Subliminal semantic priming in speech

Numerous studies have reported subliminal repetition and semantic priming in the visual modality. We transferred this paradigm to the auditory modality. Prime awareness was manipulated by a reduction of sound intensity level. Uncategorized prime words (according to a post-test) were followed by semantically related, unrelated, or repeated target words (presented without intensity reduction) and participants performed a lexical decision task (LDT). Participants with slower reaction times in the LDT showed semantic priming (faster reaction times for semantically related compared to unrelated targets) and negative repetition priming (slower reaction times for repeated compared to semantically related targets). This is the first report of semantic priming in the auditory modality without conscious categorization of the prime.     

From Local Surveys to Global Surveillance: Three High-Throughput Genotyping Methods for Epidemiological Monitoring of Xanthomonas citri pv. citri Pathotypes

Asiatic citrus canker is a major disease worldwide, and its causal agent, Xanthomonas citri pv. citri, is listed as a quarantine organism in many countries. Analysis of the molecular epidemiology of this bacterium is hindered by a lack of molecular typing techniques suitable for surveillance and outbreak investigation. We report a comparative evaluation of three typing techniques, amplified fragment length polymorphism (AFLP) analysis, insertion sequence ligation-mediated PCR (IS-LM-PCR) typing, and multilocus variable-number tandem-repeat analysis (MLVA), with 234 strains originating from Asia, the likely center of origin of the pathogen, and reference strains of pathotypes A, A*, and A^w, which differ in host range. The typing techniques were congruent in describing the diversity of this strain collection, suggesting that the evolution pattern of the bacterium may be clonal. Based on a hierarchical analysis of molecular variance, the AFLP method best described the genetic variation found among pathotypes whereas MLVA best described the variation found among individual strains from the same countries or groups of neighboring countries. IS-LM-PCR data suggested that the transposition of insertion sequences in the genome of X. citri pv. citri occurs rarely enough not to disturb the phylogenetic signal. This technique may be useful for the global surveillance of non-epidemiologically related strains. Although pathological characteristics of strains could be most often predicted from genotyping data, we report the occurrence in the Indian peninsula of strains genetically related to pathotype A* strains but with a host range similar to that of pathotype A, which makes the classification of this bacterium even more complicated.The definition of host range is a central parameter for the understanding and, ultimately, the control of infectious diseases in general and bacterial plant diseases in particular. In phytobacteriology, host range is an important aspect of pathogenicity. Control of diseases can be achieved with resistance genes which reduce host range (50, 64). Epidemiological characteristics are highly dependent on host range, and the emergence of new diseases is sometimes correlated with broadened host ranges (74). Xanthomonads have the particularity of an extremely narrow host range (sometimes reduced to a single plant genus), although a very large number of plant families can be hosts when all members of the genus are considered (33), which led plant pathologists to create the concept of pathovar at an infrasubspecific level. Pathovars were defined as groups of strains sharing several pathological characteristics, such as their host range and the disease facies they cause (18). Based on molecular data, strains classified as a single pathovar usually form a discrete monomorphic or weakly polymorphic cluster, suggesting that strains of a pathovar have a common ancestral origin (3, 56). Xanthomonas citri pv. citri is the causal agent of Asiatic canker, a severe disease infecting most commercial citrus cultivars and some genera in the Rutaceae family in many citrus-producing areas worldwide (6, 60, 61). This pathovar has two types of strains, which differ in their host ranges: pathotype A has a wide host range and a worldwide distribution and is a permanent threat for citriculture (29); in contrast, the more recently characterized pathotype A* causes citrus canker on Mexican lime (Citrus aurantifolia) and has a much less severe impact on citriculture (72). Strains of this pathotype were considered to belong to the pathovar citri because of their phenotypic and genetic relatedness to pathotype A. Their distribution was initially reported to include Saudi Arabia, Oman, Iran, and