Mismatch Correction Acts as a Barrier to Homeologous Recombination in Saccharomyces Cerevisiae

A homeologous mitotic recombination assay was used to test the role of Saccharomyces cerevisiae mismatch repair genes PMS1, MSH2 and MSH3 on recombination fidelity. A homeologous gene pair consisting of S. cerevisiae SPT15 and its S. pombe homolog were present as a direct repeat on chromosome V, with the exogenous S. pombe sequences inserted either upstream or downstream of the endogenous S. cerevisiae gene. Each gene carried a different inactivating mutation, rendering the starting strain Spt15(-). Recombinants that regenerated SPT15 function were scored after nonselective growth of the cells. In strains wild type for mismatch repair, homeologous recombination was depressed 150- to 180-fold relative to homologous controls, indicating that recombination between diverged sequences is inhibited. In one orientation of the homeologous gene pair, msh2 or msh3 mutations resulted in 17- and 9.6-fold elevations in recombination and the msh2 msh3 double mutant exhibited an 43-fold increase, implying that each MSH gene can function independently in trans to prevent homeologous recombination. Homologous recombination was not significantly affected by the msh mutations. In the other orientation, only msh2 strains were elevated (12-fold) for homeologous recombination. A mutation in MSH3 did not affect the rate of recombination in this orientation. Surprisingly, a pms1 deletion mutant did not exhibit elevated homeologous recombination.     

A comparative study of cell classifiers for image-based high-throughput screening

Background

Millions of cells are present in thousands of images created in high-throughput screening (HTS). Biologists could classify each of these cells into a phenotype by visual inspection. But in the presence of millions of cells this visual classification task becomes infeasible. Biologists train classification models on a few thousand visually classified example cells and iteratively improve the training data by visual inspection of the important misclassified phenotypes. Classification methods differ in performance and performance evaluation time. We present a comparative study of computational performance of gentle boosting, joint boosting CellProfiler Analyst (CPA), support vector machines (linear and radial basis function) and linear discriminant analysis (LDA) on two data sets of HT29 and HeLa cancer cells.

Results

For the HT29 data set we find that gentle boosting, SVM (linear) and SVM (RBF) are close in performance but SVM (linear) is faster than gentle boosting and SVM (RBF). For the HT29 data set the average performance difference between SVM (RBF) and SVM (linear) is 0.42 %. For the HeLa data set we find that SVM (RBF) outperforms other classification methods and is on average 1.41 % better in performance than SVM (linear).

Conclusions

Our study proposes SVM (linear) for iterative improvement of the training data and SVM (RBF) for the final classifier to classify all unlabeled cells in the whole data set.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-342) contains supplementary material, which is available to authorized users.     

Interaction of FANCD2 and NBS1 in the DNA damage response

Fanconi anaemia (FA) and Nijmegen breakage syndrome (NBS) are autosomal recessive chromosome instability syndromes with distinct clinical phenotypes. Cells from individuals affected with FA are hypersensitive to mitomycin C (MMC), and cells from those with NBS are hypersensitive to ionizing radiation. Here we report that both NBS cell lines and individuals with NBS are hypersensitive to MMC, indicating that there may be functional linkage between FA and NBS. In wild-type cells, MMC activates the colocalization of the FA subtype D2 protein (FANCD2) and NBS1 protein in subnuclear foci. Ionizing radiation activates the ataxia telangiectasia kinase (ATM)-dependent and NBS1-dependent phosphorylation of FANCD2, resulting in an S-phase checkpoint. NBS1 and FANCD2 therefore cooperate in two distinct cellular functions, one involved in the DNA crosslink response and one involved in the S-phase checkpoint response.     

Characteristics of Shelter-Relinquished Animals and Their Owners Compared With Animals and Their Owners in U.S. Pet-Owning Households

Animal shelters in the United States annually receive millions of relinquished dogs and cats, and risk factors for relinquishment are not fully understood. Investigators sponsored by the National Council on Pet Population Study and Policy interviewed people who relinquished dogs and cats at 12 shelters in four regions. We collected similar data from a sample of U.S. households with companion animals. Data collected included nonhuman animal characteristics such as age, sex, and frequency of selected behaviors. We also obtained data on keepers' (owners') age, sex, and level of education as well as their general knowledge of pet care and behavior. We found that relinquishment was associated with physical and behavioral characteristics of the animals and owner characteristics and knowledge. Relinquished animals were more likely to be intact, younger, and mixed bred. People relinquishing animals were significantly more likely to be men and younger than 35 years. Duration of ownership was significantly shorter for relinquished animals.     

