scholarly journals Transcriptomic analysis of sea star development through metamorphosis to the highly derived pentameral body plan with a focus on neural transcription factors

DNA Research ◽  
2020 ◽  
Vol 27 (1) ◽  
Author(s):  
Maria Byrne ◽  
Demian Koop ◽  
Dario Strbenac ◽  
Paula Cisternas ◽  
Regina Balogh ◽  
...  
Keyword(s):  
Gene Expression ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Expression Patterns ◽  
Body Plan ◽  
Sea Star ◽  
Neural Genes ◽  
Transcription Factor Genes ◽  
Juvenile Stages ◽  
Sensory Structures

Abstract The Echinodermata is characterized by a secondarily evolved pentameral body plan. While the evolutionary origin of this body plan has been the subject of debate, the molecular mechanisms underlying its development are poorly understood. We assembled a de novo developmental transcriptome from the embryo through metamorphosis in the sea star Parvulastra exigua. We use the asteroid model as it represents the basal-type echinoderm body architecture. Global variation in gene expression distinguished the gastrula profile and showed that metamorphic and juvenile stages were more similar to each other than to the pre-metamorphic stages, pointing to the marked changes that occur during metamorphosis. Differential expression and gene ontology (GO) analyses revealed dynamic changes in gene expression throughout development and the transition to pentamery. Many GO terms enriched during late metamorphosis were related to neurogenesis and signalling. Neural transcription factor genes exhibited clusters with distinct expression patterns. A suite of these genes was up-regulated during metamorphosis (e.g. Pax6, Eya, Hey, NeuroD, FoxD, Mbx, and Otp). In situ hybridization showed expression of neural genes in the CNS and sensory structures. Our results provide a foundation to understand the metamorphic transition in echinoderms and the genes involved in development and evolution of pentamery.

scholarly journals Viral Gene Expression Patterns in Human Herpesvirus 6B-Infected T Cells

2002 ◽  
Vol 76 (15) ◽  
pp. 7578-7586 ◽  
Author(s):  
Bodil Øster ◽  
Per Höllsberg
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
Protein Synthesis ◽  
De Novo ◽  
Expression Patterns ◽  
Human Herpesvirus ◽  
Viral Gene Expression ◽  
Polymerase Activity ◽  
Viral Gene ◽  
De Novo Protein Synthesis

ABSTRACT Herpesvirus gene expression is divided into immediate-early (IE) or α genes, early (E) or β genes, and late (L) or γ genes on the basis of temporal expression and dependency on other gene products. By using real-time PCR, we have investigated the expression of 35 human herpesvirus 6B (HHV-6B) genes in T cells infected by strain PL-1. Kinetic analysis and dependency on de novo protein synthesis and viral DNA polymerase activity suggest that the HHV-6B genes segregate into six separate kinetic groups. The genes expressed early (groups I and II) and late (groups V and VI) corresponded well with IE and L genes, whereas the intermediate groups III and IV contained E and L genes. Although HHV-6B has characteristics similar to those of other roseoloviruses in its overall gene regulation, we detected three B-variant-specific IE genes. Moreover, genes that were independent of de novo protein synthesis clustered in an area of the viral genome that has the lowest identity to the HHV-6A variant. The organization of IE genes in an area of the genome that differs from that of HHV-6A underscores the distinct differences between HHV-6B and HHV-6A and may provide a basis for further molecular and immunological analyses to elucidate their different biological behaviors.

scholarly journals Transcriptome Analysis of Ramie (Boehmeria niveaL. Gaud.) in Response to Ramie Moth (Cocytodes coeruleaGuenée) Infestation

2016 ◽  
Vol 2016 ◽  
pp. 1-10 ◽  
Author(s):  
Liangbin Zeng ◽  
Airong Shen ◽  
Jia Chen ◽  
Zhun Yan ◽  
Touming Liu ◽  
...  
Keyword(s):  
Protein Function ◽  
Molecular Mechanisms ◽  
Defense Mechanism ◽  
Natural Fiber ◽  
De Novo ◽  
Average Length ◽  
Expression Patterns ◽  
Transcriptome Profiling ◽  
Cdna Libraries ◽  
Pcr Analysis

