bluuebunny/crossref_metadata_2025 huggingface dataset:
Hepatozelluläres Karzinom: Innovative Therapieansätze
Authors: Mohr
Published: April 2007

Nur für Patienten mit kleinen hepatozellulären Karzinomen (HCC) bestehen befriedigende therapeutische Möglichkeiten durch Resektion, Lebertransplantation und lokalablative Verfahren. Die systemische Behandlung des weiter fortgeschrittenen HCC stellt aufgrund der hohen Resistenz der Tumorzellen gegenüber Chemotherapien und der Strahlentherapie sowie durch die Toxizität dieser Therapieformen bei der meist vorliegenden deutlichen Leberfunktionseinschränkung der Patienten ein bisher ungelöstes Problem dar. Innovative Therapiestrategien machen sich das zunehmende Wissen über molekulare Mechanismen der Tumorbiologie des HCC zunutze. Diese Therapien sind gezielt gegen spezifische molekulare und zelluläre Strukturen gerichtet, die für die Entstehung, Progression und Metastasierung des HCC von Bedeutung sind. Sie richten sich z.B. gegen Wachstumsfaktoren und ihre Rezeptoren, die intrazelluläre Signaltransduktion oder versuchen in den Zellzyklus einzugreifen. Die Hemmung der Tumor-Angiogenese ist ein weiterer therapeutischer Ansatz, der sich nicht gegen die Tumorzellen sondern gegen die Gefässneubildung richtet. Gentherapeutische Ansätze zielen darauf, nach Gentransfer «therapeutischer Gene» in Zielzellen biologisch hochaktive Proteine zu exprimieren. So genannte onkolytische Viren sind in der Lage, sich spezifisch in Tumorzellen zu vermehren und diese durch Zell-Lyse abzutöten. Ihre Effizienz kann durch zusätzliche gentherapeutische Mechanismen deutlich verstärkt werden. Die Induktion einer immunologischen Tumorabstossung ist das Ziel immuntherapeutischer Ansätze. Durch Immunisierung mit Tumorantigenen oder mit Tumor-Lysaten oder durch adoptiven Transfer aktivierter Immunzellen soll eine gegen das Tumorgewebe gerichtete Immunreaktion erzeugt werden, die zu einer Destruktion der Tumorzellen durch spezifische Effektorzellen führt.
Heterogeneous crust and upper mantle across southern Kenya and the relationship to surface deformation as inferred from magnetotelluric imaging
Authors: Meju Max A. , Sakkas Vassilis
Published: April 2007

We have used magnetotelluric data imaging to determine the resistivity structure across southern Kenya and our results suggest the presence of a buckled blocky or segmented lithosphere across the region. Prominent steep conductive zones at the Oloololo (OLO) escarpment and eastern rift margin allow us to subdivide the region into three crustal domains. West of OLO, a bow‐shaped conductor underlies a 10 km thick resistive upper crustal unit spatially correlating with an exposed Archaean greenstone belt. Between OLO and the eastern rift margin are found steeply dipping alternating conductive and resistive zones that appear buckled. East of this belt are found prominent, 5 to 20 km deep, subhorizontal conductors atop steep resistive blocks with flanking conductors. The main steep features in the crust appear to extend below the seismic Moho and thus suggest the presence of anomalously thick crust across the region. A 50 km‐wide and 4–8 km deep w‐shaped (double half‐graben) structure is suggested at the position of the Kenyan rift. We show that our inferred lateral zoning is consistent with collocated gravity and seismic measurements. We propose a link between the deep resistivity heterogeneity and surface deformation pattern in the area.
Impact of elevated CO2 on shellfish calcification
Authors: Gazeau Frédéric , Quiblier Christophe , Jansen Jeroen M. , Gattuso Jean‐Pierre , Middelburg Jack J. , Heip Carlo H. R.
Published: April 2007

Ocean acidification resulting from human emissions of carbon dioxide has already lowered and will further lower surface ocean pH. The consequent decrease in calcium carbonate saturation potentially threatens calcareous marine organisms. Here, we demonstrate that the calcification rates of the edible mussel (Mytilus edulis) and Pacific oyster (Crassostrea gigas) decline linearly with increasing pCO2. Mussel and oyster calcification may decrease by 25 and 10%, respectively, by the end of the century, following the IPCC IS92a scenario (∼740 ppmv in 2100). Moreover, mussels dissolve at pCO2 values exceeding a threshold value of ∼1800 ppmv. As these two species are important ecosystem engineers in coastal ecosystems and represent a large part of worldwide aquaculture production, the predicted decrease of calcification in response to ocean acidification will probably have an impact on coastal biodiversity and ecosystem functioning as well as potentially lead to significant economic loss.
Role of poleward moving auroral forms in the dawn‐dusk auroral precipitation asymmetries induced by IMF By
Authors: Sandholt P. E. , Farrugia C. J.
Published: April 2007

