bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel early response genes in osteoblasts exposed to dynamic fluid flow
Authors: Shivaram Giridhar M. , Kim Chi Hyun , Batra Nikhil N. , Yang Wuchen , Harris Stephen E. , Jacobs Christopher R. 
Published: January 2010

Cyclic mechanical loads applied to the skeleton from habitual physical activity result in increased bone formation. These loads lead to dynamic pressure gradients and oscillatory flow of bone interstitial fluid, which, in turn, exposes cells resident in the bony matrix to oscillatory fluid shear stress. Dynamic fluid flow has previously been shown to be a potent anabolic stimulus for cultured osteoblasts. In this study, we used cDNA microarrays to examine early phase, broad-spectrum gene expression in MC3T3-E1 osteoblasts in response to physical stimulation. RNA was harvested at 30 min and 1 h post-stimulation. RNA was used for microarray hybridization as well as subsequent reverse transcription polymerase chain reaction (RT-PCR) validation of expression levels for selected genes. Microarray results were analysed by both functional and expression profile clustering. We identified a small number of genes at both the 30 min and 1 h timepoints that were either upregulated or downregulated with flow compared to no-flow control by twofold or more. From the group of genes upregulated at 30 min, we selected nine for RT-PCR confirmation. All were found to be upregulated by at least twofold. We identify a novel set of early response genes potentially involved in mediating the anabolic response of MC3T3 osteoblasts to flow, and provide functional groupings of these genes that may shed light on the relevant mechanosensory pathways involved.
The Rabbit(Oryctolagus cuniculus):A Model for Mammalian Reproduction and Early Embryology
Authors: Püschel Bernd , Daniel Nathalie , Bitzer Eva , Blum Martin , Renard Jean-Paul , Viebahn Christoph 
Published: January 2010

INTRODUCTIONThe rabbit is a valuable animal model for a variety of biomedical research areas including in vitro fertilization, early embryology and organogenesis, neurophysiology, ophthalmology, and cardiovascular research. The rabbit is also used as a model for toxicology studies and analyses of drug effects on embryo and fetal development, as well as for research involving the immune system (e.g., host/pathogen interactions, asthma, arthritis, systemic lupus erythematosus). The rabbit’s most prominent use as a laboratory animal is antibody production; most biomedical research institutions thus provide the infrastructure and veterinary expertise for keeping rabbits. This article discusses current advances in applying modern life science research methods to basic and applied embryological research using the rabbit as a model for early intrauterine development in mammals, including state-of-the-art genomic tools and the sequencing data available (and planned) for the rabbit.
Phenotypic Analysis of Arabidopsis Mutants: Electrolyte Leakage after Freezing Stress
Authors: Lee Byeong-ha , Zhu Jian-Kang 
Published: January 2010

INTRODUCTIONAbiotic stress such as high salt or low temperature adversely affects plant growth and development. Salt stress inhibits seed germination, retards plant growth, and accelerates senescence. Freezing or drought stress can cause cell damage and plant death. The following parameters can be used to evaluate plant tolerance to salt, drought, or freezing stress: root elongation, fresh weight gain, seed germination, electrolyte leakage (described here), or water-loss measurement. Several stress mutants have been characterized using these tests, including hos1 and hos2, which show higher expression of some stress-regulated genes when exposed to low-temperature stress; hos5, which shows higher expression of some stress-regulated genes under abscisic acid (ABA) and salt treatments; sfr mutants, which are deficient in freezing tolerance; and eskimo1, which is constitutively freezing tolerant. This protocol describes an electrolyte leakage assay that can be used to measure the degree of cell damage after freezing stress in Arabidopsis. The levels of stress suggested in this protocol may need to be adjusted, depending on the ecotype and growth conditions used.
Dissection and Fixation of Rabbit Embryos
Authors: Püschel Bernd , Viebahn Christoph 
Published: January 2010

INTRODUCTIONThis protocol describes general methods for dissection and fixation of rabbit embryos. Depending on the investigation, embryos can be dissected either alive or after fixation. Some embryonic stages are surrounded by an envelope, the zona pellucida, which might have to be removed for some applications (e.g., immunohistochemistry). Fixation methods vary according to different experimental needs, such as structure preservation (morphology), antigen preservation (immunoreactivity), or mRNA accessibility (in situ hybridization).
Whole-Mount In Situ Hybridization of Early Rabbit Embryos
Authors: Püschel Bernd , Blum Martin , Viebahn Christoph 
Published: January 2010

