Recently, a unique behavior of T7 RNA polymerase has expanded its functionality as a biosensing platform. Various biosensors utilizing T7 RNA polymerase, combined with fluorescent aptamers, electrochemical probes, or CRISPR/Cas systems, have been developed to detect analytes, including nucleic acids and non-nucleic acid target, with high specificity and low detection limits. Each approach demonstrates unique strengths, such as real-time monitoring and minimal interference, but also presents challenges in stability, cost, and reaction optimization. This review provides an overview of T7 RNA polymerase's role in biosensing technology, highlighting its potential to advance diagnostics and molecular detection in diverse fields.
{"title":"Current biosensing strategies based on in vitro T7 RNA polymerase reaction","authors":"David Septian Sumanto Marpaung , Ayu Oshin Yap Sinaga , Damayanti Damayanti , Taharuddin Taharuddin , Setyadi Gumaran","doi":"10.1016/j.biotno.2025.01.002","DOIUrl":"10.1016/j.biotno.2025.01.002","url":null,"abstract":"<div><div>Recently, a unique behavior of T7 RNA polymerase has expanded its functionality as a biosensing platform. Various biosensors utilizing T7 RNA polymerase, combined with fluorescent aptamers, electrochemical probes, or CRISPR/Cas systems, have been developed to detect analytes, including nucleic acids and non-nucleic acid target, with high specificity and low detection limits. Each approach demonstrates unique strengths, such as real-time monitoring and minimal interference, but also presents challenges in stability, cost, and reaction optimization. This review provides an overview of T7 RNA polymerase's role in biosensing technology, highlighting its potential to advance diagnostics and molecular detection in diverse fields.</div></div>","PeriodicalId":100186,"journal":{"name":"Biotechnology Notes","volume":"6 ","pages":"Pages 59-66"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11788683/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143124309","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}
Pub Date : 2025-01-01DOI: 10.1016/j.biotno.2024.12.002
S.A. Razzak
This study investigates the potential of phototrophic microalgae, specifically Chlorella protothecoides, for biological wastewater treatment, with a focus on the effects of air temperature and CO2 concentration on nutrient removal from tertiary municipal wastewater. Utilizing both the Monod and Arrhenius kinetic models, the research examines how temperature and nutrient availability influence microalgal growth and nutrient removal. The study finds that optimal biomass productivity occurs at 25 °C, with growth slowing at higher temperatures (30 °C, 40 °C, and 45 °C). The Monod and Arrhenius models, which showed strong agreement with experimental data, revealed that temperature significantly impacted growth kinetics, with the Arrhenius model accurately predicting growth rates at lower temperatures. Activation energies for growth and cell death were determined as 5.4 kJ mol⁻1 and 88.4 kJ mol⁻1, respectively. The study also demonstrated that optimal nitrogen and phosphorus removal occurred at 25°C-30 °C, with 100 % total nitrogen (TN) removal and 85 % total phosphorus (TP) removal achieved at 30 °C. Additionally, CO2 concentration influenced biomass productivity, with peak productivity and nutrient removal at 6 % CO2, highlighting the importance of CO2 levels in optimizing growth and nutrient elimination. These findings provide valuable insights into optimizing conditions for microalgae-based wastewater treatment, particularly in seasonal cultivation strategies, and contribute to improving biodiesel production and nutrient removal efficiency.
