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Abhinandan Mani Tripathi, Abhishek Niranjan, Sribash Roy
Development of flower color in plants is a complex process. Among others, it is an important trait for ornamental flowering plants. Canna is a flowering ornamental plant of family Cannaceae. To understand the molecular mechanism of flower color development in Canna, RNA sequencing from flower tissues of two contrasting flower color cultivars, Red President (RP) and Tropical Sunrise (TS) was performed. More than 27.0 million and 19.0 million clean reads were obtained from RP and TS, respectively. The combined clean reads were assembled into 147,295 unigenes...
March 7, 2018: Plant Physiology and Biochemistry: PPB
Ian Hewson, Kalia S I Bistolas, Jason B Button, Elliot W Jackson
Decades of research have demonstrated the crucial importance of viruses in freshwater ecosystems. However, few studies have focused on the seasonal dynamics and potential hosts of RNA viruses. We surveyed microbial-sized (i.e. 5-0.2 μm) mixed community plankton transcriptomes for RNA viral genomes and investigated their distribution between microbial and macrobial plankton over a seasonal cycle across three temperate lakes by quantitative reverse transcriptase PCR (qRT-PCR). A total of 30 contigs bearing similarity to RNA viral genomes were recovered from a global assembly of 30 plankton RNA libraries...
2018: PloS One
Dilyana Filipova, Margit Henry, Tamara Rotshteyn, Anna Brunn, Mariana Carstov, Martina Deckert, Jürgen Hescheler, Agapios Sachinidis, Gabriele Pfitzer, Symeon Papadopoulos
In skeletal muscle the coordinated actions of two mechanically coupled Ca2+ channels-the 1,4-dihydropyridine receptor (Cav1.1) and the type 1 ryanodine receptor (RYR1)-underlie the molecular mechanism of rapid cytosolic [Ca2+] increase leading to contraction. While both [Ca2+]i and contractile activity have been implicated in the regulation of myogenesis, less is known about potential specific roles of Cav1.1 and RYR1 in skeletal muscle development. In this study, we analyzed the histology and the transcriptomic changes occurring at E14...
2018: PloS One
Aurore Quinault, Corinne Leloup, Geoffrey Denwood, Coralie Spiegelhalter, Marianne Rodriguez, Philippe Lefebvre, Nadia Messaddeq, Quan Zhang, Catherine Dacquet, Luc Pénicaud, Stephan C Collins
The rhythmic nature of insulin secretion over the 24h cycle in pancreatic islets has been mostly investigated using transcriptomics studies showing that modulation of insulin secretion over this cycle is achieved via distal stages of insulin secretion. We set out to measure β-cell exocytosis using in depth cell physiology techniques at several time points. In agreement with the activity and feeding pattern of nocturnal rodents, we find that C57/Bl6J islets in culture for 24h exhibit higher insulin secretion during the corresponding dark phase than in the light phase (Zeitgeber Time ZT20 and ZT8, respectively, in vivo)...
2018: PloS One
Nilam Borah, Emad Albarouki, Jan Schirawski
Many plant-pathogenic fungi are highly host-specific. In most cases, host-specific interactions evolved at the time of speciation of the respective host plants. However, host jumps have occurred quite frequently, and still today the greatest threat for the emergence of new fungal diseases is the acquisition of infection capability of a new host by an existing plant pathogen. Understanding the mechanisms underlying host-switching events requires knowledge of the factors determining host-specificity. In this review, we highlight molecular methods that use a comparative approach for the identification of host-specificity factors...
March 15, 2018: International Journal of Molecular Sciences
Laura Jeacock, Joana Faria, David Horn
Protein abundance differs from a few to millions of copies per cell. Trypanosoma brucei presents an excellent model for studies on codon bias and differential gene expression because transcription is broadly unregulated and uniform across the genome. T. brucei is also a major human and animal protozoal pathogen. Here, an experimental assessment, using synthetic reporter genes, revealed that GC3 codons have a major positive impact on both mRNA and protein abundance. Our estimates of relative expression, based on coding sequences alone (codon usage and sequence length), are within 2-fold of the observed values for the majority of measured cellular mRNAs (n>7000) and proteins (n>2000)...
March 15, 2018: ELife
Janaina de Freitas Nascimento, Steven Kelly, Jack Sunter, Mark Carrington
Selective transcription of individual protein coding genes does not occur in trypanosomes and the cellular copy number of each mRNA must be determined post-transcriptionally. Here, we provide evidence that codon choice directs the levels of constitutively expressed mRNAs. First, a novel codon usage metric, the gene expression codon adaptation index (geCAI), was developed that maximised the relationship between codon choice and the measured abundance for a transcriptome. Second, geCAI predictions of mRNA levels were tested using differently coded GFP transgenes and were successful over a 25-fold range, similar to the variation in endogenous mRNAs...
