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Amy D. Anderson and Bruce S. Weir
The availability of technologies for scoring genotypes of vast numbers of markers in the human genome places a premium on methods for estimating the degree of genetic relatedness. These methods generally assume that the individuals are from a randomly mating population with known allele frequencies. The authors develop a maximum-likelihood estimator that enables analysis of individuals from a cryptically structured population, a common problem in human genetics.
Experimental estimate of the abundance and effects of nearly neutral mutations in the RNA virus 
6, pp. 467–476
Christina L. Burch, Sebastien Guyader, Daniel Samarov and Haipeng Shen
Many mutations have a small effect, making it a challenge to study their impact on distributions of allele frequency and mutational variance. The authors make use of a virus with a rapid generation time to make accurate estimates of the natural mutational parameters, and test the hypothesis that few mutations have a large effect on laboratory fitness. In contrast to recent observations in eukaryotes that very few (1–4%) mutations have detectable effects on fitness, here more than one-third of spontaneous mutations in this RNA virus have detectable effects, suggesting that effect estimates based on laboratory fitness measures can be substantially underestimated.
LIN-61, one of two Caenorhabditis elegans malignant-brain-tumor-repeat-containing proteins, acts with the DRM and NuRD-like protein complexes in vulval development but not in certain other biological processes, pp. 255–271
Melissa M. Harrison, Xiaowei Lu and H. Robert Horvitz
Malignant-brain-tumor (MBT)-repeat-containing proteins are transcriptional repressors that bind to modified histones. This article describes the analysis of the two MBT-repeat-containing proteins in Caenorhabiditis elegans. One of them was found to interact with two different transcriptional-regulatory complexes that contain the retinoblastoma protein or a histone deactylase. These findings suggest that other MBT-repeat-containing proteins, including those in Drosophila and humans, might also interact with the Rb and HDAC proteins.
Suppressors of zyg-1 define regulators of centrosome duplication and nuclear association in Caenorhabditis elegans, pp. 95–113
Catherine A. Kemp, Mi Hye Song, Murali Krishna Addepalli, Ginger Hunter and Kevin O'Connell
The protein kinase ZYG-1 is required for centrosome duplication in Caenorhabditis elegans. To identify factors that interact with ZYG-1, the authors identify suppressors of a zyg-1 mutant. They define genes that function in a variety of cellular processes critical to cell division. Interestingly, several of the suppressors affect genes that play a role in attaching the centrosome to the nuclear envelope. One such gene is sun-1, encoding a nuclear envelope component. Surprisingly, the role of SUN-1 in centrosome duplication is distinct from its role in attachment to the nuclear envelope.
Genomewide association analysis in diverse inbred mice: Power and population structure, pp. 675–683
Phillip McClurg, Jeff Janes, Chunlei Wu, David L. Delano, John R. Walker, Serge Batalov, Joseph S. Takahashi, Kazuhiro Shimomura, Akira Kohsaka, Joseph Bass, Tim Wiltshire and Andrew I. Su
Genomewide association for genetic mapping remains a significant challenge. The authors make use of cis-acting expression quantitative trait loci inferences to optimize an algorithm for genomewide association testing. Their approach employs a panel of diverse inbred mouse strains that are phenotypically diverse and have high recombination rates, but are genetically stratified. An algorithm based on genomewide genetic similarity is shown to perform well in substructured samples like these. Other merits of the mouse diversity panel for association mapping are elaborated.
Genetic positioning of centromeres using half-tetrad analysis in a 4x–2x cross population of potato, pp. 85–94
Tae-Ho Park, Jong-Bo Kim, Ronald C. B. Hutten, Herman J. van Eck, Evert Jacobsen and Richard G. F. Visser
The positions of the centromere in 12 potato chromosomes are identified by half-tetrad analysis, and they are the same as those identified by marker density in the ultra-high density genetic map, showing that both methods are powerful tools for centromere localization. Additionally, the authors prove that a single crossover occurs per chromosome arm.
Neurospora spore killers Sk-2 and Sk-3 suppress meiotic silencing by unpaired DNA, pp. 43–52
Namboori B. Raju, Robert L. Metzenberg and Patrick K. T. Shiu
A fascinating link between the seemingly unrelated phenomena of meiotic drive and meiotic silencing is revealed in this article. In Neurospora, the diploid zygote monitors the pairing of DNA segments during meiotic prophase I. Any gene found not paired with a homolog, as well as sequences homologous to it, will be silenced. The authors identify two suppressors of this silencing that were first discovered as meiotic drive elements.
Role of the mod(mdg4) common region in homolog segregation in Drosophila male meiosis, pp. 161–180
Morvarid Soltani-Bejnood, Sharon E. Thomas, Louisa Villeneuve, Kierstyn Schwartz, Chia-sin Hong and Bruce D. McKee
Homologous chromosomes of Drosophila find each other in meiosis with the help of the Modifier of Mdg4 in Meiosis (MNM) proteins. The authors show that mutations in the N-terminal BTB domain that is common to all MNM proteins disrupt chromosome pairing and segregation, indicating that BTB-mediated oligomerization contributes to homolog pairing.
Genetic similarities within and between human populations, pp. 351–359
D. J. Witherspoon, S. Wooding, A. R. Rogers, E. E. Marchani, W. S. Watkins, M. A. Batzer and L. B. Jorde
Surprisingly, random pairs of people from two different populations are often genetically more similar than random pairs from the same population. This observation lies at the focal point of a recurring controversy between geneticists who stress the relative similarity of all humans and those who focus on the power of genetic data to classify people into populations. Using accessible statistical methods and large data sets from diverse populations, the authors compare and reconcile these views of human genetic variation and show that individuals can be safely assigned to their population of origin provided that hundreds of markers are used.
Proofreading and secondary structure processing determine the orientation dependence of CAG·CTG trinucleotide repeat instability in Escherichia coli, pp. 27–41
Rabaab Zahra, John K. Blackwood, Jill Sales and David R. F. Leach
Expansion of trinucleotide repeats in the genome is the cause of several inherited diseases, including Huntington's disease, fragile-X syndrome, and myotonic dystrophy. In Escherichia coli, instability depends on the orientation of the repeat with respect to replication. The authors show that the nature of deletion events in CAG•CTG repeat arrays in the E. coli genome is likely due to formation of large misfolded DNA structures. The orientation dependence of instability is caused by DNA proofreading in the presence of the structure-directed nuclease SbcCD.
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