bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Compatible-Solute-Binding Protein OpuAC from
Bacillus subtilis
: Ligand Binding, Site-Directed Mutagenesis, and Crystallographic Studies
Authors: Smits Sander H. J. , Höing Marina , Lecher Justin , Jebbar Mohamed , Schmitt Lutz , Bremer Erhard 
Published: June 2008

ABSTRACT

In the soil bacterium
Bacillus subtilis
, five transport systems work in concert to mediate the import of various compatible solutes that counteract the deleterious effects of increases in the osmolarity of the environment. Among these five systems, the ABC transporter OpuA, which catalyzes the import of glycine betaine and proline betaine, has been studied in detail in the past. Here, we demonstrate that OpuA is capable of importing the sulfobetaine dimethylsulfonioacetate (DMSA). Since OpuA is a classic ABC importer that relies on a substrate-binding protein priming the transporter with specificity and selectivity, we analyzed the OpuA-binding protein OpuAC by structural and mutational means with respect to DMSA binding. The determined crystal structure of OpuAC in complex with DMSA at a 2.8-Å resolution and a detailed mutational analysis of these residues revealed a hierarchy within the amino acids participating in substrate binding. This finding is different from those for other binding proteins that recognize compatible solutes. Furthermore, important principles that enable OpuAC to specifically bind various compatible solutes were uncovered.
Autoregulation ofswrAAand Motility inBacillus subtilis
Authors: Calvio Cinzia , Osera Cecilia , Amati Giuseppe , Galizzi Alessandro 
Published: June 2008

ABSTRACTWe demonstrate that transcription of the geneswrAA, required for swarming migration inBacillus subtilis, is driven by two promoters: asigD-dependent promoter and a putativesigA-dependent promoter, which is inactive during growth in liquid Luria-Bertani medium and becomes active in the presence of the phosphorylated form of the response regulator DegU or on semisolid surfaces. SincesigDtranscription is enhanced by SwrAA, this finding reveals thatswrAexpression is controlled by a positive feedback loop. We also demonstrate that the positive action of SwrAA in swimming and swarming motility is prevented in strains carrying a deletion of the two-component systemdegS-degUand that this effect is independent ofswrAAtranscription. Therefore, both DegU and SwrAA must be present to achieve full motility inB. subtilis.
The Uncharacterized Transcription Factor YdhM Is the Regulator of the
nemA
Gene, Encoding
N
-Ethylmaleimide Reductase
Authors: Umezawa Yoshimasa , Shimada Tomohiro , Kori Ayako , Yamada Kayoko , Ishihama Akira 
Published: June 2008

ABSTRACT

N
-Ethylmaleimide (NEM) has been used as a specific reagent of Cys modification in proteins and thus is toxic for cell growth. On the
Escherichia coli
genome, the
nemA
gene coding for NEM reductase is located downstream of the gene encoding an as-yet-uncharacterized transcription factor, YdhM. Disruption of the
ydhM
gene results in reduction of
nemA
expression even in the induced state, indicating that the two genes form a single operon. After in vitro genomic SELEX screening, one of the target recognition sequences for YdhM was identified within the promoter region for this
ydhM
-
nemA
operon. Both YdhM binding in vitro to the
ydhM
promoter region and transcription repression in vivo of the
ydhM-nemA
operon by YdhM were markedly reduced by the addition of NEM. Taken together, we propose that YdhM is the repressor for the
nemA
gene, thus hereafter designated NemR. The repressor function of NemR was inactivated by the addition of not only NEM but also other Cys modification reagents, implying that Cys modification of NemR renders it inactive. This is an addition to the mode of controlling activity of transcription factors by alkylation with chemical agents.
The Terminally Redundant, Nonpermuted Genome ofListeriaBacteriophage A511: a Model for the SPO1-Like Myoviruses of Gram-Positive Bacteria
Authors: Klumpp Jochen , Dorscht Julia , Lurz Rudi , Bielmann Regula , Wieland Matthias , Zimmer Markus , Calendar Richard , Loessner Martin J. 
Published: June 2008