India and was recently found to extend to southeast Asia, with reports of these strains in Thailand (10) and Cambodia (11). Finally, strains genetically related to pathotypes A and A* but able to infect Mexican lime and Citrus macrophylla naturally were recently detected in Florida and classified as a pathotype designated A^w (68). The molecular basis of the specific interaction of X. citri pv. citri pathotypes A* and A^w with a restricted range of citrus hosts is not known (5). An interaction between a host resistance gene and an avr gene product from the pathogen inducing host-pathogen incompatibility has not yet been demonstrated for the X. citri pv. citri-citrus pathosystem, as it has been previously for other plant pathogenic bacteria (43).No assumption can be made about whether the apparent contemporary emergence of pathotype A* strains is due to a change in virulence or to environmental or human factors. Host range shifts have sometimes been related to modifications in the repertoire of virulence genes by horizontal gene transfer or intragenomic recombinations or mutations (20, 32, 75). A clear understanding of the evolutionary relationships among pathotypes A, A*, and A^w and of the diversity among strains of each pathotype would be helpful for assessing these issues.Due to the extreme difficulty and cost of the complete eradication of Asiatic citrus canker, several canker-threatened citrus-producing regions rely on integrated pest management strategies for control (30). Data derived from the huge effort put into the molecular typing of human bacterial pathogens (46, 63, 67, 69) suggest that an extensive knowledge of populations of plant pathogenic bacteria may improve our understanding of epidemic situations.The tools most often used for the molecular epidemiology of citrus canker have been repetitive-element-based PCR (rep-PCR) and pulsed-field gel electrophoresis (PFGE) (13, 16, 19, 28, 68). The lack of discriminatory power of rep-PCR and the high labor requirement for PFGE make it difficult to use these techniques extensively for outbreak investigations or regional or global surveillance (67). Therefore, alternative high-resolution and high-throughput molecular typing systems for X. citri pv. citri should be developed. Amplified fragment length polymorphism (AFLP) analysis of an Iranian collection of strains causing Asiatic citrus canker suggested previously that this technique has better discriminatory power than the rep-PCR method (39). AFLP has the advantage of generating a large number of randomly located markers over the whole genome. The detected polymorphism may arise from point mutations at the targeted restriction sites or from insertions and/or deletions in the amplified region (73). The determination of the complete sequence of X. citri pv. citri strain 306 (17) should facilitate the development of molecular typing tools well-suited for deciphering taxonomy, evolution, and/or epidemiology. For instance, it gave access to specific primers associated with transposable elements present in this bacterium (45), which were used for typing DNA from herbarium specimens showing canker-like symptoms and originating from different geographical origins. This technique revealed an unexpectedly high degree of genetic diversity. However, this typing scheme requires more than 50 PCRs for the full analysis of unknown DNA. A new insertion sequence ligation-mediated PCR (IS-LM-PCR) scheme (9) also revealed considerable diversity and is less labor-intensive. This technique amplifies DNA fragments between an insertion sequence element and a selected restriction site (9). We also recently developed a multilocus variable-number tandem-repeat analysis (MLVA) approach for this bacterium, a promising technique targeting tandem repeats (minisatellite-like loci) for fine-scale epidemiology with distinctive advantages, such as high discriminatory power, maximal reproducibility of results, and portability of equipment (12). The characteristics of these newly developed techniques need to be subjected to a comparative evaluation in order to determine which methods would be most useful for global surveillance and molecular epidemiology on small spatial scales. In this study, we compared the AFLP, MLVA, and IS-LM-PCR techniques to explore the genetic diversity of a collection of pathotype A, A*, and A^w strains originating from Asia. Furthermore, we sought to determine the genetic diversity and structure of X. citri pv. citri strains, including a large collection of pathotype A* strains for which no extensive characterization study is available at the moment, from the area of origin of the pathogen.     

The antiapoptotic protein AAC‐11 interacts with and regulates Acinus‐mediated DNA fragmentation

