Exploring the authentication of COVID-19 vaccines using Surface-enhanced handheld Raman spectroscopy (SERS) equipped with orbital Raster scattering and machine learning

COVID-19 is a novel coronavirus first emerging in Wuhan, China in December 2019 and has since spread rapidly across the globe escalating into a worldwide pandemic causing millions of fatalities. Emergency response to the pandemic included social distancing and isolation measures as well as the escalation of vaccination programmes. The most popular COVID-19 vaccines are nucleic acid-based. The vast spread and struggles in containment of the virus has allowed a gap in the market to emerge for counterfeit vaccines. This study investigates the use of handheld Raman spectroscopy as a method for nucleic acid-based vaccine authentication and utilises machine learning analytics to assess the efficacy of the method. Conventional Raman spectroscopy requires a large workspace, is cumbersome and energy consuming, and handheld Raman systems show limitations with regards to sensitivity and sample detection. Surface Enhanced Raman spectroscopy (SERS) however, shows potential as an authentication technique for vaccines, allowing identification of characteristic nucleic acid bands in spectra. SERS showed strong identification potential through Correlation in Wavelength Space (CWS) with all vaccine samples obtaining an r value of approximately 1 when plotted against themselves. Variance was observed between some excipients and a selected number of DNA-based vaccines, possibly attributed to the stability of the SERS colloid where the colloid-vaccine complex had been measured over different time intervals. Further development of the technique would include optimisation of the SERS method, stability studies and more comprehensive analysis and interpretation of a greater sample size. © 2023 IEEE.

Antiviral compounds from seaweeds: An overview

The interest in macroalgae has been growing worldwide in the recent years, due to the new discoveries regarding the numerous health benefits they provide to consumers, namely anti-viral, antibacterial, and anti-inflammatory properties that enhance resistance and ability to combat disease to consumers, granted by algae's bioactive molecules. In the light of the ongoing COVID-19 pandemic, there is a renewed need to find cures, treatments or novel means to create immunity in the population against not only to the recently emerging severe acute respiratory syndrome-related coronavirus (SARS-CoV-2) but also to other viruses, in order to allow world populations to safely recover daily life routines. The aim of this chapter is to report the research and developments of possible treatments against virus, based on seaweed's bioactive compounds, from the first stage of development up to commercial products. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2022. All rights reserved.

Sensitivity assessment of dielectric modulated GaN material based SOI-FinFET for label-free biosensing applications

This work presents the sensitivity assessment of gallium nitride (GaN) material-based silicon-on-insulator fin field effect transistor by dielectric modulation in the nanocavity gap for label-free biosensing applications. The significant deflection is observed on the electrical characteristics such as drain current, transconductance, surface potential, energy band profile, electric field, sub-threshold slope, and threshold voltage in the presence of biomolecules owing to GaN material. Further, the device sensitivity is evaluated to identify the effectiveness of the proposed biosensor and its capability to detect the biomolecules with high precision or accuracy. The higher sensitivity is observed for Gelatin (k = 12) in terms of on-current, threshold voltage, and switching ratio by 104.88%, 82.12%, and 119.73%, respectively. This work is performed using a powerful tool, three-dimensional (3D) Sentaurus Technology computer-aided design using a well-calibrated structure. The results pave the way for GaN-SOI-FinFET to be a viable candidate for label-free dielectric modulated biosensor applications.

Biosurfactant: A Biodegradable Antimicrobial Substance

The coronavirus pandemic in 2020 increased the use of cleaning agents by residential individuals and businesses that maintained their operation even remotely. In formulating these products, one of the key ingredients is the surfactant molecule. Surfactants, in general, due to their characteristics, can act as antimicrobial agents. The presence of this active in cleaning products facilitates the process of removing dirt and reduces the occurrence of infections and health risks. However, most surfactants present in the consumer market, when used, require high consumption of water for removal and are also discharged into domestic sewage, without treatment, causing toxicity in different organisms due to their recalcitrance in the environment. Thus, the knowledge and use of biosurfactants, amphipathic molecules that can be obtained by plants and microbes, is important. Since, in addition to the same properties found in common surfactants, biosurfactants are highly biodegradable. This chapter discusses biosurfactants with a focus on their biodegradability, the different types of tests applied to assess this parameter and recent studies with importance in the applications of biosurfactants as antimicrobial agents. © 2022 Scrivener Publishing LLC.

