bluuebunny/crossref_metadata_2025_split huggingface dataset:
fosB Gene Products Trigger Cell Proliferation and Morphological Alteration with an Increased Expression of a Novel Processed Form of Galectin-1 in the Rat 3Y1 Embroyo Cell Line
Authors: Nishioka Tomoko , Sakumi Kunihiko , Miura Tomofumi , Tahara Kazuki , Horie Hidenori , Kadoya Toshihiko , Nakabeppu Yusaku 
Published: January 2012

Abstract
In this study, we established rat 3Y1 embryo cell lines expressing FosB and AFosB as fusion proteins (ER-FosB, ER-AFosB) with the ligand-binding domain of human estrogen receptor (ER). The binding of estrogen to the fusion proteins resulted in their nuclear translocation. After estrogen administration, exponentially growing cells expressing ER-AFosB, and to a lesser extent ER-FosB, underwent morphological alteration from the flat fibroblastic shape to an extended bipolar shape, and ceased proliferating. Such morphological alteration was also induced in quiescent cells expressing ER-AFosB and ER-FosB after one round of cell division triggered by estrogen administration. The cells expressing ER-AFosB changed shape frequently, and the content of F-actin in the cytoplasm detected by binding of Alexa 488-phalloidin significantly decreased after the morphological alteration. By two-dimensional gel electrophoresis analysis of cellular proteins from the cells expressing ER-AFosB, we identified several proteins whose expression either increased or decreased after estrogen administration. Two of these proteins were identified from their amino acid sequences as novel processed form of galectin-1.
Hill-Robertson Interference is a Minor Determinant of Variations in Codon Bias Across Drosophila melanogaster and Caenorhabditis elegans Genomes
Authors: Marais Gabriel , Piganeau Gwenaël 
Published: January 2012

Abstract
According to population genetics models, genomic regions with lower crossing-over rates are expected to experience less effective selection because of Hill-Robertson interference (HRi). The effect of genetic linkage is thought to be particularly important for a selection of weak intensity such as selection affecting codon usage. Consistent with this model, codon bias correlates positively with recombination rate in Drosophila melanogaster and Caenorhabditis elegans. However, in these species, the G+C content of both noncoding DNA and synonymous sites correlates positively with recombination, which suggests that mutation patterns and recombination are associated. To remove this effect of mutation patterns on codon bias, we used the synonymous sites of lowly expressed genes that are expected to be effectively neutral sites. We measured the differences between codon biases of highly expressed genes and their lowly expressed neighbors. In D. melanogaster we find that HRi weakly reduces selection on codon usage of genes located in regions of very low recombination; but these genes only comprise 4% of the total. In C. elegans we do not find any evidence for the effect of recombination on selection for codon bias. Computer simulations indicate that HRi poorly enhances codon bias if the local recombination rate is greater than the mutation rate. This prediction of the model is consistent with our data and with the current estimate of the mutation rate in D. melanogaster. The case of C. elegans, which is highly self-fertilizing, is discussed. Our results suggest that HRi is a minor determinant of variations in codon bias across the genome.
Common Origin and Evolution of Glycosyltransferases Using Dol-P-monosaccharides as Donor Substrate
Authors: Oriol Rafael , Martinez-Duncker Ivan , Chantret Isabelle , Mollicone Rosella , Codogno Patrice 
Published: January 2012

Abstract
On the basis of the analysis of 64 glycosyltransferases from 14 species we propose that several successive duplications of a common ancestral gene, followed by divergent evolution, have generated the mannosyltransferases and the glucosyltransferases involved in asparagine-linked glycosylation (ALG) and phosphatidyl-inositol glycan anchor (PIG or GPI), which use lipid-related donor and acceptor substrates. Long and short conserved peptide motifs were found in all enzymes. Conserved and identical amino acid positions were found for the α2/6- and the α3/4-mannosyltransferases and for the α2/3-glucosyltransferases, suggesting unique ancestors for these three superfamilies. The three members of the α2-mannosyltransferase family (ALG9, PIG-B, and SMP3) and the two members of the α3-glucosyltransferase family (ALG6 and ALG8) shared 11 and 30 identical amino acid positions, respectively, suggesting that these enzymes have also originated by duplication and divergent evolution. This model predicts a common genetic origin for ALG and PIG enzymes using dolichyl-phospho-monosaccharide (Dol-P-monosaccharide) donors, which might be related to similar spatial orientation of the hydroxyl acceptors. On the basis of the multiple sequence analysis and the prediction of transmembrane topology we propose that the endoplasmic reticulum glycosyltransferases using Dol-P-monosaccharides as donor substrate have a multispan transmembrane topology with a first large luminal conserved loop containing the long motif and a small cytosolic conserved loop containing the short motif, different from the classical type II glycosyltransferases, which are anchored in the Golgi by a single transmembrane domain.
Sequence Variation and Haplotype Structure at the Putative Flowering-Time Locus COL1 of Brassica nigra
Authors: Lagercrantz Ulf , Kruskopf Osterberg Marita , Lascoux Martin 
Published: January 2012

