The genus Elaphomyces (Ascomycota, Eurotiales): a ribosomal DNA-based phylogeny and revised systematics of European 'deer truffles'

Elaphomyces ('deer truffles') is one of the most important ectomycorrhizal fungal genera in temperate and subarctic forest ecosystems, but also one of the least documented in public databases. The current systematics are mainly based on macromorphology, and is not significantly different from that proposed by Vittadini (1831). Within the 49 species recognised worldwide, 23 were originally described from Europe and 17 of these were described before the 20th century. Moreover, very recent phylogenetic treatments of the genus are mainly based on a few extra-European species and most common European species are still poorly documented. Based on an extensive taxonomic sampling mainly made in the biogeographically rich Cantabrian area (Spain), complemented with collections from France, Greece, Italy, Norway, Portugal and Sweden, all currently recognized species in Europe have been sequenced at the ITS and 28S of the rDNA. Combined phylogenetic analyses yielded molecular support to sections Elaphomyces and Ceratogaster (here emended), while a third, basal lineage encompasses the sections Malacodermei and Ascoscleroderma as well as the tropical genus Pseudotulostoma. Species limits are discussed and some taxa formerly proposed as genuine species based on morphology and biogeography are re-evaluated as varieties or forms. Spore size and ornamentation, features of the peridial surface, structure of the peridium, and the presence of mycelium patches attached to the peridial surface emerge as the most significant systematic characters. Four new species: E. barrioi, E. quercicola, E. roseolus and E. violaceoniger, one new variety: E. papillatus var. sulphureopallidus, and two new forms: E. granulatus forma pallidosporus and E. anthracinus forma talosporus are introduced, as well as four new combinations in the genus: E. muricatus var. reticulatus, E. muricatus var. variegatus, E. papillatus var. striatosporus and E. morettii var. cantabricus. Lectotypes and epitypes are designated for most recognised species. For systematic purposes, new infrageneric taxa are introduced: E. sect. Ascoscleroderma stat. nov., E. subsect. Sclerodermei stat. nov., E. subsect. Maculati subsect. nov., E. subsect. Muricati subsect. nov., and E. subsect. Papillati subsect. nov. Lastly, E.laevigatus, E. sapidus, E. sulphureopallidus and E. trappei are excluded from the genus and referred to Rhizopogon roseolus, Astraeus sapidus comb. nov., Astraeus hygrometricus and Terfezia trappei comb. nov. (syn.: Terfezia cistophila), respectively.

Cryptic diversity revealed by DNA barcoding in Colombian illegally traded bird species

Colombia is the country with the largest number of bird species worldwide, yet its avifauna is seriously threatened by habitat degradation and poaching. We built a DNA barcode library of nearly half of the bird species listed in the CITES appendices for Colombia, thereby constructing a species identification reference that will help in global efforts for controlling illegal species trade. We obtained the COI barcode sequence of 151 species based on 281 samples, representing 46% of CITES bird species registered for Colombia. The species analysed belong to nine families, where Trochilidae and Psittacidae are the most abundant ones. We sequenced for the first time the DNA barcode of 47 species, mainly hummingbirds endemic of the Northern Andes region. We found a correct match between morphological and genetic identification for 86-92% of the species analysed, depending on the cluster analysis performed (BIN, ABGD and TaxonDNA). Additionally, we identified eleven cases of high intraspecific divergence based on K2P genetic distances (up to 14.61%) that could reflect cryptic diversity. In these cases, the specimens were collected in geographically distant sites such as different mountain systems, opposite flanks of the mountain or different elevations. Likewise, we found two cases of possible hybridization and incomplete lineage sorting. This survey constitutes the first attempt to build the DNA barcode library of endangered bird species in Colombia establishing as a reference for management programs of illegal species trade, and providing major insights of phylogeographic structure that can guide future taxonomic research.

Importance of early absolute lymphocyte count after allogeneic stem cell transplantation: a retrospective study

INTRODUCTION

Early lymphocyte recovery after allogeneic hematopoietic stem cell transplantation (HSCT) is related to the prevention of serious infections and the clearing of residual tumor cells.

METHODS

We analyzed the absolute lymphocyte count at 20 (D+20) and 30 (D+30) days after HSCT in 100 patients with malignant hematologic diseases and correlated with the risk of transplant-related mortality, overall survival (OS), disease-free survival (DFS), nonrelapsed mortality (NRM), and risk of infection.

RESULTS

Patients presenting with lymphocyte counts of <300 × 103/μL on D+30 have a 3.76 times greater risk of death in <100 days. Over a medium follow-up of 20 months OS, DFS, and NRM were similar between the groups.

