scholarly journals Muscle and neuronal guidepost-like cells facilitate planarian visual system regeneration

Science ◽  
2020 ◽  
Vol 368 (6498) ◽  
pp. eaba3203 ◽  
Author(s):  
M. Lucila Scimone ◽  
Kutay D. Atabay ◽  
Christopher T. Fincher ◽  
Ashley R. Bonneau ◽  
Dayan J. Li ◽  
...  
Keyword(s):  
Visual System ◽  
De Novo Assembly ◽  
De Novo ◽  
Muscle Cells ◽  
Positional Information ◽  
Neuronal Population ◽  
Neuronal Circuits ◽  
Schmidtea Mediterranea ◽  
Information Cues

Neuronal circuits damaged or lost after injury can be regenerated in some adult organisms, but the mechanisms enabling this process are largely unknown. We used the planarian Schmidtea mediterranea to study visual system regeneration after injury. We identify a rare population of muscle cells tightly associated with photoreceptor axons at stereotyped positions in both uninjured and regenerating animals. Together with a neuronal population, these cells promote de novo assembly of the visual system in diverse injury and eye transplantation contexts. These muscle guidepost-like cells are specified independently of eyes, and their position is defined by an extrinsic array of positional information cues. These findings provide a mechanism, involving adult formation of guidepost-like cells typically observed in embryos, for axon pattern restoration in regeneration.

scholarly journals Peripherin expression in hippocampal neurons induced by muscle soluble factor(s).

1993 ◽  
Vol 123 (5) ◽  
pp. 1197-1206 ◽  
Author(s):  
K Djabali ◽  
A Zissopoulou ◽  
M J de Hoop ◽  
S D Georgatos ◽  
C G Dotti
Keyword(s):  
Skeletal Muscle ◽  
De Novo Assembly ◽  
Hippocampal Neurons ◽  
De Novo ◽  
Muscle Cells ◽  
Skeletal Muscle Cells ◽  
Phenotypic Change ◽  
Target Cells ◽  
Soluble Factor

Previous studies have shown that neuronal cells in culture can switch neurotransmitters when grown in the presence of different target cells. To examine whether this plasticity extends to structural proteins, we cocultured hippocampal neurons and pituitary-derived neuroendocrine (AtT20) cells with astrocytes, kidney epithelial cells, or skeletal muscle cells. As a marker of phenotypic change we used the cytoskeletal protein peripherin, a type III intermediate filament (IF) subunit which is not expressed in hippocampal neurons and AtT20 cells. We show here that soluble factor(s) secreted specifically from skeletal muscle cells can induce the expression and de novo assembly of peripherin in a subset of post-mitotic neurons. We further demonstrate that one of these factors is the Leukemia Inhibitory Factor/Cholinergic Neuronal Differentiation Factor. The environmentally regulated expression of peripherin implies a remarkable degree of plasticity in the cytoskeletal organization of postmitotic CNS cells and provides a noninvasive model system to examine the de novo assembly of IF proteins under in vivo conditions.

scholarly journals Initial Steps of Photosystem II de Novo Assembly and Preloading with Manganese Take Place in Biogenesis Centers in Synechocystis

2012 ◽  
Vol 24 (2) ◽  
pp. 660-675 ◽  
Author(s):  
Anna Stengel ◽  
Irene L. Gügel ◽  
Daniel Hilger ◽  
Birgit Rengstl ◽  
Heinrich Jung ◽  
...  
Keyword(s):  
Photosystem Ii ◽  
De Novo Assembly ◽  
De Novo

scholarly journals Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

2021 ◽  
Vol 18 (2) ◽  
pp. 170-175 ◽  
Author(s):  
Haoyu Cheng ◽  
Gregory T. Concepcion ◽  
Xiaowen Feng ◽  
Haowen Zhang ◽  
Heng Li
Keyword(s):  
De Novo Assembly ◽  
De Novo

scholarly journals A long reads-based de-novo assembly of the genome of the Arlee homozygous line reveals chromosomal rearrangements in rainbow trout

2021 ◽  
Author(s):  
Guangtu Gao ◽  
Susana Magadan ◽  
Geoffrey C Waldbieser ◽  
Ramey C Youngblood ◽  
Paul A Wheeler ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Chromosome Number ◽  
Genome Assembly ◽  
De Novo Assembly ◽  
De Novo ◽  
Sequence Data ◽  
Structural Variations ◽  
High Coverage ◽  
Haploid Chromosome Number ◽  
Long Reads

Abstract Currently, there is still a need to improve the contiguity of the rainbow trout reference genome and to use multiple genetic backgrounds that will represent the genetic diversity of this species. The Arlee doubled haploid line was originated from a domesticated hatchery strain that was originally collected from the northern California coast. The Canu pipeline was used to generate the Arlee line genome de-novo assembly from high coverage PacBio long-reads sequence data. The assembly was further improved with Bionano optical maps and Hi-C proximity ligation sequence data to generate 32 major scaffolds corresponding to the karyotype of the Arlee line (2 N = 64). It is composed of 938 scaffolds with N50 of 39.16 Mb and a total length of 2.33 Gb, of which ∼95% was in 32 chromosome sequences with only 438 gaps between contigs and scaffolds. In rainbow trout the haploid chromosome number can vary from 29 to 32. In the Arlee karyotype the haploid chromosome number is 32 because chromosomes Omy04, 14 and 25 are divided into six acrocentric chromosomes. Additional structural variations that were identified in the Arlee genome included the major inversions on chromosomes Omy05 and Omy20 and additional 15 smaller inversions that will require further validation. This is also the first rainbow trout genome assembly that includes a scaffold with the sex-determination gene (sdY) in the chromosome Y sequence. The utility of this genome assembly is demonstrated through the improved annotation of the duplicated genome loci that harbor the IGH genes on chromosomes Omy12 and Omy13.

scholarly journals De Novo Assembly and Characterization of the Xenocatantops brachycerus Transcriptome

2018 ◽  
Vol 19 (2) ◽  
pp. 520 ◽  
Author(s):  
Le Zhao ◽  
Xinmei Zhang ◽  
Zhongying Qiu ◽  
Yuan Huang
Keyword(s):  
De Novo Assembly ◽  
De Novo

scholarly journals Dataset of de novo assembly and functional annotation of the transcriptomes of three native oleaginous microalgae from the Peruvian Amazon

Data in Brief ◽  
2020 ◽  
Vol 31 ◽  
pp. 105917
Author(s):  
Marianela Cobos ◽  
Hicler N. Rodríguez ◽  
Segundo L. Estela ◽  
Carlos G. Castro ◽  
J. Dylan Maddox ◽  
...  
Keyword(s):  
De Novo Assembly ◽  
Functional Annotation ◽  
De Novo ◽  
Peruvian Amazon ◽  
Oleaginous Microalgae
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