scholarly journals Expanding the miRNA Repertoire in Atlantic Salmon; Discovery of IsomiRs and miRNAs Highly Expressed in Different Tissues and Developmental Stages

Cells ◽  
2019 ◽  
Vol 8 (1) ◽  
pp. 42 ◽  
Author(s):  
Nardos Woldemariam ◽  
Oleg Agafonov ◽  
Bjørn Høyheim ◽  
Ross Houston ◽  
John Taggart ◽  
...  
Keyword(s):  
Atlantic Salmon ◽  
Target Gene ◽  
Hox Genes ◽  
Developmental Stages ◽  
Allelic Variation ◽  
Gene Diversity ◽  
Analysis Pipeline ◽  
Mirna Genes ◽  
Target Diversity ◽  
Predominant Expression

MicroRNAs (miRNAs) are important post-transcriptional gene expression regulators. Here, 448 different miRNA genes, including 17 novel miRNAs, encoding for 589 mature Atlantic salmon miRNAs were identified after sequencing 111 samples (fry, pathogen challenged fry, various developmental and adult tissues). This increased the reference miRNAome with almost one hundred genes. Prior to isomiR characterization (mature miRNA variants), the proportion of erroneous sequence variants (ESVs) arising in the analysis pipeline was assessed. The ESVs were biased towards 5’ and 3’ end of reads in unexpectedly high proportions indicating that measurements of ESVs rather than Phred score should be used to avoid misinterpreting ESVs as isomiRs. Forty-three isomiRs were subsequently discovered. The biological effect of the isomiRs measured as increases in target diversity was small (<3%). Five miRNA genes showed allelic variation that had a large impact on target gene diversity if present in the seed. Twenty-one miRNAs were ubiquitously expressed while 31 miRNAs showed predominant expression in one or few tissues, indicating housekeeping or tissue specific functions, respectively. The miR-10 family, known to target Hox genes, were highly expressed in the developmental stages. The proportion of miR-430 family members, participating in maternal RNA clearance, was high at the earliest developmental stage.

scholarly journals Wnt/β-catenin Pathway-Mediated PPARδ Expression during Embryonic Development Differentiation and Disease

2021 ◽  
Vol 22 (4) ◽  
pp. 1854
Author(s):  
Tabinda Sidrat ◽  
Zia-Ur Rehman ◽  
Myeong-Don Joo ◽  
Kyeong-Lim Lee ◽  
Il-Keun Kong
Keyword(s):  
Embryonic Development ◽  
Transcriptional Activation ◽  
Target Gene ◽  
Developmental Stages ◽  
Embryonic Stem ◽  
Hereditary Diseases ◽  
Peroxisome Proliferator ◽  
Peroxisome Proliferator Activated Receptor ◽  
Stem Cell Regulation ◽  
Early Developmental

The Wnt/β-catenin signaling pathway plays a crucial role in early embryonic development. Wnt/β-catenin signaling is a major regulator of cell proliferation and keeps embryonic stem cells (ESCs) in the pluripotent state. Dysregulation of Wnt signaling in the early developmental stages causes several hereditary diseases that lead to embryonic abnormalities. Several other signaling molecules are directly or indirectly activated in response to Wnt/β-catenin stimulation. The crosstalk of these signaling factors either synergizes or opposes the transcriptional activation of β-catenin/Tcf4-mediated target gene expression. Recently, the crosstalk between the peroxisome proliferator-activated receptor delta (PPARδ), which belongs to the steroid superfamily, and Wnt/β-catenin signaling has been reported to take place during several aspects of embryonic development. However, numerous questions need to be answered regarding the function and regulation of PPARδ in coordination with the Wnt/β-catenin pathway. Here, we have summarized the functional activation of the PPARδ in co-ordination with the Wnt/β-catenin pathway during the regulation of several aspects of embryonic development, stem cell regulation and maintenance, as well as during the progression of several metabolic disorders.

scholarly journals Safe-Site Effects on Rhizosphere Bacterial Communities in a High-Altitude Alpine Environment

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Sonia Ciccazzo ◽  
Alfonso Esposito ◽  
Eleonora Rolli ◽  
Stefan Zerbe ◽  
Daniele Daffonchio ◽  
...  
Keyword(s):  
High Altitude ◽  
Developmental Stage ◽  
Bacterial Communities ◽  
Developmental Stages ◽  
Gene Diversity ◽  
Intergenic Spacer ◽  
Intermediate Stage ◽  
Plant Colonization ◽  
Early Developmental Stage ◽  
Rrna Gene