{"title":"Effect of temperature and CO2 concentration on biological nutrient removal from tertiary municipal wastewater using microalgae Chlorella prototheocoides","authors":"S.A. Razzak","doi":"10.1016/j.biotno.2024.12.002","DOIUrl":"10.1016/j.biotno.2024.12.002","url":null,"abstract":"<div><div>This study investigates the potential of phototrophic microalgae, specifically Chlorella protothecoides, for biological wastewater treatment, with a focus on the effects of air temperature and CO<sub>2</sub> concentration on nutrient removal from tertiary municipal wastewater. Utilizing both the Monod and Arrhenius kinetic models, the research examines how temperature and nutrient availability influence microalgal growth and nutrient removal. The study finds that optimal biomass productivity occurs at 25 °C, with growth slowing at higher temperatures (30 °C, 40 °C, and 45 °C). The Monod and Arrhenius models, which showed strong agreement with experimental data, revealed that temperature significantly impacted growth kinetics, with the Arrhenius model accurately predicting growth rates at lower temperatures. Activation energies for growth and cell death were determined as 5.4 kJ mol⁻<sup>1</sup> and 88.4 kJ mol⁻<sup>1</sup>, respectively. The study also demonstrated that optimal nitrogen and phosphorus removal occurred at 25°C-30 °C, with 100 % total nitrogen (TN) removal and 85 % total phosphorus (TP) removal achieved at 30 °C. Additionally, CO<sub>2</sub> concentration influenced biomass productivity, with peak productivity and nutrient removal at 6 % CO<sub>2</sub>, highlighting the importance of CO<sub>2</sub> levels in optimizing growth and nutrient elimination. These findings provide valuable insights into optimizing conditions for microalgae-based wastewater treatment, particularly in seasonal cultivation strategies, and contribute to improving biodiesel production and nutrient removal efficiency.</div></div>","PeriodicalId":100186,"journal":{"name":"Biotechnology Notes","volume":"6 ","pages":"Pages 32-43"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11728070/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142981030","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}
Indian tick typhus is an infectious disease caused by intracellular gram-negative bacteria Rickettsia conorii (R. conorii). The bacterium is transmitted to humans through bite of infected ticks and sometimes by lice, fleas or mites. The disease is restricted to some areas with few cases but in last decade it is re-emerging with large number of cases from different areas of India. The insight in to genetic makeup of bacterial pathogens can be derived from their metabolic pathways. In the current study 18 metabolic pathways were found to be unique to the pathogen (R. conorii). A comprehensive analysis revealed 163 proteins implicated in 18 unique metabolic pathways of R. conorii. 140 proteins were reported to be essential for the bacterial survival, 46 were found virulent and 10 were found involved in resistance which can enhance the bacterial pathogenesis. The functional analysis of unique metabolic pathway proteins showed the abundance of plasmid conjugal transfer TrbL/VirB6, aliphatic acid kinase short chain, signal transduction response regulator receiver and components of type IV transporter system domains. The proteins were classified into six broad categories on the basis of predicted domains, i.e., metabolism, transport, gene expression and regulation, antimicrobial resistance, cell signalling and proteolysis. Further, in silico analysis showed that 88 proteins were suitable therapeutic targets which do not showed homology with host proteins. The 43 proteins showed hits with the DrugBank database showing their druggable nature and remaining 45 proteins were classified as novel drug targets that require further validation. The study will help to provide the better understanding of pathogens survival and embark on the development of successful therapies for the management of Indian tick typhus.
{"title":"Deciphering Rickettsia conorii metabolic pathways: A treasure map to therapeutic targets","authors":"Brijesh Prajapat , Ankita Sharma , Sunil Kumar , Dixit Sharma","doi":"10.1016/j.biotno.2024.11.006","DOIUrl":"10.1016/j.biotno.2024.11.006","url":null,"abstract":"<div><div>Indian tick typhus is an infectious disease caused by intracellular gram-negative bacteria <em>Rickettsia conorii</em> (<em>R. conorii</em>). The bacterium is transmitted to humans through bite of infected ticks and sometimes by lice, fleas or mites. The disease is restricted to some areas with few cases but in last decade it is re-emerging with large number of cases from different areas of India. The insight in to genetic makeup of bacterial pathogens can be derived from their metabolic pathways. In the current study 18 metabolic pathways were found to be unique to the pathogen (<em>R. conorii</em>). A comprehensive analysis revealed 163 proteins implicated in 18 unique metabolic pathways of <em>R. conorii</em>. 140 proteins were reported to be essential for the bacterial survival, 46 were found virulent and 10 were found involved in resistance which can enhance the bacterial pathogenesis. The functional analysis of unique metabolic pathway proteins showed the abundance of plasmid conjugal transfer TrbL/VirB6, aliphatic acid kinase short chain, signal transduction response regulator receiver and components of type IV transporter system domains. The proteins were classified into six broad categories on the basis of predicted domains, <em>i.e.