JCVI: A versatile toolkit for comparative genomics analysis.

The life cycle of genome builds spans interlocking pillars of assembly, annotation, and comparative genomics to drive biological insights. While tools exist to address each pillar separately, there is a growing need for tools to integrate different pillars of a genome project holistically. For example, comparative approaches can provide quality control of assembly or annotation; genome assembly, in turn, can help to identify artifacts that may complicate the interpretation of genome comparisons.

Phased chromosome-scale genome assembly of an asexual, allopolyploid root-knot nematode reveals complex subgenomic structure.

We present the chromosome-scale genome assembly of the allopolyploid root-knot nematode Meloidogyne javanica. We show that the M. javanica genome is predominantly allotetraploid, comprising two subgenomes, A and B, that most likely originated from hybridisation of two ancestral parental species.

Marine phycotoxin levels in shellfish-14 years of data gathered along the Italian coast.

Along the Italian coasts, toxins of algal origin in wild and cultivated shellfish have been reported since the 1970s. In this study, we used data gathered by the Veterinary Public Health Institutes (IZS) and the Italian Environmental Health Protection Agencies (ARPA) from 2006 to 2019 to investigate toxicity events along the Italian coasts and relate them to the distribution of potentially toxic species. Among the detected toxins (OA and analogs, YTXs, PTXs, STXs, DAs, AZAs), OA and YTX were those most frequently reported.

Development of Potential Multi-Target Inhibitors for Human Cholinesterases and Beta-Secretase 1: A Computational Approach.

Alzheimer's disease causes chronic neurodegeneration and is the leading cause of dementia in the world. The causes of this disease are not fully understood but seem to involve two essential cerebral pathways: cholinergic and amyloid. The simultaneous inhibition of AChE, BuChE, and BACE-1, essential enzymes involved in those pathways, is a promising therapeutic approach to treat the symptoms and, hopefully, also halt the disease progression.

Identification of Potential Multitarget Compounds against Alzheimer's Disease through Pharmacophore-Based Virtual Screening.

Alzheimer's disease (AD) is a neurodegenerative disease characterized by progressive loss of cognitive functions, and it is the most prevalent type of dementia worldwide, accounting for 60 to 70% of cases. The pathogenesis of AD seems to involve three main factors: deficiency in cholinergic transmission, formation of extracellular deposits of β-amyloid peptide, and accumulation of deposits of a phosphorylated form of the TAU protein. The currently available drugs are prescribed for symptomatic treatment and present adverse effects such as hepatotoxicity, hypertension, and weight loss.

Monitoring of polyphosphate levels in animal source products collected in Italy by means of ion chromatography with suppressed conductivity detection.

Polyphosphates (PPs) constitute a class of food additives widely used due to their ability to exercise different useful activities. The food safety concern about the use of PPs in food is both the possible non-declared addition and some health effects, such as bile duct stones, decrease in oligo-element absorption, and allergic reactions in susceptible people. In this study, an analytical method based on ion chromatography with conductivity detection was applied for the detection and quantification of PPs in 238 samples of animal-derived products such as meat, dairy, and fish products.

Molecular Multi-Target Approach for Human Acetylcholinesterase, Butyrylcholinesterase and -Secretase 1: Next Generation for Alzheimer's Disease Treatment.

Alzheimer's Disease (AD) is a neurodegenerative condition characterized by progressive memory loss and other affected cognitive functions. Pharmacological therapy of AD relies on inhibitors of the enzymes acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), offering only a palliative effect and being incapable of stopping or reversing the neurodegenerative process. However, recent studies have shown that inhibiting the enzyme β-secretase 1 (BACE-1) may be able to stop neurodegeneration, making it a promising target.

Rational-Based Discovery of Novel β-Carboline Derivatives as Potential Antimalarials: From In Silico Identification of Novel Targets to Inhibition of Experimental Cerebral Malaria.

Malaria is an infectious disease widespread in underdeveloped tropical regions. The most severe form of infection is caused by Plasmodium falciparum, which can lead to development of cerebral malaria (CM) and is responsible for deaths and significant neurocognitive sequelae throughout life. In this context and considering the emergence and spread of drug-resistant P.

