Evidence for functional hemizygosity at the Emtr locus in CHO cells through segregation analysis

The hypothesis of functional hemizygosity at the emetine-resistant (Emt^r, a non-X-linked recessive marker) locus in Chinese hamster ovary (CHO) cells has been examined by segregation analysis. The frequencies and the rates of segregation of the Emt^r and Thg^r (thioguanine-resistant, an X-linked recessive mutation) markers were determined from hybrids constructed between an Emt^r-Thg^r CHO cell line and various other Chinese hamster lines (V79, M3-1, CHO, GM7S, CHW and CHL). Thg^r segregants were obtained at similar frequencies (10^?2–10^?3) from all the hybrids. The frequency of segregation of the Emt^r marker, however, was similar to that of Thg^r only in the CHO × CHO hybrids and was much lower (10^?4–10^?6) than the CHO × other Chinese hamster hybrids. Similar results were obtained when the segregation rates for the two markers from various hybrids were determined. These results are consistent with the hypothesis that in CHO cells, the gene responsible for Emt^r is present in a single (functional) copy, whereas two copies of this gene are present in other Chinese hamster lines examined.     

Leaf non-structural carbohydrates and leaf dry weight per area in three altitudinal populations ofEspeletia schultzii WEDD

The leaf non-structural carbohydrate (NSC) content and total non-structural carbohydrate content (TNC) were measured on a dry weight basis and on a leaf area basis in three altitudinal (3100, 3550 and 4200 m a.s.l.) populations ofE. schultzii. The values of leaf dry weight per area (LWA) increase with altitude. The leaf non-structural carbohydrate content (expressed as g/kg dry weight) does not show statistically significant difference among populations, but the values expressed on an area basis (g/m²) show a statistically significant increase with altitude. Significant correlations were observed between LWA and TNC (r ²=0.65); insoluble carbohydrate (r ²=0.78); total soluble carbohydrate (r ²=0.53); reducing sugars (r ²=0.47) expressed on area basis. Correlations between LWA and NSC for any fraction and TNC on a dry weight basis were not significant. It appears that along this altitudinal gradient the leaf area is more affected than the leaf dry weight. Since the NSC is known to play a role in the freezing tolerance of plants, the results indicate that the freezing tolerance does not change among the populations along the gradient.     

Experimental Population Genetics of Meiotic Drive Systems I. Pseudo-Y Chromosomal Drive as a Means of Eliminating Cage Populations of DROSOPHILA MELANOGASTER

The experimental population genetics of Y-chromosome drive in Drosophila melanogaster is approximated by studying the behavior of T(Y;2),SD lines. These exhibit "pseudo-Y" drive through the effective coupling of the Y chromosome to the second chromosome meiotic drive locus, Segregation distorter (SD). T(Y;2),SD males consequently produce only male offspring. When such lines are allowed to compete against structurally normal SD⁺ flies in population cages, T(Y;2),SD males increase in frequency according to the dynamics of a simple haploid selection model until the cage population is eliminated as a result of a deficiency in the number of adult females. Cage population extinction generally occurs within about seven generations.—Several conclusions can be drawn from these competition cage studies:

(1) Fitness estimates for the T(Y;2),SD lines (relative to SD⁺ ) are generally in the range of 2–4, and these values are corroborated by independent estimates derived from studies of migration-selection equilibrium.

(2) Fitness estimates are unaffected by cage replication, sample time, or the starting frequency of T(Y;2),SD males, indicating that data from diverse cages can be legitimately pooled to give an overall fitness estimate.

(3) Partitioning of the T(Y;2),SD fitnesses into components of viability, fertility, and frequency of alternate segregation (Y + SD from X + SD⁺) suggests that most of the T(Y;2),SD advantage derives from the latter two components. Improvements in the system might involve increasing both the viability and the alternate segregation to increase the total fitness.

