The genus Pseudobagrus represents a group of economically and ecologically significant freshwater bagrid catfishes in East Asia, yet its taxonomy remains contentious. This study employed the complete mitochondrial genomes of 15 Pseudobagrus species t...
As indicator organisms for water pollution detection, Pseudogasteromyzon species play a vital role in aquatic environment monitoring. We have successfully sequenced the mitogenomes of P. fasciatus jiulongjiangensis and P. myersi and downloaded the mi...
Codon optimization is widely used to improve heterologous gene expression in Escherichia coli. However, many existing methods focus primarily on maximizing the codon adaptation index (CAI) and neglect broader aspects of biological context. In this st...
Codon optimization is a cornerstone technique in synthetic biology and biotechnological production, aimed at enhancing heterologous protein expression through synonymous codon substitutions. While optimization traditionally focuses on forward-strand...
The efficient expression of recombinant proteins in aquaculture fish poses a significant challenge, partly due to the lack of dedicated bioinformatics tools for species-specific codon usage analysis and optimization. RiboScan (v1.0.0), a portable, si...
Tea polyphenol oxidase (CsPPO) is a crucial enzyme involved in the production of tea and tea products. However, the recombinant expression of CsPPO in microorganisms is often hindered by challenges such as inclusion body formation and extremely low e...
Minimal gene set design, reducing a system to its smallest functional part set, is a core synthetic biology strategy. Bacteriophages are attractive but underused chassis, yet wild-type phages are difficult to engineer. We present a comparative genomi...
Persistent and efficient therapeutic protein expression in the specific target cell is a significant concern in gene therapy. The controllable integration site, suitable promoter, and proper codon usage influence the effectiveness of the therapeutic...
The aim of the present study was to improve the expression level of Trichoderma reesei xylanase (XynB) in Pichia pastoris through a codon optimization strategy and evaluate its effects on the growth performance and carcass characteristics of broiler....
Most common industrial xylanases are produced from filamentous fungi. In this study, the codon-optimized xynA gene encoding xylanase A from the fungus Penicilium citrinum was successfully synthesized and expressed in the yeast Pichia pastoris. The le...
Type III interferons (IFN–λs) exhibit potent antiviral activity and immunomodulatory effects in specific cells. Nucleotide fragments of the bovine ifn–λ (boifn–λ) gene were synthetized after codon optimization....
Recombinant lactoferrin (LF) production in Escherichia coli (E. coli) is limited by poor solubility and inclusion body formation. To address this, a computational-experimental workflow was established, combining protein redesign and structural screen...
In this study, we applied bacterial artificial chromosome (BAC) technology with PRVΔTK/gE/gI as the base material to replace the first, central, and terminal segments of the US3 gene with codon-deoptimized fragments via two-step Red-mediated re...
The tRNA epitranscriptome has been recognized as an important player in mRNA translation regulation. Our knowledge of the role of the tRNA epitranscriptome in fine-tuning translation via codon decoding at tissue or cell levels remains incomplete. We...
Ophiocordyceps sinensis, a fungus parasitic on insects, attracts interest due to its unique medicinal applications and complex ecological interactions. The potential relationship between codon usage bias and the parasitic relationship between O. sine...
Analysis of codon usage data has both practical and theoretical applications in understanding the basics of molecular biology. Differences in codon usage patterns among genes reflect variations in local base compositional biases and the intensity of...
Marine viral sequence space is immense and presents a promising resource for the discovery of new enzymes interesting for research and biotechnology. However, bottlenecks in the functional annotation of viral genes and soluble heterologous production...
Xyloglucan endotransglycosylase (XET) genes are widely distributed in most plants, but the codon usage bias of XET genes has remained uncharacterized. Thus, we analyzed the codon usage bias using 4500 codons of 20 XET genes to elucidate the genetic a...
Dryas octopetala var. asiatica, a dwarf shrub belonging to the Rosaceae family and native to Asia, exhibits notable plasticity in photosynthesis in response to temperature variations. However, the codon usage patterns and factors influencing them in...
Cucumber is the most important vegetable crop in the Cucurbitaceae family. Condon usage bias (CUB) is a valuable character of species evolution. However, there is little research on the CUB of cucumber. Thus, this study analyzes the codon usage patte...
The plant Actinostemma tenerum is endemic to East Asia and has been used as a traditional medicinal herb for over 1400 years. Investigating the chloroplast genome characteristics and codon usage bias (CUB) is essential for advancing research on molec...
Background: Codon usage bias (CUB), which is shaped by mutation pressure, natural selection, and genetic drift, provides valuable insights into phylogenetic relationships and molecular evolution. This study investigated the patterns and determinants...
To investigate the codon usage bias (CUB) and its influencing factors in the chloroplast genome of Styphnolobium japonicum f. oligophyllum, we sequenced, assembled and annotated the genome using Illumina high-throughput sequencing, and systematically...
In the natural host, most of the synonymous codons of a gene have been evolutionarily selected and related to protein expression and function. However, for the design of a new gene, most of the existing codon optimization tools select the high-freque...
Giardia duodenalis, a flagellated parasitic protozoan, the most common cause of parasite-induced diarrheal diseases worldwide. Codon usage bias (CUB) is an important evolutionary character in most species. However, G. duodenalis CUB remains unclear....
Enhancing the soluble expression of heterologous proteins in chassis microorganisms is critical for fundamental biological research and synthetic biology-driven industrial applications. Current methods for designing DNA sequences to ensure high solub...
