Article
Biochemistry & Molecular Biology
Chiara M. A. Cefalo, Teresa Mezza, Andrea Giaccari, Rohit N. Kulkarni
Summary: This study compared four methods for RNA extraction and found that the RNeasy MicroKit + Carrier (Qiagen) method provided the highest yield and purity.
Article
Plant Sciences
Oliver Berkowitz, Yue Xu, Lim Chee Liew, Yan Wang, Yanqiao Zhu, Bhavna Hurgobin, Mathew G. Lewsey, James Whelan
Summary: The research investigated the transcriptomes of different leaf tissues in Arabidopsis under various stress pathways, revealing a decrease in the overall number of expressed genes in response to stress stimuli. While no common stress response was identified, there was overlap of differentially expressed genes between tissues for individual treatments. Specific analysis indicated an interaction between auxin and ethylene in mediating retrograde signaling during mitochondrial dysfunction in the epidermis.
Article
Cell Biology
Xiaodan Zhang, Chuansheng Hu, Chen Huang, Ying Wei, Xiaowei Li, Miaomiao Hu, Hua Li, Ji Wu, Daniel M. Czajkowsky, Yan Guo, Zhifeng Shao
Summary: This method presents a robust approach for acquiring finely resolved transcriptional programs from clinical tissues using immunofluorescence-guided laser capture microdissection. It allows analysis of transcriptional networks and signaling pathways of specific cell types within native tissues. The use of a small molecule inhibitor, RVC, protects the RNA from degradation during the procedure.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Medicine, General & Internal
Melissa J. J. Alldred, Stephen D. D. Ginsberg
Summary: Single-cell and single-population RNA sequencing is a valuable tool in studying the transcriptomic profiles of neurons based on their spatial localization. Laser capture microdissection and RNA purification allow for the isolation of desired neurons for downstream analysis, such as differential gene expression and pathway exploration.
JOURNAL OF CLINICAL MEDICINE
(2023)
Article
Multidisciplinary Sciences
Min Chen, Jer-Young Lin, Xiaomeng Wu, Nestor R. Apuya, Kelli F. Henry, Brandon H. Le, Anhthu Q. Bui, Julie M. Pelletier, Shawn Cokus, Matteo Pellegrini, John J. Harada, Robert B. Goldberg
Summary: In this study, the transcriptomes of embryo proper and suspensor regions from different plant species were compared, revealing that genes involved in hormone synthesis and transport are mainly active in the giant scarlet runner bean and common bean suspensors, while genes controlling transcriptional regulation and cell division are primarily active in the embryo proper. Additionally, a set of suspensor- and embryo proper-specific transcription factors were identified, suggesting their involvement in early differentiation processes common to all plants.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Oncology
Quang Ong, Shingo Sakashita, Emi Hanawa, Naomi Kaneko, Masayuki Noguchi, Masafumi Muratani
Summary: The study conducted RNA-Seq and ChIP-Seq integrative analysis of clinical lung tissue samples to capture transcriptomic profiles and identify somatically altered regions marked by H3K4me3 in lung cancer. Differential expressions of cancer-related genes and enhancer activity annotations of cancer regulatory genes were observed near the altered H3K4me3 regions. The study demonstrated a practical workflow of using LMD on clinical samples for integrative analyses, improving the understanding of genetic and epigenetic dysregulation in malignancy.
Article
Biochemistry & Molecular Biology
Rita Costa Pires, Ana Ferro, Tiago Capote, Ana Usie, Barbara Correia, Gloria Pinto, Esther Menendez, Liliana Marum
Summary: This article introduces a technique of tissue isolation using laser microdissection, which is used to isolate specific plant cell types from woody tissues of cork oak and conduct RNA-Seq analysis. Through the optimized method, the molecular pathways associated with different developmental processes of xylem and phellem in oaks can be better understood.
MOLECULAR BIOTECHNOLOGY
(2023)
Article
Urology & Nephrology
Lihe Chen, Chun-Lin Chou, Mark A. Knepper
Summary: This study used a full-length, small-sample RNA-seq protocol to profile transcriptomes for all 14 renal tubule segments microdissected from mouse kidneys, identifying over 34,000 transcripts and 3709 segment-specific transcripts. Gene-expression patterns of solute carriers, transcription factors, and G protein-coupled receptors along the renal tubule were found to be important for segment-specific function.
JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
(2021)
Article
Genetics & Heredity
Hui-Hui Jia, Yuan-Tao Xu, Zhao-Ping Yin, Xiao-Meng Wu, Mei Qing, Yan-Jie Fan, Xin Song, Kai-Dong Xie, Zong-Zhou Xie, Qiang Xu, Xiu-Xin Deng, Wen-Wu Guo
Summary: Citrus nucellar poly-embryony is achieved through activation of ribosome biogenesis, protein degradation, and embryogenic development processes, while repressing auxin polar transport and increasing DNA methylation levels to regulate cell fate and NEI cell identity.
