JOE R. DELANEY^*

BIOCELL, Vol.45, No.5, pp. 1167-1170, 2021, DOI:10.32604/biocell.2021.017296 - 12 July 2021

Abstract Single-cell sequencing data has transformed the understanding of biological heterogeneity. While many flavors of single-cell sequencing have been developed, single-cell RNA sequencing (scRNA-seq) is currently the most prolific form in published literature. Bioinformatic analysis of differential biology within the population of cells studied relies on inferences and grouping of cells due to the spotty nature of data within individual cell scRNA-seq gene counts. One biologically relevant variable is readily inferred from scRNA-seq gene count tables regardless of individual gene representation within single cells: aneuploidy. Since hundreds of genes are present on chromosome arms, high-quality inferences More >

Qi Zhang^1,#, Pengtao Li^2,#, Aiying Liu¹, Shaoqi Li¹, Quanwei Lu², Qun Ge¹, Junwen Li¹, Wankui Gong¹, Xiaoying Deng¹, Haihong Shang^1,3, Yuzhen Shi^1,*, Youlu Yuan^1,3,*

Phyton-International Journal of Experimental Botany, Vol.90, No.3, pp. 837-858, 2021, DOI:10.32604/phyton.2021.014437 - 30 March 2021

Abstract Cotton is the most widely cultivated commercial crop producing natural fiber around the world. As a critical trait for fiber quality, fiber strength principally determined during the secondary wall thickening period. Based on the developed BC₅F_3:5 CSSLs (chromosome segment substitution lines) from Gossypium hirsutum CCRI36 × G. barbadense Hai 1, the superior MBI9915 was chosen to construct the secondary segregated population BC₇F₂ with its recurrent parent CCRI36, which was subsequently subjected to Bulk segregant RNA-sequencing (BSR-seq) for rapid identification of candidate genes related to fiber strength. A total of 4 fiber-transcriptome libraries were separately constructed and sequenced, including… More >

TIANXIANG ZHANG^1,#, MEISHAN ZHANG^1,#, MINGHUI SHI^1,#, WEIJIANG JIN^1,#, SHUMIAO ZHANG^2,#, MENGYUAN FAN³, YIMENG LI¹, YUPING MENG², XUELIN TIAN⁴, SHUQIANG LIU^1,*, DEFU HU^1,*

BIOCELL, Vol.45, No.2, pp. 281-306, 2021, DOI:10.32604/biocell.2021.010277 - 19 February 2021

Abstract Male muskrats (Ondatra zibethicus L.) secrete musk from their scent glands during musk secretion season. Musk plays an important role as a communication pheromone during the breeding season. In this study, gas chromatography–mass spectrometry (GC–MS) was used to analyze the main components of musk. The GC–MS results after methyl esterification showed that 71.55% of the musk is composed of fatty acids. The other components of muskrat musk include cholesterol (9.31%) and other organics. Transcriptome comparison between musk secretion and non-secretion seasons showed significant changes in the scent glands for 53 genes involved in fatty acid and More >

Pengtao Li^1,2,#,*, Quanwei Lu^1,#, Xianghui Xiao³, Rui Yang³, Xixi Duan¹

Phyton-International Journal of Experimental Botany, Vol.90, No.1, pp. 129-144, 2021, DOI:10.32604/phyton.2021.012928 - 20 November 2020

Abstract Fiber length is a critical trait that principally determines cotton spinning quality, while Upland cotton as the most widely cultivated Gossypium species around the world subjects to the relatively ordinary fiber performance. Chromosome segment substitution lines (CSSLs) have been introduced in cotton breeding to take full advantages of superior fiber quality and high yield from Sea Island and Upland cotton, respectively, which serve as ideal materials for elucidating the genetic mechanism of complex quantitative traits. Here, three CSSLs derived from CCRI45 (G. hirsutum) × Hai1 (G. barbadense), two superior (MBI7561 and MBI7747) and one (MBI7285) with ordinary… More >

XIANLIANG HOU^1,2,3,#, DONGE TANG^1,#, FENGPING ZHENG^1,#, MINGLIN OU³, YONG XU¹, HUIXUAN XU¹, XIAOPING HONG⁴, XINZHOU ZHANG¹, WEIER DAI⁵, DONGZHOU LIU^4,*, YONG DAI^1,*

BIOCELL, Vol.44, No.4, pp. 559-582, 2020, DOI:10.32604/biocell.2020.011022 - 24 December 2020

Abstract Systemic lupus erythematosus (SLE) is a systemic autoimmune disease characterized by abnormal cellular and humoral immune responses and excessive autoantibody production. The precise pathologic mechanism of SLE remains elusive. The advent of single-cell RNA sequencing (scRNA-seq) enables unbiased analysis of the molecular differences of cell populations at the single-cell level. We used scRNA-seq to profile the transcriptomes of peripheral blood mononuclear cells from an SLE patient compared with a healthy control (HC). A total of 16,021 cells were analyzed and partitioned into 12 distinct clusters. The marker genes of each cluster and the four major… More >

