bluuebunny/crossref_metadata_2025 huggingface dataset:
P-cadherin is a p63 target gene with a crucial role in the developing human limb bud and hair follicle
Authors: Shimomura Yutaka , Wajid Muhammad , Shapiro Lawrence , Christiano Angela M.
Published: January 2008

P-cadherin is a member of the classical cadherin family that forms the transmembrane core of adherens junctions. Recently, mutations in the P-cadherin gene (CDH3) have been shown to cause two inherited diseases in humans: hypotrichosis with juvenile macular dystrophy (HJMD) and ectodermal dysplasia, ectrodactyly, macular dystrophy (EEM syndrome). The common features of both diseases are sparse hair and macular dystrophy of the retina, while only EEM syndrome shows the additional finding of split hand/foot malformation (SHFM). We identified five consanguineous Pakistani families with either HJMD or EEM syndrome, and detected pathogenic mutations in the CDH3 gene of all five families. In order to define the role of P-cadherin in hair follicle and limb development, we performed expression studies on P-cadherin in the mouse embryo, and demonstrated the predominant expression of P-cadherin not only in the hair follicle placode, but also at the apical ectodermal ridge (AER) of the limb bud. Based on the evidence that mutations in the p63 gene also result in hypotrichosis and SHFM, and that the expression patterns of p63 and P-cadherin overlap in the hair follicle placode and AER, we postulated that CDH3 could be a direct transcriptional target gene of p63. We performed promoter assays and ChIP,which revealed that p63 directly interacts with two distinct regions of the CDH3 promoter. We conclude that P-cadherin is a newly defined transcriptional target gene of p63, with a crucial role in hair follicle morphogenesis as well as the AER during limb bud outgrowth in humans, whereas it is not required for either in mice.
Recombinase-mediated cassette exchange reveals the selective use of Gq/G11-dependent and -independent endothelin 1/endothelin type A receptor signaling in pharyngeal arch development
Authors: Sato Takahiro , Kawamura Yumiko , Asai Rieko , Amano Tomokazu , Uchijima Yasunobu , Dettlaff-Swiercz Dagmara A. , Offermanns Stefan , Kurihara Yukiko , Kurihara Hiroki
Published: January 2008

The endothelin (Edn) system comprises three ligands (Edn1, Edn2 and Edn3)and their G-protein-coupled type A (Ednra) and type B (Ednrb) receptors. During embryogenesis, the Edn1/Ednra signaling is thought to regulate the dorsoventral axis patterning of pharyngeal arches via Dlx5/Dlx6upregulation. To further clarify the underlying mechanism, we have established mice in which gene cassettes can be efficiently knocked-in into the Ednra locus using recombinase-mediated cassette exchange (RMCE) based on the Cre-lox system. The first homologous recombination introducing mutant lox-flanked Neo resulted in homeotic transformation of the lower jaw to an upper jaw, as expected. Subsequent RMCE-mediated knock-in of lacZ targeted its expression to the cranial/cardiac neural crest derivatives as well as in mesoderm-derived head mesenchyme. Knock-in of Ednra cDNA resulted in a complete rescue of craniofacial defects of Ednra-null mutants. By contrast, Ednrb cDNA could not rescue them except for the most distal pharyngeal structures. At early stages, the expression of Dlx5, Dlx6 and their downstream genes was downregulated and apoptotic cells distributed distally in the mandible of Ednrb-knock-in embryos. These results, together with similarity in craniofacial defects between Ednrb-knock-in mice and neural-crest-specific Gαq/Gα11-deficient mice, indicate that the dorsoventral axis patterning of pharyngeal arches is regulated by the Ednra-selective, Gq/G11-dependent signaling, while the formation of the distal pharyngeal region is under the control of a Gq/G11-independent signaling, which can be substituted by Ednrb. This RMCE-mediated knock-in system can serve as a useful tool for studies on gene functions in craniofacial development.
Mechanism of asymmetric ovarian development in chick embryos
Authors: Ishimaru Yoshiyasu , Komatsu Tomoko , Kasahara Megumi , Katoh-Fukui Yuko , Ogawa Hidesato , Toyama Yoshiro , Maekawa Mamiko , Toshimori Kiyotaka , Chandraratna Roshantha A. S. , Morohashi Ken-ichirou , Yoshioka Hidefumi
Published: January 2008

In most animals, the gonads develop symmetrically, but most birds develop only a left ovary. A possible role for estrogen in this asymmetric ovarian development has been proposed in the chick, but the mechanism underlying this process is largely unknown. Here, we identify the molecular mechanism responsible for this ovarian asymmetry. Asymmetric PITX2 expression in the left presumptive gonad leads to the asymmetric expression of the retinoic-acid (RA)-synthesizing enzyme, RALDH2, in the right presumptive gonad. Subsequently, RA suppresses expression of the nuclear receptors Ad4BP/SF-1 and estrogen receptor α in the right ovarian primordium. Ad4BP/SF-1 expressed in the left ovarian primordium asymmetrically upregulates cyclin D1 to stimulate cell proliferation. These data suggest that early asymmetric expression of PITX2 leads to asymmetric ovarian development through up- or downregulation of RALDH2,Ad4BP/SF-1, estrogen receptor α and cyclin D1.
Polo kinases regulateC. elegansembryonic polarity via binding to DYRK2-primed MEX-5 and MEX-6
Authors: Nishi Yuichi , Rogers Eric , Robertson Scott M. , Lin Rueyling
Published: January 2008

