BioTech

21 pages, 1220 KiB

Open AccessEditor’s ChoiceReview

Spirulina as a Key Ingredient in the Evolution of Eco-Friendly Cosmetics

by Sergiana dos Passos Ramos, Monize Bürck, Stephanie Fabrícia Francisco da Costa, Marcelo Assis and Anna Rafaela Cavalcante Braga

BioTech 2025, 14(2), 41; https://doi.org/10.3390/biotech14020041 - 30 May 2025

Viewed by 1623

Abstract

Limnospira spp., commercially known as spirulina, is widely recognized for its remarkable benefits due to its rich composition of bioactive compounds like phycobiliproteins, carotenoids, and phenolic compounds. These natural bioactive compounds not only serve as colorants but also offer potent antioxidant, anti-inflammatory, immunomodulatory, [...] Read more.

Limnospira spp., commercially known as spirulina, is widely recognized for its remarkable benefits due to its rich composition of bioactive compounds like phycobiliproteins, carotenoids, and phenolic compounds. These natural bioactive compounds not only serve as colorants but also offer potent antioxidant, anti-inflammatory, immunomodulatory, anticancer, antimicrobial, and anti-aging properties. As a result, spirulina and its components are increasingly used in cosmetic formulations to promote skin hydration, reduce wrinkles, and protect against UV radiation damage. Its bioactive components enhance fibroblast growth, boost collagen production, and prevent premature skin aging by inhibiting enzymes responsible for elastin degradation. Additionally, spirulina-based cosmetics have demonstrated wound-healing properties without genotoxic effects, with formulations containing C-phycocyanin particularly effective in shielding skin cells from UV-induced apoptosis. Despite these well-established benefits, there remains significant potential for the cosmetic industry to harness spirulina’s capabilities further. Research into the molecular mechanisms underlying its bioactive compounds in cosmetic formulations is still in its early stages, offering many opportunities for innovation. Emerging fields of biotechnology, such as nanotechnology and biocosmetics, could enhance the stability, efficacy, and delivery of spirulina-based ingredients, unlocking new possibilities for skin protection and rejuvenation. Furthermore, its proven biological properties align perfectly with the increasing consumer demand for safe, sustainable, and nature-inspired skincare solutions. Full article

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32 pages, 957 KiB

Open AccessEditor’s ChoiceReview

Broomrapes in Major Mediterranean Crops: From Management Strategies to Novel Approaches for Next-Generation Control

by Demosthenis Chachalis, Eleni Tani, Aliki Kapazoglou, Maria Gerakari, Angeliki Petraki, Francisco Pérez-Alfocea, Purificación A. Martínez-Melgarejo, Markus Albert, Khalil Khamassi and Mohamed Kharrat

BioTech 2025, 14(2), 40; https://doi.org/10.3390/biotech14020040 - 25 May 2025

Viewed by 1298

Abstract

Broomrapes (Orobanche and Phelipanche spp.) are parasitic weeds that significantly impact the productivity of major crops in the Mediterranean region, like tomato (Solanum spp.) and faba bean (Vicia faba) species. This review article extensively discusses management strategies to control [...] Read more.

Broomrapes (Orobanche and Phelipanche spp.) are parasitic weeds that significantly impact the productivity of major crops in the Mediterranean region, like tomato (Solanum spp.) and faba bean (Vicia faba) species. This review article extensively discusses management strategies to control broomrapes, which range from preventive measures to curative approaches. Additionally, it includes meaningful information on the intricate molecular mechanisms underlying the broomrape–host interaction, focusing on the host recognition of parasitic plant molecular patterns and the hormonal crosstalk that regulates the establishment of parasitism. Moreover, this article highlights the potential of breeding for resistance in cultivated crops, such as tomato and faba bean, as a sustainable, long-term solution to combat broomrape infestation. This review serves as a valuable resource for both researchers and farmers, offering insights for developing, implementing, and adapting effective and environmentally sustainable management practices for broomrape in Mediterranean agricultural systems. Full article

(This article belongs to the Special Issue BioTech: 5th Anniversary)

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27 pages, 10074 KiB

Open AccessEditor’s ChoiceArticle

Innovations in Proteomic Technologies and Artificial Neural Networks: Unlocking Milk Origin Identification

by Achilleas Karamoutsios, Emmanouil D. Oikonomou, Chrysoula (Chrysa) Voidarou, Lampros Hatzizisis, Konstantina Fotou, Konstantina Nikolaou, Evangelia Gouva, Evangelia Gkiza, Nikolaos Giannakeas, Ioannis Skoufos and Athina Tzora

BioTech 2025, 14(2), 33; https://doi.org/10.3390/biotech14020033 - 28 Apr 2025

Viewed by 1486

Abstract

Milk’s biological origin determination, including its adulteration and authenticity, presents serious limitations, highlighting the need for innovative advanced solutions. The utilisation of proteomic technologies combined with personalised algorithms creates great potential for a more comprehensive approach to analysing milk samples effectively. The current [...] Read more.

Milk’s biological origin determination, including its adulteration and authenticity, presents serious limitations, highlighting the need for innovative advanced solutions. The utilisation of proteomic technologies combined with personalised algorithms creates great potential for a more comprehensive approach to analysing milk samples effectively. The current study presents an innovative approach utilising proteomics and neural networks to classify and distinguish bovine, ovine and caprine milk samples by employing advanced machine learning techniques; we developed a precise and reliable model capable of distinguishing the unique mass spectral signatures associated with each species. Our dataset includes a diverse range of mass spectra collected from milk samples after MALDI-TOF MS (Matrix-assisted laser desorption/ionization-time of flight mass spectrometry) analysis, which were used to train, validate, and test the neural network model. The results indicate a high level of accuracy in species identification, underscoring the model’s potential applications in dairy product authentication, quality assurance, and food safety. The current research offers a significant contribution to agricultural science, providing a cutting-edge method for species-specific classification through mass spectrometry. The dataset comprises 648, 1554, and 2392 spectra, represented by 16,018, 38,394, and 55,055 eight-dimensional vectors from bovine, caprine, and ovine milk, respectively. Full article

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21 pages, 2688 KiB

Open AccessEditor’s ChoiceArticle

Production of Multifunctional Hydrolysates from the Lupinus mutabilis Protein Using a Micrococcus sp. PC7 Protease

by Keyla Sofía Llontop-Bernabé, Arturo Intiquilla, Carlos Ramirez-Veliz, Marco Santos, Karim Jiménez-Aliaga, Amparo Iris Zavaleta, Samuel Paterson and Blanca Hernández-Ledesma

BioTech 2025, 14(2), 32; https://doi.org/10.3390/biotech14020032 - 27 Apr 2025

Cited by 1 | Viewed by 1055

Abstract

The growing demand for functional foods has driven the search for bioactive compounds derived from plant proteins. Lupinus mutabilis “Tarwi”, a legume native to the Peruvian Andes, stands out for its high protein content and potential as a source of bioactive peptides (BPs). [...] Read more.

The growing demand for functional foods has driven the search for bioactive compounds derived from plant proteins. Lupinus mutabilis “Tarwi”, a legume native to the Peruvian Andes, stands out for its high protein content and potential as a source of bioactive peptides (BPs). In this study, the functionality of the proteins contained in the albumin fraction (AF) isolated by tangential ultrafiltration (TFF) was investigated by using the OmicsBox software. The identified proteins were functionally classified into three groups: cellular component (35.57%), molecular function (33.45%), and biological process (30.97%). The isolated AF was hydrolysed with the native protease PC7 (HAP), optimizing the E/S ratio and time parameters. Additionally, sequential hydrolysis of the PC7 protease and alcalase (HAPA) was performed. In vitro multifunctionality assays, HAP and HAPA demonstrated the ability to scavenge radicals (ABTS and ORAC) and inhibit angiotensin-converting enzyme (ACE)-I and dipeptidyl peptidase IV (DPP-IV). The findings of this study highlight the potential of L. mutabilis albumin hydrolysate as a multifunctional ingredient for functional foods aimed at managing chronic conditions associated with oxidative stress, hypertension, and/or metabolic disorders. Full article

(This article belongs to the Special Issue Natural Antioxidants: Determination in Food and Nutraceuticals and Implications on Human Health)

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26 pages, 1171 KiB

Open AccessEditor’s ChoiceReview

Matrix Metalloproteinases in Glioma: Drivers of Invasion and Therapeutic Targets

by Ella E. Aitchison, Alexandra M. Dimesa and Alireza Shoari

BioTech 2025, 14(2), 28; https://doi.org/10.3390/biotech14020028 - 15 Apr 2025

Viewed by 1367

Abstract

Matrix metalloproteinases (MMPs) are a family of zinc-dependent proteolytic enzymes that are crucial for the remodeling of the extracellular matrix, a process that is often co-opted by cancers, including brain tumors, to facilitate growth, invasion, and metastasis. In gliomas, MMPs contribute to a [...] Read more.

Matrix metalloproteinases (MMPs) are a family of zinc-dependent proteolytic enzymes that are crucial for the remodeling of the extracellular matrix, a process that is often co-opted by cancers, including brain tumors, to facilitate growth, invasion, and metastasis. In gliomas, MMPs contribute to a complex interplay involving tumor proliferation, angiogenesis, and immune modulation, thereby influencing tumor progression and patient prognosis. This review provides a comprehensive analysis of the roles of various MMPs in different types of gliomas, from highly malignant gliomas to metastatic lesions. Emphasis is placed on how the dysregulation of MMPs impacts tumor behavior, the association between specific MMPs and the tumor grade, and their potential as biomarkers for diagnosis and prognosis. Additionally, the current therapeutic approaches targeting MMP activity are discussed, exploring both their challenges and future potential. By synthesizing recent findings, this paper aims to clarify the broad significance of MMPs in gliomas and propose avenues for translational research that could enhance treatment strategies and clinical outcomes. Full article

(This article belongs to the Section Medical Biotechnology)

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20 pages, 1727 KiB

Open AccessEditor’s ChoiceReview

Developments in Extracellular Matrix-Based Angiogenesis Therapy for Ischemic Heart Disease: A Review of Current Strategies, Methodologies and Future Directions

by Jad Hamze, Mark Broadwin, Christopher Stone, Kelsey C. Muir, Frank W. Sellke and M. Ruhul Abid

BioTech 2025, 14(1), 23; https://doi.org/10.3390/biotech14010023 - 19 Mar 2025

Cited by 1 | Viewed by 779

Abstract

Ischemic heart disease (IHD) is the leading cause of mortality worldwide, underscoring the urgent need for innovative therapeutic strategies. The cardiac extracellular matrix (ECM) undergoes extreme transformations during IHD, adversely influencing the heart’s structure, mechanics, and cellular signaling. Researchers investigating the regenerative capacity [...] Read more.

Ischemic heart disease (IHD) is the leading cause of mortality worldwide, underscoring the urgent need for innovative therapeutic strategies. The cardiac extracellular matrix (ECM) undergoes extreme transformations during IHD, adversely influencing the heart’s structure, mechanics, and cellular signaling. Researchers investigating the regenerative capacity of the diseased heart have turned their attention to exploring the modulation of ECM to improve therapeutic outcomes. In this review, we thoroughly examine the current state of knowledge regarding the cardiac ECM and its therapeutic potential in the ischemic myocardium. We begin by providing an overview of the fundamentals of cardiac ECM, focusing on the structural, functional, and regulatory mechanisms that drive its modulation. Subsequently, we examine the ECM’s interactions within both chronically ischemic and acutely infarcted myocardium, emphasizing key ECM components and their roles in modulating angiogenesis. Finally, we discuss recent ECM-based approaches in biomedical engineering, focusing on different types of scaffolds as delivery tools and their compositions, and conclude with future directions for therapeutic research. By harnessing the potential of these emerging ECM-based therapies, we aim to contribute to the development of novel therapeutic modalities for IHD. Full article

(This article belongs to the Section Medical Biotechnology)

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17 pages, 608 KiB

Open AccessEditor’s ChoiceArticle

A Coupled Model of the Cardiovascular and Immune Systems to Analyze the Effects of COVID-19 Infection

by Camila Ribeiro Passos, Alexandre Altamir Moreira, Ruy Freitas Reis, Rodrigo Weber dos Santos, Marcelo Lobosco and Bernardo Martins Rocha

BioTech 2025, 14(1), 19; https://doi.org/10.3390/biotech14010019 - 12 Mar 2025

Cited by 1 | Viewed by 784

Abstract

The COVID-19 pandemic has underscored the importance of understanding the interplay between the cardiovascular and immune systems during viral infections. SARS-CoV-2 enters human cells via the ACE-2 enzyme, initiating a cascade of immune responses. This study presents a coupled mathematical model that integrates [...] Read more.