Chongchong Yan¹, Qianqian Wang¹, Nan Zhang², Jiajia Wang¹, Xuexiang Ren¹, Bingjie Xue³, Xiaojing Pu⁴, Zhihong Xu⁴, Huajun Liao^1,*

Phyton-International Journal of Experimental Botany, Vol.89, No.3, pp. 561-586, 2020, DOI:10.32604/phyton.2020.010322 - 22 June 2020

Abstract Since potato cultivars are sensitive to low temperature, cold injury severely affects the geographical distribution and yield of potato. Although some miRNAs have been identified in response to cold stress in plants, there is no report about the role of miRNAs in the response to cold stress in potato. Here, via high throughput sequencing, we described the profiling of cold stress response to miRNA and mRNA in potato. Two small RNA and six mRNA libraries were constructed and sequenced. 296 known and 211 novel miRNAs were identified, in which 34 miRNAs in Cold Group (CG)… More >

Jingsen Liu^1,2, Jinqi Ma^1,2, Ai Lin^1,2, Chao Zhang^1,2, Bo Yang^1,2, Liyuan Zhang^1,2, Lin Huang^1,2, Jiana Li^1,2,*

Phyton-International Journal of Experimental Botany, Vol.89, No.2, pp. 253-273, 2020, DOI:10.32604/phyton.2020.09334 - 22 April 2020

Abstract Invertase (INV), a key enzyme in sucrose metabolism, irreversibly catalyzes the hydrolysis of sucrose to glucose and fructose, thus playing important roles in plant growth, development, and biotic and abiotic stress responses. In this study, we identified 27 members of the BnaINV family in Brassica napus. We constructed a phylogenetic tree of the family and predicted the gene structures, conserved motifs, cis-acting elements in promoters, physicochemical properties of encoded proteins, and chromosomal distribution of the BnaINVs. We also analyzed the expression of the BnaINVs in different tissues and developmental stages in the B. napus cultivar Zhongshuang 11 using qRT-PCR.… More >

Amin Einipour¹, Mohammad Mosleh^{1, *}, Karim Ansari-Asl^{1, 2}

CMES-Computer Modeling in Engineering & Sciences, Vol.122, No.1, pp. 377-397, 2020, DOI:10.32604/cmes.2020.08496 - 01 January 2020

Abstract The emergence of single-cell RNA-sequencing (scRNA-seq) technology has introduced new information about the structure of cells, diseases, and their associated biological factors. One of the main uses of scRNA-seq is identifying cell populations, which sometimes leads to the detection of rare cell populations. However, the new method is still in its infancy and with its advantages comes computational challenges that are just beginning to address. An important tool in the analysis is dimensionality reduction, which transforms high dimensional data into a meaningful reduced subspace. The technique allows noise removal, visualization and compression of high-dimensional data.… More >

Fan Feng¹, Tingting Xia¹, Runze Zhao¹, Mengyue Wang¹, Li Yang^1,*

Molecular & Cellular Biomechanics, Vol.16, Suppl.2, pp. 131-131, 2019, DOI:10.32604/mcb.2019.07211

Abstract Objective: To study the effects of different substrate stiffness on human hepatocytes using RNA sequencing (RNA-Seq) technology. The stiffness was corresponding to physiology and pathology stiffness of liver tissues.
Results: With the aid of RNA-Seq technology, our study characterizes the transcriptome of hepatocytes cultured on soft, moderate, stiff and plastic substrates. Compared to soft substrate, our RNA-Seq results revealed 1131 genes that were up-regulated and 2534 that were down-regulated on moderate substrate, 1370 genes that were up-regulated and 2677 down-regulated genes on stiff substrate. Functional enrichment analysis indicated that differentially expressed genes were associated with More >

Sufang Wang^1,2, Wenjuan Zhao^1,2, Guolin Shi^1,2, Nu Zhang^1,2, Chen Zhang^1,2, Hui Yang^1,2,*

Molecular & Cellular Biomechanics, Vol.16, Suppl.2, pp. 100-100, 2019, DOI:10.32604/mcb.2019.07112

Abstract Long-term space flight will be a major mission for International Space Administration. However, it has been shown that exposure to space flight result in immune system dysfunction. Therefore, understand the mechanism of immune response under microgravity condition is a key topic. Macrophage is one of the most important immune cells in human body, playing key roles in both innate and adaptive immune systems. In this research, we used mouse macrophages (RAW264.7) and collected samples at short-term (8 hour), mediate-term (24 hour) and long-term (48 hour) microgravity treatment. We measured cell proliferation, phagocytosis function and used More >