bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhanced levels of stimulated Brillouin reflectivity from non-Maxwellian plasmas
Authors: BAWA'ANEH M.S. , BOYD T.J.M. 
Published: March 2006

Abstract.A model that counts for temperature gradients in the target plasma, which leads to higher ion acoustic noise and enhanced levels of stimulated Brillouin scattering (SBS) gain and SBS reflectivity, has been adopted. Enhanced Brillouin gain leading to higher SBS reflectivity levels has been computed for non-homogeneous, non-Maxwellian plasmas. SBS reflectivity levels obtained are higher than those predicted by linear convective gain theory by several orders of magnitude and coincide with the high values of experimental data known in literature, which could not be interpreted by the linear convective gain theory.
Rosetta error model for gene expression analysis
Authors: Weng Lee , Dai Hongyue , Zhan Yihui , He Yudong , Stepaniants Sergey B. , Bassett Douglas E. 
Published: March 2006

Abstract
Motivation: In microarray gene expression studies, the number of replicated microarrays is usually small because of cost and sample availability, resulting in unreliable variance estimation and thus unreliable statistical hypothesis tests. The unreliable variance estimation is further complicated by the fact that the technology-specific variance is intrinsically intensity-dependent.
Results: The Rosetta error model captures the variance-intensity relationship for various types of microarray technologies, such as single-color arrays and two-color arrays. This error model conservatively estimates intensity error and uses this value to stabilize the variance estimation.
We present two commonly used error models: the intensity error-model for single-color microarrays and the ratio error model for two-color microarrays or ratios built from two single-color arrays. We present examples to demonstrate the strength of our error models in improving statistical power of microarray data analysis, particularly, in increasing expression detection sensitivity and specificity when the number of replicates is limited.
Availability: Rosetta error models are available in the Rosetta Resolver® system for gene expression analysis. These technology-specific error models are designed and optimized for different microarray technologies, such as Affymetrix® and Agilent Technologies.
Contact: lee_weng@rosettabio.com
Supplementary information: Supplementary data and Appendices are available at Bioinformatics online.
ArabidopsisTEBICHI, with Helicase and DNA Polymerase Domains, Is Required for Regulated Cell Division and Differentiation in Meristems
Authors: Inagaki Soichi , Suzuki Takamasa , Ohto Masa-aki , Urawa Hiroko , Horiuchi Takashi , Nakamura Kenzo , Morikami Atsushi 
Published: March 2006

AbstractIn plant meristems, each cell divides and differentiates in a spatially and temporally regulated manner, and continuous organogenesis occurs using cells derived from the meristem. We report the identification of the Arabidopsis thaliana TEBICHI (TEB) gene, which is required for regulated cell division and differentiation in meristems. The teb mutants show morphological defects, such as short roots, serrated leaves, and fasciation, as well as defective patterns of cell division and differentiation in the meristem. The TEB gene encodes a homolog of Drosophila MUS308 and mammalian DNA polymerase θ, which prevent spontaneous or DNA damage–induced production of DNA double strand breaks. As expected from the function of animal homologs, teb mutants show constitutively activated DNA damage responses. Unlike other fasciation mutants with activated DNA damage responses, however, teb mutants do not activate transcriptionally silenced genes. teb shows an accumulation of cells expressing cyclinB1;1:GUS in meristems, suggesting that constitutively activated DNA damage responses in teb lead to a defect in G2/M cell cycle progression. Furthermore, other fasciation mutants, such as fasciata2 and tonsoku/mgoun3/brushy1, also show an accumulation of cells expressing cyclinB1;1:GUS in meristems. These results suggest that cell cycle progression at G2/M is important for the regulation of the pattern of cell division and of differentiation during plant development.
Nuclear Photosynthetic Gene Expression Is Synergistically Modulated by Rates of Protein Synthesis in Chloroplasts and Mitochondria
Authors: Pesaresi Paolo , Masiero Simona , Eubel Holger , Braun Hans-Peter , Bhushan Shashi , Glaser Elzbieta , Salamini Francesco , Leister Dario 
Published: March 2006