Polo kinases are known key regulators of cell divisions. Here we report a novel, non-cell division function for polo kinases in embryonic polarity of newly fertilized Caenorhabditis elegans embryos. We show that polo kinases, via their polo box domains, bind to and regulate the activity of two key polarity proteins, MEX-5 and MEX-6. These polo kinases are asymmetrically localized along the anteroposterior axis of newly fertilized C. elegans embryos in a pattern identical to that of MEX-5 and MEX-6. This asymmetric localization of polo kinases depends on MEX-5 and MEX-6, as well as genes regulating MEX-5 and MEX-6 asymmetry. We identify an amino acid of MEX-5, T186, essential for polo binding and show that T186 is important for MEX-5 function in vivo. We also show that MBK-2, a developmentally regulated DYRK2 kinase activated at meiosis II,primes T186 for subsequent polo kinase-dependent phosphorylation. Prior phosphorylation of MEX-5 at T186 greatly enhances phosphorylation of MEX-5 by polo kinases in vitro. Our results provide a mechanism by which MEX-5 and MEX-6 function is temporally regulated during the crucial oocyte-to-embryo transition.
The role of Polycomb-group response elements in regulation ofengrailedtranscription inDrosophila
Authors: DeVido Sarah K. , Kwon Deborah , Brown J. Lesley , Kassis Judith A.
Published: January 2008

Polycomb group proteins are required for long-term repression of many genes in Drosophila and all metazoans. In Drosophila, DNA fragments called Polycomb-group response elements (PREs) have been identified that mediate the action of Polycomb-group proteins. Previous studies have shown that a 2 kb fragment located from -2.4 kb to -395 bp upstream of the Drosophila engrailed promoter contains a multipartite PRE that can mediate mini-white silencing and act as a PRE in an Ubx-reporter construct. Here, we study the role of this 2 kb fragment in the regulation of the engrailed gene itself. Our results show that within this 2 kb fragment, there are two subfragments that can act as PREs in embryos. In addition to their role in gene silencing, these two adjacent PRE fragments can facilitate the activation of the engrailed promoter by distant enhancers. The repressive action of the engrailed PRE can also act over a distance. A 181 bp subfragment can act as a PRE and also mediate positive effects in an enhancer-detector construct. Finally, a deletion of 530 bp of the 2 kb PRE fragment within the endogenous engrailed gene causes a loss-of-function phenotype, showing the importance of the positive regulatory effects of this PRE-containing fragment. Our data are consistent with the model that engrailed PREs bring chromatin together, allowing both positive and negative regulatory interactions between distantly located DNA fragments.
Inactivation of nuclear Wnt-β-catenin signaling limits blastocyst competency for implantation
Authors: Xie Huirong , Tranguch Susanne , Jia Xiangxu , Zhang Hao , Das Sanjoy K. , Dey Sudhansu K. , Kuo Calvin J. , Wang Haibin
Published: January 2008

The activation of the blastocyst, a process by which it gains competency to attach with the receptive uterus, is a prerequisite for successful implantation. However, the molecular basis of blastocyst activation remains largely unexplored. Combining molecular, pharmacological and physiological approaches, we show here that silencing of Wnt-β-catenin signaling in mice does not adversely affect the development of preimplantation embryos to blastocysts and uterine preparation for receptivity, but, remarkably, blocks blastocyst competency to implantation. Using the physiologically relevant delayed implantation model and trophoblast stem cells in culture, we further demonstrate that a coordinated activation of canonical Wnt-β-catenin signaling with attenuation of the non-canonical Wnt-RhoA signaling pathway ensures blastocyst competency to implantation. These findings constitute novel evidence that Wnt signaling is at least one pathway that determines blastocyst competency for implantation.
Ectopic histone H3S10 phosphorylation causes chromatin structure remodeling inDrosophila
Authors: Deng Huai , Bao Xiaomin , Cai Weili , Blacketer Melissa J. , Belmont Andrew S. , Girton Jack , Johansen Jørgen , Johansen Kristen M.
Published: January 2008

Histones are subject to numerous post-translational modifications that correlate with the state of higher-order chromatin structure and gene expression. However, it is not clear whether changes in these epigenetic marks are causative regulatory factors in chromatin structure changes or whether they play a mainly reinforcing or maintenance role. In Drosophilaphosphorylation of histone H3S10 in euchromatic chromatin regions by the JIL-1 tandem kinase has been implicated in counteracting heterochromatization and gene silencing. Here we show, using a LacI-tethering system, that JIL-1 mediated ectopic histone H3S10 phosphorylation is sufficient to induce a change in higher-order chromatin structure from a condensed heterochromatin-like state to a more open euchromatic state. This effect was absent when a `kinase dead' LacI-JIL-1 construct without histone H3S10 phosphorylation activity was expressed. Instead, the `kinase dead' construct had a dominant-negative effect, leading to a disruption of chromatin structure that was associated with a global repression of histone H3S10 phosphorylation levels. These findings provide direct evidence that the epigenetic histone tail modification of H3S10 phosphorylation at interphase can function as a causative regulator of higher-order chromatin structure in Drosophilain vivo.
Loss ofseven-upfromDrosophilaR1/R6 photoreceptors reveals a stochastic fate choice that is normally biased by Notch
Authors: Miller Adam C. , Seymour Heather , King Christopher , Herman Tory G.
Published: January 2008