Article
Biochemical Research Methods
Daniel Almeida, Gustavo Turecki
Summary: The transcriptome of a cell plays a vital role in the complexity and heterogeneity of cell-types in the mammalian brain. However, using bulk-tissue homogenates makes it difficult to distinguish whether observed differences in gene expression are due to disease or cellular composition. Laser capture microdissection (LCM) is a strategy that allows for the capture of specific cell-types or regions of interest.
Article
Neurosciences
Regina T. Martuscello, Karthigayini Sivaprakasam, Whitney Hartstone, Sheng-Han Kuo, Genevieve Konopka, Elan D. Louis, Phyllis L. Faust
Summary: Through RNA sequencing analysis of the cerebellar cortex of essential tremor patients, we identified abnormal expression of genes and pathways related to tremor. These findings suggest that the pathogenesis of essential tremor may involve dysregulation of multiple cellular processes, and that essential tremor may be a family of disorders consisting of different types.
Article
Environmental Sciences
Shanshan Huang, Renlu Liu, Menglin Sun, Xiaofang Li, Yong Guan, Bin Lian
Summary: This study used RNA-Seq technology to reveal the molecular mechanism of microbial mineralization by Bacillus velezensis LB002 under cadmium pollution. The results showed that bacteria can induce mineralization by up-regulating specific genes, reducing Cd2+ toxicity and promoting bacterial growth.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Plant Sciences
Nathan M. Rowarth, Bruce A. Curtis, Anthony L. Einfeldt, John M. Archibald, Christian R. Lacroix, Arunika H. L. A. N. Gunawardena
Summary: Transcriptomic analysis of lace plant leaves revealed distinct gene expression profiles at different developmental stages and cell types, suggesting potential involvement of differential gene regulation in leaf remodeling and programmed cell death. The data generated from this study will be valuable for future research on plant leaf development and PCD.
Article
Environmental Sciences
Bingjian Cui, Chuncheng Liu, Chao Hu, Shengxian Liang
Summary: This study explores the physiological and gene expression characteristics of perennial ryegrass under cadmium (Cd) stress. High concentrations of Cd significantly inhibit the growth of ryegrass, while lower concentrations have minor effects. The activity levels of antioxidant enzymes increase in Cd-treated ryegrass leaves. The transcriptomic analysis identifies 1103 differentially expressed genes (DEGs) and reveals significant changes in molecular regulatory pathways.
Article
Obstetrics & Gynecology
Jiaqi Zhou, Lin Lin, Longping Liu, Jianbin Wang, Guoliang Xia, Chao Wang
Summary: The objective of this experimental study was to explore the dynamic transcriptional regulatory network of primordial follicle fate in obese mice and elucidate the potential mechanism of primordial follicle depletion. The study found that primordial follicle depletion was increased in obese mice, and it was associated with higher fat deposition and increased proliferation of granulosa cells. Furthermore, specific gene signatures associated with the primordial to primary follicle transition were identified in obese mice. The study also revealed that ferroptosis, a form of cell death, was a key pathway activated within immature ovarian follicles in the context of obesity.
FERTILITY AND STERILITY
(2023)
Article
Environmental Sciences
Wolde Tefera Beri, Weldemariam Seifu Gesessew, Shengke Tian
SCIENCE OF THE TOTAL ENVIRONMENT
(2020)
Article
Environmental Sciences
Wolde Tefera, Ting Liu, Lingli Lu, Jun Ge, Samuel M. Webb, Weldemariam Seifu, Shengke Tian
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2020)
Article
Plant Sciences
Ruohan Xie, Jianqi Zhao, Lingli Lu, Patrick Brown, Xianyong Lin, Samuel M. Webb, Jun Ge, Olga Antipova, Luxi Li, Shengke Tian
Article
Plant Sciences
Jie Zhang, Min Zhang, Haiyan Song, Jianqi Zhao, Sergey Shabala, Shengke Tian, Xiaoe Yang
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2020)
Article
Environmental Sciences
Lingling Xv, Jun Ge, Shengke Tian, Haixin Wang, Haiyue Yu, Jianqi Zhao, Lingli Lu
ENVIRONMENTAL POLLUTION
(2020)
Article
Environmental Sciences
Runze Wang, Dandi Hou, Jiuzhou Chen, Jiahao Li, Yingyi Fu, Sen Wang, Wei Zheng, Lingli Lu, Shengke Tian
ENVIRONMENT INTERNATIONAL
(2020)
Article
Environmental Sciences
Wolde Tefera, Lin Tang, Lingli Lu, Ruohan Xie, Weldemariam Seifu, Shengke Tian
Summary: This study elucidates the differences in bioaccessibility and toxicity of Cd in rice grains to humans, with significant variations among different cultivars, particularly the LA rice. Results indicate that LA rice is an effective agronomic approach to prevent Cd from entering the food chain and alleviate Cd toxicity in humans.