In a case study we document the detailed spatial/temporal structure of the aurora in the 0900–1500 magnetic local time (MLT) sector during an interval of steady southeast IMF orientation. Emphasis is placed on ground‐based observations of structure that is often averaged out in large statistical studies. A central feature is the phenomenon of poleward moving auroral forms (PMAFs), an ionospheric manifestation of pulsed magnetopause reconnection in the form of flux transfer events, FTEs, whose evolution in both prenoon and postnoon MLTs can be monitored under similar interplanetary conditions. Differences in auroral precipitation associated with PMAFs about the noon meridian related to IMF By are documented. While the prenoon PMAFs develop in three stages spanning a latitude range of ≥500 km, the highest‐latitude stage is absent in postnoon PMAFs for By > 0, which, after the initial intensification, progressively fade. We suggest that this auroral precipitation asymmetry is closely related to the different field‐aligned current configuration in PMAFs/prenoon and PMAFs/postnoon and the underlying plasma convection pattern. We detail the association between the high‐latitude component of PMAFs in the prenoon sector (By > 0) and a channel of plasma convection located in the dawnside convection cell. The latter convection channel, located in the regime of old open flux, represents an aspect of the Svalgaard‐Mansurov effect which is not included in the traditional description. The auroral and plasma convection data are placed in the context of recent work on solar wind‐magnetosphere interconnection topology for a southward pointing IMF with a strong By‐component.
Simultaneous ground and satellite observations of an isolated proton arc at subauroral latitudes
Authors: Sakaguchi K. , Shiokawa K. , Ieda A. , Miyoshi Y. , Otsuka Y. , Ogawa T. , Connors M. , Donovan E. F. , Rich F. J.
Published: April 2007

We observed an isolated proton arc at the Athabasca station (MLAT: 62°N) in Canada on 5 September 2005, using a ground‐based all‐sky imager at wavelengths of 557.7 nm, 630.0 nm, and 486.1 nm (Hβ). This arc is similar to the detached proton arc recently observed by the IMAGE satellite [Immel et al., 2002]. The arc appeared at 0500–0640 UT (2100–2240 MLT), coincident with strong Pc 1 geomagnetic pulsations in the frequency range of the electromagnetic ion cyclotron (EMIC) wave. The isolated arc did not change its structure and intensity during the late growth and expansive phases of a small substorm that occurred at 0550 UT. From particle data obtained by the NOAA 17 satellite, we found that the isolated arc was associated with the localized enhancement of ion precipitation fluxes at an energy range of 30–80 keV at L ∼ 4. Trapped ion flux enhancements (ring current ions) were also observed at two latitudinally separated regions. The localized ion precipitation was located at the outer boundary of the inner ring current ions. The DMSP F13 satellite observed signatures of an ionospheric plasma trough near the conjugate point of the arc in the Southern Hemisphere. The trough is considered to be connected to the plasmapause. These results indicate that the source region of the isolated arc was located near the plasmapause and in the ring current. We conclude that the observed isolated proton arc at subauroral latitudes was caused by the EMIC waves, which were generated near the plasmapause and resonantly scattered the ring current protons into the loss cone.
History of the Cretaceous Osbourn spreading center
Authors: Downey Nathan J. , Stock Joann M. , Clayton Robert W. , Cande Steven C.
Published: April 2007

The Osbourn Trough is a fossil spreading center that rifted apart the Manihiki and Hikurangi Plateaus during Cretaceous time. Previous models of the Osbourn spreading center are based on data collected near the trough axis, and therefore only constrain the history of the Osbourn spreading center during the last few Ma of spreading. Our data set includes multibeam data collected northward to the Manihiki Plateau, allowing us to examine seafloor morphology created during the entire active period of the Osbourn spreading center, as well as several additional multibeam data sets that provide the opportunity to examine the relationship between the Osbourn paleospreading center and the Cretaceous Pacific‐Phoenix ridge. The axial gravity of the trough is similar to the gravity found at other extinct slow‐intermediate spreading rate ridges. Magnetic field measurements indicate that spreading at the trough ceased during Chron C34. Abyssal‐hill trends indicate that spreading during the early history of the Osbourn spreading center occurred at 15°–20°. The east‐west component of this spreading explains the modern east‐west offset of the Manihiki and Hikurangi Plateaus. Spreading rotated to 2°–5° prior to extinction. Abyssal‐hill RMS amplitudes show that a decrease in spreading rate, from >7 cm/yr to 2–6 cm/yr full‐spreading rate, occurred ∼2–6 Ma prior to ridge extinction. Our data analysis is unable to determine the exact spreading rate of the Osbourn spreading center prior to the slowing event. The temporal constraints provided by our data show that the Osbourn spreading center ceased spreading prior to 87 Ma or 93 Ma, depending on whether the Manihiki and Hikurangi Plateaus rifted at 115 Ma or 121 Ma. Our model resolves the conflict between regional models of Osbourn spreading with models based on trough characteristics by showing that spreading at the Osbourn spreading center was decoupled from Pacific‐Phoenix spreading.
Circulation on the western South Atlantic continental shelf: 2. Spring and autumn realistic simulations
Authors: Soares I. D. , Kourafalou V. , Lee T. N.
Published: April 2007

Buoyancy‐driven currents are here investigated in a complex scenario, where two river plumes (the La Plata River and the Patos Lagoon plumes) occur in the vicinity of two opposing western boundary currents (the Malvinas and the Brazil currents). The study addresses the contrasting scenarios found during the austral spring and fall seasons, due to variations in river discharge, in wind stress, and in the boundary current transport. The winds blow preferably from the northeast during the spring and from the southwest during the fall. The Brazil Current transport is stronger during the spring, when the Brazil‐Malvinas Confluence is displaced southward, and weaker during the fall when the confluence moves northward. The study is conducted as a series of numerical simulations which consider the river discharges, the tides, variable wind stress, and thermohaline fields which are realistic in terms of the Brazil‐Malvinas Confluence. Our discussion focuses on the riverine water distribution in each season. The austral fall scenario shows coastally trapped plumes, and the spring scenario shows significant offshore removal, but our fall plumes are not too elongated and narrow as other authors found in the presence of constant winds, no tides, and no boundary currents, and our spring offshore removal is not as strong as found by others.
On the boundary conditions applied to the sea‐ice coupled model
Authors: Huang Rui Xin , Jin Xiangze
Published: April 2007