ABSTRACTOnly little information on a particular class of myoviruses, the SPO1-like bacteriophages infecting low-G+C-content, gram-positive host bacteria (Firmicutes), is available. We present the genome analysis and molecular characterization of the large, virulent, broad-host-rangeListeriaphage A511. A511 contains a unit (informational) genome of 134,494 bp, encompassing 190 putative open reading frames (ORFs) and 16 tRNA genes, organized in a modular fashion common among theCaudovirales. Electron microscopy, enzymatic fragmentation analyses, and sequencing revealed that the A511 DNA molecule contains linear terminal repeats of a total of 3,125 bp, encompassing nine small putative ORFs. This particular genome structure explains why A511 is unable to perform general transduction. A511 features significant sequence homologies toListeriaphage P100 and other morphologically related phages infectingFirmicutessuch asStaphylococcusphage K andLactobacillusphage LP65. Equivalent but more-extensive terminal repeats also exist in phages P100 (∼6 kb) and K (∼20 kb). High-resolution electron microscopy revealed, for the first time, the presence of long tail fibers organized in a sixfold symmetry in these viruses. Mass spectrometry-based peptide fingerprinting permitted assignment of individual proteins to A511 structural components. On the basis of the data available for A511 and relatives, we propose that SPO1-like myoviruses are characterized by (i) their infection of gram-positive, low-G+C-content bacteria; (ii) a wide host range within the host bacterial genus and a strictly virulent lifestyle; (iii) similar morphology, sequence relatedness, and collinearity of the phage genome organization; and (iv) large double-stranded DNA genomes featuring nonpermuted terminal repeats of various sizes.
Precise Determination, Cross-Recognition, and Functional Analysis of the Double-Strand Origins of the Rolling-Circle Replication Plasmids in Haloarchaea
Authors: Zhou Ligang , Zhou Meixian , Sun Chaomin , Han Jing , Lu Qiuhe , Zhou Jian , Xiang Hua 
Published: June 2008

ABSTRACT

The precise nick site in the double-strand origin (DSO) of pZMX201, a 1,668-bp rolling-circle replication (RCR) plasmid from the haloarchaeon
Natrinema
sp. CX2021, was determined by electron microscopy and DSO mapping. In this plasmid, DSO nicking occurred between residues C404 and G405 within a heptanucleotide sequence (TCTC/GGC) located in the stem region of an imperfect hairpin structure. This nick site sequence was conserved among the haloarchaeal RCR plasmids, including pNB101, suggesting that the DSO nick site might be the same for all members of this plasmid family. Interestingly, the DSOs of pZMX201 and pNB101 were found to be cross-recognized in RCR initiation and termination in a hybrid plasmid system. Mutation analysis of the DSO from pZMX201 (DSO
Z
) in this hybrid plasmid system revealed that: (i) the nucleotides in the middle of the conserved TCTCGGC sequence play more-important roles in the initiation and termination process; (ii) the left half of the hairpin structure is required for initiation but not for termination; and (iii) a 36-bp sequence containing TCTCGGC and the downstream sequence is essential and sufficient for termination. In conclusion, these haloarchaeal plasmids, with novel features that are different from the characteristics of both single-stranded DNA phages and bacterial RCR plasmids, might serve as a good model for studying the evolution of RCR replicons.
UvrD and UvrD252 Counteract RecQ, RecJ, and RecFOR in a
rep
Mutant of
Escherichia coli
Authors: Lestini Roxane , Michel Bénédicte 
Published: June 2008

ABSTRACT

Rep and UvrD are two related
Escherichia coli
helicases, and inactivating both is lethal. Based on the observation that the synthetic lethality of
rep
and
uvrD
inactivation is suppressed in the absence of the recombination presynaptic proteins RecF, RecO, or RecR, it was proposed that UvrD is essential in the
rep
mutant to counteract a deleterious RecFOR-dependent RecA binding. We show here that the synthetic lethality of
rep
and
uvrD
mutations is also suppressed by
recQ
and
recJ
inactivation but not by
rarA
inactivation. Furthermore, it is independent of the action of UvrD in nucleotide excision repair and mismatch repair. These observations support the idea that UvrD counteracts a deleterious RecA binding to forks blocked in the
rep
mutant. An ATPase-deficient mutant of UvrD [
uvrD(R284A)
] is dominant negative in a
rep
mutant, but only in the presence of all RecQJFOR proteins, suggesting that the UvrD(R284A) mutant protein is deleterious when it counteracts one of these proteins. In contrast, the
uvrD252
mutant (G30D), which exhibits a strongly decreased ATPase activity, is viable in a
rep
mutant, where it allows replication fork reversal. We conclude that the residual ATPase activity of UvrD252 prevents a negative effect on the viability of the
rep
mutant and allows UvrD to counteract the action of RecQ, RecJ, and RecFOR at forks blocked in the
rep
mutant. Models for the action of UvrD at blocked forks are proposed.
Direct Visualization of the Outer Membrane of Mycobacteria and Corynebacteria in Their Native State
Authors: Zuber Benoît , Chami Mohamed , Houssin Christine , Dubochet Jacques , Griffiths Gareth , Daffé Mamadou 
Published: June 2008

