bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neonatal and Adult Neurogenesis Provide Two Distinct Populations of Newborn Neurons to the Mouse Olfactory Bulb
Authors: Lemasson Morgane , Saghatelyan Armen , Olivo-Marin Jean-Christophe , Lledo Pierre-Marie 
Published: July 2005

In mammals, the olfactory bulb (OB) constitutes one of two regions of the postnatal brain with continuous neurogenesis throughout life. Despite intense explorations of neuronal replacement in the adult OB, little is known about the mechanisms that operate at earlier postnatal stages. This question is particularly pertinent, because the majority of local interneurons are born in the neonate, when olfaction controls vital functions. Here, we analyzed the recruitment of newborn cells to the granule cell (GC) layer (GCL) and found that the postnatal mouse OB is supplied with two spatiotemporally distinct populations of newborn interneurons.Early born [postnatal day 3 (P3) to P7] GCs constitute a threefold larger population compared with those generated later (P14-P60), and some of them are produced locally within the OB itself. Newborn interneurons generated at P3-P7 were predominantly targeted to the external edge of the GCL, whereas newly generated cells were positioned deeper in older mice. Additionally, although ∼50% of adult newborn cells were eliminated within a few weeks of reaching the OB, almost the entire population of early born GCs survived until adulthood. Importantly, early olfactory experience specifically modifies the number of newborn GCs in neonates but leaves unaltered the amount of neurons generated during adulthood. Together, these results demonstrate that early postnatal neurogenesis endows the neonate bulbar circuit with newborn GCs that differ morphologically and functionally from those produced in the adult.
lin-8, Which Antagonizes Caenorhabditis elegans Ras-Mediated Vulval Induction, Encodes a Novel Nuclear Protein That Interacts With the LIN-35 Rb Protein
Authors: Davison Ewa M , Harrison Melissa M , Walhout Albertha J M , Vidal Marc , Horvitz H Robert 
Published: July 2005

Abstract
Ras-mediated vulval development in C. elegans is inhibited by the functionally redundant sets of class A, B, and C synthetic Multivulva (synMuv) genes. Three of the class B synMuv genes encode an Rb/DP/E2F complex that, by analogy with its mammalian and Drosophila counterparts, has been proposed to silence genes required for vulval specification through chromatin modification and remodeling. Two class A synMuv genes, lin-15A and lin-56, encode novel nuclear proteins that appear to function as a complex. We show that a third class A synMuv gene, lin-8, is the defining member of a novel C. elegans gene family. The LIN-8 protein is nuclear and can interact physically with the product of the class B synMuv gene lin-35, the C. elegans homolog of mammalian Rb. LIN-8 likely acts with the synMuv A proteins LIN-15A and LIN-56 in the nucleus, possibly in a protein complex with the synMuv B protein LIN-35 Rb. Other LIN-8 family members may function in similar complexes in different cells or at different stages. The nuclear localization of LIN-15A, LIN-56, and LIN-8, as well as our observation of a direct physical interaction between class A and class B synMuv proteins, supports the hypothesis that the class A synMuv genes control vulval induction through the transcriptional regulation of gene expression.
Epistatic Pleiotropy and the Genetic Architecture of Covariation Within Early and Late-Developing Skull Trait Complexes in Mice
Authors: Wolf Jason B , Leamy Larry J , Routman Eric J , Cheverud James M 
Published: July 2005

Abstract
The role of epistasis as a source of trait variation is well established, but its role as a source of covariation among traits (i.e., as a source of “epistatic pleiotropy”) is rarely considered. In this study we examine the relative importance of epistatic pleiotropy in producing covariation within early and late-developing skull trait complexes in a population of mice derived from an intercross of the Large and Small inbred strains. Significant epistasis was found for several pairwise combinations of the 21 quantitative trait loci (QTL) affecting early developing traits and among the 20 QTL affecting late-developing traits. The majority of the epistatic effects were restricted to single traits but epistatic pleiotropy still contributed significantly to covariances. Because of their proportionally larger effects on variances than on covariances, epistatic effects tended to reduce within-group correlations of traits and reduce their overall degree of integration. The expected contributions of single-locus and two-locus epistatic pleiotropic QTL effects to the genetic covariance between traits were analyzed using a two-locus population genetic model. The model demonstrates that, for single-locus or epistatic pleiotropy to contribute to trait covariances in the study population, both traits must show the same pattern of single-locus or epistatic effects. As a result, a large number of the cases where loci show pleiotropic effects do not contribute to the covariance between traits in this population because the loci show a different pattern of effect on the different traits. In general, covariance patterns produced by single-locus and epistatic pleiotropy predicted by the model agreed well with actual values calculated from the QTL analysis. Nearly all single-locus and epistatic pleiotropic effects contributed positive components to covariances between traits, suggesting that genetic integration in the skull is achieved by a complex combination of pleiotropic effects.
The Evolution of Plastic Recombination
Authors: Agrawal Aneil F , Hadany Lilach , Otto Sarah P 
Published: July 2005

