A high-throughput method for unbiased quantitation and categorization of nuclear morphology

Abstract The physical arrangement of chromatin in the nucleus is cell type and species-specific, a fact particularly evident in sperm, in which most of the cytoplasm has been lost. Analysis of the characteristic falciform (“hook shaped”) sperm in mice is important in studies of sperm development, hybrid sterility, infertility, and toxicology. However, quantification of sperm shape differences typically relies on subjective manual assessment, rendering comparisons within and between samples difficult. We have developed an analysis program for morphometric analysis of asymmetric nuclei and characterized the sperm of mice from a range of inbred, outbred, and wild-derived mouse strains. We find that laboratory strains have elevated sperm shape variability both within and between samples in comparison to wild-derived inbred strains, and that sperm shape in F1 offspring from a cross between CBA and C57Bl6J strains is subtly affected by the direction of the cross. We further show that hierarchical clustering can discriminate distinct sperm shapes with greater efficiency and reproducibility than even experienced manual assessors, and is useful both to distinguish between samples and also to identify different morphological classes within a single sample. Our approach allows for the analysis of nuclear shape with unprecedented precision and scale and will be widely applicable to different species and different areas of biology.

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A high-throughput method for unbiased quantitation and categorisation of nuclear morphology

10.1101/312470 ◽

2018 ◽

Cited By ~ 3

Author(s):

Benjamin Matthew Skinner ◽

Claudia Cattoni Rathje ◽

Joanne Bacon ◽

Emma Elizabeth Philippa Johnson ◽

Erica Lee Larson ◽

...

Keyword(s):

Inbred Lines ◽

Analysis Program ◽

Shape Variation ◽

Cell Type ◽

Manual Measurement ◽

High Throughput Method ◽

Sperm Development ◽

Morphological Defects ◽

Mouse Species ◽

Species Specific

AbstractThe physical arrangement of chromatin in the nucleus is cell type and species specific. This is particularly evident in sperm, in which most of the cytoplasm has been lost; the shape of the nucleus reflects the shape of the cell. Mice have distinctive falciform (‘hook shaped’) sperm heads and nuclei. Quantification of the differences in shape variation between mouse species and lines often relies on manual measurement and classification that leads to subjective results, making comparisons within and between samples difficult.We have developed an analysis program for assessing the morphology of asymmetric nuclei, and characterised the sperm of mice from a range of inbred, outbred and wild-derived mouse lines. We find that laboratory lines have elevated sperm shape variability both within and between samples in comparison to wild-derived inbred lines, and that sperm shape in the F1 offspring of CBA and C57Bl6J lines is subtly affected by the direction of the cross.Hierarchical clustering can distinguish distinct sperm shapes with greater efficiency and reproducibility than even experienced manual assessors. We quantified the range of morphological defects in the inbred BALB/c line, demonstrating we can identify different morphological subgroups. This approach has applications for studies of sperm development, infertility and toxicology.

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Genetic Control of Mammalian Meiotic Recombination. I. Variation in Exchange Frequencies Among Males From Inbred Mouse Strains

Genetics ◽

10.1093/genetics/162.1.297 ◽

2002 ◽

Vol 162 (1) ◽

pp. 297-306 ◽

Cited By ~ 13

Author(s):

Kara E Koehler ◽

Jonathan P Cherry ◽

Audrey Lynn ◽

Patricia A Hunt ◽

Terry J Hassold

Keyword(s):

