bluuebunny/crossref_metadata_2025 huggingface dataset:
Community Structure in Time-Dependent, Multiscale, and Multiplex Networks
Authors: Mucha Peter J. , Richardson Thomas , Macon Kevin , Porter Mason A. , Onnela Jukka-Pekka
Published: May 2010

Network Notation

Networks are often characterized by clusters of constituents that interact more closely with each other and have more connections to one another than they do with the rest of the components of the network. However, systematically identifying and studying such community structure in complicated networks is not easy, especially when the network interactions change over time or contain multiple types of connections, as seen in many biological regulatory networks or social networks.Muchaet al.(p.876) developed a mathematical method to allow detection of communities that may be critical functional units of such networks. Application to real-world tasks—like making sense of the voting record in the U.S. Senate—demonstrated the promise of the method.
The Selection Landscape of Malaria Parasites
Authors: Mackinnon M. J. , Marsh K.
Published: May 2010

Malaria parasites have to survive and transmit within a highly selective and ever-changing host environment. Because immunity to malaria is nonsterilizing and builds up slowly through repeated infections, commonly the parasite invades a host that is immunologically and physiologically different from its previous host. During the course of infection, the parasite must also keep pace with changes in host immune responses and red-blood-cell physiology. Here, we describe the “selection landscape” of the most virulent of the human malaria parasites,
Plasmodium falciparum
, and the adaptive mechanisms it uses to navigate through that landscape. Taking a cost-benefit view of parasite fitness, we consider the evolutionary outcomes of the most important forces of selection operating on the parasite, namely immunity, host death, drugs, mosquito availability, and coinfection. Given the huge potential for malaria parasite evolution in the context of the recently renewed effort to eradicate malaria, a deeper understanding of
P. falciparum
adaptation is essential.
Carbon Dioxide Enrichment Inhibits Nitrate Assimilation in Wheat and
Arabidopsis
Authors: Bloom Arnold J. , Burger Martin , Asensio Jose Salvador Rubio , Cousins Asaph B.
Published: May 2010

Nitrate for Me, Ammonium for You

The interdependence of plant nitrogen uptake and plant responses to carbon dioxide is well established, but the influence of inorganic nitrogen form—i.e., whether nitrate or ammonium—has been largely ignored.

Bloom
et al.

(p.
899
) present evidence from five independent methods in both a monocot and dicot species that carbon dioxide inhibition of nitrate assimilation is a major determinant of plant responses to rising atmospheric concentrations of carbon dioxide. This finding explains several phenomena, including carbon dioxide acclimation and decline in food quality. The large variation in these phenomena among species, locations, or years derives from the large variation in the relative dependence of plants on nitrate and ammonium as nitrogen sources among species, locations, or years. The relative importance of ammonium and nitrate for plant N nutrition in future cropping systems will be critical for quantity and quality of food.
Additive Genetic Breeding Values Correlate with the Load of Partially Deleterious Mutations
Authors: Tomkins Joseph L. , Penrose Marissa A. , Greeff Johan , LeBas Natasha R.
Published: May 2010

Pedigree Weevils

The phenotype of an organism is related to its additive genetic phenotype, the small but numerous genetic differences between individuals affecting their phenotype, and its mutational load, which is the number of mutations an individual carries. How these two factors affect an individual's ability to leave offspring in the next generation is a major component of evolutionary theory, but evidence for a direct relationship has been lacking. By estimating the contribution of partially recessive mutations to additive genetic variation in seed-feeding cow-pea weevils over a seven-generation pedigree breeding program involving variation in levels of inbreeding,

Tomkins
et al.

(p.
892
) demonstrate an association between genetic quality and the mutational load carried, especially for males.
High-NOON States by Mixing Quantum and Classical Light
Authors: Afek Itai , Ambar Oron , Silberberg Yaron
Published: May 2010

All and Nothing

Entanglement, where a system can be in a superposition of a number of distinct states simultaneously, is a principle at the foundation of quantum mechanics (recall Schrödinger's cat, which is both dead and alive). It can also be used in many applications—imaging, communication, patterning, and metrology—with the effect being amplified by entangling larger systems. However, the systematic generation of “large” entangled systems is challenging.

Afek
et al.

(p.
879
; see the Perspective by

Wildfeuer

) present a technique for generating many-photon entanglement in so-called NOON states, where there are two possible paths and
N
photons in one path and 0 in the other—the system being a superposition of “all and nothing” states. Mixing of entangled pairs with classical light at a beam splitter formed up to five photon-entangled states. The technique should be generally applicable to generate higher-order entangled states.
Beyond Access vs. Protection in Trials of Innovative Therapies
Authors: London Alex John , Kimmelman Jonathan , Emborg Marina Elena
Published: May 2010

Review of first-in-human trials should safeguard the integrity of the scientific enterprise through a focus on preclinical and clinical study quality.
Oil Peak or Panic?
Oil Panic and the Global Crisis
Predictions and Myths

by Steven M. Gorelick

Wiley-Blackwell, Oxford, 2010. 255 pp., illus. $54.95, £32.50. ISBN 9781405195485.
Authors: Greene David Lloyd
Published: May 2010

In this balanced consideration of the peak-oil controversy, Gorelick comes down on the side of the optimists.
Support for Global Health
Authors: Bloom Barry R.
Published: May 2010