Recent evidence suggests that stochasticism is important for generating cell type diversity. We have identified a novel stochastic fate choice as part of the mechanism by which Delta/Notch (Dl/N) signaling specifies R7 fate in the Drosophila eye. The equivalence of R1/R6/R7 precursors is normally broken by the activation of N, which specifies the R7 fate. The orphan nuclear hormone receptor Seven-up (Svp) is necessary and sufficient to direct R1/R6/R7 precursors to adopt the R1/R6 fate. A simple model, therefore,is that N represses Svp, which otherwise prevents adoption of the R7 fate. However, we have found that R1/R6s lacking svp stochastically adopt either the R7 or the R8 fate with equal likelihood. We show that N specifies the R7 fate by a novel branched pathway: N represses Svp expression, thereby exposing an underlying stochastic choice between the R7 and R8 fates, and then tips this choice towards the R7 fate.
Restriction Site–Specific Methylation Studies of Imprinted Genes with Quantitative Real-Time PCR
Authors: Bruce Sara , Hannula-Jouppi Katariina , Lindgren Cecilia M , Lipsanen-Nyman Marita , Kere Juha
Published: January 2008

Background: Epigenetic studies, such as the measurement of DNA methylation, are important in the investigation of syndromes influenced by imprinted genes. Quick and accurate quantification of methylation at such genes can be of appreciable diagnostic aid.

Methods: We first digested genomic DNA with methylation-sensitive restriction enzymes and used DNA without digestion as a control and nonmethylated λ DNA as an internal control for digestion efficiency. We then performed quantitative real-time PCR analyses with 6 unique PCR assays to investigate 4 imprinting control regions on chromosomes 7 and 11 in individuals with uniparental disomy of chromosome 7 (UPD7) and in control individuals.

Results: Our validation of the method demonstrated both quantitative recovery and low methodologic imprecision. The imprinted loci on chromosome 7 behaved as expected in maternal UPD7 (100% methylation) and paternal UPD7 (<10% methylation). In controls, the mean (SD) for percent methylation at 2 previously well-studied restriction sites were 46% (6%) for both H19 and KCNQ1OT1, a result consistent with the previously observed methylation rate of approximately 50%. The methylation percentages of all investigated imprinted loci were normally distributed, implying that the mean and SD can be used as a reference for screening methylation loss or gain.

Conclusion: The investigated loci are of particular importance for investigating the congenital Silver–Russell and Beckwith–Wiedemann syndromes; however, the method can also be applied to other imprinted regions. This method is easy to set up, has no PCR bias, requires small amounts of DNA, and can easily be applied to large patient populations for screening the loss or gain of methylation.
Systematic Search for Placental DNA-Methylation Markers on Chromosome 21: Toward a Maternal Plasma-Based Epigenetic Test for Fetal Trisomy 21
Authors: Chim Stephen S C , Jin Shengnan , Lee Tracy Y H , Lun Fiona M F , Lee Wing S , Chan Lisa Y S , Jin Yongjie , Yang Ningning , Tong Yu K , Leung Tak Y , Lau Tze K , Ding Chunming , Chiu Rossa W K , Lo Y M Dennis
Published: January 2008

Background: The presence of fetal DNA in maternal plasma represents a source of fetal genetic material for noninvasive prenatal diagnosis; however, the coexisting background maternal DNA complicates the analysis of aneuploidy in such fetal DNA. Recently, the SERPINB5 gene on chromosome 18 was shown to exhibit different DNA-methylation patterns in the placenta and maternal blood cells, and the allelic ratio for placenta-derived hypomethylated SERPINB5 in maternal plasma was further shown to be useful for noninvasive detection of fetal trisomy 18.

Methods: To develop a similar method for the noninvasive detection of trisomy 21, we used methylation-sensitive single nucleotide primer extension and/or bisulfite sequencing to systematically search 114 CpG islands (CGIs)—76% of the 149 CGIs on chromosome 21 identified by bioinformatic criteria—for differentially methylated DNA patterns. The methylation index (MI) of a CpG site was estimated as the proportion of molecules methylated at that site.

Results: We identified 22 CGIs which were shown to contain CpG sites that were either completely unmethylated (MI = 0.00) in maternal blood cells and methylated in the placenta (MI range, 0.22–0.65), or completely methylated (MI = 1.00) in maternal blood cells and hypomethylated in the placenta (MI range, 0.00–0.75). We detected, for the first time, placental DNA-methylation patterns on chromosome 21 in maternal plasma during pregnancy and observed their postpartum clearance.

Conclusion: Twenty-two (19%) of the 114 studied CGIs on chromosome 21 showed epigenetic differences between samples of placenta and maternal blood cells; these CGIs may provide a rich source of markers for noninvasive prenatal diagnosis.
Noninvasive Prenatal Diagnosis of Fetal Chromosomal Aneuploidies by Maternal Plasma Nucleic Acid Analysis
Authors: Dennis Lo Y M , Chiu Rossa W K
Published: January 2008

Background: The discovery of circulating cell-free fetal nucleic acids in maternal plasma has opened up new possibilities for noninvasive prenatal diagnosis. The potential application of this technology for the noninvasive prenatal detection of fetal chromosomal aneuploidies is an aspect of this field that is being actively investigated. The main challenge of work in this area is the fact that cell-free fetal nucleic acids represent only a minor fraction of the total nucleic acids in maternal plasma.

