bluuebunny/crossref_metadata_2025 huggingface dataset:
Shiga Toxin, Cytolethal Distending Toxin, and Hemolysin Repertoires in Clinical
Escherichia coli
O91 Isolates
Authors: Bielaszewska Martina , Stoewe Franziska , Fruth Angelika , Zhang Wenlan , Prager Rita , Brockmeyer Jens , Mellmann Alexander , Karch Helge , Friedrich Alexander W.
Published: April 2009

Shiga toxin (Stx)-producing
Escherichia coli
(STEC) strains of serogroup O91 are the most common human pathogenic
eae
-negative STEC strains. To facilitate diagnosis and subtyping of these pathogens, we genotypically and phenotypically characterized 100 clinical STEC O91 isolates. Motile strains expressed flagellar antigens H8 (1 strain), H10 (2 strains), H14 (52 strains), and H21 (20 strains) or were H nontypeable (Hnt) (10 strains); 15 strains were nonmotile. All nonmotile and Hnt strains possessed the
fliC
gene encoding the flagellin subunit of the H14 antigen (
fliC
H14
). Most STEC O91 strains possessed enterohemorrhagic
E. coli
hlyA
and expressed an enterohemolytic phenotype. Among seven
stx
alleles identified,
stx
2dact
, encoding mucus- and elastase-activatable Stx2d, was present solely in STEC O91:H21, whereas most strains of the other serotypes possessed
stx
1
. Moreover, only STEC O91:H21 possessed the
cdt-
V cluster, encoding cytolethal distending toxin V; the toxin was regularly expressed and was lethal to human microvascular endothelial cells. Infection with STEC O91:H21 was associated with hemolytic-uremic syndrome (
P
= 0.0015), whereas strains of the other serotypes originated mostly in patients with nonbloody diarrhea. We conclude that STEC O91 clinical isolates belong to at least four lineages that differ by H antigens/
fliC
types,
stx
genotypes, and non-
stx
putative virulence factors, with accumulation of virulence determinants in the O91:H21 lineage. Isolation of STEC O91 from patients' stools on enterohemolysin agar and the rapid initial subtyping of these isolates using
fliC
genotyping facilitate the identification of these emerging pathogens in clinical and epidemiological studies and enable prediction of the risk of a severe clinical outcome.
Pyrosequencing Analysis of 20 Nucleotides of Internal Transcribed Spacer 2 Discriminates
Candida parapsilosis
,
Candida metapsilosis
, and
Candida orthopsilosis
Authors: Borman Andrew M. , Linton Christopher J. , Oliver Debra , Palmer Michael D. , Szekely Adrien , Odds Frank C. , Johnson Elizabeth M.
Published: April 2009

Two new cryptic sister species,
Candida orthopsilosis
and
Candida metapsilosis
, were recently identified by consistent DNA sequence differences among several genes within the genetically heterogeneous
Candida parapsilosis
complex. Here, we present data demonstrating that Pyrosequencing analysis of 20 nucleotides of internal transcribed spacer region 2 rapidly and robustly distinguishes between these three closely related
Candida
species.
Evaluation of Five Commercial Real-Time PCR Assays for Detection of
Mycoplasma pneumoniae
in Respiratory Tract Specimens
Authors: Touati A. , Benard A. , Hassen A. Ben , Bébéar C. M. , Pereyre S.
Published: April 2009

The performances of five commercial TaqMan real-time PCR assays for the detection of
Mycoplasma pneumoniae
in respiratory tract specimens were evaluated in comparison with an in-house real-time PCR. All kits allowed prompt and specific results, validated by the use of an internal control. The Nanogen kit showed the best clinical sensitivity.
Vancomycin MICs for
Staphylococcus aureus
Vary by Detection Method and Have Subtly Increased in a Pediatric Population Since 2005
Authors: Mason Edward O. , Lamberth Linda B. , Hammerman Wendy A. , Hulten Kristina G. , Versalovic James , Kaplan Sheldon L.
Published: April 2009

Vancomycin MICs for
Staphylococcus aureus
isolates in a pediatric hospital with a high rate of staphylococcal infections were examined for any increase over a 7-year period. A broth microdilution scheme allowed direct comparison of the MICs generated by this method to MICs generated by Etest. MICs generated by both methods were determined with the same inoculum suspension. One hundred sixty-five
S
.
aureus
isolates were selected on the basis of the patients having been bacteremic or having received vancomycin as the definitive therapy for their infections. Of the 165 isolates, 117 were methicillin-resistant
S
.
aureus
and 48 were methicillin-susceptible
S
.
aureus
. Forty-seven were acquired in the hospital (nosocomial), 56 were community acquired, and 62 were community onset-health care associated. All but one isolate tested by broth microdilution had MICs of <1.0 μg/ml, while 96% of these same isolates tested by Etest had MICs of ≥1 μg/ml. A significant increase in MICs that occurred after study year 4 (2004 to 2005) was demonstrated by the Etest (
P
< 0.00007) but not by broth microdilution. MICs were not different for isolates of community or health care origin, regardless of methodology. The proportion of isolates with Etest MICs of <1 and ≥1 μg/ml between children with bacteremia for ≤5 days and >5 days (
P
= 0.3) was not different. We conclude that MICs for pediatric isolates have increased slightly since 2005 and therapeutic decisions based on vancomycin MICs need to be made by considering the methodology used.
Reverse Transcription-Loop-Mediated Isothermal Amplification Assay for Rapid Detection of Hepatitis E Virus
Authors: Lan Xi , Yang Bin , Li Bao Yu , Yin Xiang Ping , Li Xue Rui , Liu Ji Xing
Published: April 2009

