scholarly journals Microarray analysis of gene expression during early development: a cautionary overview

Reproduction ◽  
2010 ◽  
Vol 140 (6) ◽  
pp. 787-801 ◽  
Author(s):  
Claude Robert
Keyword(s):  
Gene Expression ◽  
Early Development ◽  
Microarray Analysis ◽  
Developmental Stages ◽  
Sample Handling ◽  
Early Embryos ◽  
High Throughput Method ◽  
Full Benefit ◽  
Key Steps ◽  
Early Developmental

The rise of the ‘omics’ technologies started nearly a decade ago and, among them, transcriptomics has been used successfully to contrast gene expression in mammalian oocytes and early embryos. The scarcity of biological material that early developmental stages provide is the prime reason why the field of transcriptomics is becoming more and more popular with reproductive biologists. The potential to amplify scarce mRNA samples and generate the necessary amounts of starting material enables the relative measurement of RNA abundance of thousands of candidates simultaneously. So far, microarrays have been the most commonly used high-throughput method in this field. Microarray platforms can be found in a wide variety of formats, from cDNA collections to long or short oligo probe sets. These platforms generate large amounts of data that require the integration of comparative RNA abundance values in the physiological context of early development for their full benefit to be appreciated. Unfortunately, significant discrepancies between datasets suggest that direct comparison between studies is difficult and often not possible. We have investigated the sample-handling steps leading to the generation of microarray data produced from prehatching embryo samples and have identified key steps that significantly impact the downstream results. This review provides a discussion on the best methods for the preparation of samples from early embryos for microarray analysis and focuses on the challenges that impede dataset comparisons from different platforms and the reasons why methodological benchmarking performed using somatic cells may not apply to the atypical nature of prehatching development.

Dynamics of gene expression patterns during early development of the European seabass (Dicentrarchus labrax)

2015 ◽  
Vol 47 (5) ◽  
pp. 158-169 ◽  
Author(s):  
E. Kaitetzidou ◽  
J. Xiang ◽  
E. Antonopoulou ◽  
C. S. Tsigenopoulos ◽  
E. Sarropoulou
Keyword(s):  
Gene Expression ◽  
Early Development ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Dicentrarchus Labrax ◽  
Larval Rearing ◽  
Poor Growth ◽  
European Seabass ◽  
Early Developmental Stages ◽  
Early Developmental

Larval and embryonic stages are the most critical period in the life cycle of marine fish. Key developmental events occur early in development and are influenced by external parameters like stress, temperature, salinity, and photoperiodism. Any failure may cause malformations, developmental delays, poor growth, and massive mortalities. Advanced understanding of molecular processes underlying marine larval development may lead to superior larval rearing conditions. Today, the new sequencing and bioinformatic methods allow transcriptome screens comprising messenger (mRNA) and microRNA (miRNA) with the scope of detecting differential expression for any species of interest. In the present study, we applied Illumina technology to investigate the transcriptome of early developmental stages of the European seabass ( Dicentrarchus labrax). The European seabass, in its natural environment, is a euryhaline species and has shown high adaptation processes in early life phases. During its embryonic and larval phases the European seabass lives in a marine environment and as a juvenile it migrates to coastal zones, estuaries, and lagoons. Investigating the dynamics of gene expression in its early development may shed light on factors promoting phenotypic plasticity and may also contribute to the improvement and advancement of rearing methods of the European seabass, a species of high economic importance in European and Mediterranean aquaculture. We present the identification, characterization, and expression of mRNA and miRNA, comprising paralogous genes and differentially spliced transcripts from early developmental stages of the European seabass. We further investigated the detection of possible interactions of miRNA with mRNA.

scholarly journals Comparison of fecundity and offspring immunity in zebrafish fed Lactobacillus rhamnosus CICC 6141 and Lactobacillus casei BL23

