BioTech

18 pages, 325 KiB

Open AccessEditor’s ChoiceReview

Cyanidiales-Based Bioremediation of Heavy Metals

by Hari Lal Kharel, Ina Shrestha, Melissa Tan, Mohammad Nikookar, Negar Saraei and Thinesh Selvaratnam

BioTech 2023, 12(2), 29; https://doi.org/10.3390/biotech12020029 - 18 Apr 2023

Cited by 8 | Viewed by 3777

Abstract

With growing urbanization and ongoing development activities, the consumption of heavy metals has been increasing globally. Although heavy metals are vital for the survival of living beings, they can become hazardous when they surpass the permissible limit. The effect of heavy metals varies [...] Read more.

With growing urbanization and ongoing development activities, the consumption of heavy metals has been increasing globally. Although heavy metals are vital for the survival of living beings, they can become hazardous when they surpass the permissible limit. The effect of heavy metals varies from normal to acute depending on the individual, so it is necessary to treat the heavy metals before releasing them into the environment. Various conventional treatment technologies have been used based on physical, chemical, and biological methods. However, due to technical and economic constraints and poor sustainability towards the environment, the use of these technologies has been limited. Microalgal-based heavy metal removal has been explored for the past few decades and has been seen as an effective, environment-friendly, and inexpensive method compared to conventional treatment technology. Cyanidiales that belong to red algae have the potential for remediation of heavy metals as they can withstand and tolerate extreme stresses of heat, acid salts, and heavy metals. Cyanidiales are the only photosynthetic organisms that can survive and thrive in acidic mine drainage, where heavy metal contamination is often prevalent. This review focuses on the algal species belonging to three genera of Cyanidiales: Cyanidioschyzon, Cyanidium, and Galdieria. Papers published after 2015 were considered in order to examine these species’ efficiency in heavy metal removal. The result is summarized as maximum removal efficiency at the optimum experimental conditions and based on the parameters affecting the metal ion removal efficiency. This study finds that pH, initial metal concentration, initial algal biomass concentration, algal strains, and growth temperature are the major parameters that affect the heavy metal removal efficiency of Cyanidiales. Full article

23 pages, 5787 KiB

Open AccessEditor’s ChoiceArticle

Protein Delivery to Insect Epithelial Cells In Vivo: Potential Application to Functional Molecular Analysis of Proteins in Butterfly Wing Development

by Yugo Nakazato and Joji M. Otaki

BioTech 2023, 12(2), 28; https://doi.org/10.3390/biotech12020028 - 16 Apr 2023

Cited by 5 | Viewed by 3267

Abstract

Protein delivery to cells in vivo has great potential for the functional analysis of proteins in nonmodel organisms. In this study, using the butterfly wing system, we investigated a method of protein delivery to insect epithelial cells that allows for easy access, treatment, [...] Read more.

Protein delivery to cells in vivo has great potential for the functional analysis of proteins in nonmodel organisms. In this study, using the butterfly wing system, we investigated a method of protein delivery to insect epithelial cells that allows for easy access, treatment, and observation in real time in vivo. Topical and systemic applications (called the sandwich and injection methods, respectively) were tested. In both methods, green/orange fluorescent proteins (GFP/OFP) were naturally incorporated into intracellular vesicles and occasionally into the cytosol from the apical surface without any delivery reagent. However, the antibodies were not delivered by the sandwich method at all, and were delivered only into vesicles by the injection method. A membrane-lytic peptide, L17E, appeared to slightly improve the delivery of GFP/OFP and antibodies. A novel peptide reagent, ProteoCarry, successfully promoted the delivery of both GFP/OFP and antibodies into the cytosol via both the sandwich and injection methods. These protein delivery results will provide opportunities for the functional molecular analysis of proteins in butterfly wing development, and may offer a new way to deliver proteins into target cells in vivo in nonmodel organisms. Full article

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20 pages, 1566 KiB

Open AccessEditor’s ChoiceReview

Biomolecular Liquid–Liquid Phase Separation for Biotechnology

by Sumit Shil, Mitsuki Tsuruta, Keiko Kawauchi and Daisuke Miyoshi

BioTech 2023, 12(2), 26; https://doi.org/10.3390/biotech12020026 - 1 Apr 2023

Cited by 7 | Viewed by 8026

Abstract

The liquid–liquid phase separation (LLPS) of biomolecules induces condensed assemblies called liquid droplets or membrane-less organelles. In contrast to organelles with lipid membrane barriers, the liquid droplets induced by LLPS do not have distinct barriers (lipid bilayer). Biomolecular LLPS in cells has attracted [...] Read more.

The liquid–liquid phase separation (LLPS) of biomolecules induces condensed assemblies called liquid droplets or membrane-less organelles. In contrast to organelles with lipid membrane barriers, the liquid droplets induced by LLPS do not have distinct barriers (lipid bilayer). Biomolecular LLPS in cells has attracted considerable attention in broad research fields from cellular biology to soft matter physics. The physical and chemical properties of LLPS exert a variety of functions in living cells: activating and deactivating biomolecules involving enzymes; controlling the localization, condensation, and concentration of biomolecules; the filtration and purification of biomolecules; and sensing environmental factors for fast, adaptive, and reversible responses. The versatility of LLPS plays an essential role in various biological processes, such as controlling the central dogma and the onset mechanism of pathological diseases. Moreover, biomolecular LLPS could be critical for developing new biotechnologies such as the condensation, purification, and activation of a series of biomolecules. In this review article, we introduce some fundamental aspects and recent progress of biomolecular LLPS in living cells and test tubes. Then, we discuss applications of biomolecular LLPS toward biotechnologies. Full article

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14 pages, 4062 KiB

Open AccessEditor’s ChoiceArticle

Computational Screening of Approved Drugs for Inhibition of the Antibiotic Resistance Gene mecA in Methicillin-Resistant Staphylococcus aureus (MRSA) Strains

by Benson Otarigho and Mofolusho O. Falade

BioTech 2023, 12(2), 25; https://doi.org/10.3390/biotech12020025 - 31 Mar 2023

Cited by 7 | Viewed by 4031

Abstract

Antibiotic resistance is a critical problem that results in a high morbidity and mortality rate. The process of discovering new chemotherapy and antibiotics is challenging, expensive, and time-consuming, with only a few getting approved for clinical use. Therefore, screening already-approved drugs to combat [...] Read more.

Antibiotic resistance is a critical problem that results in a high morbidity and mortality rate. The process of discovering new chemotherapy and antibiotics is challenging, expensive, and time-consuming, with only a few getting approved for clinical use. Therefore, screening already-approved drugs to combat pathogens such as bacteria that cause serious infections in humans and animals is highly encouraged. In this work, we aim to identify approved antibiotics that can inhibit the mecA antibiotic resistance gene found in methicillin-resistant Staphylococcus aureus (MRSA) strains. The MecA protein sequence was utilized to perform a BLAST search against a drug database containing 4302 approved drugs. The results revealed that 50 medications, including known antibiotics for other bacterial strains, targeted the mecA antibiotic resistance gene. In addition, a structural similarity approach was employed to identify existing antibiotics for S. aureus, followed by molecular docking. The results of the docking experiment indicated that six drugs had a high binding affinity to the mecA antibiotic resistance gene. Furthermore, using the structural similarity strategy, it was discovered that afamelanotide, an approved drug with unclear antibiotic activity, had a strong binding affinity to the MRSA-MecA protein. These findings suggest that certain already-approved drugs have potential in chemotherapy against drug-resistant pathogenic bacteria, such as MRSA. Full article

(This article belongs to the Special Issue Feature Papers in Medical Biotechnology)

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12 pages, 6659 KiB

Open AccessEditor’s ChoiceArticle

A Thermostable Lipase Isolated from Brevibacillus thermoruber Strain 7 Degrades Ɛ-Polycaprolactone

by Nikolina Atanasova, Tsvetelina Paunova-Krasteva, Margarita Kambourova and Ivanka Boyadzhieva

BioTech 2023, 12(1), 23; https://doi.org/10.3390/biotech12010023 - 14 Mar 2023

Cited by 12 | Viewed by 3750

Abstract

The tremendous problem with plastic waste accumulation has determined an interest in biodegradation by effective degraders and their enzymes, such as thermophilic enzymes, which are characterized by high catalytic rates, thermostability, and optimum temperatures close to the melting points of some plastics. In [...] Read more.

The tremendous problem with plastic waste accumulation has determined an interest in biodegradation by effective degraders and their enzymes, such as thermophilic enzymes, which are characterized by high catalytic rates, thermostability, and optimum temperatures close to the melting points of some plastics. In the present work, we report on the ability of a thermophilic lipase, by Brevibacillus thermoruber strain 7, to degrade Ɛ-polycaprolactone (PCL), as well as the enzyme purification, the characterization of its physicochemical properties, the product degradation, and its disruptive effect on the PCL surface. The pure enzyme showed the highest reported optimum temperature at 55 °C and a pH of 7.5, while its half-life at 60 °C was more than five hours. Its substrate specificity referred the enzyme to the subgroup of lipases in the esterase group. A strong inhibitory effect was observed by detergents, inhibitors, and Fe³⁺ while Ca²⁺ enhanced its activity. The monomer Ɛ-caprolactone was a main product of the enzyme degradation. Similar elution profiles of the products received after treatment with ultra-concentrate and pure enzyme were observed. The significant changes in PCL appearance comprising the formation of shallower or deeper in-folds were observed after a week of incubation. The valuable enzyme properties of the lipase from Brevibacillus thermoruber strain 7, which caused a comparatively quick degradation of PCL, suggests further possible exploration of the enzyme for effective and environment-friendly degradation of PCL wastes in the area of thermal basins, or in thermophilic remediation processes. Full article

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11 pages, 1772 KiB

Open AccessEditor’s ChoiceArticle

Production, Kinetic/Thermodynamic Study, and Evaluation of the Influence of Static Magnetic Field on Kinetic Parameters of β-Fructofuranosidase from Aspergillus tamarii Kita UCP 1279 Produced by Solid-State Fermentation

by Rodrigo Lira de Oliveira, Aldeci França Araújo dos Santos, Bianca Alencar Cardoso, Thayanne Samille da Silva Santos, Galba Maria de Campos-Takaki, Tatiana Souza Porto and Camila Souza Porto

BioTech 2023, 12(1), 21; https://doi.org/10.3390/biotech12010021 - 3 Mar 2023

Cited by 3 | Viewed by 2692

Abstract

β-fructofuranosidases (FFases) are enzymes involved in sucrose hydrolysis and can be used in the production of invert sugar and fructo-oligosaccharides (FOS). This last is an important prebiotic extensively used in the food industry. In the present study, the FFase production by Aspergillus tamarii [...] Read more.

β-fructofuranosidases (FFases) are enzymes involved in sucrose hydrolysis and can be used in the production of invert sugar and fructo-oligosaccharides (FOS). This last is an important prebiotic extensively used in the food industry. In the present study, the FFase production by Aspergillus tamarii Kita UCP 1279 was assessed by solid-state fermentation using a mixture of wheat and soy brans as substrate. The FFase presents optimum pH and temperature at 5.0–7.0 and 60 °C, respectively. According to the kinetic/thermodynamic study, the FFase was relatively stable at 50 °C, a temperature frequently used in industrial FOS synthesis, using sucrose as substrate, evidenced by the parameters half-life (115.52 min) and D-value (383.76 min) and confirmed by thermodynamic parameters evaluated. The influence of static magnetic field with a 1450 G magnetic flux density presented a positive impact on FFase kinetic parameters evidenced by an increase of affinity of enzyme by substrate after exposition, observed by a decrease of 149.70 to 81.73 mM on K_m. The results obtained indicate that FFases present suitable characteristics for further use in food industry applications. Moreover, the positive influence of a magnetic field is an indicator for further developments of bioprocesses with the presence of a magnetic field. Full article

(This article belongs to the Section Industry, Agriculture and Food Biotechnology)

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11 pages, 1577 KiB

Open AccessEditor’s ChoiceArticle

In Vitro Anti-HIV-1 Activity of Chitosan Oligomers N-Conjugated with Asparagine and Glutamine

by Fatih Karadeniz

BioTech 2023, 12(1), 18; https://doi.org/10.3390/biotech12010018 - 8 Feb 2023

Cited by 6 | Viewed by 3068

Abstract

Chitosan oligomers (COS) are polysaccharides obtained by the hydrolyzation of chitosan. They are water-soluble, biodegradable, and have a wide range of beneficial properties for human health. Studies have shown that COS and its derivatives possess antitumor, antibacterial, antifungal, and antiviral activities. The goal [...] Read more.

