scholarly journals Expression patterns of Fgf8 and Shh in the developing external genitalia of Suncus murinus

Reproduction ◽  
2017 ◽  
Vol 153 (2) ◽  
pp. 187-195 ◽  
Author(s):  
Mami Miyado ◽  
Kenji Miyado ◽  
Akihiro Nakamura ◽  
Maki Fukami ◽  
Gen Yamada ◽  
...  
Keyword(s):  
Gene Expression ◽  
Developmental Process ◽  
Morphological Changes ◽  
Expression Patterns ◽  
External Genitalia ◽  
Signalling Pathways ◽  
Suncus Murinus ◽  
Fibroblast Growth Factor 8 ◽  
Male External Genitalia ◽  
Species Specific

Reciprocal epithelial–mesenchymal interactions and several signalling pathways regulate the development of the genital tubercle (GT), an embryonic primordium of external genitalia. The morphology of the adult male external genitalia of the Asian house musk shrew Suncus murinus (hereafter, laboratory name: suncus) belonging to the order Eulipotyphla (the former order Insectivora or Soricomorpha) differs from those of mice and humans. However, the developmental process of the suncus GT and its regulatory genes are unknown. In the present study, we explored the morphological changes and gene expression patterns during the development of the suncus GT. Morphological observations suggested the presence of common (during the initial outgrowth) and species-specific (during the sexual differentiation of GT) developmental processes of the suncus GT. In gene expression analysis, fibroblast growth factor 8 (Fgf8) and sonic hedgehog (Shh), an indicator and regulator of GT development in mice respectively, were found to be expressed in the cloacal epithelium and the developing urethral epithelium of the suncus GT. This pattern of expression specifically in GT epithelium is similar to that observed in the developing mouse GT. Our results indicate that the mechanism of GT formation regulated by the FGF and SHH signalling pathways is widely conserved in mammals.

Identification of Differentially Expressed Genes Using cDNA-AFLP During Six Days In Vitro Tuberization of Potato

Zuriat ◽  
2015 ◽  
Vol 14 (1) ◽  
Author(s):  
Nono Carsono ◽  
Christian Bachem
Keyword(s):  
Gene Expression ◽  
Developmental Process ◽  
Expression Patterns ◽  
Induction Medium ◽  
In Vitro Tuberization ◽  
Storage Organ ◽  
Developmentally Regulated ◽  
Study Gene Expression ◽  
Differential Pattern

Tuberization in potato is a complex developmental process resulting in the differentiation of stolon into the storage organ, tuber. During tuberization, change in gene expression has been known to occur. To study gene expression during tuberization over the time, in vitro tuberization system provides a suitable tool, due to its synchronous in tuber formation. An early six days axillary bud growing on tuber induction medium is a crucial development since a large number of genes change in their expression patterns during this period. In order to identify, isolate and sequencing the genes which displaying differential pattern between tuberizing and non-tuberizing potato explants during six days in vitro tuberization, cDNA-AFLP fingerprint, method for the visualization of gene expression using cDNA as template which is amplified to generate an RNA-fingerprinting, was used in this experiment. Seventeen primer combinations were chosen based on their expression profile from cDNA-AFLP fingerprint. Forty five TDFs (transcript derived fragment), which displayed differential expressions, were obtained. Tuberizing explants had much more TDFs, which developmentally regulated, than those from non tuberizing explants. Seven TDFs were isolated, cloned and then sequenced. One TDF did not find similarity in the current databases. The nucleotide sequence of TDF F showed best similarity to invertase ezymes from the databases. The homology of six TDFs with known sequences is discussed in this paper.

scholarly journals Growth, Development, and Gene Expression in a Persistent Streptococcus gordonii Biofilm

2003 ◽  
Vol 71 (8) ◽  
pp. 4759-4766 ◽  
Author(s):  
Keeta S. Gilmore ◽  
Pravina Srinivas ◽  
Darrin R. Akins ◽  
Kenneth L. Hatter ◽  
Michael S. Gilmore
Keyword(s):  
Gene Expression ◽  
Biofilm Formation ◽  
Bacterial Population ◽  
Morphological Changes ◽  
Expression Patterns ◽  
Nutrient Flux ◽  
Gene Expression Patterns ◽  
Significant Shift ◽  
Streptococcus Gordonii ◽  
Growth Development

