Efficient generation of targeted point mutations in the Brassica oleracea var.botrytis genome via a modified CRISPR/Cas9 system

In this study,we used the modified CRISPR/Cas9 system to produce targeted point mutations in cauliflower.Acetolactate synthase(ALS)and Centromere-specific histone H3 variant(CENH3)genes were selected as the base-editing targets and hypocotyls of cauliflower were used as explants.For ALS gene,a C-to-T conversion in the Pro182 codon(CCT)can alter the encoded amino acid,likely resulting in herbicide resistance,and a C-to-T mutation in the Leu133 codon(CTT)in the CENH3 gene may produce a haploid inducer.Results indicated that the transformation efficiency was 1.8%–4.5%and the mutation efficiencies for the ALS and CENH3 genes were approximately 22%and 87%,respectively.The ALS mutant cauliflower showed strong herbicide resistance,with possible immediate implications for broadleaf weed control in cauliflower fields.

Detection of Low-abundance Point Mutations by Competitive Strand Assisted Endonuclease Ⅳ Signal Amplification System

Genetic mutations are important molecular biomarkers for cancer diagnosis and surveillance. Therefore, the development of methods for mutation detection characterized with straightforward, highly specific and sensitive to low-level mutations within various sequence contexts is extremely needed. Although some of the currently available methods have shown very encouraging results, their discrimination efficiency is still very low. Herein, we demonstrate a fluorescent probe coupled with blocker and property of melting temperature discrimination, which is able to identify the presence of known or unknown single-base variations at abundances down to 0.1% within 20 min. The discrimination factors between the perfect-match target and single-base mismatched target are determined to be 10.15–38.48. The method is sequence independent, which assures a wide range of application. The new method would be an ideal choice for high-throughput in vitro diagnosis and precise clinical treatment.

Naturally occurring PA^(E206K)point mutation in 2009 H1N1 pandemic influenza viruses impairs viral replication at high temperatures

The emergence of influenza virus A pandemic H1N1 in April 2009 marked the first pandemic of the 21st century.In this study,we observed significant differences in the polymerase activities of two clinical 2009 H1N1 influenza A virus isolates from Chinese and Japanese patients.Sequence comparison of the three main protein subunits(PB2,PB1,and PA)of the viral RNA-dependent RNA polymerase complex and subsequent mutational analysis revealed that a single amino acid substitution(E206K)was responsible for the observed impaired replication phenotype.Further in vitro experiments showed that presence of PAE206K decreased the replication of influenza A/WSN/33 virus in mammalian cells and a reduction in the virus’s pathogenicity in vivo.Mechanistic studies revealed that PAE206K is a temperature-sensitive mutant associated with the inability to transport PB1–PA complex to the nucleus at high temperature(39.5℃).Hence,this naturally occurring variant in the PA protein represents an ideal candidate mutation for the development of live attenuated influenza vaccines.

Single-cell level point mutation analysis of circulating tumor cells through droplet microfluidics

Tumor heterogeneity plays a critical role in the determination of appropriate anticancer therapy.As cir-culating tumor cells(CTCs)contain all tumor-related information,the genetic changes on CTCs could help us choose the appropriate treatments for different patients.Single-base mutations are very common in tumor genetic changes which may result in drug resistance.Here,we introduce a single-cell mutation de-tection platform based on droplet microfluidics.This platform integrates cell capsulation,cell lysis,poly-merase chain reaction(PCR)and the observation process.The droplets’generation speed is over 6000 per minute and more than 600 cells could be encapsulated in one second.To verify the performance of our platform in practical use,we performed the mutation analysis of 4 kinds of cells with our platform and noted that the genetic status of each single cell was clearly discriminated.Moreover,these results agreed with those from direct sequencing.Compared with other forms of single-cell mutation detection techniques,our platform has high throughput,short experimental time and less experimental operations.

