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Identification of transition factors in myotube formation from proteome and transcriptome analyses
ZHENG Qi, HU Rong-cui, ZHU Cui-yun, JING Jing, LOU Meng-yu, ZHANG Si-huan, LI Shuang, CAO Hong-guo, ZHANG Xiao-rong, LING Ying-hui
2023, 22 (10): 3135-3147.   DOI: 10.1016/j.jia.2023.08.001
Abstract282)      PDF in ScienceDirect      

Muscle fibers are the main component of skeletal muscle and undergo maturation through the formation of myotubes.  During early development, a population of skeletal muscle satellite cells (SSCs) proliferate into myoblasts.  The myoblasts then undergo further differentiation and fusion events, leading to the development of myotubes.  However, the mechanisms involved in the transition from SSCs to myotube formation remain unclear.  In this study, we characterized changes in the proteomic and transcriptomic expression profiles of SSCs, myoblasts (differentiation for 2 d) and myotubes (differentiation for 10 d).  Proteomic analysis identified SLMAP and STOM as potentially associated with myotube formation.  In addition, some different changes in MyoD, MyoG, Myosin7 and Desmin occurred after silencing SLMAP and STOM, suggesting that they may affect changes in the myogenic marker.  GO analysis indicated that the differentiation and migration factors SVIL, ENSCHIG00000026624 (AQP1) and SERPINE1 enhanced the transition from SSCs to myoblasts, accompanied by changes in the apoptotic balance.  In the myoblast vs. myotube group, candidates related to cell adhesion and signal transduction were highly expressed in the myotubes.  Additionally, CCN2, TGFB1, MYL2 and MYL4 were identified as hub-candidates in this group.  These data enhance our existing understanding of myotube formation during early development and repair.

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IPM - Biological and integrated management of desert locust
LI Shuang, FENG Shi-qian, Hidayat ULLAH, TU Xiong-bing, ZHANG Ze-hua
2022, 21 (12): 3467-3487.   DOI: 10.1016/j.jia.2022.09.017
Abstract355)      PDF in ScienceDirect      

Locusts have caused periodic disasters in the recorded history of humankind.  Up to now, locust disaster is still the biggest threat to the world’s agricultural production.  The desert locust Schistocerca gregaria is one of the most harmful locusts, which has caused massive food crises, economic losses, and ecological disasters.  The desert locust is a migratory insect pest that occurs year-round in the tropic and subtropical regions.  Under the wind and seasonal alternation, it moves and flies in the African continent and West Asia.  Desert locust damages the stems and leaves of more than 300 plants, including Gramineae, Tribulus terrestris, and Euphorbiaceae.  Locusts cause devastating disasters to local plants, especially field crops, and significantly threaten food security.  To date, voluminous research has been conducted regarding the ecology and management of desert locusts.  This review represents an effort to summarize the basic information on the biology and ecology, distribution, damage, and economic impact of desert locusts, examine the recent developments in integrated locust management, and make recommendations for future research.  

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Transcriptional search to identify and assess reference genes for expression analysis in Solanum lycopersicum under stress and hormone treatment conditions
DUAN Yao-ke, HAN Rong, SU Yan, WANG Ai-ying, LI Shuang, SUN Hao, GONG Hai-jun
2022, 21 (11): 3216-3229.   DOI: 10.1016/j.jia.2022.07.051
Abstract338)      PDF in ScienceDirect      

