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Developmental transcriptome

Shahid Y Khan, Muhammad Ali, Firoz Kabir, Santosh Renuse, Chan Hyun Na, C Conover Talbot, Sean F Hackett, S Amer Riazuddin
Purpose: We previously completed a comprehensive profile of the mouse lens transcriptome. Here, we investigate the proteome of the mouse lens through mass spectrometry-based protein sequencing at the same embryonic and postnatal time points. Methods: We extracted mouse lenses at embryonic day 15 (E15) and 18 (E18) and postnatal day 0 (P0), 3 (P3), 6 (P6), and 9 (P9). The lenses from each time point were preserved in three distinct pools to serve as biological replicates for each developmental stage...
January 1, 2018: Investigative Ophthalmology & Visual Science
Satnam Singh, Mridula Gupta, Suneet Pandher, Gurmeet Kaur, Pankaj Rathore, Subba Reddy Palli
Amrasca biguttula biguttula (Ishida) commonly known as cotton leafhopper is a severe pest of cotton and okra. Not much is known on this insect at molecular level due to lack of genomic and transcriptomic data. To prepare for functional genomic studies in this insect, we evaluated 15 common housekeeping genes (Tub, B-Tub, EF alpha, GADPH, UbiCF, RP13, Ubiq, G3PD, VATPase, Actin, 18s, 28s, TATA, ETF, SOD and Cytolytic actin) during different developmental stages and under starvation stress. We selected early (1st and 2nd), late (3rd and 4th) stage nymphs and adults for identification of stable housekeeping genes using geNorm, NormFinder, BestKeeper and RefFinder software...
2018: PloS One
Tingting Li, Genxi Zhang, Pengfei Wu, Lian Duan, Guohui Li, Qiuhong Liu, Jinyu Wang
A series of elaborately regulated and orchestrated changes in gene expression profiles leads to muscle growth and development. In this study, RNA sequencing was used to profile embryonic chicken myoblasts and fused myotube transcriptomes, long non-coding RNAs (lncRNAs), and messenger RNAs (mRNAs) at four stages of myoblast differentiation. Of a total of 2484 lncRNA transcripts, 2288 were long intergenic non-coding RNAs (lincRNAs) and 198 were antisense lncRNAs. Additionally, 1530 lncRNAs were neighboring 2041 protein-coding genes (<10 kb upstream and downstream) and functionally enriched in several pathways related to skeletal muscle development that have been extensively studied, indicating that these genes may be in cis-regulatory relationships...
January 11, 2018: Genes
Huijing Liu, Yu Xi, Guorong Liu, Yuqiang Zhao, Ji Li, Minggang Lei
Myogenesis is accompanied by a number of changes in gene expression in mammals, and the transcriptional events that underlie these processes have not been yet fully elucidated. In this study, RNA-seq was used to comprehensively compare the transcription profiles of skeletal muscle between Tongcheng (TC) and Yorkshire (YK) pigs at 40, 55, 63, 70, and 90 days of gestation. One thousand three hundred seventeen and 691 differentially expressed genes (DEGs) were detected in TC and YK, respectively, among which 321 DEGs were shown to be common in TC and YK...
January 10, 2018: Functional & Integrative Genomics
Krystyna Cwiklinski, Heather Jewhurst, Paul McVeigh, Tara Barbour, Aaron G Maule, Jose Tort, Sandra M O'Neill, Mark W Robinson, Sheila Donnelly, John P Dalton
The parasite Fasciola hepatica infects a broad range of mammals with impunity.  Following ingestion of parasites (metacercariae) by the host, newly excysted juveniles (NEJ) emerge from their cysts, rapidly penetrate the duodenal wall and migrate to the liver.  Successful infection takes just a few hours and involves negotiating hurdles presented by host macromolecules, tissues and micro-environments, as well as the immune system.  Here, transcriptome and proteome analysis of ex vivo F. hepatica metacercariae and NEJ reveal the rapidity and multitude of metabolic and developmental alterations that take place in order for the parasite to establish infection...
January 10, 2018: Molecular & Cellular Proteomics: MCP
Iván Balic, Paula Vizoso, Ricardo Nilo-Poyanco, Dayan Sanhueza, Patricio Olmedo, Pablo Sepúlveda, Cesar Arriagada, Bruno G Defilippi, Claudio Meneses, Reinaldo Campos-Vargas
Ripening is one of the key processes associated with the development of major organoleptic characteristics of the fruit. This process has been extensively characterized in climacteric fruit, in contrast with non-climacteric fruit such as grape, where the process is less understood. With the aim of studying changes in gene expression during ripening of non-climacteric fruit, an Illumina based RNA-Seq transcriptome analysis was performed on four developmental stages, between veraison and harvest, on table grapes berries cv Thompson Seedless...
2018: PloS One
Ping Wang, Dejian Zhao, Herbert M Lachman, Deyou Zheng
Autism spectrum disorder (ASD) is highly heritable but genetically heterogeneous. The affected neural circuits and cell types remain unclear and may vary at different developmental stages. By analyzing multiple sets of human single cell transcriptome profiles, we found that ASD candidates showed relatively enriched gene expression in neurons, especially in inhibitory neurons. ASD candidates were also more likely to be the hubs of the co-expression gene module that is highly expressed in inhibitory neurons, a feature not detected for excitatory neurons...
