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Developmental transcriptome

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https://www.readbyqxmd.com/read/29785929/dissection-of-the-in-vitro-developmental-program-of-hammondia-hammondi-reveals-a-link-between-stress-sensitivity-and-life-cycle-flexibility-in-toxoplasma-gondii
#1
Sarah L Sokol, Abby S Primack, Sethu C Nair, Zhee S Wong, Maiwase Tembo, Shiv K Verma, Camila K Cerqueira-Cezar, J P Dubey, Jon P Boyle
Most eukaryotic parasites are obligately heteroxenous, requiring sequential infection of different host species in order to survive. Toxoplasma gondii is a rare exception to this rule, having a uniquely facultative heteroxenous life cycle. To understand the origins of this phenomenon, we compared development and stress responses in T. gondii to those of its its obligately heteroxenous relative, Hammondia hammondi and have identified multiple H. hammondi growth states that are distinct from those in T. gondii...
May 22, 2018: ELife
https://www.readbyqxmd.com/read/29785409/-de-novo-genome-and-transcriptome-resources-of-the-adzuki-bean-borer-ostrinia-scapulalis-lepidoptera-crambidae
#2
B Gschloessl, F Dorkeld, P Audiot, A Bretaudeau, C Kerdelhué, R Streiff
We present a draft genome assembly with a de novo prediction and automated functional annotation of coding genes, and a reference transcriptome of the Adzuki bean borer, Ostrinia scapulalis , based on RNA sequencing of various tissues and developmental stages. The genome assembly spans 419 Mb, has a GC content of 37.4% and includes 26,120 predicted coding genes. The reference transcriptome holds 33,080 unigenes and contains a high proportion of a set of genes conserved in eukaryotes and arthropods, used as quality assessment of the reconstructed transcripts...
April 2018: Data in Brief
https://www.readbyqxmd.com/read/29784955/integration-of-large-scale-data-for-extraction-of-integrated-arabidopsis-root-cell-type-specific-models
#3
Michael Scheunemann, Siobhan M Brady, Zoran Nikoloski
Plant organs consist of multiple cell types that do not operate in isolation, but communicate with each other to maintain proper functions. Here, we extract models specific to three developmental stages of eight root cell types or tissue layers in Arabidopsis thaliana based on a state-of-the-art constraint-based modeling approach with all publicly available transcriptomics and metabolomics data from this system to date. We integrate these models into a multi-cell root model which we investigate with respect to network structure, distribution of fluxes, and concordance to transcriptomics and proteomics data...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29784807/oocyte-stage-specific-effects-of-mtor-determine-granulosa-cell-fate-and-oocyte-quality-in-mice
#4
Jing Guo, Teng Zhang, Yueshuai Guo, Tao Sun, Hui Li, Xiaoyun Zhang, Hong Yin, Guangyi Cao, Yaoxue Yin, Hao Wang, Lanying Shi, Xuejiang Guo, Jiahao Sha, John J Eppig, You-Qiang Su
MTOR (mechanistic target of rapamycin) is a widely recognized integrator of signals and pathways key for cellular metabolism, proliferation, and differentiation. Here we show that conditional knockout (cKO) of Mtor in either primordial or growing oocytes caused infertility but differentially affected oocyte quality, granulosa cell fate, and follicular development. cKO of Mtor in nongrowing primordial oocytes caused defective follicular development leading to progressive degeneration of oocytes and loss of granulosa cell identity coincident with the acquisition of immature Sertoli cell-like characteristics...
May 21, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29781253/developmental-plasticity-in-reptiles-insights-from-temperature-dependent-gene-expression-in-wall-lizard-embryos
#5
Nathalie Feiner, Alfredo Rago, Geoffrey M While, Tobias Uller
Many features of the development of reptiles are affected by temperature, but very little is known about how incubation temperature affects gene expression. Here, we provide a detailed case study of gene expression profiles in common wall lizard (Podarcis muralis) embryos developing at stressfully low (15°C) versus benign (24°C) temperature. For maximum comparability between the two temperature regimes, we selected a precise developmental stage early in embryogenesis defined by the number of somites. We used a split-clutch design and lizards from four different populations to evaluate the robustness of temperature-responsive gene expression profiles...
