bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Marker Systems for Oenothera Genetics
Authors: Rauwolf Uwe , Golczyk Hieronim , Meurer Jörg , Herrmann Reinhold G , Greiner Stephan 
Published: September 2008

AbstractThe genus Oenothera has an outstanding scientific tradition. It has been a model for studying aspects of chromosome evolution and speciation, including the impact of plastid nuclear co-evolution. A large collection of strains analyzed during a century of experimental work and unique genetic possibilities allow the exchange of genetically definable plastids, individual or multiple chromosomes, and/or entire haploid genomes (Renner complexes) between species. However, molecular genetic approaches for the genus are largely lacking. In this study, we describe the development of efficient PCR-based marker systems for both the nuclear genome and the plastome. They allow distinguishing individual chromosomes, Renner complexes, plastomes, and subplastomes. We demonstrate their application by monitoring interspecific exchanges of genomes, chromosome pairs, and/or plastids during crossing programs, e.g., to produce plastome–genome incompatible hybrids. Using an appropriate partial permanent translocation heterozygous hybrid, linkage group 7 of the molecular map could be assigned to chromosome 9·8 of the classical Oenothera map. Finally, we provide the first direct molecular evidence that homologous recombination and free segregation of chromosomes in permanent translocation heterozygous strains is suppressed.
A Novel Septin-Associated Protein, Syp1p, Is Required for Normal Cell Cycle-Dependent Septin Cytoskeleton Dynamics in Yeast
Authors: Qiu Wenjie , Neo Suat Peng , Yu Xianwen , Cai Mingjie 
Published: September 2008

AbstractSeptins are a family of GTP-binding proteins whose heterooligomeric complex is the basic structural element of the septin filaments found in many eukaryotic organisms. In budding yeast, septins are mainly confined at the mother–daughter junction and are required for cell morphogenesis and division. Septins undergo assembly and disassembly in accordance with the progression of the cell cycle. In this report, we identified the yeast protein Syp1p as a new regulator of septin dynamics. Syp1p colocalizes with septins throughout most of the cell cycle. Syp1p interacts with the septin subunit Cdc10p and can be precipitated by Cdc10p and Cdc12p. In the syp1Δ mutant, both formation of a complete septin ring at the incipient bud site and disassembly of the septin ring in later stages of cell division are significantly delayed. In addition, overexpression of Syp1p causes marked acceleration of septin disassembly. The fluorescence recovery after photobleaching (FRAP) assay further showed that Syp1p promotes septin turnover in different cell cycle stages. These results suggest that Syp1p is involved in the regulation of cell cycle-dependent dynamics of the septin cytoskeleton in yeast.
Components of the RNAi Machinery That Mediate Long-Distance Chromosomal Associations Are Dispensable for Meiotic and Early Somatic Homolog Pairing inDrosophila melanogaster
Authors: Blumenstiel Justin P , Fu Roxana , Theurkauf William E , Hawley R Scott 
Published: September 2008

AbstractHomolog pairing is indispensable for the proper segregation of chromosomes in meiosis but the mechanism by which homologs uniquely pair with each other is poorly understood. In Drosophila, somatic chromosomes also undergo full homolog pairing by an unknown mechanism. It has been recently demonstrated that both insulator function and somatic long-distance interactions between Polycomb response elements (PREs) are stabilized by the RNAi machinery in Drosophila. This suggests the possibility that long-distance pairing interactions between homologs, either during meiosis or in the soma, may be stabilized by a similar mechanism. To test this hypothesis, we have characterized meiotic and early somatic chromosome pairing of homologous chromosomes in flies that are mutant for various components of the RNAi machinery. Despite the identification of a novel role for the piRNA machinery in meiotic progression and synaptonemal complex (SC) assembly, we have found that the components of the RNAi machinery that mediate long-distance chromosomal interactions are dispensable for homologous chromosome pairing. Thus, there appears to be at least two mechanisms that bring homologous sequences together within the nucleus: those that act between dispersed homologous sequences and those that act to align and pair homologous chromosomes.
Cross-Species Bacterial Artificial Chromosome–Fluorescence in Situ Hybridization Painting of the Tomato and Potato Chromosome 6 Reveals Undescribed Chromosomal Rearrangements
Authors: Tang Xiaomin , Szinay Dóra , Lang Chunting , Ramanna Munikote S , van der Vossen Edwin A G , Datema Erwin , Lankhorst René Klein , de Boer Jan , Peters Sander A , Bachem Christian , Stiekema Willem , Visser Richard G F , de Jong Hans , Bai Yuling 
Published: September 2008