While pseudo-Y drive operates quite effectively against laboratory stocks, it is less successful in eliminating wild-type populations which are already segregating for suppressors of SD action. This observation suggests that further studies into the origin and rate of accumulation of suppressors of meiotic drive are needed before an overall assessment can be made of the potential of Y-chromosome drive as a tool for population control.

     

A Multi-Megabase Copy Number Gain Causes Maternal Transmission Ratio Distortion on Mouse Chromosome 2

Significant departures from expected Mendelian inheritance ratios (transmission ratio distortion, TRD) are frequently observed in both experimental crosses and natural populations. TRD on mouse Chromosome (Chr) 2 has been reported in multiple experimental crosses, including the Collaborative Cross (CC). Among the eight CC founder inbred strains, we found that Chr 2 TRD was exclusive to females that were heterozygous for the WSB/EiJ allele within a 9.3 Mb region (Chr 2 76.9 – 86.2 Mb). A copy number gain of a 127 kb-long DNA segment (designated as responder to drive, R2d) emerged as the strongest candidate for the causative allele. We mapped R2d sequences to two loci within the candidate interval. R2d1 is located near the proximal boundary, and contains a single copy of R2d in all strains tested. R2d2 maps to a 900 kb interval, and the number of R2d copies varies from zero in classical strains (including the mouse reference genome) to more than 30 in wild-derived strains. Using real-time PCR assays for the copy number, we identified a mutation (R2d2^WSBdel1) that eliminates the majority of the R2d2^WSB copies without apparent alterations of the surrounding WSB/EiJ haplotype. In a three-generation pedigree segregating for R2d2^WSBdel1, the mutation is transmitted to the progeny and Mendelian segregation is restored in females heterozygous for R2d2^WSBdel1, thus providing direct evidence that the copy number gain is causal for maternal TRD. We found that transmission ratios in R2d2^WSB heterozygous females vary between Mendelian segregation and complete distortion depending on the genetic background, and that TRD is under genetic control of unlinked distorter loci. Although the R2d2^WSB transmission ratio was inversely correlated with average litter size, several independent lines of evidence support the contention that female meiotic drive is the cause of the distortion. We discuss the implications and potential applications of this novel meiotic drive system.     

Some notes on the distribution and certain modifications of Mahalanobis' generalized distance (D2)

Different modifications of Mahalanobis' generalized distance (D²) utilized in anthropological research are given, and it is shown that they all derive from the distribution of D² when the distances between the populations investigated are real. To investigate whether observed distances are real, testing of D² for significance is stressed. It is demonstrated that D² ought to be tested for significance according to its relation to the F-distribution, but that it may be related to the chi-squared distribution as an approximation when the numbers of individuals in the samples are very large. The great disadvantages of utilizing this approximation for smaller numbers of individuals in the samples are demonstrated, as well as the dependence of D² on sample size and the number of measurements used when testing for significance.     

Prioritizing Tiger Conservation through Landscape Genetics and Habitat Linkages

Even with global support for tiger (Panthera tigris) conservation their survival is threatened by poaching, habitat loss and isolation. Currently about 3,000 wild tigers persist in small fragmented populations within seven percent of their historic range. Identifying and securing habitat linkages that connect source populations for maintaining landscape-level gene flow is an important long-term conservation strategy for endangered carnivores. However, habitat corridors that link regional tiger populations are often lost to development projects due to lack of objective evidence on their importance. Here, we use individual based genetic analysis in combination with landscape permeability models to identify and prioritize movement corridors across seven tiger populations within the Central Indian Landscape. By using a panel of 11 microsatellites we identified 169 individual tigers from 587 scat and 17 tissue samples. We detected four genetic clusters within Central India with limited gene flow among three of them. Bayesian and likelihood analyses identified 17 tigers as having recent immigrant ancestry. Spatially explicit tiger occupancy obtained from extensive landscape-scale surveys across 76,913 km² of forest habitat was found to be only 21,290 km². After accounting for detection bias, the covariates that best explained tiger occupancy were large, remote, dense forest patches; large ungulate abundance, and low human footprint. We used tiger occupancy probability to parameterize habitat permeability for modeling habitat linkages using least-cost and circuit theory pathway analyses. Pairwise genetic differences (F _ST) between populations were better explained by modeled linkage costs (r>0.5, p<0.05) compared to Euclidean distances, which was in consonance with observed habitat fragmentation. The results of our study highlight that many corridors may still be functional as there is evidence of contemporary migration. Conservation efforts should provide legal status to corridors, use smart green infrastructure to mitigate development impacts, and restore habitats where connectivity has been lost.     

