DISTRIBUTIONS OF TRIPLET CODONS IN MESSENGER RNA SECONDARY STRUCTURES

Analysis of the secondary structures of mRNAs which encode mature peptides shows that the location of each codon in mRNA secondary structure has a trend, which appears to be in agreement with the conformational property of the corresponding amino acid to some extent. Most of the codons that encode hydrophobic amino acids are located in stable stem regions of mRNA secondary structures, and vice versa, most of the codons that encode hydrophilic amino acids are located in flexible loop regions. This result supports the recent conclusion that there may be the information transfer between the three dimensional structures of mRNA and the encoded protein.

Evolutionary selection on synonymous codons in RNA G-quadruplex structural region

To investigate how synonymous codons have been adapted to the formation of ribonucleic acid(RNA)G-quadruplex(rG4)structure,a computational searching algorithm G4Hunter was applied to detect rG4 structures in protein-coding sequences of mRNAs in five eukaryotic species.The native sequences forming rG4s were then compared with randomized sequences to evaluate selection on synonymous codons.Factors that may influence the formation of rG4 were also investigated,and the selection pressures of rG4 in different gene regions were compared to explore its potential roles in gene regulation.The results show universal selective pressure acts on synonymous codons in rG4 regions to facilitate rG4 formation in five eukaryotic organisms.While G-rich codon combinations are preferred in the rG4 structural region,C-rich codon combinations are selectively unfavorable for rG4 formation.Gene's codon usage bias,nucleotide composition,and evolutionary rate can account for the selective variations on synonymous codons among rG4 structures within a species.Moreover,rG4 structures in the translational initiation region showed significantly higher selective pressures than those in the translational elongation region.

mRNA Dependent Virtual-Real Substitutions of Nucleotides in Codons: The Dynamics of Their Meanings in the Genome Language

This is an attempt to explain mRNA-dependent non-stationary semantic values of codons (triplets) and nucleotides (letters) in codon composition during protein biosynthesis. This explanation is realized by comparing the different protein codes of various biosystem taxa, and, comparing mitochondrial code with the standard code. An initial mRNA transcriptional virtuality (Virtual-Reality) is transformed into material reality at the level of translation of virtual triplets into real (material) amino acids or into a real stop command of protein biosynthesis. The transformation of virtuality into reality occurs de facto when the linguistic sign1 functions of the codon syhoms are realized in the 3’ nucleotide (wobbling nucleotide according to F. Crick) in the process of protein biosynthesis. This corresponds to the theoretical works of the authors of this article. Despite the illusory appearance of semantic arbitrariness during the operation of ribosomes in the mode of codon semantic non-stationarity, this phenomenon probably provides biosystems with an unusually high level of adaptability to changes in the external environment as well as to internal (mental) dynamics of neuron’s genome in the cerebral cortex. The genome’s non-stationarity properties at the nucleotide, codon, gene and mental levels have fractal structure and corresponding dimensions. The highest form of such fractality (with maximum dimension) is probably realized in the genomic continuum of neurons in the human cerebral cortex through this semantic Virtual-to-Real (VR) codon transcoding with the biosynthesis of short-living semantic proteins, as the equivalents of material thinking-consciousness. In fact, this is the language of the brain’s genome, that is, our own language. In this case, the same thing happens in natural, primarily mental (non-verbal) languages. Their materialization is recorded in vocables (sounding words) and in writing. Such writing is the amino acid sequence in the semantic proteins of the human cerebral cortex. Rapidly decaying, such proteins can leave a long-lasting “so-called” Schrödinger wave holographic memory in the cerebral cortex. The presented below study is purely theoretical and based on a logical approach. The topic of the study is very complex and is subject to further development.

Dependence of nucleotide physical properties on their placement in codons and determinative degree

Various physical properties such as dipole moment, heat of formation and energy of the most stable formation of nucleotides and bases were calculated by PM3 (modified neglect of diatomic overlap, parametric method number 3) and AM1 (austin model 1) methods. As distinct from previous calculations, for nucleotides the interaction with neighbours is taken into account up to gradient of convergence equaling 1. The dependencies of these variables from the place in the codon and the de- terminative degree were obtained. The difference of these variables for codons and anticodons is shown.

