Modern Biotechnology Research Articles

Application of modern biotechnology and bioinformatics approaches in agricultural sciences; A systematic review

In recent times, there has been a substantial surge in biological data owing to remarkable progress in molecular biology and genomic technology. With the growing demand for data storage and management tools, coupled with the surge in genetic data, there has been a corresponding rise in the availability of tools for analyzing, visualizing, modeling, and predicting large datasets. The proliferation of diverse datasets derived from a multitude of plant species has significantly broadened our comprehension, particularly within the realm of plant biotechnology. In the realm of "omics" methodology, proficient bioinformatics methodologies and tools are presently under development to facilitate expedited genome sequencing and the comprehensive analysis of plant genomes. The present investigation centers on the diverse applications of plant biotechnology bioinformatics and their potential to augment agricultural productivity. This study aims to analyze and assess the obstacles or constraints encountered in the field of plant biotechnology, which have impeded the advancement of plant genomes at a slower pace compared to animal genomes. To successfully examine the intricate details of the plant genome, bioinformatics methods must be strong egough which provides longer coverage. The area in plant biotechnology including the agricultural industry are expected to advance from the development of bioinformatics, as would mankind as a whole. The inclusion of computer based programs and data analysis tools in plant biotechnology has facilitated the indepth study of crop plants important for commerce and trade. Improved algorithm development is necessary to facilitate tasks such as data mining, analysis, comparison, and etc. Hence, the integration of novel techniques and information into bioinformatics for the advancement of plant biotechnology, the agricultural industry, and the future of humanity will heavily rely on the expertise of bioinformaticians.

Associations of somatotropin (GH) gene polymorphism with lactation performance of cows

The research was conducted in the laboratory of molecular genetic expertise in 2018 and 2019 within the framework of the state assignment on the topic "Development of genetic-selection and theoretical foundations for the conservation and effective use of the gene pool of cattle in the Ural region with the use of modern biotechnologies". The object of the study is the cattle of Holsteinized black-and-white breed. The main task is to analyze the degree of influence of the somatotropin (GH) gene polymorphism on lactation performance indicators. In the course of the study, DNA from 270 cows was isolated, the polymorphism of the somatotropin gene was determined based on the obtained data, and the relationship between different genotypes and indicators of live weight, milk yield, protein mass fraction and fat mass fraction in milk was established. The results were biometrically processed using IBM SPSS Statistics 23 software program. It was revealed that LL is the main genotype of the GH gene among the representatives of the Holsteinized black-and-white breed (frequency of occurrence 77.0%). The proportion of LV and VV genotypes in the population is 21.9 and 1.1%, respectively. During the observation period, cows carrying the LL genotype showed higher milk yields in the first and third lactations. The difference with their peers was 202-2334 kg (p ≤ 0.05). A tendency towards increased protein content in milk was recorded in animals with the VV genotype. In the first lactation, the difference with LL and LV genotype carriers was 0.03 and 0.06%, respectively. In the third lactation, individuals with the VV genotype surpassed their female counterparts in protein content by 0.07 and 0.12%, respectively.

The Dawn of a New Era: Targeting the "Undruggables" with Antibody-Based Therapeutics.

The high selectivity and affinity of antibodies toward their antigens have made them a highly valuable tool in disease therapy, diagnosis, and basic research. A plethora of chemical and genetic approaches have been devised to make antibodies accessible to more "undruggable" targets and equipped with new functions of illustrating or regulating biological processes more precisely. In this Review, in addition to introducing how naked antibodies and various antibody conjugates (such as antibody-drug conjugates, antibody-oligonucleotide conjugates, antibody-enzyme conjugates, etc.) work in therapeutic applications, special attention has been paid to how chemistry tools have helped to optimize the therapeutic outcome (i.e., with enhanced efficacy and reduced side effects) or facilitate the multifunctionalization of antibodies, with a focus on emerging fields such as targeted protein degradation, real-time live-cell imaging, catalytic labeling or decaging with spatiotemporal control as well as the engagement of antibodies inside cells. With advances in modern chemistry and biotechnology, well-designed antibodies and their derivatives via size miniaturization or multifunctionalization together with efficient delivery systems have emerged, which have gradually improved our understanding of important biological processes and paved the way to pursue novel targets for potential treatments of various diseases.

