bluuebunny/crossref_metadata_2025_split huggingface dataset:
Throughput and energy performance of TCP on a wideband CDMA air interface
Authors: Zorzi Michele , Rossi Michele , Mazzini Gianluca 
Published: January 2005

AbstractIn this paper, we present a study on the performance of TCP, in terms of both throughput and energy consumption, in the presence of a wideband CDMA radio interface typical of third generation wireless systems. The results show that the relationship between throughput and average error rate is largely independent of the network load, making it possible to introduce a universal throughput curve, empirically characterized, which gives throughput predictions for each value of the user error probability. Furthermore, the study of the energy efficiency shows the possibility to select an optimal power control threshold to maximize the trade‐off between throughput and energy, thereby potentially achieving very significant energy gains. Copyright © 2001 John Wiley & Sons, Ltd.
Performance evaluation of TCP algorithms in multi‐hop wireless packet networks
Authors: Xu Shugong , Saadawi Tarek 
Published: January 2005

AbstractWireless packet ad hoc networks are characterized by multi‐hop wireless connectivity and limited bandwidth competed among neighboring nodes. In this paper, we investigate and evaluate the performance of several prevalent TCP algorithms in this kind of network over the wireless LAN standard IEEE 802.11 MAC layer. After extensively comparing the existing TCP versions (including Tahoe, Reno, New Reno, Sack and Vegas) in simulations, we show that, in most cases, the Vegas version works best. We reveal the reason why other TCP versions perform worse than Vegas and show a method to avoid this by tuning a TCP parameter— maximum window size. Furthermore, we investigate the performance of these TCP algorithms when they run with the delayed acknowledgment (DA) option defined in IETF RFC 1122, which allows the TCP receiver to transmit an ACK for every two incoming packets. We show that the TCP connection can gain 15 to 32 per cent good‐put improvement by using the DA option. For all the TCP versions investigated in this work, the simulation results show that with the maximum window size set at approximately 4, TCP connections perform best and then all these TCP variants differ little in performance. Copyright © 2001 John Wiley & Sons, Ltd.
Using statistical data for reliable mobile communications
Authors: Jobin J. , Tripathi Satish K. , Faloutsos Michalis , Gokhale Swapna 
Published: January 2005

AbstractWe examine the extent to which statistical mobility information can increase the reliability of the service experienced by users in mobile networks. Interrupted or dropped calls are an aspect of reliability that stems from the mobility of users. An existing user can move to a cell where there are no resources available to support their call. A natural solution is the reservation of resources in multiple cells that the user is likely to move to. This scheme is calledselective reservationsand it relies on predicting the next move of the user. Recently, there has been some work on estimating the movement probabilities (also known as themobility profile) of the user. In this paper, we quantify the usefulness of the mobility profile to improve the reliability of the service perceived by the mobile users. We identify two parameters which characterize the profile:Accuracy and Focus. Accuracy expresses the probability that the host will move as we expect it to. Focus describes how well we can identify patterns in the movement of the users. In our simulations, we examine the effect of the quality of the predictions on the performance of the system. We show that Accuracy and Focus have great impact on the performance of selective reservations. We also show how flexibility in hand‐offs can help in decreasing the dropping probability, and how this can be facilitated by letting the users make a second try at moving in case it fails the first time. Copyright © 2001 John Wiley & Sons, Ltd.
Effect of crystal structure on the background intensity in XRF
Authors: Verkhovodov Petro O. 
Published: January 2005

AbstractA new model for the origin of diffraction peaks in x‐ray fluorescence was developed, using the concept of a virtual primary radiation source. The method offers the possibility of calculating the background intensity formed by characteristic radiation and bremsstrahlung. Bragg diffraction may significantly modify the intensity of primary radiation reflected by crystal planes of a polycrystalline material. Copyright © 2005 John Wiley & Sons, Ltd.
Identification and functional analysis of the Saccharomyces cerevisiae nicotinamidase gene, PNC1
Authors: Ghislain Michel , Talla Emmanuel , François Jean M. 
Published: January 2005