The ramie mothCocytodes coeruleaGuenée (RM) is an economically important pest that seriously impairs the yield of ramie, an important natural fiber crop. The molecular mechanisms that underlie the ramie-pest interactions are unclear up to date. Therefore, a transcriptome profiling analysis would aid in understanding the ramie defense mechanisms against RM. In this study, we first constructed two cDNA libraries derived from RM-challenged (CH) and unchallenged (CK) ramie leaves. The subsequent sequencing of the CH and CK libraries yielded 40.2 and 62.8 million reads, respectively. Furthermore,de novoassembling of these reads generated 26,759 and 29,988 unigenes, respectively. An integrated assembly of data from these two libraries resulted in 46,533 unigenes, with an average length of 845 bp per unigene. Among these genes, 24,327 (52.28%) were functionally annotated by predicted protein function. A comparative analysis of the CK and CH transcriptome profiles revealed 1,980 differentially expressed genes (DEGs), of which 750 were upregulated and 1,230 were downregulated. A quantitative real-time PCR (qRT-PCR) analysis of 13 random selected genes confirmed the gene expression patterns that were determined by Illumina sequencing. Among the DEGs, the expression patterns of transcription factors, protease inhibitors, and antioxidant enzymes were studied. Overall, these results provide useful insights into the defense mechanism of ramie against RM.

scholarly journals Integrative Transcriptomics Reveals Activation of Innate Immune Responses and Inhibition of Inflammation During Oral Immunotherapy for Egg Allergy in Children

2021 ◽  
Vol 12 ◽  
Author(s):  
Piia Karisola ◽  
Kati Palosuo ◽  
Victoria Hinkkanen ◽  
Lukas Wisgrill ◽  
Terhi Savinko ◽  
...  
Keyword(s):  
Gene Expression ◽  
Clinical Outcome ◽  
Immune Responses ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Oral Immunotherapy ◽  
Innate Immune ◽  
Egg Allergy ◽  
Innate Immune Responses ◽  
Open Label

We previously reported the results of a randomized, open-label trial of egg oral immunotherapy (OIT) in 50 children where 44% were desensitized and 46% were partially desensitized after 8 months of treatment. Here we focus on cell-mediated molecular mechanisms driving desensitization during egg OIT. We sought to determine whether changes in genome-wide gene expression in blood cells during egg OIT correlate with humoral responses and the clinical outcome. The blood cell transcriptome of 50 children receiving egg OIT was profiled using peripheral blood mononuclear cell (PBMC) samples obtained at baseline and after 3 and 8 months of OIT. We identified 467 differentially expressed genes (DEGs) after 3 or 8 months of egg OIT. At 8 months, 86% of the DEGs were downregulated and played a role in the signaling of TREM1, IL-6, and IL-17. In correlation analyses, Gal d 1–4-specific IgG4 antibodies associated positively with DEGs playing a role in pathogen recognition and antigen presentation and negatively with DEGs playing a role in the signaling of IL-10, IL-6, and IL-17. Desensitized and partially desensitized patients had differences in their antibody responses, and although most of the transcriptomic changes were shared, both groups had also specific patterns, which suggest slower changes in partially desensitized and activation of NK cells in the desensitized group. OIT for egg allergy in children inhibits inflammation and activates innate immune responses regardless of the clinical outcome at 8 months. Changes in gene expression patterns first appear as posttranslational protein modifications, followed by more sustained epigenetic gene regulatory functions related to successful desensitization.

Axial specification for sensory organs versus non-sensory structures of the chicken inner ear

Development ◽  
1998 ◽  
Vol 125 (1) ◽  
pp. 11-20 ◽  
Author(s):  
D.K. Wu ◽  
F.D. Nunes ◽  
D. Choo
Keyword(s):  
Gene Expression ◽  
Inner Ear ◽  
Expression Patterns ◽  
Growth Factor Receptor ◽  
Gross Anatomy ◽  
Sensory Organ ◽  
Sensory Organs ◽  
Organ Formation ◽  
Sensory Structures ◽  
Axial Specification

A mature inner ear is a complex labyrinth containing multiple sensory organs and nonsensory structures in a fixed configuration. Any perturbation in the structure of the labyrinth will undoubtedly lead to functional deficits. Therefore, it is important to understand molecularly how and when the position of each inner ear component is determined during development. To address this issue, each axis of the otocyst (embryonic day 2.5, E2.5, stage 16–17) was changed systematically at an age when axial information of the inner ear is predicted to be fixed based on gene expression patterns. Transplanted inner ears were analyzed at E4.5 for gene expression of BMP4 (bone morphogenetic protein), SOHo-1 (sensory organ homeobox-1), Otx1 (cognate of Drosophila orthodenticle gene), p75NGFR (nerve growth factor receptor) and Msx1 (muscle segment homeobox), or at E9 for their gross anatomy and sensory organ formation. Our results showed that axial specification in the chick inner ear occurs later than expected and patterning of sensory organs in the inner ear was first specified along the anterior/posterior (A/P) axis, followed by the dorsal/ventral (D/V) axis. Whereas the A/P axis of the sensory organs was fixed at the time of transplantation, the A/P axis for most non-sensory structures was not and was able to be re-specified according to the new axial information from the host. The D/V axis for the inner ear was not fixed at the time of transplantation. The asynchronous specification of the A/P and D/V axes of the chick inner ear suggests that sensory organ formation is a multi-step phenomenon, rather than a single inductive event.