Family resemblance for serum uric acid in a Jerusalem sample of families

Summary Familial aggregation of serum uric acid was studied in a sample of families examined in the Jerusalem Lipid Research Clinic. We first examined homogeneity of familial correlations across the major origin groups in the Israeli population sample. In general correlations were homogeneous across origin groups, except for spouse pairs. Pooled correlations among biological relatives across the origin groups were all statistically significant. Spouse correlation upon adjustment for concomitant variables was moderately positive (r=0.115), yet significantly different from zero. Genetic and cultural determinants of uric acid were estimated utilizing a path model with 10 parameters to be estimated from a total of 16 correlations. Under a reduced model, genetic heritability (h²) was estimated to be 0.47±0.05 and cultural heritability (c²) was 0.11±0.03. However, our data gave suggestive evidence that cultural heritability was higher in parents (c²=0.28) than in children (c²=0.10). Commingling analysis and segregation analysis were also performed, and our findings imply that in the Israeli population there is no evidence for a major gene for high uric acid levels segregating in families.     

Breast glandularity and mean glandular dose assessment using a deep learning framework: Virtual patients study

PurposeBreast dosimetry in mammography is an important aspect of radioprotection since women are exposed periodically to ionizing radiation due to breast cancer screening programs. Mean glandular dose (MGD) is the standard quantity employed for the establishment of dose reference levels in retrospective population studies. However, MGD calculations requires breast glandularity estimation. This work proposes a deep learning framework for volume glandular fraction (VGF) estimations based on mammography images, which in turn are converted to glandularity values for MGD calculations.Methods208 virtual breast phantoms were generated and compressed computationally. The mammography images were obtained with Monte Carlo simulations (MC-GPU code) and a ray-tracing algorithm was employed for labeling the training data. The architectures of the neural networks are based on the XNet and multilayer perceptron, adapted for each task. The network predictions were compared with the ground truth using the coefficient of determination (r²).ResultsThe results have shown a good agreement for inner breast segmentation (r² = 0.999), breast volume prediction (r² = 0.982) and VGF prediction (r² = 0.935). Moreover, the DgN coefficients using the predicted VGF for the virtual population differ on average 1.3% from the ground truth values. Afterwards with the obtained DgN coefficients, the MGD values were estimated from exposure factors extracted from the DICOM header of a clinical cohort, with median(75 percentile) values of 1.91(2.45) mGy.ConclusionWe successfully implemented a deep learning framework for VGF and MGD calculations for virtual breast phantoms.     

Late-quaternary spruce decline and rise in Japan and Sakhalin

The late-glacial logistic decline of spruce (Picea) populations (the intrinsic growth rate,r in yr^?1=?0.0015) was progressively delayed toward cooler sites in Japan; spruce populations expanded asymptotically (r=0.0040?0.0045) in Sakhalin early in the Holocene. Such a time-transgressive range shift in spruce distribution, covering a wide latitudinal range (ca. 35–50°N), implies that the regional temperature rise was not instantaneous, but was rapid, being 0.0015–0.0025 C yr^?1 from 13,000 to 10,000 years B.P. Spruce populations increased in response to Neoglacial cooling only at the margin of its distribution (r=0.0036), but then declined logistically 1,000 years B.P. (r=?0.0022).     

