bluuebunny/crossref_metadata_2025 huggingface dataset:
Agouti-Related Peptide and MC3/4 Receptor Agonists Both Inhibit Excitatory Hypothalamic Ventromedial Nucleus Neurons
Authors: Fu Li-Ying , van den Pol Anthony N.
Published: May 2008

Anorexigenic melanocortins decrease food intake by activating MC3/MC4 receptors (MC3/4R); the prevailing view is that the orexigenic neuropeptide agouti-related peptide (AgRP) exerts the opposite action by acting as an antagonist at MC3/MC4 receptors. A total of 370 hypothalamic ventromedial nucleus (VMH) glutamatergic neurons was studied using whole-cell recording in hypothalamic slices from a novel mouse expressing green fluorescent protein (GFP) under control of the vesicular glutamate transporter 2 (vGluT2) promoter. Massive numbers of GFP-expressing VMH dendrites extended out of the core of the nucleus into the surrounding cell-poor shell. VMH dendrites received frequent appositions from AgRP-immunoreactive axons in the shell of the nucleus, but not the core, suggesting that AgRP may influence target VMH neurons. α-MSH, melanotan II (MTII), and selective MC3R or MC4R agonists were all inhibitory, reducing the spontaneous firing rate and hyperpolarizing vGluT2 neurons. The MC3/4R antagonist SHU9119 was excitatory. Unexpectedly, AgRP did not attenuate MTII actions on these neurons; instead, these two compounds showed an additive inhibitory effect. In the absence of synaptic activity, no hyperpolarization or change in input resistance was evoked by either MTII or AgRP, suggesting indirect actions. Consistent with this view, MTII increased the frequency of spontaneous and miniature IPSCs. In contrast, the mechanism of AgRP inhibition was dependent on presynaptic inhibition of EPSCs mediated by Gi/Go-proteins, and was attenuated by pertussis toxin and NF023, inconsistent with mediation by Gs-proteins associated with MC receptors. Together, our data suggest that the mechanism of AgRP actions on these excitatory VMH cells appears to be independent of the actions of melanocortins on MC receptors.
Evidence That Vesicles Undergo Compound Fusion on the Synaptic Ribbon
Authors: Matthews Gary , Sterling Peter
Published: May 2008

The ribbon synapse can release a stream of transmitter quanta at very high rates. Although the ribbon tethers numerous vesicles near the presynaptic membrane, most of the tethered vesicles are held at a considerable distance from the plasma membrane. Therefore, it remains unclear how their contents are released. We evoked prolonged bouts of exocytosis from a retinal bipolar cell, fixed within seconds, and then studied the ribbons by electron microscopy. Vesicle density on ribbons was reduced by ∼50% compared with cells where exocytosis was blocked with intracellular ATP-γS. Large, irregularly shaped vesicles appeared on the ribbon in cells fixed during repetitive stimulation of exocytosis, and in some cases the large vesicles could be traced in adjacent sections to cisternae open to the medium. The large cisternal structures were attached to the ribbon by filaments similar to those that tether synaptic vesicles to the ribbon, and they occupied the base of the ribbon near the plasma membrane, where normal synaptic vesicles are found in resting cells. We suggest that the cisternae attached to ribbons represent synaptic vesicles that fused by compound exocytosis during strong repetitive stimulation and, thus, that vesicles tethered to the ribbon can empty their contents by fusing to other vesicles docked at the presynaptic membrane. Such compound fusion could explain the extremely high release rates and the multivesicular release reported for auditory and visual ribbon synapses.
P2X1and P2X5Subunits Form the Functional P2X Receptor in Mouse Cortical Astrocytes
Authors: Lalo Ulyana , Pankratov Yuri , Wichert Sven P. , Rossner Moritz J. , North R. Alan , Kirchhoff Frank , Verkhratsky Alexei
Published: May 2008

ATP plays an important role in signal transduction between neuronal and glial circuits and within glial networks. Here we describe currents activated by ATP in astrocytes acutely isolated from cortical brain slices by non-enzymatic mechanical dissociation. Brain slices were prepared from transgenic mice that express enhanced green fluorescent protein under the control of the human glial fibrillary acidic protein promoter. Astrocytes were studied by whole-cell voltage clamp. Exogenous ATP evoked inward currents in 75 of 81 astrocytes. In the majority (∼65%) of cells, ATP-induced responses comprising a fast and delayed component; in the remaining subpopulation of astrocytes, ATP triggered a smoother response with rapid peak and slowly decaying plateau phase. The fast component of the response was sensitive to low concentrations of ATP (with EC50of ∼40 nm). All ATP-induced currents were blocked by pyridoxal-phosphate-6-azophenyl-2′,4′-disulfonate (PPADS); they were insensitive to ivermectin. Quantitative real-time PCR demonstrated strong expression of P2X1and P2X5receptor subunits and some expression of P2X2subunit mRNAs. The main properties of the ATP-induced response in cortical astrocytes (high sensitivity to ATP, biphasic kinetics, and sensitivity to PPADS) were very similar to those reported for P2X1/5heteromeric receptors studied previously in heterologous expression systems.
Midbrain Auditory Neurons Integrate Excitation and Inhibition to Generate Duration Selectivity: AnIn VivoWhole-Cell Patch Study in Anurans
Authors: Leary Christopher J. , Edwards Christofer J. , Rose Gary J.
Published: May 2008