Comparative transcriptomic analysis of flowering induction in pitaya induced by supplementary lighting

2019 ◽  
Author(s):  
Rui Xiong ◽  
Liu Chengli ◽  
Min Xu ◽  
Shuang-Shuang Wei ◽  
Hua Tang
Keyword(s):  
Time Course ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Floral Induction ◽  
Transcriptomic Analysis ◽  
Pcr Analysis ◽  
Reverse Transcription Pcr ◽  
Transcription Factor Genes ◽  
Supplementary Lighting ◽  
Transcriptomic Level

Abstract Background Pitayas are currently attracting considerable interest as a fruit with many health benefits. However, the lack of natural light after November in Hainan, China, severely restricts the production of pitaya in winter. To further explore the molecular mechanisms regulating flowering in pitaya, we used de novo RNA sequencing-based transcriptomic analysis for four stages of pitaya subjected to light induction. Results We assembled 68113 unigenes in total, comprising 29782 unigenes with functional annotations in the NR database, 20716 annotations in SwissProt, 18088 annotations in KOG, and 11059 annotations in KEGG. Comparison between different samples revealed different numbers of significantly differentially expressed genes (DEGs). A number of DEGs involved in energy metabolism-related processes and plant hormones were detected. Moreover, we discovered many CONSTANS-LIKE, FLOWERING LOCUS T and other DEGs involved in direct regulation of flowering, along with CDF and TCP, which function as typical transcription factor genes in the flowering process. At the transcriptomic level, we confirmed 13 DEGs with different functions in the time-course response to light-induced flowering by quantitative reverse-transcription PCR analysis. Conclusions These DEGs may include some key genes that control the floral-induction network, increasing our understanding of the molecular mechanism of floral regulation in pitaya. These findings will also aid the development of biotechnologies aimed at creating a variant of pitaya that is less sensitive to light conditions and blooms throughout the year.

scholarly journals An animal model study on the gene expression profile of meniscal degeneration

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Yehan Fang ◽  
Hui Huang ◽  
Gang Zhou ◽  
Qinghua Wang ◽  
Feng Gao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Pathway Analysis ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Control Group ◽  
Ion Binding ◽  
Endoplasmic Reticulum Membrane ◽  
Rt Pcr ◽  
Go Analysis ◽  
Meniscal Degeneration

AbstractMeniscal degeneration is a very common condition in elderly individuals, but the underlying mechanisms of its occurrence are not completely clear. This study examines the molecular mechanisms of meniscal degeneration. The anterior cruciate ligament (ACL) and lateral collateral ligament (LCL) of the right rear limbs of seven Wuzhishan mini-pigs were resected (meniscal degeneration group), and the left rear legs were sham-operated (control group). After 6 months, samples were taken for gene chip analysis, including differentially expressed gene (DEG) analysis, gene ontology (GO) analysis, clustering analysis, and pathway analysis. The selected 12 DEGs were validated by real time reverse transcription-polymerase chain reaction (RT-PCR). The two groups showed specific and highly clustered DEGs. A total of 893 DEGs were found, in which 537 are upregulated, and 356 are downregulated. The GO analysis showed that the significantly affected biological processes include nitric oxide metabolic process, male sex differentiation, and mesenchymal morphogenesis, the significantly affected cellular components include the endoplasmic reticulum membrane, and the significantly affected molecular functions include transition metal ion binding and iron ion binding. The pathway analysis showed that the significantly affected pathways include type II diabetes mellitus, inflammatory mediator regulation of TRP channels, and AMPK signaling pathway. The results of RT-PCR indicate that the microarray data accurately reflects the gene expression patterns. These findings indicate that several molecular mechanisms are involved in the development of meniscal degeneration, thus improving our understanding of meniscal degeneration and provide molecular therapeutic targets in the future.

scholarly journals Gene Expression Patterns Underlying the Reinstatement of Plasticity in the Adult Visual System