Methods and Results: We performed a review of the literature, which revealed that investigators have applied methods based on the physical and molecular enrichment of fetal nucleic acid targets from maternal plasma. The former includes the use of size fractionation of plasma DNA and the use of the controversial formaldehyde treatment method. The latter has been achieved through the development of fetal epigenetic and fetal RNA markers. The aneuploidy status of the fetus has been explored through the use of allelic ratio analysis of plasma fetal epigenetic and RNA markers. Digital PCR has been shown to offer high precision for allelic ratio and relative chromosome dosage analyses.

Conclusions: After a decade of work, the theoretical and practical feasibility of prenatal fetal chromosomal aneuploidy detection by plasma nucleic acid analysis has been demonstrated in studies using small sample sets. Larger scale independent studies will be needed to validate these initial observations. If these larger scale studies prove successful, it is expected that with further development of new fetal DNA/RNA markers and new analytical methods, molecular noninvasive prenatal diagnosis of the major chromosomal aneuploidies could become a routine practice in the near future.
IGF-1: Analytik und Referenzbereiche / Measurement of IGF-1 and reference ranges
Authors: Spilcke-Liss Elisabeth , Friedrich Nele , Wallaschofski Henri
Published: January 2008

Der Insulin-ähnliche Wachstumsfaktor IGF-1 (insulin-like growth factor 1) ist der ausschlaggebende Faktor zur Beurteilung des Wachstumshormonhaushalts. Da der IGF-1-Spiegel zahlreichen Einflüssen wie z. B. dem Alter, Geschlecht, genetischen Faktoren, der Ernährung oder Erkrankungen ausgesetzt ist, ist es notwendig, exakte normative Daten als Grundlage für die Diagnostik und Therapiekontrolle bei Patienten mit Störungen der Wachstumshormonachse zu haben. Obwohl die bisher genutzten Referenzwerte anhand großer Kohorten gesunder Personen entwickelt wurden, zeigt die Abhängigkeit dieser Werte von den verwendeten Labormethoden, dass methodenspezifische Referenzwerte für IGF-1 erforderlich sind.
Neuartiger Lymphozyten-Transformations-Test (LTT-MELISA®) zum Nachweis einer Lyme-Borreliose / A novel lymphocyte transformation test (LTT-MELISA®) for Lyme borreliosis
Authors: Valentine-Thon Elizabeth , Ilsemann Karsten , Sandkamp Martin
Published: January 2008

Die Diagnose einer aktiven Lyme-Borreliose (LB) stellt immer noch eine Herausforderung bei klinisch nicht eindeutigen, serologisch nicht zuordnungsfähigen und PCR-negativen Patienten dar. Verschiedene Lymphozyten-Transformations-Tests (LTT) wurden zur Feststellung einer zellulären Reaktivität eingesetzt, deren klinische Anwendbarkeit jedoch erheblich durch den Einsatz ungenügend definierter Borrelien-Antigene und nichtstandardisierter LTT-Verfahren eingeschränkt war. In der vorliegenden Studie stellen wir die Entwicklung und klinische Relevanz eines neuen LTT unter Einsatz eines validierten Verfahrens (MELISA®) und der Verwendung definierter rekombinanter Borrelien-Antigene vor. Nach einem initialen Screening von 244 Patienten mit Verdacht auf eine Borrelien-Infektion bzw. -Erkrankung wurden vier aussagefähige rekombinante Antigene ausgewählt: OspC (Borrelia afzelii), p41-int 1 (Borrelia garinii), p41-int 2 (B. afzelii) und p100 (B. afzelii). Anschließend wurden 30 seronegative gesunde Probanden im LTT-MELISA® untersucht, um die Spezifität festzustellen, 68 Patienten parallel analysiert, um die Reproduzierbarkeit zu überprüfen, und 54 Lymphozyten-reaktive, symptomatische Patienten vor und nach Antibiotikatherapie getestet, um die klinische Relevanz des Tests zu evaluieren. Die Mehrzahl (86,2%), der im initialen Screening untersuchten und LTT-MELISA®-positiven Patienten (36,9%), waren seropositiv und zeigten Symptome einer aktiven LB. Die Spezifität betrug 96,7%, die Reproduzierbarkeit 92,6%. Nach Therapie zeigten die meisten Patienten (90,7%) keine persistierende oder eine erheblich reduzierte Lymphozyten-Reaktivität, welche mit einer klinischen Besserung einherging. Der vorgestellte neuartige LTT-MELISA® scheint mit aktiver LB zu korrelieren und dürfte diagnostische Relevanz in der Abklärung klinisch und serologisch nicht eindeutiger Fälle aufweisen.
Evaluating Sustainability Using Standard Approaches: The BEES Tool
Authors: Lippiatt Barbara C.
Published: January 2008

In support of the ASTM International, Symposium on Common Ground, Consensus Building and Continual Improvement, this paper describes the BEES (Building for Environmental and Economic Sustainability) software that integrates standard approaches for selecting cost-effective, environmentally-preferable building products. Version 4.0 of the Windows-based decision support software, aimed at designers, builders, and product manufacturers, includes actual environmental and economic performance data for over 230 building products across a range of functional applications. BEES measures the environmental performance of building products using the environmental life-cycle assessment approach specified in International Organization for Standardization (ISO) 14040 standards. All stages in the life of a product are analyzed: raw material acquisition, manufacture, transportation, installation, use, and waste management. Economic performance is measured using the ASTM International standard life-cycle cost method (E 917), which covers the costs of initial investment, replacement, operation, maintenance and repair, and disposal. Environmental and economic performance are combined into an overall performance measure using the ASTM standard for Multiattribute Decision Analysis (E 1765). For the entire BEES analysis, building products are defined and classified based on the ASTM standard classification for building elements known as UNIFORMAT II (E 1557).
The Cyber Worlds of Self‐Injurers: Deviant Communities, Relationships, and Selves
Authors: Adler Patricia A. , Adler Peter
Published: January 2008

