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https://www.readbyqxmd.com/read/29677476/cd4-helper-and-cd8-cytotoxic-t-cell-differentiation
#1
Ichiro Taniuchi
A fundamental question in developmental immunology is how bipotential thymocyte precursors generate both CD4+ helper and CD8+ cytotoxic T cell lineages. The MHC specificity of αβ T cell receptors (TCRs) on precursors is closely correlated with cell fate-determining processes, prompting studies to characterize how variations in TCR signaling are linked with genetic programs establishing lineage-specific gene expression signatures, such as exclusive CD4 or CD8 expression. The key transcription factors ThPOK and Runx3 have been identified as mediating development of helper and cytotoxic T cell lineages, respectively...
April 26, 2018: Annual Review of Immunology
https://www.readbyqxmd.com/read/29677473/signaling-and-function-of-interleukin-2-in-t-lymphocytes
#2
Sarah H Ross, Doreen A Cantrell
The discovery of interleukin-2 (IL-2) changed the molecular understanding of how the immune system is controlled. IL-2 is a pleiotropic cytokine, and dissecting the signaling pathways that allow IL-2 to control the differentiation and homeostasis of both pro- and anti-inflammatory T cells is fundamental to determining the molecular details of immune regulation. The IL-2 receptor couples to JAK tyrosine kinases and activates the STAT5 transcription factors. However, IL-2 does much more than control transcriptional programs; it is a key regulator of T cell metabolic programs...
April 26, 2018: Annual Review of Immunology
https://www.readbyqxmd.com/read/29677185/patterning-mechanisms-diversify-neuroepithelial-domains-in-the-drosophila-optic-placode
#3
Abhishek Kumar Mishra, F Javier Bernardo-Garcia, Cornelia Fritsch, Tim-Henning Humberg, Boris Egger, Simon G Sprecher
The central nervous system develops from monolayered neuroepithelial sheets. In a first step patterning mechanisms subdivide the seemingly uniform epithelia into domains allowing an increase of neuronal diversity in a tightly controlled spatial and temporal manner. In Drosophila, neuroepithelial patterning of the embryonic optic placode gives rise to the larval eye primordium, consisting of two photoreceptor (PR) precursor types (primary and secondary), as well as the optic lobe primordium, which during larval and pupal stages develops into the prominent optic ganglia...
April 20, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29676826/epidermal-auxin-biosynthesis-facilitates-rhizobial-infection-in-lotus-japonicus
#4
Marcin Nadzieja, Simon Kelly, Jens Stougaard, Dugald Reid
Symbiotic nitrogen fixation in legumes requires nodule organogenesis to be coordinated with infection by rhizobia. The plant hormone auxin influences symbiotic infection, but the precise timing of auxin accumulation and the genetic network governing it remain unclear. We used a Lotus japonicus optimised variant of the DII-based auxin accumulation sensor and identify a rapid accumulation of auxin in the epidermis, specifically in the root hair cells. This auxin accumulation occurs in the infected root hairs during rhizobia invasion, while Nod factor application induces this response across a broader range of root hairs...
April 20, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29676801/prolonged-prenatal-hypoxia-selectively-disrupts-collecting-duct-patterning-and-postnatal-function-in-male-mouse-offspring
#5
Sarah L Walton, Reetu R Singh, Melissa H Little, Josephine Bowles, Joan Li, Karen M Moritz
KEY POINTS SUMMARY: In this study we investigated whether hypoxia during late pregnancy impairs kidney development in mouse offspring, and also whether this has long-lasting consequences affecting kidney function in adulthood. Hypoxia disrupted growth of the kidney, particularly the collecting duct network, in juvenile male offspring. By mid-late adulthood, these mice developed early signs of kidney disease, notably a compromised response to water deprivation. Female offspring showed no obvious signs of impaired kidney development and did not develop kidney disease, suggesting a underlying protection mechanism from the hypoxia insult...
April 20, 2018: Journal of Physiology
https://www.readbyqxmd.com/read/29676774/the-architecture-of-an-empirical-genotype-phenotype-map
#6
José Aguilar-Rodríguez, Leto Peel, Massimo Stella, Andreas Wagner, Joshua L Payne
Recent advances in high-throughput technologies are bringing the study of empirical genotype-phenotype (GP) maps to the fore. Here, we use data from protein binding microarrays to study an empirical GP map of transcription factor (TF) binding preferences. In this map, each genotype is a DNA sequence. The phenotype of this DNA sequence is its ability to bind one or more TFs. We study this GP map using genotype networks, in which nodes represent genotypes with the same phenotype, and edges connect nodes if their genotypes differ by a single small mutation...
