bluuebunny/crossref_metadata_2025 huggingface dataset:
Unique in the shopping mall: On the reidentifiability of credit card metadata
Authors: de Montjoye Yves-Alexandre , Radaelli Laura , Singh Vivek Kumar , Pentland Alex “Sandy”
Published: January 2015

Large-scale data sets of human behavior have the potential to fundamentally transform the way we fight diseases, design cities, or perform research. Metadata, however, contain sensitive information. Understanding the privacy of these data sets is key to their broad use and, ultimately, their impact. We study 3 months of credit card records for 1.1 million people and show that four spatiotemporal points are enough to uniquely reidentify 90% of individuals. We show that knowing the price of a transaction increases the risk of reidentification by 22%, on average. Finally, we show that even data sets that provide coarse information at any or all of the dimensions provide little anonymity and that women are more reidentifiable than men in credit card metadata.
Constrained work output of the moist atmospheric heat engine in a warming climate
Authors: Laliberté F. , Zika J. , Mudryk L. , Kushner P. J. , Kjellsson J. , Döös K.
Published: January 2015

Because the rain falls and the wind blows

Global warming is expected to intensify the hydrological cycle, but it might also make the atmosphere less energetic. Laliberté
et al.
modeled the atmosphere as a classical heat engine in order to evaluate how much energy it contains and how much work it can do (see the Perspective by Pauluis). They then used a global climate model to project how that might change as climate warms. Although the hydrological cycle may increase in intensity, it does so at the expense of its ability to do work, such as powering large-scale atmospheric circulation or fueling more very intense storms.

Science
, this issue p.
540
; see also p.
475
The bubble-like interior of the core-collapse supernova remnant Cassiopeia A
Authors: Milisavljevic Dan , Fesen Robert A.
Published: January 2015

Burbling explosions blow metallic bubbles

Stars more than about eight times the mass of the Sun don't go out quietly. Asymmetric explosions are kicked off by the collapse of their iron cores when no more fusion energy can sustain them. Exactly how this stellar catastrophe proceeds is difficult to probe. Milisavljevic
et al.
have now peered into the supernova remnant Cas A in the near-infrared and present a three-dimensional map of its interior unshocked ejecta. The bubble-like structure points to turbulent mixing, which may help us understand other supernova remnants whose structure cannot be seen in such detail.

Science
, this issue p.
526
India's costly neutrino gamble
Authors: Stone Richard , Bagla Pallava
Published: January 2015

The country splurges on a bid to regain leadership in neutrino physics.
DARPA sets out to automate research
Authors: You Jia
Published: January 2015

Crash program aims to teach computers to read journals and hatch new ideas.
A new drug war
Authors: Underwood Emily
Published: January 2015

As a growing wave of designer drugs hits the streets, researchers try to forecast which will prove most popular—and dangerous.
Alarm over synthetic cannabinoids
Authors: Underwood Emily
Published: January 2015

Marketed as mimicking the effects of marijuana, synthetic cannabinoids are far from benign.
Unmasked
Authors: Bohannon John
Published: January 2015

Facial recognition software could soon ID you in any photo.
When your voice betrays you
Authors: Shultz David
Published: January 2015

"Voiceprints" offer convenience and security, but they may pose privacy issues.
Breach of trust
Authors: Bohannon John
Published: January 2015

After the Snowden revelations, U.S. mathematicians are questioning their long-standing ties with the secretive National Security Agency.
Trust me, I'm a medical researcher
Authors: Couzin-Frankel Jennifer
Published: January 2015

Scientists can no longer guarantee patients' privacy. They're looking for new ways to build trust.
Replication-transcription switch in human mitochondria
Authors: Agaronyan Karen , Morozov Yaroslav I. , Anikin Michael , Temiakov Dmitry
Published: January 2015

Switching transcription and replication

Because mitochondrial DNA is circular, the transcription and replication machinery might be expected to collide. A single mitochondrial RNA polymerase (mtRNAP) transcribes the mitochondrial DNA and also generates primers for replication. Agaronyan
et al.
now show that transcription and replication are kept separate in human mitochondria, with the mitochondrial transcription elongation factor TEFM serving as a key player in the switch. In the absence of TEFM, mtRNAP terminates downstream from the promoter, forming primers to promote replication. In the presence of TEFM, the primers are not formed, and the overall processivity of mtRNAP elongation complexes is enhanced, promoting genome transcription. These mutually exclusive mechanisms allow the processes to proceed independently as needed by the cell.

