Analysis of evolutionary patterns of genes in Campylobacter jejuni and C. coli

BACKGROUND: The thermophilic Campylobacter jejuni and Campylobacter coli are considered weakly clonal populations where incongruences between genetic markers are assumed to be due to random horizontal transfer of genomic DNA. In order to investigate the population genetics structure we extracted a set of 1180 core gene families (CGF) from 27 sequenced genomes of C. jejuni and C. coli. We adopted a principal component analysis (PCA) on the normalized evolutionary distances in order to reveal any patterns in the evolutionary signals contained within the various CGFs. RESULTS: The analysis indicates that the conserved genes in Campylobacter show at least two, possibly five, distinct patterns of evolutionary signals, seen as clusters in the score-space of our PCA. The dominant underlying factor separating the core genes is the ability to distinguish C. jejuni from C. coli. The genes in the clusters outside the main gene group have a strong tendency of being chromosomal neighbors, which is natural if they share a common evolutionary history. Also, the most distinct cluster outside the main group is enriched with genes under positive selection and displays larger than average recombination rates. CONCLUSIONS: The Campylobacter genomes investigated here show that subsets of conserved genes differ from each other in a more systematic way than expected by random horizontal transfer, and is consistent with differences in selection pressure acting on different genes. These findings are indications of a population of bacteria characterized by genomes with a mixture of evolutionary patterns

Geographic structure in a symbiotic mutualism

An increasing number of studies analyze the geographic structure of species interactions, including symbioses, but few address mutualistic symbioses, systems where phylogenetic congruence can be expected when there is vertical inheritance of symbiotic partners. In this study, I examine fungal-algal partnership patterns and geographic structure of the fungus Letharia vulpina s. lat. (Ascomycota) and its partners, multiple clades of Trebouxia jamesii (Chlorophyta), across Western North America. Letharia lichens are unusual in that multiple gene genealogies delimiting taxa on both sides of the symbiosis are available from a prior study. This previous work provides a robust phylogenetic context for the study of a multi-species interaction network that occurs at a large geographic scale. The primary methodology employed is DNA sequencing of seven fungal loci and two algal loci. The study provides: (1) Formal description of a lichenized fungus, Letharia lupina sp. nov., that is distinct from Letharia vulpina s. str., based on morphology, geographic distribution, fungal DNA sequences, and algal partner. L. lupina and its algal partners form "Mountain Wolf" lichens. (2) A map of the geographic distribution of five clades of Mountain Wolf algae in Western North America. (3) A comparison of geographic structure of Mountain Wolf fungi with Mountain Wolf algae. (4) A comparison of the geographic structure of Mountain Wolf algae with co-distributed plant and animal taxa in Western North America

Solid Phase-Based Cross-Matching as Solution for Kidney Allograft Recipients Pretreated with Therapeutic Antibodies

In order to select recipients without donor-specific anti-HLA antibodies, the complement-dependent cytotoxicity crossmatch (CDC-CM) was established as the standard procedure about 40 years ago. However, the interpretability of this functional assay strongly depends on the vitality of isolated donors’ lymphocytes. Since the application of therapeutic antibodies for the immunosuppressive regimen falsifies the outcome of the CDC-crossmatch as a result of these antibodies’ complement-activating capacity in the recipients’ sera, we looked for an alternative methodical approach. We here present 27 examples of AB0 blood group-incompatible living kidney allograft recipients who, due to their treatment with the humanized chimeric monoclonal anti-CD20 antibody Rituximab, did not present valid outcomes of CDC-based pretransplant cross-matching. Additionally, four cases of posttransplant cross-matching after living kidney allografting and consequent treatment with the therapeutic anti-CD25 antibody Basiliximab (Simulect) due to acute biopsy-proven rejection episodes are presented and compared regarding CDC- and ELISA-based crossmatch outcomes. In all cases, it became evident that the classical CDC-based crossmatch was completely unfeasible for the detection of donor-specific anti-HLA antibodies, whereas ELISA-based cross-matching not requiring vital cells was not artificially affected. We conclude that ELISA-based cross-matching is a valuable tool to methodically circumvent false positive CDC-based crossmatch results in the presence of therapeutically applied antibodies

One hundred new species of lichenized fungi: a signature of undiscovered global diversity

