bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Stenotrophomonas maltophilia Strain Evades a Major Caenorhabditis elegans Defense Pathway
Authors: White Corin V. , Darby Brian J. , Breeden Robert J. , Herman Michael A. 
Published: December 2015

ABSTRACT

Stenotrophomonas maltophilia
is a ubiquitous bacterium and an emerging nosocomial pathogen. This bacterium is resistant to many antibiotics, associated with a number of infections, and a significant health risk, especially for immunocompromised patients. Given that
Caenorhabditis elegans
shares many conserved genetic pathways and pathway components with higher organisms, the study of its interaction with bacterial pathogens has biomedical implications.
S. maltophilia
has been isolated in association with nematodes from grassland soils, and it is likely that
C. elegans
encounters this bacterium in nature. We found that a local
S. maltophilia
isolate, JCMS, is more virulent than the other
S. maltophilia
isolates (R551-3 and K279a) tested. JCMS virulence correlates with intestinal distension and bacterial accumulation and requires the bacteria to be alive. Many of the conserved innate immune pathways that serve to protect
C. elegans
from various pathogenic bacteria also play a role in combating
S. maltophilia
JCMS. However,
S. maltophilia
JCMS is virulent to normally pathogen-resistant DAF-2/16 insulin-like signaling pathway mutants. Furthermore, several insulin-like signaling effector genes were not significantly differentially expressed between
S. maltophilia
JCMS and avirulent bacteria (
Escherichia coli
OP50). Taken together, these findings suggest that
S. maltophilia
JCMS evades the pathogen resistance conferred by the loss of DAF-2/16 pathway components. In summary, we have discovered a novel host-pathogen interaction between
C. elegans
and
S. maltophilia
and established a new animal model with which to study the mode of action of this emerging nosocomial pathogen.
The Surface Sensor NlpE of Enterohemorrhagic Escherichia coli Contributes to Regulation of the Type III Secretion System and Flagella by the Cpx Response to Adhesion
Authors: Shimizu Takeshi , Ichimura Kimitoshi , Noda Masatoshi 
Published: December 2015

ABSTRACT

Although the adhesion of enterohemorrhagic
Escherichia coli
(EHEC) is central to the EHEC-host interaction during infection, it remains unclear how such adhesion regulates virulence factors. Adhesion to abiotic surfaces by
E. coli
has been reported to be an outer membrane lipoprotein NlpE-dependent activation cue of the Cpx pathway. Therefore, we investigated the role of NlpE in EHEC on the adhesion-mediated expression of virulence genes. NlpE in EHEC contributed to upregulation of the locus of enterocyte effacement (LEE) genes encoded type III secretion system and to downregulated expression of the flagellin gene by activation of the Cpx pathway during adherence to hydrophobic glass beads and undifferentiated Caco-2 cells. Moreover, LysR homologue A (LrhA) in EHEC was involved in regulating the expression of the LEE genes and flagellin gene in response to adhesion. Gel mobility shift analysis revealed that response regulator CpxR bound to the
lrhA
promoter region and thereby regulated expressions of the LEE genes and flagellin gene via the transcriptional regulator LrhA in EHEC. Therefore, these results suggest that the sensing of adhesion signals via NlpE is important for regulation of the expression of the type III secretion system and flagella in EHEC during infection.
Interleukin-22-Induced Antimicrobial Phospholipase A2 Group IIA Mediates Protective Innate Immunity of Nonhematopoietic Cells against Listeria monocytogenes
Authors: Okita Yamato , Shiono Takeru , Yahagi Ayano , Hamada Satoru , Umemura Masayuki , Matsuzaki Goro 
Published: December 2015