Science
, this issue p.
548
Number-space mapping in the newborn chick resembles humans’ mental number line
Authors: Rugani Rosa , Vallortigara Giorgio , Priftis Konstantinos , Regolin Lucia
Published: January 2015

Even chicks may count from left to right

For the most part, humans represent numbers across a mental number line, with smaller numbers on the left and larger numbers on the right. Some have argued that this is due to culture rather than being innate. Rugani
et al.
, however, show that 3-day-old chicks share this representation of numbers, consistently seeking lower numbers to the left of a target and larger numbers to the right (see the Perspective by Brugger). These results suggest that there may be an innate spatial representation of numerical values that we share with other animals.

Science
, this issue p.
534
; see also p.
477
Structure and activity of tryptophan-rich TSPO proteins
Authors: Guo Youzhong , Kalathur Ravi C. , Liu Qun , Kloss Brian , Bruni Renato , Ginter Christopher , Kloppmann Edda , Rost Burkhard , Hendrickson Wayne A.
Published: January 2015

Structural clues to protein function

Translocator protein (TSPO) is a mitochondrial membrane protein thought to transport cholesterol and porphyrins. Its detailed function remains unclear, but interest in it is high because TSPO is involved in a variety of human diseases. Two papers now present crystal structures of bacterial TSPOs. Li
et al.
show that a mutant that mimics a human single polymorphism associated with psychiatric disorders has structural changes in a region implicated in cholesterol binding. Guo
et al.
suggest that TSPO may be more than a transporter. They show how it catalyzes the degradation of porphyrins, a function that could be important in protection against oxidative stress.

Science
, this issue p.
555
, p.
551
The selfish voter
The Hidden Agenda of the Political Mind: How Self-Interest Shapes Our Opinions and Why We Won't Admit It
Jason Weeden and Robert Kurzban
Princeton University Press, 2014. 369 pp.
Authors: Hibbing John R.
Published: January 2015

A closer look at the factors that influence our political preferences
Low trap-state density and long carrier diffusion in organolead trihalide perovskite single crystals
Authors: Shi Dong , Adinolfi Valerio , Comin Riccardo , Yuan Mingjian , Alarousu Erkki , Buin Andrei , Chen Yin , Hoogland Sjoerd , Rothenberger Alexander , Katsiev Khabiboulakh , Losovyj Yaroslav , Zhang Xin , Dowben Peter A. , Mohammed Omar F. , Sargent Edward H. , Bakr Osman M.
Published: January 2015

Large-crystal perovskite films

The performance of organic-inorganic hybrid perovskite planar solar cells has steadily improved. One outstanding issue is that grain boundaries and defects in polycrystalline films degrade their output. Now, two studies report the growth of millimeter-scale single crystals. Nie
et al.
grew continuous, pinhole-free, thin iodochloride films with a hot-casting technique and report device efficiencies of 18%. Shi
et al.
used antisolvent vapor-assisted crystallization to grow millimeter-scale bromide and iodide cubic crystals with charge-carrier diffusion lengths exceeding 10 mm.

Science
, this issue p.
522
, p.
519
Balancing privacy versus accuracy in research protocols
Authors: Goroff Daniel L.
Published: January 2015

Restricting data at collection, processing, or release
What the “right to be forgotten” means for privacy in a digital age
Authors: Newman Abraham L.
Published: January 2015

Despite the attention the right has received, we should not forget that it is just one innovative piece of a comprehensive privacy framework that must be implemented locally and enforced globally.
Chicks with a number sense
Authors: Brugger Peter
Published: January 2015

Chicks and humans map numbers to space in a similar way

[Also see Report by

Rugani
et al.