The COVID-19 pandemic has underscored the importance of understanding the interplay between the cardiovascular and immune systems during viral infections. SARS-CoV-2 enters human cells via the ACE-2 enzyme, initiating a cascade of immune responses. This study presents a coupled mathematical model that integrates the cardiovascular system (CVS) and immune system (IS), capturing their complex interactions during infection. The CVS model, based on ordinary differential equations, describes heart dynamics and pulmonary and systemic circulation, while the IS model simulates immune responses to SARS-CoV-2, including immune cell interactions and cytokine production. A coupling strategy transfers information from the IS to the CVS at specific intervals, enabling the exploration of immune-driven cardiovascular effects. Numerical simulations examined how these interactions influence infection severity and recovery. The coupled model accurately replicated the evolution of cardiac function in survivors and non-survivors of COVID-19. Survivors exhibited a left ventricular ejection fraction (LVEF) reduction of up to

25 %

while remaining within normal limits, whereas non-survivors showed a severe 4-fold decline, indicative of myocardial dysfunction. Similarly, the right ventricular ejection fraction (RV EF) decreased by approximately

50 %

in survivors but underwent a drastic 5-fold reduction in non-survivors. These findings highlight the model’s capacity to distinguish differential cardiac dysfunction across clinical outcomes and its potential to enhance our understanding of COVID-19 pathophysiology. Full article

(This article belongs to the Section Computational Biology)

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18 pages, 1301 KiB

Open AccessEditor’s ChoiceArticle

Prediction of Lupus Classification Criteria via Generative AI Medical Record Profiling

by Sandeep Nair, Gerald H. Lushington, Mohan Purushothaman, Bernard Rubin, Eldon Jupe and Santosh Gattam

BioTech 2025, 14(1), 15; https://doi.org/10.3390/biotech14010015 - 6 Mar 2025

Cited by 1 | Viewed by 1309

Abstract

Systemic lupus erythematosus (SLE) is a complex autoimmune disease that poses serious long-term patient burdens. (1) Background: SLE patient classification and care are often complicated by case heterogeneity (diverse variations in symptoms and severity). Large language models (LLMs) and generative artificial intelligence (genAI) [...] Read more.

Systemic lupus erythematosus (SLE) is a complex autoimmune disease that poses serious long-term patient burdens. (1) Background: SLE patient classification and care are often complicated by case heterogeneity (diverse variations in symptoms and severity). Large language models (LLMs) and generative artificial intelligence (genAI) may mitigate this challenge by profiling medical records to assess key medical criteria. (2) Methods: To demonstrate genAI-based profiling, ACR (American College of Rheumatology) 1997 SLE classification criteria were used to define medically relevant LLM prompts. Records from 78 previously studied patients (45 classified as having SLE; 33 indeterminate or negative) were computationally profiled, via five genAI replicate runs. (3) Results: GenAI determinations of the “Discoid Rash” and “Pleuritis or Pericarditis” classification criteria yielded perfect concurrence with clinical classification, while some factors such as “Immunologic Disorder” (56% accuracy) were statistically unreliable. Compared to clinical classification, our genAI approach achieved a 72% predictive success rate. (4) Conclusions: GenAI classifications may prove sufficiently predictive to aid medical professionals in evaluating SLE patients and structuring care strategies. For individual criteria, accuracy seems to correlate inversely with complexities in clinical determination, implying that improvements in AI patient profiling tools may emerge from continued advances in clinical classification efficacy. Full article

(This article belongs to the Topic Computational Intelligence and Bioinformatics (CIB))

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Graphical abstract

28 pages, 1169 KiB

Open AccessEditor’s ChoiceReview

Phytohormonal Regulation of Abiotic Stress Tolerance, Leaf Senescence and Yield Response in Field Crops: A Comprehensive Review

by Anna Panozzo, Pranay Kumar Bolla, Giuseppe Barion, Alessandro Botton and Teofilo Vamerali

BioTech 2025, 14(1), 14; https://doi.org/10.3390/biotech14010014 - 27 Feb 2025

Cited by 3 | Viewed by 1505

Abstract

Field crops are expected to be increasingly threatened by climate change, which will negatively impact plant development, growth and yield. Phytohormones play a crucial role in regulating specific signalling pathways to induce rapid adaptive responses to environmental stresses. Exogenous phytohormone application alters hormonal [...] Read more.

Field crops are expected to be increasingly threatened by climate change, which will negatively impact plant development, growth and yield. Phytohormones play a crucial role in regulating specific signalling pathways to induce rapid adaptive responses to environmental stresses. Exogenous phytohormone application alters hormonal balance, thereby enhancing plant adaptation to adverse conditions. While several studies have advanced our understanding of the use of phytohormones in field crops, yield responses and species-specific application strategies remain inconsistent and rarely assessed under field conditions. The application of cytokinins (CKs), abscisic acid (ABA), and gibberellic acid (GA) has been shown to maintain prolonged photosynthetic activity, stabilize plasma membrane, and reduce lipid peroxidation and ion accumulation under salinity stress in wheat. Additionally, inhibitors of ethylene synthesis and receptors can mitigate stress symptoms under drought and heat stress, which typically accelerates senescence and shortens the grain-filling period in cereal crops. In this way, exogenous application of CKs, GA, and ethylene inhibitors can delay senescence by sustaining leaf photosynthetic activity and postponing nutrient remobilization. However, these benefits may not consistently translate into improvements in grain yield and quality. This review explores the molecular mechanisms of phytohormones in abiotic stress tolerance, delineates their specific functions and evaluates experimental findings from field applications. It also summarizes the potential of phytohormone applications in field crops, emphasizing the need for species-specific investigations on application timing and dosages under open-field conditions to optimize their agronomic potential. Full article

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

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15 pages, 3580 KiB

Open AccessEditor’s ChoiceArticle

Enhanced Bioactive Compounds and Antioxidant Activity in Germinated Seeds of the New Peanut Variety

by Hwan-Hee Yu, Jong-Suk Park and Sanghyun Lee

BioTech 2025, 14(1), 12; https://doi.org/10.3390/biotech14010012 - 25 Feb 2025

Cited by 1 | Viewed by 862

Abstract

The sprout market in Korea is expanding as consumers seek healthier food options and farmers strive to increase added value and competitiveness. This study examined the changes in the phytochemical composition of Sinpalkwang (SPK), a peanut variety developed in Korea, during germination. Four [...] Read more.

The sprout market in Korea is expanding as consumers seek healthier food options and farmers strive to increase added value and competitiveness. This study examined the changes in the phytochemical composition of Sinpalkwang (SPK), a peanut variety developed in Korea, during germination. Four samples (SPK1, SPK2, SPK3, and SPK4) were collected at different growth stages and analyzed for total polyphenol content (TPC), total flavonoid content (TFC), and antioxidant activities using ABTS⁺ and DPPH assays. The levels of trans-resveratrol and soyasaponin Bb were quantified using high-performance liquid chromatography (HPLC) with a photo-diode array (PDA). Among the samples, SPK2 exhibited the highest TFC (1.61 mg QE/g ext.) and trans-resveratrol content (0.054 mg/g ext.), while SPK4 showed the highest TPC (29.38 mg TAE/g ext.) and soyasaponin Bb content (6.543 mg/g ext.). In terms of radical scavenging activities, SPK2 and SPK3 performed best in the ABTS⁺ and DPPH assays, respectively. Germinated samples demonstrated strong results across all analyses, highlighting the benefits of germination in enhancing phytochemical properties. This study provides foundational information on the phytochemical composition of SPK and the effects of germination. Future research will focus on optimizing germination conditions to further enhance the functionality and value of this Korean-bred variety as a source of high-value bioactive ingredients. Full article

(This article belongs to the Special Issue Natural Antioxidants: Determination in Food and Nutraceuticals and Implications on Human Health)

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16 pages, 1345 KiB

Open AccessEditor’s ChoiceReview

STXBP1 Syndrome: Biotechnological Advances, Challenges, and Perspectives in Gene Therapy, Experimental Models, and Translational Research

by Silvestre Ruano-Rodríguez, Mar Navarro-Alonso, Benito Domínguez-Velasco, Manuel Álvarez-Dolado and Francisco J. Esteban

BioTech 2025, 14(1), 11; https://doi.org/10.3390/biotech14010011 - 20 Feb 2025

Viewed by 2148

Abstract

STXBP1 syndrome is a severe early-onset epileptic encephalopathy characterized by developmental delay and intellectual disability. This review addresses key challenges in STXBP1 syndrome research, focusing on advanced therapeutic approaches and experimental models. We explore gene therapy strategies, including CRISPR-Cas9, adeno-associated viral (AAV) vectors, [...] Read more.

STXBP1 syndrome is a severe early-onset epileptic encephalopathy characterized by developmental delay and intellectual disability. This review addresses key challenges in STXBP1 syndrome research, focusing on advanced therapeutic approaches and experimental models. We explore gene therapy strategies, including CRISPR-Cas9, adeno-associated viral (AAV) vectors, and RNA therapies such as antisense oligonucleotides (ASOs), aimed at correcting STXBP1 genetic dysfunctions. This review presents in vivo and in vitro models, highlighting their contributions to understanding disease mechanisms. Additionally, we provide a proposal for a detailed bioinformatic analysis of a Spanish cohort of 41 individuals with STXBP1-related disorders, offering insights into specific mutations and their biological implications. Clinical and translational perspectives are discussed, emphasizing the potential of personalized medicine approaches. Future research directions and key challenges are outlined, including the identification of STXBP1 interactors, unexplored molecular pathways, and the need for clinically useful biomarkers. This comprehensive review underscores the complexity of STXBP1-related infantile epileptic encephalopathy and opens new avenues for advancing the understanding and treatment of this heterogeneous disease. Full article

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34 pages, 1515 KiB

Open AccessEditor’s ChoiceReview

The Use of Biologics for Targeting GPCRs in Metastatic Cancers

by Cian McBrien and David J. O’Connell

BioTech 2025, 14(1), 7; https://doi.org/10.3390/biotech14010007 - 30 Jan 2025

Cited by 1 | Viewed by 3902

Abstract

A comprehensive review of studies describing the role of G-protein coupled receptor (GPCR) behaviour contributing to metastasis in cancer, and the developments of biotherapeutic drugs towards targeting them, provides a valuable resource toward improving our understanding of the opportunities to effectively target this [...] Read more.

