Modern Biotechnology Research Articles

Potential Impacts of Artificial Intelligence (AI) in Biotechnology

The impact of artificial intelligence (AI) in biotechnology has become increasingly significant, driving advancements across multiple subfields in several areas of science. The demand for faster data analysis, integration of extensive databases, pattern recognition, problem solving, and even hypothesis generation has fueled the development of AI technologies in subjects like modern biotechnology, which AI has revolutionized, where the main goal is to develop new advanced products and technologies through the manipulation of biological organisms. The main impacts of AI observed in biotechnology are focused on four colors of biotechnology: green (agricultural sector); red (health sector); white (industries); and blue (marine sector). Numerous AI tools have been developed and made freely available, significantly reducing researchers’ workloads. However, the application of AI in biotechnology also raises questions that must be addressed. This review exhibits and discusses the impacts of AI on biotechnology, the advantages and disadvantages of its current presence, and the potential ethical issues and social impacts.

Upskilling the cell therapy manufacturing workforce: design, implementation, and evaluation of a massive open online course.

Cell therapies have gained prominence as a promising therapeutic modality for treating a range of diseases. Despite the recent clinical successes of cell therapy products, very few formal training programs exist for cell therapy manufacturing. To meet the demand for a well-trained workforce, we assembled a team of university researchers and industry professionals to develop an online course on the principles and practice of cell therapy manufacturing. The course covers the basic cell and systems physiology underlying cell therapy products, in addition to explaining end-to-end manufacturing from cell acquisition through to patient treatment, industrialization, and regulatory processes. As of September 2023, >10,000 learners have enrolled in the course, and >90% of respondents to the course exit survey indicated that they were "very likely" or "likely" to recommend the course to a peer. In this article, we discuss our experience in the collaborative design and implementation of the online course as well as lessons learned from quantitative and qualitative student feedback. We believe that this course can serve as a model for how academia and industry can collaborate to create innovative, scalable training programs to meet the demands of the modern biotechnology workforce.NEW & NOTEWORTHY We assembled a team of university researchers and industry professionals to develop an online course on the principles and practice of cell therapy manufacturing. We believe that this course can serve as a model for how academia and industry can collaborate to create innovative, scalable training programs to meet the demands of the modern biotechnology workforce.

Antibacterial efficacy of berry juices against Bacillus cereus relative to their phytochemical composition and antioxidant properties

Ensuring the safety and stability of minimally processed foods using natural preservatives is of great scientific and commercial interest in modern biotechnology. Berry juice supplementation is increasingly recognized within this field. This study investigated the effectiveness of juices from four berry species Aronia melanocarpa, Ribes nigrum, Vaccinium macrocarpon, and Sambucus nigra, against the food pathogen Bacillus cereus. Overall, the antibacterial potency of juice supplements (up to 10% v/v in tryptic soy broth) followed the order of chokeberry > blackcurrant > cranberry > elderberry, with the latter showing no inhibitory effects. Notably, chokeberry and elderberry juices presented lower acidity and significantly greater phenolic contents (p < 0.05) than blackcurrant and cranberry juices did, suggesting that B. cereus susceptibility is not strictly dependent upon low extracellular pH or elevated anthocyanin levels. Instead, it is inferred to correlate with pro-oxidative effects induced directly at the intracellular level. Accordingly, this paper discusses the antioxidative, acidic, and lipophilic attributes of juices and their constituent fractions, including anthocyanins, to elucidate their biopreservative potential. The results of this study increase our understanding of the antibacterial susceptibility of B. cereus.

Latin America: A hub for agrobiotechnological innovations.