Modelling the impact of hen harrier management measures on a red grouse population in the UK

Human‐wildlife conflict is one of the greatest barriers to effective conservation. The recovery of the hen harrier Circus cyaneus in the United Kingdom has been limited due to illegal persecution, a consequence of the raptors’ predation on the economically valuable game‐bird, the red grouse Lagopus lagopus scoticus. To improve management of the system it is necessary to understand the interactions between the two species in their broader community context. We therefore developed a multi‐species model in which the life history and interactions of each of the two bird species are described through linked process models. This model was fit to population data using a Bayesian state–space framework and used to investigate the effectiveness of a conflict–mitigation technique known as diversionary feeding, in which harrier nests are provided with food in an attempt to reduce consumption of grouse chicks. To explore the utility of diversionary feeding we specified four scenarios in which 1) harriers were absent from the system, 2) there was no diversionary feeding of harriers, 3) only a portion of the harrier nests were provided with diversionary food and 4) all nests were provided with diversionary food. The results from fitting the model under the different scenarios were used to determine the strength of harriers’ impact on grouse density, as well as the effectiveness of diversionary feeding. Given the lack of information on other grouse predators and only two years of data on supplementary feeding, our results need to be implanted with caution. However, we found theoretical support for the hen harriers’ suppression of grouse cycle amplitude and average density. Furthermore, our results suggest that on grouse estates where diversionary feeding is the only active management, diversionary feeding is only marginally successful and not sufficient to mitigate the consequences of hen harrier predation on red grouse chicks.     

Reproductive parameters of the Taiwan monkey (Macaca cyclopis)

The following parameters of the Taiwan monkey,Macaca cyclopis, are presented and compared with other species ofMacaca: the menstrual cycle, sexual skin and vaginal desquamation changes during the menstrual cycle, time of ovulation, gestation period, breeding season, body weight of the newborn, age and body weight at menarche, body weight at first conception, spermatozoa count in the ejaculate, and the body weight at sexual maturity of the male.The many similarities in reproductive biology ofMacaca cyclopis, the rhesus monkey (Macaca mulatta), and the cynomolgus monkey (Macaca irus) include sexual skin and vaginal desquamation changes during the menstrual cycle, time of ovulation, gestation period, and placental sign. Body weight ofM. cyclopis is lower thanM. mulatta at birth, at menarche and at the first conception in females and at sexual maturation in males, is heavier thanM. irus at birth and is not different fromM. radiata at birth. No difference in menstrual cycle ofM. cyclopis was observed in animals housed in air-conditioned rooms compared to those housed in nonair-conditioned rooms. Summer amenorrhea was not observed inM. cyclopis but a high incidence of low vaginal desquamation was noted to occur in summer months. The mode of length of the menstrual cycle ofM. cyclopis is shorter thanM. mulatta and other species ofMacaca. The breeding season ofM. cyclopis in the wild extends from the end of September to January. In laboratory conditions their fertile period extends throughout the year.This study was supported in part by the National Council on Science Development, Republic of China, and in part by the Damon Runyon Memorial Fund for Cancer Research, U. S. A. (DRG-841 B and C). The paper was presented at the ICLA Asian Pacific Meeting on Laboratory Animals held at Tokyo and Inuyama, Japan, on September 20–25, 1971.     

Central connections of the olfactory bulb in the weakly electric fish,Gnathonemus petersii

Summary We have investigated the central connections of the classical olfactory system in the weakly electric fish Gnathonemus petersii using HRP and cobalt labelling techniques. The olfactory bulb projects bilaterally via the medial and lateral olfactory tracts to restricted areas of the telencephalon, namely to its rostromedial, lateral and posterior medial parts. The most extensive telencephalic target is the posterior terminal field, which arcs around the lateral forebrain bundle at levels posterior to the anterior commissure. Projections to the contralateral hemisphere cross in the ventral telencephalon rostral to the anterior commissure and via the posterior dorsal part of the anterior commissure; endings are also present within the anterior commissure. Bilateral projections to the preoptic area, to the nucleus posterior tuberis and to an area in the thalamus are apparent. In all cases, contralateral projections are less extensive than those on the side ipsilateral to the injected bulb. A projection via the medial olfactory tract can be followed to the contralateral bulb. Following injections into the olfactory bulb, retrogradely labelled neurons are found in the contralateral bulb and in six telencephalic areas; they are also present in the periventricular diencephalon and in an area lateral to the nucleus posterior tuberis. The present results support the suggestion that a reduction in olfactory input to the telencephalon occurs together with increased telencephalic differentiation in actinopterygian fishes.