</em>, metabolism, transport, gene expression and regulation, antimicrobial resistance, cell signalling and proteolysis. Further, <em>in silico</em> analysis showed that 88 proteins were suitable therapeutic targets which do not showed homology with host proteins. The 43 proteins showed hits with the DrugBank database showing their druggable nature and remaining 45 proteins were classified as novel drug targets that require further validation. The study will help to provide the better understanding of pathogens survival and embark on the development of successful therapies for the management of Indian tick typhus.</div></div>","PeriodicalId":100186,"journal":{"name":"Biotechnology Notes","volume":"6 ","pages":"Pages 1-9"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11667008/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142901547","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}
Pub Date : 2025-01-01DOI: 10.1016/j.biotno.2024.12.001
Nkanyiso C. Nkosi , Albertus K. Basson , Zuzingcebo G. Ntombela , Nkosinathi G. Dlamini , Rajasekhar V.S.R. Pullabhotla
Nanotechnology is a rapidly expanding field with diverse healthcare, agriculture, and industry applications. Central to this discipline is manipulating materials at the nanoscale, particularly nanoparticles (NPs) ranging from 1 to 100 nm. These NPs can be synthesized through various methods, including chemical, physical, and biological processes. Among these, biological synthesis has gained significant attention due to its eco-friendly nature, utilizing natural resources such as microbes and plants as reducing and capping agents. However, information is scarce regarding the production of iron nanoparticles (FeNPs) using biological approaches, and even less is available on the synthesis of FeNPs employing microbial bioflocculants. This review aims to provide a comprehensive examination of the synthesis of FeNPs using microbial bioflocculants, highlighting the methodologies involved and their implications for environmental applications. Recent findings indicate that microbial bioflocculants enhance the stability and efficiency of FeNP synthesis while promoting environmentally friendly production methods. The synthesized FeNPs demonstrated effective removal of contaminants from wastewater, achieving removal rates of up to 93 % for specific dyes and significant reductions in chemical oxygen demand (COD) and biological oxygen demand (BOD). Additionally, these FeNPs exhibited notable antimicrobial properties against both Gram-positive and Gram-negative bacteria.
This review encompasses studies conducted between January 2015 and December 2023, providing detailed characterization of the synthesized FeNPs and underscoring their potential applications in wastewater treatment and environmental remediation.
{"title":"Green synthesis and characterization of iron nanoparticles synthesized from bioflocculant for wastewater treatment: A review","authors":"Nkanyiso C. Nkosi , Albertus K. Basson , Zuzingcebo G. Ntombela , Nkosinathi G. Dlamini , Rajasekhar V.S.R. Pullabhotla","doi":"10.1016/j.biotno.2024.12.001","DOIUrl":"10.1016/j.biotno.2024.12.001","url":null,"abstract":"<div><div>Nanotechnology is a rapidly expanding field with diverse healthcare, agriculture, and industry applications. Central to this discipline is manipulating materials at the nanoscale, particularly nanoparticles (NPs) ranging from 1 to 100 nm. These NPs can be synthesized through various methods, including chemical, physical, and biological processes. Among these, biological synthesis has gained significant attention due to its eco-friendly nature, utilizing natural resources such as microbes and plants as reducing and capping agents. However, information is scarce regarding the production of iron nanoparticles (FeNPs) using biological approaches, and even less is available on the synthesis of FeNPs employing microbial bioflocculants. This review aims to provide a comprehensive examination of the synthesis of FeNPs using microbial bioflocculants, highlighting the methodologies involved and their implications for environmental applications. Recent findings indicate that microbial bioflocculants enhance the stability and efficiency of FeNP synthesis while promoting environmentally friendly production methods. The synthesized FeNPs demonstrated effective removal of contaminants from wastewater, achieving removal rates of up to 93 % for specific dyes and significant reductions in chemical oxygen demand (COD) and biological oxygen demand (BOD). Additionally, these FeNPs exhibited notable antimicrobial properties against both Gram-positive and Gram-negative bacteria.</div><div>This review encompasses studies conducted between January 2015 and December 2023, providing detailed characterization of the synthesized FeNPs and underscoring their potential applications in wastewater treatment and environmental remediation.</div></div>","PeriodicalId":100186,"journal":{"name":"Biotechnology Notes","volume":"6 ","pages":"Pages 10-31"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11731503/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142985957","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}
