Iranian Journal of Biotechnology最新文献

{"title":"Evaluation of lncRNAs as Potential Biomarkers for Diagnosis of Metastatic Triple-Negative Breast Cancer through Bioinformatics and Machine Learning.","authors":"Shiva Soleimani, Farkhondeh Pouresmaeili, Iman Salahshoori Far","doi":"10.30498/ijb.2024.432171.3853","DOIUrl":"10.30498/ijb.2024.432171.3853","url":null,"abstract":"<p><strong>Background: </strong>Triple-negative breast cancer (TNBC) is highly invasive and metastatic to the lymph nodes. Therefore, it is an urgent priority to distinguish novel biomarkers and molecular mechanisms of lymph node metastasis as the first step to the disease investigation. Long non-coding RNAs (lncRNAs) have widely been explored in cancer tumorigenesis, progression, and invasion.</p><p><strong>Objectives: </strong>This study aimed to identify and evaluate lncRNAs in the signaling pathway of <i>MMP11</i> gene in both metastatic and non-metastatic TNBC samples. The potential of lncRNAs in prognosis and diagnosis of the disease was also assessed using bioinformatics analysis, machine learning, and quantitative real-time PCR.</p><p><strong>Materials and methods: </strong>Using machine learning algorithms, we analyzed the available BC data from the Cancer Genome Atlas Network (TCGA) and identified three potential lncRNAs, gastric adenocarcinoma-associated, positive CD44 regulator, long intergenic noncoding RNA (<i>GAPLINC</i>), <i>TPT1-AS1</i>, and <i>EIF1B</i> antisense RNA 1 (<i>EIF1B-AS1</i>) that could successfully distinguish between metastatic and non-metastatic TNBC.</p><p><strong>Results: </strong>The results showed the upregulation of <i>GAPLINC</i> lncRNA in metastatic BC tissues, compared to non-metastatic (P<0.01) and normal samples, though <i>TPT1-AS1</i> and <i>EIF1B-AS1</i> were downregulated in metastatic TNBC samples (P<0.01).</p><p><strong>Conclusion: </strong>Given the aberrant expression of candidate lncRNAs and the underlying mechanisms, the above-mentioned RNAs could act as novel diagnostic and prognostic biomarkers in metastatic BC.</p>","PeriodicalId":14492,"journal":{"name":"Iranian Journal of Biotechnology","volume":"22 3","pages":"e3853"},"PeriodicalIF":1.6,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11682528/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142906846","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}

{"title":"Hypoxic Preconditioning Prevents Oxidative Stress-Induced Cell Death in Human Hair Follicle Stem Cells.","authors":"Mohammad Saied Salehi, Fatemeh Changiz Khani, Sanaz Ansari, Mohammad Javad Mokhtari, Mahintaj Dara, Mahnaz Bayat, Etrat Hooshmandi, Nahid Ashjazadeh, Afshin Borhani-Haghighi, Gökhan Ünal, Sareh Pandamooz","doi":"10.30498/ijb.2024.447077.3888","DOIUrl":"10.30498/ijb.2024.447077.3888","url":null,"abstract":"<p><strong>Objectives: </strong>This study investigated the impact of hypoxic preconditioning on the survival and oxidative stress tolerance of nestin-expressing hair follicle stem cells (hHFSCs) and SH-SY5Y neuroblastoma cells, two crucial cell types for central nervous system therapies. The study also examined the relative expression of three key genes, HIF1α, BDNF, and VEGF following hypoxic preconditioning.</p><p><strong>Materials and methods: </strong>hHFSCs were isolated from human hair follicles, characterized, and subjected to hypoxia for up to 72 hours. SH-SY5Y cells were similarly preconditioned for up to 72 hours. Cell viability under hypoxic conditions and oxidative stress was assessed. The relative expression of key genes was evaluated using qRT-PCR.</p><p><strong>Results: </strong>hHFSCs exhibited remarkable resilience to hypoxic conditions, while SH-SY5Y cells displayed lower tolerance. Hypoxic preconditioning improved the viability of both cell types under oxidative stress. HIF1α mRNA was significantly downregulated, and VEGF transcripts increased after preconditioning, suggesting adaptations to prolonged hypoxia.</p><p><strong>Conclusion: </strong>Hypoxic preconditioning enhances the survival and oxidative stress resilience of hHFSCs and SH-SY5Y cells, offering potential benefits for central nervous system cell therapy. The differential responses observed emphasize the need for tailored preconditioning strategies for specific cell types. These findings underscore the importance of hypoxic preconditioning and warrant further research into the underlying mechanisms, bringing us closer to effective neurological disorder treatments.</p>","PeriodicalId":14492,"journal":{"name":"Iranian Journal of Biotechnology","volume":"22 3","pages":"e3888"},"PeriodicalIF":1.6,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11682525/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142906909","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}

