: a tool for integrated differential expression analysis.

One of the fundamental aspects of genomic research is the identification of differentially expressed (DE) genes between two conditions. In the past decade, numerous DE analysis tools have been developed, employing various normalization methods and statistical modelling approaches. In this article, we introduce , an R package that leverages the capabilities of four state-of-the-art DE tools: edgeR, limma, DESeq2, and dearseq.

Extracellular Biosynthesis, Characterization and Antimicrobial Activity of Silver Nanoparticles Synthesized by Filamentous Fungi.

The green synthesis of metal nanoparticles has received substantial attention due to their applications in various domains. The aim of the study was to obtain silver nanoparticles (AgNPs) by green synthesis with filamentous fungi, such as , , and . Fungal species were grown on nutrient media and aqueous mycelium extracts were used to reduce Ag to Ag (0).

Proximal and Classic Epithelioid Sarcomas are Distinct Molecular Entities Defined by MYC/GATA3 and SOX17/Endothelial Markers, Respectively.

Epithelioid sarcoma (ES) is a rare tumor hallmarked by the loss of INI1/SMARCB1 expression. Apart from this alteration, little is known about the biology of ES. Despite recent advances in treatment, the prognosis of ES remains unsatisfactory.

Microbial Removal of Heavy Metals from Contaminated Environments Using Metal-Resistant Indigenous Strains.

Contamination of soil with heavy metals has become a matter of global importance due to its impact on agriculture, environmental integrity, and therefore human health and safety. Several microbial strains isolated from soil contaminated by long-term chemical and petrochemical activities were found to manifest various levels of tolerance to Cr, Pb, and Zn, out of which and exhibited above-moderate tolerance. The concentrations of target heavy metals before and after bioremediation were determined using electrochemical screen-printed electrodes (SPE) modified with different nanomaterials.

-Mediated Green Synthesis of Silver Nanoparticles with Antimicrobial Activity.

"Green chemistry" is a simple and easily reproductible method that provides nanoparticles characterized by better stability and good dispersion in an aqueous solution. Nanoparticles can be synthesized by algae, bacteria, fungi, and plant extracts. is a commonly used medicinal mushroom with distinctive biological properties, such as antibacterial, antifungal, antioxidant, anti-inflammatory, anticancer, etc.

Highlighting Bacteria with Calcifying Abilities Suitable to Improve Mortar Properties.

Biomineralization, the use of microorganisms to produce calcium carbonate, became a green solution for application in construction materials to improve their strength and durability. The calcifying abilities of several bacteria were investigated by culturing on a medium with urea and calcium ions. The characterization of the precipitates from bacterial cultures was performed using X-ray diffraction, Fourier transform infrared spectroscopy, and thermogravimetric analysis.

A Short Overview of Recent Developments in the Application of Polymeric Materials for the Conservation of Stone Cultural Heritage Elements.

Stones are ones of the most ancient natural materials exploited by humans, with different uses, from tools to buildings, that have endured over time in better conditions than other objects belonging to cultural heritage. Given the importance of those silent witnesses of our past, as well as our duty to preserve all parts of cultural heritage for future generations, much effort was put into the development of materials for their consolidation, protection, self-cleaning, or restoration. Protection of ancient stone monuments and objects has gained the interest of researchers in the last decades in the field of conservation of cultural heritage.

Polycomb group ring finger protein 6 suppresses Myc-induced lymphomagenesis.

Max is an obligate dimerization partner for the Myc transcription factors and for several repressors, such as Mnt, Mxd1-4, and Mga, collectively thought to antagonize Myc function in transcription and oncogenesis. Mga, in particular, is part of the variant Polycomb group repressive complex PRC1.6.

Targeting mitochondrial respiration and the BCL2 family in high-grade MYC-associated B-cell lymphoma.