Sound duration can play a pivotal role in the reproductive behavior of anuran amphibians. Here, we report the first whole-cell recordings from duration-selective neurons in the anuran torus semicircularis,in vivo. We show that most short-pass duration-selective cells exhibited short-latency inhibition and delayed excitation. The duration of the inhibition increased with tone burst duration. Hence, for long-duration tone bursts, inhibition overlapped with excitation, reducing or eliminating spikes; no postinhibitory rebound was present. Other short-pass cells, however, showed inhibition only for long-duration tone bursts. Bandpass duration selectivity also involved interplay between inhibition and excitation; inhibition negated excitation with tone bursts that exceeded the optimum duration. Additionally, however, bandpass selectivity arose from stimulus-dependent excitation; tone bursts of sufficiently long duration were required to elicit excitation. Similarly, long-pass neurons showed inhibition and duration-dependent enhancement of excitation; long-pass selectivity resulted from enhanced excitation outlasting the transient inhibition or, in some cases, excitation overriding concurrent inhibition. Last, we evaluated the stimulus specificity of duration-selective neurons to variations in pulse repetition rate. We show that (1) most neurons that exhibited long-pass selectivity for tone-burst duration nonetheless responded to short-duration pulses when repeated at particular rates, and (2) some neurons that showed selectivity for tone burst duration also showed selectivity for pulse train duration. These novel response profiles appear to result from interplay between inhibition and time- and activity-dependent changes in excitation strength. These findings are discussed in the context of prevailing models of duration selectivity and acoustic communication in anurans.
Increased Dopamine Level Enhances Male–Male Courtship inDrosophila
Authors: Liu Tong , Dartevelle Laurence , Yuan Chunyan , Wei Hongping , Wang Ying , Ferveur Jean-François , Guo Aike
Published: May 2008

Sexual behavior between males is observed in many species, but the biological factors involved are poorly known. In mammals, manipulation of dopamine has revealed the role of this neuromodulator on male sexual behavior. We used genetic and pharmacological approaches to manipulate the dopamine level in dopaminergic cells inDrosophilaand investigated the consequence of this manipulation on male–male courtship behavior. Males with increased dopamine level showed enhanced propensity to court other males but did not change their courtship toward virgin females, general olfactory response, general gustatory response, or locomotor activity. Our results indicate that the high intensity of male–male interaction shown by these manipulated males was related to their altered sensory perception of other males.
Blockade of Endogenous Opioid Neurotransmission Enhances Acquisition of Conditioned Fear in Humans
Authors: Eippert Falk , Bingel Ulrike , Schoell Eszter , Yacubian Juliana , Büchel Christian
Published: May 2008

The endogenous opioid system is involved in fear learning in rodents, as opioid agonists attenuate and opioid antagonists facilitate the acquisition of conditioned fear. It has been suggested that an opioidergic signal, which is engaged through conditioning and acts inhibitory on unconditioned stimulus input, is the source of these effects. To clarify whether blockade of endogenous opioid neurotransmission enhances acquisition of conditioned fear in humans, and to elucidate the neural underpinnings of such an effect, we used functional magnetic resonance imaging in combination with behavioral recordings and a double-blind pharmacological intervention. All subjects underwent the same classical fear-conditioning paradigm, but subjects in the experimental group received the opioid antagonist naloxone before and during the experiment, in contrast to subjects in the control group, who received saline. Blocking endogenous opioid neurotransmission with naloxone led to more sustained responses to the unconditioned stimulus across trials, evident in both behavioral and blood oxygen level-dependent responses in pain responsive cortical regions. This effect was likely caused by naloxone blocking conditioned responses in a pain-inhibitory circuit involving opioid-rich areas such as the rostral anterior cingulate cortex, amygdala, and periaqueductal gray. Most importantly, naloxone enhanced the acquisition of fear on the behavioral level and changed the activation profile of the amygdala: whereas the control group showed rapidly decaying conditioned responses across trials, the naloxone group showed sustained conditioned responses in the amygdala. Together, these results demonstrate that in humans the endogenous opioid system has an inhibitory role in the acquisition of fear.
Visual–Procedural Memory Consolidation during Sleep Blocked by Glutamatergic Receptor Antagonists
Authors: Gais Steffen , Rasch Björn , Wagner Ullrich , Born Jan
Published: May 2008

Visual cortex plasticity is enhanced by sleep. It is hypothesized that a reactivation of glutamatergic synapses is essential for this form of plasticity to occur after learning. To test this hypothesis, human subjects practiced a visual texture discrimination skill known to require post-training sleep for improvements to occur. During sleep, glutamatergic transmission was inhibited by administration of the two glutamate antagonists, caroverine and ketamine, targeting the ionotropic NMDA and AMPA receptors. Both substances given during consolidation sleep in a placebo controlled crossover design were able to prevent improvement of the skill measured the next morning. An off-line activation of glutamatergic synapses therefore seems to play a critical part in the consolidation of plastic changes in the visual cortex.
Postsynaptic Action of Brain-Derived Neurotrophic Factor Attenuates α7 Nicotinic Acetylcholine Receptor-Mediated Responses in Hippocampal Interneurons
Authors: Fernandes Catarina C. , Pinto-Duarte António , Ribeiro Joaquim Alexandre , Sebastião Ana M.
Published: May 2008

