scholarly journals Peer Review #1 of "Brain transcriptome sequencing and assembly of three songbird model systems for the study of social behavior (v0.1)"

2014 ◽  
Keyword(s):  
Social Behavior ◽  
Peer Review ◽  
Transcriptome Sequencing ◽  
Model Systems ◽  
Brain Transcriptome

scholarly journals Brain transcriptome sequencing and assembly of three songbird model systems for the study of social behavior

PeerJ ◽  
2014 ◽  
Vol 2 ◽  
pp. e396 ◽  
Author(s):  
Christopher N. Balakrishnan ◽  
Motoko Mukai ◽  
Rusty A. Gonser ◽  
John C. Wingfield ◽  
Sarah E. London ◽  
...  
Keyword(s):  
Social Behavior ◽  
Transcriptome Sequencing ◽  
Model Systems ◽  
Brain Transcriptome

scholarly journals Brain transcriptome sequencing and assembly of three songbird model systems for the study of social behavior

2014 ◽  
Author(s):  
Christopher N Balakrishnan ◽  
Motoko Mukai ◽  
Rusty A Gonser ◽  
John C Wingfield ◽  
Sarah E London ◽  
...  
Keyword(s):  
Social Behavior ◽  
Vocal Communication ◽  
Bird Species ◽  
Model Systems ◽  
Zonotrichia Albicollis ◽  
Protein Coding ◽  
Brain Transcriptome ◽  
Successful Isolation ◽  
Primary Determinant ◽  
Zonotrichia Leucophrys Gambelii

Emberizid sparrows (emberizidae) have played a prominent role in the study of avian vocal communication and social behavior. We present here brain transcriptomes for three emberizid model systems, song sparrow Melospiza melodia, white-throated sparrow Zonotrichia albicollis, and Gambel’s white-crowned sparrow Zonotrichia leucophrys gambelii. Each of the assemblies covered fully or in part, 80% of the previously annotated protein coding genes in the zebra finch Taeniopygia guttata, with transcript assembly N50s ranging from 2,557 to 4,072. As in previous studies, we find tissue of origin (auditory forebrain versus hypothalamus and whole brain) as a primary determinant of overall expression profile. We also demonstrate the successful isolation of RNA and RNA-sequencing from post-mortem samples from building strikes and suggest that such an approach could be useful when traditional sampling opportunities are limited. These transcriptomes will be an important resource for the study of social behavior in birds and for data driven annotation of forthcoming whole genome sequences for these and other bird species.

scholarly journals Brain transcriptome sequencing and assembly of three songbird model systems for the study of social behavior

2014 ◽  
Author(s):  
Christopher N Balakrishnan ◽  
Motoko Mukai ◽  
Rusty A Gonser ◽  
Elaina M Tuttle ◽  
David F Clayton ◽  
...  
Keyword(s):  
Social Behavior ◽  
Vocal Communication ◽  
Bird Species ◽  
Model Systems ◽  
Zonotrichia Albicollis ◽  
Protein Coding ◽  
Brain Transcriptome ◽  
Successful Isolation ◽  
Primary Determinant ◽  
Zonotrichia Leucophrys Gambelii

Emberizid sparrows (emberizidae) have played a prominent role in the study of avian vocal communication and social behavior. We present here brain transcriptomes for three emberizid model systems, song sparrow Melospiza melodia, white-throated sparrow Zonotrichia albicollis, and Gambel’s white-crowned sparrow Zonotrichia leucophrys gambelii. Each of the assemblies covered fully or in part, 80% of the previously annotated protein coding genes in the zebra finch Taeniopygia guttata, with transcript assembly N50s ranging from 2,557 to 4,072. As in previous studies, we find tissue of origin (auditory forebrain versus hypothalamus and whole brain) as a primary determinant of overall expression profile. We also demonstrate the successful isolation of RNA and RNA-sequencing from post-mortem samples from building strikes and suggest that such an approach could be useful when traditional sampling opportunities are limited. These transcriptomes will be an important resource for the study of social behavior in birds and for data driven annotation of forthcoming whole genome sequences for these and other bird species.

scholarly journals Brain transcriptome sequencing and assembly of three songbird model systems for the study of social behavior

2014 ◽  
Author(s):  
Christopher N Balakrishnan ◽  
Motoko Mukai ◽  
Rusty A Gonser ◽  
John C Wingfield ◽  
Sarah E London ◽  
...  
Keyword(s):  
Social Behavior ◽  
Vocal Communication ◽  
Bird Species ◽  
Model Systems ◽  
Zonotrichia Albicollis ◽  
Protein Coding ◽  
Brain Transcriptome ◽  
Successful Isolation ◽  
Primary Determinant ◽  
Zonotrichia Leucophrys Gambelii

Emberizid sparrows (emberizidae) have played a prominent role in the study of avian vocal communication and social behavior. We present here brain transcriptomes for three emberizid model systems, song sparrow Melospiza melodia, white-throated sparrow Zonotrichia albicollis, and Gambel’s white-crowned sparrow Zonotrichia leucophrys gambelii. Each of the assemblies covered fully or in part, over 89% of the previously annotated protein coding genes in the zebra finch Taeniopygia guttata, with 16,846, 15,805, and 16,646 unique BLAST hits in song, white-throated and white-crowned sparrows, respectively. As in previous studies, we find tissue of origin (auditory forebrain versus hypothalamus and whole brain) as a primary determinant of overall expression profile. We also demonstrate the successful isolation of RNA and RNA-sequencing from post-mortem samples from building strikes and suggest that such an approach could be useful when traditional sampling opportunities are limited. These transcriptomes will be an important resource for the study of social behavior in birds and for data driven annotation of forthcoming whole genome sequences for these and other bird species.