DNA origami-based nano-hunter enriches low-abundance point mutations by targeting wild-type gene segments

Point mutations can be used as biomarkers to perform diagnosis for diseases. In this study, a nanorobot for low-abundance point mutation enrichment was constructed using DNA origami. The novel design achieved limits of detection of 0.1% and 1% for synthesized DNA samples and clinical gene samples, respectively. Resettability was a key property of this method, which also involved a simpler process, lower cost and shorter detection duration than traditional enrichment methods. This novel DNA nanorobot may enable the detection of tumor markers, potentially facilitating early cancer diagnosis.

Mutational analysis of Ras hotspots in patients with urothelial carcinoma of the bladder

BACKGROUND Mutational activation of Ras genes is established as a prognostic factor for the genesis of a constitutively active RAS-mitogen activated protein kinase pathway that leads to cancer.Heterogeneity among the distribution of the most frequent mutations in Ras isoforms is reported in different patient populations with urothelial carcinoma of the bladder(UCB).AIM To determine the presence/absence of mutations in Ras isoforms in patients with UCB in order to predict disease outcome.METHODS This study was performed to determine the mutational spectrum at the hotspot regions of H-Ras,K-Ras and N-Ras genes by polymerase chain reaction-restriction fragment length polymorphism(PCR-RFLP)and DNA sequencing followed by their clinical impact(if any)by examining the relationship of mutational spectrum with clinical histopathological variables in 87 UCB patients.RESULTS None of the 87 UCB patients showed point mutations in codon 12 of H-Ras gene;codon 61 of N-Ras gene and codons 12,13 of K-Ras gene by PCR-RFLP.Direct DNA sequencing of tumor and normal control bladder mucosal specimens followed by Blastn alignment with the reference wild-type sequences failed to identify even one nucleotide difference in the coding exons 1 and 2 of H-Ras,NRas and K-Ras genes in the tumor and control bladder mucosal specimens.CONCLUSION Our findings on the lack of mutations in H-Ras,K-Ras and N-Ras genes could be explained on the basis of different etiological mechanisms involved in tumor development/progression,inherent genetic susceptibility,tissue specificity or alternative Ras dysfunction such as gene amplification and/or overexpression in a given cohort of patients.

Idiopathic basal ganglia calcification associated with new MYORG mutation site:A case report

BACKGROUND Idiopathic basal ganglia calcification(IBGC)is a neurodegenerative disease characterized by symmetrical calcification of basal ganglia and other brain region,also known as Fahr’s disease.It can be sporadic or familial,and there is no definite etiology at present.With the development of neuroimaging,the number of reports of IBGC has increased in recent years.However,due to its hidden onset,diverse clinical manifestations,and low incidence,it is likely to be misdiagnosed or ignored by potential patients and their family.CASE SUMMARY We report a case of a 61-year-old man who presented with symptoms of dysphagia and alalia.His computed tomography scan of the brain revealed bilateral symmetric calcifications of basal ganglia,cerebellum,thalamus,and periventricular area.The genetic test showed a new mutation sites of MYORG,c.1438T>G mutation and c.1271_1272 TGGTGCGC insertion mutation.He was finally diagnosed with IBGC.CONCLUSION It is important to detect MYORG mutation when IBGC is suspected,especially in those without an obvious family history,for better understanding of the underlying mechanism and identifying potential treatments.

Resistance risk and molecular mechanism associated with resistance to picoxystrobin in Colletotrichum truncatum and Colletotrichum gloeosporioides

Anthracnose,caused by Colletotrichum truncatum and C.gloeosporioides,is amongst the most serious diseases of soybean in China.Picoxystrobin,a quinone outside inhibitor fungicide,is commonly used for the control of anthracnose.Its resistance risk and mechanism in C.truncatum and C.gloeosporioides are unclear.In this study,the sensitivities of 128 C.truncatum and 121 C.gloeosporioides isolates to picoxystrobin were investigated,and unimodal distributions were observed with average EC_(50)values of 0.7740 and 1.1561μg mL^(-1),respectively.Eleven picoxystrobin-resistant mutants of C.truncatum and six mutants of C.gloeosporioides were acquired,with EC_(50)values varying from 5.40-152.96 and 13.53-28.30μg mL^(-1),respectively.Compared to the parental isolates,mutants showed similar or higher relative fitness in conidial production and germination,and pathogenicity.Collectively,the resistance risk of C.truncatum and C.gloeosporioides to picoxystrobin is moderate to high.There was positive cross-resistance between picoxystrobin and pyraclostrobin,but not between picoxystrobin and fluazinam,difenoconazole,or propiconazole.The G143S mutation in Cyt b protein was detected in seven high-resistant mutants of C.truncatum(RF>100),and G137R occurred in four moderate-resistant mutants(RF<_(50)).Contrastingly,there were no point mutations in Cyt b of any C.gloeosporioides mutants.Molecular docking confirmed that two mutations conferred different resistance levels to picoxystrobin.Under greenhouse trials,picoxystrobin did not control mutants with the G143S mutation,those bearing G137R or no point mutation were somewhat controlled,but at a lower level compared to wild-type isolates.These results showed that integrated management strategies should be implemented to preserve fungicide effectiveness.

