scholarly journals Tissue-specific expression profiles and positive selection analysis in the tree swallow (Tachycineta bicolor) using a de novo transcriptome assembly

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Alexandra B. Bentz ◽  
Gregg W. C. Thomas ◽  
Douglas B. Rusch ◽  
Kimberly A. Rosvall
Keyword(s):  
Positive Selection ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Tachycineta Bicolor ◽  
Tree Swallow ◽  
Specific Expression ◽  
Tissue Specific ◽  
Tissue Specific Expression

Abstract Tree swallows (Tachycineta bicolor) are one of the most commonly studied wild birds in North America. They have advanced numerous research areas, including life history, physiology, and organismal responses to global change; however, transcriptomic resources are scarce. To further advance the utility of this system for biologists across disciplines, we generated a transcriptome for the tree swallow using six tissues (brain, blood, ovary, spleen, liver, and muscle) collected from breeding females. We de novo assembled 207,739 transcripts, which we aligned to 14,717 high confidence protein-coding genes. We then characterized each tissue with regard to its unique genes and processes and applied this transcriptome to two fundamental questions in evolutionary biology and endocrinology. First, we analyzed 3,015 single-copy orthologs and identified 46 genes under positive selection in the tree swallow lineage, including those with putative links to adaptations in this species. Second, we analyzed tissue-specific expression patterns of genes involved in sex steroidogenesis and processing. Enzymes capable of synthesizing these behaviorally relevant hormones were largely limited to the ovary, whereas steroid binding genes were found in nearly all other tissues, highlighting the potential for local regulation of sex steroid-mediated traits. These analyses provide new insights into potential sources of phenotypic variation in a free-living female bird and advance our understanding of fundamental questions in evolutionary and organismal biology.

Differential expression of the closely linked KISS1, REN, and FLJ10761 genes in transgenic mice

2004 ◽  
Vol 17 (1) ◽  
pp. 4-10 ◽  
Author(s):  
Ravi Nistala ◽  
Xiaoji Zhang ◽  
Curt D. Sigmund
Keyword(s):  
Transgenic Mice ◽  
Human Chromosome ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Artificial Chromosome ◽  
Chromosome 1 ◽  
Specific Expression ◽  
Tissue Specific ◽  
Tissue Specific Expression ◽  
Human Chromosome 1

We previously reported the development and characterization of transgenic mice containing a large 160-kb P1 artificial chromosome (PAC) encompassing the renin (REN) locus from human chromosome 1. Here we demonstrate that PAC160 not only encodes REN, but also complete copies of the next upstream (KISS1) and downstream ( FLJ10761 ) gene along human chromosome 1. Incomplete copies of the second upstream (PEPP3) and downstream (SOX13) genes are also present. The gene order PEPP3-KISS1-REN-FLJ10761-SOX13 is conserved in mice containing either one or two copies of the REN locus. Despite the close localization of KISS1, REN, and FLJ10761 , they each exhibit distinct, yet overlapping tissue-specific expression profiles in humans. The tissue-specific expression patterns of REN and FLJ10761 were retained in transgenic mice containing PAC160. Expression of REN and FLJ10761 were also proportional to copy number. Expression of KISS1 in PAC160 mice showed both similarities and differences to humans. These data suggest that expression of gene blocks encoded on large genomic clones are retained when the clones are used to generate transgenic mice. Genomic elements which act to insulate genes from their neighbors are also apparently retained.

scholarly journals Identification and functional characterization of ABCC transporters for Cd tolerance and accumulation in Sedum alfredii Hance

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Tongyu Feng ◽  
Xuelian He ◽  
Renying Zhuo ◽  
Guirong Qiao ◽  
Xiaojiao Han ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Uniform Domain ◽  
Sedum Alfredii ◽  
Specific Expression ◽  
Cd Accumulation ◽  
Tissue Specific ◽  
Tissue Specific Expression ◽  
Transporter Family

