18 research outputs found
Draft Whole-Genome Sequence of Trichoderma gamsii T6085, a Promising Biocontrol Agent of Fusarium Head Blight on Wheat
No full textTrichoderma 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
No full textTrichoderma 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
Genomica comparata di isolati di Trichoderma agenti di biocontrollo
No full textMolti 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
The 8q24 region hosts miRNAs altered in biospecimens of colorectal and bladder cancer patients
No full textBackground: 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
Evaluation of DNA methylation in leukocyte subpopulations associated with tobacco smoking exposure
No full textSmall noncoding RNAs and sperm nuclear basic proteins reflect the environmental impact on germ cells
No full textBackground: Molecular techniques can complement conventional spermiogram analyses to provide new information on the fertilizing potential of spermatozoa and to identify early alterations due to environmental pollution. Methods: Here, we present a multilevel molecular profiling by small RNA sequencing and sperm nuclear basic protein analysis of male germ cells from 33 healthy young subjects residing in low and high-polluted areas. Results: Although sperm motility and sperm concentration were comparable between samples from the two sites, those from the high-pollution area had a higher concentration of immature/immune cells, a lower protamine/histone ratio, a reduced ability of sperm nuclear basic proteins to protect DNA from oxidative damage, and an altered copper/zinc ratio in sperm. Sperm levels of 32 microRNAs involved in intraflagellar transport, oxidative stress response, and spermatogenesis were different between the two areas. In parallel, a decrease of Piwi-interacting RNA levels was observed in samples from the high-polluted area. Conclusions: This comprehensive analysis provides new insights into pollution-driven epigenetic alterations in sperm not detectable by spermiogram
Fecal miRNA profiles and gut metagenome composition in Lynch syndrome: results from a mouse model study and human subjects
No full textSmall noncoding RNAs and sperm nuclear basic proteins reflect the environmental impact on germ cells
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