Effect of different cooking treatments on the residual level of sulphites in shrimps.

Sulphiting agents (or sulphites) are a class of food additives identified in Europe by codes E220-E228. Their addition in crustaceans is permitted with specific legal limits for avoiding the so-called "blackspot" that is a defect that compromises the marketability of these products. High levels of ingested sulphites may cause pseudoallergenic reactions in susceptible people.

Determination of Nitrate and Nitrite in Swiss Chard ( L. subsp. ) and Wild Rocket ( (L.) DC.) and Food Safety Evaluations.

Nitrite and nitrate levels in vegetables are a matter of concern due to their toxicity at high levels and nitrate high accumulation. Moreover, there is a lack of knowledge about their levels in some types of widely consumed vegetables such as chard and rocket. In this study, 124 Swiss chard and wild rocket samples were analyzed for determining nitrite and nitrate using validated and accredited analytical methods by ion chromatography with conductivity detection.

Evaluation of antiplasmodial activity in silico and in vitro of N-acylhydrazone derivatives.

N-acylhydrazones are considered privileged structures in medicinal chemistry, being part of antimicrobial compounds (for example). In this study we show the activity of N-acylhydrazone compounds, namely AH1, AH2, AH4, AH5 in in vitro tests against the chloroquine-resistant strain of Plasmodium falciparum (W2) and against WI26 VA-4 human cell lines. All compounds showed low cytotoxicity (LC > 100 µM).

Identification of potential human beta-secretase 1 inhibitors by hierarchical virtual screening and molecular dynamics.

Alzheimer's disease (AD) is a neurodegenerative pathology responsible for 70% of dementia cases worldwide. Despite its relevance, the few drugs available for the treatment of this disease offer only symptomatic relief, with limited efficacy and serious adverse effects. The most accepted hypothesis about the pathogenesis involves the aggregation and deposition of β-amyloid peptides, mainly in the cerebral cortex and hippocampus, through the catalytic action of beta-secretase 1 (BACE-1), making this enzyme a promising target for the development of new drugs.

Optimization and Validation of a High Throughput UHPLC-MS/MS Method for Determination of the EU Regulated Lipophilic Marine Toxins and Occurrence in Fresh and Processed Shellfish.

Under the name of lipophilic marine toxins, there are included more than 1000 toxic secondary metabolites, produced by phytoplankton, with the common chemical property of lipophilicity. Due to toxicological effects and geographical distribution, in European legislation relevant compounds are regulated, and their determination is accomplished with the reference liquid chromatography-tandem mass spectrometry method. In this study a modified ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) method has been developed for the identification and quantification of EU-regulated lipophilic toxins.

Evaluation of Docking Machine Learning and Molecular Dynamics Methodologies for DNA-Ligand Systems.

DNA is a molecular target for the treatment of several diseases, including cancer, but there are few docking methodologies exploring the interactions between nucleic acids with DNA intercalating agents. Different docking methodologies, such as AutoDock Vina, DOCK 6, and Consensus, implemented into Molecular Architect (MolAr), were evaluated for their ability to analyze those interactions, considering visual inspection, redocking, and ROC curve. Ligands were refined by Parametric Method 7 (PM7), and ligands and decoys were docked into the minor DNA groove (PDB code: 1VZK).

Synthesis, docking, machine learning and antiproliferative activity of the 6-ferrocene/heterocycle-2-aminopyrimidine and 5-ferrocene-1H-Pyrazole derivatives obtained by microwave-assisted Atwal reaction as potential anticancer agents.

A simple and fast methodology under microwave irradiation for the synthesis of 2-aminopyrimidine and pyrazole derivatives using Atwal reaction is reported. After the optimization of the reaction conditions, eight 2-aminolpyrimidines containing ferrocene and heterocycles and three ferrocene pyrazoles were synthesized from the respective chalcones in good yields. Eight compounds had their structure determined by X-ray diffraction.

Immunoinformatics Design of Multi-Epitope Peptide-Based Vaccine Against Using Transmembrane Proteins as a Target.