April 20, 2018: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/29676772/functional-roles-of-eriocalyxin-b-in-zebrafish-revealed-by-transcriptome-analysis
#7
Xunian Zhou, Cyanne Ye Cao, Angel Tsz-Yau Wan, Grace Gar-Lee Yue, Frankie Hin-Fai Kwok, Kwok-Pui Fung, Handong Sun, Clara Bik-San Lau, Pema-Tenzin Puno, Stephen Kwok-Wing Tsui
BACKGROUND: Eriocalyxin B (EriB) is a natural ent-kaurane diterpenoid obtained from Isodon eriocalyx var. laxiflora (family Lamiaceae), which has multiple biological activities (e.g. anti-tumor and anti-inflammatory) via the alteration of gene expression and signaling transduction. Recently, RNA sequencing (RNA-seq) has been developed as a dynamic transcriptome approach to analyze the transcriptional profile and in addition use such gene expression profiles to identify novel candidate genes in a zebrafish model...
April 20, 2018: Molecular omics
https://www.readbyqxmd.com/read/29676458/an-optimized-method-to-measure-human-foxp3-regulatory-t-cells-from-multiple-tissue-types-using-mass-cytometry
#8
Nicholas A J Dawson, Avery J Lam, Laura Cook, Romy E Hoeppli, Raewyn Broady, Anne M Pesenacker, Megan K Leving
Mass cytometry has facilitated the discovery of complex immunological networks and immune cell interactions; however, there are limited reports of using this technology to measure expression of intranuclear antigens such as transcription factors. Herein we describe testing of multiple staining methods to detect FOXP3, the lineage-defining transcription factor for regulatory T cells (Tregs), by mass cytometry. A custom paraformaldehyde/saponin-based fixation and permeabilization method was found to be the optimal method for mass cytometry-based Treg detection, yielding the best balance of FOXP3 detection and preserved cell surface marker expression...
April 20, 2018: European Journal of Immunology
https://www.readbyqxmd.com/read/29675796/construction-of-transcriptional-regulatory-network-of-alzheimer-s-disease-based-on-panda-algorithm
#9
Jieyuan Ding, Wei Kong, Xiaoyang Mou, Shuaiqun Wang
The focus of modern biomedical research concentrates on molecular level regulatory mechanisms and how the normal and abnormal phenotypes of tissue functional are affected by regulatory mechanisms. Most of the research on regulatory mechanism starts from the reconstruction of gene regulation network. At present, a large number of reconstruction methods construct the network using a single data set. These methods of inferring and predicting the relationship between the target gene and the transcription factor (TF) can be used to identify individual interactions between genes, while there is not much research on the interaction of many functional-related genes...
April 19, 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29675032/fspp-a-tool-for-genome-wide-prediction-of-smorf-encoded-peptides-and-their-functions
#10
Hui Li, Li Xiao, Lili Zhang, Jiarui Wu, Bin Wei, Ninghui Sun, Yi Zhao
smORFs are small open reading frames of less than 100 codons. Recent low throughput experiments showed a lot of smORF-encoded peptides (SEPs) played crucial rule in processes such as regulation of transcription or translation, transportation through membranes and the antimicrobial activity. In order to gather more functional SEPs, it is necessary to have access to genome-wide prediction tools to give profound directions for low throughput experiments. In this study, we put forward a functional smORF-encoded peptides predictor (FSPP) which tended to predict authentic SEPs and their functions in a high throughput method...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29675029/aaein3-mediates-the-downregulation-of-artemisinin-biosynthesis-by-ethylene-signaling-through-promoting-leaf-senescence-in-artemisia-annua
#11
Yueli Tang, Ling Li, Tingxiang Yan, Xueqing Fu, Pu Shi, Qian Shen, Xiaofen Sun, Kexuan Tang
Artemisinin is an important drug for malaria treatment, which is exclusively produced in Artemisia annua . It's important to dissect the regulatory mechanism of artemisinin biosynthesis by diverse plant hormones and transcription factors. Our study shows ethylene, a plant hormone which accelerates flower and leaf senescence and fruit ripening, suppressed the expression of genes encoding three key enzymes ADS, DBR2, CYP71AV1, and a positive regulator AaORA involved in artemisinin biosynthesis. Then we isolated the gene encoding ETHYLENE-INSENSITIVE3 (EIN3), a key transcription factor in ethylene signaling pathway, by screening the transcriptome and genome database from Artemisia annua , named AaEIN3 ...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29674963/a-bivalent-securinine-compound-sn3-l6-induces-neuronal-differentiation-via-translational-upregulation-of-neurogenic-transcription-factors