ABSTRACT

The cell envelope of mycobacteria, which include the causative agents of tuberculosis and leprosy, is crucial for their success as pathogens. Despite a continued strong emphasis on identifying the multiple chemical components of this envelope, it has proven difficult to combine its components into a comprehensive structural model, primarily because the available ultrastructural data rely on conventional electron microscopy embedding and sectioning, which are known to induce artifacts. The existence of an outer membrane bilayer has long been postulated but has never been directly observed by electron microscopy of ultrathin sections. Here we have used cryo-electron microscopy of vitreous sections (CEMOVIS) to perform a detailed ultrastructural analysis of three species belonging to the
Corynebacterineae
suborder, namely,
Mycobacterium bovis
BCG,
Mycobacterium smegmatis
, and
Corynebacterium glutamicum
, in their native state. We provide new information that accurately describes the different layers of the mycobacterial cell envelope and challenges current models of the organization of its components. We show a direct visualization of an outer membrane, analogous to that found in gram-negative bacteria, in the three bacterial species examined. Furthermore, we demonstrate that mycolic acids, the hallmark of mycobacteria and related genera, are essential for the formation of this outer membrane. In addition, a granular layer and a low-density zone typifying the periplasmic space of gram-positive bacteria are apparent in CEMOVIS images of mycobacteria and corynebacteria. Based on our observations, a model of the organization of the lipids in the outer membrane is proposed. The architecture we describe should serve as a reference for future studies to relate the structure of the mycobacterial cell envelope to its function.
Genome-Wide Analysis of Ruminant
Staphylococcus aureus
Reveals Diversification of the Core Genome
Authors: Ben Zakour Nouri L. , Sturdevant Daniel E. , Even Sergine , Guinane Caitriona M. , Barbey Corinne , Alves Priscila D. , Cochet Marie-Françoise , Gautier Michel , Otto Michael , Fitzgerald J. Ross , Le Loir Yves 
Published: June 2008

ABSTRACT

Staphylococcus aureus
causes disease in humans and a wide array of animals. Of note,
S. aureus
mastitis of ruminants, including cows, sheep, and goats, results in major economic losses worldwide. Extensive variation in genome content exists among
S. aureus
pathogenic clones. However, the genomic variation among
S. aureus
strains infecting different animal species has not been well examined. To investigate variation in the genome content of human and ruminant
S. aureus
, we carried out whole-genome PCR scanning (WGPS), comparative genomic hybridizations (CGH), and the directed DNA sequence analysis of strains of human, bovine, ovine, and caprine origin. Extensive variation in genome content was discovered, including host- and ruminant-specific genetic loci. Ovine and caprine strains were genetically allied, whereas bovine strains were heterogeneous in gene content. As expected, mobile genetic elements such as pathogenicity islands and bacteriophages contributed to the variation in genome content between strains. However, differences specific for ruminant strains were restricted to regions of the conserved core genome, which contained allelic variation in genes encoding proteins of known and unknown function. Many of these proteins are predicted to be exported and could play a role in host-pathogen interactions. The genomic regions of difference identified by the whole-genome approaches adopted in the current study represent excellent targets for studies of the molecular basis of
S. aureus
host adaptation.
Locally produced C5a binds to T cell–expressed C5aR to enhance effector T-cell expansion by limiting antigen-induced apoptosis
Authors: Lalli Peter N. , Strainic Michael G. , Yang Min , Lin Feng , Medof M. Edward , Heeger Peter S. 
Published: June 2008

