Organization of regionally expressed silkmoth chorion genes

1986 ◽  
Vol 6 (9) ◽  
pp. 3215-3220
Author(s):  
A K Hatzopoulos ◽  
J C Regier
Keyword(s):  
Gene Expression ◽  
Follicle Cells ◽  
Gene Copy ◽  
Late Period ◽  
Chorion Genes ◽  
Copy Numbers ◽  
Total Dna ◽  
Dna Strand ◽  
Gene Copy Numbers ◽  
Silkmoth Chorion

We described the organization of two silkmoth chorion genes, called E1 and E2, whose expression is largely restricted in time to the very late period of choriogenesis and in space to one of two major subpopulations of follicle cells. Using E1 and E2 clone cDNAs as probes, we showed that gene copy numbers per haploid genome remain constant throughout silkmoth development despite major changes in total DNA content per nucleus. Furthermore, gene copy numbers are the same in both cellular regions of the choriogenic follicle despite differences in nuclear size and levels of E gene expression. Southern analysis indicated between two and four copies each for E1 and E2 genes. Analysis of chromosomal clones showed that single copies of E1 and E2 are separated by about 7.5 kilobases and are transcribed from the same DNA strand. Two distinct pairs of cloned E1 and E2 genes were characterized. No other chorion genes were in their immediate vicinity.

scholarly journals Organization of regionally expressed silkmoth chorion genes.

1986 ◽  
Vol 6 (9) ◽  
pp. 3215-3220 ◽  
Author(s):  
A K Hatzopoulos ◽  
J C Regier
Keyword(s):  
Gene Expression ◽  
Follicle Cells ◽  
Gene Copy ◽  
Late Period ◽  
Chorion Genes ◽  
Copy Numbers ◽  
Total Dna ◽  
Dna Strand ◽  
Gene Copy Numbers ◽  
Silkmoth Chorion

We described the organization of two silkmoth chorion genes, called E1 and E2, whose expression is largely restricted in time to the very late period of choriogenesis and in space to one of two major subpopulations of follicle cells. Using E1 and E2 clone cDNAs as probes, we showed that gene copy numbers per haploid genome remain constant throughout silkmoth development despite major changes in total DNA content per nucleus. Furthermore, gene copy numbers are the same in both cellular regions of the choriogenic follicle despite differences in nuclear size and levels of E gene expression. Southern analysis indicated between two and four copies each for E1 and E2 genes. Analysis of chromosomal clones showed that single copies of E1 and E2 are separated by about 7.5 kilobases and are transcribed from the same DNA strand. Two distinct pairs of cloned E1 and E2 genes were characterized. No other chorion genes were in their immediate vicinity.

scholarly journals CopySwitch -in vivooptimization of gene copy numbers for heterologous gene expression inBacillus subtilis

2018 ◽  
Author(s):  
Florian Nadler ◽  
Felix Bracharz ◽  
Johannes Kabisch
Keyword(s):  
Gene Expression ◽  
Bacillus Subtilis ◽  
Gene Dosage ◽  
Heterologous Gene Expression ◽  
Heterologous Gene ◽  
Gene Copy ◽  
Positive Bacterium ◽  
Gram Positive ◽  
Copy Numbers ◽  
Gene Copy Numbers

1.AbstractThe Gram-positive bacteriumBacillus subtilishas long been used as a host for production and secretion of industrially relevant enzymes like amylases and proteases. It is imperative for optimal efficiency, to balance protein yield and correct folding. Gene copy numbers are an important tuning valve for the optimization of heterologous gene expression. While some genes are best expressed from many gene copies, for other genes, medium or even single copy numbers are the only way to avoid formation of inclusion bodies, toxic gene dosage effects or achieve desired levels for metabolic engineering. In order to provide a simple and robust method to address above-mentioned issues in the Gram-positive bacteriumBacillus subtilis, we have developed an automatable system for the tuning of heterologous gene expression based on the host’s intrinsic natural competence and homologous recombination capabilities. By supplying our reporter strains with a linearized, low copy number plasmid containing homology regions left and right of the reporter genes and an antibiotic resistance marker, we could show an up to 3.6-fold highergfp(green fluorescent protein) expression and up to 1.3-fold highermPLC(mature phospholipase C) expression after successful recombination and thus circularization of our plasmid. Furthermore, the plasmid-bornegfpexpression seems to be more stable, since over the whole cultivation period the share of fluorescent cells compared to all measured cells is consistently higher.

