scholarly journals Frequent monoallelic or skewed expression for developmental genes in CNS-derived cells and evidence for balancing selection

2018 ◽  
Vol 115 (44) ◽  
pp. E10379-E10386 ◽  
Author(s):  
Sergio Branciamore ◽  
Zuzana Valo ◽  
Min Li ◽  
Jinhui Wang ◽  
Arthur D. Riggs ◽  
...  
Keyword(s):  
Balancing Selection ◽  
Developmental State ◽  
Mouse Strains ◽  
Cpg Dinucleotides ◽  
Clonal Cell Lines ◽  
Cell Type Specific ◽  
Selection For ◽  
Overlapping Classes ◽  
Two Populations ◽  
Development And Evolution

Cellular mosaicism due to monoallelic autosomal expression (MAE), with cell selection during development, is becoming increasingly recognized as prevalent in mammals, leading to interest in understanding its extent and mechanism(s). We report here use of clonal cell lines derived from the CNS of adult female F1 hybrid (C57BL/6 X JF1) mice to characterize MAE as neural stem cells (nscs) differentiate to astrocyte-like cells (asls). We found that different subsets of genes show MAE in the two populations of cells; in each case, there is strong enrichment for genes specific to the respective developmental state. Genes that exhibit MAE are 22% of nsc-specific genes and 26% of asl-specific genes. Moreover, the promoters of genes with MAE have reduced CpG dinucleotides but increased CpG differences between the two parental mouse strains. Extending the study of variability to wild populations of mice, we found evidence for balancing selection as a contributing force in evolution of those genes showing developmental specificity (i.e., expressed in either nsc or asl), not just for genes showing MAE. Furthermore, we found that genes showing skewed allelic expression (SKE) were similarly enriched among cell type-specific genes and also showed a heightened probability of balancing selection. Thus, developmental stage-specific genes and genes with MAE or SKE seem to make up overlapping classes subject to selection for increased diversity. The implications of these results for development and evolution are discussed in the context of a model with stochastic epigenetic modifications taking place only during a relatively brief developmental window.

scholarly journals Selection for Ethanol Tolerance in Two Populations of Drosophila Melanogaster Segregating Alcohol Dehydrogenase Allozymes

1979 ◽  
Vol 32 (3) ◽  
pp. 387 ◽  
Author(s):  
John B Gibson ◽  
NigeI Lewis ◽  
MichaeI Adena ◽  
Susan R Wilson
Keyword(s):  
Drosophila Melanogaster ◽  
Alcohol Dehydrogenase ◽  
Ethanol Tolerance ◽  
Selection For ◽  
Two Populations

Selection for ethanol tolerance was equally successful in two populations of D. melanogaster in both of which the frequency of AdhF was 0�5 at the start of the experiment.

scholarly journals The kinetics of T cell antigen receptor expression by subgroups of CD4+8+ thymocytes: delineation of CD4+8+3(2+) thymocytes as post-selection intermediates leading to mature T cells.

1991 ◽  
Vol 173 (2) ◽  
pp. 323-332 ◽  
Author(s):  
K Shortman ◽  
D Vremec ◽  
M Egerton
Keyword(s):  
T Cell ◽  
Cell Receptor ◽  
Receptor Expression ◽  
Mouse Strains ◽  
Adult Mice ◽  
Small Subgroup ◽  
Dividing Cells ◽  
Blast Cells ◽  
Selection For