The one-step single-tube betaine-free reverse transcription (RT)-loop-mediated isothermal amplification assay was developed for rapid diagnosis of hepatitis E virus. This assay amplified the target gene in less than 45 min (even as short as 20 min) under isothermal conditions at 63°C, and the sensitivity of this assay was 100-fold greater than that of RT-PCR. This assay demonstrated a detection limit of 0.045 fg (nine copies/reaction).
The First Vancomycin-Intermediate
Staphylococcus aureus
Strains Isolated from Patients in Thailand
Authors: Lulitanond Aroonlug , Engchanil Chulapan , Chaimanee Prajuab , Vorachit Malai , Ito Teruyo , Hiramatsu Keiichi
Published: April 2009

We screened 533 and 361 methicillin (meticillin)-resistant
Staphylococcus aureus
strains isolated in a university hospital in 2002 and 2003 and in 2006 and 2007, respectively, and identified 4 (0.8%) of the strains in the first group and 8 (2.2%) of the strains in second group as heterogeneous vancomycin-resistant
S. aureus
(heterogeneous VISA) strains and 3 (0.8%) of the strains in the second group as VISA strains. This is the first report of VISA strains isolated from patients in Thailand.
Putative Adhesins of Enteropathogenic and EnterohemorrhagicEscherichia coliof Serogroup O26 Isolated from Humans and Cattle
Authors: Bardiau Marjorie , Labrozzo Sabrina , Mainil Jacques G.
Published: April 2009

EnterohemorrhagicEscherichia coli(EHEC) strains are responsible for food poisoning in developed countries via consumption of vegetal and animal food sources contaminated by ruminant feces, and some strains (O26, O111, and O118 serogroups) are also responsible for diarrhea in young calves. The prevalence of 27 putative adhesins of EHEC and of bovine necrotoxigenicE. coli(NTEC) was studied with a collection of 43 bovine and 29 human enteropathogenic (EPEC) and EHEC strains and 5 non-EPEC/non-EHEC (1 bovine and 4 human) O26 strains, using specific PCRs. Four “groups” of adhesins exist, including adhesins present in all O26 strains, adhesins present in most O26 strains, adhesins present in a few O26 strains, and adhesins not present in O26 strains. The common profile of EHEC/EPEC strains was characterized by the presence ofloc3,loc5,loc7,loc11,loc14,paa,efa1,iha,lpfAO26, andlpfAO113genes and the absence ofloc1,loc2,loc6,loc12,loc13,saa, andeibGgenes. Except for thelpfAO26gene, which was marginally associated with bovine EHEC/EPEC strains in comparison with human strains (P= 0.012), none of the results significantly differentiated bovine strains from human strains. One adhesin gene (ldaE) was statistically (P< 0.01) associated with O26 EHEC/EPEC strains isolated from diarrheic calves in comparison with strains isolated from healthy calves.ldaE-positive strains could therefore represent a subgroup possessing the specific property of producing diarrhea in young calves. This is the first time that the distribution of putative adhesins has been described for such a large collection of EHEC/EPEC O26 strains isolated from both humans and cattle.
Rapid Real-Time Nucleic Acid Sequence-Based Amplification-Molecular Beacon Platform To Detect Fungal and Bacterial Bloodstream Infections
Authors: Zhao Yanan , Park Steven , Kreiswirth Barry N. , Ginocchio Christine C. , Veyret Raphaël , Laayoun Ali , Troesch Alain , Perlin David S.
Published: April 2009

Bloodstream infections (BSIs) are a significant cause of morbidity and mortality. Successful patient outcomes are diminished by a failure to rapidly diagnose these infections and initiate appropriate therapy. A rapid and reliable diagnostic platform of high sensitivity is needed for the management of patients with BSIs. The combination of an RNA-dependent nucleic acid sequence-based amplification and molecular beacon (NASBA-MB) detection system in multiplex format was developed to rapidly detect medically important BSI organisms. Probes and primers representing pan-gram-negative, pan-gram-positive, pan-fungal, pan-
Candida
, and pan-
Aspergillus
organisms were established utilizing 16S and 28S rRNA targets for bacteria and fungi, respectively. Two multiplex panels were developed to rapidly discriminate bacterial or fungal infections at the subkingdom/genus level with a sensitivity of 1 to 50 genomes. A clinical study was performed to evaluate the accuracy of this platform by evaluating 570 clinical samples from a tertiary-care hospital group using blood bottle samples. The sensitivity, specificity, and Youden's index values for pan-gram-positive detection and pan-gram-negative detection were 99.7%, 100%, 0.997 and 98.6%, 95.9%, 0.945, respectively. The positive predictive values (PPV) and the negative predictive values (NPV) for these two probes were 100, 90.7, and 99.4, 99.4, respectively. Pan-fungal and pan-
Candida
probes showed 100% sensitivity, specificity, PPV, and NPV, and the pan-
Aspergillus
probe showed 100% NPV. Robust signals were observed for all probes in the multiplex panels, with signal detection in <15 min. The multiplex real-time NASBA-MB assay provides a valuable platform for the rapid and specific diagnosis of bloodstream pathogens, and reliable pathogen identification and characterization can be obtained in under 3 h.
Use of Reverse Transcriptase PCR To Subtype N1 to N9 Neuraminidase Genes of Avian Influenza Viruses
Authors: Tsukamoto Kenji , Ashizawa Takayoshi , Nakanishi Koji , Kaji Noriyuki , Suzuki Kotaro , Shishido Makiko , Okamatsu Masatoshi , Mase Masaji
Published: April 2009

