Apoer2/Lrp8:the undercover cop of synaptic homeostasis

Apolipoprotein E receptor 2(ApoER2)is a receptor for the protein ApoE,the most common genetic risk factor for late-onset Alzheimer's disease(AD).It is also a key modulator of syna ptic homeostasis,in part through its effect on the expression of neuronal genes including those implicated in AD and other neuropsychiatric disorders.In this perspective,we highlight several genes affected by ApoER2 and its alternatively spliced forms and how aberrant expression can be rescued by the reintroduction of the ApoER2 intracellular domain in the mouse hippocampus.

Negative feedback regulation of PROG1 in rice

Cultivated rice(Oryza sativa L.),one of the most widely grown and important crops worldwide,is believed to have been domesticated from the ancestral wild rice(Oryza rufipogon Griff.)thousands of years ago(Cheng et al.2003;Khush 1997;Fuller et al.2010).

Genome editing for horticultural crop improvement

Horticultural crops provide humans with many valuable products.The improvement of the yield and quality of horticultural crops has been receiving increasing research attention.Given the development and advantages of genome-editing technologies,research that uses genome editing to improve horticultural crops has substantially increased in recent years.Here,we briefly review the different genome-editing systems used in horticultural research with a focus on clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated 9(Cas9)-mediated genome editing.We also summarize recent progress in the application of genome editing for horticultural crop improvement.The combination of rapidly advancing genome-editing technology with breeding will greatly increase horticultural crop production and quality.

Clinical features, endoscopic polypectomy and STK11 gene mutation in a nine-month-old Peutz-Jeghers syndrome Chinese infant

AIM: To investigate multiple polyps in a Chinese PeutzJeghers syndrome(PJS) infant. METHODS: A nine-month-old PJS infant was admitted to our hospital for recurrent prolapsed rectal polyps for one month. The clinical characteristics, a colonoscopic image, the pathological characteristics of the polyps and X-ray images of the intestinal perforation were obtained. Serine threonine-protein kinase 11(STK11) gene analysis was also performed using a DNA sample from this infant.RESULTS: Here we describe the youngest known Chinese infant with PJS. Five polyps, including a giant polyp of approximately 4 cm × 2 cm in size, were removed from the infant's intestine. Laparotomy was performed to repair a perforation caused by pneumoperitoneum. The pathological results showed that this child had PJS. Molecular analysis of the STK11 gene further revealed a novel frameshift mutation(c.64_65het_del AT) in exon 1 in this PJS infant.CONCLUSION: The appropriate treatment method for multiple polyps in an infant must be carefully considered. Our results also show that the STK11 gene mutation is the primary cause of PJS.

Alternatively spliced BobCAL transcripts alter curd morphotypes in a collection of Chinese cauliflower accessions

The curd of cauliflower(Brassica oleracea L.var.botrytis)is a modified inflorescence that is consumed as a vegetable.Curd formation is proposed to be due to a mutation in the BobCAULIFLOWER(BobCAL)gene,but the genetic relationship between BobCAL variation and curd morphotypes remains obscure.To address this question,we collected and classified a collection of 78 cauliflower accessions into four subpopulations according to curd surface features:smooth,coarse,granular,and hairy curd morphotypes.Through the cDNA sequencing of BobCAL alleles,we showed that smooth and coarse accessions characterized by inflorescence meristem arrest presented a strong association with the 451T SNP(BobCAL_T),whereas granular and hairy accessions marked with floral organ arrest presented an association with 451G(BobCAL_G).Interestingly,all BobCAL alleles were alternatively spliced,resulting in a total of four alternative splice(AS)variants due to the retention of the fourth and/or seventh introns.Among accessions with BobCAL_G alleles,the total expression of all these AS variants in granular plants was almost equal to that in hairy plants;however,the expression of the individual AS variants encoding intact proteins relative to those encoding truncated proteins differed.Hairy accessions showed relatively high expression of the individual variants encoding intact proteins,whereas granular accessions displayed relatively low expression.In smooth cauliflower,the overexpression of the BobCAL_Ga variant caused an alteration in the curd morphotype from smooth to hairy,concurrent with an increase in the expression levels of downstream floral identity genes.These results reveal that alternative splicing of BobCAL transcripts is involved in the determination of cauliflower curd morphotypes.

