SPR), and tree bisection reconnection (TBR) metrics—demonstrate that this is related to the search strategy and consensus method of each technique. The amount and structure of homoplasy in character data differ between models. Morphological coherence, which has previously not been considered in this context, proves to be a more important factor for phylogenetic accuracy than homoplasy. Selection-based models exhibit relatively lower homoplasy, lower morphological coherence, and higher inaccuracy in inferred trees. Selection is a dominant driver of morphological evolution, but we demonstrate that it has a confounding effect on numerous character properties which are fundamental to phylogenetic inference. We suggest that the current debate should move beyond considerations of parsimony versus Bayesian, toward identifying modes of morphological evolution and using these to build models for probabilistic search methods. [Bayesian; evolution; morphology; parsimony; phylogenetics; selection; simulation.]

A megacheiran arthropod, Enalikter aphson, was recently described by Siveter et al. (2014) from the mid-Silurian (late Wenlock) of Herefordshire. Previously, megacheirans had only been recognized from the Cambrian. Struck et al. (2015) considered the body plan of Enalikter to be incompatible with this affinity, arguing that many of the arthropod features were either not present or misinterpreted. Instead, they compared Enalikter to polychaete annelids, identifying characters from numerous polychaete lineages which they considered to be present in Enalikter. A reply to this critique by Siveter et al. (2015) reaffirmed arthropod affinities for Enalikter by presenting additional evidence for key arthropod features, such as arthropodized appendages. Here, we augment Siveter et al. by critically addressing the putative annelid characters of Enalikter presented by Struck et al. and additionally explore the morphological and phylogenetic implications of their hypothesis. We conclude that similarities between Enalikter and polychaetes are superficial and that character combinations proposed by Struck et al. are not present in any annelid, living or extinct. This taxon highlights the importance of using a phylogenetic framework for interpreting fossils that present unusual morphologies, such that proposed shared characters are hypotheses of homology rather than merely phenotypic similarities. Crucially, we argue that autapomorphic characters of subgroups of large taxa (like families or classes within phyla) should not be used to diagnose problematic fossils.

The ATP-bound form of the Escherichia coli DnaA replication initiator protein remodels the chromosomal origin of replication, oriC, to load the replicative helicase. The primary mechanism for regulating the activity of DnaA involves the Hda and β clamp proteins, which act together to dramatically stimulate the intrinsic DNA-dependent ATPase activity of DnaA via a process termed Regulatory Inactivation of DnaA. In addition to hyperinitiation, strains lacking hda function also exhibit cold sensitive growth at 30°C. Strains impaired for the other regulators of initiation (i.e., ΔseqA or ΔdatA) fail to exhibit cold sensitivity. The goal of this study was to gain insight into why loss of hda function impedes growth. We used a genetic approach to isolate 9 suppressors of Δhda cold sensitivity, and characterized the mechanistic basis by which these suppressors alleviated Δhda cold sensitivity. Taken together, our results provide strong support for the view that the fundamental defect associated with Δhda is diminished levels of DNA precursors, particularly dGTP and dATP. We discuss possible mechanisms by which the suppressors identified here may regulate dNTP pool size, as well as similarities in phenotypes between the Δhda strain and hda+ strains exposed to the ribonucleotide reductase inhibitor hydroxyurea.

Regulatory inactivation of DnaA (RIDA) is one of the major regulatory mechanisms of prokaryotic replication licensing. In RIDA, the Hda–sliding clamp complex loaded onto DNA directly interacts with adenosine triphosphate (ATP)-bound DnaA and stimulates the hydrolysis of ATP to inactivate DnaA. A prediction is that the activity of Hda is tightly controlled to ensure that replication initiation occurs only once per cell cycle. Here, we determined the crystal structure of the Hda–β clamp complex. This complex contains two pairs of Hda dimers sandwiched between two β clamp rings to form an octamer that is stabilized by three discrete interfaces. Two separate surfaces of Hda make contact with the β clamp, which is essential for Hda function in RIDA. The third interface between Hda monomers occludes the active site arginine finger, blocking its access to DnaA. Taken together, our structural and mutational analyses of the Hda–β clamp complex indicate that the interaction of the β clamp with Hda controls the ability of Hda to interact with DnaA. In the octameric Hda–β clamp complex, the inability of Hda to interact with DnaA is a novel mechanism that may regulate Hda function.

Sponges (Porifera), as one of the earliest-branching animal phyla, are crucial for understanding early metazoan phylogeny. Recent studies of Lower Palaeozoic sponges have revealed a variety of character states and combinations unknown in extant taxa, challenging our views of early sponge morphology. The Herefordshire Konservat–Lagerstätte yields an abundant, diverse sponge fauna with three-dimensional preservation of spicules and soft tissue. Carduispongia pedicula gen. et sp. nov. possesses a single layer of hexactine spicules arranged in a regular orthogonal network. This spicule type and arrangement is characteristic of the reticulosans, which have traditionally been interpreted as early members of the extant siliceous Class Hexactinellida. However, the unusual preservation of the spicules of C . pedicula reveals an originally calcareous composition, which would be diagnostic of the living Class Calcarea. The soft tissue architecture closely resembles the complex sylleibid or leuconid structure seen in some modern calcareans and homoscleromorphs. This combination of features strongly supports a skeletal continuum between primitive calcareans and hexactinellid siliceans, indicating that the last common ancestor of Porifera was a spiculate, solitary, vasiform animal with a thin skeletal wall.

Reconstructing the evolutionary assembly of animal body plans is challenging when there are large morphological gaps between extant sister taxa, as in the case of echinozoans (echinoids and holothurians). However, the inclusion of extinct taxa can help bridge these gaps. Here we describe a new species of echinozoan, Sollasina cthulhu , from the Silurian Herefordshire Lagerstätte, UK. Sollasina cthulhu belongs to the ophiocistioids, an extinct group that shares characters with both echinoids and holothurians. Using physical–optical tomography and computer reconstruction, we visualize the internal anatomy of S. cthulhu in three dimensions, revealing inner soft tissues that we interpret as the ring canal, a key part of the water vascular system that was previously unknown in fossil echinozoans. Phylogenetic analyses strongly suggest that Sollasina and other ophiocistioids represent a paraphyletic group of stem holothurians, as previously hypothesized. This allows us to reconstruct the stepwise reduction of the skeleton during the assembly of the holothurian body plan, which may have been controlled by changes in the expression of biomineralization genes.

