How genomics can help biodiversity conservation.

The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species.

Global SARS-CoV-2 genomic surveillance: What we have learned (so far).

The COVID-19 pandemic has brought significant challenges for genomic surveillance strategies in public health systems worldwide. During the past thirty-four months, many countries faced several epidemic waves of SARS-CoV-2 infections, driven mainly by the emergence and spread of novel variants. In that line, genomic surveillance has been a crucial toolkit to study the real-time SARS-CoV-2 evolution, for the assessment and optimization of novel diagnostic assays, and to improve the efficacy of existing vaccines.

Sulfated Polysaccharides from Macroalgae-A Simple Roadmap for Chemical Characterization.

The marine environment presents itself as a treasure chest, full of a vast diversity of organisms yet to be explored. Among these organisms, macroalgae stand out as a major source of natural products due to their nature as primary producers and relevance in the sustainability of marine ecosystems. Sulfated polysaccharides (SPs) are a group of polymers biosynthesized by macroalgae, making up part of their cell wall composition.

Polymorphisms predicting phylogeny in hepatitis B virus.

Hepatitis B viruses (HBVs) are compact viruses with circular genomes of ∼3.2 kb in length. Four genes () generating seven products are encoded on overlapping reading frames.

Antiulcerogenic Potential of the Ethanolic Extract of (A. St.-Hil.) Ravenna Evaluated by In Vitro and In Vivo Studies.

Gastrointestinal diseases, such as peptic ulcers, are caused by a damage in the gastric mucosa provoked by several factors. This stomach injury is regulated by many inflammatory mediators and is commonly treated with proton-pump inhibitors, histamine H2 receptor blockers and antacids. However, various medicinal plants have demonstrated positive effects on gastric ulcer treatment, including plants of the genus.

Untargeted Metabolomics Reveals Antidepressant Effects in a Marine Photosynthetic Organism: The Diatom as a Case Study.

The increased use of antidepressants, along with their increased occurrence in aquatic environments, is of concern for marine organisms. Although these pharmaceutical compounds have been shown to negatively affect marine diatoms, their mode of action in these non-target, single-cell phototrophic organisms is yet unknown. Using a Fourier-transform ion cyclotron-resonance mass spectrometer (FT-ICR-MS) we evaluated the effects of fluoxetine in the metabolomics of the model diatom , as well as the potential use of the identified metabolites as exposure biomarkers.

Virulence-related metabolism is activated in mostly in the interaction with tolerant green grapes that remain largely unaffected in contrast with susceptible green grapes.

is responsible for the gray mold disease, severely affecting grapevine and hundreds of other economically important crops. However, many mechanisms of this fruit-pathogen interaction remain unknown. The combined analysis of the transcriptome and metabolome of green fruits infected with from susceptible and tolerant genotypes was never performed in any fleshy fruit, mostly because green fruits are widely accepted to be resistant to this fungus.

On the not so anomalous water-induced structural transformations of choline chloride-urea (reline) deep eutectic system.

The choline chloride-urea binary mixture in the molar ratio (1 : 2), commonly known as reline, is an archetypal solvent among deep eutectic solvents (DES). Neutron diffraction (ND) and empirical potential structure refinement (EPSR) results provided evidence that reline exhibits a peculiar structural transformation upon water addition that manifests in a sudden dewetting of the choline cations at ∼51 wt% water and, therefore, a non-monotonic variation of the choline-water and choline-choline coordination. Here, we study, through molecular dynamics (MD), the influence of water on the structure of a choline chloride : urea : water DES (1 : 2 : ; = 0 to 40), to gain additional insight into the molecular source of this peculiar structural transformation.

A Note on the Effects of Linear Topology Preservation in Monte Carlo Simulations of Knotted Proteins.

Monte Carlo simulations are a powerful technique and are widely used in different fields. When applied to complex molecular systems with long chains, such as those in synthetic polymers and proteins, they have the advantage of providing a fast and computationally efficient way to sample equilibrium ensembles and calculate thermodynamic and structural properties under desired conditions. Conformational Monte Carlo techniques employ a move set to perform the transitions in the simulation Markov chain.

