Publisher's Note: Demonstrating universal scaling for dynamics of Yukawa one-component plasmas after an interaction quench [Phys. Rev. E 93, 023201 (2016)].

This corrects the article DOI: 10.1103/PhysRevE.93.023201.

Demonstrating universal scaling for dynamics of Yukawa one-component plasmas after an interaction quench.

The Yukawa one-component plasma (OCP) model is a paradigm for describing plasmas that contain one component of interest and one or more other components that can be treated as a neutralizing, screening background. In appropriately scaled units, interactions are characterized entirely by a screening parameter, κ. As a result, systems of similar κ show the same dynamics, regardless of the underlying parameters (e.g., density and temperature). We demonstrate this behavior using ultracold neutral plasmas (UNPs) created by photoionizing a cold (T≤10 mK) gas. The ions in UNP systems are well described by the Yukawa model, with the electrons providing the screening. Creation of the plasma through photoionization can be thought of as a rapid quench of the interaction potential from κ=∞ to a final κ value set by the electron density and temperature. We demonstrate experimentally that the postquench dynamics are universal in κ over a factor of 30 in density and an order of magnitude in temperature. Results are compared with molecular-dynamics simulations. We also demonstrate that features of the postquench kinetic energy evolution, such as disorder-induced heating and kinetic-energy oscillations, can be used to determine the plasma density and the electron temperature.

Polymorphism pattern at a miniature inverted-repeat transposable element locus downstream of the domestication gene Teosinte-branched1 in wild and domesticated pearl millet.

Unravelling the mechanisms involved in adaptation to understand plant morphological evolution is a challenging goal. For crop species, identification of molecular causal polymorphisms involved in domestication traits is central to this issue. Pearl millet, a domesticated grass mostly found in semi-arid areas of Africa and India, is an interesting model to address this topic: the domesticated form shares common derived phenotypes with some other cereals such as a decreased ability to develop basal and axillary branches in comparison with the wild phenotype. Two recent studies have shown that the orthologue of the maize gene Teosinte-Branched1 in pearl millet (PgTb1) was probably involved in branching evolution during domestication and that a miniature inverted-repeat transposable element (MITE) of the Tuareg family was inserted in the 3' untranslated region of PgTb1. For a set of 35 wild and domesticated populations, we compared the polymorphism patterns at this MITE and at microsatellite loci. The Tuareg insertion was nearly absent in the wild populations, whereas a strong longitudinal frequency cline was observed in the domesticated populations. The geographical pattern revealed by neutral microsatellite loci clearly demonstrated that isolation by distance does not account for the existence of this cline. However, comparison of population differentiation at the microsatellite and the MITE loci and analyses of the nucleotide polymorphism pattern in the downstream region of PgTb1 did not show evidence that the cline at the MITE locus has been shaped by selection, suggesting the implication of a neutral process. Alternative hypotheses are discussed.

Real-time dynamics of single vortex lines and vortex dipoles in a Bose-Einstein condensate.

Understanding the behavior of quantized vortices is essential to gaining insight into diverse superfluid phenomena, from critical-current densities in superconductors to quantum turbulence in superfluids. We observe the real-time dynamics of quantized vortices in trapped dilute-gas Bose-Einstein condensates by repeatedly imaging the vortex cores. The precession frequency of a single vortex is measured by explicitly observing its time dependence and is found to be in good agreement with theory. We further characterize the dynamics of vortex dipoles in two distinct configurations: (i) an asymmetric configuration, in which the vortex trajectories are dynamic and nontrivial, and (ii) a stable, symmetric configuration, in which the dipole is stationary.

Characterization of expressed NBS-LRR resistance gene candidates from common bean.