We explore how self‐injurers, a group of deviants who primarily were loners, now use the Internet to form subcultural and collegial relations. Drawing on virtual participant‐observation in cyber self‐injury groups, over eighty face‐to‐face and telephone in‐depth interviews, and over ten thousand e‐mail postings to groups and bulletin boards, we describe and analyze the online subcultures of self‐injurers. Via the Web, they have become cyber “colleagues,” simultaneously enacting two deviant organizational forms and challenging the idea that deviant loners can exist in a cyber society. We further analyze these individuals and their interactions to compare and contrast the venues that they use, the communities and relationships that they form, and their relation to real life. We contribute to symbolic interactionism through our social constructionist stance toward the creation of virtual communities and relationships, our focus on identity and stigma, our view of social organization as grounded in the panoply of human interpersonal relationships, our contrast of the competing reality claims posed by virtual as opposed to the solid world, and our discussion of the modern versus postmodern self.
Constructing Threat and Appropriating “Civil Rights”: Rhetorical Strategies of Gun Rights and English Only Leaders
Authors: Lio Shoon , Melzer Scott , Reese Ellen
Published: January 2008

Using a grounded theory method, we analyze the framing strategies of organizational leaders of the gun rights and English Only movements. Although we find greater variability in the framing strategies of English Only leaders, leaders of both movements mobilize fear by rhetorically constructing moral threats to American society in ways that draw on, and uphold, the ideals and practices of dominant social groups. In doing so, they appeal to their constituents' status anxieties. We also find that these movements engage in a particular form of frame transformation that we call “frame appropriation” to counter opponents' claims and broaden their support. Future research should examine when and how, and to what effect, other social movements similarly mobilize fear and engage in frame appropriation.
Doing Difference/Doing Power: Negotiations of Race and Gender in a Mentoring Program
Authors: Schippers Mimi
Published: January 2008

This study is an empirical exploration of how people negotiate structural inequality and interpersonal power relations through the interactive accomplishment of difference. The author presents data on a mentoring program in which college women were paired with middle school girls across race, class, and age differences. The data show white mentors' status and authority depended less on the program's structure and more on the middle school girls' interactional maneuvers to make race difference particularly salient in the mentoring relationships and, more important, to establish a set of meanings for racial difference that made African American higher in status than white. Bridging research and theory on “doing difference” and status relations, the author argues that the accomplishment of difference alone is not the main mechanism by which structural inequalities are produced in everyday life. Instead, the accomplishment of difference is reflective, productive, and sometimes divergent of structural inequalities when, within interaction, people (1) accomplish difference in a way that raises the salience of that difference for defining the situation and (2) establish meanings that define that difference as a status hierarchy.
Estimating the Per-Base-Pair Mutation Rate in the YeastSaccharomyces cerevisiae
Authors: Lang Gregory I , Murray Andrew W
Published: January 2008

Although mutation rates are a key determinant of the rate of evolution they are difficult to measure precisely and global mutations rates (mutations per genome per generation) are often extrapolated from the per-base-pair mutation rate assuming that mutation rate is uniform across the genome. Using budding yeast, we describe an improved method for the accurate calculation of mutation rates based on the fluctuation assay. Our analysis suggests that the per-base-pair mutation rates at two genes differ significantly (3.80 × 10−10 at URA3 and 6.44 × 10−10 at CAN1) and we propose a definition for the effective target size of genes (the probability that a mutation inactivates the gene) that acknowledges that the mutation rate is nonuniform across the genome.
Determination of Mitochondrial Genetic Diversity in Mammals
Authors: Nabholz Benoit , Mauffrey Jean-François , Bazin Eric , Galtier Nicolas , Glemin Sylvain
Published: January 2008

Mitochondrial DNA (mtDNA) is one of the most popular population genetic markers. Its relevance as an indicator of population size and history has recently been questioned by several large-scale studies in animals reporting evidence for recurrent adaptive evolution, at least in invertebrates. Here we focus on mammals, a more restricted taxonomic group for which the issue of mtDNA near neutrality is crucial. By analyzing the distribution of mtDNA diversity across species and relating it to allozyme diversity, life-history traits, and taxonomy, we show that (i) mtDNA in mammals does not reject the nearly neutral model; (ii) mtDNA diversity, however, is unrelated to any of the 14 life-history and ecological variables that we analyzed, including body mass, geographic range, and The World Conservation Union (IUCN) categorization; (iii) mtDNA diversity is highly variable between mammalian orders and families; (iv) this taxonomic effect is most likely explained by variations of mutation rate between lineages. These results are indicative of a strong stochasticity of effective population size in mammalian species. They suggest that, even in the absence of selection, mtDNA genetic diversity is essentially unpredictable, knowing species biology, and probably uncorrelated to species abundance.
Naive Application of Permutation Testing Leads to Inflated Type I Error Rates
Authors: Churchill G A , Doerge R W
Published: January 2008

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.
cin-4, a Gene With Homology to Topoisomerase II, Is Required for Centromere Resolution by Cohesin Removal From Sister Kinetochores During Mitosis
Authors: Stanvitch Gerald , Moore Landon L
Published: January 2008

