bluuebunny/crossref_metadata_2025 huggingface dataset:
Lower Extremity Muscular Strength and Leukocyte Telomere Length: Implications of Muscular Strength in Attenuating Age-Related Chronic Disease
Authors: Loprinzi Paul D. , Loenneke Jeremy P.
Published: August 2015

Objective:

Leukocyte telomere length (LTL) shortening is characteristic of aging and is associated with morbidity and mortality, independent of age. Research demonstrates that lower extremity muscular strength is associated with mobility, morbidity and mortality; however, no study, to our knowledge, had examined the association between lower extremity muscular strength and LTL, which was the purpose of this brief study.

Methods:

Data from the 1999–2002 NHANES was used (N = 2410; 50–85 years). Peak isokinetic knee extensor strength (IKES) was objectively measured with LTL assessed from a blood sample.

Results:

After adjustments, for every 50 N increase in IKES, participants had a 9% reduced odds (P = .04) of being in the 1st (vs. 4th) LTL quartile.

Discussion:

Lower extremity muscular strength is associated with LTL, suggesting a possible mechanism through which lower extremity muscular strength may be associated with morbidity and mortality.
Colloidal matter: Packing, geometry, and entropy
Authors: Manoharan Vinothan N.
Published: August 2015

Learning from the packing of particles

Colloidal particles, which consist of clusters of hundreds or thousands of atoms, can still resemble atomic systems. In particular, colloids have been used to study the packing of spheres and the influence of short-range interactions on crystallization and melting. Manoharan reviews these similarities, as well as the cases in which colloidal particles show behavior not seen in atomic systems. For example, the packing of nonspherical objects, where geometry or topology may matter, can give insights into the role of entropy in packing.

Science
, this issue
10.1126/science.1253751
Fiscal crisis has Brazilian scientists scrambling
Authors: Escobar Herton
Published: August 2015

Government makes deep cuts in research budgets as economy stumbles.
Plugged pores may underlie some ALS, dementia cases
Authors: Underwood Emily
Published: August 2015

Multiple groups reveal that “stutter” mutation kills nerve cells by clogging channels into the nucleus.
Dark horse scores a fusion coup
Authors: Clery Daniel
Published: August 2015

California company shows new approach to trapping hot plasma.
The missing mudbug
Authors: DeMarco Emily
Published: August 2015

As threats to crayfish mount, researchers push to document the enigmatic crustaceans.
Titin mutations in iPS cells define sarcomere insufficiency as a cause of dilated cardiomyopathy
Authors: Hinson John T. , Chopra Anant , Nafissi Navid , Polacheck William J. , Benson Craig C. , Swist Sandra , Gorham Joshua , Yang Luhan , Schafer Sebastian , Sheng Calvin C. , Haghighi Alireza , Homsy Jason , Hubner Norbert , Church George , Cook Stuart A. , Linke Wolfgang A. , Chen Christopher S. , Seidman J. G. , Seidman Christine E.
Published: August 2015

A giant disruption of the heart

Certain forms of heart failure originate from genetic mutations. Understanding how the culprit mutant proteins alter normal heart function could lead to more effective treatments. One candidate is the giant protein tintin, which is mutated in a subset of patients with dilated cardiomyopathy. Through a combination of patient-derived stem cells, tissue engineering, and gene editing, Hinson
et al.
found that disease-associated titin mutations disrupt the function of the contractile unit in heart muscle. As a result, the heart does not respond properly to mechanical and other forms of stress.

Science
, this issue p.
982
Scalable
T
2
resistivity in a small single-component Fermi surface
Authors: Lin Xiao , Fauqué Benoît , Behnia Kamran
Published: August 2015

Trying to break a stubborn law

The electrical resistivity of most metals at low temperatures has a characteristic quadratic dependence on temperature. This law is typically ascribed to the scattering of electrons off each other in the presence of a crystal lattice. By measuring the resistivity of SrTiO
3
with varying dopant concentrations, Lin
et al.
test the applicability of the law for metals with low carrier densities. The law persists down to the lowest carrier concentrations, into the regime where the conditions for this behavior were previously thought to break down.

Science
, this issue p.
945
Irrationality in mate choice revealed by túngara frogs
Authors: Lea Amanda M. , Ryan Michael J.
Published: August 2015

A third option leads to poor mates

A “decoy” effect decreases rational decision-making in humans. Irrational decisions in this case are a result of a choice between two options being affected by the introduction of a suboptimal third choice. Lea and Ryan show that tungara frogs are also subject to a decoy effect, choosing a male with a less appealing call when presented with a third, inferior calling male. These results suggest that the choice of mates by animals may be context dependent. It appears that rational choice may not always drive sexual selection.

Science
, this issue p.
964
Base triplet stepping by the Rad51/RecA family of recombinases
Authors: Lee Ja Yil , Terakawa Tsuyoshi , Qi Zhi , Steinfeld Justin B. , Redding Sy , Kwon YoungHo , Gaines William A. , Zhao Weixing , Sung Patrick , Greene Eric C.
Published: August 2015

Matching DNA three bases at a time

The exchange of genetic information between DNA strands is vital for accurate DNA repair and effective meiotic cell division. Using single-molecule methods and molecular dynamics simulations, Lee
et al.
show that members of the family of recombinase enzymes responsible for these strand exchange reactions search for and recognize matching DNA strands three bases at a time. A single mismatch abolishes triplet recognition, except for the meiosis-specific recombinase. This enzyme can stabilize a partially mismatched triplet, reflecting the partial homology of the DNA substrates in meiosis.