INTRODUCTIONThis protocol describes whole-mount in situ hybridization of early rabbit embryos. The method allows specific mRNA expression to be localized with respect to position and intensity in predefined embryonic areas. Optimal resolution of mRNA distribution can be achieved by subsequently embedding in situ hybridized embryos for histological sectioning.
Artificial Fertilization in Rabbits by Intracytoplasmic Sperm Injection (ICSI): Figure 1.
Authors: Daniel Nathalie , Renard Jean-Paul 
Published: January 2010

INTRODUCTIONIntracytoplasmic sperm injection (ICSI) consists of the injection, under microscopic observation, of a single spermatozoon directly into the cytoplasm of an oocyte using an injection capillary. This technique is used commonly in human medicine in cases of infertility. The advantage of ICSI is that the technique requires only one spermatozoon per oocyte for fertilization. Spermatozoa used for ICSI do not require high motility; ICSI works as long as the sperm nucleus is genetically intact. This protocol describes methods for performing ICSI in rabbits using either fresh or frozen/thawed sperm.
Cryopreservation of Rabbit Embryos
Authors: Daniel Nathalie , Renard Jean-Paul 
Published: January 2010

INTRODUCTIONIn the rabbit, the technique most frequently used for embryo transfer involves cryopreservation by slow freezing of morulae, followed by surgical implantation of thawed embryos. This method has the advantage of being well controlled and validated: It helps to maintain mitochondrial genomes, preserves the genetic integrity of biological material under sanitary conditions, and allows for such material to be passed along beyond the normal reproductive lifespan of a given animal, which can be advantageous in the case of rare or valuable strains. Furthermore, because litters of pups can be obtained 1 mo after embryo transfer without the need for additional backcrossings, genotyping is rapid and simple. However, the technique is not without its drawbacks: It requires expensive equipment (e.g., specialized programmable freezers), and producing large numbers of stored embryos requires the sacrifice of many donor females. Although alternative methods of embryo recovery (e.g., surgical or vaginal collection) are possible, such procedures produce fewer embryos.
Maintaining Clonal Paramecium tetraurelia Cell Lines of Controlled Age through Daily Reisolation
Authors: Beisson Janine , Bétermier Mireille , Bré Marie-Hélène , Cohen Jean , Duharcourt Sandra , Duret Laurent , Kung Ching , Malinsky Sophie , Meyer Eric , Preer John R. , Sperling Linda 
Published: January 2010

INTRODUCTIONThe sexual cycle of Paramecium tetraurelia can be managed by controlling food uptake, allowing the study of developmentally regulated differentiation in synchronous cultures. Clonal cell lines can be established easily by single cell isolation and can be grown in bacterized grass infusion medium for a large number of vegetative divisions before entering senescence. Sexual reproduction is triggered by starvation and therefore can be induced or prevented as needed by controlling the availability of food. Given a constant supply of food, P. tetraurelia cells will remain in the vegetative phase of their life cycle and, at 27°C, will divide by binary fission every 6 h. The daily reisolation procedure described here results in populations of P. tetraurelia of known age and produced under reproducible physiological conditions, which can help to standardize experiments. Paramecia produced under these conditions are suitable for immunocytochemical studies or use in genetic cross experiments.
Fluorescence In Situ Hybridization for the Identification of Environmental Microbes
Authors: Wendeberg Annelie 
Published: January 2010

INTRODUCTIONThis protocol presents methods for the phylogenetic identification of microorganisms in environmental samples (e.g., water and sediments) by means of fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes, followed by signal amplification with catalyzed reporter deposition (CARD). In this procedure, FISH probes are conjugated with the enzyme horseradish peroxidase (HRP). After hybridization, the subsequent deposition of fluorescently labeled tyramides results in substantially higher signal intensities on target cells than after FISH with probes labeled directly with fluorochromes. This protocol describes the custom labeling of tyramides with different fluorochromes, as well as sample preparation and cell permeabilization strategies for various microbial cell wall types. A protocol for sequential multicolor CARD-FISH for the simultaneous detection of different phylogenetic groups is also presented.
Meta‐analysis: targeting the intestinal microbiota in prophylaxis for post‐operative Crohn’s disease
Authors: DOHERTY G. A. , BENNETT G. C. , CHEIFETZ A. S. , MOSS A. C. 
Published: January 2010