Although it is generally accepted that δ15N in lichen reflects predominating N isotope sources in the environment, confirmation of the direct correlation between lichen δ15N and atmospheric δ15N is still missing, especially under field conditions with most confounding factors controlled. To fill this gap and investigate the response of lichens with different tolerance to atmospheric N deposition, thalli of the sensitive Evernia prunastri and the tolerant Xanthoria parietina were exposed for ten weeks to different forms and doses of N in a field manipulation experiment where confounding factors were minimized. During this period, several parameters, namely total N, δ15N and chlorophyll a fluorescence, were measured. Under the experimental conditions, δ15N in lichens quantitatively responded to the δ15N of released gaseous ammonia (NH3). Although a high correlation between the isotopic signatures in lichen tissue and supplied N was found both in tolerant and sensitive species, chlorophyll a fluorescence indicated that the sensitive species very soon lost its photosynthetic functionality with increasing N availability. The most damaging response to the different N chemical forms was observed with dry deposition of NH3, although wet deposition of ammonium ions had a significant observable physiological impact. Conversely, there was no significant effect of nitrate ions on chlorophyll a fluorescence, implying differential sensitivity to dry deposition versus wet deposition and to ammonium versus nitrate in wet deposition. Evernia prunastri was most sensitive to NH3, then NH4+, with lowest sensitivity to NO3−. Moreover, these results confirm that lichen δ15N can be used to indicate the δ15N of atmospheric ammonia, providing a suitable tool for the interpretation of the spatial distribution of NH3 sources in relation to their δ15N signal.

As a label for a distinct category of life, “living fossil” is controversial. The term has multiple definitions, and it is unclear whether the label can be genuinely used to delimit biodiversity. Even taking a purely phylogenetic perspective in which a proxy for the living fossil is evolutionary distinctness (ED), an inconsistency arises: Does it refer to “dead-end” lineages doomed to extinction or “panchronic” lineages that survive through multiple epochs? Recent tree-growth model studies indicate that speciation rates must have been unequally distributed among species in the past to produce the shape of the tree of life. Although an uneven distribution of speciation rates may create the possibility for a distinct group of living fossil lineages, such a grouping could only be considered genuine if extinction rates also show a consistent pattern, be it indicative of dead-end or panchronic lineages. To determine whether extinction rates also show an unequal distribution, we developed a tree-growth model in which the probability of speciation and extinction is a function of a tip’s ED. We simulated thousands of trees in which the ED function for a tip is randomly and independently determined for speciation and extinction rates. We find that simulations in which the most evolutionarily distinct tips have lower rates of speciation and extinction produce phylogenetic trees closest in shape to empirical trees. This implies that a distinct set of lineages with reduced rates of diversification, indicative of a panchronic definition, is required to create the shape of the tree of life.

Micro-organisms express a wide range of transmembrane pumps known as multidrug efflux pumps that improve the micro-organism's ability to survive in severe environments and contribute to resistance against antibiotic and antimicrobial agents. There is significant interest in developing efflux inhibitors as an adjunct to treatment with current and next generation of antibiotics. A greater understanding of drug recognition and transport by multidrug efflux pumps is needed to develop clinically useful inhibitors, given the breadth of molecules that can be effluxed by these systems. We summarize some structural and functional data that could provide insights into the inhibition of transport mechanisms of these intricate molecular nanomachines with a focus on the advances in computational approaches.

Macroevolutionary processes dictate the generation and loss of biodiversity. Understanding them is a key challenge when interrogating the earth–life system in deep time. Model-based approaches can reveal important macroevolutionary patterns and generate hypotheses on the underlying processes. Here we present and document a novel model called REvoSim (Rapid Evolutionary Simulator) coupled with a software implementation of this model. The latter is available here as both source code (C++/Qt, GNU General Public License) and as distributables for a variety of operating systems. REvoSim is an individual-based model with a strong focus on computational efficiency. It can simulate populations of 10 5 –10 7 digital organisms over geological timescales on a typical desktop computer, and incorporates spatial and temporal environmental variation, recombinant reproduction, mutation and dispersal. Whilst microevolutionary processes drive the model, macroevolutionary phenomena such as speciation and extinction emerge. We present results and analysis of the model focusing on validation, and note a number potential applications. REvoSim can serve as a multipurpose platform for studying both macro and microevolution, and bridges this divide. It will be continually developed by the authors to expand its capabilities and hence its utility.

The SOS response is a conserved response to DNA damage that is found in Gram-negative and Gram-positive bacteria. When DNA damage is sustained and severe, activation of error-prone DNA polymerases can induce a higher mutation rate than is normally observed, which is called the SOS mutator phenotype or hypermutation. We previously showed that zinc blocked the hypermutation response induced by quinolone antibiotics and mitomycin C in Escherichia coli and Klebsiella pneumoniae. In this study, we demonstrate that zinc blocks the SOS-induced development of chloramphenicol resistance in Enterobacter cloacae. Zinc also blocked the transfer of an extended spectrum beta-lactamase (ESBL) gene from Enterobacter to a susceptible E. coli strain. A zinc ionophore, zinc pyrithione, was ~100-fold more potent than zinc salts in inhibition of ciprofloxacin-induced hypermutation in E. cloacae. Other divalent metals, such as iron and manganese, failed to inhibit these responses. Electrophoretic mobility shift assays (EMSAs) revealed that zinc, but not iron or manganese, blocked the ability of the E. coli RecA protein to bind to single-stranded DNA, an important early step in the recognition of DNA damage in enteric bacteria. This suggests a mechanism for zinc's inhibitory effects on bacterial SOS responses, including hypermutation.