Science
, this issue p.
977
Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics
Authors: Li Dong , Shao Lin , Chen Bi-Chang , Zhang Xi , Zhang Mingshu , Moses Brian , Milkie Daniel E. , Beach Jordan R. , Hammer John A. , Pasham Mithun , Kirchhausen Tomas , Baird Michelle A. , Davidson Michael W. , Xu Pingyong , Betzig Eric
Published: August 2015

Adding to the super-resolution arsenal

Structured illumination microscopy (SIM) uses light intensities that are orders of magnitude lower than other super-resolution methods. SIM is also far faster over cellular-sized fields of view. Li
et al.
used two approaches to improve the resolution of SIM to allow live cell imaging of dynamic cellular processes, including endocytosis and cytoskeleton remodeling. The contrast in performance between SIM and other techniques is due to a few key differences. Defining the practical resolution at the limited signal-to-noise ratios necessary for live cell imaging will require better imaging metrics.

Science
, this issue
10.1126/science.aab3500
Glycerophospholipid regulation of modality-specific sensory axon guidance in the spinal cord
Authors: Guy Adam T. , Nagatsuka Yasuko , Ooashi Noriko , Inoue Mariko , Nakata Asuka , Greimel Peter , Inoue Asuka , Nabetani Takuji , Murayama Akiho , Ohta Kunihiro , Ito Yukishige , Aoki Junken , Hirabayashi Yoshio , Kamiguchi Hiroyuki
Published: August 2015

Axon paths in developing spinal cords

Sensory neurons entering the spinal cord take different paths as inputs for pain and proprioception diverge. Working with chick and mouse embryos, Guy
et al.
found that glycerophospholipids produced by radial glial cells guide these neural fibers, or axons, in the developing spinal cord. A soluble glycerophospholipid released by the cells provided an inhibitory signal to the pain-sensitive axons, keeping them on their own unique pathway.

Science
, this issue p.
974
Quantum squeezing of motion in a mechanical resonator
Authors: Wollman E. E. , Lei C. U. , Weinstein A. J. , Suh J. , Kronwald A. , Marquardt F. , Clerk A. A. , Schwab K. C.
Published: August 2015

Manipulation of a quantum squeeze

The uncertainty principle of quantum mechanics dictates that even when a system is cooled to its ground state, there are still fluctuations. This zero-point motion is unavoidable but can be manipulated. Wollman
et al.
demonstrate such manipulation with the motion of a micrometer-sized mechanical system. By driving up the fluctuations in one of the variables of the system, they are able to squeeze the other related variable below the expected zero-point limit. Quantum squeezing will be important for realizing ultrasensitive sensors and detectors.

Science
, this issue p.
952
Preparing for the next Katrina
Authors: McNutt Marcia
Published: August 2015

Ten years ago, Katrina, a category 5 hurricane at peak strength, slammed into New Orleans. Its associated storm surge breached the extensive levee system that had protected the city. Nearly 2000 residents died, and damages exceeded $100 billion. The storm remains the costliest natural disaster in U.S. history, and the resulting economic, social, and environmental turmoil led to the largest mass migration since the U.S. Civil War. A distinguished panel
*
of scientists and engineers who had been on the scene of Katrina was convened on the eve of the 10th anniversary of this event to address the question: Are American cities better prepared for the next major hurricane?
Activation of Autophagy by Metals in Chlamydomonas reinhardtii
Authors: Pérez-Martín Marta , Blaby-Haas Crysten E. , Pérez-Pérez María Esther , Andrés-Garrido Ascensión , Blaby Ian K. , Merchant Sabeeha S. , Crespo José L.
Published: August 2015

Autophagy is an intracellular self-degradation pathway by which eukaryotic cells recycle their own material in response to specific stress conditions. Exposure to high concentrations of metals causes cell damage, although the effect of metal stress on autophagy has not been explored in photosynthetic organisms. In this study, we investigated the effect of metal excess on autophagy in the model unicellular green alga
Chlamydomonas reinhardtii
. We show in cells treated with nickel an upregulation of ATG8 that is independent of CRR1, a global regulator of copper signaling in
Chlamydomonas
. A similar effect on ATG8 was observed with copper and cobalt but not with cadmium or mercury ions. Transcriptome sequencing data revealed an increase in the abundance of the protein degradation machinery, including that responsible for autophagy, and a substantial overlap of that increased abundance with the hydrogen peroxide response in cells treated with nickel ions. Thus, our results indicate that metal stress triggers autophagy in
Chlamydomonas
and suggest that excess nickel may cause oxidative damage, which in turn activates degradative pathways, including autophagy, to clear impaired components and recover cellular homeostasis.
Comparison of Phenotypic and Genotypic Approaches to Capsule Typing of Neisseria meningitidis by Use of Invasive and Carriage Isolate Collections
Authors: Jones C. Hal , Mohamed Naglaa , Rojas Eduardo , Andrew Lubomira , Hoyos Johanna , Hawkins Julio C. , McNeil Lisa K. , Jiang Qin , Mayer Leonard W. , Wang Xin , Gilca Rodica , De Wals Philippe , Pedneault Louise , Eiden Joseph , Jansen Kathrin U. , Anderson Annaliesa S.
Published: August 2015

