BioTech最新文献

{"title":"From Sequence to Solution: Intelligent Learning Engine Optimization in Drug Discovery and Protein Analysis.","authors":"Jamal Raiyn, Adam Rayan, Saleh Abu-Lafi, Anwar Rayan","doi":"10.3390/biotech13030033","DOIUrl":"10.3390/biotech13030033","url":null,"abstract":"<p><p>This study introduces the intelligent learning engine (ILE) optimization technology, a novel approach designed to revolutionize screening processes in bioinformatics, cheminformatics, and a range of other scientific fields. By focusing on the efficient and precise identification of candidates with desirable characteristics, the ILE technology marks a significant leap forward in addressing the complexities of candidate selection in drug discovery, protein classification, and beyond. The study's primary objective is to address the challenges associated with optimizing screening processes to efficiently select candidates across various fields, including drug discovery and protein classification. The methodology employed involves a detailed algorithmic process that includes dataset preparation, encoding of protein sequences, sensor nucleation, and optimization, culminating in the empirical evaluation of molecular activity indexing, homology-based modeling, and classification of proteins such as G-protein-coupled receptors. This process showcases the method's success in multiple sequence alignment, protein identification, and classification. Key results demonstrate the ILE's superior accuracy in protein classification and virtual high-throughput screening, with a notable breakthrough in drug development for assessing drug-induced long QT syndrome risks through hERG potassium channel interaction analysis. The technology showcased exceptional results in the formulation and evaluation of novel cancer drug candidates, highlighting its potential for significant advancements in pharmaceutical innovations. The findings underline the ILE optimization technology as a transformative tool in screening processes due to its proven effectiveness and broad applicability across various domains. This breakthrough contributes substantially to the fields of systems optimization and holds promise for diverse applications, enhancing the process of selecting candidate molecules with target properties and advancing drug discovery, protein classification, and modeling.</p>","PeriodicalId":34490,"journal":{"name":"BioTech","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11417716/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142297152","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Auxin-Producing Bacteria Used as Microbial Biostimulants Improve the Growth of Tomato (<i>Solanum lycopersicum</i> L.) Seedlings in Hydroponic Systems.","authors":"Livia Pappalettere, Susanna Bartolini, Annita Toffanin","doi":"10.3390/biotech13030032","DOIUrl":"10.3390/biotech13030032","url":null,"abstract":"<p><p>Seven auxin-producing endophytic bacterial strains (<i>Azospirillum</i> spp., <i>Methylobacterium symbioticum</i>, <i>Bacillus</i> spp.), and two different combinations of these strains were used to verify their influence on tomato during germination and development in hydroponic conditions where, as a novelty for Canestrino di Lucca cultivar, endophytic bacteria were inoculated. To emphasize the presence of bacterial auxins in roots and stems of seedlings, both in situ staining qualitative assessment and quantitative analysis were carried out. Moreover, hypogeal and epigeal growth of the plantlets were measured, and correlation analyses were conducted to examine the relationship between the amount of indolacetic acid (IAA) produced by the bacterial strains and root and stem parameters. Plantlets treated with microbial inoculants showed a significant increase in the survival rate compared to the control treatment. The best results as IAA producers were from <i>Azospirillum baldaniorum</i> Sp245 and <i>A. brasilense</i> Cd, which also induced significant root growth. On the other hand, <i>Bacillus amyloliquefaciens</i> and <i>B. licheniformis</i> induced the best rates in stem growth. These findings highlight the potential for using endophytic bacterial strains in a hydroponic co-cultivation system that enables inoculating plantlets, at an early stage of growth (5 days old).</p>","PeriodicalId":34490,"journal":{"name":"BioTech","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11348165/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142074064","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Principle Investigation and Method Standardization of Inhibition Zone Assay Based on Antimicrobial Peptides Extracted from Black Soldier Fly Larvae","authors":"Wenyue Shen, Ranxia Xue, Yanxia Liu, Shibo Sun, Xi Chen, Dongye Sun, Ouyang Han, Yuxin Li, Jianqiang Xu, Xiaoying Dong, Fengyun Ji, Weiping Xu","doi":"10.3390/biotech13030031","DOIUrl":"https://doi.org/10.3390/biotech13030031","url":null,"abstract":"The black soldier fly is a valuable resource insect capable of transforming organic waste while producing antimicrobial peptides (AMPs). The inhibition zone assay (IZA) is a method used to demonstrate the antimicrobial activity of AMPs. This