bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and Application of a Universal Hemoplasma Screening Assay Based on the SYBR Green PCR Principle
Authors: Willi Barbara , Meli Marina L. , Lüthy Ruedi , Honegger Hanspeter , Wengi Nicole , Hoelzle Ludwig E. , Reusch Claudia E. , Lutz Hans , Hofmann-Lehmann Regina 
Published: October 2009

ABSTRACTHemotropic mycoplasmas (hemoplasmas) are the causative agents of infectious anemia in several mammalian species. Their zoonotic potential has recently been substantiated by the identification of a feline hemoplasma isolate in an immunocompromised human patient. Although species-specific diagnostic molecular methods have been developed, their application as screening tools is limited due to the species diversity of hemoplasmas. The goals of this study were to develop a universal hemoplasma screening assay with broad specificity based on the SYBR green PCR principle, to compare the assay with hemoplasma-specific TaqMan PCR, and to analyze potential tick vectors and human blood samples to address the zoonotic potential. The newly developed PCR assay based on the 16S rRNA gene amplified feline, canine, bovine, porcine, camelid, and murine hemoplasmas, as well asMycoplasma penetransandMycoplasma pneumoniae. The lower detection limit for feline and canine hemoplasmas was 1 to 10 copies/PCR. The assay exhibited 98.2% diagnostic sensitivity and 92.1% diagnostic specificity for feline hemoplasmas. All 1,950Ixodesticks were PCR negative, suggesting thatIxodesticks are not relevant vectors for the above-mentioned hemoplasma species in Switzerland. None of the 414 blood samples derived from anemic or immunocompromised human patients revealed a clear positive result. The SYBR green PCR assay described here is a suitable tool to screen for known and so-far-undiscovered hemoplasma species. Positive results should be confirmed by specific TaqMan PCR or sequencing.
Lymphocytic Choriomeningitis Virus-Induced Mortality in Mice Is Triggered by Edema and Brain Herniation
Authors: Matullo Christine M. , O'Regan Kevin J. , Hensley Harvey , Curtis Mark , Rall Glenn F. 
Published: October 2009

ABSTRACT
Although much is known about lymphocytic choriomeningitis virus (LCMV) infection and the subsequent immune response in its natural murine host, some crucial aspects of LCMV-mediated pathogenesis remain undefined, including the underlying basis of the characteristic central nervous system disease that occurs following intracerebral (i.c.) challenge. We show that the classic seizures and paresis that occur following i.c. infection of adult, immunocompetent mice with LCMV are accompanied by anatomical and histological changes that are consistent with brain herniation, likely of the uncal subtype, as a causative basis for disease and precipitous death. Both by water weight determinations and by magnetic resonance imaging of infected brain tissues, edema was detected only at the terminal stages of disease, likely caused by the leakage of cerebrospinal fluid from the ventricles into the parenchyma. Furthermore, death was accompanied by unilateral pupillary dilation, which is indicative of uncal herniation. While immunohistochemical analysis revealed periventricular inflammation and a loss of integrity of the blood-brain barrier (BBB), these events preceded seizures by 2 to 3 days. Moreover, surviving perforin knockout mice showed barrier permeability equivalent to that of moribund, immunocompetent mice; thus, BBB damage does not appear to be the basis of LCMV-induced neuropathogenesis. Importantly, brain herniation can occur in humans as a consequence of injuries that would be predicted to increase intracranial pressure, including inflammation, head trauma, and brain tumors. Thus, a mechanistic dissection of the basis of LCMV neuropathogenesis may be informative for the development of interventive therapies to prevent this typically fatal human condition.
Anti-Glycoprotein H Antibody Impairs the Pathogenicity of Varicella-Zoster Virus in Skin Xenografts in the SCID Mouse Model
Authors: Vleck Susan E. , Oliver Stefan L. , Reichelt Mike , Rajamani Jaya , Zerboni Leigh , Jones Carol , Zehnder James , Grose Charles , Arvin Ann M. 
Published: October 2009

