Genome characterization of the selected long- and short-sleep mouse lines

Dowell, Robin D.; Odell, Aaron; Richmond, Phillip A.; Malmer, Daniel; Halper-Stromberg, Eitan; Bennett, Beth; Larson, Colin; Leach, Sonia M.; Radcliffe, Richard A.

doi:10.1007/s00335-016-9663-6

Cited by 6 publications

(6 citation statements)

References 56 publications

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“…Furthermore, mice and rats during peri-adolescent period show shorter sleep time compared to matured rodents [ 32 , 34 ]. In this study, short sleeping of ICR mice at the peri-adolescent period (5−6 weeks old) was similar to previous findings [ 31 - 33 ].…”

Section: Discussionsupporting

confidence: 92%

“…One comprehensive review reported that total sleep times ranged from 6.2 to 14.9 hours in mice and from 13.2 to 15.3 hours in rats [ 31 ]. Total sleep time could be influenced by various factors such as light conditions, genetic strains and ages [ 31 - 33 ]. If there was a longer light period, nocturnal animals slept more [ 31 ].…”

Section: Discussionmentioning

confidence: 99%

“…If there was a longer light period, nocturnal animals slept more [ 31 ]. In addition, it is possible to have different genetic strains between short and long sleepers [ 33 ]. Furthermore, mice and rats during peri-adolescent period show shorter sleep time compared to matured rodents [ 32 , 34 ].…”

Section: Discussionmentioning

confidence: 99%

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Prediction of Locomotor Activity by Infrared Motion Detector on Sleep-wake State in Mice

Park

Jung

Moon

et al. 2021

Clin Psychopharmacol Neurosci

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Objective Behavioral assessments that effectively predict sleep-wake states were tried in animal research. This study aimed to examine the prediction power of an infrared locomotion detector on the sleep-wake states in ICR (Institute Cancer Research) mice. We also explored the influence of the durations and ways of data processing on the prediction power. Methods The locomotor activities of seven male mice in home cages were recorded by infrared detectors. Their sleep-wake states were assessed by video analysis. Using the receiver operating characteristic curve analysis, the cut-off score was determined, then the area under the curve (AUC) values of the infrared motion detector that predicted sleep-wake states were calculated. In order to improve the prediction power, the four ways of data processing on the prediction power were performed by Matlab 2013b. Results In the initial analysis of raw data, the AUC value was 0.785, but it gradually reached to 0.942 after data summation. The simple data averaging and summation among four different methods showed the maximal AUC value. The 10-minute data summation improved sensitivity (0.889) and specificity (0.901) significantly from the baseline value (sensitivity 0.615; specificity 0.936) ( p < 0.001). Conclusion This study suggests that the locomotor activity measured by an infrared motion detector might be useful to predict the sleep-wake states in ICR mice. It also revealed that only simple data summation may improve the predictive power. Using daily locomotor activities measured by an infrared motion detector is expected to facilitate animal research related to sleep-wake states.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionmentioning

confidence: 99%

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Prediction of Locomotor Activity by Infrared Motion Detector on Sleep-wake State in Mice

Park

Jung

Moon

et al. 2021

Clin Psychopharmacol Neurosci

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“…The results about the percentages of properly mapped reads (99%), the capture efficiency (62%), the average on–target sequencing depth (169–178), the exome coverage (99.9%), and the percentages of exome regions read at least 10 times (98.5%) indicate the reliability of alignment. The Ts/Tv ratio (1.7) is consistent with the general Ts/Tv ratio in the mouse genome (1.5–1.7) 16 , indicating a high overall quality of the identified SNVs. The quality score of variant calling is 20–228, providing statistical confidence for variant calling.…”

Section: Resultssupporting

confidence: 78%

Whole‑exome sequencing reveals Lewis lung carcinoma is a hypermutated Kras/Nras–mutant cancer with extensive regional mutation clusters in its genome