study aimed to examine the experimental principles and establish a standardized IZA method. Results indicated that the AMPs extract consisted of proteins ranging in molecular weights from 0 to 40 kDa. The AMPs diffused radially on an agar plate through an Oxford cup. The diffusion radius was influenced by the concentration and volume of the AMPs but ultimately determined by the mass of the AMPs. The swabbing method was found to be effective for inoculating bacteria on the agar plate. Among the conditions tested, the plate nutrient concentration was the most sensitive factor for the IZA, followed by bacterial concentration and incubation time. Optimal conditions for the IZA included a nutrient plate of 0.5× TSA, a bacterial concentration of 106 CFU/mL, and an incubation time of 12 h, with oxytetracycline (OTC) at 0.01 mg/mL serving as the positive control. The antimicrobial-specific activity of AMPs could be standardized by the ratio of inhibition zone diameters between AMPs and OTC. These findings contribute to the standardization of the IZA method for profiling the antimicrobial activity of AMPs.","PeriodicalId":34490,"journal":{"name":"BioTech","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141925362","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CleanUpRNAseq: An R/Bioconductor Package for Detecting and Correcting DNA Contamination in RNA-Seq Data.","authors":"Haibo Liu, Kai Hu, Kevin O'Connor, Michelle A Kelliher, Lihua Julie Zhu","doi":"10.3390/biotech13030030","DOIUrl":"10.3390/biotech13030030","url":null,"abstract":"<p><p>RNA sequencing (RNA-seq) has become a standard method for profiling gene expression, yet genomic DNA (gDNA) contamination carried over to the sequencing library poses a significant challenge to data integrity. Detecting and correcting this contamination is vital for accurate downstream analyses. Particularly, when RNA samples are scarce and invaluable, it becomes essential not only to identify but also to correct gDNA contamination to maximize the data's utility. However, existing tools capable of correcting gDNA contamination are limited and lack thorough evaluation. To fill the gap, we developed CleanUpRNAseq, which offers a comprehensive set of functionalities for identifying and correcting gDNA-contaminated RNA-seq data. Our package offers three correction methods for unstranded RNA-seq data and a dedicated approach for stranded data. Through rigorous validation on published RNA-seq datasets with known levels of gDNA contamination and real-world RNA-seq data, we demonstrate CleanUpRNAseq's efficacy in detecting and correcting detrimental levels of gDNA contamination across diverse library protocols. CleanUpRNAseq thus serves as a valuable tool for post-alignment quality assessment of RNA-seq data and should be integrated into routine workflows for RNA-seq data analysis. Its incorporation into OneStopRNAseq should significantly bolster the accuracy of gene expression quantification and differential expression analysis of RNA-seq data.</p>","PeriodicalId":34490,"journal":{"name":"BioTech","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11348166/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142074065","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular Insight into the Response of Lactic Acid Bacteria to Bile Acids.","authors":"Caren N Moreno, Jorge N Gomez, María P Taranto, Ana E Ledesma, Ana Y Bustos","doi":"10.3390/biotech13030029","DOIUrl":"10.3390/biotech13030029","url":null,"abstract":"<p><p>Bile acids (BAs) are the main endogenous modulators of the composition and metabolic activity of the intestinal microbiota. In the present work, the effect of conjugated (glycodeoxycholic, glycocholic, taurodeoxycholic, taurocholic acids) and free BAs [cholic acid (CA) and deoxycholic acid (DCA)] on the survival, biological molecules, and structural and surface properties of two potential probiotic lactic acid bacteria (LAB) was evaluated. For this, viability assays, Raman spectroscopy, scanning electron microscopy (SEM), and zeta potential (ZP) measurements were employed. Our results evidenced that free BAs were more toxic than conjugates, with CA being significantly more harmful than deoxycholic acid (DCA). RAMAN studies show that BAs modify the bands corresponding to proteins, lipids, carbohydrates, and DNA. SEM showed that BAs cause surface distortions with depressions and fold formation, as well as incomplete cell division. DCA was the one that least altered the ZP of bacteria when compared to CA and taurodeoxycholic acid, with gradual changes towards more positive values. In general, the magnitude of these effects was different according to the BA and its concentration, being more evident in the presence of CA, even at low concentrations, which would explain its greater inhibitory effect. This work provides solid evidence on the effects of BAs on LAB that will allow for the development of strategies by which to modulate the composition of the microbiota positively.