ABSTRACTVaricella-zoster virus (VZV) infection is usually mild in healthy individuals but can cause severe disease in immunocompromised patients. Prophylaxis with varicella-zoster immunoglobulin can reduce the severity of VZV if given shortly after exposure. Glycoprotein H (gH) is a highly conserved herpesvirus protein with functions in virus entry and cell-cell spread and is a target of neutralizing antibodies. The anti-gH monoclonal antibody (MAb) 206 neutralizes VZV in vitro. To determine the requirement for gH in VZV pathogenesis in vivo, MAb 206 was administered to SCID mice with human skin xenografts inoculated with VZV. Anti-gH antibody given at 6 h postinfection significantly reduced the frequency of skin xenograft infection by 42%. Virus titers, genome copies, and lesion size were decreased in xenografts that became infected. In contrast, administering anti-gH antibody at 4 days postinfection suppressed VZV replication but did not reduce the frequency of infection. The neutralizing anti-gH MAb 206 blocked virus entry, cell fusion, or both in skin in vivo. In vitro, MAb 206 bound to plasma membranes and to surface virus particles. Antibody was internalized into vacuoles within infected cells, associated with intracellular virus particles, and colocalized with markers for early endosomes and multivesicular bodies but not thetrans-Golgi network. MAb 206 blocked spread, altered intracellular trafficking of gH, and bound to surface VZV particles, which might facilitate their uptake and targeting for degradation. As a consequence, antibody interference with gH function would likely prevent or significantly reduce VZV replication in skin during primary or recurrent infection.
Human Regulatory T Cells Are Targets for Human Immunodeficiency Virus (HIV) Infection, and Their Susceptibility Differs Depending on the HIV Type 1 Strain
Authors: Moreno-Fernandez Maria E. , Zapata Wildeman , Blackard Jason T. , Franchini Genoveffa , Chougnet Claire A. 
Published: October 2009

ABSTRACT

Regulatory T cells (Treg) are a subpopulation of CD4
+
T cells characterized by the suppressive activity they exert on effector immune responses, including human immunodeficiency virus (HIV)-specific immune responses. Because Treg express CXCR4 and CCR5, they represent potential targets for HIV; however, Treg susceptibility to HIV infection is still unclear. We therefore performed an extensive study of Treg susceptibility to HIV, using lab strains and primary isolates with either CCR5 or CXCR4 tropism. Furthermore, we quantified HIV infection at early and late time points of the virus life cycle. We found that Treg were clearly susceptible to HIV infection. Circulating Treg were not preferentially infected with HIV compared to effector T cells (Teff) in vivo. Conversely, in vitro infection with either CCR5-using (R5) or CXCR4-using (X4) viruses occurred with different dynamics. For instance, HIV infection by R5 viruses (lab strains and primary isolates) resulted in lower levels of infection in Treg compared with Teff at both early and late time points. In contrast, X4 viruses induced higher levels of infection in Treg compared to Teff at early time points, but this difference disappeared at the late time points of the virus life cycle. Our results suggest that the relative susceptibility of Treg to HIV infection compared to Teff varies, depending on both viral and host factors. These variations may play an important role in HIV pathogenesis.
Nanodisc-Incorporated Hemagglutinin Provides Protective Immunity against Influenza Virus Infection
Authors: Bhattacharya Palash , Grimme Steve , Ganesh Balaji , Gopisetty Anupama , Sheng Jian Rong , Martinez Osvaldo , Jayarama Shankar , Artinger Michael , Meriggioli Matthew , Prabhakar Bellur S. 
Published: October 2009

