COVIDomics: The Proteomic and Metabolomic Signatures of COVID-19.

Omics-based technologies have been largely adopted during this unprecedented global COVID-19 pandemic, allowing the scientific community to perform research on a large scale to understand the pathobiology of the SARS-CoV-2 infection and its replication into human cells. The application of omics techniques has been addressed to every level of application, from the detection of mutations, methods of diagnosis or monitoring, drug target discovery, and vaccine generation, to the basic definition of the pathophysiological processes and the biochemical mechanisms behind the infection and spread of SARS-CoV-2. Thus, the term COVIDomics wants to include those efforts provided by omics-scale investigations with application to the current COVID-19 research. This review summarizes the diverse pieces of knowledge acquired with the application of COVIDomics techniques, with the main focus on proteomics and metabolomics studies, in order to capture a common signature in terms of proteins, metabolites, and pathways dysregulated in COVID-19 disease. Exploring the multiomics perspective and the concurrent data integration may provide new suitable therapeutic solutions to combat the COVID-19 pandemic.

The challenge of ecophysiological biodiversity for biotechnological applications of marine microalgae.

In this review, we aim to explore the potential of microalgal biodiversity and ecology for biotechnological use. A deeper exploration of the biodiversity richness and ecophysiological properties of microalgae is crucial for enhancing their use for applicative purposes. After describing the actual biotechnological use of microalgae, we consider the multiple faces of taxonomical, morphological, functional and ecophysiological biodiversity of these organisms, and investigate how these properties could better serve the biotechnological field. Lastly, we propose new approaches to enhancing microalgal growth, photosynthesis, and synthesis of valuable products used in biotechnological fields, mainly focusing on culture conditions, especially light manipulations and genetic modifications.

Marine polysaccharides, proteins, lipids, and silica for drug delivery systems: A review.

Marine environments represent an incredible source of biopolymers with potential biomedical applications. Recently, drug delivery studies have received great attention for the increasing need to improve site specificity, therapeutic value, and bioavailability, reducing off-target effects. Marine polymers, such as alginate, carrageenan, collagen, chitosan, and silica, have reported unique biochemical features, allowing an efficient binding with drugs, and a controlled release to the target tissue, also obtainable through "green processes". In the present review, we i) analysed the last ten years of scientific peer-reviewed literature; ii) divided the articles based on the achieved experimental phases, tagged as chemistry, drug release, and drug delivery, and iii) compared the best performances among marine polymers extracted from micro- and macro-organisms. Many reviews describe drug carriers from marine organisms, focusing on a single biopolymer or a chemical class. Our study is a groundbreaking literature collection, representing the first thorough investigation of all marine biopolymers described. Most articles report experimental results on the chemical characterisation of marine biopolymers and their in vitro behaviour as drug carriers, although development processes and commercial applications are still in the early stages. Hence, the next efforts should be focused on the sustainable production of marine polymers and final product development.

Copper Effect on Microalgae: Toxicity and Bioremediation Strategies.

Microalgae are increasingly recognised as suitable microorganisms for heavy metal (HM) removal, since they are able to adsorb them onto their cell wall and, in some cases, compartmentalise them inside organelles. However, at relatively high HM concentrations, they could also show signs of stress, such as organelle impairments and increased activities of antioxidant enzymes. The main aim of this review is to report on the mechanisms adopted by microalgae to counteract detrimental effects of high copper (Cu) concentrations, and on the microalgal potential for Cu bioremediation of aquatic environments. Studying the delicate balance between beneficial and detrimental effects of Cu on microalgae is of particular relevance as this metal is widely present in aquatic environments facing industrial discharges. This metal often induces chloroplast functioning impairment, generation of reactive oxygen species (ROS) and growth rate reduction in a dose-dependent manner. However, microalgae also possess proteins and small molecules with protective role against Cu and, in general, metal stress, which increase their resistance towards these pollutants. Our critical literature analysis reveals that microalgae can be suitable indicators of Cu pollution in aquatic environments, and could also be considered as components of eco-sustainable devices for HM bioremediation in association with other organisms.

Identification of a Green Algal Strain Collected from the Sarno River Mouth (Gulf of Naples, Italy) and Its Exploitation for Heavy Metal Remediation.