PREFMoDeL: A Systematic Review and Proposed Taxonomy of Biomolecular Features for Deep Learning

Of fundamental importance in biochemical and biomedical research is understanding a molecule's biological properties—its structure, its function(s), and its activity(ies). To this end, computational methods in Artificial Intelligence, in particular Deep Learning (DL), have been applied to further biomolecular understanding—from analysis and prediction of protein–protein and protein–ligand interactions to drug discovery and design. While choosing the most appropriate DL architecture is vitally important to accurately model the task at hand, equally important is choosing the features used as input to represent molecular properties in these DL models. Through hypothesis testing, bioinformaticians have created thousands of engineered features for biomolecules such as proteins and their ligands. Herein we present an organizational taxonomy for biomolecular features extracted from 808 articles from across the scientific literature. This objective view of biomolecular features can reduce various forms of experimental and/or investigator bias and additionally facilitate feature selection in biomolecular analysis and design tasks. The resulting dataset contains 1360 nondeduplicated features, and a sample of these features were classified by their properties, clustered, and used to suggest new features. The complete feature dataset (the Public Repository of Engineered Features for Molecular Deep Learning, PREFMoDeL) is released for collaborative sourcing on the web.

Chemistry towards Biology-Instruct: Snapshot.

The knowledge of interactions between different molecules is undoubtedly the driving force of all contemporary biomedical and biological sciences. Chemical biology/biological chemistry has become an important multidisciplinary bridge connecting the perspectives of chemistry and biology to the study of small molecules/peptidomimetics and their interactions in biological systems. Advances in structural biology research, in particular linking atomic structure to molecular properties and cellular context, are essential for the sophisticated design of new medicines that exhibit a high degree of druggability and very importantly, druglikeness. The authors of this contribution are outstanding scientists in the field who provided a brief overview of their work, which is arranged from in silico investigation through the characterization of interactions of compounds with biomolecules to bioactive materials.

Experimental study on the heating/cooling and temperature uniformity performance of the microchannel temperature control device for nucleic acid PCR amplification reaction of COVID-19

The nucleic acid detection is an effective way for the prevention and control of COVID-19. PCR amplification is an important process in the nucleic acid detection. At present, PCR amplification has the problem of low heating/cooling rates, and poor temperature uniformity. This paper proposes a microchannel temperature control device for the nucleic acid detection. Five groups of parallel serpentine channels are used to increase the cooling rate of the PCR amplification. A gradual thermal conductivity design is applied to the reaction module to increase the temperature uniformity. The experimental results show that the best temperature uniformity is obtained when the materials of the inner and outer layers of the reaction module are copper and aluminum alloys, respectively. The limit and average heating/cooling rate are 7.2, 6.12, 5.52 and 5.28 °C/s, respectively, when the input power of the thermoelectric cooler is 11.07 W/cm2, the temperature and flow rate of the cooling water are 15℃ and 700 ml/min, and the thermal conductivity of the thermal grease is 6 W/(m·K). Compared with the commercial fan-fin cooling method, the limit and average heating/cooling rates are increased by 38.02%, 80.82%, 86.49% and 208.77%, respectively, with the help of microchannel cooling method. © 2023 Elsevier Ltd

Research progress on the analysis of active ingredients and elements in Fritillaria ussuriensis Bulbus

Fritillaria ussuriensis Bulbus, a genuine medicinal material of Northeast China, is the dry bulb of Fritillaria ussuriensis Maxim. It contains various active ingredients, such as alkaloids, alkaloids glycosides, adenosines, polysaccharides, and trace elements . It has antitussive, eliminating phlegm, antiasthmatic, antiulcer, antiplatelet aggregation, and anti-inflammatory. The qualitative and quantitative analysis of alkaloids, polysaccharides, nucleosides, and trace elements in Fritillaria ussuriensis Bulbus were reviewed, which is helpful for its cultivation and accurate application, and would provide a new choice for the treatment of coronavirus disease 2019 (COVID-19). © 2022