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
Ettore Tiraboschi ◽  
Ramon Guirado ◽  
Dario Greco ◽  
Petri Auvinen ◽  
Jose Fernando Maya-Vetencourt ◽  
...  
Keyword(s):  
Gene Expression ◽  
Visual Cortex ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Monocular Deprivation ◽  
Adult Brain ◽  
Gene Expression Patterns ◽  
Postnatal Life ◽  
Critical Periods

The nervous system is highly sensitive to experience during early postnatal life, but this phase of heightened plasticity decreases with age. Recent studies have demonstrated that developmental-like plasticity can be reactivated in the visual cortex of adult animals through environmental or pharmacological manipulations. These findings provide a unique opportunity to study the cellular and molecular mechanisms of adult plasticity. Here we used the monocular deprivation paradigm to investigate large-scale gene expression patterns underlying the reinstatement of plasticity produced by fluoxetine in the adult rat visual cortex. We found changes, confirmed with RT-PCRs, in gene expression in different biological themes, such as chromatin structure remodelling, transcription factors, molecules involved in synaptic plasticity, extracellular matrix, and excitatory and inhibitory neurotransmission. Our findings reveal a key role for several molecules such as the metalloproteases Mmp2 and Mmp9 or the glycoprotein Reelin and open up new insights into the mechanisms underlying the reopening of the critical periods in the adult brain.

scholarly journals Effects of Cutting, Pruning, and Grafting on the Expression of Age-Related Genes in Larix kaempferi

Forests ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 218
Author(s):  
Yao Zhang ◽  
Qiao-Lu Zang ◽  
Li-Wang Qi ◽  
Su-Ying Han ◽  
Wan-Feng Li
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Regular Expression ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Reproductive Development ◽  
Larix Kaempferi ◽  
Clonal Forestry ◽  
Cdna Sequences ◽  
Age Related

Grafting, cutting, and pruning are important horticultural techniques widely used in the establishment of clonal forestry. After the application of these techniques, some properties of the plants change, however, the underlying molecular mechanisms are still unclear. In our previous study, 27 age-related transcripts were found to be expressed differentially between the juvenile vegetative (1- and 2-year-old) and adult reproductive (25- and 50-year-old) phases of Larix kaempferi. Here, we re-analyzed the 27 age-related transcripts, cloned their full-length cDNA sequences, and measured their responses to grafting, cutting, and pruning. After sequence analysis and cloning, 20 transcription factors were obtained and annotated, most of which were associated with reproductive development, and six (LaAGL2-1, LaAGL2-2, LaAGL2-3, LaSOC1-1, LaAGL11, and LaAP2-2) showed regular expression patterns with L. kaempferi aging. Based on the expression patterns of these transcription factors in L. kaempferi trees subjected to grafting, cutting, and pruning, we concluded that (1) cutting and pruning rejuvenate the plants and change their expression, and the effects of cutting on gene expression are detectable within 14 years, although the cutting seedlings are still maturing during these years; (2) within three months after grafting, the rootstock is more sensitive to grafting than the scion and readily becomes mature with the effect of the scion, while the scion is not readily rejuvenated by the effect of the rootstock; and (3) LaAGL2-2 and LaAGL2-3 are more sensitive to grafting, while LaAP2-2 is impervious to it. These findings not only provide potential molecular markers to assess the state of plants but also aid in studies of the molecular mechanisms of rejuvenation.

scholarly journals Comparative Genomics and Transcriptomics To Analyze Fruiting Body Development in Filamentous Ascomycetes

Genetics ◽  
2019 ◽  
Vol 213 (4) ◽  
pp. 1545-1563 ◽  
Author(s):  
Ramona Lütkenhaus ◽  
Stefanie Traeger ◽  
Jan Breuer ◽  
Laia Carreté ◽  
Alan Kuo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fruiting Body ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Comparative Transcriptomics ◽  
Fruiting Bodies ◽  
Body Development ◽  
Fruiting Body Development ◽  
Genes Encoding

Many filamentous ascomycetes develop three-dimensional fruiting bodies for production and dispersal of sexual spores. Fruiting bodies are among the most complex structures differentiated by ascomycetes; however, the molecular mechanisms underlying this process are insufficiently understood. Previous comparative transcriptomics analyses of fruiting body development in different ascomycetes suggested that there might be a core set of genes that are transcriptionally regulated in a similar manner across species. Conserved patterns of gene expression can be indicative of functional relevance, and therefore such a set of genes might constitute promising candidates for functional analyses. In this study, we have sequenced the genome of the Pezizomycete Ascodesmis nigricans, and performed comparative transcriptomics of developing fruiting bodies of this fungus, the Pezizomycete Pyronema confluens, and the Sordariomycete Sordaria macrospora. With only 27 Mb, the A. nigricans genome is the smallest Pezizomycete genome sequenced to date. Comparative transcriptomics indicated that gene expression patterns in developing fruiting bodies of the three species are more similar to each other than to nonsexual hyphae of the same species. An analysis of 83 genes that are upregulated only during fruiting body development in all three species revealed 23 genes encoding proteins with predicted roles in vesicle transport, the endomembrane system, or transport across membranes, and 13 genes encoding proteins with predicted roles in chromatin organization or the regulation of gene expression. Among four genes chosen for functional analysis by deletion in S. macrospora, three were shown to be involved in fruiting body formation, including two predicted chromatin modifier genes.

