bluuebunny/crossref_metadata_2025_split huggingface dataset:
Atypical Roles for
Campylobacter jejuni
Amino Acid ATP Binding Cassette Transporter Components PaqP and PaqQ in Bacterial Stress Tolerance and Pathogen-Host Cell Dynamics
Authors: Lin Ann E. , Krastel Kirsten , Hobb Rhonda I. , Thompson Stuart A. , Cvitkovitch Dennis G. , Gaynor Erin C. 
Published: August 2009

ABSTRACT

Campylobacter jejuni
is a human pathogen causing severe diarrheal disease; however, our understanding of the survival of
C. jejuni
during disease and transmission remains limited. Amino acid ATP binding cassette (AA-ABC) transporters in
C. jejuni
have been proposed as important pathogenesis factors. We have investigated a novel AA-ABC transporter system, encoded by cj0467 to cj0469, by generating targeted deletions of cj0467 (the membrane transport component) and cj0469 (the ATPase component) in
C. jejuni
81-176. The analyses described here have led us to designate these genes
paqP
and
paqQ
, respectively (pathogenesis-associated glutamine [
q
] ABC transporter permease [
P
] and ATPase [
Q
]). We found that loss of either component resulted in amino acid uptake defects, most notably diminished glutamine uptake. Altered resistance to a series of environmental and in vivo stresses was also observed: both mutants were hyperresistant to aerobic and organic peroxide stress, and while the Δ
paqP
mutant was also hyperresistant to heat and osmotic shock, the Δ
paqQ
mutant was more susceptible than the wild type to the latter two stresses. The Δ
paqP
and Δ
paqQ
mutants also displayed a surprising but statistically significant increase in recovery from macrophages and epithelial cells in short-term intracellular survival assays. Annexin V, 4′,6-diamidino-2-phenylindole (DAPI), and Western blot analyses revealed that macrophages infected with the Δ
paqP
or Δ
paqQ
mutant exhibited transient but significant decreases in cell death and extracellular signal-regulated kinase-mitogen-activated protein kinase activation compared to levels in wild-type-infected cells. The Δ
paqP
mutant was not defective in either short-term or longer-term mouse colonization, consistent with its increased stress survival and diminished host cell damage phenotypes. Collectively, these results demonstrate a unique correlation of an AA-ABC transporter with bacterial stress tolerances and host cell responses to pathogen infection.
Comprehensive Evaluation of
Streptococcus sanguinis
Cell Wall-Anchored Proteins in Early Infective Endocarditis
Authors: Turner Lauren Senty , Kanamoto Taisei , Unoki Takeshi , Munro Cindy L. , Wu Hui , Kitten Todd 
Published: August 2009

ABSTRACT

Streptococcus sanguinis
is a member of the viridans group of streptococci and a leading cause of the life-threatening endovascular disease infective endocarditis. Initial contact with the cardiac infection site is likely mediated by
S. sanguinis
surface proteins. In an attempt to identify the proteins required for this crucial step in pathogenesis, we searched for surface-exposed, cell wall-anchored proteins encoded by
S. sanguinis
and then used a targeted signature-tagged mutagenesis (STM) approach to evaluate their contributions to virulence. Thirty-three predicted cell wall-anchored proteins were identified—a number much larger than those found in related species. The requirement of each cell wall-anchored protein for infective endocarditis was assessed in the rabbit model. It was found that no single cell wall-anchored protein was essential for the development of early infective endocarditis. STM screening was also employed for the evaluation of three predicted sortase transpeptidase enzymes, which mediate the cell surface presentation of cell wall-anchored proteins. The sortase A mutant exhibited a modest (∼2-fold) reduction in competitiveness, while the other two sortase mutants were indistinguishable from the parental strain. The combined results suggest that while cell wall-anchored proteins may play a role in
S. sanguinis
infective endocarditis, strategies designed to interfere with individual cell wall-anchored proteins or sortases would not be effective for disease prevention.
Memory T-Cell Responses to
Vibrio cholerae
O1 Infection
Authors: Weil Ana A. , Arifuzzaman Mohammad , Bhuiyan Taufiqur R. , LaRocque Regina C. , Harris Aaron M. , Kendall Emily A. , Hossain Azim , Tarique Abdullah A. , Sheikh Alaullah , Chowdhury Fahima , Khan Ashraful I. , Murshed Farhan , Parker Kenneth C. , Banerjee Kalyan K. , Ryan Edward T. , Harris Jason B. , Qadri Firdausi , Calderwood Stephen B. 
Published: August 2009