Nicotinic mechanisms acting on the hippocampus influence attention, learning, and memory and constitute a significant therapeutic target for many neurodegenerative, neurological, and psychiatric disorders. Here, we report that brain-derived neurotrophic factor (BDNF) (1–100 ng/ml), a member of the neurotrophin gene family, rapidly decreases α7 nicotinic acetylcholine receptor responses in interneurons of the hippocampal CA1 stratum radiatum. Such effect is dependent on the activation of the TrkB receptor and involves the actin cytoskeleton; noteworthy, it is compromised when the extracellular levels of the endogenous neuromodulator adenosine are reduced with adenosine deaminase (1 U/ml) or when adenosine A2Areceptors are blocked with SCH 58261 (2-(2-furanyl)-7-(2-phenylethyl)-7H-pyrazolo[4,3-e][1,2,4]triazolo[1,5-c]pyrimidin-5-amine) (100 nm). The intracellular application of U73122 (1-[6[[(17β)-3-methoxyestra-1,3,5(10)-trien-17-yl]amino]hexyl]-1H-pyrrole-2,5-dione) (5 μm), a broad-spectrum inhibitor of phospholipase C, or GF 109203X (bisindolylmaleimide I) (2 μm), a general inhibitor of protein kinase C isoforms, blocks BDNF-induced inhibition of α7 nicotinic acetylcholine receptor function. Moreover, in conditions of simultaneous intracellular dialysis of the fast Ca2+chelator BAPTA (10 mm) and removal of extracellular Ca2+ions, the inhibitory action of BDNF is further prevented. The present findings disclose a novel target for rapid actions of BDNF that might play important roles on synaptic transmission and plasticity in the brain.
CAPS Facilitates Filling of the Rapidly Releasable Pool of Large Dense-Core Vesicles
Authors: Liu Yuanyuan , Schirra Claudia , Stevens David R. , Matti Ulf , Speidel Dina , Hof Detlef , Bruns Dieter , Brose Nils , Rettig Jens
Published: May 2008

Calcium-activator protein for secretion (CAPS) is a cytosolic protein that associates with large dense-core vesicles and is involved in their secretion. Mammals express two CAPS isoforms, which share a similar domain structure including a Munc13 homology domain that is believed to be involved in the priming of secretory vesicles. A variety of studies designed to perturb CAPS function indicate that CAPS is involved in the secretion of large dense-core vesicles, but where in the secretory pathway CAPS acts is still under debate. Mice in which one allele of theCAPS-1gene is deleted exhibit a deficit in catecholamine secretion from chromaffin cells. We have examined catecholamine secretion from chromaffin cells in which bothCAPSgenes were deleted and show that the deletion of both CAPS isoforms causes a strong reduction in the pool of rapidly releasable chromaffin granules and of sustained release during ongoing stimulation. We conclude that CAPS is required for the adequate refilling and/or maintenance of a rapidly releasable granule pool.
Excitatory Actions of GABA in the Suprachiasmatic Nucleus
Authors: Choi Hee Joo , Lee C. Justin , Schroeder Analyne , Kim Yoon Sik , Jung Seung Hoon , Kim Jeong Sook , Kim Do Young , Son Eun Ju , Han Hee Chul , Hong Seung Kil , Colwell Christopher S. , Kim Yang In
Published: May 2008

Neurons in the suprachiasmatic nucleus (SCN) are responsible for the generation of circadian oscillations, and understanding how these neurons communicate to form a functional circuit is a critical issue. The neurotransmitter GABA and its receptors are widely expressed in the SCN where they mediate cell-to-cell communication. Previous studies have raised the possibility that GABA can function as an excitatory transmitter in adult SCN neurons during the day, but this work is controversial. In the present study, we first tested the hypothesis that GABA can evoke excitatory responses during certain phases of the daily cycle by broadly sampling how SCN neurons respond to GABA using extracellular single-unit recording and gramicidin-perforated-patch recording techniques. We found that, although GABA inhibits most SCN neurons, some level of GABA-mediated excitation was present in both dorsal and ventral regions of the SCN, regardless of the time of day. These GABA-evoked excitatory responses were most common during the night in the dorsal SCN region. The Na+-K+-2Cl−cotransporter (NKCC) inhibitor, bumetanide, prevented these excitatory responses. In individual neurons, the application of bumetanide was sufficient to change GABA-evoked excitation to inhibition. Calcium-imaging experiments also indicated that GABA-elicited calcium transients in SCN cells are highly dependent on the NKCC isoform 1 (NKCC1). Finally, Western blot analysis indicated that NKCC1 expression in the dorsal SCN is higher in the night. Together, this work indicates that GABA can play an excitatory role in communication between adult SCN neurons and that this excitation is critically dependent on NKCC1.
Annam Uplifted: The First Vietnamese Catholic Bishops and the Birth of a National Church, 1919–1945
Authors: Keith Charles
Published: May 2008

This article explores the place of the first Vietnamese Catholic bishops in the politics and society of late colonial Vietnam. It places the rise of these influential figures in the broader contexts of the decline of missionary Catholicism, the Vatican's push to form national Churches in Asia, and institutional and cultural changes in Vietnamese Catholicism during the interwar years. By doing so, the article explores the links between faith and politics in colonial Vietnam, showing how changes in Vietnamese Catholicism reflect a growing contestation of colonial rule and greater ties to global Catholicism that help explain the Church's place in Vietnamese society after independence.
Witnessing Trauma: Abjection and Sadomasochism in Trần Vũ's Short Stories
Authors: Cao Christine
Published: May 2008