ABSTRACTListeria monocytogenesis a bacterial pathogen which establishes intracellular parasitism in various cells, including macrophages and nonhematopoietic cells, such as hepatocytes. It has been reported that several proinflammatory cytokines have pivotal roles in innate protection againstL. monocytogenesinfection. We found that a proinflammatory cytokine, interleukin 22 (IL-22), was expressed by CD3+CD4+T cells at an early stage ofL. monocytogenesinfection in mice. To assess the influence of IL-22 onL. monocytogenesinfection in hepatocytes, cells of a human hepatocellular carcinoma line, HepG2, were treated with IL-22 beforeL. monocytogenesinfectionin vitro. Gene expression analysis of the IL-22-treated HepG2 cells identified phospholipase A2 group IIA (PLA2G2A) as an upregulated antimicrobial molecule. Addition of recombinant PLA2G2A to the HepG2 culture significantly suppressedL. monocytogenesinfection. Culture supernatant of the IL-22-treated HepG2 cells contained bactericidal activity againstL. monocytogenes, and the activity was abrogated by a specific PLA2G2A inhibitor, demonstrating that HepG2 cells secreted PLA2G2A, which killed extracellularL. monocytogenes. Furthermore, colocalization of PLA2G2A andL. monocytogeneswas detected in the IL-22-treated infected HepG2 cells, which suggests involvement of PLA2G2A in the mechanism of intracellular killing ofL. monocytogenesby HepG2 cells. These results suggest that IL-22 induced at an early stage ofL. monocytogenesinfection enhances innate immunity againstL. monocytogenesin the liver by stimulating hepatocytes to produce an antimicrobial molecule, PLA2G2A.
Hypothetical Protein BB0569 Is Essential for Chemotaxis of the Lyme Disease Spirochete Borrelia burgdorferi
Authors: Zhang Kai , Liu Jun , Charon Nyles W. , Li Chunhao 
Published: December 2015

ABSTRACT

The Lyme disease spirochete
Borrelia burgdorferi
has five putative methyl-accepting chemotaxis proteins (MCPs). In this report, we provide evidence that a hypothetical protein, BB0569, is essential for the chemotaxis of
B. burgdorferi
. While BB0569 lacks significant homology to the canonical MCPs, it contains a conserved domain (spanning residues 110 to 170) that is often evident in membrane-bound MCPs such as Tar and Tsr of
Escherichia coli
. Unlike Tar and Tsr, BB0569 lacks transmembrane regions and recognizable HAMP and methylation domains and is similar to TlpC, a cytoplasmic chemoreceptor of
Rhodobacter sphaeroides
. An isogenic mutant of
BB0569
constantly runs in one direction and fails to respond to attractants, indicating that BB0569 is essential for chemotaxis. Immunofluorescence, green fluorescent protein (GFP) fusion, and cryo-electron tomography analyses demonstrate that BB0569 localizes at the cell poles and is required for chemoreceptor clustering at the cell poles. Protein cross-linking studies reveal that BB0569 forms large protein complexes with MCP3, indicative of its interactions with other MCPs. Interestingly, analysis of
B. burgdorferi
mcp
mutants shows that inactivation of either
mcp
2
or
mcp
3
reduces the level of BB0569 substantially and that such a reduction is caused by protein turnover. Collectively, these results demonstrate that the domain composition and function of BB0569 are similar in some respects to those of TlpC but that these proteins are different in their cellular locations, further highlighting that the chemotaxis of
B. burgdorferi
is unique and different from the
Escherichia coli
and
Salmonella enterica
paradigm.

IMPORTANCE
Spirochete chemotaxis differs substantially from the
Escherichia coli
and
Salmonella enterica
paradigm, and the basis for controlling the rotation of the bundles of periplasmic flagella at each end of the cell is unknown. In recent years,
Borrelia burgdorferi
, the causative agent of Lyme disease, has been used as a model organism to understand spirochete chemotaxis and its role in infectious processes of the disease. In this report, BB0569, a hypothetical protein of
B. burgdorferi
, has been investigated by using an approach of genetic, biochemistry, and cryo-electron tomography analyses. The results indicate that BB0569 has a distinct role in chemotaxis that may be unique to spirochetes and represents a novel paradigm.
The Effect of Downwelling Longwave and Shortwave Radiation on Arctic Summer Sea Ice
Authors: Kapsch Marie-Luise , Graversen Rune Grand , Tjernström Michael , Bintanja Richard 
Published: December 2015

