Efficacy of a new carvacrol-based product on Campylobacter jejuni in challenge test in vivo and impact on the whole caecal microbiota

Efficacy of a new carvacrol-based product on Campylobacter jejuni in challenge test in vivo and impact on the whole caecal microbiota. 6. International Conference on Poultry Intestinal Healt

Monomeric PcrA helicase processively unwinds plasmid lengths of DNA in the presence of the initiator protein RepD

The helicase PcrA unwinds DNA during asymmetric replication of plasmids, acting with an initiator protein, in our case RepD. Detailed kinetics of PcrA activity were measured using bulk solution and a single-molecule imaging technique to investigate the oligomeric state of the active helicase complex, its processivity and the mechanism of unwinding. By tethering either DNA or PcrA to a microscope coverslip surface, unwinding of both linear and natural circular plasmid DNA by PcrA/RepD was followed in real-time using total internal reflection fluorescence microscopy. Visualization was achieved using a fluorescent single-stranded DNA-binding protein. The single-molecule data show that PcrA, in combination with RepD, can unwind plasmid lengths of DNA in a single run, and that PcrA is active as a monomer. Although the average rate of unwinding was similar in single-molecule and bulk solution assays, the single-molecule experiments revealed a wide distribution of unwinding speeds by different molecules. The average rate of unwinding was several-fold slower than the PcrA translocation rate on single-stranded DNA, suggesting that DNA unwinding may proceed via a partially passive mechanism. However, the fastest dsDNA unwinding rates measured in the single-molecule unwinding assays approached the PcrA translocation speed measured on ssDNA

DNA cruciform arms nucleate through a correlated but non-synchronous cooperative mechanism

Inverted repeat (IR) sequences in DNA can form non-canonical cruciform structures to relieve torsional stress. We use Monte Carlo simulations of a recently developed coarse-grained model of DNA to demonstrate that the nucleation of a cruciform can proceed through a cooperative mechanism. Firstly, a twist-induced denaturation bubble must diffuse so that its midpoint is near the centre of symmetry of the IR sequence. Secondly, bubble fluctuations must be large enough to allow one of the arms to form a small number of hairpin bonds. Once the first arm is partially formed, the second arm can rapidly grow to a similar size. Because bubbles can twist back on themselves, they need considerably fewer bases to resolve torsional stress than the final cruciform state does. The initially stabilised cruciform therefore continues to grow, which typically proceeds synchronously, reminiscent of the S-type mechanism of cruciform formation. By using umbrella sampling techniques we calculate, for different temperatures and superhelical densities, the free energy as a function of the number of bonds in each cruciform along the correlated but non-synchronous nucleation pathways we observed in direct simulations.Comment: 12 pages main paper + 11 pages supplementary dat

Λ\LambdaCDM not dead yet: massive high-z Balmer break galaxies are less common than previously reported

Early JWST observations that targeted so-called double-break sources (attributed to Lyman and Balmer breaks at $z>7$), reported a previously unknown population of very massive, evolved high-redshift galaxies. This surprising discovery led to a flurry of attempts to explain these objects' unexpected existence including invoking alternatives to the standard $\Lambda$CDM cosmological paradigm. To test these early results, we adopted the same double-break candidate galaxy selection criteria to search for such objects in the JWST images of the CAnadian NIRISS Unbiased Cluster Survey (CANUCS), and found a sample of 19 sources over five independent CANUCS fields that cover a total effective area of $\sim60\,$arcmin$^2$ at $z\sim8$. However, (1) our SED fits do not yield exceptionally high stellar masses for our candidates, while (2) spectroscopy of five of the candidates shows that while all five are at high redshifts, their red colours are due to high-EW emission lines in star-forming galaxies rather than Balmer breaks in massive, evolved systems. Additionally, (3) field-to-field variance leads to differences of $\sim 1.5$ dex in the maximum stellar masses measured in the different fields, suggesting that the early single-field JWST observations may have suffered from cosmic variance and/or sample bias. Finally, (4) we show that the presence of even a single massive outlier can dominate conclusions from small samples such as those in early JWST observations. In conclusion, we find that the double-break sources in CANUCS are not sufficiently massive or numerous to warrant questioning the standard $\Lambda$CDM paradigm.Comment: V2: correction of display problem of Fig.1 in Chrome browser. Submitted to MNRAS, 10 pages (+4 in Appendix), 5 figures (+4), 1 table (+1