The back-to-back geometry of sister kinetochores is essential in preventing loss or damage of chromosomes during mitosis. Kinetochore orientation is generated in part by a process of resolving kinetochores at the centromere (centromere resolution) prior to spindle interactions. Because few of the genes required for centromere resolution are known, we used Caenorhabditis elegans to screen for conditional mutants defective in orienting sister kinetochores during mitosis. C. elegans is ideal for such screens because its chromosomes are holocentric. Here we identified an essential gene, cin-4, required for centromere resolution and for removal of cohesin from sites near sister kinetochores during mitosis. Given that compromised cohesin function restores centromere resolution in the absence of cin-4, CIN-4 likely acts to remove cohesin from the CENP-A chromatin enabling centromere resolution. CIN-4 has a high amino acid identity to the catalytic domain of topoisomerase II, suggesting a partial gene duplication of the C. elegans topoisomerase II gene, top-2. Similar to CIN-4, TOP-2 is also required for centromere resolution; however, the loss of TOP-2 is phenotypically distinct from the loss of CIN-4, suggesting that CIN-4 and TOP-2 are topoisomerase II isoforms that perform separate essential functions in centromere structure and function.
An Accurate Model for Genetic Hitchhiking
Authors: Eriksson Anders , Fernström Pontus , Mehlig Bernhard , Sagitov Serik
Published: January 2008

We suggest a simple deterministic approximation for the growth of the favored-allele frequency during a selective sweep. Using this approximation we introduce an accurate model for genetic hitchhiking. Only when Ns < 10 (N is the population size and s denotes the selection coefficient) are discrepancies between our approximation and direct numerical simulations of a Moran model notable. Our model describes the gene genealogies of a contiguous segment of neutral loci close to the selected one, and it does not assume that the selective sweep happens instantaneously. This enables us to compute SNP distributions on the neutral segment without bias.
Integrating Phylogenetic and Population Genetic Analyses of Multiple Loci to Test Species Divergence Hypotheses in Passerina Buntings
Authors: Carling Matt D , Brumfield Robb T
Published: January 2008

Phylogenetic and population genetic analyses of DNA sequence data from 10 nuclear loci were used to test species divergence hypotheses within Passerina buntings, with special focus on a strongly supported, but controversial, sister relationship between Passerina amoena and P. caerulea inferred from a previous mitochondrial study. Here, a maximum-likelihood analysis of a concatenated 10-locus data set, as well as minimize-deep-coalescences and maximum-likelihood analyses of the locus-specific gene trees, recovered the traditional sister relationship between P. amoena and P. cyanea. In addition, a more recent divergence time estimate between P. amoena and P. cyanea than between P. amoena and P. caerulea provided evidence for the traditional sister relationship. These results provide a compelling example of how lineage sorting stochasticity can lead to incongruence between gene trees and species trees, and illustrate how phylogenetic and population genetic analyses can be integrated to investigate evolutionary relationships between recently diverged taxa.
Quantitative Trait Loci for Grain Yield and Adaptation of Durum Wheat (Triticum durum Desf.) Across a Wide Range of Water Availability
Authors: Maccaferri Marco , Sanguineti Maria Corinna , Corneti Simona , Ortega José Luis Araus , Salem Moncef Ben , Bort Jordi , DeAmbrogio Enzo , del Moral Luis Fernando Garcia , Demontis Andrea , El-Ahmed Ahmed , Maalouf Fouad , Machlab Hassan , Martos Vanessa , Moragues Marc , Motawaj Jihan , Nachit Miloudi , Nserallah Nasserlehaq , Ouabbou Hassan , Royo Conxita , Slama Amor , Tuberosa Roberto
Published: January 2008

Grain yield is a major goal for the improvement of durum wheat, particularly in drought-prone areas. In this study, the genetic basis of grain yield (GY), heading date (HD), and plant height (PH) was investigated in a durum wheat population of 249 recombinant inbred lines evaluated in 16 environments (10 rainfed and 6 irrigated) characterized by a broad range of water availability and GY (from 5.6 to 58.8 q ha−1). Among the 16 quantitative trait loci (QTL) that affected GY, two major QTL on chromosomes 2BL and 3BS showed significant effects in 8 and 7 environments, with R2 values of 21.5 and 13.8% (mean data of all 16 environments), respectively. In both cases, extensive overlap was observed between the LOD profiles of GY and PH, but not with those for HD. QTL specific for PH were identified on chromosomes 1BS, 3AL, and 7AS. Additionally, three major QTL for HD on chromosomes 2AS, 2BL, and 7BS showed limited or no effects on GY. For both PH and GY, notable epistasis between the chromosome 2BL and 3BS QTL was detected across several environments.
Novel x-Type High-Molecular-Weight Glutenin Genes From Aegilops tauschii and Their Implications on the Wheat Origin and Evolution Mechanism of Glu-D1-1 Proteins
Authors: Zhang Yanzhen , Li Xiaohui , Wang Aili , An Xueli , Zhang Qian , Pei Yuhe , Gao Liyan , Ma Wujun , Appels Rudi , Yan Yueming
Published: January 2008