ABSTRACT A model for the protracted (30-day) colonization of smooth surfaces by Streptococcus gordonii that incorporates the nutrient flux that occurs in the oral cavity was developed. This model was used to characterize the biphasic expansion of the adherent bacterial population, which corresponded with the emergence of higher-order architectures characteristic of biofilms. Biofilm formation by S. gordonii was observed to be influenced by the presence of simple sugars including sucrose, glucose, and fructose. Real-time PCR was used to quantify changes in expression of S. gordonii genes known or thought to be involved in biofilm formation. Morphological changes were accompanied by a significant shift in gene expression patterns. The majority of S. gordonii genes examined were observed to be downregulated in the biofilm phase. Genes found to be upregulated in the biofilm state were observed to encode products related to environmental sensing and signaling.

110 Temporal Changes in Endometrial Gene Expression Between Ipsi- and Contralateral Uterine Horns in Cattle

2018 ◽  
Vol 30 (1) ◽  
pp. 194
Author(s):  
J. M. Sánchez ◽  
C. Passaro ◽  
N. Forde ◽  
S. Behura ◽  
J. A. Browne ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Luteal Phase ◽  
Expression Patterns ◽  
Uterine Horn ◽  
Oestrous Cycle ◽  
Signalling Pathway ◽  
Signalling Pathways ◽  
Robust Analysis ◽  
The Impact

The transfer of an embryo into the uterine horn contralateral to the ovary bearing the corpus luteum has been associated with a decreased pregnancy rate in cattle compared with transfer into the ipsilateral horn. These findings suggest that the environment in the contralateral horn is less conducive to supporting conceptus development than that of the ipsilateral horn. Therefore, this study compared the endometrial transcriptome of the ipsi- and contralateral uterine horns during the luteal phase. Endometrial samples from the ipsi- (IPSI) and contralateral (CONTRA) horns were collected from synchronized nonpregnant beef heifers on Days 5, 7, 13 or 16 post-oestrus (n = 5 heifers per time point). Total RNA was isolated and sequenced. Differences in the transcriptome were determined by edgeR-robust analysis. Principal component analysis found that IPSI and CONTRA have distinct patterns of gene expression on each day, with Day 5 exhibiting the most variation and Day 16 being least variable. Further, the 2 uterine horns had distinct expression patterns on Day 5, with IPSI exhibiting significantly higher variation in gene expression compared twitho CONTRA. EdgeR-robust analysis found 217 (201 up- and 16 down-regulated), 54 (44 up- and 10 down-regulated), 14 (13 up- and 1 down-regulated), and 18 (14 up- and 4 down-regulated) differentially expressed genes (DEG; >2-fold change, false discovery rate P < 0.05) between IPSI and CONTRA endometria on Days 5, 7, 13, and 16 of the oestrous cycle, respectively. The top 5 canonical pathways associated with DEG between IPSI and CONTRA during the luteal phase of the oestrous cycle were involved in signalling pathways regulating pluripotency of stem cells (73/138), progesterone-mediated oocyte maturation (55/89), endometrial cancer (31/51), ErbB signalling pathway (50/87), and mTOR signalling pathway (36/61). The impact of DEG on signalling pathways was assessed using a pathway perturbation algorithm called Signalling Pathway Impact Analysis (SPIA). This topology-based pathway analysis was conducted using the Bioconductor ToPAseq package (https://bioconductor.org/packages/release/bioc/html/ToPASeq.html) and revealed that signalling pathways regulating pluripotency of stem cells showed the highest perturbation score when IPSI was compared with CONTRA irrespective of day. Discovering and cataloguing which pathways are perturbed in each uterine horn throughout the oestrous cycle may contribute to our understanding of the mechanisms underlying early embryonic loss. Ths study was supported by Science Foundation Ireland (13/IA/1983) and the Irish Department of Agriculture, Food and The Marine (13S528).

scholarly journals Symbiotic Outcome Modified by the Diversification from 7 to over 700 Nodule-Specific Cysteine-Rich Peptides

