Metatranscriptomics sheds light on the links between the functional traits of fungal guilds and ecological processes in forest soil ecosystems.

Soil fungi belonging to different functional guilds, such as saprotrophs, pathogens, and mycorrhizal symbionts, play key roles in forest ecosystems. To date, no study has compared the actual gene expression of these guilds in different forest soils. We used metatranscriptomics to study the competition for organic resources by these fungal groups in boreal, temperate, and Mediterranean forest soils. Using a dedicated mRNA annotation pipeline combined with the JGI MycoCosm database, we compared the transcripts of these three fungal guilds, targeting enzymes involved in C- and N mobilization from plant and microbial cell walls. Genes encoding enzymes involved in the degradation of plant cell walls were expressed at a higher level in saprotrophic fungi than in ectomycorrhizal and pathogenic fungi. However, ectomycorrhizal and saprotrophic fungi showed similarly high expression levels of genes encoding enzymes involved in fungal cell wall degradation. Transcripts for N-related transporters were more highly expressed in ectomycorrhizal fungi than in other groups. We showed that ectomycorrhizal and saprotrophic fungi compete for N in soil organic matter, suggesting that their interactions could decelerate C cycling. Metatranscriptomics provides a unique tool to test controversial ecological hypotheses and to better understand the underlying ecological processes involved in soil functioning and carbon stabilization.

Effect of Atomic Layer Coating on the Stability of Solid Myoglobin Formulations.

The effects of atomic layer (ALC) coating on physical properties and storage stability were examined in solid powders containing myoglobin, a model protein. Powders containing myoglobin and mannitol (1:1 w/w) were prepared by lyophilization or spray drying and subjected to aluminum oxide or silicon oxide ALC coating. Uncoated samples of these powders as well as coated and uncoated samples of myoglobin as received served as controls. After preparation (t0), samples were analyzed for moisture content, reconstitution time, myoglobin secondary structure, crystallinity, and protein aggregate content. Samples were stored for 3 months (t3) under controlled conditions (53% RH, 40 °C) in both open and closed vials and then analyzed as above. At t3, the recovery of soluble native (i.e., monomeric) protein depended on formulation, coating type, and drying method and was up to 2-fold greater in coated samples than in uncoated controls. Promisingly, some samples with high recovery also showed low soluble aggregate content (<10%) at t3 and low total monomer loss; the latter was correlated to sample moisture content. Overall, the results demonstrate that ALC coatings can stabilize solid protein formulations during storage, providing benefits over uncoated controls.

Transcriptome Metabolic Characterization of Tuber borchii SP1-A New Spanish Strain for In Vitro Studies of the Bianchetto Truffle.

Truffles are ascomycete hypogeous fungi belonging to the Tuberaceae family of the Pezizales order that grow in ectomycorrhizal symbiosis with tree roots, and they are known for their peculiar aromas and flavors. The axenic culture of truffle mycelium is problematic because it is not possible in many cases, and the growth rate is meager when it is possible. This limitation has prompted searching and characterizing new strains that can be handled in laboratory conditions for basic and applied studies. In this work, a new strain of Tuber borchii (strain SP1) was isolated and cultured, and its transcriptome was analyzed under different in vitro culture conditions. The results showed that the highest growth of T. borchii SP1 was obtained using maltose-enriched cultures made with soft-agar and in static submerged cultures made at 22 °C. We analyzed the transcriptome of this strain cultured in different media to establish a framework for future comparative studies, paying particular attention to the central metabolic pathways, principal secondary metabolite gene clusters, and the genes involved in producing volatile aromatic compounds (VOCs). The results showed a transcription signal for around 80% of the annotated genes. In contrast, most of the transcription effort was concentrated on a limited number of genes (20% of genes account for 80% of the transcription), and the transcription profile of the central metabolism genes was similar in the different conditions analyzed. The gene expression profile suggests that T. borchii uses fermentative rather than respiratory metabolism in these cultures, even in aerobic conditions. Finally, there was a reduced expression of genes belonging to secondary metabolite clusters, whereas there was a significative transcription of those involved in producing volatile aromatic compounds.

Genomic Analysis Enlightens Agaricales Lifestyle Evolution and Increasing Peroxidase Diversity.