Drosophila models used to simulate human ATP1A1 gene mutations that cause Charcot-Marie-Tooth type 2 disease and refractory seizures

Certain amino acids changes in the human Na^(+)/K^(+)-ATPase pump,ATPase Na^(+)/K^(+)transporting subunit alpha 1(ATP1A1),cause Charcot-Marie-Tooth disease type 2(CMT2)disease and refractory seizures.To develop in vivo models to study the role of Na^(+)/K^(+)-ATPase in these diseases,we modified the Drosophila gene homolog,Atpα,to mimic the human ATP1A1 gene mutations that cause CMT2.Mutations located within the helical linker region of human ATP1A1(I592T,A597T,P600T,and D601F)were simultaneously introduced into endogenous Drosophila Atpαby CRISPR/Cas9-mediated genome editing,generating the Atpα^(TTTF)model.In addition,the same strategy was used to generate the corresponding single point mutations in flies(Atpα^(I571T),Atpα^(A576T),Atpα^(P579T),and Atpα^(D580F)).Moreover,a deletion mutation(Atpα^(mut))that causes premature termination of translation was generated as a positive control.Of these alleles,we found two that could be maintained as homozygotes(Atpα^(I571T)and Atpα^(P579T)).Three alleles(Atpα^(A576T),Atpα^(P579)and Atpα^(D580F))can form heterozygotes with the Atpαmut allele.We found that the Atpαallele carrying these CMT2-associated mutations showed differential phenotypes in Drosophila.Flies heterozygous for Atpα^(TTTF)mutations have motor performance defects,a reduced lifespan,seizures,and an abnormal neuronal morphology.These Drosophila models will provide a new platform for studying the function and regulation of the sodium-potassium pump.

Fast genetic mapping in barley:case studies of cuticle mutants using RNA-sequencing

Barley(Hordeum vulgare L.)is one of the earliest domesticated crop species and ranked as the fourth largest cereal production worldwide.Forward genetic studies in barley have greatly advanced plant genetics during the last century;however,most genes are identified by the conventional mapping method.Array genotyping and exome-capture sequencing have also been successfully used to target the causal mutation in barley populations,but these techniques are not widely adopted because of associated costs and partly due to the huge genome size of barley.This review summarizes three mapping cases of barley cuticle mutants in our laboratory with the help of RNA-sequencing.The causal mutations have been successfully identified for two of them and the target genes are located in the pericentromeric regions.Detailed information on the mapping-by-sequencing,mapping-and-sequencing,and RNA-sequencing assisted linkage mapping are presented and some limitations and challenges on the mapping assisted by RNA sequencing are also discussed.The alternative and elegant methods presented in this review may greatly accelerate forward genetics of barley mapping,especially for laboratories without large funding.

2+0 CYP21A2 deletion carrier—a limitation of the genetic testing and counseling:A case report

BACKGROUND CYP21A2 gene mutations may all cause reduction or loss of 21-hydroxylase activity,leading to development of congenital adrenal hyperplasia(CAH)with different clinical phenotypes.For families with CAH children,genetic testing of the parents and genetic counseling are recommended to assess the risk of recurrence.CASE SUMMARY We report a case of CAH with a high suspicion before delivery.The risk of the child suffering from CAH during the pregnancy had been underestimated due to the deviation of genetic counseling and genetic testing results.Our report confirmed a CYP21A2 homozygous deletion in this case,CYP21A2 heterozygous deletion in the mother,and a rare 2+0 CYP21A2 deletion in the father.CONCLUSION It is important to analyze the distribution of CYP21A2 gene in the two alleles of parents of children with CAH.