The amidases (EC 3.5.1.4) are versatile hydrolase biocatalysts that have been the attention of academia and industries for stereo-selective synthesis and bioremediation. These are categorized based on the amino acid sequence and substrate specificity. Notably, the Signature amidase family is distinguished by a characteristic signature sequence, GGSS(S/G)GS, which encompasses highly conserved Ser-Ser-Lys catalytic residues, and the amidases belonging to this family typically demonstrate a broad substrate spectrum activity. The amidases classified within the nitrilase superfamily possess distinct Glu-Lys-Cys catalytic residues and exhibit activity towards small aliphatic substrates. Recent discoveries have underscored the potential role of amidases in the degradation of toxic amides present in polymers, insecticides, and food products. This expands the horizons for amidase-mediated biodegradation of amide-laden pollutants and fosters sustainable development alongside organic synthesis. The burgeoning global production facilities are expected to drive a heightened demand for this enzyme, attributable to its promising chemo-, regio-, and enantioselective hydrolysis capabilities for a variety of amides. Advances in protein engineering have enhanced the catalytic efficiency, structural stability, and substrate selectivity of amidases. Concurrently, the heterologous expression of amidase genes sourced from thermophiles has facilitated the development of highly stable amidases with significant industrial relevance. Beyond their biotransformation capabilities concerning amides, through amido-hydrolase and acyltransferase activities, recent investigations have illuminated the potential of amidase-mediated degradation of amide-containing pollutants in soil and aquatic environments. This review offers a comprehensive overview of recent advancements pertaining to microbial amidases (EC 3.5.1.4), focusing on aspects such as their distribution, gene mining methodologies, enzyme stability, protein engineering, reusability, and biocatalytic efficacy in organic synthesis and biodegradation.
{"title":"Microbial amidases: Characterization, advances and biotechnological applications","authors":"Rajendra Singh , Refana Shahul , Vijay Kumar , Ashok Kumar Yadav , Praveen Kumar Mehta","doi":"10.1016/j.biotno.2024.12.003","DOIUrl":"10.1016/j.biotno.2024.12.003","url":null,"abstract":"<div><div>The amidases (EC 3.5.1.4) are versatile hydrolase biocatalysts that have been the attention of academia and industries for stereo-selective synthesis and bioremediation. These are categorized based on the amino acid sequence and substrate specificity. Notably, the Signature amidase family is distinguished by a characteristic signature sequence, GGSS(S/G)GS, which encompasses highly conserved Ser-Ser-Lys catalytic residues, and the amidases belonging to this family typically demonstrate a broad substrate spectrum activity. The amidases classified within the nitrilase superfamily possess distinct Glu-Lys-Cys catalytic residues and exhibit activity towards small aliphatic substrates. Recent discoveries have underscored the potential role of amidases in the degradation of toxic amides present in polymers, insecticides, and food products. This expands the horizons for amidase-mediated biodegradation of amide-laden pollutants and fosters sustainable development alongside organic synthesis. The burgeoning global production facilities are expected to drive a heightened demand for this enzyme, attributable to its promising chemo-, regio-, and enantioselective hydrolysis capabilities for a variety of amides. Advances in protein engineering have enhanced the catalytic efficiency, structural stability, and substrate selectivity of amidases. Concurrently, the heterologous expression of amidase genes sourced from thermophiles has facilitated the development of highly stable amidases with significant industrial relevance. Beyond their biotransformation capabilities concerning amides, through amido-hydrolase and acyltransferase activities, recent investigations have illuminated the potential of amidase-mediated degradation of amide-containing pollutants in soil and aquatic environments. This review offers a comprehensive overview of recent advancements pertaining to microbial amidases (EC 3.5.1.4), focusing on aspects such as their distribution, gene mining methodologies, enzyme stability, protein engineering, reusability, and biocatalytic efficacy in organic synthesis and biodegradation.</div></div>","PeriodicalId":100186,"journal":{"name":"Biotechnology Notes","volume":"6 ","pages":"Pages 44-58"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11732141/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142985958","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}
Microbiome engineering has emerged as a transformative approach to enhancing food safety and quality by strategically modulating microbial communities. This review critically examines state-of-the-art techniques, including synthetic biology, artificial intelligence (AI), and systems biology, that are revolutionizing our ability to improve nutritional profiles, extend shelf life, and optimize food production processes. The review further explores complex social, ethical, and regulatory considerations, emphasizing the importance of robust public engagement and the establishment of standardized frameworks to ensure safe and effective implementation. While microbiome engineering holds significant promise for revolutionizing food safety and quality control, further research is needed to address critical challenges, including understanding microbial dynamics in complex food systems and developing harmonized regulatory frameworks. By bridging interdisciplinary gaps, this paper underscores the necessity of collaborative efforts to unlock the full potential of microbiome-driven innovations for a more resilient and sustainable food industry.