Aliment Pharmacol Ther 31, 802–809SummaryBackground  Enteric bacteria play an important early role in the pathogenesis of Crohn’s disease.Aim  To perform a meta‐analysis of trials testing antibiotics or probiotics for prevention of post‐operative recurrence of Crohn’s disease.Methods  Review of all randomized controlled trials comparing antibiotics or probiotics with placebo in prevention of endoscopic or clinical recurrence of Crohn’s disease after surgical resection. Fixed‐effect meta‐analysis was performed with dichotomous data summarized using relative risk with 95% confidence intervals, where appropriate.Results  Seven studies were identified as suitable for inclusion (two comparing antibiotics with placebo, five comparing probiotics with placebo). The use of nitroimidazole antibiotics (metronidazole, ornidazole) reduced the risk of clinical (RR 0.23; 95% CI 0.09–0.57, NNT = 4) and endoscopic (RR 0.44; 95% CI 0.26–0.74, NNT = 4) recurrence relative to placebo. However, these agents were associated with higher risk of adverse events (RR 2.39, 95% CI 1.5–3.7) and patient withdrawal. Probiotic administration was not associated with any significant difference in risk of recurrence compared with placebo.Conclusions  Nitroimidazole antibiotics are effective in the prevention of post‐operative Crohn’s disease recurrence, but their side‐effects limit acceptability. Probiotics have failed to show efficacy for post‐operative prophylaxis, but may merit further study.
The pattern of linkage disequilibrium in German Holstein cattle
Authors: Qanbari S. , Pimentel E. C. G. , Tetens J. , Thaller G. , Lichtner P. , Sharifi A. R. , Simianer H. 
Published: January 2010

SummaryThis study presents a second generation of linkage disequilibrium (LD) map statistics for the whole genome of the Holstein–Friesian population, which has a four times higher resolution compared with that of the maps available so far. We used DNA samples of 810 German Holstein–Friesian cattle genotyped by the Illumina Bovine SNP50K BeadChip to analyse LD structure. A panel of 40 854 (75.6%) markers was included in the final analysis. The pairwise r2 statistic of SNPs up to 5 Mb apart across the genome was estimated. A mean value of r2 = 0.30 ± 0.32 was observed in pairwise distances of <25 kb and it dropped to 0.20 ± 0.24 at 50–75 kb, which is nearly the average inter‐marker space in this study. The proportion of SNPs in useful LD (r2 ≥ 0.25) was 26% for the distance of 50 and 75 kb between SNPs. We found a lower level of LD for SNP pairs at the distance ≤100 kb than previously thought. Analysis revealed 712 haplo‐blocks spanning 4.7% of the genome and containing 8.0% of all SNPs. Mean and median block length were estimated as 164 ± 117 kb and 144 kb respectively. Allele frequencies of the SNPs have a considerable and systematic impact on the estimate of r2. It is shown that minimizing the allele frequency difference between SNPs reduces the influence of frequency on r2 estimates. Analysis of past effective population size based on the direct estimates of recombination rates from SNP data showed a decline in effective population size to Ne = 103 up to ∼4 generations ago. Systematic effects of marker density and effective population size on observed LD and haplotype structure are discussed.
Intranidal mating, gyne polymorphism, polygyny, and supercoloniality as factors for sympatric and parapatric speciation in ants
Authors: SEIFERT BERNHARD 
Published: January 2010