The formulation of suitable boundary conditions at the water‐ice interface during ice formation (melting) is an important aspect of the sea‐ice coupled model. The transfer of water and salt through the water‐ice can be posed as different boundary conditions. Behavior of the model under these boundary conditions is illustrated through simple analytical models and a numerical model based on pressure‐η coordinate. It is emphasized that the correct handling of the boundary conditions associated with sea ice formation requires an accurate treatment of the equivalent pressure on the top of water column and the total volume (mass) of the water column in the ice formation regime. Improper treatment of these boundary conditions may lead to an artificial loop current near the edge of ice in numerical simulations of oceanic circulation in the Arctic Ocean or near the Antarctica.
Subtidal flow structure at the turning region of a wide outflow plume
Authors: Valle‐Levinson Arnoldo , Holderied Kristine , Li Chunyan , Chant Robert J.
Published: April 2007

A series of underway current velocity profiles and near‐surface temperature and salinity measurements were combined with temperature and salinity profiles to characterize the subtidal flow structure at the turning region of a wide plume, the Chesapeake Bay outflow plume. In this context, “wide” refers to the ratio of lateral plume expansion to internal radius of deformation being greater than one. Observations were obtained in September and November of 1996 and in February and May of 1997 with the idea of capturing the variability in forcing conditions typically associated with these seasons. However, regional precipitation patterns yielded similar buoyancy forcing conditions for the four surveys and among the wettest years on record. This buoyancy forcing produced a well‐delineated outflow plume that separated from the coast on its way out the estuary. The plume separation acted in conjunction with frictional effects to delineate an inshore front, in addition to the customarily described offshore front. The outflow plume was markedly constrained by the Chesapeake Channel, which was also the main conduit of shelf waters toward the estuary. The bathymetric influence was also evident in the surface salinity field, the mean flows and the volume fluxes. The offshore extent of the plume was found between the scale predicted by geostrophic dynamics (internal Rossby radius) and that predicted by cyclostrophic dynamics. Such offshore extent was most likely linked to the plume interactions with the bathymetrically steered up‐estuary flow. This was corroborated by an analytical solution that explored the dynamical balance among pressure gradient, Coriolis accelerations and friction. In addition to being influenced by bathymetry, the Chesapeake Bay outflow plume was modified by local and remote effects related to atmospheric forcing.
Pressurized oceans and the eruption of liquid water on Europa and Enceladus
Authors: Manga M. , Wang C.‐Y.
Published: April 2007

It is difficult for liquid water to erupt onto the surface of icy satellites, such as Europa and Enceladus, because liquid water is more dense than ice. If the ice shell thickens, the volume expansion of ice upon freezing increases pressure in the subsurface ocean. The excess pressure is determined by a balance between compression of ocean water and elastic expansion of the ice shell. We show that on Europa the freezing of ∼ 1–10 km of ice generates tangential stresses that exceed the tensile strength of ice. Excess pressure, however, is insufficient for liquid water to erupt to the surface. Within smaller icy satellites, such as Enceladus, ocean pressure can become large enough to cause an eruption of large amounts of liquid water.
Connexin30 deficiency causes instrastrial fluid–blood barrier disruption within the cochlear stria vascularis
Authors: Cohen-Salmon Martine , Regnault Béatrice , Cayet Nadège , Caille Dorothée , Demuth Karine , Hardelin Jean-Pierre , Janel Nathalie , Meda Paolo , Petit Christine
Published: March 2007

The endocochlear potential (EP) is essential to hearing, because it provides approximately half of the driving force for the mechanoelectrical transduction current in auditory hair cells. The EP is produced by the stria vascularis (SV), a vascularized bilayer epithelium of the cochlea lateral wall. The absence of the gap junction protein connexin30 (Cx30) in
Cx30
−/−
mice results in the SV failure to produce an EP, which mainly accounts for the severe congenital hearing impairment of these mice. Here, we show that the SV components of the EP electrogenic machinery and the epithelial barriers limiting the intrastrial fluid space, which are both necessary for the EP production, were preserved in
Cx30
−/−
mice. In contrast, the endothelial barrier of the capillaries supplying the SV was disrupted before EP onset. This disruption is expected to result in an intrastrial electric shunt that is sufficient to account for the absence of the EP production. Immunofluorescence analysis of wild-type mice detected Cx30 in the basal and intermediate cells of the SV but not in the endothelial cells of the SV capillaries. Moreover, dye-coupling experiments showed that endothelial cells were not coupled to the SV basal, intermediate, and marginal cells. SV transcriptome analysis revealed a significant down-regulation of betaine homocysteine
S
-methyltransferase (
Bhmt
) in the
Cx30
−/−
mice, which was restricted to the SV and resulted in a local increase in homocysteine, a known factor of endothelial dysfunction. Disruption of the SV endothelial barrier is a previously undescribed pathogenic process underlying hearing impairment.
Killer T cells regulate antigen presentation for early expansion of memory, but not naive, CD8+T cell
Authors: Belz Gabrielle T. , Zhang Lei , Lay Matthew D. H. , Kupresanin Fiona , Davenport Miles P.
Published: March 2007