May 20, 2018: Journal of Experimental Zoology. Part A, Ecological and Integrative Physiology
https://www.readbyqxmd.com/read/29778942/transcriptomic-and-methylomic-analysis-reveal-the-toxicological-effect-of-2-3-7-8-tetrachlorodibenzodioxin-on-human-embryonic-stem-cell
#6
Keng Po Lai, Jing Woei Li, Ting Fung Chan, Andy Chen, Cherie Yin Lau Lee, William Shu Biu Yeung, Chris Kong Chu Wong
Cumulating epidemiological studies demonstrated that environmental exposure to endocrine disrupting chemicals (EDCs) during the early stages of fetal development is associated with the increase in disease susceptibility in later life. The fetal developmental plasticity is considered as a protective mechanism against an undesirable prenatal environment. Dioxin is one of the environmental contaminants and is considered a diabetogenic factor. Experimental animal and human epidemiological studies have revealed that dioxin exposure was associated with insulin resistance and altered beta cell function...
May 10, 2018: Chemosphere
https://www.readbyqxmd.com/read/29776340/the-developmental-transcriptomes-of-two-sea-biscuit-species-with-differing-larval-types
#7
Anne Frances Armstrong, Richard K Grosberg
BACKGROUND: Larval developmental patterns are extremely varied both between and within phyla, however the genetic mechanisms leading to this diversification are poorly understood. We assembled and compared the developmental transcriptomes for two sea biscuit species (Echinodermata: Echinoidea) with differing patterns of larval development, to provide a resource for investigating the evolution of alternate life cycles. One species (Clypeaster subdepressus) develops via an obligately feeding larva which metamorphoses 3-4 weeks after fertilization; the other (Clypeaster rosaceus) develops via a rare, intermediate larval type-facultative feeding- and can develop through metamorphosis entirely based on egg provisioning in under one week...
May 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29776339/differential-gene-transcription-across-the-life-cycle-in-daphnia-magna-using-a-new-all-genome-custom-made-microarray
#8
Bruno Campos, Danielle Fletcher, Benjamín Piña, Romà Tauler, Carlos Barata
BACKGROUND: Unravelling the link between genes and environment across the life cycle is a challenging goal that requires model organisms with well-characterized life-cycles, ecological interactions in nature, tractability in the laboratory, and available genomic tools. Very few well-studied invertebrate model species meet these requirements, being the waterflea Daphnia magna one of them. Here we report a full genome transcription profiling of D. magna during its life-cycle. The study was performed using a new microarray platform designed from the complete set of gene models representing the whole transcribed genome of D...
May 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29774045/transposon-derived-non-coding-rnas-and-their-function-in-plants
#9
REVIEW
Jungnam Cho
Transposable elements (TEs) are often regarded as harmful genomic factors and indeed they are strongly suppressed by the epigenetic silencing mechanisms. On the other hand, the mobilization of TEs brings about variability of genome and transcriptome which are essential in the survival and evolution of the host species. The vast majority of such controlling TEs influence the neighboring genes in cis by either promoting or repressing the transcriptional activities. Although TEs are highly repetitive in the genomes and transcribed in specific stress conditions or developmental stages, the trans -acting regulatory roles of TE-derived RNAs have been rarely studied...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29772090/lcm-seq-reveals-the-crucial-role-of-lssoc1-in-heat-promoted-bolting-of-lettuce-lactuca-sativa-l
#10
Zijing Chen, Wensheng Zhao, Danfeng Ge, Yingyan Han, Kang Ning, Chen Luo, Shenglin Wang, Renyi Liu, Xiaolan Zhang, Qian Wang
Lettuce (Lactuca sativa L.) is one of the most economically important vegetables. The floral transition in lettuce is accelerated under high temperatures, which can significantly decrease yields. However, the molecular mechanism underlying the floral tranition in lettuce is poorly known. Using laser capture microdissection coupled with RNA sequencing, we isolated shoot apical meristem cells from the bolting-sensitive lettuce line S39 at four critical stages of development. Subsequently, we screened specifically for the flowering-related gene LsSOC1 during the floral transition through comparative transcriptomic analysis...
