bluuebunny/crossref_metadata_2025 huggingface dataset:
Admittance study of GaAs high-k metal-insulator-semiconductor capacitors with Si interface control layer
Authors: Akazawa Masamichi , Hasegawa Hideki
Published: August 2008

Admittance behavior of high-k GaAs metal-insulator-semiconductor (MIS) capacitors having an ultrathin SiNx∕Si interface control double layer has been investigated in detail. The measured admittance showed characteristic features that are difficult to explain by the standard Si metal-oxide-semiconductor theory. They include (1) vertical and horizontal types of frequency dispersion in C-V curves, (2) presence of offset conductance in G∕ω-f plot, and (3) discrepancy between the surface potential from the high-frequency capacitance and the corresponding relaxation frequency of interface states. All of these features are tentatively explained in a unified manner by a new distributed pinning spot (DPS) model where the MIS interface consists of DPSs in addition to pinning-free regions. When the separation of pinning spots is small, the sample shows vertical type of frequency dispersion with almost bias-independent high-frequency capacitance corresponding to pinning near midgap. When pinning spots are widely separated, the C-V curves show horizontal type of frequency dispersion, each curve showing large capacitance variation with bias. This is due to flatband voltage shifts caused by effective interface state charge at the pinning spots. The pinning spot also gives rise to conductance offset. The discrepancy related to the relaxation frequency of interface states is explained by appearance of saddle points in the potential due to interaction between pinning spots and pinning-free region.
Optimum ambient N2 pressure during HfAlO pulsed-laser deposition in Pt∕SBT∕HfAlO∕Si field effect transistors
Authors: Takahashi M. , Horiuchi T. , Wang S. , Li Q.-H. , Sakai S.
Published: August 2008

The authors report on optimization of the Hf–Al oxide (HfAlO) buffer-layer deposition conditions in a Pt∕SrBi2Ta2O9∕HfAlO∕Si field effect transistor intended for nonvolatile memory applications. The N2 pressure during pulsed-laser deposition of the HfAlO buffer layer is found to primarily affect the subthreshold swing and the width of the memory window with no significant impact on the data retention behavior of the devices. Scanning transmission electron microscopy was used to investigate the gate stack structure and the electrical properties are correlated with the observed structural variations.
Etching of TiN-based gates for advanced complementary metal-oxide-semiconductor devices
Authors: Bliznetsov V. , Singh N. , Kumar R. , Balasubramanian N. , Guo P. , Lee S. J. , Cai Y.
Published: August 2008

This article presents results of study and optimization of plasma etching of TiN and TiN-TaN gates for sub-45 mm CMOS technology. By design of experiment in decoupled plasma source using HBr/Cl2 plasma, etching parameters were established providing smooth post-etch surface.
Differentiation of
Streptococcus pneumoniae
Conjunctivitis Outbreak Isolates by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry
Authors: Williamson Yulanda M. , Moura Hercules , Woolfitt Adrian R. , Pirkle James L. , Barr John R. , Carvalho Maria Da Gloria , Ades Edwin P. , Carlone George M. , Sampson Jacquelyn S.
Published: August 2008

Streptococcus pneumoniae
(pneumococcus [Pnc]) is a causative agent of many infectious diseases, including pneumonia, septicemia, otitis media, and conjunctivitis. There have been documented conjunctivitis outbreaks in which nontypeable (NT), nonencapsulated Pnc has been identified as the etiological agent. The use of mass spectrometry to comparatively and differentially analyze protein and peptide profiles of whole-cell microorganisms remains somewhat uncharted. In this report, we discuss a comparative proteomic analysis between NT
S. pneumoniae
conjunctivitis outbreak strains (cPnc) and other known typeable or NT pneumococcal and streptococcal isolates (including Pnc TIGR4 and R6,
Streptococcus oralis
,
Streptococcus mitis
,
Streptococcus pseudopneumoniae
, and
Streptococcus pyogenes
) and nonstreptococcal isolates (including
Escherichia coli
,
Enterococcus faecalis
, and
Staphylococcus aureus
) as controls. cPnc cells and controls were grown to mid-log phase, harvested, and subsequently treated with a 10% trifluoroacetic acid-sinapinic acid matrix mixture. Protein and peptide fragments of the whole-cell bacterial isolate-matrix combinations ranging in size from 2 to 14 kDa were evaluated by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Additionally Random Forest analytical tools and dendrogramic representations (Genesis) suggested similarities and clustered the isolates into distinct clonal groups, respectively. Also, a peak list of protein and peptide masses was obtained and compared to a known Pnc protein mass library, in which a peptide common and unique to cPnc isolates was tentatively identified. Information gained from this study will lead to the identification and validation of proteins that are commonly and exclusively expressed in cPnc strains which could potentially be used as a biomarker in the rapid diagnosis of pneumococcal conjunctivitis.
Resolution of Culture
Clostridium bifermentans
DPH-1 into Two Populations, a
Clostridium
sp. and Tetrachloroethene-Dechlorinating
Desulfitobacterium hafniense
Strain JH1
Authors: Fletcher Kelly E. , Ritalahti Kirsti M. , Pennell Kurt D. , Takamizawa Kazuhiro , Löffler Frank E.
Published: August 2008