Identification of the ryanodine receptor mutation I4743M and its contribution to diamide insecticide resistance in Spodoptera exigua (Lepidoptera: Noctuidae)

Insect ryanodine receptors(RyRs)are the targets of diamide insecticides.Two point mutations G4946E and I4790M(numbering according to Plutella xylostella,PxRyR)in the transmembrane domain of the insect RyRs associated with diamide resistance have so far been identified in three lepidopteran pests,P.xylostella,Tuta absoluta and Chilo suppressalis.In this study,we identified one of the known RyR target site resistance mutations(I4790M)in a field-collected population of Spodoptera exigua.The field-collected WF population of S.exigua exhibited 154 fold resistance to chlorantraniliprole when compared with the susceptible WH-S strain.Sequencing the transmembrane domains of S.exigua RyR(SeRyR)revealed that the resistant WF strain was homozygous for the 14743M mutation(corresponding to I4790M in PxRyR),whereas the G4900E allele(corresponding to G4946E of PxRyR)was not detected.The 4743M allele was introgressed into the susceptible WH-S strain by crossing WF with WH-S,followed by three rounds of backcrossing with WH-S.The introgressed strain 4743M was homozygous for the mutant 4743M allele and shared about 94%of its genetic background with that of the recipient WH-S strain.Compared with WH-S,the near-isogenic 4743M strain showed moderate levels of resistance to chlorantraniliprole(21 fold),cyantraniliprole(25 fold)and flubendiamide(22 fold),suggesting that the I4743M mutation confers medium levels of resistance to all three diamides.Genetic analysis showed diamide resistance in the 4743M strain was inherited as an autosomal and recessive trait.Results from this study have direct implications for the design of appropriate resistance monitoring and management practices to sustainably control S.exigua.

Effective generation of maternal genome point mutated porcine embryos by injection of cytosine base editor into germinal vesicle oocytes

Cytosine and adenine base editors are promising new tools for introducing precise genetic modifications that are required to generate disease models and to improve traits in pigs. Base editors can catalyze the conversion of C→T(C>T) or A→G(A>G) in the target site through a single guide RNA. Injection of base editors into the zygote cytoplasm can result in the production of offspring with precise point mutations, but most F0 are mosaic, and breeding of F1 heterozygous pigs is time-intensive. Here, we developed a method called germinal vesicle oocyte base editing(GVBE) to produce point mutant F0 porcine embryos by editing the maternal alleles during the GV to MⅡ transition. Injection of cytosine base editor 3(BE3) mRNA and X-linked Dmdspecific guide RNAs into GVoocytes efficiently edited maternal Dmd during in vitro maturation and did not affect the maturation potential of the oocytes. The edited MⅡ oocytes developed into blastocysts after parthenogenetic activation(PA) or in vitro fertilization(IVF). However, BE3 may reduce the developmental potential of IVF blastocysts from 31.5%±0.8% to 20.4%±2.1%. There 40%–78.3% diploid PA blastocysts had no more than two different alleles, including up to 10% embryos that had only C>T mutation alleles. Genotyping of IVF blastocysts indicated that over 70% of the edited embryos had one allele or two different alleles of Dmd. Since the male embryos had only a copy of Dmd allele, all five(5/19) F0 male embryos are homozygous and three of them were Dmd precise C>T mutation. Nine(9/19) female IVF embryos had two different alleles including a WT and a C>T mutation. DNA sequencing showed that some of them might be heterozygous embryos. In conclusion, the GVBE method is a valuable method for generating F0 embryos with maternal point mutated alleles in a single step.