The number of undescribed species of lichenized fungi has been estimated at roughly 10,000. Describing and cataloging these would take the existing number of taxonomists several decades; however, the support for taxonomy is in decline worldwide. In this paper we emphasize the dire need for taxonomic expertise in lichenology. We bring together 103 colleagues from institutions worldwide to describe a total of 100 new species of lichenized fungi, representing a wide taxonomic and geographic range. The newly described species are: Acarospora flavisparsa, A. janae, Aderkomyces thailandicus, Amandinea maritima, Ampliotrema cocosense, Anomomorpha lecanorina, A. tuberculata, Aspicilia mansourii, Bacidina sorediata, Badimia multiseptata, B. vezdana, Biatora epirotica, Buellia sulphurica, Bunodophoron pinnatum, Byssoloma spinulosum, Calopadia cinereopruinosa, C. editae, Caloplaca brownlieae, C. decipioides, C. digitaurea, C. magnussoniana, C. mereschkowskiana, C. yorkensis, Calvitimela uniseptata, Chapsa microspora, C. psoromica, C. rubropulveracea, C. thallotrema, Chiodecton pustuliferum, Cladonia mongkolsukii, Clypeopyrenis porinoides, Coccocarpia delicatula, Coenogonium flammeum, Cresponea ancistrosporelloides, Crocynia microphyllina, Dictyonema hernandezii, D. hirsutum, Diorygma microsporum, D. sticticum, Echinoplaca pernambucensis, E. schizidiifera, Eremithallus marusae, Everniastrum constictovexans, Fellhanera borbonica, Fibrillithecis sprucei, Fissurina astroisidiata, F. nigrolabiata, F. subcomparimuralis, Graphis caribica, G. cerradensis, G. itatiaiensis, G. marusa, Gyalideopsis chicaque, Gyrotrema papillatum, Harpidium gavilaniae, Hypogymnia amplexa, Hypotrachyna guatemalensis, H. indica, H. lueckingii, H. paracitrella, H. paraphyscioides, H. parasinuosa, Icmadophila eucalypti, Krogia microphylla, Lecanora mugambii, L. printzenii, L. xanthoplumosella, Lecidea lygommella, Lecidella greenii, Lempholemma corticola, Lepraria sekikaica, Lobariella sipmanii, Megalospora austropacifica, M. galapagoensis, Menegazzia endocrocea, Myriotrema endoflavescens, Ocellularia albobullata, O. vizcayensis, Ochrolechia insularis, Opegrapha viridipruinosa, Pannaria phyllidiata, Parmelia asiatica, Pertusaria conspersa, Phlyctis psoromica, Placopsis imshaugii, Platismatia wheeleri, Porina huainamdungensis, Ramalina hyrcana, R. stoffersii, Relicina colombiana, Rhizocarpon diploschistidina, Sticta venosa, Sagenidiopsis isidiata, Tapellaria albomarginata, Thelotrema fijiense, Tricharia nigriuncinata, Usnea galapagona, U. pallidocarpa, Verrucaria rhizicola, and Xanthomendoza rosmarieae. In addition, three new combinations are proposed: Fibrillithecis dehiscens, Lobariella botryoides, and Lobariella pallida.Fil: Messuti, Maria Ines. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Patagonia Norte. Instituto de Investigación en Biodiversidad y Medioambiente; ArgentinaFil: Lumbsch, H.T.. The Field Museum. Department Of Botany; Estados UnidosFil: Luecking, R.. The Field Museum. Department Of Botany; Estados UnidosFil: Altermann, Susanne. University of California; Estados UnidosFil: et. all

How Do You Solve a Problem like <i>Letharia</i>? A New Look at Cryptic Species in Lichen-Forming Fungi Using Bayesian Clustering and SNPs from Multilocus Sequence Data

