bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cytotoxic T Cells Are the Predominant Players Providing Cross-Protective Immunity Induced by γ-Irradiated Influenza A Viruses
Authors: Furuya Yoichi , Chan Jennifer , Regner Matthias , Lobigs Mario , Koskinen Aulikki , Kok Tuckweng , Manavis Jim , Li Peng , Müllbacher Arno , Alsharifi Mohammed 
Published: February 2010

ABSTRACTWe previously demonstrated that a single dose of nonadjuvanted intranasal γ-irradiated influenza A virus can provide robust protection in mice against both homologous and heterosubtypic challenges, including challenge with an H5N1 avian virus strain. We investigated the mechanism behind the observed cross-protection to define which arms of the adaptive immune response are involved in mediating this protection. Studies with gene knockout mice showed the cross-protective immunity to be mediated mainly by T cells and to be dependent on the cytolytic effector molecule perforin. Adoptive transfer of memory T cells from immunized mice, but not of memory B cells, protected naïve recipients against lethal heterosubtypic influenza virus challenge. Furthermore, γ-irradiated influenza viruses induced cross-reactive Tc-cell responses but not cross-neutralizing or cross-protective antibodies. In addition, histological analysis showed reduced lung inflammation in vaccinated mice compared to that in unvaccinated controls following heterosubtypic challenge. This reduced inflammation was associated with enhanced early recruitment of T cells, both CD4+and CD8+, and with early influenza virus-specific cytotoxic T-cell responses. Therefore, cross-protective immunity induced by vaccination with γ-irradiated influenza A virus is mediated mainly by Tc-cell responses.
Dengue Virus Inhibits the Production of Type I Interferon in Primary Human Dendritic Cells
Authors: Rodriguez-Madoz Juan R. , Bernal-Rubio Dabeiba , Kaminski Dorota , Boyd Kelley , Fernandez-Sesma Ana 
Published: February 2010

ABSTRACTDengue virus (DENV) infects human immune cellsin vitroand likely infects dendritic cells (DCs)in vivo. DENV-2 productive infection induces activation and release of high levels of chemokines and proinflammatory cytokines in monocyte-derived DCs (moDCs), with the notable exception of alpha/beta interferon (IFN-α/β). Interestingly, DENV-2-infected moDCs fail to prime T cells, most likely due to the lack of IFN-α/β released by moDCs, since this effect was reversed by addition of exogenous IFN-β. Together, our data show that inhibition of IFN-α/β production by DENV in primary human moDCs is a novel mechanism of immune evasion.
Rotavirus Differentially Infects and Polyclonally Stimulates Human B Cells Depending on Their Differentiation State and Tissue of Origin
Authors: Narváez Carlos F. , Franco Manuel A. , Angel Juana , Morton John M. , Greenberg Harry B. 
Published: February 2010

ABSTRACTWe have shown previously that rotavirus (RV) can infect murine intestinal B220+cellsin vivo(M. Fenaux, M. A. Cuadras, N. Feng, M. Jaimes, and H. B. Greenberg, J. Virol. 80:5219-5232, 2006) and human blood B cellsin vitro(M. C. Mesa, L. S. Rodriguez, M. A. Franco, and J. Angel, Virology366:174-184, 2007). However, the effect of RV on B cells, especially those present in the human intestine, the primary site of RV infection, is unknown. Here, we compared the effects of thein vitroRV infection of human circulating (CBC) and intestinal B cells (IBC). RV infected four times more IBC than CBC, and in both types of B cells the viral replication was highly restricted to the memory subset. RV induced cell death in 30 and 3% of infected CBC and IBC, respectively. Moreover, RV induced activation and differentiation into antibody-secreting cells (ASC) of CBC but not IBC when the B cells were present with other mononuclear cells. However, RV did not induce these effects in purified CBC or IBC, suggesting the participation of other cells in activating and differentiating CBC. RV infection was associated with enhanced interleukin-6 (IL-6) production by CBC independent of viral replication. The infection of the anti-B-cell receptor, lipopolysaccharide, or CpG-stimulated CBC reduced the secretion of IL-6 and IL-8 and decreased the number of ASC. These inhibitory effects were associated with an increase in viral replication and cell death and were observed in polyclonally stimulated CBC but not in IBC. Thus, RV differentially interacts with primary human B cells depending on their tissue of origin and differentiation stage, and it affects their capacity to modulate the local and systemic immune responses.
Role of Herpes Simplex Virus ICP0 in the Transactivation of Genes Introduced by Infection or Transfection: a Reappraisal
Authors: Kalamvoki Maria , Roizman Bernard 
Published: February 2010