]
Protective Immunogenicity of Group A Streptococcal M-Related Proteins
Authors: Dale James B. , Niedermeyer Shannon E. , Agbaosi Tina , Hysmith Nicholas D. , Penfound Thomas A. , Hohn Claudia M. , Pullen Matthew , Bright Michael I. , Murrell Daniel S. , Shenep Lori E. , Courtney Harry S.
Published: January 2015

Many previous studies have focused on the surface M proteins of group A streptococci (GAS) as virulence determinants and protective antigens. However, the majority of GAS isolates express M-related protein (Mrp) in addition to M protein, and both have been shown to be required for optimal virulence. In the current study, we evaluated the protective immunogenicity of Mrp to determine its potential as a vaccine component that may broaden the coverage of M protein-based vaccines. Sequence analyses of 33mrpgenes indicated that there are three families of structurally related Mrps (MrpI, MrpII, and MrpIII). N-terminal peptides of Mrps were cloned, expressed, and purified from M type 2 (M2) (MrpI), M4 (MrpII), and M49 (MrpIII) GAS. Rabbit antisera against the Mrps reacted at high titers with the homologous Mrp, as determined by enzyme-linked immunosorbent assay, and promoted bactericidal activity against GASemmtypes expressing Mrps within the same family. Mice passively immunized with rabbit antisera against MrpII were protected against challenge infections with M28 GAS. Assays for Mrp antibodies in serum samples from 281 pediatric subjects aged 2 to 16 indicated that the Mrp immune response correlated with increasing age of the subjects. Affinity-purified human Mrp antibodies promoted bactericidal activity against a number of GAS representing differentemmtypes that expressed an Mrp within the same family but showed no activity againstemmtypes expressing an Mrp from a different family. Our results indicate that Mrps have semiconserved N-terminal sequences that contain bactericidal epitopes which are immunogenic in humans. These findings may have direct implications for the development of GAS vaccines.
Mycobacterial DNA Extraction for Whole-Genome Sequencing from Early Positive Liquid (MGIT) Cultures
Authors: Votintseva Antonina A. , Pankhurst Louise J. , Anson Luke W. , Morgan Marcus R. , Gascoyne-Binzi Deborah , Walker Timothy M. , Quan T. Phuong , Wyllie David H. , Del Ojo Elias Carlos , Wilcox Mark , Walker A. Sarah , Peto Tim E. A. , Crook Derrick W.
Published: January 2015

We developed a low-cost and reliable method of DNA extraction from as little as 1 ml of early positive mycobacterial growth indicator tube (MGIT) cultures that is suitable for whole-genome sequencing to identify mycobacterial species and predict antibiotic resistance in clinical samples. The DNA extraction method is based on ethanol precipitation supplemented by pretreatment steps with a MolYsis kit or saline wash for the removal of human DNA and a final DNA cleanup step with solid-phase reversible immobilization beads. The protocol yielded ≥0.2 ng/μl of DNA for 90% (MolYsis kit) and 83% (saline wash) of positive MGIT cultures. A total of 144 (94%) of the 154 samples sequenced on the MiSeq platform (Illumina) achieved the target of 1 million reads, with <5% of reads derived from human or nasopharyngeal flora for 88% and 91% of samples, respectively. A total of 59 (98%) of 60 samples that were identified by the national mycobacterial reference laboratory (NMRL) as
Mycobacterium tuberculosis
were successfully mapped to the H37Rv reference, with >90% coverage achieved. The DNA extraction protocol, therefore, will facilitate fast and accurate identification of mycobacterial species and resistance using a range of bioinformatics tools.
Reevaluation of Commercial Reagents for Detection of Histoplasma capsulatum Antigen in Urine
Authors: Theel Elitza S. , Harring Julie A. , Dababneh Ala S. , Rollins Leonard O. , Bestrom Jeannie E. , Jespersen Deborah J.
Published: January 2015