Contribution to the linkage theory of autopolyploids: I

A theory of linkage of autopolyploids is developed under consideration ofm loci andr alleles. The simplifying assumption of chromosome segregation, which may be considered as an approximation to the more adequate theory of chromatid segregation, is made throughout. Random mating and distinct, non-overlapping generations are assumed. Under these assumptions the problem is determined by three basic probability distributions—the distributions of genotypes and of gametes, and the segregation distribution. The segregation distribution is assumed to be the same for males and for females. The aim of the paper is to establish recurrence formulas (which allow to find the distributions of gametes and of genotypes from generation to generation, if the distribution of genotypes for an initial generation is known) and to investigate the limit behavior of these distributions as the number of generations increases indefinitely. In the present paper (hereafter referred to as I) the problem is explained, and the three characteristic distributions are introduced for the general case of a 2s-ploid,m loci, andr alleles. Recurrence relations are established for tetraploids,s=2 andm=2 loci, while the recurrence relations for the general case as well as the limit theorems will be given in the second part of this paper (hereafter referred to as II).     

The accuracy of Bartlett's small-fluctuation approximation for stochastic-difference-equation population models

A heuristic approximation procedure devised by Bartlett has often been used to estimate the stationary first- and second-order moments of difference-equation population models perturbed by “small” noise. Here, the approximation is proved to be valid under quite general assumptions: the exact and approximate moments differ by an amount of order σ³ as σ → 0, where σ² is the mean-square norm of the noise process. The existence of stationary solutions to the perturbed difference equation is also considered. If the noise is Markovian, stationary solutions satisfying the assumptions of the error analysis are proved to exist if the noise is “small” with probability 1. The results are applied to a population model with two age classes and variable recruitment.     

Imputation-Based Population Genetics Analysis of Plasmodium falciparum Malaria Parasites

Whole-genome sequencing technologies are being increasingly applied to Plasmodium falciparum clinical isolates to identify genetic determinants of malaria pathogenesis. However, genome-wide discovery methods, such as haplotype scans for signatures of natural selection, are hindered by missing genotypes in sequence data. Poor correlation between single nucleotide polymorphisms (SNPs) in the P. falciparum genome complicates efforts to apply established missing-genotype imputation methods that leverage off patterns of linkage disequilibrium (LD). The accuracy of state-of-the-art, LD-based imputation methods (IMPUTE, Beagle) was assessed by measuring allelic r² for 459 P. falciparum samples from malaria patients in 4 countries: Thailand, Cambodia, Gambia, and Malawi. In restricting our analysis to 86k high-quality SNPs across the populations, we found that the complete-case analysis was restricted to 21k SNPs (24.5%), despite no single SNP having more than 10% missing genotypes. The accuracy of Beagle in filling in missing genotypes was consistently high across all populations (allelic r², 0.87-0.96), but the performance of IMPUTE was mixed (allelic r², 0.34-0.99) depending on reference haplotypes and population. Positive selection analysis using Beagle-imputed haplotypes identified loci involved in resistance to chloroquine (crt) in Thailand, Cambodia, and Gambia, sulfadoxine-pyrimethamine (dhfr, dhps) in Cambodia, and artemisinin (kelch13) in Cambodia. Tajima’s D-based analysis identified genes under balancing selection that encode well-characterized vaccine candidates: apical merozoite antigen 1 (ama1) and merozoite surface protein 1 (msp1). In contrast, the complete-case analysis failed to identify any well-validated drug resistance or candidate vaccine loci, except kelch13. In a setting of low LD and modest levels of missing genotypes, using Beagle to impute P. falciparum genotypes is a viable strategy for conducting accurate large-scale population genetics and association analyses, and supporting global surveillance for drug resistance markers and candidate vaccine antigens.     

