Article
Plant Sciences
Juncheng Zhang, Huan Mei, Hejun Lu, Rui Chen, Yan Hu, Tianzhen Zhang
Summary: By integrating a large number of samples and time points, this study reveals the genetic basis of fiber quality differences between Gossypium hirsutum and Gossypium barbadense. Key genes involved in fiber development were identified, providing a theoretical basis for breeding high-quality cotton and gene function analysis.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Marina Naoumkina, Gregory N. Thyssen, David D. Fang, Christopher B. Florane, Ping Li
Summary: In this study, it was found that the elongation of fiber cells in the Ligon lintless-2 (Li-2) cotton mutant is inhibited by siRNAs. This inhibition is caused by a large structural rearrangement at the end of chromosome D13, which leads to the production of self-complementary transcripts and generation of siRNAs. This finding reveals the regulatory mechanism of the Ran Binding Protein 1 family in cotton fiber growth.
Article
Biology
Madeleine Birgersson, Rajitha Indukuri, Linnea Lindquist, Lina Stepanauskaite, Qing Luo, Qiaolin Deng, Amena Archer, Cecilia Williams
Summary: By analyzing the genome-wide binding, gene regulation, and interaction between ERβ and LRH-1, this study provides a genome-wide mechanistic understanding of ovarian physiology and fertility.
Article
Plant Sciences
Sudthana Khlaimongkhon, Sriprapai Chakhonkaen, Keasinee Tongmark, Numphet Sangarwut, Natjaree Panyawut, Thiwawan Wasinanon, Kannika Sikaewtung, Samart Wanchana, Chareerat Mongkolsiriwatana, Julapark Chunwonges, Amorntip Muangprom
Summary: Rice is a crucial food crop for nearly half of the world's population, and its grain yields are affected by temperature changes. Thermosensitive genic male sterility (TGMS) rice is sterile at high temperatures and fertile at low temperatures, making it a good model for studying the effects of temperature on male development. Transcriptomic analysis revealed differential gene expression in TGMS rice panicles under sterile and fertile conditions, with some genes showing unique responses to temperature in TGMS plants compared to wild-type rice. These findings provide insights into the molecular mechanisms controlling TGMS and rice responses to temperature alterations.
Article
Plant Sciences
Yang Liu, Xiaomei Fang, Tian Tang, Yudong Wang, Yinhuan Wu, Jinyu Luo, Haotian Wu, Yingqian Wang, Jian Zhang, Renwu Ruan, Meiliang Zhou, Kaixuan Zhang, Zelin Yi
Summary: This study sequenced the transcriptome of common buckwheat and Ukrainian daliqiao using high-throughput sequencing technology, obtaining a large amount of gene information and differentially expressed genes. SSR and EST-SSR loci were also detected. The clustering results verified the genetic relationship between common buckwheat and Ukrainian daliqiao. These findings are important for enriching the genetic information and marker-assisted selection breeding of buckwheat.
Article
Entomology
Guan-Feng Xu, Cheng-Cheng Gong, Hao Lyu, Hui-Min Deng, Si-Chun Zheng
Summary: This study investigated the gene expression control of Bombyx mori embryonic development stages using RNA sequencing, identifying key genes related to DNA replication, transcription, and various developmental pathways. The findings indicate distinct gene expression patterns in early and late embryos, with a focus on organogenesis. These results enhance our understanding of the molecular mechanisms underlying embryonic development and B. mori regulation.
Article
Biochemistry & Molecular Biology
Zhiquan Fan, Guanwen Huang, Yourong Fan, Jiangyi Yang
Summary: Compared with annual crops, perennial crops with longer growing seasons and deeper root systems can fix more sunlight energy, reducing soil erosion and saving water, fertilizer, and pesticides. Oryza longistaminata (OL), a rhizomatous wild rice with an AA genome, shows strong resistance to biotic and abiotic factors, making it an ideal donor material for perennial rice breeding. Sucrose of appropriate concentrations promotes the sprout of basal axillary buds and subsequent rhizome development in OL. Comparative transcriptome analysis reveals that the boost in sucrose to rhizome elongation is due to the hydrolyzed glucose and fructose from absorbed sucrose, which increases osmotic pressure and promotes water absorption.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Xu Shi, Xiao Wang, Andrew F. Neuwald, Leena Halakivi-Clarke, Robert Clarke, Jianhua Xuan
Summary: BayesDenovo addresses the challenge of de novo transcriptome assembly by accurately reconstructing splicing graphs using a read-guided and Bayesian strategy, achieving higher accuracy and reducing false positives, especially for alternatively spliced genes and highly/lowly expressed transcripts. Additionally, it is more robust on multiple replicates and can identify phenotype-specific transcripts associated with breast cancer recurrence.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
August Guang, Mark Howison, Felipe Zapata, Charles Lawrence, Casey W. Dunn
Summary: treeinform is a method that utilizes phylogenetic information across species to improve transcriptome assemblies within species. It helps identify and correct the error of mistaking different transcripts of the same gene as transcripts from multiple closely related genes.
