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Improving error-correcting capability in DNA digital storage via soft-decision decoding

National Science Review 2024年第2期11卷 135-144页

作者：丁璐璐伍世刚候志浩李阿伦许亚苹冯虎潘玮华阮珏 Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural Sciences Guangdong Provincial Key Laboratory of Plant Molecular Breeding State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesSouth China Agricultural University

Error-correcting codes(ECCs) employed in the state-of-the-art DNA digital storage(DDS) systems suffer from a trade-off between error-correcting capability and the proportion of redundancy. To address this issue, in this study, we introduce soft-decision decoding approach into DDS by proposing a DNA-specific error prediction model and a series of novel strategies. We demonstrate the effectiveness of our approach through a proof-of-concept DDS system based on Reed-Solomon(RS) code, named as Derrick. Derrick shows significant improvement in error-correcting capability without involving additional redundancy in both in vitro and in silico experiments, using various sequencing technologies such as Illumina, Pac Bio and Oxford Nanopore Technology(ONT). Notably, in vitro experiments using ONT sequencing at a depth of 7× reveal that Derrick, compared with the traditional hard-decision decoding strategy, doubles the error-correcting capability of RS code, decreases the proportion of matrices with decoding-failure by 229-fold, and amplifies the potential maximum storage volume by impressive 32 388-fold. Also, Derrick surpasses ‘state-of-the-art' DDS systems by comprehensively considering the information density and the minimum sequencing depth required for complete information recovery. Crucially, the soft-decision decoding strategy and key steps of Derrick are generalizable to other ECCs' decoding algorithms.

关键词： DNA digital storage (DDS) error-correcting code (ECC) soft-decision decoding error-correcting capability storage volume

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Molecular cloning,characterization and promoter analysis of LbgCWIN1 and its expression profiles in response to exogenous sucrose during in vitro bulblet initiation in lily

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Horticultural Plant Journal 2024年第2期10卷 545-555页

作者： Cong Gao Shiqi Li Yunchen Xu Yue Liu Yiping Xia Ziming Ren Yun Wu genomics and Genetic Engineering Laboratory of Ornamental Plants Institute of Landscape ArchitectureCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouZhejiang 310058China Laboratory of Flower Bulbs Department of Landscape ArchitectureSchool of Civil Engineering and ArchitectureZhejiang Sci-Tech UniversityHangzhouZhejiang 310018China

Lily(Lilium spp.) is an important ornamental flower, which is mainly propagated by bulbs. Cell wall invertases(CWINs), which catalyze the irreversibly conversion of sucrose into glucose and fructose in the extracellular space, are key enzymes participating in sucrose allocation in higher plants. Previous studies have shown that CWINs play an essential role in bulblet initiation process in bulbous crops, but the underlying molecular mechanism remains unclear. Here, a CWIN gene of Lilium brownii var. giganteum(Lbg) was identified and amplified from genomic DNA. Quantitative RT-PCR assays revealed that the expression level of LbgCWIN1 was highly upregulated exactly when the endogenous starch degraded in non-sucrose medium during in vitro bulblet initiation in Lbg. Phylogenetic relationship, motif, and domain analysis of LbgCWIN1 protein and CWINs in other plant species showed that all sequences of these CWIN proteins were highly conserved. The promoter sequence of LbgCWIN1 possessed a number of alpha-amylase-, phytohormone-, light-and stress-responsive cis-elements. Meanwhile, β-glucuronidase(GUS) assay showed that the 459 bp upstream fragment from the translational start site displayed maximal promoter activity. These results revealed that LbgCWIN1 might function in the process of in vitro bulblet initiation and be in the response to degradation of endogenous starch.

关键词： Lilium brownii var.giganteum LbgCWIN1 Phylogenetic analysis Promoter analysis Bulblet initiation

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Phase separation of S-RNase promotes self-incompatibility in Petunia hybrida

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Journal of Integrative Plant Biology 2024年第5期66卷 986-1006页

作者： Huayang Tian Hongkui Zhang Huaqiu Huang Yu'e Zhang Yongbiao Xue The State Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental Biologythe Chinese Academy of SciencesBeijing 100101China University of the Chinese Academy of Sciences Beijing 100049China Beiing Institute of genomics Chinese Academy of SciencesNational Center for BioinformationBeijing 100101China

