scholarly journals EST analysis of gene expression in early cleavage-stage sea urchin embryos

Development ◽  
1999 ◽  
Vol 126 (17) ◽  
pp. 3857-3867
Author(s):  
Y.H. Lee ◽  
G.M. Huang ◽  
R.A. Cameron ◽  
G. Graham ◽  
E.H. Davidson ◽  
...  
Keyword(s):  
Sea Urchin ◽  
Expressed Sequence Tags ◽  
Early Embryo ◽  
Cytoskeletal Proteins ◽  
Open Reading Frames ◽  
Protein Coding ◽  
Est Analysis ◽  
Signaling Systems ◽  
Sea Urchin Embryos ◽  
Expressed Sequence

A set of 956 expressed sequence tags derived from 7-hour (mid-cleavage) sea urchin embryos was analyzed to assess biosynthetic functions and to illuminate the structure of the message population at this stage. About a quarter of the expressed sequence tags represented repetitive sequence transcripts typical of early embryos, or ribosomal and mitochondrial RNAs, while a majority of the remainder contained significant open reading frames. A total of 232 sequences, including 153 different proteins, produced significant matches when compared against GenBank. The majority of these identified sequences represented ‘housekeeping’ proteins, i.e., cytoskeletal proteins, metabolic enzymes, transporters and proteins involved in cell division. The most interesting finds were components of signaling systems and transcription factors not previously reported in early sea urchin embryos, including components of Notch and TGF signal transduction pathways. As expected from earlier kinetic analyses of the embryo mRNA populations, no very prevalent protein-coding species were encountered; the most highly represented such sequences were cDNAs encoding cyclins A and B. The frequency of occurrence of all sequences within the database was used to construct a sequence prevalence distribution. The result, confirming earlier mRNA population analyses, indicated that the poly(A) RNA of the early embryo consists mainly of a very complex set of low-copy-number transcripts.

scholarly journals Analysis of Expressed Sequence Tags from Uromyces appendiculatus Hyphae and Haustoria and Their Comparison to Sequences from Other Rust Fungi

2008 ◽  
Vol 98 (10) ◽  
pp. 1126-1135 ◽  
Author(s):  
D. P. Puthoff ◽  
A. Neelam ◽  
M. L. Ehrenfried ◽  
B. E. Scheffler ◽  
L. Ballard ◽  
...  
Keyword(s):  
Expressed Sequence Tags ◽  
Sequence Data ◽  
Cellular Function ◽  
Rust Fungi ◽  
Open Reading Frames ◽  
Uromyces Appendiculatus ◽  
Data Set ◽  
Uromyces Fabae ◽  
Expressed Sequence ◽  
Reading Frames

Hyphae, 2 to 8 days postinoculation (dpi), and haustoria, 5 dpi, were isolated from Uromyces appendiculatus infected bean leaves (Phaseolus vulgaris cv. Pinto 111) and a separate cDNA library prepared for each fungal preparation. Approximately 10,000 hyphae and 2,700 haustoria clones were sequenced from both the 5′ and 3′ ends. Assembly of all of the fungal sequences yielded 3,359 contigs and 927 singletons. The U. appendiculatus sequences were compared with sequence data for other rust fungi, Phakopsora pachyrhizi, Uromyces fabae, and Puccinia graminis. The U. appendiculatus haustoria library included a large number of genes with unknown cellular function; however, summation of sequences of known cellular function suggested that haustoria at 5 dpi had fewer transcripts linked to protein synthesis in favor of energy metabolism and nutrient uptake. In addition, open reading frames in the U. appendiculatus data set with an N-terminal signal peptide were identified and compared with other proteins putatively secreted from rust fungi. In this regard, a small family of putatively secreted RTP1-like proteins was identified in U. appendiculatus and P. graminis.

scholarly journals EST Analysis for the Study of Cold Stress in Blueberry (Vaccinium spp.)

HortScience ◽  
2004 ◽  
Vol 39 (4) ◽  
pp. 861D-862
Author(s):  
Anik L. Dhanaraj* ◽  
Janet P. Slovin ◽  
Lisa J. Rowland
Keyword(s):  
Cold Stress ◽  
Expressed Sequence Tags ◽  
The Other ◽  
Cdna Libraries ◽  
Functional Categories ◽  
High Quality ◽  
Est Analysis ◽  
Woody Perennial ◽  
Winter Conditions ◽  
Expressed Sequence

To gain a better understanding of changes in gene expression associated with cold stress in the woody perennial blueberry (Vaccinium spp.), a genomics approach based on the analysis of expressed sequence tags (ESTs) was undertaken. Two cDNA libraries were constructed using RNA from cold acclimated (mid winter conditions when the plants are cold stressed) and non-acclimated (before they received any chilling) floral buds of the blueberry cultivar Bluecrop. About 600 5'-end ESTs were generated from each of the libraries. Putative functions were assigned to 57% of the cDNAs that yielded high quality sequences based on homology to other genes/ESTs from Genbank, and these were classified into 14 functional categories. From a contig analysis, which clustered sequences derived from the same or very similar genes, 430 and 483 unique transcripts were identified from the cold acclimated and non-acclimated libraries, respectively. Of the total unique transcripts, only 4.3% were shared between the libraries, suggesting marked differences in the genes expressed under the two conditions. The most highly abundant cDNAs that were picked many more times from one library than from the other were identified as representing potentially differentially expressed transcripts. Northern analyses were performed to examine expression of eight selected transcripts and seven of these were confirmed to be preferentially expressed under either cold acclimating or non-acclimating conditions. Only one of the seven transcripts, encoding a dehydrin, had been found previously to be up-regulated during cold stress of blueberry. This study demonstrates that analysis of ESTs is an effective strategy to identify candidate cold-responsive transcripts in blueberry.