Chitosan oligomers (COS) are polysaccharides obtained by the hydrolyzation of chitosan. They are water-soluble, biodegradable, and have a wide range of beneficial properties for human health. Studies have shown that COS and its derivatives possess antitumor, antibacterial, antifungal, and antiviral activities. The goal of the current study was to investigate the anti-human immunodeficiency virus-1 (HIV-1) potential of amino acid-conjugated COS compared to COS itself. The HIV-1 inhibitory effects of asparagine-conjugated (COS-N) and glutamine-conjugated (COS-Q) COS were evaluated by their ability to protect C8166 CD4+ human T cell lines from HIV-1 infection and infection-mediated death. The results show that the presence of COS-N and COS-Q was able to prevent cells from HIV-1-induced lysis. Additionally, p24 viral protein production was observed to be suppressed in COS conjugate-treated cells compared to COS-treated and untreated groups. However, the protective effect of COS conjugates diminished by delayed treatment indicated an early stage inhibitory effect. COS-N and COS-Q did not show any inhibitory effect on the activities of HIV-1 reverse transcriptase and protease enzyme. The results suggest that COS-N and COS-Q possess an HIV-1 entry inhibition activity compared to COS and further studies to develop different peptide and amino acid conjugates containing N and Q amino acids might yield more effective compounds to battle HIV-1 infection. Full article

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13 pages, 1814 KiB

Open AccessFeature PaperEditor’s ChoiceArticle

Separating and Purifying Mycosporine-like Amino Acids from Cyanobacteria for Application in Commercial Sunscreen Formulations

by Valeria Candelo and Carole Anne Llewellyn

BioTech 2023, 12(1), 16; https://doi.org/10.3390/biotech12010016 - 3 Feb 2023

Cited by 6 | Viewed by 4293

Abstract

Using algal-derived mycosporine-like amino acids (MAAs) in sunscreen formulations is constrained by low cellular concentrations of MAAs and by the high costs associated with harvesting algal cells and extracting the MAAs. Here, we report an industrial scalable method using a membrane filtration approach [...] Read more.

Using algal-derived mycosporine-like amino acids (MAAs) in sunscreen formulations is constrained by low cellular concentrations of MAAs and by the high costs associated with harvesting algal cells and extracting the MAAs. Here, we report an industrial scalable method using a membrane filtration approach to purify and concentrate aqueous extracts of MAAs. The method includes an additional biorefinery step enabling purification of phycocyanin, an established valuable natural product. Cultivated cells of the cyanobacterium Chlorogloeopsis fritschii (PCC 6912) were concentrated and homogenised to produce a feed for sequential processing through three membranes of decreasing pore size to obtain a retentate and permeate for each step. Microfiltration (0.2 µm) was used to remove cell debris. Ultrafiltration (10,000 Da) was used to remove large molecules and recover phycocyanin. Finally, nanofiltration (300–400 Da) was used to remove water and other small molecules. Permeate and retentate were analysed using UV-visible spectrophotometry and HPLC. The initial homogenised feed had a shinorine concentration of 5.6 ± 07 mg L⁻¹. The final nanofiltered retentate resulted in a 3.3 times-purified concentrate (shinorine concentration of 18.71 ± 0.29 mg L⁻¹). Significant process losses (35%) highlight scope for improvement. Results confirm the potential of membrane filtration to purify and concentrate aqueous solutions of MAAs with simultaneous separation of phycocyanin highlighting a biorefinery approach. Full article

(This article belongs to the Section Industry, Agriculture and Food Biotechnology)

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15 pages, 1351 KiB

Open AccessEditor’s ChoiceReview

Cell Immortalization: In Vivo Molecular Bases and In Vitro Techniques for Obtention

by Javier Curi de Bardet, Celeste Ramírez Cardentey, Belkis López González, Deanira Patrone, Idania Lores Mulet, Dario Siniscalco and María de los Angeles Robinson-Agramonte

BioTech 2023, 12(1), 14; https://doi.org/10.3390/biotech12010014 - 28 Jan 2023

Cited by 17 | Viewed by 7618

Abstract

Somatic human cells can divide a finite number of times, a phenomenon known as the Hayflick limit. It is based on the progressive erosion of the telomeric ends each time the cell completes a replicative cycle. Given this problem, researchers need cell lines [...] Read more.

Somatic human cells can divide a finite number of times, a phenomenon known as the Hayflick limit. It is based on the progressive erosion of the telomeric ends each time the cell completes a replicative cycle. Given this problem, researchers need cell lines that do not enter the senescence phase after a certain number of divisions. In this way, more lasting studies can be carried out over time and avoid the tedious work involved in performing cell passes to fresh media. However, some cells have a high replicative potential, such as embryonic stem cells and cancer cells. To accomplish this, these cells express the enzyme telomerase or activate the mechanisms of alternative telomere elongation, which favors the maintenance of the length of their stable telomeres. Researchers have been able to develop cell immortalization technology by studying the cellular and molecular bases of both mechanisms and the genes involved in the control of the cell cycle. Through it, cells with infinite replicative capacity are obtained. To obtain them, viral oncogenes/oncoproteins, myc genes, ectopic expression of telomerase, and the manipulation of genes that regulate the cell cycle, such as p53 and Rb, have been used. Full article

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13 pages, 1531 KiB

Open AccessEditor’s ChoiceArticle

Formulation of a Simulated Wastewater Influent Composition for Use in the Research of Technologies for Managing Wastewaters Generated during Manned Long-Term Space Exploration and Other Similar Situations—Literature-Based Composition Development

by Bimi Shrestha, Rafael Hernandez, Dhan Lord B. Fortela, Wayne Sharp, Andrei Chistoserdov, Daniel Gang, Emmanuel Revellame, William E. Holmes and Mark E. Zappi

BioTech 2023, 12(1), 8; https://doi.org/10.3390/biotech12010008 - 10 Jan 2023

Cited by 3 | Viewed by 3907

Abstract

The prospect of humans inhabiting planetary bodies is gaining interest among research and development communities, with the moon being considered as a transitory base camp and Mars the next planet humans will inhabit. NASA’s Mission to Mars program is set to have humans [...] Read more.

The prospect of humans inhabiting planetary bodies is gaining interest among research and development communities, with the moon being considered as a transitory base camp and Mars the next planet humans will inhabit. NASA’s Mission to Mars program is set to have humans inhabiting Mars within on-planet space camps by the Year 2030, which has tremendously increased research and development for space exploration—including research oriented toward human life support in long-term planetary lodging camps. The sustenance of human life on Mars will not be trivial due to the unavailability of an appropriate atmosphere and usable water. This situation requires a self-sustaining human life support system that can provide the basic needs such are breathable air, potable water, food, and energy. The feasibility of sending a payload with resources adequate to support long-term human inhabitation is not reasonable, which means every resource within a Mars space camp is valuable, including human-produced wastes. A biorefinery system that treats wastewater and can also produce valuable products such as oxygen, food, and energy offers a form of circular utilization of valuable resources. To conduct research for such systems requires a wastewater influent that is representative of the wastewater to be generated by the space crew within this isolated, confined environment, which is different from what is generated on Earth due to limited variability in diet, human activity, and lifestyle in this confined area. Collection of actual wastewater influent from an isolated environment supporting humans is challenging. Additionally, to ensure a safe working environment in the laboratory and avoid the imposed threat of handling actual human feces, the proposed synthetic, non-human feces containing wastewater influent formulation offers an easy-to-produce and safer-to-handle option. This paper reviews several synthetic wastewater compositions that have been formulated for space exploration purposes. None of the formulations were found to be realistic nor adequate for a space-camp-type scenario. Thus, the formulation of a synthetic wastewater for simulating a wastewater influent from a human space-based camp is proposed in this paper. In addition, the physical, chemical, and biodegradation characteristics of the final formulation designed are presented to illustrate the value of the proposed influent formulation. Full article

(This article belongs to the Topic Advances in Environmental Biotechnology (AEB))

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12 pages, 1366 KiB

Open AccessEditor’s ChoiceArticle

An Optimized CoBRA Method for the Microfluidic Electrophoresis Detection of Breast Cancer Associated RASSF1 Methylation

by Claire Aibel, Adriana Coll De Peña and Anubhav Tripathi

BioTech 2023, 12(1), 7; https://doi.org/10.3390/biotech12010007 - 9 Jan 2023

Cited by 5 | Viewed by 3595

Abstract

Although breast cancer screening assays exist, many are inaccessible and have high turnaround times, leaving a significant need for better alternatives. Hypermethylation of tumor suppressor genes is a common epigenetic marker of breast cancer. Methylation tends to occur most frequently in the promoter [...] Read more.

Although breast cancer screening assays exist, many are inaccessible and have high turnaround times, leaving a significant need for better alternatives. Hypermethylation of tumor suppressor genes is a common epigenetic marker of breast cancer. Methylation tends to occur most frequently in the promoter and first exon regions of genes. Preliminary screening tests are crucial for informing patients whether they should pursue more involved testing. We selected RASSF1, previously demonstrated to be aberrantly methylated in liquid biopsies from breast cancer patients, as our gene of interest. Using CoBRA as our method for methylation quantification, we designed unique primer sets that amplify a portion of the CpG island spanning the 5′ end of the RASSF1 first exon. We integrated the CoBRA approach with a microfluidics-based electrophoresis quantification system (LabChip) and optimized the assay such that insightful results could be obtained without post-PCR purification or concentration, two steps traditionally included in CoBRA assays. Circumventing these steps resulted in a decreased turnaround time and mitigated the laboratory machinery and reagent requirements. Our streamlined technique has an estimated limit of detection of 9.1 ng/μL of input DNA and was able to quantify methylation with an average error of 4.3%. Full article

(This article belongs to the Section Medical Biotechnology)

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Graphical abstract

9 pages, 210 KiB

Open AccessEditor’s ChoiceArticle

Genome Editing in Human Gametes and Embryos: The Legal Dimension in Europe

by Takis Vidalis

BioTech 2023, 12(1), 1; https://doi.org/10.3390/biotech12010001 - 23 Dec 2022

Cited by 13 | Viewed by 3719

Abstract

To date, the legal aspects of the ongoing debate on the application of genome editing in human gametes and early embryos have attracted little attention. In Europe, this seems to have changed with a recent official position that clarifies the meaning of the [...] Read more.

To date, the legal aspects of the ongoing debate on the application of genome editing in human gametes and early embryos have attracted little attention. In Europe, this seems to have changed with a recent official position that clarifies the meaning of the relevant provision of the common legal instrument on Human Rights and Biomedicine (Oviedo Convention). This provision explicitly prohibits modifications to the genome of future persons and adoptes a precautionary stance with regard to genetic interventions in the human reproductive material. In this article, we examine relevant interpretative options, following the new official clarifications, focusing on the research/clinical application distinctions that characterize their approach. From this viewpoint, we propose an approach that favors basic research activities involving genome editing, even for exploring potential clinical applications under conditions of safety, which may justify a future legislative amendment. Furthermore, we explore the patenting issue, based on the current approach of European case law, and give reasons that may justify patent rights in this ethically sensitive area. Full article

(This article belongs to the Section Biotechnology Regulation)

15 pages, 2046 KiB

Open AccessEditor’s ChoiceArticle

Plasma versus Serum Analysis by FTIR Spectroscopy to Capture the Human Physiological State

by Rúben Araújo, Luís Ramalhete, Edna Ribeiro and Cecília Calado

BioTech 2022, 11(4), 56; https://doi.org/10.3390/biotech11040056 - 9 Dec 2022

Cited by 12 | Viewed by 4107

Abstract

Fourier Transform InfraRed spectroscopy of serum and plasma has been highly explored for medical diagnosis, due to its general simplicity, and high sensitivity and specificity. To evaluate the plasma and serum molecular fingerprint, as obtained by FTIR spectroscopy, to acquire the system metabolic [...] Read more.