Two new x-type high-molecular-weight glutenin subunits with similar size to 1Dx5, designated 1Dx5*t and 1Dx5.1*t in Aegilops  tauschii, were identified by SDS–PAGE, RP-HPLC, and MALDI-TOF-MS. The coding sequences were isolated by AS-PCR and the complete ORFs were obtained. Allele 1Dx5*t consists of 2481 bp encoding a mature protein of 827 residues with deduced Mr of 85,782 Da whereas 1Dx5.1*t comprises 2526 bp encoding 842 residues with Mr of 87,663 Da. The deduced Mr's of both genes were consistent with those determined by MALDI-TOF-MS. Molecular structure analysis showed that the repeat motifs of 1Dx5*t were correspondingly closer to the consensus compared to 1Dx5.1*t and 1Dx5 subunits. A total of 11 SNPs (3 in 1Dx5*t and 8 in 1Dx5.1*t) and two indels in 1Dx5*t were identified, among which 8 SNPs were due to C-T or A-G transitions (an average of 73%). Expression of the cloned ORFs and N-terminal sequencing confirmed the authenticities of the two genes. Interestingly, several hybrid clones of 1Dx5*t expressed a slightly smaller protein relative to the authentic subunit present in seed proteins; this was confirmed to result from a deletion of 180 bp through illegitimate recombination as well as an in-frame stop codon. Network analysis demonstrated that 1Dx5*t, 1Dx2t, 1Dx1.6t, and 1Dx2.2* represent a root within a network and correspond to the common ancestors of the other Glu-D-1-1 alleles in an associated star-like phylogeny, suggesting that there were at least four independent origins of hexaploid wheat. In addition to unequal homologous recombination, duplication and deletion of large fragments occurring in Glu-D-1-1 alleles were attributed to illegitimate recombination.
Enhancer Blocking and Transvection at the DrosophilaapterousLocus
Authors: Gohl Daryl , Müller Martin , Pirrotta Vincenzo , Affolter Markus , Schedl Paul
Published: January 2008

Intra- and interchromosomal interactions have been implicated in a number of genetic phenomena in diverse organisms, suggesting that the higher-order structural organization of chromosomes in the nucleus can have a profound impact on gene regulation. In Drosophila, homologous chromosomes remain paired in somatic tissues, allowing for trans interactions between genes and regulatory elements on the two homologs. One consequence of homolog pairing is the phenomenon of transvection, in which regulatory elements on one homolog can affect the expression of a gene in trans. We report a new instance of transvection at the Drosophila apterous (ap) locus. Two different insertions of boundary elements in the ap regulatory region were identified. The boundaries are inserted between the ap wing enhancer and the ap promoter and have highly penetrant wing defects typical of mutants in ap. When crossed to an ap promoter deletion, both boundary inserts exhibit the interallelic complementation characteristic of transvection. To confirm that transvection occurs at ap, we generated a deletion of the ap wing enhancer by FRT-mediated recombination. When the wing-enhancer deletion is crossed to the ap promoter deletion, strong transvection is observed. Interestingly, the two boundary elements, which are inserted ∼10 kb apart, fail to block enhancer action when they are present in trans to one another. We demonstrate that this is unlikely to be due to insulator bypass. The transvection effects described here may provide insight into the role that boundary element pairing plays in enhancer blocking both in cis and in trans.
Identification of the Minus-Dominance Gene Ortholog in the Mating-Type Locus of Gonium pectorale
Authors: Hamaji Takashi , Ferris Patrick J , Coleman Annette W , Waffenschmidt Sabine , Takahashi Fumio , Nishii Ichiro , Nozaki Hisayoshi
Published: January 2008

The evolution of anisogamy/oogamy in the colonial Volvocales might have occurred in an ancestral isogamous colonial organism like Gonium pectorale. The unicellular, close relative Chlamydomonas reinhardtii has a mating-type (MT) locus harboring several mating-type-specific genes, including one involved in mating-type determination and another involved in the function of the tubular mating structure in only one of the two isogametes. In this study, as the first step in identifying the G. pectorale MT locus, we isolated from G. pectorale the ortholog of the C. reinhardtii mating-type-determining minus-dominance (CrMID) gene, which is localized only in the MT− locus. 3′- and 5′-RACE RT–PCR using degenerate primers identified a CrMID-orthologous 164-amino-acid coding gene (GpMID) containing a leucine-zipper RWP-RK domain near the C-terminal, as is the case with CrMID. Genomic Southern blot analysis showed that GpMID was coded only in the minus strain of G. pectorale. RT–PCR revealed that GpMID expression increased during nitrogen starvation. Analysis of F1 progeny suggested that GpMID and isopropylmalate dehydratase LEU1S are tightly linked, suggesting that they are harbored in a chromosomal region under recombinational suppression that is comparable to the C. reinhardtii MT locus. However, two other genes present in the C. reinhardtii MT locus are not linked to the G. pectorale LEU1S/MID, suggesting that the gene content of the volvocalean MT loci is not static over time. Inheritance of chloroplast and mitochondria genomes in G. pectorale is uniparental from the plus and minus parents, respectively, as is also the case in C. reinhardtii.
Precision of Recombination Frequency Estimates After Random Intermating With Finite Population Sizes
Authors: Frisch Matthias , Melchinger Albrecht E
Published: January 2008

Random intermating of F2 populations has been suggested for obtaining precise estimates of recombination frequencies between tightly linked loci. In a simulation study, sampling effects due to small population sizes in the intermating generations were found to abolish the advantages of random intermating that were reported in previous theoretical studies considering an infinite population size. We propose a mating scheme for intermating with planned crosses that yields more precise estimates than those under random intermating.
Characterization of Interactions Between and Among Components of the Meiotic Silencing by Unpaired DNA Machinery in Neurospora crassa Using Bimolecular Fluorescence Complementation
Authors: Bardiya Nirmala , Alexander William G , Perdue Tony D , Barry Edward G , Metzenberg Robert L , Pukkila Patricia J , Shiu Patrick K T
Published: January 2008