Abstract
The Arctic summer sea ice has diminished fast in recent decades. A strong year-to-year variability on top of this trend indicates that sea ice is sensitive to short-term climate fluctuations. Previous studies show that anomalous atmospheric conditions over the Arctic during spring and summer affect ice melt and the September sea ice extent (SIE). These conditions are characterized by clouds, humidity, and heat anomalies that all affect downwelling shortwave (SWD) and longwave (LWD) radiation to the surface. In general, positive LWD anomalies are associated with cloudy and humid conditions, whereas positive anomalies of SWD appear under clear-sky conditions. Here the effect of realistic anomalies of LWD and SWD on summer sea ice is investigated by performing experiments with the Community Earth System Model. The SWD and LWD anomalies are studied separately and in combination for different seasons. It is found that positive LWD anomalies in spring and early summer have significant impact on the September SIE, whereas winter anomalies show only little effect. Positive anomalies in spring and early summer initiate an earlier melt onset, hereby triggering several feedback mechanisms that amplify melt during the succeeding months. Realistic positive SWD anomalies appear only important if they occur after the melt has started and the albedo is significantly reduced relative to winter conditions. Simulations where both positive LWD and negative SWD anomalies are implemented simultaneously, mimicking cloudy conditions, reveal that clouds during spring have a significant impact on summer sea ice while summer clouds have almost no effect.
Different Responses of Sea Surface Temperature in the South China Sea to Various El Niño Events during Boreal Autumn
Authors: Tan Wei , Wang Xin , Wang Weiqiang , Wang Chunzai , Zuo Juncheng 
Published: December 2015

Abstract
This study investigates variations of sea surface temperature (SST) anomalies in the South China Sea (SCS) during developing autumn of various El Niño events. The warm SST anomalies are observed in the SCS for canonical El Niño and El Niño Modoki I, whereas the cold SST anomalies are found for El Niño Modoki II. The ocean heat budget analyses show that the latent heat flux change induced by various types of El Niño events is a major contributor to the SCS SST variations. An anomalous anticyclone resides near the Philippine Sea for canonical El Niño and El Niño Modoki I, which induces the southerly wind anomalies over the SCS and thus weakens the climatological northeasterly in boreal autumn. The weakened surface wind speed reduces heat loss from the ocean, leading to a warmer state in the SCS. However, for El Niño Modoki II, the anomalous anticyclone shifts westward to the west of the SCS, and thus the northeasterly wind anomalies appear in the SCS. The northeasterly anomalies enhance the climatological northeasterly monsoon, increase the wind speed, and increase heat loss from the ocean, thus resulting in a cooling in the SCS. The anomalous anticyclone associated with El Niño events also increases shortwave radiation. The increases of the shortwave radiation can also contribute to the SCS warming for canonical El Niño and El Niño Modoki I in addition to the warm effect from the latent heat flux. Because the cooling effect from the latent heat flux is larger than that of the shortwave radiation for El Niño Modoki II, the SCS for El Niño Modoki II tends to be cool.
Internal Waves and Mixing near the Kerguelen Plateau
Authors: Meyer Amelie , Polzin Kurt L. , Sloyan Bernadette M. , Phillips Helen E. 
Published: December 2015

AbstractIn the stratified ocean, turbulent mixing is primarily attributed to the breaking of internal waves. As such, internal waves provide a link between large-scale forcing and small-scale mixing. The internal wave field north of the Kerguelen Plateau is characterized using 914 high-resolution hydrographic profiles from novel Electromagnetic Autonomous Profiling Explorer (EM-APEX) floats. Altogether, 46 coherent features are identified in the EM-APEX velocity profiles and interpreted in terms of internal wave kinematics. The large number of internal waves analyzed provides a quantitative framework for characterizing spatial variations in the internal wave field and for resolving generation versus propagation dynamics. Internal waves observed near the Kerguelen Plateau have a mean vertical wavelength of 200 m, a mean horizontal wavelength of 15 km, a mean period of 16 h, and a mean horizontal group velocity of 3 cm s−1. The internal wave characteristics are dependent on regional dynamics, suggesting that different generation mechanisms of internal waves dominate in different dynamical zones. The wave fields in the Subantarctic/Subtropical Front and the Polar Front Zone are influenced by the local small-scale topography and flow strength. The eddy-wave field is influenced by the large-scale flow structure, while the internal wave field in the Subantarctic Zone is controlled by atmospheric forcing. More importantly, the local generation of internal waves not only drives large-scale dissipation in the frontal region but also downstream from the plateau. Some internal waves in the frontal region are advected away from the plateau, contributing to mixing and stratification budgets elsewhere.
Rossby Waves and Eddies Observed at a Temperature Mooring in Northern South China Sea
Authors: Lin Y.-C. , Oey L.-Y. , Wang J. , Liu K.-K. 
Published: December 2015