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 348 ◽  
Author(s):  
Proyash Roy ◽  
Mingkee Achom ◽  
Helen Wilkinson ◽  
Beatriz Lagunas ◽  
Miriam L. Gifford
Keyword(s):  
Morphological Changes ◽  
Expression Patterns ◽  
Terminal State ◽  
Rapid Expansion ◽  
Bacterial Cells ◽  
Positive Regulators ◽  
Bacterial Cell Cycle ◽  
Species Specific ◽  
Secreted Peptides

Legume-rhizobium symbiosis represents one of the most successfully co-evolved mutualisms. Within nodules, the bacterial cells undergo distinct metabolic and morphological changes and differentiate into nitrogen-fixing bacteroids. Legumes in the inverted repeat lacking clade (IRLC) employ an array of defensin-like small secreted peptides (SSPs), known as nodule-specific cysteine-rich (NCR) peptides, to regulate bacteroid differentiation and activity. While most NCRs exhibit bactericidal effects in vitro, studies confirm that inside nodules they target the bacterial cell cycle and other cellular pathways to control and extend rhizobial differentiation into an irreversible (or terminal) state where the host gains control over bacteroids. While NCRs are well established as positive regulators of effective symbiosis, more recent findings also suggest that NCRs affect partner compatibility. The extent of bacterial differentiation has been linked to species-specific size and complexity of the NCR gene family that varies even among closely related species, suggesting a more recent origin of NCRs followed by rapid expansion in certain species. NCRs have diversified functionally, as well as in their expression patterns and responsiveness, likely driving further functional specialisation. In this review, we evaluate the functions of NCR peptides and their role as a driving force underlying the outcome of rhizobial symbiosis, where the plant is able to determine the outcome of rhizobial interaction in a temporal and spatial manner.

scholarly journals Beyond the ENCODE project: using genomics and epigenomics strategies to study enhancer evolution

2013 ◽  
Vol 368 (1632) ◽  
pp. 20130022 ◽  
Author(s):  
Noboru Jo Sakabe ◽  
Marcelo A. Nobrega
Keyword(s):  
Gene Expression ◽  
Target Genes ◽  
Expression Patterns ◽  
Dna Interaction ◽  
Regulatory Elements ◽  
Specific Gene ◽  
Genome Wide ◽  
Identify Transcription Factor ◽  
Specific Proteins ◽  
Species Specific

The complex expression patterns observed for many genes are often regulated by distal transcription enhancers. Changes in the nucleotide sequences of enhancers may therefore lead to changes in gene expression, representing a central mechanism by which organisms evolve. With the development of the experimental technique of chromatin immunoprecipitation (ChIP), in which discrete regions of the genome bound by specific proteins can be identified, it is now possible to identify transcription factor binding events (putative cis -regulatory elements) in entire genomes. Comparing protein–DNA binding maps allows us, for the first time, to attempt to identify regulatory differences and infer global patterns of change in gene expression across species. Here, we review studies that used genome-wide ChIP to study the evolution of enhancers. The trend is one of high divergence of cis -regulatory elements between species, possibly compensated by extensive creation and loss of regulatory elements and rewiring of their target genes. We speculate on the meaning of the differences observed and discuss that although ChIP experiments identify the biochemical event of protein–DNA interaction, it cannot determine whether the event results in a biological function, and therefore more studies are required to establish the effect of divergence of binding events on species-specific gene expression.

scholarly journals Evolution of gene expression across species and specialized zooids in Siphonophora

2021 ◽  
Author(s):  
Catriona Munro ◽  
Felipe Zapata ◽  
Mark Howison ◽  
Stefan Siebert ◽  
Casey W Dunn
Keyword(s):  
Gene Expression ◽  
Large Scale ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Gene Trees ◽  
Species Trees ◽  
Examine Gene Expression ◽  
Specialized Tissue ◽  
Species Specific

