A generic hidden Markov model for multi-parent populations

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab396 ◽

2021 ◽

Author(s):

Karl W Broman

Keyword(s):

Meiotic Recombination ◽

Relative Frequency ◽

Hidden Markov ◽

Probability Model ◽

Approximate Model ◽

Marker Data ◽

Diversity Outbred ◽

Precise Characterization ◽

Dense Marker

Abstract A common step in the analysis of multi-parent populations is genotype reconstruction: identifying the founder origin of haplotypes from dense marker data. This process often makes use of a probability model for the pattern of founder alleles along chromosomes, including the relative frequency of founder alleles and the probability of exchanges among them, which depend on a model for meiotic recombination and on the mating design for the population. While the precise experimental design used to generate the population may be used to derive a precise characterization of the model for exchanges among founder alleles, this can be tedious, particularly given the great variety of experimental designs that have been proposed. We describe an approximate model that can be applied for a variety of multi-parent populations. We have implemented the approach in the R/qtl2 software, and we illustrate its use in applications to publicly-available data on Diversity Outbred and Collaborative Cross mice.

Download Full-text

A general hidden Markov model for multi-parent populations

10.1101/2021.08.03.454963 ◽

2021 ◽

Author(s):

Karl W Broman

Keyword(s):

Relative Frequency ◽

Hidden Markov ◽

Exchange Process ◽

Approximate Model ◽

Experimental Designs ◽

Marker Data ◽

Diversity Outbred ◽

Precise Characterization ◽

Dense Marker

A common step in the analysis of multi-parent populations is genotype reconstruction: identifying the founder origin of haplotypes from dense marker data. This process often makes use of a model for the exchange process along chromosomes, including the relative frequency of founder alleles and of the probability of exchanges among them. While the precise experimental design used to generate the population may be used to derive a precise characterization of the exchange process, this can be tedious, particularly given the great variety of experimental designs that have been proposed. We describe an approximate model that can be applied for a variety of multi-parent populations. We have implemented the approach in the R/qtl2 software, and we illustrate its use in applications to publicly available data on Diversity Outbred and Collaborative Cross mice.

Download Full-text

Genetic Studies of mei-P26 Reveal a Link Between the Processes That Control Germ Cell Proliferation in Both Sexes and Those That Control Meiotic Exchange in Drosophila

Genetics ◽

10.1093/genetics/155.4.1757 ◽

2000 ◽

Vol 155 (4) ◽

pp. 1757-1772 ◽

Cited By ~ 7

Author(s):

Scott L Page ◽

Kim S McKim ◽

Benjamin Deneen ◽

Tajia L Van Hook ◽

R Scott Hawley

Keyword(s):

Meiotic Recombination ◽

Double Mutant ◽

P Element ◽

Genetic Studies ◽

Germline Differentiation ◽

Males And Females ◽

Bag Of Marbles ◽

Differentiation And Proliferation

Abstract We present the cloning and characterization of mei-P26, a novel P-element-induced exchange-defective female meiotic mutant in Drosophila melanogaster. Meiotic exchange in females homozygous for mei-P261 is reduced in a polar fashion, such that distal chromosomal regions are the most severely affected. Additional alleles generated by duplication of the P element reveal that mei-P26 is also necessary for germline differentiation in both females and males. To further assess the role of mei-P26 in germline differentiation, we tested double mutant combinations of mei-P26 and bag-of-marbles (bam), a gene necessary for the control of germline differentiation and proliferation in both sexes. A null mutation at the bam locus was found to act as a dominant enhancer of mei-P26 in both males and females. Interestingly, meiotic exchange in mei-P261; bamΔ86/+ females is also severely decreased in comparison to mei-P261 homozygotes, indicating that bam affects the meiotic phenotype as well. These data suggest that the pathways controlling germline differentiation and meiotic exchange are related and that factors involved in the mitotic divisions of the germline may regulate meiotic recombination.

Download Full-text

Highly precise characterization of the hydration state upon thermal denaturation of human serum albumin using a 65 GHz dielectric sensor

Physical Chemistry Chemical Physics ◽

10.1039/d0cp02265a ◽

2020 ◽

Vol 22 (35) ◽

pp. 19468-19479 ◽

Cited By ~ 1

Author(s):

Keiichiro Shiraga ◽

Mako Urabe ◽

Takeshi Matsui ◽

Shojiro Kikuchi ◽

Yuichi Ogawa

Keyword(s):

Human Serum Albumin ◽

Serum Albumin ◽

Human Serum ◽

Thermal Denaturation ◽

Hydration Water ◽

Biological Functions ◽

Dielectric Sensor ◽

Hydration State ◽

Precise Characterization

The biological functions of proteins depend on harmonization with hydration water surrounding them.

Download Full-text

Distorted chiolite crystal structures of α-Na5M3F14 (M=Cr,Fe,Ga) studied by X-ray powder diffraction

Powder Diffraction ◽

10.1154/1.1556990 ◽

2003 ◽

Vol 18 (2) ◽

pp. 128-134 ◽

Cited By ~ 4

Author(s):

A. Le Bail ◽

A.-M. Mercier

Keyword(s):

Crystal Structures ◽

Powder Diffraction ◽

Room Temperature ◽

Rietveld Refinements ◽

Space Group ◽

X Ray ◽

Precise Characterization

The crystal structures of the chiolite-related room temperature phases α-Na5M3F14 (MIII=Cr,Fe,Ga) are determined. For all of them, the space group is P21/n, Z=2; a=10.5096(3) Å, b=7.2253(2) Å, c=7.2713(2) Å, β=90.6753(7)° (M=Cr); a=10.4342(7) Å, b=7.3418(6) Å, c=7.4023(6) Å, β=90.799(5)° (M=Fe), and a=10.4052(1) Å, b=7.2251(1) Å, c=7.2689(1), β=90.6640(4)° (M=Ga). Rietveld refinements produce final RF factors 0.036, 0.033, and 0.035, and RWP factors, 0.125, 0.116, and 0.096, for MIII=Cr, Fe, and Ga, respectively. The MF6 polyhedra in the defective isolated perovskite-like layers deviate very few from perfect octahedra. Subtle octahedra tiltings lead to the symmetry decrease from the P4/mnc space group adopted by the Na5Al3F14 chiolite aristotype to the P21/n space group adopted by the title series. Facile twinning precluded till now the precise characterization of these compounds.

