Fungal ecological strategies reflected in gene transcription - a case study of two litter decomposers.

Microbial communities interplay with their environment through their functional traits that can be a response or an effect on the environment. Here, we explore how a functional trait-the decomposition of organic matter, can be addressed based on genetic markers and how the expression of these markers reflect ecological strategies of two fungal litter decomposer Gymnopus androsaceus and Chalara longipes. We sequenced the genomes of these two fungi, as well as their transcriptomes at different steps of Pinus sylvestris needles decomposition in microcosms. Our results highlighted that if the gene content of the two species could indicate similar potential decomposition abilities, the expression levels of specific gene families belonging to the glycoside hydrolase category reflected contrasting ecological strategies. Actually, C. longipes, the weaker decomposer in this experiment, turned out to have a high content of genes involved in cell wall polysaccharides decomposition but low expression levels, reflecting a versatile ecology compare to the more competitive G. androsaceus with high expression levels of keystone functional genes. Thus, we established that sequential expression of genes coding for different components of the decomposer machinery indicated adaptation to chemical changes in the substrate as decomposition progressed

The transcriptional landscape of basidiosporogenesis in mature Pisolithus microcarpus basidiocarp

Changes in gene expression of gene families related with basidiocarp formation. (DOCX 124 kb

O poder e a luta pela propriedade da terra no vale do rio Iconha/Piúma: o caso Thomaz Dutton Junior (1870-1906)

Ao chegar ao povoado de Piúma, região sul capixaba, por volta dos anos iniciais da década de 1870, Thomaz Dutton Junior, inglês de nascimento e mais tarde naturalizado brasileiro, desejava fazer parte da boa sociedade e ter direito a todas as prerrogativas que o grupo proporcionaria. No território de Piúma, adquiriu boa parte da massa falida de João Baptista Rodocanachi, um comerciante grego de grosso trato que explorava madeiras de lei e as comercializava para construção civil e naval. Na fazenda Monte Bello, após instalar colonos ingleses, Thomaz Dutton se envolveu em querelas jurídico-fundiárias com mandões do lugar com quem tinha relações interdependentes, sobretudo com Alexandrino Pires Martins e José Gonçalves Costa Beiriz, que ocultavam, ao fim e ao cabo, um complexo jogo por disputas políticas locais, por prestígio, por boa reputação e poder. No seio dessas disputas estava a propriedade da terra, símbolo de poder e mando, que o levou à insolvência. Este estudo investiga a trajetória de Thomaz Dutton, pautando-se na teoria da Configuração de Norbert Elias associada à teoria do Poder Simbólico de Pierre Bourdier. Objetiva compreender a maneira como as práticas do poder são materializadas nas relações sociais, identificando a aprendizagem extraída de relações interdependentes bem como os valores construídos a partir delas. Parte de análises de fontes documentais, como relatórios presidenciais provinciais, requerimentos, atas, cartas e artigos de jornais corpus documental, dominante nesta investigação , buscando vestígios no conteúdo dos discursos ali inseridos para poder descortinar as tramas do tecido social com lentes de objetivas aumentadas. Desse modo, torna possível trazer à tona a história local do território do vale do Iconha/Piúma no espaço de tempo entre 1870 e 1906 e assim expor suas particularidades e singularidades, inserindo-a no contexto da história regional capixaba e nacional. Destarte, usando o alicerce teórico-metodológico já apresentado, destaca as particularidades e feitos do passado da sociedade piumense que ainda estavam fora do campo de experiência e precisavam ser conhecidas para fazer parte da História do Espírito Santo

Insight into trade‐off between wood decay and parasitism from the genome of a fungal forest pathogen

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/91191/1/j.1469-8137.2012.04128.x.pd

Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis

LetterInternational audienceThe Périgord black truffle ($Tuber\ melanosporum$ Vittad.) and the Piedmont white truffle dominate today's truffle market. The hypogeous fruiting body of $T.\ melanosporum$ is a gastronomic delicacy produced by an ectomycorrhizal symbiont endemic to calcareous soils in southern Europe. The worldwide demand for this truffle has fuelled intense efforts at cultivation. Identification of processes that condition and trigger fruit body and symbiosis formation, ultimately leading to efficient crop production, will be facilitated by a thorough analysis of truffle genomic traits. In the ectomycorrhizal $Laccaria\ bicolor$, the expansion of gene families may have acted as a 'symbiosis toolbox'. This feature may however reflect evolution of this particular taxon and not a general trait shared by all ectomycorrhizal species. To get a better understanding of the biology and evolution of the ectomycorrhizal symbiosis, we report here the sequence of the haploid genome of $T.\ melanosporum$, which at $\sim$125 megabases is the largest and most complex fungal genome sequenced so far. This expansion results from a proliferation of transposable elements accounting for $\sim$58% of the genome. In contrast, this genome only contains $\sim$7,500 protein-coding genes with very rare multigene families. It lacks large sets of carbohydrate cleaving enzymes, but a few of them involved in degradation of plant cell walls are induced in symbiotic tissues. The latter feature and the upregulation of genes encoding for lipases and multicopper oxidases suggest that $T.\ melanosporum$ degrades its host cell walls during colonization. Symbiosis induces an increased expression of carbohydrate and amino acid transporters in both $L.\ bicolor$ and $T.\ melanosporum$, but the comparison of genomic traits in the two ectomycorrhizal fungi showed that genetic predispositions for symbiosis $-$'the symbiosis toolbox'$-$ evolved along different ways in ascomycetes and basidiomycete

Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits

Mycorrhizal fungi are mutualists that play crucial roles in nutrient acquisition in terrestrial ecosystems. Mycorrhizal symbioses arose repeatedly across multiple lineages of Mucoromycotina, Ascomycota, and Basidiomycota. Considerable variation exists in the capacity of mycorrhizal fungi to acquire carbon from soil organic matter. Here, we present a combined analysis of 135 fungal genomes from 73 saprotrophic, endophytic and pathogenic species, and 62 mycorrhizal species, including 29 new mycorrhizal genomes. This study samples ecologically dominant fungal guilds for which there were previously no symbiotic genomes available, including ectomycorrhizal Russulales, Thelephorales and Cantharellales. Our analyses show that transitions from saprotrophy to symbiosis involve (1) widespread losses of degrading enzymes acting on lignin and cellulose, (2) co-option of genes present in saprotrophic ancestors to fulfill new symbiotic functions, (3) diversification of novel, lineage-specific symbiosis-induced genes, (4) proliferation of transposable elements and (5) divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild. Mycorrhizal symbioses have evolved repeatedly in diverse fungal lineages. A large phylogenomic analysis sheds light on genomic changes associated with transitions from saprotrophy to symbiosis, including divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild.Peer reviewe

Common variants in Alzheimer’s disease and risk stratification by polygenic risk scores

Funder: Funder: Fundación bancaria ‘La Caixa’ Number: LCF/PR/PR16/51110003 Funder: Grifols SA Number: LCF/PR/PR16/51110003 Funder: European Union/EFPIA Innovative Medicines Initiative Joint Number: 115975 Funder: JPco-fuND FP-829-029 Number: 733051061Genetic discoveries of Alzheimer's disease are the drivers of our understanding, and together with polygenetic risk stratification can contribute towards planning of feasible and efficient preventive and curative clinical trials. We first perform a large genetic association study by merging all available case-control datasets and by-proxy study results (discovery n = 409,435 and validation size n = 58,190). Here, we add six variants associated with Alzheimer's disease risk (near APP, CHRNE, PRKD3/NDUFAF7, PLCG2 and two exonic variants in the SHARPIN gene). Assessment of the polygenic risk score and stratifying by APOE reveal a 4 to 5.5 years difference in median age at onset of Alzheimer's disease patients in APOE ɛ4 carriers. Because of this study, the underlying mechanisms of APP can be studied to refine the amyloid cascade and the polygenic risk score provides a tool to select individuals at high risk of Alzheimer's disease

Multiancestry analysis of the HLA locus in Alzheimer’s and Parkinson’s diseases uncovers a shared adaptive immune response mediated by HLA-DRB1*04 subtypes

Across multiancestry groups, we analyzed Human Leukocyte Antigen (HLA) associations in over 176,000 individuals with Parkinson’s disease (PD) and Alzheimer’s disease (AD) versus controls. We demonstrate that the two diseases share the same protective association at the HLA locus. HLA-specific fine-mapping showed that hierarchical protective effects of HLA-DRB1*04 subtypes best accounted for the association, strongest with HLA-DRB1*04:04 and HLA-DRB1*04:07, and intermediary with HLA-DRB1*04:01 and HLA-DRB1*04:03. The same signal was associated with decreased neurofibrillary tangles in postmortem brains and was associated with reduced tau levels in cerebrospinal fluid and to a lower extent with increased Aβ42. Protective HLA-DRB1*04 subtypes strongly bound the aggregation-prone tau PHF6 sequence, however only when acetylated at a lysine (K311), a common posttranslational modification central to tau aggregation. An HLA-DRB1*04-mediated adaptive immune response decreases PD and AD risks, potentially by acting against tau, offering the possibility of therapeutic avenues

