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Bethany Vice Bowling, Erin E. Acra, Lihshing Wang, Melanie F. Myers, Gary E. Dean, Glenn C. Markle, Christine L. Moskalik and Carl A. Huether
Do you want to understand what your students know before your course starts (to help you decide what to teach them) and what they know after taking the course (so you can know where you succeeded and where you might improve)? You will want to consider using the Genetics Literacy Assessment Instrument, a multiple choice diagnostic test that addresses concepts identified as central to genetic literacy. Designed on the basis of reviews by 25 genetic professionals, the instrument has been piloted with almost 400 students, resulting in a valid and reliable method for assessing the genetic literacy of undergraduate students.
Naive application of permutation testing leads to inflated type I error rates, pp. 609–610
G. A. Churchill and R. W. Doerge
Failure to account for family structure within populations or in complex mating designs via uninformed applications of permutation testing will lead to inflated type I error rates. Careful consideration of the design factors is essential since some situations allow several valid permutation strategies and the choice that maximizes statistical power will not always be intuitive.
Testing for archaic hominin admixture on the X chromosome: Model likelihoods for the modern human RRM2P4region from summaries of genealogical topology under the structured coalescent, pp. 427–437
Murray P. Cox, Fernando L. Mendez, Tatiana M. Karafet, Maya Metni Pilkington, Sarah B. Kingan, Giovanni Destro-Bisol, Beverly I. Strassmann and Michael F. Hammer
The extent to which anatomically modern humans hybridized with, or completely replaced, archaic hominins (such as Homo erectus or Neanderthals) remains an open question. In this article, models of modern human demography are parameterized using approximate Bayesian computation on a 12 Mb multilocus resequencing data set. This model is applied to a locus on the human X chromosome, RRM2P4, which was recently identified as a possible candidate for ancient admixture. The observed genealogy is consistent with a range of scenarios, including archaic admixture.
Enhancer blocking and transvection at the Drosophila apterouslocus, pp. 127–143
Daryl Gohl, Martin Müller, Vincenzo Pirrotta, Markus Affolter and Paul Schedl
Homologous chromosomes remain paired in somatic tissues of Drosophila. One consequence of this is transvection: regulatory elements on one chromosome affecting expression of a gene in trans on the other chromosome. This article reports a new instance of transvection at the Drosophila apterous (ap) gene and provides insights into the mechanism of enhancer blocking by boundary elements in cis and in trans.
Estimating the per-base-pair mutation rate in the yeast Saccharomyces cerevisiae, pp. 67–82
Gregory I. Lang and Andrew W. Murray
The global frequency of mutations per genome per generation is often extrapolated from the per-base-pair mutation rate, assuming that it is uniform across the genome. Lang and Murray revisited Luria and Delbrück's fluctuation test (GENETICS 1943) and developed an improved method for calculating mutation rates in budding yeast. They show that the per-base-pair mutation rates for two yeast genes differ by almost twofold. The authors propose a definition for the effective target size of genes (the probability that a mutation inactivates the gene) that acknowledges a nonuniform mutation rate.
Mitochondrial DNA transfer to the nucleus generates extensive insertion site variation in maize, pp. 47–55
Ashley N. Lough, Leah M. Roark, Akio Kato, Thomas S. Ream, Jonathan C. Lamb, James A. Birchler and Kathleen J. Newton
Mitochondrial DNA (mtDNA) insertions into nuclear chromosomes have been documented in a number of eukaryotes. Fluorescence in situ hybridization (FISH) was used to survey mtDNA insertion sites in multiple inbred lines of maize. This article reveals extensive variation among cultivars and frequent changes in insertion sites, demonstrating how FISH can be used to investigate organellar DNA insertion site variation in species that have not been sequenced but for which karyotype analysis is possible.
The telotype defines the telomere state in Saccharomyces cerevisiaeand is inherited as a dominant non-Mendelian characteristic in cells lacking telomerase, pp. 245–257
Svetlana Makovets, Tanya L. Williams and Elizabeth H. Blackburn
As with many important processes, cells have several ways to maintain their telomeres. Cells use telomerase or two alternative mechanisms for preserving their telomeres, and the switch between these three "telotypes" is a heritable stochastic change that occurs in response to a life-threatening challenge. This article describes epigenetic-like mechanisms of telotype switching that provide cells flexibility in responding to the crisis of telomerase loss, enabling them to sustain a viable population. It is likely that epigenetic diversity is used by both prokaryotes and eukaryotes to increase their flexibility as a population to adjust to multiple environmental conditions.
Examination of interchromosomal interactions in vegetatively growing diploid Schizosaccharomyces pombe cells by Cre/loxP site-specific recombination, pp. 99–112
Monika Molnar and Nancy Kleckner
How do chromosomes interact throughout growth of the cell? These authors probe chromosome arrangement in diploid Schizosaccharomyces pombe cells with Cre/loxP site-specific recombination. They find that homologs are coaligned, largely due to pairing at telomeres and nonspecific centromere clustering. They also find evidence for chromosome territories and make the intriguing finding that the probability of interaction of nonhomologous sequences is enhanced if they occur at similar relative positions within their respective arms, thus implicating nonhomologous effects involving both centromeres and telomeres.
Distinct activities of the germline and somatic reproductive tissues in the regulation of Caenorhabditis elegans' longevity, pp. 513–526
Tracy M. Yamawaki, Nuno Arantes-Oliveira, Jennifer R. Berman, Peichuan Zhang and Cynthia Kenyon
Removing germ cells of Caenorhabditis elegans increases an individual's longevity, but only if it has somatic reproductive tissues. The life span increase produced by loss of the germ cells requires the DAF-16/FOXO transcription factor, which accumulates in nuclei in response to germ-cell removal. The somatic reproductive tissues are not required for DAF-16 nuclear accumulation, but they are required for the expression of specific DAF-16 target genes. Thus, the somatic gonad is required for some, but not all, of the life span-extending events that occur upon germline removal.
Genetic design and statistical power of nested association mapping in maize, pp. 539–551
Jianming Yu, James B. Holland, Michael D. McMullen and Edward S. Buckler
Nested association mapping (NAM) is a novel approach that takes advantages of both linkage analysis and association mapping. This strategy is being realized with 5000 maize recombinant inbred lines derived from the crossing of a common inbred to a set of diverse founders. With empirical SNP genotypes from the founders as the primary data, computer simulations demonstrated that the high power of this integrated approach can be realized with cost-efficient genotyping strategy.
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