Heavy metals (HMs) can induce both chronic and acute harmful effects on marine and freshwater biota. The environmental impact of HMs in freshwater, seawater, soil, and wastewater can be limited using microbes, including microalgae, that are able to remove metals from environmental matrices. Indeed, they can passively adsorb and actively accumulate these persistent pollutants within their organelles, limiting their detrimental effects on cellular metabolism. The Sarno River is a 30 km long freshwater stream located in Southern Italy, polluted by partially untreated municipal, agricultural, and industrial wastewaters. In spite of this, microalgal cultures from Sarno River or Sarno River Mouth have never been established. In the present study, we isolated a green algal strain from the Sarno River Mouth and determined its ability to grow in polluted seawater containing different concentrations of cadmium, lead, or zinc. This strain was found to be able to accumulate these elements within its biomass in a dose-dependent manner. Growth inhibition experiments confirm the relatively low toxicity of Cd and Pb below 50 µM, while algal growth was seriously affected in Zn-amended media. To the best of our knowledge, this is the first study focused on the ability of microalgae from Sarno River Mouth to tolerate and uptake HMs.

Periosteal chondrosarcoma: A case series in a referral center with survivorship analysis.

BACKGROUND: Periosteal chondrosarcomas are among the rarest types of chondrosarcomas dealt with in few small series of cases. In this study, we aimed to present our experience with this chondrosarcoma, seek for prognostic factors for OS and DFS and survey the status of IDH1 and IDH2. RESULTS: 55 periosteal chondrosarcomas were retrospectively identified. Median age was 37 years, there was a male predominance (62%). The great majority of cases involved the metaphysis of long bones of the extremities. The median size of the tumors was 7.5 cm. Thirty patients underwent to subtotal surgical resection, 22 to tangential resection and the remaining 3 to amputation. The margins, reported in 54 cases, were wide/radical in 38 patients (70.4%), marginal in 9 (16.7%) and intralesional in 7 (12.9%). Histologically, 23 (42%) were grade 1; 27 (49%), grade 2; 3 (5%), grade 3 and 2 (4%) were dedifferentiated. A third of cases in which mutational analysis was feasible harbored heterozygous mutations in codon 132 of IDH1. Fifty-four cases were included for follow-up (median, 137 months). Four patients had local recurrences and six patients developed metastasis to the lungs. All patients that developed metastasis died of disease, two died of unrelated causes and 46 were alive without disease. OS and DFS was not found to be statistically associated with clinical and pathological parameters considered. CONCLUSIONS: periosteal chondrosarcomas exhibit a low-grade behavior that can be adequately treated with marginal excisions. Clinical and morphologic parameters do not seem to predict their outcome.

Histone hyperacetylation affects meiotic recombination and chromosome segregation in Arabidopsis.

In this study, the meiotic role of MEIOTIC CONTROL OF CROSSOVERS1 (MCC1), a GCN5-related histone N-acetyltransferase, is described in Arabidopsis. Analysis of the over-expression mutant obtained by enhancer activation tagging revealed that acetylation of histone H3 increased in male prophase I. MCC1 appeared to be required in meiosis for normal chiasma number and distribution and for chromosome segregation. Overall, elevated MCC1 did not affect crossover number per cell, but has a differential effect on individual chromosomes elevating COs for chromosome 4, in which there is also a shift in chiasma distribution, and reducing COs for chromosome 1 and 2. For the latter there is a loss of the obligate CO/chiasma in 8% of the male meiocytes. The meiotic defects led to abortion in about half of the male and female gametes in the mutant. In wild type, the treatment with trichostatin A, an inhibitor of histone deacetylases, phenocopies MCC1 over-expression in meiosis. Our results provide evidence that histone hyperacetylation has a significant impact on the plant meiosis.

Meiocyte Isolation by INTACT and Meiotic Transcriptome Analysis in Arabidopsis.

Isolation of nuclei tagged in specific cell types (INTACT) is a method developed to isolate cell-type-specific nuclei that are tagged through in vivo biotin labeling of a nuclear targeting fusion (NTF) protein. In our work, INTACT was used to capture nuclei of meiocytes and to generate a meiotic transcriptome in Arabidopsis. Using the promoter of AtDMC1 recombinase to label meiotic nuclei, we generated transgenic plants carrying AtDMC1:NTF along with biotin ligase enzyme (BirA) under the constitutive ACTIN2 (ACT2) promoter. AtDMC1-driven expression of biotin-labeled NTF allowed us to collect nuclei of meiocytes by streptavidin-coated magnetic beads. The nuclear meiotic transcriptome was obtained by RNA-seq using low-quantity input RNA. Transcripts grouped into different categories according to their expression levels were investigated by gene ontology enrichment analysis (GOEA). The most enriched GO term "DNA demethylation" in mid/high-expression classes suggests that this biological process is particularly relevant to meiosis onset. The majority of genes with established roles in meiosis were distributed in the classes of mid/high and high expression. Meiotic transcriptome was compared with public available transcriptomes from other tissues in Arabidopsis. Bioinformatics analysis by expression network identified a core of more than 1,500 genes related to meiosis landmarks.