ABSTRACTEvery year, influenza virus infection causes significant mortality and morbidity in human populations. Although egg-based inactivated viral vaccines are available, their effectiveness depends on the correct prediction of the circulating viral strains and is limited by the time constraint of the manufacturing process. Recombinant subunit vaccines are easier to manufacture with a relatively short lead time but are limited in their efficacy partly because the purified recombinant membrane proteins in the soluble form most likely do not retain their native membrane-bound structure. Nanodisc (ND) particles are soluble, stable, and reproducibly prepared discoid shaped nanoscale structures that contain a discrete lipid bilayer bound by two amphipathic scaffold proteins. Because ND particles permit the functional reconstitution of membrane/envelope proteins, we incorporated recombinant hemagglutinin (HA) from influenza virus strain A/New Caledonia/20/99 (H1N1) into NDs and investigated their potential to elicit an immune response to HA and confer immunity to influenza virus challenge relative to the commercial vaccines Fluzone and FluMist. HA-ND vaccination induced a robust anti-HA antibody response consisting of predominantly the immunoglobulin G1 (IgG1) subclass and a high hemagglutination inhibition titer. Intranasal immunization with HA-ND induced an anti-HA IgA response in nasal passages. HA-ND vaccination conferred protection that was comparable to that of Fluzone and FluMist against challenge with influenza virus strain A/Puerto Rico/8/1934 (H1N1).
The Bovine Immunodeficiency Virus Rev Protein: Identification of a Novel Lentiviral Bipartite Nuclear Localization Signal Harboring an Atypical Spacer Sequence
Authors: Gomez Corredor Andrea , Archambault Denis 
Published: October 2009

ABSTRACT
The bovine immunodeficiency virus (BIV) Rev protein (186 amino acids [aa] in length) is involved in the nuclear exportation of partially spliced and unspliced viral RNAs. Previous studies have shown that BIV Rev localizes in the nucleus and nucleolus of infected cells. Here we report the characterization of the nuclear/nucleolar localization signals (NLS/NoLS) of this protein. Through transfection of a series of deletion mutants of BIV Rev fused to enhanced green fluorescent protein and fluorescence microscopy analyses, we were able to map the NLS region between aa 71 and 110 of the protein. Remarkably, by conducting alanine substitution of basic residues within the aa 71 to 110 sequence, we demonstrated that the BIV Rev NLS is bipartite, maps to aa 71 to 74 and 95 to 101, and is predominantly composed of arginine residues. This is the first report of a bipartite Rev (or Rev-like) NLS in a lentivirus/retrovirus. Moreover, this NLS is atypical, as the length of the sequence between the motifs composing the bipartite NLS, e.g., the spacer sequence, is 20 aa. Further mutagenesis experiments also identified the NoLS region of BIV Rev. It localizes mainly within the NLS spacer sequence. In addition, the BIV Rev NoLS sequence differs from the consensus sequence reported for other viral and cellular nucleolar proteins. In summary, we conclude that the nucleolar and nuclear localizations of BIV Rev are mediated via novel NLS and NoLS motifs.
The Effects of Influenza A Virus PB1-F2 Protein on Polymerase Activity Are Strain Specific and Do Not Impact Pathogenesis
Authors: McAuley Julie L. , Zhang Kelly , McCullers Jonathan A. 
Published: October 2009

ABSTRACT
The influenza A virus PB1-F2 protein has been implicated as a virulence factor, but the mechanism by which it enhances pathogenicity is not understood. The PB1 gene segment of the H1N1 swine-origin influenza virus pandemic strain codes for a truncated PB1-F2 protein which terminates after 11 amino acids but could acquire the full-length form by mutation or reassortment. It is therefore important to understand the function and impact of this protein. We systematically assessed the effect that PB1-F2 expression has on viral polymerase activity, accumulation and localization of PB1, and replication in vitro and in mice. We used both the laboratory strain PR8 and a set of viruses engineered to study clinically relevant PB1-F2 proteins. PB1-F2 expression had modest effects on polymerase activity, PB1 accumulation, and replication that were cell type and virus strain dependent. Disruption of the PB1-F2 reading frame in a recent, seasonal H3N2 influenza virus strain did not affect these parameters, suggesting that this is not a universal function of the protein. Disruption of PB1-F2 expression in several backgrounds or expression of PB1-F2 from the 1918 pandemic strain or a 1956 H1N1 strain had no effect on viral lung loads in mice. Alternate mechanisms besides alterations to replication are likely responsible for the enhanced virulence in mammalian hosts attributed to PB1-F2 in previous studies.
On a Protrusion of Silurian Rock in the North of Ayrshire
Authors: Moore J. C. 
Published: October 2009