{"title":"The role of Micro-biome engineering in enhancing Food safety and quality","authors":"Anand Kumar , Abhishek Bisht , SammraMaqsood , SaiqaAmjad , Sapna baghel , Swapnil Ganesh Jaiswal , Shuai wei","doi":"10.1016/j.biotno.2025.01.001","DOIUrl":"10.1016/j.biotno.2025.01.001","url":null,"abstract":"<div><div>Microbiome engineering has emerged as a transformative approach to enhancing food safety and quality by strategically modulating microbial communities. This review critically examines state-of-the-art techniques, including synthetic biology, artificial intelligence (AI), and systems biology, that are revolutionizing our ability to improve nutritional profiles, extend shelf life, and optimize food production processes. The review further explores complex social, ethical, and regulatory considerations, emphasizing the importance of robust public engagement and the establishment of standardized frameworks to ensure safe and effective implementation. While microbiome engineering holds significant promise for revolutionizing food safety and quality control, further research is needed to address critical challenges, including understanding microbial dynamics in complex food systems and developing harmonized regulatory frameworks. By bridging interdisciplinary gaps, this paper underscores the necessity of collaborative efforts to unlock the full potential of microbiome-driven innovations for a more resilient and sustainable food industry.</div></div>","PeriodicalId":100186,"journal":{"name":"Biotechnology Notes","volume":"6 ","pages":"Pages 67-78"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143132795","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}
MicroRNAs (miRNAs) have been implicated in the pathogenesis of human diseases including sleep disorders. The aim of this study is to address the involvement of miRNAs (miR-21 and miR-29) in the pathophysiology of obstructive sleep apnea (OSA). In this study we have done integrated analysis of miRNAs with their potential gene targets as a strategy for management of OSA.
Methods
miRNA expression levels were quantified in healthy control group and obese vs. Non-obese OSA subjects by Quantitative real-time PCR. In-silico analysis of interplay of miRNAs with potential gene targets was done using Schrödinger Release 2023-1.
Results
The real time expression analysis revealed a differential expression pattern in miRNAs indicating down-regulation of miR-21 in obese OSA while miR-29 showed upregulation as compared to non-obese OSA and healthy subjects with p values of ≤0.01 and <0.0001respectively. A trend was observed where target genes TGFBR2, NAMPT, and NPPB were significantly increased with p-value of ≤0.0001 and TGFBR3 and INSIG2 showed decreasing trend with p-value of ≤0.0001 between obese and non-obese OSA respectively. MD simulation analysis provided valuable information regarding the stability, flexibility, compactness and solvent exposure of the complexes over time.
Conclusion
miR-21 and miR-29 possesses differential expressions in obese OSA subject and exihbits strong molecular interactions with potential target genes, such as TGFBR2, NPPB, NAMPT and INSIG2. Identifying the miRNAs, genes and pathways associated with OSA can help to expand our understanding of the risk factors for the disease as well as provide new avenues for potential treatment.