As more nations struggle with stressed economies, aid to the developing world becomes increasingly vulnerable to governments' budgetary cuts. The industrialized world is recognizing that coordinating global development assistance is the most efficient way to maximize effectiveness and minimize duplication. Earlier this year, the United States, the largest funder of global health assistance, announced that it seeks to expand multilateral efforts to address the major health problems of developing countries. One of the triumphs of multilateral cooperation has been the Global Fund to Fight AIDS, Tuberculosis and Malaria, a program that has saved millions of lives in developing countries. That is why the $50 million reduction in funding for the Global Fund requested by the U.S. government for fiscal year 2011, in the face of increased requests for expanded coverage by those countries, would be a major setback.
Are Lizards Toast?
Authors: Huey Raymond B. , Losos Jonathan B. , Moritz Craig
Published: May 2010

Warming is held responsible for a rash of extinctions of global lizard populations.
Managing Multistate Quantum Entanglement
Authors: Wildfeuer Christoph
Published: May 2010

A general route for creating entangled states of large numbers of photons may be relevant to other applications of interferometry, such as gravity wave detection.
Herschel's First Images Spark Star-Formation Debate
Authors: Reed Sarah
Published: May 2010

The Herschel telescope has passed its commissioning phase and is starting to deliver on its promised new insights into our universe, scientists reported at the Herschel First Results Symposium in the Netherlands last week.
Sweden Bets on New Lab to Spruce Up Its Bioscience Future
Authors: Travis John
Published: May 2010

Next week, officials in Stockholm will inaugurate a new building with cutting-edge DNA sequencing machines that by 2013 should produce a rough draft of the genome of the Norway spruce, the country's most economically important species.
Taking Laser Science To the Extreme
Authors: Clery Daniel
Published: May 2010

Europe wants to leap to the next generation of laser facilities with a 200-petawatt laser that will create new areas of research, and could rip open the vacuum.
Laser Fusion Energy Poised to Ignite
Authors: Clery Daniel
Published: May 2010

Once lasers have shown that they can spark fusion, what next? Projects in Japan, Europe, and the United States are working to build lasers with the necessary power and repetition rate to make energy from laser fusion a reality.
Smallest of the Small?
Authors: Service Robert F.
Published: May 2010

Lasers have been shrinking ever since they were invented 50 years ago. But the 44-nanometer "spaser" will be hard to beat.
Putting Light's Light Touch to Work As Optics Meets Mechanics
Authors: Cho Adrian
Published: May 2010

Forces exerted by light can set tiny objects aquiver, a phenomenon scientists hope to harness in the burgeoning field of cavity optomechanics.
Redrawing Africa's Malaria Map
Authors: Enserink Martin
Published: May 2010

Smaller countries on the hardest-hit continent have shown how aggressive malaria control can slash cases and deaths. Can the big ones follow?
Malaria's Drug Miracle in Danger
Authors: Enserink Martin
Published: May 2010

Like many others before it, the latest generation of malaria drugs is losing its punch. This time, can global disaster be averted?
Variation in Gamma Interferon Responses to Different Infecting Strains of
Mycobacterium tuberculosis
in Acid-Fast Bacillus Smear-Positive Patients and Household Contacts in Antananarivo, Madagascar
Authors: Rakotosamimanana Niaina , Raharimanga Vaomalala , Andriamandimby Soa Fy , Soares Jean-Louis , Doherty T. Mark , Ratsitorahina Maherisoa , Ramarokoto Herimanana , Zumla Alimuddin , Huggett Jim , Rook Graham , Richard Vincent , Gicquel Brigitte , Rasolofo-Razanamparany Voahangy
Published: May 2010

The majority of healthy individuals exposed to
Mycobacterium tuberculosis
will not develop tuberculosis (TB), though many may become latently infected. More precise measurement of the human immune response to
M. tuberculosis
infection may help us understand this difference and potentially identify those subjects most at risk of developing active disease. Gamma interferon (IFN-γ) production has been widely used as a proxy marker to study infection and to examine the human immune response to specific
M. tuberculosis
antigens. It has been suggested that genetically distinct
M. tuberculosis
strains may invoke different immune responses, although how these differences influence the immune responses and clinical outcome in human tuberculosis is still poorly understood. We therefore evaluated the antigen-specific IFN-γ production responses in peripheral blood mononuclear cells from two cohorts of subjects recruited in Antananarivo, Madagascar, from 2004 to 2006 and examined the influence of the infecting
M. tuberculosis
strains on this response. The cohorts were sputum-positive index cases and their household contacts. Clinical strains isolated from the TB patients were typed by spoligotyping. Comparison of the IFN-γ responses with the spoligotype of the infecting clinical strains showed that “modern”
M. tuberculosis
strains, like Beijing and Central Asian (CAS) strains, tended to induce lower IFN-γ responses than “ancient” strains, like East African-Indian (EAI) strains, in index cases and their household contacts. These results suggest that new strains may have evolved to induce a host response different from that of ancient strains. These findings could have important implications in the development of therapeutic and diagnostic strategies.
Correlates of Protection Induced by Vaccination
Authors: Plotkin Stanley A.
Published: May 2010

This paper attempts to summarize current knowledge about immune responses to vaccines that correlate with protection. Although the immune system is redundant, almost all current vaccines work through antibodies in serum or on mucosa that block infection or bacteremia/viremia and thus provide a correlate of protection. The functional characteristics of antibodies, as well as quantity, are important. Antibody may be highly correlated with protection or synergistic with other functions. Immune memory is a critical correlate: effector memory for short-incubation diseases and central memory for long-incubation diseases. Cellular immunity acts to kill or suppress intracellular pathogens and may also synergize with antibody. For some vaccines, we have no true correlates, but only useful surrogates, for an unknown protective response.
Geosmithia argillacea
: an Emerging Pathogen in Patients with Cystic Fibrosis
Authors: Giraud Sandrine , Pihet Marc , Razafimandimby Bienvenue , Carrère Jacqueline , Degand Nicolas , Mely Laurent , Favennec Loïc , Dannaoui Eric , Bouchara Jean-Philippe , Calenda Alphonse
Published: May 2010