January 10, 2018: Translational Psychiatry
Neil E Robbins, José R Dinneny
Water availability is a potent regulator of plant development and induces root branching through a process termed hydropatterning. Hydropatterning enables roots to position lateral branches toward regions of high water availability, such as wet soil or agar media, while preventing their emergence where water is less available, such as in air. The mechanism by which roots perceive the spatial distribution of water during hydropatterning is unknown. Using primary roots of Zea mays (maize) we reveal that developmental competence for hydropatterning is limited to the growth zone of the root tip...
January 9, 2018: Proceedings of the National Academy of Sciences of the United States of America
Xyrus X Maurer-Alcalá, Rob Knight, Laura A Katz
Separate germline and somatic genomes are found in numerous lineages across the eukaryotic tree of life, often separated into distinct tissues (e.g., in plants, animals, and fungi) or distinct nuclei sharing a common cytoplasm (e.g., in ciliates and some foraminifera). In ciliates, germline-limited (i.e., micronuclear-specific) DNA is eliminated during the development of a new somatic (i.e., macronuclear) genome in a process that is tightly linked to large-scale genome rearrangements, such as deletions and reordering of protein-coding sequences...
January 9, 2018: MBio
Ximena Ibarra-Soria, Wajid Jawaid, Blanca Pijuan-Sala, Vasileios Ladopoulos, Antonio Scialdone, David J Jörg, Richard C V Tyser, Fernando J Calero-Nieto, Carla Mulas, Jennifer Nichols, Ludovic Vallier, Shankar Srinivas, Benjamin D Simons, Berthold Göttgens, John C Marioni
During gastrulation, cell types from all three germ layers are specified and the basic body plan is established 1 . However, molecular analysis of this key developmental stage has been hampered by limited cell numbers and a paucity of markers. Single-cell RNA sequencing circumvents these problems, but has so far been limited to specific organ systems 2 . Here, we report single-cell transcriptomic characterization of >20,000 cells immediately following gastrulation at E8.25 of mouse development. We identify 20 major cell types, which frequently contain substructure, including three distinct signatures in early foregut cells...
January 8, 2018: Nature Cell Biology
Peter G Y Zhang, Joanna Yeung, Ishita Gupta, Miguel Ramirez, Thomas Ha, Douglas J Swanson, Sayaka Nagao-Sato, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Carsten O Daub, Erik Arner, Michiel de Hoon, Piero Carninci, Alistair R R Forrest, Yoshihide Hayashizaki, Dan Goldowitz
Laser-capture microdissection was used to isolate external germinal layer tissue from three developmental periods of mouse cerebellar development: embryonic days 13, 15, and 18. The cerebellar granule cell-enriched mRNA library was generated with next-generation sequencing using the Helicos technology. Our objective was to discover transcriptional regulators that could be important for the development of cerebellar granule cells-the most numerous neuron in the central nervous system. Through differential expression analysis, we have identified 82 differentially expressed transcription factors (TFs) from a total of 1311 differentially expressed genes...
January 6, 2018: Cerebellum
Tianli Wu, Yunying Cheng, Zhilong Liu, Wenjing Tao, Shuqing Zheng, Deshou Wang
Zona pellucida (ZP) genes encode ZP glycoproteins which constitute the coat surrounding oocytes and early embryos. Genome-wide identification of ZP genes is still lacking in vertebrates, especially in fish species. Herein, we conducted bioinformatic analyses of the ZP genes of the Nile tilapia and other vertebrates. Totally 16, 9, 17, 27, 21, 20, 26, 19, 14,11, 24, 17, 9, 18, 8, 11, 9, 8, 5, and 4 ZP genes belonging to 5 subfamilies (ZPA, ZPB, ZPC, ZPD, and ZPAX) were found in the sea lamprey, elephant shark, coelacanth, spotted gar, zebrafish, medaka, stickleback, Nile tilapia, Amazon molly, platyfish, seahorse, Northern snakehead, cavefish, tetraodon, clawed frog, turtle, chicken, platypus, kangaroo rat, and human genomes, respectively...
January 6, 2018: Fish Physiology and Biochemistry
Ping Lin, Kailiang Wang, Changfu Zhou, Yunhai Xie, Xiaohua Yao, Hengfu Yin
Camellia oleifera is a major tree species for producing edible oil. Its seed oil is well known for the high level of oleic acids; however, little is known regarding the molecular mechanism of lipid biosynthesis in C. oleifera. Here, we measured the oil contents and fatty acid (FA) compositions at four developmental stages and investigated the global gene expression profiles through transcriptomics sequencing. We identified differentially-expressed genes (DEGs) among the developmental stages and found that the distribution of numbers of DEGs was associated with the accumulation pattern of seed oil...