{"title":"Integrative analysis of candidate MicroRNAs and gene targets for OSA management using in silico and in-vitro approach","authors":"Gaganjyot Kaur Bakshi , Sartaj Khurana , Shambhavee Srivastav , Rohit Kumar , Mukesh Chourasia , Sudeep Bose","doi":"10.1016/j.biotno.2025.01.003","DOIUrl":"10.1016/j.biotno.2025.01.003","url":null,"abstract":"<div><div>MicroRNAs (miRNAs) have been implicated in the pathogenesis of human diseases including sleep disorders. The aim of this study is to address the involvement of miRNAs (miR-21 and miR-29) in the pathophysiology of obstructive sleep apnea (OSA). In this study we have done integrated analysis of miRNAs with their potential gene targets as a strategy for management of OSA.</div></div><div><h3>Methods</h3><div>miRNA expression levels were quantified in healthy control group and obese vs. Non-obese OSA subjects by Quantitative real-time PCR. In-silico analysis of interplay of miRNAs with potential gene targets was done using Schrödinger Release 2023-1.</div></div><div><h3>Results</h3><div>The real time expression analysis revealed a differential expression pattern in miRNAs indicating down-regulation of miR-21 in obese OSA while miR-29 showed upregulation as compared to non-obese OSA and healthy subjects with p values of ≤0.01 and <0.0001respectively. A trend was observed where target genes TGFBR2, NAMPT, and NPPB were significantly increased with p-value of ≤0.0001 and TGFBR3 and INSIG2 showed decreasing trend with p-value of ≤0.0001 between obese and non-obese OSA respectively. MD simulation analysis provided valuable information regarding the stability, flexibility, compactness and solvent exposure of the complexes over time.</div></div><div><h3>Conclusion</h3><div>miR-21 and miR-29 possesses differential expressions in obese OSA subject and exihbits strong molecular interactions with potential target genes, such as TGFBR2, NPPB, NAMPT and INSIG2. Identifying the miRNAs, genes and pathways associated with OSA can help to expand our understanding of the risk factors for the disease as well as provide new avenues for potential treatment.</div></div>","PeriodicalId":100186,"journal":{"name":"Biotechnology Notes","volume":"6 ","pages":"Pages 79-88"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143132794","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}
Pub Date : 2024-01-01DOI: 10.1016/j.biotno.2024.10.001
Scott A. Wegner , José L. Avalos
Isoprenoids are highly valued targets for microbial chemical production, allowing the creation of fragrances, biofuels, and pharmaceuticals from renewable carbon feedstocks. To increase isoprenoid production, previous efforts have manipulated pyruvate dehydrogenase (PDH) bypass pathway flux to increase cytosolic acetyl-coA; however, this results in mevalonate secretion and does not necessarily translate into higher isoprenoid production. Identification and disruption of the transporter mediating mevalonate secretion would allow us to determine whether increasing PDH bypass activity in the absence of secretion improves conversion of mevalonate into downstream isoprenoids. Attempted identification of the mevalonate transporter was accomplished using a pooled CRISPR library targeting all nonessential transporters and two different screening methods. Using a high throughput screen, based on growth of a mevalonate auxotrophic Escherichia coli strain, it was found that ZRT3 disruption largely abolished accumulation of extracellular mevalonate. However, disruption of ZRT3 was found to lower overall mevalonate pathway activity, rather than prevent secretion, indicating a previously unreported interaction between zinc availability and the mevalonate pathway. In a second screen, significant differences in PDR5/15 and QDR1/2 library representation were found between wild-type and mevalonate secreting Saccharomyces cerevisiae strains. However, no single deletion (or selected pair of double deletions) abolishes mevalonate secretion, indicating that this process appears to be mediated through multiple redundant transporters.
{"title":"Mevalonate secretion is not mediated by a singular non-essential transporter in Saccharomyces cerevisiae","authors":"Scott A. Wegner , José L. Avalos","doi":"10.1016/j.biotno.2024.10.001","DOIUrl":"10.1016/j.biotno.2024.10.001","url":null,"abstract":"<div><div>Isoprenoids are highly valued targets for microbial chemical production, allowing the creation of fragrances, biofuels, and pharmaceuticals from renewable carbon feedstocks. To increase isoprenoid production, previous efforts have manipulated pyruvate dehydrogenase (PDH) bypass pathway flux to increase cytosolic acetyl-coA; however, this results in mevalonate secretion and does not necessarily translate into higher isoprenoid production. Identification and disruption of the transporter mediating mevalonate secretion would allow us to determine whether increasing PDH bypass activity in the absence of secretion improves conversion of mevalonate into downstream isoprenoids. Attempted identification of the mevalonate