As actors of global carbon cycle, Agaricomycetes (Basidiomycota) have developed complex enzymatic machineries that allow them to decompose all plant polymers, including lignin. Among them, saprotrophic Agaricales are characterized by an unparalleled diversity of habitats and lifestyles. Comparative analysis of 52 Agaricomycetes genomes (14 of them sequenced de novo) reveals that Agaricales possess a large diversity of hydrolytic and oxidative enzymes for lignocellulose decay. Based on the gene families with the predicted highest evolutionary rates-namely cellulose-binding CBM1, glycoside hydrolase GH43, lytic polysaccharide monooxygenase AA9, class-II peroxidases, glucose-methanol-choline oxidase/dehydrogenases, laccases, and unspecific peroxygenases-we reconstructed the lifestyles of the ancestors that led to the extant lignocellulose-decomposing Agaricomycetes. The changes in the enzymatic toolkit of ancestral Agaricales are correlated with the evolution of their ability to grow not only on wood but also on leaf litter and decayed wood, with grass-litter decomposers as the most recent eco-physiological group. In this context, the above families were analyzed in detail in connection with lifestyle diversity. Peroxidases appear as a central component of the enzymatic toolkit of saprotrophic Agaricomycetes, consistent with their essential role in lignin degradation and high evolutionary rates. This includes not only expansions/losses in peroxidase genes common to other basidiomycetes but also the widespread presence in Agaricales (and Russulales) of new peroxidases types not found in wood-rotting Polyporales, and other Agaricomycetes orders. Therefore, we analyzed the peroxidase evolution in Agaricomycetes by ancestral-sequence reconstruction revealing several major evolutionary pathways and mapped the appearance of the different enzyme types in a time-calibrated species tree.

Comparative and transcriptional analysis of the predicted secretome in the lignocellulose-degrading basidiomycete fungus Pleurotus ostreatus.

Fungi interact with their environment by secreting proteins to obtain nutrients, elicit responses and modify their surroundings. Because the set of proteins secreted by a fungus is related to its lifestyle, it should be possible to use it as a tool to predict fungal lifestyle. To test this hypothesis, we bioinformatically identified 538 and 554 secretable proteins in the monokaryotic strains PC9 and PC15 of the white rot basidiomycete Pleurotus ostreatus. Functional annotation revealed unknown functions (37.2%), glycosyl hydrolases (26.5%) and redox enzymes (11.5%) as the main groups in the two strains. When these results were combined with RNA-seq analyses, we found that the relative importance of each group was different in different strains and culture conditions and the relevance of the unknown function proteins was enhanced. Only a few genes were actively expressed in a given culture condition in expanded multigene families, suggesting that family expansi on could increase adaptive opportunities rather than activity under a specific culture condition. Finally, we used the set of P. ostreatus secreted proteins as a query to search their counterparts in other fungal genomes and found that the secretome profiles cluster the tested basidiomycetes into lifestyle rather than phylogenetic groups.

Automated system for lung nodules classification based on wavelet feature descriptor and support vector machine.

BACKGROUND: Lung cancer is a leading cause of death worldwide; it refers to the uncontrolled growth of abnormal cells in the lung. A computed tomography (CT) scan of the thorax is the most sensitive method for detecting cancerous lung nodules. A lung nodule is a round lesion which can be either non-cancerous or cancerous. In the CT, the lung cancer is observed as round white shadow nodules. The possibility to obtain a manually accurate interpretation from CT scans demands a big effort by the radiologist and might be a fatiguing process. Therefore, the design of a computer-aided diagnosis (CADx) system would be helpful as a second opinion tool. METHODS: The stages of the proposed CADx are: a supervised extraction of the region of interest to eliminate the shape differences among CT images. The Daubechies db1, db2, and db4 wavelet transforms are computed with one and two levels of decomposition. After that, 19 features are computed from each wavelet sub-band. Then, the sub-band and attribute selection is performed. As a result, 11 features are selected and combined in pairs as inputs to the support vector machine (SVM), which is used to distinguish CT images containing cancerous nodules from those not containing nodules. RESULTS: The clinical data set used for experiments consists of 45 CT scans from ELCAP and LIDC. For the training stage 61 CT images were used (36 with cancerous lung nodules and 25 without lung nodules). The system performance was tested with 45 CT scans (23 CT scans with lung nodules and 22 without nodules), different from that used for training. The results obtained show that the methodology successfully classifies cancerous nodules with a diameter from 2 mm to 30 mm. The total preciseness obtained was 82%; the sensitivity was 90.90%, whereas the specificity was 73.91%. CONCLUSIONS: The CADx system presented is competitive with other literature systems in terms of sensitivity. The system reduces the complexity of classification by not performing the typical segmentation stage of most CADx systems. Additionally, the novelty of the algorithm is the use of a wavelet feature descriptor.

Highly expressed captured genes and cross-kingdom domains present in Helitrons create novel diversity in Pleurotus ostreatus and other fungi.