1. The syndrome of intranidal mating, morpho‐ethological gyne polymorphism, and polygyny is found in less than 5% of European ant species, but is considered as an important precondition for sympatric and parapatric speciation.2. This idea is discussed in three cases that represent example of evolution below the species level: (1) the polygynous—polydomous form of Lasius turcicus as a model of how speciation of the supercolonial Lasius neglectus could have taken place; (2) the microgyne form of Myrmica rubra as a model for sympatric speciation of socially parasitic species; and (3) hybridisation and rapid genotype selection in supercolonial wood ants of the Formica rufa group as a model for hybrid speciation.3. The first step of the evolutionary scenario is transition to polygyny followed by development of morpho‐ethological gyne polymorphism: smaller gynes with weaker wing muscles and body reserves shift to intranidal mating and reduce dispersal flight, while larger gynes with bigger wing muscles and body reserves retain nuptial and dispersal flight. This scenario leads to mating place separation and facilitates further genotype divergence.4. There is much less gene flow between conspecific supercolonies of Formica rufa group ants with dominance of intranidal or intracolonial mating than between conspecific monogynous colonies performing a nuptial flight. If two supercolonial species occasionally hybridise and if landscape structure provides some isolation of the resulting hybrid supercolony, very strong selection for genotypes takes place within this cohesive system of thousands of reproductive females eventually leading to novel genotypes and new species.
Shift happens! Shifting balance and the evolution of diversity in warning colour and mimicry
Authors: MALLET JAMES 
Published: January 2010

1. At first sight, it seems most unlikely thatHeliconiuswarning colour races have evolved by means of stochastic peak shift or shifting balance.2. Phase I, random local processes (including genetic drift and idiosyncratic selection), and phase III, interdemic selection are the most controversial phases of the shifting balance. Phase II consists of ordinary natural selection to a new adaptive peak within populations, and is uncontroversial.3.Heliconiushave bold patterns of iridescent blue, black, yellow, white, and red. These are clearly warning patterns, and near‐perfect Müllerian mimicry has evolved among species, suggesting tight control by natural selection. Field experiments have also demonstrated strong selection (oftens >0.1 on single colour pattern loci), and the population structure ofHeliconiusis typically not conducive to phase I. Yet the colour patterns are clearly somewhat independent and incompatible signals of unpalatability.4. There is empirical evidence inHeliconiusfor both controversial phases. For phase I, occasional and local polymorphisms of colour pattern in a number of species go against the generally expected (and generally observed) monomorphism for Müllerian mimics.5. For phase III, one of the few colour pattern clines mapped in detail has been observed to move rapidly over a period of 20 years. There are also a number of curious ‘leapfrog’ geographical disjunctions in colour pattern races. Disjunctions are expected if successful races have spread from the centre of the range (e.g. the Amazonian rayed races) via phase III, in competition with earlier races that are now distributed in scattered places along the periphery of the range.6. Evidence from the genomes ofHeliconiusmay in the near future aid in understanding colour pattern ‘supergenes’ and to help test for origin and spread via shifting balance.
The roles and interactions of reproductive isolation mechanisms in fall armyworm (Lepidoptera: Noctuidae) host strains
Authors: GROOT ASTRID T. , MARR MELANIE , HECKEL DAVID G. , SCHÖFL GERHARD 
Published: January 2010

1. The moth Spodoptera frugiperda presents an interesting opportunity to study the evolution of reproductive isolation, because it consists of two host races that may be in the process of speciation.2. The two races exhibit habitat isolation through host‐plant preference, and two types of behavioural isolation, i.e. differences in sex pheromone composition and timing of mating activity at night.3. In this paper, we review the selection pressures acting upon these three barriers as well as their genetic bases, to address the question of how divergence of the two strains may have evolved.4. We also address possible interactions between the three barriers, whether and how they may have evolved in concert, and we view the evolution of these three prezygotic isolation barriers in the light of postzygotic isolation.
Rapid genetic changes in natural insect populations
Authors: LOXDALE HUGH D. 
Published: January 2010

1. The insects represent around 75% of the world's fauna and as such provide especially good examples of the evolutionary process in action, aided by their often rapid generation time and high rate of reproduction.2. Here, I review some of the main mechanisms of mutational, ecological, and evolutionary change in insects. All those described, whether allo‐ para‐ or sympatric, involve changes in the genome or in behaviour that may ultimately isolate newly changed individuals from the parental population/s. They include: loss of sexuality by various means, including (potentially) mutation of the gene/s controlling sexuality; karyotypic changes, both in terms of the number of chromosomes, translocation, polyploidy, and hybridisation; host shifts as pre‐ and post‐zygotic isolating mechanisms, and in asexuals such as aphids, ‘divergence hitchhiking’ around key quantitative trait loci (QTL), and in moths, selection acting at a few linkage groups; enzyme‐based adaptive changes; sex and contact pheromone‐based isolating mechanisms; phenotypic plastic changes; and epigenetic changes. These last such changes are brought about by stress inducers, and may be transgenerational in their effects.3. Of the above mechanisms, probably chromosomal changes and host shifts represent the commonest mechanisms.
Reinforcement in hybrids among once isolated semispecies ofDanaus chrysippus(L.) and evidence for sex chromosome evolution
Authors: SMITH DAVID A. S. , GORDON IAN J. , ALLEN JOHN A. 
Published: January 2010