Cortical thymocytes from adult mice, separated on the basis of coexpression of CD4 and CD8 or of binding of high levels of peanut agglutinin (PNA), were subdivided according to the level of expression of the T cell receptor (TCR)-CD3 complex. The incidence of dividing cells in the resultant subpopulations was determined by DNA staining. Precursor-product relationships and the timing of TCR-CD3 acquisition were studied using continuous in vivo [3H]TdR labeling and radioautography. The extent of intrathymic selection for TCR specificity in the subpopulations was determined from the incidence of cells bearing V beta 6 or V beta 17a in different mouse strains. The majority of dividing CD4+8+ blast cells expressed extremely low levels of TCR-CD3, indicating that TCR expression and specificity selection generally occurred after division ceased. The [3H]TdR-labeling studies indicated that postdivision TCR expression was rapid, and that those nondividing cortical thymocytes which had not expressed significant levels of TCR by day 1, remained extremely low or negative for their entire 3.6-d lifespan. Small cortical thymocytes which expressed moderate levels of TCR-CD3, were predominantly an unselected population with a lifespan of 3.8 d. A small subgroup of CD4+8+ PNA+ cortical thymocytes expressing high levels of TCR-CD3 was identified as a nondividing intermediate between the small cortical thymocytes expressing moderate levels of TCR and mature medullary thymocytes. These intermediates showed a 1-d lag in [3H]TdR labeling, then a 3.4-d transit time. The cell flux through this intermediate subpopulation was approximately 10(6) cells/d, similar to the rate of turnover of mature thymocytes; thus, although only 3-4% of thymocytes progressed to this intermediate state, once reaching it most then progressed to full maturity. In accordance with this, the incidence of the V beta selection markers within the intermediate subpopulation indicated that both positive and negative selection had already occurred. Selection for TCR specificity in the systems studied appeared to take place among CD4+8+ thymocytes expressing intermediate levels of TCR.

scholarly journals Germination Patterns in Seeds Produced in Apical and Basal Fruits of Two Thlaspi arvense Populations

Agronomy ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 756
Author(s):  
Eva Edo-Tena ◽  
Russ W. Gesch ◽  
Aritz Royo-Esnal
Keyword(s):  
Germination Percentage ◽  
Temperate Climate ◽  
Oilseed Crop ◽  
Seed Selection ◽  
Thlaspi Arvense ◽  
Production Site ◽  
Field Pennycress ◽  
Selection For ◽  
The One ◽  
Two Populations

The aim of the present work is to study possible differences in the germination behavior of apical and basal seeds (produced in the upper and lower fruits of the infruitescence), of two populations of field pennycress (Thlaspi arvense), both produced in a Mediterranean and a continental temperate climate. The results showed that among the three studied factors (population, seed type, production site), only the production site was relevant for the total germination, germinating those produced in Morris in a greater amount than those produced in Lleida. Germination models could be applied only to seeds produced at Morris (>10% germination), and despite the lack of differences in the total germination percentage, germination rates (speed—b parameter—and time to 50% germination—G50) differed between population and seed types—apical seeds from the Spanish population germinated faster (lower b parameter) than the rest, while apical seeds of both populations germinated faster than the corresponding basal seeds (lower G50). The results show, on the one hand, the importance of the seed production site if this species was considered as a commercial oilseed crop and, on the other hand, differences that will help seed selection for seed germination and establishment improvement of pennycress.

Limitations of the Avp-IRES2-Cre (JAX #023530) and Vip-IRES-Cre (JAX #010908) Models for Chronobiological Investigations

2019 ◽  
Vol 34 (6) ◽  
pp. 634-644 ◽  
Author(s):  
Arthur H. Cheng ◽  
Samuel W. Fung ◽  
Hai-Ying Mary Cheng
Keyword(s):  
Confounding Factor ◽  
The Body ◽  
Mouse Strains ◽  
Extreme Caution ◽  
Specific Manner ◽  
A Cell ◽  
Peripheral Clocks ◽  
Cell Type Specific ◽  
Encoding Gene ◽  
The Impact