Reverse transcriptase PCR designed to amplify the N1 to N9 neuraminidase (NA) genes of avian influenza viruses detected 118 of the 119 NA genes tested (99.2%) in a subtype-specific manner. This technique successfully subtyped all 167 recent avian influenza viruses isolated from birds. Subtype specificity was confirmed by sequence analyses of all 285 PCR products.
Comparison of a Variable-Number Tandem-Repeat (VNTR) Method for TypingMycobacterium aviumwith Mycobacterial Interspersed Repetitive-Unit-VNTR and IS1245Restriction Fragment Length Polymorphism Typing
Authors: Inagaki Takayuki , Nishimori Kei , Yagi Tetsuya , Ichikawa Kazuya , Moriyama Makoto , Nakagawa Taku , Shibayama Takami , Uchiya Kei-ichi , Nikai Toshiaki , Ogawa Kenji
Published: April 2009

Mycobacterium aviumcomplex (MAC) infections are increasing annually in various countries, including Japan, but the route of transmission and pathophysiology of the infection remain unclear. Currently, a variable-number tandem-repeat (VNTR) typing method using theMycobacterium aviumtandem repeat (MATR) loci (MATR-VNTR) is employed in Japan for epidemiological studies using clinical isolates ofM. avium. In this study, the usefulness of this MATR-VNTR typing method was compared with that of the IS1245-restriction fragment length polymorphism (IS1245-RFLP) typing method and a mycobacterial interspersed repetitive-unit (MIRU)-VNTR typing method reported previously (V. C. Thibault, M. Grayon, M. L. Boschiroli, C. Hubbans, P. Overduin, K. Stevenson, M. C. Gutierrez, P. Supply, and F. Biet, J. Clin. Microbiol.45:2404-2410, 2007). Seventy clinical isolates identified asM. aviumfrom human immunodeficiency virus-negative patients with MAC infections were used. MATR-VNTR typing using 15 loci distinguished 56 patterns of different allele profiles, yielding a Hunter-Gaston discriminatory index (HGDI) of 0.990. However, IS1245-RFLP and MIRU-VNTR typing yielded HGDIs of 0.960 and 0.949, respectively, indicating that MATR-VNTR has an excellent discriminatory power compared with MIRU-VNTR and IS1245-RFLP typing. Moreover, concomitant use of the MATR-VNTR method and IS1245-RFLP typing increased the HGDI to 0.999. MATR-VNTR typing is inexpensive and easy to perform and could thus be useful in establishing a digital multifacility database that will greatly contribute to the clarification of the transmission route and pathophysiology ofM. aviuminfections.
Divergent Bro1 Domains Share the Capacity To Bind Human Immunodeficiency Virus Type 1 Nucleocapsid and To Enhance Virus-Like Particle Production
Authors: Popov Sergei , Popova Elena , Inoue Michio , Göttlinger Heinrich G.
Published: April 2009

To promote the release of infectious virions, human immunodeficiency virus type 1 (HIV-1) exploits the endosomal sorting complex required for transport (ESCRT) pathway by engaging Tsg101 and ALIX through late assembly (L) domains in p6 Gag. An LYPx
n
L motif in p6 serves as docking site for the central V domain of ALIX and is required for its ability to stimulate HIV-1 budding. Additionally, the nucleocapsid (NC) domain of Gag binds to the N-terminal Bro1 domain of ALIX, which connects ALIX to the membrane-deforming ESCRT-III complex via its CHMP4 subunits. Since the isolated Bro1 domain of ALIX is sufficient to markedly stimulate virus-like particle (VLP) production in a minimal Gag rescue assay, we examined whether the Bro1 domains of other human proteins possess a similar activity. We now show that the Bro1 domain-only protein Brox and the isolated Bro1 domains of HD-PTP and rhophilin all bind to HIV-1 NC. Furthermore, all shared the capacity to stimulate VLP production by a minimal HIV-1 Gag molecule, and Brox in particular was as potent as the Bro1 domain of ALIX in this assay. Unexpectedly, Brox retained significant activity even if its CHMP4 binding site was disrupted. Thus, the ability to assist in VLP production may be an intrinsic property of the boomerang-shaped Bro1 domain.
Downregulation of RUNX1 by RUNX3 Requires the RUNX3 VWRPY Sequence and Is Essential for Epstein-Barr Virus-Driven B-Cell Proliferation
Authors: Brady Gareth , Whiteman Hannah J. , Spender Lindsay C. , Farrell Paul J.
Published: April 2009

Cross-regulation of RUNX1 expression by RUNX3 plays a critical role in regulating proliferation of human B cells infected with Epstein-Barr virus (EBV). When EBV infection induces RUNX3, the consequent reduction in RUNX1 levels is required for the ensuing cell proliferation because forced expression of RUNX1 in an EBV lymphoblastoid cell line prevented cell proliferation. The TEL-RUNX1 fusion gene from acute B-lymphocytic leukemia retains almost all of the RUNX1 sequence but does not prevent B-cell proliferation in the same assay. B-cell maturation antigen (BCMA) was found to be induced by conditionally expressed RUNX3 in a lymphoma cell line. Chromatin immunoprecipitation assays confirmed that RUNX3 binds to the RUNX1 promoter in a lymphoblastoid cell line and a Burkitt's lymphoma cell line. The TLE binding VWRPY sequence from the C terminus of RUNX3 was found to be required for repression of the RUNX1 P1 promoter in a B-lymphoma cell line. The mechanism of repression in B-cell lines most likely involves recruitment of corepressor TLE3 or TLE4 to the RUNX1 promoter. The results demonstrate the importance of RUNX3-mediated repression of RUNX1 for EBV-driven B-cell proliferation and identify functional differences between human RUNX family proteins.
Novel MicroRNAs (miRNAs) Encoded by Herpesvirus of Turkeys: Evidence of miRNA Evolution by Duplication
Authors: Yao Yongxiu , Zhao Yuguang , Smith Lorraine P. , Watson Michael , Nair Venugopal
Published: April 2009