Background: Siphonophores are complex colonial animals, consisting of asexually-produced bodies (called zooids) that are functionally specialized for specific tasks, including feeding, swimming, and sexual reproduction. Though this extreme functional specialization has captivated biologists for generations, its genomic underpinnings remain unknown. We use RNA-seq to investigate gene expression patterns in five zooids and one specialized tissue (pneumatophore) across seven siphonophore species. Analyses of gene expression across species present several challenges, including identification of comparable expression changes on gene trees with complex histories of speciation, duplication, and loss. Here, we conduct three analyses of expression. First, we examine gene expression within species. Then, we conduct classical analyses examining expression patterns between species. Lastly, we introduce Speciation Branch Filtering, which allows us to examine the evolution of expression in a phylogenetic framework. Results: Within and across species, we identified hundreds of zooid-specific and species-specific genes, as well as a number of putative transcription factors showing differential expression in particular zooids and developmental stages. We found that gene expression patterns tended to be largely consistent in zooids with the same function across species, but also some large lineage-specific shifts in gene expression. Conclusions: Our findings show that patterns of gene expression have the potential to define zooids in colonial organisms. We also show that traditional analyses of the evolution of gene expression focus on the tips of gene phylogenies, identifying large-scale expression patterns that are zooid or species variable. The new explicit phylogenetic approach we propose here focuses on branches (not tips) offering a deeper evolutionary perspective into specific changes in gene expression within zooids along all branches of the gene (and species) trees.

scholarly journals Gene expression and DNA methylation altering lead to the high oil content in wild allotetraploid peanut (A. monticola)

2022 ◽  
Author(s):  
Nian Liu ◽  
Manish Pandey ◽  
Bei Wu ◽  
Li Huang ◽  
Huaiyong Luo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Transcription Factors ◽  
Arachis Hypogaea ◽  
Oil Content ◽  
Expression Patterns ◽  
Gene Clusters ◽  
Oil Accumulation ◽  
Species Specific ◽  
Wild Peanut

Abstract The wild allotetraploid peanut Arachis monticola contains higher oil content than cultivated allotetraploid Arachis hypogaea. To investigate its molecular mechanism controlling oil accumulation, we performed comparative transcriptomics from developing seeds between three Arachis monticola and five Arachis hypogaea varieties. The analysis not only showed species-specific grouping based on transcriptional profiles but also detected two gene clusters with divergent expression patterns enriched in lipid metabolism. Further, the differential expression gene analysis also indicated expression alteration in wild peanut leading to enhanced activity of oil biogenesis and limiting the rate of lipid degradation. We also constructed a regulatory network of lipid metabolic DEGs with co-expressed transcription factors. In addition, bisulfite sequencing was conducted to characterize the variation of DNA methylation between wild allotetraploid (245, WH 10025) and cultivated allotetraploid (Z16, Zhh 7720) genotypes. Genome-wide DNA methylation was found antagonistically correlated with gene expression during seed development. The results indicated that CG and CHG contexts methylation may negatively regulate specific lipid metabolic genes and transcription factors to subtly affect the difference of oil accumulation. Our work provided the first glimpse on the regulatory mechanism of gene expression altering for oil accumulation in wild peanut and gene resources for future breeding applications.

Gene expression profiling of mouse postnatal cerebellar development

2000 ◽  
Vol 4 (2) ◽  
pp. 155-164 ◽  
Author(s):  
RYO MATOBA ◽  
SAKAE SAITO ◽  
NORIKO UENO ◽  
CHIYURI MARUYAMA ◽  
KENICHI MATSUBARA ◽  
...  
Keyword(s):  
Gene Expression ◽  
Developmental Process ◽  
Expression Patterns ◽  
Hierarchical Cluster ◽  
Cerebellar Development ◽  
Functional Categories ◽  
Stages Of Development ◽  
Neurotransmitter Receptor ◽  
Brain Functions ◽  
Or Groups

Expression patterns of 1,869 genes were determined using adapter-tagged competitive PCR (ATAC-PCR) at 6 time points during mouse postnatal cerebellar development. The expression patterns were classified into 12 clusters that were further assembled into 3 groups by hierarchical cluster analysis. Among the 1,869 genes, 1,053 known genes were assigned to 90 functional categories. Statistically significant correlation between the clusters or groups of gene expression and the functional categories was ascertained. Genes involved in oncogenesis or protein synthesis were highly expressed during the earlier stages of development. Those responsible for brain functions such as neurotransmitter receptor and synapse components were more active during the later stages of development. Many other genes also showed expression patterns in accordance with literature information. The gene expression patterns and the inferred functions were in good agreement with anatomical as well as physiological observations made during the developmental process.