Neisseria meningitidis
serogroup B (MnB) is a leading cause of bacterial meningitis; however, MnB is most commonly associated with asymptomatic carriage in the nasopharyngeal cavity, as opposed to the disease state. Two vaccines are now licensed for the prevention of MnB disease; a possible additional benefit of these vaccines could be to protect against disease indirectly by disrupting nasopharyngeal carriage (e.g., herd protection). To investigate this possibility, accurate diagnostic approaches to characterize MnB carriage isolates are required. In contrast to invasive meningococcal disease (IMD) isolates, which can be readily serogrouped, carriage isolates often lack capsule expression, making standard phenotypic assays unsuitable for strain characterization. Several antibody-based methods were evaluated for their abilities to serogroup isolates and were compared with two genotyping methods (real-time PCR [rt-PCR] and whole-genome sequencing [WGS]) to identify which approach would most accurately ascertain the polysaccharide groups associated with carriage isolates. WGS and rt-PCR were in agreement for 99% of IMD isolates, including those with coding sequences for MnB, MnC, MnW, and MnY, and the phenotypic methods correctly identified serogroups for 69 to 98% of IMD isolates. In contrast, only 47% of carriage isolates were groupable by genotypic methods, due to mutations within the capsule operon; of the isolates identified by genotypic methods, ≤43% were serogroupable with any of the phenotypic methods tested. These observations highlight the difficulties in the serogrouping and capsular genogrouping of meningococcal carriage isolates. Based on our findings, WGS is the most suitable approach for the characterization of meningococcal carriage isolates.
Comparison of Diagnostic Accuracy of PCR Targeting the 47-Kilodalton Protein Membrane Gene of Treponema pallidum and PCR Targeting the DNA Polymerase I Gene: Systematic Review and Meta-analysis
Authors: Gayet-Ageron Angèle , Combescure Christophe , Lautenschlager Stephan , Ninet Béatrice , Perneger Thomas V.
Published: August 2015

Treponema pallidum
PCR (
Tp
-PCR) testing now is recommended as a valid tool for the diagnosis of primary or secondary syphilis. The objectives were to systematically review and determine the optimal specific target gene to be used for
Tp
-PCR. Comparisons of the performance of the two main targets are
tpp47
and
polA
genes were done using meta-analysis. Three electronic bibliographic databases, representing abstract books from five conferences specialized in infectious diseases from January 1990 to March 2015, were searched. Search keywords included (“syphilis” OR “
Treponema pallidum
” OR “neurosyphilis”) AND (“PCR” OR “PCR” OR “molecular amplification”). We included diagnostic studies assessing the performance of
Tp
-PCR targeting
tpp47
(
tpp
47-
Tp
-PCR) or the
polA
gene (
polA-Tp
-PCR) in ulcers from early syphilis. All studies were assessed against quality criteria using the QUADAS-2 tool. Of 37 studies identified, 62.2% were judged at low risk of bias or applicability. Most used the U.S. Centers for Disease Control and Prevention (CDC) case definitions for primary or secondary (early) syphilis (89.2%;
n
= 33); 15 (40.5%) used darkfield microscopy (DFM). We did not find differences in sensitivity and specificity between the two
Tp
-PCR methods in the subgroup of studies using adequate reference tests. Among studies using DFM as the reference test, sensitivities were 79.8% (95% confidence intervals [CI], 72.7 to 85.4%) and 71.4% (46.0 to 88.0%) for
tpp47-Tp
-PCR and
polA-Tp
-PCR (
P
= 0.217), respectively; respective specificities were 95.3% (93.5 to 96.6%) and 93.7% (91.8 to 95.2%) (
P
= 0.304). Our findings suggest that the two
Tp
-PCR methods have similar accuracy and could be used interchangeably.
Infectious Bursal Disease Virus VP3 Upregulates VP1-Mediated RNA-Dependent RNA Replication
Authors: Ferrero Diego , Garriga Damià , Navarro Aitor , Rodríguez José F. , Verdaguer Núria
Published: August 2015

Genome replication is a critical step in virus life cycles. Here, we analyzed the role of the infectious bursal disease virus (IBDV) VP3, a major component of IBDV ribonucleoprotein complexes, on the regulation of VP1, the virus-encoded RNA-dependent RNA polymerase (RdRp). Data show that VP3, as well as a peptide mimicking its C-terminal domain, efficiently stimulates the ability of VP1 to replicate synthetic single-stranded RNA templates containing the 3′ untranslated regions (UTRs) from the IBDV genome segments.
Selective Removal of FG Repeat Domains from the Nuclear Pore Complex by Enterovirus 2A
pro
Authors: Park Nogi , Schweers Nicholas J. , Gustin Kurt E.
Published: August 2015

Enteroviruses proteolyze nuclear pore complex (NPC) proteins (Nups) during infection, leading to disruption of host nuclear transport pathways and alterations in nuclear permeability. To better understand how enteroviruses exert these effects on nuclear transport, the mechanisms and consequences of Nup98 proteolysis were examined. The results indicate that Nup98 is rapidly targeted for degradation following enterovirus infection and that this is mediated by the enterovirus 2A protease (2A
pro
). Incubation of bacterially expressed or
in vitro
-translated Nup98 with 2A
pro
results in proteolytic cleavage at multiple sites
in vitro
, indicating that 2A
pro
cleaves Nup98 directly. Site-directed mutagenesis of putative cleavage sites identified Gly374 and Gly552 as the sites of 2A
pro
proteolysis in Nup98
in vitro
and in infected cells. Indirect immunofluorescence assays using an antibody that recognizes the N terminus of Nup98 revealed that proteolysis releases the N-terminal FG-rich region from the NPC. In contrast, similar analyses using an antibody to the C terminus indicated that this region is retained at the nuclear rim. Nup88, a core NPC component that serves as a docking site for Nup98, also remains at the NPC in infected cells. These findings support a model whereby the selective removal of Nup FG repeat domains leads to increased NPC permeability and inhibition of certain transport pathways, while retention of structural domains maintains the overall NPC structure and leaves other transport pathways unaffected.