The productive coal-fields of Ayrshire terminate abruptly to the north at the town of Ardrossan, from whence, for some miles along the coast, red sandstones and conglomerates prevail. These are correctly coloured in the maps of Phillips and of Sharpe as Old Red Sandstone, though I am not aware upon what precise grounds. At Ardrossan, and for two or three miles at least to the north, the two formations are caused by a fault to abut against each other; so that proof by superposition is wanting: no fossils, I believe, have been found in the red sandstones; and the coast of Arran opposite gives an example of sandstones and conglomerates indistinguishable in mineral type, some superior to, and others underlying the coal-measures. Having lately discovered a patch of Silurian rock in this district, which appears to me conclusive of the age of the sandstone series, it may be worth while to give details of the section.
From Saltcoats to Ardrossan (see fig.) the coal-measures are seen on the shore, dipping S.E., and consisting of the usual alternations of sandstones and shales with imbedded plants, beds of coal, and limestone. Approaching the harbour of Ardrossan, these beds dip S.E. at an angle of 45°, when a mass of trap sets in, which, running out to sea, forms a natural breakwater. To the north of the trap begin the red sandstones, also dipping S.E., but at a lower angle. They are well exhibited in a quarry immediately north of the town. The top
On a Section of a part of the Fifeshire Coast
Authors: Brown Thomas 
Published: October 2009

This section of the Carboniferous strata, as exposed on the northern shore of the Firth of Forth, from Anstruther to Burntisland, represents the strata, at about high-water mark, arranged as occupying the space due to their real thickness only.
The Carboniferous rocks in this section present three great natural groups:—1, the Lower Carboniferous; 2, the Mountain-limestone; and 3, the Upper Carboniferous, or the workable coal-measures.

From Anstruther, on the cast, to beyond Pittenweem the sequence of strata is clear, exhibiting a magnificent series of the Lower Carboniferous rocks (approximately 3800 feet thick), consisting of freshwater or estuarine shales and sandstones, with a few bands of limestone, one of which latter is of marine origin. The comparative abundance of
Sphenopteris affinis
characterizes the upper portion of this inferior group; and of
Cyclopteris
, its lower portion. The Burdiehouse limestone belongs to the upper portion; and, like the other calcareous bands, gets thinner eastwardly. The Granton beds, on the contrary, appear to belong to the lower portion.

The lowest portion of this Lower Carboniferous series has
Cyclopteris
,
Stigmaria
,
Carpolithes
, and
Cypridœ
. The marine band—an argillaceous limestone, in the middle of the series—has
Encrinites
,
Fenestella
,
Nucula tumida
,
N. attenuata
, and
Productus semirecticulatus
. The upper half of the series contains
Sphenopteris affinis
,
Cypridœ
in abudance, and
Palœoniscus
.

The strata have a westward inclination, with a gradually increasing angle of dip, which is still greater towards St. Monance, as the section traverses the “Mountain-limestone” series. This consists of sandstones and shales, with five or six beds
On Arborescent Native Copper in the Llandudno Mine, near Great Ormshead, North Wales
Authors: Vivian William 
Published: October 2009

It is well known that copper, like some other native metals, sometimes crystallizes in filiform and arborescent shapes; but in these forms they are mostly diffused through masses of mineral gauge, or spread out upon the matrix, apparently unable to bear their own weight. The symmetrical forms, however, to which we now refer are seen by a microscope to stand up like a crystalline grove of trunks and branches.
The entire group is composed of separate crystals, strung out in axial lines; the crystals under high magnifying powers show the flat wedge-like octahedron; but there is no uniformity; each crystal, or spike of crystals, varies more or less in size and modification. In the small cavities containing these crystallizations, are associated crystals of ruby copper; the latter never run out into spikes or branching forms, but exist in single perfect or modified octahedrons, or are dotted about in irregular clusters of crystals.
The whole of these minute crystallizations occur in a bed of brown limestone, yielding a soft, rich, yellow bisulphuret of copper, —the rich ore, however, being very intimately mixed up with the crystalline limestone, something like the material of a fine-grained granite or porphyry. The ore contained in this bed seems to be a medium or transition between the harder and more sulphureous ore of the bed below and the carbonates and oxides of copper of the bed above. The copper crystallizations here are peculiar to this bed alone, and are doubtless the result of the decomposition of
On an Outlier of Lias in Aberdeenshire
Authors: Jamieson T. F. 
Published: October 2009