Plant regeneration via protoplast electrofusion in cassava

Protoplast electrofusion between callus protoplasts of cultivar TMS60444 and mesophyll protoplasts of cultivar SC8 was performed as an approach for the genetic improvement of cassava.The fusion products were subsequently cultured in protoplast culture medium(TM2 G) with gradual dilution for approximately 1-2 months.Then the protoplast-derived compact calli were transferred to suspension culture medium(SH) for suspension culture.The cultured products developed successively into embryos,mature embryos,and shoots on somatic embryo emerging medium(MSN),embryo maturation medium(CMM),and shoot elongation medium(CEM),respectively.And the shoots were then rooted on Murashige and Skoog(1962) medium(MS).Sixty-six cell lines were obtained and 12 of them developed into plantlets.Based on assessment of ploidy level and chromosome counting,four of these plantlets were tetraploid and the remaining eight were diploid.Based on assessment of ploidy level and simple sequence repeat(SSR) analysis,nine tetraploid cell lines,one diploid variant plant line and nine variant cell lines were obtained.The diploid variant plant line and the nine variant cell lines all showed partial loss of genetic material compared to that of the parent TMS60444,based on SSR patterns.These results showed that some new germplasm of cassava were created.In this study,a protocol for protoplast electrofusion was developed and validated.Another important conclusion from this work is the confirmation of a viable protocol for the regeneration of plants from cassava protoplasts.Going forward,we hope to provide technical guidance for cassava tissue culture,and also provide some useful inspiration and reference for further genetic improvement of cassava.

Insights into Late Embryogenesis Abundant (LEA) Proteins in Plants: From Structure to the Functions

Late Embryogenesis Abundant (LEA) proteins, a group of hydrophilic proteins, have been linked to survival in plants and animals in periods of stress, putatively through safeguarding enzymatic function and prevention of aggregation in times of dehydration/heat. Yet despite decades of effort, the molecular-level mechanisms defining this protective function remain unknown. In this paper, we summarize and review research discoveries of the classification of the LEA protein groups based on their amino acid sequence similarity and on the presence of distinctive conserved motifs. Moreover, we focus on high correlation between their accumulation and water deficit, reinforcing their functional relevance under abiotic stresses. We also discuss the biochemical properties of LEA proteins arising from their hydrophilic nature and by amino acid composition. Although significant similarities have not been found between the members of the different groups, a unifying and outstanding feature of most of them is their high hydrophilicity and high content of glycine. Therefore, we have highlighted the biotechnological applications of LEA genes, and the effects of over-expressing LEA genes from all LEA groups from different species of origin into different plant hosts. Apart from agronomical purposes, LEA proteins could be useful for other biotechnological applications in relation to their capacity to prevent aggregation of proteins.

Potential protein–phenotype correlation in three lipopolysaccharideresponsive beige-like anchor protein-deficient patients

BACKGROUND Patients with lipopolysaccharide(LPS)-responsive beige-like anchor protein(LRBA)deficiency have a variety of clinical symptoms,but there is no apparent genotype–phenotype correlation,and patients carrying the same mutations may have different phenotypes.Therefore,it is not easy for doctors to make a decision regarding hematopoietic stem cell transplantation(HSCT)for LRBA-deficient patients.We hypothesized that there may be a protein–phenotype correlation to indicate HSCT for LRBA-deficient patients.AIM To report on three Chinese LRBA-deficient patients and determine the correlation between residual protein expression and disease phenotypes.METHODS Clinical data of three Chinese LRBA-deficient patients were collected,and protein levels were detected by Western blot analysis.In addition,LRBA mutation information of another 83 previously reported patients was summarized.RESULTS All the major clinical findings indicated enteropathy,but patients 1 and 3 presented with more severe symptoms than patient 2.Endoscopy and histology indicated nonspecific colitis for patients 1 and 3 but Crohn's disease-like colitis for patient 2.Compound heterozygous mutations in LRBA were found in patient 1,and homozygous mutations in LRBA were found in patient 2 and patient 3.Only patient 2 responded well to traditional immunosuppressive treatment.Residual expression of the LRBA protein in patients 1 and 3 was very low,but in patient 2,a more than 0.5-fold in expression of the LRBA protein was found compared to that in the control.After HSCT,patient 1 had increased LRBA protein expression.We summarized the genetic information of 86 patients,and the mutations in patients 1 and 3 were novel mutations.CONCLUSION We described three Chinese LRBA-deficient patients,two of whom carried novel mutations.These patients had no genotype-phenotype correlations,but their residual LRBA protein expression might be associated with disease outcome and could be an indicator for HSCT.