BACKGROUND: Helitrons are class-II eukaryotic transposons that transpose via a rolling circle mechanism. Due to their ability to capture and mobilize gene fragments, they play an important role in the evolution of their host genomes. We have used a bioinformatics approach for the identification of helitrons in two Pleurotus ostreatus genomes using de novo detection and homology-based searching. We have analyzed the presence of helitron-captured genes as well as the expansion of helitron-specific helicases in fungi and performed a phylogenetic analysis of their conserved domains with other representative eukaryotic species. RESULTS: Our results show the presence of two helitron families in P. ostreatus that disrupt gene colinearity and cause a lack of synteny between their genomes. Both putative autonomous and non-autonomous helitrons were transcriptionally active, and some of them carried highly expressed captured genes of unknown origin and function. In addition, both families contained eukaryotic, bacterial and viral domains within the helitron's boundaries. A phylogenetic reconstruction of RepHel helicases using the Helitron-like and PIF1-like helicase conserved domains revealed a polyphyletic origin for eukaryotic helitrons. CONCLUSION: P. ostreatus helitrons display features similar to other eukaryotic helitrons and do not tend to capture host genes or gene fragments. The occurrence of genes probably captured from other hosts inside the helitrons boundaries pose the hypothesis that an ancient horizontal transfer mechanism could have taken place. The viral domains found in some of these genes and the polyphyletic origin of RepHel helicases in the eukaryotic kingdom suggests that virus could have played a role in a putative lateral transfer of helitrons within the eukaryotic kingdom. The high similarity of some helitrons, along with the transcriptional activity of its RepHel helicases indicates that these elements are still active in the genome of P. ostreatus.

SECRETOOL: integrated secretome analysis tool for fungi.

The secretome (full set of secreted proteins) has been studied in multiple fungal genomes to elucidate the potential role of those protein collections involved in a number of metabolic processes from host infection to wood degradation. Being aminoacid composition a key factor to recognize secretory proteins, SECRETOOL comprises a group of web tools that enable secretome predictions out of aminoacid sequence files, up to complete fungal proteomes, in one step. SECRETOOL is freely available on the web at http://genomics.cicbiogune.es/SECRETOOL/Secretool.php .

Transcriptional and enzymatic profiling of Pleurotus ostreatus laccase genes in submerged and solid-state fermentation cultures.

The genome of the white rot basidiomycete Pleurotus ostreatus includes 12 phenol oxidase (laccase) genes. In this study, we examined their expression profiles in different fungal strains under different culture conditions (submerged and solid cultures) and in the presence of a wheat straw extract, which was used as an inducer of the laccase gene family. We used a reverse transcription-quantitative PCR (RT-qPCR)-based approach and focused on determining the reaction parameters (in particular, the reference gene set for the normalization and reaction efficiency determinations) used to achieve an accurate estimation of the relative gene expression values. The results suggested that (i) laccase gene transcription is upregulated in the induced submerged fermentation (iSmF) cultures but downregulated in the solid fermentation (SSF) cultures, (ii) the Lacc2 and Lacc10 genes are the main sources of laccase activity in the iSmF cultures upon induction with water-soluble wheat straw extracts, and (iii) an additional, as-yet-uncharacterized activity (Unk1) is specifically induced in SSF cultures that complements the activity of Lacc2 and Lacc10. Moreover, both the enzymatic laccase activities and the Lacc gene family transcription profiles greatly differ between closely related strains. These differences can be targeted for biotechnological breeding programs for enzyme production in submerged fermentation reactors.

Genomics and transcriptomics characterization of genes expressed during postharvest at 4°C by the edible basidiomycete Pleurotus ostreatus.

Pleurotus ostreatus is an industrially cultivated basidiomycete with nutritional and environmental applications. Its genome, which was sequenced by the Joint Genome Institute, has become a model for lignin degradation and for fungal genomics and transcriptomics studies. The complete P. ostreatus genome contains 35 Mbp organized in 11 chromosomes, and two different haploid genomes have been individually sequenced. In this work, genomics and transcriptomics approaches were employed in the study of P. ostreatus under different physiological conditions. Specifically, we analyzed a collection of expressed sequence tags (EST) obtained from cut fruit bodies that had been stored at 4°C for 7 days (postharvest conditions). Studies of the 253 expressed clones that had been automatically and manually annotated provided a detailed picture of the life characteristics of the self-sustained fruit bodies. The results suggested a complex metabolism in which autophagy, RNA metabolism, and protein and carbohydrate turnover are increased. Genes involved in environment sensing and morphogenesis were expressed under these conditions. The data improve our understanding of the decay process in postharvest mushrooms and highlight the use of high-throughput techniques to construct models of living organisms subjected to different environmental conditions.

