bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Evidence for the Importance of Protein Acetylation and Protein Deacetylation in the Halophilic Archaeon
Haloferax volcanii
Authors: Altman-Price Neta , Mevarech Moshe 
Published: December 2008

ABSTRACT

Protein acetylation and deacetylation reactions are involved in many regulatory processes in eukaryotes. Recently, it was found that similar processes occur in bacteria and archaea. Sequence analysis of the genome of the haloarchaeon
Haloferax volcanii
led to the identification of three putative protein acetyltransferases belonging to the Gcn5 family, Pat1, Pat2, and Elp3, and two deacetylases, Sir2 and HdaI. Intriguingly, the gene that encodes HdaI shares an operon with an archaeal histone homolog. We performed gene knockouts to determine whether the genes encoding these putative acetyltransferases and deacetylases are essential. A
sir2
deletion mutant was able to grow normally, whereas an
hdaI
deletion mutant was nonviable. The latter is consistent with the finding that trichostatin A, a specific inhibitor of HdaI, inhibits cell growth in a concentration-dependent manner. We also showed that each of the acetyltransferases by itself is dispensable for growth but that deletion of both
pat2
and
elp3
could not be achieved. The corresponding genes are therefore “synthetic lethals,” and the protein acetyltransferases probably have a common and essential substrate.
Ferredoxin-NADP
+
Reductase from
Pseudomonas putida
Functions as a Ferric Reductase
Authors: Yeom Jinki , Jeon Che Ok , Madsen Eugene L. , Park Woojun 
Published: December 2008

ABSTRACT

Pseudomonas putida
harbors two ferredoxin-NADP
+
reductases (Fprs) on its chromosome, and their functions remain largely unknown. Ferric reductase is structurally contained within the Fpr superfamily. Interestingly, ferric reductase is not annotated on the chromosome of
P. putida
. In an effort to elucidate the function of the Fpr as a ferric reductase, we used a variety of biochemical and physiological methods using the wild-type and mutant strains. In both the ferric reductase and flavin reductase assays, FprA and FprB preferentially used NADPH and NADH as electron donors, respectively. Two Fprs prefer a native ferric chelator to a synthetic ferric chelator and utilize free flavin mononucleotide (FMN) as an electron carrier. FprB has a higher
k
cat
/

K
m

value for reducing the ferric complex with free FMN. The growth rate of the
fprB
mutant was reduced more profoundly than that of the
fprA
mutant, the growth rate of which is also lower than the wild type in ferric iron-containing minimal media. Flavin reductase activity was diminished completely when the cell extracts of the
fprB
mutant plus NADH were utilized, but not the
fprA
mutant with NADPH. This indicates that other NADPH-dependent flavin reductases may exist. Interestingly, the structure of the NAD(P) region of FprB, but not of FprA, resembled the ferric reductase (Fre) of
Escherichia coli
in the homology modeling. This study demonstrates, for the first time, the functions of Fprs in
P. putida
as flavin and ferric reductases. Furthermore, our results indicated that FprB may perform a crucial role as a NADH-dependent ferric/flavin reductase under iron stress conditions.
Growth Phase- and Cell Division-Dependent Activation and Inactivation of the σ
32
Regulon in
Escherichia coli
Authors: Wagner Maria Anna , Zahrl Doris , Rieser Gernot , Koraimann Günther 
Published: December 2008

ABSTRACT

Alternative sigma factors allow bacteria to reprogram global transcription rapidly and to adapt to changes in the environment. Here we report on growth- and cell division-dependent σ
32
regulon activity in
Escherichia coli
in batch culture. By analyzing σ
32
expression in growing cells, an increase in σ
32
protein levels is observed during the first round of cell division after exit from stationary phase. Increased σ
32
protein levels result from transcriptional activation of the
rpoH
gene. After the first round of bulk cell division,
rpoH
transcript levels and σ
32
protein levels decrease again. The late-logarithmic phase and the transition to stationary phase are accompanied by a second increase in σ
32
levels and enhanced stability of σ
32
protein but not by enhanced transcription of
rpoH
. Throughout growth, σ
32
target genes show expression patterns consistent with oscillating σ
32
protein levels. However, during the transition to early-stationary phase, despite high σ
32
protein levels, the transcription of σ
32
target genes is downregulated, suggesting functional inactivation of σ
32
. It is deduced from these data that there may be a link between σ
32
regulon activity and cell division events. Further support for this hypothesis is provided by the observation that in cells in which FtsZ is depleted, σ
32
regulon activation is suppressed.
Regulation of Cyclic Lipopeptide Biosynthesis inPseudomonas fluorescensby the ClpP Protease
Authors: de Bruijn I. , Raaijmakers J. M. 
Published: December 2008