Interaction of nonsense suppressor tRNAs and codon nonsense mutations or termination codons

Codon nonsense mutations include amber, ochre, or opal mutations according to termination codon consisting of three types (TAG, TAA and TGA). Codon nonsense mutations are also divided into natural and artificial mutations. We discussed the interaction of codon nonsense mutations and suppressor tRNAs in vitro and in vivo. Nonsense suppressions do not only happen in prokaryotes but also in eukaryotes. Meanwhile, the misreading of termination codon and in-corporation of nonnatural amino acids into proteins are also introduced.

罕见β-珠蛋白基因Codon 24(GGT>GGA)突变导致β-地中海贫血1例及文献分析

目的:分析罕见β-珠蛋白基因突变类型、血液学及临床特征。方法:收集疑为β-地中海贫血的病例120例。对病例进行全血细胞分类及计数、血红蛋白(Hb)电泳分析检测。用跨越断裂点PCR方法、荧光PCR熔解曲线方法、DNA测序等分析α-和β-珠蛋白基因突变类型。结果:120例β-地中海贫血病例中,检出1例为罕见β-珠蛋白基因突变,基因分析为Codon 24(GGT>GGA,HBB:c.75T>A)杂合子。该病例为男性,39岁,血常规检测显示:Hb 127.3 g/L,血红细胞(RBC)5.81×10^(12)/L,红细胞平均体积(MCV)70.29 fL,红细胞平均血红蛋白量(MCH)21.94 pg,红细胞平均血红蛋白浓度(MCHC)312.10 g/L。Hb分析显示Hb A_(2)4.5%,Hb F 0.4%。a-地中海贫血基因分析未发现常见的基因突变类型。结论:首次在国内发现罕见β-珠蛋白基因Codon 24(GGT>GGA,HBB:c.75T>A)突变导致β-地中海贫血。该病例在临床上易漏诊,应引起重视。

Epidemiological Surveillance: Genetic Diversity of Rotavirus Group A in the Pearl River Delta, Guangdong, China in 2019

Objective This study aimed to understand the epidemic status and phylogenetic relationships of rotavirus group A(RVA)in the Pearl River Delta region of Guangdong Province,China.Methods This study included individuals aged 28 days–85 years.A total of 706 stool samples from patients with acute gastroenteritis collected between January 2019 and January 2020 were analyzed for 17 causative pathogens,including RVA,using a Gastrointestinal Pathogen Panel,followed by genotyping,virus isolation,and complete sequencing to assess the genetic diversity of RVA.Results The overall RVA infection rate was 14.59%(103/706),with an irregular epidemiological pattern.The proportion of co-infection with RVA and other pathogens was 39.81%(41/103).Acute gastroenteritis is highly prevalent in young children aged 0–1 year,and RVA is the key pathogen circulating in patients 6–10 months of age with diarrhea.G9P[8](58.25%,60/103)was found to be the predominant genotype in the RVA strains,and the 41 RVA-positive strains that were successfully sequenced belonged to three different RVA genotypes in the phylogenetic analysis.Recombination analysis showed that gene reassortment events,selection pressure,codon usage bias,gene polymorphism,and post-translational modifications(PTMs)occurred in the G9P[8]and G3P[8]strains.Conclusion This study provides molecular evidence of RVA prevalence in the Pearl River Delta region of China,further enriching the existing information on its genetics and evolutionary characteristics and suggesting the emergence of genetic diversity.Strengthening the surveillance of genotypic changes and gene reassortment in RVA strains is essential for further research and a better understanding of strain variations for further vaccine development.

The variable codons of H5N1 avian influenza A virus haemagglutinin genes

We investigated the selection pressures on the haemagglutinin genes of H5N1 avian influenza viruses using fixed effects likelihood models. We found evidence of positive selection in the sequences from isolates from 1997 to 2007, except viruses from 2000. The haemagglutinin sequences of viruses from southeast Asia, Hong Kong and China's Mainland were the most polymorphic and had similar nonsyn-onymous profiles. Some sites were positively selected in viruses from most regions and a few of these sites displayed different amino acid patterns. Selection appeared to produce different outcomes in vi-ruses from Europe, Africa and Russia and from different host types. One position was found to be positively selected for human isolates only. Although the functions of some positively selected posi-tions are unknown, our analysis provided evidence of different temporal, spatial and host adaptations for H5N1 avian influenza viruses.