This article analyzes three short stories of refugee expulsion, immigrant displacement, and exilic return by contemporary writer Trần Vũ. Beyond the binary of nostalgia and assimilation, Vietnamese diasporic identity emerges in these narratives as the tenuous subject of physical and psychic trauma. Informed by postcolonial theories of diasporic identity, Asian American scholarship on racial abjection, and psychoanalytic and feminist analyses of trauma and sexual deviance, I argue that the characters in these stories either succumb to or subvert the unwitting repetition of trauma in their attempts to challenge, if only precariously, patterns of domination through sadomasochism and counternationalist historiography.
RNA-Based 5-Fluorouracil Toxicity Requires the Pseudouridylation Activity of Cbf5p
Authors: Hoskins Jason , Butler J Scott
Published: May 2008

The chemotherapeutic drug 5-fluorouracil (5FU) disrupts DNA synthesis by inhibiting the enzymatic conversion of dUMP to dTMP. However, mounting evidence indicates that 5FU has important effects on RNA metabolism that contribute significantly to the toxicity of the drug. Strains with mutations in nuclear RNA-processing exosome components, including Rrp6p, exhibit strong 5FU hypersensitivity. Studies also suggest that 5FU-containing RNA can inhibit pseudouridylation, the most abundant post-transcriptional modification of noncoding RNA. We examined the effect of modulating the expression and activity of the essential yeast rRNA pseudouridylase Cbf5p on the 5FU hypersensitivity of an rrp6-Δ mutant strain. Depletion of Cbf5p suppressed the 5FU hypersensitivity of an rrp6-Δ strain, while high-copy expression enhanced sensitivity to the drug. A mutation in the catalytic site of Cbf5p also suppressed the 5FU hypersensitivity in the rrp6-Δ mutant, suggesting that RNA-based 5FU toxicity requires the pseudouridylation activity of Cbf5p. High-copy expression of box H/ACA snoRNAs also suppressed the 5FU hypersensitivity of an rrp6-Δ strain, suggesting that sequestration of Cbf5p to a particular guide RNA reduces Cbf5p-dependent 5FU toxicity. On the basis of these results and previous reports that certain pseudouridylases form stable adducts with 5FU-containing RNA, we suggest that Cbf5p binds tightly to substrates containing 5FU, causing their degradation by the TRAMP/exosome-mediated RNA surveillance pathway.
A Thermodynamic Switch for Chromosome Colocalization
Authors: Nicodemi Mario , Panning Barbara , Prisco Antonella
Published: May 2008

A general model for the early recognition and colocalization of homologous DNA sequences is proposed. We show, on thermodynamic grounds, how the distance between two homologous DNA sequences is spontaneously regulated by the concentration and affinity of diffusible mediators binding them, which act as a switch between two phases corresponding to independence or colocalization of pairing regions.
Impact of Amplified Fragment Length Polymorphism Size Homoplasy on the Estimation of Population Genetic Diversity and the Detection of Selective Loci
Authors: Caballero Armando , Quesada Humberto , Rolán-Alvarez Emilio
Published: May 2008

AFLP markers are becoming one of the most popular tools for genetic analysis in the fields of evolutionary genetics and ecology and conservation of genetic resources. The technique combines a high-information content and fidelity with the possibility of carrying out genomewide scans. However, a potential problem with this technique is the lack of homology of bands with the same electrophoretic mobility, what is known as fragment-size homoplasy. We carried out a theoretical analysis aimed at quantifying the impact of AFLP homoplasy on the estimation of within- and between-neutral population genetic diversity in a model of a structured finite population with migration among subpopulations. We also investigated the performance of a currently used method (DFDIST software) to detect selective loci from the comparison between genetic differentiation and heterozygosis of dominant molecular markers, as well as the impact of AFLP homoplasy on its effectiveness. The results indicate that the biases produced by homoplasy are: (1) an overestimation of the frequency of the allele determining the presence of the band, (2) an underestimation of the degree of differentiation between subpopulations, and (3) an overestimation or underestimation of the heterozygosis, depending on the allele frequency of the markers. The impact of homoplasy is quickly diminished by reducing the number of fragments analyzed per primer combination. However, substantial biases on the expected heterozygosity (up to 15–25%) may occur with ∼50–100 fragments per primer combination. The performance of the DFDIST software to detect selective loci from dominant markers is highly dependent on the number of selective loci in the genome and their average effects, the estimate of genetic differentiation chosen to be used in the analysis, and the critical bound probability used to detect outliers. Overall, the results indicate that the software should be used with caution. AFLP homoplasy can produce a reduction of up to 15% in the power to detect selective loci.
Management of Subdivided Populations in Conservation Programs: Development of a Novel Dynamic System
Authors: Fernández J , Toro M A , Caballero A
Published: May 2008

Within the context of a conservation program the management of subdivided populations implies a compromise between the control of the global genetic diversity, the avoidance of high inbreeding levels, and, sometimes, the maintenance of a certain degree of differentiation between subpopulations. We present a dynamic and flexible methodology, based on genealogical information, for the maximization of the genetic diversity (measured through the global population coancestry) in captive subdivided populations while controlling/restricting the levels of inbreeding. The method is able to implement specific restrictions on the desired relative levels of coancestry between and within subpopulations. By accounting for the particular genetic population structure, the method determines the optimal contributions (i.e., number of offspring) of each individual, the number of migrants, and the particular subpopulations involved in the exchange of individuals. Computer simulations are used to illustrate the procedure and its performance in a range of reasonable scenarios. The method performs well in most situations and is shown to be more efficient than the commonly accepted one-migrant-per-generation strategy.
Barren inflorescence1 Functions in Organogenesis During Vegetative and Inflorescence Development in Maize
Authors: Barazesh Solmaz , McSteen Paula
Published: May 2008