ABSTRACTCyclic lipopeptides produced byPseudomonasspecies exhibit potent surfactant and broad-spectrum antibiotic properties. Their biosynthesis is governed by large multimodular nonribosomal peptide synthetases, but little is known about the genetic regulatory network. This study provides, for the first time, evidence that the serine protease ClpP regulates the biosynthesis of massetolides, cyclic lipopeptides involved in swarming motility, biofilm formation, and antimicrobial activity ofPseudomonas fluorescensSS101. The results show that ClpP affects the expression ofluxR(mA), the transcriptional regulator of the massetolide biosynthesis genesmassABC, thereby regulating biofilm formation and swarming motility ofP. fluorescensSS101. Transcription ofluxR(mA) was significantly repressed in theclpPmutant, and introduction ofluxR(mA) restored, in part, massetolide biosynthesis and swarming motility of theclpPmutant. Site-directed mutagenesis and expression analyses indicated that the chaperone subunit ClpX and the Lon protease are not involved in regulation of massetolide biosynthesis and are transcribed independently ofclpP. Addition of Casamino Acids enhanced the transcription ofluxR(mA) andmassABCin theclpPmutant, leading to a partial rescue of massetolide production and swarming motility. The results further suggested that, at the transcriptional level, ClpP-mediated regulation of massetolide biosynthesis operates independently of regulation by the GacA/GacS two-component system. The role of amino acid metabolism and the putative mechanisms underlying ClpP-mediated regulation of cyclic lipopeptide biosynthesis, swarming motility, and growth inP. fluorescensare discussed.
MIXING OF QUANTUM WALKS ON GENERALIZED HYPERCUBES
Authors: BEST ANA , KLIEGL MARKUS , MEAD-GLUCHACKI SHAWN , TAMON CHRISTINO 
Published: December 2008

We study continuous-time quantum walks on graphs which generalize the hypercube. The only known family of graphs whose quantum walk instantaneously mixes to uniform is the Hamming graphs with small arities. We show that quantum uniform mixing on the hypercube is robust under the addition of perfect matchings but not much else. Our specific results include:• The graph obtained by augmenting the hypercube with an additive matching x ↦ x ⊕ η is instantaneous uniform mixing whenever |η| is even, but with a slower mixing time. This strictly includes the result of Moore and Russell1on the hypercube.• The class of Hamming graphs H(n,q) is not uniform mixing if and only if q ≥ 5. This is a tight characterization of quantum uniform mixing on Hamming graphs; previously, only the status of H(n,q) with q < 5 was known.• The bunkbed graph [Formula: see text] whose adjacency matrix is I ⊗ Qn+ X ⊗ Af, where Afis a [Formula: see text]-circulant matrix defined by a Boolean function f, is not uniform mixing if the Fourier transform of f has support of size smaller than 2n-1. This explains why the hypercube is uniform mixing and why the join of two hypercubes is not.Our work exploits the rich spectral structure of the generalized hypercubes and relies heavily on Fourier analysis of group-circulants.
MeanField analysis for the evaluation of gossip protocols
Authors: Bakhshi Rena , Cloth Lucia , Fokkink Wan , Haverkort Boudewijn R. 
Published: December 2008

Gossip protocols are designed to operate in very large, decentralised networks. A node in such a network bases its decision to interact (gossip) with another node on its partial view of the global system. Because of the size of these networks, analysis of gossip protocols is mostly done using simulation, which tend to be expensive in computation time and memory consumption.
We introduce mean-field analysis as an analytical method to evaluate gossip protocols. Nodes in the network are represented by small identical stochastic models. Joining all nodes would result in an enormous stochastic process. If the number of nodes goes to infinity, however, mean-field analysis allows us to replace this intractably large stochastic process by a small deterministic process. This process approximates the behaviour of very large gossip networks, and can be evaluated using simple matrix-vector multiplications.
A distributed evolutionary method to design scheduling policies for volunteer computing
Authors: Estrada Trilce , Fuentes Olac , Taufer Michela 
Published: December 2008