Adherens Junction Integrity Is a Critical Determinant of Sodium Iodide Symporter Residency at the Plasma Membrane of Thyroid Cells.

While most cases of differentiated thyroid carcinoma (DTC) are associated with a good prognosis, a significant number progress to advanced disease exhibiting aggressive clinical characteristics and often becoming refractory to radioactive iodine (RAI) treatment, the current gold-standard therapeutic option for metastatic disease. RAI-refractoriness is caused by defective functional expression of the sodium-iodide symporter (NIS), which is responsible for the active transport of iodide across the plasma membrane (PM) into thyroid follicles. NIS deficiency in these tumors often reflects a transcriptional impairment, but also its defective targeting and retention at the cells' PM.

Satellite Noncoding RNAs (ncRNA) as Cancer Biomarkers? New Insights from ncRNA Molecular and Clinical Profiles in Feline Mammary Tumors.

Satellite noncoding RNAs (ncRNAs) are a new frontier of cancer biology research and biomarkers. While the knowledge on ncRNAs in human cancers is still limited, studies in other species can be informative to guide future translational research and development for cancer molecular targets and diagnostics. In this context, is the major satellite DNA of the cat genome, which is also present in humans, being transcribed in both species.

Drug Repurposing for Cystic Fibrosis: Identification of Drugs That Induce CFTR-Independent Fluid Secretion in Nasal Organoids.

Individuals with cystic fibrosis (CF) suffer from severe respiratory disease due to a genetic defect in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which impairs airway epithelial ion and fluid secretion. New CFTR modulators that restore mutant CFTR function have been recently approved for a large group of people with CF (pwCF), but ~19% of pwCF cannot benefit from CFTR modulators Restoration of epithelial fluid secretion through non-CFTR pathways might be an effective treatment for all pwCF. Here, we developed a medium-throughput 384-well screening assay using nasal CF airway epithelial organoids, with the aim to repurpose FDA-approved drugs as modulators of non-CFTR-dependent epithelial fluid secretion.

Unravelling the Portuguese Coastal and Transitional Waters' Microbial Resistome as a Biomarker of Differential Anthropogenic Impact.

Portugal mainland and Atlantic archipelagos (Madeira and Azores) provide a wide array of coastal ecosystems with varying typology and degrees of human pressure, which shape the microbial communities thriving in these habitats, leading to the development of microbial resistance traits. The samples collected on the Portuguese northeast Atlantic coast waters show an unequivocal prevalence of Bacteria over Archaea with a high prevalence of Proteobacteria, Cyanobacteria, Bacteroidetes and Actinobacteria. Several taxa, such as the genus, showed significant correlations with anthropogenic pollution.

Bromoditerpenes from the Red Seaweed as Potential Cytotoxic Agents and Proteasome Inhibitors and Related Mechanisms of Action.

Seaweeds are a great source of compounds with cytotoxic properties with the potential to be used as anticancer agents. This study evaluated the cytotoxic and proteasome inhibitory activities of 12-hydroxy-bromosphaerol, 12-hydroxy-bromosphaerol, and bromosphaerol isolated from . The cytotoxicity was evaluated on malignant cell lines (A549, CACO-2, HCT-15, MCF-7, NCI-H226, PC-3, SH-SY5Y, and SK-MEL-28) using the MTT and LDH assays.

Unravelling the binding affinity and selectivity of molybdenum(II) phenanthroline complexes with DNA G-quadruplexes by using linear-scaling DFT studies. The important role of ancillary ligands.

We have used near linear-scaling density functional theory (LS-DFT) methods including dispersion, for the first time, to study the interaction of two isomers, equatorial (Eq) and axial (Ax), of the [Mo(η-CH)Br(CO)(phen)] metal complex with the DNA G-quadruplexes (GQ) to gain insight into its cytotoxicity. The LMKLL/DZDP level of calculation, which includes van der Waals contributions, with the SIESTA software was used to treat by means of first-principles computations the whole biological studied model system with ∼1000 atoms. Computed formation energies point to systems containing the Ax isomer as the most stable although the nearest system in energy containing the Eq isomer is only 7.

Food inauthenticity: Authority activities, guidance for food operators, and mitigation tools.