AbstractAnnual Rossby waves in northern South China Sea had previously been studied using altimetry and model data; however, how they connect to subsurface temperature fluctuations has not been examined. This study analyzed a 22-month, surface to −500-m temperature time series at 18.3°N, 115.5°E, together with satellite and other data, to show the arrivals near z ≈ −300 m and deeper cool (warm) Rossby waves after their generation near the Luzon Strait in winter (summer). Temperature fluctuations with time scales of a few weeks, and with maximum anomalies near z ≈ −100 m, were also found embedded in the smooth Rossby waves and caused by propagating eddies. Eddy fluctuations and propagation past the mooring were of two types: southwestward from southwestern Taiwan, triggered by Kuroshio intrusion that produced anticyclone–cyclone pairs in late fall and winter, and eddies propagating westward from Luzon forced by annual anomalies of wind stress curl and Kuroshio path in the Luzon Strait
Tropical Transition of an Unnamed, High-Latitude, Tropical Cyclone over the Eastern North Pacific
Authors: Bentley Alicia M. , Metz Nicholas D. 
Published: December 2015

Abstract
In early November 2006, an unnamed tropical cyclone (TC) formed via the tropical transition (TT) process at 42°N over the eastern North Pacific. An extratropical cyclone (EC), developing downstream of a thinning upper-tropospheric trough over the eastern North Pacific, served as the precursor disturbance that would ultimately undergo TT. The TT of the unnamed TC was extremely unusual—occurring over ~16°C sea surface temperatures in a portion of the eastern North Pacific basin historically devoid of TC activity.
This paper 1) identifies the upper- and lower-tropospheric features linked to the formation of the EC that transitions into the unnamed TC, 2) provides a synoptic overview of the features and processes associated with the unnamed TC’s TT, and 3) discusses the landfall of the weakening cyclone along the west coast of North America. As observed in previous studies of TT, the precursor EC progresses through the life cycle of a marine extratropical frontal cyclone, developing a bent-back warm front on its northern and western sides and undergoing a warm seclusion process. Backward air parcel trajectories suggest that air parcels isolated in the center of the transitioning cyclone were warmed in the lower troposphere via sensible heating from the underlying sea surface. Vertical cross sections taken through the center of the cyclone during its life cycle reveal its transformation from an asymmetric, cold-core, EC into an axisymmetric, warm-core, TC during TT. Ensemble reforecasts initialized after TT highlight the relatively low forecast skill associated with the landfall of the weakening cyclone.
Precipitation Nowcasting with Three-Dimensional Space–Time Extrapolation of Dense and Frequent Phased-Array Weather Radar Observations
Authors: Otsuka Shigenori , Tuerhong Gulanbaier , Kikuchi Ryota , Kitano Yoshikazu , Taniguchi Yusuke , Ruiz Juan Jose , Satoh Shinsuke , Ushio Tomoo , Miyoshi Takemasa 
Published: December 2015

Abstract
The phased-array weather radar (PAWR) is a new-generation weather radar that can make a 100-m-resolution three-dimensional (3D) volume scan every 30 s for 100 vertical levels, producing ~100 times more data than the conventional parabolic-antenna radar with a volume scan typically made every 5 min for 15 scan levels. This study takes advantage of orders of magnitude more rapid and dense observations by PAWR and explores high-precision nowcasting of 3D evolution at 1–10-km scales up to several minutes, which are compared with conventional horizontal two-dimensional (2D) nowcasting typically at O(100) km scales up to 1–6 h. A new 3D precipitation extrapolation system was designed to enhance a conventional algorithm for dense and rapid PAWR volume scans. Experiments show that the 3D extrapolation successfully captured vertical motions of convective precipitation cores and outperformed 2D nowcasting with both simulated and real PAWR data.
Transnational Histories and Subcontinental Pasts: A Review Essay
Authors: Balachandran G. 
Published: December 2015

Nico Slate, Coloured Cosmopolitanism: The Shared Struggle for Freedom in the United States and India, Ranikhet: Permanent Black, 2012, pp. 321. Vivek Bald, Bengali Harlem and the Lost Histories of South Asian America, Cambridge, MA: Harvard University Press, 2013, pp. 294. Seema Sohi, Echoes of Mutiny: Race, Surveillance and Anticolonialism in North America, New York: Oxford University Press, 2014, pp. 271.
Book Review: Philip Oldenburg, India, Pakistan, and Democracy: Solving the Puzzle of Divergent Paths and William Gould, Taylor C. Sherman and Sarah Ansari, eds, From Subjects to Citizens: Society and Everyday State in India and Pakistan
Authors: Malik Anushay 
Published: December 2015

