This review discusses the eco-friendly and cost-effective biosynthesis of gold nanoparticles (AuNPs) in viable microorganisms, focusing on microbes-mediated AuNP biosynthesis. This process suits agricultural, environmental, and biomedical applications, offering renewable, eco-friendly, non-toxic, sustainable, and time-efficient methods. Microorganisms are increasingly used in green technology, nanotechnology, and RNAi technology, but several microorganisms have not been fully identified and characterized. Bio-nanotechnology offers eco-friendly and sustainable solutions for nanomedicine, with microbe-mediated nanoparticle biosynthesis producing AuNPs with anti-oxidation activity, stability, and biocompatibility. Ultrasmall AuNPs offer rapid distribution, renal clearance, and enhanced permeability in biomedical applications. The review explores nano-size dependent biosynthesis of AuNPs by bacteria, fungi, and viruses revealing their non-toxic, non-genotoxic, and non-oxidative properties on human cells. AuNPs with varying sizes and shapes, from nitrate reductase enzymes, have shown potential as a promising nano-catalyst. The synthesized AuNPs, with negative charge capping molecules, have demonstrated antibacterial activity against drug-resistant Pseudomonas aeruginosa, and Acinetobacter baumannii strains, and were non-toxic to Vero cell lines, indicating potential antibiotic resistance treatments. A green chemical method for the biosynthesis of AuNPs using reducing chloroauric acid and Rhizopus oryzae protein extract has been described, demonstrating excellent stability and strong catalytic activity. AuNPs are eco-friendly, non-toxic, and time-efficient, making them ideal for biomedical applications due to their antioxidant, antidiabetic, and antibacterial properties. In addition to the biomedical application, the review also highlights the role of microbially synthesized AuNPs in sustainable management of plant diseases, and environmental bioremediation.
{"title":"Biotechnological advances in microbial synthesis of gold nanoparticles: Optimizations and applications.","authors":"Jyoti Verma, Chitranjan Kumar, Monica Sharma, Sangeeta Saxena","doi":"10.1007/s13205-024-04110-7","DOIUrl":"10.1007/s13205-024-04110-7","url":null,"abstract":"<p><p>This review discusses the eco-friendly and cost-effective biosynthesis of gold nanoparticles (AuNPs) in viable microorganisms, focusing on microbes-mediated AuNP biosynthesis. This process suits agricultural, environmental, and biomedical applications, offering renewable, eco-friendly, non-toxic, sustainable, and time-efficient methods. Microorganisms are increasingly used in green technology, nanotechnology, and RNAi technology, but several microorganisms have not been fully identified and characterized. Bio-nanotechnology offers eco-friendly and sustainable solutions for nanomedicine, with microbe-mediated nanoparticle biosynthesis producing AuNPs with anti-oxidation activity, stability, and biocompatibility. Ultrasmall AuNPs offer rapid distribution, renal clearance, and enhanced permeability in biomedical applications. The review explores nano-size dependent biosynthesis of AuNPs by bacteria, fungi, and viruses revealing their non-toxic, non-genotoxic, and non-oxidative properties on human cells. AuNPs with varying sizes and shapes, from nitrate reductase enzymes, have shown potential as a promising nano-catalyst. The synthesized AuNPs, with negative charge capping molecules, have demonstrated antibacterial activity against drug-resistant <i>Pseudomonas aeruginosa,</i> and <i>Acinetobacter baumannii</i> strains, and were non-toxic to Vero cell lines, indicating potential antibiotic resistance treatments. A green chemical method for the biosynthesis of AuNPs using reducing chloroauric acid and <i>Rhizopus oryzae</i> protein extract has been described, demonstrating excellent stability and strong catalytic activity. AuNPs are eco-friendly, non-toxic, and time-efficient, making them ideal for biomedical applications due to their antioxidant, antidiabetic, and antibacterial properties. In addition to the biomedical application, the review also highlights the role of microbially synthesized AuNPs in sustainable management of plant diseases, and environmental bioremediation.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 11","pages":"263"},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11458872/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142387130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-01Epub Date: 2024-10-14DOI: 10.1007/s13205-024-04086-4
Donald A Fernandes
The diagnosis and treatment of cancer can often be challenging requiring more attractive options. Some types of cancers are more aggressive than others and symptoms for many cancers are subtle, especially in the early stages. Nanotechnology provides high sensitivity, specificity and multimodal capability for cancer detection, treatment and monitoring. In particular, metal nanoparticles (NPs) such as gold nanoparticles (AuNPs) are attractive nanosystems for researchers interested in bioimaging and therapy. The size, shape and surface of AuNPs can be modified for improving targeting and accumulation in cancer cells, for example through introduction of ligands and surface charge. The interactions of AuNPs with electromagnetic radiation (e.g., visible-near-infrared, X-rays) can be used for photothermal therapy and radiation therapy, through heat generated from light absorption and emission of Auger electrons, respectively. The subsequent expansion and high X-ray attenuation from AuNPs can be used for enhancing contrast for tumor detection (e.g., using photoacoustic, computed tomography imaging). Multi-functionality can be further extended through covalent/non-covalent functionalization, for loading additional imaging/therapeutic molecules for combination therapy and multimodal imaging. In order to cover the important aspects for designing and using AuNPs for cancer theranostics, this review focuses on the synthesis, functionalization and characterization methods that are important for AuNPs, and presents their unique properties and different applications in cancer theranostics.
