Liang Yang

Sichuan Academy of Agricultural Sciences

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Wei Chang

Anhui Medical University

Mingjun Miao

Ministry of Agriculture and Rural Affairs

Zhibin Liu

Sichuan University

Yi Yang

Sichuan University

Vladimir B. Bajić

King Abdullah University of Science and Technology

Haicheng Long

Ministry of Agriculture and Rural Affairs

Piero Carninci

RIKEN Center for Integrative Medical Sciences

Jun Kawai

Kyoto University

Chikatoshi Kai

RIKEN Center for Integrative Medical Sciences

Sin Lam Tan

Minnan University of Science and Technology

Cooperative Institutions

Sichuan University

Ministry of Agriculture and Rural Affairs

Chinese Academy of Sciences

Chinese Academy of Agricultural Sciences

Sichuan Agricultural University

Yangzhou University

Ministry of Education of the People's Republic of China

Huazhong University of Science and Technology

Southern University of Science and Technology

Sichuan Academy of Agricultural Sciences

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Nitrogen Fertilizers Affect Microbial Hitchhiking to the Plant Roots

Journal of Agricultural and Food Chemistry (2024)

Zhibin Liu Qini Xia Jing Cai Ziyuan Wang Kexin Yang

The phenomenon of microbial hitchhiking, where nonmotile microbes utilize transspecies motility to navigate within their environment, has been observed. However, the underlying factors driving microbial hitchhiking remain unclear. Our study explored how nitrogen fertilizers affect microbial hitchhiking in soil through an in situ planting experiment. We established twelve treatments encompassing the presence and absence of plants, the presence and absence of a filter membrane that is used to prevent hitchhiking, and three nitrogen levels. Results showed that nitrogen influenced bacterial diversity in all soils, an effect thwarted by filter membranes. In the presence of plants, nitrogen significantly affected the bacterial mobility, Bacillus abundance, and plant biomass, but these effects vanished when filters were used. The correlation between motile Bacillus and rhizosphere bacteria was strong without filters at the proper nitrogen levels but weakened with membrane treatments. Thus, plants and nitrogen together, not nitrogen alone, alter the soil microbiome via hitchhiking.

Nitrogen Cycle

10.1021/acs.jafc.3c07623

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Citations (2)

Fine location of theS-5locus responsible for wide compatibility in rice using SSR markers

Cereal Research Communications (2007)

Xiaoying ZHANG Yajun Chen Yang Wei Weizhong Lu Hong Liao

Bulked segregant analysis

Genetic linkage

10.1556/crc.35.2007.1.1

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Genetic mapping of bph20(t) and bph21(t) loci conferring brown planthopper resistance to Nilaparvata lugens Stål in rice (Oryza sativa L.)

Euphytica (2011)

Liang Yang Ruiding LI Y. R. Li Fengkuang Huang Yu-Hao Chen

Brown planthopper

Oryza rufipogon

Introgression

Oryza

10.1007/s10681-011-0437-7

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Citations (38)

Model Study of Segment Market on Internet of Vehicles Big Data

2022 Asia Conference on Algorithms, Computing and Machine Learning (CACML) (2022)

Huajun Wang Liang Yang Wenbin Wang Xiaolin Zhang

At present, there are many problems in China's commercial vehicle enterprise, such as large subjective judgment deviation and lack of scientific calculation method. In order to solve the above problems, this paper takes the data of internet of vehicles in June 2021 collected by heavy truck of a commercial vehicle based on GB/T 17691–2018 as the experimental sample, and mining the scientific calculation model and system of commercial vehicle market segment by using algorithms such as parking point analysis and processing, word segmentation processing, DBSCAN clustering and Apriori association. The experimental results show that the effectiveness and accuracy of the model are 98.18% and 94.4% respectively. At the same time, we designed a 100,000-magnitude platform technology scheme, which reached the enterprise-level usability requirements and verified the feasibility of the research method in this paper.

10.1109/cacml55074.2022.00096

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Identification and characterization of REC66, a Ty1-copia-like retrotransposon in the genome of red flower of Mirabilis jalapa L.

Archives of Biological Sciences (2016)

Jiang Shun-ri Liang Joshua Feng Haiyan Luo Dan Blake R. Shester

Mirabilis jalapa Lis the most commonly grown ornamental species of Mirabilis and is available in a range of brilliant colors. However, genetic research on Mirabilis jalapa Lis limited. Using fluorescent differential display (FDD) screening, we report the identification of a novel Ty1-copia-like retrotransposon in the genome of the red flower of Mirabilis jalapa L, and we named it REC66based on its sequence homology to the GAG protein from Ty1-copiaretrotransposon. Using degenerate primers based on the DNA sequence of REC66, a total of fourteen different variants in reverse transcriptase (RT) sequence were recovered from the genomic DNA. These RT sequences show a high degree of heterogeneity characterized mainly by deletion mutation; they can be divided into three subfamilies, of which the majority encode defective RT. This is the first report of a Ty1-copiaretrotransposon in Mirabilis jalapa L. The finding could be helpful for the development of new molecular markers for genetic studies, particularly on the origin and evolutionary relationships of M. jalapa L, and the study of Ty1-copiaretrotransposons and plant genome evolution in the genus Mirabilisor family Nyctaginaceae.