Meiotic Recombination ◽

Inbred Mouse ◽

Inbred Strains ◽

Male Meiosis ◽

Mouse Strains ◽

Recombination Rates ◽

The Mean ◽

Genetic Background Effects ◽

Exchange Patterns ◽

Positive Interference

AbstractGenetic background effects on the frequency of meiotic recombination have long been suspected in mice but never demonstrated in a systematic manner, especially in inbred strains. We used a recently described immunostaining technique to assess meiotic exchange patterns in male mice. We found that among four different inbred strains—CAST/Ei, A/J, C57BL/6, and SPRET/Ei—the mean number of meiotic exchanges per cell and, thus, the recombination rates in these genetic backgrounds were significantly different. These frequencies ranged from a low of 21.5 exchanges in CAST/Ei to a high of 24.9 in SPRET/Ei. We also found that, as expected, these crossover events were nonrandomly distributed and displayed positive interference. However, we found no evidence for significant differences in the patterns of crossover positioning between strains with different exchange frequencies. From our observations of >10,000 autosomal synaptonemal complexes, we conclude that achiasmate bivalents arise in the male mouse at a frequency of 0.1%. Thus, special mechanisms that segregate achiasmate chromosomes are unlikely to be an important component of mammalian male meiosis.

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EVIDENCE THAT TWO LOCI PREDOMINANTLY DETERMINE THE DIFFERENCE IN SUSCEPTIBILITY TO THE HIGH PRESSURE NEUROLOGIC SYNDROME TYPE I SEIZURE IN MICE

Genetics ◽

10.1093/genetics/99.2.285 ◽

1981 ◽

Vol 99 (2) ◽

pp. 285-307

Author(s):

R D McCall ◽

D Frierson

Keyword(s):

High Pressure ◽

Inbred Mouse ◽

Inbred Strains ◽

Chromosome 17 ◽

Seizure Threshold ◽

Mouse Strains ◽

Compression Rate ◽

Type I ◽

Major Locus ◽

The Difference

ABSTRACT Most mammals tested, when exposed to increasing pressure in helium/oxygen atmospheres, exhibit progressive motor disturbances culminating in two, usually successive, well-differentiated convulsive seizures. The seizures are highly reproducible components of the constellation of events that collectively constitute the High Pressure Neurologic Syndrome (HPNS). In the present study, we present evidence that the mean difference in seizure threshold pressures of the first seizure to occur (HPNS Type I) between inbred mouse strains DBA/2J and C57BL/6J is predominantly determined (> 60%) by the expression of a major locus—possibly linked to the H-2 locus on chromosome 17—and a minor locus, probably unlinked. This outcome is derived from applications of the maximum likelihood modeling procedure of Elston and Stewart (1973) and Stewart and Elston (1973) to eleven models of genetic determinacy and tests (including breeding tests) of "preferred" models so derived using BXD recombinant inbred strains that show the following: The major locus exhibits conditional dominance characteristics depending upon compression rate and minor locus genotype. At a constant mean compression rate of 100 atm hr-1, the major locus manifests strong, though incomplete, dominance apparently independent of minor locus genotype. Its expression is, however, highly sensitive to compression rate, losing its dominance altogether at a linear rate of 1,000 atm hr-1. The major locus interacts with the weakly dominant and relatively compression-rate-insensitive minor locus to retain dominance at fast compression only when the dominant alleles of both loci are present. A principal finding of this study is that employing two compression rates permits fuller genetic characterization of murine high-pressure seizure susceptibility differences than could be achieved by use of a single compression rate.

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Discovery and refinement of muscle weight QTLs in B6 × D2 advanced intercross mice

Physiological Genomics ◽

10.1152/physiolgenomics.00055.2014 ◽

2014 ◽

Vol 46 (16) ◽

pp. 571-582 ◽

Cited By ~ 9

Author(s):

P. Carbonetto ◽

R. Cheng ◽

J. P. Gyekis ◽

C. C. Parker ◽

D. A. Blizard ◽

...