Clostridium bifermentans
strain DPH-1 reportedly dechlorinates tetrachloroethene (PCE) to
cis
-1,2-dichloroethene. Cultivation-based approaches resolved the DPH-1 culture into two populations: a nondechlorinating
Clostridium
sp. and PCE-dechlorinating
Desulfitobacterium hafniense
strain JH1. Strain JH1 carries
pceA
, encoding a PCE reductive dehalogenase, and shares other characteristics with
Desulfitobacterium hafniense
strain Y51.
Meta-Analysis of Experimental Data Concerning Antimicrobial Resistance Gene Transfer Rates during Conjugation
Authors: Hunter Paul R. , Wilkinson Dawn C. , Catling Louise A. , Barker Gary C.
Published: August 2008

This paper presents the results of a meta-analysis of published transfer rates of antimicrobial resistance genes. A total of 34 papers were identified, of which 28 contained rates estimated in relation to either donor or recipient bacterial counts. The published rates ranged from 10
−2
to 10
−9
. Generalized linear modeling was conducted to identify the factors influencing this variation. Highly significant associations between transfer frequency and both the donor (
P
= 1.2 × 10
−4
) and recipient (
P
= 1.0 × 10
−5
) genera were found. Also significant was whether the donor and recipient strains were of the same genus (
P
= 0.023) and the nature of the genetic element (
P
= 0.0019). The type of experiment, in vivo or in vitro, approached statistical significance (
P
= 0.12). Parameter estimates from a general linear model were used to estimate the probability of transfer of antimicrobial resistance genes to potential pathogens in the intestine following oral ingestion. The mean logarithms of these probabilities are in the range of [−7.0, −3.1]. These probability distributions are suitable for use in the quantitative assessment of the risk of transfer of antimicrobial resistance genes to the intestinal flora of humans and animals.
Recovery and Sequence Analysis of Hepatitis A Virus from Springwater Implicated in an Outbreak of Acute Viral Hepatitis
Authors: Tallon Lindsay A. , Love David C. , Moore Zack S. , Sobsey Mark D.
Published: August 2008

An outbreak of acute hepatitis A virus in North Carolina was linked to drinking water from a contaminated shallow spring by phylogenetic analysis of hepatitis A virus (HAV) genomic sequences. Detection of HAV and fecal indicators in the water provided useful and timely information to assist with public health prevention and control measures.
Selection of Antigens and Development of Prototype Tests for Point-of-Care Leprosy Diagnosis
Authors: Duthie Malcolm S. , Ireton Greg C. , Kanaujia Ganga V. , Goto Wakako , Liang Hong , Bhatia Ajay , Busceti Jean Marie , Macdonald Murdo , Neupane Kapil Dev , Ranjit Chaman , Sapkota Bishwa Raj , Balagon Marivic , Esfandiari Javan , Carter Darrick , Reed Steven G.
Published: August 2008

Leprosy can be a devastating chronic infection that causes nerve function impairment and associated disfigurement. Despite the recent reduction in the number of registered worldwide leprosy cases as a result of the widespread use of multidrug therapy, the number of new cases detected each year remains relatively stable. The diagnosis of leprosy is currently based on the appearance of clinical signs and requires expert clinical, as well as labor-intensive and time-consuming laboratory or histological, evaluation. For the purpose of developing an effective, simple, rapid, and low-cost diagnostic alternative, we have analyzed the serologic antibody response to identify
Mycobacterium leprae
proteins that are recognized by leprosy patients. More than 100 recombinant antigens were analyzed in a protein array format to select those with discriminatory properties for leprosy diagnosis. As expected, multibacillary leprosy patients recognized more antigens with stronger antibody responses than paucibacillary leprosy patients. Our data indicate, however, that multibacillary patients can be distinguished from paucibacillary patients, and both of these groups can be segregated from endemic control groups. We went on to confirm the diagnostic properties of antigens ML0405 and ML2331 and the LID-1 fusion construct of these two proteins by enzyme-linked immunosorbent assay. We then demonstrated the performance of these antigens in rapid test formats with a goal of developing a point-of-care diagnostic test. A serological diagnostic test capable of identifying and allowing treatment of leprosy could reduce transmission, prevent functional disabilities and stigmatizing deformities, and facilitate leprosy eradication.
The Putative α-1,2-Mannosyltransferase AfMnt1 of the Opportunistic Fungal Pathogen
Aspergillus fumigatus
Is Required for Cell Wall Stability and Full Virulence
Authors: Wagener Johannes , Echtenacher Bernd , Rohde Manfred , Kotz Andrea , Krappmann Sven , Heesemann Jürgen , Ebel Frank
Published: August 2008

Proteins entering the eukaryotic secretory pathway commonly are glycosylated. Important steps in this posttranslational modification are carried out by mannosyltransferases. In this study, we investigated the putative α-1,2-mannosyltransferase AfMnt1 of the human pathogenic mold
Aspergillus fumigatus.
AfMnt1 belongs to a family of enzymes that comprises nine members in
Saccharomyces cerevisiae
but only three in
A. fumigatus
. A Δ
afmnt1
mutant is viable and grows normally at 37°C, but its hyphal cell wall appears to be thinner than that of the parental strain. The lack of AfMnt1 leads to a higher sensitivity to calcofluor white and Congo red but not to sodium dodecyl sulfate. The growth of the mutant is abrogated at 48°C but can be restored by osmotic stabilization. The resulting colonies remain white due to a defect in the formation of conidia. Electron and immunofluorescence microscopy further revealed that the observed growth defect of the mutant at 48°C can be attributed to cell wall instability resulting in leakage at the hyphal tips. Using a red fluorescence fusion protein, we localized AfMnt1 in compact, brefeldin A-sensitive organelles that most likely represent fungal Golgi equivalents. The tumor necrosis factor alpha response of murine macrophages to hyphae was not affected by the lack of the
afmnt1
gene, but the corresponding mutant was attenuated in a mouse model of infection. This and the increased sensitivity of the Δ
afmnt1
mutant to azoles, antifungal agents that currently are used to treat
Aspergillus
infections, suggest that α-1,2-mannosyltransferases are interesting targets for novel antifungal drugs.
Substrate Specificities and Availability of Fucosyltransferase and β-Carotene Hydroxylase for Myxol 2′-Fucoside Synthesis in
Anabaena
sp. Strain PCC 7120 Compared with
Synechocystis
sp. Strain PCC 6803
Authors: Mochimaru Mari , Masukawa Hajime , Maoka Takashi , Mohamed Hatem E. , Vermaas Wim F. J. , Takaichi Shinichi
Published: August 2008