A comprehensive review of studies describing the role of G-protein coupled receptor (GPCR) behaviour contributing to metastasis in cancer, and the developments of biotherapeutic drugs towards targeting them, provides a valuable resource toward improving our understanding of the opportunities to effectively target this malignant tumour cell adaptation. Focusing on the five most common metastatic cancers of lung, breast, colorectal, melanoma, and prostate cancer, we highlight well-studied and characterised GPCRs and some less studied receptors that are also implicated in the development of metastatic cancers. Of the approximately 390 GPCRs relevant to therapeutic targeting, as many as 125 of these have been identified to play a role in promoting metastatic disease in these cancer types. GPCR signalling through the well-characterised pathways of chemokine receptors, to emerging data on signalling by orphan receptors, is integral to many aspects of the metastatic phenotype. Despite having detailed information on many receptors and their ligands, there are only thirteen approved therapeutics specifically for metastatic cancer, of which three are small molecules with the remainder including synthetic and non-synthetic peptides or monoclonal antibodies. This review will cover the existing and potential use of monoclonal antibodies, proteins and peptides, and nanobodies in targeting GPCRs for metastatic cancer therapy. Full article

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30 pages, 884 KiB

Open AccessEditor’s ChoiceReview

Aromatic Amino Acids: Exploring Microalgae as a Potential Biofactory

by Archana Niraula, Amir Danesh, Natacha Merindol, Fatma Meddeb-Mouelhi and Isabel Desgagné-Penix

BioTech 2025, 14(1), 6; https://doi.org/10.3390/biotech14010006 - 29 Jan 2025

Viewed by 2406

Abstract

In recent times, microalgae have emerged as powerful hosts for biotechnological applications, ranging from the production of lipids and specialized metabolites (SMs) of pharmaceutical interest to biofuels, nutraceutical supplements, and more. SM synthesis through bioengineered pathways relies on the availability of aromatic amino [...] Read more.

In recent times, microalgae have emerged as powerful hosts for biotechnological applications, ranging from the production of lipids and specialized metabolites (SMs) of pharmaceutical interest to biofuels, nutraceutical supplements, and more. SM synthesis through bioengineered pathways relies on the availability of aromatic amino acids (AAAs) as an essential precursor. AAAs, phenylalanine, tyrosine, and tryptophan are also the building blocks of proteins, maintaining the structural and functional integrity of cells. Hence, they are crucial intermediates linking the primary and specialized metabolism. The biosynthesis pathway of AAAs in microbes and plants has been studied for decades, but not much is known about microalgae. The allosteric control present in this pathway has been targeted for metabolic engineering in microbes. This review focuses on the biosynthesis of AAAs in eukaryotic microalgae and engineering techniques for enhanced production. All the putative genes involved in AAA pathways in the model microalgae Chlamydomonas reinhardtii and Phaeodactylum tricornutum are listed in this review. Full article

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

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19 pages, 3649 KiB

Open AccessEditor’s ChoiceArticle

Evaluating TcAs for Use in Biotechnology Applications

by Cole L. Martin, John H. Hill, Brian D. Wright, Solana R. Fernandez, Aubrey L. Miller, Karina J. Yoon, Suzanne E. Lapi and Stephen G. Aller

BioTech 2025, 14(1), 5; https://doi.org/10.3390/biotech14010005 - 25 Jan 2025

Viewed by 1449

Abstract

ABC toxin complexes (Tcs) are tripartite complexes that come together to form nano-syringe-like translocation systems. ABC Tcs are often compared with Bacillus thuringiensis (Bt) toxins, and as such, they have been highly studied as a potential novel pesticide to combat growing insect resistance. [...] Read more.

ABC toxin complexes (Tcs) are tripartite complexes that come together to form nano-syringe-like translocation systems. ABC Tcs are often compared with Bacillus thuringiensis (Bt) toxins, and as such, they have been highly studied as a potential novel pesticide to combat growing insect resistance. Moreover, it is possible to substitute the cytotoxic hypervariable region with alternative peptides, which promise potential use as a novel peptide delivery system. These toxins possess the unique ability to form active chimeric holotoxins across species and display the capability to translocate a variety of payloads across membrane bilayers. Additionally, mutagenesis on the linker region and the receptor binding domains (RBDs) show that mutations do not inherently cause a loss of functionality for translocation. For these reasons, Tcs have emerged as an ideal candidate for targeted protein engineering. However, elucidation of the specific function of each RBD in relation to target receptor recognition currently limits the use of a rational design approach with any ABC Tc. Additionally, there is a distinct lack of targeting and biodistribution data for many Tcs among mammals and mammalian cell lines. Here, we outline two separate strategies for modifying the targeting capabilities of the A subunit (TcA) from Xenorhabdus nematophilus, Xn-XptA2. We identify novel structural differences that make Xn-XptA2 different than other characterized TcAs and display the modular capabilities of substituting RBDs from alternative TcAs into the Xn-XptA2 scaffold. Finally, we show the first, to our knowledge, biodistribution data of any TcA in mice. Full article

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20 pages, 2534 KiB

Open AccessEditor’s ChoiceArticle

Discovery of Innate Immune Response mRNAs That Are Impacted by Structure-Specific Oral Baker’s Yeast Beta Glucan Consumption

by Brian K. McFarlin, John H. Curtis, Jakob L. Vingren, David W. Hill and Elizabeth A. Bridgeman

BioTech 2025, 14(1), 4; https://doi.org/10.3390/biotech14010004 - 13 Jan 2025

Cited by 1 | Viewed by 1349

Abstract

The study of nutritional compounds with the potential to train the innate immune response has implications for human health. The objective of the current study was to discover by what means 6 weeks of oral baker’s yeast beta glucan (BYBG) supplementation altered the [...] Read more.

The study of nutritional compounds with the potential to train the innate immune response has implications for human health. The objective of the current study was to discover by what means 6 weeks of oral baker’s yeast beta glucan (BYBG) supplementation altered the mRNA expression of genes that reflect innate immune training in the absence of a physical stressor. Nineteen adults were randomly assigned to either a Wellmune^® BYBG or Placebo for 6 weeks. BYBG uniquely altered the expression of 40 mRNAs associated with Dectin-1 and trained innate immunity, the innate immune response, the pathogen-associated (PAMP) and damage-associated molecular pattern (DAMP), and the inflammatory response. The observed changes were classified as immune training rather than immune priming due to the progressive increase in the expression of myeloid immune-associated mRNA. Combined with the findings of previous research, the findings of the present study support the claim that oral BYBG supplementation may be associated with trained innate immunity during resting homeostasis. Further, the key findings associated with BYBG may reflect improved responsiveness to future infection (exogenous) and/or sterile-inflammatory (endogenous) challenge. Full article

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29 pages, 2633 KiB

Open AccessEditor’s ChoiceReview

Current Approaches for Genetic Manipulation of Streptomyces spp.—Key Bacteria for Biotechnology and Environment

by Sergii Krysenko

BioTech 2025, 14(1), 3; https://doi.org/10.3390/biotech14010003 - 2 Jan 2025

Cited by 3 | Viewed by 2423

Abstract

Organisms from the genus Streptomyces feature actinobacteria with complex developmental cycles and a great ability to produce a variety of natural products. These soil bacteria produce more than 2/3 of antibiotics used in medicine, and a large variety of bioactive compounds for industrial, [...] Read more.

Organisms from the genus Streptomyces feature actinobacteria with complex developmental cycles and a great ability to produce a variety of natural products. These soil bacteria produce more than 2/3 of antibiotics used in medicine, and a large variety of bioactive compounds for industrial, medical and agricultural use. Although Streptomyces spp. have been studied for decades, the engineering of these bacteria remains challenging, and the available genetic tools are rather limited. Furthermore, most biosynthetic gene clusters in these bacteria are silent and require strategies to activate them and exploit their production potential. In order to explore, understand and manipulate the capabilities of Streptomyces spp. as a key bacterial for biotechnology, synthetic biology strategies emerged as a valuable component of Streptomyces research. Recent advancements in strategies for genetic manipulation of Streptomyces involving proposals of a large variety of synthetic components for the genetic toolbox, as well as new approaches for genome mining, assembly of genetic constructs and their delivery into the cell, allowed facilitation of the turnaround time of strain engineering and efficient production of new natural products at an industrial scale, but still have strain- and design-dependent limitations. A new perspective offered recently by technical advances in DNA sequencing, analysis and editing proposed strategies to overcome strain- and construct-specific difficulties in the engineering of Streptomyces. In this review, challenges and recent developments of approaches for Streptomyces engineering are discussed, an overview of novel synthetic biology strategies is provided and examples of successful application of new technologies in molecular genetic engineering of Streptomyces are highlighted. Full article

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

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18 pages, 518 KiB

Open AccessEditor’s ChoiceReview

Climate Resilience in Farm Animals: Transcriptomics-Based Alterations in Differentially Expressed Genes and Stress Pathways

by Chikamagalore Gopalakrishna Shashank, Veerasamy Sejian, Mullakkalparambil Velayudhan Silpa, Chinnasamy Devaraj, Aradotlu Parameshwarappa Madhusoodan, Ebenezer Binuni Rebez, Gajendirane Kalaignazhal, Artabandhu Sahoo and Frank Rowland Dunshea

BioTech 2024, 13(4), 49; https://doi.org/10.3390/biotech13040049 - 15 Nov 2024

Cited by 3 | Viewed by 1878

Abstract

The livestock sector, essential for maintaining food supply and security, encounters numerous obstacles as a result of climate change. Rising global populations exacerbate competition for natural resources, affecting feed quality and availability, heightening livestock disease risks, increasing heat stress, and contributing to biodiversity [...] Read more.

The livestock sector, essential for maintaining food supply and security, encounters numerous obstacles as a result of climate change. Rising global populations exacerbate competition for natural resources, affecting feed quality and availability, heightening livestock disease risks, increasing heat stress, and contributing to biodiversity loss. Although various management and dietary interventions exist to alleviate these impacts, they often offer only short-lived solutions. We must take a more comprehensive approach to understanding how animals adapt to and endure their environments. One such approach is quantifying transcriptomes under different environments, which can uncover underlying pathways essential for livestock adaptation. This review explores the progress and techniques in studies that apply gene expression analysis to livestock production systems, focusing on their adaptation to climate change. We also attempt to identify various biomarkers and transcriptomic differences between species and pure/crossbred animals. Looking ahead, integrating emerging technologies such as spatialomics could further accelerate genetic improvements, enabling more thermoresilient and productive livestock in response to future climate fluctuations. Ultimately, insights from these studies will help optimize livestock production systems by identifying thermoresilient/desired animals for use in precise breeding programs to counter climate change. Full article

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

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18 pages, 3391 KiB

Open AccessEditor’s ChoiceReview

Honey Bioactive Molecules: There Is a World Beyond the Sugars

by Gregorio Bonsignore, Simona Martinotti and Elia Ranzato

BioTech 2024, 13(4), 47; https://doi.org/10.3390/biotech13040047 - 14 Nov 2024

Cited by 6 | Viewed by 3298

Abstract

Honey’s many bioactive compounds have been utilized historically to cure infectious diseases. Beneficial effects are its antiviral, antibacterial, anti-inflammatory, antioxidant, and immune-stimulating qualities. The bee species, geographic location, botanical origin, harvest season, processing, and storage conditions all affect honey’s potential for therapeutic use. [...] Read more.

Honey’s many bioactive compounds have been utilized historically to cure infectious diseases. Beneficial effects are its antiviral, antibacterial, anti-inflammatory, antioxidant, and immune-stimulating qualities. The bee species, geographic location, botanical origin, harvest season, processing, and storage conditions all affect honey’s potential for therapeutic use. Honey contains a number of antioxidants and active compounds, such as polyphenols, which have been shown to have disease-preventive properties. Based on their origins, categories, and functions, the main polyphenols found in various honey varieties are examined in this review. Full article

(This article belongs to the Special Issue Natural Antioxidants: Determination in Food and Nutraceuticals and Implications on Human Health)

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27 pages, 943 KiB

Open AccessEditor’s ChoiceReview

Data Management in Biobanking: Strategies, Challenges, and Future Directions

by Ramez Alkhatib and Karoline I. Gaede

BioTech 2024, 13(3), 34; https://doi.org/10.3390/biotech13030034 - 2 Sep 2024

Cited by 17 | Viewed by 7079

Abstract

Biobanking plays a pivotal role in biomedical research by providing standardized processing, precise storing, and management of biological sample collections along with the associated data. Effective data management is a prerequisite to ensure the integrity, quality, and accessibility of these resources. This review [...] Read more.