Effect of Nutritional Factors and Copper on the Regulation of Laccase Enzyme Production in Pleurotus ostreatus.

This research aimed to establish the relationship between carbon-nitrogen nutritional factors and copper sulfate on laccase activity (LA) by Pleurotus ostreatus. Culture media composition was tested to choose the nitrogen source. Yeast extract (YE) was selected as a better nitrogen source than ammonium sulfate. Then, the effect of glucose and YE concentrations on biomass production and LA as response variables was evaluated using central composite experimental designs with and without copper. The results showed that the best culture medium composition was glucose 45 gL-1 and YE 15 gL-1, simultaneously optimizing these two response variables. The fungal transcriptome was obtained in this medium with or without copper, and the differentially expressed genes were found. The main upregulated transcripts included three laccase genes (lacc2, lacc6, and lacc10) regulated by copper, whereas the principal downregulated transcripts included a copper transporter (ctr1) and a regulator of nitrogen metabolism (nmr1). These results suggest that Ctr1, which facilitates the entry of copper into the cell, is regulated by nutrient-sufficiency conditions. Once inside, copper induces transcription of laccase genes. This finding could explain why a 10-20-fold increase in LA occurs with copper compared to cultures without copper when using the optimal concentration of YE as nitrogen sources.

Glucose counteracts wood-dependent induction of lignocellulolytic enzyme secretion in monokaryon and dikaryon submerged cultures of the white-rot basidiomycete Pleurotus ostreatus.

The secretome complexity and lignocellulose degrading capacity of Pleurotus ostreatus monokaryons mkPC9 and mkPC15 and mated dikaryon dkN001 were studied in submerged liquid cultures containing wood, glucose, and wood plus glucose as carbon sources. The study revealed that this white-rot basidiomycete attacks all the components of the plant cell wall. P. ostreatus secretes a variety of glycoside hydrolases, carbohydrate esterases, and polysaccharide lyases, especially when wood is the only carbon source. The presence of wood increased the secretome complexity, whereas glucose diminished the secretion of enzymes involved in cellulose, hemicellulose and pectin degradation. In contrast, the presence of glucose did not influence the secretion of redox enzymes or proteases, which shows the specificity of glucose on the secretion of cellulolytic enzymes. The comparison of the secretomes of monokaryons and dikaryons reveals that secretome complexity is unrelated to the nuclear composition of the strain.

The burden of 14 hr-HPV genotypes in women attending routine cervical cancer screening in 20 states of Mexico: a cross-sectional study.

In Mexico, HPV vaccines available immunize against genotypes 16/18 and 16/18/6/11; however, there is limited surveillance about carcinogenic subtypes in different states of the country that allow evaluating the effectiveness of vaccination and cervical cancer screening programs. Here, we report the regional and age-specific prevalence of 14 hr-HPV genotypes as well as their prevalence in abnormal cytology (from ASCUS to cervical cancer) among Mexican women which were undergoing from cervical cancer screening in the Salud Digna clinics in 20 states of the country. This study includes women with social security from the majority of public health institutions (IMSS, ISSSTE, SEMAR, and PEMEX), and women without social security. For cervical cancer screening, we used the SurePath liquid-based cytology and the BD Onclarity HPV Assay. From December 1, 2016, to August 2, 2018, the hr-HPV prevalence among 60,135 women was 24.78%, the most prevalent types were HPV 16 (4.13%), HPV 31 (4.12%) and HPV 51 (3.39%), while HPV 18 (1.70%) was less prevalent among infected women. Interestingly, the genotypes not covered by current vaccines in Mexico were commonly found in precancerous lesions, evidencing their carcinogenic potential, so it is necessary to increase their surveillance and inclusion in cervical cancer screening triage.

Comparative analysis of secretomes in basidiomycete fungi.