A complex ancestral resistance (R) gene cluster, localized at the end of linkage group B4, and referred to as the B4 R gene cluster, has been previously genetically characterized. The B4 R gene cluster existed prior to the separation of the two major gene pools of cultivated common bean and contains several resistance specificities effective against the fungus Colletotrichum lindemuthianum. In this paper we report the molecular analysis of four expressed resistance gene candidates (RGCs) that map at the B4 R-cluster and co-localize with R-specificities or R-QTLs effective against C. lindemuthianum. These RGCs have been isolated from two genotypes that are representative of the two major gene pools of common bean: the BA8 and BA11 RGCs originating from the Mesoamerican BAT93 genotype, and the JA71 and JA78 RGCs originating from the Andean JaloEEP558 genotype. These RGCs encode NBS-LRR resistance-like proteins that are closely similar to the tomato I2 R-protein. Based upon sequence comparisons and genetic localization, we established that these four bean RGCs belong to two different subfamilies of R-sequences independently of their gene pool of origin. No feature discriminating the four RGCs according to their gene pool of origin has been observed yet. Comparative sequence analyses of the full-length RGCs and their flanking genomic sequences confirmed the ancestral origin of the B4 R-cluster.

Polymorphism of a complex resistance gene candidate family in wild populations of common bean (Phaseolus vulgaris) in Argentina: comparison with phenotypic resistance polymorphism.

Fifteen populations of wild bean (Phaseolus vulgaris), located in three provinces in Argentina, were analysed for their polymorphism for a complex resistance gene candidate (RGC) family clustered on the genome and for resistance phenotypes to strains of Colletotrichum lindemuthianum. Results indicate that RGC polymorphism is high. Population structure obtained for markers related to resistance was compared to population structure obtained for RAPD markers in order to infer the evolutionary forces driving polymorphism for resistance in wild populations at both molecular and phenotypic levels. Hierarchical analysis of differentiation showed that, within provinces, populations were differentiated for RAPD as well as for molecular and phenotypic markers of resistance. In contrast, provinces were differentiated only for RAPD and RGC markers and not for resistance phenotypes. The discrepancies found between diversity structures for molecular markers (RAPD and RGCs) and for resistance phenotypes suggest an effect of selection and indicate that diversity for resistance may not be driven by the same selective forces at the molecular and phenotypic levels. We further discuss whether specific selective forces are exerted on RGC markers and underline the importance of spatial scale of analysis for demonstrating an impact of selection.

clap1, a gene encoding a copper-transporting ATPase involved in the process of infection by the phytopathogenic fungus Colletotrichum lindemuthianum.

A screen for insertional mutants of Colletrichum lindemuthianum, the causative agent of common bean anthracnose, led to the identification of a non-pathogenic, lightly colored transformant. This mutant is unable to induce disease symptoms on intact or wounded primary leaves of seedlings and plantlets of Phaseolus vulgaris. In vitro, it exhibits normal vegetative growth, sporulation and conidial germination, but the cultures remain beige instead of becoming black. Microscopic examination revealed that this mutant forms fewer appressoria than the wild-type strain, and these are misshapen and poorly melanized. Molecular analyses indicated that the mutagenic plasmid had targeted clap1, a gene encoding a putative copper-transporting ATPase sharing 35% identity with the human Menkes and Wilson proteins and the product of the CCC2 gene of Saccharomyces cerevisiae. Complementation of the non-pathogenic beige mutant with a wild-type allele of clap1 restored both pathogenicity and pigmentation. Conversely, replacement of the wild-type allele with a disrupted clap1 gene gave rise to non-pathogenic beige transformants. Compared with the wild-type strain, extracts from clap1 mutants were found to have very low levels of phenol oxidase activity. These observations suggest that the clap1 gene product may be involved in the pathogenicity of C. lindemuthianum strains because of its role in delivering copper to secreted cuproenzymes, such as the phenol oxidases that mediate the polymerization of 1,8-dihydroxynaphthalene to melanin.

A new class of tetraspanins in fungi.