Keyword(s):

Inbred Strains ◽

Mouse Strains ◽

Missense Mutations ◽

Muscle Weight ◽

Hindlimb Muscles ◽

Hindlimb Muscle ◽

Causal Genes ◽

Snp Panel ◽

Genomic Regions ◽

Genetic Contributions

The genes underlying variation in skeletal muscle mass are poorly understood. Although many quantitative trait loci (QTLs) have been mapped in crosses of mouse strains, the limited resolution inherent in these conventional studies has made it difficult to reliably pinpoint the causal genetic variants. The accumulated recombination events in an advanced intercross line (AIL), in which mice from two inbred strains are mated at random for several generations, can improve mapping resolution. We demonstrate these advancements in mapping QTLs for hindlimb muscle weights in an AIL ( n = 832) of the C57BL/6J (B6) and DBA/2J (D2) strains, generations F8–F13. We mapped muscle weight QTLs using the high-density MegaMUGA SNP panel. The QTLs highlight the shared genetic architecture of four hindlimb muscles and suggest that the genetic contributions to muscle variation are substantially different in males and females, at least in the B6D2 lineage. Out of the 15 muscle weight QTLs identified in the AIL, nine overlapped the genomic regions discovered in an earlier B6D2 F2 intercross. Mapping resolution, however, was substantially improved in our study to a median QTL interval of 12.5 Mb. Subsequent sequence analysis of the QTL regions revealed 20 genes with nonsense or potentially damaging missense mutations. Further refinement of the muscle weight QTLs using additional functional information, such as gene expression differences between alleles, will be important for discerning the causal genes.

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Effect of murine strain on metabolic pathways of glucose production after brief or prolonged fasting

AJP Endocrinology and Metabolism ◽

10.1152/ajpendo.00601.2004 ◽

2005 ◽

Vol 289 (1) ◽

pp. E53-E61 ◽

Cited By ~ 46

Author(s):

Shawn C. Burgess ◽

F. Mark H. Jeffrey ◽

Charles Storey ◽

Angela Milde ◽

Natasha Hausler ◽

...

Keyword(s):

Genetic Manipulation ◽

Glucose Production ◽

Tca Cycle ◽

Inbred Strains ◽

Mouse Strains ◽

Background Strain ◽

Metabolic Fluxes ◽

Inbred Strains Of Mice ◽

Total Glucose

Background strain is known to influence the way a genetic manipulation affects mouse phenotypes. Despite data that demonstrate variations in the primary phenotype of basic inbred strains of mice, there is limited data available about specific metabolic fluxes in vivo that may be responsible for the differences in strain phenotypes. In this study, a simple stable isotope tracer/NMR spectroscopic protocol has been used to compare metabolic fluxes in ICR, FVB/N (FVB), C57BL/6J (B6), and 129S1/SvImJ (129) mouse strains. After a short-term fast in these mice, there were no detectable differences in the pathway fluxes that contribute to glucose synthesis. However, after a 24-h fast, B6 mice retain some residual glycogenolysis compared with other strains. FVB mice also had a 30% higher in vivo phospho enolpyruvate carboxykinase flux and total glucose production from the level of the TCA cycle compared with B6 and 129 strains, while total body glucose production in the 129 strain was ∼30% lower than in either FVB or B6 mice. These data indicate that there are inherent differences in several pathways involving glucose metabolism of inbred strains of mice that may contribute to a phenotype after genetic manipulation in these animals. The techniques used here are amenable to use as a secondary or tertiary tool for studying mouse models with disruptions of intermediary metabolism.

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A Review of Murine Cytomegalovirus as a Model for Human Cytomegalovirus Disease—Do Mice Lie?

International Journal of Molecular Sciences ◽

10.3390/ijms22010214 ◽

2020 ◽

Vol 22 (1) ◽

pp. 214

Author(s):

Michelle A. Fisher ◽

Megan L. Lloyd

Keyword(s):