Fourier Transform InfraRed spectroscopy of serum and plasma has been highly explored for medical diagnosis, due to its general simplicity, and high sensitivity and specificity. To evaluate the plasma and serum molecular fingerprint, as obtained by FTIR spectroscopy, to acquire the system metabolic state, serum and plasma spectra were compared to characterize the metabolic state of 30 human volunteers, between 90 days consumption of green tea extract rich in Epigallocatechin-3-gallate (EGCG). Both plasma and serum spectra enabled the high impact of EGCG consumption on the biofluid spectra to be observed, as analyzed by the spectra principal component analysis, hierarchical-cluster analysis, and univariate data analysis. Plasma spectra resulted in the prediction of EGCG consumption with a slightly higher specificity, accuracy, and precision, also pointing to a higher number of significant spectral bands that were different between the 90 days period. Despite this, the lipid regions of the serum spectra were more affected by EGCG consumption than the corresponding plasma spectra. Therefore, in general, if no specific compound analysis is highlighted, plasma is in general the advised biofluid to capture by FTIR spectroscopy the general metabolic state. If the lipid content of the biofluid is relevant, serum spectra could present some advantages over plasma spectra. Full article

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13 pages, 3395 KiB

Open AccessFeature PaperEditor’s ChoiceArticle

Development of a Prediction Method of Cell Density in Autotrophic/Heterotrophic Microorganism Mixtures by Machine Learning Using Absorbance Spectrum Data

by Akihito Nakanishi, Hiroaki Fukunishi, Riri Matsumoto and Fumihito Eguchi

BioTech 2022, 11(4), 46; https://doi.org/10.3390/biotech11040046 - 12 Oct 2022

Cited by 8 | Viewed by 3243

Abstract

Microflora is actively used to produce value-added materials in industry, and each cell density should be controlled for stable microflora use. In this study, a simple system evaluating the cell density was constructed with artificial intelligence (AI) using the absorbance spectra data of [...] Read more.

Microflora is actively used to produce value-added materials in industry, and each cell density should be controlled for stable microflora use. In this study, a simple system evaluating the cell density was constructed with artificial intelligence (AI) using the absorbance spectra data of microflora. To set up the system, the prediction system for cell density based on machine learning was constructed using the spectra data as the feature from the mixture of Saccharomyces cerevisiae and Chlamydomonas reinhardtii. As the results of predicting cell density by extremely randomized trees, when the cell densities of S. cerevisiae and C. reinhardtii were shifted and fixed, the coefficient of determination (R²) was 0.8495; on the other hand, when the cell densities of S. cerevisiae and C. reinhardtii were fixed and shifted, the R² was 0.9232. To explain the prediction system, the randomized trees regressor of the decision tree-based ensemble learning method as the machine learning algorithm and Shapley additive explanations (SHAPs) as the explainable AI (XAI) to interpret the features contributing to the prediction results were used. As a result of the SHAP analyses, not only the optical density, but also the absorbance of the Soret and Q bands derived from the chloroplasts of C. reinhardtii could contribute to the prediction as the features. The simple cell density evaluating system could have an industrial impact. Full article

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11 pages, 663 KiB

Open AccessEditor’s ChoiceArticle

Omicron BA.2.75 Subvariant of SARS-CoV-2 Is Expected to Have the Greatest Infectivity Compared with the Competing BA.2 and BA.5, Due to Most Negative Gibbs Energy of Binding

by Marko Popovic

BioTech 2022, 11(4), 45; https://doi.org/10.3390/biotech11040045 - 11 Oct 2022

Cited by 19 | Viewed by 3959

Abstract

Omicron BA.2.75 may become the next globally dominant strain of COVID-19 in 2022. The BA.2.75 sub-variant has acquired more mutations (9) in spike protein and other genes of SARS-CoV-2 than any other variant. Thus, its chemical composition and thermodynamic properties have changed compared [...] Read more.

Omicron BA.2.75 may become the next globally dominant strain of COVID-19 in 2022. The BA.2.75 sub-variant has acquired more mutations (9) in spike protein and other genes of SARS-CoV-2 than any other variant. Thus, its chemical composition and thermodynamic properties have changed compared with earlier variants. In this paper, the Gibbs energy of the binding and antigen-receptor binding rate was reported for the BA.2.75 variant. Gibbs energy of the binding of the Omicron BA.2.75 variant is more negative than that of the competing variants BA.2 and BA.5. Full article

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21 pages, 1646 KiB

Open AccessEditor’s ChoiceReview

A Review of Recent Advances in Microbial Fuel Cells: Preparation, Operation, and Application

by Jianfei Wang, Kexin Ren, Yan Zhu, Jiaqi Huang and Shijie Liu

BioTech 2022, 11(4), 44; https://doi.org/10.3390/biotech11040044 - 30 Sep 2022

Cited by 59 | Viewed by 12689

Abstract

The microbial fuel cell has been considered a promising alternative to traditional fossil energy. It has great potential in energy production, waste management, and biomass valorization. However, it has several technical issues, such as low power generation efficiency and operational stability. These issues [...] Read more.

The microbial fuel cell has been considered a promising alternative to traditional fossil energy. It has great potential in energy production, waste management, and biomass valorization. However, it has several technical issues, such as low power generation efficiency and operational stability. These issues limit the scale-up and commercialization of MFC systems. This review presents the latest progress in microbial community selection and genetic engineering techniques for enhancing microbial electricity production. The summary of substrate selection covers defined substrates and some inexpensive complex substrates, such as wastewater and lignocellulosic biomass materials. In addition, it also includes electrode modification, electron transfer mediator selection, and optimization of operating conditions. The applications of MFC systems introduced in this review involve wastewater treatment, production of value-added products, and biosensors. This review focuses on the crucial process of microbial fuel cells from preparation to application and provides an outlook for their future development. Full article

(This article belongs to the Topic Advances in Environmental Biotechnology (AEB))

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17 pages, 3385 KiB

Open AccessEditor’s ChoiceReview

Immunomodulation, Toxicity, and Therapeutic Potential of Nanoparticles

by Ashutosh Pandey and Abhinava K. Mishra

BioTech 2022, 11(3), 42; https://doi.org/10.3390/biotech11030042 - 9 Sep 2022

Cited by 26 | Viewed by 5286

Abstract

Altered immune responses associated with human disease conditions, such as inflammatory and infectious diseases, cancers, and autoimmune diseases, are among the primary causes of morbidity across the world. A wealth of studies has demonstrated the efficiency of nanoparticles (NPs)-based immunotherapy strategies in different [...] Read more.

Altered immune responses associated with human disease conditions, such as inflammatory and infectious diseases, cancers, and autoimmune diseases, are among the primary causes of morbidity across the world. A wealth of studies has demonstrated the efficiency of nanoparticles (NPs)-based immunotherapy strategies in different laboratory model systems. Nanoscale dimensions (<100 nm) enable NPs to have increased surface area to volume ratio, surface charge, and reactivity. Physicochemical properties along with the shapes, sizes, and elasticity influence the immunomodulatory response induced by NPs. In recent years, NPs-based immunotherapy strategies have attained significant focus in the context of cancers and autoimmune diseases. This rapidly growing field of nanomedicine has already introduced ~50 nanotherapeutics in clinical practices. Parallel to wide industrial applications of NPs, studies have raised concerns about their potential threat to the environment and human health. In past decades, a wealth of in vivo and in vitro studies has demonstrated the immunotoxicity potential of various NPs. Given that the number of engineered/designed NPs in biomedical applications is continuing to increase, it is pertinent to establish the toxicity profile for their safe and intelligent use in biomedical applications. The review is intended to summarize the NPs-induced immunomodulation pertaining to toxicity and therapeutic development in human health. Full article

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14 pages, 787 KiB

Open AccessEditor’s ChoiceArticle

Investigating Topic Modeling Techniques to Extract Meaningful Insights in Italian Long COVID Narration

by Ileana Scarpino, Chiara Zucco, Rosarina Vallelunga, Francesco Luzza and Mario Cannataro

BioTech 2022, 11(3), 41; https://doi.org/10.3390/biotech11030041 - 3 Sep 2022

Cited by 23 | Viewed by 5346

Abstract

Through an adequate survey of the history of the disease, Narrative Medicine (NM) aims to allow the definition and implementation of an effective, appropriate, and shared treatment path. In the present study different topic modeling techniques are compared, as Latent Dirichlet Allocation (LDA) [...] Read more.

Through an adequate survey of the history of the disease, Narrative Medicine (NM) aims to allow the definition and implementation of an effective, appropriate, and shared treatment path. In the present study different topic modeling techniques are compared, as Latent Dirichlet Allocation (LDA) and topic modeling based on BERT transformer, to extract meaningful insights in the Italian narration of COVID-19 pandemic. In particular, the main focus was the characterization of Post-acute Sequelae of COVID-19, (i.e., PASC) writings as opposed to writings by health professionals and general reflections on COVID-19, (i.e., non-PASC) writings, modeled as a semi-supervised task. The results show that the BERTopic-based approach outperforms the LDA-base approach by grouping in the same cluster the 97.26% of analyzed documents, and reaching an overall accuracy of 91.97%. Full article

(This article belongs to the Special Issue Bioinformatics and High-Performance Computing Methods for Deciphering and Fighting COVID-19)

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10 pages, 285 KiB

Open AccessEditor’s ChoiceCommentary

Predictive Modelling in Clinical Bioinformatics: Key Concepts for Startups

by Ricardo J. Pais

BioTech 2022, 11(3), 35; https://doi.org/10.3390/biotech11030035 - 17 Aug 2022

Cited by 6 | Viewed by 4065

Abstract

Clinical bioinformatics is a newly emerging field that applies bioinformatics techniques for facilitating the identification of diseases, discovery of biomarkers, and therapy decision. Mathematical modelling is part of bioinformatics analysis pipelines and a fundamental step to extract clinical insights from genomes, transcriptomes and [...] Read more.

Clinical bioinformatics is a newly emerging field that applies bioinformatics techniques for facilitating the identification of diseases, discovery of biomarkers, and therapy decision. Mathematical modelling is part of bioinformatics analysis pipelines and a fundamental step to extract clinical insights from genomes, transcriptomes and proteomes of patients. Often, the chosen modelling techniques relies on either statistical, machine learning or deterministic approaches. Research that combines bioinformatics with modelling techniques have been generating innovative biomedical technology, algorithms and models with biotech applications, attracting private investment to develop new business; however, startups that emerge from these technologies have been facing difficulties to implement clinical bioinformatics pipelines, protect their technology and generate profit. In this commentary, we discuss the main concepts that startups should know for enabling a successful application of predictive modelling in clinical bioinformatics. Here we will focus on key modelling concepts, provide some successful examples and briefly discuss the modelling framework choice. We also highlight some aspects to be taken into account for a successful implementation of cost-effective bioinformatics from a business perspective. Full article

(This article belongs to the Special Issue Bioinformatics: Present and Future Biotechnology)

25 pages, 1186 KiB

Open AccessEditor’s ChoiceArticle

Bio-Strings: A Relational Database Data-Type for Dealing with Large Biosequences

by Sergio Lifschitz, Edward H. Haeusler, Marcos Catanho, Antonio B. de Miranda, Elvismary Molina de Armas, Alexandre Heine, Sergio G. M. P. Moreira and Cristian Tristão

BioTech 2022, 11(3), 31; https://doi.org/10.3390/biotech11030031 - 30 Jul 2022

Cited by 14 | Viewed by 3529

Abstract

DNA sequencers output a large set of very long biological data strings that we should persist in databases rather than basic text file systems. Many different data models and database management systems (DBMS) may deal with both storage and efficiency issues regarding genomic [...] Read more.