Analysis of environmental selection pressure of superoxide dismutase in deep-sea sea cucumber

Manganese superoxide dismutase(MnSOD)is an antioxidant that exists in mitochondria and can effectively remove superoxide anions in mitochondria.In a dark,high-pressure,and low-temperature deep-sea environment,MnSOD is essential for the survival of sea cucumbers.Six MnSODs were identified from the transcriptomes of deep and shallow-sea sea cucumbers.To explore their environmental adaptation mechanism,we conducted environmental selection pressure analysis through the branching site model of PAML software.We obtained night positive selection sites,and two of them were significant(97F→H,134K→V):97F→H located in a highly conservative characteristic sequence,and its polarity c hange might have a great impact on the function of MnSOD;134K→V had a change in piezophilic a bility,which might help MnSOD adapt to the environment of high hydrostatic pressure in the deepsea.To further study the effect of these two positive selection sites on MnSOD,we predicted the point mutations of F97H and K134V on shallow-sea sea cucumber by using MAESTROweb and PyMOL.Results show that 97F→H,134K→V might improve MnSOD’s efficiency of scavenging superoxide a nion and its ability to resist high hydrostatic pressure by moderately reducing its stability.The above results indicated that MnSODs of deep-sea sea cucumber adapted to deep-sea environments through their amino acid changes in polarity,piezophilic behavior,and local stability.This study revealed the correlation between MnSOD and extreme environment,and will help improve our understanding of the organism’s adaptation mechanisms in deep sea.

The amino acid residue E96 of Ghd8 is crucial for the formation of the flowering repression complex Ghd7-Ghd8-OsHAP5C in rice

Ghd7 is an important gene involved in the photoperiod flowering pathway in rice.A Ghd7-involved transcriptional regulatory network has been established,but its translational regulatory pathway is poorly understood.The mutant suppressor of overexpression of Ghd7(sog7)was identified from EMS-induced mutagenesis on the background of ZH11 overexpressing Ghd7.Mut Map analysis revealed that SOG7 is allelic to Ghd8 and delayed flowering under long-day(LD)conditions.Biochemical assays showed that Ghd8 interacts with OsHAP5C and Ghd7 both in vivo and in vitro.Surprisingly,a point mutation E96K in theα2 helix of the Ghd8 histone fold domain(HFD)destroyed its ability to interact with Ghd7.The prediction of the structure shows that mutated amino acid is located in the interaction region of CCT/NF-YB/YC complexes,which alter the structure ofα4 of Ghd8.This structural difference prevents the formation of complex NF-YB/YC.The triple complex of Ghd8-OsHAP5C-Ghd7 directly bound to the promotor of Hd3a and downregulated the expression of Ehd1,Hd3a and RFT1,and finally resulted in a delayed heading.These findings are helpful in deeply understanding the Ghd7-involved photoperiod flowering pathway and promote the elucidation of rice heading.

Changing Gly311 to an acidic amino acid in the MATE family protein DTX6 enhances Arabidopsis resistance to the dihydropyridine herbicides

In modern agriculture,frequent application of herbicides may induce the evolution of resistance in plants,but the mechanisms underlying herbicide resistance remain largely unexplored.Here,we report the char-acterization of rtp 1(resistant to paraquat 1),an Arabidopsis mutant showing strong resistance to the widely used herbicides paraquat and diquat.The rtp1 mutant is semi-dominant and carries a point mutation in the gene encoding the multidrug and toxic compound extrusion family protein DTX6,leading to the change of glycine to glutamic acid at residue 311(G311E).The wild-type DTX6 with glycine 311 conferred weak para-quat and diquat resistance when overexpressed,while mutation of glycine 311 to a negatively charged amino acid(G311E or G311D)markedly increased the paraquat and diquat resistance of plants,whereas mutation to a positively charged amino acid(G311R or G311K)compromised the resistance,suggesting that the charge property of residue 311 of DTX6 is critical for the paraquat and diquat resistance of Arabi-dopsis plants.DTX6 is localized in the endomembrane trafficking system and may undergo the endosomal sorting to localize to the vacuole and plasma membrane.Treatment with the V-ATPase inhibitor ConA reduced the paraquat resistance of the rtp1 mutant.Paraquat release and uptake assays demonstrated that DTX6 is involved in both exocytosis and vacuolar sequestration of paraquat.DTX6 and DTX5 show functional redundancy as the dtx5 dtx6 double mutant but not the dtx6 single mutant plants were more sen-sitive to paraquat and diquat than the wild-type plants.Collectively,our work reveals a potential mecha-nism for the evolution of herbicide resistance in weeds and provides a promising gene for the manipulation of plant herbicide resistance.