Philip Oldenburg, India, Pakistan, and Democracy: Solving the Puzzle of Divergent Paths, Delhi: Manohar, 2010, pp. 288. William Gould, Taylor C. Sherman and Sarah Ansari, eds, From Subjects to Citizens: Society and Everyday State in India and Pakistan, 1947–1970, Delhi: Cambridge University Press, 2014, pp. 258.
Distribution of mutational fitness effects and of epistasis in the 5’ untranslated region of a plant RNA virus
Authors: Bernet Guillermo P. , Elena Santiago F. 
Published: December 2015

AbstractBackgroundUnderstanding the causes and consequences of phenotypic variability is a central topic of evolutionary biology. Mutations within non-codingcis-regulatory regions are thought to be of major effect since they affect the expression of downstream genes. To address the evolutionary potential of mutations affecting such regions in RNA viruses, we explored the fitness properties of mutations affecting the 5’-untranslated region (UTR) of a prototypical member of the picorna-like superfamily,Tobacco etch virus(TEV). This 5’ UTR acts as an internal ribosomal entry site (IRES) and is essential for expression of all viral genes.ResultsWe determined in vitro the folding of 5’ UTR using the selective 2’-hydroxyl acylation analyzed by primer extension (SHAPE) technique. Then, we created a collection of single-nucleotide substitutions on this region and evaluated the statistical properties of their fitness effects in vivo. We found that, compared to random mutations affecting coding sequences, mutations at the 5’ UTR were of weaker effect. We also created double mutants by combining pairs of these single mutations and found variation in the magnitude and sign of epistatic interactions, with an enrichment of cases of positive epistasis. A correlation exists between the magnitude of fitness effects and the size of the perturbation made in the RNA folding structure, suggesting that the larger the departure from the predicted fold, the more negative impact in viral fitness.ConclusionsEvidence that mutational fitness effects on the short 5’ UTR regulatory sequence of TEV are weaker than those affecting its coding sequences have been found. Epistasis among pairs of mutations on the 5’ UTR ranged between the extreme cases of synthetic lethal and compensatory. A plausible hypothesis to explain all these observations is that the interaction between the 5’ UTR and the host translational machinery was shaped by natural selection to be robust to mutations, thus ensuring the homeostatic expression of viral genes even at high mutation rates.
Impact of Ipsilateral Blood Draws, Injections, Blood Pressure Measurements, and Air Travel on the Risk of Lymphedema for Patients Treated for Breast Cancer
Authors: Ferguson Chantal M. , Swaroop Meyha N. , Horick Nora , Skolny Melissa N. , Miller Cynthia L. , Jammallo Lauren S. , Brunelle Cheryl , O’Toole Jean A. , Salama Laura , Specht Michelle C. , Taghian Alphonse G. 
Published: December 2015

Purpose The goal of this study was to investigate the association between blood draws, injections, blood pressure readings, trauma, cellulitis in the at-risk arm, and air travel and increases in arm volume in a cohort of patients treated for breast cancer and screened for lymphedema. Patients and Methods Between 2005 and 2014, patients undergoing treatment of breast cancer at our institution were screened prospectively for lymphedema. Bilateral arm volume measurements were performed preoperatively and postoperatively using a Perometer. At each measurement, patients reported the number of blood draws, injections, blood pressure measurements, trauma to the at-risk arm(s), and number of flights taken since their last measurement. Arm volume was quantified using the relative volume change and weight-adjusted change formulas. Linear random effects models were used to assess the association between relative arm volume (as a continuous variable) and nontreatment risk factors, as well as clinical characteristics. Results In 3,041 measurements, there was no significant association between relative volume change or weight-adjusted change increase and undergoing one or more blood draws (P = .62), injections (P = .77), number of flights (one or two [P = .77] and three or more [P = .91] v none), or duration of flights (1 to 12 hours [P = .43] and 12 hours or more [P = .54] v none). By multivariate analysis, factors significantly associated with increases in arm volume included body mass index ≥ 25 (P = .0236), axillary lymph node dissection (P < .001), regional lymph node irradiation (P = .0364), and cellulitis (P < .001). Conclusion This study suggests that although cellulitis increases risk of lymphedema, ipsilateral blood draws, injections, blood pressure readings, and air travel may not be associated with arm volume increases. The results may help to educate clinicians and patients on posttreatment risk, prevention, and management of lymphedema.