ABSTRACT

ICP0, a promiscuous transactivator that enhances the expression of genes introduced by infection or transfection, functions in both nucleus and cytoplasm. The nuclear functions include degradation and dispersal of ND10 bodies and suppression of silencing of viral DNA. Subsequently, ICP0 shifts to the cytoplasm. Transfection of DNA prior to infection has no effect on the localization of ICP0 in cells that are efficient expressers of transgenes (e.g., Vero and HEK293) but results in delayed cytoplasmic localization of ICP0 in cells (e.g., HEp-2 and HEL) that are poor transgene expressers. Here, we examined by real-time PCR (qPCR) the accumulation of a transgene and of viral gI mRNAs in Vero or HEp-2 cells that were transfected and then infected with wild-type or ΔICP0 mutant viruses. The accumulation of transgene mRNA was unaffected by a ΔICP0 mutant, gradually increased in HEp-2 cells, but increased and then decreased in Vero cells infected with wild-type virus. In both cell lines, accumulation of gI mRNA increased with time and was less affected by the transfected DNA in Vero cells than in HEp-2 cells. The relative kinetics of mRNA accumulation reflected continued synthesis and degradation of the transgene and gI mRNAs. We conclude that the role of ICP0 is to render the DNA templates introduced by transfection or infection accessible by transcriptional factors, that the two cell lines differ with respect to the transcription-ready status of entering foreign DNA in the nucleus, and that ICP0 is not
per se
the recruiter of transcriptional factors to the accessible DNA templates.
Modeling Seasonal Changes in the Temperature Lapse Rate in a Northern Thailand Mountainous Area
Authors: Komatsu Hikaru , Hashimoto Hirofumi , Kume Tomonori , Tanaka Nobuaki , Yoshifuji Natsuko , Otsuki Kyoichi , Suzuki Masakazu , Kumagai Tomo’omi 
Published: February 2010

AbstractTemperature data in the mountain forest regions are often extrapolated from temperature data recorded at base stations at lower elevation. Such extrapolation is often based on elevation differences between target regions and base stations at low elevation assuming a constant temperature lapse rate throughout the year. However, this assumption might be problematic where slope circulation is active and decoupled from the regional circulation. To model the seasonal change in the lapse rate, the authors compared daily maximum (Tmax) and minimum temperatures (Tmin) observed at a mountain forest site (Kog–Ma; 1300-m altitude) with those observed at the bottom of the basin (Chiang–Mai; 314-m altitude) in northern Thailand, where slope circulation is active and decoupled from the regional circulation. The difference in Tmax between Kog–Ma and Chiang–Mai (ΔTmax; Kog–Ma minus Chiang–Mai) was relatively unchanged throughout the year. However, the difference in Tmin between Kog–Ma and Chiang–Mai (ΔTmin) changed seasonally. Thus, assuming a constant lapse rate throughout the year could cause large errors in extrapolating Tmin data in mountainous areas in northern Thailand. The difference ΔTmin was related to nighttime net radiation (Rn), suggesting that nocturnal drainage flow affects the determination of ΔTmin. This relationship would be useful in formulating seasonal changes in the lapse rate for Tmin. As Rn data are generally unavailable for meteorological stations, an index that relates to the lapse rate for Tmin and is calculated from Tmax and Tmin data is proposed. This index might be useful for accurately estimating Tmin values in mountainous regions in northern Thailand.
A Conserved Minimal Adjustment Scheme for Stabilization of Hydrographic Profiles
Authors: Chu Peter C. , Fan Chenwu 
Published: February 2010