DNA cytosine methylation dynamics and functional roles in horticultural crops

Methylation of cytosine is a conserved epigenetic modification that maintains the dynamic balance of methylation in plants under the regulation of methyltransferases and demethylases.In recent years,the study of DNA methylation in regulating the growth and development of plants and animals has become a key area of research.This review describes the regulatory mechanisms of DNA cytosine methylation in plants.It summarizes studies on epigenetic modifications of DNA methylation in fruit ripening,development,senescence,plant height,organ size,and under biotic and abiotic stresses in horticultural crops.The review provides a theoretical basis for understanding the mechanisms of DNA methylation and their relevance to breeding,genetic improvement,research,innovation,and exploitation of new cultivars of horticultural crops.

廉价基因组学

霍华德·雅各布现在基因组测序成本已经降到100美元,这可以让更多的病人受益,霍华德·雅各布说。

Down-regulation of MeMYB2 leads to anthocyanin accumulation and increases chilling tolerance in cassava(Manihot esculenta Crantz)

Chilling-induced accumulation of reactive oxygen species(ROS) is harmful to plants,which usually produce anthocyanins to scavenge ROS as protection from chilling stress.As a tropical crop,cassava is hypersensitive to chilling,but the biochemical basis of this hypersensitivity remains unclear.We previously generated Me MYB2-RNAi transgenic cassava with increased chilling tolerance.Here we report that Me MYB2-RNAi transgenic cassava accumulated less ROS but more cyanidin-3-O-glucoside than the wild type under early chilling stress.Under this stress,the anthocyanin biosynthesis pathway was more active in Me MYB2-RNAi lines than in the wild type,and several genes involved in the pathway,including Me TT8,were up-regulated by Me MYB2-RNAi in the transgenic cassava.Me MYB2 bound to the Me TT8 promoter and blocked its expression under both normal and chilling conditions,thereby inhibiting anthocyanin accumulation.Me TT8 was shown to bind to the promoter of Dihydroflavonol 4-reductase(Me DFR-2)and increased Me DFR-2 expression.Me MYB2 appears to act as an inhibitor of chilling-induced anthocyanin accumulation during the rapid response of cassava to chilling stress.

Rice Genetically Engineered to Stand Heat Stress is also More Productive

Global warming imposes a serious threat to global crop production and may cripple the outcome of a successful breeding program.Because the photosystem II(PSII)complex,a protein supercomplex that acts to harvest sunlight energy for photosynthetic plants,is sensitive to thermal damage.

Gene Interaction that Contributes to Rice Heat Tolerance Identified

Rice is one of the most important staple crops,on which more than half of the world’s population depends.But as temperatures rise and extreme weather events increase,rice becomes more vulnerable.Genetically modified strains can withstand some flooding,but few,if any,can survive the heat stress caused by the combination of high temperatures and drought.There may be hardier crops on the horizon,though,with the help of a molecular map that details the specific gene interactions that control how tolerant rice is to heat.

Molecular and structural characterization of a promiscuous chalcone synthase from the fern species Stenoloma chusanum