AbstractNicotinamidase (NAMase) from the budding yeast, Saccharomyces cerevisiae, was purified by Ni2+ affinity chromatography and gel filtration. N‐terminal microsequencing revealed sequence identity with a hypothetical polypeptide encoded by the yeast YGL037C open reading frame sharing 30% sequence identity with Escherichia coli pyrazinamidase/nicotinamidase. A yeast strain in which the NAMase gene, hereafter named PNC1, was deleted shows a decreased intracellular NAD+ concentration, consistent with the loss of NAMase activity in the null mutant. In wild‐type strains, NAMase activity is stimulated during the stationary phase of growth, by various hyperosmotic shocks or by ethanol treatment. Using a PPNC1::lacZ gene fusion, we have shown that this stimulation of NAMase activity results from increased levels of the protein and requires stress response elements in the 5′ non‐coding region of PNC1. These results suggest that NAMase helps yeast cells to adapt to various stress conditions and nutrient depletion, most likely via the activation of NAD‐dependent biological processes. Copyright © 2002 John Wiley & Sons, Ltd.
Phenotypic analysis of gene deletant strains for sensitivity to oxidative stress
Authors: Higgins Vincent J. , Alic Nazif , Thorpe Geoffrey W. , Breitenbach Michael , Larsson Veronica , Dawes Ian W. 
Published: January 2005

AbstractAscertaining the impact of inhibitors on the growth phenotype of yeast mutants can beuseful in elucidating the function of genes within the cell. Microtitre plates and robotics have been used to screen over 600 deletions from EUROSCARF, constructed in an FY1679 strain background, for sensitivity to various oxidants. These included the inorganic hydroperoxide, H2O2, an organic peroxide (cumene hydroperoxide) and a lipid hydroperoxide (linoleic acid hydroperoxide). These produce within the cell several different reactive oxygen species that can cause damage to DNA, proteins and lipids. Approximately 14% of deletants displayed sensitivity to at least one of the oxidants and there was also a distribution of deletants that showed sensitivity to all or different combinations of the oxidants. Deletants included genes encoding proteins involved in stress responses, heavy metal homeostasis and putative cell wall proteins. Although global mechanisms have been identified that provide general stress responses, these results imply that there are also distinct mechanisms involved in the protection of the cell against specific damage caused bydifferent oxidants. Further analysis of these genes may reveal unknown mechanisms protecting the cell against reactive oxygen species. Copyright © 2002 John Wiley & Sons, Ltd.
Involvement of Nst1p/YNL091w and Msl1p, a U2B″ splicing factor, in Saccharomyces cerevisiae salt tolerance
Authors: Goossens Alain , Forment Javier , Serrano Ramon 
Published: January 2005

AbstractCell tolerance to salt stress depends on many physiological functions, including the best characterized of osmotic adjustment, ion transport and sodium‐sensitive sulphate metabolism. From a screening designed to identify novel determinants of salt tolerance we have isolated the YNL091w gene, probably an Ascomycete‐specific gene encoding a protein of unknown function. This gene negatively affects salt tolerance and therefore has been designated NST1. The salt tolerance mechanism of nst1 mutants is novel because it is not related to osmoregulation, altered cation accumulation or sulphate metabolism. Genome‐wide two‐hybrid analysis has suggested that Nst1p interacts with the splicing factor Msl1p and, accordingly, the impact of NST1 on salt tolerance is dependent on a functional MSL1 gene. Loss of MSL1 and NST1 function has pleiotropic phenotypes including increased sensitivity to divalent cations (manganese and zinc) and to caffeine (a cell wall‐weakening agent). On the other hand, msl1 mutants but not nst1 mutants are sensitive to thiabendazole (a microtubule‐destabilizing agent) and to osmotic stress. Copyright © 2002 John Wiley & Sons, Ltd.
Analysis of the RAP1 protein binding to homogeneous telomeric repeats in Saccharomyces castellii
Authors: Wahlin Johan , Cohn Marita 
Published: January 2005

AbstractThe repressor activator protein 1 (RAP1) plays a role in telomere structure and function inS. cerevisiae. Here, the RAP1 homologue was identified and cloned from the budding yeast Saccharomyces castellii (scasRAP1). The scasRAP1 gene encodes a protein of 826 amino acids and shares an overall high degree of similarity with the S. cerevisiae RAP1 (scerRAP1). We demonstrate that the scasRAP1 is able to complement scerRAP1 in temperature‐sensitive S. cerevisiae strains and is able to function as a regulator to maintain the original telomere lengths. Binding analyses of the E. coli‐expressed scasRAP1 protein demonstrate that it needs two consecutive telomeric repeats in order to bind the S. castellii telomeric DNA sequences, and that it binds adjacent sites having a 16 bp centre‐to‐centre spacing. The binding affinity to telomeric DNA of several other yeasts is similar to that of scerRap1p. However, in contrast to scerRap1p, scasRap1p was found to bind the human telomeric sequence. Moreover, the scasRap1p was found to incorporate a variant repeat in its binding to the otherwise homogeneous telomeric DNA of S. castellii. This ability to bind various sites differing in DNA sequence indicates a high degree of adjustability in the binding of scasRap1p to DNA. The GenBank Accession No. for scasRAP1 is AF401990. Copyright © 2002 John Wiley & Sons, Ltd.
Efficient PCR‐based gene disruption in Saccharomyces strains using intergenic primers
Authors: Reid Robert J.D. , Sunjevaric Ivana , Kedacche Mehdi , Rothstein Rodney 
Published: January 2005