The principal circadian pacemaker in mammals, the suprachiasmatic nucleus (SCN), expresses a number of neuropeptides that facilitate intercellular synchrony, helping to generate coherent outputs to peripheral clocks throughout the body. In particular, arginine vasopressin (AVP)– and vasoactive intestinal peptide (VIP)–expressing neurons have been recognized as crucial subpopulations within the SCN and have thus been the focus of many chronobiological studies. Here, we analyze the neuropeptide expression of 2 popular transgenic mouse strains commonly used to direct or restrict Cre-mediated recombination to AVP- and VIP-ergic neurons. The Avp-IRES2-Cre (JAX #023530) and Vip-IRES-Cre (JAX #010908) “driver” mouse strains express the Cre recombinase under the control of the endogenous Avp or Vip gene, respectively, allowing scientists either to ablate their gene of interest or to overexpress a transgene in a cell type–specific manner. Although these are potentially very powerful tools for chronobiologists and other scientists studying AVP- and VIP-ergic neurons, we found that neuropeptide expression in these mice is significantly decreased when an IRES(2)-Cre cassette is inserted downstream of the neuropeptide-encoding gene locus. The impact of IRES(2)-Cre cassette insertion on neuropeptide expression may be a confounding factor in many experimental designs. Our findings suggest that extreme caution must be exercised when using these mouse models to avoid misinterpretation of empirical results.

EFFECTS OF SELECTION FOR SPEED OF GERMINATION ON ESTABLISHMENT, VIGOR, AND YIELD IN ALTAI WILD RYEGRASS

1977 ◽  
Vol 57 (4) ◽  
pp. 1085-1090 ◽  
Author(s):  
T. LAWRENCE
Keyword(s):  
Field Test ◽  
Seed Yield ◽  
Dry Matter ◽  
Germination Index ◽  
Dry Matter Yield ◽  
Stand Establishment ◽  
Greenhouse Test ◽  
Selection For ◽  
Two Populations

Selection for fast and slow germination in Altai wild ryegrass (Elymus angustus Trin.) through three cycles of selection resulted in significant differences in the speed of germination index between the two populations. The fast germinating population established significantly better in a field test than the slow germinating population. Significant differences, although not large, were also found between the populations for spring vigor, seed yield and dry matter yield. However, observations from a greenhouse test indicate that these differences were attributable to differences in stand establishment in the field test rather than directly attributable to selection for speed of germination. It is suggested that selection for fast germination would be useful in breeding better establishing strains of Altai wild ryegrass. This would have little effect on either spring vigor or yield of seed and forage.

scholarly journals Heritable variation in colour patterns mediating individual recognition

2017 ◽  
Vol 4 (2) ◽  
pp. 161008 ◽  
Author(s):  
Michael J. Sheehan ◽  
Juanita Choo ◽  
Elizabeth A. Tibbetts
Keyword(s):  
Genetic Diversity ◽  
Balancing Selection ◽  
Phenotypic Diversity ◽  
Individual Recognition ◽  
Genetic Correlations ◽  
Colour Pattern ◽  
Heritable Variation ◽  
Pattern Diversity ◽  
Selection For ◽  
Colour Patterns

Understanding the developmental and evolutionary processes that generate and maintain variation in natural populations remains a major challenge for modern biology. Populations of Polistes fuscatus paper wasps have highly variable colour patterns that mediate individual recognition. Previous experimental and comparative studies have provided evidence that colour pattern diversity is the result of selection for individuals to advertise their identity. Distinctive identity-signalling phenotypes facilitate recognition, which reduces aggression between familiar individuals in P. fuscatus wasps. Selection for identity signals may increase phenotypic diversity via two distinct modes of selection that have different effects on genetic diversity. Directional selection for increased plasticity would greatly increase phenotypic diversity but decrease genetic diversity at associated loci. Alternatively, heritable identity signals under balancing selection would maintain genetic diversity at associated loci. Here, we assess whether there is heritable variation underlying colour pattern diversity used for facial recognition in a wild population of P. fuscatus wasps. We find that colour patterns are heritable and not Mendelian, suggesting that multiple loci are involved. Additionally, patterns of genetic correlations among traits indicated that many of the loci underlying colour pattern variation are unlinked and independently segregating. Our results support a model where the benefits of being recognizable maintain genetic variation at multiple unlinked loci that code for phenotypic diversity used for recognition.