Reproduction ◽  
2014 ◽  
Vol 147 (1) ◽  
pp. 53-64 ◽  
Author(s):  
Chubin Qin ◽  
Li Xu ◽  
Yalin Yang ◽  
Suxu He ◽  
Yingying Dai ◽  
...  
Keyword(s):  
Gene Expression ◽  
Oocyte Maturation ◽  
Lactobacillus Casei ◽  
Developmental Stages ◽  
Lactobacillus Rhamnosus ◽  
Reproductive Process ◽  
Beneficial Effects ◽  
Larval Stages ◽  
Probiotic Strains ◽  
Early Developmental

To increase the knowledge of probiotic effects on zebrafish (Danio rerio), we compare the effects of two probiotic strains, Lactobacillus rhamnosus CICC 6141 (a highly adhesive strain) and Lactobacillus casei BL23 (a weakly adhesive strain), on zebrafish reproduction and their offsprings' innate level of immunity to water-borne pathogens. During probiotics treatments from 7 to 28 days, both the Lactobacillus strains, and especially L. casei BL23, significantly increased fecundity in zebrafish: higher rates of egg ovulation, fertilization, and hatching were observed. Increased densities of both small and large vitellogenic follicles, seen in specimens fed either Lactobacillus strain, demonstrated accelerated oocyte maturation. Feeding either strain of Lactobacillus upregulated gene expression of leptin, kiss2, gnrh3, fsh, lh, lhcgr, and paqr8, which were regarded to enhance fecundity and encourage oocyte maturation. Concomitantly, the gene expression of bmp15 and tgfb1 was inhibited, which code for local factors that prevent oocyte maturation. The beneficial effects of the Lactobacillus strains on fecundity diminished after feeding of the probiotics was discontinued, even for the highly adhesive gut Lactobacillus strain. Administering L. rhamnosus CICC 6141 for 28 days was found to affect the innate immunity of offspring derived from their parents, as evinced by a lower level of alkaline phosphatase activity in early larval stages. This study highlights the effects of probiotics both upon the reproductive process and upon the offsprings' immunity during early developmental stages.

Microarray analysis of gene expression patterns in the leaf during potato tuberization in the potato somatic hybrid Solanum tuberosum and Solanum etuberosum

Genome ◽  
2015 ◽  
Vol 58 (6) ◽  
pp. 305-313 ◽  
Author(s):  
Jagesh Kumar Tiwari ◽  
Sapna Devi ◽  
S. Sundaresha ◽  
Poonam Chandel ◽  
Nilofer Ali ◽  
...  
Keyword(s):  
Gene Expression ◽  
Candidate Genes ◽  
Microarray Analysis ◽  
Somatic Hybrid ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Gene Expression Patterns ◽  
Potato Tuberization ◽  
Solanum Etuberosum

Genes involved in photoassimilate partitioning and changes in hormonal balance are important for potato tuberization. In the present study, we investigated gene expression patterns in the tuber-bearing potato somatic hybrid (E1-3) and control non-tuberous wild species Solanum etuberosum (Etb) by microarray. Plants were grown under controlled conditions and leaves were collected at eight tuber developmental stages for microarray analysis. A t-test analysis identified a total of 468 genes (94 up-regulated and 374 down-regulated) that were statistically significant (p ≤ 0.05) and differentially expressed in E1-3 and Etb. Gene Ontology (GO) characterization of the 468 genes revealed that 145 were annotated and 323 were of unknown function. Further, these 145 genes were grouped based on GO biological processes followed by molecular function and (or) PGSC description into 15 gene sets, namely (1) transport, (2) metabolic process, (3) biological process, (4) photosynthesis, (5) oxidation-reduction, (6) transcription, (7) translation, (8) binding, (9) protein phosphorylation, (10) protein folding, (11) ubiquitin-dependent protein catabolic process, (12) RNA processing, (13) negative regulation of protein, (14) methylation, and (15) mitosis. RT-PCR analysis of 10 selected highly significant genes (p ≤ 0.01) confirmed the microarray results. Overall, we show that candidate genes induced in leaves of E1-3 were implicated in tuberization processes such as transport, carbohydrate metabolism, phytohormones, and transcription/translation/binding functions. Hence, our results provide an insight into the candidate genes induced in leaf tissues during tuberization in E1-3.