ENVIRONMENTAL POLLUTION
(2021)
Article
Environmental Sciences
Jun Ge, Shengke Tian, Haiyue Yu, Jianqi Zhao, Junwen Chen, Lijia Pan, Ruohan Xie, Lingli Lu
Summary: Sedum alfredii, a Cd/Zn hyperaccumulator native to China, showed high tolerance and accumulation ability to Mn while also significantly affecting the hyperaccumulation of Cd. High Mn exposure reduced the plant uptake of Cd, but at the same time increased its accumulation in the roots and shoots of the plant.
ENVIRONMENTAL POLLUTION
(2021)
Article
Plant Sciences
Haiyue Yu, Shengke Tian, Qianbin Huang, Jiuzhou Chen, Yuping Wu, Runze Wang, Lingli Lu
Summary: This study found that using insect-proof nets and insect- and rain-proof nets can effectively reduce Drosophila infestation in Chinese bayberry production, improving fruit growth and development while also reducing bacterial levels on the fruits. Therefore, the use of insect- and rain-proof nets is recommended for enhancing Chinese bayberry production and quality.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Agronomy
Di Liu, Rukhsanda Aziz, Md Jahidul Islam Shohag, Lingli Lu, Yuyan Wang, Ying Feng, Tingqiang Li, Mei Wang, Shengke Tian, Xiaoe Yang, Siyu Chen, Mingguang Tu, Zhiqiang Wang
Summary: Tetracycline has cytotoxic effects on human liver cells and extracellular ALT activity can be used as an indicator for monitoring soil TC contamination.
Article
Biology
Jun Ge, Jiayu Lin, Zhiying Wu, Kuan Xu, Jingyu Tao, Haizhong Lin, Shengke Tian, Lingli Lu
Summary: This study identified the function of SaPCR2 in the zinc uptake of S. alfredii through gene expression analysis and transgenic plant experiments. The results showed that SaPCR2 was highly expressed in the root elongation zone and significantly increased the zinc uptake in transgenic plants. Additionally, overexpression of SaPCR2 altered root morphology and inhibited root growth.
Article
Environmental Sciences
Jun Ge, Jingyu Tao, Jianqi Zhao, Zhiying Wu, Hewan Zhang, Yuxiao Gao, Shengke Tian, Ruohan Xie, Shengyang Xu, Lingli Lu
Summary: Sedum alfredii Hance, a Cd/Zn hyperaccumulator native to China, shows high tolerance to Pb, Cu, Ni, and Mn, making it valuable for phytoremediation of soils contaminated with multiple heavy metals. Transcriptomic analysis reveals unique and flexible strategies employed by this species in response to different heavy metals, with some genes found to be associated with heavy metal tolerance for the first time.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2022)
Article
Environmental Sciences
Jianqi Zhao, Ruohan Xie, Jiayu Lin, Lingling Xu, Xiaoyu Gao, Xianyong Lin, Shengke Tian, Lingli Lu
Summary: This study functionally characterized SaMT3 in the Cd/Zn hyperaccumulator S. alfredii. The C- and N-terminal regions of SaMT3 exhibited differential functional roles in Cd adaptation, with the C-terminal region involved in Cd sensing and binding and the N-terminal region responsible for ROS scavenging. Overexpression of SaMT3 increased Cd tolerance in transgenic plants, while knockout of SaMT3 led to decreased Cd concentrations and increased ROS levels. These findings provide valuable insights into the role of SaMT3 in Cd hyperaccumulation and the molecular mechanisms underlying Cd detoxification in plants.
ENVIRONMENTAL POLLUTION
(2022)
Article
Engineering, Environmental
Lingling Xu, Shengke Tian, Yan Hu, Jun Ge, Jianqi Zhao, Lingli Lu
Summary: This study found that Cd can improve the heat resistance of the hyperaccumulator plant Sedum alfredii. Cd penetrates the guard cells, restores stomatal function, and mitigates water loss under heat stress. Additionally, Cd activates antioxidant enzymes, promotes phytohormone biosynthesis, and upregulates a series of genes, enhancing the heat resistance of S. alfredii.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Environmental Sciences
Haiyun Xie, Jiuzhou Chen, Yabei Qiao, Kuan Xu, Zhi Lin, Shengke Tian
Summary: This study explores the effect of biofortification on soil cadmium (Cd) remediation using a fruit tree Sedum alfredii Hance and oil sunflower crop rotation and relay cropping mode. The results show that biofortification measures can significantly improve the Cd extraction effect and do not affect the safe production of crops. This has important guiding significance for Cd pollution remediation and safe production in farmland.