Biology Technology Research Articles

Principles and research progress of gene editing technology

Gene editing is a new genetic engineering technology. Given the quick development of molecular biology technology, genome editing tools have made great progress from the initial ZFNs and TALEN technology to CRISPR-Cas9 technology in recent years. Gene editing is the modification of specific targets in the genome of an organism to change its genetic information and phenotypic characteristics. This study analyzed the principle and research progress of gene editing technology through the data. For example, CRISPR-Cas9 can protect against secondary viral attacks, and ZFNs can be cleaved on any genomic sequence. Studies have found that there are still great challenges in the clinical field of genetic technology. Including the need for standardized safety protocols, regulatory transparency, and pricing frameworks, which increase the risk of further mutations. This article elaborates on the role and future development of gene editing in medicine, and provides a reference for the future field of gene editing technology.

Effects of Storm Runoff on Bacterial Community Structure and Metabolic Activity and Water Quality in a Drinking Water Reservoir

To explore the influence of storm runoff on bacterial metabolic activity and water quality in Jinpen Reservoir, three-dimensional fluorescence spectroscopy parallel factor analysis, high-throughput DNA sequencing technology, and Biolog technology were used to analyze variations in the components of dissolved organic matter, bacterial community composition, and microbial metabolic activity during three periods （before, during, and one month after runoff）. The results showed that after storm runoff into the reservoir, the water temperature decreased, and dissolved oxygen in the middle of the water column increased significantly. Finally, the aerobic and low-temperature state in the middle water and anaerobic and low-temperature state in the bottom water was formed. Simultaneously, the concentration of total nitrogen, total phosphorus, organic matter, and turbidity increased significantly. After one month of runoff, the concentration of pollutant decreased, however, was still higher than that before runoff. Further, during the runoff period, the proportion of Proteobacteria and Bacteroidetes increased significantly and the sum of their relative abundance accounted for 63.6% of the bacterial community. The bacterial metabolic activity was also higher than that before. One month after runoff, the bacterial population structure did not recover and the bacterial metabolic activity still remained at a high level.

The Internet of Bio-Nano Things with Insulin-Glucose, Security and Research Challenges: A Survey

The Internet of Bio-Nano Things (IoBNT) is collaborative cell biology and nanodevice technology interacting through Molecular Communication (MC). The IoBNT can be accomplished by using the Information and Communication Theory (ICT) study of biological networks. Various technologies such as the Internet of Nano Things (IoNT), the Internet of Bio-degradable Things (IoBDT) and the Internet of Ingestible Things (IoIT) contribute to the development of IoBNT. Our survey discussed the Bio-Nano network and the role of IoT-based technologies along with a comparative study from various literature. We surveyed the various applications of IoNT in which the drug delivery for Insulin-Glucose system is prominent. Our survey aims to provide information about the Insulin-Glucose system involving the IoBNT and MC. We described the details of various factors for a diabetes analysis. We surveyed the diffusion coefficients of Insulin, Glucose and the various parameters that influence insulin production in the body. Our survey identifies the security aspects of IoBNT such as attacks in nanonetworks, bio-cyber interface, Insulin-Glucose system and their possible mitigation techniques. Our survey also provides a hierarchical model of the Bio-Nano network collaborating all the related technologies. Finally, our survey includes the research challenges involved in the proper handling of the IoBNT.

Role of Computer-Aided Design and Development in Modern Pharmaceuticals

The integration of molecular biology and computational technologies has transformed modern drug discovery and development processes. Advanced computational methodologies, particularly artificial intelligence (AI) and machine learning (ML), have reshaped traditional drug development approaches through unprecedented access to ligand property data, target binding interactions, three-dimensional protein structures, and virtual libraries containing billions of drug-like molecules. AI and deep learning (DL) implementations have enhanced multiple stages of drug discovery, from target identification to lead optimization. These computational advances, backed by improved hardware capabilities and sophisticated algorithms, now enable targeting of previously "undruggable" proteins. This review presents modern computational approaches in pharmaceutical development, including strategies for challenging protein targets through covalent regulation, allosteric inhibition, protein-protein interaction modulation, and targeted protein degradation. AI-driven methods have accelerated drug discovery pipelines, reduced development costs, and improved clinical trial success rates. The transition from traditional broad-spectrum approaches to precision medicine, supported by computational tools, has enabled personalized therapeutic strategies. Current limitations in computer-aided drug design persist, yet the combination of computational predictions with experimental validation continues to advance therapeutic development. Recent developments in quantum computing and advanced neural networks promise to further enhance drug discovery efficiency and success rates in the coming decades.