The rhizosphere effect on bacterial communities associated with three floristic communities (RW, FI, and M sites) which differed for the developmental stages was studied in a high-altitude alpine ecosystem. RW site was an early developmental stage, FI was an intermediate stage, M was a later more matured stage. The N and C contents in the soils confirmed a different developmental stage with a kind of gradient from the unvegetated bare soil (BS) site through RW, FI up to M site. The floristic communities were composed of 21 pioneer plants belonging to 14 species. Automated ribosomal intergenic spacer analysis showed different bacterial genetic structures per each floristic consortium which differed also from the BS site. When plants of the same species occurred within the same site, almost all their bacterial communities clustered together exhibiting a plant species effect. Unifrac significance value (P<0.05) on 16S rRNA gene diversity revealed significant differences (P<0.05) between BS site and the vegetated sites with a weak similarity to the RW site. The intermediate plant colonization stage FI did not differ significantly from the RW and the M vegetated sites. These results pointed out the effect of different floristic communities rhizospheres on their soil bacterial communities.

scholarly journals Genetic population structure of mangrove jack, Lutjanus argentimaculatus (Forsskål)

2003 ◽  
Vol 54 (2) ◽  
pp. 127 ◽  
Author(s):  
Jennifer R. Ovenden ◽  
Raewyn Street
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Allelic Variation ◽  
Gene Diversity ◽  
Haplotype Diversity ◽  
Genetic Population Structure ◽  
Western Coast ◽  
Base Pairs ◽  
Genetic Population ◽  
Lutjanus Argentimaculatus

Translocations of mangrove jack, Lutjanus argentimaculatus (Forsskål 1775), to increase angling opportunities in artificial impoundments are foreshadowed in Queensland. To evaluate genetic population structure before translocations occur, mangrove jack were collected from three sites on the Queensland coast and from one site on the north-western coast of Western Australia. Allelic variation at four dinucleotide microsatellite loci was high: gene diversity (heterozygosity) ranged from 0.602 to 0.930 and allelic counts from 10 to 24. Genetic differentiation among collection sites was weak: estimates of FST were 0.002 for all four sites, and less (FST = 0.001) across a major biogeographical boundary (the Torres Strait region). Nucleotide sequence from two mitochondrial regions (control, 375 base pairs, and ATPase, 415 base pairs) was obtained from a subset of the Australian and additional Indo-Pacific (Indonesian and Samoan) mangrove jack. Haplotype diversity was high (control region, 33 haplotypes for 34 fish; ATPase region, 13 haplotypes for 56 fish). Phylogenetic analysis of mitochondrial DNA sequence data could not discern a relationship between tree topology and geography. These results suggest that mangrove jack in Queensland, and possibly throughout Australia, experience high levels of gene flow. The artificial gene flow caused by permitted translocations is unlikely to exceed natural levels. Fine-scale ecological matching between donor and recipient populations may increase stocking success, and is important if translocation is needed as a species recovery tool in the future.

scholarly journals A Preliminary Single-Cell RNA-Seq Analysis of Embryonic Cells That Express Brachyury in the Amphioxus, Branchiostoma japonicum

2021 ◽  
Vol 9 ◽  
Author(s):  
Noriyuki Satoh ◽  
Hitoshi Tominaga ◽  
Masato Kiyomoto ◽  
Kanako Hisata ◽  
Jun Inoue ◽  
...  
Keyword(s):  
Single Cell ◽  
Hox Genes ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Embryonic Cells ◽  
Rna Seq ◽  
Tail Bud ◽  
Developmental Features ◽  
Number Of Cells ◽  
In Cells