Modern biotechnology is one of the last century's major advances in human science. Particularly in the agronomical field, the landscape of crop improvement technologies has witnessed a great expansion, driven by the integration of molecular and genetic engineering methodologies into the breeding toolbox. Latin America (LATAM) serves as a pioneering region in incorporating such techniques with several countries swiftly embracing these technologies. This review aims to give a comprehensive overview of the elements that influenced agrobiotech acceptance in LATAM countries and how such cases could provide support for upcoming technologies to be considered worldwide. Nearly 50 years of biotech breakthroughs have provided humankind with an impressive portfolio of tools already integrated into several life-sciences areas. The agronomical field has greatly progressed thanks to technologies derived from Genetically Modified Organisms (GMOs) and high promises are being made to also incorporate genome -editing products. LATAM's case is a prime example of how early introduction of novelties in the crop production chain can result in improved yields, paving the way for future developments to be easily integrated into the technological ecosystem of a region. The example set by LATAM can also be useful for the present gene-editing regulatory scenario. With several countries presently on the path to approving these methods in their current crop systems, basing their next steps on the southern continent's example, could represent a safe and practical pathway towards a new agronomical revolution.

Link Between Individual Codon Frequencies and Protein Expression: Going Beyond Codon Adaptation Index.

An important role of a particular synonymous codon composition of a gene in its expression level is well known. There are a number of algorithms optimizing codon usage of recombinant genes to maximize their expression in host cells. Nevertheless, the underlying mechanism remains unsolved and is of significant relevance. In the realm of modern biotechnology, directing protein production to a specific level is crucial for metabolic engineering, genome rewriting and a growing number of other applications. In this study, we propose two new simple statistical and empirical methods for predicting the protein expression level from the nucleotide sequence of the corresponding gene: Codon Expression Index Score (CEIS) and Codon Productivity Score (CPS). Both of these methods are based on the influence of each individual codon in the gene on the overall expression level of the encoded protein and the frequencies of isoacceptors in the species. Our predictions achieve a correlation level of up to r = 0.7 with experimentally measured quantitative proteome data of Escherichia coli, which is superior to any previously proposed methods. Our work helps understand how codons determine protein abundances. Based on these methods, it is possible to design proteins optimized for expression in a particular organism.

Obtaining and Characterizing Thermostable α-Amylases Secreted by Bacillus subtilis, Originating from Bacillus amyloliquefaciens and Bacillus subtilis

The production of recombinant enzymes, primarily used for obtaining pure and functional target molecules, holds significant importance in modern biotechnology. This study aimed to obtain and characterize recombinant, extracellularly expressed α-amylases (Amy3500 and Amy1974), derived from B. amyloliquefaciens MDC1974 and B. subtilis MDC3500, respectively, using the pBE-S shuttle vector. Both α-amylase genes were molecularly cloned into the E. coli/B. subtilis pBE-S shuttle vector, both with (Amy1974sig and Amy3500sig) and without their signal peptides (Amy1974 and Amy3500), along with a signal peptide originating from the plasmid, and tested in flask fermentations. For recombinant Amy3500, the amylase variants resulted in similar levels of volumetric activity (700–750 U/mL). In contrast, the expression of Amy1974 nearly doubled compared to Amy1974sig with double signal peptides, reaching 2000 U/mL. SDS-PAGE estimated the molecular weight of Amy1974 α-amylase to be 54.6 kDa, which is consistent with the theoretical molecular mass calculations. However, the estimated molecular weight of Amy3500 α-amylase was significantly lower upon exiting the producer cells. Ca2⁺ ions exhibit a modest activating effect on the activities of Amy1974 and Amy3500 amylases, likely due to their tight binding to the protein scaffold. Both enzymes exhibited broad activity peaks between 45 and 70 °C, with a maximum at 65 °C. The Amy1974 and Amy3500 α-amylases demonstrated broad pH optima and pH-dependent thermostability, with optimum pH values at 6.5 and 5.8, and thermal stability peaks at pH 7.6 and 5.9, respectively. Both α-amylases displayed high relative activity against various starches, including corn amylopectin and potato amylose, while showing comparatively lower activity towards α-, β-, and γ-cyclodextrins. The Amy1974 amylase is effective in converting starch into dextrins of varying lengths, while Amy3500 primarily converts starch into glucose. These characteristics make them promising candidate enzymes for industrial applications.