March 15, 2018: ELife
Jared M Dickinson, Andrew C D'Lugos, Marcus A Naymik, Ashley L Siniard, Amanda J Wolfe, Donald P Curtis, Matthew J Huentelman, Chad C Carroll
Aerobic (AE) and resistance exercise (RE) elicit unique adaptations in skeletal muscle that have distinct implications for health and performance. The purpose of this study was to identify the unique transcriptome response of skeletal muscle to acute AE and RE. In a counter-balanced, cross-over design, six healthy, recreationally active young men (27{plus minus}3y) completed acute AE (40 min cycling, ~70% maximal HR) and RE (8 sets, 10 reps, ~65% 1RM), separated by ~1wk. Muscle biopsies ( vastus lateralis) were obtained before and at 1 and 4h post exercise...
March 15, 2018: Journal of Applied Physiology
Luhong He, Jairav Xolo Desai, Jinxin Gao, Laurie B Hazeltine, Zhirui Lian, John N Calley, Christopher C Frye
Oxidation of monoclonal antibodies (mAb) is a common chemical modification with potential impact on a therapeutic protein's activity and immunogenicity. In a previous study, it was found that tryptophan oxidation (Trp-ox) levels of two mAb produced in Chinese hamster ovary (CHO) cells were significantly lowered by modifying cell culture medium/feed. In this study, transcriptome analysis by RNA-Seq was applied to further elucidate the underlying mechanism of those changes in lowering the Trp-ox levels. Cell samples from the 5L fed-batch conditions were harvested and subjected to RNA-Seq analysis...
March 15, 2018: Biotechnology Journal
Margarita Villar, Lourdes Mateos-Hernandez, Jose de la Fuente
BACKGROUND: Why an autoimmune disease that is the main cause of the acute neuromuscular paralysis worldwide has not yet a well-characterized cause or an effective treatment? The existence of different clinical variants for the Guillain-Barré syndrome (GBS) coupled with the fact that a high number of pathogens can cause an infection that sometimes, but not always, precedes the development of the syndrome, confers a high degree of uncertainty for both prognosis and treatment. In the post-genomic era, the development of omics technologies for the high-throughput analysis of biological molecules is allowing the characterization of biological systems in a degree of depth unimaginable before...
March 14, 2018: Current Medicinal Chemistry
Carina Strell, Markus M Hilscher, Navya Laxman, Jessica Svedlund, Chenglin Wu, Chika Yokota, Mats Nilsson
Single-cell transcriptomics provides us with completely new insights into the molecular diversity of different cell-types and the different states they can adopt. The technique generates inventories of cells that constitute the building blocks of multicellular organisms. However, since the method requires isolation of discrete cells, information about the original location within tissue is lost. Therefore, it is not possible to draw detailed cellular maps of tissue architecture and their positioning in relation to other cells...
March 14, 2018: FEBS Journal
Peng He, Patamarerk Engsontia, Guang-Lei Chen, Qian Yin, Jun Wang, Xu Lu, Ya-Nan Zhang, Zhao-Qun Li, Ming He
BACKGROUND: The white-backed planthopper (WBPH) Sogatella furcifera Horváth, the brown planthopper (BPH) Nilaparvata lugens, and the small brown planthopper (SBPH) Laodelphax striatellus (Hemiptera: Delphacidae) are rice pests that damage rice plants by sap-sucking and by transmitting viruses. Host-seeking behavior involves chemosensory receptor genes, which include odorant receptors (ORs), ionotropic receptors (IRs) and gustatory receptors (GRs). RESULTS: We used genome and transcriptome data to identify 141 ORs, 28 GRs and 25 IRs in BPH, 135 ORs, 18 GRs and 16 IRs in WBPH and 37 ORs, 14 GRs and 6 IRs in SBPH...
March 15, 2018: Pest Management Science
Hitoyoshi Yasuo, Alex McDougall
Phallusia mammillata has recently emerged as a new ascidian model. Its unique characteristics, including the optical transparency of eggs and embryos and efficient translation of exogenously introduced mRNA in eggs, make the Phallusia system suitable for fluorescent protein (FP)-based imaging approaches. In addition, genomic and transcriptomic resources are readily available for this ascidian species, facilitating functional gene studies. Microinjection is probably the most versatile technique for introducing exogenous molecules such as plasmids, mRNAs, and proteins into ascidian eggs/embryos...
2018: Advances in Experimental Medicine and Biology
John R Apps, Gabriela Carreno, Jose Mario Gonzalez-Meljem, Scott Haston, Romain Guiho, Julie E Cooper, Saba Manshaei, Nital Jani, Annett Hölsken, Benedetta Pettorini, Robert J Beynon, Deborah M Simpson, Helen C Fraser, Ying Hong, Shirleen Hallang, Thomas J Stone, Alex Virasami, Andrew M Donson, David Jones, Kristian Aquilina, Helen Spoudeas, Abhijit R Joshi, Richard Grundy, Lisa C D Storer, Márta Korbonits, David A Hilton, Kyoko Tossell, Selvam Thavaraj, Mark A Ungless, Jesus Gil, Rolf Buslei, Todd Hankinson, Darren Hargrave, Colin Goding, Cynthia L Andoniadou, Paul Brogan, Thomas S Jacques, Hywel J Williams, Juan Pedro Martinez-Barbera
Adamantinomatous craniopharyngiomas (ACPs) are clinically challenging tumours, the majority of which have activating mutations in CTNNB1. They are histologically complex, showing cystic and solid components, the latter comprised of different morphological cell types (e.g. β-catenin-accumulating cluster cells and palisading epithelium), surrounded by a florid glial reaction with immune cells. Here, we have carried out RNA sequencing on 18 ACP samples and integrated these data with an existing ACP transcriptomic dataset...