Multiple molecular features, such as activation of specific oncogenes (e.g., MYC, BCL2) or a variety of gene expression signatures, have been associated with disease course in diffuse large B-cell lymphoma (DLBCL), although their relationships and implications for targeted therapy remain to be fully unraveled.

The Scavenging Effect of Myoglobin from Meat Extracts toward Peroxynitrite Studied with a Flow Injection System Based on Electrochemical Reduction over a Screen-Printed Carbon Electrode Modified with Cobalt Phthalocyanine: Quantification and Kinetics.

The scavenging activity of myoglobin toward peroxynitrite (PON) was studied in meat extracts, using a new developed electrochemical method (based on cobalt phthalocyanine-modified screen-printed carbon electrode, SPCE/CoPc) and calculating kinetic parameters of PON decay (such as half-time and apparent rate constants). As reactive oxygen/nitrogen species (ROS/RNS) affect the food quality, the consumers can be negatively influenced. The discoloration, rancidity, and flavor of meat are altered in the presence of these species, such as PON.

Fungal Based Biopolymer Composites for Construction Materials.

Environmental contamination, extensive exploitation of fuel sources and accessibility of natural renewable resources represent the for the development of composite biomaterials. These materials have controlled properties, being obtained through processes operated in mild conditions with low costs, and contributing to the valorization of byproducts from agriculture and industry fields. A novel board composite including lignocelullosic substrate as wheat straws, fungal mycelium and polypropylene embedded with bacterial spores was developed and investigated in the present study.

Integrated requirement of non-specific and sequence-specific DNA binding in Myc-driven transcription.

Eukaryotic transcription factors recognize specific DNA sequence motifs, but are also endowed with generic, non-specific DNA-binding activity. How these binding modes are integrated to determine select transcriptional outputs remains unresolved. We addressed this question by site-directed mutagenesis of the Myc transcription factor.

WhatsApp video call communication between oncological patients and their families during COVID-19 outbreak.

Background: On March 8, 2020 the Italian Government implemented extraordinary measures to limit COVID-19 viral transmission. The aim of the study was to verify if the use of WhatsApp facilitates communication, improves health information, perception of safe and security, reduce emotional stress during the COVID-19 emergency.

Methods: In this study we identified two period, in the pre-COVID 1-month period (February 9 - March 8, 2020) 34 patients underwent elective surgery for malignancies (21) and benign (13) diseases, respectively.

Cooperation Between MYC and β-Catenin in Liver Tumorigenesis Requires Yap/Taz.

Background And Aims: Activation of MYC and catenin beta-1 (CTNNB1, encoding β-catenin) can co-occur in liver cancer, but how these oncogenes cooperate in tumorigenesis remains unclear.

Approach And Results: We generated a mouse model allowing conditional activation of MYC and WNT/β-catenin signaling (through either β-catenin activation or loss of APC - adenomatous polyposis coli) upon expression of CRE recombinase in the liver and monitored their effects on hepatocyte proliferation, apoptosis, gene expression profiles, and tumorigenesis. Activation of WNT/β-catenin signaling strongly accelerated MYC-driven carcinogenesis in the liver.

An early Myc-dependent transcriptional program orchestrates cell growth during B-cell activation.

Upon activation, lymphocytes exit quiescence and undergo substantial increases in cell size, accompanied by activation of energy-producing and anabolic pathways, widespread chromatin decompaction, and elevated transcriptional activity. These changes depend upon prior induction of the Myc transcription factor, but how Myc controls them remains unclear. We addressed this issue by profiling the response to LPS stimulation in wild-type and c-myc-deleted primary mouse B-cells.

Therapeutic synergy between tigecycline and venetoclax in a preclinical model of / double-hit B cell lymphoma.

High-grade B cell lymphomas with concurrent activation of the and oncogenes, also known as double-hit lymphomas (DHL), show dismal prognosis with current therapies. activation sensitizes cells to inhibition of mitochondrial translation by the antibiotic tigecycline, and treatment with this compound provides a therapeutic window in a mouse model of -driven lymphoma. We now addressed the utility of this antibiotic for treatment of DHL.

