keyword
https://read.qxmd.com/read/38522573/strategy-for-the-optimization-of-read-through-therapy-for-junctional-epidermolysis-bullosa-with-col17a1-nonsense-mutation
#1
JOURNAL ARTICLE
Saliha Beyza Sayar, Cristina Has
The read-through therapy suppresses premature termination codons and induces read-through activity consequently restoring missing proteins. Aminoglycosides are widely studied as read-through drugs in different human genetic disorders including hereditary skin diseases. Our previous work revealed that aminoglycosides have effect on COL17A1 nonsense mutations and represent a therapeutic option to alleviate disease severity. However, the amount of restored type XVII collagen (C17) in C17 deficient junctional epidermolysis bullosa (JEB-C17) keratinocytes was less than 1% relative to normal keratinocytes and was achieved only after high dose gentamicin treatment, which induced deep transcriptional changes...
March 22, 2024: Journal of Investigative Dermatology
https://read.qxmd.com/read/38521922/adsorption-of-hg-2-cr-6-by-metal-binding-proteins-heterologously-expressed-in-escherichia-coli
#2
JOURNAL ARTICLE
Shuting Hu, Zixiang Wei, Teng Liu, Xinyu Zuo, Xiaoqiang Jia
BACKGROUND: Removal of heavy metals from water and soil is a pressing challenge in environmental engineering, and biosorption by microorganisms is considered as one of the most cost-effective methods. In this study, the metal-binding proteins MerR and ChrB derived from Cupriavidus metallidurans were separately expressed in Escherichia coli BL21 to construct adsorption strains. To improve the adsorption performance, surface display and codon optimization were carried out. RESULTS: In this study, we constructed 24 adsorption engineering strains for Hg2+ and Cr6+ , utilizing different strategies...
March 23, 2024: BMC Biotechnology
https://read.qxmd.com/read/38509572/modifications-of-the-5-region-of-the-caspon-tm-tag-s-mrna-further-enhance-soluble-recombinant-protein-production-in-escherichia-coli
#3
JOURNAL ARTICLE
Christoph Köppl, Wolfgang Buchinger, Gerald Striedner, Monika Cserjan-Puschmann
BACKGROUND: Escherichia coli is one of the most commonly used host organisms for the production of biopharmaceuticals, as it allows for cost-efficient and fast recombinant protein expression. However, challenging proteins are often produced with low titres or as inclusion bodies, and the manufacturing process needs to be developed individually for each protein. Recently, we developed the CASPONTM technology, a generic fusion tag-based platform process for high-titer soluble expression including a standardized downstream processing and highly specific enzymatic cleavage of the fusion tag...
March 20, 2024: Microbial Cell Factories
https://read.qxmd.com/read/38509174/enhancing-explainable-sars-cov-2-vaccine-development-leveraging-bee-colony-optimised-bi-lstm-bi-gru-models-and-bioinformatic-analysis
#4
JOURNAL ARTICLE
Dilber Uzun Ozsahin, Zubaida Said Ameen, Abdurrahman Shuaibu Hassan, Auwalu Saleh Mubarak
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a single-stranded RNA virus that caused the outbreak of the coronavirus disease 2019 (COVID-19). The COVID-19 outbreak has led to millions of deaths and economic losses globally. Vaccination is the most practical solution, but finding epitopes (antigenic peptide regions) in the SARS-CoV-2 proteome is challenging, costly, and time-consuming. Here, we proposed a deep learning method based on standalone Recurrent Neural networks to predict epitopes from SARS-CoV-2 proteins easily...