CONCLUSION

In our group of patients delayed lymphocyte recovery after HSCT was a predictor of early death post-HSCT.

Predicted altitudinal shifts and reduced spatial distribution of Leishmania infantum vector species under climate change scenarios in Colombia

Visceral leishmaniasis (VL) is caused by the trypanosomatid parasite Leishmania infantum (=Leishmania chagasi), and is epidemiologically relevant due to its wide geographic distribution, the number of annual cases reported and the increase in its co-infection with HIV. Two vector species have been incriminated in the Americas: Lutzomyia longipalpis and Lutzomyia evansi. In Colombia, L. longipalpis is distributed along the Magdalena River Valley while L. evansi is only found in the northern part of the Country. Regarding the epidemiology of the disease, in Colombia the incidence of VL has decreased over the last few years without any intervention being implemented. Additionally, changes in transmission cycles have been reported with urban transmission occurring in the Caribbean Coast. In Europe and North America climate change seems to be driving a latitudinal shift of leishmaniasis transmission. Here, we explored the spatial distribution of the two known vector species of L. infantum in Colombia and projected its future distribution into climate change scenarios to establish the expansion potential of the disease. An updated database including L. longipalpis and L. evansi collection records from Colombia was compiled. Ecological niche models were performed for each species using the Maxent software and 13 Worldclim bioclimatic coverages. Projections were made for the pessimistic CSIRO A2 scenario, which predicts the higher increase in temperature due to non-emission reduction, and the optimistic Hadley B2 Scenario predicting the minimum increase in temperature. The database contained 23 records for L. evansi and 39 records for L. longipalpis, distributed along the Magdalena River Valley and the Caribbean Coast, where the potential distribution areas of both species were also predicted by Maxent. Climate change projections showed a general overall reduction in the spatial distribution of the two vector species, promoting a shift in altitudinal distribution for L. longipalpis and confining L. evansi to certain regions in the Caribbean Coast. Altitudinal shifts have been reported for cutaneous leishmaniasis vectors in Colombia and Peru. Here, we predict the same outcome for VL vectors in Colombia. Changes in spatial distribution patterns could be affecting local abundances due to climatic pressures on vector populations thus reducing the incidence of human cases.

Seroprevalence of Toxoplasma gondii and Neospora caninum in wild and domestic ruminants sharing pastures in Galicia (Northwest Spain)

The prevalence of antibodies to the protozoan parasites Toxoplasma gondii and Neospora caninum were investigated by the direct agglutination test (DAT) and cELISA, respectively, in 160 roe deer (Capreolus capreolus), 177 sheep and 178 cattle sharing pastures in Galicia (Northwest Spain). The seroprevalence for T. gondii was 13.7% in roe deer, 57% in sheep and 7.3% in cattle. The seroprevalence for N. canimum was 6.8%, 10.1% and 24.1% in roe deer, sheep and cattle, respectively. Statistically significant differences were observed between sheep and the other species for T. gondii and between cattle and the other ruminants for N. caninum. Only 19/515 animals were positive for both, T. gondii and N. caninum. Statistically significant differences were observed among different geographical areas for T. gondii but not for Neospora, seroprevalence being higher in the coastal area lower than in other areas. This study reveals a widespread exposure to T. gondii in Galician ruminants, and therefore, those species, particularly sheep, should be regarded as a potential source of infection for humans.

Different clustering of genomes across life using the A-T-C-G and degenerate R-Y alphabets: early and late signaling on genome evolution?

In this study, we have calculated distances between genomes based on our previously developed compositional spectra (CS) analysis. The study was conducted using genomes of 39 species of Eukarya, Eubacteria, and Archaea. Based on CS distances, we produced two different consensus dendrograms for four- and two-letter (purine-pyrimidine) alphabets. A comparison of the obtained structure using purine-pyrimidine alphabet with the standard three-kingdom (3K) scheme reveals substantial similarity. Surprisingly, this is not the case when the same procedure is based on the four-letter alphabet. In this situation, we also found three main clusters-but different from those in the 3K scheme. In particular, one of the clusters includes Eukarya and thermophilic bacteria and a part of the considered Archaea species. We speculate that the key factor in the last classification (based on the A-T-G-C alphabet) is related to ecology: two ecological parameters, temperature and oxygen, distinctly explain the clustering revealed by compositional spectra in the four-letter alphabet. Therefore, we assume that this result reflects two interdependent processes: evolutionary divergence and superimposed ecological convergence of the genomes, albeit another process, horizontal transfer, cannot be excluded as an important contributing factor.