Antigen presentation within the lymph node draining a site of infection is crucial for initiation of cytotoxic T cell responses. Precisely how this antigen presentation regulates T cell expansionin vivois unclear. Here, we show that, in primary infection, antigen presentation peaks ≈3 days postinfection and then slowly decays until day 12. This prolonged antigen presentation is required for optimal expansion of naive CD8+T cells, because early ablation of dendritic cells reduces the later CD8+T cell response. Antigen presentation during secondary infection was 10-fold lower in magnitude and largely terminated by day 4 postinfection. Expansion of memory, but not naive, antigen-specific T cells was tightly controlled by perforin-dependent cytolysis of antigen-presenting cells. The ability of the memory T cells to remove antigen-presenting cells provides a negative-feedback loop to directly limit the duration of antigen presentationin vivo.
Time-resolved infrared (TRIR) study on the formation and reactivity of organometallic methane and ethane complexes in room temperature solution
Authors: Cowan Alexander J. , Portius Peter , Kawanami Hajime K. , Jina Omar S. , Grills David C. , Sun Xue-Zhong , McMaster Jonathan , George Michael W.
Published: April 2007

We have used fast time-resolved infrared spectroscopy to characterize a series of organometallic methane and ethane complexes in solution at room temperature: W(CO)
5
(CH
4
) and M(η
5

C
5
R
5
)(CO)
2
(L) [where M = Mn or Re, R = H or CH
3
(Re only); and L = CH
4
or C
2
H
6
]. In all cases, the methane complexes are found to be short-lived and significantly more reactive than the analogous
n
-heptane complexes. Re(Cp)(CO)
2
(CH
4
) and Re(Cp*)(CO)
2
(L) [Cp* = η
5

C
5
(CH
3
)
5
and L = CH
4
, C
2
H
6
] were found to be in rapid equilibrium with the alkyl hydride complexes. In the presence of CO, both alkane and alkyl hydride complexes decay at the same rate. We have used picosecond time-resolved infrared spectroscopy to directly monitor the photolysis of Re(Cp*)(CO)
3
in
sc
CH
4
and demonstrated that the initially generated Re(Cp*)(CO)
2
(CH
4
) forms an equilibrium mixture of Re(Cp*)(CO)
2
(CH
4
)/Re(Cp*)(CO)
2
(CH
3
)H within the first few nanoseconds (τ = 2 ns). The ratio of alkane to alkyl hydride complexes varies in the order Re(Cp)(CO)
2
(C
2
H
6
):Re(Cp)(CO)
2
(C
2
H
5
)H > Re(Cp*)(CO)
2
(C
2
H
6
):Re(Cp*)(CO)
2
(C
2
H
5
)H ≈ Re(Cp)(CO)
2
(CH
4
):Re(Cp)(CO)
2
(CH
3
)H > Re(Cp*)(CO)
2
(CH
4
):Re(Cp*)(CO)
2
(CH
3
)H. Activation parameters for the reactions of the organometallic methane and ethane complexes with CO have been measured, and the ΔH
‡
values represent lower limits for the CH
4
binding enthalpies to the metal center of W

CH
4
(30 kJ·mol
−1
), Mn

CH
4
(39 kJ·mol
−1
), and Re

CH
4
(51 kJ·mol
−1
) bonds in W(CO)
5
(CH
4
), Mn(Cp)(CO)
2
(CH
4
), and Re(Cp)(CO)
2
(CH
4
), respectively.
Inhibition of CFTR Cl
−
channel function caused by enzymatic hydrolysis of sphingomyelin
Authors: Ramu Yajamana , Xu Yanping , Lu Zhe
Published: March 2007

Numerous mutations in the cystic fibrosis (CF) transmembrane conductance regulator (CFTR, a Cl
−
channel) disrupt salt and fluid transport and lead to the formation of thick mucus in patients' airways. Obstruction by mucus predisposes CF patients to chronic infections and inflammation, which become gradually harder to control and eventually fatal. Aggressive antibiotic therapy and supportive measures have dramatically lengthened CF patients' lives. Here, we report that sphingomyelinases (SMase) from human respiratory pathogens strongly inhibit CFTR function. The hydrolysis of sphingomyelin by SMase makes it more difficult to activate CFTR by phosphorylation of its regulatory domain. By inhibiting CFTR currents, SMase-producing respiratory tract bacteria may not only aggravate pulmonary infection in some CF patients but may also elicit a condition, analogous to CFTR deficiency, in non-CF patients suffering from bacterial lung infection.
Caspase 1 deficiency reduces inflammation-induced brain transcription
Authors: Mastronardi Claudio , Whelan Fiona , Yildiz Ozlem A. , Hannestad Jonas , Elashoff David , McCann Samuel M. , Licinio Julio , Wong Ma-Li
Published: April 2007

The systemic inflammatory response syndrome (SIRS) is a life-threatening medical condition characterized by a severe and generalized inflammatory state that can lead to multiple organ failure and shock. The CNS regulates many features of SIRS such as fever, cardiovascular, and neuroendocrine responses. Central and systemic manifestations of SIRS can be induced by LPS or IL-1β administration. The crucial role of IL-1β in inflammation has been further highlighted by studies of mice lacking caspase 1 (casp1, also known as IL-1β convertase), a protease that cleaves pro-IL-1β into mature IL-1β. Indeed, casp1 knockout (casp1−/−) mice survive lethal doses of LPS. The key role of IL-1β in sickness behavior and itsde novoexpression in the CNS during inflammation led us to test the hypothesis that IL-1β plays a major role modulating the brain transcriptome during SIRS. We show a gene–environment effect caused by LPS administration in casp1−/−mice. During SIRS, the expression of several genes, such as chemokines, GTPases, the metalloprotease ADAMTS1, IL-1RA, the inducible nitric oxide synthase, and cyclooxygenase-2, was differentially increased in casp1−/−mice. Our findings may contribute to the understanding of the molecular changes that take place within the CNS during sepsis and SIRS and the development of new therapies for these serious conditions. Our results indicate that those genes may also play a role in several neuropsychiatric conditions in which inflammation has been implicated and indicate that casp1 might be a potential therapeutic target for such disorders.
Management, presentation and interpretation of genome scans using GSCANDB
Authors: Taylor Martin , Valdar William , Kumar Ashish , Flint Jonathan , Mott Richard
Published: March 2007

Motivation: Advances in high-throughput genotyping have made it possible to carry out genome-wide association studies using very high densities of genetic markers. This has led to the problem of the storage, management, quality control, presentation and interpretation of results. In order to achieve a successful outcome, it may be necessary to analyse the data in different ways and compare the results with genome annotations and other genome scans.