To elucidate the biosynthetic pathways of carotenoids, especially myxol 2′-glycosides, in cyanobacteria,
Anabaena
sp. strain PCC 7120 (also known as
Nostoc
sp. strain PCC 7120) and
Synechocystis
sp. strain PCC 6803 deletion mutants lacking selected proposed carotenoid biosynthesis enzymes and GDP-fucose synthase (WcaG), which is required for myxol 2′-fucoside production, were analyzed. The carotenoids in these mutants were identified using high-performance liquid chromatography, field desorption mass spectrometry, and
1
H nuclear magnetic resonance. The
wcaG
(all4826) deletion mutant of
Anabaena
sp. strain PCC 7120 produced myxol 2′-rhamnoside and 4-ketomyxol 2′-rhamnoside as polar carotenoids instead of the myxol 2′-fucoside and 4-ketomyxol 2′-fucoside produced by the wild type. Deletion of the corresponding gene in
Synechocystis
sp. strain PCC 6803 (sll1213; 79% amino acid sequence identity with the
Anabaena
sp. strain PCC 7120 gene product) produced free myxol instead of the myxol 2′-dimethyl-fucoside produced by the wild type. Free myxol might correspond to the unknown component observed previously in the same mutant (H. E. Mohamed, A. M. L. van de Meene, R. W. Roberson, and W. F. J. Vermaas, J. Bacteriol.
187:
6883-6892, 2005). These results indicate that in
Anabaena
sp. strain PCC 7120, but not in
Synechocystis
sp. strain PCC 6803, rhamnose can be substituted for fucose in myxol glycoside. The β-carotene hydroxylase orthologue (CrtR, Alr4009) of
Anabaena
sp. strain PCC 7120 catalyzed the transformation of deoxymyxol and deoxymyxol 2′-fucoside to myxol and myxol 2′-fucoside, respectively, but not the β-carotene-to-zeaxanthin reaction, whereas CrtR from
Synechocystis
sp. strain PCC 6803 catalyzed both reactions. Thus, the substrate specificities or substrate availabilities of both fucosyltransferase and CrtR were different in these species. The biosynthetic pathways of carotenoids in
Anabaena
sp. strain PCC 7120 are discussed.
Helcococcus ovis
, an Emerging Pathogen in Bovine Valvular Endocarditis
Authors: Kutzer Peter , Schulze Christoph , Engelhardt Andreas , Wieler Lothar H. , Nordhoff Marcel
Published: August 2008

The initial isolation of
Helcococcus ovis
from a valvular thrombus prompted us to investigate the prevalence of this bacterium in bovine valvular endocarditis. Specimens from 55 affected hearts were examined by culture using Columbia blood agar and cross streaking the inoculated plate with a
Staphylococcus aureus
strain. As confirmed by 16S rRNA gene sequencing,
H. ovis
was isolated with an unexpectedly high frequency of 33%, predominantly as heavy growth and pure culture. The majority of
H. ovis
isolates showed distinct satellitism around
S. aureus
and pyridoxal dependency, resembling “nutritionally variant streptococci” (now assigned to the genera
Abiotrophia
and
Granulicatella
). Using the API rapid ID 32 Strep, API ZYM, and Rosco Diatabs systems, incongruent results were obtained for alkaline phosphatase, β-galactosidase, β-glucuronidase, and leucine aminopeptidase activities. Based on the satellitism/pyridoxal dependency; hemolysis on blood agar; the API rapid ID 32 Strep results for arginine dihydrolase, α-galactosidase, β-galactosidase, β-glucuronidase, and pyroglutamic acid arylamidase activities; hippurate hydrolysis; and acidification of sucrose, a scheme for the identification of
H. ovis
and its differentiation from other members of the
Helcococcus
genus and the pyridoxal-dependent species
Abiotrophia defectiva, Granulicatella adiacens
, and
Granulicatella elegans
is proposed. By establishing specific fluorescence in situ hybridization, large
H. ovis
aggregates were specifically detected within the fibrinous exudate of the valvular thrombi. Our results demonstrate for the first time that
H. ovis
represents an emerging pathogen in bovine valvular endocarditis that is frequently isolated if appropriate culture conditions are used.
Molecular Characterization of Equine Rotavirus in Ireland
Authors: Collins P. J. , Cullinane A. , Martella V. , O'Shea H.
Published: August 2008