We report eight cases of airway colonization by
Geosmithia argillacea
in patients with cystic fibrosis. This filamentous fungus, resembling members of the genera
Penicillium
and
Paecilomyces
, was identified by molecular analysis. All patients carried a mutation on each
CFTR
(cystic fibrosis transmembrane conductance regulator) allele, with at least one copy of the F508del mutation. The first isolation of this fungus occurred from F508del-homozygous patients at a younger age than in F508del-heterozygous patients. Before recovery of
G. argillacea
, all patients were treated with itraconazole; two of them had also received voriconazole for an
Aspergillus fumigatus
infection. However, antifungal susceptibility patterns showed high MICs of voriconazole for all isolates, and high MICs of amphotericin B and itraconazole for the majority of them, but mostly low minimum effective concentrations (MECs) of caspofungin. The appearance and persistence of
G. argillacea
in the airways were not associated with exacerbation of the disease. However, the clinical implications of
G. argillacea
, particularly in immunocompromised patients, remain a concern, particularly given recent observations suggesting that this fungus may also cause disseminated infections.
Nasopharyngeal Carriage of
Haemophilus haemolyticus
in Otitis-Prone and Healthy Children
Authors: Kirkham Lea-Ann S. , Wiertsema Selma P. , Mowe Eva N. , Bowman Jacinta M. , Riley Thomas V. , Richmond Peter C.
Published: May 2010

Haemophilus haemolyticus
is often incorrectly categorized as nontypeable
Haemophilus influenzae
(NTHI) upon culture. PCR analyses of 266 NTHI-like nasopharyngeal isolates from children with and without recurrent acute otitis media (rAOM) revealed that 11.7% were
H. haemolyticus
and 9.4% gave equivocal results. Children with rAOM were more likely to carry
H. haemolyticus
.
Nucleic Acid Sequence-Based Amplification Assay for Human Papillomavirus mRNA Detection and Typing: Evidence for DNA Amplification
Authors: Boulet Gaëlle A. V. , Micalessi Isabel M. , Horvath Caroline A. J. , Benoy Ina H. , Depuydt Christophe E. , Bogers Johannes J.
Published: May 2010

Human papillomavirus (HPV) E6/E7 mRNA has been proposed as a more specific marker for cervical dysplasia and cancer than HPV DNA. This study evaluated the RNA specificity of nucleic acid sequence-based amplification (NASBA)-based HPV detection using HPV DNA plasmids (HPV type 16 [HPV16], HPV18, HPV31, HPV33, and HPV45) and nucleic acid extracts of several cell lines, which were systematically subjected to enzymatic treatments with DNase and RNase. HPV plasmid dilutions (106to 100copies/μl) and nucleic acid extracts (total DNA, RNA-free DNA, total RNA, and DNA-free RNA) of unfixed and fixed (PreServCyt and SurePath) HaCaT, HeLa, and CaSki cells were tested with the NucliSENS EasyQ HPV test. The RNA-free DNA extracts of HeLa and CaSki cells could be amplified by HPV18 and -16 NASBA, respectively. Fixation of the cells did not influence NASBA. All HPV plasmids could be detected with NASBA. Based on the plasmid dilution series, a lower detection limit of 5 × 103HPV DNA copies could be determined. Our study identified viral double-stranded DNA as a possible target for NASBA-based HPV detection. The differences in diagnostic accuracy between the NASBA-based tests and conventional HPV DNA detection assays seem to be attributable not to the more specific amplification of viral mRNA but to the limited type range and the lower analytical sensitivity for HPV DNA.
The
Streptococcus milleri
Population of a Cystic Fibrosis Clinic Reveals Patient Specificity and Intraspecies Diversity
Authors: Sibley Christopher D. , Sibley Kristen A. , Leong Tara A. , Grinwis Margot E. , Parkins Michael D. , Rabin Harvey R. , Surette Michael G.
Published: May 2010

The genetic relatedness of
Streptococcus milleri
group isolates from the airways of cystic fibrosis patients was determined by using pulsed-field gel electrophoresis. This study reveals no evidence for patient-to-patient transmission in our patient population; however, within individual patients, complex inter- and intraspecies diversity and dynamics can be observed.
Perinatal Sepsis Caused by
Williamsia serinedens
Infection in a 31-Year-Old Pregnant Woman
Authors: Yassin Atteyet F. , Lombardi Salvatore J. , Fortunato Stephen J. , McNabb Paul C. , Carr Mark B. , Trabue Christopher H.
Published: May 2010

Williamsia serinedens
has been isolated from soil but has not yet been implicated in human disease. We report the first case of perinatal sepsis caused by a dual-morphotype form of
Williamsia serinedens
in a 31-year-old pregnant woman hospitalized with preterm labor.
Phylogenetic Analysis of a Virulent
Borrelia
Species Isolated from Patients with Relapsing Fever
Authors: Toledo A. , Anda P. , Escudero R. , Larsson C. , Bergstrom S. , Benach J. L.
Published: May 2010