Seabird colonies alter the biogeochemistry of nearby ecosystems, while the associated emissions of ammonia (NH3) may cause acidification and eutrophication of finely balanced biomes. To examine the possible effects of future climate change on the magnitude and distribution of seabird NH3 emissions globally, a global seabird database was used as input to the GUANO model, a dynamic mass-flow process-based model that simulates NH3 losses from seabird colonies at an hourly resolution in relation to environmental conditions. Ammonia emissions calculated by the GUANO model were in close agreement with measured NH3 emissions across a wide range of climates. For the year 2010, the total global seabird NH3 emission is estimated at 82 [37–127] Gg year−1. This is less than previously estimated using a simple temperature-dependent empirical model, mainly due to inclusion of nitrogen wash-off from colonies during precipitation events in the GUANO model. High precipitation, especially between 40° and 60° S, results in total emissions for the penguin species that are 82% smaller than previously estimated, while for species found in dry tropical areas, emissions are 83–133% larger. Application of temperature anomalies for several IPCC scenarios for 2099 in the GUANO model indicated a predicted net increase in global seabird NH3 emissions of 27% (B1 scenario) and 39% (A2 scenario), compared with the 2010 estimates. At individual colonies, the net change was the result of influences of temperature, precipitation and relative humidity change, with smaller effects of wind-speed changes. The largest increases in NH3 emissions (mean: 60% [486 to −50] increase; A2 scenario for 2099 compared with 2010) were found for colonies 40°S to 65°N, and may lead to increased plant growth and decreased biodiversity by eliminating nitrogen sensitive plant species. Only 7% of the seabird colonies assessed globally (mainly limited to the sub-polar Southern Ocean) were estimated to experience a reduction in NH3 emission (average: −18% [-50 to 0] reduction between 2010 and 2099, A2 scenario), where an increase in precipitation was found to more than offset the effect of rising temperatures.

The Herefordshire (Silurian) Lagerstätte (approx. 430 Myr BP) has yielded, among many exceptionally preserved invertebrates, a wide range of new genera belonging to crown-group Panarthropoda. Here, we increase this panarthropod diversity with the lobopodian Thanahita distos , a new total-group panarthropod genus and species. This new lobopodian preserves at least nine paired, long, slender appendages, the anterior two in the head region and the posterior seven representing trunk lobopods. The body ends in a short post-appendicular extension. Some of the trunk lobopods bear two claws, others a single claw. The body is covered by paired, tuft-like papillae. Thanahita distos joins only seven other known three-dimensionally preserved lobopodian or onychophoran (velvet worm) fossil specimens and is the first lobopodian to be formally described from the Silurian. Phylogenetic analysis recovered it, together with all described Hallucigenia species, in a sister-clade to crown-group panarthropods. Its placement in a redefined Hallucigeniidae, an iconic Cambrian clade, indicates the survival of this clade to Silurian times.

Extant aplacophorans, a group of shell-less vermiform molluscs, respire through appendages within or projecting from a posterior cavity. Respiratory structures differ between the subclasses Caudofoveata (ctenidia within the cavity) and Solenogastres (folds of the mantle itself). Acaenoplax hayae, a Silurian vermiform mollusc from the Herefordshire Lagerstatte, England, exhibits characteristics of both these groups. While recent work places it within the crown group Aplacophora, near the caudofoveates, initial observations suggested that its respiratory structures were closer to those of the solenogastres. Here, we present new reconstructions of the posterior of Acaenoplax prepared with the aim of resolving features obscured when prior studies were undertaken. These reconstructions detail a novel posterior architecture, not closely comparable to that of either extant aplacophoran group, in which respiratory projections arise from a membrane that partly encloses a central posterior cavity. The posterior membrane is flanked by small spherical projections; both membrane and spherical projections are apparently unique within the Aplacophora. The existence of this previously undocumented respiratory system underlines the diversity of the aplacophoran clade during the Palaeozoic.

The widespread dissemination of CTX-M extended spectrum β-lactamases among Escherichia coli bacteria, both in nosocomial and community environments, is a challenge for diagnostic bacteriology laboratories. We describe a rapid and sensitive detection system for analysis of DNA containing the blaCTX-M-15 gene using isothermal DNA amplification by recombinase polymerase amplification (RPA) on a digital microfluidic platform; active matrix electrowetting-on-dielectric (AM-EWOD). The devices have 16,800 electrodes that can be independently controlled to perform multiple and simultaneous droplet operations. The device includes an in-built impedance sensor for real time droplet position and size detection, an on-chip thermistor for temperature sensing and an integrated heater for regulating the droplet temperature. Automatic dispensing of droplets (45 nL) from reservoir electrodes is demonstrated with a coefficient of variation (CV) in volume of approximately 2%. The RPA reaction is monitored in real-time using exonuclease fluorescent probes. Continuous mixing of droplets during DNA amplification significantly improves target DNA detection by at least 100 times compared to a benchtop assay, enabling the detection of target DNA over four-order-of-magnitude with a limit of detection of a single copy within ~15 minutes.

Proteus mirabilis forms extensive crystalline biofilms on indwelling urethral catheters that block urine flow and lead to serious clinical complications. The Bcr/CflA efflux system has previously been identified as important for development of P. mirabilis crystalline biofilms, highlighting the potential for efflux pump inhibitors (EPIs) to control catheter blockage. Here we evaluate the potential for drugs already used in human medicine (fluoxetine and thioridazine) to act as EPIs in P. mirabilis, and control crystalline biofilm formation. Both fluoxetine and thioridazine inhibited efflux in P. mirabilis, and molecular modelling predicted both drugs interact strongly with the biofilm-associated Bcr/CflA efflux system. Both EPIs were also found to significantly reduce the rate of P. mirabilis crystalline biofilm formation on catheters, and increase the time taken for catheters to block. Swimming and swarming motilies in P. mirabilis were also significantly reduced by both EPIs. The impact of these drugs on catheter biofilm formation by other uropathogens (Escherichia coli, Pseudomonas aeruginosa) was also explored, and thioridazine was shown to also inhibit biofilm formation in these species. Therefore, repurposing of existing drugs with EPI activity could be a promising approach to control catheter blockage, or biofilm formation on other medical devices.

Many studies in recent years have highlighted the ecological implications of adding reactive nitrogen (Nr) to terrestrial ecosystems. Seabird colonies represent a situation with concentrated sources of Nr, through excreted and accumulated guano, often occurring in otherwise nutrient-poor areas. To date, there has been little attention given to modelling N flows in this context, and particularly to quantifying the relationship between ammonia (NH3) emissions and meteorology. This paper presents a dynamic mass-flow model (GUANO) that simulates temporal variations in NH3 emissions from seabird guano. While the focus is on NH3 emissions, the model necessarily also treats the interaction with wash-off as far as this affects NH3. The model is validated using NH3 emissions measurements from seabird colonies across a range of climates, from sub-polar to tropical. In simulations for hourly time-resolved data, the model is able to capture the observed dependence of NH3 emission on environmental variables. With temperature and wind speed having the greatest effects on emission for the cases considered. In comparison with empirical data, the percentage of excreted nitrogen that volatilizes as NH3 is found to range from 2% to 67% (based on measurements), with the GUANO model providing a range of 2%–82%. The model provides a tool that can be used to investigate the meteorological dependence of NH3 emissions from seabird guano and provides a starting point to refine models of NH3 emissions from other sources.