Among chordate taxa, the cephalochordates diverged earlier than urochordates and vertebrates; thus, they retain unique, primitive developmental features. In particular, the amphioxus notochord has muscle-like properties, a feature not seen in urochordates or vertebrates. Amphioxus contains two Brachyury genes, Bra1 and Bra2. Bra2 is reportedly expressed in the blastopore, notochord, somites, and tail bud, in contrast to a low level of Bra1 expression only in notochord. To distinguish the expression profiles of the two Brachyury genes at the single-cell level, we carried out single-cell RNA-seq (scRNA-seq) analysis using the amphioxus, Branchiostoma japonicum. This scRNA-seq analysis classified B. japonicum embryonic cells into 15 clusters at developmental stages from midgastrula to early swimming larva. Brachyury was expressed in cells of clusters 4, 5, 8, and 9. We first confirmed that cluster 8 comprises cells that form somites since this cluster specifically expresses four myogenic factor genes. Cluster 9 contains a larger number of cells with high levels of Bra2 expression and a smaller number of cells with Bra1 expression. Simultaneous expression in cluster 9 of tool-kit genes, including FoxA, Goosecoid, and hedgehog, showed that this cluster comprises cells that form the notochord. Expression of Bra2, but not Bra1, in cells of clusters 4 and 5 at the gastrula stage together with expression of Wnt1 and Caudal indicates that clusters 4 and 5 comprise cells of the blastopore, which contiguously form the tail bud. In addition, Hox1, Hox3, and Hox4 were highly expressed in Bra2-expressing clusters 4, 5, 8, and 9 in a temporally coordinated manner, suggesting roles of anterior Hox genes in specification of mesodermal organs, including somites, notochord, and tail bud. This scRNA-seq analysis therefore highlights differences between the two Brachyury genes in relation to embryonic regions in which they are expressed and their levels of expression. Bra2 is the ancestral Brachyury in amphioxus, since expression in the blastopore is shared with other deuterostomes. On the other hand, Bra1 is a duplicate copy and likely evolved a supplementary function in notochord and somite formation in the Branchiostoma lineage.

scholarly journals Identification and Allelic Variation of Genes Involved in the Potato Glycoalkaloid Biosynthetic Pathway

2012 ◽  
Author(s):  
Idit Ginzberg ◽  
Richard E. Veilleux ◽  
James G. Tokuhisa
Keyword(s):  
Transgenic Plants ◽  
Candidate Genes ◽  
Biosynthetic Pathway ◽  
Developmental Stages ◽  
Allelic Variation ◽  
Mevalonic Acid ◽  
Transcript Abundance ◽  
Primary Metabolism ◽  
E Coli ◽  
Isoprenoid Pathway

Steroidal glycoalkaloids (SGAs) are secondary metabolites being part of the plant defense response. The two major SGAs in cultivated potato (Solanum tuberosum) are α-chaconine and α-solanine, which exhibit strong cellular lytic properties and inhibit acetylcholinesterase activity, and are poisonous at high concentrations for humans. As SGAs are not destroyed during cooking and frying commercial cultivars have been bred to contain low levels, and their content in tubers should not exceed 20 mg/100 g fresh weight. However, environmental factors can increase tuber SGA content above the safe level. The focus of the proposed research was to apply genomic approaches to identify candidate genes that control potato SGA content in order to develop tools for potato improvement by marker-assisted selection and/or transgenic approaches. To this end, the objectives of the proposal included identification of genes, metabolic intermediates and allelic variations in the potato SGAbiosynthetic pathway.   The SGAs are biosynthesized by the sterol branch of the mevalonic acid/isoprenoid pathway. Transgenic potato plants that overexpress 3-hydroxy-3-methylglutaryl-CoA reductase 1 (HMG1) or squalene synthase 1 (SQS1), key enzymes of the mevalonic acid/isoprenoid pathway, exhibited elevated levels of solanine and chaconine as well as induced expression of genes downstream the pathway. These results suggest of coordinated regulation of isoprenoid (primary) metabolism and SGA secondary metabolism. The transgenic plants were further used to identify new SGA-related candidate genes by cDNA-AFLP approach and a novel glycosyltransferase was isolated. In addition, genes involved in phytosterol biosynthesis may have dual role and synthesize defense-related steroidal metabolites, such as SGAs, via lanosterol pathway. Potato lanosterol synthase sequence (LAS) was isolated and used to prepare transgenic plants with overexpressing and silencing constructs. Plants are currently being analyzed for SGA content.   The dynamics of SGA accumulation in the various organs of a potato species with high SGA content gave insights into the general regulation of SGA abundance. Leaf SGA levels in S. chacoense were 10 to 20-fold greater than those of S. tuberosum. The leptines, SGAs with strong antifeedant properties against Colorado potato beetles, were present in all aerial tissues except for early and mid-developmental stages of above ground stolons, and accounted for the high SGA content of S. chacoense. These results indicate the presence of regulatory mechanisms in most tissues except in stolons that limit the levels of α-solanine and α-chaconine and confine leptine accumulation to the aerial tissues.   The genomes of cultivated and wild potato contain a 4-member gene family coding for SQS. Three orthologs were cloned as cDNAs from S. chacoense and heterologously expressed in E. coli. Squalene accumulated in all E. coli lines transformed with each of the three gene constructs. Differential transcript abundance in various organs and amino acid sequence differences in the conserved domains of three isoenzymes indicate subfunctionalization of SQS activity and triterpene/sterol metabolism.   Because S. chacoense and S. phureja differ so greatly for presence and accumulation of SGAs, we selected four candidate genes from different points along the biosynthetic pathway to determine if chcor phuspecific alleles were associated with SGA expression in a segregating interspecific diploid population. For two of the four genes (HMG2 and SGT2) F2 plants with chcalleles expressed significantly greater total SGAs compared with heterozygotes and those with phualleles. Although there are other determinants of SGA biosynthesis and composition in potato, the ability of allelic states at two genes to affect SGA levels confirms some of the above transgenic work where chcalleles at two other loci altered SGA expression in Desiree.   Present results reveal new opportunities to manipulate triterpene/sterol biosynthesis in more targeted ways with the objective of altering SGA content for both human health concerns and natural pesticide content without disrupting the essential metabolism and function of the phytosterol component of the membranes and the growth regulating brassinosteroids.