Multilocus sequence analysis (MLSA) was used to clarify the taxonomic status of a virulent
Borrelia
organism previously isolated from patients with relapsing fever and from ticks in Spain that is designated the Spanish relapsing fever (SRF)
Borrelia
. This species has been used extensively in experimental infection models because of its continued virulence. Seven genes were amplified to analyze the phylogenetic relationships among several Spanish isolates of SRF
Borrelia
and other relapsing fever
Borrelia
species. The genes targeted in this study included
rrs
and
flaB
, which have commonly been used in phylogenetic studies; the
rrf-rrl
intergenic spacer (IGS), which is highly discriminatory; and four additional genes,
p66
,
groEL
,
glpQ
, and
recC
, which are located on the chromosome and which have therefore evolved in a clonal way. The species included in this study were
Borrelia duttonii
,
B. recurrentis
,
B. crocidurae
, and
B. hispanica
as Old World
Borrelia
species and
B. turicatae
and
B. hermsii
as New World
Borrelia
species. The results obtained by MLSA of the SRF
Borrelia
on the basis of 1% of the genomic sequence data analyzed confirmed that the SRF
Borrelia
isolates are
B. hispanica
. However, the prototype isolates of
B. hispanica
used in this study have an uncertain history and display unique phenotypic characteristics that are not shared with the SRF
Borrelia
. Therefore, we propose to use strain SP1, isolated from a relapsing fever patient in 1994 in southern Spain, as the type strain for
B. hispanica
.
Multilocus Sequence Types of Carbapenem-Resistant
Pseudomonas aeruginosa
in Singapore Carrying Metallo-β-Lactamase Genes, Including the Novel
bla
IMP-26
Gene
Authors: Koh Tse Hsien , Khoo Cheng Teng , Tan Thuan Tong , Mohamed Arshad Mohamed Amir Bin , Ang Li Ping , Lau Lee Jin , Hsu Li-Yang , Ooi Eng Eong
Published: May 2010

Nine imipenem-resistant
Pseudomonas aeruginosa
isolates were found to contain a variety of metallo-β-lactamase genes, including
bla
IMP-1
,
bla
IMP-7
,
bla
VIM-2
,
bla
VIM-6
, and the novel
bla
IMP-26
. Multilocus sequence typing showed a diversity of sequence types. Comparison with isolates from an earlier study showed that the epidemic clones from 2000 have not become established.
Clinical and Etiological Characteristics of Enterovirus 71-Related Diseases during a Recent 2-Year Period in Korea
Authors: Ryu Wi-Sun , Kang Byounghak , Hong Jiyoung , Hwang Seoyeon , Kim Jonghyun , Cheon Doo-Sung
Published: May 2010

Human enterovirus 71 (EV 71) has caused large-scale outbreaks of hand-foot-and-mouth disease (HFMD), particularly in the Asian-Pacific region. In this study, we report a major outbreak of EV 71 infection in Korea and describe the clinical differences between EV 71 and non-EV 71 enterovirus infections. We prospectively enrolled patients with suspected viral infections during a recent 2-year period through a nationwide surveillance system. We identified 719 patients with suspected HFMD or herpangina using real-time PCR and genotyping based on VP1 sequence analysis. The major pathogen causing HFMD changed substantially from 2008 to 2009, with EV 71 becoming the most common cause of HFMD in Korea in 2009. We successfully identified the enteroviral genotypes for 218 of the 719 patients. Patients with EV 71 infections tended to be younger than those with non-EV 71 enteroviral infections and presented with HFMD and meningoencephalitis. In addition, the occurrence of fever, headache, and neck stiffness was significantly higher in patients with EV 71 infections. Multivariable analysis showed that for patients presenting with HFMD, fever, or a sore throat, each covariate was independently associated with EV 71 infection; the adjusted odds ratios (with 95% confidence intervals in parentheses) for these variables were 31.86 (10.04 to 101.09), 4.76 (1.71 to 13.25), and 0.18 (0.04 to 0.77), respectively. Our results indicate that EV 71 was a major cause of HFMD in Korea during the study period. In addition, we found that clinical symptoms may be helpful in the early identification of patients with EV 71 infections.
Detection of
Anaplasma marginale
and
A. phagocytophilum
in Bovine Peripheral Blood Samples by Duplex Real-Time Reverse Transcriptase PCR Assay
Authors: Reinbold James B. , Coetzee Johann F. , Sirigireddy Kamesh R. , Ganta Roman R.
Published: May 2010

Insufficient diagnostic sensitivity and specificity coupled with the potential for cross-reactivity among closely related
Anaplasma
species has made the accurate determination of infection status problematic. A method for the development of simplex and duplex real-time quantitative reverse transcriptase PCR (qRT-PCR) assays for the detection of
A. marginale
and
A. phagocytophilum
16S rRNA in plasma-free bovine peripheral blood samples is described. The duplex assay was able to detect as few as 100 copies of 16S rRNA of both
A. marginale
and
A. phagocytophilum
in the same reaction. The ratio of 16S rRNA to 16S DNA copies for
A.
marginale was determined to be 117.9:1 (95% confidence interval [95% CI], 100.7:1, 135.2:1). Therefore, the detection limit is the minimum infective unit of one
A. marginale
bacterium. The duplex assay detected nonequivalent molar ratios as high as 100-fold. Additionally, the duplex assay and a competitive enzyme-linked immunosorbent assay (cELISA) were used to screen 237 samples collected from herds in which anaplasmosis was endemic. When the cELISA was evaluated by the results of the qRT-PCR, its sensitivity and specificity for the detection of
A. marginale
infection were found to be 65.2% (95% CI, 55.3%, 75.1%) and 97.3% (95% CI, 94.7%, 99.9%), respectively.
A. phagocytophilum
infection was not detected in the samples analyzed. One- and two-way receiver operator characteristic curves were constructed in order to recommend the optimum negative cutoff value for the cELISA. Percentages of inhibition of 20 and 15.3% were recommended for the one- and two-way curves, respectively. In conclusion, the duplex real-time qRT-PCR assay is a highly sensitive and specific diagnostic tool for the accurate and precise detection of
A. marginale
and
A. phagocytophilum
infections in cattle.
Prevalence of
Haemophilus influenzae
Type b Genetic Islands among Clinical and Commensal
H. influenzae
and
H. haemolyticus
Isolates
Authors: Sandstedt Sara A. , Marrs Carl F. , Patel Mayuri , Hirasawa Hitomi , Zhang Lixin , Davis Gregg S. , Gilsdorf Janet R.
Published: May 2010