</p>","PeriodicalId":34490,"journal":{"name":"BioTech","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11348023/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142074066","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Removal of Cadmium (II) from Aqueous Solution Using <i>Galdieria sulphuraria</i> CCMEE 5587.1.","authors":"Hari Lal Kharel, Lina Jha, Melissa Tan, Thinesh Selvaratnam","doi":"10.3390/biotech13030028","DOIUrl":"10.3390/biotech13030028","url":null,"abstract":"<p><p>The release of cadmium into the environment is a significant global concern due to its toxicity, non-biodegradability, and persistence in nature. There is an urgent need for effective, eco-friendly, and cost-effective systems for removing Cd because of the many drawbacks of conventional physicochemical techniques. This study investigated the ability of the extremophile red microalgal strain <i>Galdieria sulphuraria</i> CCMEE 5587.1 to tolerate and remove Cd (II) ions at acidic pH in a controlled laboratory environment. Three distinct concentrations of Cd (1.5 mg L^-1, 3 mg L^-1, and 6 mg L^-1) were introduced to the cyanidium medium, and <i>G. sulphuraria</i> cells were introduced in the medium and grown for ten days. Four distinct aspects were identified regarding Cd removal: time course Cd removal, total Cd removal, extracellular Cd removal, and intracellular Cd removal. The inhibitory effects of Cd on <i>G. sulphuraria</i> growth were observed using a daily growth profile. Initial incubation days showed an inhibition of <i>G. sulphuraria</i> growth. In addition, increasing the Cd concentration in the medium decreased the growth rate of <i>G. sulphuraria</i>. Rapid Cd removal occurred on the first day of the experiment, followed by a steady removal of Cd until the last day. The highest total removal efficiency occurred in a medium containing 3 mg L^-1 of Cd ions, which was 30%. In contrast, the highest sorption capacity occurred in a medium containing 6 mg L^-1 of Cd ions, which was 1.59 mg g^-1 of dry biomass. In all media compositions, a major fraction (>80%) of Cd removal occurred via adsorption on the cell surface (extracellular). These results showed that <i>G. sulphuraria</i> cells can remove Cd ions from aqueous solution, which makes them a potential bioremediation option for heavy metal removal.</p>","PeriodicalId":34490,"journal":{"name":"BioTech","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11348382/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142074067","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hydroponics with Microalgae and Cyanobacteria: Emerging Trends and Opportunities in Modern Agriculture.","authors":"Prabhaharan Renganathan, Edgar Omar Rueda Puente, Natalia V Sukhanova, Lira A Gaysina","doi":"10.3390/biotech13030027","DOIUrl":"10.3390/biotech13030027","url":null,"abstract":"<p><p>The global population is expected to reach 9.5 billion, which means that crop productivity needs to double to meet the growing population's food demand. Soil degradation and environmental factors, such as climate events, significantly threaten crop production and global food security. Furthermore, rapid urbanization has led to 55% of the world's population migrating to cities, and this proportion is expected to increase to 75% by 2050, which presents significant challenges in producing staple foods through conventional hinterland farming. Numerous studies have proposed various sustainable farming techniques to combat the shortage of farmable land and increase food security in urban areas. Soilless farming techniques such as hydroponics have gained worldwide popularity due to their resource efficiency and production of superior-quality fresh products. However, using chemical nutrients in a conventional hydroponic system can have significant environmental impacts, including eutrophication and resource depletion. Incorporating microalgae into hydroponic systems as biostimulants offers a sustainable and ecofriendly approach toward circular bioeconomy strategies. The present review summarizes the plant growth-promoting activity of microalgae as biostimulants and their mechanisms of action. We discuss their effects on plant growth parameters under different applications, emphasizing the significance of integrating microalgae into a closed-loop circular economy model to sustainably meet global food demands.</p>","PeriodicalId":34490,"journal":{"name":"BioTech","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11270261/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141761416","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Strategies for Increasing the Throughput of Genetic Screening: Lessons Learned from the COVID-19 Pandemic within a University Community","authors":"Fernanda Miguel, A. R. Baleizão, A. G. Gomes, Helena Caria, Fátima N. Serralha, Marta C. Justino","doi":"10.3390/biotech13030026","DOIUrl":"https://doi.org/10.3390/biotech13030026","url":null,"abstract":"Amidst the COVID-19 pandemic, the Polytechnic University of Setúbal (IPS) used its expertise in molecular genetics to establish a COVID-19 laboratory, addressing the demand for community-wide testing. Following standard protocols, the IPS COVID Lab received national accreditation in October 2020 and was registered in February 2021. With the emergence of new SARS-CoV-2 variants and safety concerns