International audience; Over the past two decades, the development of methods for visualizing and analysing specimens digitally, in three and even four dimensions, has transformed the study of living and fossil organisms. However, the initial promise that the widespread application of such methods would facilitate access to the underlying digital data has not been fully achieved. The underlying datasets for many published studies are not readily or freely available, introducing a barrier to verification and reproducibility, and the reuse of data. There is no current agreement or policy on the amount and type of data that should be made available alongside studies that use, and in some cases are wholly reliant on, digital morphology. Here, we propose a set of recommendations for minimum standards and additional best practice for three-dimensional digital data publication, and review the issues around data storage, management and accessibility.

Significance DNA damage can be a potent block to replication. One pathway to bypass damage is translesion synthesis (TLS) by specialized DNA polymerases. These conserved TLS polymerases have higher error rates than replicative polymerases, requiring careful regulation of polymerase exchange. By reconstituting the full polymerase exchange reaction at the single-molecule level, we show how distinct sets of binding sites on the β processivity clamp regulate exchange between the Escherichia coli replicative polymerase (Pol) III and the TLS Pol IV. At low concentrations, Pol IV binds β in an inactive binding mode, promoting rapid bypass of a cognate DNA lesion, whereas at high concentrations (corresponding to SOS damage response levels), association at a low-affinity sites facilitates Pol III displacement.

Wet deposition of nitrogen (N) occurs in oxidized (nitrate) and reduced (ammonium) forms. Whether one form drives vegetation change more than the other is widely debated, as field evidence has been lacking. We are manipulating N form in wet deposition to an ombrotrophic bog, Whim (Scottish Borders), and here report nine years of results. Ammonium and nitrate were provided in rainwater spray as NH4 Cl or NaNO3 at 8, 24 or 56 kg N ha(-1) yr(-1) , plus a rainwater only control, via an automated system coupled to site meteorology. Detrimental N effects were observed in sensitive nonvascular plant species, with higher cumulative N loads leading to more damage at lower annual doses. Cover responses to N addition, both in relation to form and dose, were species specific and mostly dependent on N dose. Some species were generally indifferent to N form and dose, while others were dose sensitive. Calluna vulgaris showed a preference for higher N doses as ammonium N and Hypnum jutlandicum for nitrate N. However, after 9 years, the magnitude of change from wet deposited N on overall species cover is small, indicating only a slow decline in key species. Nitrogen treatment effects on soil N availability were likewise small and rarely correlated with species cover. Ammonium caused most N accumulation and damage to sensitive species at lower N loads, but toxic effects also occurred with nitrate. However, because different species respond differently to N form, setting of ecosystem level critical loads by N form is challenging. We recommend implementing the lowest value of the critical load range where communities include sensitive nonvascular plants and where ammonium dominates wet deposition chemistry. In the context of parallel assessment at the same site, N treatments for wet deposition showed overall much smaller effects than corresponding inputs of dry deposition as ammonia.

A new species of Medullosan ovule from the Mazon Creek Carboniferous lagerstatte is documented using a novel combination of non-invasive X-Ray Micro-Tomography (XMT) and orientated precision sectioning based on the XMT results. 3-D reconstruction of the ovule has correlated geometries of different layers with tissue characteristics gathered from wafered sections, with the methodological combination presenting a virtual reconstruction of the specimen and also enabling positioning of serial sections of the holotype in pre-determined positions. Stephanospermum braidwoodensis sp. nov. has four longitudinally orientated sarcotestal wings, two to each side of the major plane that demonstrate 180° rotational (bilateral) symmetry, while the sclerotesta has three prominent longitudinal commissural ribs and the pollen chamber has three small ribs and triangular nucellar beak, both demonstrating radial (threefold) symmetry. This demonstration of both radial and bilateral symmetries in different tissues emphasises the complexities of inferring systematic affinities of fossil seeds from symmetry alone. We consider S. braidwoodensis to be closely related to the co-occurring S. konopeonus Drinnan et al., and postulate that it was born on a fertile truss similar to that of the latter species. Finally implications of our findings for the utility of these methods in identifying additional species from the Mazon Creek biota are discussed, and the advantages and disadvantages of different methods of nodule preparation are considered. We conclude that additional species are likely to be recognised from the Mazon Creek flora by application of the same methodologies used in this investigation.

Xylokorys chledophilia , a new arthropod with three-dimensionally preserved soft tissues, is described from the Herefordshire (Silurian) Lagerstätte of England. The head and trunk are covered by a relatively featureless ovoid carapace, which comprises a domed central part and a flange-like border. The head bears five pairs of appendages. The first is uniramous, with dorsal and ventral projections distally. Appendages two to four are biramous and each endopod terminates in two projections. Appendage five is possibly biramous. The hypostome is very long and subrectangular in outline. There are approximately 35 pairs of biramous trunk appendages. Each exopod comprises a long slender shaft bearing numerous fine filaments; each endopod comprises a ribbon-like shaft bearing paddle-like endites. Morphological comparisons and cladistic analyses of X. chledophilia indicate affinity with Vachonisia rogeri from the Lower Devonian Hunsrück Slate, within the marrellomorphs, but assignment to Marrellomorpha is provisional pending revision of other members of this clade. Xylokorys is the first ‘marrellomorph’ to be reported from the Silurian. It is interpreted as a benthic particle filter feeder, which may also have consumed prey items.

Pycnogonids (sea spiders) are marine arthropods numbering some 1,160 extant species. They are globally distributed in depths of up to 6,000 metres, and locally abundant; however, their typically delicate form and non-biomineralized cuticle has resulted in an extremely sparse fossil record that is not accepted universally. There are two opposing views of their phylogenetic position: either within Chelicerata as sister group to the euchelicerates, or as a sister taxon to all other euarthropods. The Silurian Herefordshire Konservat-Lagerstatte in England (approximately 425 million years (Myr) bp) yields exceptionally preserved three-dimensional fossils that provide unrivalled insights into the palaeobiology of a variety of invertebrates. The fossils are preserved as calcitic void in-fills in carbonate concretions within a volcaniclastic horizon, and are reconstructed digitally. Here we describe a new pycnogonid from this deposit, which is the oldest adult sea spider by approximately 35 Myr and the most completely known fossil species. The large chelate first appendage is consistent with a chelicerate affinity for the pycnogonids. Cladistic analyses place the new species near the base of the pycnogonid crown group, implying that the latter had arisen by the Silurian period.

