keyword
MENU ▼
Read by QxMD icon Read
search

Developmental transcriptome

keyword
https://www.readbyqxmd.com/read/28439475/transcriptomic-resources-for-an-endemic-neotropical-plant-lineage-gesneriaceae
#1
Martha L Serrano-Serrano, Anna Marcionetti, Mathieu Perret, Nicolas Salamin
PREMISE OF THE STUDY: Despite the extensive phenotypic variation that characterizes the Gesneriaceae family, there is a lack of genomic resources to investigate the molecular basis of their diversity. We developed and compared the transcriptomes for two species of the Neotropical lineage of the Gesneriaceae. METHODS AND RESULTS: Illumina sequencing and de novo assembly of floral and leaf samples were used to generate multigene sequence data for Sinningia eumorpha and S...
April 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28439397/transcriptomic-analysis-of-maternally-provisioned-cues-for-phenotypic-plasticity-in-the-annual-killifish-austrofundulus-limnaeus
#2
Amie L Romney, Jason E Podrabsky
BACKGROUND: Genotype and environment can interact during development to produce novel adaptive traits that support life in extreme conditions. The development of the annual killifish Austrofundulus limnaeus is unique among vertebrates because the embryos have distinct cell movements that separate epiboly from axis formation during early development, can enter into a state of metabolic dormancy known as diapause and can survive extreme environmental conditions. The ability to enter into diapause can be maternally programmed, with young females producing embryos that do not enter into diapause...
2017: EvoDevo
https://www.readbyqxmd.com/read/28439089/transcriptome-analysis-on-the-exoskeleton-formation-in-early-developmetal-stages-and-reconstruction-scenario-in-growth-moulting-in-litopenaeus-vannamei
#3
Yi Gao, Jiankai Wei, Jianbo Yuan, Xiaojun Zhang, Fuhua Li, Jianhai Xiang
Exoskeleton construction is an important issue in shrimp. To better understand the molecular mechanism of exoskeleton formation, development and reconstruction, the transcriptome of the entire developmental process in Litopenaeus vannamei, including nine early developmental stages and eight adult-moulting stages, was sequenced and analysed using Illumina RNA-seq technology. A total of 117,539 unigenes were obtained, with 41.2% unigenes predicting the full-length coding sequence. Gene Ontology, Clusters of Orthologous Group (COG), the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and functional annotation of all unigenes gave a better understanding of the exoskeleton developmental process in L...
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28438675/integrating-cell-biology-and-proteomic-approaches-in-plants
#4
Tomáš Takáč, Olga Šamajová, Jozef Šamaj
Significant improvements of protein extraction, separation, mass spectrometry and bioinformatics nurtured advancements of proteomics during the past years. The usefulness of proteomics in the investigation of biological problems can be enhanced by integration with other experimental methods from cell biology, genetics, biochemistry, pharmacology, molecular biology and other omics approaches including transcriptomics and metabolomics. This review aims to summarize current trends integrating cell biology and proteomics in plant science...
April 21, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28436429/human-fetal-heart-specific-coexpression-network-involves-congenital-heart-disease-defect-candidate-genes
#5
Bo Wang, Guoling You, Qihua Fu
Heart development is a complex process requiring dynamic transcriptional regulation. Disturbance of this process will lead to severe developmental defects such as congenital heart disease/defect (CHD). CHD is a group of complex disorder with high genetic heterogeneity, common pathways associated with CHD remains largely unknown. In the manuscript, we focused on the tissue specific genes in human fetal heart samples to explore such pathways. We used the RNA microarray dataset of human fetal tissues from ENCODE project to identify genes with heart tissue specific expression...
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28428870/gene-expression-profiling-during-the-embryo-to-larva-transition-in-the-giant-red-sea-urchin-mesocentrotus-franciscanus
#6
Juan Diego Gaitán-Espitia, Gretchen E Hofmann
In echinoderms, major morphological transitions during early development are attributed to different genetic interactions and changes in global expression patterns that shape the regulatory program for the specification of embryonic territories. In order more thoroughly to understand these biological and molecular processes, we examined the transcriptome structure and expression profiles during the embryo-to-larva transition of a keystone species, the giant red sea urchin Mesocentrotus franciscanus. Using a de novo assembly approach, we obtained 176,885 transcripts from which 60,439 (34%) had significant alignments to known proteins...