Abstract
Ongoing genomics projects of tomato (Solanum lycopersicum) and potato (S. tuberosum) are providing unique tools for comparative mapping studies in Solanaceae. At the chromosomal level, bacterial artificial chromosomes (BACs) can be positioned on pachytene complements by fluorescence in situ hybridization (FISH) on homeologous chromosomes of related species. Here we present results of such a cross-species multicolor cytogenetic mapping of tomato BACs on potato chromosomes 6 and vice versa. The experiments were performed under low hybridization stringency, while blocking with Cot-100 was essential in suppressing excessive hybridization of repeat signals in both within-species FISH and cross-species FISH of tomato BACs. In the short arm we detected a large paracentric inversion that covers the whole euchromatin part with breakpoints close to the telomeric heterochromatin and at the border of the short arm pericentromere. The long arm BACs revealed no deviation in the colinearity between tomato and potato. Further comparison between tomato cultivars Cherry VFNT and Heinz 1706 revealed colinearity of the tested tomato BACs, whereas one of the six potato clones (RH98-856-18) showed minor putative rearrangements within the inversion. Our results present cross-species multicolor BAC–FISH as a unique tool for comparative genetic studies across Solanum species.
Genetic Analysis of MraY Inhibition by the ϕX174 Protein E
Authors: Zheng Yi , Struck Douglas K , Bernhardt Thomas G , Young Ry 
Published: September 2008

Abstract
Protein E, the lysis protein of bacteriophage ϕX174, is a specific inhibitor of MraY, the phospho-MurNAc-pentapeptide translocase that catalyzes the synthesis of lipid I in the conserved pathway for peptidoglycan biosynthesis. The original evidence for this inhibition was the isolation of two spontaneous E-resistance mraY mutants. Here we report further genetic studies aimed at dissecting the interaction between E and MraY, using a genetic strategy that is facile, rapid, and does not depend on the availability of purified E, purified MraY, or its substrates. This system relies on the ability of mraY or its enzymatically inactive D267N allele to protect cells from lysis after induction of a chimeric λ∷E prophage. Using this approach, the MraY protein from Bacillus subtilis, which shares 43% sequence identity with the Escherichia coli enzyme, was found to interact weakly, if at all, with E. A potential E binding site defined by transmembrane domains 5 and 9 has been identified by isolating more mraY mutants resistant to E inhibition. Genetic analysis indicates that these E-resistant alleles fall into three classes on the basis of the affinity of the encoded proteins for MraY.
Accurate Discovery of Expression Quantitative Trait Loci Under Confounding From Spurious and Genuine Regulatory Hotspots
Authors: Kang Hyun Min , Ye Chun , Eskin Eleazar 
Published: September 2008

Abstract
In genomewide mapping of expression quantitative trait loci (eQTL), it is widely believed that thousands of genes are trans-regulated by a small number of genomic regions called “regulatory hotspots,” resulting in “trans-regulatory bands” in an eQTL map. As several recent studies have demonstrated, technical confounding factors such as batch effects can complicate eQTL analysis by causing many spurious associations including spurious regulatory hotspots. Yet little is understood about how these technical confounding factors affect eQTL analyses and how to correct for these factors. Our analysis of data sets with biological replicates suggests that it is this intersample correlation structure inherent in expression data that leads to spurious associations between genetic loci and a large number of transcripts inducing spurious regulatory hotspots. We propose a statistical method that corrects for the spurious associations caused by complex intersample correlation of expression measurements in eQTL mapping. Applying our intersample correlation emended (ICE) eQTL mapping method to mouse, yeast, and human identifies many more cis associations while eliminating most of the spurious trans associations. The concordances of cis and trans associations have consistently increased between different replicates, tissues, and populations, demonstrating the higher accuracy of our method to identify real genetic effects.
A Targeted Deleterious Allele of the Splicing Factor SCNM1 in the Mouse
Authors: Howell Viive M , de Haan Georgius , Bergren Sarah , Jones Julie M , Culiat Cymbeline T , Michaud Edward J , Frankel Wayne N , Meisler Miriam H 
Published: September 2008