The key enzymes involved in the flavonoid biosynthesis pathway have been extensively studied in seed plants,but relatively less in ferns.In this study,two 4-Coumarate:coenzyme A ligases(Sc4CL1 and Sc4CL2)and one novel chalcone synthase(ScCHS1)were functionally characterized by mining the Stenoloma chusanum transcriptome database.Recombinant Sc4CLs were able to esterify various hydroxycinnamic acids to corresponding acyl-coenzyme A(CoA).ScCHS1could catalyze p-coumaroyl-CoA,cinnamoyl-CoA,caffeoyl-CoA,and feruloyl-CoA to form naringenin,pinocembrin,eriodictyol,and homoeriodictyol,respectively.Moreover,enzymatic kinetics studies revealed that the optimal substrates of ScCHS1were feruloyl-CoA and caffeoyl-CoA,rather than p-coumaroyl-CoA,which was substantially different from the common CHSs.Crystallographic and sitedirected mutagenesis experiments indicated that the amino acid residues,Leu87,Leu97,Met165,and Ile200,located in the substrate-binding pocket near the B-ring of products,could exert a significant impact on the unique catalytic activity of ScCHS1.Furthermore,overexpression of ScCHS1 in tt4 mutants could partially rescue the mutant phenotypes.Finally,ScCHS1 and Sc4CL1 were used to synthesize flavanones and flavones with multi-substituted hydroxyl and methoxyl B-ring in Escherichia coli,which can effectively eliminate the need for the cytochrome P450 hydroxylation/O-methyltransferase from simple phenylpropanoid acids.In summary,the identification of these important Stenoloma enzymes provides a springboard for the future production of various flavonoids in E.coli.

Molecular Basis for Sesterterpene Diversity Produced by Plant Terpene Synthases

Class I terpene synthase(TPS)generates bioactive terpenoids with diverse backbones.Sesterterpene synthase(sester-TPS,C25),a branch of class I TPSs,was recently identified in Brassicaceae.However,the catalytic mechanisms of sester-TPSs are not fully understood.Here,we first identified three nonclustered functional sester-TPSs(AtTPS06,AtTPS22,and AtTPS29)in Arabidopsis thaliana.AtTPS06 utilizes a type-B cyclization mechanism,whereas most other sester-TPSs produce various sesterterpene backbones via a type-A cyclization mechanism.We then determined the crystal structure of the AtTPS18–FSPP complex to explore the cyclization mechanism of plant sester-TPSs.We used structural comparisons and site-directed mutagenesis to further elucidate the mechanism:(1)mainly due to the outward shift of helix G,plant sester-TPSs have a larger catalytic pocket than do mono-,sesqui-,and di-TPSs to accommodate GFPP;(2)type-A sester-TPSs have more aromatic residues(five or six)in their catalytic pocket than classic TPSs(two or three),which also determines whether the type-A or type-B cyclization mechanism is active;and(3)the other residues responsible for product fidelity are determined by interconversion of AtTPS18 and its close homologs.Altogether,this study improves our understanding of the catalytic mechanism of plant sester-TPS,which ultimately enables the rational engineering of sesterterpenoids for future applications.

The mechanism and function of active DNA demethylation in plants

DNA methylation is a conserved and important epigenetic mark in both mammals and plants.DNA methylation can be dynamically established,maintained,and removed through different pathways.In plants,active DNA demethylation is initiated by the RELEASE OF SILENCING 1(ROS1)family of bifunctional DNA glycosylases/lyases.Accumulating evidence suggests that DNA demethylation is important in many processes in plants.In this review,we summarize recent studies on the enzymes and regulatory factors that have been identified in the DNA demethylation pathway.We also review the functions of active DNA demethylation in plant development as well as biotic and abiotic stress responses.Finally,we highlight those aspects of DNA demethylation that require additional research.

Phytochrome Signaling in Green Arabidopsis Seedlings： Impact Assessment of a Mutually Negative phyB-PIF Feedback Loop