DNA sequencers output a large set of very long biological data strings that we should persist in databases rather than basic text file systems. Many different data models and database management systems (DBMS) may deal with both storage and efficiency issues regarding genomic datasets. Specifically, there is a need for handling strings with variable sizes while keeping their biological meaning. Relational database management systems (RDBMS) provide several data types that could be further explored for the genomics context. Besides, they enforce integrity, consistency, and enable good abstractions for more conventional data. We propose the relational text data type to represent and manipulate biological sequences and their derivatives. We present a logical schema for representing the core biological information, which may be inferred from a given biological conceptual data schema and the corresponding function manipulations. We implement and evaluate these stored functions into an actual RDBMS for both efficacy and efficiency. We show that it is possible to enforce basic and complex requirements for the genomic domain. We claim that the well-established relational text data type in RDBMS may appropriately handle the representation and persistency of biological sequences. We base our approach on the idea of domain-specific abstract data types that can store data with semantically defined functions while hiding those details from non-technical end-users. Full article

(This article belongs to the Special Issue Bioinformatics: Present and Future Biotechnology)

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14 pages, 2794 KiB

Open AccessEditor’s ChoiceArticle

Setup and Characterization of a High-Throughput Luminescence-Based Serum Bactericidal Assay (L-SBA) to Determine Functionality of Human Sera against Shigella flexneri

by Francesca Mancini, Francesca Micoli and Omar Rossi

BioTech 2022, 11(3), 29; https://doi.org/10.3390/biotech11030029 - 27 Jul 2022

Cited by 7 | Viewed by 3445

Abstract

Shigellosis represents a major public health problem worldwide. The morbidity of the disease, especially in children in developing countries, together with the increase of antimicrobial resistance make a vaccine against Shigella an urgent medical need. Several vaccines under development are targeting Shigella lipopolysaccharide [...] Read more.

Shigellosis represents a major public health problem worldwide. The morbidity of the disease, especially in children in developing countries, together with the increase of antimicrobial resistance make a vaccine against Shigella an urgent medical need. Several vaccines under development are targeting Shigella lipopolysaccharide (LPS), whose extreme diversity renders necessary the development of multivalent vaccines. Immunity against Shigella LPS can elicit antibodies capable of killing bacteria in a serotype-specific manner. Therefore, although a correlation of protection against shigellosis has not been established, demonstration of vaccine-elicited antibody bactericidal activity may provide one means of vaccine protection against Shigella. To facilitate Shigella vaccine development, we have set up a high-throughput serum bactericidal assay based on luminescence readout (L-SBA), which has been already used to determine the functionality of antibodies against S. sonnei in multiple clinical trials. Here we present the setup and intra-laboratory characterization of L-SBA against three epidemiologically relevant Shigella flexneri serotypes using human sera. We assessed the linearity, repeatability and reproducibility of the method, demonstrating high assay specificity to detect the activity of antibodies against each homologous strain without any heterologous aspecificity against species-related and non-species-related strains; this assay is ready to be used to determine bactericidal activity of clinical sera raised by multivalent vaccines and in sero-epidemiological studies. Full article

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9 pages, 955 KiB

Open AccessEditor’s ChoiceCommunication

Rethinking the Intrinsic Sensitivity of Fungi to Glyphosate

by Tuomas Tall and Pere Puigbò

BioTech 2022, 11(3), 28; https://doi.org/10.3390/biotech11030028 - 26 Jul 2022

Cited by 7 | Viewed by 3163

Abstract

The 5-enolpyruvylshikimate 3-phosphate synthase (EPSPS) is the central enzyme of the shikimate pathway to synthesize the three aromatic amino acids in fungi, plants, and prokaryotes. This enzyme is the target of the herbicide glyphosate. In most plants and prokaryotes, the EPSPS protein is [...] Read more.

The 5-enolpyruvylshikimate 3-phosphate synthase (EPSPS) is the central enzyme of the shikimate pathway to synthesize the three aromatic amino acids in fungi, plants, and prokaryotes. This enzyme is the target of the herbicide glyphosate. In most plants and prokaryotes, the EPSPS protein is constituted by a single domain family, the EPSP synthase (PF00275) domain, whereas in fungi, the protein is formed by a multi-domain structure from combinations of 22 EPSPS-associated domains. The most common multi-domain EPSPS structure in fungi involves five EPSPS-associated domains of the shikimate pathway. In this article, we analyze 390 EPSPS proteins of fungi to determine the extent of the EPSPS-associated domains. Based on the current classification of the EPSPS protein, most fungal species are intrinsically sensitive to glyphosate. However, complex domain architectures may have multiple responses to the herbicide. Further empirical studies are needed to determine the effect of glyphosate on fungi, taking into account the diversity of multi-domain architectures of the EPSPS. This research opens the door to novel biotechnological applications for microbial degradation of glyphosate. Full article

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14 pages, 822 KiB

Open AccessEditor’s ChoiceReview

Closing the Door with CRISPR: Genome Editing of CCR5 and CXCR4 as a Potential Curative Solution for HIV

by Julian J. Freen-van Heeren

BioTech 2022, 11(3), 25; https://doi.org/10.3390/biotech11030025 - 14 Jul 2022

Cited by 13 | Viewed by 7870

Abstract

Human immunodeficiency virus (HIV) infection can be controlled by anti-retroviral therapy. Suppressing viral replication relies on life-long medication, but anti-retroviral therapy is not without risks to the patient. Therefore, it is important that permanent cures for HIV infection are developed. Three patients have [...] Read more.

Human immunodeficiency virus (HIV) infection can be controlled by anti-retroviral therapy. Suppressing viral replication relies on life-long medication, but anti-retroviral therapy is not without risks to the patient. Therefore, it is important that permanent cures for HIV infection are developed. Three patients have been described to be completely cured from HIV infection in recent years. In all cases, patients received a hematopoietic stem cell (HSC) transplantation due to a hematological malignancy. The HSCs were sourced from autologous donors that expressed a homozygous mutation in the CCR5 gene. This mutation results in a non-functional receptor, and confers resistance to CCR5-tropic HIV strains that rely on CCR5 to enter host cells. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated (Cas) system is one of the methods of choice for gene editing, and the CRISPR/Cas system has been employed to target loci of interest in the context of HIV. Here, the current literature regarding CRISPR-mediated genome editing to render cells resistant to HIV (re)-infection by knocking out the co-receptors CCR5 and CXCR4 is summarized, and an outlook is provided regarding future (research) directions. Full article

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21 pages, 356 KiB

Open AccessEditor’s ChoiceArticle

Challenges and Limitations of Biological Network Analysis

by Marianna Milano, Giuseppe Agapito and Mario Cannataro

BioTech 2022, 11(3), 24; https://doi.org/10.3390/biotech11030024 - 7 Jul 2022

Cited by 20 | Viewed by 4497

Abstract

High-Throughput technologies are producing an increasing volume of data that needs large amounts of data storage, effective data models and efficient, possibly parallel analysis algorithms. Pathway and interactomics data are represented as graphs and add a new dimension of analysis, allowing, among other [...] Read more.

High-Throughput technologies are producing an increasing volume of data that needs large amounts of data storage, effective data models and efficient, possibly parallel analysis algorithms. Pathway and interactomics data are represented as graphs and add a new dimension of analysis, allowing, among other features, graph-based comparison of organisms’ properties. For instance, in biological pathway representation, the nodes can represent proteins, RNA and fat molecules, while the edges represent the interaction between molecules. Otherwise, biological networks such as Protein–Protein Interaction (PPI) Networks, represent the biochemical interactions among proteins by using nodes that model the proteins from a given organism, and edges that model the protein–protein interactions, whereas pathway networks enable the representation of biochemical-reaction cascades that happen within the cells or tissues. In this paper, we discuss the main models for standard representation of pathways and PPI networks, the data models for the representation and exchange of pathway and protein interaction data, the main databases in which they are stored and the alignment algorithms for the comparison of pathways and PPI networks of different organisms. Finally, we discuss the challenges and the limitations of pathways and PPI network representation and analysis. We have identified that network alignment presents a lot of open problems worthy of further investigation, especially concerning pathway alignment. Full article

(This article belongs to the Special Issue Bioinformatics: Present and Future Biotechnology)

12 pages, 2309 KiB

Open AccessEditor’s ChoiceArticle

Xylanase Production by Talaromyces amestolkiae Valuing Agroindustrial Byproducts

by Giórgia S. Barbieri, Heitor B. S. Bento, Fernanda de Oliveira, Flávio P. Picheli, Lídia M. Dias, Fernando Masarin and Valéria C. Santos-Ebinuma

BioTech 2022, 11(2), 15; https://doi.org/10.3390/biotech11020015 - 17 May 2022

Cited by 15 | Viewed by 4264

Abstract

In general, agroindustrial byproducts can be easily assimilated by several microorganisms due to their composition, which is rich in carbohydrates. Therefore, they could be appropriate for use as raw materials in a sustainable refinery concept, including the production of hydrolytic enzymes with industrial [...] Read more.

In general, agroindustrial byproducts can be easily assimilated by several microorganisms due to their composition, which is rich in carbohydrates. Therefore, they could be appropriate for use as raw materials in a sustainable refinery concept, including the production of hydrolytic enzymes with industrial applicability. In this work, xylanase production by the filamentous fungi Talaromyces amestolkiae in submerged culture was evaluated using five agroindustrial byproducts, namely, wheat bran, citrus pulp, rice bran, peanut skin, and peanut shell. Firstly, the aforementioned byproducts were characterized in terms of cellulose, xylan, lignin, and extractives. Next, production studies were performed, and wheat bran generated the highest enzymatic activity (5.4 U·mL⁻¹), probably because of its large amount of xylan. Subsequently, a factorial design was performed to evaluate the independent variables yeast extract, wheat bran, K₂HPO₄, and pH, aiming to improve the variable response, xylanase activity. The condition that promoted the highest production, 13.02 U·mL⁻¹ (141% higher than the initial condition), was 20 g·L⁻¹ wheat bran, 2.5 g·L⁻¹ yeast extract, 3 g·L⁻¹ K₂HPO₄, and pH 7. Thus, industrial byproducts with a high content of xylan can be used as a culture medium to produce xylanase enzymes with a Talaromyces strain through an economical and sustainable approach. Full article

(This article belongs to the Section Industry, Agriculture and Food Biotechnology)

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16 pages, 2145 KiB

Open AccessEditor’s ChoiceArticle

A Freeze-Dried Cranberry Powder Consistently Enhances SCFA Production and Lowers Abundance of Opportunistic Pathogens In Vitro

by Christina Khoo, Cindy Duysburgh, Massimo Marzorati, Pieter Van den Abbeele and Derek Zhang

BioTech 2022, 11(2), 14; https://doi.org/10.3390/biotech11020014 - 6 May 2022

Cited by 7 | Viewed by 4167

Abstract

The American cranberry, Vaccinium macrocarpon, contains fibers and (poly)phenols that could exert health-promoting effects through modulation of gut microbiota. This study aimed to investigate how a freeze-dried whole cranberry powder (FCP) modulated metabolite production and microbial composition using both a 48-h incubation [...] Read more.

