RESUMO
The greater amberjack Seriola dumerili is a promising candidate for aquaculture production. This study compares the ovary transcriptome of greater amberjack sampled in the wild (WILD) with hatchery-produced breeders reared in aquaculture sea cages in the Mediterranean Sea. Among the seven sampled cultured fish, three were classified as reproductively dysfunctional (DysF group), while four showed no signs of reproductive alteration (NormalF group). The DysF fish showed 1,166 differentially expressed genes (DEGs) compared to WILD females, and 755 DEGs compared to the NormalF. According to gene ontology (GO) analysis, DysF females exhibited enrichment of genes belonging to the biological categories classified as Secreted, ECM-receptor interaction, and Focal adhesion. Protein-protein interaction analysis revealed proteins involved in the biological categories of ECM-receptor interaction, Enzyme-linked receptor protein signaling, Wnt signal transduction pathways, and Ovulation cycle. KEGG pathway analysis showed DEGs involved in 111 pathways, including Neuroactive ligand-receptor interaction, Steroid hormone biosynthesis, Cell cycle, Oocyte meiosis, Necroptosis, Ferroptosis, Apoptosis, Autophagy, Progesterone-mediated oocyte maturation, Endocytosis and Phagosome, as well as Hedgehog, Apelin, PPAR, Notch, and GnRH signalling pathways. Additionally, DysF females exhibited factors encoded by upregulated genes associated with hypogonadism and polycystic ovary syndrome in mammals. This study -which is part of a broader research effort examining the transcriptome of the entire reproductive axis in greater amberjack of both sexes-, enhances our comprehension of the mechanisms underlying the appearance of reproductive dysfunctions when fish are reared under aquaculture conditions.
Assuntos
Ovário , Transcriptoma , Animais , Feminino , Ovário/metabolismo , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Aquicultura , Peixes/genética , Perfilação da Expressão Gênica , Ontologia GenéticaRESUMO
Amyotrophic Lateral Sclerosis (ALS) is a progressive disease with prevalent mitochondrial dysfunctions affecting both upper and lower motor neurons in the motor cortex, brainstem, and spinal cord. Despite mitochondria having their own genome (mtDNA), in humans, most mitochondrial genes are encoded by the nuclear genome (nDNA). Our study aimed to simultaneously screen for nDNA and mtDNA genomes to assess for specific variant enrichment in ALS compared to control tissues. Here, we analysed whole exome (WES) and whole genome (WGS) sequencing data from spinal cord tissues, respectively, of 6 and 12 human donors. A total of 31,257 and 301,241 variants in nuclear-encoded mitochondrial genes were identified from WES and WGS, respectively, while mtDNA reads accounted for 73 and 332 variants. Despite technical differences, both datasets consistently revealed a specific enrichment of variants in the mitochondrial Control Region (CR) and in several of these genes directly associated with mitochondrial dynamics or with Sirtuin pathway genes within ALS tissues. Overall, our data support the hypothesis of a variant burden in specific genes, highlighting potential actionable targets for therapeutic interventions in ALS.
