Biology Technology Research Articles

Current Technologies in Snake Venom Analysis and Applications

This comprehensive review explores the cutting-edge advancements in snake venom research, focusing on the integration of proteomics, genomics, transcriptomics, and bioinformatics. Highlighting the transformative impact of these technologies, the review delves into the genetic and ecological factors driving venom evolution, the complex molecular composition of venoms, and the regulatory mechanisms underlying toxin production. The application of synthetic biology and multi-omics approaches, collectively known as venomics, has revolutionized the field, providing deeper insights into venom function and its therapeutic potential. Despite significant progress, challenges such as the functional characterization of toxins and the development of cost-effective antivenoms remain. This review also discusses the future directions of venom research, emphasizing the need for interdisciplinary collaborations and new technologies (mRNAs, cryo-electron microscopy for structural determinations of toxin complexes, synthetic biology, and other technologies) to fully harness the biomedical potential of venoms and toxins from snakes and other animals.

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

Background and Objectives: 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 immuno- genic 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. Materials and Methods: 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. Results: The induction of strong humoral immune responses proved the strong immunoreactivity of the recombinant protein. Conclusion: 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.

Characterizing Marine Medaka (Oryzias melastigma) Haploid Embryonic Stem Cells: A Valuable Tool for Marine Fish Genetic Research.

Haploid embryonic stem cells (ESCs), which combine the properties of haploidy and pluripotency, hold significant potential for advancing developmental biology and reproductive technology. However, while previous research has largely focused on haploid ESCs in freshwater species like Japanese medaka (Oryzias latipes), little is known about their counterparts in marine species. This study hypothesizes that haploid ESCs from marine fish could offer unique insights and tools for genetic and virological research. To address this, we successfully established and characterized a novel haploid ESC line, hMMES1, derived from marine medaka (Oryzias melastigma). The hMMES1 cells contain 24 chromosomes, exhibit core stem cell characteristics, and express key pluripotency markers. In vitro, hMMES1 cells form embryonic bodies (EBs) capable of differentiating into the three germ layers. In vivo, hMMES1 cells were successfully transplanted into marine medaka and zebrafish, resulting in the generation of interspecies and interordinal chimeras. Additionally, hMMES1 cells demonstrate high efficiency in transfection and transduction, and show susceptibility to major aquaculture viruses, nodavirus (NNV) and iridovirus (SGIV). These findings suggest that hMMES1 cells represent a valuable model for genetic manipulation and virological studies in marine fish species.

Recent Toolboxes for Chemoselective Dual Modifications of Proteins.

Site-selective chemical modifications of proteins have emerged as a potent technology in chemical biology, materials science, and medicine, facilitating precise manipulation of proteins with tailored functionalities for basic biology research and developing innovative therapeutics. Compared to traditional recombinant expression methods, one of the prominent advantages of chemical protein modification lies in its capacity to decorate proteins with a wide range of functional moieties, including non-genetically encoded ones, enabling the generation of novel protein conjugates with enhanced or previously unexplored properties. Among these, approaches for dual or multiple modifications of proteins are increasingly garnering attention, as it has been found that single modification of proteins is inadequate to meet current demands. Therefore, in light of the rapid developments in this field, this review provides a timely and comprehensive overview of the latest advancements in chemical and biological approaches for dual functionalization of proteins. It further discusses their advantages, limitations, and potential future directions in this relatively nascent area.

Fire needle therapy for the treatment of cancer pain: a protocol for the systematic review and meta-analysis.

Cancer patients frequently suffer pain as one of their symptoms. It includes acute and chronic pain and is one of the most feared symptoms for patients. About one-third of adults actively undergoing cancer treatment suffer from pain related to their condition. Cancer pain control remains suboptimal due to a lack of assessment, knowledge, and access. Fire needle therapy, a traditional Chinese medicine, offers a potentially beneficial addition to current pain management approaches. This protocol outlines a systematic review and meta-analysis to compile evidence and examine the pain-relieving effects and safety of fire needle therapy for cancer patients. We will systematically search China National Knowledge Infrastructure (CNKI), Wanfang Database, China Biology Medicine disc (CBM), China Science and Technology Journal Database (CSTJ or VIP), PubMed, Web of Science, Embase, Cochrane Central Registry of Controlled Trials (CENTRAL), Chinese Clinical Trial Registry (Chictr), Opengrey, Worldcat, and Scopus from inception through July 2023. Random control trials (RCTs) include all types of cancer patients (age ≥ 18 years) complaining of pain. The primary outcome will be changes in pain intensity measured by Visual Analogue Scale (VAS), Numerical Rating Scale (NRS), Neuropathic Pain Scale (NPS), or Brief Pain Inventory (BPI). Secondary outcomes include quality of life (EORTC QLQ-C30 and GCQ), performance status (KPS), times of burst pain, treatment response rate, the dose reduction of analgesic drugs, and side effects rates. Utilizing the Cochrane risk bias measurement tool: Risk of Bias 2 (RoB 2), the trials' quality will be evaluated, and meta-analysis will be performed using RevMan software (version 5.4). This systematic review will be the first comprehensive review of the literature to provide a meta-analysis of fire needle therapy for cancer pain, including only Random control trials (RCTs). For the sake of transparency and to avoid future duplication, the publication of this protocol offers a clear illustration of the procedures utilized in this evaluation. The results of our future studies may provide a new approach and theoretical basis for the treatment of cancer pain by medical oncology professionals. https://www.crd.york.ac.uk/prospero/, identifier CRD42023418609.