Visualizing helicases unwinding DNA at the single molecule level

DNA helicases are motor proteins that catalyze the unwinding of double-stranded DNA into single-stranded DNA using the free energy from ATP hydrolysis. Single molecule approaches enable us to address detailed mechanistic questions about how such enzymes move processively along DNA. Here, an optical method has been developed to follow the unwinding of multiple DNA molecules simultaneously in real time. This was achieved by measuring the accumulation of fluorescent single-stranded DNA-binding protein on the single-stranded DNA product of the helicase, using total internal reflection fluorescence microscopy. By immobilizing either the DNA or helicase, localized increase in fluorescence provides information about the rate of unwinding and the processivity of individual enzymes. In addition, it reveals details of the unwinding process, such as pauses and bursts of activity. The generic and versatile nature of the assay makes it applicable to a variety of DNA helicases and DNA templates. The method is an important addition to the single-molecule toolbox available for studying DNA processing enzymes

Maternal Behavior is Impaired in Female Mice Lacking Type 3 Adenylyl Cyclase

Although chemosensory signals generated by mouse pups may trigger maternal behavior of females, the mechanism for detection of these signals has not been fully defined. As some odorant receptors are coupled to the type 3 adenylyl cyclase (AC3), we evaluated the role of AC3 for maternal behavior using AC3−/− female mice. Here, we report that maternal behavior is impaired in virgin and postpartum AC3−/− mice. Female AC3−/− mice failed the pup retrieval assay, did not construct well-defined nests, and did not exhibit maternal aggression. Furthermore, AC3−/− females could not detect odorants or pup urine in the odorant habituation test and were unable to detect pups by chemoreception. In contrast to wild-type mice, AC activity in main olfactory epithelium (MOE) preparations from AC3−/− female mice was not stimulated by odorants or pheromones. Moreover, odorants and pheromones did not evoke electro-olfactogram (EOG) responses in the MOE of AC3−/− female mice. We hypothesize that the detection of chemical signals that trigger maternal behavior in female mice depends upon AC3 in the MOE

Cell Size and the Initiation of DNA Replication in Bacteria

In eukaryotes, DNA replication is coupled to the cell cycle through the actions of cyclin-dependent kinases and associated factors. In bacteria, the prevailing view, based primarily from work in Escherichia coli, is that growth-dependent accumulation of the highly conserved initiator, DnaA, triggers initiation. However, the timing of initiation is unchanged in Bacillus subtilis mutants that are ∼30% smaller than wild-type cells, indicating that achievement of a particular cell size is not obligatory for initiation. Prompted by this finding, we re-examined the link between cell size and initiation in both E. coli and B. subtilis. Although changes in DNA replication have been shown to alter both E. coli and B. subtilis cell size, the converse (the effect of cell size on DNA replication) has not been explored. Here, we report that the mechanisms responsible for coordinating DNA replication with cell size vary between these two model organisms. In contrast to B. subtilis, small E. coli mutants delayed replication initiation until they achieved the size at which wild-type cells initiate. Modest increases in DnaA alleviated the delay, supporting the view that growth-dependent accumulation of DnaA is the trigger for replication initiation in E. coli. Significantly, although small E. coli and B. subtilis cells both maintained wild-type concentration of DnaA, only the E. coli mutants failed to initiate on time. Thus, rather than the concentration, the total amount of DnaA appears to be more important for initiation timing in E. coli. The difference in behavior of the two bacteria appears to lie in the mechanisms that control the activity of DnaA

The GLEAMing of the first supermassive black holes: II. A new sample of high-redshift radio galaxy candidates