Abstract
The auxiliary spliceosomal protein SCNM1 contributes to recognition of nonconsensus splice donor sites. SCNM1 was first identified as a modifier of the severity of a sodium channelopathy in the mouse. The most severely affected strain, C57BL/6J, carries the variant allele SCNM1R187X, which is defective in splicing the mutated donor site in the Scn8amedJ transcript. To further probe the in vivo function of SCNM1, we constructed a floxed allele and generated a mouse with constitutive deletion of exons 3–5. The SCNM1Δ3-5 protein is produced and correctly localized to the nucleus, but is more functionally impaired than the C57BL/6J allele. Deficiency of SCNM1 did not significantly alter other brain transcripts. We characterized an ENU-induced allele of Scnm1 and evaluated the ability of wild-type SCNM1 to rescue lethal mutations of I-mfa and Brunol4. The phenotypes of the Scnm1Δ3-5 mutant confirm the role of this splice factor in processing the Scn8amedJ transcript and provide a new allele of greater severity for future studies.
A Simple Polymerase Chain Reaction-Based Method for the Construction of Recombinase-Mediated Cassette Exchange Donor Vectors
Authors: Bateman Jack R , Wu C-ting 
Published: September 2008

Abstract
Here we describe a simple method for generating donor vectors suitable for targeted transgenesis via recombinase-mediated cassette exchange (RMCE) using the ΦC31 integrase. This PCR-based strategy employs small attB “tails” on the primers used to amplify a sequence of interest, permitting the rapid creation of transgenes for in vivo analysis.
Nonsense-Mediated Decay of ash1 Nonsense Transcripts in Saccharomyces cerevisiae
Authors: Zheng Wei , Finkel Jonathan S , Landers Sharon M , Long Roy M , Culbertson Michael R 
Published: September 2008

Abstract
Nonsense-mediated mRNA decay (NMD) performs two functions in eukaryotes, one in controlling the expression level of a substantial subset of genes and the other in RNA surveillance. In the vast majority of genes, nonsense mutations render the corresponding transcripts prone to surveillance and subject to rapid degradation by NMD. To examine whether some classes of nonsense transcripts escape surveillance, we asked whether NMD acts on mRNAs that undergo subcellular localization prior to translation. In Saccharomyces cerevisiae, wild-type ASH1 mRNA is one of several dozen transcripts that are exported from the mother-cell nucleus during mitotic anaphase, transported to the bud tip on actin cables, anchored at the bud tip, and translated. Although repressed during transport, translation is a prerequisite for NMD. We found that ash1 nonsense mutations affect transport and/or anchoring independently of NMD. The nonsense transcripts respond to NMD in a manner dependent on the position of the mutation. Maximal sensitivity to NMD occurs when transport and translational repression are simultaneously impaired. Overall, our results suggest a model in which ash1 mRNAs are insensitive to NMD while translation is repressed during transport but become sensitive once repression is relieved.
Differential Gene Expression between Fall‐ and Spring‐Run Chinook Salmon Assessed by Long Serial Analysis of Gene Expression
Authors: Bernier Jeremiah C. , Birkeland Shanda R. , Cipriano Michael J. , McArthur Andrew G. , Banks Michael A. 
Published: September 2008

AbstractOf all Pacific salmonids, Chinook salmon Oncorhynchus tshawytscha display the greatest variability in return times to freshwater. The molecular mechanisms of these differential return times have not been well described. Current methods, such as long serial analysis of gene expression (LongSAGE) and microarrays, allow gene expression to be analyzed for thousands of genes simultaneously. To investigate whether differential gene expression is observed between fall‐ and spring‐run Chinook salmon from California's Central Valley, LongSAGE libraries were constructed. Three libraries containing between 25,512 and 29,372 sequenced tags (21 base pairs/tag) were generated using messenger RNA from the brains of adult Chinook salmon returning in fall and spring and from one ocean‐caught Chinook salmon. Tags were annotated to genes using complementary DNA libraries from Atlantic salmon Salmo salar and rainbow trout O. mykiss. Differentially expressed genes, as estimated by differences in the number of sequence tags, were found in all pairwise comparisons of libraries (freshwater versus saltwater = 40 genes; fall versus spring = 11 genes; and spawning versus nonspawning = 51 genes). The gene for ependymin, an extracellular glycoprotein involved in behavioral plasticity in fish, exhibited the most differential expression among the three groupings. Reverse transcription polymerase chain reaction analysis verified the differential expression of ependymin between the fall‐ and spring‐run samples. These LongSAGE libraries, the first reported for Chinook salmon, provide a window of the transcriptional changes during Chinook salmon return migration to freshwater and spawning and increase the amount of expressed sequence data.
Evaluation of Half‐Heusler Compounds as Thermoelectric Materials Based on the Calculated Electrical Transport Properties
Authors: Yang Jiong , Li Huanming , Wu Ting , Zhang Wenqing , Chen Lidong , Yang Jihui 
Published: September 2008