March 14, 2018: Acta Neuropathologica
Francesca Finotello, Zlatko Trajanoski
By exerting pro- and anti-tumorigenic actions, tumor-infiltrating immune cells can profoundly influence tumor progression, as well as the success of anti-cancer therapies. Therefore, the quantification of tumor-infiltrating immune cells holds the promise to unveil the multi-faceted role of the immune system in human cancers and its involvement in tumor escape mechanisms and response to therapy. Tumor-infiltrating immune cells can be quantified from RNA sequencing data of human tumors using bioinformatics approaches...
March 14, 2018: Cancer Immunology, Immunotherapy: CII
Wei Liu, Hua Ye, Ying-Fu Liu, Chao-Qun Xu, Yue-Xian Zhong, Tian Tian, Shi-Wei Ma, Huan Tao, Ling Li, Li-Chun Xue, Hua-Qin He
The stromal and immune cells that form the tumor microenvironment serve a key role in the aggressiveness of tumors. Current tumor-centric interpretations of cancer transcriptome data ignore the roles of stromal and immune cells. The aim of the present study was to investigate the clinical utility of stromal and immune cells in tissue-based transcriptome data. The 'Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data' (ESTIMATE) algorithm was used to probe diverse cancer datasets and the fraction of stromal and immune cells in tumor tissues was scored...
April 2018: Oncology Letters
Min Yang, Youcong Chuan, Cunwu Guo, Jingjing Liao, Yanguo Xu, Xinyue Mei, Yixiang Liu, Huichuan Huang, Xiahong He, Shusheng Zhu
Panax notoginseng is a highly valuable medicinal herb, but its culture is strongly hindered by replant failure, mainly due to autotoxicity. Deciphering the response mechanisms of plants to autotoxins is critical for overcoming the observed autotoxicity. Here, we elucidated the response of P. notoginseng to the autotoxic ginsenoside Rg1 via transcriptomic and cellular approaches. Cellular analyses demonstrated that Rg1 inhibited root growth by disrupting the cell membrane and wall. Transcriptomic analyses confirmed that genes related to the cell membrane, cell wall decomposition and reactive oxygen species (ROS) metabolism were up-regulated by Rg1 stress...
2018: Frontiers in Plant Science
Fei Tao, Junjuan Wang, Zhongfeng Guo, Jingjing Hu, Xiangming Xu, Jiarong Yang, Xianming Chen, Xiaoping Hu
Stripe rust, caused by Puccinia striiformis f. sp. tritici ( Pst ), is a destructive disease of wheat worldwide. The disease is preferably controlled by growing resistant cultivars. Wheat cultivar Xiaoyan 6 (XY 6) has been resistant to stripe rust since its release. In the previous studies, XY 6 was found to have higher-temperature seedling-plant (HTSP) resistance. However, the molecular mechanisms of HTSP resistance were not clear. To identify differentially expressed genes (DEGs) involved in HTSP resistance, we sequenced 30 cDNA libraries constructed from XY 6 seedlings exposed to several temperature treatments...
2018: Frontiers in Plant Science
Christian Haselmair-Gosch, Silvija Miosic, Daria Nitarska, Barbara L Roth, Benjamin Walliser, Renate Paltram, Rares C Lucaciu, Lukas Eidenberger, Thomas Rattei, Klaus Olbricht, Karl Stich, Heidi Halbwirth
A recall campaign for commercial, orange flowering petunia varieties in spring 2017 caused economic losses worldwide. The orange varieties were identified as undeclared genetically engineered (GE)-plants, harboring a maize dihydroflavonol 4-reductase ( DFR, A 1 ), which was used in former scientific transgenic breeding attempts to enable formation of orange pelargonidin derivatives from the precursor dihydrokaempferol (DHK) in petunia. How and when the A 1 cDNA entered the commercial breeding process is unclear...
2018: Frontiers in Plant Science
Rebecca K Shears, Allison J Bancroft, Catherine Sharpe, Richard K Grencis, David J Thornton
Trichuris trichiura (whipworm) is one of the four major soil-transmitted helminth infections of man, affecting an estimated 465 million people worldwide. An effective vaccine that induces long-lasting protective immunity against T. trichiura would alleviate the morbidity associated with this intestinal-dwelling parasite, however the lack of known host protective antigens has hindered vaccine development. Here, we show that vaccination with ES products stimulates long-lasting protection against chronic infection in male C57BL/6 mice...
March 14, 2018: Scientific Reports
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