Five genetic islands (HiGI) found in
Haemophilus influenzae
type b strain Eagan were used as hybridization probes on type b,
Haemophilus haemolyticus
, and nontypeable
H. influenzae
(NTHi) isolates. HiGI2 and HiGI7 were significantly more prevalent in NTHi isolates from children with otitis media than in those from the throats of healthy children.
Disseminated Infection with a New Genovar of
Encephalitozoon cuniculi
in a Renal Transplant Recipient
Authors: Talabani Hana , Sarfati Claudine , Pillebout Evangeline , van Gool Tom , Derouin Francis , Menotti Jean
Published: May 2010

Disseminated microsporidiosis is a life-threatening opportunistic infection. Here, we report about a previously undescribed genovar of
Encephalitozoon cuniculi
causing disseminated infection in a non-HIV-infected renal transplant recipient. Disseminated microsporidiosis must be considered in the differential diagnosis of chronic fever in renal allograft recipients, even those without urinary symptoms.
Dissection of the HIV Vif Interaction with Human E3 Ubiquitin Ligase
Authors: Wolfe Leslie S. , Stanley Bradford J. , Liu Chang , Eliason William K. , Xiong Yong
Published: May 2010

The human immunodeficiency virus type 1 (HIV-1) protein Vif recruits the host E3 ubiquitin ligase, composed of cullin 5 (Cul5), Rbx2, Elongin B, and Elongin C (EloBC), to polyubiquitinate the antiviral protein APOBEC3G. Multiple regions in the C-terminal half of Vif interact with the E3 ligase. We have purified individual regions of Vif and investigated their thermodynamic contributions to the ligase assembly
in vitro
using isothermal titration calorimetry and fluorescence anisotropy. Our results quantify the high-affinity interactions between the Vif BC box and EloBC and between the Vif zinc finger and Cul5, as well as the modest interaction between the Vif cullin box and Cul5. Our purified Vif constructs also provide direct biochemical evidence that the Vif cullin box, containing the PPLP region, leads to the dimerization of Vif-EloBC complexes but not Cul5-Vif-EloBC complexes.
APOBEC3G Contributes to HIV-1 Variation through Sublethal Mutagenesis
Authors: Sadler Holly A. , Stenglein Mark D. , Harris Reuben S. , Mansky Louis M.
Published: May 2010

The mammalian APOBEC3 proteins are an important component of the cellular innate immune response to retroviral infection. APOBEC3G can extinguish HIV-1 infectivity by its incorporation into virus particles and subsequent cytosine deaminase activity that attacks the nascent viral cDNA during reverse transcription, causing lethal mutagenesis. It has been suggested, but not formally shown, that APOBEC3G can also induce sublethal mutagenesis, which would maintain virus infectivity and contribute to HIV-1 variation. To test this, we developed a novel model system utilizing an HIV-1 vector and a panel of APOBEC3G-expressing cells. We observed proviruses with single APOBEC3G-mediated mutations (in the presence or absence of Vif), occurring at distinct hot spots and which could be rescued and shown to have infectivity. These data indicate that APOBEC3G-dependent restriction of HIV-1 can result in viable viral progeny that harbor sublethal levels of G-to-A mutations. Such mutations have the potential to contribute significantly to HIV-1 evolution, pathogenesis, immune escape, and drug resistance.
Splicing Diversity of the Human
OCLN
Gene and Its Biological Significance for Hepatitis C Virus Entry
Authors: Kohaar Indu , Ploss Alexander , Korol Evgenia , Mu Kathy , Schoggins John W. , O'Brien Thomas R. , Rice Charles M. , Prokunina-Olsson Ludmila
Published: May 2010

Persistent hepatitis C virus (HCV) infection is a primary etiological factor for the development of chronic liver disease, including cirrhosis and cancer. A recent study identified occludin (OCLN), an integral tight junction protein, as one of the key factors for HCV entry into cells. We explored the splicing diversity of
OCLN
in normal human liver and observed variable expression of alternative splice variants, including two known forms (
WT-OCLN
and
OCLN-ex4del
) and six novel forms (
OCLN-ex7ext
,
OCLN-ex3pdel
,
OCLN-ex3del
,
OCLN-ex3
-
4del
,
OCLN-ex3p-9pdel
, and
OCLN-ex3p-7pdel
). Recombinant protein isoforms WT-OCLN and OCLN-ex7ext, which retained the HCV-interacting MARVEL domain, were expressed on the cell membrane and were permissive for HCV infection in
in vitro
infectivity assays. All other forms lacked the MARVEL domain, were expressed in the cytoplasm, and were nonpermissive for HCV infection. Additionally, we observed variable expression of
OCLN
splicing forms across human tissues and cell lines. Our study suggests that the remarkable natural splicing diversity of
OCLN
might contribute to HCV tissue tropism and possibly modify the outcome of HCV infection in humans. Genetic factors crucial for regulation of
OCLN
expression and susceptibility to HCV infection remain to be elucidated.
Genetically Engineered, Biarsenically Labeled Influenza Virus Allows Visualization of Viral NS1 Protein in Living Cells
Authors: Li Yang , Lu Xinya , Li Junwei , Bérubé Nathalie , Giest Kerri-Lane , Liu Qiang , Anderson Deborah H. , Zhou Yan
Published: May 2010