Fungal and algal gene expression in early developmental stages of lichen-symbiosis

Mycologia ◽  
2011 ◽  
Vol 103 (2) ◽  
pp. 291-306 ◽  
Author(s):  
Suzanne Joneson ◽  
Daniele Armaleo ◽  
François Lutzoni
Keyword(s):  
Gene Expression ◽  
Developmental Stages ◽  
Lichen Symbiosis ◽  
Early Developmental Stages ◽  
Early Developmental ◽  
Algal Gene

scholarly journals Physical constraints on early blastomere packings

2021 ◽  
Vol 17 (1) ◽  
pp. e1007994
Author(s):  
James Giammona ◽  
Otger Campàs
Keyword(s):  
Cell Division ◽  
Developmental Stages ◽  
Physical Parameters ◽  
Cell Stage ◽  
Physical Constraints ◽  
Equilibrium Dynamics ◽  
Deformable Particles ◽  
Early Embryos ◽  
Early Developmental Stages ◽  
Early Developmental

At very early embryonic stages, when embryos are composed of just a few cells, establishing the correct packing arrangements (contacts) between cells is essential for the proper development of the organism. As early as the 4-cell stage, the observed cellular packings in different species are distinct and, in many cases, differ from the equilibrium packings expected for simple adherent and deformable particles. It is unclear what are the specific roles that different physical parameters, such as the forces between blastomeres, their division times, orientation of cell division and embryonic confinement, play in the control of these packing configurations. Here we simulate the non-equilibrium dynamics of cells in early embryos and systematically study how these different parameters affect embryonic packings at the 4-cell stage. In the absence of embryo confinement, we find that cellular packings are not robust, with multiple packing configurations simultaneously possible and very sensitive to parameter changes. Our results indicate that the geometry of the embryo confinement determines the packing configurations at the 4-cell stage, removing degeneracy in the possible packing configurations and overriding division rules in most cases. Overall, these results indicate that physical confinement of the embryo is essential to robustly specify proper cellular arrangements at very early developmental stages.

Chromatin diminution is strictly correlated to somatic cell behavior in early development of the nematode Parascaris univalens

1995 ◽  
Vol 108 (6) ◽  
pp. 2393-2404
Author(s):  
M.R. Esteban ◽  
G. Giovinazzo ◽  
C. Goday
Keyword(s):  
Somatic Cell ◽  
Early Development ◽  
Cytochalasin B ◽  
Developmental Stages ◽  
Cell Behavior ◽  
Chromatin Diminution ◽  
Developmental Behavior ◽  
Licl Treatment ◽  
The Relationship ◽  
Early Developmental

We have studied the relationship between the occurrence of chromatin diminution and the developmental behavior of somatic blastomeres in early development of the nematode Parascaris univalens. A cytological and immunocytochemical analysis of chromatin diminution was performed in P. univalens embryos exposed to ‘vegetalizing’ (LiCl) and ‘animalizing’ (NaSCN) substances during early developmental stages. We have also analyzed chromatin diminution in embryos displaying only symmetrical ‘somatic-like’ divisions due to a brief cytochalasin B treatment at the pronuclear stage. The results show that LiCl treatment induces chromatin diminution in P0-P4 pregerminal blastomeres while NaSCN treatment prevents it. Pregerminal cells undergoing chromatin diminution in ‘vegetalized’ embryos behaved like somatic cells with respect to division and cleavage patterns. NaSCN treatment results in undiminuted polynucleated embryos that are not capable of cleavage. In cytochalasin B-pulsed embryos, chromatin diminution occurs in all blastomeres. From our results we conclude that chromatin diminution and somatic cell behavior are not separable and constitute strictly correlated events in Parascaris. Moreover, the results indicate that the segregation of the cytoplasmic factors involved in chromatin diminution in early Parascaris development are microfilament-mediated. Here, we also report the formation of a latter pregerminal cell precursor (P5) not susceptible to LiCl-induced chromatin diminution.