癌症的诊断和治疗往往具有挑战性,需要更具吸引力的选择。某些类型的癌症比其他类型的癌症更具侵袭性,许多癌症的症状并不明显,尤其是在早期阶段。纳米技术为癌症检测、治疗和监测提供了高灵敏度、高特异性和多模式能力。尤其是金属纳米粒子(NPs),如金纳米粒子(AuNPs),对于对生物成像和治疗感兴趣的研究人员来说是一种极具吸引力的纳米系统。AuNPs 的大小、形状和表面可以通过引入配体和表面电荷等方式进行修饰,以提高在癌细胞中的靶向性和蓄积性。AuNPs 与电磁辐射(如可见光-近红外和 X 射线)的相互作用可分别通过光吸收和奥杰电子发射产生的热量用于光热疗法和放射治疗。AuNPs 随后产生的膨胀和高 X 射线衰减可用于增强肿瘤检测的对比度(例如,利用光声学和计算机断层扫描成像)。还可通过共价/非共价功能化进一步扩展其多功能性,装载额外的成像/治疗分子,用于联合治疗和多模式成像。为了涵盖设计和使用 AuNPs 进行癌症治疗的重要方面,本综述重点介绍对 AuNPs 十分重要的合成、功能化和表征方法,并介绍 AuNPs 的独特性质及其在癌症治疗中的不同应用。
{"title":"Multifunctional gold nanoparticles for cancer theranostics.","authors":"Donald A Fernandes","doi":"10.1007/s13205-024-04086-4","DOIUrl":"10.1007/s13205-024-04086-4","url":null,"abstract":"<p><p>The diagnosis and treatment of cancer can often be challenging requiring more attractive options. Some types of cancers are more aggressive than others and symptoms for many cancers are subtle, especially in the early stages. Nanotechnology provides high sensitivity, specificity and multimodal capability for cancer detection, treatment and monitoring. In particular, metal nanoparticles (NPs) such as gold nanoparticles (AuNPs) are attractive nanosystems for researchers interested in bioimaging and therapy. The size, shape and surface of AuNPs can be modified for improving targeting and accumulation in cancer cells, for example through introduction of ligands and surface charge. The interactions of AuNPs with electromagnetic radiation (e.g., visible-near-infrared, X-rays) can be used for photothermal therapy and radiation therapy, through heat generated from light absorption and emission of Auger electrons, respectively. The subsequent expansion and high X-ray attenuation from AuNPs can be used for enhancing contrast for tumor detection (e.g., using photoacoustic, computed tomography imaging). Multi-functionality can be further extended through covalent/non-covalent functionalization, for loading additional imaging/therapeutic molecules for combination therapy and multimodal imaging. In order to cover the important aspects for designing and using AuNPs for cancer theranostics, this review focuses on the synthesis, functionalization and characterization methods that are important for AuNPs, and presents their unique properties and different applications in cancer theranostics.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 11","pages":"267"},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11473483/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142455456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
In the present study, a novel series of sulfamethoxazole and 1-(2-fluorophenyl) piperazine derivatives were designed, synthesized and characterized by FTIR, IH NMR,13C NMR, Mass spectrometry, CHN data, and evaluated for their efficiency as BCL2 inhibitors that could lead to potential antiproliferative activity. The ten newly synthesized compounds were screened for their therapeutic activity using MDA-MB-231 breast cancer cell lines. All the test compounds exhibited moderate to high cytotoxic activity in MTT assay. Among them, compounds 3e and 6b exhibited promising antitumor activity, as evidenced by their IC50 values of 16.98 and 17.33 μM respectively. In addition, both compounds 3e and 6b displayed potential antioxidant and apoptosis induction properties. The qRT-PCR analysis showed down regulation of BCL2 expression and up regulation of Casp3 expression in 3e and 6b treated MDA-MB-231 cells. Further, the interaction between critical amino acids of the active domains of BCL2 and 3e and 6b was evaluated by MD simulation, and the results reflected the potent inhibitory activities of 3e and 6b. In summary, the novel compounds 3e and 6b demonstrate their potent anti-cancer properties by inducing apoptosis and selectively targeting BCL2 and caspases-3.
Supplementary information: The online version contains supplementary material available at 10.1007/s13205-024-04111-6.