The nuclear factor Acinus has been suggested to mediate apoptotic chromatin condensation after caspase cleavage. However, this role has been challenged by recent observations suggesting a contribution of Acinus in apoptotic internucleosomal DNA cleavage. We report here that AAC‐11, a survival protein whose expression prevents apoptosis that occurs on deprivation of growth factors, physiologically binds to Acinus and prevents Acinus‐mediated DNA fragmentation. AAC‐11 was able to protect Acinus from caspase‐3 cleavage in vivo and in vitro, thus interfering with its biological function. Interestingly, AAC‐11 depletion markedly increased cellular sensitivity to anticancer drugs, whereas its expression interfered with drug‐induced cell death. AAC‐11 possesses a leucine‐zipper domain that dictates, upon oligomerization, its interaction with Acinus as well as the antiapoptotic effect of AAC‐11 on drug‐induced cell death. A cell permeable peptide that mimics the leucine‐zipper subdomain of AAC‐11, thus preventing its oligomerization, inhibited the AAC‐11–Acinus complex formation and potentiated drug‐mediated apoptosis in cancer cells. Our results, therefore, show that targeting AAC‐11 might be a potent strategy for cancer treatment by sensitization of tumour cells to chemotherapeutic drugs.     

Preventing physical interactions between parturient ewes and their neonate differentially impairs the development of maternal responsiveness and selectivity depending on maternal experience

The present study investigated whether deprivation of nursing or of any physical interaction with the lamb impairs the onset of maternal responsiveness and the establishment of selectivity in primiparous and multiparous ewes. Just after parturition, ewes could interact freely with their lamb, or could only lick their lamb but not nurse them, or could neither lick nor nurse them for the first 4 h. At 4 h, mothers were successively observed for 3 min with an alien lamb and then with their own lamb. Only 5/14 primiparous mothers accepted their own lamb following deprivation of all physical contact whereas all multiparous mothers did so (19/19). Also, deprivation of all physical contact resulted in a significantly higher proportion of multiparous mothers accepting an alien lamb (6/18) than following deprivation of nursing only (0/19) indicating an impairment in selectivity. Finally, there was no indication that preventing only nursing led to a deficit either in maternal responsiveness or selectivity, neither in primiparous nor in multiparous ewes. These findings underline the importance of perception of olfactory cues from amniotic fluids through licking and/or physical contact and interacting with the lamb for the development of maternal responsiveness and selectivity.     

Bicelles: A natural ‘molecular goniometer’ for structural,dynamical and topological studies of molecules in membranes

Major biological processes occur at the biological membrane. One of the great challenges is to understand the function of chemical or biological molecules inside the membrane; as well of those involved in membrane trafficking. This requires obtaining a complete picture of the in situ structure and dynamics as well as the topology and orientation of these molecules in the membrane lipid bilayer. These led to the creation of several innovative models of biological membranes in order to investigate the structure and dynamics of amphiphilic molecules, as well as integral membrane proteins having single or multiple transmembrane segments. Because the determination of the structure, dynamics and topology of molecules in membranes requires a macroscopic alignment of the system, a new membrane model called ‘bicelles’ that represents a crossover between lipid vesicles and classical micelles has become very popular due to its property of spontaneous self-orientation in magnetic fields. In addition, crucial factors involved in mimicking natural membranes, such as sample hydration, pH and salinity limits, are easy to control in bicelle systems. Bicelles are composed of mixtures of long chain (14–18 carbons) and short chain phospholipids (6–8 carbons) hydrated up to 98% with buffers and may adopt various morphologies depending on lipid composition, temperature and hydration. We have been developing bicelle systems under the form of nano-discs made of lipids with saturated or biphenyl-containing fatty acyl chains. Depending on the lipid nature, these membranous nano-discs may be macroscopically oriented with their normal perpendicular or parallel to the magnetic field, providing a natural ‘molecular goniometer’ for structural and topological studies, especially in the field of NMR. Bicelles can also be spun at the magic angle and lead to the 3D structural determination of molecules in membranes.     

Asymmetric DNA requirements in Xer recombination activation by FtsK

In bacteria with circular chromosomes, homologous recombination events can lead to the formation of chromosome dimers. In Escherichia coli, chromosome dimers are resolved by the addition of a crossover by two tyrosine recombinases, XerC and XerD, at a specific site on the chromosome, dif. Recombination depends on a direct contact between XerD and a cell division protein, FtsK, which functions as a hexameric double stranded DNA translocase. Here, we have investigated how the structure and composition of DNA interferes with Xer recombination activation by FtsK. XerC and XerD each cleave a specific strand on dif, the top and bottom strand, respectively. We found that the integrity and nature of eight bottom-strand nucleotides and three top-strand nucleotides immediately adjacent to the XerD-binding site of dif are crucial for recombination. These nucleotides are probably not implicated in FtsK translocation since FtsK could translocate on single stranded DNA in both the 5′–3′ and 3′–5′ orientation along a few nucleotides. We propose that they are required to stabilize FtsK in the vicinity of dif for recombination to occur because the FtsK–XerD interaction is too transient or too weak in itself to allow for XerD catalysis.     