Advances in the detection technology of vegetable soil borne fungi and bacteria

Soil borne diseases are one of the most serious diseases which often results the decline of vegetables quality and loss of production. Moreover, it is difficult for plants to exhibit disease symptoms in the early stages attributing to strong concealment of soil borne pathogens. Therefore, early detection of pathogens and their physiological races plays an important role in reducing the harm of pathogens associated with diseases of vegetable crops. The traditional diagnostic techniques relied on the time consuming and less accurate methods like disease symptom observation, microscopic diagnosis, and culture techniques etc. The development of molecular biology technology has brought revolutionary changes to the diagnosis of vegetable soil borne diseases, improving the accuracy and efficiency of diagnosis. This paper reviews the various molecular detection techniques for vegetable soil borne pathogens (PCR, nested-PCR, multiplex PCR, etc.) and their physiological races (host identification, DNA molecular markers, transposon detection, etc.), explains the advantages and disadvantages of each detection technique. Furthermore, the paper comprehensively introduces the application of molecular detection technology for soil borne pathogen detection in soil, plants, and seeds. Finally, we put forward important perspectives for the future development of rapid detection methods, aiming to promote rapid diagnosis of soil pathogenic microorganisms and provide guidance for the control of biological risks.

Biomimetic Materials to Fabricate Artificial Cells.

As the foundation of life, a cell is generally considered an advanced microreactor with a complicated structure and function. Undeniably, this fascinating complexity motivates scientists to try to extricate themselves from natural living matter and work toward rebuilding artificial cells in vitro. Driven by synthetic biology and bionic technology, the research of artificial cells has gradually become a subclass. It is not only held import in many disciplines but also of great interest in its synthesis. Therefore, in this review, we have reviewed the development of cell and bionic strategies and focused on the efforts of bottom-up strategies in artificial cell construction. Different from starting with existing living organisms, we have also discussed the construction of artificial cells based on biomimetic materials, from simple cell scaffolds to multiple compartment systems, from the construction of functional modules to the simulation of crucial metabolism behaviors, or even to the biomimetic of communication networks. All of them could represent an exciting advance in the field. In addition, we will make a rough analysis of the bottlenecks in this field. Meanwhile, the future development of this field has been prospecting. This review may bridge the gap between materials engineering and life sciences, forming a theoretical basis for developing various life-inspired assembly materials.

Photocleavable Guide crRNAs for a Light-Controllable CRISPR/Cas9 System.

The design of controllable and precise RNA-targeted CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats) systems is an important problem of modern molecular biology and genetic technology. Herein, we have designed a series of photocleavable guide CRISPR RNAs (crRNA) and their 2'-modified (2'-fluoro and locked nucleic acid) analogs containing one or two 1-(2-nitrophenyl)-1,2-ethanediol photolabile linkers (PL). We have demonstrated that these crRNAs can be destroyed by relatively mild UVA irradiation with the rate constants 0.24-0.77 min-1 and that the photocleavage markedly slows down the action of Cas9 nuclease in the model in vitro system. Two PLs provide more rapid crRNA destruction than a single linker. PLs in the crRNA structure improve the specificity of DNA cleavage by Cas9 nuclease for the fully complementary target. The application of photocleavable crRNA in CRISPR/Cas9 genome editing permits the system to be switched off in a spatiotemporally controlled manner, thus alleviating its off-target effects.

Construction of engineered probiotic that adhere and display nanobody to neutralize porcine reproductive and respiratory syndrome virus.