Istihalah and Its Impacts on Food According to the Islamic Perspective

Issues related to istihalah (transformation) are not only limited to matters of food and drink, but they are also concerned with the purity rulings of a human-need product in Islam. Nevertheless, this matter becomes more prevalent today when science and technology move forward swiftly with the latest diverse products. It has dramatically shifted the original form of food production through modern biotechnology methods, mixing ingredients from animal sources in food until it alters its original properties to new physical features such as cake, cultured meat, and genetically modified food. Following the realisation of the extensive mixing of halal and haram ingredients, the contemporary fatwa is being discussed among scholars in the food and beverage industry. Therefore, this research aimed to examine the process of istihalah that takes place, which can be categorised as istihalah tammah (perfect transformation) or istihalah naqisah (incomplete transformation), as well as explore the impacts on food that has gone through the process of istihalah. Next, the study also intended to examine the rulings of food that change in terms of properties, taste, smell, colour, physicality, and chemistry. The statements of fiqh scholars have been quoted and studied to address this concern. The analysis used a qualitative method by collecting sources from the Quran and Sunnah and the ijtihad of scholars obtained from reading such books as fiqh, food science, and websites. Ultimately, the study data substantiated that the process of istihalah is permissible in Islam if it is istihalah tammah and totally met. Nonetheless, deciding the halal status of a food product that has gone through istihalah is tricky because the PCR process in the laboratory needs to be done to confirm that the study results are authentic.

Fruit Wastes and Crop Residues as Nutrient Sources for Bacterial Nanocellulose Production: A Review

Nanocellulose has been developed and used as a bio-based advanced material in modern biotechnology. Lately, bacterial nanocellulose (BNC) emerged as a prominent biopolymer because of its multi-functional application in various industries, such as food, biomedical, cosmetics, and environmental. The emerging concern for large-scale BNC production is the high fermentation costs, low productivity, and expensive culture medium. To minimise this issue, agro-industrial wastes can be used as feedstock. Recently, many studies have investigated the utilization of agro-industrial wastes as potential nutrient sources for BNC production. However, a comprehensive review of BNC production from fruit wastes and crop residues is lacking. To address this gap, the current review focuses on the utilization of fruit wastes and crop residues for BNC production, including its advantages and disadvantages. This study contributes to the scientific community by (a) providing an insight into fruit waste and crop residue utilization for BNC synthesis (b) an overview on its advantages and disadvantages (c) providing recommendations and future perspectives on BNC production from agro-industrial waste utilization. The sustainable concept of BNC production utilizing agro-industrial wastes opens a way for industries to produce BNC on a larger scale.

Evaluating the concentration dependent dual effects of β-Glucan on cancerous skin cells and mitochondria isolated from melanoma-induced animal model

Introduction Melanoma is still one of the deadliest cancers whose prevalence has increased in recent decades. Today, many polysaccharides and their bioactive compounds have been of special importance in modern biotechnology. They have various biological and therapeutic properties. they can regulate and strengthen the immune system, lower blood pressure and cholesterol, and reduce bacterial and viral infections. According to studies, these compounds also have antitumor properties. we investigated the cytotoxic effects of β-Glucan obtained from solid-state fermentation (SSF) of edible medicinal mushroom Lentinus edodes on cancerous skin cells. Materials and methods The mitochondria were isolated from melanoma cells via differential centrifugation and treated with various concentrations (30, 45, 60, 90, 120, and 240 µg/ml) of β-Glucan extract. Then, they were subjected to MTT, ROS, MMP decline, mitochondrial swelling, cytochrome c release, and flow cytometry assays. Results The results of the MTT assay showed that IC50 of β-Glucan extract was 60 μg/ml, and it induced a selectively significant (P < 0.05) concentration-dependent decrease in the SDH activity in cancerous skin mitochondria. At higher concentrations, no such effect was observed. The ROS results also showed that 30, 45, and 60 µg/ml concentrations of β-Glucan extract significantly increased ROS. However, no such effect was observed at higher concentrations. MMP decline and the release of cytochrome c in cancer groups mitochondria and swelling were significantly increased at 30, 45, and 60 µg/ml compared to the control group. At higher concentrations, no such effect was observed. β-Glucan extract at 60 µg/ml concentration increased apoptosis on melanoma cells, while it had no effect on control non-tumour cells. Discussion and conclusion Based on these results, β-Glucan extract at 30, 45, and 60 µg/ml showed a cytotoxic effect, while no such effect was observed at higher concentrations. Overall, it seems that β-Glucan has antioxidant and free radical scavenging effects on cancer cells at higher concentrations.