April 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28419974/prediction-and-feature-analysis-of-intron-retention-events-in-plant-genome
#7
Ying Cui, Chao Zhang, Meng Cai
Alternative splicing (AS) is a major contributor to increase the potential informational content of eukaryotic genomes by creating multiple mRNA species and proteins from a single gene. In plants, up to 60% genes are alternatively spliced and the most common type of AS is intron retention (IR). Genomic analyses of IR have illuminated its crucial role in shaping the evolution of genomes, in the control of developmental processes, and in the dynamic regulation of the transcriptome to influence phenotype. To explore the relationship between the sequence feature and the formation mechanism of IR, we statistically analyzed the retained introns and proposed an improved random forest-based hybrid method to predict intron retention events in plant genome...
April 13, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28419137/transcriptional-changes-in-litchi-litchi-chinensis-sonn-inflorescences-treated-with-uniconazole
#8
Yongzan Wei, Chen Dong, Hongna Zhang, Xuewen Zheng, Bo Shu, Shengyou Shi, Weicai Li
In Arabidopsis, treating shoots with uniconazole can result in enhanced primary root elongation and bolting delay. Uniconazole spraying has become an important cultivation technique in controlling the flowering and improving the fruit-setting of litchi. However, the mechanism by which uniconazole regulates the complicated developmental processes in litchi remains unclear. This study aimed to determine which signal pathways and genes drive the responses of litchi inflorescences to uniconazole treatment. We monitored the transcriptional activity in inflorescences after uniconazole treatment by Illumina sequencing technology...
2017: PloS One
https://www.readbyqxmd.com/read/28414820/transcriptome-analysis-of-the-epidermis-of-the-purple-quail-like-q-lp-mutant-of-silkworm-bombyx-mori
#9
Pingyang Wang, Zhiyong Qiu, Dingguo Xia, Shunming Tang, Xingjia Shen, Qiaoling Zhao
A new purple quail-like (q-lp) mutant found from the plain silkworm strain 932VR has pigment dots on the epidermis similar to the pigment mutant quail (q). In addition, q-lp mutant larvae are inactive, consume little and grow slowly, with a high death rate and other developmental abnormalities. Pigmentation of the silkworm epidermis consists of melanin, ommochrome and pteridine. Silkworm development is regulated by ecdysone and juvenile hormone. In this study, we performed RNA-Seq on the epidermis of the q-lp mutant in the 4th instar during molting, with 932VR serving as the control...
2017: PloS One
https://www.readbyqxmd.com/read/28412460/characterization-of-transcriptome-in-the-indian-meal-moth-plodia-interpunctella-lepidoptera-pyralidae-and-gene-expression-analysis-during-developmental-stages
#10
Pei-An Tang, Hai-Jing Wu, Hao Xue, Xing-Rong Ju, Wei Song, Qi-Lin Zhang, Ming-Long Yuan
The Indian meal moth Plodia interpunctella (Lepidoptera: Pyralidae) is a worldwide pest that causes serious damage to stored foods. Although many efforts have been conducted on this species due to its economic importance, the study of genetic basis of development, behavior and insecticide resistance has been greatly hampered due to lack of genomic information. In this study, we used high throughput sequencing platform to perform a de novo transcriptome assembly and tag-based digital gene expression profiling (DGE) analyses across four different developmental stages of P...
April 13, 2017: Gene
https://www.readbyqxmd.com/read/28406933/transcriptomic-profiling-of-taproot-growth-and-sucrose-accumulation-in-sugar-beet-beta-vulgaris-l-at-different-developmental-stages
#11
Yong-Feng Zhang, Guo-Long Li, Xue-Feng Wang, Ya-Qing Sun, Shao-Ying Zhang
In sugar beet (Beta vulgaris L.), taproot weight and sucrose content are the important determinants of yield and quality. However, high yield and low sucrose content are two tightly bound agronomic traits. The advances in next-generation sequencing technology and the publication of sugar beet genome have provided a method for the study of molecular mechanism underlying the regulation of these two agronomic traits. In this work, we performed comparative transcriptomic analyses in the high taproot yield cultivar SD13829 and the high sucrose content cultivar BS02 at five developmental stages...
