Mass Spectrometry Approaches for SARS-CoV-2 Detection: Harnessing for Application in Food and Environmental Samples

The public health crisis caused by the emergence of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in 2019 has drastically changed our lifestyle in virtually all contexts around the world. SARS-CoV-2 is mainly airborne, transmitted by the salivary droplets produced when infected people cough or sneeze. In addition, diarrhea symptoms and the detection of SARS-CoV-2 in feces suggest a fecal–oral route of contagion. Currently, the high demand for SARS-CoV-2 diagnosis has surpassed the availability of PCR and immunodetection probes and has prompted the development of other diagnostic alternatives. In this context, mass spectrometry (MS) represents a mature, robust alternative platform for detection of SARS-CoV-2 and other human viruses. This possibility has raised great interest worldwide. Therefore, it is time for the global application of MS as a feasible option for detecting SARS-CoV-2, not only in human fluids, but also in other matrices such as foods and wastewater. This review covers the most relevant established methods for MS-based SARS-CoV-2 detection and discusses the future application of these tools in different matrices. Significance: The Coronavirus Disease 2019 (COVID-19) pandemic highlighted the pros and cons of currently available PCR and immunodetection tools. The great concern over the infective potential of SARS-CoV-2 viral particles that can persist for several hours on different surfaces under various conditions further evidenced the need for reliable alternatives and high-throughput methods to meet the needs for mass detection of SARS-CoV-2. In this context, MS-based proteomics emerging from fundamental studies in life science can offer a robust option for SARS-CoV-2 detection in human fluids and other matrices. In addition, the substantial efforts towards detecting SARS-CoV-2 in clinal samples, position MS to support the detection of this virus in different matrices such as the surfaces of the packing food process, frozen foods, and wastewaters. Proteomics and mass spectrometry are, therefore, well positioned to play a role in the epidemiological control of COVID-19 and other future diseases. We are currently witnessing the opportunity to generate technologies to overcome prolonged pandemics for the first time in human history

Characterization of the Technofunctional Properties and Three-Dimensional Structure Prediction of 11S Globulins from Amaranth (Amaranthus hypochondriacus L.) Seeds

Amaranth 11S globulins (Ah11Sn) are an excellent source of essential amino acids; however, there have been no investigations on the characterization of their techno-functional properties at different pH conditions and NaCl concentrations, which are necessary for food formulations. In this work, we report a new two-step purification method for native Ah11Sn with purity levels of ~95%. LC–MS/MS analysis revealed the presence of three different Ah11Sn paralogs named Ah11SB, A11SC, and Ah11SHMW, and their structures were predicted with Alphafold2. We carried out an experimental evaluation of Ah11Sn surface hydrophobicity, solubility, emulsifying properties, and assembly capacity to provide an alternative application of these proteins in food formulations. Ah11Sn showed good surface hydrophobicity, solubility, and emulsifying properties at pH values of 2 and 3. However, the emulsions became unstable at 60 min. The assembly capacity of Ah11Sn evaluated by DLS analysis showed mainly the trimeric assembly (~150–170 kDa). This information is beneficial to exploit and utilize Ah11Sn rationally in food systems

Differences in the Abundance of Auxin Homeostasis Proteins Suggest Their Central Roles for In Vitro Tissue Differentiation in Coffea arabica

Coffea arabica is one of the most important crops worldwide. In vitro culture is an alternative for achieving Coffea regeneration, propagation, conservation, genetic improvement, and genome editing. The aim of this work was to identify proteins involved in auxin homeostasis by isobaric tandem mass tag (TMT) and the synchronous precursor selection (SPS)-based MS3 technology on the Orbitrap Fusion™ Tribrid mass spectrometer™ in three types of biological materials corresponding to C. arabica: plantlet leaves, calli, and suspension cultures. Proteins included in the β-oxidation of indole butyric acid and in the signaling, transport, and conjugation of indole-3-acetic acid were identified, such as the indole butyric response (IBR), the auxin binding protein (ABP), the ATP-binding cassette transporters (ABC), the Gretchen-Hagen 3 proteins (GH3), and the indole-3-acetic-leucine-resistant proteins (ILR). A more significant accumulation of proteins involved in auxin homeostasis was found in the suspension cultures vs. the plantlet, followed by callus vs. plantlet and suspension culture vs. callus, suggesting important roles of these proteins in the cell differentiation process