AbstractAn Erratum has been published for this article in Yeast 19(9) 2002, 803.Gene disruptions are a vital tool for understanding Saccharomyces cerevisiae gene function. An arrayed library of gene disruption strains has been produced by a consortium of yeast laboratories; however their use is limited to a single genetic background. Since the yeast research community works with several different strain backgrounds, disruption libraries in other common laboratory strains are desirable. We have developed simple PCR‐based methods that allow transfer of gene disruptions from the S288C‐derived strain library into any Saccharomyces strain. One method transfers the unique sequence tags that flank each of the disrupted genes and replaces the kanamycin resistance marker with a recyclable URA3 gene from Kluyveromyces lactis. All gene‐specific PCR amplifications for this method are performed using a pre‐existing set of primers that are commercially available. We have also extended this PCR technique to develop a second general gene disruption method suitable for any transformable strain of Saccharomyces. Copyright © 2002 John Wiley & Sons, Ltd.
ABC transporters Cdr1p, Cdr2p and Cdr3p of a human pathogen Candida albicans are general phospholipid translocators
Authors: Smriti  , Krishnamurthy S. , Dixit B.L. , Gupta C.M. , Milewski S. , Prasad R. 
Published: January 2005

AbstractWe have used fluorescent 7‐nitrobenz‐2‐oxa‐1,3‐diazol‐4‐yl (NBD)‐tagged phospholipid analogues, NBD‐PE (phosphatidylethanolamine), NBD‐PC (phosphatidylcholine) and NBD‐PS (phosphatidylserine), to demonstrate that Cdr1p and its other homologues, Cdr2p and Cdr3p, belonging to the ATP‐binding cassette (ABC) superfamily behave as general phospholipid translocators. Interestingly, CDR1 and CDR2, whose overexpression leads to azole resistance in C. albicans, elicit in‐to‐out transbilayer phospholipid movement, while CDR3, which is not involved in drug resistance, carries out‐to‐in translocation of phospholipids between the two monolayers of plasma membrane. Cdr1p, Cdr2p and Cdr3p could be further distinguished on the basis of their sensitivities to different inhibitors. For example, the in‐to‐out activity associated with Cdr1p and Cdr2p is energy‐dependent and sensitive to sulphydryl blocking agents such as N‐ethylmaleimide (NEM) and cytoskeleton disrupting agent cytochalasin E, while Cdr3p‐associated out‐to‐in activity is energy‐dependent but insensitive to NEM and cytochalasin E. We found that certain drugs, such as fluconazole, cycloheximide and miconazole, to which Cdr1p confers resistance could also affect in‐to‐out transbilayer movement of NBD‐PE, while the same drugs had no effect on Cdr3p‐mediated out‐to‐in translocation of NBD‐PE. The ineffectiveness of these drugs to affect Cdr3p mediated out‐to‐in phospholipid translocation further confirms the inherent difference in the directionality of phospholipid translocation between these pumps. Notwithstanding the role of some of the Cdrps in drug resistance, this study clearly demonstrates that these ABC transporters of C. albicans are phospholipid translocators and this function could represent one of the physiological functions of such large family of proteins. Copyright © 2002 John Wiley & Sons, Ltd.
HSP12 is essential for biofilm formation by a Sardinian wine strain of S. cerevisiae
Authors: Zara Severino , Antonio Farris G. , Budroni Marilena , Bakalinsky Alan T. 
Published: January 2005

AbstractSardinian sherry strains of S. cerevisiae form a biofilm on the surface of wine at the end of the ethanolic fermentation, when grape sugar is depleted and when further growth becomes dependent on access to oxygen. A point mutation in HSP12 or deletion of the entire gene results in inability to form this film. HSP12 encodes a heat‐shock protein previously foundby others to be active during stationary phase, in cells depleted for glucose, and in cells metabolizing ethanol and fatty acids, all conditions associated with sherry biofilms. The DNA sequence of HSP12 allele of strain Ar5‐H12 has GenBank Accession No. AY046957. Copyright © 2002 John Wiley & Sons, Ltd.
Overproduction of pentose phosphate pathway enzymes using a new CRE–loxP expression vector for repeated genomic integration in Saccharomyces cerevisiae
Authors: Johansson Björn , Hahn‐Hägerdal Bärbel 
Published: January 2005