Herpesviruses account for 134 out of the 140 virus-encoded microRNAs (miRNAs) known today. Here we report the identification of 11 novel miRNAs encoded by herpesvirus of turkey (HVT), a virus used as a live vaccine in poultry against the highly oncogenic Marek's disease virus type 1. Ten of these miRNAs were clustered together within the repeat long region of the viral genome, demonstrating some degree of positional conservation with other mardiviruses. Close sequence and phylogenetic relationships of some miRNAs in this cluster indicate evolution by duplication. HVT miRNAs represent the first example of virus-encoded miRNAs that show evolution by duplication.
Molecular Determinants for Subcellular Localization of the Severe Acute Respiratory Syndrome Coronavirus Open Reading Frame 3b Protein
Authors: Freundt Eric C. , Yu Li , Park Elizabeth , Lenardo Michael J. , Xu Xiao-Ning
Published: April 2009

Viruses such as hepatitis C and the severe acute respiratory syndrome coronavirus (SARS-CoV) encode proteins that are distributed between mitochondria and the nucleus, but little is known about the factors that control partitioning between these sites. SARS-CoV encodes a unique accessory gene called open reading frame (ORF) 3b that, like other unique accessory genes in SARS-CoV, likely contributes to viral pathogenicity. The ORF 3b protein is 154 amino acids and is predicted to express from the second ORF in subgenomic RNA3. In this report, we have characterized the molecular components that regulate intracellular localization of the ORF 3b protein. We demonstrate unique shuttling behavior of ORF 3b, whereby the protein initially accumulates in the nucleus and subsequently translocates to mitochondria. Following nuclear localization, ORF 3b traffics to the outer membrane of mitochondria via a predicted amphipathic α-helix. Additionally, ORF 3b contains a consensus nuclear export sequence, and we demonstrate that nuclear export and thus mitochondrial translocation are dependent on a leptomycin B-sensitive nuclear export mechanism. We further show that ORF 3b inhibits induction of type I interferon induced by retinoic acid-induced gene 1 and the mitochondrial antiviral signaling protein. Our observations provide insights into the cellular localization of ORF 3b that may enhance our understanding of the mechanisms by which ORF 3b contributes to SARS-CoV pathogenesis. The findings reported here reveal that for multilocalized proteins, consideration of the spatiotemporal distribution may be crucial for understanding viral protein behavior and function.
Ebolavirus VP35 Interacts with the Cytoplasmic Dynein Light Chain 8
Authors: Kubota Toru , Matsuoka Mayumi , Chang Tsung-Hsien , Bray Mike , Jones Steven , Tashiro Masato , Kato Atsushi , Ozato Keiko
Published: April 2009

The viral protein VP35 of ebolavirus (EBOV) is implicated to have diverse roles in the viral life cycle. We employed a yeast two-hybrid screen to search for VP35 binding partners and identified the cytoplasmic dynein light chain (DLC8) as a protein that interacts with VP35. Mapping analysis unraveled a consensus motif, SQTQT, within VP35 through which VP35 binds to DLC8. The disruption of DLC8 binding does not affect the ability of VP35 to inhibit type I IFN production. Given that VP35 from various EBOV species interacts with DLC8, this interaction may have a role in regulating the EBOV life cycle.
Human Immunodeficiency Virus Type 1 Nef Protein Targets CD4 to the Multivesicular Body Pathway
Authors: daSilva Luis L. P. , Sougrat Rachid , Burgos Patricia V. , Janvier Katy , Mattera Rafael , Bonifacino Juan S.
Published: April 2009

The Nef protein of human immunodeficiency virus type 1 downregulates the CD4 coreceptor from the surface of host cells by accelerating the rate of CD4 endocytosis through a clathrin/AP-2 pathway. Herein, we report that Nef has the additional function of targeting CD4 to the multivesicular body (MVB) pathway for eventual delivery to lysosomes. This targeting involves theendosomalsortingcomplexrequired fortransport (ESCRT) machinery. Perturbation of this machinery does not prevent removal of CD4 from the cell surface but precludes its lysosomal degradation, indicating that accelerated endocytosis and targeting to the MVB pathway are separate functions of Nef. We also show that both CD4 and Nef are ubiquitinated on lysine residues, but this modification is dispensable for Nef-induced targeting of CD4 to the MVB pathway.
Antibodies to the Buried N Terminus of Rhinovirus VP4 Exhibit Cross-Serotypic Neutralization
Authors: Katpally Umesh , Fu Tong-Ming , Freed Daniel C. , Casimiro Danilo R. , Smith Thomas J.
Published: April 2009