Prokaryotic expression of goldfish Tgf2 transposase with optimal codons and its enzyme activity

Tgf2 transposase(Tgf2-TPase),a hAT transposase from goldfish,plays an important role in fish transgenic applications.Previously,the production of the recombinant Tgf2-TPase protein required rigorous fermentation at low temperatures(22℃)and early log phase induction(OD600=0.3–0.4)in Rosetta 1(DE3)Escherichia coli lines.In order to better express the Tgf2-TPase and detect its enzyme activity,83 rare codons in Tgf2-TPase were optimized and designated Tgf2-TPase^(83).The expression results showed that the soluble recombinant Tgf2-TPase83 was highly expressed at 30℃ and was inducible at an OD600 of 0.5–0.6 in the same prokaryotic expression system.After purification by affinity chromatography,Tgf2-TPase83 with codon optimization had higher enzyme activity than the Tgf2-TPase control.Comparison of different preservation methods(freezedrying at−80℃,storage in 20%-glycerol,8%-sucrose,4%-mannitol),revealed storage of Tgf2-TPase^(83) in glycerol helped to preserve its DNase digestion activity.Furthermore,size exclusion chromatography suggested that the purified Tgf2-TPase^(83) could recognize and bind to DNA probes containing a terminal inverted repeat(TIR)and a subterminal repeat(STR)sequence of the Tgf2 transposon.Overall,the results showed that optimizing the 83 codons of Tgf2 transposase can simplify the fermentation process and improve the enzyme activity.We propose that the production of the Tgf2-Tpase83 protein in a soluble and active form could provide an alternative tool for genetic modification of fish.

Genomic Landscape of Rare Codon Usage at Start Region in the Pacific Oyster Genome

Synonymous codons have different frequencies of usage in many species.Based on the frequency of usage,the codons can be divided into two groups,rare codons and abundant codons.Rare codons are found to be enriched at the start regions of genes,and it is assumed that these codons can reduce elongation speed of genes.However,the rare codon usage in different genomic regions of mollusks and their relationship with selective pressure has not been systematically investigated.In this study,the patterns of rare codon usage are characterized at whole genome level,and their relationship with selective pressures is investigated in Crassostrea gigas.The rare codons are enriched at the start regions of genes with high and medium expression levels,and their proportion is higher than those in the genes with low expression level.The genes with longer coding sequences and more exon numbers have lower fraction of rare codons at start regions.Rare codons have lower level of nucleotide diversity and higher frequency of rare mutations at start regions.This work is the first comprehensive investigation of the relationships between rare codon usage and some intrinsic genetic factors in mollusca species.The results suggest that the selective pressures play an important role in shaping the rare codon usage in the C.gigas genome.

Different oncological features of colorectal cancer codon-specific KRAS mutations:Not codon 13 but codon 12 have prognostic value

BACKGROUND Approximately 40%of colorectal cancer(CRC)cases are linked to Kirsten rat sarcoma viral oncogene homolog(KRAS)mutations.KRAS mutations are associated with poor CRC prognosis,especially KRAS codon 12 mutation,which is associated with metastasis and poorer survival.However,the clinicopathological characteristics and prognosis of KRAS codon 13 mutation in CRC remain unclear.AIM To evaluate the clinicopathological characteristics and prognostic value of codonspecific KRAS mutations,especially in codon 13.METHODS This retrospective,single-center,observational cohort study included patients who underwent surgery for stage I-III CRC between January 2009 and December 2019.Patients with KRAS mutation status confirmed by molecular pathology reports were included.The relationships between clinicopathological characteristics and individual codon-specific KRAS mutations were analyzed.Survival data were analyzed to identify codon-specific KRAS mutations as recurrence-related factors using the Cox proportional hazards regression model.RESULTS Among the 2203 patients,the incidence of KRAS codons 12,13,and 61 mutations was 27.7%,9.1%,and 1.3%,respectively.Both KARS codons 12 and 13 mutations showed a tendency to be associated with clinical characteristics,but only codon 12 was associated with pathological features,such as stage of primary tumor(T stage),lymph node involvement(N stage),vascular invasion,perineural invasion,tumor size,and microsatellite instability.KRAS codon 13 mutation showed no associations(77.2%vs 85.3%,P=0.159),whereas codon 12 was associated with a lower 5-year recurrence-free survival rate(78.9%vs 75.5%,P=0.025).In multivariable analysis,along with T and N stages and vascular and perineural invasion,only codon 12(hazard ratio:1.399;95%confidence interval:1.034-1.894;P=0.030)among KRAS mutations was an independent risk factor for recurrence.CONCLUSION This study provides evidence that KRAS codon 13 mutation is less likely to serve as a prognostic biomarker than codon 12 mutation for CRC in a large-scale cohort.