本研究设计、合成了一系列新型磺胺甲噁唑和 1-(2-氟苯基)哌嗪衍生物,并通过傅立叶变换红外光谱(FTIR)、IH NMR、13C NMR、质谱分析和 CHN 数据对其进行了表征,评估了它们作为 BCL2 抑制剂的效率,这可能会导致潜在的抗增殖活性。利用 MDA-MB-231 乳腺癌细胞系对这十种新合成的化合物进行了治疗活性筛选。在 MTT 试验中,所有受试化合物都表现出中等到较高的细胞毒性活性。其中,化合物 3e 和 6b 的 IC50 值分别为 16.98 和 17.33 μM,显示出良好的抗肿瘤活性。此外,化合物 3e 和 6b 还具有潜在的抗氧化和诱导细胞凋亡的特性。qRT-PCR 分析表明,在 3e 和 6b 处理的 MDA-MB-231 细胞中,BCL2 表达下调,Casp3 表达上调。此外,通过 MD 模拟评估了 BCL2 活性域的关键氨基酸与 3e 和 6b 之间的相互作用,结果显示 3e 和 6b 具有很强的抑制活性。总之,新型化合物 3e 和 6b 通过诱导细胞凋亡和选择性靶向 BCL2 和 caspases-3 显示了其强大的抗癌特性:在线版本包含补充材料,可查阅 10.1007/s13205-024-04111-6。
{"title":"Novel sulfamethoxazole and 1-(2-fluorophenyl) piperazine derivatives as potential apoptotic and antiproliferative agents by inhibition of BCL2; design, synthesis, biological evaluation, and docking studies.","authors":"Nagalakshmamma Vadabingi, Venkataswamy Mallepogu, Rani E Mallapu, Chiranjeevi Pasala, Sumithra Poreddy, Poojitha Bellala, Umamaheswari Amineni, Suresh Reddy Cirandur, Balaji Meriga","doi":"10.1007/s13205-024-04111-6","DOIUrl":"10.1007/s13205-024-04111-6","url":null,"abstract":"<p><p>In the present study, a novel series of sulfamethoxazole and 1-(2-fluorophenyl) piperazine derivatives were designed, synthesized and characterized by FTIR, <sup>I</sup>H NMR,<sup>13</sup>C NMR, Mass spectrometry, CHN data, and evaluated for their efficiency as BCL2 inhibitors that could lead to potential antiproliferative activity. The ten newly synthesized compounds were screened for their therapeutic activity using MDA-MB-231 breast cancer cell lines. All the test compounds exhibited moderate to high cytotoxic activity in MTT assay. Among them, compounds <b>3e</b> and <b>6b</b> exhibited promising antitumor activity, as evidenced by their IC<sub>50</sub> values of 16.98 and 17.33 μM respectively. In addition, both compounds <b>3e</b> and <b>6b</b> displayed potential antioxidant and apoptosis induction properties. The qRT-PCR analysis showed down regulation of BCL2 expression and up regulation of Casp3 expression in <b>3e</b> and <b>6b</b> treated MDA-MB-231 cells. Further, the interaction between critical amino acids of the active domains of BCL2 and <b>3e</b> and <b>6b</b> was evaluated by MD simulation, and the results reflected the potent inhibitory activities of <b>3e</b> and <b>6b</b>. In summary, the novel compounds <b>3e</b> and <b>6b</b> demonstrate their potent anti-cancer properties by inducing apoptosis and selectively targeting BCL2 and caspases-3.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s13205-024-04111-6.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 11","pages":"269"},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11480306/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142455457","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-01Epub Date: 2024-10-29DOI: 10.1007/s13205-024-04122-3
Nootjalee Supromin, Siraporn Potivichayanon
The purpose of this study was to investigate the optimum conditions, including aerobic and anoxic conditions, for operating a long-term bioreactor system to decrease the toxicity of industrial electroplating wastewater effluents containing metal cyanide using Agrobacterium tumefaciens SUTS 1 and Pseudomonas monteilii SUTS 2. The initial results revealed that bacteria performed better under aerobic conditions than under anoxic conditions. An aerobic bioreactor system was subsequently set up in a long-term study lasting 30 days under optimum operating conditions. Both mixed-culture bacteria and indigenous bacteria promoted the high-efficiency treatment of cyanide and metals in the first 7 days of the study. When the system had high removal rates, cyanide removal was greater than that of zinc, copper, nickel, and chromium (CN- > Zn > Cu > Ni > Cr), with removal efficiencies of 96.67%, 93.93%, 74.17%, 63.43%, and 44.65%, respectively, with residual concentrations of 0.15 ± 0.01, 0.24 ± 0.005, 0.03 ± 0.002, 18.41 ± 0.06 and 14.26 ± 0.15 mg/L, respectively. The cell concentration in the bioreactor increased to approximately 107 CFU/mL over 30 days from initial cell concentrations of 6.15 × 105 CFU/mL and 1.05 × 103 CFU/mL for the mixed culture and indigenous inoculation, respectively. These results implied that the bacteria were resistant to heavy metal toxicity. The addition of an appropriate carbon source with sufficient aeration to a bioreactor resulted in increased cyanide degradation.