Development of a vaccine for the common cold has been thwarted by the fact that there are more than 100 serotypes of human rhinovirus (HRV). We previously demonstrated that the HRV14 capsid is dynamic and transiently displays the buried N termini of viral protein 1 (VP1) and VP4. Here, further evidence for this “breathing” phenomenon is presented, using antibodies to several peptides representing the N terminus of VP4. The antibodies form stable complexes with intact HRV14 virions and neutralize infectivity. Since this region of VP4 is highly conserved among all of the rhinoviruses, antiviral activity by these anti-VP4 antibodies is cross-serotypic. The antibodies inhibit HRV16 infectivity in a temperature- and time-dependent manner consistent with the breathing behavior. Monoclonal and polyclonal antibodies raised against the 30-residue peptide do not react with peptides shorter than 24 residues, suggesting that these peptides are adopting three-dimensional conformations that are highly dependent upon the length of the peptide. Furthermore, there is evidence that the N termini of VP4 are interacting with each other upon extrusion from the capsid. A Ser5Cys mutation in VP4 yields an infectious virus that forms cysteine cross-links in VP4 when the virus is incubated at room temperature but not at 4°C. The fact that all of the VP4s are involved in this cross-linking process strongly suggests that VP4 forms specific oligomers upon extrusion. Together these results suggest that it may be possible to develop a pan-serotypic peptide vaccine to HRV, but its design will likely require details about the oligomeric structure of the exposed termini.
Nuclear-Cytoplasmic Shuttling Is Not Required for the Epstein-Barr Virus EBNA-LP Transcriptional Coactivation Function
Authors: Ling Paul D. , Tan Jie , Peng RongSheng
Published: April 2009

Epstein-Barr virus (EBV) EBNA-LP is a transcriptional coactivator of EBNA2 that works though interaction with the promyelocytic leukemia nuclear-body-associated protein Sp100A. EBNA-LP localizes predominantly in the nucleus through the action of nuclear localization signals in the repeated regions of the protein. EBNA-LP has also been detected in the cytoplasm, and a previous study suggested that some of the EBNA-LP coactivation function is mediated by relocalizing histone deacetylase 4 (HDAC4) from the nucleus to the cytoplasm. Although EBNA-LP can be found in the cytoplasm, it has no obvious nuclear export signal, and there is no direct evidence for active shuttling between these cellular compartments. Whether active shuttling between the nucleus and cytoplasm is required for coactivation remains to be clarified. To address these issues, we tested a variety of EBNA-LP isoforms and mutants for nuclear-cytoplasmic shuttling activity in an interspecies heterokaryon assay and for the ability to associate with HDAC4. EBNA-LP isoforms smaller than 42 kDa shuttle efficiently in the heterokaryon assay via a crm-1-independent mechanism. In addition, no specific EBNA-LP domain that mediates nuclear export could be identified. In contrast, an EBNA-LP 62-kDa isoform does not demonstrate detectable shuttling in the heterokaryon assay yet still coactivates EBNA2 similarly to the smaller EBNA-LP isoforms. All of the EBNA-LP mutants tested, including the coactivation-deficient ΔCR3 mutant and the nonshuttling 62-kDa isoform, were capable of associating with HDAC4. Taken together, our results suggest that simple diffusion may account for the nuclear export observed with smaller isoforms of EBNA-LP, that nuclear-cytoplasmic shuttling is not required for efficient EBNA-LP coactivation function, and that competence for HDAC4 association is not sufficient to mediate nuclear-cytoplasmic shuttling or EBNA-LP coactivation in the absence of a functional interaction with Sp100A.
Rhinovirus 3C Protease Can Localize in the Nucleus and Alter Active and Passive Nucleocytoplasmic Transport
Authors: Ghildyal Reena , Jordan Benjamin , Li Dongsheng , Dagher Hayat , Bardin Phillip G. , Gern James E. , Jans David A.
Published: April 2009

The degradation of nuclear pore components and disruption of nucleocytoplasmic trafficking during rhinovirus infection have been attributed to viral 2A protease. Here we show for the first time that rhinovirus 3C protease may also have a role. Specifically, we show that 3C and its precursor, 3CD, can target green fluorescent protein to the nucleus of living cells, leading to degradation of nuclear pore components, and that incubation with recombinant 3C disrupts active and passive nucleocytoplasmic transport in a semi-intact cell nuclear transport system dependent on 3C protease activity. 3C may thus contribute to host cell shutoff in infected cells by localizing in the nucleus and facilitating nuclear pore breakdown.
Ethical issues in funding research and development of drugs for neglected tropical diseases
Authors: Oprea L , Braunack-Mayer A , Gericke C A
Published: April 2009

Neglected and tropical diseases, pervasive in developing countries, are important contributors to global health inequalities. They remain largely untreated due to lack of effective and affordable treatments. Resource-poor countries cannot afford to develop the public health interventions needed to control neglected diseases. In addition, neglected diseases do not represent an attractive market for pharmaceutical industry. Although a number of international commitments, stated in the Millennium Development Goals, have been made to avert the risk of communicable diseases, tropical diseases still remain neglected due to delays in international assistance. This delay can be explained by the form international cooperation has generally taken, which is limited to promoting countries’ national interests, rather than social justice at a global level. This restricts the international responsibility for global inequalities in health to a humanitarian assistance.

We propose an alternative view, arguing that expanding the scope of international cooperation by promoting shared health and economic value at a global level will create new opportunities for innovative, effective and affordable interventions worldwide. It will also promote neglected diseases as a global research priority. We build our argument on a proposal to replace the patenting system that currently regulates pharmaceutical research with a global fund to reward this research based on actual decreases in morbidity and mortality at a global level. We argue that this approach is beneficent because it will decrease global health inequalities and promote social justice worldwide.
Iran’s experience with surrogate motherhood: an Islamic view and ethical concerns
Authors: Aramesh K
Published: April 2009

Gestational surrogacy as a treatment for infertility is being practised in some well-known medical institutions in Tehran and some other cities in Iran. While the majority of Muslims in the world are Sunni, the majority of Iranians are Shiite. Most Sunni scholars do not permit surrogate motherhood, since it involves introducing the sperm of a man into the uterus of a woman to whom he is not married. Most Shiite scholars, however, have issued jurisprudential decrees (fatwas) that allow surrogate motherhood as a treatment for infertility, albeit only for legal couples. They regard this practice as transferring an embryo or fetus from one womb to another, which is not forbidden in Shiite jurisprudence. Nevertheless, there are some controversies concerning some issues such as kinship and inheritance. The main ethical concern of Iran’s experience with gestational surrogacy is the monetary relation between the intended couple and the surrogate mother. While monetary remuneration is practised in Iran and allowed by religious authorities, it seems to suffer from ethical problems. This article proposes that this kind of monetary relation should be modified and limited to reimbursement of normal costs. Such modification requires new legislation and religious decrees.
Stimulating brains, altering minds
Authors: Glannon W
Published: April 2009