Schistosomiasis remains a serious health issue nowadays for an estimated one billion people in 79 countries around the world. Great efforts have been made to identify good vaccine candidates during the last decades, but only three molecules reached clinical trials so far. The reverse vaccinology approach has become an attractive option for vaccine design, especially regarding parasites like spp.

Treatment of Catatonia with Asenapine in a Patient with Schizotypal Personality Disorder, Psychotic Depression and Septic Shock from SARSCoV- 2 - A Case Report.

Introduction: Catatonia is a psychomotor syndrome that presents with severe symptoms which can lead to dangerous and lethal conditions if not diagnosed and treated properly. SARS-- CoV-2 is a positive-sense single-stranded RNA virus that can occur in severe cases with acute pneumonia, ARDS, sepsis and septic shock. In these cases, ICU admission is necessary.

A novel antiplasmodial compound: integration of and assays.

Malaria is a disease caused by genus. which is responsible for the most severe form of the disease, cerebral malaria. In 2018, 405,000 people died of malaria.

Dehydrobufotenin extracted from the Amazonian toad (Anura: Bufonidae) as a prototype molecule for the development of antiplasmodial drugs.

Background: The resistance against antimalarial drugs represents a global challenge in the fight and control of malaria. The Brazilian biodiversity can be an important tool for research and development of new medicinal products. In this context, toxinology is a multidisciplinary approach on the development of new drugs, including the isolation, purification, and evaluation of the pharmacological activities of natural toxins.

Sulfites in meat: Occurrence, activity, toxicity, regulation, and detection. A comprehensive review.

Sulfites are a class of chemical compounds, SO releasers, widely used as additives in food industry, due to their antimicrobial, color stabilizing, antibrowning, and antioxidant properties. As the results of these pleiotropic functions they can be added to a broad range of products including dried fruits and vegetables, seafood, juices, alcoholic and nonalcoholic beverage, and in few meat products. Sulfites ingestion has been correlated with several adverse and toxic reactions, such as hypersensitivity, allergic diseases, vitamin deficiency, and may lead to dysbiotic events of gut and oral microbiota.

Antiplasmodial activity of sulfonylhydrazones: and approaches.

Malaria is still a life-threatening public health issue, and the upsurge of resistant strains requires continuous generation of active molecules. In this work, 35 sulfonylhydrazone derivatives were synthesized and evaluated against chloroquine-sensitive (3D7) and resistant (W2) strains. The most promising compound, 5b, had an IC of 0.

Accelerating the identification of subtype selective inhibitors via Three-Dimensional Biologically Relevant Spectrum (BRS-3D): The monoamine oxidase subtypes as a case study.

Subtype-selective drugs are of great therapeutic importance as they are expected to be more effective and with less side-effects. However, discovery of subtype selective inhibitors was hampered by the high similarity of the binding sites within subfamilies. In this study, we further evaluated the applicability of "Three-Dimensional Biologically Relevant Spectrum (BRS-3D)" for the identification of subtype-selective inhibitors.

Reverse and structural vaccinology approach to design a highly immunogenic multi-epitope subunit vaccine against Streptococcus pneumoniae infection.

Streptococcus pneumoniae is a pathogen that resides in the upper respiratory tract of healthy individuals, maintaining a commensal relationship with its host. However, the virulent form may be the etiology of pneumonia, meningitis, bacteremia, and other respiratory tract infections. Streptococcal diseases are preventable by vaccination; but currently available vaccines have some drawbacks, especially due to the high capsule variability of streptococci strains.

Structure-Based Virtual Screening: From Classical to Artificial Intelligence.

The drug development process is a major challenge in the pharmaceutical industry since it takes a substantial amount of time and money to move through all the phases of developing of a new drug. One extensively used method to minimize the cost and time for the drug development process is computer-aided drug design (CADD). CADD allows better focusing on experiments, which can reduce the time and cost involved in researching new drugs.

The analytical determination of polyphosphates in food: A point-to-point comparison between direct ion chromatography and indirect photometry.

Being an indirect approach, the standard method for the determination of polyphosphates (PPs) in food maybe characterized by high variability which can lead to significant errors in the final measurement. In this study, this method was validated and then compared to the ion chromatography-based approach. Method trueness and measurement uncertainty resulted comparable, while the precision of ion chromatography approach was higher.