{"title":"Inhibition of Chitinase-3-like Protein 1 Reduced Epithelial-Mesenchymal Transition and Vascular Epithelial Cadherin Expression in Oesophageal Squamous Cell Carcinoma.","authors":"Yanzi Qin, Wenjun Zhao, Qicai Li, Zhaogeng Cai, Guowen Wang, Nan Wang, Li Ma","doi":"10.30498/ijb.2024.394737.3693","DOIUrl":"10.30498/ijb.2024.394737.3693","url":null,"abstract":"<p><strong>Background: </strong>Oesophageal cancer (EC) is one of the common malignant tumors, and the prognosis of patients is poor. Further exploration of EC pathogenesis remains warranted.</p><p><strong>Objective: </strong>The relationship between vascular epithelial cadherin (VE-cadherin) and chitinase-3-like protein 1 (CHI3L1) in EC is currently unknown. To further explore the relationship, immunohistochemical staining was performed to detect the expression level of CHI3L1 and VE-cadherin in oesophageal squamous cell carcinoma ( ESCC).</p><p><strong>Materials and methods: </strong>Small interfering RNAs (siRNAs) inhibited CHI3L1 expression in KYSE-150 and TE1 cells. Western blot and quantitative fluorescence polymerase chain reaction were used to detect the levels of CHI3L1, VE-cadherin and epithelial-mesenchymal transition (EMT)-related proteins <i>in vitro</i> and <i>in vivo</i>, and KYSE-150 cells were used to establish an <i>in-vivo</i> model and observe tumour growth.</p><p><strong>Results: </strong>High levels of CHI3L1 and VE-cadherin expression were closely associated with the progression of ESCC; the pathologic tumour-node-metastasis stage was also closely related with the progression of ESCC (<i>p</i> < 0.05). High levels of CHI3L1 and VE-cadherin expression led to poor prognosis in patients with EC. In KYSE-150 and TE1 EC cell lines, the invasion, migration and proliferation of cells decreased, and the apoptotic rate increased after CHI3L1 expression was decreased using siRNA. The CHI3L1, VE-cadherin, Snail, Twist1 protein and mRNA expression levels decreased, whereas the E-cadherin levels increased.</p><p><strong>Conclusions: </strong>Chitinase-3-like protein 1 could promote the EMT of ESCC, and the inhibition of CHI3L1 decreases the expression of VE-cadherin, which inhibits tumour angiogenesis and tumour progression in ESCC.</p>","PeriodicalId":14492,"journal":{"name":"Iranian Journal of Biotechnology","volume":"22 3","pages":"e3693"},"PeriodicalIF":1.6,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11682521/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142906915","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}

{"title":"Optimization of Green Synthesis Formulation of Selenium Nanoparticles (SeNPs) Using Peach Tree Leaf Extract and Investigating its Properties and Stability.","authors":"Sepideh Shayan, Donya Hajihajikolai, Fateme Ghazale, Fatemeh Gharahdaghigharahtappeh, Amirhossein Faghih, Omid Ahmadi, Gity Behbudi","doi":"10.30498/ijb.2024.413943.3786","DOIUrl":"10.30498/ijb.2024.413943.3786","url":null,"abstract":"<p><strong>Background: </strong>Selenium nanoparticles (SeNPs) are highly sought after in diverse industries for their distinct properties and advantages. SeNPs can be synthesized via several methods, including the use of microwave, bain-marie, autoclave, and heater.</p><p><strong>Objective: </strong>The objective is to optimize the SeNP synthesis formulation, emphasizing stability, concentration, particle size minimization, and uniformity using central composite design.