Biobanking plays a pivotal role in biomedical research by providing standardized processing, precise storing, and management of biological sample collections along with the associated data. Effective data management is a prerequisite to ensure the integrity, quality, and accessibility of these resources. This review provides a current landscape of data management in biobanking, discussing key challenges, existing strategies, and potential future directions. We explore multiple aspects of data management, including data collection, storage, curation, sharing, and ethical considerations. By examining the evolving technologies and methodologies in biobanking, we aim to provide insights into addressing the complexities and maximizing the utility of biobank data for research and clinical applications. Full article

(This article belongs to the Section Biotechnology Regulation)

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14 pages, 4119 KiB

Open AccessEditor’s ChoiceArticle

Auxin-Producing Bacteria Used as Microbial Biostimulants Improve the Growth of Tomato (Solanum lycopersicum L.) Seedlings in Hydroponic Systems

by Livia Pappalettere, Susanna Bartolini and Annita Toffanin

BioTech 2024, 13(3), 32; https://doi.org/10.3390/biotech13030032 - 21 Aug 2024

Cited by 3 | Viewed by 2981

Abstract

Seven auxin-producing endophytic bacterial strains (Azospirillum spp., Methylobacterium symbioticum, Bacillus spp.), and two different combinations of these strains were used to verify their influence on tomato during germination and development in hydroponic conditions where, as a novelty for Canestrino di Lucca [...] Read more.

Seven auxin-producing endophytic bacterial strains (Azospirillum spp., Methylobacterium symbioticum, Bacillus spp.), and two different combinations of these strains were used to verify their influence on tomato during germination and development in hydroponic conditions where, as a novelty for Canestrino di Lucca cultivar, endophytic bacteria were inoculated. To emphasize the presence of bacterial auxins in roots and stems of seedlings, both in situ staining qualitative assessment and quantitative analysis were carried out. Moreover, hypogeal and epigeal growth of the plantlets were measured, and correlation analyses were conducted to examine the relationship between the amount of indolacetic acid (IAA) produced by the bacterial strains and root and stem parameters. Plantlets treated with microbial inoculants showed a significant increase in the survival rate compared to the control treatment. The best results as IAA producers were from Azospirillum baldaniorum Sp245 and A. brasilense Cd, which also induced significant root growth. On the other hand, Bacillus amyloliquefaciens and B. licheniformis induced the best rates in stem growth. These findings highlight the potential for using endophytic bacterial strains in a hydroponic co-cultivation system that enables inoculating plantlets, at an early stage of growth (5 days old). Full article

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

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14 pages, 1611 KiB

Open AccessEditor’s ChoiceArticle

Removal of Cadmium (II) from Aqueous Solution Using Galdieria sulphuraria CCMEE 5587.1

by Hari Lal Kharel, Lina Jha, Melissa Tan and Thinesh Selvaratnam

BioTech 2024, 13(3), 28; https://doi.org/10.3390/biotech13030028 - 1 Aug 2024

Cited by 3 | Viewed by 1831

Abstract

The release of cadmium into the environment is a significant global concern due to its toxicity, non-biodegradability, and persistence in nature. There is an urgent need for effective, eco-friendly, and cost-effective systems for removing Cd because of the many drawbacks of conventional physicochemical [...] Read more.

The release of cadmium into the environment is a significant global concern due to its toxicity, non-biodegradability, and persistence in nature. There is an urgent need for effective, eco-friendly, and cost-effective systems for removing Cd because of the many drawbacks of conventional physicochemical techniques. This study investigated the ability of the extremophile red microalgal strain Galdieria sulphuraria CCMEE 5587.1 to tolerate and remove Cd (II) ions at acidic pH in a controlled laboratory environment. Three distinct concentrations of Cd (1.5 mg L⁻¹, 3 mg L⁻¹, and 6 mg L⁻¹) were introduced to the cyanidium medium, and G. sulphuraria cells were introduced in the medium and grown for ten days. Four distinct aspects were identified regarding Cd removal: time course Cd removal, total Cd removal, extracellular Cd removal, and intracellular Cd removal. The inhibitory effects of Cd on G. sulphuraria growth were observed using a daily growth profile. Initial incubation days showed an inhibition of G. sulphuraria growth. In addition, increasing the Cd concentration in the medium decreased the growth rate of G. sulphuraria. Rapid Cd removal occurred on the first day of the experiment, followed by a steady removal of Cd until the last day. The highest total removal efficiency occurred in a medium containing 3 mg L⁻¹ of Cd ions, which was 30%. In contrast, the highest sorption capacity occurred in a medium containing 6 mg L⁻¹ of Cd ions, which was 1.59 mg g⁻¹ of dry biomass. In all media compositions, a major fraction (>80%) of Cd removal occurred via adsorption on the cell surface (extracellular). These results showed that G. sulphuraria cells can remove Cd ions from aqueous solution, which makes them a potential bioremediation option for heavy metal removal. Full article

(This article belongs to the Section Environmental Biotechnology)

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14 pages, 2059 KiB

Open AccessEditor’s ChoiceArticle

A Machine Learning-Based Web Tool for the Severity Prediction of COVID-19

by Avgi Christodoulou, Martha-Spyridoula Katsarou, Christina Emmanouil, Marios Gavrielatos, Dimitrios Georgiou, Annia Tsolakou, Maria Papasavva, Vasiliki Economou, Vasiliki Nanou, Ioannis Nikolopoulos, Maria Daganou, Aikaterini Argyraki, Evaggelos Stefanidis, Gerasimos Metaxas, Emmanouil Panagiotou, Ioannis Michalopoulos and Nikolaos Drakoulis

BioTech 2024, 13(3), 22; https://doi.org/10.3390/biotech13030022 - 1 Jul 2024

Cited by 2 | Viewed by 2739

Abstract

Predictive tools provide a unique opportunity to explain the observed differences in outcome between patients of the COVID-19 pandemic. The aim of this study was to associate individual demographic and clinical characteristics with disease severity in COVID-19 patients and to highlight the importance [...] Read more.

Predictive tools provide a unique opportunity to explain the observed differences in outcome between patients of the COVID-19 pandemic. The aim of this study was to associate individual demographic and clinical characteristics with disease severity in COVID-19 patients and to highlight the importance of machine learning (ML) in disease prognosis. The study enrolled 344 unvaccinated patients with confirmed SARS-CoV-2 infection. Data collected by integrating questionnaires and medical records were imported into various classification machine learning algorithms, and the algorithm and the hyperparameters with the greatest predictive ability were selected for use in a disease outcome prediction web tool. Of 111 independent features, age, sex, hypertension, obesity, and cancer comorbidity were found to be associated with severe COVID-19. Our prognostic tool can contribute to a successful therapeutic approach via personalized treatment. Although at the present time vaccination is not considered mandatory, this algorithm could encourage vulnerable groups to be vaccinated. Full article

(This article belongs to the Topic Advances in Bioinformatics and Computational Biology of Human Disease)

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6 pages, 339 KiB

Open AccessEditor’s ChoiceCommunication

Spectrofluorimetric Analysis of Riboflavin Content during Kombucha Fermentation

by Mojca Čakić Semenčić, Adrianna Biedrzycka, Anna Kiczor, Sunčica Beluhan and Filip Šupljika

BioTech 2024, 13(2), 20; https://doi.org/10.3390/biotech13020020 - 11 Jun 2024

Cited by 2 | Viewed by 2011

Abstract

Kombucha is a traditional beverage obtained by the microbial fermentation of tea using a symbiotic culture of bacteria and yeasts. In addition to several documented functional properties, such as anti-inflammatory activity and antioxidant activity, kombucha is often credited with high levels of vitamins, [...] Read more.

Kombucha is a traditional beverage obtained by the microbial fermentation of tea using a symbiotic culture of bacteria and yeasts. In addition to several documented functional properties, such as anti-inflammatory activity and antioxidant activity, kombucha is often credited with high levels of vitamins, including riboflavin. To our knowledge, the vitamin B2 content in traditionally prepared kombucha has been determined in only two studies, in which the concentration measured by the HPLC technique ranged from 2.2 × 10⁻⁷ to 2.1 × 10⁻⁴ mol dm⁻³. These unexplained differences of three orders of magnitude in the vitamin B2 content prompted us to determine its concentration during the cultivation of kombucha under very similar conditions by spectrofluorimetry. The B2 concentrations during the 10-day fermentation of black tea ranged from 7.6 × 10⁻⁸ to 3.3 × 10⁻⁷ mol dm⁻³. Full article

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

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24 pages, 5154 KiB

Open AccessEditor’s ChoiceArticle

Simulation of Radiation-Induced DNA Damage and Protection by Histones Using the Code RITRACKS

by Ianik Plante, Devany W. West, Jason Weeks and Viviana I. Risca

BioTech 2024, 13(2), 17; https://doi.org/10.3390/biotech13020017 - 5 Jun 2024

Cited by 3 | Viewed by 2335

Abstract

(1) Background: DNA damage is of great importance in the understanding of the effects of ionizing radiation. Various types of DNA damage can result from exposure to ionizing radiation, with clustered types considered the most important for radiobiological effects. (2) Methods: The code [...] Read more.

(1) Background: DNA damage is of great importance in the understanding of the effects of ionizing radiation. Various types of DNA damage can result from exposure to ionizing radiation, with clustered types considered the most important for radiobiological effects. (2) Methods: The code RITRACKS (Relativistic Ion Tracks), a program that simulates stochastic radiation track structures, was used to simulate DNA damage by photons and ions spanning a broad range of linear energy transfer (LET) values. To perform these simulations, the transport code was modified to include cross sections for the interactions of ions or electrons with DNA and amino acids for ionizations, dissociative electron attachment, and elastic collisions. The radiochemistry simulations were performed using a step-by-step algorithm that follows the evolution of all particles in time, including reactions between radicals and DNA structures and amino acids. Furthermore, detailed DNA damage events, such as base pair positions, DNA fragment lengths, and fragment yields, were recorded. (3) Results: We report simulation results using photons and the ions ¹H⁺, ⁴He²⁺, ¹²C⁶⁺, ¹⁶O⁸⁺, and ⁵⁶Fe²⁶⁺ at various energies, covering LET values from 0.3 to 164 keV/µm, and performed a comparison with other codes and experimental results. The results show evidence of DNA protection from damage at its points of contacts with histone proteins. (4) Conclusions: RITRACKS can provide a framework for studying DNA damage from a variety of ionizing radiation sources with detailed representations of DNA at the atomic scale, DNA-associated proteins, and resulting DNA damage events and statistics, enabling a broader range of future comparisons with experiments such as those based on DNA sequencing. Full article

(This article belongs to the Section Computational Biology)

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19 pages, 3199 KiB

Open AccessEditor’s ChoiceArticle

In Silico and In Vitro Evaluation of the Antifungal Activity of a New Chromone Derivative against Candida spp.

by Gleycyelly Rodrigues Araújo, Palloma Christine Queiroga Gomes da Costa, Paula Lima Nogueira, Danielle da Nóbrega Alves, Alana Rodrigues Ferreira, Pablo R. da Silva, Jéssica Cabral de Andrade, Natália F. de Sousa, Paulo Bruno Araujo Loureiro, Marianna Vieira Sobral, Damião P. Sousa, Marcus Tullius Scotti, Ricardo Dias de Castro and Luciana Scotti

BioTech 2024, 13(2), 16; https://doi.org/10.3390/biotech13020016 - 25 May 2024

Cited by 4 | Viewed by 2545

Abstract

Candida species are frequently implicated in the development of both superficial and invasive fungal infections, which can impact vital organs. In the quest for novel strategies to combat fungal infections, there has been growing interest in exploring synthetic and semi-synthetic products, particularly chromone [...] Read more.