ABSTRACT

Vibrio cholerae
O1 can cause diarrheal disease that may be life-threatening without treatment. Natural infection results in long-lasting protective immunity, but the role of T cells in this immune response has not been well characterized. In contrast, robust B-cell responses to
V. cholerae
infection have been observed. In particular, memory B-cell responses to T-cell-dependent antigens persist for at least 1 year, whereas responses to lipopolysaccharide, a T-cell-independent antigen, wane more rapidly after infection. We hypothesize that protective immunity is mediated by anamnestic responses of memory B cells in the gut-associated lymphoid tissue, and T-cell responses may be required to generate and maintain durable memory B-cell responses. In this study, we examined B- and T-cell responses in patients with severe
V. cholerae
infection. Using the flow cytometric assay of the specific cell-mediated immune response in activated whole blood, we measured antigen-specific T-cell responses using
V. cholerae
antigens, including the toxin-coregulated pilus (TcpA), a
V. cholerae
membrane preparation, and the
V. cholerae
cytolysin/hemolysin (VCC) protein. Our results show that memory T-cell responses develop by day 7 after infection, a time prior to and concurrent with the development of B-cell responses. This suggests that T-cell responses to
V. cholerae
antigens may be important for the generation and stability of memory B-cell responses. The T-cell proliferative response to VCC was of a higher magnitude than responses observed to other
V. cholerae
antigens.
Borrelia burgdorferi
BmpA Is a Laminin-Binding Protein
Authors: Verma Ashutosh , Brissette Catherine A. , Bowman Amy , Stevenson Brian 
Published: August 2009

ABSTRACT

The
Borrelia burgdorferi
BmpA outer surface protein plays a significant role in mammalian infection by the Lyme disease spirochete and is an important antigen for the serodiagnosis of human infection.
B. burgdorferi
adheres to host extracellular matrix components, including laminin. The results of our studies indicate that BmpA and its three paralogous proteins, BmpB, BmpC, and BmpD, all bind to mammalian laminin. BmpA did not bind mammalian type I or type IV collagens or fibronectin. BmpA-directed antibodies significantly inhibited the adherence of live
B. burgdorferi
to laminin. The laminin-binding domain of BmpA was mapped to the carboxy-terminal 80 amino acids. Solubilized collagen inhibited BmpA-laminin binding, suggesting interactions through the collagen-binding domains of laminin. These results, together with previous data, indicate that BmpA and its paralogs are targets for the development of preventative and curative therapies for Lyme disease.
Pathogen Profiling: Rapid Molecular Characterization of
Staphylococcus aureus
by PCR/Electrospray Ionization-Mass Spectrometry and Correlation with Phenotype
Authors: Wolk Donna M. , Blyn Lawrence B. , Hall Thomas A. , Sampath Rangarajan , Ranken Raymond , Ivy Cristina , Melton Rachael , Matthews Heather , White Neill , Li Feng , Harpin Vanessa , Ecker David J. , Limbago Brandi , McDougal Linda K. , Wysocki Vicki H. , Cai Mian , Carroll Karen C. 
Published: August 2009

ABSTRACT

There are few diagnostic methods that readily distinguish among community-acquired methicillin (meticillin)-resistant
Staphylococcus aureus
strains, now frequently transmitted within hospitals. We describe a rapid and high-throughput method for bacterial profiling of staphylococcal isolates. The method couples PCR to electrospray ionization-mass spectrometry (ESI-MS) and is performed on a platform suitable for use in a diagnostic laboratory. This profiling technology produces a high-resolution genetic signature indicative of the presence of specific genetic elements that represent distinctive phenotypic features. The PCR/ESI-MS signature accurately identified genotypic determinants consistent with phenotypic traits in well-characterized reference and clinical isolates of
S. aureus
. Molecular identification of the antibiotic resistance genes correlated strongly with phenotypic in vitro resistance. The identification of toxin genes correlated with independent PCR analyses for the toxin genes. Finally, isolates were correctly classified into genotypic groups that correlated with genetic clonal complexes, repetitive-element-based PCR patterns, or pulsed-field gel electrophoresis types. The high-throughput PCR/ESI-MS assay should improve clinical management of staphylococcal infections.
Endophthalmitis Caused byVibrio alginolyticus
Authors: Li Xiao Chun , Xiang Zhen Yang , Xu Xiao Ming , Yan Wei Hua , Ma Jian Min 
Published: August 2009