A small, non–biomineralized, macrophagous arthropod with chelicerate affinities, Offacolus kingi gen. et sp. nov., from the Silurian (Wenlock Series) of Herefordshire, UK, is described. The dorsal exoskeleton comprises an arch–like cephalic shield, a thorax of three free tergites and a triangular posterior tagma of five fused tergites, the last with a stout postero–dorsally directed medial spine. Seven pairs of appendages beneath the cephalic shield surround a postero–medially sited oral cavity on the ventral surface of the head. Appendages I and, probably, II are uniramous and project antero–ventrally; I was sensory and II sensory and7sol;or ambulatory. Appendages III VI are biramous, each with an antero–ventrally projecting ramus and a robust, highly geniculate, hdorizontally oriented ramus that projects through an anterior gape.The former rami were ambulatory and the latter have spinose terminal podomeres and functioned as a unit for trapping food and transferring it towards the oral cavity. Appendage VII, which is probably uniramous, is posteroventrally directed and flap like. Each tergite of the thorax and posterior tagma covers at least a pair (probably two pairs) of probably biramous appendages with each ramus flap like and setose.

Ostracod crustaceans are the most abundant fossil arthropods. The Silurian Pauline avibella gen. et sp. nov., from the Herefordshire Lagerstätte, UK, is an extremely rare Palaeozoic example with soft-part preservation. Based on its soft-part morphology, especially the exceptionally preserved limbs and presence of lateral eyes, it is assigned to the myodocopid myodocopes. The ostracod is very large, with an epipod on the fifth limb pair, as well as gills implying the presence of a heart and an integrated respiratory–circulatory system as in living cylindroleberidid myodocopids. Features of its shell morphology, however, recall halocyprid myodocopes and palaeocopes, encouraging caution in classifying ostracods based on the carapace alone and querying the interpretation of their shell-based fossil record, especially for the Palaeozoic, where some 500 genera are presently assigned to the Palaeocopida.

A new arthropod with three-dimensionally preserved soft parts, Tanazios dokeron , is described from the Wenlock Series (Silurian) of Herefordshire, England, UK. Serial grinding, digital photographic and computer rendering techniques yielded ‘virtual fossils’ in the round for study. The body tagmata of T. dokeron comprise a head shield and a long trunk. The head shield bears six pairs of horn-like spines and the head bears five pairs of appendages. The antennule, antenna and mandible are all uniramous, and the mandible includes a gnathobasic coxa. Appendages four and five are biramous and similar to those of the trunk: each comprises a limb base with an endite, an enditic membrane, and two epipodites, plus an endopod and exopod. The hypostome bears a large cone-like projection centrally, and there may be a short labrum. The trunk has some 64 segments and at least 60 appendage pairs. A very small telson has the anus sited ventrally in its posterior part and also bears a caudal furca. Comparative morphological and cladistic analyses of T. dokeron indicate a crustacean affinity, with a probable position in the eucrustacean stem group. As such the epipodites in T. dokeron are the first recorded in a eucrustacean stem taxon. The new species is interpreted as a benthic or nektobenthic scavenger.

An exceptionally well-preserved ostracode from the Silurian of Herefordshire, United Kingdom, provides a rare view of the fossilized soft-part anatomy of this important group of living crustaceans and confirms that Ostracoda were extant in the Paleozoic. The fossil has striking similarity to the extant myodocopid family Cylindroleberididae, to which it is assigned, and demonstrates remarkable evolutionary stasis over 425 million years. The fossil is identified as a male on the basis of its copulatory organ.

The chemical breakdown of marine derived reactive nitrogen transported to the land as seabird guano represents a significant source of ammonia (NH3) in areas far from other NH3 sources. Measurements made at tropical and temperate seabird colonies indicate substantial NH3 emissions, with emission rates larger than many anthropogenic point sources. However, several studies indicate that thermodynamic processes limit the amount of NH3 emitted from guano, suggesting that the percentage of guano volatilizing as NH3 may be considerably lower in colder climates. This study undertook high resolution temporal ammonia measurements in the field and coupled results with modelling to estimate NH3 emissions at a temperate puffin colony and two sub-polar penguin colonies (Signy Island, South Orkney Islands and Bird Island, South Georgia) during the breeding season. These emission rates are then compared with NH3 volatilization rates from other climates. Ammonia emissions were calculated using a Lagrangian atmospheric dispersion model, resulting in mean emissions of 5 μg m−2 s−1 at the Isle of May, 12 μg m−2 s−1 at Signy Island and 9 μg m−2 s−1 at Bird Island. The estimated percentage of total guano nitrogen volatilized was 5% on the Isle of May, 3% on Signy and 2% on Bird Island. These values are much smaller than the percentage of guano nitrogen volatilized in tropical contexts (31–65%). The study confirmed temperature, wind speed and water availability have a significant influence on the magnitude of NH3 emissions, which has implications for reactive nitrogen in both modern remote regions and pre-industrial atmospheric composition and ecosystem interactions.

Piper (1) offers the fascinating observation that the attachment of small arthropods by threads to the Silurian arthropod Aquilonifer (2) is similar to that of the nymphs of Uropodina mites to larger arthropods (e.g., beetles) to facilitate their dispersal in patchy habitats (phoresy). Clearly these two examples are profoundly separated by time (∼430 Mya) and ecology (the one fully marine, the other terrestrial), but it is worth considering the possibility that the adherence of tiny arthropods to Aquilonifer represents the behavior of some sort of marine mite ancestor. The oldest unequivocal fossil mites are from the Lower Devonian … [↵][1]1To whom correspondence should be addressed. Email: derek.briggs{at}yale.edu. [1]: #xref-corresp-1-1

Examples of dynamic polymerase exchange have been previously characterized in model systems provided by coliphages T4 and T7. Using a dominant negative D403E polymerase (Pol) III α that can form initiation complexes and sequester primer termini but not elongate, we investigated the possibility of exchange at the Escherichia coli replication fork on a rolling circle template. Unlike other systems, addition of polymerase alone did not lead to exchange. Only when D403E Pol III was bound to a τ-containing DnaX complex did exchange occur. In contrast, addition of Pol IV led to rapid exchange in the absence of bound DnaX complex. Examination of Pol III* with varying composition of τ or the alternative shorter dnaX translation product γ showed that τ-, τ2-, or τ3-DnaX complexes supported equivalent levels of synthesis, identical Okazaki fragment size, and gaps between fragments, possessed the ability to challenge pre-established replication forks, and displayed equivalent susceptibility to challenge by exogenous D403E Pol III*. These findings reveal that redundant interactions at the replication fork must stabilize complexes containing only one τ. Previously, it was thought that at least two τs in the trimeric DnaX complex were required to couple the leading and lagging strand polymerases at the replication fork. Possible mechanisms of exchange are discussed.