Historically, food fraud was a major public health concern which helped drive the development of early food regulations in many markets including the US and EU market. In the past 10 years, the integrity of food chains with respect to food fraud has again been questioned due to high profile food fraud cases. We provide an overview of the resulting numerous authoritative activities underway within different regions to counter food fraud, and we describe the guidance available to the industry to understand how to assess the vulnerability of their businesses and implement appropriate mitigation.

-A Source of Natural Active Ingredients for Greener Skincare Formulations.

The growing knowledge about the harmful effects caused by some synthetic ingredients present in skincare products has led to an extensive search for natural bioactives. Thus, this study aimed to investigate the dermatological potential of five fractions (F1-F5), obtained by a sequential extraction procedure, from the brown seaweed . The antioxidant (DPPH, FRAP, ORAC and TPC), anti-enzymatic (collagenase, elastase, hyaluronidase and tyrosinase), antimicrobial (, and ), anti-inflammatory (nitric oxide, tumor necrosis factor-α, interleukin-6 and interleukin-10) and photoprotective (reactive oxygen species) properties of all fractions were evaluated.

European and American chestnuts: An overview of the main threats and control efforts.

Chestnuts are multipurpose trees significant for the economy and wildlife. These trees are currently found around the globe, demonstrating their genetic adaptation to different environmental conditions. Several biotic and abiotic stresses have challenged these species, contributing to the decline of European chestnut production and the functional extinction of the American chestnut.

Sandfly-Borne Phleboviruses in Portugal: Four and Still Counting.

According to ICTV, there are currently 66 known phlebovirus species. More than 40 of these viruses were isolated or detected in phlebotomine sandflies and some of them are known pathogens. In Portugal, information about sandfly-borne phleboviruses is scarce and scattered sandfly-borne diseases are neglected and often not considered in differential diagnoses.

A Drug Screening Reveals Minocycline Hydrochloride as a Therapeutic Option to Prevent Breast Cancer Cells Extravasation across the Blood-Brain Barrier.

Among breast cancer (BC) patients, 15-25% develop BC brain metastases (BCBM), a severe condition due to the limited therapeutic options, which points to the need for preventive strategies. We aimed to find a drug able to boost blood-brain barrier (BBB) properties and prevent BC cells (BCCs) extravasation, among PI3K, HSP90, and EGFR inhibitors and approved drugs. We used BCCs (4T1) and BBB endothelial cells (b.

Effects of Glyphosate-Based Herbicide on Primary Production and Physiological Fitness of the Macroalgae .

The use of glyphosate-based herbicides (GBHs) worldwide has increased exponentially over the last two decades increasing the environmental risk to marine and coastal habitats. The present study investigated the effects of GBHs at environmentally relevant concentrations (0, 10, 50, 100, 250, and 500 μg·L) on the physiology and biochemistry (photosynthesis, pigment, and lipid composition, antioxidative systems and energy balance) of , a cosmopolitan marine macroalgae species. Although GBHs cause deleterious effects such as the inhibition of photosynthetic activity, particularly at 250 μg·L, due to the impairment of the electron transport in the chloroplasts, these changes are almost completely reverted at the highest concentration (500 μg·L).

Measuring cystic fibrosis drug responses in organoids derived from 2D differentiated nasal epithelia.

Cystic fibrosis is caused by genetic defects that impair the CFTR channel in airway epithelial cells. These defects may be overcome by specific CFTR modulating drugs, for which the efficacy can be predicted in a personalized manner using 3D nasal-brushing-derived airway organoids in a forskolin-induced swelling assay. Despite of this, previously described CFTR function assays in 3D airway organoids were not fully optimal, because of inefficient organoid differentiation and limited scalability.

Effect Biomarkers of the Widespread Antimicrobial Triclosan in a Marine Model Diatom.

The present-day COVID-19 pandemic has led to the increasing daily use of antimicrobials worldwide. Triclosan is a manmade disinfectant chemical used in several consumer healthcare products, and thus frequently detected in surface waters. In the present work, we aimed to evaluate the effect of triclosan on diatom cell photophysiology, fatty acid profiles, and oxidative stress biomarkers, using the diatom as a model organism.