Group A rotaviruses are important causative agents of severe, acute dehydrating diarrhea in foals. A total of 86 rotavirus-positive fecal samples, collected from diarrheic foals from 11 counties in three of the four provinces of Ireland, were obtained from the Irish Equine Centre in Kildare during a 7-year (1999 to 2005) passive surveillance study and were characterized molecularly to establish the VP7 (G type) and VP4 (P type) antigenic specificities. Fifty-eight samples (67.5%) were found to contain G3 viruses, while in 26 samples (30.2%) the rotaviruses were typed as G14 and in 2 samples (2.3%) there was a mixed infection, G3 plus G14. All samples except for two, which were untypeable, were characterized as P[12]. Fifty-eight percent of the samples were obtained from County Kildare, the center of the Irish horse industry, where an apparent shift from G3P[12] to G14P[12] was observed in 2003. By sequence analysis of the VP7 protein, the G3 Irish strains were shown to resemble viruses of the G3A subtype (H2-like) (97.1 to 100% amino acid [aa] identity), while the G14 Irish strains displayed 93.9 to 97.1% aa identity to other G14 viruses. In the VP8* fragment of the VP4 protein, the P[12] Irish viruses displayed high conservation (92.3 to 100% aa) with other equine P[12] viruses. Worldwide, G3P[12] and G14P[12] are the most prevalent equine rotavirus strains, and G3P[12] vaccines have been developed for prevention of rotavirus-associated diarrhea in foals. Investigations of the VP7/VP4 diversity of the circulating equine viruses and the dynamics of strain replacement are important for better assessing the efficacies of the vaccines.
Kinetic Analysis by Real-Time PCR of Hepatitis C Virus (HCV)-Specific T Cells in Peripheral Blood and Liver after Challenge with HCV
Authors: Ramalingam Ramesh K. , Meyer-Olson Dirk , Shoukry Naglaa H. , Bowen David G. , Walker Christopher M. , Kalams Spyros A.
Published: August 2008

Intrahepatic virus-specific CD8
+
T cells are thought to be important for the control of hepatitis C virus (HCV) infection, yet the precise kinetics for the expansion of epitope-specific T cells over the course of infection are difficult to determine with currently available methods. We used a real-time PCR assay to measure the frequency of clonotypic HCV-specific CD8
+
T cells in peripheral blood and snap-frozen liver biopsy specimens of two chimpanzees (
Pan troglodytes
) with previously resolved HCV infection who were rechallenged with HCV. In response to rechallenge, the magnitude of each clonotypic response was 10-fold higher in the liver than in the blood, and the peak clonotype frequency was concurrent with the peak viral load. The higher frequency of HCV-specific clonotypes in the liver than in peripheral blood was maintained for at least 3 months after the clearance of viremia. After antibody-mediated CD8
+
T-cell depletion and another viral challenge, the rebound of these clonotypes was seen prior to an appreciable reconstitution of CD8
+
T-cell values and, again, at higher frequencies in the liver than in peripheral blood. These data demonstrate the importance of intrahepatic virus-specific CD8
+
T cells for the clearance of infection and the rapid kinetics of expansion after virus challenge.
Hidden Virulence Determinants in a Viral Quasispecies In Vivo
Authors: Sanz-Ramos Marta , Díaz-San Segundo Fayna , Escarmís Cristina , Domingo Esteban , Sevilla Noemí
Published: August 2008

The characterization of virulence determinants of pathogenic agents is of utmost relevance for the design of disease control strategies. So far, two classes of virulence determinants have been characterized for viral populations: those imprinted in the nucleotide sequence of some specific genomic regions and those that depend on the complexity of the viral population as such. Here we provide evidence of a virulence determinant that depends neither on a genomic sequence nor on detectable differences in population complexity. Foot-and-mouth disease virus is lethal for C57BL/6 mice showing the highest viral load in pancreas. Virus isolated from pancreas after one passage in mice showed an attenuated phenotype, with no lethality even at the highest dose tested. By contrast, virus from sera of the same mice displayed a virulence similar to that of the parental wild-type clone and virus isolated from spleen displayed an intermediate phenotype. However, viral populations from pancreas, spleen, and serum showed indistinguishable consensus genomic nucleotide sequences and mutant spectrum complexities, as quantified according to the mutation frequencies of both entire genomic nucleotide sequences of biological clones. The results show that the populations with differing virulences cannot be distinguished either by the consensus sequence or by the average complexity of the mutant spectrum. Differential harvesting of virus generated by cell transfection of RNA from serum and pancreas failed to reveal genetic differences between subpopulations endowed with differing virulences. In addition to providing evidence of hidden virulence determinants, this study underlines the capacity of a clone of an RNA virus to rapidly diversify phenotypically in vivo.
Insertion of an EYFP-pp71 (UL82) Coding Sequence into the Human Cytomegalovirus Genome Results in a Recombinant Virus with Enhanced Viral Growth
Authors: Tavalai Nina , Kraiger Martina , Kaiser Nina , Stamminger Thomas
Published: August 2008

The human cytomegalovirus (HCMV) UL82-encoded tegument protein pp71 has recently been shown to activate viral immediate-early (IE) gene expression by neutralizing a cellular intrinsic immune defense instituted by the ND10 protein hDaxx. Pp71 localizes to ND10 upon infection and induces the degradation of hDaxx. Here, we report the successful generation of a recombinant HCMV expressing enhanced yellow fluorescent protein (EYFP) fused to the N terminus of pp71. Intriguingly, insertion of the EYFP-UL82 coding sequence into the HCMV AD169 genome gave rise to a recombinant virus, termed AD169/EYFP-pp71, that replicates to significantly higher titers than wild-type AD169. In particular, we noticed strongly increased protein levels of pp71 after AD169/EYFP-pp71 inoculation. Although the high abundance of pp71 resulted in augmented packaging of the tegument protein into viral particles, no increased hDaxx degradation was detectable upon AD169/EYFP-pp71 infection. In contrast, further investigation revealed a significantly enhanced viral DNA replication compared to wild-type AD169. Thus, we hypothesize that an as-yet-unidentified function of pp71 contributes to the enhanced infectivity of AD169/EYFP-pp71. This assumption is additionally supported by the observation that increased early and late gene expression after AD169/EYFP-pp71 infection occurs independent of elevated IE protein levels. Finally, immunofluorescence analyses confirmed that hDaxx determines the ND10-localization of pp71 upon infection, since pp71 exhibited a nucleolar distribution in the absence of hDaxx. Taken together, we generated a recombinant HCMV that constitutes a useful tool not only to dissect the in vivo dynamics of pp71 subnuclear localization more precisely but also to explore new features of this viral transactivator.
Identification of Direct Transcriptional Targets of the Kaposi's Sarcoma-Associated Herpesvirus Rta Lytic Switch Protein by Conditional Nuclear Localization
Authors: Bu Wei , Palmeri Diana , Krishnan Raghu , Marin Roxana , Aris Virginie M. , Soteropoulos Patricia , Lukac David M.
Published: August 2008