Development of pigment-cup eyes in the polychaetePlatynereis dumeriliiand evolutionary conservation of larval eyes in Bilateria

Development ◽  
2002 ◽  
Vol 129 (5) ◽  
pp. 1143-1154 ◽  
Author(s):  
Detlev Arendt ◽  
Kristin Tessmar ◽  
Maria-Ines Medeiros de Campos-Baptista ◽  
Adriaan Dorresteijn ◽  
Joachim Wittbrodt
Keyword(s):  
Visual System ◽  
Early Development ◽  
Developmental Stages ◽  
Photoreceptor Cells ◽  
Evolutionary Conservation ◽  
Early Developmental Stages ◽  
Platynereis Dumerilii ◽  
Differentiation Marker ◽  
Early Developmental

The role of Pax6 in eye development in insects and vertebrates supports the view that their eyes evolved from simple pigment-cup ocelli present in their last common ancestors (Urbilateria). The cerebral eyes in errant polychaetes represent prototype invertebrate pigment-cup ocelli and thus resemble the presumed ancestral eyes. We have analysed expression of conserved eye specification genes in the early development of larval and adult pigment-cup eyes in Platynereis dumerilii (Polychaeta, Annelida, Lophotrochozoa). Both larval and adult eyes form in close vicinity of the optic anlagen on both sides of the developing brain ganglia. While pax6 is expressed in the larval, but not in the developing, adult eyes, expression of six1/2 from trochophora stages onwards specifically outlines the optic anlagen and thus covers both the developing larval and adult eyes. Using Platynereis rhabdomeric opsin as differentiation marker, we show that the first pair of adult eye photoreceptor cells is detected within bilateral clusters that transitorily express ath, the Platynereis atonal orthologue, thus resembling proneural sensory clusters. Our data indicate that – similar to insects, but different from the vertebrates – polychaete six1/2 expression outlines the entire visual system from early developmental stages onwards and ath-positive clusters generate the first photoreceptor cells to appear. We propose that pax6-, six1/2- and ath-positive larval eyes, as found in today’s trochophora, were present already in Urbilateria.

scholarly journals Zebrafish lipid droplets regulate embryonic ATP homeostasis to power early development

Open Biology ◽  
2017 ◽  
Vol 7 (7) ◽  
pp. 170063 ◽  
Author(s):  
Asmita Dutta ◽  
Deepak Kumar Sinha
Keyword(s):  
Fatty Acids ◽  
Early Development ◽  
Lipid Droplets ◽  
Developmental Stages ◽  
Fatty Acyl ◽  
Zebrafish Embryos ◽  
Early Developmental Stages ◽  
Successful Execution ◽  
Acyl Coenzyme A ◽  
Early Developmental

In zebrafish embryos, the maternally supplied pool of ATP is insufficient to power even the earliest of developmental events (0–3 hpf) such as oocyte-to-embryo transition (OET). The embryos generate an additional pulse (2.5 h long) of ATP (1.25–4 hpf) to achieve the embryonic ATP homeostasis. We demonstrate that the additional pulse of ATP is needed for successful execution of OET. The maternally supplied yolk lipids play a crucial role in maintaining the embryonic ATP homeostasis. In this paper, we identify the source and trafficking routes of free fatty acids (FFAs) that feed the mitochondria for synthesis of ATP. Interestingly, neither the maternally supplied pool of yolk-FFA nor the yolk-FACoA (fatty acyl coenzyme A) is used for ATP homeostasis during 0–5 hpf in zebrafish embryos. With the help of lipidomics, we explore the link between lipid droplet (LD)-mediated lipolysis and ATP homeostasis in zebrafish embryos. Until 5 hpf, the embryonic LDs undergo extensive lipolysis that generates FFAs. We demonstrate that these newly synthesized FFAs from LDs are involved in the maintenance of embryonic ATP homeostasis, rather than the FFAs/FACoA present in the yolk. Thus, the LDs are vital embryonic organelles that maintain the ATP homeostasis during early developmental stages (0–5 hpf) in zebrafish embryos. Our study highlights the important roles carried on by the LDs during the early development of the zebrafish embryos.