{"title":"Bioremediation of metal cyanide complexes from electroplating wastewater for long-term application using <i>Agrobacterium tumefaciens</i> SUTS 1 and <i>Pseudomonas monteilii</i> SUTS 2.","authors":"Nootjalee Supromin, Siraporn Potivichayanon","doi":"10.1007/s13205-024-04122-3","DOIUrl":"10.1007/s13205-024-04122-3","url":null,"abstract":"<p><p>The purpose of this study was to investigate the optimum conditions, including aerobic and anoxic conditions, for operating a long-term bioreactor system to decrease the toxicity of industrial electroplating wastewater effluents containing metal cyanide using <i>Agrobacterium tumefaciens</i> SUTS 1 and <i>Pseudomonas monteilii</i> SUTS 2. The initial results revealed that bacteria performed better under aerobic conditions than under anoxic conditions. An aerobic bioreactor system was subsequently set up in a long-term study lasting 30 days under optimum operating conditions. Both mixed-culture bacteria and indigenous bacteria promoted the high-efficiency treatment of cyanide and metals in the first 7 days of the study. When the system had high removal rates, cyanide removal was greater than that of zinc, copper, nickel, and chromium (CN<sup>-</sup> > Zn > Cu > Ni > Cr), with removal efficiencies of 96.67%, 93.93%, 74.17%, 63.43%, and 44.65%, respectively, with residual concentrations of 0.15 ± 0.01, 0.24 ± 0.005, 0.03 ± 0.002, 18.41 ± 0.06 and 14.26 ± 0.15 mg/L, respectively. The cell concentration in the bioreactor increased to approximately 10<sup>7</sup> CFU/mL over 30 days from initial cell concentrations of 6.15 × 10<sup>5</sup> CFU/mL and 1.05 × 10<sup>3</sup> CFU/mL for the mixed culture and indigenous inoculation, respectively. These results implied that the bacteria were resistant to heavy metal toxicity. The addition of an appropriate carbon source with sufficient aeration to a bioreactor resulted in increased cyanide degradation.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 11","pages":"283"},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11522241/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142556881","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-01Epub Date: 2024-10-29DOI: 10.1007/s13205-024-04119-y
Banisha Phukela, Hanna Leonard, Yuval Sapir
R2R3-MYBs are an important group of transcription factors that regulate crucial developmental processes across the plant kingdom; yet no comprehensive analysis of the R2R3-MYBs in the early-diverging eudicot clade of Ranunculaceae has been conducted so far. In the present study, Aquilegia coerulea is chosen to understand the extent of conservation and divergence of R2R3-MYBs as a representative of the family by analysing the genomic distribution, organization, gene structure, physiochemical properties, protein architecture, evolution and possible mode of expansion. Genome-wide analysis showed the presence of 82 putative homologues classified into 21 subgroups, based on phylogenetic analysis of full-length protein sequences. The domain has remained largely conserved across all homologues with few differences from the characterized Arabidopsis thaliana R2R3-MYBs. The topology of the phylogenetic tree remains the same when full-length protein sequences are used, indicating that the evolution of R2R3-MYBs is driven by the domain region only. This is supported by the presence of similar structures of exon-intron and conserved motifs within the same subgroup. Furthermore, comparisons of the AqcoeR2R3-MYB members with monocots and core-eudicots revealed the evolutionary expansion of a few functional clades, such as A. thaliana R2R3-MYB subgroup 6 (SG6), the upstream regulatory factors of floral pigment biosynthesis and floral color. The reconstructed evolutionary history of SG6-like genes across angiosperms highlights the occurrence of independent duplication events in the genus Aquilegia. AqcoeR2R3-MYB genes are present in all seven chromosomes of A. coerulea, most of which result from local and segmental duplications. Selection analysis of these duplicated gene pairs indicates purifying selection except one, and the physiochemical analyses of R2R3-MYBs reveal differences among the MYBs signifying their functional diversification. This study paves the way for further investigation of paralogous copies and their probable role in the evolution of different floral traits in A. coerulea. It lays the foundation for functional genomic studies of R2R3-MYBs in the basal eudicots and facilitates comparative studies among angiosperms. The work also provides a framework for deciphering novel genetic regulatory pathways that govern the diversity of floral morphology.
Supplementary information: The online version contains supplementary material available at 10.1007/s13205-024-04119-y.