AbstractArabidopsis thaliana mutants prors1-1 and -2 were identified on the basis of a decrease in effective photosystem II quantum yield. Mutations were localized to the 5′-untranslated region of the nuclear gene PROLYL-tRNA SYNTHETASE1 (PRORS1), which acts in both plastids and mitochondria. In prors1-1 and -2, PRORS1 expression is reduced, along with protein synthesis in both organelles. PRORS1 null alleles (prors1-3 and -4) result in embryo sac and embryo development arrest. In mutants with the leaky prors1-1 and -2 alleles, transcription of nuclear genes for proteins involved in photosynthetic light reactions is downregulated, whereas genes for other chloroplast proteins are upregulated. Downregulation of nuclear photosynthetic genes is not associated with a marked increase in the level of reactive oxygen species in leaves and persists in the dark, suggesting that the transcriptional response is light and photooxidative stress independent. The mrpl11 and prpl11 mutants are impaired in the mitochondrial and plastid ribosomal L11 proteins, respectively. The prpl11 mrpl11 double mutant, but neither of the single mutants, resulted in strong downregulation of nuclear photosynthetic genes, like that seen in leaky mutants for PRORS1, implying that, when organellar translation is perturbed, signals derived from both types of organelles cooperate in the regulation of nuclear photosynthetic gene expression.
Reactive Oxygen Species Play a Role in Regulating a Fungus–Perennial Ryegrass Mutualistic Interaction
Authors: Tanaka Aiko , Christensen Michael J. , Takemoto Daigo , Park Pyoyun , Scott Barry 
Published: March 2006

AbstractAlthough much is known about the signals and mechanisms that lead to pathogenic interactions between plants and fungi, comparatively little is known about fungus–plant mutualistic symbioses. We describe a novel role for reactive oxygen species (ROS) in regulating the mutualistic interaction between a clavicipitaceous fungal endophyte, Epichloë festucae, and its grass host, Lolium perenne. In wild-type associations, E. festucae grows systemically in intercellular spaces of leaves as infrequently branched hyphae parallel to the leaf axis. A screen to identify symbiotic genes isolated a fungal mutant that altered the interaction from mutualistic to antagonistic. This mutant has a single-copy plasmid insertion in the coding region of a NADPH oxidase gene, noxA. Plants infected with the noxA mutant lose apical dominance, become severely stunted, show precocious senescence, and eventually die. The fungal biomass in these associations is increased dramatically, with hyphae showing increased vacuolation. Deletion of a second NADPH oxidase gene, noxB, had no effect on the E. festucae–perennial ryegrass symbiosis. ROS accumulation was detected cytochemically in the endophyte extracellular matrix and at the interface between the extracellular matrix and host cell walls of meristematic tissue in wild-type but not in noxA mutant associations. These results demonstrate that fungal ROS production is critical in maintaining a mutualistic fungus–plant interaction.
The D-Type Cyclin CYCD3;1 Is Limiting for the G1-to-S-Phase Transition inArabidopsis
Authors: Menges Margit , Samland Anne K. , Planchais Séverine , Murray James A.H. 
Published: March 2006

AbstractThe G1-to-S-phase transition is a key regulatory point in the cell cycle, but the rate-limiting component in plants is unknown. Overexpression of CYCLIN D3;1 (CYCD3;1) in transgenic plants increases mitotic cycles and reduces endocycles, but its effects on cell cycle progression cannot be unambiguously determined. To analyze the cell cycle roles of plant D-type cyclins, we overexpressed CYCD3;1 in Arabidopsis thaliana cell suspension cultures. Changes in cell number and doubling time were insignificant, but cultures exhibited an increased proportion of G2- over G1-phase cells, as well as increased G2 arrest in response to stationary phase and sucrose starvation. Synchronized cultures confirm that CYCD3;1-expressing (but not CYCD2;1-expressing) cells show increased G2-phase length and delayed activation of mitotic genes such as B-type cyclins, suggesting that CYCD3;1 has a specific G1/S role. Analysis of putative cyclin-dependent kinase phosphorylation sites within CYCD3;1 shows that mutating Ser-343 to Ala enhances CYCD3;1 potency without affecting its rate of turnover and results in a fivefold increase in the level of cell death in response to sucrose removal. We conclude that CYCD3;1 dominantly drives the G1/S transition, and in sucrose-depleted cells the decline in CYCD3;1 levels leads to G1 arrest, which is overcome by ectopic CYCD3;1 expression. Ser-343 is likely a key residue in modulating CYCD3;1 activity in response to sucrose depletion.
A family of oligopeptide transporters is required for growth of Candida albicans on proteins
Authors: Reuß Oliver , Morschhäuser Joachim 
Published: March 2006