scholarly journals Single-nuclei chromatin profiling of ventral midbrain reveals cell identity transcription factors and cell-type-specific gene regulatory variation

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Yujuan Gui ◽  
Kamil Grzyb ◽  
Mélanie H. Thomas ◽  
Jochen Ohnmacht ◽  
Pierre Garcia ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Cell Types ◽  
Mouse Strains ◽  
Cell Type ◽  
Data Set ◽  
Cell Identity ◽  
Regulatory Variation ◽  
Ventral Midbrain ◽  
Cell Type Specific

Abstract Background Cell types in ventral midbrain are involved in diseases with variable genetic susceptibility, such as Parkinson’s disease and schizophrenia. Many genetic variants affect regulatory regions and alter gene expression in a cell-type-specific manner depending on the chromatin structure and accessibility. Results We report 20,658 single-nuclei chromatin accessibility profiles of ventral midbrain from two genetically and phenotypically distinct mouse strains. We distinguish ten cell types based on chromatin profiles and analysis of accessible regions controlling cell identity genes highlights cell-type-specific key transcription factors. Regulatory variation segregating the mouse strains manifests more on transcriptome than chromatin level. However, cell-type-level data reveals changes not captured at tissue level. To discover the scope and cell-type specificity of cis-acting variation in midbrain gene expression, we identify putative regulatory variants and show them to be enriched at differentially expressed loci. Finally, we find TCF7L2 to mediate trans-acting variation selectively in midbrain neurons. Conclusions Our data set provides an extensive resource to study gene regulation in mesencephalon and provides insights into control of cell identity in the midbrain and identifies cell-type-specific regulatory variation possibly underlying phenotypic and behavioural differences between mouse strains.

scholarly journals Evidence for strong mutation bias towards, and selection against, T/U content in SARS-CoV2: implications for attenuated vaccine design

2020 ◽  
Author(s):  
Alan M. Rice ◽  
Atahualpa Castillo Morales ◽  
Alexander T. Ho ◽  
Christine Mordstein ◽  
Stefanie Mühlhausen ◽  
...  
Keyword(s):  
Large Scale ◽  
Mutation Bias ◽  
Cpg Dinucleotides ◽  
Synonymous Codons ◽  
Universal Feature ◽  
Neutral Equilibrium ◽  
Synonymous Sites ◽  
Selection For ◽  
Attenuated Viruses ◽  
Codon Pairs

ABSTRACTLarge-scale re-engineering of synonymous sites is a promising strategy to generate attenuated viruses for vaccines. Attenuation typically relies on de-optimisation of codon pairs and maximization of CpG dinculeotide frequencies. So as to formulate evolutionarily-informed attenuation strategies, that aim to force nucleotide usage against the estimated direction favoured by selection, here we examine available whole-genome sequences of SARS-CoV2 to infer patterns of mutation and selection on synonymous sites. Analysis of mutational profiles indicates a strong mutation bias towards T with concomitant selection against T. Accounting for dinucleotide effects reinforces this conclusion, observed TT content being a quarter of that expected under neutrality. A significantly different mutational profile at CDS sites that are not 4-fold degenerate is consistent with contemporaneous selection against T mutations more widely. Although selection against CpG dinucleotides is expected to drive synonymous site G+C content below mutational equilibrium, observed G+C content is slightly above equilibrium, possibly because of selection for higher expression. Consistent with gene-specific selection against CpG dinucleotides, we observe systematic differences of CpG content between SARS-CoV2 genes. We propose an evolutionarily informed gene-bespoke approach to attenuation that, unusually, seeks to increase usage of the already most common synonymous codons. Comparable analysis of H1N1 and Ebola finds that GC3 deviated from neutral equilibrium is not a universal feature, cautioning against generalization of results.

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