Retrotransposon

Homology

genomic DNA

10.2298/abs160326103j

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Construction of genomic DNA library of the mirror carp

Liang Yang

High molecular weight genomic DNA from the mirror carp was extracted and partially digested with Sau3A Ⅰ.9- 23kb DNA fragments were collected by 10% -40% sucrose gradient centrifugation and ligated into λDASH Ⅱ vector. Recombination DNA was packaged. The construction of the genomic DNA library in mirror carp was completed. 5 separated plaques were selected randomly. The extracted DNA was analyzed by the digestion of EcoR Ⅰ and BamH Ⅰ . The results show the recombination rate is 100% . The titer of the library is 108pfu/mL and according to the formula N = ln(l - P)/ln(l - f) , the genomic DNA library consists 99% genome of mirror carp. The Southern blot were carried out with the probe of common carp IGF - Ⅱ in the library. Many positive clones proved that this is a completed genomic DNA library of mirror carp.

genomic DNA

Southern blot

Source

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Mice and Men: Their Promoter Properties

PLoS Genetics (2006)

Vladimir B. Bajić Sin Lam Tan Alan Christoffels Christian Schönbach Leonard Lipovich

Using the two largest collections of Mus musculus and Homo sapiens transcription start sites (TSSs) determined based on CAGE tags, ditags, full-length cDNAs, and other transcript data, we describe the compositional landscape surrounding TSSs with the aim of gaining better insight into the properties of mammalian promoters. We classified TSSs into four types based on compositional properties of regions immediately surrounding them. These properties highlighted distinctive features in the extended core promoters that helped us delineate boundaries of the transcription initiation domain space for both species. The TSS types were analyzed for associations with initiating dinucleotides, CpG islands, TATA boxes, and an extensive collection of statistically significant cis-elements in mouse and human. We found that different TSS types show preferences for different sets of initiating dinucleotides and cis-elements. Through Gene Ontology and eVOC categories and tissue expression libraries we linked TSS characteristics to expression. Moreover, we show a link of TSS characteristics to very specific genomic organization in an example of immune-response-related genes (GO:0006955). Our results shed light on the global properties of the two transcriptomes not revealed before and therefore provide the framework for better understanding of the transcriptional mechanisms in the two species, as well as a framework for development of new and more efficient promoter- and gene-finding tools.

CpG site

Homo sapiens

TATA box

Transcription

10.1371/journal.pgen.0020054

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Citations (120)

Efficient plant genome engineering using a probiotic sourced CRISPR-Cas9 system

Nature Communications (2023)

Zhaohui Zhong Guanqing Liu Zhongjie Tang Shuyue Xiang Liang Yang

Abstract Among CRISPR-Cas genome editing systems, Streptococcus pyogenes Cas9 (SpCas9), sourced from a human pathogen, is the most widely used. Here, through in silico data mining, we have established an efficient plant genome engineering system using CRISPR-Cas9 from probiotic Lactobacillus rhamnosus . We have confirmed the predicted 5’-NGAAA-3’ PAM via a bacterial PAM depletion assay and showcased its exceptional editing efficiency in rice, wheat, tomato, and Larix cells, surpassing LbCas12a, SpCas9-NG, and SpRY when targeting the identical sequences. In stable rice lines, LrCas9 facilitates multiplexed gene knockout through coding sequence editing and achieves gene knockdown via targeted promoter deletion, demonstrating high specificity. We have also developed LrCas9-derived cytosine and adenine base editors, expanding base editing capabilities. Finally, by harnessing LrCas9’s A/T-rich PAM targeting preference, we have created efficient CRISPR interference and activation systems in plants. Together, our work establishes CRISPR-LrCas9 as an efficient and user-friendly genome engineering tool for diverse applications in crops and beyond.

Genome Engineering

10.1038/s41467-023-41802-9

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Citations (16)

Molecular determinants responsible for recognition of the single-stranded DNA regulatory sequence, χ, by RecBCD enzyme

Proceedings of the National Academy of Sciences (2012)

Naofumi Handa Liang Yang Mark S. Dillingham Ichizo Kobayashi Dale B. Wigley

The RecBCD enzyme is important for both restriction of foreign DNA and recombinational DNA repair. Switching enzyme function from the destructive antiviral state to the productive recombinational state is regulated by the recombination hotspot, χ (5′-GCTGGTGG-3′). Recognition of χ is unique in that it is recognized as a specific sequence within single-stranded DNA (ssDNA) during DNA translocation and unwinding by RecBCD. The molecular determinants of χ recognition and the subsequent alteration in function are unknown. Consequently, we mutated residues within the RecC subunit that comprise a channel where ssDNA is thought to be scanned for a χ sequence. These mutants were characterized in vivo with regard to χ recognition, UV-sensitivity, phage degradation, and recombination proficiency. Of 38 residues mutated, 11 were previously undescribed mutations that altered χ recognition. The mutants fell into two classes: five that failed to respond to χ, and six that suggested a relaxed specificity for χ recognition. The location of the first set of mutations defines a recognition structure responsible for sequence-specific binding of ssDNA. The second set defines a highly conserved structure, linked to the recognition structure, which we hypothesize regulates conversion of RecBCD from a molecular machine that destroys DNA to one that repairs it. These findings offer insight into the evolution of enzymes with alternate χ recognition specificities.

RecBCD

Recognition sequence

Sequence motif

10.1073/pnas.1206076109

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Citations (59)

Inorganic polyphosphates stimulate FGF23 expression through the FGFR pathway

Biochemical and Biophysical Research Communications (2012)

Ningyuan Sun Huawei Zou Liang Yang Koji Morita Ping Gong

Polyphosphate

10.1016/j.bbrc.2012.10.051

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Citations (9)