Abstract
Empirical data suggest that recombination rates may change in response to stress. To study the evolution of plastic recombination, we develop a modifier model using the same theoretical framework used to study conventional (nonplastic) modifiers, thus allowing direct comparison. We examine the evolution of plastic recombination in both haploid and diploid systems. In haploids, a plastic modifier spreads by forming associations with selectively favored alleles. Relative to nonplastic effects, selection on the plastic effects of a modifier is both much stronger and less sensitive to the specifics of the selection regime (e.g., epistasis). In contrast, the evolution of plastic recombination in diploids is much more restricted. Selection on plasticity requires the ability to detect DNA damage or cis-trans effects as may occur through maternal effects on fitness.
Genetic Analysis of Variation in Gene Expression inArabidopsis thaliana
Authors: Vuylsteke Marnik , van Eeuwijk Fred , Van Hummelen Paul , Kuiper Martin , Zabeau Marc 
Published: July 2005

AbstractIn Arabidopsis thaliana, significant efforts to determine the extent of genomic variation between phenotypically divergent accessions are under way, but virtually nothing is known about variation at the transcription level. We used microarrays to examine variation in transcript abundance among three inbred lines and two pairs of reciprocal F1 hybrids of the highly self-fertilizing species Arabidopsis. Composite additive genetic effects for gene expression were estimated from pairwise comparisons of the three accessions Columbia (Col), Landsberg erecta (Ler), and Cape Verde Islands (Cvi). For the pair Col and Ler, 27.0% of the 4876 genes exhibited additive genetic effects in their expression (α = 0.001) vs. 32.2 and 37.5% for Cvi with Ler and Col, respectively. Significant differential expression ranged from 32.45 down to 1.10 in fold change and typically differed by a factor of 1.56. Maternal or paternal transmission affected only a few genes, suggesting that the reciprocal effects observed in the two crosses analyzed were minimal. Dominance effects were estimated from the comparisons of hybrids with the corresponding midparent value. The percentage of genes showing dominance at the expression level in the F1 hybrids ranged from 6.4 to 21.1% (α = 0.001). Breakdown of these numbers of genes according to the magnitude of the dominance ratio revealed heterosis for expression for on average 9% of the genes. Further advances in the genetic analysis of gene expression variation may contribute to a better understanding of its role in affecting quantitative trait variation at the phenotypic level.
RNA Cleavage Linked With Ribosomal Action
Authors: Yamanishi Haruyo , Yonesaki Tetsuro 
Published: July 2005

Abstract
Ribonuclease LS in Escherichia coli is a potential antagonist of bacteriophage T4. When T4 dmd is mutated, this RNase efficiently cleaves T4 mRNAs and leads to the silencing of late genes, thus blocking T4 growth. We previously found that, when two consecutive ochre codons were placed in the open reading frame of T4 soc, RNase LS cleaved soc mRNA at a specific site downstream of the ochre codons. Here, we demonstrate that RNase LS cleaves soc RNA at the same site even when only a single ochre codon is present or is replaced with either an amber or an opal codon. On the other hand, disruption of the Shine-Dalgarno sequence, a ribosome-binding site required for the initiation of translation, eliminates the cleavage. These results strongly suggest that RNase LS cleaves in a manner dependent on translation termination. Consistent with this suggestion, the cleavage dependency on an amber codon was considerably reduced in the presence of amber-codon-suppressing tRNA. Instead, two other cleavages that depend on translation of the region containing the target sites occurred farther downstream. Additional analysis suggests that an interaction of the ribosome with a stop codon might affect the site of cleavage by RNase LS in an mRNA molecule. This effect of the ribosome could reflect remodeling of the high-order structure of the mRNA molecule.
Eu-heterochromatic Rearrangements Induce Replication of Heterochromatic Sequences Normally Underreplicated in Polytene Chromosomes of Drosophila melanogaster
Authors: Abramov Yuri A , Kogan Galina L , Tolchkov Eugenii V , Rasheva Vanya I , Lavrov Sergei A , Bonaccorsi Silvia , Kramerova Irina A , Gvozdev Vladimir A 
Published: July 2005