Eco-Friendly Hierarchical Nanoporous Microfiber Respirator Filters Fabricated Using Rotary Jet Spinning Technology (RJS)

The current global health crisis caused by the SARS-CoV-2 virus (COVID-19) has increased the use of personal protective equipment, especially face masks, leading to the disposal of a large amount of plastic waste causing an environmental crisis due to the use of non-biodegradable and non-recyclable polymers, such as polypropylene and polyester. In this work, an eco-friendly biopolymer, polylactic acid (PLA), was used to manufacture hierarchical nanoporous microfiber biofilters via a single-step rotary jet spinning (RJS) technique. The process parameters that aid the formation of nanoporosity within the microfibers were discussed. The microstructure of the fibers was analyzed by scanning electron microscopy (SEM) and a noninvasive X-ray microtomography (XRM) technique was employed to study the three-dimensional (3D) morphology and the porous architecture. Particulate matter (PM) and aerosol filtration efficiency were tested by OSHA standards with a broad range (10-1000 nm) of aerosolized saline droplets. The viral penetration efficiency was tested using the ΦX174 bacteriophage (∼25 nm) with an envelope, mimicking the spike protein structure of SARS-CoV-2. Although these fibers have a similar size used in N95 filters, the developed biofilters present superior filtration efficiency (∼99%) while retaining better breathability (<4% pressure drop) than N95 respirator filters. © 2023 American Chemical Society

Recent Trends in SERS-Based Plasmonic Sensors for Disease Diagnostics, Biomolecules Detection, and Machine Learning Techniques.

Surface-enhanced Raman spectroscopy/scattering (SERS) has evolved into a popular tool for applications in biology and medicine owing to its ease-of-use, non-destructive, and label-free approach. Advances in plasmonics and instrumentation have enabled the realization of SERS's full potential for the trace detection of biomolecules, disease diagnostics, and monitoring. We provide a brief review on the recent developments in the SERS technique for biosensing applications, with a particular focus on machine learning techniques used for the same. Initially, the article discusses the need for plasmonic sensors in biology and the advantage of SERS over existing techniques. In the later sections, the applications are organized as SERS-based biosensing for disease diagnosis focusing on cancer identification and respiratory diseases, including the recent SARS-CoV-2 detection. We then discuss progress in sensing microorganisms, such as bacteria, with a particular focus on plasmonic sensors for detecting biohazardous materials in view of homeland security. At the end of the article, we focus on machine learning techniques for the (a) identification, (b) classification, and (c) quantification in SERS for biology applications. The review covers the work from 2010 onwards, and the language is simplified to suit the needs of the interdisciplinary audience.

Design and Optimize of Campus Nucleic Acid Tests Queuing System

Covid-19 is more likely to spread in campus than it in other places because students live together without masks. In this case, it is necessary to take nucleic acid tests in a unified time regularly. To make nucleic acid tests efficient and convenient to manage students and the testing time, this article would apply queuing theory to design a nucleic acid tests queuing system by using the data from Sanda University in April 2022. According to the special conditions on campus, such as course schedule, students' daily activities, and campus management, students would be grouped by several management styles. The system would calculate the start time and waiting time for each group and would strive to take nucleic acid tests in an orderly manner with minimal waiting time. © 2022 IEEE.

Significance of Insilco Approaches in Finding Novel Biomolecules Challenging Newly Emerging, Resurging, Deliberately Emerging Global Outbreaks

Pandemics are large-scale outbreaks of contagious disease that can significantly raise ill health and promote death. Pandemics can spread through, wide range of geographical areas across the globe and capable of disrupting social and economic status of the countries affected. With the scientific testimony available it is evidenced that the rate of occurrence of pandemics has been drastically increased over the last two decades and presently witnessing the impact of COVID-19 disease globally. Anthropogenic activities such as urbanization conditions, increased global travel, abnormal land usage, exploitation of natural environment, are some of the significant causative factors that promote the rate of occurrence of pandemics. Rapid spread of SARS-CoV-2 virus highlighted the importance such as, be ready for any imminent event, need of detecting new bacterial and viral pathogens at initial stages of contagion and focus on the risk elements that promote the occurrence and spread of the outbreaks to humankind. It is evidenced from the literature that, there is a great demand to institute the methodological process using smart approaches such as Insilco based studies to investigate the emergence of future pandemics. Globally there is a great demand for the robust and efficient procedures to develop novel biomolecule in quick period. With this significance, the present paper aimed to survey the occurrence of global pandemics and the applications of Insilco methods in identifying newer routes to develop novel biomolecules in challenge the existing, newly emerging, resurging, deliberately emerging global outbreaks. © 2022 Published by ISRES Publishing: www.isres.org.