ABSTRACTVibrio alginolyticusis a facultative anaerobic gram-negative bacillus found in normal marine flora. Ocular infections induced byV. alginolyticusare extremely rare. We report a case of endophthalmitis caused byV. alginolyticusto draw attention toV. alginolyticusinfections following ocular injuries.
Sharing of
Escherichia coli
Sequence Type ST131 and Other Multidrug-Resistant and Urovirulent
E. coli
Strains among Dogs and Cats within a Household
Authors: Johnson James R. , Miller Sybille , Johnston Brian , Clabots Connie , DebRoy Chitrita 
Published: August 2009

ABSTRACT

A multidrug-resistant (MDR)
Escherichia coli
strain from a human-associated pulsotype within sequence type ST131 (O25:H4) colonized three of five dogs and cats within a household. Of the four other colonizing strains identified, two were MDR and two colonized multiple hosts. The ST131 strain uniquely exhibited high resistance and virulence scores.
Sequence Analysis of Unusual P[7]G5 Bovine Rotavirus Strains Reveals Evidence of Interspecies Transmission
Authors: Ha Thi Phuong Mai , Kim Hyun-Jeong , Saif Linda J. , Jeong Young-Ju , Kim Ha-Hyun , Kwon Hyung-Jun , Park Su-Jin , Cho Kyoung-Oh 
Published: August 2009

ABSTRACT
By sequence and phylogenetic analyses, the 11 genomic segments of two bovine rotaviruses isolated from clinically infected calves were proven to be derived from the swine-like P[7]G5 genotype. This finding reinforced the hypothesis that interspecies transmission of completely heterologous strains can occur in nature.
Rhesus Theta-Defensin Prevents Death in a Mouse Model of Severe Acute Respiratory Syndrome Coronavirus Pulmonary Disease
Authors: Wohlford-Lenane Christine L. , Meyerholz David K. , Perlman Stanley , Zhou Haixia , Tran Dat , Selsted Michael E. , McCray Paul B. 
Published: August 2009

ABSTRACT
We evaluated the efficacy of rhesus theta-defensin 1 (RTD-1), a novel cyclic antimicrobial peptide, as a prophylactic antiviral in a mouse model of severe acute respiratory syndrome (SARS) coronavirus (CoV) lung disease. BALB/c mice exposed to a mouse-adapted strain of SARS-CoV demonstrated 100% survival and modest reductions in lung pathology without reductions in virus titer when treated with two intranasal doses of RTD-1, while mortality in untreated mice was ∼75%. RTD-1-treated, SARS-CoV-infected mice displayed altered lung tissue cytokine responses 2 and 4 days postinfection compared to those of untreated animals, suggesting that one possible mechanism of action for RTD-1 is immunomodulatory.
Genetic Heterogeneity and Recombination in Canine Noroviruses
Authors: Martella Vito , Decaro Nicola , Lorusso Eleonora , Radogna Arianna , Moschidou Paschalina , Amorisco Francesca , Lucente Maria Stella , Desario Costantina , Mari Viviana , Elia Gabriella , Banyai Krisztian , Carmichael Leland Eugene , Buonavoglia Canio 
Published: August 2009

ABSTRACTAlphatronlike (genogroup IV [GIV]) noroviruses (NoVs) have been recently identified in carnivores. By screening a collection of 183 fecal samples collected during 2007 from dogs with enteric signs, the overall NoV prevalence was found to be 2.2% (4/183). A unique strain, Bari/91/07/ITA, resembled GIV.2 NoVs in its ORF1 (polymerase complex), while it was genetically unrelated in its full-length ORF2 (capsid gene) to GIV animal and human NoVs (54.0 to 54.4% amino acid identity) and to any other NoV genogroup (<54.7% amino acid identity). It displayed the highest identity (58.1% amino acid identity) to unclassified human strain Chiba/040502/04/Jp. Interestingly, the very 5′ end of ORF2 of the canine virus matched short noroviral sequences (88.9% nucleotide identity and 98.9% amino acid identity) identified from oysters in Japan, indicating that similar viruses may be common environmental contaminants.
Mutational Analysis of the Bunyamwera Orthobunyavirus Nucleocapsid Protein Gene
Authors: Eifan Saleh A. , Elliott Richard M. 
Published: August 2009