AbstractTwo new vectors are described, the expression vector pB3 PGK and the CRE recombinase vector pCRE3. The pB3 PGK has a zeocin‐selectable marker flanked by loxP sequences and an expression cassette consisting of the strong PGK1 promoter and the GCY1 terminator. The S. cerevisiae genes RKI1, RPE1, TAL1 and TKL1 were cloned in pB3 PGK and integrated in the locus of the respective gene, resulting in overexpression of the genes. S. cerevisiae TMB 3026, simultaneously overexpressing the RKI1, RPE1, TAL1 and TKL1 genes, was created by successive integrations and removal of the loxP–zeocin–loxP cassette using pCRE3. The 2µ‐based pCRE3 carries the aureobasidin A, zeocin and URA3 markers. pCRE3 proved to be easily cured without active counter‐selection. The zeocin marker is present on both the pB3 PGK and on pCRE3, so that screening for zeocin sensitivity indicates both chromosomal marker loss and loss of the pCRE3 vector. This feature saves time, since only one screening step is needed between successive chromosomal integrations. Marker recycling did not lead to increased zeocin resistance, indicating that the zeocin marker could be used for more than four rounds of transformation. The use of the CRE/loxP system proved to be a practical strategy to overexpress multiple genes without exhausting available markers. Copyright © 2002 John Wiley & Sons, Ltd.
Decreasing acetic acid accumulation by a glycerol overproducing strain of Saccharomyces cerevisiae by deleting the ALD6 aldehyde dehydrogenase gene
Authors: Eglinton Jeffrey M. , Heinrich Anthony J. , Pollnitz Alan P. , Langridge Peter , Henschke Paul A. , de Barros Lopes Miguel 
Published: January 2005

AbstractGlycerol is a major fermentation product of Saccharomyces cerevisiae that contributes to the sensory character of wine. Diverting sugar to glycerol overproduction and away from ethanol production by overexpressing the glycerol 3‐phosphate dehydrogenase gene,GPD2, caused S. cerevisiae to produce more than twice as much acetic acid as the wild‐type strain (S288C background) in anaerobic cell culture. Deletion of the aldehyde dehydrogenase gene, ALD6, in wild‐type and GPD2 overexpressing strains (GPD2‐OP) decreased acetic acid production by three‐ and four‐fold, respectively. In conjunction with reduced acetic acid production, the GPD2‐OP ald6Δ strain produced more glycerol and less ethanol than the wild‐type. The growth rate and fermentation rate were similar for the modified and wild‐type strains, although the fermentation rate for the GPD2 ald6Δ strain was slightly less than that of the other strains from 24 h onwards. Analysis of the metabolome of the mutants revealed that genetic modification affected the production of some secondary metabolites of fermentation, including acids, esters, aldehydes and higher alcohols, many of which are flavour‐active in wine. Modification of GPD2 and ALD6 expression represents an effective strategy to increase the glycerol and decrease the ethanol concentration during fermentation, and alters the chemical composition of the medium such that, potentially, novel flavour diversity is possible. The implications for the use of these modifications in commercial wine production require further investigation in wine yeast strains. Copyright © 2002 John Wiley & Sons, Ltd.
The adaptive response of Saccharomyces cerevisiae to mercury exposure
Authors: Westwater John , McLaren Niall F. , Dormer Ulla H. , Jamieson Derek J. 
Published: January 2005

AbstractThe budding yeast Saccharomyces cerevisiae has been shown to possess a number of discrete but overlapping adaptive stress responses. We show here that yeast has an adaptive stress response towards mercury and that this response overlaps to some extent with the H2O2 and cadmium‐inducible stress responses. Expression of the yeast GSH1 gene, encoding γ‐glutamylcysteine synthetase, is known to be regulated by hydrogen peroxide; in this study we show that expression of a GSH1–lacZ reporter gene is shown to be regulated by exposure to heavy metals, such as mercury and cadmium. Other redox‐active metals, including copper and iron, were found not to induce GSH1 expression. We show that mercury‐mediated regulation of the GSH1 gene is not by the same mechanism used by cadmium. Moreover, our experiments suggest the possibility that the oxidative stress produced by mercury exposure is similar to that produced by treatment with H2O2, consistent with our finding that the Yap1 protein is also involved in the response of yeast towards mercury. Copyright © 2002 John Wiley & Sons, Ltd.
Inhibitory effect of nikkomycin Z on chitin synthases in Candida albicans
Authors: Kim Min‐Kyoung , Park Hyun‐Sook , Kim Chi‐Hwa , Park Hee‐Moon , Choi Wonja 
Published: January 2005

