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PubMed1997

Estimating meiotic exchange patterns from recombination data: an application to humans.

We present analytical methods to estimate the recombinational history of chromosomes in a human population. Our analysis, similar to those utilized in Drosophila, can be used to construct meiotic maps based upon crossover frequencies observed in family data. We apply this method of exchange estimation to a population of paternally and maternally inherited chromosomes 21. The patterns of chromosomal exchange estimated by this type of analysis are comparable to those obtained by the more technically difficult method of cytologically counting chiasmata among human male meiotic events (sperm). This type of analysis can be applied to both male and female meiosis, circumventing many technical problems inherent to cytological counting. Moreover, the distribution of exchange locations along a chromosome for each exchange type (i.e., single, double, or triple exchanges) can be examined individually, an advantage compared to examination of genetic maps that only provide a summary of these distributions. We discuss how this analysis can be used to examine various assumptions concerning meiotic exchange in humans and investigate properties of the analysis that contribute to the accuracy of the results.

Female↗
PubMed2003

Aberrant interchromosomal exchanges are the predominant cause of the 22q11.2 deletion.

Chromosome 22q11.2 deletions are found in almost 90% of patients with DiGeorge/velocardiofacial syndrome (DGS/VCFS). Large, chromosome-specific low copy repeats (LCRs), flanking and within the deletion interval, are presumed to lead to misalignment and aberrant recombination in meiosis resulting in this frequent microdeletion syndrome. We traced the grandparental origin of regions flanking de novo 3 Mb deletions in 20 informative three-generation families. Haplotype reconstruction showed an unexpectedly high number of proximal interchromosomal exchanges between homologs, occurring in 19/20 families. Instead, the normal chromosome 22 in these probands showed interchromosomal exchanges in 2/15 informative meioses, a rate consistent with the genetic distance. Meiotic exchanges, visualized as MLH1 foci, localize to the distal long arm of chromosome 22 in 75% of human spermatocytes tested, also reflecting the genetic map. Additionally, we found no effect of proband gender or parental age on the crossover frequency. Parental origin studies in 65 de novo 3 Mb deletions (including these 20 patients) demonstrated no bias. Unlike Williams syndrome, we found no chromosomal inversions flanked by LCRs in 22 sets of parents of 22q11 deleted patients, or in eight non-deleted patients with a DGS/VCFS phenotype using FISH. Our data are consistent with significant aberrant interchromosomal exchange events during meiosis I in the proximal region of the affected chromosome 22 as the likely etiology for the deletion. This type of exchange occurs more often than is described for deletions of chromosomes 7q11, 15q11, 17p11 and 17q11, implying a difference in the meiotic behavior of chromosome 22.

Chromosome Aberrations↗
PubMedDate not supplied

Genetic variability and mapping of peptidase-4 in Anopheles albimanus.

Field-collected and laboratory populations of Anopheles albimanus were analyzed for the presence of variability for the enzyme, peptidase. Four zones of peptidase electromorphs were observed. The Peptidase-4 (Pep-4) locus was analyzed genetically and assigned to a location adjacent to the centromere on the right arm of chromosome 2 by employing crosses involving morphological mutants, allozyme markers, a holandric translocation, and pericentric inversions. The gene sequence (and map distances) on chromosome 2 beginning from the left arm is: brown larva--40--ebony (eb)--centromere--pep-4--?--bent(be)--?--Glutamate oxaloacetate transaminase (Got)--11--Glucose oxidase-2(Go-2)--17--green larva (gl)--9--amber (am)--2--propoxur resistance (prr)--2--red eye (re)--21--6-Phosphogluconate dehydrogenase (6-Pgd)--1--yellow. The crossover frequencies between eb and Pep-4 and Pep-4 and Got were 34 and 16, respectively.

Alleles↗
PubMed2002

Propagation of acoustic waves in nematic elastomers.

We develop a theory of elastic waves in oriented monodomain nematic elastomers. The effect of soft elasticity, combined with the Leslie-Ericksen version of dissipation function, results in an unusual dispersion and anomalous anisotropy of shear acoustic waves. A characteristic time scale of nematic rotation determines the crossover frequency, below which waves of some polarizations have a very strong attenuation while others experience no dissipation at all. We study the anisotropy of low-frequency Poynting vectors and wave fronts, and discuss a "squeeze" effect of energy transfer nonparallel to the wave vector. Based on these theoretical results, an application, the acoustic polarizer, is proposed.