Tomato (Solanum lycopersicum) is a model plant for research on fruit development and stress response, in which gene expression analysis is frequently conducted.  Quantitative PCR (qPCR) is a widely used technique for gene expression analysis, and the selection of reference genes may affect the accuracy of results and even conclusions.  Although there have been some frequently used reference genes in tomato, it has been shown that the expressions of some of these genes are not constant in different tissues and environmental conditions.  Moreover, little information on genomic identification of reference genes is available in tomato.  Here, we mined the publicly available transcriptional sequencing data and screened out fifteen candidate reference genes, and the expression stability of these candidate genes and seven traditionally used ones were evaluated under stress and hormone treatment.  The results showed that over half of the selected candidate references were housekeeping genes in tomato cells.  Among the candidate reference genes and the traditionally used ones, the most stably expressed genes varied under different treatments, and most of these genes were recommended as preferred reference genes at least once except Solyc04g009030 and Solyc07g066610, two traditionally used reference genes.  This study provides some novel reference genes in tomato, and the preferred reference genes under different environmental stimuli, which may be useful for future research.  Our study suggests that excavating stably expressed genes from transcriptome sequencing data is a reliable approach to screening reference genes for qPCR analysis.  

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Effects of long-term straw incorporation on nematode community composition and metabolic footprint in a rice–wheat cropping system
CHEN Yun-feng, XIA Xian-ge, HU Cheng, LIU Dong-hai, QIAO Yan, LI Shuang-lai, FAN Xian-peng
2021, 20 (8): 2265-2276.   DOI: 10.1016/S2095-3119(20)63435-9
Abstract156)      PDF in ScienceDirect      
Soil nematode communities can provide valuable information about the structure and functions of soil food webs, and are sensitive to agricultural practices, including short-term straw incorporation.  However, currently, such effects under long-term straw incorporation conditions at different fertility levels are largely unknown.  Thus, we conducted a 13-year ongoing experiment to evaluate the effects of long-term straw incorporation on the structure and functions of the soil food web in low and high fertility soils through analyzing its effects on nematode communities, food web indices and metabolic footprints.  Four treatments were included: straw removal (–S) under non-fertilized (–NPK) or fertilized (+NPK) conditions; and straw incorporation (+S) under –NPK or +NPK conditions.  Soil samples from a 0–20 cm depth layer were collected when wheat and rice were harvested.  Compared with straw removal, straw incorporation increased the abundances of total nematodes, bacterivores, plant-parasites and omnivores-predators, as well the relative abundances of omnivores-predators with increases of 73.06, 89.29, 95.31, 238.98, and 114.61% in –NPK soils and 16.23, 2.23, 19.01, 141.38, and 90.23% in +NPK soils, respectively.  Regardless of sampling times and fertilization effects, straw incorporation increased the diversity and community stability of nematodes, as indicated by the Shannon-Weaver diversity index and maturity index.  Enrichment and structure index did not show significant responses to straw incorporation, but a slight increase was observed in the structure index.  The analysis of nematode metabolic footprints showed that straw incorporation increased the plant-parasite footprint and structure footprint by 97.27 and 305.39% in –NPK soils and by 11.29 and 149.56% in +NPK soils, but did not significantly influence enrichment, bacterivore and fungivore footprints.  In conclusion, long-term straw incorporation, particularly under a low fertility level, favored the soil nematodes and regulated the soil food web mainly via a top-down effect.   
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Genome-wide pedigree analysis of elite rice Shuhui 527 reveals key regions for breeding
REN Yun, CHEN Dan, LI Wen-jie, TAO Luo, YUAN Guo-qiang, CAO Ye, LI Xue-mei, DENG Qi-ming, WANG Shi-quan, ZHENG Ai-ping, ZHU Jun, LIU Huai-nian, WANG Ling-xia, LI Ping, LI Shuang-cheng
2021, 20 (1): 35-45.   DOI: 10.1016/S2095-3119(20)63256-7
Abstract226)      PDF in ScienceDirect      
Hybrid rice significantly contributes to the food supply worldwide.  Backbone parents play important roles in elite hybrid rice breeding systems.  In this study, we performed pedigree-based analysis of the elite backbone parent rice variety, namely, Shuhui 527 (SH527, Oryza sativa), to exploit key genome regions during breeding.  Twenty-four cultivars (including SH527, its six progenitors and 17 derived cultivars) were collected and analyzed with high-density single nucleotide polymorphism (SNP) array.  Scanning all these cultivars with genome-wide SNP data indicated the unique contributions of progenitors to the SH527 genome and identified the key genomic regions of SH527 conserved within all its derivatives.  These findings were further supported by known rice yield-related genes or unknown QTLs identified by genome-wide association study.  This study reveals several key regions for SH527 and provides insights into hybrid rice breeding.
 