Pathogenic blue ear disease caused by porcine reproductive and respiratory syndrome virus (PRRSV) bring severe loss to breeding industry due to high infectivity and mortality. L. plantarum serves as the probiotic host strain, known for its beneficial properties in the gut microbiota. E. coli is used as a cloning host for the initial genetic engineering steps, facilitating the construction and amplification of the desired genetic constructs. In this study, using synthetic biology technology, we constructed engineered probiotics which could adhere and display nanobody on the surface to neutralize virus. Firstly, we screen an optimal nanobody to effectively bind with PRRSV by building library, expression and purification. Then, the integration of adhesion protein and nanobody into the genome of probiotics significantly improved its adhesion to IPEC-J2 cells. In addition, this engineered probiotic is almost non-toxic to cells with good safety, which can be used as a daily probiotics to prevent virus fecal transmission. Our study proposed this novel construction strategy of engineering probiotics with both adhesion and neutralization effects, which provided a new therapeutic view for intestinal virus clearance.

Identification of rice samples with rice blast resistance genes Pi-2 and Pi-b

Since rice blast is a disease that causes significant damage to rice all over the world, the intensive development of disease-resistant genotypes is of great urgency. The use of molecular biology technologies, new biotechnological approaches and molecular genetic methods allows creating disease-resistant varieties while reducing the time of their development, which plays an important role in growing competitive products. The current paper has highlighted the results of estimating rice samples developed at the FSBSI “ARC “Donskoy” for blast resistance. The objects of the study were new samples developed in the laboratory of rice breeding and seed production. In 2022–2023, there were screened one hundred eighty-seven rice samples. They were identified on a presence of the blast resistance gene Pi-2. One hundred fifteen samples were estimated for the blast resistance gene Pi-b. Genomic DNA was isolated from young rice leaves. After estimating the quantity and quality of the isolated DNA there was conducted a polymerase chain reaction for the target genes Pi-2 and Pi-b. In order to identify the alleles of the desired genes there were used specific intragenic molecular SSR markers of dominant (for Pi-2) and codominant (for Pi-b) types. Electrophoresis of the obtained amplicons was performed on 2 % agarose gels during an hour. The results of the analysis were recorded in ultraviolet light and processed in ImageLab 5.1 software. As a result of the conducted study, there were identified new rice breeding samples that carry blast resistance genes Pi-2 and Pi-b. These samples are recommended for use in the further breeding process for blast resistance.

An Advancement in Postharvest Biology and Fresh-Keeping Technology of Kiwifruit (Actinidia spp.): A Review

Kiwifruit is a climacteric fruit that may decay rapidly and softens after harvest if not stored properly. How to expand the storage time of kiwifruit to maintain the quality, is a critical challenge for the kiwifruit industry development. Kiwifruit’s post-harvest life is tied closely to post-harvest management, such as scientific harvesting, green preservation, ethylene management, and low-temperature storage, as well as texture and quality. This study focuses on the advancement of related research from four perspectives and explores their impacts on kiwifruit storage in order to give a theoretical foundation for breeding varieties with superior storage capacity, and the development of storage and preservation technologies. Hayward and Hort16A varieties of kiwifruit had been cultivated largely in past but now, yellow-fleshed Sun Gold, Gold 3 and Gold 9, Hongyang, Maohua Cuixiang, Xuxiang, etc. are becoming significantly famous in international commerce. For the best postharvest quality, kiwifruit must be stored at low temperatures. Fruit quality, harvesting maturity, ethylene production, storage life, green preservation, and pathology are the priorities in breeding projects. To take advantage of adequate germplasm resources, reproductive biology understandings are needed.

Halogen substitution effects in Chlorostannate(II) hybrid material: Insights from DFT study on 2(C4H4FN3O)·SnX6·2(H2O), (X = F, Cl, Br, I)

The development of new materials is crucial for advancing technologies in material science, energy, and biology. In this study, we investigate the effect of Halogen-substitution on the compound 2(C4H4FN3O)·SnX6·2(H2O) (where X = F, Cl, Br, and I). Using extensive theoretical analysis, we examined the impact of halogen substitution on the structural properties, band gap energy (Eg), and chemical behavior. Our results show that the Eg decreases with the increasing atomic number of halogens. The I-substituted compound is the most reactive and exhibits significant intramolecular charge transfer, enhancing its antioxidant properties. The spatial distribution of electron density in the Frontier Molecular Orbitals (FMOs) indicates that the HOMO is localized on the inorganic anion and the LUMO on the organic cation, a pattern consistent across all substituted compounds. These findings highlight the potential of these compounds in electron transfer reactions and provide insights for tailoring them for specific chemical and biochemical applications.