AbstractA theoretical evaluation of the thermoelectric‐related electrical transport properties of 36 half‐Heusler (HH) compounds, selected from more than 100 HHs, is carried out in this paper. The electronic structures and electrical transport properties are studied using ab initio calculations and the Boltzmann transport equation under the constant relaxation time approximation for charge carriers. The electronic structure results predict the band gaps of these HH compounds, and show that many HHs are narrow‐band‐gap semiconductors and, therefore, are potentially good thermoelectric materials. The dependence of Seebeck coefficient, electrical conductivity, and power factor on the Fermi level is investigated. Maximum power factors and the corresponding optimal p‐ or n‐type doping levels, related to the thermoelectric performance of materials, are calculated for all HH compounds investigated, which certainly provide guidance to experimental work. The estimated optimal doping levels and Seebeck coefficients show reasonable agreement with the measured results for some HH systems. A few HHs are recommended to be potentially good thermoelectric materials based on our calculations.
Evidence that SIZN1 is a candidate X‐linked mental retardation gene
Authors: Cho Ginam , Bhat Shambhu S. , Gao Jinsong , Collins Julianne S. , Rogers R. Curtis , Simensen Richard J. , Schwartz Charles E. , Golden Jeffrey A. , Srivastava Anand K. 
Published: September 2008

AbstractAn estimated 1–3% of individuals within the United States are diagnosed with mental retardation (MR), yet the cause is unknown in nearly 50% of the patients. While several environmental, genetic and combined teratogenetic etiologies have been identified, many causative genes remain to be identified. Furthermore, the pathogenetic mechanisms underlying MR are known for very few of these genes. Males have a much higher incidence of MR implicating genes on the X‐chromosome. We have recently identified a novel gene, SIZN1, on the X‐chromosome and showed that it functions in modulating the BMP signaling pathway. Furthermore, we have shown this gene is necessary for basal forebrain cholinergic neuron (BFCN) specific gene expression. Given that cognitive function is impaired when BFCNs are lost or functionally disrupted, we undertook a screen of cognitively impaired males for SIZN1 mutations. We report on four different sequence variants in SIZN1 in 11 individuals with nonsyndromic X‐linked mental retardation(XLMR). Our data implicate SIZN1 as a candidate gene for XLMR and/or as a neurocognitive functional modifier. © 2008 Wiley‐Liss, Inc.
High prevalence of orofacial clefts in Shanxi Province in northern China, 2003–2004
Authors: Li Zhiwen , Ren Aiguo , Liu Jianmeng , Zhang Le , Ye Rongwei , Li Song , Li Zhu 
Published: September 2008

AbstractShanxi Province in northern China has been identified as an area with the highest prevalence of neural tube defects in the world; however, few reports exist on the prevalence of orofacial clefts (OFC). We examined the prevalence of OFC and their association with selected characteristics. Data came from a population‐based birth defects surveillance system in four counties of Shanxi Province. The system captures information on all live births, stillbirths of at least 20 weeks gestation, and pregnancy terminations at any gestational age after prenatal diagnosis of a birth defect. Out of 25,355 births in 2003–2004, 83 cases with orofacial clefts were identified resulting in a birth prevalence of 3.27 per 1,000. Other major external birth defects were present in 12 (14.5%) OFC cases. Cleft lip with palate (CLP), cleft lip alone (CL) and cleft palate alone (CP) accounted for 62.0%, 29.6% and 8.4% of OFC cases without additional external defects, respectively. The male to female ratio was 1.04 (95%CI: 0.67–1.60) for all OFC, 1.46 (95%CI: 0.80–2.68) for CLP, 1.23 (95%CI: 0.52–2.91) for CL, 0.46 (95%CI: 0.08–2.51) for CP without additional major external defects, and 0.31(95%CI: 0.08–1.13) for OFC with additional external defects. The prevalence of OFC without additional external defects was increased with decreased maternal age (P < 0.05) and increased maternal education (P < 0.05). The birth prevalence of OFC in Shanxi Province of northern China is among the highest worldwide. Further studies are required to define the factors associated with excess risk of clefts. © 2008 Wiley‐Liss, Inc.
Genetic counseling in Robertsonian translocations der(13;14): Frequencies of reproductive outcomes and infertility in 101 pedigrees
Authors: Engels Hartmut , Eggermann Thomas , Caliebe Almut , Jelska Anna , Schubert Regine , Schüler Herdit M. , Panasiuk Barbara , Zaremba Jacek , Latos‐Bieleńska Anna , Jakubowski Lucjusz , Zerres Klaus P. , Schwanitz Gesa , Midro Alina T. 
Published: September 2008