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).

A fossil of an aplacophoran from the Silurian of Herefordshire, England, is shown to have armour plating, supporting recent studies that have allied the worm-like, shell-less Aplacophora with the multi-shelled Polyplacophora, or chitons. The interrelationships of the Mollusca — one of the most diverse and species-rich animal phyla — have been contentious. Recent molecular work has allied the wormlike, shell-less Aplacophora with the multi-shelled Polyplacophora, or chitons. This is now corroborated with fossil evidence: the fossil of an aplacophoran from the Silurian of Herefordshire displays armour plating, suggesting a close link with chitons. The Mollusca is one of the most diverse, important and well-studied invertebrate phyla; however, relationships among major molluscan taxa have long been a subject of controversy1,2,3,4,5,6,7,8,9. In particular, the position of the shell-less vermiform Aplacophora and its relationship to the better-known Polyplacophora (chitons) have been problematic: Aplacophora has been treated as a paraphyletic or monophyletic group at the base of the Mollusca3,6,8, proximate to other derived clades such as Cephalopoda2,3,10, or as sister group to the Polyplacophora, forming the clade Aculifera1,5,7,11,12. Resolution of this debate is required to allow the evolutionary origins of Mollusca to be reconstructed with confidence. Recent fossil finds13,14,15,16 support the Aculifera hypothesis, demonstrating that the Palaeozoic-era palaeoloricate ‘chitons’ included taxa combining certain polyplacophoran and aplacophoran characteristics5. However, fossils combining an unambiguously aplacophoran-like body with chiton-like valves have remained elusive. Here we describe such a fossil, Kulindroplax perissokomos gen. et sp. nov., from the Herefordshire Lagerstatte17,18 (about 425 million years bp), a Silurian deposit preserving a marine biota18 in unusual three-dimensional detail. The specimen is reconstructed three-dimensionally through physical–optical tomography19. Phylogenetic analysis indicates that this and many other palaeoloricate chitons are crown-group aplacophorans.

The preservation of polygonal imprints of epithelial cells in acrotretoid brachiopods is reviewed and supplemented by new data from the Cambrian of southern Great Britain. The imprints are confirmed as representing moulds of epithelial cells rather than an artefact of microstructure or preserved soft tissues, as they are (1) recorded in most taxa reviewed, (2) best preserved in areas where the shell has been thickened and (3) similar in size to cells recorded in Lingula, the closest living relative to the now extinct acrotretoids. Analysis of the morphology and sizes of epithelial cell moulds demonstrates that there is no consistent relationship between cell width and valve size, and that epithelial cells are not a useful taxonomic character within this group.

Summary The ATP-bound form of the Escherichia coli DnaA protein binds ‘DnaA boxes’ present in the origin of replication (oriC) and operator sites of several genes, including dnaA, to co-ordinate their transcription with initiation of replication. The Hda protein, together with the β sliding clamp, stimulates the ATPase activity of DnaA via a process termed regulatory inactivation of DnaA (RIDA), to regulate the activity of DnaA in DNA replication. Here, we used the mutant dnaN159 strain, which expresses the β159 clamp protein, to gain insight into how the actions of Hda are co-ordinated with replication. Elevated expression of Hda impeded growth of the dnaN159 strain in a Pol II- and Pol IV-dependent manner, suggesting a role for Hda managing the actions of these Pols. In a wild-type strain, elevated levels of Hda conferred sensitivity to nitrofurazone, and suppressed the frequency of −1 frameshift mutations characteristic of Pol IV, while loss of hda conferred cold sensitivity. Using the dnaN159 strain, we identified 24 novel hda alleles, four of which supported E. coli viability despite their RIDA defect. Taken together, these findings suggest that although one or more Hda functions are essential for cell viability, RIDA may be dispensable.

The palaeoloricate ‘polyplacophorans’ are an extinct paraphyletic group of basal chiton-like organisms known primarily from their fossilized valves. Their phylogenetic placement remains contentious, but they are likely to include both stem-group Polyplacophora and stem-group Aplacophora. Candidates for the latter position include ‘Helminthochiton’thraivensis from the Ordovician of Scotland, which we redescribe here through a combined optical and micro-CT (XMT) restudy of the type material. The 11 specimens in the type series are all articulated, presenting partial or complete valve series as well as mouldic preservation of the girdle armature; they demonstrate a vermiform body plan. The valves are typically palaeoloricate in aspect, but differ in detail from all existing palaeoloricate genera; we hence erect Phthipodochiton gen. nov. to contain the species. The most notable feature of the fossils is the spicular girdle; this is impersistently preserved, but demonstrably wraps entirely around the ventral surface of the animal, implying that a ‘true’ (i.e. polyplacophoran like) foot was absent, although we do not exclude the possibility of a narrow solenogastre-like median pedal groove having been present. Phthipodochiton thraivensis presents an apparent mosaic of aplacophoran and polyplacophoran features and as such will inform our understanding of the relationship between these groups of extant molluscs. An inference may also be drawn that at least some other palaeoloricates possessed an ‘armoured aplacophoran’ body plan, in contrast to the ‘limpet-like’ body plan of extant Polyplacophora.