Phylogeny,molecular evolution,and dating of divergences in Lagerstroemia using plastome sequences

Lagerstroemia L.(Lythraceae)is a widely distributed genus of trees and shrubs native to tropical and subtropical environments from Southeast Asia to Australia,with numerous species highly valued as ornamentals.Although the plastomes of many species in this genus have been sequenced,the rates of functional gene evolution and their effect on phylogenetic analyses have not been thoroughly examined.We compared three plastome sequence matrices to elucidate how differences in these datasets affected phylogenetic analyses.Robust phylogenetic relationships for Lagerstroemia species were reconstructed based on different plastome sequence partitions and multiple phylogenetic methods.Identification of single-nucleotide variants within different genes also provides basic data on the patterns of functional gene evolution in Lagerstroemia and may provide insights into how those mutations affect protein structure and potentially drive divergence via cytonuclear incompatibility.These results as well as analyses of non-synonymous and synonymous mutations,indicate that heterotachic modes of evolution are present in functional plastome genes and should be accounted for in the analyses of molecular evolution.In addition,divergence events within the Lagerstroemia were dated for the first time.Several of the divergence estimates corresponded to well-known Earth history events,such as the reduction in global temperatures at the Eocene/Oligocene boundary.Our analyses conducted in Lagerstroemia here dissects the various patterns in the divergence of Lagerstroemia and may provide a useful guide to help plant breeders,as well as the necessity of using plastomic data and as possible as to combine evidence from morphological characteristics to investigate the complicated interspecies relationship and the evolutionary dynamics of species.

Bioorthogonal Engineered Virus‑Like Nanoparticles for Efficient Gene Therapy

Gene therapy offers potentially transformative strategies for major human diseases.However,one of the key challenges in gene therapy is developing an effective strategy that could deliver genes into the specific tissue.Here,we report a novel virus-like nanoparticle,the bioorthgonal engineered viruslike recombinant biosome(reBiosome),for efficient gene therapies of cancer and inflammatory diseases.The mutant virus-like biosome(mBiosome)is first prepared by site-specific codon mutation for displaying 4-azido-L-phenylalanine on vesicular stomatitis virus glycoprotein of eBiosome at a rational site,and the reBiosome is then prepared by clicking weak acid-responsive hydrophilic polymer onto the mBiosome via bioorthogonal chemistry.The results show that the reBiosome exhibits reduced virus-like immunogenicity,prolonged blood circulation time and enhanced gene delivery efficiency to weakly acidic foci(like tumor and arthritic tissue).Furthermore,reBiosome demonstrates robust therapeutic efficacy in breast cancer and arthritis by delivering gene editing and silencing systems,respectively.In conclusion,this study develops a universal,safe and efficient platform for gene therapies for cancer and inflammatory diseases.