Would edible insects become part of our gastronomic quest?

Global food security status has been contested in recent times with claims of efficient food production by the proponents and severe to moderate food insecurity by the opponents. The current population growth prediction of 9.7 billion by 2050 requires additional food production due to the impact of climate change leading to diminished yield rates. Novel food sources such as cellular agriculture utilizing modern biotechnology are at various trial and commercialization stages. Old traditions of insects as a reliable food (entomophagy) source are gaining momentum in recent times. This article explores various aspects of entomophagy. The ecological footprint of entomophagy on its animal counterparts is presented. Since religious factors have a major impact on eating habits that privileges certain elements, perspectives from major religions on entomophagy have been discussed. The regulatory standpoint of Anglo-Saxon, Western and Eastern societies are given. Consumer knowledge and commercialization challenges are also discussed with concluding remarks.

TEMPRO: nanobody melting temperature estimation model using protein embeddings

Single-domain antibodies (sdAbs) or nanobodies have received widespread attention due to their small size (~ 15 kDa) and diverse applications in bio-derived therapeutics. As many modern biotechnology breakthroughs are applied to antibody engineering and design, nanobody thermostability or melting temperature (Tm) is crucial for their successful utilization. In this study, we present TEMPRO which is a predictive modeling approach for estimating the Tm of nanobodies using computational methods. Our methodology integrates various nanobody biophysical features to include Evolutionary Scale Modeling (ESM) embeddings, NetSurfP3 structural predictions, pLDDT scores per sdAb region from AlphaFold2, and each sequence’s physicochemical characteristics. This approach is validated with our combined dataset containing 567 unique sequences with corresponding experimental Tm values from a manually curated internal data and a recently published nanobody database, NbThermo. Our results indicate the efficacy of protein embeddings in reliably predicting the Tm of sdAbs with mean absolute error (MAE) of 4.03 °C and root mean squared error (RMSE) of 5.66 °C, thus offering a valuable tool for the optimization of nanobodies for various biomedical and therapeutic applications. Moreover, we have validated the models’ performance using experimentally determined Tms from nanobodies not found in NbThermo. This predictive model not only enhances nanobody thermostability prediction, but also provides a useful perspective of using embeddings as a tool for facilitating a broader applicability of downstream protein analyses.

A MATLAB-based simulator for the study of process control of fed-batch yeast fermentations

This paper presents a MATLAB-based simulator for the study of process control of fed-batch yeast fermentations that meets the educational needs of undergraduate and graduate students. Against the background of challenges in interdisciplinary education, the paper examines the evolving environment of simulation tools in the field of bioprocesses. It emphasizes the need for interdisciplinarity to prepare students for the complexities of the modern biotechnology industry. Built with accessibility and flexibility in mind, the simulator offers a modular structure with a graphical user interface (GUI) for novice users and direct access to MATLAB functions for advanced users. This design choice ensures ease of use for students with different programming backgrounds and allows for adaptability to alternative software environments. The introductory sections provide a detailed overview of the simulator development, including the mathematical models that govern biomass growth kinetics, mass transfer, and process quality indicators. Selected process control strategies such as rule-based and feedforward approaches are incorporated in the simulator to enhance the learning experience by allowing students to experiment with different scenarios. The paper concludes by emphasizing the simulator's adaptability, modularity, and user-friendly interface as a valuable asset in educating students about the complexities of bioprocess control.