</p><p><strong>Materials and methods: </strong>The method involves autoclave heating at 121 °C under 1.5 bar pressure for 15 minutes. Prunus persica tree leaf extract and Aloe Vera gel serve as a regenerating agent and stabilizer, respectively. Four responses including SeNPs concentration, average particle size, zeta potential, and dispersion index (PDI), were assessed according to the experimental design. The optimal synthesis point was determined and evaluated for SeNP imaging, antioxidant, and antifungal properties.</p><p><strong>Results: </strong>Results indicate that the optimal SeNPs formulation includes 5.73 mL of Prunus persica tree leaf extract, 13.45 mL of sodium selenite salt solution, and 0.80 mL of Aloe Vera gel.</p><p><strong>Conclusion: </strong>The optimal formulation of selenium nanoparticles (SeNPs) achieved in this study, using Prunus persica tree leaf extract as a reducing agent and Aloe Vera gel as a stabilizer, demonstrates superior properties including high stability, a small average particle size, and a favorable zeta potential. These characteristics make the SeNPs well-suited for applications requiring enhanced antioxidant and antifungal activities. The findings underscore the importance of optimizing synthesis parameters to maximize the functional properties of SeNPs.</p>","PeriodicalId":14492,"journal":{"name":"Iranian Journal of Biotechnology","volume":"22 3","pages":"e3786"},"PeriodicalIF":1.6,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11682526/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142906952","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}

{"title":"Resistance Induced by Viral Sense, Anti-sense, and Hairpin Constructs Against Beet Curly Top Virus and Beet Curly Top Iran Virus.","authors":"Razieh Montazeri, Mohammad Ali Malboobi, Masoud Shams-Bakhsh","doi":"10.30498/ijb.2024.425159.3831","DOIUrl":"10.30498/ijb.2024.425159.3831","url":null,"abstract":"<p><strong>Background: </strong>RNA silencing-based antiviral breeding is a promising strategy for developing virus-resistant plants.</p><p><strong>Objectives: </strong>This study employed viral sense, anti-sense, and hairpin constructs to induce resistance against beet curly top virus (BCTV) and beet curly top Iran virus (BCTIV).</p><p><strong>Materials and methods: </strong>For this purpose, a 120-bp conserved sequence of Rep- and C2-BCTV and a 222-bp conserved sequence of CP-, Reg-, and MP-BCTIV were selected for construct production. The efficiency of constructs was investigated in transient expression in <i>Nicotiana benthamiana</i> and sugar beet plants and stable expression in <i>N. benthamiana</i>.</p><p><strong>Results: </strong>In transient expression, all designed constructs induced effective resistance to BCTV and BCTIV; the hairpin constructs were more effective against both viruses. The stability of the achieved resistance by hairpin constructs was also confirmed in the T1 generation of transgenic plants.</p><p><strong>Conclusions: </strong>This study showed that employing conserved coding sequences of BCTVs leads to effective resistance against BCTVs infection. The lack of protein production from transgene and degradation of its transcript due to the gene silencing mechanism makes this method safe for biosecurity. In stable transformation, the inheritance of induced resistance against BCTVs was confirmed in the T1 generation. These advantages make this mechanism commercially useful for the production of resistant plants to viruses.</p>","PeriodicalId":14492,"journal":{"name":"Iranian Journal of Biotechnology","volume":"22 3","pages":"e3831"},"PeriodicalIF":1.6,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11682523/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142907002","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}