Lytic reactivation from latency is critical for the pathogenesis of Kaposi's sarcoma-associated herpesvirus (KSHV). We previously demonstrated that the 691-amino-acid (aa) KSHV Rta transcriptional transactivator is necessary and sufficient to reactivate the virus from latency. Viral lytic cycle genes, including those expressing additional transactivators and putative oncogenes, are induced in a cascade fashion following Rta expression. In this study, we sought to define Rta's direct targets during reactivation by generating a conditionally nuclear variant of Rta. Wild-type Rta protein is constitutively localized to cell nuclei and contains two putative nuclear localization signals (NLSs). Only one NLS (NLS2; aa 516 to 530) was required for the nuclear localization of Rta, and it relocalized enhanced green fluorescent protein exclusively to cell nuclei. The results of analyses of Rta NLS mutants demonstrated that proper nuclear localization of Rta was required for transactivation and the stimulation of viral reactivation. RTA with NLS1 and NLS2 deleted was fused to the hormone-binding domain of the murine estrogen receptor to generate an Rta variant whose nuclear localization and ability to transactivate and induce reactivation were tightly controlled posttranslationally by the synthetic hormone tamoxifen. We used this strategy in KSHV-infected cells treated with protein synthesis inhibitors to identify direct transcriptional targets of Rta. Rta activated only eight KSHV genes in the absence of de novo protein synthesis. These direct transcriptional targets of Rta were transactivated to different levels and included the genes nut-1/PAN, ORF57/Mta, ORF56/Primase, K2/viral interleukin-6 (vIL-6), ORF37/SOX, K14/vOX, K9/vIRF1, and ORF52. Our data suggest that the induction of most of the KSHV lytic cycle genes requires additional protein expression after the expression of Rta.
Persistent Propagation of Variant Creutzfeldt-Jakob Disease Agent in Murine Spleen Stromal Cell Culture with Features of Mesenchymal Stem Cells
Authors: Akimov Sergey , Yakovleva Oksana , Vasilyeva Irina , McKenzie Carroll , Cervenakova Larisa
Published: August 2008

The transmission of variant Creutzfeldt-Jakob disease (vCJD) through blood transfusions has created new concerns about the iatrogenic spread of transmissible spongiform encephalopathies (TSEs)/prion diseases through blood and plasma-derived products and has increased the need to develop efficient methods for detection of the agent in biologics. Here, we report the first successful generation of spleen-derived murine stromal cell cultures that persistently propagate two mouse-adapted isolates of human TSE agents, mouse-adapted vCJD, and Fukuoka 1. These new cell cultures can be used efficiently for studies of the pathogenesis of the disease, for development of diagnostics and therapeutics, and as a rapid ex vivo assay for TSE inactivation/removal procedures.
Structural Rearrangement within an Enveloped Virus upon Binding to the Host Cell
Authors: Meckes David G. , Wills John W.
Published: August 2008

We have made the surprising discovery that the interactions of herpes simplex virus with its initial cell attachment receptor induce a rapid and highly efficient structural change in the tegument, the region of the virion situated between the membrane and the capsid. It has been known for nearly a decade that viruses can trigger host signaling pathways when they bind to receptors on the cell surface; however, until now there has been no evidence that a signal can be sent in reverse—from the “outside in”—across a viral membrane. Evidence for this signaling event was found during studies of UL16, a tegument protein that is conserved among all the herpesviruses. Previous work has demonstrated that UL16 is bound to capsids isolated from the cytoplasm of infected cells, but this interaction is destabilized during subsequent egress steps, leading to release of the extracellular virion. Pretreatment with
N
-ethylmaleimide, a small, membrane-permeating compound that covalently modifies free cysteines, restabilizes the interaction, thereby permitting the capsid-UL16 complex to be isolated following disruption of virions with NP-40. In the experiments described here, we found that the natural signal for release of UL16 from capsids is sent when virions merely bind to cells at 4°C. The internal change was also observed upon binding to immobilized heparin in a manner that requires viral glycoprotein C. This represents the first example of signaling across a viral envelope following receptor binding.
Analysis of the Interaction between the UL11 and UL16 Tegument Proteins of Herpes Simplex Virus
Authors: Yeh Pei-Chun , Meckes David G. , Wills John W.
Published: August 2008