{"title":"In silico analysis of R2R3-MYB transcription factors in the basal eudicot model, <i>Aquilegia coerulea</i>.","authors":"Banisha Phukela, Hanna Leonard, Yuval Sapir","doi":"10.1007/s13205-024-04119-y","DOIUrl":"10.1007/s13205-024-04119-y","url":null,"abstract":"<p><p>R2R3-MYBs are an important group of transcription factors that regulate crucial developmental processes across the plant kingdom; yet no comprehensive analysis of the R2R3-MYBs in the early-diverging eudicot clade of Ranunculaceae has been conducted so far. In the present study, <i>Aquilegia coerulea</i> is chosen to understand the extent of conservation and divergence of R2R3-MYBs as a representative of the family by analysing the genomic distribution, organization, gene structure, physiochemical properties, protein architecture, evolution and possible mode of expansion. Genome-wide analysis showed the presence of 82 putative homologues classified into 21 subgroups, based on phylogenetic analysis of full-length protein sequences. The domain has remained largely conserved across all homologues with few differences from the characterized <i>Arabidopsis thaliana</i> R2R3-MYBs. The topology of the phylogenetic tree remains the same when full-length protein sequences are used, indicating that the evolution of R2R3-MYBs is driven by the domain region only. This is supported by the presence of similar structures of exon-intron and conserved motifs within the same subgroup. Furthermore, comparisons of the AqcoeR2R3-MYB members with monocots and core-eudicots revealed the evolutionary expansion of a few functional clades, such as <i>A. thaliana</i> R2R3-MYB subgroup 6 (SG6), the upstream regulatory factors of floral pigment biosynthesis and floral color. The reconstructed evolutionary history of SG6-like genes across angiosperms highlights the occurrence of independent duplication events in the genus <i>Aquilegia</i>. AqcoeR2R3-MYB genes are present in all seven chromosomes of <i>A. coerulea</i>, most of which result from local and segmental duplications. Selection analysis of these duplicated gene pairs indicates purifying selection except one, and the physiochemical analyses of R2R3-MYBs reveal differences among the MYBs signifying their functional diversification. This study paves the way for further investigation of paralogous copies and their probable role in the evolution of different floral traits in <i>A. coerulea</i>. It lays the foundation for functional genomic studies of R2R3-MYBs in the basal eudicots and facilitates comparative studies among angiosperms. The work also provides a framework for deciphering novel genetic regulatory pathways that govern the diversity of floral morphology.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s13205-024-04119-y.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 11","pages":"284"},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11522220/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-01Epub Date: 2024-10-21DOI: 10.1007/s13205-024-04127-y
Prithvi Singh, Gulnaz Tabassum, Mohammad Masood, Saleha Anwar, Mansoor Ali Syed, Kapil Dev, Md Imtaiyaz Hassan, Mohammad Mahfuzul Haque, Ravins Dohare, Indrakant Kumar Singh
As one of the most prevalent malignancies, lung cancer displays considerable biological variability in both molecular and clinical characteristics. Lung cancer is broadly categorized into small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC) with the latter being most prevalent. The primary histological subtypes of NSCLC are lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). In the present work, we primarily extracted mRNA count data from a publicly accessible database followed by differentially expressed genes (DEGs) and differentially expressed mitophagy-related genes (DEMRGs) identification in case of both LUAD and LUSC cohorts. Next, we identified important DEMRGs via clustering approach followed by enrichment, survival, and mutational analyses. Lastly, the finalized prognostic biomarker was validated using wet-lab experimentations. Primarily, we obtained 986 and 1714 DEGs across LUAD and LUSC cohorts. Only 7 DEMRGs from both cohorts had significant membership values as indicated by the clustering analysis. Most significant pathway, Gene Ontology (GO)-biological process (BP), GO-molecular function (MF), GO-cellular compartment (CC) terms were macroautophagy, GTP metabolic process, magnesium ion binding, mitochondrial outer membrane. Among all, only TDRKH reported significant overall survival (OS) and 14% amplification across LUAD patients. Lastly, we validated TDRKH via immunohistochemistry (IHC) and semi-quantitative polymerase chain reaction (PCR). In conclusion, our findings advocate for the exploration of TDRKH and their genetic alterations in precision oncology therapeutic approaches for LUAD, emphasizing the potential for target-driven therapy and early diagnostics.
Supplementary information: The online version contains supplementary material available at 10.1007/s13205-024-04127-y.
{"title":"Investigating the role of prognostic mitophagy-related genes in non-small cell cancer pathogenesis via multiomics and network-based approach.","authors":"Prithvi Singh, Gulnaz Tabassum, Mohammad Masood, Saleha Anwar, Mansoor Ali Syed, Kapil Dev, Md Imtaiyaz Hassan, Mohammad Mahfuzul Haque, Ravins Dohare, Indrakant Kumar Singh","doi":"10.1007/s13205-024-04127-y","DOIUrl":"10.1007/s13205-024-04127-y","url":null,"abstract":"<p><p>As one of the most prevalent malignancies, lung cancer displays considerable biological variability in both molecular and clinical characteristics. Lung cancer is broadly categorized into small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC) with the latter being most prevalent. The primary histological subtypes of NSCLC are lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). In the present work, we primarily extracted mRNA count data from a publicly accessible database followed by differentially expressed