2017: PloS One
https://www.readbyqxmd.com/read/28404879/developmental-transcriptome-profiling-of-bovine-muscle-tissue-reveals-an-abundant-gosb-that-regulates-myoblast-proliferation-and-apoptosis
#12
Hui Li, Xuefeng Wei, Jiameng Yang, Dong Dong, Yongzhen Huang, Xianyong Lan, Martin Plath, Chuzhao Lei, Xinglei Qi, Yueyu Bai, Hong Chen
The formation of bovine skeletal muscle involves complex developmental and physiological processes that play a vital role in determining the quality of beef; however, the regulatory mechanisms underlying differences in meat quality are largely unknown. We conducted transcriptome analysis of bovine muscle tissues to compare gene expression profiles between embryonic and adult stages. Total RNAs from skeletal muscle of Qinchuan cattle at fetal and adult stages were used to construct libraries for Illumina next-generation sequencing using the Ribo-Zero RNA sequencing (RNA-Seq) method...
March 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28400510/malate-dependent-fe-accumulation-is-a-critical-checkpoint-in-the-root-developmental-response-to-low-phosphate
#13
Javier Mora-Macías, Jonathan Odilón Ojeda-Rivera, Dolores Gutiérrez-Alanís, Lenin Yong-Villalobos, Araceli Oropeza-Aburto, Javier Raya-González, Gabriel Jiménez-Domínguez, Gabriela Chávez-Calvillo, Rubén Rellán-Álvarez, Luis Herrera-Estrella
Low phosphate (Pi) availability constrains plant development and seed production in both natural and agricultural ecosystems. When Pi is scarce, modifications of root system architecture (RSA) enhance the soil exploration ability of the plant and lead to an increase in Pi uptake. In Arabidopsis, an iron-dependent mechanism reprograms primary root growth in response to low Pi availability. This program is activated upon contact of the root tip with low-Pi media and induces premature cell differentiation and the arrest of mitotic activity in the root apical meristem, resulting in a short-root phenotype...
April 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28399811/transcriptome-dynamics-in-early-zebrafish-embryogenesis-determined-by-high-resolution-time-course-analysis-of-180-successive-individual-zebrafish-embryos
#14
Han Rauwerda, Johanna F B Pagano, Wim C de Leeuw, Wim Ensink, Ulrike Nehrdich, Mark de Jong, Martijs Jonker, Herman P Spaink, Timo M Breit
BACKGROUND: Recently, much progress has been made in the field of gene-expression in early embryogenesis. However, the dynamic behaviour of transcriptomes in individual embryos has hardly been studied yet and the time points at which pools of embryos are collected are usually still quite far apart. Here, we present a high-resolution gene-expression time series with 180 individual zebrafish embryos, obtained from nine different spawns, developmentally ordered and profiled from late blastula to mid-gastrula stage...
April 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28396539/transcriptome-analysis-of-human-reninomas-as-an-approach-to-understanding-juxtaglomerular-cell-biology
#15
Alexandre G Martini, Lucie K Xa, Marie-Josée Lacombe, Alexis Blanchet-Cohen, Chantal Mercure, Benjamin Haibe-Kains, Edith C H Friesema, Anton H van den Meiracker, Kenneth W Gross, Michel Azizi, Pierre Corvol, Geneviève Nguyen, Timothy L Reudelhuber, A H Jan Danser
Renin, a key component in the regulation of blood pressure in mammals, is produced by the rare and highly specialized juxtaglomerular cells of the kidney. Chronic stimulation of renin release results in a recruitment of new juxtaglomerular cells by the apparent conversion of adjacent smooth muscle cells along the afferent arterioles. Because juxtaglomerular cells rapidly dedifferentiate when removed from the kidney, their developmental origin and the mechanism that explains their phenotypic plasticity remain unclear...