Maize (Zea mays) has a highly branched inflorescence due to the production of different types of axillary meristems. Characterization of the barren inflorescence class of mutants has led to the discovery of genes required for axillary meristem initiation in the inflorescence. Previous studies showed that barren inflorescence2 (bif2) encodes a serine/threonine protein kinase that regulates auxin transport, and barren stalk1 (ba1) encodes a basic helix-loop-helix transcription factor that acts downstream of auxin transport. Here, we characterize Barren inflorescence1 (Bif1), a classical semidominant mutation of maize. Developmental, histological, and genetic analyses show that Bif1 mutants are defective in the initiation of all axillary meristems in the inflorescence. Real time RT–PCR experiments show that both bif2 and ba1 are expressed at lower levels in Bif1 mutants. Double-mutant analyses demonstrate that Bif1 exhibits an epistatic interaction with ba1 and a synergistic interaction with bif2. The dramatic phenotypic enhancement observed in Bif1; bif2 double mutants implies that bif1 plays an overlapping role with bif2 in the initiation of lateral organs during vegetative development. The phenotypic resemblance of Bif1 to bif2 mutants and the reduction of auxin transport in Bif1 mutants suggest that bif1 functions as a regulator of auxin transport in maize.
Linkage Disequilibrium Decay and Haplotype Block Structure in the Pig
Authors: Amaral Andreia J , Megens Hendrik-Jan , Crooijmans Richard P M A , Heuven Henri C M , Groenen Martien A M
Published: May 2008

Linkage disequilibrium (LD) may reveal much about domestication and breed history. An investigation was conducted, to analyze the extent of LD, haploblock partitioning, and haplotype diversity within haploblocks across several pig breeds from China and Europe and in European wild boar. In total, 371 single-nucleotide-polymorphisms located in three genomic regions were genotyped. The extent of LD differed significantly between European and Chinese breeds, extending up to 2 cM in Europe and up to 0.05 cM in China. In European breeds, LD extended over large haploblocks up to 400 kb, whereas in Chinese breeds the extent of LD was smaller and generally did not exceed 10 kb. The European wild boar showed an intermediate level of LD between Chinese and European breeds. In Europe, the extent of LD also differed according to genomic region. Chinese breeds showed a higher level of haplotype diversity and shared high levels of frequent haplotypes with Large White, Landrace, and Duroc. The extent of LD differs between both centers of pig domestication, being higher in Europe. Two hypotheses can explain these findings. First, the European ancestral stock had a higher level of LD. Second, modern breeding programs increased the extent of LD in Europe and caused differences of LD between genomic regions. Large White, Landrace, and Duroc showed evidence of past introgression from Chinese breeds.
De Novo Origination of a New Protein-Coding Gene in Saccharomyces cerevisiae
Authors: Cai Jing , Zhao Ruoping , Jiang Huifeng , Wang Wen
Published: May 2008

Origination of new genes is an important mechanism generating genetic novelties during the evolution of an organism. Processes of creating new genes using preexisting genes as the raw materials are well characterized, such as exon shuffling, gene duplication, retroposition, gene fusion, and fission. However, the process of how a new gene is de novo created from noncoding sequence is largely unknown. On the basis of genome comparison among yeast species, we have identified a new de novo protein-coding gene, BSC4 in Saccharomyces cerevisiae. The BSC4 gene has an open reading frame (ORF) encoding a 132-amino-acid-long peptide, while there is no homologous ORF in all the sequenced genomes of other fungal species, including its closely related species such as S. paradoxus and S. mikatae. The functional protein-coding feature of the BSC4 gene in S. cerevisiae is supported by population genetics, expression, proteomics, and synthetic lethal data. The evidence suggests that BSC4 may be involved in the DNA repair pathway during the stationary phase of S. cerevisiae and contribute to the robustness of S. cerevisiae, when shifted to a nutrient-poor environment. Because the corresponding noncoding sequences in S. paradoxus, S. mikatae, and S. bayanus also transcribe, we propose that a new de novo protein-coding gene may have evolved from a previously expressed noncoding sequence.
Estimation of 2Nes From Temporal Allele Frequency Data
Authors: Bollback Jonathan P , York Thomas L , Nielsen Rasmus
Published: May 2008

We develop a new method for estimating effective population sizes, Ne, and selection coefficients, s, from time-series data of allele frequencies sampled from a single diallelic locus. The method is based on calculating transition probabilities, using a numerical solution of the diffusion process, and assuming independent binomial sampling from this diffusion process at each time point. We apply the method in two example applications. First, we estimate selection coefficients acting on the CCR5-Δ32 mutation on the basis of published samples of contemporary and ancient human DNA. We show that the data are compatible with the assumption of s = 0, although moderate amounts of selection acting on this mutation cannot be excluded. In our second example, we estimate the selection coefficient acting on a mutation segregating in an experimental phage population. We show that the selection coefficient acting on this mutation is ∼0.43.
Regulators of Cellular Levels of Histone Acetylation in Saccharomyces cerevisiae
Authors: Peng Weimin , Togawa Cynthia , Zhang Kangling , Kurdistani Siavash K
Published: May 2008