Abstract
Motivated by a previous study indicating that polymorphism at an indel, Ind2, within the Brassica nigraCOL1 gene is significantly associated with flowering time, we searched for evidence of selection in a sample of 41 complete sequences of B. nigraCOL1. The within–gene population recombination rate is moderate, and all neutrality tests used in the present study failed to detect departure from the standard neutral model or evidence of selection. The haplotype structure of the 5′-half of the gene is primarily associated with the demographic history of the species and more specifically with the split between European and Ethiopian populations, whereas the structure of the 3′-half reflects the polymorphism at Ind2. This could be the result of selection or a combination of recombination and migration during the history of the sample of sequences. Without additional information on polymorphism in flanking areas, these two alternatives are difficult to tell apart. If selection acted on the gene, we suggest that if the indel itself is not the target of selection, among the polymorphic sites cosegregating with the polymorphism at Ind2, replacement polymorphisms around sites 890 and 1260 are the most likely quantitative trait nucleotides within the gene.
Testing for Differences in Rates-Across-Sites Distributions in Phylogenetic Subtrees
Authors: Susko Edward , Inagaki Yuji , Field Chris , Holder Michael E. , Roger Andrew J. 
Published: January 2012

Abstract
It has long been recognized that the rates of molecular evolution vary amongst sites in proteins. The usual model for rate heterogeneity assumes independent rate variation according to a rate distribution. In such models the rate at a site, although random, is assumed fixed throughout the evolutionary tree. Recent work by several groups has suggested that rates at sites often vary across subtrees of the larger tree as well as across sites. This phenomenon is not captured by most phylogenetic models but instead is more similar to the covarion model of Fitch and coworkers. In this article we present methods that can be useful in detecting whether different rates occur in two different subtrees of the larger tree and where these differences occur. Parametric bootstrapping and orthogonal regression methodologies are used to test for rate differences and to make statements about the general differences in the rates at sites. Confidence intervals based on the conditional distributions of rates at sites are then used to detect where the rate differences occur. Such methods will be helpful in studying the phylogenetic, structural, and functional bases of changes in evolutionary rates at sites, a phenomenon that has important consequences for deep phylogenetic inference.
GAI Homologues in the Hawaiian Silversword Alliance (Asteraceae-Madiinae): Molecular Evolution of Growth Regulators in a Rapidly Diversifying Plant Lineage
Authors: Remington David L. , Purugganan Michael D. 
Published: January 2012

Abstract
Accelerated evolution of regulatory genes has been proposed as an explanation for decoupled rates of morphological and molecular evolution. The Hawaiian silversword alliance (Asteraceae-Madiinae) has evolved drastic differences in growth form, including rosette plants, cushion plants, shrubs, and trees, since its origin ∼6 MYA. We have isolated genes in the DELLA subfamily of putative growth regulators from 13 taxa of Hawaiian and North American Madiinae. The Hawaiian taxa contain two copies of DaGAI that form separate clades within the Madiinae, consistent with an allotetraploid origin for the silversword alliance. DaGAI retains conserved features that have previously been identified in DELLA genes. Selective constraint in the Hawaiian DaGAI copies remains strong in spite of rapid growth form divergence in the silversword alliance, although the constraint was somewhat relaxed in the Hawaiian copies relative to the North American lineages. We failed to detect evidence for positive selection on individual codons. Notably, selective constraint remained especially strong in the gibberellin-responsive DELLA region for which the gene subfamily is named, which is truncated or deleted in all identified dwarf mutants in GAI homologues in different angiosperm species. In contrast with the coding region, however, ∼900 bp of the upstream flanking region shows variable rates and patterns of evolution, which might reflect positive selection on regulatory regions.
The Extent of Nucleotide Polymorphism is Highly Variable Across a 3-kb Region on Plasmodium falciparum Chromosome 2
Authors: Jongwutiwes Somchai , Putaporntip Chaturong , Friedman Robert , Hughes Austin L. 
Published: January 2012