Results: We created GSCANDB, a database for genome scan data, using a MySQL backend and Perl-CGI web interface. It displays genome scans of multiple phenotypes analysed in different ways and projected onto genome annotations derived from EnsMart. The current version is optimized for analysis of mouse data, but is customizable to other species.

Availability: Source code and example data are available under the GPL, in versions tailored to either human or mouse association studies, from http://gscan.well.ox.ac.uk/software.

Contact:  Richard.Mott@well.ox.ac.uk

Supplementary information: The GSCANDB database of mouse genome scans is accessible from http://gscan.well.ox.ac.uk.
SCEPTRANS: an online tool for analyzing periodic transcription in yeast
Authors: Kudlicki Andrzej , Rowicka Maga , Otwinowski Zbyszek
Published: March 2007

Summary: SCEPTRANS is designed for analysis of microarray timecourse data related to periodic phenomena in the budding yeast. The server allows for easy viewing of temporal profiles of multiple genes in a number of datasets. Additional functionality includes searching for coexpressed genes, periodicity and correlation analysis, integrating functional annotation and localization data as well as advanced operations on sets of genes.

Availability: Available online at http://sceptrans.org/

Contact:  andrzej@work.swmed.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Evaluation of Antioxidant and Wound Healing Effects of Alcoholic and Aqueous Extract of Ocimum sanctum Linn in Rats
Authors: Shetty Somashekar , Udupa Saraswati , Udupa Laxminarayana
Published: April 2007

In recent years, oxidative stress and free radicals have been implicated in impaired wound healing. Ocimum sanctum (O. sanctum), a plant widely used in Ayurveda, possesses anti‐inflammatory and antioxidant properties. The present study was undertaken to assess the potential of alcoholic and aqueous extracts in wound healing in Wistar albino rats. The rats were divided into five groups of six animals each. Group 1 is normal wounded control and the other four groups were treated with two different doses each of alcoholic and aqueous extract of O. sanctum. The wound healing parameters were evaluated by using incision, excision and dead space wounds in extract‐treated rats and controls. Both the doses of alcoholic and aqueous extract significantly increased wound breaking strength, hydroxyproline, hexuronic acid, hexosamines, superoxide dismutase, catalase, reduced glutathione and significantly decreased percentage of wound contraction and lipid peroxidation when compared with the control group. The results suggest that O. sanctum has antioxidant properties, which may be responsible and favorable for faster wound healing and this plant extract may be useful in the management of abnormal healing and hypertropic scars.
Activity/Stability of Human Pepsin: Implications for Reflux Attributed Laryngeal Disease
Authors: Johnston Nikki , Dettmar Peter W. , Bishwokarma Bimjhana , Lively Mark O. , Koufman Jamie A.
Published: April 2007

Objectives/Hypothesis: Exposure of laryngeal epithelia to pepsin during extra‐esophageal reflux causes depletion of laryngeal protective proteins, carbonic anhydrase isoenzyme III (CAIII), and squamous epithelial stress protein Sep70. The first objective of this study was to determine whether pepsin has to be enzymatically active to deplete these proteins. The second objective was to investigate the effect of pH on the activity and stability of human pepsin 3b under conditions that might be found in the human esophagus and larynx.

Study Design: Prospective translational research study.

Methods: An established porcine in vitro model was used to examine the effect of active/inactive pepsin on laryngeal CAIII and Sep70 protein levels. The activity and stability of pepsin was determined by kinetic assay, measuring the rate of hydrolysis of a synthetic pepsin‐specific substrate after incubation at various pH values for increasing duration.

Results: Active pepsin is required to deplete laryngeal CAIII and Sep70. Pepsin has maximum activity at pH 2.0 and is inactive at pH 6.5 or higher. Although pepsin is inactive at pH 6.5 and above, it remains stable until pH 8.0 and can be reactivated when the pH is reduced. Pepsin is stable for at least 24 hours at pH 7.0, 37°C and retains 79% ± 11% of its original activity after re‐acidification at pH 3.0.

Conclusions: Detectable levels of pepsin remain in laryngeal epithelia after a reflux event. Pepsin bound there would be enzymatically inactive because the mean pH of the laryngopharynx is pH 6.8. Significantly, pepsin could remain in a form that would be reactivated by a subsequent decrease in pH, such as would occur during an acidic reflux event or possibly after uptake into intracellular compartments of lower pH.
Induction of apoptosis in Saccharomyces cerevisiae results in the spontaneous maturation of tetravirus procapsids in vivo
Authors: Tomasicchio Michele , Venter Philip Arno , H. J. Gordon Karl , N. Hanzlik Terry , Dorrington Rosemary Ann
Published: April 2007

