摘要：
Flowering time is an important improvement target in cotton breeding. The photoperiod is one of the significant factors affecting flowering in plant. Here, we conducted an exploration of how day length affects flowering and early maturating in upland cotton. After subjecting leaf samples of two cotton varieties, L19 (an early-maturity genotype) and L37 (a late-maturity genotype), to long-day (LD) and short-day (SD) conditions, we observed that the flowering time of both cotton varieties exhibited 7 - 11 days earlier under LD than SD. To investigate the underlying molecular mechanism, 8595 shared differentially expressed genes (DEGs) were identified in L19 and L37 based on transcriptome sequencing. Principal components analysis (PCA) showed the leaf stage and photoperiod treatment contributed the main differences between L19 and L37. KEGG analysis demonstrated that the DEGs were significantly enriched in circadian rhythms pathway and hormones signal transduction pathway, and the results of WGCNA further showed that green, darkgreen and lightgreen modules were significantly associated with day length. According to GO analysis, these DEGs in the three modules were involved in photoperiod related biological process such as rhythmic process, long-day photoperiodism and flowering process. A total of 75 hub genes were determined associated with each leaf developmental stage, and 8 genes were related to photoperiodic flowering pathway, including GhTOC1 , GhCCA1/LHY and GhFKF1 , etc. Finally, GhFKF1 , one of the hub genes, which highly expressed under long-day conditions, were selected for functional verification by virus induced gene silencing (VIGS). The results showed the flowering time of the silenced plants was delayed by 4.62 days. qPCR analysis indicated the expression of GhFKF1 in silenced plants was significantly reduced compared with the control and the expression levels of downstream genes GhFT and GhCO also decrease accordingly. Our research provides fresh insights into the molecular mechanisms of photoperiodic pathwaydepended flowering in cotton.
摘要：
Proline biosynthesis and catabolism pathways are executed by powerful action of specific enzymes that are subjected to environmental fluctuations at the transcriptional level. Previous researches have demonstrated that osmotic stress-induced upstream events can affect the expression of proline metabolism-related genes, which results in adjustable free proline accumulation to protect plant cells from severe damage. Here, we mainly describe the mechanisms for how some key factors, such as transcription factors, ABA (abscisic acid), Ca(2+), MAPK cascades, CK (cytokinin) and phospholipase, in a phosphorylated manner, vividly function in the transcriptional regulation of proline metabolism under osmotic stress. These mechanisms reveal that sustaining of proline homeostasis is an efficient way for plants to adapt to osmotic stress.
通讯机构：
[Zhi Liu] C;[Junhua Chen] N;National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China<&wdkj&>College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
摘要：
We successfully constructed several cascaded molecular logic gates (2INHIBIT-2AND, 2AND-2OR, and 2OR-2INHIBIT) using three different antibiotics as the inputs. In the presence of kanamycin (KAN), chloramphenicol (CHL), or oxytetracycline (OXY), the aptamer-antibiotic recognition will release the trigger DNA to active the hairpin DNA hybridization. Exonuclease III (Exo III)-mediated catalysis reaction was introduced in the logic system to generate Mg2+-dependent DNAzyme, which was used to cleave the fluorescence signal reporter probe. For input, the presence and absence of the antibiotic was defined as 1 and 0, respectively. For output, the fluorescence intensity higher or lower than the threshold value was defined as 1 and 0, respectively. In the 2INHIBIT-2AND logic circuit, the 101 input combination generates an output of 1 and other input combinations generate an output of 0. In the 2AND-2OR logic circuit, the input combinations of 001, 011, 110, 101, and 111 generate an output of 1 and other input combinations generate an output of 0. In the 2OR-2INHIBIT logic circuit, the input combinations of 010, 100, and 110 generate an output of 1 and other input combinations generate an output of 0. Our constructed logic system exhibits high selectivity and can work even in complex water samples. With the advantages of multiple biocomputation capabilities, high flexibility, and easy scalability, this logic gate system provides a new analytical method for the intelligent detection of different antibiotics.
期刊：
Science of The Total Environment,2023年881:163465 ISSN：0048-9697
通讯作者：
Zhi Liu<&wdkj&>Junhua Chen
作者机构：
[Liu, Zhi; Pan, Jiafeng; Deng, Fang] Hunan Agr Univ, Coll Biosci & Biotechnol, Changsha 410128, Peoples R China.;[Chen, Manjia; Pan, Jiafeng; Deng, Fang; Chen, Junhua] Guangdong Acad Sci, Natl Reg Joint Engn Res Ctr Soil Pollut Control &, Guangdong Key Lab Integrated Agroenvironm Pollut C, Inst Ecoenvironm & Soil Sci, Guangzhou 510650, Peoples R China.;[Liu, Chengshuai; Chen, Manjia] Guangdong Lab Lingnan Modern Agr, Guangzhou 510642, Peoples R China.;[Liu, Chengshuai] Chinese Acad Sci, Inst Geochem, State Key Lab Environm Geochem, Guiyang 550081, Peoples R China.