Human Cytomegalovirus ◽

Murine Cytomegalovirus ◽

Clinical Samples ◽

Mouse Strains ◽

Cytomegalovirus Disease ◽

Wild Mice ◽

Congenital Cytomegalovirus ◽

Non Invasive ◽

Species Specific ◽

Disseminated Disease

Since murine cytomegalovirus (MCMV) was first described in 1954, it has been used to model human cytomegalovirus (HCMV) diseases. MCMV is a natural pathogen of mice that is present in wild mice populations and has been associated with diseases such as myocarditis. The species-specific nature of HCMV restricts most research to cell culture-based studies or to the investigation of non-invasive clinical samples, which may not be ideal for the study of disseminated disease. Initial MCMV research used a salivary gland-propagated virus administered via different routes of inoculation into a variety of mouse strains. This revealed that the genetic background of the laboratory mice affected the severity of disease and altered the extent of subsequent pathology. The advent of genetically modified mice and viruses has allowed new aspects of disease to be modeled and the opportunistic nature of HCMV infection to be confirmed. This review describes the different ways that MCMV has been used to model HCMV diseases and explores the continuing difficulty faced by researchers attempting to model HCMV congenital cytomegalovirus disease using the mouse model.

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Evolutionary origin of the cell nucleus and its functional architecture

Essays in Biochemistry ◽

10.1042/bse0480001 ◽

2010 ◽

Vol 48 ◽

pp. 1-24 ◽

Cited By ~ 15

Author(s):

Jan Postberg ◽

Hans J. Lipps ◽

Thomas Cremer

Keyword(s):

Cell Nucleus ◽

Interdisciplinary Research ◽

Nuclear Organization ◽

Nuclear Architecture ◽

Evolutionary Origin ◽

Cell Type ◽

Research Strategies ◽

Evolutionarily Conserved ◽

Species Specific ◽

The Impact

Understanding the evolutionary origin of the nucleus and its compartmentalized architecture provides a huge but, as expected, greatly rewarding challenge in the post-genomic era. We start this chapter with a survey of current hypotheses on the evolutionary origin of the cell nucleus. Thereafter, we provide an overview of evolutionarily conserved features of chromatin organization and arrangements, as well as topographical aspects of DNA replication and transcription, followed by a brief introduction of current models of nuclear architecture. In addition to features which may possibly apply to all eukaryotes, the evolutionary plasticity of higher-order nuclear organization is reflected by cell-type- and species-specific features, by the ability of nuclear architecture to adapt to specific environmental demands, as well as by the impact of aberrant nuclear organization on senescence and human disease. We conclude this chapter with a reflection on the necessity of interdisciplinary research strategies to map epigenomes in space and time.

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MoG+: a database of genomic variations across three mouse subspecies for biomedical research

Mammalian Genome ◽

10.1007/s00335-021-09933-w ◽

2021 ◽

Author(s):

Toyoyuki Takada ◽

Kentaro Fukuta ◽

Daiki Usuda ◽

Tatsuya Kushida ◽

Shinji Kondo ◽

...

Keyword(s):

Phenotypic Diversity ◽

Laboratory Mouse ◽

Genomic Analysis ◽

Inbred Strains ◽

Genetic Distances ◽

Mouse Strains ◽

Comparative Genomic ◽

Genome Database ◽

Data Resource ◽

Genomic Variations

AbstractLaboratory mouse strains have mosaic genomes derived from at least three major subspecies that are distributed in Eurasia. Here, we describe genomic variations in ten inbred strains: Mus musculus musculus-derived BLG2/Ms, NJL/Ms, CHD/Ms, SWN/Ms, and KJR/Ms; M. m. domesticus-derived PGN2/Ms and BFM/Ms; M. m. castaneus-derived HMI/Ms; and JF1/Ms and MSM/Ms, which were derived from a hybrid between M. m. musculus and M. m. castaneus. These strains were established by Prof. Moriwaki in the 1980s and are collectively named the “Mishima Battery”. These strains show large phenotypic variations in body size and in many physiological traits. We resequenced the genomes of the Mishima Battery strains and performed a comparative genomic analysis with dbSNP data. More than 81 million nucleotide coordinates were identified as variant sites due to the large genetic distances among the mouse subspecies; 8,062,070 new SNP sites were detected in this study, and these may underlie the large phenotypic diversity observed in the Mishima Battery. The new information was collected in a reconstructed genome database, termed MoG+ that includes new application software and viewers. MoG+ intuitively visualizes nucleotide variants in genes and intergenic regions, and amino acid substitutions across the three mouse subspecies. We report statistical data from the resequencing and comparative genomic analyses and newly collected phenotype data of the Mishima Battery, and provide a brief description of the functions of MoG+, which provides a searchable and unique data resource of the numerous genomic variations across the three mouse subspecies. The data in MoG+ will be invaluable for research into phenotype-genotype links in diverse mouse strains.