The inclusion of molecular data is increasingly an integral part of studies assessing species boundaries. Analyses based on predefined groups may obscure patterns of differentiation, and population assignment tests provide an alternative for identifying population structure and barriers to gene flow. In this study, we apply population assignment tests implemented in the programs STRUCTURE and BAPS to single nucleotide polymorphisms from DNA sequence data generated for three previous studies of the lichenized fungal genus Letharia. Previous molecular work employing a gene genealogical approach circumscribed six species-level lineages within the genus, four putative lineages within the nominal taxon L. columbiana (Nutt.) J.W. Thomson and two sorediate lineages. We show that Bayesian clustering implemented in the program STRUCTURE was generally able to recover the same six putative Letharia lineages. Population assignments were largely consistent across a range of scenarios, including: extensive amounts of missing data, the exclusion of SNPs from variable markers, and inferences based on SNPs from as few as three gene regions. While our study provided additional evidence corroborating the six candidate Letharia species, the equivalence of these genetic clusters with species-level lineages is uncertain due, in part, to limited phylogenetic signal. Furthermore, both the BAPS analysis and the ad hoc ΔK statistic from results of the STRUCTURE analysis suggest that population structure can possibly be captured with fewer genetic groups. Our findings also suggest that uneven sampling across taxa may be responsible for the contrasting inferences of population substructure. Our results consistently supported two distinct sorediate groups, ‘L. lupina’ and L. vulpina, and subtle morphological differences support this distinction. Similarly, the putative apotheciate species ‘L. lucida’ was also consistently supported as a distinct genetic cluster. However, additional studies will be required to elucidate the relationships of other L. columbiana s.l. populations with the two sorediate genetic clusters.</p

One hundred new species of lichenized fungi: a signature of undiscovered global diversity

The number of undescribed species of lichenized fungi has been estimated at roughly 10,000. Describing and cataloging these would take the existing number of taxonomists several decades; however, the support for taxonomy is in decline worldwide. In this paper we emphasize the dire need for taxonomic expertise in lichenology. We bring together 103 colleagues from institutions worldwide to describe a total of 100 new species of lichenized fungi, representing a wide taxonomic and geographic range. The newly described species are: Acarospora flavisparsa, A. janae, Aderkomyces thailandicus, Amandinea maritima, Ampliotrema cocosense, Anomomorpha lecanorina, A. tuberculata, Aspicilia mansourii, Bacidina sorediata, Badimia multiseptata, B. vezdana, Biatora epirotica, Buellia sulphurica, Bunodophoron pinnatum, Byssoloma spinulosum, Calopadia cinereopruinosa, C. editae, Caloplaca brownlieae, C. decipioides, C. digitaurea, C. magnussoniana, C. mereschkowskiana, C. yorkensis, Calvitimela uniseptata, Chapsa microspora, C. psoromica, C. rubropulveracea, C. thallotrema, Chiodecton pustuliferum, Cladonia mongkolsukii, Clypeopyrenis porinoides, Coccocarpia delicatula, Coenogonium flammeum, Cresponea ancistrosporelloides, Crocynia microphyllina, Dictyonema hernandezii, D. hirsutum, Diorygma microsporum, D. sticticum, Echinoplaca pernambucensis, E. schizidiifera, Eremithallus marusae, Everniastrum constictovexans, Fellhanera borbonica, Fibrillithecis sprucei, Fissurina astroisidiata, F. nigrolabiata, F. subcomparimuralis, Graphis caribica, G. cerradensis, G. itatiaiensis, G. marusa, Gyalideopsis chicaque, Gyrotrema papillatum, Harpidium gavilaniae, Hypogymnia amplexa, Hypotrachyna guatemalensis, H. indica, H. lueckingii, H. paracitrella, H. paraphyscioides, H. parasinuosa, Icmadophila eucalypti, Krogia microphylla, Lecanora mugambii, L. printzenii, L. xanthoplumosella, Lecidea lygommella, Lecidella greenii, Lempholemma corticola, Lepraria sekikaica, Lobariella sipmanii, Megalospora austropacifica, M. galapagoensis, Menegazzia endocrocea, Myriotrema endoflavescens, Ocellularia albobullata, O. vizcayensis, Ochrolechia insularis, Opegrapha viridipruinosa, Pannaria phyllidiata, Parmelia asiatica, Pertusaria conspersa, Phlyctis psoromica, Placopsis imshaugii, Platismatia wheeleri, Porina huainamdungensis, Ramalina hyrcana, R. stoffersii, Relicina colombiana, Rhizocarpon diploschistidina, Sticta venosa, Sagenidiopsis isidiata, Tapellaria albomarginata, Thelotrema fijiense, Tricharia nigriuncinata, Usnea galapagona, U. pallidocarpa, Verrucaria rhizicola, and Xanthomendoza rosmarieae. In addition, three new combinations are proposed: Fibrillithecis dehiscens, Lobariella botryoides, and Lobariella pallida