Detection of the
Histoplasma capsulatum
urinary antigen (UAg) is among the most sensitive and rapid means to diagnose histoplasmosis. Previously, we evaluated analyte-specific reagents (ASR) manufactured by IMMY (Norman, OK) for detection of
Histoplasma
galactomannan (GM) in urine using an enzyme immunoassay (EIA), and we showed low positive agreement (64.5%) with the MiraVista (MVista)
Histoplasma
antigen (Ag) quantitative EIA (MiraVista Diagnostics, Indianapolis, IN). Here we reevaluated the IMMY GM ASR following modification of our original assay protocol and introduction of an indeterminate range. A total of 150 prospectively collected urine samples were tested with both the IMMY and MVista EIAs, and clinical histories were recorded for all study subjects. The IMMY GM ASR showed positive and negative agreements of 82.3% (14/17 samples) and 100% (121/121 samples), respectively (with exclusion of 12 indeterminate results), and overall agreement of 90% (135/150 samples) with respect to the MVista EIA. Of the three patients with negative IMMY GM ASR results and positive MVista EIA results, testing was performed for initial diagnostic purposes for one patient (<0.4 ng/ml by the MVista EIA) and UAg levels were being monitored for the remaining two patients (both <0.7 ng/ml by the MVista EIA). The MVista EIA results were positive for 6/12 samples that tested indeterminate by the IMMY GM ASR. We also show that the IMMY GM ASR can be used to serially monitor
Histoplasma
UAg levels. In conclusion, we demonstrate that, with modification, the IMMY GM ASR is a reliable rapid assay for detection of
Histoplasma
UAg.
Tracing Melioidosis Back to the Source: Using Whole-Genome Sequencing To Investigate an Outbreak Originating from a Contaminated Domestic Water Supply
Authors: McRobb Evan , Sarovich Derek S. , Price Erin P. , Kaestli Mirjam , Mayo Mark , Keim Paul , Currie Bart J.
Published: January 2015

Melioidosis, a disease of public health importance in Southeast Asia and northern Australia, is caused by the Gram-negative soil bacillus
Burkholderia pseudomallei
. Melioidosis is typically acquired through environmental exposure, and case clusters are rare, even in regions where the disease is endemic.
B. pseudomallei
is classed as a tier 1 select agent by the Centers for Disease Control and Prevention; from a biodefense perspective, source attribution is vital in an outbreak scenario to rule out a deliberate release. Two cases of melioidosis within a 3-month period at a residence in rural northern Australia prompted an investigation to determine the source of exposure.
B. pseudomallei
isolates from the property's groundwater supply matched the multilocus sequence type of the clinical isolates. Whole-genome sequencing confirmed the water supply as the probable source of infection in both cases, with the clinical isolates differing from the likely infecting environmental strain by just one single nucleotide polymorphism (SNP) each. For the first time, we report a phylogenetic analysis of genomewide insertion/deletion (indel) data, an approach conventionally viewed as problematic due to high mutation rates and homoplasy. Our whole-genome indel analysis was concordant with the SNP phylogeny, and these two combined data sets provided greater resolution and a better fit with our epidemiological chronology of events. Collectively, this investigation represents a highly accurate account of source attribution in a melioidosis outbreak and gives further insight into a frequently overlooked reservoir of
B. pseudomallei
. Our methods and findings have important implications for outbreak source tracing of this bacterium and other highly recombinogenic pathogens.
Evaluation of Portability and Cost of a Fluorescent PCR Ribotyping Protocol for Clostridium difficile Epidemiology
Authors: Martinson Jonathan N. V. , Broadaway Susan , Lohman Egan , Johnson Christina , Alam M. Jahangir , Khaleduzzaman Mohammed , Garey Kevin W. , Schlackman Jessica , Young Vincent B. , Santhosh Kavitha , Rao Krishna , Lyons Robert H. , Walk Seth T.
Published: January 2015