通讯机构：
[Zhi Liu] C;[Junhua Chen] N;National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China<&wdkj&>College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
摘要：
Polychlorinated biphenyls (PCBs) are ubiquitous persistent organic pollutants that cause harmful effects on environmental safety and human health. There is an urgent need to develop an intelligent method for PCBs sensing. In this work, we proposed a logic gate biosensing platform for simultaneous detection of multiple PCBs. 2,3',5,5'-tetrachlorobiphenyl (PCB72) and 3,3',4,4'-tetrachlorobiphenyl (PCB77) were used as the two inputs to construct biocomputing logic gates. We used 0 and 1 to encode the inputs and outputs. The aptamer was used to recognize the inputs and release the trigger DNA. A catalytic hairpin assembly (CHA) module is designed to convert and amplify each trigger DNA into multiple programmable DNA duplexes, which initiate the trans-cleavage activity of CRISPR/Cas12a for the signal output. The activated Cas12 cleaves the BHQ-Cy5 modified single-stranded DNA (ssDNA) to yield the fluorescence reporting signals. In the YES logic gate, PCB72 was used as the only input to carry out the logic operation. In the OR, AND, and INHIBIT logic gates, PCB72 and PCB77 were used as the two inputs. The output signals can be visualized by the naked eye under UV light transilluminators or quantified by a microplate reader. Our constructed biosensing platform possesses the merits of multiple combinations of inputs, intuitive digital output, and high flexibility and scalability, which holds great promise for the intelligent detection of different PCBs.
通讯机构：
[Chen, Junhua] N;National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China. Electronic address:
摘要：
The frequent emergence of SARS-CoV-2 variants increased viral transmissibility and reduced protection afforded by vaccines. The rapid, multichannel, and intelligent screening of variants is critical to minimizing community transmissions. DNA molecular logic gates have attracted wide attention in recent years due to the powerful information processing capabilities and molecular data biocomputing functions. In this work, some molecular switches (MSs) were connected with each other to implement arbitrary binary functions by emulating the threshold switching of MOS transistors and the decision tree model. Using specific sequences of different SARS-CoV-2 variants as inputs, the MSs net was used to build several molecular biocomputing circuits, including NOT, AND, OR, INHIBIT, XOR, half adder, half subtractor, full adder, and full subtractor. Four fluorophores (FAM, Cy3, ROX, and Cy5) were employed in the logic systems to realize the multichannel monitoring of the logic operation results. The logic response is fast and can be finished with 10 min, which facilitates the rapid wide-population screening for SARS-CoV-2 variants. Importantly, the logic results can be directly observed by the naked eye under a portable UV lamp, thus providing a simple and intelligent method to enable high-frequency point-of-care diagnostics, particularly in low-resource communities.
通讯机构：
[Junhua Chen] N;National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
关键词：
CRISPR-Cas12a;Catalytic hairpin assembly;DNAzyme;Heavy metal ions;Intelligent sensing;Logic gate
摘要：
We successfully constructed several molecular logic gates using heavy metal ions as inputs based on catalytic hairpin assembly (CHA) and CRISPR-Cas12a. The corresponding DNAzymes were used to recognize heavy metal ions (Hg(2+), Cd(2+), Pb(2+), and Mn(2+)). The specific cleavage between heavy metal ions and DNAzymes leads to the release of the trigger DNA, which can be used to activate CHA through logic computation. The CHA-generated DNA duplexes contain the protospacer adjacent motifs (PAM) sequence, which can be distinguished by CRISPR-Cas12a. The hybridization interactions between the duplexes and gRNA will activate the trans-cleavage capability of Cas12a, which can cleave the single-stranded DNA (ssDNA) reporter. The separation of the fluorescence group and quench group in ssDNA will generate a high fluorescence signal for readout. Using Hg(2+) and Cd(2+) as the two inputs, several basic logic gates were constructed, including OR, AND, and INHIBT. Using Hg(2+), Cd(2+), Pb(2+), and Mn(2+) as the four inputs, cascaded logic gates were further fabricated. With the advantages of scalability, versatility, and logic computing capability, our proposed molecular logic gates can provide an intelligent sensing system for heavy metal ions monitoring.