March 20, 2024: Scientific Reports
https://read.qxmd.com/read/38500114/new-improvements-in-grapevine-genome-editing-high-efficiency-biallelic-homozygous-knock-out-from-regenerated-plantlets-by-using-an-optimized-zcas9i
#5
JOURNAL ARTICLE
Jérémy Villette, Fatma Lecourieux, Eliot Bastiancig, Marie-Claire Héloir, Benoit Poinssot
BACKGROUND: For ten years, CRISPR/cas9 system has become a very useful tool for obtaining site-specific mutations on targeted genes in many plant organisms. This technology opens up a wide range of possibilities for improved plant breeding in the future. In plants, the CRISPR/Cas9 system is mostly used through stable transformation with constructs that allow for the expression of the Cas9 gene and sgRNA. Numerous studies have shown that site-specific mutation efficiency can vary greatly between different plant species due to factors such as plant transformation efficiency, Cas9 expression, Cas9 nucleotide sequence, the addition of intronic sequences, and many other parameters...
March 18, 2024: Plant Methods
https://read.qxmd.com/read/38498447/bioinformatic-analysis-of-codon-usage-bias-of-hsp20-genes-in-four-cruciferous-species
#6
JOURNAL ARTICLE
Huiyue Ji, Junnan Liu, Yineng Chen, Xinyi Yu, Chenlu Luo, Luxi Sang, Jiayu Zhou, Hai Liao
Heat shock protein 20 (HSP20) serves as a chaperone and plays roles in numerous biological processes, but the codon usage bias (CUB) of its genes has remained unexplored. This study identified 140 HSP20 genes from four cruciferous species, Arabidopsis thaliana , Brassica napus , Brassica rapa , and Camelina sativa , that were identified from the Ensembl plants database, and we subsequently investigated their CUB. As a result, the base composition analysis revealed that the overall GC content of HSP20 genes was below 50%...
February 6, 2024: Plants (Basel, Switzerland)
https://read.qxmd.com/read/38492609/identification-of-an-n-terminal-tag-580n-that-improves-the-biosynthesis-of-fluorescent-proteins-in-francisella-tularensis-and-other-gram-negative-bacteria
#7
JOURNAL ARTICLE
Kristen Haggerty, Stuart Cantlay, Emily Young, Mariah K Cashbaugh, Elio F Delatore Iii, Rori Schreiber, Hayden Hess, Daniel R Komlosi, Sarah Butler, Dalton Bolon, Theresa Evangelista, Takoda Hager, Claire Kelly, Katherine Phillips, Jada Voellinger, Robert M Q Shanks, Joseph Horzempa
Utilization of fluorescent proteins is widespread for the study of microbial pathogenesis and host-pathogen interactions. Here, we discovered that linkage of the 36 N-terminal amino acids of FTL_0580 (a hypothetical protein of Francisella tularensis) to fluorescent proteins increases the fluorescence emission of bacteria that express these recombinant fusions. This N-terminal peptide will be referred to as 580N. Western blotting revealed that the linkage of 580N to Emerald Green Fluorescent Protein (EmGFP) in F...
March 14, 2024: Molecular and Cellular Probes
https://read.qxmd.com/read/38491213/cellular-energy-regulates-mrna-degradation-in-a-codon-specific-manner
#8
JOURNAL ARTICLE
Pedro Tomaz da Silva, Yujie Zhang, Evangelos Theodorakis, Laura D Martens, Vicente A Yépez, Vicent Pelechano, Julien Gagneur
Codon optimality is a major determinant of mRNA translation and degradation rates. However, whether and through which mechanisms its effects are regulated remains poorly understood. Here we show that codon optimality associates with up to 2-fold change in mRNA stability variations between human tissues, and that its effect is attenuated in tissues with high energy metabolism and amplifies with age. Mathematical modeling and perturbation data through oxygen deprivation and ATP synthesis inhibition reveal that cellular energy variations non-uniformly alter the effect of codon usage...
March 15, 2024: Molecular Systems Biology
https://read.qxmd.com/read/38488603/whole-proteome-screening-to-develop-a-potent-epitope-based-vaccine-against-coxiella-burnetii-a-reverse-vaccinology-approach
#9
JOURNAL ARTICLE
Ali Forouharmehr
Coxiellosis is known as a threat to human health. This study aimed to develop an epitope-based vaccine against coxiellosis using a whole proteome investigation. In this case, the whole proteome of Coxiella burnetii was collected from the database, then different assessments were performed to select immunogenic proteins. The selected proteins were used for epitopes prediction. The epitope-based vaccine was made using the best-selected epitopes and HBHA protein. The physical and chemical features, as well as secondary and tertiary structures of the developed vaccine were analyzed...