Article
Biochemical Research Methods
Qianqian Zhang, Xing Xu, Li Lin, Jian Yang, Xing Na, Xin Chen, Lingling Wu, Jia Song, Chaoyong Yang
Summary: Cilo-seq is a high-performance platform for single-cell RNA sequencing library construction. It utilizes digital microfluidics in a single device, enabling convenient single-cell isolation, efficient nucleic acid amplification, low-loss nucleic acid purification, and high-quality library preparation.
Article
Multidisciplinary Sciences
Chaoqiong Ding, Xiang Yan, Mengying Xu, Ran Zhou, Yuancun Zhao, Dan Zhang, Zongyao Huang, Zhenzhong Pan, Peng Xiao, Huifang Li, Lu Chen, Yuan Wang
Summary: This study reports the full-length transcriptome of mouse neural stem cells (NSCs) at different developmental stages, providing an important resource for studying NSC fate determination, neural development, and disease in the neuroscience community.
Article
Plant Sciences
Chen Sheng, Shengnan Song, Wangyi Zhou, Senouwa Segla Koffi Dossou, Rong Zhou, Yanxin Zhang, Donghua Li, Jun You, Linhai Wang
Summary: This study conducted a comprehensive transcriptome analysis on two sesame varieties and identified key genes related to plant height development. The regulatory network controlling plant height was revealed, providing valuable genetic resources for optimizing plant architecture in sesame.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Article
Cell Biology
Di Wu
Summary: The germinal vesicle (GV) stage is a critical transition point in mammalian oocyte development that determines oocyte quality through active RNA degradation and transcriptome reprofiling. Oocyte RNA-seq has revealed differences between non-surrounded nucleolus (NSN) and surrounded nucleolus (SN) phases. Single oocyte RNA-seq (soRNA-seq) shows higher reproducibility and a better illustration of gene changes during oocyte development.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Yuefen Cao, Hui Huang, Yanjun Yu, Huaqin Dai, Huanfeng Hao, Hua Zhang, Yurong Jiang, Mingquan Ding, Feifei Li, Lili Tu, Zhaosheng Kong, Junkang Rong
Summary: The dynamic remodeling of the actin cytoskeleton plays a central role in cotton fiber elongation. In the Li-1 mutant, over-expression of GhACT17DM disrupts actin polymerization, affecting the establishment and dynamics of the actin cytoskeleton, resulting in defective fiber elongation and the overall dwarf and twisted phenotype.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Lin Chen, Maomao Yun, Zhenqiang Cao, Zhaojun Liang, Wenrui Liu, Min Wang, Jinqiang Yan, Songguang Yang, Xiaoming He, Biao Jiang, Qingwu Peng, Yu'e Lin
Summary: This study evaluated the changes in male flower development in cucumber under normal and heat stress conditions. It was found that heat stress led to decreased pollen fertility, abnormal tapetum and microspores, and significant changes in gene expression related to carbohydrate metabolism. Additionally, a co-expression network analysis revealed specific hub genes associated with heat stress response.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Genetics & Heredity
Mingquan Ding, Wuwei Ye, Lifeng Lin, Shae He, Xiongming Du, Aiqun Chen, Yuefen Cao, Yuan Qin, Fen Yang, Yurong Jiang, Hua Zhang, Xiyin Wang, Andrew H. Paterson, Junkang Rong
Article
Biochemistry & Molecular Biology
Yurong Jiang, Mingquan Ding, Yuefen Cao, Fen Yang, Hua Zhang, Shae He, Huaqin Dai, Huanfeng Hao, Junkang Rong
MOLECULAR GENETICS AND GENOMICS
(2015)
Article
Plant Sciences