January 2, 2018: International Journal of Molecular Sciences
Guanghui Yang, Zhenshan Liu, Lulu Gao, Kuohai Yu, Man Feng, Yingyin Yao, Huiru Peng, Zhaorong Hu, Qixin Sun, Zhongfu Ni, Mingming Xin
Genomic imprinting is an epigenetic phenomenon that causes genes to be differentially expressed depending on their parent-of-origin. To evaluate the evolutionary conservation of genomic imprinting and the effects of ploidy on this process, we investigated parent-of-origin-specific gene expression patterns in the endosperm of diploid (Aegilops spp.), tetraploid, and hexaploid wheat (Triticum spp.) at various stages of development via high-throughput transcriptome sequencing. We identified 91, 135, and 146 maternally or paternally expressed genes (MEGs or PEGs, respectively) in diploid, tetraploid, and hexaploid wheat, respectively, 52...
January 3, 2018: Plant Cell
Fengrui Wu, Limin Wu, Qingqing Wu, Linyan Zhou, Wenyong Li, Deshou Wang
β-Catenin, a key transcriptional coactivator of the Wnt pathway, plays an important role in animal embryonic development and organogenesis. In our earlier study, we have reported that two types of β-catenin (β-catenin-1 and β-catenin-2) were ubiquitously expressed in almost all the tissues examined in tilapia. However, the immunolocalization of β-catenin in those tissues, especially in extra-gonadal tissues, remains unclear. In the present study, we further confirm that these two types of β-catenin gene exist only in teleosts and are derived from 3R (third round of genome duplication) by phylogenetic and syntenic analyses...
December 30, 2017: Fish Physiology and Biochemistry
Laura Sonnack, Thorsten Klawonn, Ralf Kriehuber, Henner Hollert, Christoph Schäfers, Martina Fenske
Metal toxicity is a global environmental challenge. Fish are particularly prone to metal exposure, which can be lethal or cause sublethal physiological impairments. The objective of this study was to investigate how adverse effects of chronic exposure to non-toxic levels of essential and non-essential metals in early life stage zebrafish may be explained by changes in the transcriptome. We therefore studied the effects of three different metals at low concentrations in zebrafish embryos by transcriptomics analysis...
December 15, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
Miguel Bento, Sónia Gomes Pereira, Wanda Viegas, Manuela Silva
The predicted world population increase along with climate changes threatens sustainable agricultural supply in the coming decades. It is therefore vital to understand crops diversity associated to abiotic stress response. Heat stress is considered one of the major constrains on crops productivity thus it is essential to develop new approaches for a precocious and rigorous evaluation of varietal diversity regarding heat tolerance. Plant cell membrane thermostability (CMS) is a widely used method for wheat thermotolerance assessment although its limitations require complementary solutions...
2017: PloS One
Yasunori Ichihashi, Miyako Kusano, Makoto Kobayashi, Kenji Suetsugu, Satoko Yoshida, Takanori Wakatake, Kie Kumaishi, Arisa Shibata, Kazuki Saito, Ken Shirasu
Most of plants show remarkable developmental plasticity in the generation of diverse types of new organs upon external stimuli, allowing them to adapt to their environment. Haustorial formation in parasitic plants is an example of such developmental reprogramming, but its molecular mechanism is largely unknown. In this study, we performed field-omics using transcriptomics and metabolomics to profile the molecular switch occurring in haustorial formation of the root parasitic plant, Thesium chinense, collected from its natural habitat...
December 20, 2017: Plant & Cell Physiology
Johannes Delp, Simon Gutbier, Martin Cerff, Christin Zasada, Sebastian Niedenführ, Liang Zhao, Lena Smirnova, Thomas Hartung, Hanna Borlinghaus, Falk Schreiber, Jörg Bergemann, Jochem Gätgens, Martin Beyss, Salah Azzouzi, Tanja Waldmann, Stefan Kempa, Katharina Nöh, Marcel Leist
Developmental neurotoxicity (DNT) may be induced when chemicals disturb a key neurodevelopmental process, and many tests focus on this type of toxicity. Alternatively, DNT may occur when chemicals are cytotoxic only during a specific neurodevelopmental stage. The toxicant sensitivity is affected by the expression of toxicant targets and by resilience factors. Although cellular metabolism plays an important role, little is known how it changes during human neurogenesis, and how potential alterations affect toxicant sensitivity of mature vs...
December 24, 2017: Toxicology and Applied Pharmacology
Giovanni Iacono, Marco Benevento, Aline Dubos, Yann Herault, Hans van Bokhoven, Nael Nadif Kasri, Hendrik G Stunnenberg
The ability to assign expression patterns to the individual cell types that constitute a tissue is a major challenge. This especially applies to brain, given its plethora of different, functionally interconnected cell types. Here, we derived cell type-specific transcriptome signatures from existing single cell RNA data and integrated these signatures with a newly generated dataset of expression (bulk RNA-Seq) of the postnatal developing mouse hippocampus. This integrated analysis allowed us to provide a comprehensive and unbiased prediction of the differentiation drivers for 11 different hippocampal cell types and describe how the different cell types interact to support crucial developmental stages...
December 22, 2017: Scientific Reports
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