Abstract
Ocean (T, S) data analysis/assimilation, conducted in the three-dimensional physical space, is a generalized average of purely observed data (data analysis) or of modeled/observed data (data assimilation). Because of the high nonlinearity of the equation of the state of the seawater and nonuniform vertical distribution of the observational profile data, false static instability may be generated. A new analytical conserved adjustment scheme has been developed on the base of conservation of heat, salt, and static stability for the whole water column with predetermined (T, S) adjustment ratios. A set of well-posed combined linear and nonlinear algebraic equations has been established and is solved using Newton’s method. This new scheme can be used for ocean hydrographic data analysis and data assimilation.
Forecasting the Maintenance of Mesoscale Convective Systems Crossing the Appalachian Mountains
Authors: Letkewicz Casey E. , Parker Matthew D. 
Published: February 2010

Abstract
Forecasting the maintenance of mesoscale convective systems (MCSs) is a unique problem in the eastern United States due to the influence of the Appalachian Mountains. At times these systems are able to traverse the terrain and produce severe weather in the lee, while at other times they instead dissipate upon encountering the mountains. To differentiate between crossing and noncrossing MCS environments, 20 crossing and 20 noncrossing MCS cases were examined. The cases were largely similar in terms of their 500-hPa patterns, MCS archetypes, and orientations with respect to the barrier. Analysis of radiosonde data, however, revealed that the environment east of the mountains discriminated between case types very well. The thermodynamic and kinematic variables that had the most discriminatory power included those associated with instability, several different bulk shear vector magnitudes, and also the mean tropospheric wind. Crossing cases were characterized by higher instability, which was found to be partially attributable to the diurnal cycle. However, these cases also tended to occur in environments with weaker shear and a smaller mean wind. The potential reasons for these results, and their forecasting implications, are discussed.
Interpreting the Tropical Atlantic Climate: Diaries from the Mid-Nineteenth-Century Australian Voyage
Authors: Foxhall Katherine 
Published: February 2010

AbstractThis article analyses representations of the tropical Atlantic and its climate in diaries written during sailing voyages from Britain to the Australian colonies in the middle third of the nineteenth century. It argues that writers employed a wide range of formal and informal knowledge about weather and climate to evaluate the physical experience of sailing through the maritime tropics. These interpretive frames include geographical conventions of latitude and longitude, colonial medical topography, natural observation, sailor’s expertise, maritime culture, and literary tropes. The article’s exploration of vernacular knowledge in an underexplored social and geographic context makes two contributions: first, to historical and geographical discussions about the distinction between expertise and belief and second, to recent attempts to emphasize the material importance of the ocean in an unprecedented era of industrial, scientific, and colonial expansion.
Up-regulation of the Apo/Fas (CD95) complex on neutrophils harvested during cardiac surgery: distinct findings in patients operated on with or without the use of cardiopulmonary bypass
Authors: Kunes Pavel , Mandak Jiri , Harrer Jan , Kolackova Martina , Andrys Ctirad , Holicka Monika , Krejsek Jan 
Published: February 2010

Aims: In a group of patients undergoing cardiac surgery performed both with (“on-pump”) and without the use (“offpump”) of cardiopulmonary bypass (CPB), we studied the changes of neutrophil membrane apoptosis-inducing complex Apo/Fas. Methods: Expression of Apo/Fas (CD95) on leukocytes was evaluated by flow cytometry. Results: In “on-pump” patients, we found an increase in the expression of CD95 median intensity fluorescence (MFI) on granulocytes from a baseline level median=56, (Q 1=45.5, Q3=64) to a median=88, (Q1=62, Q 3=109.5; p<0.01) at the 3rd postoperative day and median=74, (Q1=63, Q3=84.5; p<0.01) at the 7th postoperative day. In “off-pump” patients, granulocyte CD95 MFI was median=55, (Q1=51, Q3=84) before surgery. The significant increase was found on the 3rd postoperative day only; median=90, (Q 1=66; Q3=98; p<0.05). A similar pattern in the CD95 expression was also found if percentage changes of granulocyte CD95 MFI were followed. Moreover, the significantly increased Apo/Fas expression expressed as a percentage change of CD95 MFI was found in “on-pump” patients compared to “off-pump” patients, both at the 3rd postoperative day (p<0.05) and at the 7th postoperative day (p<0.01). Conclusions: This is the first direct evidence of increasing densities of the Apo/Fas complex on neutrophils in cardiac surgical patients.
Vascular endothelial growth factor stimulates protein kinase CβII expression in chronic lymphocytic leukemia cells
Authors: Abrams Simon T. , Brown Benjamin R. B. , Zuzel Mirko , Slupsky Joseph R. 
Published: February 2010