AbstractRobertsonian translocations 13/14 are the most common chromosome rearrangements in humans. However, most studies aimed at determining risk figures are more than 20 years old. Their results are often contradictory regarding important topics in genetic counseling such as infertility and unfavorable pregnancy outcomes. Here, we present a study on a sample of 101 previously unreported pedigrees of der(13;14)(q10;q10). In order to minimize problems of partial ascertainment, we included families with a wide range of reasons of ascertainment such as birth of a child with congenital anomalies, prenatal diagnosis due to maternal age, fertility problems and recurrent pregnancy loss. No evidence of increased infertility rates of female and male carriers was found. The detected miscarriage frequency of female carriers was higher than previously reported (27.6 ± 4.0% of all spontaneous pregnancies). This may be explained by an over‐correction of earlier studies, which excluded all unkaryotyped miscarriages. In three out of 42 amniocenteses, translocation trisomies 13 were diagnosed (7.1 ± 4.0% of all amniocenteses). The frequency of stillbirths was 3.3 ± 1.6% for female carriers and 1.4 ± 1.4% for male carriers. A low risk for the live birth of translocation trisomy 13 children was confirmed since no live born children with trisomy 13 or Pätau syndrome were detected in the ascertainment‐corrected sample. © 2008 Wiley‐Liss, Inc.
Popcorn calcification in osteogenesis imperfecta: Incidence, progression, and molecular correlation
Authors: Obafemi Abimbola A. , Bulas Dorothy I. , Troendle James , Marini Joan C. 
Published: September 2008

AbstractOsteogenesis imperfecta (OI) is a heritable disorder characterized by osteoporosis and increased susceptibility to fracture. All children with severe OI have extreme short stature and some have “popcorn” calcifications, areas of disorganized hyperdense lines in the metaphysis and epiphysis around the growth plate on lower limb radiographs. Popcorn calcifications were noted on radiographs of two children with non‐lethal type VIII OI, a recessive form caused by P3H1 deficiency. To determine the incidence, progression, and molecular correlations of popcorn calcifications, we retrospectively examined serial lower limb radiographs of 45 children with type III or IV OI and known dominant mutations in type I collagen. Popcorn calcifications were present in 13 of 25 type III (52%), but only 2 of 20 type IV (10%), OI children. The mean age of onset was 7.0 years, with a range of 4–14 years. All children with popcorn calcifications had this finding in their distal femora, and most also had calcifications in proximal tibiae. While unilateral popcorn calcification contributes to femoral growth deficiency and leg length discrepancy, severe linear growth deficiency, and metaphyseal flare do not differ significantly between type III OI patients with and without popcorn calcifications. The type I collagen mutations associated with popcorn calcifications occur equally in both COL1A1 and COL1A2, and have no preferential location along the chains. These data demonstrate that popcorn calcifications are a frequent feature of severe OI, but do not distinguish cases with defects in collagen structure (primarily dominant type III OI) or modification (recessive type VIII OI). © 2008 Wiley‐Liss, Inc.
Sex reversal from functional disomy of Xp: Prenatal and post‐mortem findings
Authors: Piccione Maria , Maresi Emiliano , Zollino Marcella , Sanfilippo Cinzia , Seminara Laura , Neri Giovanni , Corsello Giovanni 
Published: September 2008

AbstractTranslocations involving the short arms of the X and Y chromosomes are uncommon and are often associated with anomalies in gonadal development. Segmental duplications of the X chromosome interfere with the formation of the testis in patients with a 46,XY karyotype. The gene products located within the duplicated segment, when present in double dose, may affect on male sex development. We report on a fetus with karyotype 46,XY,der (14)t(X;14) (p10;p10)dn. Attached to chromosome 14 is the entire short arm of the X chromosome. Therefore, the fetus is affected with a disomy of Xp, resulting in complete male to female sex reversal, as well as other structural defects. To the best of our knowledge, this is the first description of an XY fetus with a pure duplication of the entire short arm of X chromosome. © 2008 Wiley‐Liss, Inc.