May 17, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29771926/evolutionary-and-genomic-analysis-of-the-caleosin-peroxygenase-clo-pxg-gene-protein-families-in-the-viridiplantae
#11
Farzana Rahman, Mehedi Hassan, Rozana Rosli, Ibrahem Almousally, Abdulsamie Hanano, Denis J Murphy
Bioinformatics analyses of caleosin/peroxygenases (CLO/PXG) demonstrated that these genes are present in the vast majority of Viridiplantae taxa for which sequence data are available. Functionally active CLO/PXG proteins with roles in abiotic stress tolerance and lipid droplet storage are present in some Trebouxiophycean and Chlorophycean green algae but are absent from the small number of sequenced Prasinophyceaen genomes. CLO/PXG-like genes are expressed during dehydration stress in Charophyte algae, a sister clade of the land plants (Embryophyta)...
2018: PloS One
https://www.readbyqxmd.com/read/29765956/transcriptomic-profiling-of-zebrafish-hair-cells-using-ribotag
#12
Maggie S Matern, Alisha Beirl, Yoko Ogawa, Yang Song, Nikhil Paladugu, Katie S Kindt, Ronna Hertzano
The zebrafish inner ear organs and lateral line neuromasts are comprised of a variety of cell types, including mechanosensitive hair cells. Zebrafish hair cells are evolutionarily homologous to mammalian hair cells, and have been particularly useful for studying normal hair cell development and function. However, the relative scarcity of hair cells within these complex organs, as well as the difficulty of fine dissection at early developmental time points, makes hair cell-specific gene expression profiling technically challenging...
2018: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/29765414/developmental-pathways-pervade-stem-cell-responses-to-evolving-extracellular-matrices-of-3d-bioprinted-microenvironments
#13
Quyen A Tran, Visar Ajeti, Brian T Freeman, Paul J Campagnola, Brenda M Ogle
Developmental studies and 3D in vitro model systems show that the production and engagement of extracellular matrix (ECM) often precede stem cell differentiation. Yet, unclear is how the ECM triggers signaling events in sequence to accommodate multistep process characteristic of differentiation. Here, we employ transcriptome profiling and advanced imaging to delineate the specificity of ECM engagement to particular differentiation pathways and to determine whether specificity in this context is a function of long-term ECM remodeling...
2018: Stem Cells International
https://www.readbyqxmd.com/read/29765069/de-novo-characterization-of-phenacoccus-solenopsis-transcriptome-and-analysis-of-gene-expression-profiling-during-development-and-hormone-biosynthesis
#14
Surjeet Kumar Arya, Yogeshwar Vikram Dhar, Santosh Kumar Upadhyay, Mehar Hasan Asif, Praveen Chandra Verma
The cotton mealybug Phenacoccus solenopsis is a devastating pest of cotton causing tremendous loss in the yield of crops each year. Widespread physiological and biological studies on P. solenopsis have been carried out, but the lack of genetic information has constrained our understanding of the molecular mechanisms behind its growth and development. To understand and characterize the different developmental stages, RNA-Seq platform was used to execute de-novo transcriptome assembly and differential gene expression profiling for the eggs, first, second, third instar and adult female stages...
May 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29765017/assessment-of-established-techniques-to-determine-developmental-and-malignant-potential-of-human-pluripotent-stem-cells
#15
(no author information available yet)
The International Stem Cell Initiative compared several commonly used approaches to assess human pluripotent stem cells (PSC). PluriTest predicts pluripotency through bioinformatic analysis of the transcriptomes of undifferentiated cells, whereas, embryoid body (EB) formation in vitro and teratoma formation in vivo provide direct tests of differentiation. Here we report that EB assays, analyzed after differentiation under neutral conditions and under conditions promoting differentiation to ectoderm, mesoderm, or endoderm lineages, are sufficient to assess the differentiation potential of PSCs...