Download Full-text

BrdU-dye characterization of late replication and meiotic recombination in Armenian hamster germ cells

Chromosoma ◽

10.1007/bf00292272 ◽

1979 ◽

Vol 74 (2) ◽

pp. 189-207 ◽

Cited By ~ 26

Author(s):

James W. Allen

Keyword(s):

Germ Cells ◽

Meiotic Recombination ◽

Late Replication

Download Full-text

Simple and Precise Characterization of Differential Modal Group Delay arising in Few-Mode Fiber

Optics Letters ◽

10.1364/ol.423950 ◽

2021 ◽

Author(s):

Zhe Fu ◽

Junjie Zhang ◽

Ziheng Zhang ◽

Songnian Fu ◽

Yuwen Qin ◽

...

Keyword(s):

Group Delay ◽

Precise Characterization ◽

Modal Group

Download Full-text

Children hospitalized due to maltreatment in the ICU of a Public Health Service

Revista Brasileira de Enfermagem ◽

10.1590/0034-7167-2017-0502 ◽

2018 ◽

Vol 71 (suppl 3) ◽

pp. 1420-1427

Author(s):

Letícia Medeiros Santomé ◽

Sandra Maria Cezar Leal ◽

Joel Rolim Mancia ◽

Antônio Marcos Freire Gomes

Keyword(s):

Medical Records ◽

Relative Frequency ◽

Life Histories ◽

Public Health Service ◽

Physical Violence ◽

First Aid ◽

Porto Alegre ◽

Chi Square ◽

Pediatric Icu

ABSRACT Objective: to characterize children hospitalized due to violence in a pediatric ICU in 2011; to relate violence and the mechanisms of trauma with death; to know the contextualization of violence, from the records in the medical records. Method: retrospective cohort, performed in a first aid hospital, Porto Alegre city, in the records of 22 children hospitalized in the ICU due to violence. Quantitative analysis was performed by absolute and relative frequency rates, chi-square and relative risk. Results: 54.5% were boys, 81.8% were white and 50% were up to three years old. Physical violence 50% and neglect 36.4%, family of children (77.3%), highlighting the mother (35.3%). Mechanisms of aggression: fall (22.7%), burns (18.2%). Burns were at high risk for death. Discharge to go home after ICU admission (59.1%). Conclusion: It is considered that the characterization of the cases of violence reflects the complexity of the theme, mainly, in face of the life histories that surround each case of children hospitalized by this aggravation.

Download Full-text

RAD54 is essential for RAD51-mediated repair of meiotic DSB in Arabidopsis

PLoS Genetics ◽

10.1371/journal.pgen.1008919 ◽

2021 ◽

Vol 17 (5) ◽

pp. e1008919

Author(s):

Miguel Hernandez Sanchez-Rebato ◽

Alida M. Bouatta ◽

Maria E. Gallego ◽

Charles I. White ◽

Olivier Da Ines

Keyword(s):

Homologous Recombination ◽

Meiotic Recombination ◽

Dna Supercoiling ◽

Homology Search ◽

Detectable Effect ◽

Damage Repair ◽

Meiotic Dsbs ◽

Dna Translocase

An essential component of the homologous recombination machinery in eukaryotes, the RAD54 protein is a member of the SWI2/SNF2 family of helicases with dsDNA-dependent ATPase, DNA translocase, DNA supercoiling and chromatin remodelling activities. It is a motor protein that translocates along dsDNA and performs multiple functions in homologous recombination. In particular, RAD54 is an essential cofactor for regulating RAD51 activity. It stabilizes the RAD51 nucleofilament, remodels nucleosomes, and stimulates homology search and strand invasion activity of RAD51. Accordingly, deletion of RAD54 has dramatic consequences on DNA damage repair in mitotic cells. In contrast, its role in meiotic recombination is less clear. RAD54 is essential for meiotic recombination in Drosophila and C. elegans, but plays minor roles in yeast and mammals. We present here characterization of the roles of RAD54 in meiotic recombination in the model plant Arabidopsis thaliana. Absence of RAD54 has no detectable effect on meiotic recombination in otherwise wild-type plants but RAD54 becomes essential for meiotic DSB repair in absence of DMC1. In Arabidopsis, dmc1 mutants have an achiasmate meiosis, in which RAD51 repairs meiotic DSBs. Lack of RAD54 leads to meiotic chromosomal fragmentation in absence of DMC1. The action of RAD54 in meiotic RAD51 activity is thus mainly downstream of the role of RAD51 in supporting the activity of DMC1. Equivalent analyses show no effect on meiosis of combining dmc1 with the mutants of the RAD51-mediators RAD51B, RAD51D and XRCC2. RAD54 is thus required for repair of meiotic DSBs by RAD51 and the absence of meiotic phenotype in rad54 plants is a consequence of RAD51 playing a RAD54-independent supporting role to DMC1 in meiotic recombination.

Download Full-text