IMPORTANCE
Enteroviruses are dependent upon host nuclear RNA binding proteins for efficient replication. This study examines the mechanisms responsible for alterations in nuclear transport in enterovirus-infected cells that lead to the cytoplasmic accumulation of these proteins. The results demonstrate that the enterovirus 2A protease directly cleaves the nuclear pore complex (NPC) protein, Nup98, at amino acid positions G374 and G552 both
in vitro
and in infected cells. Cleavage at these positions results in the selective removal of the FG-containing N terminus of Nup98 from the NPC, while the C terminus remains associated. Nup88, a core component of the NPC that serves as a docking site for the C terminus of Nup98, remains associated with the NPC in infected cells. These findings help to explain the alterations in permeability and nuclear transport in enterovirus-infected cells and how NPCs remain functional for certain trafficking pathways despite significant alterations to their compositions.
Differences in Processing Determinants of Nonstructural Polyprotein and in the Sequence of Nonstructural Protein 3 Affect Neurovirulence of Semliki Forest Virus
Authors: Saul Sirle , Ferguson Mhairi , Cordonin Colette , Fragkoudis Rennos , Ool Margit , Tamberg Nele , Sherwood Karen , Fazakerley John K. , Merits Andres
Published: August 2015

The A7(74) strain of Semliki Forest virus (SFV; genus
Alphavirus
) is avirulent in adult mice, while the L10 strain is virulent in mice of all ages. It has been previously demonstrated that this phenotypic difference is associated with nonstructural protein 3 (nsP3). Consensus clones of L10 (designated SFV6) and A7(74) (designated A774wt) were used to construct a panel of recombinant viruses. The insertion of nsP3 from A774wt into the SFV6 backbone had a minor effect on the virulence of the resulting recombinant virus. Conversely, insertion of nsP3 from SFV6 into the A774wt backbone or replacement of A774wt nsP3 with two copies of nsP3 from SFV6 resulted in virulent viruses. Unexpectedly, duplication of nsP3-encoding sequences also resulted in elevated levels of nsP4, revealing that nsP3 is involved in the stabilization of nsP4. Interestingly, replacement of nsP3 of SFV6 with that of A774wt resulted in a virulent virus; the virulence of this recombinant was strongly reduced by functionally coupled substitutions for amino acid residues 534 (P4 position of the cleavage site between nsP1 and nsP2) and 1052 (S4 subsite residue of nsP2 protease) in the nonstructural polyprotein. Pulse-chase experiments revealed that A774wt and avirulent recombinant virus were characterized by increased processing speed of the cleavage site between nsP1 and nsP2. A His534-to-Arg substitution specifically activated this cleavage, while a Val1052-to-Glu substitution compensated for this effect by reducing the basal protease activity of nsP2. These findings provide a link between nonstructural polyprotein processing and the virulence of SFV.

IMPORTANCE
SFV infection of mice provides a well-characterized model to study viral encephalitis. SFV also serves as a model for studies of alphavirus molecular biology and host-pathogen interactions. Thus far, the genetic basis of different properties of SFV strains has been studied using molecular clones, which often contain mistakes originating from standard cDNA synthesis and cloning procedures. Here, for the first time, consensus clones of SFV strains were used to map virulence determinants. Existing data on the importance of nsP3 for virulent phenotypes were confirmed, another determinant of neurovirulence and its molecular basis was characterized, and a novel function of nsP3 was identified. These findings provide links between the molecular biology of SFV and its biological properties and significantly increase our understanding of the basis of alphavirus-induced pathology. In addition, the usefulness of consensus clones as tools for studies of alphaviruses was demonstrated.
Middle East Respiratory Syndrome Coronavirus nsp1 Inhibits Host Gene Expression by Selectively Targeting mRNAs Transcribed in the Nucleus while Sparing mRNAs of Cytoplasmic Origin
Authors: Lokugamage Kumari G. , Narayanan Krishna , Nakagawa Keisuke , Terasaki Kaori , Ramirez Sydney I. , Tseng Chien-Te K. , Makino Shinji
Published: August 2015

The newly emerged Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome CoV (SARS-CoV) represent highly pathogenic human CoVs that share a property to inhibit host gene expression at the posttranscriptional level. Similar to the nonstructural protein 1 (nsp1) of SARS-CoV that inhibits host gene expression at the translational level, we report that MERS-CoV nsp1 also exhibits a conserved function to negatively regulate host gene expression by inhibiting host mRNA translation and inducing the degradation of host mRNAs. Furthermore, like SARS-CoV nsp1, the mRNA degradation activity of MERS-CoV nsp1, most probably triggered by its ability to induce an endonucleolytic RNA cleavage, was separable from its translation inhibitory function. Despite these functional similarities, MERS-CoV nsp1 used a strikingly different strategy that selectively targeted translationally competent host mRNAs for inhibition. While SARS-CoV nsp1 is localized exclusively in the cytoplasm and binds to the 40S ribosomal subunit to gain access to translating mRNAs, MERS-CoV nsp1 was distributed in both the nucleus and the cytoplasm and did not bind stably to the 40S subunit, suggesting a distinctly different mode of targeting translating mRNAs. Interestingly, consistent with this notion, MERS-CoV nsp1 selectively targeted mRNAs, which are transcribed in the nucleus and transported to the cytoplasm, for translation inhibition and mRNA degradation but spared exogenous mRNAs introduced directly into the cytoplasm or virus-like mRNAs that originate in the cytoplasm. Collectively, these data point toward a novel viral strategy wherein the cytoplasmic origin of MERS-CoV mRNAs facilitates their escape from the inhibitory effects of MERS-CoV nsp1.