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Uptake of fluorescent-labeled BSA into root cells: endocytosis?

Acta Societatis Botanicorum Poloniae ◽

10.5586/asbp.1997.037 ◽

2014 ◽

Vol 66 (3-4) ◽

pp. 319-324 ◽

Cited By ~ 1

Author(s):

A. Kaźmierczak ◽

J. Maszewski

Keyword(s):

Zea Mays ◽

Bovine Serum Albumin ◽

Serum Albumin ◽

Bovine Serum ◽

Cytochalasin B ◽

Fluorescein Isothiocyanate ◽

Cell Type ◽

Root Cells ◽

Root Zones ◽

Species Specific

Incorporation of rhodamine- and fluorescein-isothiocyanate labeled bovine serum albumin (BSA-TRITC, BSA-FITC) was examined in different root zones of the 3-day-old seedlings in Melandrium noctiflorum, Allium cepa and Zea mays. The uptake of fluorescent-labeled BSA was found: (1) species-specific, (2) cell-type dependent, and (3) cytochalasin B-sensitive. The characteristic punctute distribution of vesicles within the cytoplasm suggests the internalization of labeled proteins by endocytosis.

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Influence of genetic background on ex vivo and in vivo cardiac function in several commonly used inbred mouse strains

Physiological Genomics ◽

10.1152/physiolgenomics.00071.2010 ◽

2010 ◽

Vol 42A (2) ◽

pp. 103-113 ◽

Cited By ~ 54

Author(s):

Matthew S. Barnabei ◽

Nathan J. Palpant ◽

Joseph M. Metzger

Keyword(s):

Cardiac Function ◽

Genetic Divergence ◽

Ex Vivo ◽

Inbred Mouse ◽

Critical Role ◽

Inbred Strains ◽

Mouse Strains ◽

Inbred Mouse Strains ◽

Cardiac Decompensation

Inbred mouse strains play a critical role in biomedical research. Genetic homogeneity within inbred strains and their general amenability to genetic manipulation have made them an ideal resource for dissecting the physiological function(s) of individual genes. However, the inbreeding that makes inbred mice so useful also results in genetic divergence between them. This genetic divergence is often unaccounted for but may be a confounding factor when comparing studies that have utilized distinct inbred strains. Here, we compared the cardiac function of C57BL/6J mice to seven other commonly used inbred mouse strains: FVB/NJ, DBA/2J, C3H/HeJ, BALB/cJ, 129X1/SvJ, C57BL/10SnJ, and 129S1/SvImJ. The assays used to compare cardiac function were the ex vivo isolated Langendorff heart preparation and in vivo real-time hemodynamic analysis using conductance micromanometry. We report significant strain-dependent differences in cardiac function between C57BL/6J and other commonly used inbred strains. C57BL/6J maintained better cardiac function than most inbred strains after ex vivo ischemia, particularly compared with 129S1/SvImJ, 129X1/SvJ, and C57BL/10SnJ strains. However, during in vivo acute hypoxia 129X1/SvJ and 129S1/SvImJ maintained relatively normal cardiac function, whereas C57BL/6J animals showed dramatic cardiac decompensation. Additionally, C3H/HeJ showed rapid and marked cardiac decompensation in response to esmolol infusion compared with effects of other strains. These findings demonstrate the complex effects of genetic divergence between inbred strains on cardiac function. These results may help inform analysis of gene ablation or transgenic studies and further demonstrate specific quantitative traits that could be useful in discovery of genetic modifiers relevant to cardiac health and disease.

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