Cold-Adapted Proteases: An Efficient and Energy-Saving Biocatalyst.

The modern biotechnology industry has a demand for macromolecules that can function in extreme environments. One example is cold-adapted proteases, possessing advantages such as maintaining high catalytic efficiency at low temperature and low energy input during production and inactivation. Meanwhile, cold-adapted proteases are characterised by sustainability, environmental protection, and energy conservation; therefore, they hold significant economic and ecological value regarding resource utilisation and the global biogeochemical cycle. Recently, the development and application of cold-adapted proteases have gained gaining increasing attention; however, their applications potential has not yet been fully developed, which has seriously restricted the promotion and application of cold-adapted proteases in the industry. This article introduces the source, related enzymology characteristics, cold resistance mechanism, and the structure-function relationship of cold-adapted proteases in detail. This is in addition to discussing related biotechnologies to improve stability, emphasise application potential in clinical medical research, and the constraints of the further developing of cold-adapted proteases. This article provides a reference for future research and the development of cold-adapted proteases.

CRISPR/Cas9-based gene activation and base editing in Populus.

The genus Populus has long been used for environmental, agroforestry and industrial applications worldwide. Today Populus is also recognized as a desirable crop for biofuel production and a model tree for physiological and ecological research. As such, various modern biotechnologies, including CRISPR/Cas9-based techniques, have been actively applied to Populus for genetic and genomic improvements for traits such as increased growth rate and tailored lignin composition. However, CRISPR/Cas9 has been primarily used as the active Cas9 form to create knockouts in the hybrid poplar clone "717-1B4" (P. tremula x P. alba clone INRA 717-1B4). Alternative CRISPR/Cas9-based technologies, e.g. those involving modified Cas9 for gene activation and base editing, have not been evaluated in most Populus species for their efficacy. Here we employed a deactivated Cas9 (dCas9)-based CRISPR activation (CRISPRa) technique to fine-tune the expression of two target genes, TPX2 and LecRLK-G which play important roles in plant growth and defense response, in hybrid poplar clone "717-1B4" and poplar clone "WV94" (P. deltoides "WV94"), respectively. We observed that CRISPRa resulted in 1.2-fold to 7.0-fold increase in target gene expression through transient expression in protoplasts and Agrobacterium-mediated stable transformation, demonstrating the effectiveness of dCas9-based CRISPRa system in Populus. In addition, we applied Cas9 nickase (nCas9)-based cytosine base editor (CBE) to precisely introduce premature stop codons via C-to-T conversion, with an efficiency of 13%-14%, in the target gene PLATZ which encodes a transcription factor involved in plant fungal pathogen response in hybrid poplar clone "717-1B4". Overall, we showcase the successful application of CRISPR/Cas-based technologies in gene expression regulation and precise gene engineering in two Populus species, facilitating the adoption of emerging genome editing tools in woody species.

Guarding Against Catastrophic Biological Risks: Preventing State Biological Weapon Development and Use by Shaping Intentions.

Guarding Against Catastrophic Biological Risks: Preventing State Biological Weapon Development and Use by Shaping Intentions.

Evolution-strengthened knowledge graph enables predicting the targetability and druggability of genes.

Identifying promising targets is a critical step in modern drug discovery, with causative genes of diseases that are an important source of successful targets. Previous studies have found that the pathogeneses of various diseases are closely related to the evolutionary events of organisms. Accordingly, evolutionary knowledge can facilitate the prediction of causative genes and further accelerate target identification. With the development of modern biotechnology, massive biomedical data have been accumulated, and knowledge graphs (KGs) have emerged as a powerful approach for integrating and utilizing vast amounts of data. In this study, we constructed an evolution-strengthened knowledge graph (ESKG) and validated applications of ESKG in the identification of causative genes. More importantly, we developed an ESKG-based machine learning model named GraphEvo, which can effectively predict the targetability and the druggability of genes. We further investigated the explainability of the ESKG in druggability prediction by dissecting the evolutionary hallmarks of successful targets. Our study highlights the importance of evolutionary knowledge in biomedical research and demonstrates the potential power of ESKG in promising target identification. The data set of ESKG and the code of GraphEvo can be downloaded from https://github.com/Zhankun-Xiong/GraphEvo.