March 15, 2024: Journal of Biomolecular Structure & Dynamics
https://read.qxmd.com/read/38486475/a-novel-immunoinformatics-approach-for-developing-a-poly-epitope-vaccine-targeting-foot-and-mouth-disease-virus-exploiting-structural-vp-proteins
#10
JOURNAL ARTICLE
Muhammad Saad Bhutta, Muhammad Awais, Sahar Sadaqat, Fernando Berton Zanchi, Naila Shahid, Abdul Qayyum Rao
Foot and mouth Disease virus (FMDV) belongs to Picornaviridae family and Aphthovirus genus causing Foot and mouth disease (FMD) in cloven-hoofed animals. FMDV, a prevalent virus induces both acute and chronic infections with high mutation rates resulting in seven primary serotypes, making vaccine development indispensable. Due to time and cost effectiveness of the immunoinformatic approach, we designed in-silico polyepitope vaccine (PEV) for the curtailment of FMDV. Structural and immunogenic parts of FMDV (Viral Protein 1 (VP1), Viral Protein 2 (VP2), Viral Protein 3 (VP3), and Viral Protein 4 (VP4)) were used to design the cytotoxic T Lymphocyte (CTL), Helper T Lymphocyte (HTL), and B-cell epitopes, followed by screening for antigenic, non-allergenic, Interferon (IFN) simulator, and non-toxicity, which narrowed down to 7 CTL, 3 HTL, and 12 B-cell epitopes...
March 15, 2024: Journal of Biomolecular Structure & Dynamics
https://read.qxmd.com/read/38481819/hypoxia-activated-selectivity-improved-anti-pkm2-antibody-combined-with-prodrug-th-302-for-potentiated-targeting-therapy-in-hepatocellular-carcinoma
#11
JOURNAL ARTICLE
Bo Wang, Fang-Zheng Qi, Ping Chen, Luo-Meng Qian, Hui-Shan Su, Yang Wang, Chen-Hui Wang, Ya-Xin Hou, Qing Zhang, Ding Li, Zhe-Sheng Chen, Si-He Zhang
Background: Hypoxia induces hepatocellular carcinoma (HCC) malignancies; yet it also offers treatment opportunities, exemplified by developing hypoxia-activated prodrugs (HAPs). Although HAP TH-302 combined with therapeutic antibody (Ab) has synergistic effects, the clinical benefits are limited by the on-target off-tumor toxicity of Ab. Here, we sought to develop a hypoxia-activated anti-M2 splice isoform of pyruvate kinase (PKM2) Ab combined with TH-302 for potentiated targeting therapy. Methods: Codon-optimized and hypoxia-activation strategies were used to develop H103 Ab-azo-PEG5k (HAP103) Ab...
2024: International Journal of Biological Sciences
https://read.qxmd.com/read/38480976/adeno-associated-virus-mediated-trastuzumab-delivery-to-the-central-nervous-system-for-human-epidermal-growth-factor-receptor-2-brain-metastasis
#12
JOURNAL ARTICLE
Marcela S Werner, Shweta Aras, Ashleigh R Morgan, Jillian Roamer, Nesteene J Param, Kanyin Olagbegi, R Jason Lamontagne, Jenny A Greig, James M Wilson
Trastuzumab improves overall survival for HER2+ breast cancer, but its short half-life in the cerebrospinal fluid (~2-4 days) and delivery limitations restrict the ability to target HER2+ central nervous system (CNS) disease. We developed an adeno-associated virus (AAV) vector expressing a codon-optimized, ubiquitin C (UbC)-promoter-driven trastuzumab sequence (AAV9.UbC.trastuzumab) for intrathecal administration. Transgene expression was evaluated in adult Rag1 knockout mice and rhesus nonhuman primates (NHPs) after a single intracerebroventricular (ICV) or intra-cisterna magna (ICM) AAV9...