Volunteer Computing (VC) is a paradigm that takes advantage of idle cycles from computing resources donated by volunteers and connected through the Internet to compute large-scale, loosely coupled simulations. A big challenge in VC projects is the scheduling of work-units across heterogeneous, volatile, and error-prone computers. The design of efficient scheduling policies for VC projects involves subjective and time-demanding tuning that is driven by knowledge of the project designer. VC projects are in need of a faster and project-independent method to automate the scheduling design.
To automatically generate a scheduling policy, we must explore the extremely large space of syntactically valid policies. Given the size of this search space, exhaustive search is not feasible. Thus in this paper we propose to solve the problem using an evolutionary method to automatically generate a set of scheduling policies that are project-independent, minimize errors, and maximize throughput in VC projects. Our method includes a genetic algorithm where the representation of individuals, the fitness function, and the genetic operators are specifically tailored to get effective policies in a short time. The effectiveness of our method is evaluated with SimBA, a Simulator of BOINC Applications. In contrast with manually designed scheduling policies that often perform well only for the specific project they were designed for and require months of tuning, our resulting scheduling policies provide better overall throughput across the different VC projects considered in this work and were generated by our method in a time window of one week.
African Theology of Reconstruction: The Painful Realities and Practical Options!
Authors: Gunda Masiiwa Ragies 
Published: December 2008

AbstractReconstruction theology in Africa has been the latest theological project coming out of Africa, beginning in 1990 it has gradually established itself and from 2003 a number of publications have come out on the subject. This paper seeks to make an addition to this growing list of publications. In this paper, I question the validity of the blame of external forces for all the woes that Africa is going through now. I instead propose that a functional reconstruction theology should primarily tackle the evil that we commit against ourselves. When we deal with this evil we have a likelihood of bringing African people into a proper unified group that can stand together against foreign elements. I also take issue with the selection of Nehemiah as the model upon which we can do our reconstruction theology. It is in this context that this paper suggests the prophet Amos over and above Jesus as the right model needed to confront the sort of problems we face as Africans. There is need for the church in Africa to undergo a reconstruction of its own after which the church can lead in the African reconstruction. This paper brings to the fore the painful realities of internally perpetrated evils, which are bigger than has been appreciated in many earlier contributions.
Medication Reconciliation in Hospice: A Pilot Study
Authors: Kemp Leonette O. , Narula Priyanka , McPherson Mary Lynn , Zuckerman Ilene 
Published: December 2008

Background: The Joint Commission required implementation of medication reconciliation processes by January 2006. Medication reconciliation is the practice of acquiring an accurate medication history at each transitional point of care. Potential for errors increases with inaccurate medication histories. This study determined the extent of medication reconciliation errors in hospice. Methods: Patients were enrolled from 2 hospices in Maryland (January 2007). An initial medication history was completed by the nurse on hospice admission. The pharmacist did another medication history within 5 days of admission and compared the medication histories. All differences were reported as medication discrepancies. Results: There were 504 medication discrepancies. Medication omissions occurred most commonly. All patients had at least 1 medication discrepancy (average 8.7 per patient). Overall, 190 drug interactions were identified; most were moderately severe. Conclusion: Terminal patients often use numerous medications increasing the risk of medication errors. Accurate medication histories reduce errors and potential for harm.
IFN-γ, IL-4 and IL-13 modulate responsiveness of human airway smooth muscle cells to IL-13
Authors: Moynihan Barry J , Tolloczko Barbara , Bassam Souad El , Ferraro Pascale , Michoud Marie-Claire , Martin James G , Laberge Sophie 
Published: December 2008