Abstract
In polytene chromosomes of D. melanogaster the heterochromatic pericentric regions are underreplicated (underrepresented). In this report, we analyze the effects of eu-heterochromatic rearrangements involving a cluster of the X-linked heterochromatic (Xh) Stellate repeats on the representation of these sequences in salivary gland polytene chromosomes. The discontinuous heterochromatic Stellate cluster contains specific restriction fragments that were mapped along the distal region of Xh. We found that transposition of a fragment of the Stellate cluster into euchromatin resulted in its replication in polytene chromosomes. Interestingly, only the Stellate repeats that remain within the pericentric Xh and are close to a new eu-heterochromatic boundary were replicated, strongly suggesting the existence of a spreading effect exerted by the adjacent euchromatin. Internal rearrangements of the distal Xh did not affect Stellate polytenization. We also demonstrated trans effects exerted by heterochromatic blocks on the replication of the rearranged heterochromatin; replication of transposed Stellate sequences was suppressed by a deletion of Xh and restored by addition of Y heterochromatin. This phenomenon is discussed in light of a possible role of heterochromatic proteins in the process of heterochromatin underrepresentation in polytene chromosomes.
Adaptation in Sexuals vs. Asexuals: Clonal Interference and the Fisher-Muller Model
Authors: Kim Yuseob , Orr H Allen 
Published: July 2005

Abstract
Fisher and Muller's theory that recombination speeds adaptation by eliminating competition among beneficial mutations has proved a popular explanation for the advantage of sex. Recent theoretical studies have attempted to quantify the speed of adaptation under the Fisher-Muller model, partly in an attempt to understand the role of “clonal interference” in microbial experimental evolution. We reexamine adaptation in sexuals vs. asexuals, using a model of DNA sequence evolution. In this model, a modest number of sites can mutate to beneficial alleles and the fitness effects of these mutations are unequal. We study (1) transition probabilities to different beneficial mutations; (2) waiting times to the first and the last substitutions of beneficial mutations; and (3) trajectories of mean fitness through time. We find that some of these statistics are surprisingly similar between sexuals and asexuals. These results highlight the importance of the choice of substitution model in assessing the Fisher-Muller advantage of sex.
Drosophila ATM and Mre11 Are Essential for the G2/M Checkpoint Induced by Low-Dose Irradiation
Authors: Bi Xiaolin , Gong Min , Srikanta Deepa , Rong Yikang S 
Published: July 2005

Abstract
Others have suggested recently that the conserved ATM checkpoint kinase is minimally involved in controlling the G2/M checkpoint in Drosophila that serves to prevent mitotic entry in the presence of DNA damage. Our data indicate that both ATM and its regulator Mre11 are important for the checkpoint and that their roles become essential when animals are challenged with a low dose of X rays or when they have compromised checkpoint function of the ATM-related ATR kinase.
The Extent of Linkage Disequilibrium Caused by Selection on G6PD in Humans
Authors: Saunders Matthew A , Slatkin Montgomery , Garner Chad , Hammer Michael F , Nachman Michael W 
Published: July 2005