The UL11 and UL16 tegument proteins of herpes simplex virus are conserved throughout the herpesvirus family. Previous studies have shown that these proteins interact, perhaps to link UL16-bound nucleocapsids to UL11, which resides on the cytoplasmic face of the
trans
-Golgi network, where maturation budding occurs. Little is known about the interaction except that it requires the leucine-isoleucine (LI) and acidic cluster motifs in UL11 and that no other viral proteins are involved. In particular, the important question of whether these two proteins bind to each other directly has not been addressed. Accordingly, UL11 and UL16 were expressed in bacteria, and the purified proteins were found to retain the ability to interact in a manner that was dependent upon the LI and acidic cluster. In an attempt to map the UL11-binding site contained in UL16, a large number of deletion mutants were constructed. The first 40 (nonconserved) amino acids were found to be dispensable, but all the other constructs failed to bind UL11 or had poor expression in transfected cells, suggesting that UL16 is very sensitive to alterations and probably lacks a multidomain structure. As an alternative strategy for identifying residues that are important for the interaction, the cysteines of UL16 were investigated, because many of these are highly conserved. Approximately half of the 20 cysteines in UL16 have been shown to be covalently modified by
N
-ethylmaleimide, and this treatment was found to block the interaction with UL11. Moreover, individual serine replacements of six of the most conserved cysteine residues were made, and four of these disrupted the interaction with UL11 without affecting protein stability. However, the UL11-UL16 interaction does not involve the formation of interspecies disulfide bonds, because binding occurred even when all the cysteines in UL11 were eliminated. Thus, UL16 directly interacts with UL11 and does so in a manner that requires free cysteines.
Minority Human Immunodeficiency Virus Type 1 Variants in Antiretroviral-Naive Persons with Reverse Transcriptase Codon 215 Revertant Mutations
Authors: Mitsuya Yumi , Varghese Vici , Wang Chunlin , Liu Tommy F. , Holmes Susan P. , Jayakumar Prerana , Gharizadeh Baback , Ronaghi Mostafa , Klein Daniel , Fessel W. Jeffrey , Shafer Robert W.
Published: August 2008

T215 revertant mutations such as T215C/D/E/S that evolve from the nucleoside reverse transcriptase (RT) inhibitor mutations T215Y/F have been found in about 3% of human immunodeficiency virus type 1 (HIV-1) isolates from newly diagnosed HIV-1-infected persons. We used a newly developed sequencing method—ultradeep pyrosequencing (UDPS; 454 Life Sciences)—to determine the frequency with which T215Y/F or other RT inhibitor resistance mutations could be detected as minority variants in samples from untreated persons that contain T215 revertants (“revertant” samples) compared with samples from untreated persons that lack such revertants (“control” samples). Among the 22 revertant and 29 control samples, UDPS detected a mean of 3.8 and 4.8 additional RT amino acid mutations, respectively. In 6 of 22 (27%) revertant samples and in 4 of 29 control samples (14%;P= 0.4), UDPS detected one or more RT inhibitor resistance mutations. T215Y or T215F was not detected in any of the revertant or control samples; however, 4 of 22 revertant samples had one or more T215 revertants that were detected by UDPS but not by direct PCR sequencing. The failure to detect viruses with T215Y/F in the 22 revertant samples in this study may result from the overwhelming replacement of transmitted T215Y variants by the more fit T215 revertants or from the primary transmission of a T215 revertant in a subset of persons with T215 revertants.
SOME EFFECTS OF ETHYLENE ON GERMINATING WHEAT
Authors: Roberts D. W. A.
Published: August 2008

Ethylene at concentrations of 0.2% to 1.0% in air causes inhibition of the elongation of the shoots and roots of germinating wheat without any Inhibition of the rate of carbon dioxide emission. Gassing does not cause any major disturbances in gross protein hydrolysis in the endosperm, protein synthesis in the embryo, or translocation of nitrogenous substances as judged by soluble and protein nitrogen determinations. The dry weight of treated embryos is similar to that of untreated embryos of similar age during the first five days of germination. Treatment inhibits the water uptake of the embryos during the second, third, and fourth days of germination but increases the water uptake during the fifth day.
VARIATION IN THE CULTURAL CHARACTERISTICS AND PATHOGENICITY OF FUSARIUM AVENACEUM AND F. ARTHROSPORIOIDES
Authors: Cormack M. W.
Published: August 2008

Variants which occurred commonly in isolates of Fusarium avenaceum and F. arthrosporioides from diseased roots of alfalfa and other hosts in Alberta were of two kinds, viz., culture variants arising as sectors or patches in mycelial colonies of the parent wild type, and spore variants developing from single macroconidia. Both kinds appeared under a wide range of environmental and nutritional conditions, but they were distinct from the temporary, cultural changes which could sometimes be induced by varying these conditions. The culture variants were mostly mycelial and tended to revert partially to the wild type, or to produce other variants. Relatively stable, heavily sporulating types predominated among the spore variants. Variation followed a similar pattern in the two species studied, but isolates differed greatly in respect to number and type of variants produced. Some isolates which were relatively stable in culture produced many spore variants, and vice versa. Taxonomic comparisons indicated that classification should be based on the original characteristics of the wild types rather than on their range of cultural variation.The wild types remained viable longer than any of the variants in dried soil culture. Soil culture proved suitable for inoculum and storage purposes since variants developed infrequently in this medium.All variants proved less virulent than their parent wild types in infection tests on roots of alfalfa and sweet clover. These results emphasize the necessity of using the wild types of stable isolates in varietal resistance tests and other infection experiments.
ACID METABOLISM OF McINTOSH APPLES DURING THEIR DEVELOPMENT ON THE TREE AND IN COLD STORAGE
Authors: Krotkov G. , Wilson D. G. , Street R. W.
Published: August 2008