Candida species are frequently implicated in the development of both superficial and invasive fungal infections, which can impact vital organs. In the quest for novel strategies to combat fungal infections, there has been growing interest in exploring synthetic and semi-synthetic products, particularly chromone derivatives, renowned for their antimicrobial properties. In the analysis of the antifungal activity of the compound (E)-benzylidene-chroman-4-one against Candida, in silico and laboratory tests were performed to predict possible mechanisms of action pathways, and in vitro tests were performed to determine antifungal activity (MIC and MFC), to verify potential modes of action on the fungal cell membrane and wall, and to assess cytotoxicity in human keratinocytes. The tested compound exhibited predicted affinity for all fungal targets, with the highest predicted affinity observed for thymidylate synthase (−102.589 kJ/mol). MIC and CFM values ranged from 264.52 μM (62.5 μg/mL) to 4232.44 μM (1000 μg/mL). The antifungal effect likely occurs due to the action of the compound on the plasma membrane. Therefore, (E)-benzylidene-chroman-4-one showed fungicidal-like activity against Candida spp., possibly targeting the plasma membrane. Full article

(This article belongs to the Special Issue Feature Papers in Computational Biology)

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16 pages, 1553 KiB

Open AccessEditor’s ChoiceArticle

Valorization of Wheat Bran by Co-Cultivation of Fungi with Integrated Hydrolysis to Provide Sugars and Animal Feed

by Fabian Mittermeier, Fabienne Fischer, Sebastian Hauke, Peter Hirschmann and Dirk Weuster-Botz

BioTech 2024, 13(2), 15; https://doi.org/10.3390/biotech13020015 - 18 May 2024

Cited by 2 | Viewed by 1965

Abstract

The enzymatic hydrolysis of agricultural residues like wheat bran enables the valorization of otherwise unused carbon sources for biotechnological processes. The co-culture of Aspergillus niger and Trichoderma reesei with wheat bran particles as substrate produces an enzyme set consisting of xylanases, amylases, and [...] Read more.

The enzymatic hydrolysis of agricultural residues like wheat bran enables the valorization of otherwise unused carbon sources for biotechnological processes. The co-culture of Aspergillus niger and Trichoderma reesei with wheat bran particles as substrate produces an enzyme set consisting of xylanases, amylases, and cellulases that is suitable to degrade lignocellulosic biomass to sugar monomers (D-glucose, D-xylose, and L-arabinose). An integrated one-pot process for enzyme production followed by hydrolysis in stirred tank bioreactors resulted in hydrolysates with overall sugar concentrations of 32.3 g L⁻¹ and 24.4 g L⁻¹ at a 25 L and a 1000 L scale, respectively, within 86 h. Furthermore, the residual solid biomass consisting of fermented wheat bran with protein-rich fungal mycelium displays improved nutritional properties for usage as animal feed due to its increased content of sugars, protein, and fat. Full article

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

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24 pages, 978 KiB

Open AccessEditor’s ChoiceReview

Challenges for the Post-Market Environmental Monitoring in the European Union Imposed by Novel Applications of Genetically Modified and Genome-Edited Organisms

by Marion Dolezel, Andreas Lang, Anita Greiter, Marianne Miklau, Michael Eckerstorfer, Andreas Heissenberger, Eva Willée and Wiebke Züghart

BioTech 2024, 13(2), 14; https://doi.org/10.3390/biotech13020014 - 15 May 2024

Cited by 4 | Viewed by 3794

Abstract

Information on the state of the environment is important to achieve the objectives of the European Green Deal, including the EU’s Biodiversity Strategy for 2030. The existing regulatory provisions for genetically modified organisms (GMOs) foresee an obligatory post-market environmental monitoring (PMEM) of potential [...] Read more.

Information on the state of the environment is important to achieve the objectives of the European Green Deal, including the EU’s Biodiversity Strategy for 2030. The existing regulatory provisions for genetically modified organisms (GMOs) foresee an obligatory post-market environmental monitoring (PMEM) of potential adverse effects upon release into the environment. So far, GMO monitoring activities have focused on genetically modified crops. With the advent of new genomic techniques (NGT), novel GMO applications are being developed and may be released into a range of different, non-agricultural environments with potential implications for ecosystems and biodiversity. This challenges the current monitoring concepts and requires adaptation of existing monitoring programs to meet monitoring requirements. While the incorporation of existing biodiversity monitoring programs into GMO monitoring at the national level is important, additional monitoring activities will also be required. Using case examples, we highlight that monitoring requirements for novel GMO applications differ from those of GM crop plants previously authorized for commercial use in the European Union. Full article

(This article belongs to the Section Environmental Biotechnology)

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24 pages, 1620 KiB

Open AccessEditor’s ChoiceReview

Proteases: Importance, Immobilization Protocols, Potential of Activated Carbon as Support, and the Importance of Modifying Supports for Immobilization

by Mateus Pereira Flores Santos, Evaldo Cardozo de Souza Junior, Carolina Villadóniga, Diego Vallés, Susana Castro-Sowinski, Renata Cristina Ferreira Bonomo and Cristiane Martins Veloso

BioTech 2024, 13(2), 13; https://doi.org/10.3390/biotech13020013 - 30 Apr 2024

Cited by 5 | Viewed by 3381

Abstract

Although enzymes have been used for thousands of years, their application in industrial processes has gained importance since the 20th century due to technological and scientific advances in several areas, including biochemistry [...] Full article

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

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26 pages, 10784 KiB

Open AccessEditor’s ChoiceReview

Synthesis and Biological Activities of Some Metal Complexes of Peptides: A Review

by Petja Marinova and Kristina Tamahkyarova

BioTech 2024, 13(2), 9; https://doi.org/10.3390/biotech13020009 - 8 Apr 2024

Cited by 6 | Viewed by 4003

Abstract

Peptides, both natural and synthetic, are well suited for a wide range of purposes and offer versatile applications in different fields such as biocatalysts, injectable hydrogels, tumor treatment, and drug delivery. The research of the better part of the cited papers was conducted [...] Read more.

Peptides, both natural and synthetic, are well suited for a wide range of purposes and offer versatile applications in different fields such as biocatalysts, injectable hydrogels, tumor treatment, and drug delivery. The research of the better part of the cited papers was conducted using various database platforms such as MetalPDB. The rising prominence of therapeutic peptides encompasses anticancer, antiviral, antimicrobial, and anti-neurodegenerative properties. The metals Na, K, Mg, Ca, Fe, Mn, Co, Cu, Zn, and Mo are ten of the twenty elements that are considered essential for life. Crucial for understanding the biological role of metals is the exploration of metal-bound proteins and peptides. Aside from essential metals, there are other non-essential metals that also interact biologically, exhibiting either therapeutic or toxic effects. Irregularities in metal binding contribute to diseases like Alzheimer’s, neurodegenerative disorders, Wilson’s, and Menkes disease. Certain metal complexes have potential applications as radiopharmaceuticals. The examination of these complexes was achieved by preforming UV–Vis, IR, EPR, NMR spectroscopy, and X-ray analysis. This summary, although unable to cover all of the studies in the field, offers a review of the ongoing experimentation and is a basis for new ideas, as well as strategies to explore and gain knowledge from the extensive realm of peptide-chelated metals and biotechnologies. Full article

(This article belongs to the Section Medical Biotechnology)

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14 pages, 7442 KiB

Open AccessEditor’s ChoiceArticle

Optimization of Aqueous Extraction of Polyphenols from Cuminum cyminum Seeds Using Response Surface Methodology and Assessment of Biological Activity

by Hana El Tannir, Diana Houhou, Espérance Debs, Mohamed Koubaa, Adla Jammoul, Bilal Azakir, Mahmoud I. Khalil, Nada El Darra and Nicolas Louka

BioTech 2024, 13(1), 7; https://doi.org/10.3390/biotech13010007 - 21 Mar 2024

Cited by 7 | Viewed by 3011

Abstract

(1) Background: Cumin seeds, extracted from the plant Cuminum cyminum, are abundant in phenolic compounds and have been extensively researched for their chemical makeup and biological effects. The objective of this research is to enhance the water extraction of polyphenols through the [...] Read more.

(1) Background: Cumin seeds, extracted from the plant Cuminum cyminum, are abundant in phenolic compounds and have been extensively researched for their chemical makeup and biological effects. The objective of this research is to enhance the water extraction of polyphenols through the water bath (WB) technique and to evaluate the antiradical, antibacterial, and anticancer effects of the extract. (2) Methods: Response Surface Methodology was used to find the best parameters to extract polyphenols. Three experimental parameters, time, temperature, and solid-liquid ratio, were tested. The disc diffusion method has been used to determine the antimicrobial activities against Salmonella Typhimurium, Pseudomonas aeruginosa, Escherichia coli, Staphylococcus aureus, and Candida albicans. The antiradical activity was performed using the DPPH method, while total phenolic content was performed using Folin–Ciocalteu. High-Performance Liquid Chromatography (HPLC) was conducted to analyze the phytochemical profile of WB extracts. The anticancer activity of the lyophilized extract was assessed against three cancer cell lines (colon (HT29), lung (A549), and breast (MCF7) cancer cell lines).; (3) Results: The optimal conditions for water extraction were 130 min at 72 °C. The total phenolic compounds yield (14.7 mg GAE/g DM) and antioxidant activity (0.52 mg trolox eq./mL) were obtained using a 1:40 solid–liquid ratio. The primary polyphenols identified were the flavonoids rutin (0.1 ppm) and ellagic acid (3.78 ppm). The extract had no antibacterial or antifungal activities against the microorganisms tested. The extract showed anticancer activity of about 98% against MCF7 (breast cancer cell line), about 81% against HT29 (colon cancer cell line), and 85% against A549 (lung cancer cell line) at high doses. (4) Conclusions: Extraction time and a high solid–liquid ratio had a positive impact on polyphenol recovery and in maintaining their quantity and quality. Furthermore, the optimal aqueous extract exhibited strong antiradical activity reflected by the inhibition of free radicals in addition to a significant specificity against the tested cancer cell lines. Full article

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11 pages, 1824 KiB

Open AccessEditor’s ChoiceArticle

Effect of Chitosan Degradation Products, Glucosamine and Chitosan Oligosaccharide, on Osteoclastic Differentiation

by Tomoharu Takeuchi, Midori Oyama and Tomomi Hatanaka

BioTech 2024, 13(1), 6; https://doi.org/10.3390/biotech13010006 - 6 Mar 2024

Cited by 3 | Viewed by 2330

Abstract

Chitosan, a natural cationic polysaccharide derived from crustaceans and shellfish shells, is known for its advantageous biological properties, including biodegradability, biocompatibility, and antibacterial activity. Chitosan and its composite materials are studied for their potential for bone tissue repair. However, the effects of chitosan [...] Read more.

Chitosan, a natural cationic polysaccharide derived from crustaceans and shellfish shells, is known for its advantageous biological properties, including biodegradability, biocompatibility, and antibacterial activity. Chitosan and its composite materials are studied for their potential for bone tissue repair. However, the effects of chitosan degradation products, glucosamine (GlcN) and chitosan oligosaccharide (COS), on osteoclasts remain unclear. If these chitosan degradation products promote osteoclastic differentiation, careful consideration is required for the use of chitosan and related materials in bone repair applications. Here, we assessed the effects of high (500 μg/mL) and low (0.5 μg/mL) concentrations of GlcN and COS on osteoclastic differentiation in human peripheral blood mononuclear cells (PBMCs) and murine macrophage-like RAW264 cells. A tartrate-resistant acid phosphatase (TRAP) enzyme activity assay, TRAP staining, and actin staining were used to assess osteoclastic differentiation. High concentrations of GlcN and COS, but not low concentrations, suppressed macrophage colony-stimulating factor (M-CSF)- and RANKL-dependent increases in TRAP enzyme activity, TRAP-positive multinuclear osteoclast formation, and actin ring formation in PBMCs without cytotoxicity. Similar effects were observed in the RANKL-dependent osteoclastic differentiation of RAW264 cells. In conclusion, chitosan degradation products do not possess osteoclast-inducing properties, suggesting that chitosan and its composite materials can be safely used for bone tissue repair. Full article

(This article belongs to the Section Medical Biotechnology)

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31 pages, 9703 KiB

Open AccessEditor’s ChoiceArticle

Expression and Purification of Cp3GT: Structural Analysis and Modeling of a Key Plant Flavonol-3-O Glucosyltransferase from Citrus paradisi

by Aaron S. Birchfield and Cecilia A. McIntosh

BioTech 2024, 13(1), 4; https://doi.org/10.3390/biotech13010004 - 7 Feb 2024

Cited by 3 | Viewed by 2209

Abstract

Glycosyltransferases (GTs) are pivotal enzymes in the biosynthesis of various biological molecules. This study focuses on the scale-up, expression, and purification of a plant flavonol-specific 3-O glucosyltransferase (Cp3GT), a key enzyme from Citrus paradisi, for structural analysis and modeling. The challenges associated [...] Read more.