Distribution, occurrence and biotoxin composition of the main shellfish toxin producing microalgae within European waters: A comparison of methods of analysis.

Harmful algal blooms (HABs) are a natural global phenomena emerging in severity and extent. Incidents have many economic, ecological and human health impacts. Monitoring and providing early warning of toxic HABs are critical for protecting public health. Current monitoring programmes include measuring the number of toxic phytoplankton cells in the water and biotoxin levels in shellfish tissue. As these efforts are demanding and labour intensive, methods which improve the efficiency are essential. This study compares the utilisation of a multitoxin surface plasmon resonance (multitoxin SPR) biosensor with enzyme-linked immunosorbent assay (ELISA) and analytical methods such as high performance liquid chromatography with fluorescence detection (HPLC-FLD) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) for toxic HAB monitoring efforts in Europe. Seawater samples (n=256) from European waters, collected 2009-2011, were analysed for biotoxins: saxitoxin and analogues, okadaic acid and dinophysistoxins 1/2 (DTX1/DTX2) and domoic acid responsible for paralytic shellfish poisoning (PSP), diarrheic shellfish poisoning (DSP) and amnesic shellfish poisoning (ASP), respectively. Biotoxins were detected mainly in samples from Spain and Ireland. France and Norway appeared to have the lowest number of toxic samples. Both the multitoxin SPR biosensor and the RNA microarray were more sensitive at detecting toxic HABs than standard light microscopy phytoplankton monitoring. Correlations between each of the detection methods were performed with the overall agreement, based on statistical 2×2 comparison tables, between each testing platform ranging between 32% and 74% for all three toxin families illustrating that one individual testing method may not be an ideal solution. An efficient early warning monitoring system for the detection of toxic HABs could therefore be achieved by combining both the multitoxin SPR biosensor and RNA microarray.

Specificity of LSU rRNA-targeted oligonucleotide probes for Pseudo-nitzschia species tested through dot-blot hybridisation.

In the scope of the development of a microarray PhyloChip for the detection of toxic phytoplankton species, we designed a large series of probes specific against targets in the nuclear large subunit (LSU) rRNA of a range of Pseudo-nitzschia species and spotted these onto the microarray. Hybridisation with rRNA extracted from monoclonal cultures and from plankton samples revealed many cross-reactions. In the present work, we tested the functionality and specificity of 23 of these probes designed against ten of the species, using a dot-blot procedure. In this case, probe specificity is tested against the target region in PCR products of the LSU rRNA gene marker region blotted on nitrocellulose filters. Each filter was incubated with a species-specific oligoprobe. Eleven of the tested probes showed specific responses, identifying seven Pseudo-nitzschia species. The other probes showed non-specific responses or did not respond at all. Results of dot-blot hybridisations are more specific than those obtained with the microarray approach and the possible reasons for this are discussed.

Spectral radiation dependent photoprotective mechanism in the diatom Pseudo-nitzschia multistriata.

Phytoplankton, such as diatoms, experience great variations of photon flux density (PFD) and light spectrum along the marine water column. Diatoms have developed some rapidly-regulated photoprotective mechanisms, such as the xanthophyll cycle activation (XC) and the non-photochemical chlorophyll fluorescence quenching (NPQ), to protect themselves from photooxidative damages caused by excess PFD. In this study, we investigate the role of blue fluence rate in combination with red radiation in shaping photoacclimative and protective responses in the coastal diatom Pseudo-nitzschia multistriata. This diatom was acclimated to four spectral light conditions (blue, red, blue-red, blue-red-green), each of them provided with low and high PFD. Our results reveal that the increase in the XC pool size and the amplitude of NPQ is determined by the blue fluence rate experienced by cells, while cells require sensing red radiation to allow the development of these processes. Variations in the light spectrum and in the blue versus red radiation modulate either the photoprotective capacity, such as the activation of the diadinoxanthin-diatoxanthin xanthophyll cycle, the diadinoxanthin de-epoxidation rate and the capacity of non-photochemical quenching, or the pigment composition of this diatom. We propose that spectral composition of light has a key role on the ability of diatoms to finely balance light harvesting and photoprotective capacity.

