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Spatial search weighting information contained in cell velocity distribution

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Chinese Physics B 2024年第2期33卷 522-528页

Cell migration plays a significant role in physiological and pathological *** the characteristics of cell movement is crucial for comprehending biological processes such as cell functionality,cell migration,and cell–cell *** of the fundamental characteristics of cell movement is the specific distribution of cell speed,containing valuable information that still requires comprehensive *** article investigates the distribution of mean velocities along cell trajectories,with a focus on optimizing the efficiency of cell food search in the context of the entire *** confirm that the specific velocity distribution in the experiments corresponds to an optimal search efficiency when spatial weighting is *** simulation results indicate that the distribution of average velocity does not align with the optimal search efficiency when employing average spatial ***,when considering the distribution of central spatial weighting,the specific velocity distribution in the experiment is shown to correspond to the optimal search *** simulations reveal that for any given distribution of average velocity,a specific central spatial weighting can be identified among the possible central spatial weighting that aligns with the optimal search ***,our work presents a method for determining the spatial weights embedded in the velocity distribution of cell *** results have provided new avenues for further investigation of significant topics,such as relationship between cell behavior and environmental conditions throughout their evolutionary history,and how cells achieve collective cooperation through cell-cell communication.

关键词： cell migration foraging efficiency random walk spatial search weight

A homing rescue gene drive with multiplexed gRNAs reaches high frequency in cage populations but generates functional resistance

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Journal of Genetics and genomics 2024年第8期51卷 836-843页

作者： Shibo Hou Jingheng Chen Ruobing Feng Xuejiao Xu Nan Liang Jackson Champer center for bioinformatics Center for Life SciencesSchool of Life SciencesPeking UniversityBeijing 100871China

CRISPR homing gene drives have considerable potential for managing populations of medically and agriculturally significant *** operate by Cas9 cleavage followed by homology-directed repair,copying the drive allele to the wild-type chromosome and thus increasing in frequency and spreading throughout a ***,resistance alleles formed by end-joining repair pose a significant *** address this,we create a homing drive targeting the essential hairy gene in Drosophila *** resistance alleles are recessive lethal,while drive carriers have a recoded“rescue”version of *** drive inheritance rate is moderate,and multigenerational cage studies show drive spread to 96%–97%of the ***,the drive does not reach 100%due to the formation of functional resistance alleles despite using four *** alleles have a large deletion but likely utilize an alternate start ***,revised designs targeting more essential regions of a gene may be necessary to avoid such functional *** of the rescue element’s native 3'UTR with a homolog from another species increases drive inheritance by 13%–24%.This was possibly because of reduced homology between the rescue element and surrounding genomic DNA,which could also be an important design consideration for rescue gene drives.

关键词： Genedrive Homing drive Rescueelement Population modification Multiplexed gRNAs Resistance alleles Cage study

Plant genomic resources at National genomics Data center:assisting in data-driven breeding applications

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aBIOTECH 2024年第1期5卷 94-106页

作者： Dongmei Tian Tianyi Xu Hailong Kang Hong Luo Yanqing Wang Meili Chen Rujiao Li Lina Ma Zhonghuang Wang Lili Hao Bixia Tang Dong Zou Jingfa Xiao Wenming Zhao Yiming Bao Zhang Zhang Shuhui Song National genomics Data center Beijing Institute of GenomicsChinese Academy of Sciences&China National Center for BioinformationBeijing 100101China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences&China National Center for BioinformationBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

Genomic data serve as an invaluable resource for unraveling the intricacies of the higher plant systems,including the constituent elements within and among *** various efforts in genomic data archiving,integrative analysis and value-added curation,the National genomics Data center(NGDC),which is a part of the China National center for Bioinformation(CNCB),has successfully established and currently maintains a vast amount of database *** dedicated initiative of the NGDC facilitates a data-rich ecosystem that greatly strengthens and supports genomic research ***,we present a comprehensive overview of central repositories dedicated to archiving,presenting,and sharing plant omics data,introduce knowledgebases focused on variants or gene-based functional insights,highlight species-specific multiple omics database resources,and briefly review the online application *** intend that this review can be used as a guide map for plant researchers wishing to select effective data resources from the NGDC for their specific areas of study.