March 13, 2024: Cancer Gene Therapy
https://read.qxmd.com/read/38479588/escherichia-coli-as-a-versatile-cell-factory-advances-and-challenges-in-recombinant-protein-production
#13
REVIEW
İbrahim İncir, Özlem Kaplan
E. coli plays a substantial role in recombinant protein production. Its importance increased with the discovery of recombinant DNA technology and the subsequent production of the first recombinant insulin in E. coli. E. coli is a widely used and cost-effective host to produce recombinant proteins. It is also noteworthy that a significant portion of the approved therapeutic proteins have been produced in this organism. Despite these advantages, it has some disadvantages, such as toxicity and lack of eukaryotic post-translational modifications that can lead to the production of misfolded, insoluble, or dysfunctional proteins...
March 12, 2024: Protein Expression and Purification
https://read.qxmd.com/read/38479107/response-to-dabrafenib-plus-trametinib-in-a-patient-with-an-uncommon-activating-braf-mutation-a-first-in-non-small-cell-lung-cancer
#14
JOURNAL ARTICLE
John A Sharp, Daniel Jones, Julia K Rotow, Panos M Fidias, Erin Bertino, Dwight H Owen
Mutations in BRAF are present in 4% of non-small cell lung cancer (NSCLC), of which half are well-characterized activating variants affecting codon 600 (classified as class I). These mutations, most commonly BRAF V600E, have been associated with response to BRAF/MEK-directed small molecule kinase inhibitors. NSCLC with kinase-activating BRAF mutations occurring at other codons (class II variants) represent a substantial portion of BRAF-mutated NSCLC, but use of targeted therapy in these tumors is still under investigation...
March 13, 2024: Journal of the National Comprehensive Cancer Network: JNCCN
https://read.qxmd.com/read/38475476/overexpression-of-cry1c-enhances-resistance-against-to-soybean-pod-borer-leguminivora-glycinivorella-in-soybean
#15
JOURNAL ARTICLE
Qingxi Fang, Yingxue Cao, Thinzar Hla Oo, Chuang Zhang, Mingyu Yang, Yuecheng Tang, Meizi Wang, Wu Zhang, Ling Zhang, Yuhong Zheng, Wenbin Li, Fanli Meng
Soybean [ Glycine max (L.) Merr.], an essential staple food and oil crop worldwide, boasts abundant vegetable proteins and fats beneficial for both human and animal consumption. However, the soybean pod borer ( Leguminivora glycinivorella ) (SPB) stands as the most destructive soybean insect pest in northeast China and other northeastern Asian regions, leading to significant annual losses in soybean yield and economic burden. Therefore, this study aims to investigate the introduction of a previously tested codon-optimized cry1c gene, cry1c* , into the soybean genome and assess its effect on the SPB infestation by generating and characterizing stable transgenic soybeans overexpressing cry1c* ...
February 25, 2024: Plants (Basel, Switzerland)
https://read.qxmd.com/read/38474031/a-direct-comparison-of-raav5-variants-derived-from-the-baculovirus-expression-system-using-lc-ms-workflows-demonstrates-key-differences-in-overall-production-yield-product-quality-and-vector-efficiency
#16
JOURNAL ARTICLE
Felipe Guapo, Nicholas Donohue, Lisa Strasser, Stefano Boi, Florian Füssl, Alana Rainbow-Fletcher, Paul Getty, Ian Anderson, Niall Barron, Jonathan Bones
Gene therapy holds great promise for the treatment of severe diseases, and adeno-associated virus (AAV) vectors have emerged as valuable tools in this field. However, challenges such as immunogenicity and high production costs complicate the commercial viability of AAV-based therapies. To overcome these barriers, improvements in production yield, driven through the availability of robust and sensitive characterization techniques that allow for the monitoring of critical quality attributes to deepen product and process understanding are crucial...