#12
Yumei Liao, Xiaoji Zhuang, Xiaojie Huang, Yinghui Peng, Xuanyue Ma, Zhi-Xing Huang, Feng Liu, Junyu Xu, Ying Wang, Wei-Min Chen, Wen-Cai Ye, Lei Shi
Developing therapeutic approaches that target neuronal differentiation will be greatly beneficial for the regeneration of neurons and synaptic networks in neurological diseases. Protein synthesis (mRNA translation) has recently been shown to regulate neurogenesis of neural stem/progenitor cells (NSPCs). However, it has remained unknown whether engineering translational machinery is a valid approach for manipulating neuronal differentiation. The present study identifies that a bivalent securinine compound SN3-L6, previously designed and synthesized by our group, induces potent neuronal differentiation through a novel translation-dependent mechanism...
2018: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/29674717/a-proteomics-landscape-of-circadian-clock-in-mouse-liver
#13
Yunzhi Wang, Lei Song, Mingwei Liu, Rui Ge, Quan Zhou, Wanlin Liu, Ruiyang Li, Jingbo Qie, Bei Zhen, Yi Wang, Fuchu He, Jun Qin, Chen Ding
As a circadian organ, liver executes diverse functions in different phase of the circadian clock. This process is believed to be driven by a transcription program. Here, we present a transcription factor (TF) DNA-binding activity-centered multi-dimensional proteomics landscape of the mouse liver, which includes DNA-binding profiles of different TFs, phosphorylation, and ubiquitylation patterns, the nuclear sub-proteome, the whole proteome as well as the transcriptome, to portray the hierarchical circadian clock network of this tissue...
April 19, 2018: Nature Communications
https://www.readbyqxmd.com/read/29673687/the-brassinosteroid-regulated-transcription-factors-bzr1-bes1-function-as-a-coordinator-in-multisignal-regulated-plant-growth
#14
REVIEW
Qian-Feng Li, Jun Lu, Jia-Wen Yu, Chang-Quan Zhang, Jun-Xian He, Qiao-Quan Liu
BZR1 and BES1 are key transcription factors of brassinosteroid (BR) signaling and represent the integration node of numerous signaling cascades. Their direct target genes have been identified, and BZR1/BES1-DNA interactions have been experimentally verified. Importantly, BZR1/BES1 also integrate different growth and development events via direct protein-protein interactions. For instance, DELLAs, PIFs, ARF6, and PKL, all directly interact with BZR1/BES1, forming a BZR1/BES1-centered regulatory network to coordinate cell elongation...
April 16, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29673528/genomics-and-proteomic-techniques
#15
Jonathan Z Pan
Although general anesthesia induced by inhaled anesthetics produces definitive phenotypes (e.g., loss of mobility, amnesia, analgesia), the underlying targets of these drugs are still not clear. Genomics and proteomic techniques are discussed for measurement of global transcriptional and translational changes after inhaled anesthetic exposures. The current discussion focuses primarily on the genomic and proteomic technical methodology. We also include a discussion of network and pathway analyses for data interpretation after identification of the targets...
2018: Methods in Enzymology
https://www.readbyqxmd.com/read/29672823/developmental-disorders-with-intellectual-disability-driven-by-chromatin-dysregulation-clinical-overlaps-and-molecular-mechanisms
#16
REVIEW
L Larizza, P Finelli
Advances in genomic analyses based on next generation sequencing and integrated omics approaches, have accelerated in an unprecedented way the discovery of causative genes of developmental delay (DD) and intellectual disability (ID) disorders. Chromatin dysregulation has been recognized as common pathomechanism of mendelian DD/ID syndromes due to mutation in genes encoding chromatin regulators referred as transcriptomopathies or epigenetic disorders. Common to these syndromes are the wide phenotypic breadth and the recognition of groups of distinct syndromes with shared signs besides cognitive impairment, likely mirroring common molecular mechanisms...