TheTetraviridaeare a family of small, non-enveloped, insect RNA viruses consisting of one or two single-stranded, positive-sense genomic RNAs encapsidated in an icosahedral capsid withT=4 symmetry. Tetravirus procapsids undergo maturation when exposed to a low pH environmentin vitro. While the structural biology of the conformational changes that mediate acid-dependent maturation is well understood, little is known about the significance of acid-dependent maturationin vivo. To address this question, the capsid-coding sequence of the tetravirusHelicoverpa armigera stunt viruswas expressed inSaccharomyces cerevisiaecells. Virus-like particles were shown to assemble as procapsids that matured spontaneouslyin vivoas the cells began to age. Growth in the presence of hydrogen peroxide or acetic acid, which induced apoptosis or programmed cell death in the yeast cells, resulted in virus-like particle maturation. The results demonstrate that assembly-dependent maturation of tetravirus procapsidsin vivois linked to the onset of apoptosis in yeast cells. We propose that the reduction in pH required for tetraviral maturation may be the result of cytosolic acidification, which is associated with the early onset of programmed cell death in infected cells.
Human herpesvirus 7 infection increases the expression levels of CD46 and CD59 in target cells
Authors: Takemoto Masaya , Yamanishi Koichi , Mori Yasuko
Published: April 2007

CD46 (membrane cofactor protein; MCP) is a molecule that functions as either a complement-regulatory protein (CRP) or a receptor for some pathogens, including human herpesvirus 6. DNA microarray analysis suggested that the expression of CD46 was upregulated in T cells infected with human herpesvirus 7 (HHV-7). Northen and Western blot analyses supported this result at both the transcriptional and translational levels. Flow-cytometric analysis revealed that upregulation of CD46 occurred at a late stage of infection in both SupT1 cells and primary CD4+T cells, and also that expression of another CRP, CD59, was increased at a late stage of infection. Whether these CRPs actually function in HHV-7-infected cells was addressed and it was found that HHV-7-infected cells were more resistant to complement-dependent cytotoxicity than were uninfected cells. This study is the first report demonstrating that HHV-7 infection causes elevation of the CRPs CD46 and CD59, which may be a possible mechanism for HHV-7 to evade humoral immunity via complement.
Complete genomes for hepatitis C virus subtypes 6f, 6i, 6j and 6m: viral genetic diversity among Thai blood donors and infected spouses
Authors: Lu Ling , Li Chunhua , Fu Yongshui , Thaikruea Lakkana , Thongswat Satawat , Maneekarn Niwat , Apichartpiyakul Chatchawann , Hotta Hak , Okamoto Hiroaki , Netski Dale , Pybus Oliver G. , Murphy Donald , Hagedorn Curt H. , Nelson Kenrad E.
Published: April 2007

In this study, the first complete genome sequences for hepatitis C virus (HCV) subtypes 6f, 6i, 6j and 6m, obtained from infected blood donors in Chiang Mai, Thailand, are reported. Pairwise genome-wide nucleotide similarities between some of these isolates were higher than the 75–80 % value used previously to define different HCV subtypes. To investigate further, the entire genomes of four prototype isolates, Th602 (6i), Th553 (6j), B4/92 (6m) and D86/93 (6n), were sequenced. Pairwise comparison of these sequences gave a similar range of nucleotide similarities, thereby providing new information for HCV subtype classification. In order to study the hypothesis of interspousal HCV transmission, four additional complete HCV genome sequences were obtained from two infected Thai blood donors and their spouses, C-0044 and C-0046 (6f), and C-0192 and C-0185 (6m). Pairwise comparison of the sequences revealed that C-0044 and C-0046 share a nucleotide similarity of 98.1 %, whilst C-0185 and C-0192 have a similarity of 97.8 %. Several other studies of partial HCV sequences of different genomic regions from HCV-infected couples have shown nucleotide similarities ranging from 96.3 to 100 %. The similarities of the complete genome sequences from the two couples in the current study are consistent with HCV transmission between spouses.
Molecular dissection of the potato virus Y VPg virulence factor reveals complex adaptations to the pvr2 resistance allelic series in pepper
Authors: Ayme Valérie , Petit-Pierre Julien , Souche Sylvie , Palloix Alain , Moury Benoît
Published: April 2007

The virulence properties of potato virus Y (PVY) towards an allelic series at thepvr2locus in pepper genotypes are related to variations in the genome-linked viral protein (VPg). Eleven amino acid substitutions in the central part of the VPg were identified in strains differing by their virulenceproperties and were introduced, either singly or in combination, in an infectious PVY clone to get an in-depth genetic analysis of the virulence determinant. The virulence spectrum of these mutants was evaluated by inoculation of four pepper genotypes carrying different alleles at thepvr2locus. The mutations introduced had complex effects on virulence, including antagonisticepistasis and trade-offs for virulence towards differentpvr2alleles. In addition, several mutants showed new virulence properties that were unknown in the natural environment. Such complex effects of mutations on plant virus virulence are unprecedented. They provide a better understanding of the variable levels of durability of the resistance conferred by the differentpvr2alleles, and have important consequences for a durable management of the resistances.
Identification and functional analysis of the origins of DNA replication in the Cydia pomonella granulovirus genome
Authors: Hilton Sally , Winstanley Doreen
Published: April 2007