Tetraspanins are animal proteins involved in membrane complexes that are involved in cell adhesion, differentiation, and motility. The PLS1 gene from rice blast fungus Magnaporthe grisea encodes a protein (Pls1p) structurally related to tetraspanins that is required for pathogenicity. In Botrytis cinerea public sequences, we identified an EST homologous to PLS1. Using degenerated oligonucleotides, we amplified sequences homologous to PLS1 in fungi Colletotrichum lindemuthianum and Neurospora crassa. Analysis of N. crassa and M. grisea genome sequences revealed the presence of a single tetraspanin gene. Thus, fungi differ from animals, which contain between 20 and 37 paralogous tetraspanin genes. Fungal proteins encoded by BcPLS1, ClPLS1, and NcPLS1 display all the structural hallmarks of tetraspanins (predicted topology with four transmembrane domains, extra- and intracellular loops; conserved cysteine-based patterns in second extracellular loop). Phylogenetic analysis suggests that these genes define a new family of orthologous genes encoding fungal-specific tetraspanins.

Aberrant transposition of a Tc1-mariner element, impala, in the fungus Fusarium oxysporum.

We previously determined that the impalaD transposable element of Fusarium oxysporum was able to mobilize a non autonomous copy of impala ( niaD::imp::hph), inserted in the niaD gene encoding nitrate reductase. Generally, mobilization results in the recovery of Nia(+) revertants at low frequency. In the course of this study, we recovered a transformant that gave rise to Nia(+) revertants at a high rate. These revertants displayed atypical phenotypes and showed a niaD hybridization pattern different from that in more typical revertants. Molecular analysis of the structure of the transformant and atypical revertants indicated that (i) in the transformant, two copies of impala, one defective and one active, were inserted at the same genomic locus in a head-to-head orientation; and (ii) all the revertants analyzed presented the same chromosomal rearrangement, an inversion resulting in the replacement of the niaD promoter by a new sequence containing a cryptic promoter. We also frequently observed additional DNA rearrangements (deletion or inversion) in these revertants. The sequences at the rearrangement junctions indicated the occurrence of a transposition event that used the ITRs (Inverted Terminal Repeats) of separate transposons arranged in direct orientation. These features can be interpreted as the consequences of an aberrant transposition process. Such a process may account for the rearrangements observed in some genomic regions containing multiple transposon ends, and could serve as a mechanism for the generation of genetic diversity.

Potential role of transposable elements in the rapid reorganization of the Fusarium oxysporum genome.

The activity of several families of transposable elements (TEs) in the genome of Fusarium oxysporum represents a potential source of karyotypic instability. We investigated transposon-mediated chromosome rearrangements by analyzing the karyotypes of a set of strains in which transposition events had occurred. We uncovered exceptional electrophoretic karyotype (EK) variability, in both number and size of chromosomal bands. We showed that EK differences result from chromosomal translocations, large deletions, and even more complex rearrangements. We also revealed many duplicated chromosomal regions. By following transposition of two elements and analyzing the distribution of different families of TEs on whole chromosomes, we find (i) no evidence of chromosomal breakages induced by transposition, (ii) a clustering of TEs in some regions, and (iii) a correlation between the high level of chromosomal polymorphism and the concentration of TEs. These results suggest that chromosome length polymorphisms likely result from ectopic recombination between TEs that can serve as substrates for these changes.

Evolutionary history of the impala transposon in Fusarium oxysporum.

Impala is an active DNA transposon family that was first identified in a strain of Fusarium oxysporum pathogenic to melon. The 10 copies present in this strain define three subfamilies that differ by about 20% at the nucleotide level. This high level of polymorphism suggests the existence of an ancestral polymorphism associated with vertical transmission and/or the introduction of some subfamilies by horizontal transfer from another species. To gain insights into the molecular evolution of this family, impala distribution was investigated in strains with various host specificities by Southern blot, PCR, and sequencing. Detection of impala elements in most of the F. oxysporum strains tested indicates that impala is an ancient component of the F. oxysporum genome. Subfamily-specific amplifications and sequence and phylogenetic analyses revealed five subfamilies, several of which can be found within the same genome. This supports the hypothesis of an ancestral polymorphism followed by vertical transmission and independent evolution in the host-specific forms. Highly similar elements showing unique features (internal deletions, high rates of CG-to-TA transitions) or being present at the same genomic location were identified in several strains with different host specificities, raising questions about the phylogenetic relationships of these strains. A phylogenetic analysis performed by sequencing a portion of the EF1alpha gene showed in most cases a correlation between the presence of a particular element and a close genetic relationship. All of these data provide important information on the evolutionary origin of this element and reveal its potential as a valuable tool for tracing populations.