Although the effects of atmospheric nitrogen deposition on species composition are relatively well known, the roles of the different forms of nitrogen, in particular gaseous ammonia (NH3), have not been tested in the field. Since 2002, we have manipulated the form of N deposition to an ombrotrophic bog, Whim, on deep peat in southern Scotland, with low ambient N (wet + dry = 8 kg N ha 1 yr 1) and S (4 kg S ha 1 yr 1) deposition. A gradient of ammonia (NH3, dry N), from 70 kg N ha 1 yr 1 down to background, 3–4 kg N ha 1 yr 1 was generated by free air release. Wet ammonium (NH4 +, wet N) was provided to replicate plots in a fine rainwater spray (NH4Cl at +8, +24, +56 kg N ha 1 yr 1). Automated treatments are coupled to meteorological conditions, in a globally unique, field experiment. Ammonia concentrations were converted to NH3-N deposition (kg N ha 1) using a site/vegetation specific parameterization. Within 3 years, exposure to relatively modest deposition of NH3, 20–56 kg NH3-N ha 1 yr 1 led to dramatic reductions in species cover, with almost total loss of Calluna vulgaris, Sphagnum capillifolium and Cladonia portentosa. These effects appear to result from direct foliar uptake and interaction with abiotic and biotic stresses, rather than via effects on the soil. Additional wet N by contrast, significantly increased Calluna cover after 5 years at the 56 kg N dose, but reduced cover of Sphagnum and Cladonia. Cover reductions caused by wet N were significantly different from and much smaller than those caused by equivalent dry N doses. The effects of gaseous NH3 described here, highlight the potential for ammonia to destroy acid heathland and peat bog ecosystems. Separating the effects of gaseous ammonia and wet ammonium deposition, for a peat bog, has significant implications for regulatory bodies and conservation agencies

1. Atmospheric ammonia (NH3) is one of the main drivers for ecosystem changes world-wide, including biodiversity loss. Modelling its deposition to evaluate its impact on ecosystems has been the focus of many studies. For that, universal indicators are needed to determine and compare the early effects of NH3 across ecosystems. 2. We evaluate the effects of atmospheric NH3 in ecosystems using lichens, which are one of the most sensitive communities at the ecosystem level. Rather than measuring total diversity, we use a functional diversity approach because this is potentially a more universal tool. 3. We evaluated the spatial and temporal patterns of atmospheric NH3 concentrations ([NH3]atm) emitted from a point-source over a 1-year period in a cork oak Mediterranean woodland. We observed a temporal pattern of [NH3]atm, with maximum concentrations during autumn. 4. The distribution of lichen species was c. 90% explained by [NH3]atm. The tolerance of lichen species to atmospheric NH3, based on expert knowledge from literature, was tested for the first time against direct measurements of atmospheric NH3. Most species were well classified, with the exception of Lecanora albella and Chrysothrix candelaris, which were more tolerant than expected. Our updated lichen classification can be used to establish lichen functional groups that respond to atmospheric NH3, and these can be used in other Mediterranean countries. 5. Increasing [NH3]atm led to a complete replacement of oligotrophic by nitrophytic species within 65 m of the NH3 source. The geostatistical analysis of functional diversity variables yielded a spatial model with low non-spatial variance, indicating that these variables can cope robustly with high spatial variation in NH3. 6. Synthesis and applications. Our results support the use of functional diversity variables, such as a lichen diversity value, as accurate and robust indicators of the effects of atmospheric NH3 on ecosystems. The spatial modelling of these indicators can provide information with high spatial resolution about the effects of atmospheric NH3 around point- and diffuse sources. As this methodology is based on functional groups, it can be applied to monitor both the impact of atmospheric NH3 and the success of mitigation strategies.

Background The SOS response is a conserved response to DNA damage that is found in Gram negative and Gram-positive bacteria. When DNA damage is sustained and severe, activation of error-prone DNA polymerases can induce a higher mutation rate then normally observed, which is called the mutator phenotype or hypermutation. We previously showed that zinc blocked the hypermutation response induced by quinolone antibiotics and mitomycin C in E. coli and Klebsiella pneumoniae (Bunnell BE, Escobar JF, Bair KL, Sutton MD, Crane JK (2017). Zinc blocks SOS-induced antibiotic resistance via inhibition of RecA in Escherichia coli. PLoS ONE 12(5): e0178303. https://doi.org/10.1371/journal.pone.0178303.) In addition to causing copying errors in DNA replication, Beaber et al. showed that induction of the SOS response increased the frequency of horizontal gene transfer into Vibrio cholerae, an organism naturally competent at uptake of extracellular DNA. (Beaber JW, Hochhut B, Waldor MK. 2003. SOS response promotes horizontal dissemination of antibiotic resistance genes. Nature 427:72–74.) Methods. In this study, we tested whether induction of the SOS response could induce transfer of antibiotic resistance from Enterobacter cloacae into E. coli, and whether zinc could inhibit that inter-species transfer of antibiotic resistance. Results. Ciprofloxacin, an inducer of the SOS response, increased the rate of transfer of an extended spectrum β-lactamase (ESBL) gene from Enterobacter into a susceptible E. coli strain. Zinc blocked SOS-induced horizontal transfer of §-lactamase into E. coli. Other divalent metals, such as iron and manganese, failed to inhibit these responses. Conclusion. In vitro assays showed that zinc blocked the ability of RecA to bind to ssDNA, an early step in the SOS response, suggesting the mechanism by which zinc blocks the SOS response. Disclosures All authors: No reported disclosures.

Ostracod crustaceans are diverse and ubiquitous in aqueous environments today but relatively few known species have gills. Ostracods are the most abundant fossil arthropods but examples of soft-part preservation, especially of gills, are exceptionally rare. A new ostracod, Spiricopia aurita (Myodocopa), from the marine Silurian Herefordshire Lagerstätte (430 Mya), UK, preserves appendages, lateral eyes and gills. The respiratory system includes five pairs of gill lamellae with hypobranchial and epibranchial canals that conveyed haemolymph. A heart and associated vessels had likely evolved in ostracods by the Mid-Silurian.

Specimens of the polyplacophoran mollusk ‘ Helminthochiton ’ thraivensis Reed from the Upper Ordovician of southwest Scotland provide rare examples of complete valve series preserved in near life position, albeit as external molds. Application of high-resolution X-ray microtomography to one such specimen has revealed the exceptional preservation of its last meal, which included elements of a crinoid column, in its intestine. The interaction was either predatory or scavenging; extant chitons are not known to be crinoidivorous. This is the earliest direct record of predation or scavenging on crinoids in the fossil record. It is also the first indication that the broad axial canal of primitive crinoids may have contained nutritious tissues. The predatory or scavenging habit of H. thraivensis is consistent with its inferred phylogenetic position as a stem-group aplacophoran and provides new data suggesting an origin of carnivory early in the evolution of this clade.