p21 codon31基因多态性与宫颈癌相关性的meta分析

目的:系统评价p21 codon31基因多态性与宫颈癌发生风险的相关性。方法:检索数据库PubMed、Web of science、Medline、中国知网、万方、维普和中国生物医学文献数据库,获取2022年8月31日之前公开发表的文章,采用5种遗传模型进行meta分析,OR值和95%CI评估关联的强度。结果:共纳入19个病例对照研究,宫颈癌组3612例,对照组4135例。等位基因模型[Arg比Ser,I^(2)=80.5%,OR=1.03,95%CI0.87~1.21]、纯合比较模型[Arg/Arg比Ser/Ser,I^(2)=71.8%,OR=1.03,95%CI 0.76~1.39]、杂合比较模型[Ser/Arg比Ser/Ser,I^(2)=71.8%,OR=0.96,95%CI 0.78~1.17]、显性比较模型[(Arg/Arg+Ser/Arg)比Ser/Ser,I^(2)=83.8%,OR=0.94,95%CI 0.73~1.20]、隐性比较模型[Arg/Arg比(Ser/Ser+Ser/Arg),I^(2)=65.2%,OR=1.02,95%CI 0.80~1.30]均提示p21 codon31不会增加宫颈癌的遗传易感性。进一步对宫颈癌进行分类分析后发现,p21 codon31基因多态性与宫颈鳞癌无相关性;但纯合比较模型[Arg/Arg比Ser/Ser,I^(2)=48.4%,OR=0.53,95%CI 0.32~0.86]、显性比较模型[(Arg/Arg+Ser/Arg)比Ser/Ser,I^(2)=0.0,OR=0.61,95%CI 043~0.88]表明Arg突变型是宫颈腺癌的保护因素。结论:p21 codon31基因多态性与宫颈癌无相关性,但与宫颈腺癌有关,与宫颈鳞癌无关。

Analysis of Codon Usage Between Different Poplar Species

Codon usage is the selective and nonrandom use of synonymous codons to encode amino acids in genes for proteins. The analysis of codon usage may improve the understanding of cocion preferences between different species and allow to rebuild the codons of exogenous genes to increase the expression efficiency of exogenous genes, Here, codon DNA sequence （CDS） of four poplar species, including Populus tremuloides Michx., P. tomentosa Carr., P. deltoides Marsh., and P. trichocarpa Torr. ＆ Gray., is used to analyze the relative frequency of synonymous codon （RFSC）. High-frequency codons are selected by high-frequency （HF） codon analysis. The results indicate that the codon usage is common for all four poplar species and the codon preference is quite similar among the four poplar species. However, CCT encoding for Pro, and ACT coding for Thr are the preferred codons in P. tremuloides and P. tomentosa, whereas CCA coding for Pro, and ACA coding for Thr are preferred in P. deltoides and P. trichocarpa The codons such as TGC coding for Cys, TTC coding for Phe, and AAG coding for Lys, are preferred in the poplar species except P trichocarpa. GAG coding for Glu is preferred only in P deltoides, while the other three poplar species prefer to use GAA. The commonness of preferred codon allows exogenous gene designed by the preferred cocion of one of the different poplar species to be used in other poplar species.

p53基因codon 72多态性与乳腺癌术后放化疗疗效相关性分析

目的：分析p53基因codon 72多态性与乳腺癌患者术后放化疗的预后相关性。方法：选取北京大学肿瘤医院乳腺癌患者术后接受放化疗427例,采用聚合酶链反应-限制性片段长度多态性（PCR-RFLP）方法分析其p53基因codon 72多态性,比较不同基因型患者间复发及生存的差异。结果：全部患者基因型分布为Pro/Pro型18.3%（78/427）、Pro/Arg型44.0%（188/427）、Arg/Arg型37.7%（161/427）。3种基因型间无局部复发生存（LRFS）、无局部区域复发生存（LRRFS）、无远处转移生存（DDFS）及总生存（OS）均无显著性差异（均P〉0.05）。427例患者中雌激素受体（ER）阳性为303例,其中Arg/Arg基因型患者OS明显优于Pro/Pro基因型患者（χ2=6.330,P=0.042）。在多因素分析中p53基因codon 72多态性是ER阳性患者LRFS、LRRFS、DDFS及OS的独立预后因素,Pro/Pro基因型的患者较Arg/Arg基因型的局部复发风险增加5.9倍（HR=5.9,95%CI 1.1~31.1,P=0.036）,局部区域复发风险增加3.1倍（HR=3.1,95%CI 1.1~9.1,P=0.039）,远处转移风险增加2.8倍（HR=2.8,95%CI 1.3~6.0,P=0.010）,死亡风险增加4倍（HR=4.0,95%CI 1.3~12.0,P=0.013）。结论：在ER阳性的乳腺癌术后接受放化疗患者中,Pro/Pro基因型的局部及局部区域复发风险、远处转移风险、死亡风险均高于Arg/Arg基因型。