Clostridium difficile
is the most commonly identified pathogen among health care-associated infections in the United States. There is a need for accurate and low-cost typing tools that produce comparable data across studies (i.e., portable data) to help characterize isolates during epidemiologic investigations of
C. difficile
outbreaks and sporadic cases of disease. The most popular
C. difficile
-typing technique is PCR ribotyping, and we previously developed methods using fluorescent PCR primers and amplicon sizing on a Sanger-style sequencer to generate fluorescent PCR ribotyping data. This technique has been used to characterize tens of thousands of
C. difficile
isolates from cases of disease. Here, we present validation of a protocol for the cost-effective generation of fluorescent PCR ribotyping data. A key component of this protocol is the ability to accurately identify PCR ribotypes against an online database (
http://walklab.rcg.montana.edu
) at no cost. We present results from a blinded multicenter study to address data portability across four different laboratories and three different sequencing centers. Our standardized protocol and centralized database for typing of
C. difficile
pathogens will increase comparability between studies so that important epidemiologic linkages between cases of disease and patterns of emergence can be rapidly identified.
Disruption of Type I Interferon Signaling by the Nonstructural Protein of Severe Fever with Thrombocytopenia Syndrome Virus via the Hijacking of STAT2 and STAT1 into Inclusion Bodies
Authors: Ning Yun-Jia , Feng Kuan , Min Yuan-Qin , Cao Wu-Chun , Wang Manli , Deng Fei , Hu Zhihong , Wang Hualin
Published: January 2015

The type I interferon (IFN) system, including IFN induction and signaling, is the critical component of the host defense line against viral infection, which, in turn, is also a vulnerable target for viral immune evasion. Severe fever with thrombocytopenia syndrome virus (SFTSV) is an emerging bunyavirus. Previous data have shown that SFTSV can interfere with the early induction of type I IFNs through targeting host kinases TBK1/IKKε. In this study, we demonstrated that SFTSV also can suppress type I IFN-triggered signaling and interferon-stimulated gene (ISG) expression. Interestingly, we observed the significant inhibition of IFN signaling in cells transfected with the plasmids encoding the nonstructural protein (NSs) but not the nucleocapsid protein (NP), indicating the role of NSs as an antagonist of IFN signaling. Furthermore, coimmunoprecipitation (Co-IP) and pulldown assays indicated that NSs interacts with the cellular signal transducer and activator of transcription 2 (STAT2), and the DNA-binding domain of STAT2 may contribute to the NSs-STAT2 interaction. Combined with confocal microscopy analyses, we demonstrated that NSs sequesters STAT2 and STAT1 into viral inclusion bodies (IBs) and impairs IFN-induced STAT2 phosphorylation and nuclear translocation of both STATs, resulting in the inhibition of IFN signaling and ISG expression. SFTSV NSs-mediated hijacking of STATs in IBs represents a novel mechanism of viral suppression of IFN signaling, highlighting the role of viral IBs as the virus-built “jail” sequestering some crucial host factors and interfering with the corresponding cellular processes.

IMPORTANCE
SFTSV is an emerging bunyavirus which can cause a severe hemorrhagic fever-like disease with high case fatality rates in humans, posing a serious health threat. However, there are no specific antivirals available, and the pathogenesis and virus-host interactions are largely unclear. Here, we demonstrated that SFTSV can inhibit type I IFN antiviral signaling by the NSs-mediated hijacking of STAT2 and STAT1 into viral IBs, highlighting the interesting role of viral IBs in virus-host interactions as the virus-built jail. Sequestering signaling molecules into IBs represents a novel and, perhaps, also a general mechanism of viral suppression of IFN signaling, the understanding of which may benefit the study of viral pathogenesis and the development of antiviral therapies.
Restricted Protein Phosphatase 2A Targeting by Merkel Cell Polyomavirus Small T Antigen
Authors: Kwun Hyun Jin , Shuda Masahiro , Camacho Carlos J. , Gamper Armin M. , Thant Mamie , Chang Yuan , Moore Patrick S.
Published: January 2015