Parallel reaction monitoring targeted mass spectrometry as a fast and sensitive alternative to antibody-based protein detection

The reliable, accurate and quantitative targeted detection of proteins is a key technology in molecular and cell biology and molecular diagnostics. The current golden standard for targeted protein detection in complex mixtures such as complete cell lysates or body fluids is immunoblotting, a technology that was developed in the late 1970s and has not undergone major changes since. Although widespread, this methodology suffers from several disadvantages, such as the inability to detect low-abundant proteins or specific posttranslational modifications, the requirement for highly specific antibodies, the lack of quantitative power and the often-tedious practical procedures. Mass spectrometry (MS) based targeted protein detection is an alternative technology that could circumvent these caveats. Here, we compare immunoblotting with targeted protein mass spectrometry using a parallel reaction monitoring (PRM) regime on the Orbitrap mass spectrometer. We show that PRM based MS has superior sensitivity and quantitative accuracy over immunoblotting. The limit of detection for proteolytic peptides of a purified target protein was found to be in the mid- to low-attomole range and approximately one order of magnitude higher when embedded in a complex biological matrix. The incorporation of synthetic heavy isotope labeled (AQUA) peptides as internal calibrants into the PRM workflow allows for even higher accuracy for both the relative and absolute quantitation of tryptic target peptides. In conclusion, PRM is a versatile and sensitive technology, which can overcome the shortcomings of immunoblotting. We argue that PRM based MS could become the method of choice for the targeted detection of proteins in complex cellular matrices or body fluids and may eventually replace standard methods such as Western blotting and ELISA in biomedical research and in the clinic.

Current Treatment Methods for Charcot-Marie-Tooth Diseases.

Charcot-Marie-Tooth (CMT) disease, the most common inherited neuromuscular disorder, exhibits a wide phenotypic range, genetic heterogeneity, and a variable disease course. The diverse molecular genetic mechanisms of CMT were discovered over the past three decades with the development of molecular biology and gene sequencing technologies. These methods have brought new options for CMT reclassification and led to an exciting era of treatment target discovery for this incurable disease. Currently, there are no approved disease management methods that can fully cure patients with CMT, and rehabilitation, orthotics, and surgery are the only available treatments to ameliorate symptoms. Considerable research attention has been given to disease-modifying therapies, including gene silencing, gene addition, and gene editing, but most treatments that reach clinical trials are drug treatments, while currently, only gene therapies for CMT2S have reached the clinical trial stage. In this review, we highlight the pathogenic mechanisms and therapeutic investigations of different subtypes of CMT, and promising therapeutic approaches are also discussed.

End-to-End Technologies in Medicine, Pharmacy and Biology

The article raises the topical issue of the use of end-to-end technologies for medicine, pharmacy, and biology. The analysis of the use of new technologies in these areas is carried out at the present time. The authors are looking for ways to solve the problem of teaching humanities and natural sciences at a medical university using the capabilities of modern technologies. A random sampling method using the capabilities of Goole forms was used to conduct a survey of 2nd year students of the medical university and teachers working with them. The level of training, the needs of students for new knowledge on modern end-to-end technologies, and the possibilities of implementing training programs are discussed. The survey showed that despite the widespread introduction of end-to-end technologies, the knowledge of students and teachers in this area is extremely limited. Students have a need to acquire new knowledge that can be applied in their future profession. Several solutions to the problem of teaching student’s new technologies and their practical application in medicine, pharmacy, and biology are proposed. The survey also showed that there are two possible options: 1) the introduction of a separate optional course into the curriculum; 2) teachers can talk about the possibilities of new technologies and their use during the study of the discipline. For effective teaching, teachers must improve their skills in a timely manner by taking courses. With an integrated approach, a quick and effective solution to the task is possible.

Data Integration and Management in Bioinformatics

Bioinformatics is an interdisciplinary field that combines biology, computer science, and information technology to understand and analyze biological data. With the development of high-throughput sequencing technology and other biotechnologies, the speed and scale of biological data generation are unprecedented. Effectively integrating and managing these data has become a significant challenge. This paper explores the current state of bioinformatics data integration and management, the challenges faced, commonly used methods and tools, and future development directions.