257 Genome wide estimation of gene copy numbers in cervical carcinomas: Relationship to gene expression

2006 ◽  
Vol 78 ◽  
pp. S91-S92
Author(s):  
S.R. Brovig ◽  
O.T. Brustugun ◽  
D.H. Svendsrud ◽  
E. Galteland ◽  
P. De Angelis ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Copy ◽  
Cervical Carcinomas ◽  
Copy Numbers ◽  
Genome Wide ◽  
Gene Copy Numbers

Predominance of ammonia-oxidizing archaea andnirK-gene-bearing denitrifiers among ammonia-oxidizing and denitrifying populations in sediments of a large urban eutrophic lake (Lake Donghu)

2013 ◽  
Vol 59 (7) ◽  
pp. 456-464 ◽  
Author(s):  
Jie Hou ◽  
Xiuyun Cao ◽  
Chunlei Song ◽  
Yiyong Zhou
Keyword(s):  
Amoa Gene ◽  
Eutrophic Lake ◽  
Gene Copy ◽  
Nirs Gene ◽  
Bacterial Amoa Gene ◽  
Archaeal Amoa Gene ◽  
Copy Numbers ◽  
Significant Difference ◽  
Nirk Gene ◽  
Gene Copy Numbers

The coupled nitrification–denitrification process plays a pivotal role in cycling and removal of nitrogen in aquatic ecosystems. In the present study, the communities of ammonia oxidizers and denitrifiers in the sediments of 2 basins (Guozhenghu Basin and Tuanhu Basin) of a large urban eutrophic lake (Lake Donghu) were determined using the ammonia monooxygenase subunit A (amoA) gene and the nitrite reductase gene. At all sites of this study, the archaeal amoA gene predominated over the bacterial amoA gene, whereas the functional gene for denitrification nirK gene far outnumbered the nirS gene. Spatially, compared with the Tuanhu Basin, the Guozhenghu Basin showed a significantly greater abundance of the archaeal amoA gene but less abundance of the nirK and nirS genes, while there was no significant difference of bacterial amoA gene copy numbers between the 2 basins. Unlike the archaeal amoA gene, the nirK gene showed a significant difference in community structure between the 2 basins. Archaeal amoA diversity was limited to the water–sediment cluster of Crenarchaeota, in sharp contrast with nirK for which 22 distinct operational taxonomic units were found. Accumulation of organic substances were found to be positively related to nirK and nirS gene copy numbers but negatively related to archaeal amoA gene copy numbers, whereas the abundance of the bacterial amoA gene was related to ammonia concentration.

scholarly journals Evolution of dosage compensation does not depend on genomic background

2020 ◽  
Author(s):  
Michail Rovatsos ◽  
Lukáš Kratochvíl
Keyword(s):  
Dosage Compensation ◽  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Genomic Region ◽  
Gene Copy ◽  
Gene Dose ◽  
Copy Numbers ◽  
Compensation Mechanisms ◽  
Gene Copy Numbers ◽  
Softshell Turtles

AbstractOrganisms evolved various mechanisms to cope with the differences in the gene copy numbers between sexes caused by degeneration of Y and W sex chromosomes. Complete dosage compensation or at least expression balance between sexes was reported predominantly in XX/XY, but rarely in ZZ/ZW systems. However, this often-reported pattern is based on comparisons of lineages where sex chromosomes evolved from non-homologous genomic regions, potentially differing in sensitivity to differences in gene copy numbers. Here we document that two reptilian lineages (XX/XY iguanas and ZZ/ZW softshell turtles), which independently co-opted the same ancestral genomic region for the function of sex chromosomes, evolved different gene dose regulatory mechanisms. The independent co-option of the same genomic region for the role of sex chromosome as in the iguanas and the softshell turtles offers a great opportunity for testing evolutionary scenarios on the sex chromosome evolution under the explicit control for the genomic background and for gene identity. We showed that the parallel loss of functional genes from the Y chromosome of the green anole and the W chromosome of the Florida softshell turtle led to different dosage compensation mechanisms. Our approach controlling for genetic background thus does not support that the variability in the regulation of the gene dose differences is a consequence of ancestral autosomal gene content.