ABSTRACT

The bunyavirus nucleocapsid protein, N, is a multifunctional protein that encapsidates each of the three negative-sense genome segments to form ribonucleoprotein complexes that are the functional templates for viral transcription and replication. In addition, N protein molecules interact with themselves to form oligomers, with the viral L (RNA polymerase) protein, with the carboxy-terminal regions of either or both of the virion glycoproteins, and probably also with host cell proteins. Bunyamwera virus (BUNV), the prototype bunyavirus, encodes an N protein of 233 amino acids in length. To learn more about the roles of individual amino acids in the different interactions of N, we performed a wide-scale mutagenic analysis of the protein, and 110 single-point mutants were obtained. When the mutants were employed in a minireplicon assay to examine their effects on viral RNA synthesis, a wide range of activities compared to those of wild-type N protein were observed; changes at nine amino acid positions resulted in severely impaired RNA synthesis. Seventy-seven mutant clones were selected for use in the bunyavirus reverse genetics system, and 57 viable recombinant viruses were recovered. The recombinant viruses displayed a range of plaque sizes and titers in cell culture (from approximately 10
3
to 10
8
PFU/ml), and a number of viruses were shown to be temperature sensitive. Different assays were applied to determine why 20 mutant N proteins could not be recovered into infectious virus. Based on these results, a preliminary domain map of the BUNV N protein is proposed.
Optimistic parallelism requires abstractions
Authors: Kulkarni Milind , Pingali Keshav , Walter Bruce , Ramanarayanan Ganesh , Bala Kavita , Chew L. Paul 
Published: August 2009

The problem of writing software for multicore processors is greatly simplified if we could automatically parallelize sequential programs. Although auto-parallelization has been studied for many decades, it has succeeded only in a few application areas such as dense matrix computations. In particular, auto-parallelization of irregular programs, which are organized around large, pointer-based data structures like graphs, has seemed intractable.
The Galois project is taking a fresh look at autoparallelization. Rather than attempt to parallelize all programs no matter how obscurely they are written, we are designing programming abstractions that permit programmers to highlight opportunities for exploiting parallelism in sequential programs, and building a runtime system that uses these hints to execute the program in parallel. In this paper, we describe the design and implementation of a system based on these ideas. Experimental results for two real-world irregular applications, a Delaunay mesh refinement application and a graphics application that performs agglomerative clustering, demonstrate that this approach is promising.
Efficient memory management for hardware accelerated Java Virtual Machines
Authors: Bertels Peter , Heirman Wim , D'Hollander Erik , Stroobandt Dirk 
Published: August 2009

Application-specific hardware accelerators can significantly improve a system's performance. In a Java-based system, we then have to consider a hybrid architecture that consists of a Java Virtual Machine running on a general-purpose processor connected to the hardware accelerator. In such a hybrid architecture, data communication between the accelerator and the general-purpose processor can incur a significant cost, which may even annihilate the original performance improvement of adding the accelerator. A careful layout of the data in the memory structure is therefore of major importance to maintain the acceleration performance benefits.
This article addresses the reduction of the communication cost in a distributed shared memory consisting of the main memory of the processor and the accelerator's local memory, which are unified in the Java heap. Since memory access times are highly nonuniform, a suitable allocation of objects in either main memory or the accelerator's local memory can significantly reduce the communication cost. We propose several techniques for finding the optimal location for each Java object's data, either statically through profiling or dynamically at runtime. We show how we can reduce communication cost by up to 86% for the SPECjvm and DaCapo benchmarks. We also show that the best strategy is application dependent and also depends on the relative cost of remote versus local accesses. For a relative cost higher than 10, a self-learning dynamic approach often results in the best performance.
Leakage-aware task scheduling for partially dynamically reconfigurable FPGAs
Authors: Yuh Ping-Hung , Yang Chia-Lin , Li Chi-Feng , Lin Chung-Hsiang 
Published: August 2009