AbstractBackgroundIL-13 is a critical mediator of allergic asthma and associated airway hyperresponsiveness. IL-13 acts through a receptor complex comprised of IL-13Rα1 and IL-4Rα subunits with subsequent activation of signal transducer and activator of transcription 6 (STAT6). The IL-13Rα2 receptor may act as a decoy receptor. In human airway smooth muscle (HASM) cells, IL-13 enhances cellular proliferation, calcium responses to agonists and induces eotaxin production. We investigated the effects of pre-treatment with IL-4, IL-13 and IFN-γ on the responses of HASM cells to IL-13.MethodsCultured HASM were examined for expression of IL-13 receptor subunits using polymerase chain reaction, immunofluorescence microscopy and flow cytometry. Effects of cytokine pre-treatment on IL-13-induced cell responses were assessed by looking at STAT6 phosphorylation using Western blot, eotaxin secretion and calcium responses to histamine.ResultsIL-13Rα1, IL-4Rα and IL-13Rα2 subunits were expressed on HASM cells. IL-13 induced phosphorylation of STAT6 which reached a maximum by 30 minutes. Pre-treatment with IL-4, IL-13 and, to a lesser degree, IFN-γ reduced peak STAT6 phosphorylation in response to IL-13. IL-13, but not IFN-γ, pre-treatment abrogated IL-13-induced eotaxin secretion. Pre-treatment with IL-4 or IL-13 abrogated IL-13-induced augmentation of the calcium transient evoked by histamine. Cytokine pre-treatment did not affect expression of IL-13Rα1 and IL-4Rα but increased expression of IL-13Rα2. An anti-IL-13Rα2 neutralizing antibody did not prevent the cytokine pre-treatment effects on STAT6 phosphorylation. Cytokine pre-treatment increased SOCS-1, but not SOCS-3, mRNA expression which was not associated with significant increases in protein expression.ConclusionPre-treatment with IL-4 and IL-13, but not IFN-γ, induced desensitization of the HASM cells to IL-13 as measured by eotaxin secretion and calcium transients to histamine. The mechanism of IL-4 and IL-13 induced desensitization does not appear to involve either downregulation of receptor expression or induction of the IL-13Rα2 or the SOCS proteins.
Biomphalaria glabrata transcriptome: cDNA microarray profiling identifies resistant- and susceptible-specific gene expression in haemocytes from snail strains exposed to Schistosoma mansoni
Authors: Lockyer Anne E , Spinks Jenny , Kane Richard A , Hoffmann Karl F , Fitzpatrick Jennifer M , Rollinson David , Noble Leslie R , Jones Catherine S 
Published: December 2008

Abstract

Background

Biomphalaria glabrata is an intermediate snail host for Schistosoma mansoni, one of the important schistosomes infecting man. B. glabrata/S. mansoni provides a useful model system for investigating the intimate interactions between host and parasite. Examining differential gene expression between S. mansoni-exposed schistosome-resistant and susceptible snail lines will identify genes and pathways that may be involved in snail defences.

Results
We have developed a 2053 element cDNA microarray for B. glabrata containing clones from ORESTES (Open Reading frame ESTs) libraries, suppression subtractive hybridization (SSH) libraries and clones identified in previous expression studies. Snail haemocyte RNA, extracted from parasite-challenged resistant and susceptible snails, 2 to 24 h post-exposure to S. mansoni, was hybridized to the custom made cDNA microarray and 98 differentially expressed genes or gene clusters were identified, 94 resistant-associated and 4 susceptible-associated. Quantitative PCR analysis verified the cDNA microarray results for representative transcripts. Differentially expressed genes were annotated and clustered using gene ontology (GO) terminology and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis. 61% of the identified differentially expressed genes have no known function including the 4 susceptible strain-specific transcripts. Resistant strain-specific expression of genes implicated in innate immunity of invertebrates was identified, including hydrolytic enzymes such as cathepsin L, a cysteine proteinase involved in lysis of phagocytosed particles; metabolic enzymes such as ornithine decarboxylase, the rate-limiting enzyme in the production of polyamines, important in inflammation and infection processes, as well as scavenging damaging free radicals produced during production of reactive oxygen species; stress response genes such as HSP70; proteins involved in signalling, such as importin 7 and copine 1, cytoplasmic intermediate filament (IF) protein and transcription enzymes such as elongation factor 1α and EF-2.