Histone acetylation levels are regulated through the opposing activities of histone acetyltransferases (HATs) and deacetylases (HDACs). While much is known about gene-specific control of histone acetylation, little is understood about how total or cellular levels of histone acetylation are regulated. To identify regulators of cellular levels of histone acetylation, we developed an immunofluorescence-based approach to screen the single-gene deletion library of Saccharomyces cerevisiae for strains with significant reductions in cellular histone acetylation levels. Of the 4848 mutants screened, we identified 63 strains with considerable cellular hypoacetylation of N-terminal lysines in histones H3 and H4. The cellular hypoacetylation was validated for subsets of the identified strains through secondary screens including mass spectrometric analysis of individual lysines and chromatin immunoprecipitation of specific genomic loci. Among the identified mutants were several members of the Ccr4-Not complex, V-type ATPases, and vacuolar protein-sorting complexes as well as genes with unknown functions. We show that Gcn5, a major HAT in yeast, has diminished histone acetyltransferase activity in particular mutants, providing a plausible explanation for reduction of cellular acetylation levels in vivo. Our findings have revealed unexpected and novel links between histone acetylation, Gcn5 HAT activity, and diverse processes such as transcription, cellular ion homeostasis, and protein transport.
Quantitative Trait Loci for Urinary Albumin in Crosses Between C57BL/6J and A/J Inbred Mice in the Presence and Absence of Apoe
Authors: Doorenbos Carolien , Tsaih Shirng-Wern , Sheehan Susan , Ishimori Naoki , Navis Gerjan , Churchill Gary , DiPetrillo Keith , Korstanje Ron
Published: May 2008

We investigated the effect of apolipoprotein E (Apoe) on albuminuria in the males of two independent F2 intercrosses between C57BL/6J and A/J mice, using wild-type inbred strains in the first cross and B6-Apoe−/− animals in the second cross. In the first cross, we identified three quantitative trait loci (QTL): chromosome (Chr) 2 [LOD 3.5, peak at 70 cM, confidence interval (C.I.) 28–88 cM]; Chr 9 (LOD 2.0, peak 5 cM, C.I. 5–25 cM); and Chr 19 (LOD 1.9, peak 49 cM, C.I. 23–54 cM). The Chr 2 and Chr 19 QTL were concordant with previously found QTL for renal damage in rat and human. The Chr 9 QTL was concordant with a locus found in rat. The second cross, testing only Apoe−/− progeny, did not identify any of these loci, but detected two other loci on Chr 4 (LOD 3.2, peak 54 cM, C.I. 29–73 cM) and Chr 6 (LOD 2.6, peak 33 cM, C.I. 11–61 cM), one of which was concordant with a QTL found in rat. The dependence of QTL detection on the presence of Apoe and the concordance of these QTL with rat and human kidney disease QTL suggest that Apoe plays a role in renal damage.
Coincidence of P-Insertion Sites and Breakpoints of Deletions Induced by Activating P Elements in Drosophila
Authors: Sudi Jyotsna , Zhang Sen , Intrieri Gino , Hao Ximing , Zhang Ping
Published: May 2008

We isolated a set of seven deletions in the 67B region by activating a nearby P-element insertion. The structures of the deletions were characterized by cloning and sequencing. The results showed that the P-induced deletions occurred nonrandomly in the genomic sites. One breakpoint of the deletions was located precisely at the end of the starting element, i.e., at the end of the inverted terminal repeats. The other breakpoint was nearby the retained starting element and coincided with preferential P-element insertion sites that harbor transcription initiation activities. It is known that P elements induce male recombination near the starting elements, giving rise to deletions with one breakpoint precisely located at an inverted terminal repeat of the retained starting element. Database analyses further revealed that deletions generated in P-induced male recombination also contained the other breakpoint in genomic regions that coincided with preferential P-insertion sites. The results suggest that nonrandom distribution of the deletion breakpoints is characteristic of the mechanism by which P elements induce deletions near the starting elements.
Expressed Sequence Tags With cDNA Termini: Previously Overlooked Resources for Gene Annotation and Transcriptome Exploration in Chlamydomonas reinhardtii
Authors: Liang Chun , Liu Yuansheng , Liu Lin , Davis Adam C , Shen Yingjia , Li Qingshun Quinn
Published: May 2008

Many of Chlamydomonas reinhardtii expressed sequence tags (ESTs) in GenBank dbEST and community EST assemblies were either over- or undertrimmed in terms of their cDNA termini, which are defined as the diagnostic sequence elements that delineate 3′/5′ ends of mRNA transcripts. Overtrimming represents a loss of directional, positional, and structural information of transcript ends whereas undertrimming causes unclean spurious sequences retained in ESTs that exert deleterious impacts on downstream EST-based applications. We examined 309,278 raw EST sequencing trace files of C. reinhardtii and found that only 57% had cDNA termini that matched the expected structures specified in their cDNA library constructions while satisfying our minimum length requirement for their final clean sequences. Using GMAP, 156,963 individual ESTs were mapped to the genome successfully, with their in silico-verified cDNA termini anchored to the genome. Our data analysis suggested strong macro- and microheterogeneity of 3′/5′ end positions of individual transcripts derived from the same genes in C. reinhardtii. This work annotating differential ends of individual transcripts in the draft genome presents the research community with a new stream of data that will facilitate accurate determination of gene structures, genome annotation, and exploration of the transcriptome and mRNA metabolism in C. reinhardtii.
The Chloroplast Protein Translocation Complexes ofChlamydomonas reinhardtii: A Bioinformatic Comparison of Toc and Tic Components in Plants, Green Algae and Red Algae
Authors: Kalanon Ming , McFadden Geoffrey I
Published: May 2008