Light modulation of biomass and macromolecular composition of the diatom Skeletonema marinoi.

The biochemical profile and growth of the coastal diatom Skeletonema marinoi was investigated under four different daily blue light doses (sinusoidal light peaking at 88, 130, 250 and 450 µmol photons m(−2) s(−1), respectively). Ability of cells to regulate the light energy input caused alterations in growth and different biosynthetic pathways. The light saturation index for photosynthesis (E(k)), which governs the photoacclimative processes, ranged between 250 and 300 µmol photons m(−2) s(−1). Cells that were adapted to low light (

Strengths and weaknesses of microarray approaches to detect Pseudo-nitzschia species in the field.

The planktonic diatom genus Pseudo-nitzschia contains several genetically closely related species. Some of these can produce domoic acid, a potent neurotoxin. Thus, monitoring programs are needed to screen for the presence of these toxic species. Unfortunately, many are impossible to distinguish using light microscopy. Therefore, we assessed the applicability of microarray technology for detection of toxic and non-toxic Pseudo-nitzschia species in the Gulf of Naples (Mediterranean Sea). Here, 11 species have been detected, of which at least 5 are potentially toxic. A total of 49 genus- and species-specific DNA probes were designed in silico against the nuclear LSU and SSU rRNA of 19 species, and spotted on the microarray. The microarray was tested against total RNA of monoclonal cultures of eight species. Only three of the probes designed to be species-specific were indeed so within the limits of our experimental design. To assess the effectiveness of the microarray in detecting Pseudo-nitzschia species in environmental samples, we hybridized total RNA extracted from 11 seasonal plankton samples against microarray slides and compared the observed pattern with plankton counts in light microscopy and with expected hybridization patterns obtained with monoclonal cultures of the observed species. Presence of species in field samples generally resulted in signal patterns on the microarray as observed with RNA extracted from cultures of these species, but many a-specific signals appeared as well. Possible reasons for the numerous cross reactions are discussed. Calibration curves for Pseudo-nitzschia multistriata showed linear relationship between signal strength and cell number.

CHLOROPHYLL C PIGMENT PATTERNS IN 18 SPECIES (51 STRAINS) OF THE GENUS PSEUDO-NITZSCHIA (BACILLARIOPHYCEAE)(1).

The pigment composition of 18 species (51 strains) of the pennate diatom Pseudo-nitzschia was examined using HPLC. The carotenoid composition was typical for diatoms, with fucoxanthin (the major xanthophyll), diadinoxanthin, diatoxanthin, and ß,ß-carotene. However, a diverse array of chl c pigments was observed in the studied strains. All Pseudo-nitzschia strains contained chl a and chl c2 , traces of Mg-2,4-divinyl phaeoporphyrin a5 monomethyl ester (MgDVP), and traces of a chl c2 -like pigment originally found in the haptophyte Pavlova gyrans. The distribution of chl c1 and chl c3 was variable among species (present in seven and 14 species, respectively). Based on chl c distribution, three major pigment types were defined: type 1 (chl c1 + c2 , four species: P. australis, P. brasiliana, P. multiseries, and P. seriata), type 2 (chl c1 + c2 + c3 , three species: P. fraudulenta, P. multistriata, and P. pungens), and type 3 (chl c2 + c3 , 11 species: P. arenysensis, P. calliantha, P. cuspidata, P. decipiens, P. delicatissima, P. galaxiae, P. mannii, P. pseudodelicatissima, P. subcurvata, P. cf. subpacifica, and a novel Pseudo-nitzschia species). Type 1 and 2 species also shared the absence of a particular morphological character, the central nodule in the raphe, with the only exception of P. fraudulenta. The implications of such pigment diversity in chemotaxonomy, HAB monitoring, ecology, and phylogeny of Pseudo-nitzschia species are discussed.

A bicistronic lentiviral vector based on the 1D/2A sequence of foot-and-mouth disease virus expresses proteins stoichiometrically.

Classic IRES sequences are notorious for exerting biased expression in favor of upstream coding regions when placed into polycistronic vectors. Here, we report the development of a bicistronic lentiviral system based on the 1D/2A sequence from the foot-and-mouth disease virus that is able to maintain tightly balanced control of upstream and downstream protein expression for several days at a stoichiometry very closely approaching 1.0. Our results suggest that the 1D/2A sequence can be optimized in an FUGW lentiviral setting to coordinate expression of multiple polypeptides, presenting a potentially valuable tool to signaling network researchers and to the gene therapy community.