High-Yield-Related Genes Participate in Mushroom Production.

In recent years, the increasing global demand for mushrooms has made the enhancement of mushroom yield a focal point of research. Currently, the primary methods for developing high-yield mushroom varieties include mutation- and hybridization-based breeding. However, due to the long breeding cycles and low predictability associated with these approaches, they no longer meet the demands for high-yield and high-quality varieties in the expansive mushroom market. Modern molecular biology technologies such as RNA interference (RNAi) and gene editing, including via CRISPR-Cas9, can be used to precisely modify target genes, providing a new solution for mushroom breeding. The high-yield genes of mushrooms can be divided into four categories based on existing research results: the genes controlling mycelial growth are very suitable for genetic modification; the genes controlling primordium formation are directly or indirectly regulated by the genes controlling mycelial growth; the genes controlling button germination are more difficult to modify; and the genes controlling fruiting body development can be regulated during the mycelial stage. This article reviews the current research status for the four major categories of high-yield-related genes across the different stages of mushroom growth stages, providing a foundation and scientific basis for using molecular biology to improve mushroom yield and promote the economic development of the global edible-mushroom industry.

Development of e-Booklets making nata de pina as a learning resource for Biology Technology Innovation material in the Merdeka Phase E curriculum in high school

Research Development of e-Booklet Making Nata De Pina Research-Based Research as a Learning Source of Biological Technology Innovation Material in the Merdeka Phase E Curriculum in High School aims to analyze the influence of the concentration of sprouts extract on the quality of thickness and weight of nata de pina, as well as analyzing the validity, feasibility, and readability of E-Booklet Making Nata De Pina Developed. The development research design uses the Addie model, which consists of 5 stages, namely analysis, design, development, implementation and evaluation. In this study the implementation stage was not implemented. The results of this study were the provision of sprouts in the process of making nata de pina had a significant effect on the thickness of thickness and weight of nata de pina. The best results of the five treatments for the concentration of sprouts extract tested are trial in the K4 treatment with a concentration of sprouts of 100 ml for 500ml of media. The e-Booklet of making Nata de Pina is considered very valid with the acquisition of material validation scores of 90.90% and the validation score of media experts of 93.53%. The e-Booklet making Nata de Pina was declared very feasible with the acquisition of the teacher response score of 96.66% and the student response was 89.52%. As well as the results of the e-Booklet readability test making Nata de Pina is considered high with the acquisition of the Rumpang test score of 98.38%.

Enhanced nitrogen and phosphorus removal from mariculture water using immobilized bacteria and macroalgae

With the vigorous development of the mariculture industry, the untreated wastewater from mariculture has exerted significant pressure on the water environment. The untreated N and P in the wastewater from mariculture can deteriorate the quality of the mariculture. In this study, a composite in situ treatment system involving macroalgae (Caulerpa lentillifera/Caulerpa sertularoides f. Longipes) and immobilized degrading bacteria was established to handle wastewater from shrimp culture. The changes in nutrients in aquaculture wastewater were studied by chemical analysis, and the microbial community structure was analyzed using molecular biology technology and high-throughput sequencing technology. The removal efficacy of nutrients in aquaculture wastewater and the composition of microorganisms in the wastewater were examined, and the primary causes for the alteration of the microbial community were analyzed. The results demonstrated that when the macroalgae in the system were Caulerpa lentillifera (CL), the removal efficiencies of TN, PO43--P, and COD from shrimp culture were 59.04%, 34.26%, and 68.61% respectively. When the macroalgae was Caulerpa sertularoides f. Longipes (CSF), the removal efficiencies of TN, PO43--P, and COD generated by experimental shrimp culture were 51.50%, 33.69%, and 50.88% respectively. The biomass (wet weight) of both macroalgae species also increased, facilitating the removal of nutrients from the wastewater. Additionally, both Proteobacteria and Bacteroidetes were the dominant bacteria in the three samples, and the addition of the composite in-situ treatment system had no impact on the dominant bacteria in the water. The results of FAPROTAX analysis indicated that compared with the untreated samples, the abundances of methyl-functional bacteria and amino acid-functional bacteria in the samples increased due to organic matter such as COD produced during shrimp culture and the addition of feed, suggesting that shrimp culture can influence the abundances of functional bacteria in the water. In conclusion, the combined in situ treatment system can effectively eliminate nutrients from aquaculture wastewater, and the combined effect of macroalgae and immobilized degrading bacteria plays a vital role in this process.