AbstractChronic lymphocytic leukemia (CLL) is a malignant disease of mature B lymphocytes. We have previously shown that a characteristic feature of CLL cells are high levels of expression and activity of protein kinase CβII (PKCβII), and that this might influence disease progression by modulating signaling in response to B-cell receptor engagement. The aim of the present work was to investigate the factors involved in stimulating PKCβII expression in CLL cells. Here we show that the activation of PKCβII in CLL cells stimulated with vascular endothelial growth factor (VEGF) can drive expression of the gene for PKCβ, PRKCB1. We found that this effect of VEGF on PRKCB1 transcription is paralleled by high expression of PKCβII protein and therefore probably contributes to the malignant phenotype of CLL cells. Taken together, the data presented in this study demonstrate that VEGF, in addition to its role in providing prosurvival signals, also plays a role in overexpression of PKCβII, an enzyme with a specific pathophysiologic role in CLL.
CD160 signaling mediates PI3K-dependent survival and growth signals in chronic lymphocytic leukemia
Authors: Liu Feng-Ting , Giustiniani Jerome , Farren Timothy , Jia Li , Bensussan Armand , Gribben John G. , Agrawal Samir G. 
Published: February 2010

AbstractB-cell chronic lymphocytic leukemia (CLL) expresses CD160, a glycosylphosphatidylinositol-linked receptor found on normal natural killer (NK) and T cells, but not B cells. CD160 is a multifunctional molecule in normal lymphocytes, but its role in CLL biology is unknown. In vitro, CLL cells undergo rapid spontaneous apoptosis, which CD160 activation protected against—mean cell viability increased from 67% to 79% (P < .001). This was associated with up-regulation of Bcl-2, Bcl-xL, and Mcl-1, but not Bax. As expected from these changes in Bcl-2/Bax and Bcl-xL/Bax ratios, CD160 triggering reduced mitochondrial membrane potential collapse and cytochrome c release. CD160 stimulation also induced DNA synthesis, cell cycle progression, and proliferation. B-cell antigen receptor (BCR)–induced CLL proliferation was generally greater than with CD160, but marked variation was seen. Both BCR and CD160 signaling led to CLL secretion of interleukin-6 (IL-6) and IL-8, although CD160 induced greater increases of IL-6 (51-fold) and IL-8 (15-fold). Survival and activation signals mediated by CD160 showed dose-dependent suppression by phosphoinositide-3 kinase (PI3K) inhibitors. Thus, in vitro, CLL cells can use the CD160 pathway for survival and activation, mimicking CD160 signaling in normal NK and CD8+ T cells. Establishing the pathophysiologic relevance of these findings may reveal new therapeutic targets.
Malignant malaria and microangiopathies: merging mechanisms
Authors: López José A. 
Published: February 2010

Abstract
In this issue of Blood, Bridges and colleagues report that Plasmodium falciparum–infected erythrocytes are able to attach to the endothelial surface by binding platelet-decorated VWF strands in a CD36-dependent fashion, revealing a new mechanism for erythrocyte cytoadherence in malaria.1
Potentials 'R'Us web-server for protein energy estimations with coarse-grained knowledge-based potentials
Authors: Feng Yaping , Kloczkowski Andrzej , Jernigan Robert L 
Published: February 2010

Abstract

Background
Knowledge-based potentials have been widely used in the last 20 years for fold recognition, protein structure prediction from amino acid sequence, ligand binding, protein design, and many other purposes. However generally these are not readily accessible online.

Results
Our new knowledge-based potential server makes available many of these potentials for easy use to automatically compute the energies of protein structures or models supplied. Our web server for protein energy estimation uses four-body potentials, short-range potentials, and 23 different two-body potentials. Users can select potentials according to their needs and preferences. Files containing the coordinates of protein atoms in the PDB format can be uploaded as input. The results will be returned to the user's email address.