The entire genome ofCydia pomonellagranulovirus (CpGV) was systematically screened for origins of DNA replication, using an infection-dependent DNA replication assay in the granulovirus-permissiveCydia pomonellacell line, Cp14R. All seven cosmids in an overlapping library that covered the CpGV genome were found to replicate in the assay. A genomic library of 32 overlapping plasmids was subsequently screened. Plasmids that replicated were in turn subcloned into 1–2 kbp overlapping fragments. Eleven subclones replicated, each containing at least one of the 13 single-copy 74–76 bp imperfect palindromes, previously identified in the CpGV genome as possible origins of replication. Genome fragments of 156 bp, each containing one of the 13 palindromes, were cloned to verify replication and provided confirmation that these 13 palindromes are the only origins of replication in the genome. A real-time PCR method was developed for the quantification of DNA replication, which eliminated the need for Southern blotting and hybridization. A set of deletion clones allowed further quantitative characterization of one of the palindromes. The previously proposed non-homologous region origin of replication did not replicate in the assay.
Vaccination with a T-cell-priming Gag peptide of caprine arthritis encephalitis virus enhances virus replication transiently in vivo
Authors: Nenci Chiara , Zahno Marie-Luise , Vogt Hans-Rudolf , Obexer-Ruff Gabriela , Doherr Marcus G. , Zanoni Reto , Peterhans Ernst , Bertoni Giuseppe
Published: April 2007

CD4+ T cells are involved in several immune response pathways used to control viral infections. In this study, a group of genetically defined goats was immunized with a synthetic peptide known to encompass an immunodominant helper T-cell epitope of caprine arthritis encephalitis virus (CAEV). Fifty-five days after challenge with the molecularly cloned CAEV strain CO, the vaccinated animals had a higher proviral load than the controls. The measurement of gamma interferon and interleukin-4 gene expression showed that these cytokines were reliable markers of an ongoing immune response but their balance did not account for more or less efficient control of CAEV replication. In contrast, granulocyte–macrophage colony-stimulating factor appeared to be a key cytokine that might support virus replication in the early phase of infection. The observation of a potential T-cell-mediated enhancement of virus replication supports other recent findings showing that lentivirus-specific T cells can be detrimental to the host, suggesting caution in designing vaccine candidates.
Complete genomes of hepatitis C virus (HCV) subtypes 6c, 6l, 6o, 6p and 6q: completion of a full panel of genomes for HCV genotype 6
Authors: Lu Ling , Li Chunhua , Fu Yongshui , Gao Fengxiang , Pybus Oliver G. , Abe Kenji , Okamoto Hiroaki , Hagedorn Curt H. , Murphy Donald
Published: April 2007

Five hepatitis C virus (HCV) complete genome sequences (Th846, 537796, QC227, QC216 and QC99) from a blood donor in Thailand and three Asian immigrants and one Caucasian in North America were determined. Phylogenetically, they represent the first complete genomes for subtypes 6c, 6l, 6o, 6p and 6q, respectively. Similarity analysis showed no evidence of inter- or intrasubtype recombination. Further analysis in conjunction with partial sequences from the Los Alamos HCV database led to the identification of other closely related isolates from south-eastern Asia or immigrants from that region. However, Th846 did not cluster with any reference sequence and is the sole isolate of subtype 6c reported so far. This study completes the full genome sequencing of all 17 assigned HCV genotype 6 subtypes (6a–6q). The utility of this panel of complete sequences for accurate detection and classification of infection, and for estimating the origin of this genotype of HCV, is discussed.
Transcript Profiling of Poplar Leaves upon Infection with Compatible and Incompatible Strains of the Foliar RustMelampsora larici-populina
Authors: Rinaldi Cécile , Kohler Annegret , Frey Pascal , Duchaussoy Frédéric , Ningre Nathalie , Couloux Arnaud , Wincker Patrick , Le Thiec Didier , Fluch Silvia , Martin Francis , Duplessis Sébastien
Published: March 2007

To understand key processes governing defense mechanisms in poplar (Populus spp.) upon infection with the rust fungus Melampsora larici-populina, we used combined histological and molecular techniques to describe the infection of Populus trichocarpa × Populus deltoides ‘Beaupré’ leaves by compatible and incompatible fungal strains. Striking differences in host-tissue infection were observed after 48-h postinoculation (hpi) between compatible and incompatible interactions. No reactive oxygen species production could be detected at infection sites, while a strong accumulation of monolignols occurred in the incompatible interaction after 48 hpi, indicating a late plant response once the fungus already penetrated host cells to form haustorial infection structures. P. trichocarpa whole-genome expression oligoarrays and sequencing of cDNAs were used to determine changes in gene expression in both interactions at 48 hpi. Temporal expression profiling of infection-regulated transcripts was further compared by cDNA arrays and reverse transcription-quantitative polymerase chain reaction. Among 1,730 significantly differentially expressed transcripts in the incompatible interaction, 150 showed an increase in concentration ≥3-fold, whereas 62 were decreased by ≥3-fold. Regulated transcripts corresponded to known genes targeted by R genes in plant pathosystems, such as inositol-3-P synthase, glutathione S-transferases, and pathogenesis-related proteins. However, the transcript showing the highest rust-induced up-regulation encodes a putative secreted protein with no known function. In contrast, only a few transcripts showed an altered expression in the compatible interaction, suggesting a delay in defense response between incompatible and compatible interactions in poplar. This comprehensive analysis of early molecular responses of poplar to M. larici-populina infection identified key genes that likely contain the fungus proliferation in planta.
Rice UDP-Glucose Pyrophosphorylase1 Is Essential for Pollen Callose Deposition and Its Cosuppression Results in a New Type of Thermosensitive Genic Male Sterility
Authors: Chen Rongzhi , Zhao Xiao , Shao Zhe , Wei Zhe , Wang Yuanyuan , Zhu Lili , Zhao Jie , Sun Mengxiang , He Ruifeng , He Guangcun
Published: March 2007