February 28, 2024: International Journal of Molecular Sciences
https://read.qxmd.com/read/38463112/synthetic-biology-approach-revealed-enhancement-in-haeme-oxygenase-1-gene-expression-by-codon-pair-optimization-while-reduction-by-codon-deoptimization
#17
JOURNAL ARTICLE
Rekha Khandia, Megha Katare Pandey, Azmat Ali Khan, Igor Baklanov, Amer M Alanazi, Prakash Nepali, Pankaj Gurjar, Om Prakash Choudhary
Haem oxygenase-1 (HO-1) is a ubiquitously expressed gene involved in cellular homoeostasis, and its imbalance in expression results in various disorders. To alleviate such disorders, HO-1 gene expression needs to be modulated. Codon usage bias results from evolutionary forces acting on any nucleotide sequence and determines the gene expression. Like codon usage bias, codon pair bias also exists, playing a role in gene expression. In the present study, HO-1 gene was recoded by manipulating codon and codon pair bias, and four such constructs were made through codon/codon pair deoptimization and codon/codon pair optimization to reduce and enhance the HO-1 gene expression...
March 2024: Annals of Medicine and Surgery
https://read.qxmd.com/read/38463054/molecular-insights-into-codon-usage-analysis-of-mitochondrial-fission-and-fusion-gene-relevance-to-neurodegenerative-diseases
#18
JOURNAL ARTICLE
Rekha Khandia, Megha Katare Pandey, Rajkumar Garg, Azmat Ali Khan, Igor Baklanov, Amer M Alanazi, Prakash Nepali, Pankaj Gurjar, Om Prakash Choudhary
Mitochondrial dysfunction is the leading cause of neurodegenerative disorders like Alzheimer's disease and Parkinson's disease. Mitochondria is a highly dynamic organelle continuously undergoing the process of fission and fusion for even distribution of components and maintaining proper shape, number, and bioenergetic functionality. A set of genes governs the process of fission and fusion. OPA1, Mfn1 , and Mfn2 govern fusion, while Drp1 , Fis1 , MIEF1 , and MIEF2 genes control fission. Determination of specific molecular patterns of transcripts of these genes revealed the impact of compositional constraints on selecting optimal codons...
March 2024: Annals of Medicine and Surgery
https://read.qxmd.com/read/38458885/heterologous-production-of-a-new-lanthipeptide-boletupeptin-using-a-cryptic-biosynthetic-gene-cluster-of-the-myxobacterium-melittangium-boletus
#19
JOURNAL ARTICLE
Pratchaya Rukthanapitak, Keita Saito, Ryo Kobayashi, Issara Kaweewan, Shinya Kodani
Myxobacteria have comparatively large genomes that contain many biosynthetic genes with the potential to produce secondary metabolites. Based on genome mining, we discovered a new biosynthetic gene cluster of class III lanthipeptide in the genome of the myxobacterium Melittangium boletus. The biosynthetic gene cluster contained a precursor peptide-coding gene bolA, and a class III lanthipeptide synthetase-coding gene bolKC. The expression vector containing bolA and bolKC was constructed using synthetic DNA with codon-optimized sequences based on the commercially available vector pET29b...
March 7, 2024: Journal of Bioscience and Bioengineering
https://read.qxmd.com/read/38445904/halocin-h4-is-activated-through-cleavage-by-halolysin-hlyr4
#20
JOURNAL ARTICLE
Shaoxing Chen, Yongpei Dai, Juntao Ke, Yuqing Luo, Chuangming Wang, Yuling Hao, Aodi Zhang, Jing Han, Hua Xiang
UNLABELLED: Halocins are antimicrobial peptides secreted by haloarchaea capable of inhibiting the growth of other haloarchaea or bacteria. Halocin H4 (HalH4) is secreted by the model halophilic archaeon Haloferax mediterranei ATCC 33500. Despite attempts to express halH4 heterologously in Escherichia coli and subsequent careful renaturation procedures commonly employed for haloarchaeal proteins, no active halocin was obtained. However, it was discovered that the antihaloarchaeal activity of this halocin could be activated through cleavage by halolysin R4 (HlyR4), a serine protease also secreted by Hfx...
March 6, 2024: Applied and Environmental Microbiology
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