April 10, 2017: Hypertension
https://www.readbyqxmd.com/read/28393854/transcriptomic-analysis-of-the-biosynthesis-recycling-and-distribution-of-ascorbic-acid-during-leaf-development-in-tea-plant-camellia-sinensis-l-o-kuntze
#16
Hui Li, Wei Huang, Guang-Long Wang, Wen-Li Wang, Xin Cui, Jing Zhuang
Ascorbic acid (AsA), known as vitamin C, is an essential nutrient for humans and mainly absorbed from food. Tea plant (Camellia sinensis (L.) O. Kuntze) leaves can be a dietary source of AsA for humans. However, experimental evidence on the biosynthesis, recycling pathway and distribution of AsA during leaf development in tea plants is unclear. To gain insight into the mechanism and distribution of AsA in the tea plant leaf, we identified 18 related genes involved in AsA biosynthesis and recycling pathway based on the transcriptome database of tea plants...
April 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28390473/differential-effects-of-high-and-low-glucose-concentrations-during-lipolysis-like-conditions-on-bovine-in-vitro-oocyte-quality-metabolism-and-subsequent-embryo-development
#17
J De Bie, W F A Marei, V Maillo, L Jordaens, A Gutierrez-Adan, P E J Bols, J L M R Leroy
Lipolytic metabolic conditions are traditionally associated with elevated non-esterified fatty acid (NEFA) concentrations, but may also be accompanied by hyperglycaemia in obesity or by hypoglycaemia during a negative energy balance status. Elevated NEFA concentrations disrupt oocyte and embryo development and quality, but little is known about whether the effects of lipolytic conditions on oocyte developmental competence are modulated by glucose availability. To answer this, bovine cumulus-oocyte complexes (COCs) were matured under different conditions: physiological NEFA (72µM) and normal glucose (5...
April 10, 2017: Reproduction, Fertility, and Development
https://www.readbyqxmd.com/read/28388875/sex-specific-differences-in-transcriptome-profiles-of-brain-and-muscle-tissue-of-the-tropical-gar
#18
Kayla M Cribbin, Corey R Quackenbush, Kyle Taylor, Lenin Arias-Rodriguez, Joanna L Kelley
BACKGROUND: The tropical gar (Atractosteus tropicus) is the southernmost species of the seven extant species of gar fishes in the world. In Mexico and Central America, the species is an important food source due to its nutritional quality and low price. Despite its regional importance and increasing concerns about overexploitation and habitat degradation, basic genetic information on the tropical gar is lacking. Determining genetic information on the tropical gar is important for the sustainable management of wild populations, implementation of best practices in aquaculture settings, evolutionary studies of ancient lineages, and an understanding of sex-specific gene expression...
April 7, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28387959/high-quality-genome-assembly-of-capsella-bursa-pastoris-reveals-asymmetry-of-regulatory-elements-at-early-stages-of-polyploid-genome-evolution
#19
Artem S Kasianov, Anna V Klepikova, Ivan V Kulakovskiy, Evgeny S Gerasimov, Anna V Fedotova, Elizaveta G Besedina, Alexey S Kondrashov, Maria D Logacheva, Aleksey A Penin
Polyploidization and subsequent sub- and neofunctionalization of duplicated genes represent a major mechanism of plant genome evolution. Capsella bursa-pastoris, a widespread ruderal plant, is a recent allotetraploid, and, thus, is an ideal model organism for studying early changes following polyploidization. We constructed a high-quality assembly of C. bursa-pastoris genome and a transcriptome atlas covering a broad sample of organs and developmental stages (available online at http://travadb.org/browse/Species=Cbp)...
April 7, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28383663/transcriptomic-analysis-of-gene-cascades-involved-in-protein-kinase-a-and-c-signalling-in-the-kgn-line-of-human-ovarian-granulosa-tumour-cells1
#20
Patricia G Tremblay, Marc-André Sirard
The developmental competence of an oocyte is its capacity to resume maturation, undergo successful fertilization and reach the blastocyst stage. This competence is acquired through interaction with somatic cells of the follicle. Cumulus and granulosa cells support oocyte development while the oocyte influences follicular cell growth and differentiation. Studies suggest that follicle-stimulating hormone and luteinizing hormone play an essential role in oocyte competence acquisition through signalling initiated by protein kinases A and C (PKA and PKC) in granulosa cells...
April 5, 2017: Biology of Reproduction
keyword
keyword
42272
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"