scholarly journals Molecular Cloning ofphd1and Comparative Analysis ofphd1, 2, and3Expression inXenopus laevis

2012 ◽  
Vol 2012 ◽  
pp. 1-6 ◽  
Author(s):  
Dandan Han ◽  
Luan Wen ◽  
Yonglong Chen
Keyword(s):  
Comparative Analysis ◽  
Embryonic Development ◽  
Gall Bladder ◽  
Molecular Cloning ◽  
Gene Targeting ◽  
Expression Patterns ◽  
Systematic Analysis ◽  
Adult Tissues ◽  
Inxenopus Laevis ◽  
And Function

Intensive gene targeting studies in mice have revealed that prolyl hydroxylase domain proteins (PHDs) play important roles in murine embryonic development; however, the expression patterns and function of these genes during embryogenesis of other vertebrates remain largely unknown. Here we report the molecular cloning ofphd1and systematic analysis ofphd1,phd2, andphd3expression in embryos as well as adult tissues ofXenopus laevis. All threephdsare maternally provided duringXenopusearly development. The spatial expression patterns ofphdsgenes inXenopusembryos appear to define a distinct synexpression group. Frogphd2andphd3showed complementary expression in adult tissues withphd2transcription levels being high in the eye, brain, and intestine, but low in the liver, pancreas, and kidney. On the contrary, expression levels ofphd3are high in the liver, pancreas, and kidney, but low in the eye, brain, and intestine. All threephdsare highly expressed in testes, ovary, gall bladder, and spleen. Among threephds,phd3showed strongest expression in heart.

scholarly journals Enhancer analysis of the Drosophila zinc finger transcription factor Earmuff by gene targeting

Hereditas ◽  
2021 ◽  
Vol 158 (1) ◽  
Author(s):  
Kirsten Hildebrandt ◽  
Sabrina Kübel ◽  
Marie Minet ◽  
Nora Fürst ◽  
Christine Klöppel ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Gene Targeting ◽  
Zinc Finger ◽  
Neural Progenitor Cells ◽  
Expression Patterns ◽  
Brain Structures ◽  
Systematic Analysis ◽  
Major Function ◽  
Stem Cell Maintenance ◽  
The Brain

Abstract Background Many transcription factors are involved in the formation of the brain during the development of Drosophila melanogaster. The transcription factor Earmuff (Erm), a member of the forebrain embryonic zinc finger family (Fezf), is one of these important factors for brain development. One major function of Earmuff is the regulation of proliferation within type II neuroblast lineages in the brain; here, Earmuff is expressed in intermediate neural progenitor cells (INPs) and balances neuronal differentiation versus stem cell maintenance. Erm expression during development is regulated by several enhancers. Results In this work we show a functional analysis of erm and some of its enhancers. We generated a new erm mutant allele by gene targeting and reintegrated Gal4 to make an erm enhancer trap strain that could also be used on an erm mutant background. The deletion of three of the previously analysed enhancers showing the most prominent expression patterns of erm by gene targeting resulted in specific temporal and spatial defects in defined brain structures. These defects were already known but here could be assigned to specific enhancer regions. Conclusion This analysis is to our knowledge the first systematic analysis of several large enhancer deletions of a Drosophila gene by gene targeting and will enable deeper analysis of erm enhancer functions in the future.

scholarly journals Analysis of Medicago truncatula Nodule Expressed Sequence Tags

2000 ◽  
Vol 13 (1) ◽  
pp. 62-71 ◽  
Author(s):  
János Györgyey ◽  
Danièle Vaubert ◽  
José I. Jiménez-Zurdo ◽  
Celine Charon ◽  
Liliane Troussard ◽  
...  
Keyword(s):  
Medicago Truncatula ◽  
Expressed Sequence Tags ◽  
Sinorhizobium Meliloti ◽  
Expression Patterns ◽  
Homology Search ◽  
Cdna Clones ◽  
Systematic Analysis ◽  
And Function ◽  
Nodulin Genes ◽  
Expressed Sequence

Systematic sequencing of expressed sequence tags (ESTs) can give a global picture of the assembly of genes involved in the development and function of organs. Indeterminate nodules representing different stages of the developmental program are especially suited to the study of organogenesis. With the vector λHybriZAP, a cDNA library was constructed from emerging nodules of Medicago truncatula induced by Sinorhizobium meliloti. The 5′ ends of 389 cDNA clones were sequenced, then these ESTs were analyzed both by sequence homology search and by studying their expression in roots and nodules. Two hundred fifty-six ESTs exhibited significant similarities to characterized data base entries and 40 of them represented 26 nodulin genes, while 133 had no similarity to sequences with known function. Only 60 out of the 389 cDNA clones corresponded to previously submitted M. truncatula EST sequences. For 117 cDNAs, reverse Northern (RNA) hybridization with root and nodule RNA probes revealed enhanced expression in the nodule, 48 clones are likely to code for novel nodulins, 33 cDNAs are clones of already known nodulin genes, and 36 clones exhibit similarity to other characterized genes. Thus, systematic analysis of the EST sequences and their expression patterns is a powerful way to identify nodule-specific and nodulation-related genes.

scholarly journals Identifying Conserved Generic Aspergillus spp. Co-Expressed Gene Modules Associated with Germination Using Cross-Platform and Cross-Species Transcriptomics

