Enzymes are widely used in medical and biopharmaceuticals. They can be used not only for various disease treatments, but also clinical diagnosis. The use of microorganisms to express heterologous proteins has become the easiest and fastest way to obtain enzymes. In order to obtain high concentration and high-quality heterologous proteins, a common method is codon optimization of gene sequences. The traditional codon optimization strategy is mainly based on codon bias and GC content, ignoring complex and varied factors such as translational dynamics and metabolic levels. We provide here comprehensive codon optimization strategy based on gene level, transcriptional level, translational level, post-translational level and metabolic level, mainly including codon bias, codon harmonization, codon sensitivity, adjustment of gene sequence structure and some other influencing factors. We also summarize the aspects of strategy content, theoretical support and application. Besides, the advantages and disadvantages of each strategy are also systematically compared, providing an all-round, multi-level and multi-selection optimization strategy for heterogeneous protein expression, and also providing references for the enzyme industry and biopharmaceuticals.
Base Composition ; Codon

Human cytomegalovirus (HCMV) is a member of beta-herpesvirus and contains a double-stranded genome with longer than 230 Kbp. HCMV infection of human is mostly asymptomatic, but often causes fatal diseases in immunocompromised people. In this study, codon usages of HCMV genes were analyzed and attempted to correlate with evolutionary conservancy. Core genes are the most conserved genes common among herpesvirus family, beta-herpes genes are common to beta-herpesviruses, and CMV genes are the least conserved found only in CMVs. Core genes had higher codon adaptation index (CAI) and GC content of silent 3rd codon position (GC3s) values and lower effective number of codons (Nc) and Nc/GC3s values than CMV genes. The average length of core genes was statistically longer than CMV genes, and core genes were found to be less varied than CMV genes. beta-herpes genes could be placed between core and CMV genes. Higher CAI and GC3s values along with lower Nc and Nc/GC3s values are suggestive of higher codon usage bias and more adaptation to host cells. Thus it is concluded that core genes of HCMV are more biased in codon usage and adapted to host cells compared to CMV genes.
Base Composition ; Bias (Epidemiology)* ; Codon* ; Cytomegalovirus* ; Genome ; Humans*

Prolonged imbalance between input and output of any element in a living organism is incompatible with life. The duration of imbalance varies, but eventually balance is achieved. This rule applies to any quantifiable element in a compartment of finite capacity. Transient discrepancies occur regularly, but given sufficient time, balance is always achieved, because permanent imbalance is impossible, and the mechanism for eventual restoration of balance is foolproof. The kidney is a central player for balance restoration of fluid and electrolytes, but the smartness of the kidney is not the reason for perfect balance. The kidney merely accelerates the process. The most crucial element of the control system is that discrepancy between intake and output inevitably leads to a change in total content of the element in the system, and uncorrected balance has a cumulative effect on the overall content of the element. In a living organism, the speed of restoration of balance depends on the permissible duration of imbalance without death or severe disability. The three main factors that influence the speed of balance restoration are: magnitude of flux, basal store, and capacity for additional storage. For most electrolytes, total capacity is such that a substantial discrepancy is not possible for more than a week or two. Most control mechanisms correct abnormality partially. The infinite gain control mechanism is unique in that abnormality is completely corrected upon completion of compensation.
Acid-Base Equilibrium ; Body Composition ; Compensation and Redress ; Electrolytes ; Kidney

Amygdalus pedunculata Pall. is one of the 12 important woody oil crops in China. In this study, we determined the complete chloroplast genome sequence of A. pedunculata Pall. (MG602257) from Mu Us desert in Yulin city, Shaanxi province, China. The plastome was 157 851 bp with 36.8% GC content. Comparisons among the plastomes of MG602257 and other two MG869261 and KY101153 from Genebank of NCBI showed that the total length of these chloroplast genomes was MG602257< MG869261 Animals ; Base Composition ; China ; Genome, Chloroplast ; Phylogeny ; Thoracica

Reynoutria japonica Houtt., belonging to Polygoneae of Polygonaceae, is a Chinese medicinal herb with the functions of draining dampness and relieving jaundice, clearing heat and detoxifying, dispersing blood stasis and relieving pain, and relieving cough and resolving phlegm. In this study, we carried out high-throughput sequencing for the chloroplast genome sequences of five cultivars of R. japonica and analyzed the genome structure and variations. The chloroplast genomes of the five R. japonica cultivars had two sizes (163 376 bp and 163 371 bp) and a typical circular tetrad structure composed of a large single-copy (LSC) region of 85 784 bp, a small single-copy (SSC) region of 18 616 bp, and a pair of inverted repeat (IR) regions (IRa/IRb) which are spaced apart. A total of 161 genes were obtained by annotation, which consisted of 106 protein-coding genes, 10 rRNA-coding genes, and 45 tRNA-coding genes. The total GC content was 36.7%. Specifically, the GC content in the LSC, SSC, and IR regions were 34.8%, 30.7%, and 42.7%, respectively. Comparison of the whole chloroplast genome among the five cultivars showed that trnk-UUU, rpoC1, petD, rpl16, ndhA, and rpl12 in coding regions had sequence variations. In the phylogenetic tree constructed for the 11 samples of Polygoneae, the five cultivars of R. japonica clustered into one clade near the root and was a sister group of Fallopia multiflora (Thunb.).
Base Composition ; Genome, Chloroplast/genetics* ; Open Reading Frames ; Phylogeny ; Reynoutria