Proteometabolomic Analysis Reveals Molecular Features Associated with Grain Size and Antioxidant Properties amongst Chickpea (Cicer arietinum L.) Seeds Genotypes

Legumes are an essential source of nutrients that complement energy and protein requirements in the human diet. They also contribute to the intake of bioactive compounds such as polyphenols, whose content can vary depending on cultivars and genotypes. We conducted a comparative proteomics and metabolomics study to determine if there were significant variations in relevant nutraceutical compounds in the five genotypes of Kabuli-type chickpea grains. We performed an isobaric tandem mass tag (TMT) couple to synchronous precursor selection (SPS)-MS3 method along with a targeted and untargeted metabolomics approach based on accurate mass spectrometry. We observed an association between the overproduction of proteins involved in starch, lipid, and amino acid metabolism with gibberellin accumulation in large grains. In contrast, we visualized the over-accumulation of proteins associated with water deprivation in small grains. It was possible to visualize in small grains the over-accumulation of some phenolics such as vanillin, salicylic acid, protocatechuic acid, 4-coumaric acid, 4-hydroxybenzoic acid, vanillic acid, ferulic acid, and kaempferol 3-O-glucoside as well as the amino acid l-phenylalanine. The activated phenolic pathway was associated with the higher antioxidant capacity of small grains. Small grains consumption could be advantageous due to their nutraceutical properties

A First Glimpse of the Mexican Fruit Fly Anastrepha ludens (Diptera: Tephritidae) Antenna Morphology and Proteome in Response to a Proteinaceous Attractant

Anastrepha ludens is a key pest of mangoes and citrus from Texas to Costa Rica but the mechanisms of odorant perception in this species are poorly understood. Detection of volatiles in insects occurs mainly in the antenna, where molecules penetrate sensillum pores and link to soluble proteins in the hemolymph until reaching specific odor receptors that trigger signal transduction and lead to behavioral responses. Scrutinizing the molecular foundation of odorant perception in A. ludens is necessary to improve biorational management strategies against this pest. After exposing adults of three maturity stages to a proteinaceous attractant, we studied antennal morphology and comparative proteomic profiles using nano-LC-MS/MS with tandem mass tags combined with synchronous precursor selection (SPS)-MS3. Antennas from newly emerged flies exhibited dense agglomerations of olfactory sensory neurons. We discovered 4618 unique proteins in the antennas of A. ludens and identified some associated with odor signaling, including odorant-binding and calcium signaling related proteins, the odorant receptor co-receptor (Orco), and putative odorant-degrading enzymes. Antennas of sexually immature flies exhibited the most upregulation of odor perception proteins compared to mature flies exposed to the attractant. This is the first report where critical molecular players are linked to the odor perception mechanism of A. ludens

Migraciones sur-sur : Paradojas globales y promesas locales

Durante la primera década del siglo XX el 90% de los migrantes provenía de Europa y se dirigía a cinco países: EEUU, Argentina, Canadá, Brasil y Australia. Hoy esa misma proporción de migrantes proviene de tres continentes: Asia, África y Latinoamérica y se dirige a cuatro grandes regiones: Europa, Norteamérica, Asia Pacífico y El Golfo Pérsico. Las migraciones se han mundializado no tanto por la magnitud de los flujos, que sigue estando por debajo del 5% de la población mundial, sino por el reducido número de países que hoy permanece al margen de las redes migratorias. Estas realidades crecientes crean las condiciones para que los potenciales migrantes en países empobrecidos y en proceso de empobrecimiento quieran migrar. A esto precisamente apuntó Joaquín Arango cuando definió nuestra época como el tiempo de la inmovilidad involuntaria

The Sonozotz project: Assembling an echolocation call library for bats in a megadiverse country

Bat acoustic libraries are important tools that assemble echolocation calls to allow the comparison and discrimination to confirm species identifications. The Sonozotz project represents the first nation-wide library of bat echolocation calls for a megadiverse country. It was assembled following a standardized recording protocol that aimed to cover different recording habitats, recording techniques, and call variation inherent to individuals. The Sonozotz project included 69 species of echolocating bats, a high species richness that represents 50% of bat species found in the country. We include recommendations on how the database can be used and how the sampling methods can be potentially replicated in countries with similar environmental and geographic conditions. To our knowledge, this represents the most exhaustive effort to date to document and compile the diversity of bat echolocation calls for a megadiverse country. This database will be useful to address a range of ecological questions including the effects of anthropogenic activities on bat communities through the analysis of bat sound.</p