关键词： Plant-omics data Data repositories Data integration Knowledgebase Plant genomics

Interplant communication:an emerging battlefield in plant-aphid-virus interactions

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Science China(Life Sciences) 2024年第5期67卷 1069-1071页

作者： Yunjing Wang Qian Gong Yule Liu MOE Key Laboratory of bioinformatics and center for Plant Biology School of Life SciencesTsinghua UniversityBeijing 100084China Tsinghua-Peking center for Life Sciences Beijing 100084China

Plants constantly face threats from various organisms,including pathogens and *** the pathogens,plant viruses are obligate intracellular parasites that infect plants and cause serious crop yield losses.

关键词： plant Plants communication

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Allosteric modulation of G protein-coupled receptors as a novel therapeutic strategy in neuropathic pain

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Acta Pharmaceutica Sinica B 2024年第1期14卷 67-86页

作者： Chunhao Zhu Xiaobing Lan Zhiqiang Wei Jianqiang Yu Jian Zhang School of Pharmacy Ningxia Medical UniversityYinchuan 750004China Medicinal Chemistry and bioinformatics center Shanghai Jiao Tong University School of MedicineShanghai 200025China School of Basic Medical Science Ningxia Medical UniversityYinchuan 750004China Medicinal Chemistry and bioinformatics center Ocean University of ChinaQingdao 266100China State Key Laboratory of Pharmaceutical Biotechnology Nanjing UniversityNanjing 210023China

Neuropathic pain is a debilitating pathological condition that presents significant therapeutic challenges in clinical ***,current pharmacological treatments for neuropathic pain lack clinical efficacy and often lead to harmful adverse *** G protein-coupled receptors(GPCRs)are widely distributed throughout the body,including the pain transmission pathway and descending inhibition pathway,the development of novel neuropathic pain treatments based on GPCRs allosteric modulation theory is gaining *** research has shown that allosteric modulators targeting GPCRs on the pain pathway can effectively alleviate symptoms of neuropathic pain while reducing or eliminating adverse *** review aims to provide a comprehensive summary of the progress made in GPCRs allosteric modulators in the treatment of neuropathic pain,and discuss the potential benefits and adverse factors of this *** will also concentrate on the development of biased agonists of GPCRs,and based on important examples of biased agonist development in recent years,we will describe universal strategies for designing structure-based biased *** is foreseeable that,with the continuous improvement of GPCRs allosteric modulation and biased agonist theory,effective GPCRs allosteric drugs will eventually be available for the treatment of neuropathic pain with acceptable safety.

关键词： Neuropathic pain Allosteric modulators G protein-coupled receptors Analgesia

Dynamics and genetic regulation of macronutrient concentrations during grain development in maize

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Journal of Integrative Agriculture 2024年第3期23卷 781-794页

作者： Pengcheng Li Shuangyi Yin Yunyun Wang Tianze Zhu Xinjie Zhu Minggang Ji Wenye Rui Houmiao Wang Chenwu Xu Zefeng Yang Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional genomics Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Agricultural CollegeYangzhou UniversityYangzhou 225009China Jiangsu Co-lnnovation center for Modern Production Technology of Grain Crops Yangzhou UniversityYangzhou 225009China

Nitrogen(N), phosphorus(P), and potassium(K) are essential macronutrients that are crucial not only for maize growth and development, but also for crop yield and quality. The genetic basis of macronutrient dynamics and accumulation during grain filling in maize remains largely unknown. In this study, we evaluated grain N, P, and K concentrations in 206 recombinant inbred lines generated from a cross of DH1M and T877 at six time points after pollination. We then calculated conditional phenotypic values at different time intervals to explore the dynamic characteristics of the N, P, and K concentrations. Abundant phenotypic variations were observed in the concentrations and net changes of these nutrients. Unconditional quantitative trait locus(QTL) mapping revealed 41 non-redundant QTLs, including 17, 16, and 14 for the N, P, and K concentrations, respectively. Conditional QTL mapping uncovered 39 non-redundant QTLs related to net changes in the N, P, and K concentrations. By combining QTL, gene expression, co-expression analysis, and comparative genomic data, we identified 44, 36, and 44 candidate genes for the N, P, and K concentrations, respectively, including GRMZM2G371058 encoding a Doftype zinc finger DNA-binding family protein, which was associated with the N concentration, and GRMZM2G113967encoding a CBL-interacting protein kinase, which was related to the K concentration. The results deepen our understanding of the genetic factors controlling N, P, and K accumulation during maize grain development and provide valuable genes for the genetic improvement of nutrient concentrations in maize.