Promiscuous arbuscular mycorrhizal symbiosis of yam (Dioscorea spp.), a key staple crop in West Africa

Yam (Dioscorea spp.) is a tuberous staple food crop of major importance in the sub-Saharan savannas of West Africa. Optimal yields commonly are obtained only in the first year following slash-and-burn in the shifting cultivation systems. It appears that the yield decline in subsequent years is not merely caused by soil nutrient depletion but might be due to a loss of the beneficial soil microflora, including arbuscular mycorrhizal fungi (AMF), associated with tropical “tree-aspect” savannas and dry forests that are the natural habitats of the wild relatives of yam. Our objective was to study the AMF communities of natural savannas and adjacent yam fields in the Southern Guinea savanna of Benin. AMF were identified by morphotyping spores in the soil from the field sites and in AMF trap cultures with Sorghum bicolor and yam (Dioscorea rotundata and Dioscorea cayenensis) as bait plants. AMF species richness was higher in the savanna than in the yam-field soils (18–25 vs. 11–16 spp.), but similar for both ecosystems (29–36 spp.) according to the observations in trap cultures. Inoculation of trap cultures with soil sampled during the dry season led to high AMF root colonization, spore production, and species richness (overall 45 spp.) whereas inoculation with wet-season soil was inefficient (two spp. only). The use of D. cayenensis and D. rotundata as baits yielded 28 and 29 AMF species, respectively, and S. bicolor 37 species. AMF root colonization, however, was higher in yam than in sorghum (70–95 vs. 11–20%). After 8 months of trap culturing, the mycorrhizal yam had a higher tuber biomass than the nonmycorrhizal controls. The AMF actually colonizing D. rotundata roots in the field were also studied using a novel field sampling procedure for molecular analyses. Multiple phylotaxa were detected that corresponded with the spore morphotypes observed. It is, therefore, likely that the legacy of indigenous AMF from the natural savanna plays a crucial role for yam productivity, particularly in the low-input traditional farming systems prevailing in West Africa.     

PhyloFisher: A phylogenomic package for resolving eukaryotic relationships

Phylogenomic analyses of hundreds of protein-coding genes aimed at resolving phylogenetic relationships is now a common practice. However, no software currently exists that includes tools for dataset construction and subsequent analysis with diverse validation strategies to assess robustness. Furthermore, there are no publicly available high-quality curated databases designed to assess deep (>100 million years) relationships in the tree of eukaryotes. To address these issues, we developed an easy-to-use software package, PhyloFisher (https://github.com/TheBrownLab/PhyloFisher), written in Python 3. PhyloFisher includes a manually curated database of 240 protein-coding genes from 304 eukaryotic taxa covering known eukaryotic diversity, a novel tool for ortholog selection, and utilities that will perform diverse analyses required by state-of-the-art phylogenomic investigations. Through phylogenetic reconstructions of the tree of eukaryotes and of the Saccharomycetaceae clade of budding yeasts, we demonstrate the utility of the PhyloFisher workflow and the provided starting database to address phylogenetic questions across a large range of evolutionary time points for diverse groups of organisms. We also demonstrate that undetected paralogy can remain in phylogenomic “single-copy orthogroup” datasets constructed using widely accepted methods such as all vs. all BLAST searches followed by Markov Cluster Algorithm (MCL) clustering and application of automated tree pruning algorithms. Finally, we show how the PhyloFisher workflow helps detect inadvertent paralog inclusions, allowing the user to make more informed decisions regarding orthology assignments, leading to a more accurate final dataset.

Phylogenomic analyses of hundreds of protein-coding genes aimed at resolving phylogenetic relationships is now a common practice. This article presents PhyloFisher, a community-driven tool for phylogenomic dataset construction to infer deep and shallow phylogenetic relationships among eukaryotes.