Conclusions
Our Potentials 'R'Us server is an easily accessible, freely available tool with a web interface that collects all existing and future protein coarse-grained potentials and computes energies of multiple structural models.
Transcriptomic changes arising during light-induced sporulation in Physarum polycephalum
Authors: Barrantes Israel , Glockner Gernot , Meyer Sonja , Marwan Wolfgang 
Published: February 2010

Abstract

Background

Physarum polycephalum is a free-living amoebozoan protist displaying a complex life cycle, including alternation between single- and multinucleate stages through sporulation, a simple form of cell differentiation. Sporulation in Physarum can be experimentally induced by several external factors, and Physarum displays many biochemical features typical for metazoan cells, including metazoan-type signaling pathways, which makes this organism a model to study cell cycle, cell differentiation and cellular reprogramming.

Results
In order to identify the genes associated to the light-induced sporulation in Physarum, especially those related to signal transduction, we isolated RNA before and after photoinduction from sporulation- competent cells, and used these RNAs to synthesize cDNAs, which were then analyzed using the 454 sequencing technology. We obtained 16,669 cDNAs that were annotated at every computational level. 13,169 transcripts included hit count data, from which 2,772 displayed significant differential expression (upregulated: 1,623; downregulated: 1,149). Transcripts with valid annotations and significant differential expression were later integrated into putative networks using interaction information from orthologs.

Conclusions
Gene ontology analysis suggested that most significantly downregulated genes are linked to DNA repair, cell division, inhibition of cell migration, and calcium release, while highly upregulated genes were involved in cell death, cell polarization, maintenance of integrity, and differentiation. In addition, cell death- associated transcripts were overrepresented between the upregulated transcripts. These changes are associated to a network of actin-binding proteins encoded by genes that are differentially regulated before and after light induction.
Genomic sequencing and analyses of Lymantria xylina multiple nucleopolyhedrovirus
Authors: Nai Yu-Shin , Wu Chih-Yu , Wang Tai-Chuan , Chen Yun-Ru , Lau Wei-Hong , Lo Chu-Fang , Tsai Meng-Feng , Wang Chung-Hsiung 
Published: February 2010

Abstract

Background
Outbreaks of the casuarina moth, Lymantria xylina Swinehoe (Lepidoptera: Lymantriidae), which is a very important forest pest in Taiwan, have occurred every five to 10 years. This moth has expanded its range of host plants to include more than 65 species of broadleaf trees. LyxyMNPV (L. xylina multiple nucleopolyhedrovirus) is highly virulent to the casuarina moth and has been investigated as a possible biopesticide for controlling this moth. LdMNPV-like virus has also been isolated from Lymantria xylin a larvae but LyxyMNPV was more virulent than LdMNPV-like virus both in NTU-LY and IPLB-LD-652Y cell lines. To better understand LyxyMNPV, the nucleotide sequence of the LyxyMNPV DNA genome was determined and analysed.

Results
The genome of LyxyMNPV consists of 156,344 bases, has a G+C content of 53.4% and contains 157 putative open reading frames (ORFs). The gene content and gene order of LyxyMNPV were similar to those of LdMNPV, with 151 ORFs identified as homologous to those reported in the LdMNPV genome. Two genes (Lyxy49 and Lyxy123) were homologous to other baculoviruses, and four unique LyxyMNPV ORFs (Lyxy11, Lyxy19, Lyxy130 and Lyxy131) were identified in the LyxyMNPV genome, including a gag-like gene that was not reported in baculoviruses. LdMNPV contains 23 ORFs that are absent in LyxyMNPV. Readily identifiable homologues of the gene host range factor-1 (hrf-1), which appears to be involved in the susceptibility of L. dispar to NPV infection, were not present in LyxyMNPV. Additionally, two putative odv-e27 homologues were identified in LyxyMNPV. The LyxyMNPV genome encoded 14 bro genes compared with 16 in LdMNPV, which occupied more than 8% of the LyxyMNPV genome. Thirteen homologous regions (hr s) were identified containing 48 repeated sequences composed of 30-bp imperfect palindromes. However, they differed in the relative positions, number of repeats and orientation in the genome compared to LdMNPV.

Conclusion
The gene parity plot analysis, percent identity of the gene homologues and a phylogenetic analysis suggested that LyxyMNPV is a Group II NPV that is most closely related to LdMNPV but with a highly distinct genomic organisation.