Abstract
The gene coding for glucose-6-phosphate dehydrogenase (G6PD) is subject to positive selection by malaria in some human populations. The G6PD A− allele, which is common in sub-Saharan Africa, is associated with deficient enzyme activity and protection from severe malaria. To delimit the impact of selection on patterns of linkage disequilibrium (LD) and nucleotide diversity, we resequenced 5.1 kb at G6PD and ∼2–3 kb at each of eight loci in a 2.5-Mb region roughly centered on G6PD in a diverse sub-Saharan African panel of 51 unrelated men (including 20 G6PD A−, 11 G6PD A+, and 20 G6PD B chromosomes). The signature of selection is evident in the absence of genetic variation at G6PD and at three neighboring loci within 0.9 Mb from G6PD among all individuals bearing G6PD A− alleles. A genomic region of ∼1.6 Mb around G6PD was characterized by long-range LD associated with the A− alleles. These patterns of nucleotide variability and LD suggest that G6PD A− is younger than previous age estimates and has increased in frequency in sub-Saharan Africa due to strong selection (0.1 &lt; s &lt; 0.2). These results also show that selection can lead to nonrandom associations among SNPs over great physical and genetic distances, even in African populations.
Evaluating UV‐B Effects and EDU Protection in Soybean Leaves Using Fluorescence
Authors: Middleton Elizabeth M. , Kim Moon S. , Krizek Donald T. , Bajwa Ravinder K. S. 
Published: July 2005

ABSTRACTA growth‐chamber experiment was conducted to evaluate whether ethylenenediurea (EDU), a chemical shown to be protective against ozone pollution, could ameliorate foliar damage induced by ultraviolet‐B (UV‐B) radiation exposure in ‘Roanoke’ soybean (Glycine max L.), a UV‐B–sensitive cultivar, and whether these effects could be discriminated using fluorescence (F) observations. The experiment had four treatment groups: control; biologically effective UV‐B (18 kjm−2 day−1); EDU (500 μmol mol−1); and both UV‐B and EDU (UV/EDU). Measurements included photosynthetic pigments, F image system (FIS) images of adaxial surfaces in four spectral regions (blue, green, red and far‐red) and F emission spectra of the pigment extracts produced at two excitation wavelengths, 280 nm (280EX) and 380 nm (380EX). Several F ratios from 280EX, 380EX and the FIS images successfully separated the low UV vs high EDU group responses based on means alone, with intermediate values for controls and the combined UV/EDU groups. A UV‐B/blue emission ratio, F315/F420 (280EX), was correlated with chlorophyll content (μg cm−2)(R= 0.88, P < 0.001), as was a ratio of emissions at two UV‐A wavelengths: F330/F385 (280EX) (R= 0.87). These two 280EX ratios were also linearly correlated with emission ratios produced by 380EX, such as the far‐red/green ratio, F730/F525 (380EX) (R= 0.92, P < 0.001), and clearly distinguished the UV‐B and EDU groups separately, and which bracketed the similar intermediate responses of the UV/EDU and control groups. The FIS images additionally captured the following anatomical spatial patterns across the leaf surfaces: (1) emissions of UV‐B–irradiated leaves were more uniform but lower in intensity than those of other groups; and (2) emissions of EDU‐treated leaves exhibited the greatest variation in spatial patterns because veins had elevated blue F and leaf edges had enhanced red and far‐red F. This experiment supports the hypothesis that EDU substantially ameliorated UV‐B damage to foliage, a result that relied on the combined use of FIS images and emission spectra.
Rapid Detection of Aspergillus flavus Contamination in Peanut with Novel Delayed Luminescence Spectra
Authors: Chen WenLi , Xing Da , Chen WeiGui 
Published: July 2005

ABSTRACTEmploying a luminescence spectrometer the usefulness of light‐induced delayed luminescence (DL) for the detection of aflatoxinB1 (AfB1) contamination in whole peanut was studied. Peanut was artificially contaminated with Aspergillus flavus (7.5 × 105conidia/mL) and incubated for 0–72 h. The DL and fluorescence spectra of contaminated peanut were obtained by a luminescence spectrometer. The correlation between the spectra and contamination levels was established. The DL and fluorescence intensity has a negative correlation with the AfB1 concentration. Our results suggested that the DL technique might be useful for the rapid and noninvasive evaluation of AfB1 contamination levels in whole peanut.
Electroshocking and PIT Tagging of Juvenile Atlantic Salmon: Are There Interactive Effects on Growth and Survival?
Authors: Sigourney Douglas B. , Horton Gregg E. , Dubreuil Todd L. , Varaday Aimee M. , Letcher Benjamin H. 
Published: July 2005