Journal Article↗
PubMed2003

Dielectrophoresis of charged colloidal suspensions.

We present a theoretical study of dielectrophoretic (DEP) crossover spectrum of two polarizable particles under the action of a nonuniform ac electric field. For two approaching particles, the mutual polarization interaction yields a change in their respective dipole moments, and hence, in the DEP crossover spectrum. The induced polarization effects are captured by the multiple image method. Using spectral representation theory, an analytic expression for the DEP force is derived. We find that the mutual polarization effects can change the crossover frequency at which the DEP force changes sign. The results are found to be in agreement with recent experimental observation and as they go beyond the standard theory, they help to clarify the important question of the underlying polarization mechanisms.

Journal Article↗
PubMed2002

Novel EIS postprocessing algorithm for breast cancer diagnosis.

A new postprocessing algorithm was developed for the diagnosis of breast cancer using electrical impedance scanning. This algorithm automatically recognizes bright focal spots in the conductivity map of the breast. Moreover, this algorithm discriminates between malignant and benign/normal tissues using two main predictors: phase at 5 kHz and crossover frequency, the frequency at which the imaginary part of the admittance is at its maximum. The thresholds for these predictors were adjusted using a learning group consisting of 83 carcinomas and 378 benign cases. In addition, the algorithm was verified on an independent test group including 87 carcinomas, 153 benign cases and 356 asymptomatic cases. Biopsy was used as gold standard for determining pathology in the symptomatic cases. A sensitivity of 84% and a specificity of 52% were obtained for the test group.

Algorithms↗
PubMed1997

Estimating articulation scores.

The ability of listeners to estimate articulation scores for lists of nonsense syllables was evaluated. Normal-hearing subjects were presented with lists of from 50 to 60 nonsense syllables that were degraded with various amounts of noise or filtering and were instructed to estimate consonant-correct scores for each condition. To provide a reference for estimating, subjects were shown the accurate orthographic representation of the syllable on a computer monitor to compare with the auditory presentation. The printed version was displayed either simultaneously with the auditory presentation or 500 ms after the offset of the syllable. Estimates were collected on two occasions to examine test-retest reliability, and actual percent-correct scores were obtained to check the accuracy of the estimates. Most subjects overestimated actual scores when the printed representation was provided simultaneously, but estimates were strikingly similar to actual scores when the printed representation was delayed. The delay appeared to prevent the printed representation from favorably biasing the reception of the syllable. The average of two or three estimates gave highly repeatable results for both visual displays. Crossover frequencies derived from the filtered-speech conditions were within the range reported in the literature. This supports the conclusion that subjects based their estimates on the recognition of speech sounds rather than other percepts associated with the speech-in-noise conditions such as loudness of the noise. The estimation procedure permits the collection of articulation scores in much less time than required by traditional test procedures.

Adult↗
PubMed2003

A transcriptionally active subgenomic promoter supports homologous crossovers in a plus-strand RNA virus.

Genetic RNA recombination plays an important role in viral evolution, but its molecular mechanism is not well understood. In this work we describe homologous RNA recombination activity that is supported by a subgenomic promoter (sgp) region in the RNA3 segment of brome mosaic bromovirus (BMV), a tripartite plus-strand RNA virus. The crossover frequencies were determined by coinoculations with pairs of BMV RNA3 variants that carried a duplicated sgp region flanked by marker restriction sites. A region composed of the sgp core, a poly(A) tract, and an upstream enhancer supported homologous exchanges in 25% of the analyzed RNA3 progeny. However, mutations in the sgp core stopped both the transcription of the sgp RNA and homologous recombination. These data provide evidence for an association of RNA recombination with transcription.

Bromovirus↗
PubMed2005

A variance component analysis on recombination rate in the COGA pedigrees.