Conclusion
Production of the first cDNA microarray for profiling gene expression in B. glabrata provides a foundation for expanding our understanding of pathways and genes involved in the snail internal defence system (IDS). We demonstrate resistant strain-specific expression of genes potentially associated with the snail IDS, ranging from signalling and inflammation responses through to lysis of proteinacous products (encapsulated sporocysts or phagocytosed parasite components) and processing/degradation of these targeted products by ubiquitination.
Quantification of SLIT-ROBO transcripts in hepatocellular carcinoma reveals two groups of genes with coordinate expression
Authors: Avci Mehmet Ender , Konu Ozlen , Yagci Tamer 
Published: December 2008

Abstract

Background
SLIT-ROBO families of proteins mediate axon pathfinding and their expression is not solely confined to nervous system. Aberrant expression of SLIT-ROBO genes was repeatedly shown in a wide variety of cancers, yet data about their collective behavior in hepatocellular carcinoma (HCC) is missing. Hence, we quantified SLIT-ROBO transcripts in HCC cell lines, and in normal and tumor tissues from liver.

Methods
Expression of SLIT-ROBO family members was quantified by real-time qRT-PCR in 14 HCC cell lines, 8 normal and 35 tumor tissues from the liver. ANOVA and Pearson's correlation analyses were performed in R environment, and different clinicopathological subgroups were pairwise compared in Minitab. Gene expression matrices of cell lines and tissues were analyzed by Mantel's association test.

Results
Genewise hierarchical clustering revealed two subgroups with coordinate expression pattern in both the HCC cell lines and tissues: ROBO1, ROBO2, SLIT1 in one cluster, and ROBO4, SLIT2, SLIT3 in the other, respectively. Moreover, SLIT-ROBO expression predicted AFP-dependent subgrouping of HCC cell lines, but not that of liver tissues. ROBO1 and ROBO2 were significantly up-regulated, whereas SLIT3 was significantly down-regulated in cell lines with high-AFP background. When compared to normal liver tissue, ROBO1 was found to be significantly overexpressed, while ROBO4 was down-regulated in HCC. We also observed that ROBO1 and SLIT2 differentiated histopathological subgroups of liver tissues depending on both tumor staging and differentiation status. However, ROBO4 could discriminate poorly differentiated HCC from other subgroups.

Conclusion
The present study is the first in comprehensive and quantitative evaluation of SLIT-ROBO family gene expression in HCC, and suggests that the expression of SLIT-ROBO genes is regulated in hepatocarcinogenesis. Our results implicate that SLIT-ROBO transcription profile is bi-modular in nature, and that each module shows intrinsic variability. We also provide quantitative evidence for potential use of ROBO1, ROBO4 and SLIT2 for prediction of tumor stage and differentiation status.
mRNA expression of the DNA replication-initiation proteins in epithelial dysplasia and squamous cell carcinoma of the tongue
Authors: Li Jian-na , Feng Chong-jin , Lu Yong-jun , Li Hui-jun , Tu Zheng , Liao Gui-qing , Liang Chun 
Published: December 2008

Abstract

Background
The tongue squamous cell carcinomas (SCCs) are characterized by high mitotic activity, and early detection is desirable. Overexpression of the DNA replication-initiation proteins has been associated with dysplasia and malignancy. Our aim was to determine whether these proteins are useful biomarkers for assessing the development of tongue SCC.

Methods
We analyzed the mRNA expression of CDC6, CDT1, MCM2 and CDC45 in formalin-fixed, paraffin-embedded benign and malignant tongue tissues using quantitative real-time PCR followed by statistical analysis.

Results
We found that the expression levels are significantly higher in malignant SCC than mild precancerous epithelial dysplasia, and the expression levels in general increase with increasing grade of precancerous lesions from mild, moderate to severe epithelial dysplasia. CDC6 and CDC45 expression is dependent of the dysplasia grade and lymph node status. CDT1 expression is higher in severe dysplasia than in mild and moderate dysplasia. MCM2 expression is dependent of the dysplasia grade, lymph node status and clinical stage. The expression of the four genes is independent of tumor size or histological grade. A simple linear regression analysis revealed a linear increase in the mRNA levels of the four genes from the mild to severe dysplasia and SCC. A strong association was established between CDC6 and CDT1, and between MCM2 and CDC45 expression. The nonparametric receiver operating characteristic analysis suggested that MCM2 and CDC45 had a higher accuracy than CDC6 and CDT1 for distinguishing dysplasia from tongue SCC.

Conclusion
These proteins can be used as biomarkers to distinguish precancerous dysplasia from SCC and are useful for early detection and diagnosis of SCC as an adjunct to clinicopathological parameters.