SummaryThe human fungal pathogen Candida albicans can use proteins as the sole source of nitrogen for growth. The secretion of aspartic proteinases, which have been shown to contribute to virulence of C. albicans, allows the fungus to digest host proteins to produce peptides that must be taken up into the cell by specific transporters. To understand in more detail how C. albicans utilizes proteins as a nitrogen source, we undertook a comprehensive analysis of oligopeptide transporters encoded in the C. albicans genome. We identified eight OPT genes encoding putative oligopeptide transporters, almost all of which are represented by polymorphic alleles in strain SC5314. Expression of these genes was differentially induced when C. albicans was grown in YCB‐BSA medium, which contains bovine serum albumin as the sole nitrogen source. Whereas deletion of single OPT genes in strain SC5314 did not affect its ability to utilize proteins as a nitrogen source, opt123Δ triple mutants had a severe growth defect in YCB‐BSA which was rescued by reintroduction of a single copy of OPT1, OPT2 or OPT3. In addition, forced expression of OPT4 or OPT5 under control of the ADH1 promoter also restored growth of an opt123Δ mutant, demonstrating that at least OPT1‐OPT5 encode functional peptide transporters. The various oligopeptide transporters differ in their substrate preferences, as shown by the ability of strains expressing specific OPT genes to grow on peptides of defined length and sequence. We present evidence that in addition to the known role of oligopeptide transporters in the uptake of tetra‐ and pentapeptides these proteins can also transport longer peptides up to at least eight amino acids in length, ensuring an efficient utilization of the various peptides produced via endoproteolytic digestion of proteins by the secreted aspartic proteinases. As even transporters encoded by polymorphic alleles of a single gene exhibited differences in their efficiency to take up specific peptides, the oligopeptide transporters represent an example for how the evolution of gene families containing differentially expressed and functionally optimized members increases the nutritional versatility and, presumably, the adaptation of C. albicans to different host niches.
Evaluation of a Burdizzo Castrator for Neutering of Dogs
Authors: Ortega‐Pacheco A , Bolio‐González ME , Colin‐Flores RF , Sauri‐Arceo CH , Gutiérrez‐Blanco E , Jiménez‐Coello M , Linde Forsberg C 
Published: March 2006

ContentsA Burdizzo castrator was evaluated for the neutering of dogs. Histological and morphological changes of spermatic cells and peripheral serum testosterone after challenge with a GnRH‐analogue (gonadorelin) were assessed. There was a control group (G1), a surgically castrated group (G2) and a Burdizzo group (G3) divided in two, G3a receiving two crunches in each spermatic cord and G3b receiving one crunch in each spermatic cord. Sixteen days after application of the Burdizzo blood samples were taken from the dogs at 30 min interval during 2 h; after the second sample the dogs were treated with 1 μg/kg body weight of gonadorelin i.v. The same protocol of gonadorelin challenge was performed in G1 and G2 dogs. The G2 dogs were surgically castrated after the second blood sample, before the gonadorelin treatment, and the G1 dogs after the last blood sample. The excised gonads were examined histologically, and sperm smears were prepared from the caudae epididymidis. The testes and plexus pampiniformis of the G1 and G2 dogs had a normal histological appearance, and they had morphologically normal epididymal sperm cells. In all G3 dogs, there was an acute fibrosis with an inflammatory reaction in the plexus pampiniformis. The testes from the G3a dogs showed diffuse areas of infarction and degeneration of the parenchyma. Similar but less diffuse lesions were seen in group 3b dogs. The deferent ducts from all G3 dogs showed vasitis and/or sperm granulomas. Azoospermia or sperm malformations were observed in the epididymal smears from the G3 dogs. Testosterone concentration in the G1 dogs increased after gonadorelin application (p < 0.0001). The G2 dogs had basal testosterone levels after castration (p < 0.001) and did not respond to gonadorelin. Groups 3a and b showed a slight but non‐significant increase in testosterone concentration after gonadorelin challenge, supposedly due to the reduction of testicular blood flow and loss of testicular interstitial tissue.
Suppressed oxytocin neuron responses to immune challenge in late pregnant rats: a role for endogenous opioids
Authors: Brunton Paula J. , Sabatier Nancy , Leng Gareth , Russell John A. 
Published: March 2006