The recently completed genome of Chlamydomonas reinhardtii was surveyed for components of the chloroplast protein translocation complexes. Putative components were identified using reciprocal BlastP searches with the protein sequences of Arabidopsis thaliana as queries. As a comparison, we also surveyed the new genomes of the bryophyte Physcomitrella patens, two prasinophyte green algae (Ostreococcus lucimarinus and Ostreococcus tauri), the red alga Cyanidioschizon merolae, and several cyanobacteria. Overall, we found that the components of the import pathway are remarkably well conserved, particularly among the Viridiplantae lineages. Specifically, C. reinhardtii contained almost all the components found in A. thaliana, with two exceptions. Missing from C. reinhardtii are the C-terminal ferredoxin-NADPH-reductase (FNR) binding domain of Tic62 and a full-length, TPR-bearing Toc64. Further, the N-terminal domain of C. reinhardtii Toc34 is highly acidic, whereas the analogous region in C. reinhardtii Toc159 is not. This reversal of the vascular plant model may explain the similarity of C. reinhardtii chloroplast transit peptides to mitochondrial-targeting peptides. Other findings from our genome survey include the absence of Tic22 in both Ostreococcus genomes; the presence of only one Toc75 homolog in C. merolae; and, finally, a distinctive propensity for gene duplication in P. patens.
Contrasting Patterns of Transposable-Element Insertion Polymorphism and Nucleotide Diversity in Autotetraploid and Allotetraploid Arabidopsis Species
Authors: Hazzouri Khaled M , Mohajer Arezou , Dejak Steven I , Otto Sarah P , Wright Stephen I
Published: May 2008

It has been hypothesized that polyploidy permits the proliferation of transposable elements, due to both the masking of deleterious recessive mutations and the breakdown of host silencing mechanisms. We investigated the patterns of insertion polymorphism of an Ac-like transposable element and nucleotide diversity at 18 gene fragments in the allotetraploid Arabidopsis suecica and the autotetraploid A. arenosa. All identified insertions were fixed in A. suecica, and many were clearly inherited from the parental species A. thaliana or A. arenosa. These results are inconsistent with a rapid increase in transposition associated with hybrid breakdown but support the evidence from nucleotide polymorphism patterns of a recent single origin of this species leading to genomewide fixations of transposable elements. In contrast, most insertions were segregating at very low frequencies in A. arenosa samples, showing a significant departure from neutrality in favor of purifying selection, even when we account for population subdivision inferred from sequence variation. Patterns of nucleotide variation at reference genes are consistent with the TE results, showing evidence for higher effective population sizes in A. arenosa than in related diploid taxa but a near complete population bottleneck associated with the origins of A. suecica.
Genetic Characterization of the Drosophila jaguar322 Mutant Reveals That Complete Myosin VI Loss of Function Is Not Lethal
Authors: Morrison Julie K , Miller Kathryn G
Published: May 2008

Myosin VI is an actin-based motor that has been implicated in many cellular processes. Studies in vertebrates have demonstrated that animals lacking this ubiquitously expressed myosin are viable. However in Drosophila, myosin VI loss of function has been thought to be lethal. We show here that complete loss of myosin VI is not lethal in flies and that the previously reported lethality of the null mutation (jar322) is most likely due to deletion of a neighboring gene. Maternally provided myosin VI does not account for the survival of myosin VI null animals. Mutant animals are recovered at a lower than expected Mendelian frequency, suggesting that myosin VI participates in processes which contribute to normal development, but its participation is not essential.
The Peroxiredoxin and Glutathione Peroxidase Families in Chlamydomonas reinhardtii
Authors: Dayer Régine , Fischer Beat B , Eggen Rik I L , Lemaire Stéphane D
Published: May 2008

Thiol/selenol peroxidases are ubiquitous nonheme peroxidases. They are divided into two major subfamilies: peroxiredoxins (PRXs) and glutathione peroxidases (GPXs). PRXs are present in diverse subcellular compartments and divided into four types: 2-cys PRX, 1-cys PRX, PRX-Q, and type II PRX (PRXII). In mammals, most GPXs are selenoenzymes containing a highly reactive selenocysteine in their active site while yeast and land plants are devoid of selenoproteins but contain nonselenium GPXs. The presence of a chloroplastic 2-cys PRX, a nonselenium GPX, and two selenium-dependent GPXs has been reported in the unicellular green alga Chlamydomonas reinhardtii. The availability of the Chlamydomonas genome sequence offers the opportunity to complete our knowledge on thiol/selenol peroxidases in this organism. In this article, Chlamydomonas PRX and GPX families are presented and compared to their counterparts in Arabidopsis, human, yeast, and Synechocystis sp. A summary of the current knowledge on each family of peroxidases, especially in photosynthetic organisms, phylogenetic analyses, and investigations of the putative subcellular localization of each protein and its relative expression level, on the basis of EST data, are presented. We show that Chlamydomonas PRX and GPX families share some similarities with other photosynthetic organisms but also with human cells. The data are discussed in view of recent results suggesting that these enzymes are important scavengers of reactive oxygen species (ROS) and reactive nitrogen species (RNS) but also play a role in ROS signaling.
Genome-Based Analysis of Chlamydomonas reinhardtii Exoribonucleases and Poly(A) Polymerases Predicts Unexpected Organellar and Exosomal Features
Authors: Zimmer Sara L , Fei Zhangjun , Stern David B
Published: May 2008