Assuntos
Esclerose Lateral Amiotrófica , DNA Mitocondrial , Sirtuínas , Medula Espinal , Esclerose Lateral Amiotrófica/genética , Esclerose Lateral Amiotrófica/metabolismo , Humanos , Medula Espinal/metabolismo , Medula Espinal/patologia , DNA Mitocondrial/genética , Sirtuínas/genética , Sirtuínas/metabolismo , Masculino , Feminino , Pessoa de Meia-Idade , Mitocôndrias/genética , Mitocôndrias/metabolismo , Núcleo Celular/genética , Núcleo Celular/metabolismo , Idoso , Sequenciamento do ExomaRESUMO
BACKGROUND: Macroalgae, especially reds (Rhodophyta Division) and browns (Phaeophyta Division), are known for producing various halogenated compounds. Yet, the reasons underlying their production and the fate of these metabolites remain largely unknown. Some theories suggest their potential antimicrobial activity and involvement in interactions between macroalgae and prokaryotes. However, detailed investigations are currently missing on how the genetic information of prokaryotic communities associated with macroalgae may influence the fate of organohalogenated molecules. RESULTS: To address this challenge, we created a specialized dataset containing 161 enzymes, each with a complete enzyme commission number, known to be involved in halogen metabolism. This dataset served as a reference to annotate the corresponding genes encoded in both the metagenomic contigs and 98 metagenome-assembled genomes (MAGs) obtained from the microbiome of 2 red (Sphaerococcus coronopifolius and Asparagopsis taxiformis) and 1 brown (Halopteris scoparia) macroalgae. We detected many dehalogenation-related genes, particularly those with hydrolytic functions, suggesting their potential involvement in the degradation of a wide spectrum of halocarbons and haloaromatic molecules, including anthropogenic compounds. We uncovered an array of degradative gene functions within MAGs, spanning various bacterial orders such as Rhodobacterales, Rhizobiales, Caulobacterales, Geminicoccales, Sphingomonadales, Granulosicoccales, Microtrichales, and Pseudomonadales. Less abundant than degradative functions, we also uncovered genes associated with the biosynthesis of halogenated antimicrobial compounds and metabolites. CONCLUSION: The functional data provided here contribute to understanding the still largely unexplored role of unknown prokaryotes. These findings support the hypothesis that macroalgae function as holobionts, where the metabolism of halogenated compounds might play a role in symbiogenesis and act as a possible defense mechanism against environmental chemical stressors. Furthermore, bacterial groups, previously never connected with organohalogen metabolism, e.g., Caulobacterales, Geminicoccales, Granulosicoccales, and Microtrichales, functionally characterized through MAGs reconstruction, revealed a biotechnologically relevant gene content, useful in synthetic biology, and bioprospecting applications. Video Abstract.
Assuntos
Anti-Infecciosos , Microbiota , Rodófitas , Alga Marinha , Rodófitas/genética , Rodófitas/metabolismo , Microbiota/genética , Bactérias/genética , Bactérias/metabolismo , Alga Marinha/genética , Alga Marinha/metabolismo , Metagenoma , Halogênios/metabolismoRESUMO
Emerging evidence shows that oral squamous cell carcinoma (OSCC) invasiveness can be attributed to a small subpopulation of cancer stem cells (CSCs) in the bulk of the tumor. However, the presence of CSCs in the OSCC close resection margins is still poorly unexplored. Here, we found that BMI1, CD44, SOX2, OCT4, UBE2C, CXCR4 CSCs marker genes are significantly upregulated, while IGF1-R, KLF4, ALDH1A1, CD133, FAM3C are downregulated in the tumor core vs healthy mucosa of 24 patients with OSCC. Among these, SOX2 appears also upregulated in the tumor close margin vs healthy mucosa and this significantly correlates with tumor size and lymph node compromise. In vitro analyses in CAL27 and SCC15 tongue squamous cell carcinoma cell lines, show that SOX2 transient knockdown i) promotes the mesenchymal-to-epithelial transition, ii) smooths the invasiveness, iii) attenuates the 3D tumor sphere-forming capacity, and iv) partially increases the sensitivity to cisplatin treatment. Overall, our study highlights that the OSCC close margins can retain CSC-specific markers. Notably, SOX2 may represent a useful CSCs marker to predict a more aggressive phenotype and a suitable target to prevent local invasiveness.
Assuntos
Carcinoma de Células Escamosas , Neoplasias de Cabeça e Pescoço , Neoplasias Bucais , Neoplasias da Língua , Humanos , Carcinoma de Células Escamosas/patologia , Carcinoma de Células Escamosas de Cabeça e Pescoço/patologia , Neoplasias Bucais/patologia , Neoplasias da Língua/patologia , Neoplasias de Cabeça e Pescoço/patologia , Células-Tronco Neoplásicas/metabolismo , Fenótipo , Linhagem Celular Tumoral , Fatores de Transcrição SOXB1/genética , Fatores de Transcrição SOXB1/metabolismo , Proteínas de Neoplasias/genética , Citocinas/metabolismoRESUMO
Key Clinical Message: Conventional treatments of anaplastic meningioma include surgery and radiotherapy. Temozolomide is also an option. Metastases to extracerebral organs are very rare and hardly manageable. Antiangiogenic drugs could represent a salvage therapy. Abstract: Anaplastic meningioma is an unusual tumor subtype that rarely involves organs outside the brain. In our case, a patient with cerebral meningioma developed lung metastases after 19 years from the initial tumor appearance. This unpredictable behavior could make complex the diagnosis.