2021 ◽  
Vol 7 (4) ◽  
pp. 270
Author(s):  
Tim J. H. Baltussen ◽  
Jordy P. M. Coolen ◽  
Paul E. Verweij ◽  
Jan Dijksterhuis ◽  
Willem J. G. Melchers
Keyword(s):  
Comparative Analysis ◽  
Expression Patterns ◽  
Biological Processes ◽  
Polarized Growth ◽  
Black Module ◽  
Cross Platform ◽  
Gene Modules ◽  
Opportunistic Human Pathogen ◽  
Dependent Transport ◽  
Blue Module

Aspergillus spp. is an opportunistic human pathogen that may cause a spectrum of pulmonary diseases. In order to establish infection, inhaled conidia must germinate, whereby they break dormancy, start to swell, and initiate a highly polarized growth process. To identify critical biological processes during germination, we performed a cross-platform, cross-species comparative analysis of germinating A. fumigatus and A. niger conidia using transcriptional data from published RNA-Seq and Affymetrix studies. A consensus co-expression network analysis identified four gene modules associated with stages of germination. These modules showed numerous shared biological processes between A. niger and A. fumigatus during conidial germination. Specifically, the turquoise module was enriched with secondary metabolism, the black module was highly enriched with protein synthesis, the darkgreen module was enriched with protein fate, and the blue module was highly enriched with polarized growth. More specifically, enriched functional categories identified in the blue module were vesicle formation, vesicular transport, tubulin dependent transport, actin-dependent transport, exocytosis, and endocytosis. Genes important for these biological processes showed similar expression patterns in A. fumigatus and A. niger, therefore, they could be potential antifungal targets. Through cross-platform, cross-species comparative analysis, we were able to identify biologically meaningful modules shared by A. fumigatus and A. niger, which underscores the potential of this approach.

scholarly journals Microglial Function and Regulation during Development, Homeostasis and Alzheimer’s Disease

Cells ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 957
Author(s):  
Brad T. Casali ◽  
Erin G. Reed-Geaghan
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Immune Cells ◽  
Expression Patterns ◽  
Brain Parenchyma ◽  
Primary Role ◽  
And Function ◽  
Inflammatory Milieu ◽  
The Brain ◽  
Homeostatic State

Microglia are the resident immune cells of the brain, deriving from yolk sac progenitors that populate the brain parenchyma during development. During development and homeostasis, microglia play critical roles in synaptogenesis and synaptic plasticity, in addition to their primary role as immune sentinels. In aging and neurodegenerative diseases generally, and Alzheimer’s disease (AD) specifically, microglial function is altered in ways that significantly diverge from their homeostatic state, inducing a more detrimental inflammatory environment. In this review, we discuss the receptors, signaling, regulation and gene expression patterns of microglia that mediate their phenotype and function contributing to the inflammatory milieu of the AD brain, as well as strategies that target microglia to ameliorate the onset, progression and symptoms of AD.

scholarly journals Genome-wide identification and analysis of class III peroxidases in Betula pendula

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Kewei Cai ◽  
Huixin Liu ◽  
Song Chen ◽  
Yi Liu ◽  
Xiyang Zhao ◽  
...  
Keyword(s):  
Stress Responses ◽  
Betula Pendula ◽  
Expression Patterns ◽  
Class Iii ◽  
Physiological Processes ◽  
Plant Life ◽  
Genome Wide ◽  
Plant Life Cycle ◽  
Class Iii Peroxidases ◽  
And Function

Abstract Background Class III peroxidases (POD) proteins are widely present in the plant kingdom that are involved in a broad range of physiological processes including stress responses and lignin polymerization throughout the plant life cycle. At present, POD genes have been studied in Arabidopsis, rice, poplar, maize and Chinese pear, but there are no reports on the identification and function of POD gene family in Betula pendula. Results We identified 90 nonredundant POD genes in Betula pendula. (designated BpPODs). According to phylogenetic relationships, these POD genes were classified into 12 groups. The BpPODs are distributed in different numbers on the 14 chromosomes, and some BpPODs were located sequentially in tandem on chromosomes. In addition, we analyzed the conserved domains of BpPOD proteins and found that they contain highly conserved motifs. We also investigated their expression patterns in different tissues, the results showed that some BpPODs might play an important role in xylem, leaf, root and flower. Furthermore, under low temperature conditions, some BpPODs showed different expression patterns at different times. Conclusions The research on the structure and function of the POD genes in Betula pendula plays a very important role in understanding the growth and development process and the molecular mechanism of stress resistance. These results lay the theoretical foundation for the genetic improvement of Betula pendula.

scholarly journals The Gene Targeting Approach of Small Fragment Homologous Replacement (SFHR) Alters the Expression Patterns of DNA Repair and Cell Cycle Control Genes

2016 ◽  
Vol 5 ◽  
pp. e304 ◽  
Author(s):  
Silvia Pierandrei ◽  
Andrea Luchetti ◽  
Massimo Sanchez ◽  
Giuseppe Novelli ◽  
Federica Sangiuolo ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Dna Repair ◽  
Gene Targeting ◽  
Cell Cycle Control ◽  
Expression Patterns ◽  
Small Fragment

The utility of a burn specific measure of pain anxiety to prospectively predict pain and function: a comparative analysis

Burns ◽  
2001 ◽  
Vol 27 (4) ◽  
pp. 329-334 ◽  
Author(s):  
L.A Aaron ◽  
D.R Patterson ◽  
C.P Finch ◽  
G.J Carrougher ◽  
D.M Heimbach
Keyword(s):  
Comparative Analysis ◽  
Specific Measure ◽  
Pain Anxiety ◽  
And Function
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