Merkel cell polyomavirus (MCV) is a newly discovered human cancer virus encoding a small T (sT) oncoprotein. We performed MCV sT FLAG-affinity purification followed by mass spectroscopy (MS) analysis, which identified several protein phosphatases (PP), including PP2A A and C subunits and PP4C, as potential cellular interacting proteins. PP2A targeting is critical for the transforming properties of nonhuman polyomaviruses, such as simian virus 40 (SV40), but is not required for MCV sT-induced rodent cell transformation. We compared similarities and differences in PP2A binding between MCV and SV40 sT. While SV40 sT coimmunopurified with subunits PP2A Aα and PP2A C, MCV sT coimmunopurified with PP2A Aα, PP2A Aβ, and PP2A C. Scanning alanine mutagenesis at 29 sites across the MCV sT protein revealed that PP2A-binding domains lie on the opposite molecular surface from a previously described large T stabilization domain (LSD) loop that binds E3 ligases, such as Fbw7. MCV sT-PP2A interactions can be functionally distinguished by mutagenesis from MCV sT LSD-dependent 4E-BP1 hyperphosphorylation and viral DNA replication enhancement. MCV sT has a restricted range for PP2A B subunit substitution, inhibiting only the assembly of B56α into the phosphatase holoenzyme. In contrast, SV40 sT inhibits the assembly of B55α, B56α and B56ε into PP2A. We conclude that MCV sT is required for Merkel cell carcinoma growth, but its
in vitro
transforming activity depends on LSD interactions rather than PP2A targeting.

IMPORTANCE
Merkel cell polyomavirus is a newly discovered human cancer virus that promotes cancer, in part, through expression of its small T (sT) oncoprotein. Animal polyomavirus sT oncoproteins have been found to cause experimental tumors by blocking the activities of a group of phosphatases called protein phosphatase 2A (PP2A). Our structural analysis reveals that MCV sT also displaces the B subunit of PP2A to inhibit PP2A activity. MCV sT, however, only displaces a restricted subset of PP2A B subunits, which is insufficient to cause tumor cell formation
in vitro
. MCV sT instead transforms tumor cells through another region called the large T stabilization domain. The PP2A targeting and transforming activities lie on opposite faces of the MCV sT molecule and can be genetically separated from each other.
Zombies in TCGA
Authors: DiMaio Daniel
Published: January 2015

Next-generation sequencing results obtained to detect somatic mutations in human cancers can also be searched for viruses that contribute to cancer. Recently, human papillomavirus 18 RNA was detected in tumor types not typically associated with HPV infection. Analyses reported in this issue of
Journal of Virology
demonstrate that the apparent presence of HPV18 RNA in these atypical tumors is due in at least some cases to contamination of samples with HeLa cells, which harbor HPV18.
PA-X Decreases the Pathogenicity of Highly Pathogenic H5N1 Influenza A Virus in Avian Species by Inhibiting Virus Replication and Host Response
Authors: Hu Jiao , Mo Yiqun , Wang Xiaoquan , Gu Min , Hu Zenglei , Zhong Lei , Wu Qiwen , Hao Xiaoli , Hu Shunlin , Liu Wenbo , Liu Huimou , Liu Xiaowen , Liu Xiufan
Published: January 2015

PA-X is a newly discovered protein that decreases the virulence of the 1918 H1N1 virus in a mouse model. However, the role of PA-X in the pathogenesis of highly pathogenic avian influenza viruses (HPAIV) of the H5N1 subtype in avian species is totally unknown. By generating two PA-X-deficient viruses and evaluating their virulence in different animal models, we show here that PA-X diminishes the virulence of the HPAIV H5N1 strain A/Chicken/Jiangsu/k0402/2010 (CK10) in mice, chickens, and ducks. Expression of PA-X dampens polymerase activity and virus replication both
in vitro
and
in vivo
. Using microarray analysis, we found that PA-X blunts the global host response in chicken lungs, markedly downregulating genes associated with the inflammatory and cell death responses. Correspondingly, a decreased cytokine response was recapitulated in multiple organs of chickens and ducks infected with the wild-type virus relative to those infected with the PA-X-deficient virus. In addition, the PA-X protein exhibits antiapoptotic activity in chicken and duck embryo fibroblasts. Thus, our results demonstrated that PA-X acts as a negative virulence regulator and decreases virulence by inhibiting viral replication and the host innate immune response. Therefore, we here define the role of PA-X in the pathogenicity of H5N1 HPAIV, furthering our understanding of the intricate pathogenesis of influenza A virus.