Looking for organization patterns of highly expressed genes: purine-pyrimidine composition of precursor mRNAs

We analyzed precursor messenger RNAs (pre-mRNAs) of 12 eukaryotic species. In each species, three groups of highly expressed genes, ribosomal proteins, heat shock proteins, and amino-acyl tRNA synthetases, were compared with a control group (randomly selected genes). The purine-pyrimidine (R-Y) composition of pre-mRNAs of the three targeted gene groups proved to differ significantly from the control. The exons of the three groups tested have higher purine contents and R-tract abundance and lower abundance of Y-tracts compared to the control (R-tract-tract of sequential purines with Rn>or=5; Y-tract-tract of sequential pyrimidines with Yn>or=5). In species widely employing "intron definition" in the splicing process, the Y content of introns of the three targeted groups appeared to be higher compared to the control group. Furthermore, in all examined species, the introns of the targeted genes have a lower abundance of R-tracts compared to the control. We hypothesized that the R-Y composition of the targeted gene groups contributes to high rate and efficiency of both splicing and translation, in addition to the mRNA coding role. This is presumably achieved by (1) reducing the possibility of the formation of secondary structures in the mRNA, (2) using the R-tracts and R-biased sequences as exonic splicing enhancers, (3) lowering the amount of targets for pyrimidine tract binding protein in the exons, and (4) reducing the amount of target sequences for binding of serine/arginine-rich (SR) proteins in the introns, thereby allowing SR proteins to bind to proper (exonic) targets.

Skin immune responses in cattle after primary and secondary infections with Hypoderma lineatum (Diptera: Oestridae) larvae

Cellular immune responses were examined in the skin of cattle after primary and secondary experimental infections with Hypoderma lineatum larvae. Skin biopsies were taken at 0, 6, 12, 48 and 96 h post-infection (h.p.i.). In primary infected animals the penetration of Hypoderma larvae was characterized by moderate inflammatory responses. The pattern of cellular changes in previously infected animals suggested an allergic or rheumatic process, probably as a consequence of the development of a type III hypersensitivity reaction against the second or successive reinfections. Perivascular infiltration with CD3(+) T lymphocytes was marked in infected groups, but especially in previously infected animals, with a significant increase with respect to uninfected controls at 48 h.p.i. B cells remained close to control values during primary infection, while they increased significantly 12 h.p.i. in reinfected animals. IgG(+) plasma cells were also very abundant during secondary infections, with significant differences from primary infected and uninfected animals from 6 h.p.i. onwards. These results suggest that secondary infections allow cellular responses which may be effective in killing some of the entering larvae, resulting in a degree of resistance.

Evolutionary regulation of the blind subterranean mole rat, Spalax, revealed by genome-wide gene expression

We applied genome-wide gene expression analysis to the evolutionary processes of adaptive speciation of the Israeli blind subterranean mole rats of the Spalax ehrenbergi superspecies. The four Israeli allospecies climatically and adaptively radiated into the cooler, mesic northern domain (N) and warmer, xeric southern domain (S). The kidney and brain mRNAs of two N and two S animals were examined through cross-species hybridizations with two types of Affymetrix arrays (mouse and rat) and muscle mRNA of six N and six S animals with spotted cDNA mouse arrays. The initial microarray analysis was hypothesis-free, i.e., conducted without reference to the origin of animals. Principal component analysis revealed that 20-30% of the expression signal variability could be explained by the differentiation of N-S species. Similar N-S effects were obtained for all tissues and types of arrays: two Affymetrix microarrays using probe oligomer signals and the spotted array. Likewise, ANOVA and t test statistics demonstrated significant N-S ecogeographic divergence and region-tissue specificity in gene expression. Analysis of differential gene expression between species corroborates previous results deduced by allozymes and DNA molecular polymorphisms. Functional categories show significant N-S ecologic putative adaptive divergent up-regulation of genes highlighting a higher metabolism in N, and potential adaptive brain activity and kidney urine cycle pathways in S. The present results confirm ecologic-genomic separation of blind mole rats into N and S. Gene expression regulation appears to be central to the evolution of blind mole rats.

Coevolution of DNA-interacting proteins and genome "dialect"