Bimolecular fluorescence complementation (BiFC) is based on the complementation between two nonfluorescent fragments of the yellow fluorescent protein (YFP) when they are united by interactions between proteins covalently linked to them. We have successfully applied BiFC in Neurospora crassa using two genes involved in meiotic silencing by unpaired DNA (MSUD) and observed macromolecular complex formation involving only SAD-1 proteins, only SAD-2 proteins, and mixtures of SAD-1 and SAD-2 proteins.
Development and Evaluation of a Genetics Literacy Assessment Instrument for Undergraduates
Authors: Bowling Bethany Vice , Acra Erin E , Wang Lihshing , Myers Melanie F , Dean Gary E , Markle Glenn C , Moskalik Christine L , Huether Carl A
Published: January 2008

There is continued emphasis on increasing and improving genetics education for grades K–12, for medical professionals, and for the general public. Another critical audience is undergraduate students in introductory biology and genetics courses. To improve the learning of genetics, there is a need to first assess students' understanding of genetics concepts and their level of genetics literacy (i.e., genetics knowledge as it relates to, and affects, their lives). We have developed and evaluated a new instrument to assess the genetics literacy of undergraduate students taking introductory biology or genetics courses. The Genetics Literacy Assessment Instrument is a 31-item multiple-choice test that addresses 17 concepts identified as central to genetics literacy. The items were selected and modified on the basis of reviews by 25 genetics professionals and educators. The instrument underwent additional analysis in student focus groups and pilot testing. It has been evaluated using ∼400 students in eight introductory nonmajor biology and genetics courses. The content validity, discriminant validity, internal reliability, and stability of the instrument have been considered. This project directly enhances genetics education research by providing a valid and reliable instrument for assessing the genetics literacy of undergraduate students.
A Genetic Selection For Neurospora crassa Mutants Altered in Their Light Regulation of Transcription
Authors: Navarro-Sampedro Laura , Yanofsky Charles , Corrochano Luis M
Published: January 2008

Transcription of the Neurospora crassa gene con-10 is induced during conidiation and following exposure of vegetative mycelia to light, but light activation is transient due to photoadaptation. We describe mutational analyses of photoadaptation using a N. crassa strain bearing a translational fusion of con-10, including its regulatory region, to a selectable bacterial gene conferring hygromycin resistance (hph). Growth of this strain was sensitive to hygromycin, upon continuous culture in the light. Five mutants were isolated that were resistant to hygromycin when cultured under constant light. Three mutant strains displayed elevated, sustained accumulation of con-10∷hph mRNA during continued light exposure, suggesting that they bear mutations that reduce or eliminate the presumed light-dependent repression mechanism that blocks con-10 transcription upon prolonged illumination. These mutations altered photoadaptation for only a specific group of genes (con-10 and con-6), suggesting that regulation of photoadaptation is relatively gene specific. The mutations increased light-dependent mRNA accumulation for genes al-1, al-2, and al-3, each required for carotenoid biosynthesis, resulting in a threefold increase in carotenoid accumulation following continuous light exposure. Identification of the altered gene or genes in these mutants may reveal novel proteins that participate in light regulation of gene transcription in fungi.
Regulation of Serotonin Biosynthesis by the G Proteins Gαo and Gαq Controls Serotonin Signaling inCaenorhabditis elegans
Authors: Tanis Jessica E , Moresco James J , Lindquist Robert A , Koelle Michael R
Published: January 2008

To analyze mechanisms that modulate serotonin signaling, we investigated how Caenorhabditis elegans regulates the function of serotonergic motor neurons that stimulate egg-laying behavior. Egg laying is inhibited by the G protein Gαo and activated by the G protein Gαq. We found that Gαo and Gαq act directly in the serotonergic HSN motor neurons to control egg laying. There, the G proteins had opposing effects on transcription of the tryptophan hydroxylase gene tph-1, which encodes the rate-limiting enzyme for serotonin biosynthesis. Antiserotonin staining confirmed that Gαo and Gαq antagonistically affect serotonin levels. Altering tph-1 gene dosage showed that small changes in tph-1 expression were sufficient to affect egg-laying behavior. Epistasis experiments showed that signaling through the G proteins has additional tph-1-independent effects. Our results indicate that (1) serotonin signaling is regulated by modulating serotonin biosynthesis and (2) Gαo and Gαq act in the same neurons to have opposing effects on behavior, in part, by antagonistically regulating transcription of specific genes. Gαo and Gαq have opposing effects on many behaviors in addition to egg laying and may generally act, as they do in the egg-laying system, to integrate multiple signals and consequently set levels of transcription of genes that affect neurotransmitter release.
AfricanDrosophila melanogasterandD. simulansPopulations Have Similar Levels of Sequence Variability, Suggesting Comparable Effective Population Sizes
Authors: Nolte Viola , Schlötterer Christian
Published: January 2008

Drosophila melanogaster and D. simulans are two closely related species with a similar distribution range. Many studies suggested that D. melanogaster has a smaller effective population size than D. simulans. As most evidence was derived from non-African populations, we readdressed this question by sequencing 10 X-linked loci in five African D. simulans and six African D. melanogaster populations. Contrary to previous results, we found no evidence for higher variability, and thus larger effective population size, in D. simulans. Our observation of similar levels of variability of both species will have important implications for the interpretation of patterns of molecular evolution.