AbstractCd is one of the potential toxic elements (PTEs) exerting great threats on the environment and living organisms and arising extensive attentions worldwide. Sedum alfredii Hance, a Cd hyperaccumulator, is of great importance in studying the mechanisms of Cd hyperaccumulation and has potentials for phytoremediation. ATP-binding cassette sub-family C (ABCC) belongs to the ABC transporter family, which is deemed to closely associate with multiple physiological processes including cellular homeostasis, metal detoxification, and transport of metabolites. In the present work, ten ABCC proteins were identified in S. alfredii Hance, exhibiting uniform domain structure and divergently clustering with those from Arabidopsis. Tissue-specific expression analysis indicated that some SaABCC genes had significantly higher expression in roots (Sa23221 and Sa88F144), stems (Sa13F200 and Sa14F98) and leaves (Sa13F200). Co-expression network analysis using these five SaABCC genes as hub genes produced two clades harboring different edge genes. Transcriptional expression profiles responsive to Cd illustrated a dramatic elevation of Sa14F190 and Sa18F186 genes. Heterologous expression in a Cd-sensitive yeast cell line, we confirmed the functions of Sa14F190 gene encoding ABCC in Cd accumulation. Our study performed a comprehensive analysis of ABCCs in S. alfredii Hance, firstly mapped their tissue-specific expression patterns responsive to Cd stress, and characterized the roles of Sa14F190 genes in Cd accumulation.

Tissue-specific expression patterns of nuclear receptors

2013 ◽  
Author(s):  
AL Bookout ◽  
Y Jeong ◽  
M Downes ◽  
RT Yu ◽  
RM Evans ◽  
...  
Keyword(s):  
Nuclear Receptors ◽  
Expression Patterns ◽  
Specific Expression ◽  
Tissue Specific ◽  
Tissue Specific Expression

scholarly journals Tissue Distribution of ACE2 Protein in Syrian Golden Hamster (Mesocricetus auratus) and Its Possible Implications in SARS-CoV-2 Related Studies

2021 ◽  
Vol 11 ◽  
Author(s):  
Voddu Suresh ◽  
Deepti Parida ◽  
Aliva P. Minz ◽  
Manisha Sethi ◽  
Bhabani S. Sahoo ◽  
...  
Keyword(s):  
Expression Pattern ◽  
Golden Hamster ◽  
Expression Patterns ◽  
Mesocricetus Auratus ◽  
Syrian Golden Hamster ◽  
Surface Epithelium ◽  
Specific Expression ◽  
Tissue Specific ◽  
Tissue Specific Expression ◽  
Specific Expression Pattern

The Syrian golden hamster (Mesocricetus auratus) has recently been demonstrated as a clinically relevant animal model for SARS-CoV-2 infection. However, lack of knowledge about the tissue-specific expression pattern of various proteins in these animals and the unavailability of reagents like antibodies against this species hampers these models’ optimal use. The major objective of our current study was to analyze the tissue-specific expression pattern of angiotensin-converting enzyme 2, a proven functional receptor for SARS-CoV-2 in different organs of the hamster. Using two different antibodies (MA5-32307 and AF933), we have conducted immunoblotting, immunohistochemistry, and immunofluorescence analysis to evaluate the ACE2 expression in different tissues of the hamster. Further, at the mRNA level, the expression of Ace2 in tissues was evaluated through RT-qPCR analysis. Both the antibodies detected expression of ACE2 in kidney, small intestine, tongue, and liver. Epithelium of proximal tubules of kidney and surface epithelium of ileum expresses a very high amount of this protein. Surprisingly, analysis of stained tissue sections showed no detectable expression of ACE2 in the lung or tracheal epithelial cells. Similarly, all parts of the large intestine were negative for ACE2 expression. Analysis of tissues from different age groups and sex didn’t show any obvious difference in ACE2 expression pattern or level. Together, our findings corroborate some of the earlier reports related to ACE2 expression patterns in human tissues and contradict others. We believe that this study’s findings have provided evidence that demands further investigation to understand the predominant respiratory pathology of SARS-CoV-2 infection and disease.

scholarly journals Characterization of Embryonic Skin Transcriptome in Anser cygnoides at Three Feather Follicles Developmental Stages

2019 ◽  
Vol 10 (2) ◽  
pp. 443-454
Author(s):  
Chang Liu ◽  
Cornelius Tlotliso Sello ◽  
Yujian Sui ◽  
Jingtao Hu ◽  
Shaokang Chen ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Developmental Stages ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Mitogen Activated Protein Kinase ◽  
Receptor Interaction ◽  
Keratinocyte Proliferation ◽  
Skin Development