Enzymes from several gene families modify RNA molecules at their extremities. These reactions occur in several cellular compartments and affect every class of RNA. To assess the diversity of a subclass of these enzymes, we searched Chlamydomonas for open reading frames (ORFs) potentially encoding exoribonucleases, poly(A) polymerases, and proteins known to associate with and/or regulate them. The ORFs were further analyzed for indications of protein localization to the nucleus, cytosol, mitochondrion, and/or chloroplast. By comparing predicted proteins with homologs in Arabidopsis and yeast, we derived several tentative conclusions regarding RNA 5′- and 3′-end metabolism in Chlamydomonas. First, the alga possesses only one each of the following likely organellar enzymes: polynucleotide phosphorylase, hydrolytic exoribonuclease, poly(A) polymerase, and CCA transferase, a surprisingly small complement. Second, although the core of the nuclear/cytosolic exosome decay complex is well conserved, neither nucleus-specific activators nor the cytosolic exosome activators are present. Finally, our discovery of nine noncanonical poly(A) polymerases, a divergent family retaining the catalytic domains of conventional poly(A) polymerases, leads to the hypothesis that polyadenylation may play an especially important regulatory role throughout the Chlamydomonas cell, stabilizing some transcripts and targeting degradation machinery to others.
Variation and Evolution of Male Sex Combs in Drosophila: Nature of Selection Response and Theories of Genetic Variation for Sexual Traits
Authors: Ahuja Abha , Singh Rama S
Published: May 2008

We investigated the genetic architecture of variation in male sex comb bristle number, a rapidly evolving secondary sexual character of Drosophila. Twenty-four generations of divergent artificial selection for sex comb bristle number in a heterogeneous population of Drosophila melanogaster resulted in a significant response that was more pronounced in the direction of low bristle numbers. We observed a strong positive correlated response to selection in the corresponding female transverse bristle row. The correlated response in male abdominal and sternopleural bristle numbers, on the other hand, did not follow the same pattern as sex comb bristle number differences between selection lines. Relaxation-of-selection experiments along with mate choice and fecundity assays using the selection lines developed demonstrated the action of stabilizing selection on sex comb bristle number. Our results show (1) substantial genetic variation underlying sex comb bristle number variation; (2) a weak relationship between the sex comb and developmentally related, non-sex bristle systems; and (3) that sexual selection may be a driving force in sex comb evolution, indicating the potential of sex combs to diversify rapidly during population differentiation and speciation. We discuss the implications of these results for theories of genetic variation in display and nondisplay male sex traits.
Saccharomyces cerevisiae Yta7 Regulates Histone Gene Expression
Authors: Gradolatto Angeline , Rogers Richard S , Lavender Heather , Taverna Sean D , Allis C David , Aitchison John D , Tackett Alan J
Published: May 2008

The Saccharomyces cerevisiae Yta7 protein is a component of a nucleosome bound protein complex that maintains distinct transcriptional zones of chromatin. We previously found that one protein copurifying with Yta7 is the yFACT member Spt16. Epistasis analyses revealed a link between Yta7, Spt16, and other previously identified members of the histone regulatory pathway. In concurrence, Yta7 was found to regulate histone gene transcription in a cell-cycle-dependent manner. Association at the histone gene loci appeared to occur through binding of the bromodomain-like region of Yta7 with the N-terminal tail of histone H3. Our work suggests a mechanism in which Yta7 is localized to chromatin to establish regions of transcriptional silencing, and that one facet of this cellular mechanism is to modulate transcription of histone genes.
On the “NPD Ratio” as a Test for Crossover Interference
Authors: Stahl Franklin W
Published: May 2008

The “NPD ratio,” widely used by yeast geneticists, is of limited applicability and is prone to falsely indicate significant crossover interference in a chi-square test. A simple, better chi-square test for interference in two-factor crosses is described.
Functional Characterization of the Drosophila Hmt4-20/Suv4-20 Histone Methyltransferase
Authors: Sakaguchi Ayako , Karachentsev Dmitry , Seth-Pasricha Mansha , Druzhinina Marina , Steward Ruth
Published: May 2008

Di- and trimethylation of histone H4 lysine20 (H4K20) are thought to play an important role in controlling gene expression in vertebrates and in Drosophila. By inducing a null mutation in Drosophila Suv4-20, we show that it encodes the histone H4 lysine20 di- and trimethyltransferase. In Suv4-20 mutants, the H4K20 di- and trimethyl marks are strongly reduced or absent, and the monomethyl mark is significantly increased. We find that even with this biochemical function, Suv4-20 is not required for survival and does not control position-effect variegation (PEV).
Identification of New Quantitative Trait Loci (Other Than the PRNP Gene) Modulating the Scrapie Incubation Period in Sheep
Authors: Moreno C R , Cosseddu G M , Schibler L , Roig A , Moazami-Goudarzi K , Andreoletti O , Eychenne F , Lajous D , Schelcher F , Cribiu E P , Laurent P , Vaiman D , Elsen J M
Published: May 2008

Although susceptibility to scrapie is largely controlled by the PRNP gene, we have searched for additional genomic regions that affect scrapie incubation time in sheep, using two half-sib families with a susceptible PRNP genotype and naturally infected by scrapie. Quantitative trait loci were detected on OAR6 and OAR18.