AbstractCytokine challenge (mimicking infection) with systemic interleukin‐1β (IL‐1β) stimulates oxytocin neurons via a noradrenergic brainstem pathway similar to that involved in parturition. As the responses of oxytocin neurons to several stimuli are reduced in late pregnancy, we have investigated whether responses to IL‐1β are also suppressed. In virgin Sprague–Dawley rats, IL‐1β (500 ng/kg i.v.) rapidly increased oxytocin secretion (3.2‐fold), via a central action as the firing rate of oxytocin neurons in the supraoptic nucleus was increased. In contrast, IL‐1β had no significant effect on the electrical or secretory activity of oxytocin neurons in late pregnant rats. In pregnancy activation of a central inhibitory opioid mechanism restrains oxytocin neuron responses to various stimuli. Accordingly, we tested the effects of the opioid antagonist, naloxone, on oxytocin neuron responses to IL‐1β in pregnancy. Naloxone (5 mg/kg i.v.) did not affect the oxytocin secretory response to IL‐1β in virgin rats, whereas in late pregnant rats naloxone revealed a greater oxytocin secretory response to IL‐1β (3.5‐fold) than in virgin rats. In virgin rats, naloxone decreased oxytocin neuron firing rate after IL‐1β, however, in pregnant rats naloxone increased the firing rate response to IL‐1β to the level seen in virgin rats. Thus, systemic IL‐1β acts centrally to increase oxytocin secretion. In pregnancy this response is suppressed by endogenous opioids, thus preserving neurohypophysial oxytocin stores for parturition and minimizing the risk of preterm labour. The exaggerated oxytocin secretory response to IL‐1β in pregnancy after naloxone reflects increased oxytocin stores and/or increased efficiency of excitation‐secretion coupling at the posterior pituitary.
Estimation of microbial cover distributions at Mammoth Hot Springs using a multiple clone library resampling method
Authors: Martín Héctor García , Goldenfeld Nigel 
Published: March 2006

SummaryWe propose the use of cover as a quick, low‐resolution proxy for the abundance of microbial species, which reduces polymerase chain reaction bias. We showcase this concept in a computation that uses clone library information from travertine‐forming hot springs in Yellowstone National Park to provide estimates of relative covers at different locations within the spring system. Samples were used from two media: the water column and the travertine substrate. The cover distribution is found to approximate a power law for samples within the water column. Significant commonality of species with the highest cover is observed in the water column for all locations, but not for species present in the substrate at different locations or between media at the same location.
Site‐specific variation in Antarctic marine biofilms established on artificial surfaces
Authors: Webster Nicole S. , Negri Andrew P. 
Published: March 2006

SummaryThe community structure and composition of marine microbial biofilms established on glass surfaces was investigated across three differentially contaminated Antarctic sites within McMurdo Sound. Diverse microbial communities were revealed at all sites using fluorescence in situ hybridization (FISH) and denaturing gradient gel electrophoresis (DGGE) techniques. Sequencing of excised DGGE bands demonstrated close affiliation with known psychrophiles or undescribed bacteria also recovered from the Antarctic environment. The majority of bacterial sequences were affiliated to the Gammaproteobacteria, Cytophaga/Flavobacteria of Bacteroidetes (CFB), Verrucomicrobia and Planctomycetales. Principal components analysis of quantitative FISH data revealed distinct differences in community composition between sites. Each of the sites were dominated by different bacterial groups: Alphaproteobacteria, Gammaproteobacteria and CFB at the least impacted site, Cape Armitage; green sulfur and sulfate reducing bacteria near the semi‐impacted Scott Base and Planctomycetales and sulfate reducing bacteria near the highly impacted McMurdo Station. The highest abundance of archaea was detected near Scott Base (2.5% of total bacteria). Multivariate analyses (non‐metric multidimensional scaling and analysis of similarities) of DGGE patterns revealed greater variability in community composition between sites than within sites. This is the first investigation of Antarctic biofilm structure and FISH results suggest that anthropogenic impacts may influence the complex composition of microbial communities.
Mutational Analysis of the
Saccharomyces cerevisiae
Cytochrome
c
Oxidase Assembly Protein Cox11p
Authors: Banting Graham S. , Glerum D. Moira 
Published: March 2006