The heterologous expression of novel recombinant protein composed of HN and F moieties of Newcastle disease virus and immunogenicity evaluation in mouse model.

The rapid spread of Newcastle disease (ND), driven by extensive commercial exchange in the poultry industry, necessitates urgent preventive measures. Although effective vaccines against the Newcastle disease virus (NDV) have been used since 1940, recent outbreaks and the limitations of current vaccines highlight the need for improved solutions. Advances in synthetic biology, reverse vaccinology, molecular biology, and recombinant DNA technology over the past 20 years have led to the development of recombinant vaccines, which offer enhanced protection and broader immunogenic coverage against NDV. This study aimed to express the immunogenic domains of Hemagglutinin Neuraminidase (HN) and Fusion (F) glycoproteins, linked to the heat-labile enterotoxin B subunit (LTB) bio-adjuvant, to develop an effective and reliable recombinant vaccine for NDV. In this study, the L(HN)2F protein, composed of the LTB bio-adjuvant and the immunogenic regions of the doubled Hemagglutinin Neuraminidase (HN-HN) and Fusion (F) epitope, was expressed in Escherichia coli. Subcutaneous injection was used to evaluate the humoral immune response in mice and the result was compared with B1 vaccine. The induction of strong humoral immune responses proved the strong immunoreactivity of the recombinant protein. The IgG elicited by the recombinant proteins was comparable to that of the commercial B1 vaccine against NDV, indicating its potential as a viable candidate for further development and evaluation as a recombinant vaccine against NDV.

A Review of Antimicrobial Peptides: Structure, Mechanism of Action, and Molecular Optimization Strategies

Antimicrobial peptides (AMPs) are bioactive macromolecules that exhibit antibacterial, antiviral, and immunomodulatory functions. They come from a wide range of sources and are found in all forms of life, from bacteria to plants, vertebrates, and invertebrates, and play an important role in controlling the spread of pathogens, promoting wound healing and treating tumors. Consequently, AMPs have emerged as promising alternatives to next-generation antibiotics. With advancements in systems biology and synthetic biology technologies, it has become possible to synthesize AMPs artificially. We can better understand their functional activities for further modification and development by investigating the mechanism of action underlying their antimicrobial properties. This review focuses on the structural aspects of AMPs while highlighting their significance for biological activity. Furthermore, it elucidates the membrane targeting mechanism and intracellular targets of these peptides while summarizing molecular modification approaches aimed at enhancing their antibacterial efficacy. Finally, this article outlines future challenges in the functional development of AMPs along with proposed strategies to overcome them.

Autonomous tracking of honey bee behaviors over long-term periods with cooperating robots.

Digital and mechatronic methods, paired with artificial intelligence and machine learning, are transformative technologies in behavioral science and biology. The central element of the most important pollinator species-honey bees-is the colony's queen. Because honey bee self-regulation is complex and studying queens in their natural colony context is difficult, the behavioral strategies of these organisms have not been widely studied. We created an autonomous robotic observation and behavioral analysis system aimed at continuous observation of the queen and her interactions with worker bees and comb cells, generating behavioral datasets of exceptional length and quality. Key behavioral metrics of the queen and her social embedding within the colony were gathered using our robotic system. Data were collected continuously for 24 hours a day over a period of 30 days, demonstrating our system's capability to extract key behavioral metrics at microscopic, mesoscopic, and macroscopic system levels. Additionally, interactions among the queen, worker bees, and brood were observed and quantified. Long-term continuous observations performed by the robot yielded large amounts of high-definition video data that are beyond the observation capabilities of humans or stationary cameras. Our robotic system can enable a deeper understanding of the innermost mechanisms of honey bees' swarm-intelligent self-regulation. Moreover, it offers the possibility to study other social insect colonies, biocoenoses, and ecosystems in an automated manner. Social insects are keystone species in all terrestrial ecosystems; thus, developing a better understanding of their behaviors will be invaluable for the protection and even the restoration of our fragile ecosystems globally.