Advances in cold-adapted enzymes derived from microorganisms.

Cold-adapted enzymes, produced in cold-adapted organisms, are a class of enzyme with catalytic activity at low temperatures, high temperature sensitivity, and the ability to adapt to cold stimulation. These enzymes are largely derived from animals, plants, and microorganisms in polar areas, mountains, and the deep sea. With the rapid development of modern biotechnology, cold-adapted enzymes have been implemented in human and other animal food production, the protection and restoration of environments, and fundamental biological research, among other areas. Cold-adapted enzymes derived from microorganisms have attracted much attention because of their short production cycles, high yield, and simple separation and purification, compared with cold-adapted enzymes derived from plants and animals. In this review we discuss various types of cold-adapted enzyme from cold-adapted microorganisms, along with associated applications, catalytic mechanisms, and molecular modification methods, to establish foundation for the theoretical research and application of cold-adapted enzymes.

Bacterial biosynthesis of flavonoids: Overview, current biotechnology applications, challenges,and prospects.

Flavonoids are secondary metabolites present in plant organs and tissues. These natural metabolites are the most prevalent and display a wide range of beneficial physiological effects, making them usually intriguing in several scientific fields. Due to their safety for use and protective attributes, including antioxidant, anti-inflammatory, anticancer, and antimicrobial functions, flavonoids are broadly utilized in foods, pharmaceuticals, and nutraceuticals. However, conventional methods for producing flavonoids, such as plant extraction and chemical synthesis, entailed dangerous substances, and laborious procedures, with low product yield. Recent studies have documented the ability of microorganisms, such as fungi and bacteria, to synthesize adequate amounts of flavonoids. Bacterial biosynthesis of flavonoids from plant biomass is a viable and environmentally friendly technique for producing flavonoids on a larger scale and has recently received much attention. Still, only a few bacteria species, particularly Escherichia coli, have been extensively studied. The most recent developments in bacterial biosynthesis of flavonoids are reviewed and discussed in this article, including their various applications as natural food biocontrol agents. In addition, the challenges currently faced in bacterial flavonoid biosynthesis and possible solutions, including the application of modern biotechnology approaches for developing bacterial strains that could successfully produce flavonoids on an industrial scale, were elucidated.

The new directions in genetics, breeding and biotechnology of ornamental and berry crops in the N.I. Vavilov Institute of Plant Genetic Resources (VIR)

The use of modern breeding methods, biotechnology, and molecular genetics makes it possible to identify promising accessions with specified economically important traits at early pre-breeding stages. The success of creating new varieties depends on the availability of unique collections of plant genetic resources, information about genomes, possibility of in vitro cultivation with high regenerative capacity, and practical skills and competencies in this area. One of the advanced methods for accelerating the breeding process is genome editing using the CRISPR/Cas system. This method allows the effective modification of genes in order to obtain varieties with desired traits. In 2022, a new youth laboratory of genetics, breeding, biotechnology of ornamental and berry crops was set up at VIR as part of the National Project "Science and Universities". It is noteworthy that this event coincided with the 135th anniversary of the birth of N.I. Vavilov. The work of the laboratory is aimed at obtaining lines with desired properties for the further breeding process; identifying target genes of economically important traits for obtaining new varieties, lines, and hybrids; as well as creating protocols for the accelerated reproduction of virus-free material of commercially demanded varieties oriented towards import substitution. This review discusses current trends in breeding of ornamental and berry crops: e.g., flower color change in snapdragon and peony; flower aroma improvement in rose; architectonics change in actinidia; and increase of resistance to stress factors in blackberries, strawberries, and grapes.