We estimated the crossover frequency in 1,232 gametes from 356 subjects in pedigrees from the Collaborative Study on the Genetics on Alcoholism. We examined the effect of covariates including age, ethnicity, and years with ALDX1 on recombination rate, and found a positive correlation between recombination rate and years with ALDX1. By variance-component analysis, we estimated the heritability of recombination rate to be around 0.5, and provided suggestive evidence for a locus linked to recombination rate.

Alcoholism↗
PubMed1999

A genetic linkage map of rat chromosome 9 with a new locus for variant activity of liver aldehyde oxidase.

A genetic linkage map of rat chromosome 9 consisting of five loci including a new biochemical marker representing a genetic variation of the activity of the liver aldehyde oxidase, (Aox) was constructed. Linkage analysis of the five loci among 92 backcross progeny of (WKS/Iar x IS/Iar)F1 x WKS/Iar revealed significant linkages between these loci. Minimizing crossover frequency resulted in the best gene order: Aox-D9Mit4-Gls-Cryg-Tp53l1. The homologues of the Cryg, Gls, and Aox genes have been mapped on mouse chromosome 1 and human chromosome 2q. The present findings provide further evidence for the conservation of synteny among these regions of rat, mouse, and human chromosomes.

Aldehyde Oxidase↗
PubMed2004

[New approach in the explaining of the Morgan Law in genetics teaching].

Using the model of broad and narrow way, the paper introduces a new approach in the explaining of a few basic concepts in the Morgan Law. The paper introduces a thorough inquiry into the applying condition of the three-factor crosses, and finds the source of the difference between the crossover frequency (F(C)) and recombination frequency (F(R)) of the non-adjacent factors in the three-factor crosses in Neurospora crassa.

Alleles↗
PubMed1977

The genetic contribution of the NZB mouse to the renal disease of the NZB x NZW hybrid.

The occurrence of lupus nephritis in (NZB x NZW)F1 mice appears to depend on the action of at least two dominant or co-dominant genes (at least one gene from each parent) as neither of the inbred parental strains shows the disorder. Identifying affected animals by antemortem determinations of renal function, using improved methods of measuring proteinuria and renal clearance, we have studied the incidence of the renal disease in 230 (NZB x NZW)F1 x NZW backcross mice. The incidence was 49-6% which indicates that NZB strain contributes only one gene, or cluster of closely linked genes, to the renal disorder of the F1 hybrid. The gene(s) must be dominant or co-dominant, as it expresses its effect in the heterozygous state. Study of the H-2 status of the backcross mice showed a loose linkage of the NZB renal disease gene(s) to the D end of the H-2 complex, the crossover frequency being 32-6+/-3-1%.

Aging↗
PubMedDate not supplied

Analysis and modeling of frequency-specific habituation of the goldfish vestibulo-ocular reflex.

Modification of the vestibulo-ocular reflex (VOR) by vestibular habituation is an important paradigm in the study of neural plasticity. The VOR is responsible for rotating the eyes to maintain the direction of gaze during head rotation. The response of the VOR to sinusoidal rotation is quantified by its gain (eye rotational velocity/head rotational velocity) and phase difference (eye velocity phase--inverted head velocity phase). The frequency response of the VOR in naïve animals has been previously modeled as a high-pass filter (HPF). A HPF passes signals above its corner frequency with gain 1 and phase 0 but decreases gain and increases phase lead (positive phase difference) as signal frequency decreases below its corner frequency. Modification of the VOR by habituation occurs after prolonged low-frequency rotation in the dark. Habituation causes a reduction in low-frequency VOR gain and has been simulated by increasing the corner frequency of the HPF model. This decreases gain not only at the habituating frequency but further decreases gain at all frequencies below the new corner frequency. It also causes phase lead to increase at all frequencies below the new corner frequency (up to some asymptotic value). We show that habituation of the goldfish VOR is not a broad frequency phenomena but is frequency specific. A decrease in VOR gain is produced primarily at the habituating frequency, and there is an increase in phase lead at nearby higher frequencies and a decrease in phase lead at nearby lower frequencies (phase crossover). Both the phase crossover and the frequency specific gain decrease make it impossible to simulate habituation of the VOR simply by increasing the corner frequency of the HPF model. The simplest way to simulate our data is to subtract the output of a band-pass filter (BPF) from the output of the HPF model of the naïve VOR. A BPF passes signals over a limited frequency range only. A BPF decreases gain and imparts a phase lag and lead, respectively, as frequency increases and decreases outside this range. Our model produces both the specific decrease in gain at the habituating frequency, and the phase crossover centered on the frequency of habituation. Our results suggest that VOR habituation may be similar to VOR adaptation (in which VOR modification is produced by visual-vestibular mismatch) in that both are frequency-specific phenomena.