Electrochemical behaviour of silica basic hybrid coatings deposited on stainless steel by dipping and EPD

The aim of this work is the characterisation of the corrosion behaviour of stainless steel (AISI 304) substrates coated by dipping and electrophoretic deposition (EPD) from a sol–gel basic sol. Particulate silica sols (labelled NaSi)were prepared by basic catalysis from ethyltriethoxysilane (TEOS), methyltriethoxysilane (MTES) and sodium hydroxide. Coatings between 2 and 10 mwere prepared by using concentrated and diluted sols by dipping and EPD process and the corrosion behaviour of the coated substrates were studied through potentiodynamic and impedance spectroscopy measurements (EIS). Potentiodynamic studies of coatings produced by dipping reveal a strong dependence of the protective properties with the concentration of the sol. This behaviour was confirmed by EIS showing that only the coatings obtained from concentrated sol present enough protective properties. On the contrary, EPD coatings prepared from diluted NaSi sol showed an excellent corrosion resistance, maintaining a pure capacitive behaviour for long periods of immersion. EPD deposition is thus proposed as a good alternative method for obtaining thicker and denser coatings with good protective properties from dilute and stable sols.Peer reviewe

How Do You Solve a Problem like <i>Letharia</i>? A New Look at Cryptic Species in Lichen-Forming Fungi Using Bayesian Clustering and SNPs from Multilocus Sequence Data

<div><p>The inclusion of molecular data is increasingly an integral part of studies assessing species boundaries. Analyses based on predefined groups may obscure patterns of differentiation, and population assignment tests provide an alternative for identifying population structure and barriers to gene flow. In this study, we apply population assignment tests implemented in the programs STRUCTURE and BAPS to single nucleotide polymorphisms from DNA sequence data generated for three previous studies of the lichenized fungal genus <i>Letharia</i>. Previous molecular work employing a gene genealogical approach circumscribed six species-level lineages within the genus, four putative lineages within the nominal taxon <i>L. columbiana</i> (Nutt.) J.W. Thomson and two sorediate lineages. We show that Bayesian clustering implemented in the program STRUCTURE was generally able to recover the same six putative <i>Letharia</i> lineages. Population assignments were largely consistent across a range of scenarios, including: extensive amounts of missing data, the exclusion of SNPs from variable markers, and inferences based on SNPs from as few as three gene regions. While our study provided additional evidence corroborating the six candidate <i>Letharia</i> species, the equivalence of these genetic clusters with species-level lineages is uncertain due, in part, to limited phylogenetic signal. Furthermore, both the BAPS analysis and the ad hoc Δ<i>K</i> statistic from results of the STRUCTURE analysis suggest that population structure can possibly be captured with fewer genetic groups. Our findings also suggest that uneven sampling across taxa may be responsible for the contrasting inferences of population substructure. Our results consistently supported two distinct sorediate groups, ‘<i>L. lupina</i>’ and <i>L. vulpina</i>, and subtle morphological differences support this distinction. Similarly, the putative apotheciate species ‘<i>L. lucida</i>’ was also consistently supported as a distinct genetic cluster. However, additional studies will be required to elucidate the relationships of other <i>L. columbiana</i> s.l. populations with the two sorediate genetic clusters.</p></div

Probing the Microstructure of Methylammonium Lead Iodide Perovskite Solar Cells

The microstructure of absorber layers is pivotally important for all thin‐film solar technologies. Using electron backscattered diffraction (EBSD), the crystal orientation in methylammonium lead iodide thin films with submicrometer resolution is reported. For the vast majority of (110) oriented grains, the c‐axis of the perovskite unit cell is oriented in‐plane. Although some adjacent grains exhibit the same in‐plane horizontal orientation of the c‐axis, no universal horizontal orientation of the c‐axis within the sample plane exists. The (110) crystal orientation correlates with an in‐plane orientation of the ferroelectric polarization as investigated by vertical and lateral piezoresponse force microscopy (PFM). The individual grains with different crystal orientations that exhibit different ferroelectric patterns and surface potentials are identified. The strong correlation between crystal orientation and ferroelectric polarization allows conclusions to be drawn about the microstructure from PFM measurements and, likewise, the ferroelectric polarization to be derived from crystallographic observations by EBSD