Protein functional domain analysis enhances genotype-phenotype associations in comparative genomic studies of .

Introduction: represents a paradigm for studies on antibiotic resistance. Nevertheless, despite the considerable number of genome sequences that have been released in recent years, there is still a paucity of knowledge regarding the genomic determinants of the typical phenotypic traits associated with pulmonary infection.

Methods: The genomes of 40 strains of were sequenced over an 8-year period (2007-2014), isolated from the sputum of a single patient with cystic fibrosis in Trentino, Italy.

Bioinformatics and modelling studies of FhuD, the periplasmic siderophore binding protein from the plant pathogen Erwinia amylovora.

Erwinia amylovora, a Gram-negative phytopathogenic bacterium, is the etiological agent of fire blight in apples and pears. Key virulence factors include the exopolysaccharide amylovoran, the type III secretion system, and siderophore-mediated iron uptake. Within the iron uptake pathway, the periplasmic siderophore binding protein FhuD, unique to Erwinia species infecting Rosaceae, plays a vital role in transporting iron-loaded siderophores to the inner periplasmic membrane, making it a crucial target for structural and functional characterization.

The Genetic Background and Culture Medium Only Marginally Affect the In Vitro Evolution of Toward Colistin Resistance.

Colistin is a last-resort treatment for multidrug-resistant infections, but resistance to it is emerging. While colistin resistance in is typically associated with chromosomal mutations inducing lipopolysaccharide (LPS) aminoarabinosylation, other mutations unrelated to LPS modifications have been proposed to influence the extent of colistin resistance. Here, we examined whether the genetic background and culture conditions affect the evolution of high-level colistin resistance in this bacterium.

An in Planta Enrichment Route to Identify Bacterial Root Endophytes.

Microorganisms live in close association with plants, forming ecological interaction webs and providing beneficial traits such as nutrition, growth, and tolerance to biotic and abiotic stresses. Via the rhizosphere, plants recruit bacteria which colonise internal plant tissues, creating a spatial gradient between the rhizosphere and the endosphere. This study presents a high throughput in planta endophyte enrichment scheme designed for the identification of 'super'-endophytic bacteria which can serially colonise the rice root endosphere.

Sorghum rhizosphere bacteriome studies and generation of multistrain beneficial bacterial consortia.

The plant rhizosphere microbiome plays a crucial role in plant growth and health. Within this microbiome, bacteria dominate, exhibiting traits that benefit plants, such as facilitating nutrient acquisition, fixing nitrogen, controlling pathogens, and promoting root growth. This study focuses on designing synthetic bacterial consortia using key bacterial strains which have been mapped and then isolated from the sorghum rhizosphere microbiome.

A Longitudinal Study of Clinical Isolates from the Tracheal Aspirates of a Paediatric Patient-Strain Type Similar to Pandemic ST131.

is a Gram-negative bacterium and part of the intestinal microbiota. However, it can cause various diarrhoeal illnesses, i.e.

Overexpression of CCL-20 and CXCL-8 genes enhances tumor escape and resistance to cemiplimab, a programmed cell death protein-1 (PD-1) inhibitor, in patients with locally advanced and metastatic cutaneous squamous cell carcinoma.

Cemiplimab has demonstrated relevant clinical activity in cutaneous squamous cell carcinoma (cSCC) but mechanisms of primary and acquired resistance to immunotherapy are still unknown. We collected clinical data from locally advanced and/or metastatic cSSC patients treated with cemiplimab in two Italian University centers. In addition, gene expression analysis by using Nanostring Technologies platform to evaluate 770 cancer- and immune-related genes on 20 tumor tissue samples (9 responders and 11 non-responders to cemiplimab) was performed.

Camel Milk Resistome in Kuwait: Genotypic and Phenotypic Characterization.

Antimicrobial resistance (AMR) is one of the major global health and economic threats. There is growing concern about the emergence of AMR in food and the possibility of transmission of microorganisms possessing antibiotic resistance genes (ARGs) to the human gut microbiome. Shotgun sequencing and in vitro antimicrobial susceptibility testing were used in this study to provide a detailed characterization of the antibiotic resistance profile of bacteria and their ARGs in dromedary camel milk.

The JAK-STAT Pathway as a Therapeutic Strategy in Cancer Patients with Immune Checkpoint Inhibitor-Induced Colitis: A Narrative Review.

Immunotherapy has emerged as a pivotal component in the treatment of various malignancies, encompassing lung, skin, gastrointestinal, and head and neck cancers. The foundation of this therapeutic approach lies in immune checkpoint inhibitors (ICI). While ICIs have demonstrated remarkable efficacy in impeding the neoplastic progression of these tumours, their use may give rise to substantial toxicity, notably in the gastrointestinal domain, where ICI colitis constitutes a significant aspect.

Extracellular DNA secreted in yeast cultures is metabolism-specific and inhibits cell proliferation.

Extracellular DNA (exDNA) can be actively released by living cells and different putative functions have been attributed to it. Further, homologous exDNA has been reported to exert species-specific inhibitory effects on several organisms. Here, we demonstrate by different experimental evidence, including H-NMR metabolomic fingerprint, that the growth rate decline in fed-batch cultures is determined by the accumulation of exDNA in the medium.

Broad Genome Sequencing of Environmental and Clinical Strains and Genotyping.