Several species-specific characteristics of genome organization that are superimposed on its coding aspects were proposed earlier, including genome signature (GS), genome accent, and compositional spectrum (CS). These notions could be considered as representatives of genome dialect (GD). We measured within the Proteobacteria some GD representatives, the relative abundance of dinucleotides or GS, the profiles of occurrence of 10 nucleotide words (CS), and the profiles of occurrence of 20 nucleotide words, using a degenerate two-letter alphabet (purine-pyrimidine compositional spectra [PPCS]). Here, we show that the evolutionary distances between DNA repair and recombination orthologous enzymes (especially those of the nucleotide excision repair system) are highly correlated with PPCS and GS distances. Orthologous proteins involved in structural or metabolic processes (control group) have significantly lower correlations of their evolutionary distances with the PPCS and GS distances. We hypothesize that the high correlation of the evolutionary distances of the DNA repair orthologous enzymes with their GD is a result of the coevolution of the DNA repair enzymes' structures and GDs. Species GDs could be substantially influenced by the function of DNA polymerase I (the bacterial major DNA repair polymerase). This might cause the correlation of species GDs differentiation with evolutionary changes of species DNA polymerase I. Simultaneously, the structures of DNA repair-recombination enzymes might be evolutionarily sensitive and responsive to changes in the structure of their substrate-the DNA (including those that are represented by GD differentiation). We further discuss the rationale and mechanisms of the hypothesized coevolution. We suggest that stress might be an important cause of changes in the repair-recombination genes and the GD and the trigger of the aforementioned coevolution process. Other triggers might be massive horizontal gene transfer and ecological selection.

Larval development of Neostrongylus linearis (Nematoda, Protostrongylidae) in the mollusc Cochlicella barbara infected and maintained in a subhumid area (north-west Spain) and its possible influence on the infection of small ruminants

Twelve batches of 100 Cochlicella barbara (Mollusca, Helicidae) were deposited monthly, from January to December in plots (0.5 x 0.5 m) with faeces of sheep containing first-stage larvae of Neostrongylus linearis in order to be naturally infected, and another 12 batches acted as uninfected controls. Every 2 weeks dead molluscs were removed from the plots and three to five specimens were examined to study larval development in the snail. Infected and control snails did not differ in their mortality, which may be associated with the low rate of infection of snails. The highest number of molluscs that were infected and the maximum level of infection were observed in batches deposited in summer months. There was a positive correlation between the percentage of infected snails and temperature. Molluscs harboured higher number of infectious third-stage larvae (L3) from mid-spring to mid-autumn and especially in summer months; thus under these climatic conditions and periods small ruminants are more likely to get infected by N. linearis.

Larval development of Aelurostrongylus abstrusus (Nematoda, Angiostrongylidae) in experimentally infected Cernuella (Cernuella) virgata (Mollusca, Helicidae)

The larval development of the cat lungworm Aelurostrongylus abstrusus was studied for the first time in the helicid mollusc Cernuella (Cernuella) virgata, in order to know its performance as intermediate host (I.H.). This snail is very common in the north-west of Spain. First-stage larvae (L1) of A. abstrusus were obtained by the Baermann-Wetzel method from the faeces of a naturally infected cat. Then, 120 specimens of C. (C.) virgata were infected with 500 L1/snail and maintained under laboratory conditions (20+/-2 degrees C). Every 2 days, from day 8 to day 76 post-infection (p.i.), three snails were killed in order to study the larval development of the parasite. Morphological features of the different larval stages were also recorded. The apparent rate of penetration of L1 into the snail foot was 65.5%, but only 4.78% completed their development to the infective stage (L3). The total number of larvae was 49.8+/-28.8 larvae/snail and the average number of L3 was 23.9+/-18.4 L3/snail. The first L2 and L3 were observed on day 12 and day 18 p.i., respectively. From day 52 p.i. onwards, all larvae were at the infective stage in the snail. Considering those results, it was concluded that C. (C.) virgata is a suitable I.H. for A. abstrusus.

MAGE-A8 overexpression in transitional cell carcinoma of the bladder: identification of two tumour-associated antigen peptides

Bladder carcinoma is the fourth most common cancer in men and the eighth most common cancer among women. Our study is aimed to characterise tumour-associated antigen peptides of transitional cell carcinoma of the bladder (TCC). A DNA micro-array-based differential display analysis of 10 000 genes was carried out, and MAGE-A8 gene expression was detected in the tumour, and not in the normal bladder. High occurrence of MAGE-A8 expression was observed in fresh tumour samples (17 out of 23) and TCC lines (four of eight). The MAGE-A8 protein sequence was screened for HLA-A2.1-binding motifs, six potential peptides were synthesised, and peptides binding to HLA-A2.1 were assured. Immunogenicity and antigenicity of the MAGE-A8 peptides were examined in the HHD system, murine class I MHC knockout mice, transgenic for HLA-A2.1. The MAGE-A8 peptide immunogenicity was examined in three modes of vaccination, delivered intranasally with cholera toxin, injected into the tail base with complete Freund's adjuvant (CFA), or presented directly as loaded onto cell surface HLA-A2.1 molecules. Two peptides, 8.1 and 8.3, induce CTL that kills the T24 TCC line in vitro, and prime human lymphocyte response of healthy donors. These results demonstrate the potential use of the MAGE-A8 peptides for specific immunotherapy of TCC.