Transposition of autonomous and engineered impala transposons in Fusarium oxysporum and a related species.

The impala transposon of Fusarium oxysporum is an active element. We demonstrated that the imp160 copy, transposed into the gene encoding nitrate reductase, is an autonomous element, since it excises from this gene and reinserts at a new genomic position in backgrounds free of active elements. An element in which the transposase gene was replaced by a hygromycin B resistance gene was used (1) to demonstrate the absence of endogenous transposase in several F. oxysporum strains and (2) to check the ability of different genomic copies of impala to transactivate this defective element. This two-component system allowed the identification of autonomous elements in two impala subfamilies and revealed that transactivation can occur between highly divergent elements. We also demonstrate that the autonomous copy transposes in a closely related species complex, F. moniliforme, in a fashion similar to that observed in F. oxysporium. The ability of impala to function as a two-component system and to transpose in a heterologous host promises further advances in our understanding of the factors that modulate transposition efficiency and demonstrates the potential of impala as a means of establishing a transposon tagging system for a wide range of fungal species.

Bronchorrhea revealing cervix adenocarcinoma metastastic to the lung.

Copious bronchorrhea can be related to bronchioloalveolar carcinoma, but reports of bronchorrhea related to lung metastasis are rare. We report the case of a woman presenting lung metastases of a cervical adenocarcinoma revealed by bronchorrhea, eventually identified as ectopic cervical mucus. Treatment included anticancer drugs and erythromycin, the latter in order to reduce the bronchorrhea, with eventually poor efficacy. This observation illustrates the importance of respiratory signs in the post-therapeutic follow up of cancer, especially cough and bronchorrhea in adenocarcinoma.

A GAL4-like protein is involved in the switch between biotrophic and necrotrophic phases of the infection process of Colletotrichum lindemuthianum on common bean. .

Random insertional mutagenesis was conducted with the hemibiotrophic fungus Colletotrichum lindemuthianum, causal agent of common bean anthracnose. Nine mutants that were altered in their infection process on the host plant were generated. One of these, H433 is a nonpathogenic mutant able to induce necrotic spots on infected leaves rapidly. These spots are similar to those observed during the hypersensitive reaction. Cytological observations showed that the development of the mutant H433 is stopped at the switch between the biotrophic and the necrotrophic phases. This mutant carries two independent insertions of the transforming plasmid pAN7-1. Complementation studies using the wild-type genomic regions corresponding to the two insertions showed that one is responsible for the H433 phenotype. Sequencing analysis identified a single open reading frame that encoded a putative transcriptional activator belonging to the fungal zinc cluster (Zn[II](2)Cys(6)) family. The corresponding gene was designated CLTA1 (for C. lindemuthianum transcriptional activator 1). Expression studies showed that CLTA1 is expressed in low amounts during in vitro culture. Targeted disrupted strains were generated, and they exhibited the same phenotype as the original mutant H433. Complementation of these disrupted strains by the CLTA1 gene led to full restoration of pathogenicity. This study demonstrates that CLTA1 is both a pathogenicity gene and a regulatory gene involved in the switch between biotrophy and necrotrophy of the infection process of a hemibiotrophic fungus.

Genome organization in Fusarium oxysporum: clusters of class II transposons.