Real-time fluorescence imaging of viral proteins in living cells provides a valuable means to study virus-host interactions. The challenge of generating replication-competent fluorescent influenza A virus is that the segmented genome does not allow fusion of a fluorescent protein gene to any viral gene. Here, we introduced the tetracysteine (TC) biarsenical labeling system into influenza virus in order to fluorescently label viral protein in the virus life cycle. We generated infectious influenza A viruses bearing a small TC tag (CCPGCC) in the loop/linker regions of the NS1 proteins. In the background of A/Puerto Rico/8/34 (H1N1) (PR8) virus, the TC tag can be inserted into NS1 after amino acid 52 (AA52) (PR8-410), AA79 (PR8-412), or AA102 (PR8-413) or the TC tag can be inserted and replace amino acids 79 to 84 (AA79-84) (PR8-411). Although PR8-410, PR8-411, and PR8-412 viruses are attenuated than the wild-type (WT) virus to some extent in multiple-cycle infection, their growth potential is similar to that of the WT virus during a single cycle of infection, and their NS1 subcellular localization and viral protein synthesis rate are quite similar to those of the WT virus. Furthermore, labeling with membrane-permeable biarsenical dye resulted in fluorescent NS1 protein in the context of virus infection. We could exploit this strategy on NS1 protein of A/Texas/36/91 (H1N1) (Tx91) by successfully rescuing a TC-tagged virus, Tx91-445, which carries the TC tag replacement of AA79-84. The infectivity of Tx91-445 virus was similar to that of WT Tx91 during multiple cycles of replication and a single cycle of replication. The NS1 protein derived from Tx91-445 can be fluorescently labeled in living cells. Finally, with biarsenical labeling, the engineered replication-competent virus allowed us to visualize NS1 protein nuclear import in virus-infected cells in real time.
Establishment of an H6N2 Influenza Virus Lineage in Domestic Ducks in Southern China
Authors: Huang K. , Bahl J. , Fan X. H. , Vijaykrishna D. , Cheung C. L. , Webby R. J. , Webster R. G. , Chen H. , Smith Gavin J. D. , Peiris J. S. M. , Guan Y.
Published: May 2010

Multiple reassortment events between different subtypes of endemic avian influenza viruses have increased the genomic diversity of influenza viruses circulating in poultry in southern China. Gene exchange from the natural gene pool to poultry has contributed to this increase in genetic diversity. However, the role of domestic ducks as an interface between the natural gene pool and terrestrial poultry in the influenza virus ecosystem has not been fully characterized. Here we phylogenetically and antigenically analyzed 170 H6 viruses isolated from domestic ducks from 2000 to 2005 in southern China, which contains the largest population of domestic ducks in the world. Three distinct hemagglutinin lineages were identified. Group I contained the majority of isolates with a single internal gene complex and was endemic in domestic ducks in Guangdong from the late 1990s onward. Group II was derived from reassortment events in which the surface genes of group I viruses were replaced with novel H6 and N2 genes. Group III represented H6 viruses that undergo frequent reassortment with multiple virus subtypes from the natural gene pool. Surprisingly, H6 viruses endemic in domestic ducks and terrestrial poultry seldom reassort, but gene exchanges between viruses from domestic ducks and migratory ducks occurred throughout the surveillance period. These findings suggest that domestic ducks in southern China mediate the interaction of viruses between different gene pools and facilitate the generation of novel influenza virus variants circulating in poultry.
OrfA Downregulates Feline Immunodeficiency Virus Primary Receptor CD134 on the Host Cell Surface and Is Important in Viral Infection
Authors: Hong Yang , Fink Elizabeth , Hu Qiong-Ying , Kiosses William B. , Elder John H.
Published: May 2010

Feline immunodeficiency virus (FIV) OrfA is an accessory protein that is critical for productive viral replication and infection in T cells. Here, we show that OrfA acts to markedly reduce cell surface expression of the FIV primary binding receptor. Downregulation does not occur at the transcriptional or translational level in that the amounts of CD134 mRNA and protein in total cell lysates are not altered between parental 104-C1 T cells and the same cell line stably expressing OrfA (104-C1-OrfA). Analysis by confocal microscopy revealed significant accumulation of CD134 in the Golgi apparatus of 104-C1 cells expressing OrfA. OrfA does not cause a generalized disruption of membrane trafficking in that surface expression of CD9 is unaffected by OrfA overexpression. Consistent with the above observations, OrfA-negative FIV-34TF10 productively infects CrFK (CD134-negative) and 104-C1-OrfA (CD134 downregulated by OrfA) cells but fails to productively infect either 104-C1 (CD134-positive) cells or GFox (CrFK cells overexpressing CD134) cells. FIV-34TF10 in which the OrfA reading frame is open (OrfArep) productively infects CrFK, GFox, 104-C1, and 104-C1-OrfA cells. We hypothesize that reduced surface expression of the receptor, a hallmark of retrovirus infections, may facilitate an increase in virus release from the infected cell by minimizing receptor interactions with budding virus particles.
Epitope Mapping of Ibalizumab, a Humanized Anti-CD4 Monoclonal Antibody with Anti-HIV-1 Activity in Infected Patients
Authors: Song Ruijiang , Franco David , Kao Chia-Ying , Yu Faye , Huang Yaoxing , Ho David D.
Published: May 2010