scholarly journals Brain transcriptome sequencing and assembly of three songbird model systems for the study of social behavior

2014 ◽  
Author(s):  
Christopher N Balakrishnan ◽  
Motoko Mukai ◽  
Rusty A Gonser ◽  
John C Wingfield ◽  
Sarah E London ◽  
...  
Keyword(s):  
Social Behavior ◽  
Vocal Communication ◽  
Bird Species ◽  
Model Systems ◽  
Zonotrichia Albicollis ◽  
Protein Coding ◽  
Brain Transcriptome ◽  
Successful Isolation ◽  
Primary Determinant ◽  
Zonotrichia Leucophrys Gambelii

Emberizid sparrows (emberizidae) have played a prominent role in the study of avian vocal communication and social behavior. We present here brain transcriptomes for three emberizid model systems, song sparrow Melospiza melodia, white-throated sparrow Zonotrichia albicollis, and Gambel’s white-crowned sparrow Zonotrichia leucophrys gambelii. Each of the assemblies covered fully or in part, over 89% of the previously annotated protein coding genes in the zebra finch Taeniopygia guttata, with 16,846, 15,805, and 16,646 unique BLAST hits in song, white-throated and white-crowned sparrows, respectively. As in previous studies, we find tissue of origin (auditory forebrain versus hypothalamus and whole brain) as a primary determinant of overall expression profile. We also demonstrate the successful isolation of RNA and RNA-sequencing from post-mortem samples from building strikes and suggest that such an approach could be useful when traditional sampling opportunities are limited. These transcriptomes will be an important resource for the study of social behavior in birds and for data driven annotation of forthcoming whole genome sequences for these and other bird species.

scholarly journals Mouse Model Systems of Autism Spectrum Disorder: Replicability and Informatics Signature

2019 ◽  
Author(s):  
Patricia Kabitzke ◽  
Diana Morales ◽  
Dansha He ◽  
Kimberly Cox ◽  
Jane Sutphen ◽  
...  
Keyword(s):  
Autism Spectrum Disorder ◽  
Social Behavior ◽  
Mouse Model ◽  
Autism Spectrum ◽  
Spectrum Disorder ◽  
Model Systems ◽  
Activity Levels ◽  
Phenotypic Differences ◽  
Genetic Mouse Model ◽  
Unitary Concept

3.AbstractBackgroundPhenotyping mouse model systems of human disease has proven to be a difficult task, with frequent poor inter- and intra-laboratory replicability and translatability, particularly in behavioral domains such as social and verbal function. However, establishing robust animal model systems with strong construct validity is of fundamental importance as they are central tools for understanding disease pathophysiology and developing therapeutics. To complete our studies of mouse model systems relevant to autism spectrum disorder (ASD), we present a replication of the main findings from our two published studies comprising five genetic mouse model systems of ASD.MethodsTo assess the robustness of our previous results, we chose the two model systems that showed the greatest phenotypic differences, the Shank3/F and Cntnap2, and repeated assessments of general health, activity, and social behavior. We additionally explored all five model systems in the same framework, comparing all results obtained in this three-yearlong effort using informatics techniques to look for commonalities and differences.ResultsResults in the current study were very similar to our previously published results. The informatics signatures of the two model systems chosen for the replication showed that they were most distinguished by activity levels. Although the two model systems were opposite in this regard, those aspects of their social behavior not confounded by activity (vocalizations) were similar.ConclusionsOur results showed high intra-laboratory replicability of results, even for those with effect sizes that were not particularly large, suggesting that discrepancies in the literature may be dependent on subtle differences in testing conditions, housing enrichment, or background strains and not so much on the variability of the behavioral phenotypes. The overall informatics analysis suggests two main classes of model systems that in some aspects lie on opposite ends of the behavioral spectrum, supporting the view that autism is not a unitary concept.

scholarly journals Organoid Models for Cancer Research

2019 ◽  
Vol 3 (1) ◽  
pp. 223-234 ◽  
Author(s):  
Hans Clevers ◽  
David A. Tuveson
Keyword(s):  
Cancer Research ◽  
Tumor Microenvironment ◽  
Personalized Medicine ◽  
High Throughput ◽  
Stromal Cells ◽  
Transcriptome Sequencing ◽  
Cancer Biology ◽  
Three Dimensional ◽  
Model Systems ◽  
Liver Cancers

Organoid cultures have emerged as powerful model systems accelerating discoveries in cellular and cancer biology. These three-dimensional cultures are amenable to diverse techniques, including high-throughput genome and transcriptome sequencing, as well as genetic and biochemical perturbation, making these models well suited to answer a variety of questions. Recently, organoids have been generated from diverse human cancers, including breast, colon, pancreas, prostate, bladder, and liver cancers, and studies involving these models are expanding our knowledge of the etiology and characteristics of these malignancies. Co-cultures of cancer organoids with non-neoplastic stromal cells enable investigation of the tumor microenvironment. In addition, recent studies have established that organoids have a place in personalized medicine approaches. Here, we describe the application of organoid technology to cancer discovery and treatment.

scholarly journals Brain Transcriptome Sequencing of a Natural Model of Alzheimer's Disease

2017 ◽  
Vol 9 ◽  
Author(s):  
Francisco Altimiras ◽  
Barbara Uszczynska-Ratajczak ◽  
Francisco Camara ◽  
Anna Vlasova ◽  
Emilio Palumbo ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Transcriptome Sequencing ◽  
Brain Transcriptome ◽  
Model Of Alzheimer’S Disease
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