Single-nucleotide editing for zebra3 and wsl5 phenotypes in rice using CRISPR/Cas9-mediated adenine base editors

The CRISPR/Cas9-mediated base editing technology can efficiently generate point mutations in the genome without introducing a double-strand break(DSB)or supplying a DNA donor template for homology-directed repair(HDR).In this study,adenine base editors(ABEs)were used for rapid generation of precise point mutations in two distinct genes,OsWSL5,and OsZEBRA3(Z3),in both rice protoplasts and regenerated plants.The precisely engineered point mutations were stably inherited to subsequent generations.These single nucleotide alterations resulted in single amino acid changes and associated wsl5 and z3 phenotypes as evidenced by white stripe leaf and light green/dark green leaf pattern,respectively.Through selfing and genetic segregation,transgene-free,base edited wsl5 and z3 mutants were obtained in a short period of time.We noticed a novel mutation(V540A)in Z3 locus could also mimic the phenotype of Z3 mutation(S542P).Furthermore,we observed unexpected non-A/G or T/C mutations in the ABE editing window in a few of the edited plants.The ABE vectors and the method from this study could be used to simultaneously generate point mutations in multiple target genes in a single transformation and serve as a useful base editing tool for crop improvement as well as basic studies in plant biology.

Prediction of the next highly pathogenic avian influenza pandemic that can cause illness in humans

Background:In recent years,avian influenza viruses(AIVs)have seriously threatened human health.Questions such as:why do AIVs infect humans?,how quickly can an AIV become pandemic?,and which virus is the most dangerous?cannot be sufficiently answered using current bioinformatic studies.Method:Secondary structures and energies of representative 5′-untranslated region(UTR)of the HA gene were calculated.Then their secondary structures and energies were re-calculated after one or two nucleotide substitutions were introduced into the HA 5′-UTR.Phylogenetic trees on the basis of hemagglutinin(HA)and polymerase basic protein 2(PB2)amino acid sequences and HA 5′-UTR nucleotide sequences were constructed.The connection between the energy and translation efficiency of 5′-UTR was confirmed by in vitro coupled transcription/translation assay.Results:The simplicity of the secondary structure of the 5′-UTR of the HA gene determines the overall virus replication rate and transmission potential.Point mutation assays show that the 5′-UTR sequences of the HA gene in the influenza subtypes H2N2,H3N2,and H7N9 have greater variation potentials than other virus subtypes.Conclusion:Some high-virulent strains of avian influenza might emerge in the next two to three years.The H2N2 subtype,once disappeared in humans,may stage a comeback.The current outbreak of H7N9 may become pandemic and cause even more deaths,if one or two bases are substituted in the 5′-UTR sequence of the HA gene.

Using DelPhi Capabilities to Mimic Protein’s Conformational Reorganization with Amino Acid Specific Dielectric Constants

Many molecular events are associated with small or large conformational changes occurring in the corresponding proteins.Modeling such changes is a challenge and requires significant amount of computing time.From point of view of electrostatics,these changes can be viewed as a reorganization of local charges and dipoles in response to the changes of the electrostatic field,if the cause is insertion or deletion of a charged amino acid.Here we report a large scale investigation of modeling the changes of the folding energy due to single mutations involving charged group.This allows the changes of the folding energy to be considered mostly electrostatics in origin and to be calculated with DelPhi assigning residue-specific value of the internal dielectric constant of protein.The predicted energy changes are benchmarked against experimentally measured changes of the folding energy on a set of 257 single mutations.The best fit between experimental values and predicted changes is used to find out the effective value of the internal dielectric constant for each type of amino acid.The predicted folding free energy changes with the optimal,amino acid specific,dielectric constants are within RMSD=0.86 kcal/mol from experimentally measured changes.