Ibalizumab is a humanized monoclonal antibody that binds human CD4, the primary receptor for human immunodeficiency virus type 1 (HIV-1). With its unique specificity for domain 2 of CD4, this antibody potently and broadly blocks HIV-1 infection
in vitro
by inhibiting a postbinding step required for viral entry but without interfering with major histocompatibility complex class II (MHC-II)-mediated immune function. In clinical trials, ibalizumab has demonstrated anti-HIV-1 activity in patients without causing immunosuppression. Thus, a characterization of the ibalizumab epitope was conducted in an attempt to gain insight into the underlying mechanism of its antiviral activity as well as its safety profile. By studying mouse/human chimeric CD4 molecules and site-directed point mutants of CD4, amino acids L96, P121, P122, and Q163 in domain 2 were found to be important for ibalizumab binding, with E77 and S79 in domain 1 also contributing. All these residues appear to cluster on the interface between domains 1 and 2 of human CD4 on a surface opposite the site where gp120 and the MHC-II molecule bind on domain 1. Separately, the epitope of M-T441, a weakly neutralizing mouse monoclonal antibody that competes with ibalizumab, was localized entirely within domain 2 on residues 123 to 125 and 138 to 140. The results reported herein not only provide an appreciation for why ibalizumab has not had significant adverse immunological consequences in infected patients to date but also raise possible steric hindrance mechanisms by which this antibody blocks HIV-1 entry into a CD4-positive cell.
A Limited Number of Simian Immunodeficiency Virus (SIV)
env
Variants Are Transmitted to Rhesus Macaques Vaginally Inoculated with SIVmac251
Authors: Stone Mars , Keele Brandon F. , Ma Zhong-Min , Bailes Elizabeth , Dutra Joseph , Hahn Beatrice H. , Shaw George M. , Miller Christopher J.
Published: May 2010

Single-genome amplification (SGA) and sequencing of HIV-1 RNA in plasma of acutely infected humans allows the identification and enumeration of transmitted/founder viruses responsible for productive systemic infection. Use of this strategy as a means for identifying transmitted viruses suggested that intrarectal simian immunodeficiency virus (SIV) inoculation of macaques recapitulates key features of human rectal infection. However, no studies have used the SGA strategy to identify vaginally transmitted virus(es) in macaques or to determine how early SIV diversification in vaginally infected animals compares with HIV-1 in humans. We used SGA to amplify 227 partial
env
sequences from a SIVmac251 challenge stock and from seven rhesus macaques at the earliest plasma viral RNA-positive time point after low- and high-dose intravaginal inoculation. Sequences were analyzed phylogenetically to determine the relationship of transmitted/founder viruses within and between each animal and the challenge stock. In each animal, discrete low-diversity
env
sequence lineages were evident, and these coalesced phylogenetically to identical or near-identical
env
sequences in the challenge stock, thus confirming the validity of the SGA sequencing and modeling strategy for identifying vaginally transmitted SIV. Between 1 and 10 viruses were responsible for systemic infection, similar to humans infected by sexual contact, and the set of viruses transmitted to the seven animals studied represented the full genetic constellation of the challenge stock. These findings recapitulate many of the features of sexual HIV-1 transmission in women. Furthermore, the SIV rhesus macaque model can be used to understand the factors that influence the transmission of single versus multiple SIV variants.
Bat Guano Virome: Predominance of Dietary Viruses from Insects and Plants plus Novel Mammalian Viruses
Authors: Li Linlin , Victoria Joseph G. , Wang Chunlin , Jones Morris , Fellers Gary M. , Kunz Thomas H. , Delwart Eric
Published: May 2010

Bats are hosts to a variety of viruses capable of zoonotic transmissions. Because of increased contact between bats, humans, and other animal species, the possibility exists for further cross-species transmissions and ensuing disease outbreaks. We describe here full and partial viral genomes identified using metagenomics in the guano of bats from California and Texas. A total of 34% and 58% of 390,000 sequence reads from bat guano in California and Texas, respectively, were related to eukaryotic viruses, and the largest proportion of those infect insects, reflecting the diet of these insectivorous bats, including members of the viral families
Dicistroviridae
,
Iflaviridae
,
Tetraviridae
, and
Nodaviridae
and the subfamily
Densovirinae
. The second largest proportion of virus-related sequences infects plants and fungi, likely reflecting the diet of ingested insects, including members of the viral families
Luteoviridae
,
Secoviridae
,
Tymoviridae
, and
Partitiviridae
and the genus
Sobemovirus
. Bat guano viruses related to those infecting mammals comprised the third largest group, including members of the viral families
Parvoviridae
,
Circoviridae
,
Picornaviridae
,
Adenoviridae
,
Poxviridae
,
Astroviridae
, and
Coronaviridae
. No close relative of known human viral pathogens was identified in these bat populations. Phylogenetic analysis was used to clarify the relationship to known viral taxa of novel sequences detected in bat guano samples, showing that some guano viral sequences fall outside existing taxonomic groups. This initial characterization of the bat guano virome, the first metagenomic analysis of viruses in wild mammals using second-generation sequencing, therefore showed the presence of previously unidentified viral species, genera, and possibly families. Viral metagenomics is a useful tool for genetically characterizing viruses present in animals with the known capability of direct or indirect viral zoonosis to humans.
Neutralization Efficiency Is Greatly Enhanced by Bivalent Binding of an Antibody to Epitopes in the V4 Region and the Membrane-Proximal External Region within One Trimer of Human Immunodeficiency Virus Type 1 Glycoproteins
Authors: Wang Pengcheng , Yang Xinzhen
Published: May 2010