for students and staff, the lab was further challenged to develop rapid and sensitive diagnostic technologies. Methodologies such as sample-pooling extraction and multiplex protocols were developed to enhance testing efficiency without compromising accuracy. Through Real-Time Reverse Transcription Polymerase Chain Reaction (RT-qPCR) analysis, the effectiveness of sample pooling was validated, proving to be a clear success in COVID-19 screening. Regarding multiplex analysis, the IPS COVID Lab developed an in-house protocol, achieving a sensitivity comparable to that of standard methods while reducing operational time and reagent consumption. This approach, requiring only two wells of a PCR plate (instead of three for samples), presents a more efficient alternative for future testing scenarios, increasing its throughput and testing capacity while upholding accuracy standards. The lessons learned during the SARS-CoV-2 pandemic provide added value for future pandemic situations.","PeriodicalId":34490,"journal":{"name":"BioTech","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141658256","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In Vitro: The Extraordinary Enhancement in Rutin Accumulation and Antioxidant Activity in Philodendron “Imperial Red” Plantlets Using Ti-Mo-Ni-O Nanotubes as a Novel Elicitor","authors":"Hanan S. Ebrahim, Nourhan M. Deyab, B. Shaheen, A. Gabr, Nageh K. Allam","doi":"10.3390/biotech13030024","DOIUrl":"https://doi.org/10.3390/biotech13030024","url":null,"abstract":"Rutin, a flavonoid phytochemical compound, plays a vital role in human health. It is used in treating capillary fragility and has anti-Alzheimer, anti-inflammatory, and antioxidant effects. In this study, Ti-Mo-Ni-O nanotubes (NTs) were used, for the first time, in an unprecedented plant biotechnology application, wherein in vitro Philodendron shoots (Philodendron erubescens) known as “Imperial Red” were targeted for rutin accumulation. The antioxidant responses and the accumulation of rutin were evaluated in treated Philodendron erubescens (P. erubescens) shoots using 5.0 mg/L of Ti-Mo-Ni-O NTs. The total phenolic content and total flavonoid content were estimated, and an ABTS+ assay, FRAP assay, and iron metal chelation assay were performed. The application of Ti-Mo-Ni-O NTs enhanced the rutin content considerably from 0.02 mg/g to 2.96 mg/g for dry-weight shootlet extracts. Therefore, the use of Ti-Mo-Ni-O NTs is proposed to be a superior alternative to elevate the rutin content. The aim of the current study is to target P. erubescens shoots grown in vitro for the accumulation of rutin compounds using Ti-Mo-Ni-O NT powder, to determine the quantitative and qualitative accumulation of rutin via HPLC–DAD analysis, and to estimate the antioxidant activity of P. erubescens shoot extract. This study presents a novel methodology for utilizing nano-biotechnology in the synthesis of plant secondary metabolites.","PeriodicalId":34490,"journal":{"name":"BioTech","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141677307","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An Efficient and Rapid Protocol for Somatic Shoot Organogenesis from Juvenile Hypocotyl-Derived Callus of Castor Bean cv. Zanzibar Green","authors":"Danaya V. Demidenko, N. V. Varlamova, Taisiya M. Soboleva, A. V. Shitikova, M. Khaliluev","doi":"10.3390/biotech13030025","DOIUrl":"https://doi.org/10.3390/biotech13030025","url":null,"abstract":"Aseptic seedlings of different ages derived from surface-sterilized mature seeds were applied as an explant source. Various explants such as 7- and 21-day-old hypocotyl fragments, 42-day-old nodal stem segments, and transverse nodal segments of stem, as well as leaf petioles, were cultured on the agar-solidified Murashige and Skoog (MS) basal medium supplemented with 0.1 mg/L IAA, 5 mg/L AgNO3 and different types and concentrations of cytokinin (1 mg/L zeatin, 0.25 mg/L thidiazuron (TDZ), and 5 mg/L 6-benzylaminopurine (6-BAP)). Consequently, it was found that 7- and 21-day-old hypocotyl fragments, as well as nodal stem segments obtained from adult aseptic seedlings, are characterized by a high explant viability and callus formation capacity with a frequency of 79.7–100%. However, the success of in vitro somatic shoot organogenesis was significantly determined not only by the culture medium composition and explant type but also depending on its age, as well as on the size and explant preparation in cases of hypocotyl and age-matched nodal stem fragments, respectively. Multiple somatic shoot organogenesis (5.7 regenerants per explant) with a frequency of 67.5% was achieved during 3 subcultures of juvenile hypocotyl-derived callus tissue on MS culture medium containing 0.25 mg/L TDZ as cytokinin source. Castor bean regenerants were excised from the callus and successfully rooted on ½ MS basal medium without exogenous auxin (81%). In vitro plantlets with well-developed roots were adapted to ex vitro conditions with a frequency of 90%.","PeriodicalId":34490,"journal":{"name":"BioTech","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141680028","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}