The American cranberry, Vaccinium macrocarpon, contains fibers and (poly)phenols that could exert health-promoting effects through modulation of gut microbiota. This study aimed to investigate how a freeze-dried whole cranberry powder (FCP) modulated metabolite production and microbial composition using both a 48-h incubation strategy and a long-term human gut simulator study with the M-SHIME (Mucosal Simulator of the Human Intestinal Microbial Ecosystem). FCP was repeatedly administered over three weeks. The studies included five and three study subjects, respectively. In both models, FCP significantly increased levels of health-related short-chain fatty acids (SCFA: acetate, propionate and butyrate), while decreased levels of branched-chain fatty acids (markers of proteolytic fermentation). Interestingly, FCP consistently increased luminal Bacteroidetes abundances in the proximal colon of the M-SHIME (+17.5 ± 9.3%) at the expense of Proteobacteria (−10.2 ± 1.5%). At family level, this was due to the stimulation of Bacteroidaceae and Prevotellaceae and a decrease of Pseudomonodaceae and Enterobacteriaceae. Despite of interpersonal differences, FCP also increased the abundance of families of known butyrate producers. Overall, FCP displayed an interesting prebiotic potential in vitro given its selective utilization by host microorganisms and potential health-related effects on inhibition of pathogens and selective stimulation of beneficial metabolites. Full article

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15 pages, 2201 KiB

Open AccessEditor’s ChoiceArticle

Prebiotic Potential and Value-Added Products Derived from Spirulina laxissima SV001—A Step towards Healthy Living

by Vidya Sankarapandian, Kirubakaran Nitharsan, Kavitha Parangusadoss, Prakash Gangadaran, Prasanna Ramani, Balu Alagar Venmathi Maran and Manasi P. Jogalekar

BioTech 2022, 11(2), 13; https://doi.org/10.3390/biotech11020013 - 26 Apr 2022

Cited by 25 | Viewed by 5536

Abstract

Lately, microalgae-based value-added products have been gaining market value because they moderate the dependency on fossil fuel and high-value chemical products. To this end, the purpose of this study was to develop prebiotic products from the microalgae Spirulina sp. The microalgae were isolated [...] Read more.

Lately, microalgae-based value-added products have been gaining market value because they moderate the dependency on fossil fuel and high-value chemical products. To this end, the purpose of this study was to develop prebiotic products from the microalgae Spirulina sp. The microalgae were isolated from the fresh water and characterized at the molecular level. The dry biomass, chlorophyll content, phycocyanin, cytotoxicity and antimicrobial and antioxidant properties of the isolated strains were analyzed. Moreover, value-added products like Spirulina cake, chocolate, tea, vermicelli and Spirulina juice were made for a vulnerable population due to high nutritive value. Full article

(This article belongs to the Special Issue Applications for Biotechnology: Present and Future Improvements in Bacteria)

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15 pages, 12941 KiB

Open AccessFeature PaperEditor’s ChoiceArticle

Characterisation of Omicron Variant during COVID-19 Pandemic and the Impact of Vaccination, Transmission Rate, Mortality, and Reinfection in South Africa, Germany, and Brazil

by Carolina Ribeiro Xavier, Rafael Sachetto Oliveira, Vinícius da Fonseca Vieira, Marcelo Lobosco and Rodrigo Weber dos Santos

BioTech 2022, 11(2), 12; https://doi.org/10.3390/biotech11020012 - 26 Apr 2022

Cited by 26 | Viewed by 5651

Abstract

Several variants of SARS-CoV-2 have been identified in different parts of the world, including Gamma, detected in Brazil, Delta, detected in India, and the recent Omicron variant, detected in South Africa. The emergence of a new variant is a cause of great concern. [...] Read more.

Several variants of SARS-CoV-2 have been identified in different parts of the world, including Gamma, detected in Brazil, Delta, detected in India, and the recent Omicron variant, detected in South Africa. The emergence of a new variant is a cause of great concern. This work considers an extended version of an SIRD model capable of incorporating the effects of vaccination, time-dependent transmissibility rates, mortality, and even potential reinfections during the pandemic. We use this model to characterise the Omicron wave in Brazil, South Africa, and Germany. During Omicron, the transmissibility increased by five for Brazil and Germany and eight for South Africa, whereas the estimated mortality was reduced by three-fold. We estimated that the reported cases accounted for less than

25 %

of the actual cases during Omicron. The mortality among the nonvaccinated population in these countries is, on average, three to four times higher than the mortality among the fully vaccinated. Finally, we could only reproduce the observed dynamics after introducing a new parameter that accounts for the percentage of the population that can be reinfected. Reinfection was as high as

40 %

in South Africa, which has only

29 %

of its population fully vaccinated and as low as

13 %

in Brazil, which has over

70 %

and

80 %

of its population fully vaccinated and with at least one dose, respectively. The calibrated models were able to estimate essential features of the complex virus and vaccination dynamics and stand as valuable tools for quantifying the impact of protocols and decisions in different populations. Full article

(This article belongs to the Special Issue Bioinformatics and High-Performance Computing Methods for Deciphering and Fighting COVID-19)

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20 pages, 3166 KiB

Open AccessEditor’s ChoiceArticle

Immobilization and Characterization of L-Asparaginase over Carbon Xerogels

by Rita A. M. Barros, Raquel O. Cristóvão, Sónia A. C. Carabineiro, Márcia C. Neves, Mara G. Freire, Joaquim L. Faria, Valéria C. Santos-Ebinuma, Ana P. M. Tavares and Cláudia G. Silva

BioTech 2022, 11(2), 10; https://doi.org/10.3390/biotech11020010 - 14 Apr 2022

Cited by 13 | Viewed by 4411

Abstract

L-asparaginase (ASNase) is an aminohydrolase currently used in the pharmaceutical and food industries. Enzyme immobilization is an exciting option for both applications, allowing for a more straightforward recovery and increased stability. High surface area and customizable porosity make carbon xerogels (CXs) promising materials [...] Read more.

L-asparaginase (ASNase) is an aminohydrolase currently used in the pharmaceutical and food industries. Enzyme immobilization is an exciting option for both applications, allowing for a more straightforward recovery and increased stability. High surface area and customizable porosity make carbon xerogels (CXs) promising materials for ASNase immobilization. This work describes the influence of contact time, pH, and ASNase concentration on the immobilization yield (IY) and relative recovered activity (RRA) using the Central Composite Design methodology. The most promising results were obtained using CX with an average pore size of 4 nm (CX-4), reaching IY and RRA of 100%. At the optimal conditions (contact time 49 min, pH 6.73, and [ASNase] 0.26 mg·mL⁻¹), the ASNase-CXs biocomposite was characterized and evaluated in terms of kinetic properties and operational, thermal, and pH stabilities. The immobilized ASNase onto CX-4 retained 71% of its original activity after six continuous reaction cycles, showed good thermal stability at 37 °C (RRA of 91% after 90 min), and was able to adapt to both acidic and alkaline environments. Finally, the results indicated a 3.9-fold increase in the immobilized ASNase affinity for the substrate, confirming the potential of CXs as a support for ASNase and as a cost-effective tool for subsequent use in the therapeutic and food sectors. Full article

(This article belongs to the Section Industry, Agriculture and Food Biotechnology)

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24 pages, 391 KiB

Open AccessEditor’s ChoiceReview

Non-Viral Vectors for Delivery of Nucleic Acid Therapies for Cancer

by Shrey Kanvinde, Tanmay Kulkarni, Suyash Deodhar, Deep Bhattacharya and Aneesha Dasgupta

BioTech 2022, 11(1), 6; https://doi.org/10.3390/biotech11010006 - 7 Mar 2022

Cited by 30 | Viewed by 8302

Abstract

The research and development of non-viral gene therapy has been extensive over the past decade and has received a big push thanks to the recent successful approval of non-viral nucleic acid therapy products. Despite these developments, nucleic acid therapy applications in cancer have [...] Read more.

The research and development of non-viral gene therapy has been extensive over the past decade and has received a big push thanks to the recent successful approval of non-viral nucleic acid therapy products. Despite these developments, nucleic acid therapy applications in cancer have been limited. One of the main causes of this has been the imbalance in development of delivery vectors as compared with sophisticated nucleic acid payloads, such as siRNA, mRNA, etc. This paper reviews non-viral vectors that can be used to deliver nucleic acids for cancer treatment. It discusses various types of vectors and highlights their current applications. Additionally, it discusses a perspective on the current regulatory landscape to facilitate the commercial translation of gene therapy. Full article

20 pages, 640 KiB

Open AccessEditor’s ChoiceReview

A Systematic Review of Oral Biopsies, Sample Types, and Detection Techniques Applied in Relation to Oral Cancer Detection

by Guanghuan Yang, Luqi Wei, Benjamin K. S. Thong, Yuanyuan Fu, Io Hong Cheong, Zisis Kozlakidis, Xue Li, Hui Wang and Xiaoguang Li

BioTech 2022, 11(1), 5; https://doi.org/10.3390/biotech11010005 - 2 Mar 2022

Cited by 27 | Viewed by 9181

Abstract

Background: Early identification of the stage of oral cancer development can lead to better treatment outcomes and avoid malignant transformation. Therefore, this review aims to provide a comprehensive overview that describes the development of standardized procedures for oral sample collection, characterization, and molecular [...] Read more.

Background: Early identification of the stage of oral cancer development can lead to better treatment outcomes and avoid malignant transformation. Therefore, this review aims to provide a comprehensive overview that describes the development of standardized procedures for oral sample collection, characterization, and molecular risk assessment. This can help investigators to choose the appropriate sampling method and downstream analyses for different purposes. Methods: This systematic review was conducted according to the PRISMA guidelines. Using both PubMed and Web of Science databases, four independent authors conducted a literature search between 15 and 21 June 2021. We used key search terms to broaden the search for studies. Non-conforming articles were removed using an EndNote-based and manual approach. Reviewers used a designed form to extract data. Results: This review included a total of 3574 records, after eliminating duplicate articles and excluding papers that did not meet the inclusion criteria. Finally, 202 articles were included in this review. We summarized the sampling methods, biopsy samples, and downstream analysis. The biopsy techniques were classified into tissue and liquid biopsy. The common sequential analysis of tissue biopsy includes histopathological examination such as H&E or IHC to identify various pathogenic features. Meanwhile, liquid samples such as saliva, blood, and urine are analyzed for the purpose of screening to detect mutations in cancer. Commonly used technologies are PCR, RT-PCR, high-throughput sequencing, and metabolomic analysis. Conclusions: Currently, tissue biopsies provide increased diagnostic value compared to liquid biopsy. However, the minimal invasiveness and convenience of liquid biopsy make it a suitable method for mass screening and eventual clinical adoption. The analysis of samples includes histological and molecular analysis. Metabolite analysis is rising but remains scarce. Full article

(This article belongs to the Special Issue Recent Advances in Biobanking: New Perspectives from Laboratory to Regulation)

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18 pages, 729 KiB

Open AccessEditor’s ChoiceReview

Hacking Commensal Bacteria to Consolidate the Adaptive Mucosal Immune Response in the Gut–Lung Axis: Future Possibilities for SARS-CoV-2 Protection

by Marcela Pereira, Ju Kyoung Oh, Dae-Kyung Kang, Lars Engstrand and Valerie Diane Valeriano

BioTech 2022, 11(1), 3; https://doi.org/10.3390/biotech11010003 - 30 Jan 2022

Cited by 7 | Viewed by 6364

Abstract

Infectious diseases caused by mucosal pathogens significantly increase mortality and morbidity. Thus, the possibility to target these pathogens at their primary entry points can consolidate protective immunity. Regarding SARS-CoV-2 infection, it has been observed that the upper respiratory mucosa is highly affected and [...] Read more.