Deep-brain stimulation has been used to treat advanced Parkinson disease and other neurological and psychiatric disorders that have not responded to other treatments. While deep-brain stimulation can modulate overactive or underactive regions of the brain and thereby improve motor function, it can also cause changes in a patient’s thought and personality. This paper discusses the trade-offs between the physiological benefit of this technique and the potential psychological harm.
Abortion: Strong’s counterexamples fail
Authors: Di Nucci E
Published: April 2009

This paper shows that the counterexamples proposed by Strong in 2008 in theJournal of Medical Ethicsto Marquis’s argument against abortion fail. Strong’s basic idea is that there are cases—for example, terminally ill patients—where killing an adult human being is prima facie seriously morally wrong even though that human being is not being deprived of a “valuable future”. So Marquis would be wrong in thinking that what is essential about the wrongness of killing an adult human being is that they are being deprived of a valuable future. This paper shows that whichever way the concept of “valuable future” is interpreted, the proposed counterexamples fail: if it is interpreted as “future like ours”, the proposed counterexamples have no bearing on Marquis’s argument. If the concept is interpreted as referring to the patient’s preferences, it must be either conceded that the patients in Strong’s scenarios have some valuable future or admitted that killing them is not seriously morally wrong. Finally, if “valuable future” is interpreted as referring to objective standards, one ends up with implausible and unpalatable moral claims.
Grim news for an unoriginal position: a reply to Seth Baum
Authors: Benatar D
Published: April 2009

Seth Baum suggests that my claim that it is better never to come into existence “can readily be rejected not just out of reflexive distaste for the claim but also out of sound ethical reasoning”. In my reply, I argue that Mr Baum fails to state accurately what my arguments are, and then attempts to refute them by association with other views that he dismisses perfunctorily. Where he does actually engage in my views, his response is effectively merely to assert the opposite.
Controlling Giardia spp. and Cryptosporidium spp. in drinking water by microbial reduction processes
Authors: Finch G R , Belosevic Miodrag
Published: April 2009

Drinking water microbial reduction has evolved from simple, effective chlorination to control waterborne diseases such as cholera and typhoid fever to advanced systems using ozone, chlorine dioxide, ultraviolet radiation, and combinations of disinfectants to control waterborne diseases such as poliomyelitis, hepatitis, giardiasis, and cryptosporidiosis. Giardia spp. and Cryptosporidium spp. have posed a major challenge to the water industry from a variety of perspectives. They occur in low concentrations in source waters, their infective doses in humans are low when compared with typical waterborne viruses and bacteria, they are difficult to inactivate with chlorine compounds, and they are difficult to determine if they are dead when detected in the environment or after microbial reduction in water treatment. However, Giardia spp. and Cryptosporidium spp. are readily controlled by ozone or ultraviolet radiation over a wide range of water-quality conditions. Chlorine dioxide provides a simple alternative to chlorine in some circumstances. Using modern microbial reduction process design techniques such as the integrated disinfection design framework (IDDF) ensures the provision of drinking water with a low risk of transmitting human pathogens to the consumer. Key words: ozone, chlorine dioxide, chlorine, ultraviolet, disinfection, microbial reduction, drinking water, Giardia, Cryptosporidium, parasite.
A multi-species, process based vegetation simulation module to simulate successional forest regrowth after forest disturbance in daily time step hydrological transport models
Authors: MacDonald J.D. , Kiniry J.R. , Putz G. , Prepas E.E.
Published: April 2009

To simulate the effects of tree harvest on boreal forest catchment hydrology, the vegetation growth model within the soil and water assessment tool (SWAT) must reproduce the successional stages of forest reestablishment. The agricultural land management alternatives with numerical assessment criteria (ALMANAC), a multi-species growth model, was modified to simulate vegetation regeneration on forest sites after harvest (ALMANACBF). The model uses similar principles of vegetation growth as the current vegetation model in SWAT, and input requirements are consistent with typical forest inventory databases. This article describes the algorithms integrated into the ALMANACBF model to simulate successional stages in forest growth, provides initial estimates of parameters required to simulate multi-species forest succession, and presents examples of the type of variability in vegetation growth scenarios that these algorithms can reproduce. The model structure and modelling approach shows promise as a tool for foresters to evaluate how patterns and timing of forest management activities influence forest watershed hydrology.
Dissolved and particulate phosphorus concentration and export patterns in headwater streams draining Boreal Plain watersheds one year after experimental forest harvest and post-harvest silvicultural activities
Authors: Prepas Ellie E. , Burke Janice M. , Putz Gordon , Smith Daniel W.
Published: April 2009