The Factors Shaping Synonymous Codon Usage in the Genome of Burkholderia mallei

Burkholderia mallei is regarded as a potential biological weapon by the Centers for Disease Control and Prevention. In this study, the main factors shaping codon usage in the genome of B. mallei ATCC 23344 were firstly reported. The results showed that the primary trend in codon usage variation in the B. mallei is due to translational selection; while compositional mutation bias is relatively the weaker influence and the hydrophobicity of each protein and gene length are only the minor influences. At the same time, 21 codons defined firstly as ＇optimal codons＇ might provide more useful information for the expression of target genes and development of a vaccine to prevent glanders.

耐链霉素结核分枝杆菌rpsL基因高突变位点43Codon分子信标检测的实验研究

目的选择耐链霉素(STR)结核分枝杆菌rpsL基因主要突变位点密码子43序列设计分子信标探针及扩增体系,并建立运用荧光显微镜及图像分析软件检测荧光结果及定性判断的方法。方法运用软件Beacon designer设计43Codon分子信标探针及建立其扩增体系,采用荧光显微镜观测反应后的荧光信号及图像分析软件定性判断结果。结果包含43Codon rpsL基因聚合酶链反应(PCR)扩增产物条带清晰;通过荧光显微镜观测到标准株及耐STR株PCR产物与分子信标探针杂交后荧光信号区别明显;67株耐STR与10株H37RV标准株对照组荧光信号强度比较,P<0.05和P<0.01的耐STR组检出率为80%。结论分子信标技术是一种具有高灵敏、高特异核酸检测技术;采用荧光显微镜观测荧光信号具有更强的荧光信号识别、放大功能及结果判断更准确等优点。

p53基因codon72多态性与乳腺癌的相关性研究

目的：研究p53基因codon72多态性与乳腺癌患者的年龄、病理分期、淋巴结转移、雌激素受体（ER）、孕激素受体（PR）、c—erbB-2、P53蛋白表达情况的相关性。方法：TaqMan探针方法检测277例乳腺癌患者血液标本的p53基因codon72多态性。免疫组化SP法检测匹配肿瘤纽织中ER、PR、c-erbB-2和P53蛋白的表达情况。SPSS16．0软件行统计学分析，p53基因多态性与病理学特征关系用x^2检验，非条件Logistic回归分析基因多态性与ER、PR、c—erbB-2、P53蛋白表达的相关性，计算OR值及其95％可信区间（95％CI）。P〈0．05为差异有统计学意义。结果：p53基因codon72基因型为CC／CG／GG．频率分别为22．0％、513％和26．7％，携带CC、CG、GG基因型的患者发病年龄逐渐降低，但无统计学差异；p53基因codon72多态性与临床病理学特征无关，与ER、PR、c—erbB-2和P53蛋白表达无相关性（P〉0．05）。肿瘤组织P53蛋白表达与ER、PR、c—erbB-2蛋白表达密切相关（x^2=15．492，P=0．000；x^2=3．970，P=0．046；x^2=17．956，P=0．000）。结论：p53基因codon72多态性与P55蛋白表达及病理学特征无相关性，P53蛋白表达与ER、PR、C—erbB-2蛋白表达关系密切。p53基因codon72基因型与患者发病年龄的关系有待扩大样本量进一步研究。

p53 Codon 72多态性与宫颈癌关系的研究

目的 探讨抑癌基因 p5 3codon72多态性与宫颈癌的关系。方法 应用聚合酶链反应法分别对15例卵巢浆液性囊腺癌、15例宫颈鳞状细胞癌和 2 0例正常妇女的 p5 3codon72多态性进行检测。结果 p5 3Arg纯合子、p5 3Pro纯合子和 p5 3Arg/ p5 3Pro杂合子在正常妇女对照组分别为 38%、6 %和 5 6 % ;而在卵巢癌组分别为 38%、5 %和 5 7% ;在宫颈癌组分别为 78%、8%和 14%。上述人群中 ,宫颈癌 p5 3Arg纯合子明显高于卵巢癌组和正常妇女对照组 (P<0 .0 5 )。结论 p5 3Arg纯合子可作为与