Infectious diseases caused by mucosal pathogens significantly increase mortality and morbidity. Thus, the possibility to target these pathogens at their primary entry points can consolidate protective immunity. Regarding SARS-CoV-2 infection, it has been observed that the upper respiratory mucosa is highly affected and that dysregulation of resident microbiota in the gut–lung axis plays a crucial role in determining symptom severity. Thus, understanding the possibility of eliciting various mucosal and adaptive immune responses allows us to effectively design bacterial mucosal vaccine vectors. Such design requires rationally selecting resident bacterial candidates as potential host carriers, evaluating effective carrier proteins for stimulating an immune response, and combining these two to improve antigenic display and immunogenicity. This review investigated mucosal vaccine vectors from 2015 to present, where a few have started to utilize Salmonella and lactic acid bacteria (LAB) to display SARS-CoV-2 Spike S proteins or fragments. Although current literature is still lacking for its studies beyond in vitro or in vivo efficiency, decades of research into these vectors show promising results. Here, we discuss the mucosal immune systems focusing on the gut–lung axis microbiome and offer new insight into the potential use of alpha streptococci in the upper respiratory tract as a vaccine carrier. Full article

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16 pages, 2059 KiB

Open AccessEditor’s ChoiceArticle

Metagenomic Insights into the Composition and Function of Microbes Associated with the Rootzone of Datura inoxia

by Savanah Senn, Kelly Pangell and Adrianna L. Bowerman

BioTech 2022, 11(1), 1; https://doi.org/10.3390/biotech11010001 - 14 Jan 2022

Cited by 7 | Viewed by 5993

Abstract

The purpose of this paper is to elucidate the roles that microbes may be playing in the rootzone of the medicinal plant Daturainoxia. We hypothesized that the microbes associated with the Datura rootzone would be significantly different than the similar surrounding [...] Read more.

The purpose of this paper is to elucidate the roles that microbes may be playing in the rootzone of the medicinal plant Daturainoxia. We hypothesized that the microbes associated with the Datura rootzone would be significantly different than the similar surrounding fields in composition and function. We also hypothesized that rhizospheric and endophytic microbes would be associated with similar metabolic functions to the plant rootzone they inhabited. The methods employed were microbial barcoding, tests of essential oils against antibiotic resistant bacteria and other soil bacterial isolates, 16S Next Generation Sequencing (NGS) metabarcoding, and Whole Genome Shotgun (WGS) taxonomic and functional analyses. A few of the main bacterial genera of interest that were differentially abundant in the Datura root microbiome were Flavobacterium (p = 0.007), Chitinophaga (p = 0.0007), Pedobacter (p = 6 × 10⁻⁵), Bradyhizobium (p = 1 × 10⁻⁸), and Paenibacillus (p = 1.46 × 10⁻⁶). There was significant evidence that the microbes associated with the Datura rootzone had elevated function related to bacterial chalcone synthase (p = 1.49 × 10⁻³) and permease genes (p < 0.003). There was some evidence that microbial functions in the Datura rootzone provided precursors to important plant bioactive molecules or were beneficial to plant growth. This is important because these compounds are phyto-protective antioxidants and are precursors to many aromatic bioactive compounds that are relevant to human health. In the context of known interactions, and current results, plants and microbes influence the flavonoid biosynthetic pathways of one other, in terms of the regulation of the phenylpropanoid pathway. This is the first study to focus on the microbial ecology of the Datura rootzone. There are possible biopharmaceutical and agricultural applications of the natural interplay that was discovered during this study of the Datura inoxia rhizosphere. Full article

(This article belongs to the Special Issue Applications for Biotechnology: Present and Future Improvements in Bacteria)

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17 pages, 287 KiB

Open AccessEditor’s ChoiceArticle

Public Perceptions Regarding Genomic Technologies Applied to Breeding Farm Animals: A Qualitative Study

by Francis Z. Naab, David Coles, Ellen Goddard and Lynn J. Frewer

BioTech 2021, 10(4), 28; https://doi.org/10.3390/biotech10040028 - 3 Dec 2021

Cited by 9 | Viewed by 5234

Abstract

The societal acceptability of different applications of genomic technologies to animal production systems will determine whether their innovation trajectories will reach the commercialisation stage. Importantly, technological implementation and commercialisation trajectories, regulation, and policy development need to take account of public priorities and attitudes. [...] Read more.

The societal acceptability of different applications of genomic technologies to animal production systems will determine whether their innovation trajectories will reach the commercialisation stage. Importantly, technological implementation and commercialisation trajectories, regulation, and policy development need to take account of public priorities and attitudes. More effective co-production practices will ensure the application of genomic technologies to animals aligns with public priorities and are acceptable to society. Consumer rejection of, and limited demand for, animal products developed using novel genomic technologies will determine whether they are integration into the food system. However, little is known about whether genomic technologies that accelerate breeding but do not introduce cross-species genetic changes are more acceptable to consumers than those that do. Five focus groups, held in the north east of England, were used to explore the perceptions of, and attitudes towards, the use of genomic technologies in breeding farm animals for the human food supply chain. Overall, study participants were more positive towards genomic technologies applied to promote animal welfare (e.g., improved disease resistance), environmental sustainability, and human health. Animal “disenhancement” was viewed negatively and increased food production alone was not perceived as a potential benefit. In comparison to gene editing, research participants were most negative about genetic modification and the application of gene drives, independent of the benefits delivered. Full article

(This article belongs to the Special Issue Biotechnology and Bioethics)

13 pages, 4698 KiB

Open AccessEditor’s ChoiceArticle

VirusLab: A Tool for Customized SARS-CoV-2 Data Analysis

by Pietro Pinoli, Anna Bernasconi, Anna Sandionigi and Stefano Ceri

BioTech 2021, 10(4), 27; https://doi.org/10.3390/biotech10040027 - 6 Nov 2021

Cited by 7 | Viewed by 5477

Abstract

Since the beginning of 2020, the COVID-19 pandemic has posed unprecedented challenges to viral data analysis and connected host disease diagnostic methods. We propose VirusLab, a flexible system for analysing SARS-CoV-2 viral sequences and relating them to metadata or clinical information about the [...] Read more.

Since the beginning of 2020, the COVID-19 pandemic has posed unprecedented challenges to viral data analysis and connected host disease diagnostic methods. We propose VirusLab, a flexible system for analysing SARS-CoV-2 viral sequences and relating them to metadata or clinical information about the host. VirusLab capitalizes on two existing resources: ViruSurf, a database of public SARS-CoV-2 sequences supporting metadata-driven search, and VirusViz, a tool for visual analysis of search results. VirusLab is designed for taking advantage of these resources within a server-side architecture that: (i) covers pipelines based on approaches already in use (ARTIC, Galaxy) but entirely cutomizable upon user request; (ii) predigests analysis of raw sequencing data from different platforms (Oxford Nanopore and Illumina); (iii) gives access to public archives datasets; (iv) supplies user-friendly reporting – making it a tool that can also be integrated into a business environment. VirusLab can be installed and hosted within the premises of any organization where information about SARS-CoV-2 sequences can be safely integrated with information about hosts (e.g., clinical metadata). A system such as VirusLab is not currently available in the landscape of similar providers: our results show that VirusLab is a powerful tool to generate tabular/graphical and machine readable reports that can be integrated in more complex pipelines. We foresee that the proposed system can support many research-oriented and therapeutic scenarios within hospitals or the tracing of viral sequences and their mutational processes within organizations for viral surveillance. Full article

(This article belongs to the Special Issue Bioinformatics and High-Performance Computing Methods for Deciphering and Fighting COVID-19)

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19 pages, 2437 KiB

Open AccessEditor’s ChoiceArticle

Primer Binding Site (PBS) Profiling of Genetic Diversity of Natural Populations of Endemic Species Allium ledebourianum Schult.

by Oxana Khapilina, Ainur Turzhanova, Alevtina Danilova, Asem Tumenbayeva, Vladislav Shevtsov, Yuri Kotukhov and Ruslan Kalendar

BioTech 2021, 10(4), 23; https://doi.org/10.3390/biotech10040023 - 13 Oct 2021

Cited by 19 | Viewed by 5377

Abstract

Endemic species are especially vulnerable to biodiversity loss caused by isolation or habitat specificity, small population size, and anthropogenic factors. Endemic species biodiversity analysis has a critically important global value for the development of conservation strategies. The rare onion Allium ledebourianum is a [...] Read more.

Endemic species are especially vulnerable to biodiversity loss caused by isolation or habitat specificity, small population size, and anthropogenic factors. Endemic species biodiversity analysis has a critically important global value for the development of conservation strategies. The rare onion Allium ledebourianum is a narrow-lined endemic species, with natural populations located in the extreme climatic conditions of the Kazakh Altai. A. ledebourianum populations are decreasing everywhere due to anthropogenic impact, and therefore, this species requires preservation and protection. Conservation of this rare species is associated with monitoring studies to investigate the genetic diversity of natural populations. Fundamental components of eukaryote genome include multiple classes of interspersed repeats. Various PCR-based DNA fingerprinting methods are used to detect chromosomal changes related to recombination processes of these interspersed elements. These methods are based on interspersed repeat sequences and are an effective approach for assessing the biological diversity of plants and their variability. We applied DNA profiling approaches based on conservative sequences of interspersed repeats to assess the genetic diversity of natural A. ledebourianum populations located in the territory of Kazakhstan Altai. The analysis of natural A. ledebourianum populations, carried out using the DNA profiling approach, allowed the effective differentiation of the populations and assessment of their genetic diversity. We used conservative sequences of tRNA primer binding sites (PBS) of the long-terminal repeat (LTR) retrotransposons as PCR primers. Amplification using the three most effective PBS primers generated 628 PCR amplicons, with an average of 209 amplicons. The average polymorphism level varied from 34% to 40% for all studied samples. Resolution analysis of the PBS primers showed all of them to have high or medium polymorphism levels, which varied from 0.763 to 0.965. Results of the molecular analysis of variance showed that the general biodiversity of A. ledebourianum populations is due to interpopulation (67%) and intrapopulation (33%) differences. The revealed genetic diversity was higher in the most distant population of A. ledebourianum LD64, located on the Sarymsakty ridge of Southern Altai. This is the first genetic diversity study of the endemic species A. ledebourianum using DNA profiling approaches. This work allowed us to collect new genetic data on the structure of A. ledebourianum populations in the Altai for subsequent development of preservation strategies to enhance the reproduction of this relict species. The results will be useful for the conservation and exploitation of this species, serving as the basis for further studies of its evolution and ecology. Full article

(This article belongs to the Special Issue Recent Advances in Transposable Elements-Based Genetic Diversity Assessment, Discovery, and Analysis)

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12 pages, 1165 KiB

Open AccessEditor’s ChoiceArticle

Highly Efficient Purification of Recombinant VSV-∆G-Spike Vaccine against SARS-CoV-2 by Flow-Through Chromatography

by Elad Lerer, Ziv Oren, Yaron Kafri, Yaakov Adar, Einat Toister, Lilach Cherry, Edith Lupu, Arik Monash, Rona Levy, Eyal Dor, Eyal Epstein, Lilach Levin, Meni Girshengorn, Niva Natan, Ran Zichel and Arik Makovitzki

BioTech 2021, 10(4), 22; https://doi.org/10.3390/biotech10040022 - 12 Oct 2021

Cited by 18 | Viewed by 7158

Abstract

This study reports a highly efficient, rapid one-step purification process for the production of the recombinant vesicular stomatitis virus-based vaccine, rVSV-∆G-spike (rVSV-S), recently developed by the Israel Institute for Biological Research (IIBR) for the prevention of COVID-19. Several purification strategies are evaluated using [...] Read more.