IMPORTANCE
Middle East respiratory syndrome coronavirus (MERS-CoV) is a highly pathogenic human CoV that emerged in Saudi Arabia in 2012. MERS-CoV has a zoonotic origin and poses a major threat to public health. However, little is known about the viral factors contributing to the high virulence of MERS-CoV. Many animal viruses, including CoVs, encode proteins that interfere with host gene expression, including those involved in antiviral immune responses, and these viral proteins are often major virulence factors. The nonstructural protein 1 (nsp1) of CoVs is one such protein that inhibits host gene expression and is a major virulence factor. This study presents evidence for a strategy used by MERS-CoV nsp1 to inhibit host gene expression that has not been described previously for any viral protein. The present study represents a meaningful step toward a better understanding of the factors and molecular mechanisms governing the virulence and pathogenesis of MERS-CoV.
Sinorhizobium meliloti Phage ΦM9 Defines a New Group of T4 Superfamily Phages with Unusual Genomic Features but a Common T=16 Capsid
Authors: Johnson Matthew C. , Tatum Kelsey B. , Lynn Jason S. , Brewer Tess E. , Lu Stephen , Washburn Brian K. , Stroupe M. Elizabeth , Jones Kathryn M.
Published: August 2015

Relatively little is known about the phages that infect agriculturally important nitrogen-fixing rhizobial bacteria. Here we report the genome and cryo-electron microscopy structure of the
Sinorhizobium meliloti
-infecting T4 superfamily phage ΦM9. This phage and its close relative
Rhizobium
phage vB_RleM_P10VF define a new group of T4 superfamily phages. These phages are distinctly different from the recently characterized cyanophage-like
S. meliloti
phages of the ΦM12 group. Structurally, ΦM9 has a T=16 capsid formed from repeating units of an extended gp23-like subunit that assemble through interactions between one subunit and the adjacent E-loop insertion domain. Though genetically very distant from the cyanophages, the ΦM9 capsid closely resembles that of the T4 superfamily cyanophage Syn9. ΦM9 also has the same T=16 capsid architecture as the very distant phage SPO1 and the herpesviruses. Despite their overall lack of similarity at the genomic and structural levels, ΦM9 and
S. meliloti
phage ΦM12 have a small number of open reading frames in common that appear to encode structural proteins involved in interaction with the host and which may have been acquired by horizontal transfer. These proteins are predicted to encode tail baseplate proteins, tail fibers, tail fiber assembly proteins, and glycanases that cleave host exopolysaccharide.

IMPORTANCE
Despite recent advances in the phylogenetic and structural characterization of bacteriophages, only a small number of phages of plant-symbiotic nitrogen-fixing soil bacteria have been studied at the molecular level. The effects of phage predation upon beneficial bacteria that promote plant growth remain poorly characterized. First steps in understanding these soil bacterium-phage dynamics are genetic, molecular, and structural characterizations of these groups of phages. The T4 superfamily phages are among the most complex phages; they have large genomes packaged within an icosahedral head and a long, contractile tail through which the DNA is delivered to host cells. This phylogenetic and structural study of
S. meliloti
-infecting T4 superfamily phage ΦM9 provides new insight into the diversity of this family. The comparison of structure-related genes in both ΦM9 and
S. meliloti
-infecting T4 superfamily phage ΦM12, which comes from a completely different lineage of these phages, allows the identification of host infection-related factors.
In Vitro
Evidence Supports Membrane Alanyl Aminopeptidase N as a Receptor for a Plant Virus in the Pea Aphid Vector
Authors: Linz Lucas B. , Liu Sijun , Chougule Nanasaheb P. , Bonning Bryony C.
Published: August 2015

Insect-borne plant viruses cause significant agricultural losses and jeopardize sustainable global food production. Although blocking plant virus transmission would allow for crop protection, virus receptors in insect vectors are unknown. Here we identify membrane alanyl aminopeptidase N (APN) as a receptor for pea enation mosaic virus (PEMV) coat protein (CP) in the gut of the pea aphid,
Acyrthosiphon pisum
, using a far-Western blot method. Pulldown and immunofluorescence binding assays and surface plasmon resonance were used to confirm and characterize CP-APN interaction. PEMV virions and a peptide comprised of PEMV CP fused to a proline-rich hinge (-P-) and green fluorescent protein (CP-P-GFP) specifically bound to APN. Recombinant APN expressed in Sf9 cells resulted in internalization of CP-P-GFP, which was visualized by confocal microscopy; such internalization is an expected hallmark of a functional gut receptor. Finally, in assays with aphid gut-derived brush border membrane vesicles, binding of CP-P-GFP competed with binding of GBP3.1, a peptide previously demonstrated to bind to APN in the aphid gut and to impede PEMV uptake into the hemocoel; this finding supports the hypothesis that GBP3.1 and PEMV bind to and compete for the same APN receptor. These
in vitro
data combined with previously published
in vivo
experiments (S. Liu, S. Sivakumar, W. O. Sparks, W. A. Miller, and B. C. Bonning, Virology 401:107–116, 2010,
http://dx.doi.org/10.1016/j.virol.2010.02.009
) support the identification of APN as the first receptor in a plant virus vector. Knowledge of this receptor will provide for technologies based on PEMV-APN interaction designed to block plant virus transmission and to suppress aphid populations.