Abstract
Genomic nucleotide polymorphism in the virulent human malarial parasite Plasmodium falciparum was surveyed by sequencing a 3-kb region of chromosome 2 from 21 isolates, including the MSP4 and MSP5 genes. Extensive sequence polymorphism was observed in the coding regions of these genes and in the region downstream to MSP5, and the average pairwise divergence time of haplotypes in this region was estimated to be at least about 200,000 years. But nucleotide polymorphism was not found in the introns and was much reduced in the intergenic region. Over the entire region, nucleotide diversity was negatively correlated with a nucleotide content skewed toward thymine. Together with the previous evidence of limited nucleotide polymorphism in introns of P. falciparum, these data suggest the existence of a mechanism suppressing single-nucleotide polymorphism in regions of the P. falciparum genome with highly skewed nucleotide content.
Bayesian Phylogenetics Using an RNA Substitution Model Applied to Early Mammalian Evolution
Authors: Jow H. , Hudelot C. , Rattray M. , Higgs P. G. 
Published: January 2012

Abstract
We study the phylogeny of the placental mammals using molecular data from all mitochondrial tRNAs and rRNAs of 54 species. We use probabilistic substitution models specific to evolution in base paired regions of RNA. A number of these models have been implemented in a new phylogenetic inference software package for carrying out maximum likelihood and Bayesian phylogenetic inferences. We describe our Bayesian phylogenetic method which uses a Markov chain Monte Carlo algorithm to provide samples from the posterior distribution of tree topologies. Our results show support for four primary mammalian clades, in agreement with recent studies of much larger data sets mainly comprising nuclear DNA. We discuss some issues arising when using Bayesian techniques on RNA sequence data.
Surgery and Brain Atrophy in Cognitively Normal Elderly Subjects and Subjects Diagnosed with Mild Cognitive Impairment
Authors: Kline Richard P. , Pirraglia Elizabeth , Cheng Hao , De Santi Susan , Li Yi , Haile Michael , de Leon Mony J. , Bekker Alex 
Published: January 2012

Background
Structural magnetic resonance imaging is used to longitudinally monitor the progression of Alzheimer disease from its presymptomatic to symptomatic phases. Using magnetic resonance imaging data from the Alzheimer's Disease Neuroimaging Initiative, we tested the hypothesis that surgery would impact brain parameters associated with progression of dementia.

Methods
Brain images from the neuroimaging initiative database were used to study normal volunteer subjects and patients with mild cognitive impairment for the age group 55 to 90 inclusive. We compared changes in regional brain anatomy for three visits that defined two intervisit intervals for a surgical cohort (n = 41) and a propensity matched nonsurgical control cohort (n = 123). The first interval for the surgical cohort contained the surgical date. Regional brain volumes were determined with Freesurfer and quantitatively described with J-image software (University of California at San Francisco, San Francisco, California). Statistical analysis used Repeated Measures ANCOVA (SPSS, v.18.0; Chicago, IL).

Results
We found that surgical patients, during the first follow-up interval (5-9 months), but not subsequently, had increased rates of atrophy for cortical gray matter and hippocampus, and lateral ventricle enlargement, as compared with nonsurgical controls. A composite score of five cognitive tests during this interval showed reduced performance for surgical patients with mild cognitive impairment.

Conclusions
Elderly subjects after surgery experienced an increased rate of brain atrophy during the initial evaluation interval, a time associated with enhanced risk for postoperative cognitive dysfunction. Although there was no difference in atrophy rate by diagnosis, subjects with mild cognitive impairment suffered greater subsequent cognitive effects.
Pluripotency of a polyploid H1 (ES) cell system without leukaemia inhibitory factor
Authors: Fujikawa‐Yamamoto K. , Ota T. , Miyagoshi M. , Yamagishi H. 
Published: January 2012