Lignocellulose, the major reservoir of organic carbon on Earth, is recalcitrant to turnover and resistant to microbial and enzymatic attack because of the protective action of lignin and the crystalline structure of cellulose. Basidiomycetes are the only organisms known to degrade lignocellulose using two alternative degradation strategies: white rot basidiomycetes break down the lignin moiety extensively before attacking the cellulose, whereas brown rot basidiomycetes cause limited lignin alteration while primarily degrading cellulose. These strategies depend on complex portfolios of extracellular enzymes whose production and export are environment and substrate dependent. More than 265 fungal genomes (more than 90 corresponding to basidiomycetes) have been sequenced. These sequences can be bioinformatically screened to identify presumptive secreted proteins that, however, differ from the experimental data, stressing the importance of using complementary approaches for analyzing these complex systems. The study of fungal secretomes from the scope of their different lignin degradation strategies and lifestyles would facilitate their use in the treatment of lignocellulose as carbon feedstock for biofuel production and further biorefinery processes. In this article, we carry out a comparative review of the analytical tools and strategies used for studying basidiomycetes' secretomes and compare the available results from these two points of view. BIOLOGICAL SIGNIFICANCE: In this article, we review the tools and strategies used in the analysis of basidiomycetes' secretomes and we compare the secretome data available for this type of fungi with a special emphasis on the enzymes involved in lignocellulose degradation. This comparative study provides a basis for distinguishing different lifestyles (saprotrophs, symbionts and parasites) on the basis of their respective secretomes.

Induction of laccase activity in the white rot fungus Pleurotus ostreatus using water polluted with wheat straw extracts.

The purpose of this work was to explore the use of polluted water effluents from wheat straw using industries as inducers of lignocellulolytic enzymatic activities in cultures of white rot basidiomycetes. For this purpose, we studied the effect of a wheat straw water extract on the evolution of the laccase activity recovered from submerged cultures of Pleurotus ostreatus made in different media and under various culture conditions. Our results demonstrated an accumulative induction effect in all the cultures and conditions tested. This induction is parallel to changes in the laccase electrophoretic profiles recovered from the culture supernatants. The isoenzyme that appeared to be mainly responsible for the laccase activity under these conditions was laccase 10, as confirmed by sequencing the induced protein. These results support the idea of using wheat straw effluents as inducers in liquid cultures of P. ostreatus mycelia for the production of ligninolytic enzymatic cocktails.

Bacteriemia transitoria post Proctosigmoidoscopía. / Transient Bacteriemia post Proctosigmoidoscopy.

En el presente trabajo se han estudiado 40 personas concurrentes al servicio de Gastroenterología del Hospital Hipólito Unanue. Se tomaron una muestra basal de sangre y muestras sucesivas al minuto, cinco, diez y quince minutos después de realizada la Proctosigmidoscopía, con jeringa y aguja descartable para cada muestra. El análisis de los hemocultivos demuestra que en todos los casos el hemocultivo basal, fue negativo, de los hemocultivos posteriores a la endoscopía, 5 casos correspondieron a Estafilococo Aureus, coagulasa negativo; un caso de Neisseria y un caso de Difteroide. De los 7 hemocultivos positivos, dos lo fueron en la segunda muestra, dos casos en la tercera y los tres restantes en la cuarta muestra. No hubo positividad en la quinta muestra. La positividad de los hemocultivos nos lleva a concluir que se presenta bacteriemia como posible complicación del exámen proctosigmoidoscópico, pero con la característica especial de ser transitoria, de corta duración, ya que se presenta sólo en los primeros minutos de realizado el examen, encontrándose la sangre, libre de bacterias, quince minutos después de la endoscopía.

La histerectomía obstétrica. Evolución y cambio / Obstetric hysterectomy. evolution and change

Se analiza un grupo seleccionado de pacientes en quienes se realizó histerectomía obstétrica que presentan la tendencia institucional para el manejo del embarazo, parto y puerperio complicados. No hubo mortalidad en las series pero la morbilidad se elevó hasta 65.21 por ciento. Se mantiene parcialmente el perfil de riesgo en cuanto a edad, embarazo de término, tipo de complicación del embarazo actual y cambia en cuanto a paridad (III-IV para la más frecuente) ausencia de antecedentes de operación cesárea y el tipo de morbilidad informado. Se recomienda un manejo preventivo integral y una indicación temprana con realización de técnica quirúrgica depurada en histerectomía total y extrafascial y un reconocimiento oportuno de las dificultades o problemas surgidos durante el evento quirúrgico

Ligadura de arterias hipogástricas análisis de 400 casos / Hypogastric arteries ligation analysis of 400 cases

Se presenta la experiencia de diez años en ligadura de arterias hipogástricas medida secundaria para el control del sangrado en un grupo seleccionado de 400 pacientes; las cuales habían tenido un manejo múltiple previo al procedimiento. Se señala el tipo de patología, los grupos de riesgo y los problemas que condicionaron la indicación. Se analiza la técnica quirúrgica, sus complicaciones y secuelas; con un seguimiento de dos años a 63.5 por ciento. La mortalidad depurada fue de 1 por ciento. Se concluye que la eficacia del procedimiento depende de su oportuna realización, adecuada indicación y buena técnica.