genes (DEGs) and differentially expressed mitophagy-related genes (DEMRGs) identification in case of both LUAD and LUSC cohorts. Next, we identified important DEMRGs via clustering approach followed by enrichment, survival, and mutational analyses. Lastly, the finalized prognostic biomarker was validated using wet-lab experimentations. Primarily, we obtained 986 and 1714 DEGs across LUAD and LUSC cohorts. Only 7 DEMRGs from both cohorts had significant membership values as indicated by the clustering analysis. Most significant pathway, Gene Ontology (GO)-biological process (BP), GO-molecular function (MF), GO-cellular compartment (CC) terms were macroautophagy, GTP metabolic process, magnesium ion binding, mitochondrial outer membrane. Among all, only <i>TDRKH</i> reported significant overall survival (OS) and 14% amplification across LUAD patients. Lastly, we validated <i>TDRKH</i> via immunohistochemistry (IHC) and semi-quantitative polymerase chain reaction (PCR). In conclusion, our findings advocate for the exploration of <i>TDRKH</i> and their genetic alterations in precision oncology therapeutic approaches for LUAD, emphasizing the potential for target-driven therapy and early diagnostics<i>.</i></p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s13205-024-04127-y.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 11","pages":"273"},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11493942/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142492768","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-01Epub Date: 2024-10-19DOI: 10.1007/s13205-024-04099-z
Thaynara Lorenzoni Entringer, José Maria Rodrigues da Luz, Tomás Gomes Reis Veloso, Lucas Louzada Pereira, Karen Mirella Souza Menezes, Dério Brioschi Júnior, Maria Catarina Megumi Kasuya, Marliane de Cássia Soares da Silva
Understanding the effects of microorganisms on coffee fermentation is crucial to ensure sensory quality and food security. The analysis of the dynamics of the microbial community during fermentation can contribute to a better understanding of the beneficial and harmful effects of microorganisms and help select starter cultures to improve coffee quality. Furthermore, the anaerobic environment produced by carbonic maceration of the coffee fruits inhibits aerobic respiratory processes and stimulates fermentative metabolism, modulating the microbial community during coffee fermentation. This study evaluated the effects of carbonic maceration in the fungal community dynamics during the fermentation of Coffea arabica fruits at 18, 28, and 38 °C for 24, 48, 72, 96, and 120 h. Fungal diversity was accompanied by high-throughput sequencing (NGS) of the Internal Transcribed Spacer (ITS) region. During the coffee fermentation, the fungal community changed over time, with the most significant changes occurring at 18 and 28 °C after 72 h. However, at 38 °C, there were greater variations in fungal composition and fungal diversity was highest after 120 h. The yeast Pichia cephalocereana was predominant in the fermentations. These results indicated that temperature and fermentation conditions influence the fungal community during coffee fermentation. Lower temperatures might favor a more stable microbial environment, while higher temperatures lead to more intense changes. Thus, our data from NGS can help in the identification, isolation, and metabolic characterization of fungi for the fermentation of coffee fruits.
了解微生物对咖啡发酵的影响对于确保感官质量和食品安全至关重要。分析发酵过程中微生物群落的动态有助于更好地了解微生物的有益和有害影响,并帮助选择启动培养物以提高咖啡质量。此外,咖啡果实碳酸浸渍产生的厌氧环境会抑制有氧呼吸过程,刺激发酵代谢,从而调节咖啡发酵过程中的微生物群落。本研究评估了碳酸浸渍对阿拉比卡咖啡果实在 18、28 和 38 °C 温度下发酵 24、48、72、96 和 120 小时期间真菌群落动态的影响。在咖啡发酵过程中,真菌群落随着时间的推移而变化,在 18 和 28 °C 温度下,72 小时后的变化最为显著;但在 38 °C 温度下,真菌组成的变化更大,120 小时后真菌多样性最高。这些结果表明,温度和发酵条件会影响咖啡发酵过程中的真菌群落。较低的温度可能有利于更稳定的微生物环境,而较高的温度则会导致更剧烈的变化。因此,我们从 NGS 中获得的数据有助于咖啡果实发酵过程中真菌的鉴定、分离和代谢特征描述。
{"title":"Genetic diversity of the fungal community that contributes to the sensory quality of coffee beverage after carbonic maceration and fermentation.","authors":"Thaynara Lorenzoni Entringer, José Maria Rodrigues da Luz, Tomás Gomes Reis Veloso, Lucas Louzada Pereira, Karen Mirella Souza Menezes, Dério Brioschi Júnior, Maria Catarina Megumi Kasuya, Marliane de Cássia Soares da Silva","doi":"10.1007/s13205-024-04099-z","DOIUrl":"10.1007/s13205-024-04099-z","url":null,"abstract":"<p><p>Understanding the effects of microorganisms on coffee fermentation is crucial to ensure sensory quality and food security. The analysis of the dynamics of the microbial community during fermentation can contribute to a better understanding of the beneficial and harmful effects of microorganisms and help select starter cultures to improve coffee quality. Furthermore, the anaerobic environment produced by carbonic maceration of the coffee fruits inhibits aerobic respiratory processes and stimulates fermentative metabolism, modulating the microbial community during coffee fermentation. This study evaluated the effects of carbonic maceration in the fungal community dynamics during the fermentation of <i>Coffea arabica</i> fruits at 18, 28, and 38 °C for 24, 48, 72, 96, and 120 h. Fungal diversity was accompanied by high-throughput sequencing (NGS) of the Internal Transcribed Spacer (ITS) region. During the coffee fermentation, the fungal community changed over time, with the most significant changes occurring at 18 and 28 °C after 72 h. However, at 38 °C, there were greater variations in fungal composition and fungal diversity was highest after 120 h. The yeast <i>Pichia cephalocereana</i> was predominant in the fermentations. These results indicated that temperature and fermentation conditions influence the fungal community during coffee fermentation. Lower temperatures might favor a more stable microbial environment, while higher temperatures lead to more intense changes. Thus, our data from NGS can help in the identification, isolation, and metabolic characterization of fungi for the fermentation of coffee fruits.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 11","pages":"272"},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11490598/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142455454","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-01Epub Date: 2024-10-23DOI: 10.1007/s13205-024-04121-4
