Genomica comparata di isolati di Trichoderma agenti di biocontrollo

Molti isolati di Trichoderma sono ben noti per i loro effetti benefici che si esplicano sia in termini di protezione delle piante contro fattori biotici e abiotici che di promozione della crescita. L’isolato Trichoderma gamsii 6085 è da tempo noto come agente di lotta biologica, in condizioni di laboratorio e in campo, contro gli agenti causali del Fusarium Head Blight (FHB) o Fusariosi del frumento, in particolare Fusarium graminearum e Fusarium culmorum, di cui,grazie alla sua abilità di crescere in presenza di deossinivalenolo, ne limita la crescita e la produzione di micotossine. Trichoderma harzianum 6776 svolge la sua azione benefica stimolando la crescita di pomodoro, attraverso un effetto di stimolo dell’attività fotosintetica, produzione di ormoni e presenza di zuccheri nella pianta. Inoltre è in grado di indurre resistenza a stress biotici ed abiotici. Nella presente tesi il DNA totale genomico di entrambi gli isolati è stato sequenziato mediante la tecnologia MiSeq Illumina, con sequenze mate pair-ends di 250bp. Le sequenze ottenute (copertura media 80X per T. harzianum e 90X per T. gamsii) sono state assemblate con Velvet versione 1.2.07. Il genoma assemblato di T. gamsii 6085 è risultato essere composto da 381 scaffolds con una lunghezza totale di 37.97 Mbp mentre quello di T. harzianum 6776 da 1573 scaffolds con una lunghezza totale di 39.73 Mbp. La completezza del genoma è stata valutata utilizzando CEGMA, che ha stimato la sequenza genomica essere completa al 98.39 % per T. harzianum 6776 e 87,58% per T. gamsii 6085). I genomi sono stati annotati in modo automatico con la pipeline MAKER2. Complessivamente sono stati identificati 10.944 modelli genici codificanti proteine contenute nel genoma nucleare in T. gamsii e 11.501 in T. harzianum. I proteomi predetti dei genomi degli isolati sequenziati sono stati comparati con altre specie appartenenti al genere Trichoderma e con un insieme di organismi aventi comportamento biologico simile e differente, in modo da poter individuare le espansioni delle famiglie geniche associate alle interazioni di agente di biocontrollo e di micoparassitismo degli isolati oggetto di studio. In dettaglio sono state caratterizzate le espansioni delle famiglie geniche delle classi enzimatiche appartenenti ai CaZY (Carbohydrate-Active enZYmes) coinvolte nel processo di micoparassitismo di Trichoderma. Tale studio ha l’obiettivo di fornire una piattaforma utile per ulteriori studi futuri di genomica funzionale quali analisi di trascrittomica, metabolomica e proteomica

Draft Whole-Genome Sequence of Trichoderma gamsii T6085, a Promising Biocontrol Agent of Fusarium Head Blight on Wheat

Trichoderma gamsii T6085 is a promising beneficial isolate whose effects consist of growth inhibition of the main agents causing Fusarium head blight, reduction of mycotoxin accumulation, competition for wheat debris, and reduction of the disease in both the lab and the field. Here, we present the first genome assembly of a T. gamsii isolate, providing a useful platform for the scientific community

Draft Whole-Genome Sequence of the Biocontrol Agent Trichoderma harzianum T6776

Trichoderma harzianum T6776 is a promising beneficial isolate whose effects consist of growth promotion, positive response of photosynthetic activity, hormonal signaling, and carbon partitioning in tomato, coupled with biocontrol of plant pathogens. Here, we present the first genome assembly of T6776, providing a useful platform for the scientific community

Faecal miRNA profiles associated with age, sex, BMI, and lifestyle habits in healthy individuals