The combination of morphological characteristics and DNA barcodes was used to a systematic study of Hippocampus spinosissimus,laying the foundation for rapid and accurate identification for the medical seahorse species. According to the reported literature and observation on seahorse samples,the typical characteristics of the H. spinosissimus include highly developed spiny,much short nose,single or double cheeks and strongly developed spines bordering pouch. Genomic DNAs of H. spinosissimus and other related seahorse species were extracted using the TIANamp Marine Animals DNA Kit. The COⅠ and ATP6 genes were amplified and sequenced in both directions. After the verification by Blast,the GC content,intraspecific and interspecific genetic distance,and the Neighbor joining( NJ) phylogenetic trees were analyzed by MEGA 7. The lengths of the COⅠ and ATP6 genes were 649 bp and 602-603 bp,respectively,with the average GC content of 39. 96% and 35. 37%. The maximum intraspecific genetic distances in H. spinosissimus based on COⅠ and ATP were both far less than the minimum interspecific genetic distance between H. spinosissimus and other seahorses,suggesting a significant barcoding gap. NJ analysis results of COⅠ and ATP6 exhibited that all H. spinosissimus species clustered together,indicating that the two DNA barcode could identify H. spinosissimus from other seahorses accurately and quickly. In addition,H. spinosissimus shared a close genetic relationship between H. kelloggi according to the NJ tree. Furthermore,there exits three stable subgroup structure of H. spinosissimus,indicating that COⅠ and ATP6 barcodes could be applied the indicator for the geographical ecology research of H. spinosissimus. The results obtained the typical morphological and molecular identification characteristics of H. spinosissimus,which played central roles for the development of species identification. This study provides an important basis data for expanding the medical seahorse resources and ensuring the safety of clinical medicine.
Animals ; Base Composition ; DNA ; DNA Barcoding, Taxonomic ; Phylogeny ; Smegmamorpha/genetics*

Using the complete genome of Plasmodium falciparum 3D7 which has 14 chromosomes as an example, we have examined the distribution functions for the amount of C or G and A or T consecutively and non-overlapping blocks of m bases in this system. The function P(S) about the number of the consecutive C-G or A-T content cluster conforms to the relation P(S) proportional, variante(-alphas); values of the scaling exponent alpha(CG) are much larger than alpha(AT); and alpha(AT) of 14 chromosomes are hardly changed, whereas alpha(CG) of 14 chromosomes have a number of fluctuations. We found maximum value of A-T cluster size is much larger than C-G, which implies the existence of large A-T cluster. Our study of the width function xi(m) of cluster C-G content showed that follows good power law xi(m) proportional, variantm(-gamma). The average gamma for 14 chromosomes is 0.931. These investigations provide some insight into the nucleotide clusters of DNA sequences, and help us understand other properties of DNA sequences.
Animals ; Base Composition ; Base Sequence ; Chromosomes ; genetics ; DNA, Protozoan ; genetics ; Genome, Protozoan ; Genomics ; Nucleotides ; genetics ; Plasmodium falciparum ; genetics

The aim was to establish an effective screening microarray at genus level for Pospiviroid. We analyzed nucleotide sequences from Pospiviroid viroid and designed 19 probes with genus identification characteristics. The standards of these probes included the characters of (i) a GC content between 40 and 60%, (ii) less than 50% of single nucleotide, (iii) less than 4 continuous mononucleotides, and (iv) less than 6 nucleotides in the inner hairpin. We synthesized microarrays by using these probes on glass slides. The validation results of microarray probes show effective signals from chrysanthemum stunt viroid and tomato planta macho viroid standard samples hybridization. The sensitivity results show that the microarray detected 200 pg/microL of total RNA. The microarray can be used to screen Pospiviroid viroid.
Base Composition ; Base Sequence ; Microarray Analysis ; Nucleic Acid Hybridization ; Plant Diseases ; virology ; Plant Viruses ; classification ; RNA ; Viroids ; classification

Research into new methods for identifying highly expressed genes in anonymous genome sequences has been going on for more than 15 years. We presented here an alternative approach based on modified score of relative codon usage bias to identify highly expressed genes in crenarchaeal genomes. The proposed algorithm relies exclusively on sequence features for identifying the highly expressed genes. In this study, a comparative analysis of predicted highly expressed genes in five crenarchaeal genomes was performed using the score of Modified Relative Codon Bias Strength (MRCBS) as a numerical estimator of gene expression level. We found a systematic strong correlation between Codon Adaptation Index and MRCBS. Additionally, MRCBS correlated well with other expression measures. Our study indicates that MRCBS can consistently capture the highly expressed genes.
Anonyms and Pseudonyms ; Archaea ; Base Composition ; Bias (Epidemiology) ; Codon ; Gene Expression* ; Genome*

Expressed sequence tags (ESTs) are widely used in gene survey research these years. The EST Pipeline System, software developed by Hangzhou Genomics Institute (HGI), can automatically analyze different scalar EST sequences by suitable methods. All the analysis reports, including those of vector masking, sequence assembly, gene annotation, Gene Ontology classification, and some other analyses, can be browsed and searched as well as downloaded in the Excel format from the web interface, saving research efforts from routine data processing for biological rules embedded in the data.
Automation ; Base Composition ; Computational Biology ; methods ; Databases, Genetic ; Expressed Sequence Tags ; Software ; User-Computer Interface