Status of the Indian biopharmaceutical industry and way forward to be a dominant global player

Abstract The government promotes biotechnology in India, with the Department of Biotechnology (DBT) taking the leadership role, whereas some other departments also join in the endeavor. Modern biotechnology is no more new to India. Several therapeutic and diagnostic products are manufactured in the country from the primary stage. The emphasis is on the manufacture of patent-expired products more cost-effectively. The Indian biopharmaceutical market was approximately INR 32261 crores (US$ 4.032 billion) during 2021–2022 and approximately 1.14% of the global market. The manufacture of biopharmaceuticals needs sophisticated equipment and specialized skills. India has acquired skills in recombinant deoxyribonucleic acid (rDNA) technologies, developed capacities in genetically modifying Escherichia coli, Saccharomyces cerevisiae, Pichia pastoris, Hansenula polymorpha, and Chinese hamster ovary (CHO) cells lines, and has expertise in the multiplication of viruses in different animal and human cell lines. India produces many therapeutic and diagnostic recombinant proteins, including several therapeutic monoclonal antibodies. The more advanced areas of biopharmaceutical technology, such as mRNA-based cell therapies, including in-vitro modified somatic cell-based treatment and chimeric antigen receptor (CAR) T-cell therapy, are evolving. Genome editing technologies involving the manipulation of germ line cells are in the research and development (R&D) stage. Xenotransplantation technologies and the development of humanized transgenic animals are yet to start. Appropriate artificial intelligence programs may be included in the Indian biopharmaceutical industry to speed up the development of novel biopharmaceuticals. There are shortages of leaders adequately trained in biopharmaceutical skills in manufacturing, and the industry has constraints of abundant infrastructure and finance for deployment in R&D. India is committed to fulfilling a social objective by providing many essential medicines, including biopharmaceuticals at affordable prices through the Pradhan Mantri Bhartiya Janaushadhi Pariyojana.

Effect of Methionine on Gene Expression in Komagataella phaffii Cells.

Komagataella phaffii yeast plays a prominent role in modern biotechnology as a recombinant protein producer. For efficient use of this yeast, it is essential to study the effects of different media components on its growth and gene expression. We investigated the effect of methionine on gene expression in K. phaffii cells using RNA-seq analysis. Several gene groups exhibited altered expression when K. phaffii cells were cultured in a medium with methanol and methionine, compared to a medium without this amino acid. Methionine primarily affects the expression of genes involved in its biosynthesis, fatty acid metabolism, and methanol utilization. The AOX1 gene promoter, which is widely used for heterologous expression in K. phaffii, is downregulated in methionine-containing media. Despite great progress in the development of K. phaffii strain engineering techniques, a sensitive adjustment of cultivation conditions is required to achieve a high yield of the target product. The revealed effect of methionine on K. phaffii gene expression is important for optimizing media recipes and cultivation strategies aimed at maximizing the efficiency of recombinant product synthesis.

Diverse Repertoire and Relationship of Exopolysaccharide Genes in Cold-Adapted Acinetobacter sp. CUI-P1 Revealed by Comparative Genome Analysis.

This study focused on the exploration of microbial communities inhabiting extreme cold environments, such as the Passu and Pisan glaciers of Pakistan, and their potential utilization in industrial applications. Among the 25 initially screened strains, five were found to be suitable candidates for exopolysaccharide (EPS) production, with strain CUI-P1 displaying the highest yield of 7230.5 mg/L compared to the other four strains. The purified EPS from CUI-P1 was tested for its ability to protect probiotic bacteria and E. coli expressing green fluorescence protein (HriGFP) against extreme cold temperatures, and it exhibited excellent cryoprotectant and emulsification activity, highlighting its potential use in the biotechnological industry. Furthermore, the genome of Acinetobacter sp., CUI-P1 comprised 199 contigs, with a genome size of 10,493,143bp and a G + C content of 42%, and showed 98.197% nucleotide identity to the type genome of Acinetobacter baumannii ATCC 17978. These findings offer promising avenues for the application of EPS as a cryoprotectant, an essential tool in modern biotechnology.