Cutting-edge developments in acute myeloid leukaemia: innovations in diagnosis and treatment

Acute Myeloid Leukaemia (AML) is a fast-growing hematologic malignancy that is distinguished by the clonal proliferation of myeloid progenitors in bone marrow. Recent advances in molecular biology and genomic technology have altered the landscape of AML diagnosis and therapy, resulting in more tailored and successful therapeutic approaches. This study reviews recent innovations in the diagnosis and treatment of AML, focusing on genomic profiling, next-generation sequencing (NGS), and novel targeted therapies. Data was collected from recent clinical trials, peer-reviewed journals, and case studies. Comparative analysis was conducted to evaluate the efficacy of emerging diagnostic tools and treatments. NGS and MRD monitoring have greatly improved diagnosis accuracy and therapy customization. Targeted medicines have enhanced remission rates and decreased recurrence rates in individuals with certain genetic alterations. Immunotherapies have showed long-term efficacy and controllable safety profiles. Combining modern diagnostic technologies with customized medicines ushers in a new era of AML care, enhancing prognosis and quality of life. Ongoing research and clinical trials are critical for improving these therapies and expanding their advantages to a larger patient group.

The applications of artificial intelligence in personalized medicine

Personalized medicine provides advanced diagnostics, customized therapies, and proactive health management, taking into account the distinct genetic and socioeconomic profiles of each patient. The rapid development of contemporary technologies, such as the combination of biology and information technology, has laid a solid foundation for the development of artificial intelligence in the field of personalized medicine. This article primarily explores the application of artificial intelligence (AI) to personalized diagnosis and treatment. Firstly, AI can use big data analysis, machine learning, and especially deep learning to quickly detect early disease indicators from massive medical data to provide patients with more accurate diagnosis and prediction. Secondly, AI can help develop a more personalized treatment plans by analyzing relevant data such as patients' genetic information, lifestyle, and social environment. This article focuses on the technical advantages and current applications of AI in personalized medicine to better understand the known challenges and future potential of the field.

The molecular basis of flavonoid biosynthesis response to water, light, and temperature in grape berries.

Flavonoids, including proanthocyanidins (PAs), anthocyanins and flavonols are essential secondary metabolites that contribute to the nutritional value and sensory quality of grape berry and red wine. Advances in molecular biology technology have led to substantial progress in understanding the regulation of flavonoid biosynthesis. The influence of terroir on grape berries and wine has garnered increasing attention, yet its comprehensive regulatory network remains underexplored. In terms of application, environmental factors such as water, light, and temperature are more easily regulated in grapevines compared to soil conditions. Therefore, we summarize their effects on flavonoid content and composition, constructing a network that links environmental factors, hormones, and metabolites to provide a deeper understanding of the underlying mechanisms. This review enriches the knowledge of the regulatory network mechanisms governing flavonoid responses to environmental factors in grapes.

Integrated Review of Transcriptomic and Proteomic Studies to Understand Molecular Mechanisms of Rice's Response to Environmental Stresses.

Rice (Oryza sativa L.) is grown nearly worldwide and is a staple food for more than half of the world's population. With the rise in extreme weather and climate events, there is an urgent need to decode the complex mechanisms of rice's response to environmental stress and to breed high-yield, high-quality and stress-resistant varieties. Over the past few decades, significant advancements in molecular biology have led to the widespread use of several omics methodologies to study all aspects of plant growth, development and environmental adaptation. Transcriptomics and proteomics have become the most popular techniques used to investigate plants' stress-responsive mechanisms despite the complexity of the underlying molecular landscapes. This review offers a comprehensive and current summary of how transcriptomics and proteomics together reveal the molecular details of rice's response to environmental stresses. It also provides a catalog of the current applications of omics in comprehending this imperative crop in relation to stress tolerance improvement and breeding. The evaluation of recent advances in CRISPR/Cas-based genome editing and the application of synthetic biology technologies highlights the possibility of expediting the development of rice cultivars that are resistant to stress and suited to various agroecological environments.

Role of HSP90 in Type 2 Diabetes Mellitus and Its Association with Liver Diseases.

Non-alcoholic fatty acid liver disease (NAFLD), non-alcoholic steatohepatitis (NASH) and hepatocellular carcinoma (HCC) are the fatal liver diseases which encompass a spectrum of disease severity associated with increased risk of type 2 diabetes mellitus (T2DM), a metabolic disorder. Heat shock proteins serve as markers in early prognosis and diagnosis of early stages of liver diseases associated with metabolic disorder. This review aims to comprehensively investigate the significance of HSP90 isoforms in T2DM and liver diseases. Additionally, we explore the collective knowledge on plant-based drug compounds that regulate HSP90 isoform targets, highlighting their potential in treating T2DM-associated liver diseases. Furthermore, this review focuses on the computational systems' biology and next-generation sequencing technology approaches that are used to unravel the potential medicine for the treatment of pleiotropy of these 2 diseases and to further elucidate the mechanism.