{"title":"The Histone Deacetylase Inhibitor Trichostatin-A Modifies the Expression of Trichothecene Mycotoxin Regulatory Gene <i>Tri5</i> in <i>Fusarium graminearum</i>.","authors":"Shiva Amin, Saeed Rezaee, Amir Mousavi, Hamidreza Zamanizadeh","doi":"10.30498/ijb.2024.437331.3872","DOIUrl":"10.30498/ijb.2024.437331.3872","url":null,"abstract":"<p><strong>Background: </strong><i>Fusarium graminearum</i> is the causal agent of Fusarium Head Blight (FHB) on wheat and produces deoxynivalenol (DON), known to cause extreme human and animal toxicosis. This species' genome contains genes involved in plant-pathogen interactions and regulated by chromatin modifications. Moreover, histone deacetylase inhibitors (HDACIs), including trichostatin A (TSA), have been employed to study gene transcription regulation because they can convert the structure of chromatin.</p><p><strong>Objectives: </strong>The current study was designed to evaluate the effects of TSA on histone deacetylase (<i>HDAC</i>) and, trichodiene synthase (<i>Tri5</i>) gene expression in toxigenic and non-toxigenic <i>F. graminearum</i> isolates.</p><p><strong>Materials and methods: </strong>The mycelia were grown on potato dextrose broth (PDB) culture media supplemented with two concentrations of TSA and dimethyl sulfoxide (DMSO) (3 and 10 µg. mL^-1) for 48 h, 72 h, and 96 h. Then, the mRNA levels were estimated via real-time quantitative reverse transcription-polymerase chain reaction (real-time qRT-PCR).</p><p><strong>Results: </strong>We found that the levels of <i>HADC</i> and <i>Tri5</i> varied over time and dosage in response to the use of TSA. The toxigenic isolate showed an increase in the <i>Tri5</i> expression when treated with TSA, with the highest levels monitored when the concentration of the substance was 3 µg. mL^-1 at 48 h. The non-toxigenic isolate also showed high levels of <i>HDAC</i> and <i>Tri5</i> expression in the presence of TSA, but a sharp decrease in the <i>Tri5</i> transcription was observed at 72 h when grown on culture media containing 10 µg. mL^-1 of TSA.</p><p><strong>Conclusion: </strong>Overall, our results suggest a mode of DON biosynthesis regulation in <i>F. graminearum</i> by chromatin modifications that may help us offer new strategies for tackling fungal infections.</p>","PeriodicalId":14492,"journal":{"name":"Iranian Journal of Biotechnology","volume":"22 3","pages":"e3872"},"PeriodicalIF":1.6,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11682529/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142907004","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}

{"title":"Genetic Diversity and Population Structure of Primary Tritipyrum Lines in Comparison with Bread Wheat Varieties and Triticale Lines using SCoT Markers.","authors":"Marzia Rezai, S Ebrahim Seifati, Afagh Tabandeh Saravi, Hossein Shahsavand Hasani","doi":"10.30498/ijb.2024.447932.3889","DOIUrl":"10.30498/ijb.2024.447932.3889","url":null,"abstract":"<p><strong>Background: </strong>Triticale and tritipyrum as a new artificial cereal were investigated as potential stress-resistant alternatives within the Triticeae tribe due to their notable adaptability to environmental stresses.</p><p><strong>Objectives: </strong>The first purpose of this study was to determine the genetic variation of 14 genotypes on physiological traits in arid and semi-arid climate of Yazd province on primary trans chromosomal tritipyrum (PTCT) lines, promising triticale lines, and Iranian and Afghan bread wheat cultivars, and the second purpose was to investigate the genetic diversity and classification of genotypes using start codon targeted (SCoT) markers.</p><p><strong>Materials and methods: </strong>The photosynthesis pigments, proline, and catalase enzyme activity of 14 genotypes were determined. Also, genomic DNA of 10 genotypes was extracted using a modified CTAB protocol. The 13 primers were set-up for PCR and the studied parameters were analyzed with Excel, GenAlEx6.5, POPGen32, and STRUCTURE software.</p><p><strong>Results: </strong>Based on 14 amphidiploids, Triticale 4115 and PTCT line (Ka/b) (Cr/b) F₂ had the greatest carotenoids and photosynthesis pigments values. Proline content was highest in PTCT lines (Ka/b) (Cr/b) F₂, triticale line 4115, and La(4B/4D)/b. The PTCT lines La/b and Az/b showed the highest (0.34) and lowest (0.04) average catalase, respectively. The investigation of genetic diversity in physiological traits related to the arid and semi-arid climate conditions of Yazd province showed that there is a great diversity between the genotypes.</p>","PeriodicalId":14492,"journal":{"name":"Iranian Journal of Biotechnology","volume":"22 3","pages":"e3889"},"PeriodicalIF":1.6,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11682527/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142906772","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}