Abstract
Objectives:  Tetraploid cells are strictly biologically inhibited from composition of embryos; by the same token, only diploid cells compose embryos. However, the distinction between diploid and tetraploid cells in development has not been well explained. To examine pluripotency of polyploid ES cells, a polyploid embryonic stem (ES)‐cell system was prepared.
Materials and methods:  Diploid, tetraploid, pentaploid, hexaploid, octaploid and decaploid H1 (ES) cells (2H1, 4H1, 5H1, 6H1, 8H1 and 10H1 cells, respectively) were cultured for about 460 days in L15F10 medium without leukaemia inhibitory factor (LIF). The cells cultured under LIF‐free conditions were denoted as 2H1(−), 4H1(−), 5H1(−), 6H1(−), 8H1(−) and 10H1(−) cells, respectively. Pluripotency and gene expression were examined.
Results:  Ploidy alteration of H1(−) cells was similar to that of H1 cells. The polyploid H1(−) cells showed positive activity of alkaline phosphatase, suggesting that they maintained pluripotency in vitro without LIF. The polyploid H1(−) cells formed teratocarcinomas in mouse abdomen, suggesting they could differentiate in mouse abdomen in vivo. 2H1, 4H1 and polyploid H1(−) cells expressed nanog, oct3/4 and sox2 genes, suggesting that they fulfilled the criteria of ES cells. Nanog gene was significantly over‐expressed in 4H1 and polyploid H1(−) cells, suggesting that overexpression of nanog gene was a characteristic of polyploid H1 cells.
Conclusion:  Polyploid H1 (ES) cells retained pluripotency in vitro, without LIF with nanog over‐expression.
Photoconversion of DAPI following UV or violet excitation can cause DAPI to fluoresce with blue or cyan excitation
Authors: PITERBURG M. , PANET H. , WEISS A. 
Published: January 2012

Summary4’‐6‐Diamidino‐2‐phenylindole is a fluorescent dye commonly used to visualize deoxyribonucleic acid or cell nuclei in fixed cell preparations, and is often used together with fluorescein or green fluorescent protein, which can be excited without exciting 4’‐6‐Diamidino‐2‐phenylindole. It is assumed that when using typical fluorescein or green fluorescent protein filter cubes, 4’‐6‐Diamidino‐2‐phenylindole will not be observed. In this paper, we show that following observation of 4’‐6‐Diamidino‐2‐phenylindole using UV or violet excitation, it may become sensitive to the blue/cyan excitation used in fluorescein/green fluorescent protein filter cubes. This has serious implications for the use of 4’‐6‐Diamidino‐2‐phenylindole together with widely used green fluorophores in double labelling experiments.
Putative members of the Arabidopsis Nup107‐160 nuclear pore sub‐complex contribute to pathogen defense
Authors: Wiermer Marcel , Cheng Yu Ti , Imkampe Julia , Li Meilan , Wang Dongmei , Lipka Volker , Li Xin 
Published: January 2012

SummaryIn eukaryotic cells, transduction of external stimuli into the nucleus to induce transcription and export of mRNAs for translation in the cytoplasm is mediated by nuclear pore complexes (NPCs) composed of nucleoporin proteins (Nups). We previously reported that ArabidopsisMOS3, encoding the homolog of vertebrate Nup96, is required for plant immunity and constitutive resistance mediated by the de‐regulated Toll interleukin 1 receptor/nucleotide‐binding/leucine‐rich repeat (TNL)‐typeRgenesnc1. In vertebrates, Nup96 is a component of the conserved Nup107‐160 nuclear pore sub‐complex, and implicated in immunity‐related mRNA export. Here, we used a reverse genetics approach to examine the requirement for additional subunits of the predicted Arabidopsis Nup107‐160 complex in plant immunity. We show that, among eight putative complex members, beside MOS3, only plants with defects inNup160orSeh1are impaired in basal resistance. Constitutive resistance in thesnc1mutant and immunity mediated by TNL‐typeR genes also depend on functionalNup160and have a partial requirement forSeh1. Conversely, resistance conferred by coiled coil‐type immune receptors operates largely independently of both genes, demonstrating specific contributions to plant defense signaling. Our functional analysis further revealed that defects innup160andseh1result in nuclear accumulation of poly(A) mRNA, and, in the case ofnup160, considerable depletion of EDS1, a key positive regulator of basal and TNL‐triggered resistance. These findings suggest thatNup160is required for nuclear mRNA export and full expression of EDS1‐conditioned resistance pathways in Arabidopsis.
Relationship Between Condition, Aggression, Signaling, Courtship, and Egg Laying in the Field Cricket, Gryllus assimilis
Authors: Bertram Susan M. , Rook Vanessa 
Published: January 2012