The Next-Generation Sequencing revolution had a great impact on the genomics of Pseudomonas aeruginosa. Since the first release of the P. aeruginosa PAO1 genome, there are more than 5700 genomes published.

Real-world clinical outcome and safety of adjuvant therapy in stage III melanoma patients: Data from two Academic Italian Institutions.

Adjuvant immunotherapy (IO) and targeted therapy (TT) have improved relapse-free survival (RFS) in patients with stage III melanoma, although about 25% of them relapse within a year. However, real-world data on treatment efficacy and safety as well as management of treatment recurrences are still limited. We retrospectively analyzed 113 patients with stage III melanoma who received at least one cycle of anti-PD-1 (nivolumab or pembrolizumab) or dabrafenib + trametinib as adjuvant therapy.

Shotgun metagenomic sequencing in culture negative microbial keratitis.

Purpose: To evaluate the microbiota of culture negative Corneal Impression Membrane (CIM) microbial keratitis samples with the use of shotgun metagenomics analysis.

Methods: DNA of microbial keratitis samples were collected with CIM and extracted using the MasterPure™ Complete DNA and RNA Purification Kit (Epicentre). DNA was fragmented by sonication into fragments of 300 to 400 base pairs (bp) using Bioruptor® (Diagenode, Belgium) and then used as a template for library preparation.

Assessment of mastitis in camel using high-throughput sequencing.

Camel milk is recognized as a functional food with significant economic value. Mastitis is one of the most common and costly diseases in the dairy industry. Mastitis, which is caused by pathogens such as bacteria, viruses, fungi, and algae, has an impact on the quality and quantity of milk produced as well as animal health and welfare.

Data on microbial diversity of camel milk microbiota determined by 16S rRNA gene sequencing.

Raw camel milk samples were collected from three geographical locations (south, north and middle Kuwait) during two seasons. Next generation sequencing of the V3-V4 regions of the 16S rRNA gene was used to analyze the bacterial community in camel milk. DNA was extracted from one hundred thirty-three samples, and libraries were prepared using custom fusion primers of the 16S rRNA gene and sequenced on Illumina HiSeq 2500 platform.

Microbiome characterization of alpine water springs for human consumption reveals site- and usage-specific microbial signatures.

The microbiome of water springs is gaining increasing interest, especially in water intended for human consumption. However, the knowledge about large-scale patterns in water springs microbiome is still incomplete. The presence of bacteria in water sources used for human consumption is a major concern for health authorities; nonetheless, the standard microbiological quality checks are focused only on pathogenic species and total microbial load.

The Flavone Cirsiliol from Binds the F Moiety of ATP Synthase, Modulating Free Radical Production.

Several studies have shown that mammalian retinal rod outer segments (OS) are peculiar structures devoid of mitochondria, characterized by ectopic expression of the molecular machinery for oxidative phosphorylation. Such ectopic aerobic metabolism would provide the chemical energy for the phototransduction taking place in the OS. Natural polyphenols include a large variety of molecules having pleiotropic effects, ranging from anti-inflammatory to antioxidant and others.

Camel milk microbiota: A culture-independent assessment.

Camel milk is renowned for its nutritional value and its therapeutic properties. It is considered a promising alternative to bovine milk due to its higher nutritional benefits, hypoallergenic characteristics and greater digestibility in the human gastrointestinal system. This study reports camel milk's bacterial and fungal microbiota, and the effect of geographical location and season on its bacterial community.

Identification and Characterization of an RRM-Containing, RNA Binding Protein in .

is a Gram-negative pathogen, known to acquire resistance to antibiotics used in the clinic. The RNA-binding proteome of this bacterium is poorly characterized, in particular for what concerns the proteins containing RNA Recognition Motif (RRM). Here, we browsed the proteome for homologous proteins to the human HuR(ELAVL1), an RNA binding protein containing three RRMs.

Beneficial effect of polyphenols in COVID-19 and the ectopic F F -ATP synthase: Is there a link?

COVID-19 has been proposed to be an endothelial disease, as endothelial damage and oxidative stress contribute to its systemic inflammatory and thrombotic events. Polyphenols, natural antioxidant compounds appear as promising agents to prevent and treat COVID-19. Polyphenols bind and inhibit the F F -ATP synthase rotary catalysis.

Evolutionary Adaptation of the Thyroid Hormone Signaling Toolkit in Chordates.

The specification of the endostyle in non-vertebrate chordates and of the thyroid gland in vertebrates are fundamental steps in the evolution of the thyroid hormone (TH) signaling to coordinate development and body physiology in response to a range of environmental signals. The physiology and biology of TH signaling in vertebrates have been studied in the past, but a complete understanding of such a complex system is still lacking. Non-model species from non-vertebrate chordates may greatly improve our understanding of the evolution of this complex endocrine pathway.

sp. nov., isolated from groundwater.

Strain 3P27G6 was isolated from an artesian well connected to the thermal water basin of Comano Terme, Province of Trento, Italy. In phylogenetic analyses based on multilocus sequence analysis, strain 3P27G6 clustered together with WSM2073. Genome sequencing produced a 99.

Response to Extracellular DNA: Self Versus Nonself Exposure.

The inhibitory effect of extracellular DNA (exDNA) on the growth of conspecific individuals was demonstrated in different kingdoms. In plants, the inhibition has been observed on root growth and seed germination, demonstrating its role in plant-soil negative feedback. Several hypotheses have been proposed to explain the early response to exDNA and the inhibitory effect of conspecific exDNA.