关键词： maize nutrient concentration unconditional QTL mapping conditional QTL mapping dynamic trait

Curation,nomenclature,and topological classification of receptor-like kinases from 528 plant species for novel domain discovery and functional inference

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Molecular Plant 2024年第4期17卷 658-671页

作者： Qian Liu Qiong Fu Yujie Yan Qian Jiang Longfei Mao Long Wang Feng Yu Heping Zheng State Key Laboratory of Chemo/Biosensing and Chemometrics Hunan University College of BiologyChangshaHunan 410082China bioinformatics center Hunan University College of BiologyChangshaHunan 410082China

Receptor-like kinases(RLKs)are the most numerous signal transduction components in plants and play important roles in determining how different plants adapt to their ecological *** on RLKs has focused mainly on a small number of typical RLK members in a few model *** is an urgent need to study the composition,distribution,and evolution of RLKs at the holistic level to increase our understanding of how RLKs assist in the ecological adaptations of different plant *** this study,we collected the genome assemblies of 528 plant species and constructed an RLK *** this dataset,we identified and characterized 524948 RLK family *** member underwent systematic topological classification and was assigned a gene ID based on a unified nomenclature ***,we identified two novel extracellular domains in some RLKs,designated Xiao and *** analysis of the RLK family revealed that the RLCK-XVII and RLCK-XII-2 classes were present exclusively in dicots,suggesting that diversification of RLKs between monocots and dicots may have led to differences in downstream cytoplasmic *** also used an interaction proteome to help empower data mining for inference of new RLK functions from a global perspective,with the ultimate goal of understanding how RLKs shape the adaptation of different plants to the environments/*** assembled RLK dataset,together with annotations and analytical tools,forms an integrated foundation of multiomics data that is publicly accessible via the metaRLK web portal(http://***).

关键词： RLK RLCK domain signaling pathway receptor-protein interactions

Recurrent evolution of seaweed body plan complexity among photosynthetic eukaryotes

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Molecular Plant 2024年第7期17卷 999-1001页

作者： Elisa S.Goldbecker Iker Irisarri Jan de Vries Department of Applied bioinformatics Institute for Microbiology and GeneticsUniversity of GottingenGoldschmidtstr.137077 GottingenGermany Section Phylogenomics Center for Molecular Biodiversity ResearchLeibniz Institute for the Analysis of Biodiversity Change(LIB)Museum of Nature HamburgMartin-Luther-King-Platz 320146 HamburgGermany Department of Applied bioinformatics Campus Institute Data Science(CIDAS)University of GottingenGoldschmidtstr.137077 GottingenGermany Department of Applied bioinformatics Gottingen Center for Molecular Biosciences(GZMB)University of GottingenGoldschmidtstr.137077 GottingenGermany

The evolutionary origin of multicellularity is an age-old question in biological *** studies have delved into the evolutionary processes that led to the evolution of multicellular life forms from unicellular *** beauty and the challenge about this topic are that evolution has brought forth various forms of multicellular life,multiple times independently,scattered across the evolutionary tree of *** to the challenge,multicellular organisms exist in a diversity of forms and complexities,and the mechanisms by which multicellularity emerged are also likely different between animals,algae,or fungi(Niklas and Newman,2020).Recently,Nelson et al.(2024)presented a large-scale comparative genomics study focused on particularly intricate multicellular organisms:macroalgae(seaweeds),which emerged independently in three distinct eukaryotic lineages-green algae(Chlorophyta),red algae(Rhodophyta),and brown algae(Phaeophyceae).

关键词： algae seaweed evolution

Integrating machine learning and genome editing for crop improvement

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aBIOTECH 2024年第2期5卷 262-277页

作者： Long Chen Guanqing Liu Tao Zhang Jiangsu Key Laboratory of Crop genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional genomics of the Ministry of Education Agricultural College of Yangzhou UniversityYangzhou 225009China Jiangsu Co-Innovation center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology Yangzhou UniversityYangzhou 225009China

Genome editing is a promising technique that has been broadly utilized for basic gene function studies and trait ***,the exponential growth of computational power and big data now promote the application of machine learning for biological *** this regard,machine learning shows great potential in the refinement of genome editing systems and crop ***,we review the advances of machine learning to genome editing optimization,with emphasis placed on editing efficiency and specificity ***,we demonstrate how machine learning bridges genome editing and crop breeding,by accurate key site detection and guide RNA ***,we discuss the current challenges and prospects of these two techniques in crop *** integrating advanced genome editing techniques with machine learning,progress in crop breeding will be further accelerated in the future.

关键词： Machine learning Genome editing Crop improvement Molecular design breeding