Glycosyltransferases (GTs) are pivotal enzymes in the biosynthesis of various biological molecules. This study focuses on the scale-up, expression, and purification of a plant flavonol-specific 3-O glucosyltransferase (Cp3GT), a key enzyme from Citrus paradisi, for structural analysis and modeling. The challenges associated with recombinant protein production in Pichia pastoris, such as proteolytic degradation, were addressed through the optimization of culture conditions and purification processes. The purification strategy employed affinity, anion exchange, and size exclusion chromatography, leading to greater than 95% homogeneity for Cp3GT. In silico modeling, using D-I-TASSER and COFACTOR integrated with the AlphaFold2 pipeline, provided insights into the structural dynamics of Cp3GT and its ligand binding sites, offering predictions for enzyme–substrate interactions. These models were compared to experimentally derived structures, enhancing understanding of the enzyme’s functional mechanisms. The findings present a comprehensive approach to produce a highly purified Cp3GT which is suitable for crystallographic studies and to shed light on the structural basis of flavonol specificity in plant GTs. The significant implications of these results for synthetic biology and enzyme engineering in pharmaceutical applications are also considered. Full article

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12 pages, 932 KiB

Open AccessEditor’s ChoiceReview

Exploring DNA Damage and Repair Mechanisms: A Review with Computational Insights

by Jiawei Chen, Ravi Potlapalli, Heng Quan, Lingtao Chen, Ying Xie, Seyedamin Pouriyeh, Nazmus Sakib, Lichao Liu and Yixin Xie

BioTech 2024, 13(1), 3; https://doi.org/10.3390/biotech13010003 - 16 Jan 2024

Cited by 11 | Viewed by 15884

Abstract

DNA damage is a critical factor contributing to genetic alterations, directly affecting human health, including developing diseases such as cancer and age-related disorders. DNA repair mechanisms play a pivotal role in safeguarding genetic integrity and preventing the onset of these ailments. Over the [...] Read more.

DNA damage is a critical factor contributing to genetic alterations, directly affecting human health, including developing diseases such as cancer and age-related disorders. DNA repair mechanisms play a pivotal role in safeguarding genetic integrity and preventing the onset of these ailments. Over the past decade, substantial progress and pivotal discoveries have been achieved in DNA damage and repair. This comprehensive review paper consolidates research efforts, focusing on DNA repair mechanisms, computational research methods, and associated databases. Our work is a valuable resource for scientists and researchers engaged in computational DNA research, offering the latest insights into DNA-related proteins, diseases, and cutting-edge methodologies. The review addresses key questions, including the major types of DNA damage, common DNA repair mechanisms, the availability of reliable databases for DNA damage and associated diseases, and the predominant computational research methods for enzymes involved in DNA damage and repair. Full article

(This article belongs to the Topic Advances in Bioinformatics and Computational Biology of Human Disease)

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12 pages, 2031 KiB

Open AccessEditor’s ChoiceArticle

Styrene Production in Genetically Engineered Escherichia coli in a Two-Phase Culture

by Shuhei Noda, Ryosuke Fujiwara, Yutaro Mori, Mayumi Dainin, Tomokazu Shirai and Akihiko Kondo

BioTech 2024, 13(1), 2; https://doi.org/10.3390/biotech13010002 - 14 Jan 2024

Cited by 3 | Viewed by 3554

Abstract

Styrene is an important industrial chemical. Although several studies have reported microbial styrene production, the amount of styrene produced in batch cultures can be increased. In this study, styrene was produced using genetically engineered Escherichia coli. First, we evaluated five types of [...] Read more.

Styrene is an important industrial chemical. Although several studies have reported microbial styrene production, the amount of styrene produced in batch cultures can be increased. In this study, styrene was produced using genetically engineered Escherichia coli. First, we evaluated five types of phenylalanine ammonia lyases (PALs) from Arabidopsis thaliana (AtPAL) and Brachypodium distachyon (BdPAL) for their ability to produce trans-cinnamic acid (Cin), a styrene precursor. AtPAL2-expressing E. coli produced approximately 700 mg/L of Cin and we found that BdPALs could convert Cin into styrene. To assess styrene production, we constructed an E. coli strain that co-expressed AtPAL2 and ferulic acid decarboxylase from Saccharomyces cerevisiae. After a biphasic culture with oleyl alcohol, styrene production and yield from glucose were 3.1 g/L and 26.7% (mol/mol), respectively, which, to the best of our knowledge, are the highest values obtained in batch cultivation. Thus, this strain can be applied to the large–scale industrial production of styrene. Full article

(This article belongs to the Topic Microbial Biotechnology Products and Biocatalysis Processes for a Sustainable Bioeconomy)

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31 pages, 4942 KiB

Open AccessEditor’s ChoiceReview

Gene Therapy for Genetic Syndromes: Understanding the Current State to Guide Future Care

by Marian L. Henderson, Jacob K. Zieba, Xiaopeng Li, Daniel B. Campbell, Michael R. Williams, Daniel L. Vogt, Caleb P. Bupp, Yvonne M. Edgerly, Surender Rajasekaran, Nicholas L. Hartog, Jeremy W. Prokop and Jena M. Krueger

BioTech 2024, 13(1), 1; https://doi.org/10.3390/biotech13010001 - 3 Jan 2024

Cited by 17 | Viewed by 23984

Abstract

Gene therapy holds promise as a life-changing option for individuals with genetic variants that give rise to disease. FDA-approved gene therapies for Spinal Muscular Atrophy (SMA), cerebral adrenoleukodystrophy, β-Thalassemia, hemophilia A/B, retinal dystrophy, and Duchenne Muscular Dystrophy have generated buzz around the ability [...] Read more.

Gene therapy holds promise as a life-changing option for individuals with genetic variants that give rise to disease. FDA-approved gene therapies for Spinal Muscular Atrophy (SMA), cerebral adrenoleukodystrophy, β-Thalassemia, hemophilia A/B, retinal dystrophy, and Duchenne Muscular Dystrophy have generated buzz around the ability to change the course of genetic syndromes. However, this excitement risks over-expansion into areas of genetic disease that may not fit the current state of gene therapy. While in situ (targeted to an area) and ex vivo (removal of cells, delivery, and administration of cells) approaches show promise, they have a limited target ability. Broader in vivo gene therapy trials have shown various continued challenges, including immune response, use of immune suppressants correlating to secondary infections, unknown outcomes of overexpression, and challenges in driving tissue-specific corrections. Viral delivery systems can be associated with adverse outcomes such as hepatotoxicity and lethality if uncontrolled. In some cases, these risks are far outweighed by the potentially lethal syndromes for which these systems are being developed. Therefore, it is critical to evaluate the field of genetic diseases to perform cost–benefit analyses for gene therapy. In this work, we present the current state while setting forth tools and resources to guide informed directions to avoid foreseeable issues in gene therapy that could prevent the field from continued success. Full article

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

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17 pages, 3481 KiB

Open AccessEditor’s ChoiceArticle

Gibberellin-Producing Bacteria Isolated from Coastal Soil Enhance Seed Germination of Mallow and Broccoli Plants under Saline Conditions

by Ji-In Woo, Md. Injamum-Ul-Hoque, Nazree Zainurin, Shifa Shaffique, Eun-Hae Kwon, Ho-Jun Gam, Jin Ryeol Jeon, In-Jung Lee, Gil-Jae Joo and Sang-Mo Kang

BioTech 2023, 12(4), 66; https://doi.org/10.3390/biotech12040066 - 11 Dec 2023

Cited by 6 | Viewed by 4249

Abstract

Salinity hinders plant growth, posing a substantial challenge to sustainable agricultural yield maintenance. The application of plant growth-promoting rhizobacteria (PGPR) offers an emerging strategy to mitigate the detrimental effects of high salinity levels. This study aimed to isolate and identify gibberellin-producing bacteria and [...] Read more.

Salinity hinders plant growth, posing a substantial challenge to sustainable agricultural yield maintenance. The application of plant growth-promoting rhizobacteria (PGPR) offers an emerging strategy to mitigate the detrimental effects of high salinity levels. This study aimed to isolate and identify gibberellin-producing bacteria and their impact on the seed germination of Malva verticillata (mallow) and Brassica oleracea var. italica (broccoli) under salt stress. In this study, seven bacterial isolates (KW01, KW02, KW03, KW04, KW05, KW06, and KW07) were used to assess their capacity for producing various growth-promoting traits and their tolerance to varying amounts of salinity (100 mM and 150 Mm NaCl). The findings revealed that KW05 and KW07 isolates outperformed other isolates in synthesizing indole-3-acetic acid, siderophores, and exopolysaccharides and in solubilizing phosphates. These isolates also enhanced phosphatase activity and antioxidant levels, including superoxide dismutase and catalase. Both KW05 and KW07 isolate highlight the growth-promoting effects of gibberellin by enhancing of growth parameters of Waito-C rice. Further, gas chromatography–mass spectrometry validation confirmed the ability of KW05 and KW07 to produce gibberellins (GAs), including GA₁, GA₃, GA₄, and GA₇. Seed germination metrics were enhanced due to the inoculation of KW05 and KW07. Moreover, inoculation with KW05 increased the fresh weight (FW) (7.82%) and total length (38.61%) of mallow under salt stress. Inoculation with KW07 increased the FW (32.04%) and shoot length of mallow under salt stress. A single inoculation of these two isolates increased broccoli plants’ FW and shoot length under salt stress. Gibberellin-producing bacteria helps in plant growth promotion by improving salt tolerance by stimulating root elongation and facilitating enhanced absorption of water and nutrient uptake in salty environments. Based on these findings, they can play a role in boosting agricultural yield in salt-affected areas, which would help to ensure the long-term viability of agriculture in coastal regions. Full article

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

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11 pages, 571 KiB

Open AccessEditor’s ChoiceArticle

Detection and Characterization of Electrogenic Bacteria from Soils

by Ana Rumora, Liliana Hopkins, Kayla Yim, Melissa F. Baykus, Luisa Martinez and Luis Jimenez

BioTech 2023, 12(4), 65; https://doi.org/10.3390/biotech12040065 - 2 Dec 2023

Cited by 4 | Viewed by 4059

Abstract

Soil microbial fuel cells (SMFCs) are bioelectrical devices powered by the oxidation of organic and inorganic compounds due to microbial activity. Seven soils were randomly selected from Bergen Community College or areas nearby, located in the state of New Jersey, USA, were used [...] Read more.