NandhaGopal SoundharaPandiyan, Carlton Ranjith Wilson Alphonse, Subramoniam Thanumalaya, Samuel Gnana Prakash Vincent, Rajaretinam Rajesh Kannan
The Caridina pseudogracilirostris is commonly found in the brackish waters of the southwestern coastal regions of India. This study provides a comprehensive genomic investigation of the shrimp species C. pseudogracilirostris, offering insights into its genetic makeup, evolutionary dynamics, and functional annotations. The genomic DNA was isolated from tissue samples, sequenced using next-generation sequencing (NGS), and stored in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database (Accession No: PRJNA847710). De novo sequencing indicated a genome size of 1.31 Gbp with a low heterozygosity of about 0.81%. Repeat masking and annotation revealed that repeated elements constitute 24.60% of the genome, with simple sequence repeats (SSRs) accounting for 7.26%. Gene prediction identified 14,101 genes, with functional annotations indicating involvement in critical biological processes such as development, cellular function, immunological responses, and reproduction. Furthermore, phylogenetic analysis revealed genomic links among Malacostraca species, indicating gene duplication as a strategy for genetic diversity and adaptation. C. pseudogracilirostris has 1,856 duplicated genes, reflecting a distinct genomic architecture and evolutionary strategy within the Malacostraca branch. These findings enhance our understanding of the genetic characteristics and evolutionary relationships of C. pseudogracilirostris, providing significant insights into the overall evolutionary dynamics of the Malacostraca group.
Supplementary information: The online version contains supplementary material available at 10.1007/s13205-024-04121-4.
{"title":"Genome sequencing of <i>Caridina pseudogracilirostris</i> and its comparative analysis with malacostracan crustaceans.","authors":"NandhaGopal SoundharaPandiyan, Carlton Ranjith Wilson Alphonse, Subramoniam Thanumalaya, Samuel Gnana Prakash Vincent, Rajaretinam Rajesh Kannan","doi":"10.1007/s13205-024-04121-4","DOIUrl":"10.1007/s13205-024-04121-4","url":null,"abstract":"<p><p>The <i>Caridina pseudogracilirostris</i> is commonly found in the brackish waters of the southwestern coastal regions of India. This study provides a comprehensive genomic investigation of the shrimp species <i>C. pseudogracilirostris</i>, offering insights into its genetic makeup, evolutionary dynamics, and functional annotations. The genomic DNA was isolated from tissue samples, sequenced using next-generation sequencing (NGS), and stored in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database (Accession No: PRJNA847710). De novo sequencing indicated a genome size of 1.31 Gbp with a low heterozygosity of about 0.81%. Repeat masking and annotation revealed that repeated elements constitute 24.60% of the genome, with simple sequence repeats (SSRs) accounting for 7.26%. Gene prediction identified 14,101 genes, with functional annotations indicating involvement in critical biological processes such as development, cellular function, immunological responses, and reproduction. Furthermore, phylogenetic analysis revealed genomic links among Malacostraca species, indicating gene duplication as a strategy for genetic diversity and adaptation. <i>C. pseudogracilirostris</i> has 1,856 duplicated genes, reflecting a distinct genomic architecture and evolutionary strategy within the Malacostraca branch. These findings enhance our understanding of the genetic characteristics and evolutionary relationships of <i>C. pseudogracilirostris</i>, providing significant insights into the overall evolutionary dynamics of the Malacostraca group.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s13205-024-04121-4.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 11","pages":"276"},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11499489/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142492767","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-01Epub Date: 2024-10-24DOI: 10.1007/s13205-024-04126-z
Vinod Kumar Yata
The microbiota-gut-brain axis involves complex bidirectional communication through neural, immune, and endocrine pathways. Microbial metabolites, such as short-chain fatty acids, influence gut motility and brain function by interacting with gut receptors and modulating hormone release. Additionally, microbial components such as lipopolysaccharides and cytokines can cross the gut epithelium and the blood-brain barrier, impacting immune responses and cognitive function. Ex vivo models, which preserve gut tissue and neural segments, offer insight into localized gut-brain communication by allowing for detailed study of nerve excitability in response to microbial signals, but they are limited in systemic complexity. Miniaturized in vitro models, including organ-on-chip platforms, enable precise control of the cellular environment and simulate complex microbiota-host interactions. These systems allow for the study of microbial metabolites, immune responses, and neuronal activity, providing valuable insights into gut-brain communication. Despite challenges such as replicating long-term biological processes and integrating immune and hormonal systems, advancements in bioengineered platforms are enhancing the physiological relevance of these models, offering new opportunities for understanding the mechanisms of the microbiota-gut-brain axis. This review aims to describe the ex vivo and miniaturized in vitro models which are used to mimic the in vivo conditions and facilitate more precise studies of gut brain communication.