scholarly journals Tissue specificity of rat mitochondrial dimethylglycine dehydrogenase expression

1994 ◽  
Vol 299 (2) ◽  
pp. 393-398 ◽  
Author(s):  
H Lang ◽  
K Minaian ◽  
N Freudenberg ◽  
R Hoffmann ◽  
R Brandsch
Keyword(s):  
Liver Cell ◽  
Developmental Stages ◽  
Cell Types ◽  
Western Blots ◽  
Ito Cells ◽  
Proximal Tubule Cells ◽  
Total Rna ◽  
Liver And Kidney ◽  
High Level ◽  
Predominant Expression

Expression of mitochondrial dimethylglycine dehydrogenase (Me2GlyDH) was analysed in various tissues, liver cell types and developmental stages of the rat. Total RNA extracted from liver, spleen, brain, kidney, lung and heart was reverse-transcribed into cDNA and amplified with Me2GlyDH cDNA-specific oligonucleotides by PCR. Expression of the enzyme was observed mainly in liver and kidney. In addition, Me2GlyDH mRNA could be demonstrated in total RNA samples of lung, heart and brain but was barely detectable in spleen total RNA. In RNA prepared from 14-day rat embryos, Me2GlyDH-specific mRNA was clearly present. Among various liver cell types, besides hepatocytes, endothelial cells showed a high level of Me2GlyDH mRNA expression. There was no amplification product detectable in liver macrophages (Kupffer cells) and only a very faint one in fat-storing cells (Ito cells). Western blots confirmed at the protein level the predominant expression of the enzyme in liver and kidney, but Me2GlyDH protein was also present in the protein extract of lung, heart, spleen and brain. Immunohistochemical staining of liver slices with Me2GlyDH-specific antiserum revealed that expression of this enzyme is evenly distributed throughout the liver tissue. In the kidney, expression of the enzyme was located in the proximal tubule cells. Our results demonstrate that, contrary to the previously assumed liver-restricted expression, this enzyme is specifically expressed predominantly in the liver and kidney, but, in addition, it is detectable in many other tissues of the rat.

Body shape and fin size in juvenile Atlantic salmon (Salmo salar): effects of temperature during embryogenesis

2021 ◽  
pp. 381-389
Author(s):  
Larry Greenberg ◽  
Bror Jonsson ◽  
Johnny R. Norrgård ◽  
Ann Erlandsson ◽  
Eva Bergman
Keyword(s):  
Global Warming ◽  
Atlantic Salmon ◽  
Salmo Salar ◽  
Body Shape ◽  
Developmental Stages ◽  
Swimming Performance ◽  
Later Life ◽  
Climate Change Scenarios ◽  
Population Declines ◽  
Atlantic Salmon Salmo Salar

Temperature during egg incubation and early development influences later life stages of fishes, potentially influencing survival. Throughout its distribution, Atlantic salmon (Salmo salar Linnaeus, 1758) have experienced population declines, and in view of ongoing global warming, we tested if temperature during the earliest developmental stages modified body shape and fin size when temperatures averaged 2.6 vs. 5.6 °C. This temperature difference simulates increases predicted in climate change scenarios. Based on previous studies, we hypothesized that salmon originating from eggs subjected to cold incubation temperatures would have slimmer bodies and larger pectoral and dorsal fins than salmon from eggs that experienced warmer temperatures. After hatching, the juveniles were raised for 1 year under identical temperatures, after which we measured their body shape and fin areas. We found no support for our hypothesis regarding body shape. Indeed, we found the opposite, with cold-incubated salmon having deeper bodies than warm-incubated salmon. For fin size, the pectoral fins of cold-incubated salmon were larger than for warm-incubated salmon as predicted, but there was no difference in dorsal fin size. These results suggest that global warming may lead to altered body shape and fin size, possibly affecting swimming performance, and thus raise questions about the ecological consequences of the changes.