AbstractSexual selection theory suggests males in good condition should be more successful than males in poor condition when competing with rivals for territories and mates. Understanding how condition influences the interplay between aggression, mate attraction, and courtship displays could help explain why variation is maintained in traits that confer fitness. Using laboratory‐reared Jamaican field crickets, Gryllus assimilis, we found that fine‐scale temporal components of mate attraction signals were positively correlated with body condition (residual body mass) and body size; signaling effort was positively correlated with both body condition and fine‐scale temporal signaling components; aggression was positively correlated with signaling effort; number of eggs laid was positively correlated with female body size, male body condition and aggression. Together our correlative study suggests that variation in body condition and size may drive some of the variation in cricket mate attraction signaling and aggression. Given condition and body size are influenced by foraging ability, nutrient availability and the organism’s ability to uptake and retain these essential nutrients could explain some of the persistent variation in fitness conferring traits.
A Simple Panel‐CADF Test for Unit Roots*
Authors: Costantini Mauro , Lupi Claudio 
Published: January 2012

AbstractIn this paper, we propose a simple extension to the panel case of the covariate‐augmented Dickey–Fuller (CADF) test for unit roots developed in Hansen (1995). The panel test we propose is based on a P values combination approach that takes into account cross‐section dependence. We show that the test has good size properties and gives power gains with respect to other popular panel approaches. An empirical application is carried out for illustration purposes on international data to test the purchasing power parity (PPP) hypothesis.
Meningoencephaloradiculomyelitis after tick‐borne encephalitis virus infection: a case series
Authors: Ponfick M. , Hacker S. , Gdynia H‐J. , Linden R. , Gränz M. , Nowak D. A. 
Published: January 2012

Background:  Tick‐borne encephalitis (TBE) is caused by a RNA‐virus and is in about 50% of cases characterized by a biphasic clinical course in adults. Different clinical syndromes have been described, including meningitis, meningoencephalitis, meningoencephalomyelitis and meningoencephaloradiculomyelitis. The latter seems to be the most disabling and severe form of TBE virus infection.Methods:  Here we report five cases with meningoencephaloradiculomyelitis. Only in three patients a tick prick was remembered.Results:  Only two patients could be weaned successfully from assisted ventilation; only one patient was able to return to self‐dependent life without nursing support. The youngest patient in this case series showed the most favourable outcome.Conclusions:  Polyradiculopathy and/or myelopathy as verified by electrophysiological examination within 4 weeks from symptom onset were indicative of a more severe disease course and a greater likelihood of moderate to serious sequelae even after long‐term rehabilitation. Older age at symptom onset seems to be associated with a less favourable outcome. Because of frequent long‐term hospitalization with immobilization and invasive ventilation, secondary complications, such as ventilation associated pulmonary infections and decubiti, must be avoided.
Common nucleotide sequence of structural gene encoding fibroblast growth factor 4 in eight cattle derived from three breeds
Authors: SATO Sho , TAKAHASHI Toshikiyo , NISHINOMIYA Hiroshi , KATOH Makiko , ITOH Ryu , YOKOO Masaki , YOKOO Mari , IHA Momoe , MORI Yuki , KASUGA Kano , KOJIMA Ikuo , KOBAYASHI Masayuki 
Published: January 2012

ABSTRACTFibroblast growth factor 4 (FGF4) is considered as a crucial gene for the proper development of bovine embryos. However, the complete nucleotide sequences of the structural genes encoding FGF4 in identified breeds are still unknown. In the present study, direct sequencing of PCR products derived from genomic DNA samples obtained from three Japanese Black, two Japanese Shorthorn and three Holstein cattle, revealed that the nucleotide sequences of the structural gene encoding FGF4 matched completely among these eight cattle. On the other hand, differences in the nucleotide sequences, leading to substitutions, insertions or deletions of amino acid residues were detected when compared with the already reported sequence from unidentified breeds. We cannot rule out a possibility that the structural gene elucidated in the present study is widely distributed in cattle. To the best of our knowledge, this is the first determination of the complete nucleotide sequence of the structural gene encoding bovine FGF4 in identified breeds.