Yuefen Cao, Yurong Jiang, Mingquan Ding, Shae He, Hua Zhang, Lifeng Lin, Junkang Rong
PLANT CELL REPORTS
(2015)
Article
Multidisciplinary Sciences
Wei Zhou, Shasha Wu, Mingquan Ding, Jingjuan Li, Zhaobin Shi, Wei Wei, Jialian Guo, Hua Zhang, Yurong Jiang, Junkang Rong
Article
Biochemistry & Molecular Biology
Mingquan Ding, Jiadong Chen, Yurong Jiang, Lifeng Lin, YueFen Cao, Minhua Wang, Yuting Zhang, Junkang Rong, Wuwei Ye
MOLECULAR GENETICS AND GENOMICS
(2015)
Article
Genetics & Heredity
Yunzheng Miao, Siqing Yang, Yurong Jiang, Junkang Rong, Jinsheng Yu
JOURNAL OF GENETICS
(2018)
Article
Genetics & Heredity
Xiangge Meng, Chengping Li, Yu Hei, Xiang Zhou, Guoli Zhou
Summary: The study used IVT-SAPAS sequencing to analyze the dynamic changes of APA sites during adipogenesis in bovine subcutaneous preadipocytes and intramuscular preadipocytes. The results showed that APA plays an important role in adipocyte differentiation, and UTR-APA switching genes have different trends, with intramuscular preadipocytes tending to use shorter 3'UTR for differentiation. TRIB3, WWTR1, and INSIG1 play important roles in intramuscular preadipocyte differentiation.
Article
Genetics & Heredity
S. Alizadeh, S. Khamse, N. Tajeddin, H. R. Khorram Khorshid, A. Delbari, M. Ohadi
Summary: This study identifies a specific genotype at a CG-rich trinucleotide short tandem repeat (STR) locus that is associated with late-onset neurocognitive disorders such as Alzheimer's disease (AD).
Article
Genetics & Heredity
Shougang Liu, Zhe Zhuang, Fanghua Liu, Xiuqing Yuan, Zeqiao Zhang, Xiaoqian Liang, Xinhui Li, Yongfeng Chen
Summary: This study investigated the effect and mechanism of RPL9 and TIFA in scalp psoriasis, and identified RPL9 as a potential therapeutic target for scalp psoriasis.
Article
Genetics & Heredity
Shiting Wang, Jiaqi Chen, Zhichao Jin, Ying Xing, Ruiping Wang
Summary: This study suggests a causal association between hair color and skin cancers, with light hair colors (red, blonde, and light brown) being associated with an increased risk and dark brown hair being associated with a decreased risk.
Article
Genetics & Heredity
Joseph Hawadak, Loick Pradel Kojom Foko, Rodrigue Roman Dongang Nana, Karmveer Yadav, Veena Pande, Aparup Das, Vineeta Singh
Summary: This study investigates the genetic diversity and natural selection of the Pfama-1 gene in Plasmodium falciparum isolates from Cameroon. The study finds a considerable nucleotide and haplotype diversity, as well as specific mutations in Cameroonian isolates. Positive diversifying selection and the identification of selected codon sites suggest the potential implication of these genetic variations in host immune pressure and parasite-binding complex modulation. The findings provide valuable baseline data for malaria vaccine design.
Article
Genetics & Heredity
Emily Biernat, Mansi Verma, Chhabi K. Govind
Summary: RSC is an essential ATP-dependent chromatin remodeling complex in Saccharomyces cerevisiae. It regulates nucleosome-depleted regions (NDRs) by sliding flanking nucleosomes away from NDRs. Depletion of RSC leads to nucleosome encroachment in NDRs and transcription initiation defects. The study compared the effects of catalytic-dead Sth1 and rapid depletion of Sth1 on transcription. Rapid depletion of Sth1 reduces recruitment of TBP and Pol II, while the catalytic-dead mutant exhibits a severe reduction in TBP binding but accumulates Pol II in coding regions. The results suggest a role for RSC in transcription elongation and termination processes.