AbstractOur recent studies have shown that immune cell–produced complement provides costimulatory and survival signals to naive CD4+ T cells. Whether these signals are similarly required during effector cell expansion and what molecular pathways link locally produced complement to T-cell survival were not clarified. To address this, we stimulated monoclonal and polyclonal T cells in vitro and in vivo with antigen-presenting cells (APCs) deficient in the complement regulatory protein, decay accelerating factor (DAF), and/or the complement component C3. We found that T-cell expansion induced by DAF-deficient APCs was augmented with diminished T-cell apoptosis, whereas T-cell expansion induced by C3−/− APCs was reduced because of enhanced T-cell apoptosis. These effects were traced to locally produced C5a, which through binding to T cell–expressed C5aR, enhanced expression of Bcl-2 and prevented Fas up-regulation. The results show that C5aR signal transduction in T cells is important to allow optimal T-cell expansion, as well as to maintain naive cell viability, and does so by suppressing programmed cell death.
Solitary skull metastasis as initial manifestation of hepatocellular carcinoma
Authors: Shim Yu Shik , Ahn Jung Yong , Cho Jun Hyung , Lee Kyu Sung 
Published: June 2008

Abstract

Background
A solitary skull metastasis from hepatocellular carcinoma (HCC) prior to diagnosis of the primary tumor without liver dysfunction is a very rare event.

Case presentation
A 71-year-old male, without known liver disease, presented to our institution with a palpable occipital scalp mass. On brain magnetic resonance imaging (MRI), a highly enhanced and osteolytic skull tumor was observed. The histological diagnosis obtained from the percutaneous needle biopsy was a cranial metastasis from HCC. The metastatic tumor was removed via occipital craniectomy, and the two primary liver mass lesions were subsequently treated by transarterial chemoembolization.

Conclusion
An isolated skull metastasis may be the sole initial presentation of HCC. Early diagnosis is essential in order to treat the primary disease. A skull metastasis from HCC should be considered in the differential diagnosis in patients with subcutaneous scalp mass and osteolytic defects on X-ray.
Transcriptional patterns, biomarkers and pathways characterizing nasopharyngeal carcinoma of Southern China
Authors: Fang Weiyi , Li Xin , Jiang Qingping , Liu Zhen , Yang Huiling , Wang Shuang , Xie Siming , Liu Qiuzhen , Liu Tengfei , Huang Jing , Xie Weibing , Li Zuguo , Zhao Yingdong , Wang Ena , Marincola Francesco M , Yao Kaitai 
Published: June 2008

Abstract

Background
The pathogenesis of nasopharyngeal carcinoma (NPC) is a complicated process involving genetic predisposition, Epstein-Bar Virus infection, and genetic alterations. Although some oncogenes and tumor suppressor genes have been previously reported in NPC, a complete understanding of the pathogenesis of NPC in the context of global gene expression, transcriptional pathways and biomarker assessment remains to be elucidated.

Methods
Total RNA from 32 pathologically-confirmed cases of poorly-differentiated NPC was divided into pools inclusive of four consecutive specimens and each pool (T1 to T8) was co-hybridized with pooled RNA from 24 normal non-cancerous nasopharyngeal tissues (NP) to a human 8K cDNA array platform. The reliability of microarray data was validated for selected genes by semi-quantitative RT-PCR and immunohistochemistry.

Results
Stringent statistical filtering parameters identified 435 genes to be up-regulated and 257 genes to be down-regulated in NPC compared to NP. Seven up-regulated genes including CYC1, MIF, LAMB3, TUBB2, UBE2C and TRAP1 had been previously proposed as candidate common cancer biomarkers based on a previous extensive comparison among various cancers and normal tissues which did not, however, include NPC or NP. In addition, nine known oncogenes and tumor suppressor genes, MIF, BIRC5, PTTG1, ATM, FOXO1A, TGFBR2, PRKAR1A, KLF5 and PDCD4 were identified through the microarray literature-based annotation search engine MILANO, suggesting these genes may be specifically involved in the promotion of the malignant conversion of nasopharyngeal epithelium. Finally, we found that these differentially expressed genes were involved in apoptosis, MAPK, VEGF and B cell receptor signaling pathways and other functions associated with cell growth, signal transduction and immune system activation.