Abstract
Electroshocking and tagging of fish with passive integrated transponder (PIT) tags are two commonly used methods for conducting mark–recapture studies in freshwater environments and are frequently used in combination. We conducted an experiment to test for the effects of electroshocking, tagging, and a combination of electroshocking plus tagging on the growth and survival of Atlantic salmon Salmo salar parr. We used five treatments that included the presence or absence of PIT tags and electroshocking at 300 or 500 V plus a control group. Fish were measured, weighed, and electroshocked on four occasions separated by approximately 2-month intervals. The average (±1 SD) fork length was 62.1 ± 1.9 mm and the average weight was 2.5 ± 0.3 g at the start of the experiment; at the end of the experiment, length averaged 120.5 ± 11.6 mm and weight averaged 20.9 ± 6.1 g. We did not detect any significant effects of electroshocking on growth or survival over the course of the experiment. However, there was evidence that tagging negatively influenced survival over the first interval after initial tagging and that survival was positively correlated with fish size. In addition, tagged fish seemed to suffer a minor depression in growth over the first interval, although differences in size among tagged and untagged fish were nonsignificant throughout the course of the experiment. We suggest that the size at tagging may have a greater effect on survival and growth of small (&lt;80;eqmm) Atlantic salmon parr than the amount of exposure to electroshocking.
Extent of Anadromy in Bull Trout and Implications for Conservation of a Threatened Species
Authors: Brenkman Samuel J. , Corbett Stephen C. 
Published: July 2005

Abstract
The use of radiotelemetry revealed that adult bull trout Salvelinus confluentus moved between freshwater and the Pacific Ocean and between watersheds along coastal Washington. Forty-seven of 82 radio-tagged bull trout implanted in the Hoh River and Kalaloch Creek basins were anadromous, and 23 fish were relocated in five different estuaries up to 47 km south of their tagging locations. Anadromous bull trout typically entered the Hoh River from May to July, ascended as far as 78 km upstream to spawning areas by September, and returned to the ocean to overwinter. This is the first study to verify that anadromy is a primary life history form in coastal bull trout. The presence of anadromy and the irregular periods of freshwater, estuarine, and marine residence observed in this study are consistent with observations reported for other Salvelinus species. These results also demonstrate that anadromous bull trout inhabit a diverse range of estuarine, freshwater, and marine habitats. Their affinity to estuaries and their observed temporal movements suggest that bull trout optimize winter refugia and forage opportunities and are susceptible to incidental mortality in gill-net and recreational fisheries directed at other Pacific salmonids. An understanding of the extent of anadromy, sources of mortality, and diversity of habitats occupied by bull trout is informative in the establishment of appropriate conservation and recovery strategies for this species.
Effect of Measurement Error on Tests of Density Dependence of Catchability for Walleyes in Northern Wisconsin Angling and Spearing Fisheries
Authors: Hansen Michael J. , Beard T. Douglas , Hewett Steven W. 
Published: July 2005

Abstract
We sought to determine how much measurement errors affected tests of density dependence of spearing and angling catchability for walleye Sander vitreus by quantifying relationships between spearing and angling catch rates (catch/h) and walleye population density (number/acre) in northern Wisconsin lakes. The mean measurement error of spearing catch rates was 43.5 times greater than the mean measurement error of adult walleye population densities, whereas the mean measurement error of angling catch rates was only 5.6 times greater than the mean measurement error of adult walleye population densities. The bias-corrected estimate of the relationship between spearing catch rate and adult walleye population density was similar to the ordinary-least-squares regression estimate but differed significantly from the geometric mean (GM) functional regression estimate. In contrast, the bias-corrected estimate of the relationship between angling catch rate and total walleye population density was intermediate between ordinary-least-squares and GM functional regression estimates. Catch rates of walleyes in both spearing and angling fisheries were not linearly related to walleye population density, which indicated that catch rates in both fisheries were hyperstable in relation to walleye population density. For both fisheries, GM functional regression overestimated the degree of hyperdepletion in catch rates and ordinary-least-squares regression overestimated the degree of hyperstability in catch rates. However, ordinary-least-squares regression induced significantly less bias in tests of density dependence than GM functional regression, so it may be suitable for testing the degree of density dependence in fisheries for which fish population density is estimated with mark– recapture methods similar to those used in our study.