{"title":"LncRNA U731166 Increases the Accumulation of TGFBR1 by Sponging miR-3607-3p in Esophageal Squamous-Cell Carcinomas (ESCC) to Promote Tumor Metastasis.","authors":"Mingbo Wang, Meng Wang, Chao Huang, Yonggang Zhu, Fan Zhang, Wenda Gao, Zhenhua Li, Liangbiao Peng, Ziqiang Tian, Chao Gao, Xingpeng Han","doi":"10.30498/ijb.2024.343750.3391","DOIUrl":"10.30498/ijb.2024.343750.3391","url":null,"abstract":"<p><strong>Background: </strong>Long non-coding RNA (lncRNA) U731166 and microRNA (miR)-3607-3p are two ncRNAs with critical roles in cancer biology, while their involvement in esophageal squamous-cell carcinomas (ESCC) is unclear. We predicted that U731166 and miR-3607-3p might interact with each other. This study aimed to investigate their role and interaction in ESCC.</p><p><strong>Objectives: </strong>This study was therefore conducted to explore the involvement of U731166 and miR-3607-3p in ESCC, with a focus on the interaction between them.</p><p><strong>Materials and methods: </strong>Paired ESCC and non-tumor tissue samples were recruited from 72 ESCC patients. By RT-Qpcr, level of U731166 and miR-3607-3p in paired tissues was measured. By RNA-RNA pulldown assay, the direct interaction between U731166 and miR-3607-3p was detected. U731166 overexpression or miR-3607-3p overexpression was performed to investigate their role in regulating the expression of each other. By RT-qPCR and Western blot analysis, the role of U731166 and miR-3607-3p in regulating the level of TGFBR1 was assessed. By Transwell assays, cell invasion and migration were analyzed.</p><p><strong>Results: </strong>Compared to non-tumor tissues, U731166 was highly upregulated in ESCC, while miR-3607-3p was downregulated in ESCC. U731166 and miR-3607-3p directly interacted with each other, but they are not closely correlated and did not regulate the level of each other. Moreover, U731166 reversed the role of miR-3607-3p in downregulating TGFBR1 and inhibiting cancer cell invasion and migration. U731166 and miR-3607-3p were closely associated with patients' tumor metastasis but not tumor size.</p><p><strong>Conclusion: </strong>U731166 may upregulate TGFBR1 by sponging miR-3607-3p in ESCC cells to promote tumor metastasis.</p>","PeriodicalId":14492,"journal":{"name":"Iranian Journal of Biotechnology","volume":"22 3","pages":"e3391"},"PeriodicalIF":1.6,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11682522/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142906932","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}

{"title":"Plant Heat Shock Proteins Are More Effective in Enhancing Recombinant Alcohol Dehydrogenase Activity than Bacterial Ones <i>In Vitro</i>.","authors":"Minjae Jung, Yunjin Park, Yeh-Jin Ahn","doi":"10.30498/ijb.2024.442517.3878","DOIUrl":"10.30498/ijb.2024.442517.3878","url":null,"abstract":"<p><strong>Background: </strong>Recombinant proteins produced in the cell factories are used in biological research, pharmaceutical production, and biochemical and agricultural applications. Molecular chaperones, such as heat shock proteins (Hsps), are co-expressed with recombinant proteins to enhance their yield, stability, and activity. When <i>Escherichia coli</i> (<i>E. coli</i>) is used as a cell factory, <i>E. coli</i> Hsps are the frequently used co-expression partners.</p><p><strong>Objectives: </strong>We examined if there are differences in the molecular chaperone activities of plant and bacterial Hsps on recombinant protein activity. We compared the effects of the Hsps from carrot (<i>Daucus carota</i>) and <i>E. coli</i> on enhancing the recombinant alcohol dehydrogenase (ADH) activity and solubility under normal and heat conditions <i>in vitro</i>.