scholarly journals Transcriptional Analysis of Clostridium beijerinckii NCIMB 8052 and the Hyper-Butanol-Producing Mutant BA101 during the Shift from Acidogenesis to Solventogenesis

2008 ◽  
Vol 74 (24) ◽  
pp. 7709-7714 ◽  
Author(s):  
Zhen Shi ◽  
Hans P. Blaschek
Keyword(s):  
Gene Expression ◽  
Time Course ◽  
Genomic Sequence ◽  
Morphological Changes ◽  
Expression Patterns ◽  
Sugar Transport ◽  
Clostridium Beijerinckii ◽  
Transcriptional Analysis ◽  
Sequence Information ◽  
Phosphotransferase System

ABSTRACT Clostridium beijerinckii is an anaerobic bacterium used for the fermentative production of acetone and butanol. The recent availability of genomic sequence information for C. beijerinckii NCIMB 8052 has allowed for an examination of gene expression during the shift from acidogenesis to solventogenesis over the time course of a batch fermentation using a ca. 500-gene set DNA microarray. The microarray was constructed using a collection of genes which are orthologs of members of gene families previously found to be important to the physiology of C. acetobutylicum ATCC 824. Similar to the onset of solventogenesis in C. acetobutylicum 824, the onset of solventogenesis in C. beijerinckii 8052 was concurrent with the initiation of sporulation. However, forespores and endospores developed more rapidly in C. beijerinckii 8052 than in C. acetobutylicum 824, consistent with the accelerated expression of the sigE- and sigG-regulated genes in C. beijerinckii 8052. The comparison of gene expression patterns and morphological changes in C. beijerinckii 8052 and the hyper-butanol-producing C. beijerinckii strain BA101 indicated that BA101 was less efficient in sporulation and phosphotransferase system-mediated sugar transport than 8052 but that it exhibited elevated expression of several primary metabolic genes and chemotaxis/motility genes.

scholarly journals Imprints of independent allopolyploid formations on patterns of gene expression in two sibling yarrow species (Achillea, Asteraceae)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Duo Chen ◽  
Peng-Cheng Yan ◽  
Yan-Ping Guo
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Specific Gene ◽  
Differential Adaptation ◽  
Expression Bias ◽  
Parental Gene ◽  
Species Specific ◽  
Go Terms ◽  
Allotetraploid Species

Abstract Background Polyploid species often originate recurrently. While this is well known, there is little information on the extent to which distinct allotetraploid species formed from the same parent species differ in gene expression. The tetraploid yarrow species Achillea alpina and A. wilsoniana arose independently from allopolyploidization between diploid A. acuminata and A. asiatica. The genetics and geography of these origins are clear from previous studies, providing a solid basis for comparing gene expression patterns of sibling allopolyploid species that arose independently. Results We conducted comparative RNA-sequencing analyses on the two Achillea tetraploid species and their diploid progenitors to evaluate: 1) species-specific gene expression and coexpression across the four species; 2) patterns of inheritance of parental gene expression; 3) parental contributions to gene expression in the allotetraploid species, and homeolog expression bias. Diploid A. asiatica showed a higher contribution than diploid A. acuminata to the transcriptomes of both tetraploids and also greater homeolog bias in these transcriptomes, possibly reflecting a maternal effect. Comparing expressed genes in the two allotetraploids, we found expression of ca. 30% genes were species-specific in each, which were most enriched for GO terms pertaining to “defense response”. Despite species-specific and differentially expressed genes between the two allotetraploids, they display similar transcriptome changes in comparison to their diploid progenitors. Conclusion Two independently originated Achillea allotetraploid species exhibited difference in gene expression, some of which must be related to differential adaptation during their post-speciation evolution. On the other hand, they showed similar expression profiles when compared to their progenitors. This similarity might be expected when pairs of merged diploid genomes in tetraploids are similar, as is the case in these two particular allotetraploids.

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