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Sclerotinia sclerotiorum virulence is affected by mycelial age via reduction in oxalate biosynthesis
WANG Ji-peng, XU You-ping, ZANG Xian-peng, LI Shuang-sheng, CAI Xin-zhong
2016, 15 (05): 1034-1045.   DOI: 10.1016/S2095-3119(15)61199-6
Abstract1607)      PDF in ScienceDirect      
Sclerotinia sclerotiorum is one of the most devastating necrotrophic phytopathogens.  Virulence of the hyphae of this fungus at different ages varies significantly.  Molecular mechanisms underlying this functional distinction are largely unknown.  In this study, we confirmed the effect of mycelial culture time/age on virulence in two host plants and elucidated its molecular and morphological basis.  The virulence of the S. sclerotiorum mycelia in plants dramatically decreases along with the increase of the mycelial age.  Three-day-old mycelia lost the virulence in plants.  Comparative proteomics analyses revealed that metabolism pathways were comprehensively reprogrammed to suppress the oxalic acid (OA) accumulation in old mycelia.  The oxaloacetate acetylhydrolase (OAH), which catalyzes OA biosynthesis, was identified in the S. sclerotiorum genome.  Both gene expression and protein accumulation of OAH in old mycelia were strongly repressed.  Moreover, in planta OA accumulation was strikingly reduced in old mycelia-inoculated plants compared with young vegetative mycelia-inoculated plants.  Furthermore, supply with 10 mmol L–1 OA enabled the old mycelia infect the host plants, demonstrating that loss of virulence of old mycelia is mainly caused by being unable to accumulate OA.  Additionally, aerial mycelia started to develop from 0.5-day-old vegetative mycelia and dominated over 1-day-old mycelia grown on potato dextrose agar plates.  They were much smaller in hypha diameter and grew significantly slower than young vegetative mycelia when subcultured, which did not maintain to progenies.  Collectively, our results reveal that S. sclerotiorum aerial hyphae-dominant old mycelia fail to accumulate OA and thereby lose the virulence in host plants.
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Enhanced resistance to Botrytis cinerea and Rhizoctonia solani in transgenic broccoli with a Trichoderma viride endochitinase gene
YU Ya, ZHANG Lei, LIAN Wei-ran, XU Feng-feng, LI Shuang-tao, XIANG Juan, ZHANG Guo-zhen, HU Zan-min, ZHAO Bing, REN Shu-xin, GUO Yang-dong
2015, 14 (3): 430-437.   DOI: 10.1016/S2095-3119(14)60919-9
Abstract2010)      PDF in ScienceDirect      
A endochitinase gene (Tch) from the fungus Trichoderma viride was introduced into broccoli (Brassica oleracea var. italica) by Agrobacterium-mediated transformation. Sixty-eight putative transformants were obtained and the presence of the Tch gene was confirmed by both PCR and Southern blot analysis. RT-PCR analysis showed an accumulation of the transcript encoding the endochitinase protein in the transgenic plants. Using real-time quantitative PCR, the expression profiling of endochitinase gene was analyzed. Primary transformants and selfed progeny were examined for expression of the endochitinase using a fluorometric assay and for their resistance to the pathogenic fungi Botrytis cinerea and Rhizoctonia solani. The endochitinase activities in T0 in vitro plants, T0 mature plants and T1 mature plants were correlated with leaf lesions, and the transgenic line T618 had high endochitinse activities of 102.68, 114.53 and 120.27 nmol L–1 MU min–1 mg–1 protein in the three kinds of plants, respectively. The endochitinase activity showed a positive correlation with the resistance to the pathogens. Most transgenic T0 broccoli had increased resistance to the pathogens of B. cinerea and R. solani in leaf assays and this resistance was confirmed to be inheritable. These findings suggested that expression of the Tch gene from T. viride could enhance resistance to pathogenic fungi in Brassica species.