An Integrated Analysis of Mechanistic Insights into Biomolecular Interactions and Molecular Dynamics of Bio-Inspired Cu(II) and Zn(II) Complexes towards DNA/BSA/SARS-CoV-2 3CLpro by Molecular Docking-Based Virtual Screening and FRET Detection.

Novel constructed bioactive mixed-ligand complexes (1b) [CuII(L)2(phen)] and (2b) [ZnII(L)2(phen)] {where, L = 2-(4-morpholinobenzylideneamino)phenol), phen = 1,10-phenanthroline} have been structurally analysed by various analytical and spectroscopic techniques, including, magnetic moments, thermogravimetric analysis, and X-ray crystallography. Various analytical and spectral measurements assigned showed that all complexes appear to have an octahedral geometry. Agar gel electrophoresis's output demonstrated that the Cu(II) complex (1b) had efficient deoxyribonucleic cleavage and complex (2b) demonstrated the partial cleavage accomplished with an oxidation agent, which generates spreadable OH● through the Fenton type mechanism. The DNA binding constants observed from viscosity, UV-Vis spectral, fluorometric, and electrochemical titrations were in the following sequence: (1b) > (2b) > (HL), which suggests that the complexes (1b-2b) might intercalate DNA, a possibility that is supported by the biothermodynamic measurements. In addition, the observed binding constant results of BSA by electronic absorption and fluorometric titrations indicate that complex (1b) revealed the best binding efficacy as compared to complex (2b) and free ligand. Interestingly, all compounds are found to interact with BSA through a static approach, as further attested by FRET detection. The DFT and molecular docking calculations were also performed to realize the electronic structure, reactivity, and binding capability of all test samples with CT-DNA, BSA, and the SARS-CoV-2 3CLPro, which revealed the binding energies were in a range of -8.1 to -8.9, -7.5 to -10.5 and -6.7--8.8 kcal/mol, respectively. The higher reactivity of the complexes than the free ligand is supported by the FMO theory. Among all the observed data for antioxidant properties against DPPH᛫, ᛫OH, O2-• and NO᛫ free radicals, complex (1a) had the best biological efficacy. The antimicrobial and cytotoxic characteristics of all test compounds have been studied by screening against certain selected microorganisms as well as against A549, HepG2, MCF-7, and NHDF cell lines, respectively. The observed findings revealed that the activity enhances coordination as compared to free ligand via Overtone's and Tweedy's chelation mechanisms. This is especially encouraging given that in every case, the experimental findings and theoretical detections were in perfect accord.

Chemical Composition, In vivo Immunomodulatory and Anti-Hyperlipidaemic Properties of Rhinoceros (Rhino) Oil in Lead-Induced Immunocompromised Models

A knowledge of the chemical content of Rhinoceros (Rhino) oil and its activity on selected biomolecules of experimental models would help boost the immune system against an immunocompromised COVID-19 status. The study seeks to evaluate the chemical and biomolecular profile of Rhino oil. Chemical profile was done using standard methods of analysis. 25 rats were assigned in five groups (A-E) (n=5). Animals in group A (control) were administered 0.5 ml of distilled water while those in groups B-E which were immunocompromised (by intraperitoneal administration of 5 mg/kg body weight (b.w) of lead [Pb]) were also administered distilled water, immunomodulatory drug (5 mg/kg body weight of zinc [Zn]), 2 and 5 mg/kg b.w of Rhino oil extract respectively, once daily for 8 days followed by biomolecular assay. Proximate analysis gave moisture content (14.37+/-0.29), among others. FAMEs analysis showed hexadecanoic acid (12.80%) and other esters. Lipid profile of the oil gave LDLC to contain (32.90+/-0.53 mg/L), and others. The physicochemical properties gave iodine value as (115.80+/-0.40 mg/g), among others. The metal composition revealed Zn (0.28+/-0.06) plus others. The amnio acid profile of the oil gave ten essential amino acids and non-essential amino acids respectively. The levels of biomolecules in serum of the animals were altered at specific doses of the oil extract. Altogether, the chemical content of the oil was significantly high, with altered biomolecular effect. The rich content of vital nutrients and chemicals of Rhino oil may boost the white blood cells against COVID-19. The isolation and characterization of the active principles of the oil is encouraged. Copyright © 2007 The authors.