</p><p><strong>Materials and methods: </strong>His-tagged carrot Hsps (DcHsp17.7 and DcHsp70), <i>E. coli</i> Hsps (IbpA, IbpB, and DnaK), and ADH from a thermophile <i>Geobacillus stearothermophilus</i> were individually cloned in a pET11a or a pET26b vector, introduced into <i>E. coli</i> BL21(DE3), and expressed by isopropyl β-D-1-thiogalactopyranoside treatment (0.5 mM, 16 °C , 20 h). The recombinant proteins were purified using Ni-NTA affinity chromatography and resolved in SDS-PAGE (17%). The recombinant ADH was treated with the individual Hsps or in combination, and the enzyme activity was examined by measuring the NADH product levels at O.D.₃₄₀.</p><p><strong>Results: </strong>The recombinant ADH was expressed at high levels in <i>E. coli</i> and very thermotolerant when the purified enzyme reacted (up to 70 °C). All five Hsps enhanced the ADH activity under normal and heat conditions <i>in vitro</i>, compared to the control. DcHsp17.7 and DcHsp70 were the most effective for improving the enzyme activity by up to 13.0- and 11.6-fold, respectively, followed by IbpA (8.4-fold), DnaK (6.5-fold), and IbpB (3.4-fold), at 37 °C . Combined incubation of DcHsp17.7-DcHsp70 and DcHsp17.7-DnaK further enhanced the ADH activity by 13.8 and 14.2-fold, respectively. DcHsp70 effectively enhanced ADH's solubility at 37 °C <i>in vitro</i>.</p><p><strong>Conclusion: </strong>Our results suggest that plant Hsps can enhance recombinant protein activity, such as ADH, more effectively than their bacterial counterparts. Identifying effective molecular chaperones in the bacterial and eukaryotic domains will help enhance the production of recombinant proteins in <i>E. coli</i>.</p>","PeriodicalId":14492,"journal":{"name":"Iranian Journal of Biotechnology","volume":"22 3","pages":"e3878"},"PeriodicalIF":1.6,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11682524/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142906966","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}

{"title":"<i>In-Silico</i> Method for Predicting Pathogenic Missense Variants Using Online Tools: AURKA Gene as a Model.","authors":"Eric Jonathan Maciel-Cruz, Luis Eduardo Figuera-Villanueva, Liliana Gómez-Flores-Ramos, Rubiceli Hernández-Peña, Martha Patricia Gallegos-Arreola","doi":"10.30498/ijb.2024.413800.3787","DOIUrl":"10.30498/ijb.2024.413800.3787","url":null,"abstract":"<p><strong>Background: </strong><i>In-silico</i> analysis provides a fast, simple, and cost-free method for identifying potentially pathogenic single nucleotide variants.</p><p><strong>Objective: </strong>To propose a simple and relatively fast method for the prediction of variant pathogenicity using free online <i>in-silico</i> (IS) tools with <i>AURKA</i> gene as a model.</p><p><strong>Materials and methods: </strong>We aim to propose a methodology to predict variants with high pathogenic potential using computational analysis, using <i>AURKA</i> gene as model. We predicted a protein model and analyzed 209 out of 64,369 <i>AURKA</i> variants obtained from Ensembl database. We used bioinformatic tools to predict pathogenicity. The results were compared through the VarSome website, which includes its own pathogenicity score and the American College of Medical Genetics (ACMG) classification.</p><p><strong>Results: </strong>Out of the 209 analyzed variants, 16 were considered pathogenic, and 13 were located in the catalytic domain. The most frequent protein changes were size and hydrophobicity modifications of amino acids. Proline and Glycine amino acid substitutions were the most frequent changes predicted as pathogenic. These bioinformatic tools predicted functional changes, such as protein up or down-regulation, gain or loss of molecule interactions, and structural protein modifications. When compared to the ACMG classification, 10 out of 16 variants were considered likely pathogenic, with 7 out of 10 changes at Proline/Glycine substitutions.</p><p><strong>Conclusion: </strong>This method allows quick and cost-free bulk variant screening to identify variants with pathogenic potential for further association and/or functional studies.</p>","PeriodicalId":14492,"journal":{"name":"Iranian Journal of Biotechnology","volume":"22 2","pages":"e3787"},"PeriodicalIF":1.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364922/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142107499","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}