Конверсия пшеничных отрубей в целевые продукты биосинтеза

A more efficient bioconversion of renewable plant resources is a priority in modern biotechnology. An important aspect of the processing and pretreatment of cellulose raw materials is to obtain a high content of reducing substances in the final product. The present research objective was to determine the optimal conditions for the chemical transformation of plant polymers to obtain biologically valuable substances. The research results will reduce the final cost of biotechnological production.
 This research featured wheat bran polymers treated with sulfuric acid and relied on a set of standard research methods. The degree of polymer conversion was tested on native and mechanically activated wheat bran fractions of 600, 200, and 100 microns. The kinetics of the high-temperature chemical hydrolysis was as follows: temperature – 120–130°C, sulfuric acid concentration – 0.6–0.9%, treatment time – 30–60 min, hydromodule – 1:8;9;10. The quantitative and qualitative composition of mono- and disaccharides of hydrolysates was determined using the high performance liquid chromatography method. 
 The composition of wheat bran showed a low content of lignin (7.55%) and a high content of pentosans (17.9%). The highest content of reducing substances in hydrolysates was 640 mg/g bran. The optimal technological conditions with the highest content of reducing substances were as follows: hydromodulus – 1:10, temperature – 120°C, treatment time – 45 min, and sulfuric acid concentration – 0.9%. The greatest change in the content of mono- and disaccharides of hydrolysates belonged to pentoses: 78.2 mg/g of bran (in terms of xylose). The amount of easily hydrolysable carbohydrates and wheat bran fiber decreased by 80 and 19%, respectively.
 This research revealed the optimal parameters for the chemical hydrolysis of wheat bran to obtain biologically valuable carbohydrates. This area of research can be of practical use for producers of biofuels, chemicals, and food additives.

The emerging role of vaccines in cancer therapies

Globally, there is a severe public health issue with cancer. Comprehensive funding has been provided for the creation of medicinal vaccines against cancer. The efficiency of vaccines in preventing bacterial and viral illnesses has been demonstrated. Over the past 200 years, they have averted many fatal diseases and saved countless lives. Vaccines protect against diseases brought on by viruses and bacteria by exposing recipients to attenuated or inactivated pathogens. Thereby, the individual's immune system can identify the antigen and behave. DNA vaccines, mRNA vaccines, and synthetic peptide vaccines are just a few of the innovative vaccinations created in recent years using modern biotechnology. Immune adjuvants or drug delivery systems are utilized to enhance immunogenicity through extensive immune system research, tests on animal models, and clinical trials of vaccines. This review paper will discuss therapeutic cancer vaccine mechanisms and cancer vaccine delivery methods.

The legacies of the "Father of Hybrid Rice" and the seven representative achievements of Chinese rice research: A pioneering perspective towards sustainable development.

The "Father of Hybrid Rice", Yuan Longping, created high-yield hybrid rice that can feed tens of millions of people annually. The research achievements of Yuan and his team on low cadmium-accumulating rice and sea rice, in addition to hybrid rice, as well as those of a large number of Chinese scientists engaged in rice research in other six areas, including the rice genome, purple endosperm rice, de novo domestication of tetraploid rice, perennial rice, rice blast disease, and key genes for high nitrogen use efficiency, play an important role in promoting the realization of the United Nations Sustainable Development Goals 2 and 12. The purpose of this review is not to elaborate on the details of each research, but to innovatively summarize the significance and inspiration of these achievements to ensure global food security and achieve sustainable agriculture. In the future, cultivating new rice varieties through modern biotechnology, such as genome editing, will not only reduce hunger, but potentially reduce human-land conflicts, improve the environment, and mitigate climate change.

New promising strains of <i>Bacillus subtilis</i> isolated from frozen soils of Yakutia

Screening of natural microorganisms possessing a combination of antagonistic and enzymatic activities is one of the main tasks in the development of agrobiotechnological preparations. Microbiological studies of permafrost soils of Central Yakutia were carried out with the aim of finding bacterial strains of the Bacillus genus that are promising in modern biotechnology. 14 isolates were isolated from the middle loamy permafrost soil of the Khangalassky ulus. Of these three isolates were identified as Bacillus subtilis species by their physiological and biochemical properties which was confirmed by molecular genetic studies on 16S pPNK. The new strains of B. subtilis Bac-1p, B. subtilis Bac-2p, and B. subtilis Bac-4p were found to possess marked antagonistic properties against Salmonellosis and streptococcal pathogens: Sal. abortus equi BN-12, Str. equi 5/1. New strains are also capable of producing a number of hydrolytic enzymes (amylase, xylanase, phytase). B. subtilis TNP-3 and B. subtilis TNP-5 bacterial strains were used as controls for determining quantitative indicators of enzymatic activity. These strains are deposited in the collection of microorganisms used in animal husbandry and veterinary medicine and are the basis of probiotic preparations. B. subtilis Bac-1p, B. subtilis Bac-2p, and B. subtilis Bac-4p strains were found to be somewhat inferior to the control strains in amylolytic activity, but they were significantly superior in xylanase and phytase activities. The results of these studies have shown the potential of new B. subtilis strains for further study and the possibility of using them in the development of biological preparations for agriculture.