AbstractNikkomycin Z is a competitive inhibitor of chitin synthases in fungi. It has been reported that it inhibits chitin synthases (Chs) 1 and 3, but not 2, of Saccharomyces cerevisiae. In our study, we found that: (a) nikkomycin Z inhibited all three Chs isozymes of Candida albicans (CaChs). The IC50 value for CaChs1 is 15 µM, for CaChs2 0.8 µM, and for CaChs3 13 µM; (b) nikkomycin Z inhibits vegetative growth of C. albicans differently in different growth media; growth inhibition was observed on Spider and corn meal agar plate, but not on Lee's plate; (c) growth inhibition by nikkomycin Z accompanied by the absence of septum and cell wall chitin, which in turn brought about cell lysis. Nikkomycin Z did not lyse cells in Lee's media and lysis was partially prevented in the presence of sorbitol as an osmostabilizer in Spider medium. Therefore, nikkomycin Z prevented the formation of septum and cell wall chitin by inhibiting chitin synthase activities in a growth medium‐dependent manner. Copyright © 2002 John Wiley & Sons, Ltd.
Proliferation of the endoplasmic reticulum occurs normally in cells that lack a functional unfolded protein response
Authors: Larson Lynnelle L. , Parrish Mark L. , Koning Ann J. , Wright Robin L. 
Published: January 2005

AbstractIncreased expression of certain ER membrane proteins leads to biogenesis of novel ER membrane arrays. These structures provide models in which to explore the mechanisms by which cells control the size and organization of organelles in response to changing physiological demands. In yeast, elevated levels of HMG‐CoA reductase induce ER arrays known as karmellae. Cox and co‐workers (1997) discovered that karmellae assembly is toxic to ire1 mutants. These mutants are unable to initiate the unfolded protein response, which enables cells to adjust levels of ER chaperones in response to stresses. We sought to determine whether the karmellae‐dependent death of ire1 mutants was due to karmellae assembly or to increased levels of HMG‐CoA reductase activity. Unexpectedly, we found that ire1 cells could assemble normal levels of karmellae that were structurally identical to those of wild‐type cells. In addition, karmellae assembly did not itself induce the unfolded protein response. Certain ire1 strains produced significant numbers of transformants that were unable to utilize galactose as sole carbon source. These results suggest that the karmellae‐dependent death of certain ire1 strains may simply reflect their inability to grow on galactose. Copyright © 2002 John Wiley & Sons, Ltd.
Siderophore uptake by Candida albicans: effect of serum treatment and comparison with Saccharomyces cerevisiae
Authors: Lesuisse Emmanuel , Knight Simon A. B. , Camadro Jean‐Michel , Dancis Andrew 
Published: January 2005

AbstractIron uptake systems often function as virulence factors in pathogenic organisms. Candida albicans is a fungal pathogen that infects immunocompromised hosts, such as AIDS patients or granulocytopenic bone marrow transplant recipients. Here we show that iron uptake from siderophores occurs in C. albicans and is mediated by one or more high‐affinity transport systems. Iron carried on ferrioxamine B, triacethyl‐fusarinine, ferrichrome, or ferricrocin was actively taken up via a high‐affinity mechanism. The kinetic parameters of uptake were similar to those found in S. cerevisiae. Furthermore, for ferrichrome and ferrioxamine B, cellular uptake of fluorescent analogues was observed. In C. albicans, iron uptake from siderophores was regulated by iron availability, with iron deprivation inducing uptake. Serum exposure, which induces a morphogenic shift from yeast to filamentous forms known to be required for virulence, also resulted in induction of iron transport from ferrichrome‐type siderophores. In a tup1/tup1 strain which grows constitutively in the filamentous form, iron transport was derepressed for all siderophores tested. The genes mediating uptake and utilization of iron from siderophores in C. albicans have not been identified; however, the transcript abundance for CaSIT1 was regulated in a manner consistent with the pattern of iron uptake from ferrichrome‐type siderophores. Furthermore, CaSIT1 overexpression in S. cerevisiae resulted in inhibited siderophore iron uptake, suggesting that the expressed protein may interact with proteins of S. cerevisiae involved in iron uptake from siderophores. In summary, iron uptake from ferrichrome‐type siderophores was induced in filamentous C. albicans, and a potential role of this iron acquisition system in pathogenicity should be considered. Copyright © 2002 John Wiley & Sons, Ltd.