scholarly journals Early development of Hypogymnia physodes (L.) Nyl. in response to emissions from a copper smelter

2001 ◽  
Vol 33 (6) ◽  
pp. 527-538 ◽  
Author(s):  
Irina N. Mikhailova ◽  
Christoph Scheidegger
Keyword(s):  
Early Development ◽  
Developmental Stages ◽  
Developmental Rate ◽  
Copper Smelter ◽  
Copper Smelting ◽  
Hypogymnia Physodes ◽  
Toxic Impact ◽  
Early Developmental ◽  
Desert Zone ◽  
Copper Smelting Plant

AbstractThe early development of Hypogymnia physodes from soredia to the formation of stratified lobes has been studied experimentally in the vicinity of a copper-smelting plant in theMiddle Urals. SEM investigations combined with life table analyses of early developmental stages revealed decreases in soredial survival and developmental rate in polluted localities. Non-stricatified pre-thallus stages without an epicortex were tolerant to toxic impact and were able to survive even in the zone with the highest pollution (lichen desert zone). The sensitivity of developmental stagesancreased after stratified lobes had developed.

Changes in gene expression during development and thermogenesis in Arum

1999 ◽  
Vol 26 (5) ◽  
pp. 391 ◽  
Author(s):  
Stephen Chivasa ◽  
James O. Berry ◽  
Tom ap Rees ◽  
John P. Carr
Keyword(s):  
Gene Expression ◽  
Malic Enzyme ◽  
Alternative Oxidase ◽  
Developmental Stages ◽  
Pathogen Resistance ◽  
Protein Accumulation ◽  
Alternative Respiration ◽  
Mrna Accumulation ◽  
Bisphosphate Carboxylase ◽  
Early Developmental

Thermogenesis in Arum species is induced by salicylic acid (SA) and caused by activation of the alternative respiration pathway and the alternative oxidase (AOX), resulting in heat production. The enzymes phosphoenolpyruvate carboxylase (PEPCase) and NAD-dependent malic enzyme (NAD-ME) also show dramatic increases in activity during thermogenesis and are essential for heat generation. In this current study, we characterized the timing and localization of changes in levels of AOX, NAD-ME, and PEPCase polypeptide accumulation, and changes in Ppc and Me mRNA accumulation, in various Arum tissues during prethermogenic development and during thermogenesis. In addition, changes in ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) gene expression were analysed at the level of rbcL protein and mRNA accumulation. AOX, PEPCase, and NAD-ME all increased only in clubs during development, increasing 5–6-fold by the latest prethermogenic stage and remained at this level. The induction of thermogenesis did not cause any changes in levels of AOX, indicating that SA does not affect levels of the enzyme itself, but instead must act to stimulate activity. Reported increases in NAD-ME activity during club development correlated closely with mRNA and protein accumulation, whereas PEPCase activity appears to be determined by post-transcriptional and post-translational processes. Interestingly, Rubisco protein and mRNA were found in relatively abundant amounts in clubs during early developmental stages, and disappeared rapidly as the thermogenic enzymes began to increase in abundance. The induction of thermogenesis by a synthetic inducer of plant pathogen resistance, 2,6-dichloroisonicotinic acid, as well as the involvement of SA and AOX in both processes, reinforces evidence for a link between mechanisms controlling disease resistance in all plants and thermogenic induction in Arum.

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