IMPORTANCE
A significant proportion of global food production is lost to insect pests. Aphids, in addition to weakening plants by feeding on their sap, are responsible for transmitting about half of the plant viruses vectored by insects. Growers rely heavily on the application of chemical insecticides to manage both aphids and aphid-vectored plant viral disease. To increase our understanding of plant virus-aphid vector interaction, we provide
in vitro
evidence supporting earlier
in vivo
work for identification of a receptor protein in the aphid gut called aminopeptidase N, which is responsible for entry of the plant virus pea enation mosaic virus into the pea aphid vector. Enrichment of proteins found on the surface of the aphid gut epithelium resulted in identification of this first aphid gut receptor for a plant virus. This discovery is particularly important since the disruption of plant virus binding to such a receptor may enable the development of a nonchemical strategy for controlling aphid-vectored plant viruses to maximize food production.
A Nucleolar Protein, Ribosomal RNA Processing 1 Homolog B (RRP1B), Enhances the Recruitment of Cellular mRNA in Influenza Virus Transcription
Authors: Su Wen-Chi , Hsu Shih-Feng , Lee Yi-Yuan , Jeng King-Song , Lai Michael M. C.
Published: August 2015

Influenza A virus (IAV) undergoes RNA transcription by a unique capped-mRNA-dependent transcription, which is carried out by the viral RNA-dependent RNA polymerase (RdRp), consisting of the viral PA, PB1, and PB2 proteins. However, how the viral RdRp utilizes cellular factors for virus transcription is not clear. Previously, we conducted a genome-wide pooled short hairpin RNA (shRNA) screen to identify host factors important for influenza A virus replication. Ribosomal RNA processing 1 homolog B (RRP1B) was identified as one of the candidates. RRP1B is a nucleolar protein involved in ribosomal biogenesis. Upon IAV infection, part of RRP1B was translocated from the nucleolus to the nucleoplasm, where viral RNA synthesis likely takes place. The depletion of RRP1B significantly reduced IAV mRNA transcription in a minireplicon assay and in virus-infected cells. Furthermore, we showed that RRP1B interacted with PB1 and PB2 of the RdRp and formed a coimmunoprecipitable complex with RdRp. The depletion of RRP1B reduced the amount of capped mRNA in the RdRp complex. Taken together, these findings indicate that RRP1B is a host factor essential for IAV transcription and provide a target for new antivirals.

IMPORTANCE
Influenza virus is an important human pathogen that causes significant morbidity and mortality and threatens the human population with epidemics and pandemics every year. Due to the high mutation rate of the virus, antiviral drugs targeting viral proteins might ultimately lose their effectiveness. An alternative strategy that explores the genetic stability of host factors indispensable for influenza virus replication would thus be desirable. Here, we characterized the rRNA processing 1 homolog B (RRP1B) protein as an important cellular factor for influenza A virus transcription. We showed that silencing RRP1B hampered viral RNA-dependent RNA polymerase (RdRp) activity, which is responsible for virus transcription and replication. Furthermore, we reported that RRP1B is crucial for RdRp binding to cellular capped mRNA, which is a critical step of virus transcription. Our study not only provides a deeper understanding of influenza virus-host interplay, but also suggests a potential target for antiviral drug development.
Host Gene Expression Is Regulated by Two Types of Noncoding RNAs Transcribed from the Epstein-Barr Virus BamHI A Rightward Transcript Region
Authors: Marquitz Aron R. , Mathur Anuja , Edwards Rachel Hood , Raab-Traub Nancy
Published: August 2015

In Epstein-Barr virus-infected epithelial cancers, the alternatively spliced BamHI A rightward transcripts (BARTs) are the most abundant viral polyadenylated RNA. The BART introns form the template for the production of 44 microRNAs (miRNAs), and the spliced and polyadenylated exons form nuclear non-protein-coding RNAs. Analysis of host cell transcription by RNA-seq during latency in AGS cells identified a large number of reproducibly changed genes. Genes that were downregulated were enriched for BART miRNA targets. Bioinformatics analysis predicted activation of the myc pathway and downregulation of XBP1 as likely mediators of the host transcriptional changes. Effects on XBP1 activity were not detected in these cells; however, myc activation was confirmed through use of a myc-responsive luciferase reporter. To identify potential regulatory properties of the spliced, polyadenylated BART RNAs, a full-length cDNA clone of one of the BART isoforms was obtained and expressed in the Epstein-Barr virus (EBV)-negative AGS cells. The BART cDNA transcript remained primarily nuclear yet induced considerable and consistent changes in cellular transcription, as profiled by RNA-seq. These transcriptional changes significantly overlapped the transcriptional changes induced during latent EBV infection of these same cells, where the BARTs are exclusively nuclear and do not encode proteins. These data suggest that the nuclear BART RNAs are functional long noncoding RNAs (lncRNAs). The abundant expression of multiple forms of noncoding RNAs that contribute to growth regulation without expression of immunogenic proteins would be an important mechanism for viral oncogenesis in the presence of a functional immune system.