He,

Sun,

Pan

2024

Sci Rep

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Lewis lung carcinoma (LLC), as a widely used preclinical cancer model, has still not been genetically and genomically characterized. Here, we performed a whole–exome sequencing analysis on the LLC cell line to elucidate its molecular characteristics and etiologies. Our data showed that LLC originated from a male mouse belonging to C57BL/6L (a transitional strain between C57BL/6J and C57BL/6N) and contains substantial somatic SNV and InDel mutations (> 20,000). Extensive regional mutation clusters are present in its genome, which were caused mainly by the mutational processes underlying the SBS1, SBS5, SBS15, SBS17a, and SBS21 signatures during frequent structural rearrangements. Thirty three deleterious mutations are present in 30 cancer genes including Kras, Nras, Trp53, Dcc, and Cacna1d. Cdkn2a and Cdkn2b are biallelically deleted from the genome. Five pathways (RTK/RAS, p53, cell cycle, TGFB, and Hippo) are oncogenically deregulated or affected. The major mutational processes in LLC include chromosomal instability, exposure to metabolic mutagens, spontaneous 5–methylcytosine deamination, defective DNA mismatch repair, and reactive oxygen species. Our data also suggest that LLC is a lung cancer similar to human lung adenocarcinoma. This study lays a molecular basis for the more targeted application of LLC in preclinical research.

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“…LORR testing implicated pharmacokinetics as the underlying basis of the sleeptime differences in the congenics, yet the latent increase in drinking in the HLC2CO may be indicating the development of tolerance that potentially could be interacting with the pharmacokinetic effect. The genetic questions could be addressed through the continued development of recombinant congenics followed by a variety of genomic studies as we have done in our related mouse research (e.g., Bennett et al, 2015; Dowell et al, 2016; Dumas et al, 2014; Radcliffe et al, 2013). Regarding the question of EtOH metabolism, it would have been helpful to have conducted pharmacokinetic studies in the congenics, including the measurement of BECs during the drinking procedures.…”

Section: Discussionmentioning

confidence: 99%

Quantitative trait loci for sensitivity to acute ethanol and ethanol consummatory behaviors in rats

Mandt

Larson

Fay

et al. 2018

Alcohol

Self Cite

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Individuals with a low initial response to alcohol (i.e., ethanol) are at greater risk of developing alcohol abuse or dependence later in life. Similar to humans, individual differences in ethanol sensitivity also can be seen in rats, and several laboratories have used these individual differences to generate selectively bred rats that differ in acute ethanol sensitivity. We have worked with two sets of such rats (Inbred High or Low Alcohol Sensitivity strains, IHAS or ILAS, respectively; Inbred Alcohol Tolerant or Non-Tolerant strains, IAT and IANT, respectively) and have confirmed previously mapped quantitative trait loci (QTL) for these acute differences with the use of recombinant congenic lines; however, the relationship between acute sensitivity and ethanol drinking in these rats has yet to be determined. Thus, here we tested the hypothesis that QTLs underlying variation in initial low sensitivity to ethanol also will modulate variation in ethanol drinking behaviors. Separate groups of selectively inbred parent and congenic rats were tested for the loss of righting response (LORR) and also assessed for ethanol consummatory behavior using either operant self-administration or an intermittent-access two-bottle choice procedure. LORR testing confirmed the presence of a LORR duration QTL in all of the congenics; however, the lack of a corresponding difference in blood ethanol concentration at the regaining of the righting response suggests that these QTLs may be mediating a difference in ethanol metabolism rather than in neuronal sensitivity. IHAS/ILAS-derived congenic rats did not differ from parent rats at any point during operant self-administration. IAT/IANT-derived congenic rats showed small, but significant, increases in ethanol consumption relative to the parent strains only during the initial stages of operant self-administration. In contrast to operant testing, IHAS/ILAS-derived congenic rats showed significantly greater ethanol consumption and preference than parent rats during intermittent-access testing. There were not differences, however, between IAT/IANT congenic and parent rats during intermittent access. These data support the hypothesis that there is a genetic relationship between initial ethanol sensitivity and ethanol consumption, at least for the IHAS/ILAS-derived congenic rats. Our current studies, however, cannot eliminate pharmacokinetic or taste preference factors as contributing to the rats' responses, nor can we eliminate the possibility of a linkage effect because of the fairly large size of the QTL intervals; i.e., distinct genes may be mediating the acute sensitivity and drinking responses.

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Genome characterization of the selected long- and short-sleep mouse lines

Cited by 6 publications

References 56 publications

Prediction of Locomotor Activity by Infrared Motion Detector on Sleep-wake State in Mice

Prediction of Locomotor Activity by Infrared Motion Detector on Sleep-wake State in Mice

Whole‑exome sequencing reveals Lewis lung carcinoma is a hypermutated Kras/Nras–mutant cancer with extensive regional mutation clusters in its genome

Quantitative trait loci for sensitivity to acute ethanol and ethanol consummatory behaviors in rats

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