In order to enrich the Anser cygnoides genome and identify the gene expression profiles of primary and secondary feather follicles development, de novo transcriptome assembly of skin tissues was established by analyzing three developmental stages at embryonic day 14, 18, and 28 (E14, E18, E28). Sequencing output generated 436,730,608 clean reads from nine libraries and de novo assembled into 56,301 unigenes. There were 2,298, 9,423 and 12,559 unigenes showing differential expression in three stages respectively. Furthermore, differentially expressed genes (DEGs) were functionally classified according to genes ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and series-cluster analysis. Relevant specific GO terms such as epithelium development, regulation of keratinocyte proliferation, morphogenesis of an epithelium were identified. In all, 15,144 DEGs were clustered into eight profiles with distinct expression patterns and 2,424 DEGs were assigned to 198 KEGG pathways. Skin development related pathways (mitogen-activated protein kinase signaling pathway, extra-cellular matrix -receptor interaction, Wingless-type signaling pathway) and genes (delta like canonical Notch ligand 1, fibroblast growth factor 2, Snail family transcriptional repressor 2, bone morphogenetic protein 6, polo like kinase 1) were identified, and eight DEGs were selected to verify the reliability of transcriptome results by real-time quantitative PCR. The findings of this study will provide the key insights into the complicated molecular mechanism and breeding techniques underlying the developmental characteristics of skin and feather follicles in Anser cygnoides.

The Murine Genome Contains Two Functional Kininogen Genes Leading to Tissue Specific Expression of High Molecular Weight Kininogen (HK) and Expression of a Novel HK Splice Variant.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 3979-3979
Author(s):  
Sergei Merkoulov ◽  
Anton A. Komar ◽  
Keith R. McCrae
Keyword(s):  
Molecular Weight ◽  
High Molecular Weight ◽  
Expression Patterns ◽  
Endothelial Cell Proliferation ◽  
Head Orientation ◽  
High Molecular Weight Kininogen ◽  
Specific Expression ◽  
Tissue Specific ◽  
Tissue Specific Expression ◽  
Exon 10

Abstract High molecular weight kininogen (HK) plays an important role in the assembly and activation of the kallikrein/kinin system. While the human genome contains only a single copy of the kininogen gene, three copies are present in the rat (one K-kininogen and two T-kininogen). Here, we report that the mouse genome contains two homologous kininogen genes (overall homology 91%), denoted mHK1 and mHK2. Both genes are located on chromosome 16 in a head-to-head orientation, and contain open reading frames. The size of intronic sequences between the 11 kininogen gene exons is similar (Figure). HK mRNA transcripts derived from the mHK1 and mHK2 genes differ slightly in size due to gaps of 33 and 18 nucleotides in exon 10 of mHK2. RT-PCR analysis of HK gene expression in adult and embryonic murine tissues revealed that HK mRNA was derived from mHK1 in liver, adrenal and embryo, but from mHK2 in kidney and lung. HK mRNA derived from both genes was present in testis, brain and muscle, though expression levels were low relative to those in other tissues. HK mRNA was not detected in ovary, bone marrow, heart or bladder. mHK1-derived HK mRNA was alternatively spliced, as demonstrated by the presence of an HK mRNA transcript encoding a novel HK1 isoform, ΔmD5, that lacked the portion of exon 10 encoding Thr400 - Asp582 of HK domains 5 and 6. Examination of the putative promoter regions of the two genes using the MatInspector Professional program (Genomatix) demonstrated distinct differences, perhaps explaining in part their tissue-specific expression patterns. Like domain 5 of human HK (hD5), domain 5 of murine HK (mD5), in which the histidine and lysine-rich C-terminal region of this domain previously shown to mediate the antiangiogenic activity of domain 5 is highly conserved, inhibited endothelial cell proliferation. While the function of each of the kininogen genes in the intact animal has yet to be defined, characterization of the two genes may provide new information concerning the role of high molecular weight kininogen in development, normal physiology, and pathological processes. Figure Figure

scholarly journals Tissue-Specific Expression Patterns of MicroRNA during Acute Graft-versus-Host Disease in the Rat

2016 ◽  
Vol 7 ◽  
Author(s):  
Dasaradha Jalapothu ◽  
Margherita Boieri ◽  
Rachel E. Crossland ◽  
Pranali Shah ◽  
Isha A. Butt ◽  
...  
Keyword(s):  
Graft Versus Host Disease ◽  
Expression Patterns ◽  
Specific Expression ◽  
Tissue Specific ◽  
Host Disease ◽  
Graft Versus Host ◽  
Tissue Specific Expression ◽  
Acute Graft
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