RESUMO
Reproductive dysfunctions have been recently documented in male greater amberjack Seriola dumerili caught from the wild and reared in captivity. In the present study, we compared testis transcriptome in wild fish (WILD), hatchery-produced fish with apparently normal spermatogenesis (Normal Farmed; NormalF) and hatchery-produced fish with evident reproductive dysfunction (Dysfunctional Farmed; DysF). Gene expression analysis identified 2157, 1985 and 74 differentially expressed genes (DEGs) in DysF vs WILD, NormalF vs DysF and NormalF vs WILD comparisons, respectively. In DysF, a dysregulation of several interconnected biological processes, including cell assembly, steroidogenesis and apoptosis was found. Gene enrichment of progesterone-mediated oocyte maturation, oocyte meiosis and cell cycle pathways were identified in the DysF vs NormalF comparison. Most of the DEGs involved in the enriched pathways were downregulated in DysF. The comparison of NormalF vs WILD showed that most of the DEGs were downregulated in NormalF, including a gene that encodes for a regulatory protein with a protective role in apoptosis regulation (ptpn6), indicating that spermatogenesis was dysfunctional also in the apparently "normal" hatchery-produced fish. Hence, rearing of male greater amberjack in captivity, from eggs produced by captive breeders, did not prevent the appearance of reproductive dysfunctions, and these dysfunctions involved several biological processes and metabolic pathways.
Assuntos
Perciformes , Testículo , Masculino , Animais , Espermatogênese/genética , Meiose/genética , RNA Mensageiro/genéticaRESUMO
Fire events in agricultural soils can modify not only soil properties but also the structure of soil microbial communities, especially in soils containing high concentrations of potentially toxic elements (PTEs). The recolonization of burned soils can in fact favor the proliferation of certain microorganisms, more adaptable to post-fire soil conditions and higher PTE availability, over others. In this study, we simulated with laboratory experiments the microbial recolonization of an agricultural soil containing high Cr concentrations after heating at 500 °C for 30 min, to mimic the burning of crop residues. Changes in soil properties and Cr speciation were assessed, as well as soil microbial structure by means of 16S rRNA gene sequencing. Both altered soil conditions and increased Cr availability, especially Cr(VI), appeared to be responsible for the reduction in species diversity in heated soils and the proliferation of Firmicutes. Indeed, already after 3 days from the heat treatment, Firmicutes increased from 14% to 60% relative abundance. In particular, Paenibacillus was the most abundant genus identified after the simulation, with an average relative abundance of 40%. These bacteria are known to be good fire-responders and Cr-tolerant. These results could be useful to identify bacterial strains to be used as bioindicators of altered environments and for the recovery of fire-impacted polluted sites.
RESUMO
Staphylococcus cohnii (SC), a coagulase-negative bacterium, was first isolated in 1975 from human skin. Early phenotypic analyses led to the delineation of two subspecies (subsp.), Staphylococcus cohnii subsp. cohnii (SCC) and Staphylococcus cohnii subsp. urealyticus (SCU). SCC was considered to be specific to humans, whereas SCU apparently demonstrated a wider host range, from lower primates to humans. The type strains ATCC 29974 and ATCC 49330 have been designated for SCC and SCU, respectively. Comparative analysis of 66 complete genome sequences-including a novel SC isolate-revealed unexpected patterns within the SC complex, both in terms of genomic sequence identity and gene content, highlighting the presence of 3 phylogenetically distinct groups. Based on our observations, and on the current guidelines for taxonomic classification for bacterial species, we propose a revision of the SC species complex. We suggest that SCC and SCU should be regarded as two distinct species: SC and SU (Staphylococcus urealyticus), and that two distinct subspecies, SCC and SCB (SC subsp. barensis, represented by the novel strain isolated in Bari) should be recognized within SC. Furthermore, since large-scale comparative genomics studies recurrently suggest inconsistencies or conflicts in taxonomic assignments of bacterial species, we believe that the approach proposed here might be considered for more general application.