INTRODUCTION TO IN VITRO CULTURE OF RHAPОNTICUM CARTHAMOIDES

The article presents the results of studies on the introduction into in vitro culture of the valuable medicinal plant Rhaponticum carthamoides, growing in the territory of the Kazakhstan Altai. R. carthamoides - or maral root is a source of various biologically active compounds (flavonoids, polysaccharides, saponins, cumanins). This species is of particular value as a producer of ultra-high quantities of ecdysteroids, which have a hepatoprotective and hypoglycemic effect, acting as adaptogens. Currently, natural reserves of this species are sharply reduced due to increasing demand and, as a consequence, lead to the depletion of natural populations. Modern biotechnology methods make it possible to develop highly effective approaches for the propagation and preservation of R. carthamoides for subsequent introduction and expansion of the range of fodder and medicinal crops that meet the needs of agriculture, medicine and the food industry. Seeds collected from their natural habitats were used as research material. A seed sterilization protocol has been developed; it has been established that to obtain aseptic seedlings it is necessary to use a multi-stage sterilization protocol using various sterilizing agents. Surface-sterilized seeds were placed on MS and MS media containing ½ mineral salts with different hormonal compositions. The results showed that the percentage of seed germination varied depending on the hormonal status of the environment and ranged from 42.9 to 85.5%. Thus, the lowest percentage of germination was noted on the B0 medium option (½ MS) - 42.9%. The highest percentage of germination was in seeds on the B3 medium option (MS + 3 mg/l BAP + 3 mg/l kinetin) - 85.5%.

A Spotlight on the Potential of Microscopic Motile Algae as Novel Sources for Modern Cosmetic Products

The recognition and use of algae in the very trend-driven cosmetic industry is progressively increasing. Up to now, the main focus was on large seaweeds and a limited number of microalgae. However, motile microalgae, flagellates, remain underscored in this aspect, although some of them are utilized commercially. Flagellates from different taxonomic groups occupy various habitats and contain bioactive high-value multifunctional compounds, some of which are novel. Moreover, they may simultaneously produce different substances, which together with the development of downstream processing technologies, makes them a promising source for modern biotechnology. The present review covers data on 411 strains, 251 species from 110 genera from 6 phyla, and is oriented generally towards less explored flagellates. It demonstrates their great potential as bearers of interesting novel compounds that can be beneficially applied in modern cosmetics. Safety aspects of both sources and products are also discussed. Considering the gaps in the knowledge, the necessity to expand the research on both well-known and yet unexplored microalgae is shown, encouraging the development of upstreaming processes, including phycoprospecting. Last but not least, this paper outlines the role of living culture collections and of using good taxonomic expertise before running the biochemical tests, cultivation, and bioengineering experiments.

A REVIEW OF ANIMAL MODELS FOR BONE FRACTURE NONUNION AND THEIR ROLE IN STUDYING BIOLOGICAL THERAPY EFFICACY

The bone healing impairment, such as non-union fractures after injuries of long bones, lead to loss of working capacity and result in significant financial costs, which emphasizes the socioeconomic significance of the problem. However, it is not known which method of modeling the non-union bone fractures is more optimal for further research into the effectiveness of biological therapy aimed at treating bone healing impairment. For a detailed study of methods of non-union fracture treatment of, it is necessary to determine the developed animal models. The objective was to analyze the existing animal models of fracture nonunion in long bones in vivo and to consider the possibility of their further use to evaluate the effectiveness of the use of modern biotechnologies for the in the management of fracture nonunion. It was found that the majority of developed animal models of atrophic long bone non-union were created using small animals, namely rats, mice, and rabbits. A more common method of modeling bone non-union is performing an osteotomy with the formation of a defect of different widths between the bone fragments and subsequent removal of the periosteum proximal and distal to the osteotomy site; damage to the endosteum or removal of bone marrow. Also, in such animal models, researchers use a silicone spacer, a polysulfone plate, or a latex-silicone foil to physically prevent fracture union. In these animal models, studies using mesenchymal stromal cells, platelet-rich plasma or bone morphogenetic protein-2 (BMP-2) have already been conducted for the management of non-union bone fractures. At the same time, the clinical results of the application of various biological therapies are ambiguous, which determines the conduct of further experimental studies, in particular, in vivo. However, there are disagreements about which in vivo modeling methods give a reproducible result and prevent bone union, which determines the need for further analysis of existing modeling tools for conducting research in this direction.