Several families of transposable elements (TEs) are present in the genome of the phytopathogenic fungus Fusarium oxysporum. They are present in copy numbers ranging from just a few elements to tens or hundreds per genome. Sequence analysis of contiguous stretches of genomic DNA surrounding insertion sites of one family revealed that they are packed with repeated sequences. We have carried out a detailed study of the composition and arrangement of these repeats in three chromosomal regions. We found that they are essentially mixtures of several types of TEs, most of them being DNA transposons, different from those previously characterized. Some repeats are frequently reiterated and many of them are inserted into other elements. Parts of these regions are also duplications. These regions appear prone to rearrangement and transposition and are subject to rapid reorganization.

Inheritance of partial resistance against Colletotrichum lindemuthianum in Phaseolus vulgaris and co-localization of quantitative trait loci with genes involved in specific resistance.

Anthracnose, one of the most important diseases of common bean (Phaseolus vulgaris), is caused by the fungus Colletotrichum lindemuthianum. A "candidate gene" approach was used to map anthracnose resistance quantitative trait loci (QTL). Candidate genes included genes for both pathogen recognition (resistance genes and resistance gene analogs [RGAs]) and general plant defense (defense response genes). Two strains of C. lindemuthianum, identified in a world collection of 177 strains, displayed a reproducible and differential aggressiveness toward BAT93 and JaloEEP558, two parental lines of P. vulgaris representing the two major gene pools of this crop. A reliable test was developed to score partial resistance in aerial organs of the plant (stem, leaf, petiole) under controlled growth chamber conditions. BAT93 was more resistant than JaloEEP558 regardless of the organ or strain tested. With a recombinant inbred line (RIL) population derived from a cross between these two parental lines, 10 QTL were located on a genetic map harboring 143 markers, including known defense response genes, anthracnose-specific resistance genes, and RGAs. Eight of the QTL displayed isolate specificity. Two were co-localized with known defense genes (phenylalanine ammonia-lyase and hydroxyproline-rich glycoprotein) and three with anthracnose-specific resistance genes and/or RGAs. Interestingly, two QTL, with different allelic contribution, mapped on linkage group B4 in a 5.0 cM interval containing Andean and Mesoamerican specific resistance genes against C. lindemuthianum and 11 polymorphic fragments revealed with a RGA probe. The possible relationship between genes underlying specific and partial resistance is discussed.

Maturation of epidermal Langerhans cells: increased expression of beta- and gamma-actin isoforms as a basis of specialized cell functions.

Epidermal Langerhans cells (LC) represent immature dendritic cells. During in vitro culture in the presence of keratinocytes they mature into potent immunostimulatory cells for naive T cells. This process is thought to simulate in vivo maturation of LC following activation by antigen contact. Maturation of LC is accompanied by morphological alterations. Applying a differential screening procedure we isolated differentially expressed cDNAs involved in the maturation events including cDNAs of the cytoskeletal actin isoforms beta- and gamma-actin. Stronger signals with hybridization probes derived from cultured LC compared with probes derived from freshly isolated LC indicate upregulation of actin expression. Upregulated expression of actin was confirmed by RT-PCR, Western blot and immunofluorescence analysis. Staining with fluorescence-labelled phalloidin that selectively binds to polymerized F-actin, indicates an increase in F-actin levels in cultured LC. Thus our data show that maturation of LC, which involves formation of dendritic structures and movement of formerly immobile cells, is accompanied by augmented expression of actin and formation of additional actin filaments. Furthermore, actin mRNA, often used as reference to assess mRNA amounts for Northern blotting or competitive RT-PCR because of its high and ubiquitous expression, is an inappropriate standard for the analysis of LC and DC.

Identification of an ancestral resistance gene cluster involved in the coevolution process between Phaseolus vulgaris and its fungal pathogen Colletotrichum lindemuthianum.