Databases, DrugBank, and virtual screening platforms for therapeutic development

The upsurge of the severe acute respiratory syndrome-Coronavirus-2 (SARS-CoV-2) has turned into a global health disaster. Many remodeled medications were suggested for treatment in the early stages of this pandemic, but these dosages afterward came across with distinct offshoots. Thus, these consequences compelled the scientists to develop new drugs using various antiviral, antiinflammatory, antibacterial, and phytochemical compounds. A handful of drugs have been scrutinized in silico, in vitro, plus through human trials such as anti-SARS-CoV-2 agents and made available as various databases by various scientific communities. The SARS-CoV-2 pandemic databases are designed to allay difficulties associated with this scenario. Some of the popular databases are GESS (global evaluation of SARS-CoV-2/HCoV-19 sequences) which gives a thorough study of data based on tenfold of thousands of complete coverage and quality of SARS-CoV-2 genomes, CORona Drug InTERactions (CORDITE) database for SARS-CoV-2 which profoundly combines the understanding of potential drugs and make it available for scientists and medicos. SARSCOVIDB set one’s sights to merge all differential gene expression data, at mRNA and protein levels, helping to accelerate analysis and research on the molecular impact of covid-19. This chapter aims to provide a piece of complete information about the SARS-CoV-2 virus databases, potentially available drugs, and virtual screening methods. And also provides a different webserver to reach out for information related to the COVID-19 pandemic and its future. © 2022 Elsevier Inc. All rights reserved.

Artificial intelligence methods to repurpose and discover new drugs to fight the Coronavirus disease-2019 pandemic

The Coronavirus disease 2019 pandemic struck the world at the end of 2019 and, as of 2021, there are no specific drugs available against the causative agent, the severe acute respiratory syndrome-Coronavirus-2 (SARS-CoV-2). From the onset of the pandemic, researchers have been trying to find drugs among the current therapeutic arsenal that could target crucial viral function, and many of these efforts resulted in clinical trials to repurpose a drug for this new indication. In this scenario, artificial intelligence (AI) is of fundamental importance, allowing academia and pharmaceutical companies to accelerate the discovery of biochemical insights from the chemical and biological information available in literature databases. This chapter will cover some AI methods that are being explored to repurpose drugs against SARS-CoV-2. It will be outlined how these methods work followed by a discussion of selected examples applying them to identify promising drugs. © 2022 Elsevier Inc. All rights reserved.

Convenient Nucleic Acid Detection Method and Point-of-Care Detection Device Rased on CRISPR/Cas12a Molecular Diagnosis