scholarly journals Expanding an expanded genome: long-read sequencing ofTrypanosoma cruzi

2018 ◽  
Author(s):  
Luisa Berná ◽  
Matías Rodríguez ◽  
María Laura Chiribao ◽  
Adriana Parodi-Talice ◽  
Sebastián Pita ◽  
...  
Keyword(s):  
Repetitive Sequences ◽  
Gc Content ◽  
Gene Copy ◽  
Accurate Estimation ◽  
Sequencing Technologies ◽  
Copy Numbers ◽  
Long Reads ◽  
Long Read ◽  
Large Clusters ◽  
Gene Copy Numbers

Although the genome ofTrypanosoma cruzi, the causative agent of Chagas disease, was first made available in 2005, with additional strains reported later, the intrinsic genome complexity of this parasite (abundance of repetitive sequences and genes organized in tandem) has traditionally hindered high-quality genome assembly and annotation. This also limits diverse types of analyses that require high degree of precision. Long reads generated by third-generation sequencing technologies are particularly suitable to address the challenges associated withT. cruzi´sgenome since they permit directly determining the full sequence of large clusters of repetitive sequences without collapsing them. This, in turn, allows not only accurate estimation of gene copy numbers but also circumvents assembly fragmentation. Here, we present the analysis of the genome sequences of twoT. cruziclones: the hybrid TCC (DTU TcVI) and the non-hybrid Dm28c (DTU TcI), determined by PacBio SMRT technology. The improved assemblies herein obtained permitted us to accurately estimate gene copy numbers, abundance and distribution of repetitive sequences (including satellites and retroelements). We found that the genome ofT. cruziis composed of a "core compartment" and a "disruptive compartment" which exhibit opposite gene and GC content composition. New tandem and disperse repetitive sequences were identified, including some located inside coding sequences. Additionally, homologous chromosomes were separately assembled, allowing us to retrieve haplotypes as separate contigs instead of a unique mosaic sequence. Finally, manual annotation of surface multigene families MUC and trans-sialidases allows now a better overview of these complex groups of genes.

scholarly journals Growth of sedimentaryBathyarchaeotaon lignin as an energy source

2018 ◽  
Vol 115 (23) ◽  
pp. 6022-6027 ◽  
Author(s):  
Tiantian Yu ◽  
Weichao Wu ◽  
Wenyue Liang ◽  
Mark Alexander Lever ◽  
Kai-Uwe Hinrichs ◽  
...  
Keyword(s):  
Energy Source ◽  
Estuarine Sediments ◽  
Gene Copy ◽  
Organic Substrates ◽  
Metabolic Functions ◽  
Copy Numbers ◽  
Tetraether Lipids ◽  
Archaeal Lipids ◽  
Gene Copy Numbers ◽  
Direct Confirmation

Members of the archaeal phylumBathyarchaeotaare among the most abundant microorganisms on Earth. Although versatile metabolic capabilities such as acetogenesis, methanogenesis, and fermentation have been suggested for bathyarchaeotal members, no direct confirmation of these metabolic functions has been achieved through growth ofBathyarchaeotain the laboratory. Here we demonstrate, on the basis of gene-copy numbers and probing of archaeal lipids, the growth ofBathyarchaeotasubgroup Bathy-8 in enrichments of estuarine sediments with the biopolymer lignin. Other organic substrates (casein, oleic acid, cellulose, and phenol) did not significantly stimulate growth ofBathyarchaeota. Meanwhile, putative bathyarchaeotal tetraether lipids incorporated13C from13C-bicarbonate only when added in concert with lignin. Our results are consistent with organoautotrophic growth of a bathyarchaeotal group with lignin as an energy source and bicarbonate as a carbon source and shed light into the cycling of one of Earth’s most abundant biopolymers in anoxic marine sediment.

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