UDP-glucose pyrophosphorylase (UGPase) catalyzes the reversible production of glucose-1-phosphate and UTP to UDP-glucose and pyrophosphate. The rice (Oryza sativa) genome contains two homologous UGPase genes, Ugp1 and Ugp2. We report a functional characterization of rice Ugp1, which is expressed throughout the plant, with highest expression in florets, especially in pollen during anther development. Ugp1 silencing by RNA interference or cosuppression results in male sterility. Expressing a double-stranded RNA interference construct in Ugp1-RI plants resulted in complete suppression of both Ugp1 and Ugp2, together with various pleiotropic developmental abnormalities, suggesting that UGPase plays critical roles in plant growth and development. More importantly, Ugp1-cosuppressing plants contained unprocessed intron-containing primary transcripts derived from transcription of the overexpression construct. These aberrant transcripts undergo temperature-sensitive splicing in florets, leading to a novel thermosensitive genic male sterility. Pollen mother cells (PMCs) of Ugp1-silenced plants appeared normal before meiosis, but during meiosis, normal callose deposition was disrupted. Consequently, the PMCs began to degenerate at the early meiosis stage, eventually resulting in complete pollen collapse. In addition, the degeneration of the tapetum and middle layer was inhibited. These results demonstrate that rice Ugp1 is required for callose deposition during PMC meiosis and bridges the apoplastic unloading pathway and pollen development.
Arabidopsis Phage-Type RNA Polymerases: Accurate in Vitro Transcription of Organellar Genes
Authors: Kühn Kristina , Bohne Alexandra-Viola , Liere Karsten , Weihe Andreas , Börner Thomas
Published: March 2007

The T7 bacteriophage RNA polymerase (RNAP) performs all steps of transcription, including promoter recognition, initiation, and elongation as a single-polypeptide enzyme. Arabidopsis thaliana possesses three nuclear-encoded T7 phage-type RNAPs that localize to mitochondria (RpoTm), plastids (RpoTp), or presumably both organelles (RpoTmp). Their specific functions are as yet unresolved. We have established an in vitro transcription system to examine the abilities of the three Arabidopsis phage-type RNAPs to synthesize RNA and to recognize organellar promoters. All three RpoT genes were shown to encode transcriptionally active RNAPs. RpoTmp displayed no significant promoter specificity, whereas RpoTm and RpoTp were able to accurately initiate transcription from overlapping subsets of mitochondrial and plastidial promoters without the aid of protein cofactors. Our study strongly suggests RpoTm to be the enzyme that transcribes most, if not all, mitochondrial genes in Arabidopsis. Intrinsic promoter specificity, a feature that RpoTm and RpoTp share with the T7 RNAP, appears to have been conserved over the long period of evolution of nuclear-encoded mitochondrial and plastidial RNAPs. Selective promoter recognition by the Arabidopsis phage-type RNAPs in vitro implies that auxiliary factors are required for efficient initiation of transcription in vivo.
Genome-Wide Analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 Pathway inArabidopsisReveals Dependency on miRNA- and tasiRNA-Directed Targeting
Authors: Howell Miya D. , Fahlgren Noah , Chapman Elisabeth J. , Cumbie Jason S. , Sullivan Christopher M. , Givan Scott A. , Kasschau Kristin D. , Carrington James C.
Published: March 2007

Posttranscriptional RNA silencing of many endogenous transcripts, viruses, and transgenes involves the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 (RDR6/DCL4)-dependent short interfering RNA (siRNA) biogenesis pathway. Arabidopsis thaliana contains several families of trans-acting siRNAs (tasiRNAs) that form in 21-nucleotide phased arrays through the RDR6/DCL4-dependent pathway and that negatively regulate target transcripts. Using deep sequencing technology and computational approaches, the phasing patterns of known tasiRNAs and tasiRNA-like loci from across the Arabidopsis genome were analyzed in wild-type plants and silencing-defective mutants. Several gene transcripts were found to be routed through the RDR6/DCL4-dependent pathway after initial targeting by one or multiple miRNAs or tasiRNAs, the most conspicuous example of which was an expanding clade of genes encoding pentatricopeptide repeat (PPR) proteins. Interestingly, phylogenetic analysis using Populus trichocarpa revealed evidence for small RNA–mediated regulatory mechanisms within a similarly expanded group of PPR genes. We suggest that posttranscriptional silencing mechanisms operate on an evolutionary scale to buffer the effects of rapidly expanding gene families.
Elaboration of B Gene Function to Include the Identity of Novel Floral Organs in the Lower EudicotAquilegia
Authors: Kramer Elena M. , Holappa Lynn , Gould Billie , Jaramillo M. Alejandra , Setnikov Dimitriy , Santiago Philip M.
Published: March 2007

The basal eudicot Aquilegia (columbine) has an unusual floral structure that includes two morphologically distinct whorls of petaloid organs and a clearly differentiated fifth organ type, the staminodium. In this study, we have sought to determine how Aquilegia homologs of the B class genes APETALA3 (AP3) and PISTILLATA (PI) contribute to these novel forms of organ identity. Detailed expression analyses of the three AP3 paralogs and one PI homolog in wild-type and floral homeotic mutant lines reveal complex patterns that suggest that canonical B class function has been elaborated in Aquilegia. Yeast two-hybrid studies demonstrate that the protein products of Aquilegia's AP3 and PI homologs can form heterodimers, much like what has been observed for their core eudicot homologs. Downregulation of AqvPI using virus-induced gene silencing indicates that in addition to petal and stamen identity, this locus is essential to staminodial identity but may not control the identity of the petaloid sepals. Our findings show that preexisting floral organ identity programs can be partitioned and modified to produce additional organ types. In addition, they indicate that some types of petaloid organs are not entirely dependent on AP3/PI homologs for their identity.