Review on: Public Perception of Biotechnology on Genetically Modified Crops, Bio Policy and Intellectual Property Rights

Public discussion about genetically modified crops is strongly heavily influenced by debates over their risks and benefits. Supporters of biotechnology point to its potential to reduce hunger, prevent malnutrition, treat diseases, and improve overall health and quality of life. However, there is considerable opposition to biotechnology. Some critics argue that it poses risks to human health and the environment, while others oppose it on moral and ethical grounds. The transfer of genes between different species is often criticized as &amp;quot;playing God&amp;quot; or breaking the &amp;quot;Law of Nature.&amp;quot; Biosafety on (GM) crops is a rapidly growing field that includes scientific research, ethical issues, and policy and regulatory frameworks to assess and manage risks to human and animal health, including food and feed safety, as well as environmental risks related to modern biotechnology products. Bio-policy refers to the rules, norms, and ethical considerations that govern the development, production, and use of biotechnology products. These policies differ by country and can be influenced by international agreements and organizations. A key international agreement (TRIPS) Agreement, which sets global standards for intellectual property protection. The Trade-Related Aspects of Intellectual Property Rights (TRIPS) Agreement requires governments to issue patents in technological sectors, including modern biotechnology, to protect innovations in this field. This ensures that biotechnological advancements, including GM crops, are protected under intellectual property laws, aiding their development and commercialization while addressing ethical and safety concerns.

A Comprehensive Review on Crop Modification Techniques Using Traditional and Modern Biotechnological Approaches

A Comprehensive Review on Crop Modification Techniques Using Traditional and Modern Biotechnological Approaches

New Insights into Pseudomonas spp.-Produced Antibiotics: Genetic Regulation of Biosynthesis and Implementation in Biotechnology.

Pseudomonas bacteria are renowned for their remarkable capacity to synthesize antibiotics, namely mupirocin, gluconic acid, pyrrolnitrin, and 2,4-diacetylphloroglucinol (DAPG). While these substances are extensively employed in agricultural biotechnology to safeguard plants against harmful bacteria and fungi, their potential for human medicine and healthcare remains highly promising for common science. However, the challenge of obtaining stable producers that yield higher quantities of these antibiotics continues to be a pertinent concern in modern biotechnology. Although the interest in antibiotics of Pseudomonas bacteria has persisted over the past century, many uncertainties still surround the regulation of the biosynthetic pathways of these compounds. Thus, the present review comprehensively studies the genetic organization and regulation of the biosynthesis of these antibiotics and provides a comprehensive summary of the genetic organization of antibiotic biosynthesis pathways in pseudomonas strains, appealing to both molecular biologists and biotechnologists. In addition, attention is also paid to the application of antibiotics in plant protection.

Expanding the Scope of Ribosome‐Mediated Biosynthesis in vitro using tRNA‐Aminoacylating Ribozyme

AbstractProteins are synthesized within ribosomes through the polymerization of amino acids (AAs). This process requires prior activation of AAs through aminoacylation that attaches them to their corresponding transfer RNAs (tRNAs). Within cells, this attachment is facilitated by aminoacyl‐tRNA synthetase, resulting in a tRNA:AA conjugate. A set of ribozymes developed to acylate tRNA with non‐canonical substrates enables this process outside the confines of living cells, thereby facilitating the synthesis of novel bio‐based products. In modern biotechnology, aminoacylating ribozymes contribute to the production of innovative bio‐based materials bearing functional non‐canonical chemical substrates (NCSs) and fill the gaps in synthesizing unique polymeric backbones, extending the scope beyond traditional peptide bonds. This review summarizes current understanding of flexizymes at the molecular level and their application in generating exceptional polymeric backbones through ribosome‐mediated synthesis in vitro.

Extreme Biocatalysts: From Basic Research to Biotechnological Applications

Biocatalysis, a cornerstone of modern biotechnology, is poised to revolutionize industrial processes across diverse sectors [...]