May 15, 2018: Nature Communications
https://www.readbyqxmd.com/read/29764901/the-histone-demethylase-kdm5-is-essential-for-larval-growth-in-drosophila
#16
Coralie Drelon, Helen M Belalcazar, Julie Secombe
Regulated gene expression is necessary for developmental and homeostatic processes. The KDM5 family of transcriptional regulators are histone H3 lysine 4 demethylases that can function through both demethylase-dependent and independent mechanisms. While loss and overexpression of KDM5 proteins are linked to intellectual disability and cancer, respectively, their normal developmental functions remain less characterized. Drosophila melanogaster provides an ideal system to investigate KDM5 function, as it encodes a single ortholog in contrast to the four paralogs found in mammalian cells...
May 15, 2018: Genetics
https://www.readbyqxmd.com/read/29764377/transcriptome-display-during-tilapia-sex-determination-and-differentiation-as-revealed-by-rna-seq-analysis
#17
Wenjing Tao, Jinlin Chen, Dejie Tan, Jing Yang, Lina Sun, Jing Wei, Matthew A Conte, Thomas D Kocher, Deshou Wang
BACKGROUND: The factors determining sex in teleosts are diverse. Great efforts have been made to characterize the underlying genetic network in various species. However, only seven master sex-determining genes have been identified in teleosts. While the function of a few genes involved in sex determination and differentiation has been studied, we are far from fully understanding how genes interact to coordinate in this process. RESULTS: To enable systematic insights into fish sexual differentiation, we generated a dynamic co-expression network from tilapia gonadal transcriptomes at 5, 20, 30, 40, 90, and 180 dah (days after hatching), plus 45 and 90 dat (days after treatment) and linked gene expression profiles to both development and sexual differentiation...
May 15, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29763587/mice-exposed-to-bisphenol-a-exhibit-depressive-like-behavior-with-neurotransmitter-and-neuroactive-steroid-dysfunction
#18
Frances Xin, Erin Fischer, Christopher Krapp, Elizabeth N Krizman, Yemin Lan, Clementina Mesaros, Nathaniel W Snyder, Amita Bansal, Michael B Robinson, Rebecca A Simmons, Marisa S Bartolomei
Fetal exposure to endocrine disrupting chemicals (EDCs) has been associated with adverse neurobehavioral outcomes across the lifespan and can persist across multiple generations of offspring. However, the underlying mechanisms driving these changes are not well understood. We investigated the molecular perturbations associated with EDC-induced behavioral changes in first (F1) and second (F2) filial generations, using the model EDC bisphenol A (BPA). C57BL/6J dams were exposed to BPA from preconception until lactation through the diet at doses (10 μg/kg bw/d-lower dose or 10 mg/kg bw/d-upper dose) representative of human exposure levels...
May 18, 2018: Hormones and Behavior
https://www.readbyqxmd.com/read/29762529/combined-analysis-of-the-fruit-metabolome-and-transcriptome-reveals-candidate-genes-involved-in-flavonoid-biosynthesis-in-actinidia-arguta
#19
Yukuo Li, Jinbao Fang, Xiujuan Qi, Miaomiao Lin, Yunpeng Zhong, Leiming Sun, Wen Cui
To assess the interrelation between the change of metabolites and the change of fruit color, we performed a combined metabolome and transcriptome analysis of the flesh in two different Actinidia arguta cultivars: "HB" ("Hongbaoshixing") and "YF" ("Yongfengyihao") at two different fruit developmental stages: 70d (days after full bloom) and 100d (days after full bloom). Metabolite and transcript profiling was obtained by ultra-performance liquid chromatography quadrupole time-of-flight tandem mass spectrometer and high-throughput RNA sequencing, respectively...
May 15, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29761627/muscle-fiber-type-diversity-revealed-by-anti-myosin-heavy-chain-antibodies
#20
REVIEW
Stefano Schiaffino
Different forms of myosin heavy chains (MyHCs), coded by a large family of sarcomeric MYH genes, are expressed in striated muscles. The generation of specific anti-MyHC antibodies has provided a powerful tool to define the fiber types present in skeletal muscles, their functional properties, their response to conditions that affect muscle plasticity and their changes in muscle disorders. Cardiomyocyte heterogeneity has been revealed by the serendipitous observation that different MyHCs are present in atrial and ventricular myocardium and in heart conduction tissue...
May 14, 2018: FEBS Journal
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