Article
Genetics & Heredity
Yunxiao Wei, Yuhan Song, Muhammad Aamir Khan, Chengzhen Liang, Zhigang Meng, Yuan Wang, Sandui Guo, Rui Zhang
Summary: This study analyzed the GhTPP protein family in upland cotton for the first time and identified the important role of GhTPPA_2 in regulating sugar metabolism, improving soluble sugar accumulation, and drought stress tolerance.
Article
Genetics & Heredity
Yannan Geng, Rui Shao, Tiantong Xu, Lilong Zhang
Summary: A novel risk model based on SCUBE3, TNNC1, SPON1, SEPT12 and ULBP1 genes was developed for predicting PMOP risk, with higher risk score indicating higher risk of suffering from PMOP. Significant differences in signaling pathway activities were observed between the high-risk score group and the low-risk score group.
Article
Genetics & Heredity
Randy P. Williams, Corina Lesseur, Haoxiang Cheng, Qian Li, Maya Deyssenroth, Christopher D. Molteno, Ernesta M. Meintjes, Sandra W. Jacobson, Joseph L. Jacobson, Helen Wainwright, Ke Hao, Jia Chen, R. Colin Carter
Summary: The study suggests that heavy alcohol exposure during pregnancy may impact the proportion of fetal placental villi macrophages and increase the expression of inflammatory genes. Further research is needed to explore these effects and evaluate the potential functional roles of placental inflammation in FASD.
Article
Genetics & Heredity
Lvjing Luo, Lishuang Sun, Shu Li, Huiting Liu, Zhengyu Chen, Shi Huang, Yinyin Mo, Genliang Li
Summary: This study analyzed the expression of Ptpn1 and miR-124-3p in testicular tissues of mice and investigated their regulatory relationship. The results showed that Ptpn1 expression was up-regulated in adult mouse testis compared to juvenile mouse testis, while miR-124-3p expression showed an opposite pattern. Further analysis suggested that the down-regulation of miR-124-3p may contribute to the high expression of Ptpn1 in adult mouse testis.
Article
Genetics & Heredity
Gairui Li, Dan Zhao, Xiaolin Peng, Yashuang Zhao
Summary: MiRNA-22 shows potential as a candidate for early diagnosis of colorectal cancer (CRC). The study found higher miR-22 expression levels in the CRC and CRA groups, suggesting its potential as a biomarker for CRC early screening.
Article
Genetics & Heredity
Zhongqiu Zhu, Qianting Yang, Xiaoying Tian, Da Man, Jian Wang, Junfang Zhang, Bingshe Han
Summary: This study constructed a ceRNA network mediated by lncRNAs in cold-acclimated zebrafish ZF4 cells and revealed that upregulation of MSTRG3207 promotes apoptosis by sponging dre-miR-736 during cold acclimation.
Article
Genetics & Heredity
Weitao Chen, Denggao Xiang, Shang Gao, Shuli Zhu, Zhi Wu, Yuefei Li, Jie Li
Summary: Dam construction has negatively impacted the genetic diversity and structure of fish populations. This case study on the endangered Hemibagrus guttatus found low genetic diversity, high levels of inbreeding, and decreasing population size in fragmented populations. Genetic structure and differentiation were also observed, indicating the influence of dams on these fish populations.
Article
Genetics & Heredity
Pooja Singh, Debleena Guin, Bijay Pattnaik, Ritushree Kukreti
Summary: Through systematic literature review and meta-analysis, it was found that idiopathic pulmonary fibrosis is significantly associated with 222 polymorphisms in 118 genes. Four polymorphisms - rs35705950/MUC5B, rs2736100/TERT, rs2076295/DSP, and rs111521887/TOLLIP, exhibited substantial epidemiological evidence supporting their association with IPF risk.
Article
Genetics & Heredity
Jianping Zhang, Zhijun Cai, Fanzhe Feng, Yufeng Peng, Yi Cui, Yongiqing Xu
Summary: This study found that exosomes secreted by young BMSCs can promote the healing of tendon-bone interface after rotator cuff tears. These exosomes can improve extracellular matrix remodeling, osteogenic differentiation, angiogenesis, and stemness of tendon-derived stem cells (TDSCs). The exosomes from young BMSCs have better effects compared to those from aged BMSCs.