In a cutting of the Banff, Macduff, and Turriff Extension Railway, about four miles to the north of the latter town, close beside the turnpike-road at the Plaidy toll-bar, there has been exposed a mass of a very tenacious clay, blue in colour, and of homogeneous texture, which contains many
Ammonites, Belemnites
, and other fossils characteristic of the Lias, such as
Gryphæa, Plagiostoma,
and possibly others; these I have got myself. I also saw in the possession of one of the “navvies” a fragment of a shell resembling a
Nerinæa
, in remarkably fine preservation.

The altitude of the railway-cutting above the level of the sea, as I learn from the engineer on the line, is 250 feet. At the time of my visit the excavation had reached a depth of from 10 to 15 feet, and the “navvies” were busy at work in the “gullet,” filling their waggons with the clay, which is a mass of a fine greenish-blue colour, very compact and tenacious, and unlike any other clay in this part of the country. It consists of a fine impalpable mud, devoid of all manner of stones or pebbles, save occasionally a hard greenish nodule, enclosing the remains of a large Ammonite.
This clay is covered by a stratum of the Pleistocene Drift, of a brownish-grey colour, very sandy in some places, and of a more clayey nature in others. In this drift I found many striated fragments of clay-slate, together with bits of other primary rocks. The line
On some Fossils from South Africa
Authors: Stow C. W. 
Published: October 2009

Abstract

A
t
the close of 1850 Mr. Stow and his party fell back into the interior to avoid the Kaffirs; in making the journey he collected largely the fossils on his route, and succeeded, with much trouble, in preserving them on his return.

In a plain at the foot of the Rhenosterberg, a branch of the Sneewbergen Range (of which latter the Spitzkop is the culminating point), the author met with patches of ground strewed with nodular concretions and fossil wood (specimens 2 to 63) over an extent of about two miles in length and one in width. These fossils were on the surface, and had been probably derived from the neighbouring mountains.
The plain was of a lozenge-shape, about twelve miles broad and twenty long; and was one of several of a similar kind that he had travelled through. It was bounded by the Rhenosterberg Mountains on the N.E., on the S.W. by a nearly parallel range, and on the S.E. was contracted to a narrow valley between low rocky hills. Two low volcanic dykes crossed the plain, one on the north-western, and the other on the south-eastern side.
The strata forming the mountains are horizontal. There are about eight strata of sandstone forming the lower part of the Rhenosterberg. Immediately above there is a limestone full of rounded fragments of other calcareous and non-calcareous rocks, and sometimes containing bones (specimens 64, 65, 66). Of this pebbly limestone, or calcareous grit, there are four layers, separated one from another by several yards of strata, and varying in thickness from a few inches to about a foot.
The mountains on the opposite side of the plain are apparently composed of the same strata as the Rhenosterberg; for, taking a commanding position on one of the dykes, one can distinctly count the strata in the mountains on either side ; and so uniform are they in colour and thickness, so alike in height, and equally horizontal in position, that the idea at once forces itself upon the mind that they must at one time have been continuous.
At one spot on the side of the Rhenosterberg is a Kloof where the author found some fossils imbedded in the rock; and he often regretted when visiting the spot that the Kaffirs had left him nothing but a hammer and old chisel that were thrown into the waggon at starting, as with better tools he might have obtained many more specimens. Here he found the specimens 68, 69, which appear to be casts of stems of plants in sandstone.
The first bones he here discovered were those of the skeleton, specimen No. 83 (a small Dieynodon). They were directly in the water-course, and only a small piece of one part was at first visible. By dint of hammering and chiseling each succeeding portion revealed itself to view. Unfortunately the skull was wanting. Underneath a large part of it there was a whitish scaly appearance on the rock, which might have been the remains of the covering that the animal had when alive.
Many portions of the strata here were matted together with the stem-like fossils, such as specimens 70-75. Specimens 76 to 82 (nodular concretions)appear to have been washed from the same strata.