The recent cloning of plant resistance (R) genes and the sequencing of resistance gene clusters have shed light on the molecular evolution of R genes. However, up to now, no attempt has been made to correlate this molecular evolution with the host-pathogen coevolution process at the population level. Cross-inoculations were carried out between 26 strains of the fungal pathogen Colletotrichum lindemuthianum and 48 Phaseolus vulgaris plants collected in the three centers of diversity of the host species. A high level of diversity for resistance against the pathogen was revealed. Most of the resistance specificities were overcome in sympatric situations, indicating an adaptation of the pathogen to the local host. In contrast, plants were generally resistant to allopatric strains, suggesting that R genes that were efficient against exotic strains but had been overcome locally were maintained in the plant genome. These results indicated that coevolution processes between the two protagonists led to a differentiation for resistance in the three centers of diversity of the host. To improve our understanding of the molecular evolution of these different specificities, a recombinant inbred (RI) population derived from two representative genotypes of the Andean (JaloEEP558) and Mesoamerican (BAT93) gene pools was used to map anthracnose specificities. A gene cluster comprising both Andean (Co-y; Co-z) and Mesoamerican (Co-9) host resistance specificities was identified, suggesting that this locus existed prior to the separation of the two major gene pools of P. vulgaris. Molecular analysis revealed a high level of complexity at this locus. It harbors 11 restriction fragment length polymorphisms when R gene analog (RGA) clones are used. The relationship between the coevolution process and diversification of resistance specificities at resistance gene clusters is discussed.

Cloning and molecular characterization of three members of the NBS-LRR subfamily located in the vicinity of the Co-2 locus for anthracnose resistance in Phaseolus vulgaris.

Co-2 is one of the R-genes against anthracnose identified in common bean. A RAPD marker, cloned as PvH20, was previously shown to contain 6 imperfect leucine-rich-repeats and to reveal a family of related sequences in the vicinity of the Co-2 locus. Using PvH20 as probe, a genomic clone and 2 partial cDNAs were isolated. DNA sequencing revealed that the 6.1 kb genomic fragment contains sequences encoding both NBS-LRR (ORF1) and kinase-like (ORF2) products. The 2 partial cDNAs (cD7 and cD8) belong to the NBS-LRR subfamily as do most of the resistance genes cloned to date. The LRR domain of ORF1 is interrupted by 2 stop codons suggesting that it corresponds to a non-functional member of the multigene family and ORF2 appears to be a kinase pseudogene. The 3 NBS-LRR polypeptides share a high level of amino acid identity and represent different members of a related family. By genetic mapping ORF1, cD7, and cD8 were found to span a genetic distance of 3 cM: cD8 maps at 2 cM from Co-2 and 3 cM from ORF1, cD7 maps at 1 cM from ORF1 and co-segregates with Co-2, thus cD7 might be a putative candidate for the Co-2 R-gene.

Specific expression of the Fusarium transposon Fot1 and effects on target gene transcription.

The Fot1 transposon is active in some strains of the plant pathogenic fungus Fusarium oxysporum. In a high-copy-number strain that contains autonomous elements, we have detected a transcript of 1.7 kb hybridizing to Fot1 in very low amounts. Mapping the 3' and 5' termini of this transcript confirms that it corresponds to a Fot1-specific transcript. In this strain, five independent mutants of the transgene (niaD) encoding nitrate reductase have arisen by insertion of Fot1 into the third intron. The analysis of the effect of Fot1 insertion in these mutants shows that, depending on the orientation of Fot1 relative to niaD, different truncated chimeric niaD-Fot1 transcripts are produced. Mapping the 5' and 3' ends of these transcripts reveals (i) premature polyadenylation at sites present in the 5' and 3' untranslated regions of Fot1, and (ii) initiation of some transcripts in the 3' part of the niaD gene at sites located immediately downstream of the Fot1 insertion. Thus, a novel promoter, associated with the end of Fot1, directs transcriptional activity outwards from the element into the coding sequence of the niaD gene. These effects demonstrate that Fot1 insertion provides an additional general mechanism controlling fungal gene expression.