transporter was accomplished using a pooled CRISPR library targeting all nonessential transporters and two different screening methods. Using a high throughput screen, based on growth of a mevalonate auxotrophic <em>Escherichia coli</em> strain, it was found that <em>ZRT3</em> disruption largely abolished accumulation of extracellular mevalonate. However, disruption of <em>ZRT3</em> was found to lower overall mevalonate pathway activity, rather than prevent secretion, indicating a previously unreported interaction between zinc availability and the mevalonate pathway. In a second screen, significant differences in <em>PDR5/15</em> and <em>QDR1/2</em> library representation were found between wild-type and mevalonate secreting <em>Saccharomyces cerevisiae</em> strains. However, no single deletion (or selected pair of double deletions) abolishes mevalonate secretion, indicating that this process appears to be mediated through multiple redundant transporters.</div></div>","PeriodicalId":100186,"journal":{"name":"Biotechnology Notes","volume":"5 ","pages":"Pages 140-150"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142528967","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}
Pub Date : 2024-01-01DOI: 10.1016/j.biotno.2024.06.001
Mahalakshmi Devaraji, Punniyakoti V. Thanikachalam, Karthikeyan Elumalai
Nanotechnology is a modern scientific discipline that uses nanoparticles of metals like copper, silver, gold, platinum, and zinc for various applications. Copper oxide nanoparticles (CuONPs) are effective in biomedical settings, such as killing bacteria, speeding up reactions, stopping cancer cells, and coating surfaces. These inorganic nanostructures have a longer shelf life than their organic counterparts and are chemically inert and thermally stable. However, commercial synthesis of NPs often involves harmful byproducts and hazardous chemicals. Green synthesis for CuONPs offers numerous benefits, including being clean, harmless, economical, and environmentally friendly. Using naturally occurring organisms like bacteria, yeast, fungi, algae, and plants can make CuONPs more environmentally friendly. CuONPs are expected to be used in nanomedicine due to their potent antimicrobial properties and disinfecting agents for infectious diseases. This comprehensive review looks to evaluate research articles published in the last ten years that investigate the antioxidant, anticancer, antibacterial, wound healing, dental application and catalytic properties of copper nanoparticles generated using biological processes. Utilising the scientific approach of large-scale data analytics. However, their toxic effects on vertebrates and invertebrates raise concerns about their use for diagnostic and therapeutic purposes. Therefore, biocompatibility and non-toxicity are crucial for selecting nanoparticles for clinical research.
{"title":"The potential of copper oxide nanoparticles in nanomedicine: A comprehensive review","authors":"Mahalakshmi Devaraji, Punniyakoti V. Thanikachalam, Karthikeyan Elumalai","doi":"10.1016/j.biotno.2024.06.001","DOIUrl":"https://doi.org/10.1016/j.biotno.2024.06.001","url":null,"abstract":"<div><p>Nanotechnology is a modern scientific discipline that uses nanoparticles of metals like copper, silver, gold, platinum, and zinc for various applications. Copper oxide nanoparticles (CuONPs) are effective in biomedical settings, such as killing bacteria, speeding up reactions, stopping cancer cells, and coating surfaces. These inorganic nanostructures have a longer shelf life than their organic counterparts and are chemically inert and thermally stable. However, commercial synthesis of NPs often involves harmful byproducts and hazardous chemicals. Green synthesis for CuONPs offers numerous benefits, including being clean, harmless, economical, and environmentally friendly. Using naturally occurring organisms like bacteria, yeast, fungi, algae, and plants can make CuONPs more environmentally friendly. CuONPs are expected to be used in nanomedicine due to their potent antimicrobial properties and disinfecting agents for infectious diseases. This comprehensive review looks to evaluate research articles published in the last ten years that investigate the antioxidant, anticancer, antibacterial, wound healing, dental application and catalytic properties of copper nanoparticles generated using biological processes. Utilising the scientific approach of large-scale data analytics. However, their toxic effects on vertebrates and invertebrates raise concerns about their use for diagnostic and therapeutic purposes. Therefore, biocompatibility and non-toxicity are crucial for selecting nanoparticles for clinical research.</p></div>","PeriodicalId":100186,"journal":{"name":"Biotechnology Notes","volume":"5 ","pages":"Pages 80-99"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2665906924000102/pdfft?md5=1bd90f034c802d80d953cb65ac2eab2a&pid=1-s2.0-S2665906924000102-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141292369","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}