Self-incompatibility(SI)is an intraspecific reproductive barrier widely present in *** SI system with the broadest occurrence in angiosperms is based on an S-RNase linked to a cluster of multiple S-locus F-box(SLF)genes found in the Solanaceae,Plantaginaceae,Rosaceae,and *** studies reveal that non-self S-RNase is degraded by the Skip Cullin F-box(SCF)SLF-mediated ubiquitin–proteasome system in a collaborative manner in Petunia,but how self-RNase functions largely remains ***,we show that S-RNases form S-RNase condensates(SRCs)in the self-pollen tube cytoplasm through phase separation and the disruption of SRC formation breaks SI in self-incompatible Petunia *** further find that the pistil SI factors of a small asparagine-rich protein HT-B and thioredoxin h together with a reduced state of the pollen tube all promote the expansion of SRCs,which then sequester several actin-binding proteins,including the actin polymerization factor PhABRACL,the actin polymerization activity of which is reduced by S-RNase in ***,we find that S-RNase variants lacking condensation ability fail to recruit PhABRACL and are unable to induce actin foci formation required for pollen tube growth *** together,our results demonstrate that phase separation of S-RNase promotes SI response in ***,revealing a new mode of S-RNase action.

关键词： self-incompatibility S-RNase phase separation

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The global regulation of c-di-GMP and cAMP in bacteria

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mLife 2024年第1期3卷 42-56页

作者： Cong Liu Rui Shi Marcus S.Jensen Jingrong Zhu Jiawen Liu Xiaobo Liu Di Sun Weijie Liu Jiangsu Key Laboratory of Phylogenomics&Comparative genomics School of Life SciencesJiangsu Normal UniversityXuzhouChina Key Laboratory of Metabolic Engineering and Biosynthesis Technology Ministry of Industry and Information TechnologyNanjing University of Science and TechnologyNanjingChina

Nucleotide second messengers are highly versatile signaling molecules that regulate a variety of key biological processes in *** best-studied examples are cyclic AMP(cAMP)and bis-(3'-5')-cyclic dimeric guanosine monophosphate(c-di-GMP),which both act as global *** regulatory frameworks of c-di-GMP and cAMP in bacteria show several parallels but also significant *** this review,we llustrate the global regulatory models of the two nucleotide second messengers,compare the different regulatory frameworks between c-di-GMP and cAMP,and discuss the mechanisms and physiological significance of cross-regulation between c-di-GMP and cAMP.c-di-GMP responds to numerous signals de-pendent on a great number of metabolic enzymes,and it regulates various signal transduction pathways through its huge number of effectors with varying *** contrast,due to the limited quantity,the cAMP metabolic enzymes and its major effector are regulated at different levels by diverse *** performs its global regulatory function primarily by controlling the transcription of a large number of genes via cAMP receptor protein(CRP)in most *** review can help us understand how bacteria use the two typical nucleotide second messengers to effectively coordinate and integrate various physiological processes,providing theoretical guidelines for future research.

关键词： bacteria cAMP c-di-GMP cross-regulation CRP

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Loss of the accessory chromosome converts a pathogenic tree-root fungus into a mutualistic endophyte

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Plant Communications 2024年第1期5卷 164-180页

作者： Huanshen Wei Zhenhui Zhong Zhongfeng Li Yuwei Zhang Eva H.Stukenbrock Boping Tang Ningning Yang Riccardo Baroncelli Long Peng Zhuo Liu Xinghua He Yuzhan Yang Zhilin Yuan State Key Laboratory of Tree Genetics and Breeding Chinese Academy of ForestryBeijing 100091China Research Institute of Subtropical Forestry Chinese Academy of ForestryHangzhou 311400China State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops Fujian Agriculture and Forestry UniversityFuzhou 350002China Environmental genomics Christian-Albrechts University24118 KielGermany Max Planck Fellow Group Environmental genomics Max Planck Institute for Evolutionary Biology24306 PlonGermany Jiangsu Key Laboratory for Bioresources of Saline Soils School of WetlandsYancheng Teachers UniversityYancheng 224002China Department of Agricultural and Food Sciences(DISTAL) University of Bologna40127 BolognaItaly

Some fungal accessory chromosomes(ACs)may contribute to virulence in ***,the mecha-nisms by which ACs determine specific traits associated with lifestyle transitions along a symbiotic contin-uum are not *** we delineated the genetic divergence in two sympatric but considerably variable isolates(16B and 16W)of the poplar-associated fungus Stagonosporopsis *** identified a-0.6-Mb horizontally acquired AC in 16W that resulted in a mildly parasitic lifestyle in *** deletion of the AC(D16W)significantly altered the fungal ***,D16W was morphologically more similar to 16B,showed enhanced melanization,and established beneficial interactions with poplar plants,thereby acting as a dark septate *** sequencing(RNA-seq)analysis showed that AC loss induced the upregulation of genes related to root colonization and biosynthesis of indole acetic acid and *** observed that the AC maintained a more open status of chromatin across the genome,indicating an impressive remodeling of cis-regulatory elements upon AC loss,which potentially enhanced symbiotic *** demonstrated that the symbiotic capacities were non-host-specific through comparable experiments on Triticum–and Arabidopsis–fungus ***,the three isolates generated symbiotic interactions with a nonvascular *** summary,our study suggests that the AC is a suppressor of symbiosis and provides insights into the underlying mechanisms of mutualism with vascular plants in the absence of traits encoded by the *** speculate that AC-situ-ated effectors and other potential secreted molecules may have evolved to specifically target vascular plants and promote mild virulence.