通讯机构：
[Zhi Liu] C;[Junhua Chen] N;College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China<&wdkj&>National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, China
摘要：
【目的】通过对陆地棉酰基辅酶A氧化酶(acyl coenzyme A oxidase,ACX)基因家族进行鉴定和表达分析,为后续研究ACX基因的功能奠定基础。【方法】采用生物信息学方法对陆地棉基因组中ACX基因家族成员进行鉴定,并系统分析其理化性质、基因结构、进化关系、基因复制、启动子区顺式作用元件和表达模式等。利用病毒诱导的基因沉默技术初步探究GhACX16基因的功能。【结果】陆地棉基因组中鉴定到20个ACX基因,分布在13条染色体上,聚类分析将其分为4个亚族。非同义突变率/同义突变率(K_a/K_s)分析结果表明陆地棉ACX家族基因经历了较强烈的纯化选择。ACX基因的启动子区含有热应激、干旱、植物激素响应等相关的顺式作用元件。非生物胁迫下的表达模式分析结果显示,陆地棉ACX基因明显响应高温、低温、盐和模拟干旱胁迫;分析高温胁迫下耐高温与高温敏感棉花材料不同发育时期的花药中ACX基因的表达模式,发现GhACX5和GhACX16基因的表达量变化明显。与阴性对照相比,高温胁迫下GhACX16基因沉默的棉苗表现出明显的耐高温特征,且叶片中脯氨酸含量、叶绿素含量和过氧化氢酶活性显著升高,而丙二醛含量显著降低。【结论】陆地棉ACX基因的鉴定及表达模式分析表明,ACX基因广泛参与非生物胁迫响应;经基因沉默试验和生理生化分析初步推测其中的GhACX16基因可能在高温胁迫响应中发挥重要的功能。
通讯机构：
[Tian, Y.; Liu, H.] C;College of Bioscience and Biotechnology, China
关键词：
Lilii Bulbus;Boiling process;Total polysaccharide;heavy metal;Edible Chinese herb medicine
摘要：
<jats:p><jats:italic>Lilii Bulbus</jats:italic>, an edible Chinese herbal medicine, has a long history in medicine. However, research on effectively boiling <jats:italic>Lilii Bulbus</jats:italic> is rare. To make the more nutritious <jats:italic>Lilii Bulbus</jats:italic> soup, the optimized boiling process, using an alternate heating mode by decoction pot carrying a mixture of water and Chinese liquor at the ration of 9:1, was established in this study. Compared to the soup prepared by the daily process, the polysaccharide amount improved by 54%, and the total heavy metals decreased by 33.5% using the optimized boiling process. In addition, the total saponins at 34.3 μg/g were determined in the soup prepared by the optimized process. Meanwhile, the colchicine content in the boiled <jats:italic>Lilii Bulbus</jats:italic> soup was undetectable using the optimized process. This research performs an optimized boiling process for making <jats:italic>Lilii Bulbus</jats:italic> soup, and provides a reference for generating high commercial value from <jats:italic>Lilii Bulbus</jats:italic> soup in the future.</jats:p>
摘要：
Two fragments of the COVID-19 genome (specific and homologous) were used as two inputs to construct an AND logic gate for COVID-19 detection based on exonuclease III and DNAzyme. The detection sensitivity of the assay can reach fM levels. Satisfactory recovery values were obtained in real sample analysis.
摘要：
Cotton fibers are the main raw materials of the textile industry. Exogenous superior fiber genes have been introduced into upland cotton to develop high-yield cultivars with excellent fiber quality. We used a single chromosomal segment on the chromosome A07 substitution line SL7, with high fiber strength, to investigate the molecular mechanism underlying its fiber quality. RNA-seq and KEGG analysis showed that 70 differentially expressed genes were enriched in plant hormone transduction pathways, including auxin, ethylene and abscisic acid, in fibers at 10 days post-anthesis (DPA). Among these, fiber-development related transcription factors MYB and NAC, including Gh_A11G0981 (MYB108), Gh_A03G0887 (NAC029), and Gh_A08G1691 (NAC021), were significantly upregulated in SL7, as were numerous cellulose synthase-like (CSL) genes involved in non-cellulose polysaccharide and cell wall synthesis. The hemicellulose content of SL7 was significantly higher than that of L22, an upland cotton cultivar. These results suggest that key genes in the introgressed chromosomal segment of SL7 regulate the expression of transcription-factor genes via hormone-transduction pathways, thereby inducing the expression of genes involved in secondary wall synthesis and ultimately improving fiber quality. This study has shed light on the molecular mechanism of fiber development and will contribute to the improvement of fiber quality of upland cotton by molecular breeding. (c) 2019 Crop Science Society of China and Institute of Crop Science, CAAS. Production and hosting by Elsevier B.V. on behalf of KeAi Communications Co., Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/