From the time of fruit setting early in the spring and throughout the whole summer, samples of fruits were taken directly from the tree. In the fall several bushels of apples were picked and placed in cold storage. These constituted the source of material during the winter. Weekly samples of fruits were analyzed for pH and titratable acidity of their sap, and also for their organic acids content. Various stages in the acid metabolism of fruits were found to correspond chronologically very closely with those of carbohydrate and respiration. During the first two to four weeks of the fruit ontogeny, the pH of the apple juice falls rapidly to a value of about 2.8. Thereafter there is a slow, steady rise which continues until the next spring. This regularity makes the pH of the juice a better indicator of the physiological age of a fruit than either its chemical composition or respiratory rate. Initially, the malic acid content of a fruit is low, and some unknown organic acids predominate. This relation is reversed within the first two to four weeks of growth and during the rest of the ontogeny malic acid forms about 80% of the total organic acids of a fruit.
OBSERVATIONS ON AMYLQLYTIC BACTERIA: II. A SURVEY OF NAMED MESOPHILIC SPECIES ON FIVE DIFFERENT STARCHES
Authors: Stark Egon , Tetrault P. A.
Published: August 2008

The ability of strains of 40 mesophilic species of bacteria to hydrolyze five different starches was studied. These species are either not described in Bergey's Manual as to their action on starch or they are listed as "not hydrolyzing starch". Strains of 32 species were amylolytic, six species were not. Strains of two species failed to grow. Of the amylolytic species, 22 attacked all five starches, two attacked four, six hydrolyzed two, and two species hydrolyzed only one starch. No single starch was hydrolyzed by all strains of 32 amylolytic species. Rice and soluble starch were most readily hydrolyzed. Potato and corn starch offered the greatest resistance at first. Arrowroot starch held an intermediate position. Two weeks of incubation seemed to be a minimum period. The longer the cultures were incubated the more completely was a particular starch hydrolyzed and the more numerous were the amylolytic cultures. The implications of these observations for determinative work are discussed.
A PRELIMINARY STUDY OF CORN SEEDLING BLIGHT IN SOUTHERN ONTARIO
Authors: McKeen W. E.
Published: August 2008

In southern Ontario, seedling blight is the major factor responsible for poor stands of corn and its gradual decline in yield for the past number of years. This disease expresses itself as an uneven stunting and chlorosis throughout the field. It may be caused by Pythium arrhenomanes Drechs., Pythium debaryanum Hesse., Fusarium moniliforme Sheld., Fusarium graminearum Schw., or Rhizoctonia solani Kuehn. P. arrhenomanes, which is the most economically important pathogen encountered, produces millions of zoospores in moist soil Under natural field conditions, it seldom kills the plant, since corn possesses unusual capacity to send out new adventitious roots when tire causal organism destroys the older roots. In the course of these studies, F. graminearum was found only once and apparently is not important as a soil-borne organism in this corn–wheat-growing area. F. moniliforme was present in most lesions, but it is not an active root parasite and, in the majority of cases, is a secondary invader Studies conducted in refrigerated rooms have shown that temperature has a greater influence on the hosts (wheat and corn) than on the organism, P. arrhenomanes, because disease incidence was greatest at low temperatures for corn and at high temperatures for wheat. Although nematodes are very numerous in necrotic roots, they appear to be of little importance.
A COMPARISON OF SEED TESTING METHODS IN RELATION TO THE STEM-BREAK- AND BROWNING DISEASE OF FLAX, CAUSED BY POLYSPORA LINI LAFF.
Authors: Wallen V. R. , Skolko A. J.
Published: August 2008

A comparison of the Ulster, New Zealand, and Ottawa methods of seed examination for the presence of Polyspora lini Laff., the cause of stem-break and browning disease of flax, showed great variation in the percentage of infection obtained, depending upon the method used. The Ulster method, in which the seed is not treated before it is plated, does not differentiate deep-seated infection from superficial infection of the seed, but has proved satisfactory in actual practice with seed samples that are not contaminated seriously by saprophytic fungi. The New Zealand method, by which surface contamination is supposedly removed by washing the seed in running water, has not been found reliable. The Ottawa method, by which the seed is surface sterilized before it is plated, does not indicate the degree of superficial infection, but does give the percentage of deep-seated infection, and hence it indicates the suitability of the seed for planting purposes if the seed is treated with a fungicide. It is suggested that a centrifuge test combined with the Ottawa plating method would provide a better index of the health condition of flax seed as far as disease caused by. P. lini is concerned.
STUDIES IN THE BIOCHEMISTRY OF CELLULOLYTIC MICROORGANISMS: I. CARBON BALANCES OF WOOD-ROTTING FUNGI IN SURFACE CULTURE
Authors: Whitaker D. R.
Published: August 2008

A carbon balance study was made of the metabolic products of 40 species of wood-rotting fungi, grown in surface culture on a glass wool support in a glucose urea medium. Sixteen species were tested under both continuous and restricted aeration. The categories of product determined were: carbon in carbon dioxide evolved during incubation, carbon in mycelium, and carbon in the culture filtrate as total carbon, as residual glucose, as volatile acids, as volatile neutrals, and as carbon dioxide. The resulting carbon balances indicated that, under the conditions tested, carbon dioxide and mycelium were the only major end products of the majority of species examined.
STUDIES OF VIRUS DISEASES OF STRAWBERRIES IN BRITISH COLUMBIA: I. THE REACTION OF THE BRITISH SOVEREIGN VARIETY AND THE INDICATOR FRAGARIA VESCA TO YELLOWS
Authors: Fitzpatrick Randal E. , Mellor Frances C.
Published: August 2008