CyCadas: accelerating interactive annotation and analysis of clustered cytometry data.

Single cell profiling by cytometry has emerged as a key technology in biology, immunology and clinical-translational medicine. The correct annotation, which refers to the identification of clusters as specific cell populations based on their marker expression, of clustered high-dimensional cytometry data, is a critical step of the analysis. Its accuracy determines the correct interpretation of the biological data. Despite the progress in various clustering algorithms, the annotation of clustered data still remains a manual, time consuming and error-prone task. We developed a user-friendly cluster annotation and differential abundance detection tool that can be applied on data generated with Self Organizing Map clustering algorithms, thus simplifying the annotation process of datasets that consist of hundreds or thousands of clusters. We present Cytometry Cluster Annotation and Differential Abundance Suite (CyCadas), a semi-automated software tool that facilitates cluster annotation in cytometry data by offering both visual and computational guidance. CyCadas addresses the critical need for efficient and accurate annotation of high-resolution clustered cytometry data, significantly reducing the time needed to perform the analysis compared to both manual gating approaches and manual annotation of clustered data. The tool features a user-friendly interface, visual tools enabling data exploration and automated threshold estimation to separate negative and positive marker expression. It facilitates the definition and annotation of cell phenotypes among multiple clusters in a tree-based data structure. Finally, it calculates the abundance of various cell populations across the conditions with statistical interpretation. It is an ideal resource for researchers aiming to streamline their cytometry workflow. CyCadas is available as open source at: https://github.com/DII-LIH-Luxembourg/cycadas.

Absorbance measurement for interdisciplinary educational experiment on cytotoxicity

Abstract We propose a multidisciplinary educational experiment, linking knowledge and skills in physics, biology and information technology through the training and application of the research method by students. From a physics point of view, the experiment consists in light absorption measurement, and in terms of biology, it demonstrates the process of cytotoxicity evaluation by means of the colorimetric method neutral red uptake in vitro test. The test allows to determine the concentration of a test drug at which 50% cytotoxicity (CC50 values) of the cells is observed. After initial exposure to the tested drug, neutral red (NR) is added to the cell culture medium, it is absorbed by the living cells and subsequently released in a desorb buffer. The cell culture medium becomes coloured, and the more intensive colour corresponds to higher cell viability, while more transparent solution corresponds to lower number of living cells. The NR concentration in the solution is estimated by the absorbance value. We measure the absorbance of NR by utilizing a very affordable educational-grade spectrometer and compare its output with that of a professional microplate reader. We show that the educational spectrometer gives a result on the CC50 value that is in agreement with the acceptable values of the official protocol. We include a comment on the results when performing this laboratory exercise in one class of 18 year old students (in their last year of secondary education). The experiment can be also successfully applied in the laboratory practicum of first year university study.

Biosafety risks, control, and biocontainment of engineered microalgae

Microalgae, with the ability to harness solar energy to fix CO2 and convert it into organic compounds, have emerged as promising green cell factories. With the rapid development of cutting-edge biotechnologies, the research and application of photosynthetic microalgae have been expanding, leading to comprehensive and in-depth engineering of microalgae. The synthetic biology and genome editing technologies have enabled the applications of microalgae in medicine, agriculture, food, energy, and the environment. However, the survival and spreading of engineered microalgae in the natural environment pose potential safety risks to ecosystems and human health. To curb the risks caused by the spreading of engineered microalgae in the environment, biosafety policies should be formulated for engineered microalgae and the prevention and control technologies should be developed. Toward this goal, researchers have developed biocontainment systems, including positive strategies such as the design of toxic protein-based kill switches and passive strategies such as knocking out essential genes to construct the strains with nutritional deficiencies, thereby spatially containing engineered microalgae. This article summarizes the application of cutting-edge biotechnologies in the engineering of microalgae, the biosafety risks and management regulations associated with the escape of engineered microalgae, and the progress in novel biocontainment technologies established for engineered microalgae. Finally, this article gives insights into the future development direction of microalgae biocontainment.