Zebrafish hox genes: expression in the hindbrain region of wild-type and mutants of the segmentation gene, valentino

Development ◽  
1998 ◽  
Vol 125 (3) ◽  
pp. 393-406 ◽  
Author(s):  
V.E. Prince ◽  
C.B. Moens ◽  
C.B. Kimmel ◽  
R.K. Ho
Keyword(s):  
Gene Expression ◽  
Gene Product ◽  
Hox Genes ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Critical Role ◽  
Loss Of Function ◽  
Hox Gene ◽  
Segmentation Gene ◽  
Functional Changes

The developing hindbrain is organized into a series of segments termed rhombomeres which represent lineage restricted compartments correlating with domains of gene expression and neuronal differentiation. In this study, we investigate the processes of hindbrain segmentation and the acquisition of segmental identity by analyzing the expression of zebrafish hox genes in the hindbrains of normal fish and fish with a loss-of-function mutation in the segmentation gene valentino (val, the homologue of mouse kreisler; Moens, C. B., Cordes, S. P. Giorgianni, M. W., Barsh, G. S. and Kimmel, C. B. (1998). Development 125, 381–391). We find that zebrafish hox genes generally have similar expression profiles to their murine and avian counterparts, although there are several differences in timing and spatial extent of expression which may underlie some of the functional changes that have occurred along the separate evolutionary lineages of teleosts and tetrapods. Our analysis of hox gene expression in val- embryos confirms that the val gene product is important for subdivision of the presumptive rhombomere 5 and 6 territory into definitive rhombomeres, suggests that the val gene product plays a critical role in regulating hox gene transcription, and indicates that some neural crest cells are inappropriately specified in val- embryos. Our analysis of gene expression at several developmental stages has allowed us to infer differences between primary and secondary defects in the val mutant: we find that extended domains of expression for some hox genes are secondary, late phenomena potentially resulting from inappropriate cell mixing or lack of normal inter-rhombomeric interactions in the caudal hindbrain.

Hox repression of a target gene: extradenticle-independent, additive action through multiple monomer binding sites

Development ◽  
2002 ◽  
Vol 129 (13) ◽  
pp. 3115-3126 ◽  
Author(s):  
Ron Galant ◽  
Christopher M. Walsh ◽  
Sean B. Carroll
Keyword(s):  
Binding Sites ◽  
Target Gene ◽  
Target Genes ◽  
Hox Genes ◽  
Regulatory Element ◽  
Morphological Diversity ◽  
Hox Proteins ◽  
Cis Element ◽  
Additive Action ◽  
Hox Protein

Homeotic (Hox) genes regulate the identity of structures along the anterior-posterior axis of most animals. The low DNA-binding specificities of Hox proteins have raised the question of how these transcription factors selectively regulate target gene expression. The discovery that the Extradenticle (Exd)/Pbx and Homothorax (Hth)/Meis proteins act as cofactors for several Hox proteins has advanced the view that interactions with cofactors are critical to the target selectivity of Hox proteins. It is not clear, however, to what extent Hox proteins also regulate target genes in the absence of cofactors. In Drosophila melanogaster, the Hox protein Ultrabithorax (Ubx) promotes haltere development and suppresses wing development by selectively repressing many genes of the wing-patterning hierarchy, and this activity requires neither Exd nor Hth function. Here, we show that Ubx directly regulates a flight appendage-specific cis-regulatory element of the spalt (sal) gene. We find that multiple monomer Ubx-binding sites are required to completely repress this cis-element in the haltere, and that individual Ubx-binding sites are sufficient to mediate its partial repression. These results suggest that Hox proteins can directly regulate target genes in the absence of the cofactor Extradenticle. We propose that the regulation of some Hox target genes evolves via the accumulation of multiple Hox monomer binding sites. Furthermore, because the development and morphological diversity of the distal parts of most arthropod and vertebrate appendages involve Hox, but not Exd/Pbx or Hth/Meis proteins, this mode of target gene regulation appears to be important for distal appendage development and the evolution of appendage diversity.

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