While unobscured and radio-quiet active galactic nuclei are regularly being found at redshifts $z > 6$, their obscured and radio-loud counterparts remain elusive. We build upon our successful pilot study, presenting a new sample of low-frequency-selected candidate high-redshift radio galaxies (HzRGs) over a sky area twenty times larger. We have refined our selection technique, in which we select sources with curved radio spectra between 72-231 MHz from the GaLactic and Extragalactic All-sky Murchison Widefield Array (GLEAM) survey. In combination with the requirements that our GLEAM-selected HzRG candidates have compact radio morphologies and be undetected in near-infrared $K_{\rm s}$-band imaging from the Visible and Infrared Survey Telescope for Astronomy Kilo-degree Infrared Galaxy (VIKING) survey, we find 51 new candidate HzRGs over a sky area of approximately 1200 deg$^2$. Our sample also includes two sources from the pilot study: the second-most distant radio galaxy currently known, at $z=5.55$, with another source potentially at $z \sim 8$. We present our refined selection technique and analyse the properties of the sample. We model the broadband radio spectra between 74 MHz and 9 GHz by supplementing the GLEAM data with both publicly available data and new observations from the Australia Telescope Compact Array at 5.5 and 9 GHz. In addition, deep $K_{\rm s}$-band imaging from the High-Acuity Widefield $K$-band Imager (HAWK-I) on the Very Large Telescope and from the Southern Herschel Astrophysical Terahertz Large Area Survey Regions $K_{\rm s}$-band Survey (SHARKS) is presented for five sources. We discuss the prospects of finding very distant radio galaxies in our sample, potentially within the epoch of reionisation at $z \gtrsim 6.5$.Comment: 49 pages, 3 figures (one of which is a multi-page figure with 102 separate panels), 9 tables, accepted for publication in PAS

Classification and evolutionary history of the single-strand annealing proteins, RecT, Redβ, ERF and RAD52

BACKGROUND: The DNA single-strand annealing proteins (SSAPs), such as RecT, Redβ, ERF and Rad52, function in RecA-dependent and RecA-independent DNA recombination pathways. Recently, they have been shown to form similar helical quaternary superstructures. However, despite the functional similarities between these diverse SSAPs, their actual evolutionary affinities are poorly understood. RESULTS: Using sensitive computational sequence analysis, we show that the RecT and Redβ proteins, along with several other bacterial proteins, form a distinct superfamily. The ERF and Rad52 families show no direct evolutionary relationship to these proteins and define novel superfamilies of their own. We identify several previously unknown members of each of these superfamilies and also report, for the first time, bacterial and viral homologs of Rad52. Additionally, we predict the presence of aberrant HhH modules in RAD52 that are likely to be involved in DNA-binding. Using the contextual information obtained from the analysis of gene neighborhoods, we provide evidence of the interaction of the bacterial members of each of these SSAP superfamilies with a similar set of DNA repair/recombination protein. These include different nucleases or Holliday junction resolvases, the ABC ATPase SbcC and the single-strand-binding protein. We also present evidence of independent assembly of some of the predicted operons encoding SSAPs and in situ displacement of functionally similar genes. CONCLUSIONS: There are three evolutionarily distinct superfamilies of SSAPs, namely the RecT/Redβ, ERF, and RAD52, that have different sequence conservation patterns and predicted folds. All these SSAPs appear to be primarily of bacteriophage origin and have been acquired by numerous phylogenetically distant cellular genomes. They generally occur in predicted operons encoding one or more of a set of conserved DNA recombination proteins that appear to be the principal functional partners of the SSAPs

Modern termites inherited the potential of collective construction from their common ancestor

Animal collective behaviors give rise to various spatial patterns, such as the nests of social insects. These structures are built by individuals following a simple set of rules, slightly varying within and among species, to produce a large diversity of shapes. However, little is known about the origin and evolution of the behavioral mechanisms regulating nest structures. In this study, we discuss the perspective of inferring the evolution of collective behaviors behind pattern formations using a phylogenetic framework. We review the collective behaviors that can be described by a single set of behavioral rules, and for which variations of the environmental and behavioral parameter values produce diverse patterns. We propose that this mechanism could be at the origin of the pattern diversity observed among related species, and that, when they are placed in the proper conditions, species have the behavioral potential to form patterns observed in related species. The comparative analysis of shelter tube construction by lower termites is consistent with this hypothesis. Although the use of shelter tubes in natural conditions is variable among species, most modern species have the potential to build them, suggesting that the behavioral rules for shelter tube construction evolved once in the common ancestor of modern termites. Our study emphasizes that comparative studies of behavioral rules have the potential to shed light on the evolution of collective behaviors.journal articl