{"title":"Ex vivo and miniaturized in vitro <i>models</i> to study microbiota-gut-brain axis.","authors":"Vinod Kumar Yata","doi":"10.1007/s13205-024-04126-z","DOIUrl":"10.1007/s13205-024-04126-z","url":null,"abstract":"<p><p>The microbiota-gut-brain axis involves complex bidirectional communication through neural, immune, and endocrine pathways. Microbial metabolites, such as short-chain fatty acids, influence gut motility and brain function by interacting with gut receptors and modulating hormone release. Additionally, microbial components such as lipopolysaccharides and cytokines can cross the gut epithelium and the blood-brain barrier, impacting immune responses and cognitive function. Ex vivo models, which preserve gut tissue and neural segments, offer insight into localized gut-brain communication by allowing for detailed study of nerve excitability in response to microbial signals, but they are limited in systemic complexity. Miniaturized in vitro models, including organ-on-chip platforms, enable precise control of the cellular environment and simulate complex microbiota-host interactions. These systems allow for the study of microbial metabolites, immune responses, and neuronal activity, providing valuable insights into gut-brain communication. Despite challenges such as replicating long-term biological processes and integrating immune and hormonal systems, advancements in bioengineered platforms are enhancing the physiological relevance of these models, offering new opportunities for understanding the mechanisms of the microbiota-gut-brain axis. This review aims to describe the ex vivo and miniaturized in vitro models which are used to mimic the in vivo conditions and facilitate more precise studies of gut brain communication.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 11","pages":"280"},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11502650/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142516252","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Fusion transcripts (FTs) are well known cancer biomarkers, relatively understudied in plants. Here, we developed PFusionDB (www.nipgr.ac.in/PFusionDB), a novel plant-specific fusion-transcript database. It is a comprehensive repository of 80,170, 39,108, 83,330, and 11,500 unique fusions detected in 1280, 637, 697, and 181 RNA-Seq samples of Arabidopsis thaliana, Oryza sativa japonica, Oryza sativa indica, and Cicer arietinum respectively. Here, a total of 76,599 (Arabidopsis thaliana), 35,480 (Oryza sativa japonica), 72,099 (Oryza sativa indica), and 9524 (Cicer arietinum) fusion transcripts are non-recurrent i.e., only found in one sample. Identification of FTs was performed by using a total of five tools viz. EricScript-Plants, STAR-Fusion, TrinityFusion, SQUID, and MapSplice. At PFusionDB, available fundamental details of fusion events includes the information of parental genes, junction sequence, expression levels of fusion transcripts, breakpoint coordinates, strand information, tissue type, treatment information, fusion type, PFusionDB ID, and Sequence Read Archive (SRA) ID. Further, two search modules: 'Simple Search' and 'Advanced Search', along with a 'Browse' option to data download, are present for the ease of users. Three distinct modules viz. 'BLASTN', 'SW Align', and 'Mapping' are also available for efficient query sequence mapping and alignment to FTs. PFusionDB serves as a crucial resource for delving into the intricate world of fusion transcript in plants, providing researchers with a foundation for further exploration and analysis. Database URL: www.nipgr.ac.in/PFusionDB.
Supplementary information: The online version contains supplementary material available at 10.1007/s13205-024-04132-1.
{"title":"PFusionDB: a comprehensive database of plant-specific fusion transcripts.","authors":"Ajay Arya, Simran Arora, Fiza Hamid, Shailesh Kumar","doi":"10.1007/s13205-024-04132-1","DOIUrl":"10.1007/s13205-024-04132-1","url":null,"abstract":"<p><p>Fusion transcripts (FTs) are well known cancer biomarkers, relatively understudied in plants. Here, we developed PFusionDB (www.nipgr.ac.in/PFusionDB), a novel plant-specific fusion-transcript database. It is a comprehensive repository of 80,170, 39,108, 83,330, and 11,500 unique fusions detected in 1280, 637, 697, and 181 RNA-Seq samples of <i>Arabidopsis thaliana</i>, <i>Oryza sativa japonica</i>, <i>Oryza sativa indica</i>, and <i>Cicer arietinum</i> respectively. Here, a total of 76,599 (<i>Arabidopsis thaliana</i>), 35,480 (<i>Oryza sativa japonica</i>), 72,099 (<i>Oryza sativa indica</i>), and 9524 (<i>Cicer arietinum</i>) fusion transcripts are non-recurrent i.e., only found in one sample. Identification of FTs was performed by using a total of five tools viz. EricScript-Plants, STAR-Fusion, TrinityFusion, SQUID, and MapSplice. At PFusionDB, available fundamental details of fusion events includes the information of parental genes, junction sequence, expression levels of fusion transcripts, breakpoint coordinates, strand information, tissue type, treatment information, fusion type, PFusionDB ID, and Sequence Read Archive (SRA) ID. Further, two search modules: 'Simple Search' and 'Advanced Search', along with a 'Browse' option to data download, are present for the ease of users. Three distinct modules viz. 'BLASTN', 'SW Align', and 'Mapping' are also available for efficient query sequence mapping and alignment to FTs. PFusionDB serves as a crucial resource for delving into the intricate world of fusion transcript in plants, providing researchers with a foundation for further exploration and analysis. Database URL: www.nipgr.ac.in/PFusionDB.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s13205-024-04132-1.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 11","pages":"282"},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11519250/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542976","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}