This study reports a highly efficient, rapid one-step purification process for the production of the recombinant vesicular stomatitis virus-based vaccine, rVSV-∆G-spike (rVSV-S), recently developed by the Israel Institute for Biological Research (IIBR) for the prevention of COVID-19. Several purification strategies are evaluated using a variety of chromatography methods, including membrane adsorbers and packed-bed ion-exchange chromatography. Cell harvest is initially treated with endonuclease, clarified, and further concentrated by ultrafiltration before chromatography purification. The use of anion-exchange chromatography in all forms results in strong binding of the virus to the media, necessitating a high salt concentration for elution. The large virus and spike protein binds very strongly to the high surface area of the membrane adsorbents, resulting in poor virus recovery (<15%), while the use of packed-bed chromatography, where the surface area is smaller, achieves better recovery (up to 33%). Finally, a highly efficient chromatography purification process with Capto^TM Core 700 resin, which does not require binding and the elution of the virus, is described. rVSV-S cannot enter the inner pores of the resin and is collected in the flow-through eluent. Purification of the rVSV-S virus with Capto^TM Core 700 resulted in viral infectivity above 85% for this step, with the efficient removal of host cell proteins, consistent with regulatory requirements. Similar results were obtained without an initial ultrafiltration step. Full article

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15 pages, 337 KiB

Open AccessEditor’s ChoiceReview

Flow-FISH as a Tool for Studying Bacteria, Fungi and Viruses

by Julian J. Freen-van Heeren

BioTech 2021, 10(4), 21; https://doi.org/10.3390/biotech10040021 - 11 Oct 2021

Cited by 16 | Viewed by 7439

Abstract

Many techniques are currently in use to study microbes. These can be aimed at detecting, identifying, and characterizing bacterial, fungal, and viral species. One technique that is suitable for high-throughput analysis is flow cytometry-based fluorescence in situ hybridization, or Flow-FISH. This technique employs [...] Read more.

Many techniques are currently in use to study microbes. These can be aimed at detecting, identifying, and characterizing bacterial, fungal, and viral species. One technique that is suitable for high-throughput analysis is flow cytometry-based fluorescence in situ hybridization, or Flow-FISH. This technique employs (fluorescently labeled) probes directed against DNA or (m)RNA, for instance targeting a gene or microorganism of interest and provides information on a single-cell level. Furthermore, by combining Flow-FISH with antibody-based protein detection, proteins of interest can be measured simultaneously with genetic material. Additionally, depending on the type of Flow-FISH assay, Flow-FISH can also be multiplexed, allowing for the simultaneous measurement of multiple gene targets and/or microorganisms. Together, this allows for, e.g., single-cell gene expression analysis or identification of (sub)strains in mixed cultures. Flow-FISH has been used in mammalian cells but has also been extensively employed to study diverse microbial species. Here, the use of Flow-FISH for studying microorganisms is reviewed. Specifically, the detection of (intracellular) pathogens, studying microorganism biology and disease pathogenesis, and identification of bacterial, fungal, and viral strains in mixed cultures is discussed, with a particular focus on the viruses EBV, HIV-1, and SARS-CoV-2. Full article

14 pages, 3489 KiB

Open AccessEditor’s ChoiceCommunication

Searching for G-Quadruplex-Binding Proteins in Plants: New Insight into Possible G-Quadruplex Regulation

by Adriana Volná, Martin Bartas, Jakub Nezval, Vladimír Špunda, Petr Pečinka and Jiří Červeň

BioTech 2021, 10(4), 20; https://doi.org/10.3390/biotech10040020 - 22 Sep 2021

Cited by 10 | Viewed by 5507

Abstract

G-quadruplexes are four-stranded nucleic acid structures occurring in the genomes of all living organisms and viruses. It is increasingly evident that these structures play important molecular roles; generally, by modulating gene expression and overall genome integrity. For a long period, G-quadruplexes have been [...] Read more.

G-quadruplexes are four-stranded nucleic acid structures occurring in the genomes of all living organisms and viruses. It is increasingly evident that these structures play important molecular roles; generally, by modulating gene expression and overall genome integrity. For a long period, G-quadruplexes have been studied specifically in the context of human promoters, telomeres, and associated diseases (cancers, neurological disorders). Several of the proteins for binding G-quadruplexes are known, providing promising targets for influencing G-quadruplex-related processes in organisms. Nonetheless, in plants, only a small number of G-quadruplex binding proteins have been described to date. Thus, we aimed to bioinformatically inspect the available protein sequences to find the best protein candidates with the potential to bind G-quadruplexes. Two similar glycine and arginine-rich G-quadruplex-binding motifs were described in humans. The first is the so-called “RGG motif”-RRGDGRRRGGGGRGQGGRGRGGGFKG, and the second (which has been recently described) is known as the “NIQI motif”-RGRGRGRGGGSGGSGGRGRG. Using this general knowledge, we searched for plant proteins containing the above mentioned motifs, using two independent approaches (BLASTp and FIMO scanning), and revealed many proteins containing the G4-binding motif(s). Our research also revealed the core proteins involved in G4 folding and resolving in green plants, algae, and the key plant model organism, Arabidopsis thaliana. The discovered protein candidates were annotated using STRINGdb and sorted by their molecular and physiological roles in simple schemes. Our results point to the significant role of G4-binding proteins in the regulation of gene expression in plants. Full article

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11 pages, 1457 KiB

Open AccessEditor’s ChoiceArticle

Increasing the High Throughput of a Luminescence-Based Serum Bactericidal Assay (L-SBA)

by Maria Grazia Aruta, Martina Carducci, Francesca Micoli, Francesca Necchi and Omar Rossi

BioTech 2021, 10(3), 19; https://doi.org/10.3390/biotech10030019 - 18 Sep 2021

Cited by 9 | Viewed by 5663

Abstract

Serum bactericidal assay (SBA) is the method to investigate in vitro complement-mediated bactericidal activity of sera raised upon vaccination. The assay is based on incubating the target bacteria and exogenous complement with sera at different dilutions and the result of the assay is [...] Read more.

Serum bactericidal assay (SBA) is the method to investigate in vitro complement-mediated bactericidal activity of sera raised upon vaccination. The assay is based on incubating the target bacteria and exogenous complement with sera at different dilutions and the result of the assay is represented by the sera dilution being able to kill 50% of bacteria present in the inoculum. The traditional readout of the assay is based on measurement of colony-forming units (CFU) obtained after plating different reaction mixes on agar. This readout is at low throughput and time consuming, even when automated counting is used. We previously described a novel assay with a luminescence readout (L-SBA) based on measurement of ATP released by live bacteria, which allowed to substantially increase the throughput as well as to reduce the time necessary to perform the assay when compared to traditional methods. Here we present a further improvement of the assay by moving from a 96-well to a 384-well format, which allowed us to further increase the throughput and substantially reduce costs while maintaining the high performance of the previously described L-SBA method. The method has been successfully applied to a variety of different pathogens. Full article

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12 pages, 2137 KiB

Open AccessEditor’s ChoiceArticle

Impact of Ethyl Methane Sulphonate Mutagenesis in Artemisia vulgaris L. under NaCl Stress

by Sudheeran Pradeep Kumar and B.D. Ranjitha Kumari

BioTech 2021, 10(3), 18; https://doi.org/10.3390/biotech10030018 - 21 Aug 2021

Cited by 10 | Viewed by 4512

Abstract

The present investigation aimed to obtain salt-tolerant Artemisia vulgaris L. to develop a constant form through in vitro mutagenesis with ethyl methane sulphonate (EMS) as the chemical mutagen. NaCl tolerance was evaluated by the ability of the callus to maintain its growth under [...] Read more.

The present investigation aimed to obtain salt-tolerant Artemisia vulgaris L. to develop a constant form through in vitro mutagenesis with ethyl methane sulphonate (EMS) as the chemical mutagen. NaCl tolerance was evaluated by the ability of the callus to maintain its growth under different concentrations, ranges from (0 mM to 500 mM). However, NaCl salinity concentration at (500 mM) did not show any development of callus, slight shrinking, and brown discoloration taking place over a week. Thus, all the biochemical and antioxidant assays were limited to (0–400 mM) NaCl. On the other hand, selected calluses were treated with 0.5% EMS for 30, 60, and 90 min and further subcultured on basal media fortified with different concentrations of 0–400 mM NaCl separately. Thus, the callus was treated for 60 min and was found to induce the mutation on the callus. The maximum salt-tolerant callus from 400 mM NaCl was regenerated in MS medium fortified with suitable hormones. Biochemical parameters such as chlorophyll, carotenoids, starch, amino acids, and phenol contents decreased under NaCl stress, whereas sugar and proline increased. Peroxidase (POD) and superoxide dismutase (SOD) activities peaked at 200 mM NaCl, whereas catalase (CAT) was maximum at 100 mM NaCl. Enhanced tolerance of 0.5% the EMS-treated callus, attributed to the increased biochemical and antioxidant activity over the control and NaCl stress. As a result, the mutants were more tolerant of salinity than the control plants. Full article

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15 pages, 845 KiB

Open AccessEditor’s ChoiceReview

Calculation of Fetal Fraction for Non-Invasive Prenatal Testing

by Matthew Cserhati

BioTech 2021, 10(3), 17; https://doi.org/10.3390/biotech10030017 - 9 Aug 2021

Cited by 7 | Viewed by 7704

Abstract

Estimating the fetal fraction of DNA in a pregnant mother’s blood is a risk-free, non-invasive way of predicting fetal aneuploidy. It is a rapidly developing field of study, offering researchers a plethora of different complementary methods. Such methods include examining the differences in [...] Read more.

Estimating the fetal fraction of DNA in a pregnant mother’s blood is a risk-free, non-invasive way of predicting fetal aneuploidy. It is a rapidly developing field of study, offering researchers a plethora of different complementary methods. Such methods include examining the differences in methylation profiles between the fetus and the mother. Others include calculating the average allele frequency based on the difference in genotype of a number of single-nucleotide polymorphisms. Differences in the length distribution of DNA fragments between the mother and the fetus as well as measuring the proportion of DNA reads mapping to the Y chromosome also constitute fetal fraction estimation methods. The advantages and disadvantages of each of these main method types are discussed. Moreover, several well-known fetal fraction estimation methods, such as SeqFF, are described and compared with other methods. These methods are amenable to not only the estimation of fetal fraction but also paternity, cancer, and transplantation monitoring studies. NIPT is safe, and should aneuploidy be detected, this information can help parents prepare mentally and emotionally for the birth of a special needs child. Full article

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8 pages, 188 KiB

Open AccessEditor’s ChoiceArticle

Artificial Intelligence in Biomedicine: A Legal Insight

by Takis Vidalis

BioTech 2021, 10(3), 15; https://doi.org/10.3390/biotech10030015 - 14 Jul 2021

Cited by 7 | Viewed by 4723

Abstract

The involvement of artificial intelligence in biomedicine promises better support for decision-making both in conventional and research medical practice. Yet two important issues emerge in relation to personal data handling, and the influence of AI on patient/doctor relationships. The development of AI algorithms [...] Read more.

The involvement of artificial intelligence in biomedicine promises better support for decision-making both in conventional and research medical practice. Yet two important issues emerge in relation to personal data handling, and the influence of AI on patient/doctor relationships. The development of AI algorithms presupposes extensive processing of big data in biobanks, for which procedures of compliance with data protection need to be ensured. This article addresses this problem in the framework of the EU legislation (GDPR) and explains the legal prerequisites pertinent to various categories of health data. Furthermore, the self-learning systems of AI may affect the fulfillment of medical duties, particularly if the attending physicians rely on unsupervised applications operating beyond their direct control. The article argues that the patient informed consent prerequisite plays a key role here, not only in conventional medical acts but also in clinical research procedures. Full article

(This article belongs to the Special Issue Biotechnology and Bioethics)

7 pages, 1012 KiB

Open AccessEditor’s ChoiceArticle

New Challenges for Biobanks: Accreditation to the New ISO 20387:2018 Standard Specific for Biobanks

by Pasquale De Blasio and Ida Biunno

BioTech 2021, 10(3), 13; https://doi.org/10.3390/biotech10030013 - 2 Jul 2021

Cited by 19 | Viewed by 6007

Abstract

Background: The emergence of “multi-omics” and “multi-parametric” types of analysis based on a high number of biospecimens enforces the use of a great number of high-quality “Biological Materials and Associated Data” (BMaD). To meet the demands of biomedical research, several Biological Resource Centers [...] Read more.