IMPORTANCE
Infection with Epstein-Barr virus (EBV) is nearly ubiquitous in the human population; however, it does contribute to the formation of multiple types of cancer. In immunocompromised patients, EBV causes multiple types of lymphomas by expressing viral oncogenes that promote growth and survival of infected B lymphocytes. EBV-positive gastric carcinoma does not require immune suppression, and the viral oncoproteins that are frequent targets for an immunological response are not expressed. This study demonstrates using transcriptional analysis that the expression of various classes of viral non-protein-coding RNAs likely contribute to the considerable changes in the host transcriptional profile in the AGS gastric cancer cell line. This is the first report to show that the highly expressed polyadenylated BamHI A rightward transcripts (BART) viral transcript in gastric carcinoma is in fact a functional viral long noncoding RNA. These studies provide new insight into how EBV can promote transformation in the absence of viral protein expression.
Evolutionary Dynamics and Global Diversity of Influenza A Virus
Authors: Rejmanek Daniel , Hosseini Parviez R. , Mazet Jonna A. K. , Daszak Peter , Goldstein Tracey
Published: August 2015

The increasing number of zoonotic infections caused by influenza A virus (IAV) subtypes of avian origin (e.g., H5N1 and H7N9) in recent years underscores the need to better understand the factors driving IAV evolution and diversity. To evaluate the current feasibility of global analyses to contribute to this aim, we evaluated information in the public domain to explore IAV evolutionary dynamics, including nucleotide substitution rates and selection pressures, using 14 IAV subtypes in 32 different countries over a 12-year period (2000 to 2011). Using geospatial information from 39,785 IAV strains, we examined associations between subtype diversity and socioeconomic, biodiversity, and agricultural indices. Our analyses showed that nucleotide substitution rates for 11 of the 14 evaluated subtypes tended to be higher in Asian countries, particularly in East Asia, than in Canada and the United States. Similarly, at a regional level, subtypes H5N1, H5N2, and H6N2 exhibited significantly higher substitution rates in East Asia than in North America. In contrast, the selection pressures (measured as ratios of nonsynonymous to synonymous evolutionary changes [
dN
/
dS
ratios]) acting on individual subtypes showed little geographic variation. We found that the strongest predictors for the detected subtype diversity at the country level were reporting effort (i.e., total number of strains reported) and health care spending (an indicator of economic development). Our analyses also identified major global gaps in IAV reporting (including a lack of sequences submitted from large portions of Africa and South America and a lack of geolocation information) and in broad subtype testing which, until addressed, will continue to hinder efforts to track the evolution and diversity of IAV around the world.

IMPORTANCE
In recent years, an increasing number of influenza A virus (IAV) subtypes, including H5N1, H7N9, and H10N8, have been detected in humans. High fatality rates have led to an increased urgency to better understand where and how novel pathogenic influenza virus strains emerge. Our findings showed that mutational rates of 11 commonly encountered subtypes were higher in East Asian countries than in North America, suggesting that there may be a greater risk for the emergence of novel pathogenic strains in East Asia. In assessing the potential drivers of IAV subtype diversity, our analyses confirmed that reporting effort and health care spending were the best predictors of the observed subtype diversity at the country level. These findings underscore the need to increase sampling and reporting efforts for all subtypes in many undersampled countries throughout the world.
Bst2/Tetherin Is Induced in Neurons by Type I Interferon and Viral Infection but Is Dispensable for Protection against Neurotropic Viral Challenge
Authors: Holmgren Alicia M. , Miller Katelyn D. , Cavanaugh Sarah E. , Rall Glenn F.
Published: August 2015

In permissive mouse central nervous system (CNS) neurons, measles virus (MV) spreads in the absence of hallmark viral budding or neuronal death, with transmission occurring efficiently and exclusively via the synapse. MV infection also initiates a robust type I interferon (IFN) response, resulting in the synthesis of a large number of genes, including bone marrow stromal antigen 2 (Bst2)/tetherin/CD317. Bst2 restricts the release of some enveloped viruses, but to date, its role in viral infection of neurons has not been assessed. Consequently, we investigated how Bst2 was induced and what role it played in MV neuronal infection. The magnitude of induction of neuronal Bst2 RNA and protein following IFN exposure and viral infection was notably higher than in similarly treated mouse embryo fibroblasts (MEFs). Bst2 synthesis was both IFN and Stat1 dependent. Although Bst2 prevented MV release from nonneuronal cells, its deletion had no effect on viral pathogenesis in MV-challenged mice. Our findings underscore how cell-type-specific differences impact viral infection and pathogenesis.

IMPORTANCE
Viral infections of the central nervous system can lead to debilitating disease and death. Moreover, it is becoming increasingly clear that nonrenewable cells, including most central nervous system neurons, combat neurotropic viral infections in fundamentally different ways than other rapidly dividing and renewable cell populations. Here we identify type I interferon signaling as a key inducer of a known antiviral protein (Bst2) in neurons. Unexpectedly, the gene is dispensable for clearance of neurotropic viral infection despite its well-defined contribution to limiting the spread of enveloped viruses in proliferating cells. A deeper appreciation of the importance of cell type heterogeneity in antiviral immunity will aid in the identification of unique therapeutic targets for life-threatening viral infections.
The Combination of the R263K and T66I Resistance Substitutions in HIV-1 Integrase Is Incompatible with High-Level Viral Replication and the Development of High-Level Drug Resistance
Authors: Liang Jiaming , Mesplède Thibault , Oliveira Maureen , Anstett Kaitlin , Wainberg Mark A.
Published: August 2015

The R263K substitution in integrase has been selected in tissue culture with dolutegravir (DTG) and has been reported for several treatment-experienced individuals receiving DTG as part of salvage therapy. The R263K substitution seems to be incompatible with the presence of common resistance mutations associated with raltegravir (RAL), a different integrase strand transfer inhibitor (INSTI). T66I is a substitution that is common in individuals who have developed resistance against a different INSTI termed elvitegravir (EVG), but it is not known whether these two mutations might be compatible in the context of resistance against DTG or what impact the combination of these substitutions might have on resistance against INSTIs. E138K is a common secondary substitution observed with various primary resistance substitutions in RAL- and EVG-treated individuals. Viral infectivity, replicative capacity, and resistance against INSTIs were measured in cell-based assays. Strand transfer and 3′ processing activities were measured biochemically. The combination of the R263K and T66I substitutions decreased HIV-1 infectivity, replicative capacity, and strand transfer activity. The addition of the E138K substitution partially compensated for these deficits and resulted in high levels of resistance against EVG but not against DTG or RAL. These findings suggest that the presence of the T66I substitution will not compromise the activity of DTG and may also help to prevent the additional generation of the R263K mutation. Our observations support the use of DTG in second-line therapy for individuals who experience treatment failure with EVG due to the T66I substitution.