British Sovereign, the commercial strawberry variety of British Columbia, has shown no field evidence of degeneration from the virus disease, yellows, that is attacking the Marshall variety in the Pacific Northwest. However, experimental inoculation of British Sovereign by stolon grafting to a yellows-infected Marshall plant proved the British Sovereign to be susceptible to yellows. As with the Marshall, infected plants were reduced in size and the foliage tended to flatten towards the grounds but, unlike the Marshall, there was no pronounced yellowing. When Fragaria vesca was grafted to a yellows-infected Marshall plant the reaction was rapid and severe. The older leaves flattened to the ground, the young runner tips hooked back, the newly developing leaves, though relatively well proportioned, were minute and yellow at the margins, and the plants eventually died.
STUDIES IN THE NUTRITION OF CORYNEBACTERIUM SEPEDONICUM (SPIEK. AND KOTT.) SKAPT. AND BURKH.
Authors: MacLachlan D. S. , Thatcher F. S.
Published: August 2008

The nutritional requirements of Corynebacterium sepedonicum (Spiek. and Kott.) Skapt. and Burkh. were investigated by the use of the Warburg respiration apparatus. Pantothenic acid, in a concentration of 600 micrograms (μgm.) per liter, caused the greatest growth augmentation of nine vitamins tested. The amino acids, glutamic acid, asparagine, leucine, and lysine in concentrations of 0.001, 1. 0, 0.03, and 0.03 gm. per liter respectively, caused a marked increase in oxygen uptake, either individually or in combination. Yeast nucleic acid and thymonucleic acid had no significant effect on the growth rate of C. sepedonicum. A new medium was prepared for the isolation and maintenance of C. sepedonicum.
TWO NEW SMUTS ON CAREX IN CANADA
Authors: Savile D. B. O.
Published: August 2008

Cintractia calderi is described from ovaries of Carex backii; it has been found in Manitoba and Ontario, and is characterized by very large spores with coarse, dark warts. The genus Planetella is erected to accommodate P. lironis found in the ovaries of Carex maritima in Keewatin and C. leiophylla in Yukon; the spores have thin, pale walls except for a dark brown, thickened equatorial ring, and the sori have a hard, prosenchyma coat.
UPTAKE OF P32 BY SOME CEREALS
Authors: Naylor J. M. , Walker G. W. R. , Murray D. , Person C. O. , Spinks J. W. T. , Arnason T. J.
Published: August 2008

When wheat grains were germinated individually in test tubes containing 0.1 ml. solution in which initially 6.5-10 mrd. P32 in the form of phosphate were included, over 90% of the activity was absorbed by the grain and seedling within 13 days. At five days over 80% of the absorbed activity was in the embryo with less than 20% in the grain coats and endosperm. When plants were grown in washed sand of high quartz content about 5% of the activity added in solution to the sand at 31 days or at 40 days was absorbed by the plants. Activity added to soil in which barley plants were growing resulted in activity absorptions ranging from 0.97 to 10.4% of the amounts supplied. More P32 was absorbed when carrier P was provided than when carrier-free solutions were used. A method permitting uptake measurements to be made at intervals with the same plants was also tried. Initially, 1.66 mrd. P32 were available to each plant. At intervals, determinations of uptake were made. Then P32 was added to the solution to bring the level up to 1.66 mrd. per plant. The total energy received by individual vulgare wheat plants from decay of absorbed P32 was calculated to be 54.6 gram-roentgens.
EFFECT OF PASMO DISEASE OF FLAX ON THE YIELD AND QUALITY OF LINSEED OIL
Authors: Sackston W. E. , Carson R. B.
Published: August 2008

Heavy infections of pasmo significantly reduced the oil content of flaxseed and the iodine number of the oil. The effects of pasmo infection on oil content and iodine number of the oil were similar to those caused by a hot, dry climate. Oil content was affected similarly by pasmo infection and by flax rust infection, but the two diseases had dissimilar effects on iodine number of the oil. Greatest reductions in oil content and iodine number resulted from pasmo inoculations made when the flax plants were flowering. Inoculations made when the seed was ripening had little or no effect on yield and quality of linseed oil.
STUDIES ON THE LEGUME ROOT NODULE BACTERIA: I. DETECTION OF EFFECTIVE AND INEFFECTIVE STRAINS
Authors: Jordan D. C. , Garrard E. H.
Published: August 2008

The Virtanen technique was used to detect effective and ineffective rhizobia. The rhizobia studied varied widely in their action towards different varieties of the same host species. Maximum leghemoglobin concentrations occurred just prior to blossoming in field legumes, but much earlier in greenhouse legumes cultivated under conditions of this experiment. The nodules of the ineffective strains of legume bacteria differed from those produced by effective strains in color, size, distribution, rate of destruction of the bacteroid area, and presence or absence of rodlike bacterial forms. Experimental evidence is presented to show that a supposedly parasitic strain of alfalfa organism can exist.
OBSERVATIONS ON QUATERNARY AMMONIUM DISINFECTANTS
Authors: Chaplin C. E.
Published: August 2008

Bacterial death rate studies were carried out with several quaternary ammonium compounds. The survivor curves were found to be sigmoid. This shape was shown to be due to the difference in resistance to the QAC among the individual cells. An exponential rate was found when a more resistant strain was selected from the survivors of disinfection. Sporocidal action was not found. The reaction between substrate protein and the QAC removes the disinfectant from solution and occurs in the presence of a wide QAC–protein ratio, but the bactericidal action is dependent upon the concentration of the disinfectant. Serratia marcescens was adapted to grow in 200 times the originally lethal concentration of disinfectant, Escherichia coli in 43 times, but no increase in concentration was tolerated by Micrococcus pyogenes var. aureus.