Diversity and evolutionary history of lettuce necrotic yellows virus in Australia and New Zealand

Lettuce necrotic yellows virus (LNYV) is the type member of the genus Cytorhabdovirus, family Rhabdoviridae, and causes a severe disease of lettuce (Lactuca sativa L.). This virus has been described as endemic to Australia and New Zealand, with sporadic reports of a similar virus in Europe. Genetic variability studies of plant-infecting rhabdoviruses are scarce. We have extended a previous study on the variability of the LNYV nucleocapsid gene, comparing sequences from isolates sampled from both Australia and New Zealand, as well as analysing symptom expression on Nicotiana glutinosa. Phylogenetic and BEAST analyses confirm separation of LNYV isolates into two subgroups (I and II) and suggest that subgroup I is slightly older than subgroup II. No correlation was observed between isolate subgroup and disease symptoms on N. glutinosa. The origin of LNYV remains unclear; LNYV may have moved between native and weed hosts within Australia or New Zealand before infecting lettuce or may have appeared as a result of at least two incursions, with the first coinciding with the beginning of European agriculture in the region. The apparent extinction of subgroup I in Australia may have been due to less-efficient dispersal than that which has occurred for subgroup II – possibly a consequence of suboptimal interactions with plant and/or insect hosts. Introduction of subgroup II to New Zealand appears to be more recent. More-detailed epidemiological studies using molecular tools are needed to fully understand how LNYV interacts with its hosts and to determine where the virus originated

Succinate, iron chelation, and monovalent cations affect the transformation efficiency of Acinetobacter baylyi strain ATCC33305 during growth in complex media

Natural transformation is the acquisition of new genetic material via the uptake of exogenous DNA by competent bacteria. Acinetobacter baylyi is model for natural transformation. Here we focus on natural transformation of A. baylyi strain ATCC33305 grown in complex media and seek environmental conditions that appreciably affect transformation efficiency. We find that the transformation efficiency for A. baylyi is a resilient characteristic that remains high under most conditions tested. We do find several distinct conditions that alter natural transformation efficiency including addition of succinate, Fe2+ (ferrous) iron chelation, and substitution of sodium ions with potassium ones. These distinct conditions could be useful as control knobs for researchers using A. baylyi as a model organism to study natural transformation.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

The role of core and accessory type IV pilus genes in natural transformation and twitching motility in the bacterium Acinetobacter baylyi.

Here we present an examination of type IV pilus genes associated with competence and twitching in the bacterium Acinetobacter baylyi (strain ADP1, BD413). We used bioinformatics to identify potential competence and twitching genes and their operons. We measured the competence and twitching phenotypes of the bioinformatically-identified genes. These results demonstrate that competence and twitching in A. baylyi both rely upon a core of the same type IV pilus proteins. The core includes the inner membrane assembly platform (PilC), a periplasmic assemblage connecting the inner membrane assembly platform to the secretin (ComM), a secretin (ComQ) and its associated pilotin (PilF) that assists with secretin assembly and localization, both cytoplasmic pilus retraction ATPases (PilU, PilT), and pilins (ComP, ComB, PilX). Proteins not needed for both competence and twitching are instead found to specialize in either of the two traits. The pilins are varied in their specialization with some required for either competence (FimT) and others for twitching (ComE). The protein that transports DNA across the inner membrane (ComA) specializes in competence, while signal transduction proteins (PilG, PilS, and PilR) specialize in twitching. Taken together our results suggest that the function of accessory proteins should not be based on homology alone. In addition the results suggest that in A. baylyi the mechanisms of natural transformation and twitching are mediated by the same set of core Type IV pilus proteins with distinct specialized proteins required for each phenotype. Finally, since competence requires multiple pilins as well as both pilus retraction motors PilU and PilT, this suggests that A. baylyi employs a pilus in natural transformation

Reactive design patterns

<p><b>Twitching zones on (a) soft vs. (b) hard agar for multiple twitching phenotypes.</b> On soft agar (0.5%) in panel (a), mutants <i>fimU</i> and <i>comA</i> twitch a comparable amount to the wildtype, while <i>comP</i> and <i>comE</i> are substantially impaired in agreement with <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182139#pone.0182139.g003" target="_blank">Fig 3</a>. Panel (b) shows the same mutants but now on hard agar (1.5%). In this case all diameters are comparable.</p

Determination of N7-glycidamide guanine adducts in human blood DNA following exposure to dietary acrylamide using liquid chromatography/tandem mass spectrometry

RationaleAcrylamide is classified as a probable human carcinogen that is metabolised to glycidamide, which can covalently bind to DNA. The aim of this study was to investigate the formation of N7-glycidamide guanine (N7-GA-Gua) adducts in human blood DNA following exposure to acrylamide present in carbohydrate-rich foods as part of the normal human diet.MethodsLymphocyte DNA was extracted from blood samples obtained from healthy human volunteers. Following thermal depurination of the DNA samples, N7-GA-Gua adducts were quantified using a validated liquid chromatography/tandem mass spectrometry (LC/MS/MS) method incorporating a stable isotope labelled internal standard. Estimated dietary acrylamide intake was recorded by completion of food frequency questionnaires for the 24 hours prior to volunteer blood donation.ResultsAn LC/MS/MS method was validated with a limit of detection of 0.25 fmol and a lower limit of quantitation of 0.50 fmol on column. N7-GA-Gua adducts were detected in human blood DNA with the levels ranging between 0.3 to 6.3 adducts per 108 nucleotides. The acrylamide intake was calculated from the food frequency questionnaires ranging between 20.0 and 78.6 μg.ConclusionsIdentification and quantification of N7-GA-Gua adducts in the blood DNA of healthy volunteers suggests that dietary acrylamide exposure may lead to the formation of DNA adducts. This important finding warrants further investigation to ascertain a correlation between environmental/dietary acrylamide exposure and levels of DNA adducts.</div

Alignment of FimU and FimT pilins from ADP1.

<p>A. The length of the primary sequence is indicated above with Pfam motifs found in both proteins diagrammed below. N = PF07963.11; GspH = PF12019.7. Such motifs are identified using multiple sequence alignments. B. Pairwise alignment of FimU and FimT. Identical amino acids are indicated by a vertical line connecting them while: and. represent higher and lower degrees of chemical similarity between the two amino acids, respectively. Boldface amino acids are part of the Pfam motifs diagrammed in A.</p

Competence and twitching phenotypes of null mutations.

<p>All data in this figure were taken using complex media and incubating at 37°C. Both competence and twitching assays were performed on agar: 1.5% for competence and 0.5% for twitching. Color scheme is the same as <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182139#pone.0182139.g001" target="_blank">Fig 1</a>. Like symbols indicate that genes are part of the same operon. All data points contain multiple measurements for both competence and twitching. Error bars represent the standard deviation of multiple measurements. For the x-axis standard deviation is given by where x = log and ΔTE is defined as the standard deviation from the mean transformation efficiency, . The detection limit for competence is 10⁻⁹ and for twitching is 0.4. Data points that fall below either detection limit appear on the graph in a “below detection limit” region. Their position within this region has no physical interpretation beyond indicating that they fall below this limit.</p

Model of the ADP1 type IV pilus with associated competence and signal transduction proteins.

<p>Components of the model are predicted by homology from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182139#pone.0182139.t001" target="_blank">Table 1</a> and are supported by data in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182139#pone.0182139.g003" target="_blank">Fig 3</a>.</p