IMPORTANCEThe integrase strand transfer inhibitors (INSTIs) elvitegravir and dolutegravir are newly developed inhibitors against human immunodeficiency virus type 1 (HIV-1). HIV drug-resistant mutations in integrase that can arise in individuals treated with elvitegravir commonly include the T66I substitution, whereas R263K is a signature resistance substitution against dolutegravir. In order to determine how different combinations of integrase resistance mutations can influence the outcome of therapy, we report here the effects of the T66I, E138K, and R263K substitutions, alone and in combination, on viral replicative capacity and resistance to integrase inhibitors. Our results show that the addition of R263K to the T66I substitution diminishes viral replicative capacity and strand transfer activity while not compromising susceptibility to dolutegravir. This supports the use of dolutegravir in second-line therapy for patients failing elvitegravir therapy who harbor the T66I resistance substitution.
Remote Activation of Host Cell DNA Synthesis in Uninfected Cells Signaled by Infected Cells in Advance of Virus Transmission
Authors: Schmidt Nora , Hennig Thomas , Serwa Remigiusz A. , Marchetti Magda , O'Hare Peter
Published: August 2015

Viruses modulate cellular processes and metabolism in diverse ways, but these are almost universally studied in the infected cell itself. Here, we study spatial organization of DNA synthesis during multiround transmission of herpes simplex virus (HSV) using pulse-labeling with ethynyl nucleotides and cycloaddition of azide fluorophores. We report a hitherto unknown and unexpected outcome of virus-host interaction. Consistent with the current understanding of the single-step growth cycle, HSV suppresses host DNA synthesis and promotes viral DNA synthesis in spatially segregated compartments within the cell. In striking contrast, during progressive rounds of infection initiated at a single cell, we observe that infection induces a clear and pronounced stimulation of cellular DNA replication in remote uninfected cells. This induced DNA synthesis was observed in hundreds of uninfected cells at the extended border, outside the perimeter of the progressing infection. Moreover, using pulse-chase analysis, we show that this activation is maintained, resulting in a propagating wave of host DNA synthesis continually in advance of infection. As the virus reaches and infects these activated cells, host DNA synthesis is then shut off and replaced with virus DNA synthesis. Using nonpropagating viruses or conditioned medium, we demonstrate a paracrine effector of uninfected cell DNA synthesis in remote cells continually in advance of infection. These findings have significant implications, likely with broad applicability, for our understanding of the ways in which virus infection manipulates cell processes not only in the infected cell itself but also now in remote uninfected cells, as well as of mechanisms governing host DNA synthesis.

IMPORTANCE
We show that during infection initiated by a single particle with progressive cell-cell virus transmission (i.e., the normal situation), HSV induces host DNA synthesis in uninfected cells, mediated by a virus-induced paracrine effector. The field has had no conception that this process occurs, and the work changes our interpretation of virus-host interaction during advancing infection and has implications for understanding controls of host DNA synthesis. Our findings demonstrate the utility of chemical biology techniques in analysis of infection processes, reveal distinct processes when infection is examined in multiround transmission versus single-step growth curves, and reveal a hitherto-unknown process in virus infection, likely relevant for other viruses (and other infectious agents) and for remote signaling of other processes, including transcription and protein synthesis.
Prevalence, repairs and complications of hypospadias: an Australian population-based study
Authors: Schneuer Francisco Javier , Holland Andrew J A , Pereira Gavin , Bower Carol , Nassar Natasha
Published: August 2015

Objective

To investigate hypospadias’ prevalence and trends, rate of surgical repairs and post-repair complications in an Australian population.

Methods

Hypospadias cases were identified from all live-born infants in New South Wales, Australia, during the period 2001–2010, using routinely collected birth and hospital data. Prevalence, trends, surgical procedures or repairs, hospital admissions and complications following surgery were evaluated. Risk factors for reoperation and complications were assessed using multivariate logistic regression.

Results

There were 3186 boys with hypospadias in 2001–2010. Overall prevalence was 35.1 per 10 000 live births and remained constant during the study period. Proportions of anterior, middle, proximal and unspecified hypospadias were 41.3%, 26.2%, 5.8% and 26.6%, respectively. Surgical procedures were performed in 1945 boys (61%), with 1718 primary repairs. The overall post-surgery complication rate involving fistulas or strictures was 13%, but higher (33%) for proximal cases. Complications occurred after 1 year post-repair in 52.3% of cases and up to 5 years. Boys with proximal or middle hypospadias were at increased risk of reoperation or complications, but age at primary repair did not affect the outcome.

Conclusion

One in 285 infants were affected with hypospadias, 60% required surgical repair or correction and one in eight experienced complications. The frequency of late complications would suggest that clinical review should be maintained for >1 year post-repair.