ABSTRACT

Cox11p is an integral protein of the inner mitochondrial membrane that is essential for cytochrome
c
oxidase assembly. The bulk of the protein is located in the intermembrane space and displays high levels of evolutionary conservation. We have analyzed a collection of site-directed and random
cox11
mutants in an effort to further define essential portions of the molecule. Of the alleles studied, more than half had no apparent effect on Cox11p function. Among the respiration deficiency-encoding alleles, we identified three distinct phenotypes, which included a set of mutants with a misassembled or partially assembled cytochrome oxidase, as indicated by a blue-shifted cytochrome
aa
3
peak. In addition to the shifted spectral signal, these mutants also display a specific reduction in the levels of subunit 1 (Cox1p). Two of these mutations are likely to occlude a surface pocket behind the copper-binding domain in Cox11p, based on analogy with the
Sinorhizobium meliloti
Cox11 solution structure, thereby suggesting that this pocket is crucial for Cox11p function. Sequential deletions of the matrix portion of Cox11p suggest that this domain is not functional beyond the residues involved in mitochondrial targeting and membrane insertion. In addition, our studies indicate that Δ
cox11
, like Δ
sco1
, displays a specific hypersensitivity to hydrogen peroxide. Our studies provide the first evidence at the level of the cytochrome oxidase holoenzyme that Cox1p is the in vivo target for Cox11p and suggest that Cox11p may also have a role in the response to hydrogen peroxide exposure.
Genomic and Expression Analysis of the 3q25-q26 Amplification Unit Reveals TLOC1/SEC62 as a Probable Target Gene in Prostate Cancer
Authors: Jung Volker , Kindich Roland , Kamradt Jörn , Jung Martin , Müller Mirko , Schulz Wolfgang A. , Engers Rainer , Unteregger Gerhard , Stöckle Michael , Zimmermann Richard , Wullich Bernd 
Published: March 2006

Abstract
Gain at chromosome 3q25-q26 has been reported to commonly occur in prostate cancer. To map the 3q25-q26 amplification unit and to identify the candidate genes of amplification, we did fluorescence in situ hybridization and quantitative real-time PCR for gene copy number and mRNA expression measurements in prostate cancer cell lines and prostate cancer samples from radical prostatectomy specimens. The minimal overlapping region of DNA copy number gains in the cell lines could be narrowed down to 700 kb at 3q26.2. Of all positional and functional candidates in this region, the gene TLOC1/SEC62 revealed the highest frequency (50%) of copy number gains in the prostate cancer samples and was found to be up-regulated at the mRNA level in all samples analyzed. TLOC1/Sec62 protein was also shown to be overexpressed by Western blot analysis. Intriguingly, the TLOC1/SEC62 gene copy number was increased in prostate tumors from patients who had a lower risk of and a longer time to progression following radical prostatectomy. These findings make TLOC1/SEC62 the best candidate within the 3q amplification unit in prostate cancer. TLOC1/Sec62 protein is a component of the endoplasmic reticulum protein translocation machinery, whose function during prostate carcinogenesis remains to be determined. (Mol Cancer Res 2006;4(3):169–76)
VRK1 Signaling Pathway in the Context of the Proliferation Phenotype in Head and Neck Squamous Cell Carcinoma
Authors: Santos Claudio R. , Rodríguez-Pinilla María , Vega Francisco M. , Rodríguez-Peralto José L. , Blanco Sandra , Sevilla Ana , Valbuena Alberto , Hernández Teresa , van Wijnen André J. , Li Fengzhi , de Alava Enrique , Sánchez-Céspedes Montserrat , Lazo Pedro A. 
Published: March 2006

Abstract
The vaccinia-related kinase (VRK) proteins are a new family with three members in the human kinome. The VRK1 protein phosphorylates several transcription factors and has been postulated to be involved in regulation of cell proliferation. In normal squamous epithelium, VRK1 is expressed in the proliferation area. Because VRK1 can stabilize p53, the expression of the VRK1 protein was analyzed in the context of the p53 pathway and the proliferation phenotype in a series of 73 head and neck squamous cell carcinomas. VRK1 protein level positively correlated with p53 response proteins, particularly hdm2 and p21. The VRK1 protein also correlated positively with several proteins associated with proliferation, such as cyclin-dependent kinase 2 (CDK2), CDK6, cdc2, cyclins B1 and A, topoisomerase II, survivin, and Ki67. The level of VRK1 protein behaves like a proliferation marker in this series of head and neck squamous cell carcinomas. To identify a possible regulatory role for VRK1 and because it regulates gene transcription, the promoters of two genes were studied, CDK2 and SURVIVIN, whose proteins correlated positively with VRK1. VRK1 increases the activity of both the CDK2 and SURVIVIN gene promoters. The expression of VRK1 was analyzed in the context of regulators of the G1-S transition. VRK1 protein levels increase in response to E2F1 and are reduced by retinoblastoma and p16. These data suggest that VRK1 might play a role in cell cycle regulation and is likely to represent the beginning of a new control mechanism of cell cycle, particularly late in the G1-S phase. (Mol Cancer Res 2006;4(3):177–85)