April 19, 2018: Clinical Genetics
https://www.readbyqxmd.com/read/29672625/mechanistic-studies-of-depr-in-regulating-fk228-biosynthesis-in-chromobacterium-violaceum-no-968
#17
Yongjian Qiao, Tiantian Tong, Jiao Xue, Wenjing Lin, Zixin Deng, Yi-Qiang Cheng, Dongqing Zhu
DepR, a LysR-type transcriptional regulator encoded by the last gene of the putative min operon (orf21-20-19-depR) located at the downstream region of the anticancer agent FK228 biosynthetic gene cluster in Chromobacterium violaceum No. 968, positively regulates the biosynthesis of FK228. In this work, the mechanism underlining this positive regulation was probed by multiple approaches. Electrophoretic mobility shift assay (EMSA) and DNase I footprinting assay (DIFA) identified a conserved 35-nt DNA segment in the orf21-orf22 intergenic region where the purified recombinant DepR binds to...
2018: PloS One
https://www.readbyqxmd.com/read/29672513/rna-seq-reveals-differentially-expressed-genes-affecting-polyunsaturated-fatty-acids-percentage-in-the-huangshan-black-chicken-population
#18
Shaohua Yang, Ying Wang, Lulu Wang, Zhaoyuan Shi, Xiaoqian Ou, Dan Wu, Xinmiao Zhang, Hao Hu, Jia Yuan, Wei Wang, Fuhu Cao, Guoqing Liu
Fatty acids metabolic products determine meat quality in chickens. Identifying genes associated with fatty acids composition could provide valuable information for the complex genetic networks of genes with underlying variations in fatty acids synthesis. RNA sequencing (RNA-Seq) was conducted to explore the chicken transcriptome from the thigh muscle tissue of 6 Huangshan Black Chickens with 3 extremely high and low phenotypic values for percentage of polyunsaturated fatty acids (PUFAs). In total, we obtained 41,139,108-44,901,729 uniquely mapped reads, which covered 74...
2018: PloS One
https://www.readbyqxmd.com/read/29672183/identification-of-key-pathways-and-genes-in-l4-dorsal-root-ganglion-drg-after-sciatic-nerve-injury-via-microarray-analysis
#19
He Zhao, Li-Jun Duan, Qing-Ling Sun, Yu-Shan Gao, Yong-Dong Yang, Xiang-Sheng Tang, Ding-Yan Zhao, Yang Xiong, Zhen-Guo Hu, Chuan-Hong Li, Si-Xue Chen, Tao Liu, Xing Yu
BACKGROUND: Peripheral nerve injury (PNI) has devastating consequences. Dorsal root ganglion as a pivotal locus participates in the process of neuropathic pain and nerve regeneration. In recent years, gene sequencing technology has seen rapid rise in the biomedicine field. So, we attempt to gain insight into in the mechanism of neuropathic pain and nerve regeneration in the transcriptional level and to explore novel genes through bioinformatics analysis. METHODS: The gene expression profiles of GSE96051 were downloaded from GEO database...
April 19, 2018: Journal of Investigative Surgery: the Official Journal of the Academy of Surgical Research
https://www.readbyqxmd.com/read/29672174/th9-cells-probable-players-in-ulcerative-colitis-pathogenesis
#20
Mojtaba Shohan, Shokrollah Elahi, Hedayatollah Shirzad, Mahmoud Rafieian-Kopaei, Nader Bagheri, Emad Soltani
T lymphocytes represent an important part of adaptive immune system undertaking different functions to regulate immune responses. CD4+ T cells are the most important activator cells in inflammatory conditions. Depending on the type of induced cells and inflamed sites, expression and activity of different subtypes of helper T cells are changed. Recent studies have confirmed the existence of a new subset of helper T lymphocytes called Th9. Naive T cells can differentiate into Th9 subtypes if they are exposed simultaneously by interleukin (IL) 4 and transforming growth factor β and also secondary activation of a complicated network of transcription factors such as interferon regulatory factor 4 (IRF4) and Smads which are essential for adequate induction of this phenotype...
April 19, 2018: International Reviews of Immunology
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