Assuntos
Staphylococcus/classificação , Genes Bacterianos , Genoma Bacteriano , Genômica , Hibridização de Ácido Nucleico , Filogenia , Staphylococcus/genética , Staphylococcus/isolamento & purificação , Sequenciamento Completo do GenomaRESUMO
Coagulase Negative Staphylococci (CoNS) are becoming increasingly recognized as an important cause of human and animal infections. Notwithstanding their clinical relevance, annotation of genes potentially involved in pathogenicity and/or antibiotic resistance in the CoNS species Staphylococcus arlettae (SAR) is currently very limited. In the current work we describe the genome of a novel methicillin resistant isolate of SAR, which we named Bari, and present a comprehensive analysis of predicted antibiotic resistance profiles and virulence determinants for all the 22 currently available SAR genomes. By comparing predicted antibiotic resistance and virulence-associated genes with those obtained from a manual selection of 148 bacterial strains belonging to 14 different species of staphylococci and to two "outgroup" species, Bacillus subtilis (BS) and Macrococcus caseoliticus (MC), we derived some interesting observations concerning the types and number of antibiotic resistance-related and virulence-like genes in SAR. Interestingly, almost 50% of the putative antibiotic resistance determinants identified in this work, which include the clinically relevant mec, van, and cls genes, were shared among all the SAR strains herein considered (Bari included). Moreover, comparison of predicted antibiotic resistance profiles suggest that SAR is closely related to well-known pathogenic Staphylococcus species, such as Staphylococcus aureus (SA) and Staphylococcus epidermidis (SE). A similar analysis of predicted virulence factors, revealed that several genes associated with pathogenesis (including, for example, ica, nuc, and ssp), which are commonly found in the genomes of pathogenic staphylococci such as Staphylococcus haemolyticus (SH) and Staphylococcus saprophyticus (SS), are observed also in the SAR strains for which a genomic sequence is available. All in all, we believe that the analyses presented in the current study, by providing a consistent and comprehensive annotation of virulence and antibiotic resistance-related genes in SAR, can constitute a valuable resource for the study of molecular mechanisms of opportunistic pathogenicity in this species.
RESUMO
The genome sequences of three new strains of Staphylococcus arlettae named Bari1, Bari2, and Bari3 are presented. The strains exhibited tolerance to hexavalent chromium ions. An sprC gene encoding a putative chromium transporter was present in each of the three draft genome sequences.
RESUMO
In order to identify antifungal compounds from natural sources to be used as ingredients in the bakery industry, water/salt-soluble extracts (WSE) from different legume flour hydrolysates obtained by the use of a fungal protease were assayed against Penicillium roqueforti DPPMAF1. The agar diffusion assays allowed the selection of the pea (Pisum sativum) hydrolysate as the most active. As shown by the hyphal radial growth rate, the WSE had inhibitory activity towards several fungi isolated from bakeries. The MIC of the WSE was 9.0 mg/ml. Fungal inhibition was slightly affected by heating and variations in pH. The antifungal activity was attributed to three native proteins (pea defensins 1 and 2 and a nonspecific lipid transfer protein [nsLTP]) and a mixture of peptides released during hydrolysis. The three proteins have been reported previously as components of the defense system of the plant. Five peptides were purified from WSE and were identified as sequences encrypted in leginsulin A, vicilin, provicilin, and the nsLTP. To confirm antifungal activity, the peptides were chemically synthesized and tested. Freeze-dried WSE were used as ingredients in leavened baked goods. In particular, breads made by the addition of 1.6% (wt/wt) of the extract and fermented by baker's yeast or sourdough were characterized for their main chemical, structural, and sensory features, packed in polyethylene bags, stored at room temperature, and compared to controls prepared without pea hydrolysate. Artificially inoculated slices of a bread containing the WSE did not show contamination by fungi until at least 21 days of storage and behaved like the bread prepared with calcium propionate (0.3%, wt/wt).