Soil microbial fuel cells (SMFCs) are bioelectrical devices powered by the oxidation of organic and inorganic compounds due to microbial activity. Seven soils were randomly selected from Bergen Community College or areas nearby, located in the state of New Jersey, USA, were used to screen for the presence of electrogenic bacteria. SMFCs were incubated at 35–37 °C. Electricity generation and electrogenic bacteria were determined using an application developed for cellular phones. Of the seven samples, five generated electricity and enriched electrogenic bacteria. Average electrical output for the seven SMFCs was 155 microwatts with the start-up time ranging from 1 to 11 days. The highest output and electrogenic bacterial numbers were found with SMFC-B1 with 143 microwatts and 2.99 × 10⁹ electrogenic bacteria after 15 days. Optimal electrical output and electrogenic bacterial numbers ranged from 1 to 21 days. Microbial DNA was extracted from the top and bottom of the anode of SMFC-B1 using the ZR Soil Microbe DNA MiniPrep Protocol followed by PCR amplification of 16S rRNA V3-V4 region. Next-generation sequencing of 16S rRNA genes generated an average of 58 k sequences. BLAST analysis of the anode bacterial community in SMFC-B1 demonstrated that the predominant bacterial phylum was Bacillota of the class Clostridia (50%). However, bacteria belonging to the phylum Pseudomonadota (15%) such as Magnetospirillum sp. and Methylocaldum gracile were also part of the predominant electrogenic bacterial community in the anode. Unidentified uncultured bacteria accounted for 35% of the predominant bacterial community. Bioelectrical devices such as MFCs provide sustainable and clean alternatives to future applications for electricity generation, waste treatment, and biosensors. Full article

(This article belongs to the Topic Microbial Biotechnology Products and Biocatalysis Processes for a Sustainable Bioeconomy)

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24 pages, 4054 KiB

Open AccessEditor’s ChoiceReview

Fungicide Resistance in Botrytis spp. and Regional Strategies for Its Management in Northern European Strawberry Production

by Roland W. S. Weber and Antonios Petridis

BioTech 2023, 12(4), 64; https://doi.org/10.3390/biotech12040064 - 19 Nov 2023

Cited by 9 | Viewed by 3341

Abstract

Grey mould, caused by Botrytis cinerea and other Botrytis spp., is a major cause of fruit rot in strawberries and other fruit crops worldwide. Repeated fungicide applications are essential in order to secure harvests. However, resistance to all currently registered single-site fungicides is [...] Read more.

Grey mould, caused by Botrytis cinerea and other Botrytis spp., is a major cause of fruit rot in strawberries and other fruit crops worldwide. Repeated fungicide applications are essential in order to secure harvests. However, resistance to all currently registered single-site fungicides is widespread. The rising importance of strains with multiple resistance to most or all fungicides is of particular concern. These strains may be introduced into fields via contaminated nursery plants and/or by immigration from adjacent plots. On the basis of research conducted in northern German and Danish strawberry production, a concept to manage fungicide resistance under northern European conditions has been developed and put into regional strawberry production practice. This principally includes the testing of nursery plants for fungicide-resistant Botrytis strains prior to planting; the restricted and specific use of fungicides at flowering in the production fields, taking account of the resistance spectrum within the local Botrytis population; and crop sanitation measures such as the removal of rotting fruits at the beginning of harvest. Further options such as protected cultivation, reduced fertilisation and biological control are also discussed. The practical implementation of such a strategy in northern Germany and Denmark has been shown to reduce the occurrence of multi-resistant strains to a tolerable steady-state level. Full article

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14 pages, 381 KiB

Open AccessEditor’s ChoiceReview

The Controversial Nature of Some Non-Starter Lactic Acid Bacteria Actively Participating in Cheese Ripening

by Svetoslav G. Dimov

BioTech 2023, 12(4), 63; https://doi.org/10.3390/biotech12040063 - 9 Nov 2023

Cited by 6 | Viewed by 2904

Abstract

This mini review deals with some controversial non-starter lactic acid bacteria (NSLAB) species known to be both human and animal pathogens but also health-promoting and probiotic. The focus is on Lactococcus garvieae, two Streptococcus species (S. uberis and S. parauberis), [...] Read more.

This mini review deals with some controversial non-starter lactic acid bacteria (NSLAB) species known to be both human and animal pathogens but also health-promoting and probiotic. The focus is on Lactococcus garvieae, two Streptococcus species (S. uberis and S. parauberis), four Weissella species (W. hellenica, W. confusa, W. paramesenteroides, and W. cibaria), and Mammalicoccus sciuri, which worldwide, are often found within the microbiotas of different kinds of cheese, mainly traditional artisanal cheeses made from raw milk and/or relying on environmental bacteria for their ripening. Based on literature data, the virulence and health-promoting effects of these bacteria are examined, and some of the mechanisms of these actions are reviewed. Additionally, their possible roles in cheese ripening are also discussed. The analysis of the literature data available so far showed that, in general, the pathogenic and the beneficial strains, despite belonging to the same species, show somewhat different genetic constitutions. Yet, when the safety of a given strain is assessed, genomic analysis on its own is not enough, and a polyphasic approach including additional physiological and functional tests is needed. Full article

11 pages, 1436 KiB

Open AccessEditor’s ChoiceArticle

Assessing Curcumin Uptake and Clearance and Their Influence on Superoxide Dismutase Activity in Drosophila melanogaster

by Tammy R. Hoffman, Sarah A. Emsley, Jenna C. Douglas, Kaela R. Reed, Abigail R. Esquivel, Marc J. Koyack, Brie E. Paddock and Patrick Videau

BioTech 2023, 12(3), 58; https://doi.org/10.3390/biotech12030058 - 8 Sep 2023

Cited by 3 | Viewed by 2835

Abstract

While normal levels of reactive oxygen and nitrogen species (RONS) are required for proper organismal function, increased levels result in oxidative stress. Oxidative stress may be managed via the scavenging activities of antioxidants (e.g., curcumin) and the action of enzymes, including superoxide dismutase [...] Read more.

While normal levels of reactive oxygen and nitrogen species (RONS) are required for proper organismal function, increased levels result in oxidative stress. Oxidative stress may be managed via the scavenging activities of antioxidants (e.g., curcumin) and the action of enzymes, including superoxide dismutase (SOD). In this work, the uptake and clearance of dietary curcuminoids (consisting of curcumin, demethoxycurcumin, and bisdemethoxycurcumin) was assessed in Drosophila melanogaster larvae following chronic or acute exposure. High levels of curcuminoid uptake and loss were observed within a few hours and leveled off within eight hours post treatment onset. The addition or removal of curcuminoids from media resulted in corresponding changes in SOD activity, and the involvement of each of the three SOD genes was assessed for their contribution to total SOD activity. Taken together, these data provide insight into the uptake and clearance dynamics of curcuminoids and indicate that, while SOD activity generally increases following curcuminoid treatment, the individual SOD genes appear to contribute differently to this response. Full article

(This article belongs to the Special Issue Natural Antioxidants: Determination in Food and Nutraceuticals and Implications on Human Health)

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14 pages, 1419 KiB

Open AccessEditor’s ChoiceArticle

Characterization of Enzyme-Linked Immunosorbent Assay (ELISA) for Quantification of Antibodies against Salmonella Typhimurium and Salmonella Enteritidis O-Antigens in Human Sera

by Maria Grazia Aruta, Elisa Lari, Daniele De Simone, Bianca Semplici, Claudia Semplici, Helen Dale, Esmelda Chirwa, Innocent Kadwala, Maurice Mbewe, Happy Banda, Miren Iturriza-Gomara, Melita Gordon, Tonney Nyirenda, Pietro Piu, Mariagrazia Pizza, Francesco Berlanda Scorza, Silvia Grappi, Rocío Canals, Omar Rossi and on behalf of the Vacc-iNTS Consortium Collaborators

BioTech 2023, 12(3), 54; https://doi.org/10.3390/biotech12030054 - 11 Aug 2023

Cited by 8 | Viewed by 5281

Abstract

Nontyphoidal Salmonella (NTS) is a leading cause of morbidity and mortality caused by enteric pathogens worldwide in both children and adults, and vaccines are not yet available. The measurement of antigen-specific antibodies in the sera of vaccinated or convalescent individuals is crucial to [...] Read more.

Nontyphoidal Salmonella (NTS) is a leading cause of morbidity and mortality caused by enteric pathogens worldwide in both children and adults, and vaccines are not yet available. The measurement of antigen-specific antibodies in the sera of vaccinated or convalescent individuals is crucial to understand the incidence of disease and the immunogenicity of vaccine candidates. A solid and standardized assay used to determine the level of specific anti-antigens IgG is therefore of paramount importance. In this work, we presented the characterization of a customized enzyme-linked immunosorbent assay (ELISA) with continuous readouts and a standardized definition of EU/mL. We assessed various performance parameters: standard curve accuracy, dilutional linearity, intermediate precision, specificity, limits of blanks, and quantification. The simplicity of the assay, its high sensitivity and specificity coupled with its low cost and the use of basic consumables and instruments without the need of high automation makes it suitable for transfer and application to different laboratories, including resource-limiting settings where the disease is endemic. This ELISA is, therefore, fit for purpose to be used for quantification of antibodies against Salmonella Typhimurium and Salmonella Enteritidis O-antigens in human samples, both for vaccine clinical trials and large sero-epidemiological studies. Full article

(This article belongs to the Section Medical Biotechnology)

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16 pages, 1241 KiB

Open AccessEditor’s ChoiceArticle

Co-Producing Phycocyanin and Bioplastic in Arthrospira platensis Using Carbon-Rich Wastewater

by Hajar Shayesteh, Damian W. Laird, Leonie J. Hughes, Mohammad A. Nematollahi, Amin Mirshamsi Kakhki and Navid R. Moheimani

BioTech 2023, 12(3), 49; https://doi.org/10.3390/biotech12030049 - 3 Jul 2023

Cited by 10 | Viewed by 4132

Abstract

Microalgae can treat waste streams containing elevated levels of organic carbon and nitrogen. This process can be economically attractive if high value products are created simultaneously from the relatively low-cost waste stream. Co-production of two high value microalgal products, phycocyanin and polyhydroxybutyrate (PHB), [...] Read more.

Microalgae can treat waste streams containing elevated levels of organic carbon and nitrogen. This process can be economically attractive if high value products are created simultaneously from the relatively low-cost waste stream. Co-production of two high value microalgal products, phycocyanin and polyhydroxybutyrate (PHB), was investigated using non-axenic Arthrospira platensis MUR126 and supplemental organic carbon (acetate, oxalate, glycerol and combinations). All supplemented cultures had higher biomass yield (g/L) than photoautotrophic control. All cultures produced PHB (3.6–7.8% w/w), except the control and those fed oxalate. Supplemented cultures showed a two to three-fold increase in phycocyanin content over the eight-day cultivation. Results indicate co-production of phycocyanin and PHB is possible in A. platensis, using mixed-waste organic carbon. However, supplementation resulted in growth of extremophile bacteria, particularly in cultures fed glycerol, and this had a negative impact on culture health. Refinement of the carbon dosing rate is required to minimise impacts of native bacterial contamination. Full article

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

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20 pages, 1711 KiB

Open AccessEditor’s ChoiceReview

Ocular-Surface Regeneration Therapies for Eye Disorders: The State of the Art

by Matteo Posarelli, Davide Romano, Davide Tucci, Giuseppe Giannaccare, Vincenzo Scorcia, Andrea Taloni, Luca Pagano and Alfredo Borgia

BioTech 2023, 12(2), 48; https://doi.org/10.3390/biotech12020048 - 15 Jun 2023

Cited by 4 | Viewed by 4443

Abstract

The ocular surface is a complex structure that includes cornea, conjunctiva, limbus, and tear film, and is critical for maintaining visual function. When the ocular-surface integrity is altered by a disease, conventional therapies usually rely on topical drops or tissue replacement with more [...] Read more.