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Study on the Mitochondrial Genome of Sea Island Cotton (Gossypium barbadense) by BAC Library Screening
SU Ai-guo, LI Shuang-shuang, LIU Guo-zheng, LEI Bin-bin, KANG Ding-ming, LI Zhao-hu, MA
2014, 13 (5): 945-953.   DOI: 10.1016/S2095-3119(13)60595-X
Abstract1968)      PDF in ScienceDirect      
The plant mitochondrial genome displays complex features, particularly in terms of cytoplasmic male sterility (CMS). Therefore, research on the cotton mitochondrial genome may provide important information for analyzing genome evolution and exploring the molecular mechanism of CMS. In this paper, we present a preliminary study on the mitochondrial genome of sea island cotton (Gossypium barbadense) based on positive clones from the bacterial artificial chromosome (BAC) library. Thirty-five primers designed with the conserved sequences of functional genes and exons of mitochondria were used to screen positive clones in the genome library of the sea island cotton variety called Pima 90-53. Ten BAC clones were obtained and verified for further study. A contig was obtained based on six overlapping clones and subsequently laid out primarily on the mitochondrial genome. One BAC clone, clone 6 harbored with the inserter of approximate 115 kb mtDNA sequence, in which more than 10 primers fragments could be amplified, was sequenced and assembled using the Solexa strategy. Fifteen mitochondrial functional genes were revealed in clone 6 by gene annotation. The characteristics of the syntenic gene/exon of the sequences and RNA editing were preliminarily predicted.
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Nitrogen Use Efficiency as Affected by Phosphorus and Potassium in Long-Term Rice and Wheat Experiments
DUAN Ying-hua, SHI Xiao-jun, LI Shuang-lai, SUN Xi-fa , HE Xin-hua
2014, 13 (3): 588-596.   DOI: 10.1016/S2095-3119(13)60716-9
Abstract1801)      PDF in ScienceDirect      
Improving nitrogen use efficiency (NUE) and decreasing N loss are critical to sustainable agriculture. The objective of this research was to investigate the effect of various fertilization regimes on yield, NUE, N agronomic efficiency (NAE) and N loss in long-term (16- or 24-yr) experiments carried out at three rice-wheat rotation sites (Chongqing, Suining and Wuchang) in subtropical China. Three treatments were examined: sole chemical N, N+phosphorus (NP), and NP+potassium (NPK) fertilizations. Grain yields at three sites were significantly increased by 9.3-81.6% (rice) and 54.5-93.8% (wheat) under NP compared with N alone, 1.7-9.8% (rice) and 0-17.6% (wheat) with NPK compared with NP. Compared to NP, NUE significantly increased for wheat at Chongqing (9.3%) and Wuchang (11.8%), but not at Suining, China. No changes in NUE were observed in rice between NP and NPK at all three sites. The rice-wheat rotation’s NAE was 3.3 kg kg-1 higher under NPK than under NP at Chongqing, while NAE was similar for NP and NPK at Suining and Wuchang. We estimated that an uptake increase of 1.0 kg N ha-1 would increase 40 kg rice and 30 kg wheat ha-1. Nitrogen loss/input ratios were ~60, ~40 or ~30% under N, NP or NPK at three sites, indicating significant decrease of N loss by P or PK additions. We attribute part of the increase in NUE soil N accumulation which significantly increased by 25-55 kg ha-1 yr-1 under NPK at three sites, whereas by 35 kg ha-1 yr-1 under NP at Chongqing only. This paper illustrates that apply P and K to wheat, and reduce K application to rice is an effective nutrient management strategy for both the NUE improvement and N losses reduction in China.
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