Adaptation, Physiological↗
PubMed2006

Evidence for a crossover in the frequency dependence of the acoustic attenuation in vitreous silica.

We report measurements of the sound attenuation coefficient in vitreous silica, for sound waves of wavelength between 50 and 80 nm, performed with the new inelastic UV light scattering technique. These data indicate that in silica glass a crossover between a temperature-dependent (at low frequency) and a temperature-independent (at high frequency) acoustic attenuation mechanism occurs at Q approximately equal to 0.15 nm(-1). The absence of any signature in the static structure factor at this Q value suggests that the observed crossover should be associated with local elastic constant fluctuations.

Journal Article↗
PubMed1994

The relationship of homologous synapsis and crossing over in a maize inversion.

Frequency of homologous synapsis at pachytene for a relatively short heterozygous inversion was compared to the frequency of crossover occurrence within the inversion and to the frequency of the presence of a recombination nodule within the homologously synapsed inverted region. Crossover frequencies were estimated from bridge-fragment frequencies at anaphase I and anaphase II. Recombination nodules (RNs) were observed in electron micrographs. Results show very similar frequencies of homologous synapsis and the occurrence of reciprocal recombination within the inverted region, consistent with the interpretation that establishment of homologous synapsis in this case is related to at least commitment to the form of resolution of crossover intermediates which gives rise to reciprocal recombination, not conversion only, events. An RN was generally found at pachytene in homologously synapsed inverted regions.

Crossing Over, Genetic↗
PubMed2004

Revealing and addressing length bias and heterogeneous effects in frequency case-crossover studies.

The case-crossover design is useful for assessing whether a recurrent exposure (e.g., drug) triggers an event (e.g., myocardial infarction), using only cases, when finding good controls is impractical. In the basic frequency design, the observed exposure odds among cases, during a period immediately before the event, are compared with the expected exposure odds, based on their usual frequency of past exposures. This is equivalent to comparing observed gap times between the event and the last exposure with the expected gap times based on the subjects' exposure experience under the null hypothesis of no exposure-event relation. Such a comparison reveals two problems in the usual-frequency analyses: 1) length bias that exists even under the null hypothesis; and 2) loss of efficiency when exposure effects do exist. The first problem arises because the event will more likely fall on a longer-than-average period between exposures, even under the null hypothesis, resulting in a systematic downward bias of risk ratios. The second problem arises from categorizing cases as exposed or unexposed and from not fully using the data on gap times between events and preceding exposures. A new method of analysis is presented that is free from length bias and that efficiently uses gap time data.

Bias↗
PubMed2002

eCodonOpt: a systematic computational framework for optimizing codon usage in directed evolution experiments.

We present a systematic computational framework, eCodonOpt, for designing parental DNA sequences for directed evolution experiments through codon usage optimization. Given a set of homologous parental proteins to be recombined at the DNA level, the optimal DNA sequences encoding these proteins are sought for a given diversity objective. We find that the free energy of annealing between the recombining DNA sequences is a much better descriptor of the extent of crossover formation than sequence identity. Three different diversity targets are investigated for the DNA shuffling protocol to showcase the utility of the eCodonOpt framework: (i) maximizing the average number of crossovers per recombined sequence; (ii) minimizing bias in family DNA shuffling so that each of the parental sequence pair contributes a similar number of crossovers to the library; and (iii) maximizing the relative frequency of crossovers in specific structural regions. Each one of these design challenges is formulated as a constrained optimization problem that utilizes 0-1 binary variables as on/off switches to model the selection of different codon choices for each residue position. Computational results suggest that many-fold improvements in the crossover frequency, location and specificity are possible, providing valuable insights for the engineering of directed evolution protocols.

Aldose-Ketose Isomerases↗