Abstract For their stability and detectability faecal microRNAs represent promising molecules with potential clinical interest as non-invasive diagnostic and prognostic biomarkers. However, there is no evidence on how stool miRNA profiles change according to an individual’s age, sex, and body mass index (BMI) or how lifestyle habits influence the expression levels of these molecules. We explored the relationship between the stool miRNA levels and common traits (sex, age, BMI, and menopausal status) or lifestyle habits (physical activity, smoking status, coffee, and alcohol consumption) as derived by a self-reported questionnaire, using small RNA-sequencing data of samples from 335 healthy subjects. We detected 151 differentially expressed miRNAs associated with one variable and 52 associated with at least two. Differences in miR-638 levels were associated with age, sex, BMI, and smoking status. The highest number of differentially expressed miRNAs was associated with BMI (n = 92) and smoking status (n = 84), with several miRNAs shared between them. Functional enrichment analyses revealed the involvement of the miRNA target genes in pathways coherent with the analysed variables. Our findings suggest that miRNA profiles in stool may reflect common traits and lifestyle habits and should be considered in relation to disease and association studies based on faecal miRNA expression

Immune Trait Shifts in Association With Tobacco Smoking: A Study in Healthy Women.

Tobacco smoking is known to impact circulating levels of major immune cells populations, but its effect on specific immune cell subsets remains poorly understood. Here, using high-resolution data from 223 healthy women (25 current and 198 never smokers), we investigated the association between smoking status and 35,651 immune traits capturing immune cell subset frequencies. Our results confirmed that active tobacco smoking is associated with increased frequencies of circulating CD8+ T cells expressing the CD25 activation marker. Moreover, we identified novel associations between smoking status and relative abundances of CD8+ CD25+ memory T cells, CD8+ memory T cells expressing the CCR4 chemokine receptor, and CD4+CD8+ (double-positive) CD25+ T cells. We also observed, in current smokers, a decrease in the relative frequencies of CD4+ T cells expressing the CD38 activation marker and an increase in class-switched memory B cell isotypes IgA, IgG, and IgE. Finally, using data from 135 former female smokers, we showed that the relative frequencies of immune traits associated with active smoking are usually completely restored after smoking cessation, with the exception of subsets of CD8+ and CD8+ memory T cells, which persist partially altered. Our results are consistent with previous findings and provide further evidence on how tobacco smoking shapes leukocyte cell subsets proportion toward chronic inflammation

The 8q24 region hosts miRNAs altered in biospecimens of colorectal and bladder cancer patients

Abstract Background The 8q24 locus is enriched in cancer‐associated polymorphisms and, despite containing relatively few protein‐coding genes, it hosts the MYC oncogene and other genetic elements connected to tumorigenesis, including microRNAs (miRNAs). Research on miRNAs may provide insights into the transcriptomic regulation of this multiple cancer‐associated region. Material and methods We profiled all miRNAs located in the 8q24 region in 120 colorectal cancer (CRC) patients and 80 controls. miRNA profiling was performed on cancer/non‐malignant adjacent mucosa, stool, and plasma extracellular vesicles (EVs), and the results validated with The Cancer Genome Atlas (TCGA) data. To verify if the 8q24‐annotated miRNAs altered in CRC were dysregulated in other cancers and biofluids, we evaluated their levels in bladder cancer (BC) cases from the TCGA dataset and in urine and plasma EVs from a set of BC cases and healthy controls. Results Among the detected mature miRNAs in the region, 12 were altered between CRC and adjacent mucosa (adj. p < 0.05). Five and four miRNAs were confirmed as dysregulated in the CRC and BC TCGA dataset, respectively. A co‐expression analysis of tumor/adjacent tissue data from the CRC group revealed a correlation between the dysregulated miRNAs and CRC‐related genes (PVT1 and MYC) annotated in 8q24 region. miR‐30d‐5p and miR‐151a‐3p, altered in CRC tissue, were also dysregulated in stool of CRC patients and urine of BC cases, respectively. Functional enrichment of dysregulated miRNA target genes highlighted terms related to TP53‐mediated cell cycle control. Conclusions Altered expression of 8q24‐annotated miRNAs may be relevant for the initiation and/or progression of cancer