scholarly journals β-Catenin is essential for patterning the maternally specified animal-vegetal axis in the sea urchin embryo

1998 ◽  
Vol 95 (16) ◽  
pp. 9343-9348 ◽  
Author(s):  
Athula H. Wikramanayake ◽  
Ling Huang ◽  
William H. Klein
Keyword(s):  
Sea Urchin ◽  
Molecular Mechanisms ◽  
Early Embryo ◽  
Cell Fates ◽  
Cell Stage ◽  
Signal Transduction Cascade ◽  
Sea Urchin Embryos ◽  
Sea Urchin Embryo ◽  
Vegetal Pole ◽  
Vegetal Cell

In sea urchin embryos, the animal-vegetal axis is specified during oogenesis. After fertilization, this axis is patterned to produce five distinct territories by the 60-cell stage. Territorial specification is thought to occur by a signal transduction cascade that is initiated by the large micromeres located at the vegetal pole. The molecular mechanisms that mediate the specification events along the animal–vegetal axis in sea urchin embryos are largely unknown. Nuclear β-catenin is seen in vegetal cells of the early embryo, suggesting that this protein plays a role in specifying vegetal cell fates. Here, we test this hypothesis and show that β-catenin is necessary for vegetal plate specification and is also sufficient for endoderm formation. In addition, we show that β-catenin has pronounced effects on animal blastomeres and is critical for specification of aboral ectoderm and for ectoderm patterning, presumably via a noncell-autonomous mechanism. These results support a model in which a Wnt-like signal released by vegetal cells patterns the early embryo along the animal–vegetal axis. Our results also reveal similarities between the sea urchin animal–vegetal axis and the vertebrate dorsal–ventral axis, suggesting that these axes share a common evolutionary origin.

scholarly journals In SilicoExpressed Sequence Tag Analysis in Identification of Probable Diabetic Genes as Virtual Therapeutic Targets

2013 ◽  
Vol 2013 ◽  
pp. 1-9
Author(s):  
Pabitra Mohan Behera ◽  
Deepak Kumar Behera ◽  
Aparajeya Panda ◽  
Anshuman Dixit ◽  
Payodhar Padhi
Keyword(s):  
Expressed Sequence Tags ◽  
Therapeutic Targets ◽  
Gene Products ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Putative Gene ◽  
Est Analysis ◽  
Treatment Of Diabetes ◽  
Conceptual Translation ◽  
Expressed Sequence

The expressed sequence tags (ESTs) are major entities for gene discovery, molecular transcripts, and single nucleotide polymorphism (SNPs) analysis as well as functional annotation of putative gene products. In our quest for identification of novel diabetic genes as virtual targets for type II diabetes, we searched various publicly available databases and found 7 reported genes. Thein silicoEST analysis of these reported genes produced 6 consensus contigs which illustrated some good matches to a number of chromosomes of the human genome. Again the conceptual translation of these contigs produced 3 protein sequences. The functional and structural annotations of these proteins revealed some important features which may lead to the discovery of novel therapeutic targets for the treatment of diabetes.

scholarly journals Building the cytokinetic contractile ring in an early embryo: Initiation as clusters of myosin II, anillin and septin, and visualization of a septin filament network

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0252845
Author(s):  
Chelsea Garno ◽  
Zoe H. Irons ◽  
Courtney M. Gamache ◽  
Quenelle McKim ◽  
Gabriela Reyes ◽  
...  
Keyword(s):  
Sea Urchin ◽  
Animal Cell ◽  
Myosin Ii ◽  
Super Resolution ◽  
Early Embryo ◽  
Contractile Ring ◽  
Sea Urchin Embryos ◽  
Structural Progression ◽  
Filament Network ◽  
Septin Filament

The cytokinetic contractile ring (CR) was first described some 50 years ago, however our understanding of the assembly and structure of the animal cell CR remains incomplete. We recently reported that mature CRs in sea urchin embryos contain myosin II mini-filaments organized into aligned concatenated arrays, and that in early CRs myosin II formed discrete clusters that transformed into the linearized structure over time. The present study extends our previous work by addressing the hypothesis that these myosin II clusters also contain the crucial scaffolding proteins anillin and septin, known to help link actin, myosin II, RhoA, and the membrane during cytokinesis. Super-resolution imaging of cortices from dividing embryos indicates that within each cluster, anillin and septin2 occupy a centralized position relative to the myosin II mini-filaments. As CR formation progresses, the myosin II, septin and anillin containing clusters enlarge and coalesce into patchy and faintly linear patterns. Our super-resolution images provide the initial visualization of anillin and septin nanostructure within an animal cell CR, including evidence of a septin filament-like network. Furthermore, Latrunculin-treated embryos indicated that the localization of septin or anillin to the myosin II clusters in the early CR was not dependent on actin filaments. These results highlight the structural progression of the CR in sea urchin embryos from an array of clusters to a linearized purse string, the association of anillin and septin with this process, and provide the visualization of an apparent septin filament network with the CR structure of an animal cell.

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