Biosynthesis of anticancer phytochemical compounds and their chemistry.

Cancer is a severe health issue, and cancer cases are rising yearly. New anticancer drugs have been developed as our understanding of the molecular mechanisms behind diverse solid tumors, and metastatic malignancies have increased. Plant-derived phytochemical compounds target different oncogenes, tumor suppressor genes, protein channels, immune cells, protein channels, and pumps, which have attracted much attention for treating cancer in preclinical studies. Despite the anticancer capabilities of these phytochemical compounds, systemic toxicity, medication resistance, and limited absorption remain more significant obstacles in clinical trials. Therefore, drug combinations of new phytochemical compounds, phytonanomedicine, semi-synthetic, and synthetic analogs should be considered to supplement the existing cancer therapies. It is also crucial to consider different strategies for increased production of phytochemical bioactive substances. The primary goal of this review is to highlight several bioactive anticancer phytochemical compounds found in plants, preclinical research, their synthetic and semi-synthetic analogs, and clinical trials. Additionally, biotechnological and metabolic engineering strategies are explored to enhance the production of bioactive phytochemical compounds. Ligands and their interactions with their putative targets are also explored through molecular docking studies. Therefore, emphasis is given to gathering comprehensive data regarding modern biotechnology, metabolic engineering, molecular biology, and in silico tools.

Omne vivum ex ovo: the oocyte reprogramming and remodeling activities.

Understanding the establishment of post-fertilization totipotency has broad implications for modern biotechnologies. This review summarizes the current knowledge of putative egg components governing this process following natural fertilization and after somatic cell nuclear transfer. The mammalian oocyte is a unique cell, and comprehending its physiology and biology is essential for understanding fertilization, totipotency and early events of embryogenesis. Consequently, research in these areas influences the outcomes of various technologies, for example, the production and conservation of laboratory and large animals with rare and valuable genotypes, the rescue of the species near extinction, as well as success in human assisted reproduction. Nevertheless, even the most advanced and sophisticated reproductive technologies of today do not always guarantee a favorable outcome. Elucidating the interactions of oocyte components with its natural partner cell - the sperm or an 'unnatural' somatic nucleus, when the somatic cell nucleus transfer is used is essential for understanding how totipotency is established and thus defining the requirements for normal development. One of the crucial aspects is the stoichiometry of different reprogramming and remodeling factors present in the oocyte and their balance. Here, we discuss how these factors, in combination, may lead to the formation of a new organism. We focus on the laboratory mouse and its genetic models, as this species has been instrumental in shaping our understanding of early post-fertilization events.

Biocybersecurity and Deterrence: Hypothetical Rwandan Considerations

Digitalization and sustainability are popular words within modern disciplines as practitioners each look toward the future of their respective fields. Specifically for the African continent, which is making great strides in developmental targets, those two terms are central to core aspects of policy initiatives that may foster cooperation across its varied lands and nations. One of the underlying challenges that confront Africa is a lack of strong regional integration across socioeconomic and political programs; there is value in African regions having more regional connectedness. We assess the rate of regional integration and development in Africa and discuss how to alleviate development crises that could be accelerated by deploying a sustainable cybersecurity strategy, which increasingly includes the bioeconomy and its components. This can be done through the application of Fourth Industrial Revolution (4IR) technologies such as Artificial Intelligence (AI) and modern biotechnology. This work suggests that political and socio-economic activities associated with regional integration must be seen as an all-encompassing task that transcends beyond national boundaries towards a cyber biodefense fortification and increases in 4IR technological integration. This has the aim of thereby encompassing efforts to persuade leaders to fast-track policies that seek to promote geospatial cyberinfrastructure, integrative cybersecurity considerations, cross-border digitalization programs, and increased need for cybersecurity research and education, with mindfulness towards education and further integration of mindful automation. In conclusion, a model of integrative security is proposed for Africa.