As technology continues to shrink, reducing leakage power of Field-Programmable Gate Arrays (FPGAs) becomes a critical issue for the practical use of FPGAs. In this article, we address the leakage issue of partially dynamically reconfigurable FPGA architectures with sleep transistors embedded into FPGA fabrics. In particular, we focus on eliminating leakage waste due to the delay between reconfiguration and execution time of a task. For partially dynamically reconfigurable FPGAs, the configuration prefetching technique is commonly used to hide runtime reconfiguration overhead. With prefetching, the configuration of a task is loaded into FPGAs as early as possible. Therefore, there is often a delay between reconfiguration and execution time of a task. In this period of time, the SRAM cells allocated to a task cannot be turned off even though they are not utilized.
In this article, we propose a two-stage task scheduling methodology to reduce leakage waste due to the delay between reconfiguration and execution time of a task without sacrificing performance. In the first stage, a performance-driven task scheduler that targets at minimizing the schedule length is invoked to generate an initial placement. In the second stage, a postplacement leakage-aware task scheduling is applied to refine the initial placement such that leakage waste is minimized provided that the schedule length is not increased. To solve the postplacement leakage optimization problem, we propose two algorithms. The first one is an optimal algorithm based on Integer Linear Programming (ILP). The second algorithm is a heuristic approach that iteratively refines the placement to reduce leakage waste. Experimental results on real and synthetic designs show that the efficiency and effectiveness of the proposed postplacement leakage reduction techniques.
A Cloud-to-Ground Lightning Climatology for Romania
Authors: Antonescu Bogdan , Burcea Sorin 
Published: August 2009

Abstract
The first study of the characteristics of cloud-to-ground (CG) lightning in Romania, based on the data recorded by the Romanian National Lightning Detection Network (RNLDN), is presented. The data, more than 1.75 million CG flashes, covers the entirety of Romania and were recorded between January 2003 and December 2005 and January and December 2007. The spatial analyses (total and positive flash density, the percentage of positive flashes, and negative and positive peak currents) were done with a resolution of 20 km. The average spatial distribution shows a maximum (3.06 flashes km−2 yr−1) over the south slopes of the central meridional Carpathians possibly associated with the Romanian Plain convergence zone. The mean monthly variation shows maximum CG lightning between May and September (98%) and minimum values in December and January. High values (&gt;0.028 km−2 yr−1) for positive CG lightning density are observed in southwestern and central Romania. The monthly distribution of positive flashes shows a main maximum in May (25%) and a secondary maximum in August (23%), suggesting that positive flashes tend to occur earlier in the year than total flashes. The mean annual percentage of positive flashes has lower values at 1.3% in the central parts of the country. The percentage of positive CG flashes changes over the year from 1% in June to 19% in January. The monthly variation of the median first-strike peak currents has a maximum in winter and reaches a minimum in July, for both negative and positive currents. The mean diurnal cycle for total CG lightning flashes peaks between 1230 and 1430 UTC (2.2%) and shows a minimum between 0600 and 0800 UTC (0.3%).
Different NK cell–activating receptors preferentially recruit Rab27a or Munc13-4 to perforin-containing granules for cytotoxicity
Authors: Wood Stephanie M. , Meeths Marie , Chiang Samuel C. C. , Bechensteen Anne Grete , Boelens Jaap J. , Heilmann Carsten , Horiuchi Hisanori , Rosthøj Steen , Rutynowska Olga , Winiarski Jacek , Stow Jennifer L. , Nordenskjöld Magnus , Henter Jan-Inge , Ljunggren Hans-Gustaf , Bryceson Yenan T. 
Published: August 2009

AbstractThe autosomal recessive immunodeficiencies Griscelli syndrome type 2 (GS2) and familial hemophagocytic lymphohistiocytosis type 3 (FHL3) are associated with loss-of-function mutations in RAB27A (encoding Rab27a) and UNC13D (encoding Munc13-4). Munc13-4 deficiency abrogates NK-cell release of perforin-containing lytic granules induced by signals for natural and antibody-dependent cellular cytotoxicity. We demonstrate here that these signals fail to induce degranulation in resting NK cells from Rab27a-deficient patients. In resting NK cells from healthy subjects, endogenous Rab27a and Munc13-4 do not colocalize extensively with perforin. However, phorbol 12-myristate 13-acetate and ionomycin stimulation or conjugation to susceptible target cells induced myosin-dependent colocalization of Rab27a and Munc13-4 with perforin. Unexpectedly, individual engagement of receptors leukocyte functional antigen-1, NKG2D, or 2B4 induced colocalization of Rab27a, but not Munc13-4, with perforin. Conversely, engagement of antibody-dependent cellular cytotoxicity receptor CD16 induced colocalization of Munc13-4, but not Rab27a, with perforin. Furthermore, colocalization of Munc13-4 with perforin was Rab27a-dependent. In conclusion, Rab27a or Munc13-4 recruitment to lytic granules is preferentially regulated by different receptor signals, demonstrating that individual target cell ligands regulate discrete molecular events for lytic granule maturation. The data suggest Rab27a facilitates degranulation at an early step yet highlight a reciprocal relationship between Munc13-4 and Rab27a for degranulation.