Objective Clustered regularly interspaced short palindromic repeats (CRISPR) has shown significant promise as an emerging nucleic acid detection technology. However, it still requires improvement in terms of sensitivity, detection automation, and anti-pollution. Furthermore, CRISPR technology lacks simple and portable professional equipment to meet the high demand of rapid point-of-care testing. Therefore, this study proposes a CRISPR/Cas12a detection reaction system for SARS-CoV-2. This detection response system and innovative tube-in-tube consumables aid in developing a portable compact device for simultaneous automatic detection of several samples and a coaxial fiber-based fluorescence detection system. Finally, we developed a single-sample user-friendly nucleic acid detection APP based on smartphone recognition and detection results for the manual detection mode. Methods The target in this study was severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which was detected using the CRISPR method and enhanced via the reverse transcription-recombinase polymerase amplification (RT-RPA) technique;the feasibility was assessed using the reverse transcription-polymerase chain reaction (RT-PCR) amplification method in the early stages. Various companies customized the required reagents and the designed sequences. In the detection process, first, with the tube-in-tube consumables developed by our team in the early stage, which comprised the reaction outer and inner tubes, the amplification reagents and detection reagents were loaded into the inner and outer tubes, respectively. The temperature was regulated to 37-42 ℃ to complete the amplification. The reagents in the inner and outer tubes were then mixed by shaking or centrifugation, and the temperature was adjusted to complete the CRISPR reaction. Finally, it was possible to observe if there was any fluorescence occurrence under the illumination of a blue light. The detection instrument was composed of an optical cassette and a base, and automatic detection was realized through a printed circuit board (PCB), a human-computer interaction display screen, etc. In addition, this study also used the fluorescence image recognition algorithm to process the detection images, compared with the international standard polymerase chain reaction (PCR) technology to explore the detection limit, and increased the target types to test the specificity strength. Results and Discussions The lower part of the detection instrument designed by our team integrates the printed circuit board and the human-computer interaction display screen. In the automatic detection mode, the fluorescence recognition circuit was designed with the help of a 470 nm light-emitting diode (LED), an optical filter, a complementary metal oxide semiconductor (CMOS) camera, a collimating lens, and a coaxial fiber. At the same time, the specificity of the theoretical experiment was verified through comparative experiments on several different targets. In addition, to verify the accuracy of this method for detecting actual samples, we compared each actual sample through PCR detection and the method based on the combination of RT-RPA and CRISPR proposed in this study. The detection results showed that the two were perfectly consistent. Conclusions The current study proposed a CRISPR/Cas12a-based anti-pollution portable nucleic acid detection technique. Furthermore, a simple model was proposed based on the naked eye or smartphone to recognize results;additionally, a downsized portable device based on fluorescence detection that can simultaneously detect numerous samples was constructed. The portable device can detect numerous samples simultaneously, and it has a constant heating mechanism and fluorescence stimulation detection optical channel to enhance the detection system’s accuracy and stability. The nucleic acid of SARS-CoV-2 was verified using the proposed method and detection system. The minimum detection limit was <10 copy/μL. The test findings of our method had a good consistency with that of real- ime fluorescence quantitative PCR method, but our method took less than half the time consuming of the PCR method, and the whole detection process could be finished in 32 min. The method and technology developed in this study propose a novel approach for nucleic acid detection at health-care center and home. © 2022 Science Press. All rights reserved.

Microalgae-based approaches to overcome the effects of the COVID-19 pandemic

At the end of 2019, a new coronavirus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) began to spread rapidly worldwide, to the point of becoming a pandemic by early 2020. After almost two years of living with this new disease, humanity continues to face one of its greatest crises, not only health-wise but also environmentally and economically. To alleviate some of the effects suffered worldwide by the pandemic, it is necessary to integrate new strategies in medical therapies and economic strengthening. Under this scenario, the present review presents the functionalities of microalgae that could be exploited to boost the areas most affected by the pandemic. Among the most promising benefits are the various biomolecules derived from microalgae that could be adjuvant therapies or preventive agents and their potential to become biofactories of antibodies or vaccines through genetic engineering. Finally, the development of microalgae-based industries could become a driver of the economy and a source of local employment generation. In this way, the positive impact of microalgae-derived products in pharmacological, environmental, and industrial fields that could be exploited to counteract the consequences of two years of the pandemic is presented.

Chapter 26 - Phase separation and infectious diseases

Infectious diseases continue to represent a major threat to the humankind. This is reiterated by the current COVID-19 pandemic that affected almost 550 million people worldwide and caused more than 6.35 million deaths. It is clear that in addition to the existing preventive measures and treatments for various pathogens, better understanding is needed of the relationship between pathogen infection and the human antiinfection immune response and of the specific mechanisms underlying these complex processes. There is a constant warfare between the hosts and infectious pathogens, where humans have evolved a very effective and broadly amended antiinfection immune system, but, in their turn, pathogens have evolved a multitude of immune escape mechanisms to efficiently oppose it. It is recognized now that liquid–liquid phase separation (LLPS) occupies a special place among the important molecular mechanisms of the antiinfection immune response. Some illustrative examples of the roles of LLPS in the antiinfection immune response are considered in this chapter.