The reversibly red （R）/far-red （FR）-Iight-responsive phytochrome （phy） photosensory system initiates both the deetiolation process in dark-germinated seedlings upon first exposure to light, and the shade-avoidance process in fully deetiolated seedlings upon exposure to vegetational shade. The intracellular signaling pathway from the light-activated photoreceptor conformer （Pfr） to the transcriptional network that drives these responses involves direct, physical inter- action of Pfr with a small subfamily of bHLH transcription factors, termed Phy-lnteracting Factors （PIFs）, which induces rapid PIF proteolytic degradation. In addition, there is evidence of further complexity in light-grown seedlings, whereby phyB-PIF interaction reciprocally induces phyB degradation, in a mutually-negative, feedback-loop configuration. Here, to assess the relative contributions of these antagonistic activities to the net phenotypic readout in light-grown seedlings, we have examined the magnitude of the light- and simulated-shade-induced responses of a pentuple phyBpiflpif3pif4pif5 （phyBpifq） mutant and various multiple pif-mutant combinations. The data （1） reaffirm that phyB is the predominant, if not exclusive, photoreceptor imposing the inhibition of hypocotyl elongation in deetiolating seedlings in response to pro- longed continuous R irradiation and （2） show that the PIF quartet （PIF1, PIF3, PIF4, and PIF5） retain and exert a dual capacity to modulate hypocotyl elongation under these conditions, by concomitantly promoting cell elongation through intrinsic transcriptional-regulatory activity, and reducing phyB-inhibitory capacity through feedback-loop-induced phyB degrada- tion. In shade-exposed seedlings, immunoblot analysis shows that the shade-imposed reduction in Pfr levels induces increases in the abundance of PIF3, and mutant analysis indicates that PIF3 acts, in conjunction with PIF4 and PIF5, to promote the known shade-induced acceleration of hypocotyl elongation. Conversely, although the quadruple pifq mutant displays clearly reduced hypocotyl elongation compared to wild-type in response to prolonged shade, immunoblot analysis detects no elevation in phyB levels in the mutant seedlings compared to the wild-type during the majority of the shade-induced growth period, and phyB levels are not robustly correlated with the growth phenotype across the pif-mutant combinations compared. These results suggest that PIF feedback modulation of phyB abundance does not play a dominant role in modulating the magnitude of the PIF-promoted, shade-responsive phenotype under these conditions. In seedlings grown under diurnal light-dark cycles, the data show that FR-pulse-induced removal of Pfr at the beginning of the dark period （End-of-Day-FR （EOD-FR） treatment） results in longer hypocotyls relative to no EOD-FR treatment and that this effect is attenuated in the pif-mutant combinations tested. This result similarly indicates that the PIF quartet members are capable of intrinsically promoting hypocotyl cell elongation in light-grown plants, independently of the effects of PIF feedback modulation of photoactivated-phyB abundance.

Twenty years of rice genomics research: From sequencing and functional genomics to quantitative genomics

Since the completion of the rice genome sequencing project in 2005,we have entered the era of rice genomics,which is still in its ascendancy.Rice genomics studies can be classified into three stages:structural genomics,functional genomics,and quantitative genomics.Structural genomics refers primarily to genome sequencing for the construction of a complete map of rice genome sequence.This is fundamental for rice genetics and molecular biology research.Functional genomics aims to decode the functions of rice genes.Quantitative genomics is large-scale sequence-and statistics-based research to define the quantitative traits and genetic features of rice populations.Rice genomics has been a transformative influence on rice biological research and contributes significantly to rice breeding,making rice a good model plant for studying crop sciences.

Expanding the scope of CRISPR/Cas9-mediated genome editing in plants using an xCas9 and Cas9-NG hybrid^FA

The widely used Streptococcus pyogenes Cas9(SpCas9)requires NGG as a protospacer adjacent motif(PAM)for genome editing.Although Sp Cas9 is a powerful genome-editing tool,its use has been limited on the targetable genomic locus lacking NGG PAM.The Sp Cas9 variants xCas9 and Cas9-NG have been developed to recognize NG,GAA,and GAT PAMs in human cel s.Here,we show that xCas9 cannot recognize NG PAMs in tomato,and Cas9-NG can recognize some of our tested NG PAMs in the tomato and Arabidopsis genomes.In addition,we engineered BrSp Cas9(XNG-Cas9)based on mutations from both xCas9 and Cas9-NG,and found that XNG-Cas9 can efficiently mutagenize endogenous target sites with NG,GAG,GAA,and GAT PAMs in the tomato or Arabidopsis genomes.The PAM compatibility of XNG-Cas9 is the broadest reported to date among Cas9 s(SpCas9 and Cas9-NG)active in plant.

The βC1 Protein of Gem,n,v,rus--Betasatellite Complexes:A Target and Repressor of Host Defenses

Geminiviruses are a family of plant viruses that cause devastating diseases in many economically important crops worldwide. These pathogens encapsidate circular,single-stranded DNAs (ssDNAs)of 2.5-3.0 kb that replicate through double-stranded DNA (dsDNA)intermediates.Members of the genus Begomovirus,which comprises by far the largest number of species in the family,are transmitted by whiteflies and have genomes consisting of one or two DNAs.