The ocular surface is a complex structure that includes cornea, conjunctiva, limbus, and tear film, and is critical for maintaining visual function. When the ocular-surface integrity is altered by a disease, conventional therapies usually rely on topical drops or tissue replacement with more invasive procedures, such as corneal transplants. However, in the last years, regeneration therapies have emerged as a promising approach to repair the damaged ocular surface by stimulating cell proliferation and restoring the eye homeostasis and function. This article reviews the different strategies employed in ocular-surface regeneration, including cell-based therapies, growth-factor-based therapies, and tissue-engineering approaches. Dry eye and neurotrophic keratopathy diseases can be treated with nerve-growth factors to stimulate the limbal stem-cell proliferation and the corneal nerve regeneration, whereas conjunctival autograft or amniotic membrane are used in subjects with corneal limbus dysfunction, such as limbal stem-cell deficiency or pterygium. Further, new therapies are available for patients with corneal endothelium diseases to promote the expansion and migration of cells without the need of corneal keratoplasty. Finally, gene therapy is a promising new frontier of regeneration medicine that can modify the gene expression and, potentially, restore the corneal transparency by reducing fibrosis and neovascularization, as well as by stimulating stem-cell proliferation and tissue regeneration. Full article

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13 pages, 910 KiB

Open AccessEditor’s ChoiceArticle

Privacy Implications of Contacting the At-Risk Relatives of Patients with Medically Actionable Genetic Predisposition, with Patient Consent: A Hypothetical Australian Case Study

by Jane Tiller, Kristen Nowak, Tiffany Boughtwood and Margaret Otlowski

BioTech 2023, 12(2), 45; https://doi.org/10.3390/biotech12020045 - 2 Jun 2023

Cited by 6 | Viewed by 3081

Abstract

Genetic risk information has relevance for patients’ blood relatives. However, cascade testing uptake in at-risk families is <50%. International research supports direct notification of at-risk relatives by health professionals (HPs), with patient consent. However, HPs express concerns about the privacy implications of this [...] Read more.

Genetic risk information has relevance for patients’ blood relatives. However, cascade testing uptake in at-risk families is <50%. International research supports direct notification of at-risk relatives by health professionals (HPs), with patient consent. However, HPs express concerns about the privacy implications of this practice. Our privacy analysis, grounded in a clinically relevant hypothetical scenario, considers the types of personal information involved in direct notification of at-risk relatives and the application of Australian privacy regulations. It finds that collecting relatives’ contact details, and using those details (with patient consent) to notify relatives of possible genetic risk, does not breach Australian privacy law, providing that HPs adhere to regulatory requirements. It finds the purported “right to know” does not prevent disclosure of genetic information to at-risk relatives. Finally, the analysis confirms that the discretion available to HPs does not equate to a positive duty to warn at-risk relatives. Thus, direct notification of a patient’s at-risk relatives regarding medically actionable genetic information, with patient consent, is not a breach of Australian privacy regulations, providing it is conducted in accordance with the applicable principles set out. Clinical services should consider offering this service to patients where appropriate. National guidelines would assist with the clarification of the discretion for HPs. Full article

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

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17 pages, 2455 KiB

Open AccessEditor’s ChoiceReview

DNA Data Storage

by Tomasz Buko, Nella Tuczko and Takao Ishikawa

BioTech 2023, 12(2), 44; https://doi.org/10.3390/biotech12020044 - 1 Jun 2023

Cited by 6 | Viewed by 9709

Abstract

The demand for data storage is growing at an unprecedented rate, and current methods are not sufficient to accommodate such rapid growth due to their cost, space requirements, and energy consumption. Therefore, there is a need for a new, long-lasting data storage medium [...] Read more.

The demand for data storage is growing at an unprecedented rate, and current methods are not sufficient to accommodate such rapid growth due to their cost, space requirements, and energy consumption. Therefore, there is a need for a new, long-lasting data storage medium with high capacity, high data density, and high durability against extreme conditions. DNA is one of the most promising next-generation data carriers, with a storage density of 10¹⁹ bits of data per cubic centimeter, and its three-dimensional structure makes it about eight orders of magnitude denser than other storage media. DNA amplification during PCR or replication during cell proliferation enables the quick and inexpensive copying of vast amounts of data. In addition, DNA can possibly endure millions of years if stored in optimal conditions and dehydrated, making it useful for data storage. Numerous space experiments on microorganisms have also proven their extraordinary durability in extreme conditions, which suggests that DNA could be a durable storage medium for data. Despite some remaining challenges, such as the need to refine methods for the fast and error-free synthesis of oligonucleotides, DNA is a promising candidate for future data storage. Full article

(This article belongs to the Topic Computational Intelligence and Bioinformatics (CIB))

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20 pages, 1246 KiB

Open AccessEditor’s ChoiceReview

Trends in Biological Ammonia Production

by Adewale Adeniyi, Ibrahim Bello, Taofeek Mukaila, Niloy Chandra Sarker and Ademola Hammed

BioTech 2023, 12(2), 41; https://doi.org/10.3390/biotech12020041 - 19 May 2023

Cited by 20 | Viewed by 10520

Abstract

Food production heavily depends on ammonia-containing fertilizers to improve crop yield and profitability. However, ammonia production is challenged by huge energy demands and the release of ~2% of global CO₂. To mitigate this challenge, many research efforts have been made to [...] Read more.

Food production heavily depends on ammonia-containing fertilizers to improve crop yield and profitability. However, ammonia production is challenged by huge energy demands and the release of ~2% of global CO₂. To mitigate this challenge, many research efforts have been made to develop bioprocessing technologies to make biological ammonia. This review presents three different biological approaches that drive the biochemical mechanisms to convert nitrogen gas, bioresources, or waste to bio-ammonia. The use of advanced technologies—enzyme immobilization and microbial bioengineering—enhanced bio-ammonia production. This review also highlighted some challenges and research gaps that require researchers’ attention for bio-ammonia to be industrially pragmatic. Full article

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

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23 pages, 1493 KiB

Open AccessEditor’s ChoiceReview

Recent Developments in Protein Lactylation in PTSD and CVD: Novel Strategies and Targets

by Zisis Kozlakidis, Patricia Shi, Ganna Abarbanel, Carolina Klein and Adonis Sfera

BioTech 2023, 12(2), 38; https://doi.org/10.3390/biotech12020038 - 15 May 2023

Cited by 3 | Viewed by 5637

Abstract

In 1938, Corneille Heymans received the Nobel Prize in physiology for discovering that oxygen sensing in the aortic arch and carotid sinus was mediated by the nervous system. The genetics of this process remained unclear until 1991 when Gregg Semenza while studying erythropoietin, [...] Read more.

In 1938, Corneille Heymans received the Nobel Prize in physiology for discovering that oxygen sensing in the aortic arch and carotid sinus was mediated by the nervous system. The genetics of this process remained unclear until 1991 when Gregg Semenza while studying erythropoietin, came upon hypoxia-inducible factor 1, for which he obtained the Nobel Prize in 2019. The same year, Yingming Zhao found protein lactylation, a posttranslational modification that can alter the function of hypoxia-inducible factor 1, the master regulator of cellular senescence, a pathology implicated in both post-traumatic stress disorder (PTSD) and cardiovascular disease (CVD). The genetic correlation between PTSD and CVD has been demonstrated by many studies, of which the most recent one utilizes large-scale genetics to estimate the risk factors for these conditions. This study focuses on the role of hypertension and dysfunctional interleukin 7 in PTSD and CVD, the former caused by stress-induced sympathetic arousal and elevated angiotensin II, while the latter links stress to premature endothelial cell senescence and early vascular aging. This review summarizes the recent developments and highlights several novel PTSD and CVD pharmacological targets. They include lactylation of histone and non-histone proteins, along with the related biomolecular actors such as hypoxia-inducible factor 1α, erythropoietin, acid-sensing ion channels, basigin, and Interleukin 7, as well as strategies to delay premature cellular senescence by telomere lengthening and resetting the epigenetic clock. Full article

(This article belongs to the Section Medical Biotechnology)

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14 pages, 1247 KiB

Open AccessEditor’s ChoiceReview

Bioremediation of Organic Pollutants in Soil–Water System: A Review

by Pankaj Kumar Gupta and Manvi Gandhi

BioTech 2023, 12(2), 36; https://doi.org/10.3390/biotech12020036 - 11 May 2023

Cited by 15 | Viewed by 7130

Abstract

Soil–water pollution is of serious concern worldwide. There is a public outcry against the continually rising problems of pollution to ensure the safest and healthiest subsurface environment for living beings. A variety of organic pollutants causes serious soil–water pollution, toxicity and, therefore, the [...] Read more.

Soil–water pollution is of serious concern worldwide. There is a public outcry against the continually rising problems of pollution to ensure the safest and healthiest subsurface environment for living beings. A variety of organic pollutants causes serious soil–water pollution, toxicity and, therefore, the removal of a wide range of organic pollutants from contaminated matrix through the biological process rather than physico-chemical methods is an urgent need to protect the environment and public health. Being an ecofriendly technology, bioremediation can solve the problems of soil–water pollution due to hydrocarbons as it is a low-cost and self-driven process that utilises microorganisms and plants or their enzymes to degrade and detoxify pollutants and thus, promote sustainable development. This paper describes the updates on the bioremediation and phytoremediation techniques which have been recently developed and demonstrated at the plot-scale. Further, this paper provides details of wetland-based treatment of BTEX contaminated soils and water. The knowledge acquired in our study contributes extensively towards understanding the impact of dynamic subsurface conditions on engineered bioremediation techniques. Full article

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7 pages, 1127 KiB

Open AccessEditor’s ChoiceCommunication

Development of the Follow-Up Human 3D Oral Cancer Model in Cancer Treatment

by Kazuyo Igawa, Kenji Izumi and Yoshinori Sakurai

BioTech 2023, 12(2), 35; https://doi.org/10.3390/biotech12020035 - 11 May 2023

Cited by 4 | Viewed by 2987

Abstract

As function preservation cancer therapy, targeted radiation therapies have been developed for the quality of life of cancer patients. However, preclinical animal studies evaluating the safety and efficacy of targeted radiation therapy is challenging from the viewpoints of animal welfare and animal protection, [...] Read more.

As function preservation cancer therapy, targeted radiation therapies have been developed for the quality of life of cancer patients. However, preclinical animal studies evaluating the safety and efficacy of targeted radiation therapy is challenging from the viewpoints of animal welfare and animal protection, as well as the management of animal in radiation-controlled areas under the regulations. We fabricated the human 3D oral cancer model that considers the time axis of the follow up in cancer treatment. Therefore, in this study, the 3D model with human oral cancer cells and normal oral fibroblasts was treated based on clinical protocol. After cancer treatment, the histological findings of the 3D oral cancer model indicated the clinical correlation between tumor response and surrounding normal tissue. This 3D model has potential as a tool for preclinical studies alternative to animal studies. Full article

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

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18 pages, 4442 KiB

Open AccessEditor’s ChoiceArticle

A Bacterial Myeloperoxidase with Antimicrobial Properties

by Claire Céré, Brigitte Delord, Parfait Kenfack Ymbe, Léa Vimbert, Jean-Paul Chapel and Claire Stines-Chaumeil

BioTech 2023, 12(2), 33; https://doi.org/10.3390/biotech12020033 - 5 May 2023

Cited by 4 | Viewed by 3207

Abstract

The four mammalian peroxidases (myeloperoxidase, eosinophilperoxidase, lactoperoxidase, and thyroid peroxidase) are widely studied in the literature. They catalyze the formation of antimicrobial compounds and participate in innate immunity. Owing to their properties, they are used in many biomedical, biotechnological, and agro-food applications. We [...] Read more.

The four mammalian peroxidases (myeloperoxidase, eosinophilperoxidase, lactoperoxidase, and thyroid peroxidase) are widely studied in the literature. They catalyze the formation of antimicrobial compounds and participate in innate immunity. Owing to their properties, they are used in many biomedical, biotechnological, and agro-food applications. We decided to look for an enzyme that is easiest to produce and much more stable at 37 °C than mammalian peroxidases. To address this question, a peroxidase from Rhodopirellula baltica, identified by bioinformatics tools, was fully characterized in this study. In particular, a production and purification protocol including the study of heme reconstitution was developed. Several activity tests were also performed to validate the hypothesis that this peroxidase is a new homolog of mammalian myeloperoxidase. It has the same substrate specificities as the human one and accepts I⁻, SCN⁻, Br⁻, and Cl⁻ as (pseudo-) halides. It also exhibits other auxiliary activities such as catalase and classical peroxidase activities, and it is very stable at 37 °C. Finally, this bacterial myeloperoxidase can kill the Escherichia coli strain ATCC25922, which is usually used to perform antibiograms. Full article

(This article belongs to the Section Medical Biotechnology)

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