关键词： dark septate endophytes effectors lifestyle transition root–fungus symbioses

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Isolation and culture of human primary osteoblasts:Comparing the effects of differences in method details on osteoblast characteristics

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Genes & Diseases 2024年第2期11卷 546-549页

作者： Fei Chen Yan Zhang Pai Peng Xiao-Ting Huang Zi-Han Qiu Bao-Cheng Liu Tie-Lin Yang Bo Yang Yan Guo Key Laboratory of Biomedical Information Engineering of Ministry of Education Biomedical Informatics & Genomics CenterSchool of Life Science and TechnologyXi'an Jiaotong UniversityXi'anShaanxi 710049China Department of Orthopaedics Shannxi Provincial People's Hospital (The Third Affiliated Hospital of Xi'an Jiaotong University)Xi'anShaanxi 710068China

Osteoblasts are essential in the maintenance of human bone homeostasis.1 The abnormal formation and impaired differentiation ability of osteoblasts are pivotal factors leading to bone-related diseases,suggesting that an indepth study of osteoblasts can provide novel treatment strategies for these diseases.2 Human primary osteoblasts are precious experimental models in bone-related research.3 However,the isolation and culture of human primary osteoblasts still have some difficulties and ***,we refined a method to isolate and culture human primary osteoblasts by taking cancellous bone through a bone tissue sampler and pre-digesting it with pancreatin,which makes the process easier,cheaper,and more ***,we compared the effects of the subtle changes in isolation and culture methods on the phenotype of human primary osteoblasts and examined the differences in morphology,proliferation,and differentiation between micro-explants cultured osteoblasts(MECOBs)and explants cultured osteoblasts(EC-OBs).

关键词： impaired culture details

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OsWRKY65 enhances immunity against fungal and bacterial pathogens in rice

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The Crop Journal 2024年第2期12卷 470-481页

作者： Seungmin Son Giha Song Suhyeon Nam Jinjeong Lee Duk-Ju Hwang Eun-Jung Suh Sang Ryeol Park National Institute of Agricultural Sciences Rural Development AdministrationJeonju 54874Republic of Korea Department of Agriculture Forestry and BioresourcesPlant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesSeoul National UniversitySeoul 08826Republic of Korea Department of Crop Science and Biotechnology Jeonbuk National UniversityJeonju 54896Republic of Korea

Diverse bacterial and fungal pathogens attack plants,causing biotic stress and severe yield losses *** losses are expected to become more serious as climate change improves conditions for many ***,identifying genes conferring broad-spectrum disease resistance and elucidating their underlying mechanisms provides important resources for plant *** transcription factors affect plant growth and stress ***,the functions of many WRKY proteins remain to be ***,we demonstrated the role of rice(Oryza sativa)WRKY groupⅢtranscription factor OsWRKY65 in ***65 localized to the nucleus and acted as transcriptional *** and molecular functional analyses showed that OsWRKY65 increases resistance to the fungal pathogen Fusarium fujikuroi through downregulation of GA signaling and upregulation of JA ***,OsWRKY65 modulated the expression of the key genes that confer susceptibility or resistance to Xanthomonas oryzae *** to enhance immunity against the *** particular,OsWRKY65directly bound to the promoter region of OsSWEET13 and repressed its *** together,our findings demonstrate that the OsWRKY65 enhances resistance to fungal and bacterial pathogens in rice.

关键词： Bacterial blight Bakanae disease Broad-spectrum disease resistance Oriza sativa OsWRKY65 Rice

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Single-cell transcriptome analysis dissects lncRNA-associated gene networks in Arabidopsis

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Plant Communications 2024年第2期5卷 94-105页