This study examined total dissolved (TDP) and particulate phosphorus (PP) concentration and export in nine headwater streams draining Boreal Plain forests in Alberta, Canada, during the growing season and autumn before and in the first year after winter harvest in four of the watersheds. Mechanical and chemical site preparation was also conducted before and during the post-harvest sampling period. During the growing season, TDP and PP concentrations in streams draining harvested watersheds were higher than in the reference streams at storm peaks (P ≤ 0.08) and along the falling limbs of storm flows (P ≤ 0.03). We postulate that forestry activities enhanced TDP leaching from watershed soils after they became saturated. This promoted the growth of periphyton in streams, which subsequently sloughed off during high flows. In autumn, TDP concentrations were higher in streams draining harvested watersheds along the rising limb, at the storm peaks, and along the falling limbs (P ≤ 0.05). However, PP concentrations in autumn were similar in harvested and reference streams along the rising limb (P = 0.19) and were lower in harvested streams at the storm peaks and along the falling limbs (P ≤ 0.08). No differences in TDP or PP concentration were detected between harvested and reference streams during baseflow-dominated periods. Mean TDP and PP export coefficients tended to be higher in the post-harvest than pre-harvest year in both reference and harvested watersheds. After normalization to precipitation inputs, this change (“impact ratio”) was 153% and 130% higher in harvested than reference watersheds for TDP and PP, respectively (P ≤ 0.08). The TDP impact ratio and percent of the watershed area cut were positively related (r2 = 0.95, P = 0.02). A 30 m riparian buffer strip in two harvested watersheds did not appear to reduce the harvest response.
Development of opinion-based generic reforestation regimes and their application in vegetation management and water modelling in the Upper and Lower Foothills of Alberta
Authors: Godin Paul , Russell Jonathan S. , MacDonald J. Douglas , Putz Gordon , Prepas Ellie E.
Published: April 2009

The operational forestry practices employed by Millar Western Forest Products Ltd. in the Upper and Lower Foothills of Alberta, Canada integrate a broad range of tools to plan, implement, and manage post-harvest site regeneration of pure and mixedwood boreal forests. Following tree harvesting, mechanical site preparation is often used to improve microsite conditions to promote conifer seedling establishment or natural regeneration. Chemical and mechanical site preparation and stand tending control competing vascular weed species. To meet forest regeneration commitments, incorporating knowledge gained from forestry experimentation, long-term field data and iterative deterministic modelling into modified management approaches is employed to formulate appropriate vegetation management strategies. These strategies consider and balance multiple biodiversity (e.g., habitat supply modelling), physical environmental (e.g., streamflow), and societal (e.g., industrial fibre requirements) needs relative to a regenerated vegetation complex. From this experience and understanding, the Company developed a series of generic establishment regimes (GERs), which prescribe detailed silvicultural activities to achieve site-regenerated vegetation complexes in alignment with higher-level forest management planning. An outcome of the GER formulation was the development of corresponding plant community assembly diagrams (PCADs), which describe vegetation complexity and permit calculation of total biomass relative to the time series of silvicultural activities within each GER. In turn, these allow forest planners to model biological, physical, and societal factors, while taking into consideration specific stand growth trajectories based on impacts of silvicultural activities on vegetation biomass and species composition. The GERs and PCADs help formulate vegetation complexes over time and are used to guide the behaviour of a vegetation growth model used in conjunction with a hydrologic simulation model.
Strain rate behaviour of Saint-Jean-Vianney clay
Authors: Vaid Y. P. , Robertson P. K. , Campanella R. G.
Published: April 2009

Rate effects on one-dimensional compressibility and undrained shear strength of a heavily overconsolidated naturally cemented clay have been studied. It is shown that in constant rate-of-strain consolidation tests the compressibility increases and the apparent preconsolidation pressure decreases with progressive decrease in rate of strain. Also a decrease in undrained strength is shown to occur with slower rates of strain in constant rate-of-strain shear and with increased time of sustained loading in creep tests. Undrained strengths from the two types of shear tests have been correlated.
The use of sulphur in roadway frost applications
Authors: Gifford P. M. , Gillott J. E.
Published: April 2009

Sulphur-bound soils and a lightweight aggregate sulphur concrete have been studied for potential use as structural frost insulating base materials in roadway construction. Sulphur-bound materials show rapid strength gain and sulphur has a low thermal conductivity (0.27 W/(m ∙ K)). Laboratory studies have shown, however, that, unless specially treated, sulphur-bound soil that contains significant swelling clay disintegrates in water. The laboratory studies were more favourable for the lightweight aggregate sulphur concrete and this material was used as a base course in two test sections of roadway. The test sections and a control section instrumented with thermocouples to measure temperatures to depths of 1.52 m were monitored for 6 winter months. A Dynaflect deflection apparatus was used for structural assessment. It was found that both frost penetration and the length of the subgrade freezing period were reduced and that the structural integrity of the pavement system was improved when lightweight aggregate sulphur concrete was introduced into the base course of the roadway.
Deformation and strength properties of some rocks in southern Ontario
Authors: Lo K. Y. , Hori M.
Published: April 2009

Uniaxial compression tests were performed on sedimentary rocks of five different geological formations at various sites in southern Ontario. The deformation behaviour is analysed in terms of the cross-anisotropic elastic theory and typical sets of five independent parameters for each rock unit have been obtained. It is shown that some of the rock types are significantly anisotropic both in deformation and strength behaviour. The practical relevance of the results in the analysis and design of underground structures in these rocks is discussed.
ELECTROCHEMICAL DEPOSITION OF MAGNESIUM IN ETHEREAL GRIGNARD SALT SOLUTION WITH IONIC LIQUID ADDITIVE
Authors: LIU NING , WANG LIDONG , WU YAOMING , WANG LIMIN
Published: April 2009

The electrochemical deposition of magnesium was investigated in ethereal Grignard salt solution with tetraethylammonium bistrifluoro-methanesulfonimidate additive, using cyclic voltammetry, potentiostatic transients, and scanning electron microscope measurements. The voltammograms showed the presence of reduction and oxidation peaks associated with the deposition and dissolution of magnesium. From the analysis of the experimental current transients, it was shown that the magnesium deposition process was characterized as a three-dimensional nucleation. The deposited product obtained from potentiostatic reduction presented a generally uniform and dense film.
KINETICS OF HYDROGEN ABSORPTION IN Ti600 ALLOY
Authors: WANG XIAOLI , ZHAO YONGQING , ZENG WEIDONG , HOU HONGLIANG , WANG YAOQI
Published: April 2009