Northern peatlands cover approximately 4% of the global land surface area. Those peatlands will be particularly vulnerable to environmental and climate change and therefore it is important to investigate their total greenhouse gas (GHG) budgets, to determine the feedback on the climate. Nitrogen (N) is known to influence the GHG budget in particular by affecting the methane (CH(4)) balance. At two peatland sites in Scotland and Finland GHG fluxes of carbon dioxide (CO(2)), methane and nitrous oxide (N(2)O) and nitrogen fluxes were measured as part of the European project 'NitroEurope'. The Scottish site, Auchencorth Moss, was a GHG sink of -321, -490 and -321 g CO(2) eq m(-2) year(-1) in 2006, 2007 and 2008, respectively, with CO(2) as the dominating GHG. In contrast, the dominating GHG at the Finnish site, Lompolojankka, was CH(4), resulting in the site being a net GHG source of +485 and +431 g CO(2) eq m(-2) year(-1) in 2006 and 2007, respectively. Therefore. Auchencorth Moss had a negative global warming potential (GWP) whilst Lompolojankka had a positive GWP over the investigated time period. Initial results yielded a positive N budget for Lompolojankka of 7.1 kg N ha(-1) year(-1), meaning the site was gaining nitrogen, and a negative N budget for Auchencorth Moss of -2.4 kg N ha year(-1), meaning the site was losing nitrogen.

Schemm-Gregory, M. & Sutton, M. 2010: First report of brachiopod–brachiopod endoparasitism. Lethaia, Vol. 43, pp. 111–115. The first example of brachiopod–brachiopod endoparasitism is reported from the Lower Devonian of China. Three-dimensional reconstructions following serial sectioning show a specimen of a strophomenide (Dicoelostrophia sp.) within an articulated shell of the spiriferide Rostrospirifer tonkinensis; morphological modifications of the host and the positioning of the strophomenide with respect to the inhalant current demonstrate the in vivo nature of the association. The symbiosis is interpreted as parasitic; it appears to be facultative but demonstrates the viability of this mode of life, expanding the ecological range known to be exploitable by the Brachiopoda. □3-D reconstruction, Brachiopoda, Dicoelostrophia, endoparasitism, Lower Devonian, Rostrospirifer.

DNA synthesis is catalyzed by an ensemble of proteins designated the replicase. The efficient assembly of this multi-protein complex is essential for the continuity of DNA replication and is mediated by clamp-loading accessory proteins that use ATP binding and hydrolysis to coordinate these events. As a consequence, the ability to selectively inhibit the activity of these accessory proteins provides a rational approach to regulate DNA synthesis. Toward this goal, we tested the ability of several non-natural nucleotides to inhibit ATP-dependent enzymes associated with DNA replicase assembly. Kinetic and biophysical studies identified 5-nitro-indolyl-2'-deoxyribose-5'-triphosphate as a unique non-natural nucleotide capable of selectively inhibiting the bacteriophage T4 clamp loader versus the homologous enzyme from Escherichia coli. Modeling studies highlight the structural diversity between the ATP-binding site of each enzyme and provide a mechanism accounting for the differences in potencies for various substituted indolyl-2'-deoxyribose-5'-triphosphates. An in vivo assay measuring plaque formation demonstrates the efficacy and selectivity of 5-nitro-indolyl-2'-deoxyribose as a cytostatic agent against T4 bacteriophage while leaving viability of the E. coli host unaffected. This strategy provides a novel approach to develop agents that selectively inhibit ATP-dependent enzymes that are required for efficient DNA replication.

Fossil carpoids possess a unique anatomy that is difficult to interpret; as a result, there are a number of competing phylogenetic hypotheses for carpoid taxa. Stratigraphic congruence indices provide a quantitative means of evaluating alternative cladograms where character coding is contentious; trees that show a statistically significant fit between stratigraphy and phylogeny are better supported by the fossil record. We here test the agreement between stratigraphic and cladistic data for 27 carpoid cladograms (24 have previously been published, three are novel). The results demonstrate that in analyses of subsets of carpoid taxa, the stratigraphic congruence of trees is not strongly affected by the interpretative model followed. However, when studying the relationships of carpoids with other deuterostomes, assuming that carpoids should be interpreted by reference to chordates/hemichordates (rather than echinoderms) leads to a poorer fit with the known stratigraphic ranges of taxa. Thus, the disputed calcichordate hypothesis (carpoids interpreted as stem and crown-group chordates and stem-group hemichordates) is much less congruent with stratigraphy than alternative models interpreting carpoids as stem or crown-group echinoderms.

Sliding clamp proteins topologically encircle DNA and play vital roles in coordinating the actions of various DNA replication, repair, and damage tolerance proteins. At least three distinct surfaces of the Escherichia coli beta clamp interact physically with the DNA that it topologically encircles. We utilized mutant beta clamp proteins bearing G66E and G174A substitutions (beta159), affecting the single-stranded DNA-binding region, or poly-Ala substitutions in place of residues 148-HQDVR-152 (beta(148-152)), affecting the double-stranded DNA binding region, to determine the biological relevance of clamp-DNA interactions. As part of this work, we solved the X-ray crystal structure of beta(148-152), which verified that the poly-Ala substitutions failed to significantly alter the tertiary structure of the clamp. Based on functional assays, both beta159 and beta(148-152) were impaired for loading and retention on a linear primed DNA in vitro. In the case of beta(148-152), this defect was not due to altered interactions with the DnaX clamp loader, but rather was the result of impaired beta(148-152)-DNA interactions. Once loaded, beta(148-152) was proficient for DNA polymerase III (Pol III) replication in vitro. In contrast, beta(148-152) was severely impaired for Pol II and Pol IV replication and was similarly impaired for direct physical interactions with these Pols. Despite its ability to support Pol III replication in vitro, beta(148-152) was unable to support viability of E. coli. Nevertheless, physiological levels of beta(148-152) expressed from a plasmid efficiently complemented the temperature-sensitive growth phenotype of a strain expressing beta159 (dnaN159), provided that Pol II and Pol IV were inactivated. Although this strain was impaired for Pol V-dependent mutagenesis, inactivation of Pol II and Pol IV restored the Pol V mutator phenotype. Taken together, these results support a model in which a sophisticated combination of competitive clamp-DNA, clamp-partner, and partner-DNA interactions serve to manage the actions of the different E. coli Pols in vivo.