Background: The emergence of “multi-omics” and “multi-parametric” types of analysis based on a high number of biospecimens enforces the use of a great number of high-quality “Biological Materials and Associated Data” (BMaD). To meet the demands of biomedical research, several Biological Resource Centers (BRCs) or Biobanks world-wide have implemented a specific Quality Management System (QMS) certified ISO 9001:2015 or accredited by CAP⁹ ISO 20387:2018. For the first time, ISO, with the support of several Biobanking experts, issued the ISO 20387:2018 which is the first ISO norm specific for Biobanks. The fundamental difference with present certification/accreditation standards is that the ISO 20387:2018 focuses not only on the operational aspects of the Biobank, but also on the “competence of the Biobank to carry our specific Biobanking tasks”. Methods: The accreditation process for ISO 20387:2018 required the definition of: (1) objectives, goals and organizational structure of the Biobank, including procedures for governance, confidentiality and impartiality policies; (2) standard operating procedures (SOPs) of all activities performed, including acquisition, analysis, collection, data management, distribution, preparation, preservation, testing facility and equipment maintenance, calibration, and monitoring; (3) procedures for control of documents and records, the identification of risks and opportunities, improvements, corrective actions, nonconforming records and evaluation of external providers (4) an internal audit and management reviews, verification of QMS performance, monitoring of quality objectives and personnel qualification and competency in carrying out specific Biobanking tasks. Results: The accreditation process is performed by an independent authorized organization which certifies that all processes are performed according to the QMS, and that the infrastructure is engineered and managed according to the GDP and/or GMP guidelines. Conclusion: Accreditation is given by an accreditation body, which recognizes formally that the Biobank is “competent to carry out specific Biobanking tasks”. Full article

(This article belongs to the Special Issue Recent Advances in Biobanking: New Perspectives from Laboratory to Regulation)

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19 pages, 290 KiB

Open AccessEditor’s ChoiceArticle

Ethical Challenges in Organoid Use

by Vasiliki Mollaki

BioTech 2021, 10(3), 12; https://doi.org/10.3390/biotech10030012 - 28 Jun 2021

Cited by 50 | Viewed by 11523

Abstract

Organoids hold great promises for numerous applications in biomedicine and biotechnology. Despite its potential in science, organoid technology poses complex ethical challenges that may hinder any future benefits for patients and society. This study aims to analyze the multifaceted ethical issues raised by [...] Read more.

Organoids hold great promises for numerous applications in biomedicine and biotechnology. Despite its potential in science, organoid technology poses complex ethical challenges that may hinder any future benefits for patients and society. This study aims to analyze the multifaceted ethical issues raised by organoids and recommend measures that must be taken at various levels to ensure the ethical use and application of this technology. Organoid technology raises several serious ethics issues related to the source of stem cells for organoid creation, informed consent and privacy of cell donors, the moral and legal status of organoids, the potential acquisition of human “characteristics or qualities”, use of gene editing, creation of chimeras, organoid transplantation, commercialization and patentability, issues of equity in the resulting treatments, potential misuse and dual use issues and long-term storage in biobanks. Existing guidelines and regulatory frameworks that are applicable to organoids are also discussed. It is concluded that despite the serious ethical challenges posed by organoid use and biobanking, we have a moral obligation to support organoid research and ensure that we do not lose any of the potential benefits that organoids offer. In this direction, a four-step approach is recommended, which includes existing regulations and guidelines, special regulatory provisions that may be needed, public engagement and continuous monitoring of the rapid advancements in the field. This approach may help maximize the biomedical and social benefits of organoid technology and contribute to future governance models in organoid technology. Full article

(This article belongs to the Special Issue Biotechnology and Bioethics)

14 pages, 290 KiB

Open AccessEditor’s ChoiceReview

Biosafety of Genome Editing Applications in Plant Breeding: Considerations for a Focused Case-Specific Risk Assessment in the EU

by Michael F. Eckerstorfer, Marcin Grabowski, Matteo Lener, Margret Engelhard, Samson Simon, Marion Dolezel, Andreas Heissenberger and Christoph Lüthi

BioTech 2021, 10(3), 10; https://doi.org/10.3390/biotech10030010 - 22 Jun 2021

Cited by 21 | Viewed by 11562

Abstract

An intensely debated question is whether or how a mandatory environmental risk assessment (ERA) should be conducted for plants obtained through novel genomic techniques, including genome editing (GE). Some countries have already exempted certain types of GE applications from their regulations addressing genetically [...] Read more.

An intensely debated question is whether or how a mandatory environmental risk assessment (ERA) should be conducted for plants obtained through novel genomic techniques, including genome editing (GE). Some countries have already exempted certain types of GE applications from their regulations addressing genetically modified organisms (GMOs). In the European Union, the European Court of Justice confirmed in 2018 that plants developed by novel genomic techniques for directed mutagenesis are regulated as GMOs. Thus, they have to undergo an ERA prior to deliberate release or being placed on the market. Recently, the European Food Safety Authority (EFSA) published two opinions on the relevance of the current EU ERA framework for GM plants obtained through novel genomic techniques (NGTs). Regarding GE plants, the opinions confirmed that the existing ERA framework is suitable in general and that the current ERA requirements need to be applied in a case specific manner. Since EFSA did not provide further guidance, this review addresses a couple of issues relevant for the case-specific assessment of GE plants. We discuss the suitability of general denominators of risk/safety and address characteristics of GE plants which require particular assessment approaches. We suggest integrating the following two sets of considerations into the ERA: considerations related to the traits developed by GE and considerations addressing the assessment of method-related unintended effects, e.g., due to off-target modifications. In conclusion, we recommend that further specific guidance for the ERA and monitoring should be developed to facilitate a focused assessment approach for GE plants. Full article

(This article belongs to the Special Issue Biotechnology and Bioethics)

11 pages, 190 KiB

Open AccessEditor’s ChoiceArticle

The 3Rs Principle in Animal Experimentation: A Legal Review of the State of the Art in Europe and the Case in Italy

by Enrico Maestri

BioTech 2021, 10(2), 9; https://doi.org/10.3390/biotech10020009 - 20 May 2021

Cited by 35 | Viewed by 7956

Abstract

The aim of this paper is to describe the essential points of Italian and European legislation governing the use of animals in biomedical experimentation. A close look will be taken at the principles of the 3Rs, which represent the mainstay of the legal [...] Read more.

The aim of this paper is to describe the essential points of Italian and European legislation governing the use of animals in biomedical experimentation. A close look will be taken at the principles of the 3Rs, which represent the mainstay of the legal architecture based on which a correct interpretation may be drawn of the legislative documents on animal experimentation. Furthermore, this paper will address the ways in which Directive 2010/63/EU is implemented in Italian legislation on the welfare of laboratory animals. In addition to an assessment of legal issues (such as the scope of jurisdiction of supervisory authorities tasked with issuing authorizations), it will include a discussion of cases of inadequate and insufficient implementation of the requirements laid down by Directive 2010/63/EU. Both the consistency of the interpretation of national legislation with the Directive and the direct effectiveness of the Directive in national law, in which animal testing has been and still is the subject of heated debate between supporters and opponents, will be examined. Full article

13 pages, 1070 KiB

Open AccessEditor’s ChoiceArticle

Harmonization of Biobank Education for Biobank Technicians: Identification of Learning Objectives

by Mara Lena Hartung, Ronny Baber, Esther Herpel, Cornelia Specht, Daniel Peer Brucker, Anne Schoneberg, Theresa Winter and Sara Yasemin Nussbeck

BioTech 2021, 10(2), 7; https://doi.org/10.3390/biotech10020007 - 14 Apr 2021

Cited by 7 | Viewed by 4174

Abstract

The quality of biospecimens stored in a biobank depends tremendously on the technical personnel responsible for processing, storage, and release of biospecimens. Adequate training of these biobank employees would allow harmonization of correct sample handling and thus ensure a high and comparable quality [...] Read more.

The quality of biospecimens stored in a biobank depends tremendously on the technical personnel responsible for processing, storage, and release of biospecimens. Adequate training of these biobank employees would allow harmonization of correct sample handling and thus ensure a high and comparable quality of samples across biobank locations. However, in Germany there are no specific training opportunities for technical biobank staff. To understand the educational needs of the technical personnel a web-based survey was sent to all national biobanks via established e-mail registers. In total, 79 biobank employees completed the survey, including 43 technicians. The majority of the participating technical personnel stated that they had worked in a biobank for less than three years and had never participated in an advanced training. Three-quarters of the technicians indicated that they were not able to understand English content instantly. Based on these results and the results of a workshop with 16 biobank technicians, 41 learning objectives were formulated. These learning objectives can be used as a basis for advanced training programs for technical personnel in biobanks. Setting up courses based on the identified learning objectives for this group of biobank staff could contribute to harmonization and sustainability of biospecimen quality. Full article

(This article belongs to the Special Issue Recent Advances in Biobanking: New Perspectives from Laboratory to Regulation)

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6 pages, 750 KiB

Open AccessEditor’s ChoiceCommunication

Qiime Artifact eXtractor (qax): A Fast and Versatile Tool to Interact with Qiime2 Archives

by Andrea Telatin

BioTech 2021, 10(1), 5; https://doi.org/10.3390/biotech10010005 - 3 Mar 2021

Cited by 9 | Viewed by 4794

Abstract

Qiime2 is one of the most popular software tools used for analysis of output from metabarcoding experiments (e.g., sequencing of 16S, 18S, or ITS amplicons). Qiime2 introduced a novel and innovative data exchange format: the ‘Qiime2 artifact’. Qiime2 artifacts are structured compressed archives [...] Read more.

Qiime2 is one of the most popular software tools used for analysis of output from metabarcoding experiments (e.g., sequencing of 16S, 18S, or ITS amplicons). Qiime2 introduced a novel and innovative data exchange format: the ‘Qiime2 artifact’. Qiime2 artifacts are structured compressed archives containing a dataset and its associated metadata. Examples of datasets are FASTQ reads, representative sequences in FASTA format, a phylogenetic tree in Newick format, while examples of metadata are the command that generated the artifact, information on the execution environment, citations on the used software, and all the metadata of the artifacts used to produce it. While artifacts can improve the shareability and reproducibility of Qiime2 workflows, they are less easily integrated with general bioinformatics pipelines. Accessing metadata in the artifacts also requires full Qiime2 installation. Qiime Artifact eXtractor (qax) allows users to easily interface with Qiime2 artifacts from the command line, without needing the full Qiime2 environment installed (or activated). Full article

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19 pages, 915 KiB

Open AccessEditor’s ChoiceArticle

Integrating Multi–Omics Data for Gene-Environment Interactions

by Yinhao Du, Kun Fan, Xi Lu and Cen Wu

BioTech 2021, 10(1), 3; https://doi.org/10.3390/biotech10010003 - 29 Jan 2021

Cited by 5 | Viewed by 4787

Abstract

Gene-environment (G×E) interaction is critical for understanding the genetic basis of complex disease beyond genetic and environment main effects. In addition to existing tools for interaction studies, penalized variable selection emerges as a promising alternative for dissecting G×E interactions. Despite the success, variable [...] Read more.

Gene-environment (G×E) interaction is critical for understanding the genetic basis of complex disease beyond genetic and environment main effects. In addition to existing tools for interaction studies, penalized variable selection emerges as a promising alternative for dissecting G×E interactions. Despite the success, variable selection is limited in terms of accounting for multidimensional measurements. Published variable selection methods cannot accommodate structured sparsity in the framework of integrating multiomics data for disease outcomes. In this paper, we have developed a novel variable selection method in order to integrate multi-omics measurements in G×E interaction studies. Extensive studies have already revealed that analyzing omics data across multi-platforms is not only sensible biologically, but also resulting in improved identification and prediction performance. Our integrative model can efficiently pinpoint important regulators of gene expressions through sparse dimensionality reduction, and link the disease outcomes to multiple effects in the integrative G×E studies through accommodating a sparse bi-level structure. The simulation studies show the integrative model leads to better identification of G×E interactions and regulators than alternative methods. In two G×E lung cancer studies with high dimensional multi-omics data, the integrative model leads to an improved prediction and findings with important biological implications. Full article

(This article belongs to the Special Issue Feature Papers 2020)

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