Most antibodies are multivalent, with the potential to bind with high avidity. However, neutralizing antibodies commonly bind to virions monovalently. Bivalent binding of a monoclonal antibody (MAb) to a virion has been documented only in a single case. Thus, the role of high avidity in antibody-mediated neutralization of viruses has not been defined clearly. In this study, we demonstrated that when an artificial 2F5 epitope was inserted in the gp120 V4 region so that an HIV-1 envelope glycoprotein (Env) trimer contains a natural 2F5 epitope in the gp41 membrane-proximal envelope region (MPER) and an artificially engineered 2F5 epitope in the gp120 V4 region, bivalent 2F5 IgG achieved greatly enhanced neutralization efficiency, with a 50% inhibitory concentration (IC
50
) decrease over a 2-log scale. In contrast, the monovalent 2F5 Fab fragment did not exhibit any appreciable change in neutralization efficiency in the same context. These results demonstrate that bivalent binding of 2F5 IgG to a single HIV-1 Env trimer results in dramatic enhancement of neutralization, probably through an increase in binding avidity. Furthermore, we demonstrated that bivalent binding of MAb 2F5 to the V4 region and MPER of an HIV-1 Env trimer can be achieved only in a specific configuration, providing an important insight into the structure of a native/infectious HIV-1 Env trimer. This specific binding configuration also establishes a useful standard that can be applied to evaluate the biological relevance of structural information on the HIV-1 Env trimer.
Pathogenic Hantaviruses Andes Virus and Hantaan Virus Induce Adherens Junction Disassembly by Directing Vascular Endothelial Cadherin Internalization in Human Endothelial Cells
Authors: Gorbunova Elena , Gavrilovskaya Irina N. , Mackow Erich R.
Published: May 2010

Hantaviruses infect endothelial cells and cause 2 vascular permeability-based diseases. Pathogenic hantaviruses enhance the permeability of endothelial cells in response to vascular endothelial growth factor (VEGF). However, the mechanism by which hantaviruses hyperpermeabilize endothelial cells has not been defined. The paracellular permeability of endothelial cells is uniquely determined by the homophilic assembly of vascular endothelial cadherin (VE-cadherin) within adherens junctions, which is regulated by VEGF receptor-2 (VEGFR2) responses. Here, we investigated VEGFR2 phosphorylation and the internalization of VE-cadherin within endothelial cells infected by pathogenic Andes virus (ANDV) and Hantaan virus (HTNV) and nonpathogenic Tula virus (TULV) hantaviruses. We found that VEGF addition to ANDV- and HTNV-infected endothelial cells results in the hyperphosphorylation of VEGFR2, while TULV infection failed to increase VEGFR2 phosphorylation. Concomitant with the VEGFR2 hyperphosphorylation, VE-cadherin was internalized to intracellular vesicles within ANDV- or HTNV-, but not TULV-, infected endothelial cells. Addition of angiopoietin-1 (Ang-1) or sphingosine-1-phosphate (S1P) to ANDV- or HTNV-infected cells blocked VE-cadherin internalization in response to VEGF. These findings are consistent with the ability of Ang-1 and S1P to inhibit hantavirus-induced endothelial cell permeability. Our results suggest that pathogenic hantaviruses disrupt fluid barrier properties of endothelial cell adherens junctions by enhancing VEGFR2-VE-cadherin pathway responses which increase paracellular permeability. These results provide a pathway-specific mechanism for the enhanced permeability of hantavirus-infected endothelial cells and suggest that stabilizing VE-cadherin within adherens junctions is a primary target for regulating endothelial cell permeability during pathogenic hantavirus infection.
Counteraction of HLA-C-Mediated Immune Control of HIV-1 by Nef
Authors: Specht Anke , Telenti Amalio , Martinez Raquel , Fellay Jacques , Bailes Elizabeth , Evans David T. , Carrington Mary , Hahn Beatrice H. , Goldstein David B. , Kirchhoff Frank
Published: May 2010

A host genetic variant (−
35C
/
T
) correlates with increased human leukocyte antigen C (HLA-C) expression and improved control of HIV-1. HLA-C-mediated immunity may be particularly protective because HIV-1 is unable to remove HLA-C from the cell surface, whereas it can avoid HLA-A- and HLA-B-mediated immunity by Nef-mediated down-modulation. However, some individuals with the protective −
35CC
genotype exhibit high viral loads. Here, we investigated whether the ability of HIV-1 to replicate efficiently in the “protective” high-HLA-C-expression host environment correlates with specific functional properties of Nef. We found that high set point viral loads (sVLs) were not associated with the emergence of Nef variants that had acquired the ability to down-modulate HLA-C or were more effective in removing HLA-A and HLA-B from the cell surface. However, in individuals with the protective −
35CC
genotype we found a significant association between sVLs and the efficiency of Nef-mediated enhancement of virion infectivity and modulation of CD4, CD28, and the major histocompatibility complex class II (MHC-II)-associated invariant chain (Ii), while this was not observed in subjects with the −
35TT
genotype. Since the latter Nef functions all influence the stimulation of CD4
+
T helper cells by antigen-presenting cells, they may cooperate to affect both the activation status of infected T cells and the generation of an antiviral cytotoxic T-lymphocyte (CTL) response. In comparison, different levels of viremia in individuals with the common −
35TT
genotype were not associated with differences in Nef function but with differences in HLA-C mRNA expression levels. Thus, while high HLA-C expression may generally facilitate control of HIV-1, Nef may counteract HLA-C-mediated immune control in some individuals indirectly, by manipulating T-cell function and MHC-II antigen presentation.