The kinetics and mechanism of hydrogen absorption in Ti 600 alloy were investigated at various temperatures (873 K ≤ T ≤ 1123 K ). The rate of hydrogen absorption and equilibrium hydrogen pressure increased with the increase of temperature. Because hydriding reaction is an exothermic reaction, solubility of hydrogen decreased with increasing temperature. The experiment results were interpreted from the time dependent hydrogen absorption curves using various rate equations to reveal the mechanism of the hydrogen absorption processes. The hydriding reaction rate constants were extracted from the time-dependent hydrogen absorption curves. The mechanism of hydriding reaction in different stages has been analyzed. It was found that the chemical reaction process dominated the hydrogen absorption process at 923K. The chemical reaction process and the three-dimensional diffusion process dominated the hydrogen absorption process at 973K or higher.
ACHIEVING ULTRAFINE GRAIN SIZE IN Mg-Al-Zn ALLOY BY COLD DRAWING
Authors: CHAO HONGYING , YU YANG , WANG ERDE
Published: April 2009

Ultrafine-grain size of ~1µm was achieved in an AZ31B Mg alloy wires with high strength prepared by cold drawing and subsequent annealing in the present study. Effects of cold-drawn area reduction (CAR) on strain hardening, recrystallized grain refinement and annealing temperature were investigated. The results showed that the maximum cold area reduction as high as 65.1% could be reached at room temperature, which resulted in the notable strain hardening, grain refinement and the decrease of annealing temperature.
EFFECT OF ZIRCONIUM ON HIGH TEMPERATURE TENSILE PROPERTIES OF PRECIPITATION-HARDENEDMG-ND-ZNCASTING ALLOY
Authors: JUN JOONG-HWAN , SEONG KI-DUG , LEE MIN-HA
Published: April 2009

Influences of Zr addition on microstructure and tensile properties at ambient and elevated temperatures have been investigated for precipitation-hardened Mg -3% Nd -0.6% Zn and Mg -3% Nd -0.6% Zn -0.2% Zr casting alloys. By the addition of Zr , the average grain size of α-( Mg ) phase decreases remarkably. In T6-treated state, the Mg -3% Nd -0.6% Zn -0.2% Zr alloy shows higher YS, UTS and elongation at RT, 150°C and 200°C, compared to those of the Zr -free alloy. Better creep resistance is observed in the Zr -containing alloy at 175°C/120MPa condition, while its creep resistance becomes inferior to that of the Zr -free alloy at 215°C/80MPa and 250°C/40MPa conditions. The discrepancy between tensile and creep properties is discussed in relation to microstructural evolution.
EFFECT OF HOT EXTRUSION ON MICROSTRUCTURE AND MECHANICAL PROPERTIES OF ELECTROMAGNETIC CONTINUOUS CAST AZ31 MAGNESIUM ALLOY
Authors: CHEN GUOQING , SONG JUNHUI , FU XUESONG , ZHAO YUXIAN , ZHOU WENLONG
Published: April 2009

This paper describes the effect of hot extrusion on the microstructure and mechanical properties of electromagnetic continuous cast (EMC) AZ31 alloy. The microstructure, mechanical properties and fracture surfaces of AZ31 alloy before and after extrusion were investigated. The results demonstrate that extrusion processing gives rise to a strong basal texture. The grains are significantly refined and the average grain size of localized fine grain area is 2μm. Compared with EMC ingots, as-extruded specimens have much finer grain size and more uniform microstructure, and the second phase ( Mg 17 Al 12) becomes smaller and distributes more uniformly. The mechanical properties of the deformed AZ31 were improved after hot-extrusion. When the extrusion ratio was 10, the yield strength, ultimate tensile strength and reduction in cross-sectional area of as-extruded AZ31 alloy were 248MPa, 306MPa and 28.44%, which were respectively enhanced by 78.4%, 41% and 45.25%, compared with those of as-cast samples. With the increase of extrusion ratio, the grain refining effect was more significant and the microstructure was more uniform. The yield strength, ultimate tensile strength and reduction in cross-sectional area increased obviously with increasing the extrusion ratio. The observation on fracture surfaces demonstrates that the fracture mode changes from ductile-brittle fracture to ductile fracture after extrusion.
EFFECTS OF THERMO-MECHANICAL TREATMENTS ON MICROSTRUCTURE OF Ti-43Al-9V-Y ALLOY
Authors: KONG FANTAO , CHEN YUYONG
Published: April 2009

Ti -43 Al -9 V - Y alloy billets was prepared by the quasi-isothermal canned forging processing, and effect of heat treatment processes on the microstructure of as-forged Ti -43 Al -9 V - Y alloy was investigated. The results show that, as-forged Ti -43 Al -9 V - Y alloy has streamline microstructure including a large number of recrystallized grains and broken lamellae, and different heat treatment processes were employed to obtain different microstructures of Ti -43 Al -9 V - Y alloy. After heat treatment at 1250°C, the microstructure of as-forged Ti -43 Al -9 V - Y alloy becomes γ+ B 2 microstructure. Comparing with the microstructure after HT of 1250°C/30 min, the precipitation of B 2 lath phase in γ equiaxed grains increased and γ grains refined after HT of 1280°C/30min or 1320°C/30min. However, after the heat treatment of 1300°C/30 min, the duplex microstructures can be gained.