Magnetic Resonance Imaging (MRI) assists in studying the nervous system. MRI scans undergo significant processing before presenting the final images to medical practitioners. These processes are executed with ease due to excellent software pipelines. However, establishing software workstations is non-trivial and requires researchers in life sciences to be comfortable in downloading, installing, and scripting software that is non-user-friendly and may lack basic GUI. As researchers struggle with these skills, there is a dire need to develop software packages that can automatically install software pipelines speeding up building software workstations and laboratories. Previous solutions include NeuroDebian, BIDS Apps, Flywheel, QMENTA, Boutiques, Brainlife and Neurodesk. Overall, all these solutions complement each other. NeuroDebian covers neuroscience and has a wider scope, providing only 51 tools for MRI. Whereas, BIDS Apps is committed to the BIDS format, covering only 45 software related to MRI. Boutiques is more flexible, facilitating its pipelines to be easily installed as separate containers, validated, published, and executed. Whereas, both Flywheel and Qmenta are propriety, leaving four for users looking for ‘free for use’ tools, i.e., NeuroDebian, Brainlife, Neurodesk, and BIDS Apps. This paper presents an extensive survey of 317 tools published in MRI-based neuroimaging in the last ten years, along with ‘aXonica,’ an MRI-based neuroimaging support package that is unbiased towards any formatting standards and provides 130 applications, more than that of NeuroDebian (51), BIDS App (45), Flywheel (70), and Neurodesk (85). Using a technology stack that employs GUI as the front-end and shell scripted back-end, aXonica provides (i) 130 tools that span the entire MRI-based neuroimaging analysis, and allow the user to (ii) select the software of their choice, (iii) automatically resolve individual dependencies and (iv) installs them. Hence, aXonica can serve as an important resource for researchers and teachers working in the field of MRI-based Neuroimaging to (a) develop software workstations, and/or (b) install newer tools in their existing workstations.
{"title":"aXonica: A support package for MRI based Neuroimaging","authors":"Bilal Wajid , Momina Jamil , Fahim Gohar Awan , Faria Anwar , Ali Anwar","doi":"10.1016/j.biotno.2024.08.001","DOIUrl":"10.1016/j.biotno.2024.08.001","url":null,"abstract":"<div><p>Magnetic Resonance Imaging (MRI) assists in studying the nervous system. MRI scans undergo significant processing before presenting the final images to medical practitioners. These processes are executed with ease due to excellent software pipelines. However, establishing software workstations is non-trivial and requires researchers in life sciences to be comfortable in downloading, installing, and scripting software that is non-user-friendly and may lack basic GUI. As researchers struggle with these skills, there is a dire need to develop software packages that can automatically install software pipelines speeding up building software workstations and laboratories. Previous solutions include NeuroDebian, BIDS Apps, Flywheel, QMENTA, Boutiques, Brainlife and Neurodesk. Overall, all these solutions complement each other. NeuroDebian covers neuroscience and has a wider scope, providing only 51 tools for MRI. Whereas, BIDS Apps is committed to the BIDS format, covering only 45 software related to MRI. Boutiques is more flexible, facilitating its pipelines to be easily installed as separate containers, validated, published, and executed. Whereas, both Flywheel and Qmenta are propriety, leaving four for users looking for ‘free for use’ tools, i.e., NeuroDebian, Brainlife, Neurodesk, and BIDS Apps. This paper presents an extensive survey of 317 tools published in MRI-based neuroimaging in the last ten years, along with ‘aXonica,’ an MRI-based neuroimaging support package that is unbiased towards any formatting standards and provides 130 applications, more than that of NeuroDebian (51), BIDS App (45), Flywheel (70), and Neurodesk (85). Using a technology stack that employs GUI as the front-end and shell scripted back-end, aXonica provides (i) 130 tools that span the entire MRI-based neuroimaging analysis, and allow the user to (ii) select the software of their choice, (iii) automatically resolve individual dependencies and (iv) installs them. Hence, aXonica can serve as an important resource for researchers and teachers working in the field of MRI-based Neuroimaging to (a) develop software workstations, and/or (b) install newer tools in their existing workstations.</p></div>","PeriodicalId":100186,"journal":{"name":"Biotechnology Notes","volume":"5 ","pages":"Pages 120-136"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2665906924000126/pdfft?md5=586029896db2ec4af16780650f840978&pid=1-s2.0-S2665906924000126-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142149205","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}
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