Contraselectable Streptomycin Susceptibility Determinant for Genetic Manipulation and Analysis of Helicobacter pylori

Many Helicobacter pylori genetic studies would benefit from an ability to move DNA sequences easily between strains by transformation and homologous recombination, without needing to leave a conventional drug resistance determinant at the targeted locus. Presented here is a two-gene cassette that can be selected both (i) against, due to a Campylobacter jejuni rpsL gene (dominant streptomycin susceptibility in cells also carrying an rpsL-str^r allele), and (ii) for, due to an erm gene (erythromycin resistance). This rpsL,erm cassette's utility was assessed by using it to replace four gene loci (mdaB, frxA, fur, and nikR) in four streptomycin-resistant [Str^r] strain backgrounds (derivatives of 26695, SS1, X47, and G27MA). The resultant 16 strains (phenotypically erythromycin resistant [Erm^r] and Str^s) were each transformed with wild-type genomic DNAs, and Str^r derivatives were selected. The desired Erm^s Str^r isolates were obtained at frequencies that ranged from 17 to 96% among Str^r transformants, with the Erm^s yield apparently depending on the strain background and genome location of the targeted locus. The ease of isolating unmarked transformants described here should be valuable for many H. pylori molecular genetic and evolutionary analyses.     

Genotypic variation in carboxylation of tomatoes

The gas exchange characteristics of 24 genotypes of Lycopersicon esculentum Mill. and one of L. minutum were measured with an infrared gas analyzer and dew point hygrometer in an open system. Net carbon exchange (NCE) and transpiration rate were measured at 50, 100, 150, and 300 μ1 1⁻¹ CO₂, and a regression of NCE versus internal lead [CO₂] estimates was calculated. The slope of the regression curve at the CO₂ compensation point was used as the measure of carboxylation efficiency (CE). Significant genotypic differences for CE were obtained. Differences in CE did not appear to be due to differences in diffusive resistance defined as the sum of the boundary layer resistance (r_a) and the stomatal plus cuticular resistance (r₁). There was no correlation (r = -0.07) between (r_a + r₁) and CE. Within groups with nonsignificantly different means for (r_a + r₁) there were genotypes with extremes for CE.     

A simple proof that certain quantities are independent of the geographical structure of population

This paper gives a proof that certain quantities are independent of the geographical structure of a population. The quantities are: (1) the fixation probability of a mutant; (2) the sum of the quantity x(1 ? x), where x is the mutant frequency, while the mutant is segregating; and (3) the quantity x(1 ? x) summed over the generations during which the gene frequency in the whole population assumes a specified value. The independence of geographical structure for the latter two quantities is not exact if there is selection, but is a close approximation.The model is a geographically structured version of Moran's haploid overlapping generation model. The population consists of colonies connected genetically by migration. Each individual has the same negative exponential lifetime distribution. When an individual dies, it is immediately replaced by an individual born in the same colony with a probability proportional to the frequency and fitness of the type giving birth. In a diploid population the quantity x(1 ? x) is proportional to the heterozygosity.     

Characterization of an RNase Z nonsense mutation identified exclusively in environment-conditioned genic male sterile rice

The two-line hybrid system in rice is becoming more important and employs environment-conditioned genic male sterile (EGMS) lines sensitive to photoperiod (photoperiod-sensitive genic male sterile), temperature [temperature genic male sterile (TGMS)], or a combination of the two (photoperiod temperature genic male sterile). At least 18 EGMS genes have been mapped, and two cloned, but controversies exist. For example, three different genes were reported to underlie the TGMS trait in three independently identified progenitors, Annong S-1, Zhu 1S, and Guangzhan 63S, while another study demonstrated that the TGMS genes in Annong S-1 and Zhu 1S are allelic. In the present study, we confirmed the allelism of the three TGMS genes, which means there is a common TGMS gene(s) in these lines. Knowing there is an association between the mutant allele (RNZ ^m ) of a ribonuclease gene (RNZ) with the TGMS trait in Guangzhuan 63S, we then sequenced RNZ for 14 commercial EGMS and 21 non-EGMS lines, and we developed two derived cleaved amplified polymorphic sequence (dCAPS) markers to detect RNZ ^m alleles in 32 EGMS and 310 non-EGMS lines. The analyses showed that the RNZ ^m allele existed exclusively in EGMS lines; all non-EGMS lines contained the functional RNZ ^gc or RNZ ^tc allele. Furthermore, two segregating populations that included 2,429 individuals were developed by crossing Zhu 1S (RNZ ^m ) to two non-EGMS lines (both with RNZ ^tc ); examination of the segregation of male sterile and fertile plants indicated that the TGMS trait was under the control of a single gene; analysis of the markers revealed the RNZ ^m allele exclusively in TGMS plants and the RNZ ^tc allele only in non-TGMS plants in both populations. The dCAPS markers could therefore help select TGMS progeny in breeding programs, which will save time and labor, and improve breeding efficiency and accuracy.     