作者： Zhaohui He Yangming Lan Xinkai Zhou Bianjiong Yu Tao Zhu Fa Yang Liang-Yu Fu Haoyu Chao Jiahao Wang Rong-Xu Feng Shimin Zuo Wenzhi Lan Chunli Chen Ming Chen Xue Zhao Keming Hu Dijun Chen State Key Laboratory of Pharmaceutical Biotechnology School of Life SciencesNanjing UniversityNanjing 210023China Department of Bioinformatics College of Life SciencesZhejiang UniversityHangzhou 310058China Jiangsu Key Laboratory of Crop genomics and Molecular Breeding/Key Laboratory of Plant Functional genomics of the Ministry of Education College of AgricultureYangzhou UniversityYangzhou 225009China Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province Yangzhou UniversityYangzhou 225009China Zhejiang Zhoushan High School Zhoushan 316099China National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops Hubei Hongshan LaboratoryWuhan 430070China

The plant genome produces an extremely large collection of long noncoding RNAs(lncRNAs)that are generally expressed in a context-specific manner and have pivotal roles in regulation of diverse biological ***,we mapped the transcriptional heterogeneity of lncRNAs and their associated gene reg-ulatory networks at single-cell *** generated a comprehensive cell atlas at the whole-organism level by integrative analysis of 28 published single-cell RNA sequencing(scRNA-seq)datasets from juvenile Arabidopsis *** then provided an in-depth analysis of cell-type-related lncRNA signatures that show expression patterns consistent with canonical protein-coding gene *** further demon-strated that the cell-type-specific expression of lncRNAs largely explains their tissue *** addi-tion,we predicted gene regulatory networks on the basis of motif enrichment and co-expression analysis of lncRNAs and mRNAs,and we identified putative transcription factors orchestrating cell-type-specific expression of *** analysis results are available at the single-cell-based plant lncRNA atlas data-base(scPLAD;https://***/scPLAD/).Overall,this work demonstrates the power of inte-grative single-cell data analysis applied to plant lncRNA biology and provides fundamental insights into lncRNA expression specificity and associated gene regulation.

关键词： single-cell transcriptomics long noncoding RNAs lncRNAs gene regulatory networks GRNs plants

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Identification of TMEM217 as a novel prognostic biomarker and potential therapeutic target in acute myeloid leukemia

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Genes & Diseases 2024年第4期11卷 90-93页

作者： Yunying Yao Zhizhou Xi Min Wu Bo Jiao Jiaming Gao Donghe Li Xi Xie Pengfei Xu Jiaoyang Li Lei Yan Ruibao Ren Ping Liu Shanghai Institute of Hematology State Key Laboratory for Medical GenomicsNational Research Center for Translational MedicineCollaborative Innovation Center of HematologyRuijin Hospital affiliated with Shanghai Jiao Tong University School of MedicineShanghai 200025China International Center for Aging and Cancer Hainan Medical UniversityHaikouHainan 570102China

Despite remarkable advances in molecular and cell biology of acute myeloid leukemia(AML),AML patients still frequently relapse and have low 5-year overall survival(OS)rates.1 It is worth noting that a recent study from the registry or clinical trial compilation has reported an improvement in the OS of adult AML patients,especially those under 60 years of age.

关键词： acute myeloid leukemia

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Streamlined whole-genome genotyping through NGS-enhanced thermal asymmetric interlaced(TAIL)-PCR

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Plant Communications 2024年第9期5卷 25-37页

作者： Sheng Zhao Yue Wang Zhenghang Zhu Peng Chen Wuge Liu Chongrong Wang Hong Lu Yong Xiang Yuwen Liu Qian Qian Yuxiao Chang Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China 2 Guangdong Provincial Key Laboratory of New Technology in Rice Breeding Rice Research InstituteGuangdong Academy of Agricultural SciencesGuangzhou 510640China

Whole-genome genotyping(WGG)stands as a pivotal element in genomic-assisted plant ***theless,sequencing-based approaches for WGG continue to be costly,primarily owing to the high expenses associated with library preparation and the laborious *** prior development of foreground and background integrated genotyping by sequencing(FBI-seq),we discovered that any sequence-specific primer(SP)inherently possesses the capability to amplify a massive array of stable and reproducible non-specific PCR products across the ***,we further improved FBI-seq by replacing the adapter ligated by Tn5 transposase with an arbitrary degenerate(AD)*** protocol for the enhanced FBI-seq unexpectedly mirrors a simplified thermal asymmetric interlaced(TAIL)-PCR,a technique that is widely used for isolation of flanking ***,the improved TAIL-PCR maximizes the primer-template mismatched annealing capabilities of both SP and AD *** addition,leveraging of next-generation sequencing enhances the ability of this technique to assay tens of thousands of genome-wide loci for any *** cost-effective,user-friendly,and powerful WGG tool,which we have named TAIL-PCR by sequencing(TAIL-peq),holds great potential for widespread application in breeding programs,thereby facilitating genome-assisted crop improvement.

关键词： whole-genome genotyping primer-template mismatched annealing specific primer arbitrary degenerate primer molecular breeding

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