Achievements and Prospects in Electrochemical-Based Biosensing Platforms for Aflatoxin M₁ Detection in Milk and Dairy Products.

Aflatoxins, which are mainly produced by and growing on plants and products stored under inappropriate conditions, represent the most studied group of mycotoxins. Contamination of human and animal milk with aflatoxin M₁, the hydroxylated metabolite of aflatoxin B₁, is an important health risk factor due to its carcinogenicity and mutagenicity. Due to the low concentration of this aflatoxin in milk and milk products, the analytical methods used for its quantification have to be highly sensitive, specific and simple.

Transcriptional integration of mitogenic and mechanical signals by Myc and YAP.

Mammalian cells must integrate environmental cues to determine coherent physiological responses. The transcription factors Myc and YAP-TEAD act downstream from mitogenic signals, with the latter responding also to mechanical cues. Here, we show that these factors coordinately regulate genes required for cell proliferation.

Integrative analysis of RNA polymerase II and transcriptional dynamics upon MYC activation.

Overexpression of the MYC transcription factor causes its widespread interaction with regulatory elements in the genome but leads to the up- and down-regulation of discrete sets of genes. The molecular determinants of these selective transcriptional responses remain elusive. Here, we present an integrated time-course analysis of transcription and mRNA dynamics following MYC activation in proliferating mouse fibroblasts, based on chromatin immunoprecipitation, metabolic labeling of newly synthesized RNA, extensive sequencing, and mathematical modeling.

Smyd2 is a Myc-regulated gene critical for MLL-AF9 induced leukemogenesis.

The Smyd2 protein (Set- and Mynd domain containing protein 2) is a methyl-transferase that can modify both histones and cytoplasmic proteins. Smyd2 is over-expressed in several cancer types and was shown to be limiting for tumor development in the pancreas. However, genetic evidence for a role of Smyd2 in other cancers or in mouse development was missing to date.

The mitochondrial translation machinery as a therapeutic target in Myc-driven lymphomas.

The oncogenic transcription factor Myc is required for the progression and maintenance of diverse tumors. This has led to the concept that Myc itself, Myc-activated gene products, or associated biological processes might constitute prime targets for cancer therapy. Here, we present an in vivo reverse-genetic screen targeting a set of 241 Myc-activated mRNAs in mouse B-cell lymphomas, unraveling a critical role for the mitochondrial ribosomal protein (MRP) Ptcd3 in tumor maintenance.

Identification of MYC-Dependent Transcriptional Programs in Oncogene-Addicted Liver Tumors.

Tumors driven by activation of the transcription factor MYC generally show oncogene addiction. However, the gene expression programs that depend upon sustained MYC activity remain unknown. In this study, we employed a mouse model of liver carcinoma driven by a reversible tet-MYC transgene, combined with chromatin immunoprecipitation and gene expression profiling to identify MYC-dependent regulatory events.

Pin1 is required for sustained B cell proliferation upon oncogenic activation of Myc.

The c-myc proto-oncogene is activated by translocation in Burkitt's lymphoma and substitutions in codon 58 stabilize the Myc protein or augment its oncogenic potential. In wild-type Myc, phosphorylation of Ser 62 and Thr 58 provides a landing pad for the peptidyl prolyl-isomerase Pin1, which in turn promotes Ser 62 dephosphorylation and Myc degradation. However, the role of Pin1 in Myc-induced lymphomagenesis remains unknown.

Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis.

The c-myc proto-oncogene product, Myc, is a transcription factor that binds thousands of genomic loci. Recent work suggested that rather than up- and downregulating selected groups of genes, Myc targets all active promoters and enhancers in the genome (a phenomenon termed 'invasion') and acts as a general amplifier of transcription. However, the available data did not readily discriminate between direct and indirect effects of Myc on RNA biogenesis.