Anaerobic fungi are emerging biotechnology platforms with genomes rich in biosynthetic potential. Yet, the heterologous expression of their biosynthetic pathways has had limited success in model hosts like E. coli. We find one reason for this is that...
Oocytes from women of advanced reproductive age exhibit diminished developmental potential, but the underlying mechanisms remain incompletely defined. Oocyte maturation depends on translational control of maternal mRNA synthesized during growth. We p...
Background/Objectives: Approved mRNA vaccines commonly use sequences modified with pseudouridine to enhance translation efficiency and mRNA stability. However, this modification can result in ribosomal frameshifts, reduced immunogenicity, and higher...
Synonymous codon usage (SCU) bias in oil-tea camellia cpDNAs was determined by examining 13 South Chinese oil-tea camellia samples and performing bioinformatics analysis using GenBank sequence information, revealing conserved bias among the samples....
The design of Pfizer/BioNTech and Moderna mRNA vaccines involves many different types of optimizations. Proper optimization of vaccine mRNA can reduce dosage required for each injection leading to more efficient immunization programs. The mRNA compon...
Bispecific antibodies (bsAbs) are often composed of several polypeptide chains that have to be expressed adequately to enable optimal assembly and yield of the bsAb. κλ bodies are a bispecific format with a native IgG structure, composed...
Genomic organization and its comparative analysis throughout all major kingdoms of life are extensively studied across multiple scales, ranging from individual gene-level analyses to system-wide investigations. This work introduces a novel framework...
Personalized cancer vaccines are a promising immunotherapy targeting patient-specific tumor neoantigens, yet their design and efficacy remain challenging. Recent advances in artificial intelligence (AI) provide powerful tools to enhance multiple stag...
Cyanobacterial biosynthetic gene clusters (BGCs) remain difficult to reconstruct in heterologous systems, yet the suitability of fungal hosts for expression of cyanobacterial pathways remains largely unexplored. Here, the well-characterized lyngbyato...
Gaucher disease (GD) is an autosomal recessive disorder caused by the deficient activity of the lysosomal enzyme glucocerebrosidase (GCase). Although enzyme replacement therapy (ERT) remains the standard of care for non-neuropathic GD patients, its h...
Zearalenone (ZEN) is a thermostable, lipophilic, non-steroidal estrogenic mycotoxin produced by Fusarium spp. that persistently contaminates food and feed. Its strong estrogenic activity and resistance to conventional detoxification strategies pose s...
Cyclodextrins (CDs) are cyclic oligosaccharides composed of α(1 → 4) linked glucose units, which are widely used as solubilizers and stabilizers in the food, pharmaceutical and cosmetic industries. Among the CDs, γ-CD has attracted m...
Manganese peroxidases (MnP) from the white-rot fungi Phanerochaete chrysosporium catalyse the oxidation of Mn2+ to Mn3+, a strong oxidizer able to oxidize a wide variety of organic compounds. Different approaches have been used to unravel the enzymat...
The expression of functional, folded, and isotopically enriched membrane proteins is an enduring bottleneck for nuclear magnetic resonance (NMR) studies. Indeed, historically, protein yield optimization has been insufficient to allow NMR analysis of...
Lactate is a valuable compound used in food, chemical, and pharmaceutical industries. High-value, optically pure L- or D-lactate can be synthesized microbially via specific dehydrogenases. The non-conventional yeast Scheffersomyces stipitis, which is...
Children are at risk of infection from severe acute respiratory syndrome coronavirus-2 virus (SARS-CoV-2) resulting in coronavirus disease (COVID-19) and its more severe forms. New-born infants are expected to receive short-term protection from passi...
Codon usage bias (CUB) is a useful indicator of evolutionary forces shaping mitochondrial genomes. Codon usage bias in mitochondrial genomes of Diphyllobothriidae and especially in Ligula intestinalis was characterized. The roles of natural selection...
Codon optimization is a widely employed strategy to enhance protein expression. However, it occasionally leads to unexpected transcriptional repression despite preserving amino acid sequences. This study investigates the mechanistic basis of such tra...
Plasmodium vivax is the most widespread cause of malaria, especially in subtropical and temperate regions such as Asia-Pacific and America. P. vivax lactate dehydrogenase (PvLDH), an essential enzyme in the glycolytic pathway, is required for the dev...
Two optimization strategies, codon usage modification and glycine supplementation, were adopted to improve the extracellular production of Bacillus sp. NR5 UPM β-cyclodextrin glycosyltransferase (CGT-BS) in recombinant Escherichia coli. Several...
Botrytis cinerea can infect almost all of the important horticultural crops and cause severe economic losses globally every year. Modifying candidate genes and studying the phenotypic changes are among the most effective ways to unravel the pathogeni...
The SARS-CoV-2 delta variant (B.1.617.2) appeared for the first time in December 2020 and later spread worldwide. Currently available vaccines are not so efficacious in curbing the viral pathogenesis of the delta strain of COVID; therefore, the devel...
Lassa virus (LASV) causes a severe, often fatal, hemorrhagic fever endemic to West Africa. Presently, there are no FDA-licensed medical countermeasures for this disease. In a pilot study, we constructed a DNA vaccine (pLASV-GPC) that expressed the LA...
Bromelain is a unique enzyme-based bioactive complex containing a mixture of cysteine proteases specifically found in the stems and fruits of pineapple (Ananas comosus) with a wide range of applications. MD2 pineapple harbors a gene encoding a small...
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