Dépistage du cancer des reins natifs chez les transplantés rénaux (évaluation des pratiques nancéennes)

[L évolution des traitements immunosuppresseurs et de la prise en charge des patients transplantés rénaux, a conduit à une survie plus longue, mais également à la survenue de complications de type néoplasique, notamment les carcinomes rénaux. Un dépistage de ces cancers est donc recommandé. Celui-ci se fait historiquement par échographie annuelle, mais devant la difficulté d analyse des reins souvent atrophiques et multikystiques des insuffisants rénaux, un dépistage par scanner systématique a été proposé. Le but de cette étude est d évaluer l incidence des carcinomes rénaux chez les patients transplantés du centre de Nancy, et de déterminer les avantages éventuels apportés par le scanner. La cohorte de transplantés comprend 711 patients, parmi lesquels 19 ont présenté une tumeur rénale. Neuf patients appartiennent au groupe de dépistage échographique, et 10 au groupe de dépistage scannographique. En comparant les deux groupes en ce qui concerne le temps passé en dialyse, l âge au moment du diagnostic, le délai entre la transplantation rénale et le diagnostic de tumeur à l imagerie, et la taille des tumeurs, nous ne retrouvons pas de différence significative. Par contre nous pouvons dire que dans le groupe au dépistage scannographique il n y a pas de grosse tumeur. Dans les deux groupes la survie est bonne, avec un seul décès imputable au cancer sur les 19 patients. En ce qui concerne l imputabilité de l immunosuppression, elle n est pas seule en cause. En effet, les patients au stade d insuffisance rénale chronique et de dialyse présente un excès de risque par rapport à la population générale. En conclusion les cancers des reins natifs chez les transplantés sont de bon pronostic, et d évolution lente. Le dépistage échographique par des opérateurs entraînés donne de bons résultats][With the progress done in immunosuppressive therapies, and in the care of kidney transplant recipients, the survival of the graft gets longer and longer. Due to this low immunity, some neoplasic complications tend to occur, such as renal cell carcinoma of the native kidneys. The screening with ultrasound of the kidneys is known to be difficult, thus we suggested screening with computed tomography starting the third year post transplantation, and then every other year. The purpose of this study is to evaluate the incidence of renal cell carcinoma in kidney transplant recipients, and to determine if computed tomography is more efficient than ultrasound. 711 patients have been included in this study, amongst whom 19 have developed renal cell carcinoma. Nine of them belong to the group screened with ultrasound, and ten of them were screened with computed tomography. The time spent on dialysis, the time between the transplantation and the diagnosis of cancer, and the size of the tumours once the diagnosis is set, are not different in the two groups. We can notice in this study an increased incidence of renal cell carcinoma in the transplant population, in contrast with the general population. However the number of cancer screened with computed tomography is not significantly higher than the one screened with ustrasound. Regarding the imputability of the immunosuppression in this increased incidence, it is not the only cause, as patients with chronic renal failure, and patients on dialysis, also present a higher risk of developing renal cell carcinoma. The prognosis of suchtumour is good, since the survival rate reaches 92% after five years]NANCY1-Bib. numérique (543959902) / SudocSudocFranceF

Deep RNA sequencing improved the structural annotation of the Tuber melanosporum transcriptome

International audienceThe functional complexity of the Tuber melanosporum transcriptome has not yet been fully elucidated. Here, we applied high-throughput Illumina RNA-sequencing (RNA-Seq) to the transcriptome of T. melanosporum at different major developmental stages, that is free-living mycelium, fruiting body and ectomycorrhiza. Sequencing of cDNA libraries generated a total of c. 24 million sequence reads representing >882 Mb of sequence data. To construct a coverage signal profile across the genome, all reads were then aligned to the reference genome assembly of T. melanosporum Mel28. We were able to identify a substantial number of novel transcripts, antisense transcripts, new exons, untranslated regions (UTRs), alternative upstream initiation codons and upstream open reading frames. This RNA-Seq analysis allowed us to improve the genome annotation. It also provided us with a genome-wide view of the transcriptional and post-transcriptional mechanisms generating an increased number of transcript isoforms during major developmental transitions in T. melanosporum