Conclusion
This study identified potential candidate biomarkers, oncogenes/tumor suppressor genes involved in several pathways relevant to the oncogenesis of NPC. This information may facilitate the determination of diagnostic and therapeutic targets for NPC as well as provide insights about the molecular pathogenesis of NPC.
GMODWeb: a web framework for the generic model organism database
Authors: O'Connor Brian D , Day Allen , Cain Scott , Arnaiz Olivier , Sperling Linda , Stein Lincoln D 
Published: June 2008

AbstractThe Generic Model Organism Database (GMOD) initiative provides species-agnostic data models and software tools for representing curated model organism data. Here we describe GMODWeb, a GMOD project designed to speed the development of model organism database (MOD) websites. Sites created with GMODWeb provide integration with other GMOD tools and allow users to browse and search through a variety of data types. GMODWeb was built using the open source Turnkey web framework and is available from http://turnkey.sourceforge.net.
Multiple Part-Type Production in Robotic Cells: Equivalence of Two Real-World Models
Authors: Dawande Milind , Pinedo Michael , Sriskandarajah Chelliah 
Published: June 2008

We address the scheduling of operations in a robotic cell that produces multiple part-types. The objective is to obtain a cyclic schedule—a sequence of robot moves and an ordering of the parts—that minimizes the long-run average time to produce a part or, equivalently, maximizes the throughput. We consider two different models that are currently used in practice. The first is a single-gripper cell with a unit-capacity output buffer at each machine. The second is a bufferless dual-gripper cell. We focus our analysis on a widely used class of cyclic solutions, referred to as CRM cycles. The main outcome of our analysis is the equivalence of the two models (i.e., the maximum throughput is the same for both models) under conditions that are common in practice. The equivalence is established in two steps: (i) identification of a subset of dominating cyclic solutions for each model, and (ii) provision of a one-to-one mapping between these dominating cycles such that corresponding cycles have the same throughput. We also analyze the computational complexity of the throughput maximization problem for the two models. The enhanced capabilities (i.e., output buffers and dual gripper) of both models were motivated by a need to improve the throughput. However, the costs of acquiring these capabilities differ significantly. Our discussions with operations managers at a Dallas-area robotic cell manufacturer revealed that the total cost of designing and programming the robot's control mechanism for a cell with output buffers is about 20% less than that for a dual-gripper cell. The equivalence of the two models is, therefore, somewhat surprising and has significant practical implications. For cells that operationalize CRM cycles, the use of output buffers instead of a dual gripper can result in considerable savings without compromising throughput.
Within-Subject Variability and Analytic Imprecision of Insulinlike Growth Factor Axis and Collagen Markers: Implications for Clinical Diagnosis and Doping Tests
Authors: Nguyen Tuan V , Nelson Anne E , Howe Christopher J , Seibel Markus J , Baxter Robert C , Handelsman David J , Kazlauskas Ray , Ho Ken K 
Published: June 2008

AbstractBackground: The utility of insulinlike growth factor (IGF) axis and collagen markers for a growth hormone (GH) doping test in sport depends on their stability and reproducibility. We sought to determine short-term within-subject variability of these markers in a large cohort of healthy individuals.Methods: We measured IGF-I, IGF binding protein 3 (IGFBP-3), acid labile subunit (ALS), and the collagen markers N-terminal propeptide of type I procollagen (PINP), C-terminal telopeptide of type I collagen (ICTP), and N-terminal propeptide of type III procollagen (PIIINP) in serum samples obtained on multiple occasions (median 3 per participant) over a 2- to 3-week period from 1103 elite athletes (699 men, 404 women) ages 22.2 (5.2) years [mean (SD)]. We estimated between-subject and within-subject variances by mixed–effects ANOVA.Results: Within-subject variance accounted for 32% to 36% and 4% to 13% of the total variance in IGF markers and collagen markers, respectively. The within-subject CV ranged from 11% to 21% for the IGF axis markers and from 13% to 15% for the collagen markers. The index of individuality for the IGF axis markers was 0.66–0.76, and for the collagen markers, 0.26–0.45. For each marker, individuals with initial extreme measured values tended to regress toward the population mean in subsequent repeated measurements. We developed a Bayesian model to estimate the long-term probable value for each marker.Conclusions: These results indicate that in healthy individuals the within-subject variability was greater for IGF-I than for the collagen markers, and that where a single measurement is available, it is possible to estimate the long-term probable value of each of the markers by applying the Bayesian approach. Such an application can increase the reliability and decrease the cost of detecting GH doping.