Is the decrease of the total electron energy density a covalence indicator in hydrogen and halogen bonds?

In this work, halogen bonding (XB) and hydrogen bonding (HB) complexes were studied with the aim of analyzing the variation of the total electronic energy density H(r _b ) with the interaction strengthening. The calculations were performed at the MP2/6?311++G(2d,2p) level of approximation. To explain the nature of such interactions, the atoms in molecules theory (AIM) in conjunction with reduced variational space self-consistent field (RVS) energy decomposition analysis were carried out. Based on the local virial theorem, an equation to decompose the total electronic energy density H(r _b ) in two energy densities, (?G(r _b )) and 1/4?²ρ(r _b ), was derived. These energy densities were linked with the RVS interaction energy components. Through the connection between both decomposition schemes, it was possible to conclude that the decrease in H(r _b ) with the interaction strengthening observed in the HB as well as the XB complexes, is mainly due to the increase in the attractive electrostatic part of the interaction energy and in lesser extent to the increase in its covalent character, as is commonly considered.     

Characterization and transferability of Clostridium perfringens plasmids.

Two strains of Clostridium perfringens resistant to clindamycin (Cl), chloramphenicol (Cm), erythromycin (Em), and tetracycline (Tc) were isolated in France in 1974 and 1975. For one of these strains, curing experiments and molecular characterization of the extrachromosomal DNA clearly demonstrate the existence of two plasmids, plP401 (54 kilobases) and plP402 (63 kilobases), which, respectively, code for Tc Cm and Em Cl resistance. With mixed cultures, the Tc Cm plasmid is transferable to sensitive strains of C. perfringens; a segregation of these markers is frequently observed during mating experiments. In contrast, the transfer of the naturally occurring plasmid Em Cl does not occur at a significant rate. In performing transfer experiments in axenic mice, we obtained a Cl^r Em^r Tc^r transcipient whose chromosomal properties are those of a hybrid. When used in mating as a parental strain, this strain promotes chromosomal gene exchange. The role of the plasmid in this phenomenon is discussed, these transcipients being generally Cl^r Em^r Tc^r. The plasmid transfer is not limited to antibiotic resistance plasmids, the transferability of a bacteriocinogenic plasmid, plP404, harbored by C. perfringens BP6K-N5 being shown also. The transfer mechanism remains to be proved; it might be a conjugation process, a cell-to-cell contact being necessary for the transfer.     

Purification and characterization of the inactive Ca2+, Mg2+-activated adenosine triphosphatase of the unc A- mutant Escherichia coli AN120.

Resealing of erythrocyte ghosts in the presence of 4.5 mm Ca²⁺ induces the segregation of small membrane vesicles with a very high phospholipid:protein ratio and a high lysolecithin content. Polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate indicates that the vesicles consist mainly of the high molecular spectrin peptides, the Ca²⁺-induced increase of band IIa (M_r 198,000) which is not extractable at low ionic strength, and a weak peptide band in the 72,000 M_r region. Ca²⁺ ghosts and vesicles show significant differences with regard to the specific activities of several membrane-associated enzymes. The segregated vesicles dispose of an efficient outwarddirected Ca²⁺-transport system.