Tissue Microarray Is a Useful Tool in the Evaluation of Genes Implicated in Transformation of Follicular Lymphoma.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 2267-2267 ◽  
Author(s):  
Abigail Lee ◽  
Andrew Davies ◽  
Andrew Clear ◽  
Maria Calaminici ◽  
Janet Matthews ◽  
...  
Keyword(s):  
Gene Expression ◽  
Follicular Lymphoma ◽  
Tissue Microarray ◽  
Molecular Mechanisms ◽  
De Novo ◽  
B Cell Lymphoma ◽  
Follicular Dendritic Cell ◽  
Response To Therapy ◽  
Aurora Kinase B ◽  
General Response

Abstract A subset of patients (pts.) with follicular lymphoma (FL) will transform to a more aggressive histological sub-type, most typically diffuse large B-cell lymphoma (DLBCL). In general response to therapy is poor and survival short. Paired analysis of samples pre- and post transformation suggest that the molecular mechanisms underlying transformation (Tx) are heterogeneous. In order to independently validate recurring changes in gene/protein expression at transformation (GC phenotype of TxDLBCL, Davies et al., 2002; loss of follicular dendritic Cell (FDC) markers, Shiozawa et al., 2003) a Tx-tissue microarray (Tx-TMA) was created comprising serial samples from 35 pts. (median age 54yrs (22–81) at the time of transformation). In these pts. transformation occurred a median of 3.1years from diagnosis (range 0–15.4) and for each pt. ‘set’ at least 1 pre-Tx FL sample (1–3; n=56), and 1 (1–4; n=44) post transformation sample were represented on the array. To ensure that the Tx-TMA cores accurately represented the corresponding full tissue sections a panel of routine immunohistochemical (IHC) diagnostic markers (n=9) were scored. The concordance between Tx-TMA and full sections (n=10) was >90%. The Tx-TMA was then used to investigate the phenotype of transformed DLBCL, according to the germinal centre (GC)/non-GC like model of de novo DLBCL. Using CD10, BCL6 and MUM1 expression to discriminate between the two subclasses of DLBCL the methodology was first validated on a de novo DLBCL TMA (n=31; 20/31 (65%) non-GC, 11/31 (35%) GC phenotype; 5-yr survival for non-GC pts. 51% and for GC pts., 73%). IHC confirmed the results of gene expression profiling indicating that in 31/35 (89%) pts. transformed DLBCL was of GC phenotype (28/35 (80%) CD10+ and 3/35 (9%) CD10-, BCL6+, MUM1-). Of the remainder, 4/35 were CD10-, BCL6+, of which 3/4 were MUM1+ (3/35 (9%) non-GC phenotype; 1/4 MUM1 was not assessable). Similarly the Tx-TMA confirmed loss of FDC markers (CD21 and CD23) on transformation. Samples from 28 pts were evaluable for CD21 and CD23 IHC expression. In 71% (20/28) of pts. the FDC meshwork was lost or became more sparse on transformation (CD21 loss 15/28 (54%); CD23 loss 17/28 (61%)). The most discriminating changes in gene expression on transformation are now being assessed by IHC. Aurora kinase B (ARKB) is an attractive therapeutic target given that disruption of ARK function results in the induction of apoptosis in RL, a t(14:18) positive DLBCL cell line (Harrington et al. 2004). The observed elevation in ARKB transcription on transformation was confirmed by IHC in this series. The Tx-TMA showed ARKB expression increased on Tx in 13/33 (40%) pts., potentially defining a subset of pts. who might be considered for ARKB directed therapies. Expression of ARKB was low throughout in 18/33 (55%) pts and decreased in 2/33 (6%) pts.; difference in ARKB expression was not significantly associated with survival. These preliminary studies suggest that the availability of TMA of serial biopsies from pts. with transformed FL will provide a powerful means of assessing the relevance of gene expression, both within the tumour and the microenvironment while facilitating the selection of patients most likely to benefit from directed therapeutic approaches.

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