1. The aim of this paper is to investigate mechanisms of reinforcement between two semi‐isolated semispecies of the African savannah butterflyDanaus chrysippus. The biogeography of colour genes suggests that four semispecies evolved in once isolated refugia. They expanded their ranges in response to Holocene climatic changes to form a hybrid zone in central‐east Africa.2.Danaus chrysippusis a superspecies within which cycles of alternating cladogenesis and reticulation among semispecies have probably operated over some 4 Myr. Semispecies are inter‐fertile but show Haldane rule effects in crosses; gene flow is massive but subject to isolation by distance.3. One semispecies shows linkage disequilibrium, vis‐ à‐vis others, for haplotype, karyotype (W‐linkage of colour genes which function as reproductive isolating barriers) and all‐female broods caused by a male‐killer endosymbiont. Introgression of colour genes betweenD. c. dorippusandD. c. chrysippusis constrained by sex linkage and male killing.4. Reinforcement in hybrid zones comprises allochronic migration, assortative mating, (assumed) sex chromosome incompatibility and sex‐ratio distortion. Gene introgression fromD. c. dorippusto other semispecies is maintained by a high frequency of backcrossing between hybrid males and females of the latter.
Micro‐evolutionary change in relation to insecticide resistance in the peach–potato aphid,Myzus persicae
Authors: FENTON BRIAN , MARGARITOPOULOS JOHN T. , MALLOCH GAYNOR L. , FOSTER STEPHEN P. 
Published: January 2010

1. Phenotypic diversity is the fuel that powers evolution.2. Asexual organisms rely on mutation whereas sexual organisms combine mutation with recombination.3. Few organisms provide examples of species that are both sexual and asexual, but aphids do.4. To examine evolution on perceptible timescales requires strong evolutionary forces and, as Darwin noted, agricultural practices provide strong selection. In the case of aphids, insecticides provide a considerable force in the elimination of genotypes.5. Insecticide resistance inMyzus persicae(Sulzer) has arisen independently through point mutation and gene amplification on a number of occasions and at different times. Resistance to organophosphates, pyrethroids, and pirimicarb (a dimethyl carbamate) is now widespread.6. In this paper, we examine these three elements: sexual recombination, clonal expansion, and insecticide selection in the peach–potato aphidM. persicaein relation to the evolution of insecticide resistance and survival of the fittest clone.
In vivo transfer of plasmid pRAS1 between Aeromonas salmonicida and Aeromonas hydrophila in artificially infected Cyprinus carpio L.
Authors: Bello‐López J M , Fernández‐Rendón E , Curiel‐Quesada E 
Published: January 2010

AbstractThis study investigated the possible in vivo transfer of plasmid pRAS1 between Aeromonas salmonicida and A. hydrophila inhabiting two different organs of Cyprinus carpio L. To distinguish transconjugants from naturally occurring antibiotic resistant bacteria, twelve luminescent transposon‐tagged A. hydrophila strains using miniTn5luxCDABEKm2 transposon were generated. In conjugal transfer experiments, fish were conditioned with the donor bacteria and subsequently immersed in water containing the recipient strain. Bacteria were recovered from gills and intestines and isolated by growth on selective plates. Transconjugants were identified by their resistance to the pRAS1 encoded antimicrobials and by light emission. In vivo transfer frequencies ranged between 10−3 and 10−6 and were somewhat lower in intestines, compared to gills. Transfer frequencies were also smaller relative to those obtained in vitro. The minimal amount of donor and recipient bacteria needed to yield detectable transconjugants in vivo was 1 × 104 CFU mL−1. Implications of this plasmid transfer in natural settings and its possible consequences to human health are discussed.