IMPORTANCE
Influenza A virus (IAV) continues to pose a huge threat to global public health. Eight gene segments of the IAV genome encode as many as 17 proteins, including 8 main viral proteins and 9 accessory proteins. The presence of these accessory proteins may further complicate the pathogenesis of IAV. PA-X is a newly identified protein in segment 3 that acts to decrease the virulence of the 1918 H1N1 virus in mice by modulating host gene expression. Our study extends these functions of PA-X to H5N1 HPAIV. We demonstrated that loss of PA-X expression increases the virulence and replication of an H5N1 virus in mice and avian species and alters the host innate immune and cell death responses. Our report is the first to delineate the role of the novel PA-X protein in the pathogenesis of H5N1 viruses in avian species and promotes our understanding of H5N1 HPAIV.
Unique Glycan Signatures Regulate Adeno-Associated Virus Tropism in the Developing Brain
Authors: Murlidharan Giridhar , Corriher Travis , Ghashghaei H. Troy , Asokan Aravind
Published: January 2015

Adeno-associated viruses (AAV) are thought to spread through the central nervous system (CNS) by exploiting cerebrospinal fluid (CSF) flux and hijacking axonal transport pathways. The role of host receptors that mediate these processes is not well understood. In the current study, we utilized AAV serotype 4 (AAV4) as a model to evaluate whether ubiquitously expressed 2,3-linked sialic acid and the developmentally regulated marker 2,8-linked polysialic acid (PSA) regulate viral transport and tropism in the neonatal brain. Modulation of the levels of SA and PSA in cell culture studies using specific neuraminidases revealed possibly opposing roles of the two glycans in AAV4 transduction. Interestingly, upon intracranial injection into lateral ventricles of the neonatal mouse brain, a low-affinity AAV4 mutant (AAV4.18) displayed a striking shift in cellular tropism from 2,3-linked SA
+
ependymal lining to 2,8-linked PSA
+
migrating progenitors in the rostral migratory stream and olfactory bulb. In addition, this gain-of-function phenotype correlated with robust CNS spread of AAV4.18 through paravascular transport pathways. Consistent with these observations, altering glycan dynamics within the brain by coadministering SA- and PSA-specific neuraminidases resulted in striking changes to the cellular tropisms and transduction efficiencies of both parental and mutant vectors. We postulate that glycan signatures associated with host development can be exploited to redirect novel AAV vectors to specific cell types in the brain.

IMPORTANCE
Viruses invade the CNS through various mechanisms. In the current study, we utilized AAV as a model to study the dynamics of virus-carbohydrate interactions in the developing brain and their impact on viral tropism. Our findings suggest that carbohydrate content can be exploited to regulate viral transport and tropism in the brain.
Mechanism of Angiopoietin-1 Upregulation in Kaposi's Sarcoma-Associated Herpesvirus-Infected PEL Cell Lines
Authors: Zheng Xin , Ohsaki Eriko , Ueda Keiji
Published: January 2015

Angiopoietin-1 (ANGPT-1) is a secreted glycoprotein that was first characterized as a ligand of the Tie2 receptor. In a previous study using microarray analysis, we found that the expression of ANGPT-1 was upregulated in Kaposi's sarcoma-associated herpesvirus (KSHV)-infected primary effusion lymphoma (PEL) cell lines compared with that in uninfected Burkitt and other leukemia cell lines. Other authors have also reported focal expression of ANGPT-1 mRNA in biopsy specimens of Kaposi's sarcoma (KS) tissue from patients with AIDS. Here, to confirm these findings, we examined the expression and secretion levels of ANGPT-1 in KSHV-infected PEL cell lines and address the mechanisms of
ANGPT-1
transcriptional regulation. We also showed that ANGPT-1 was expressed and localized in the cytoplasm and secreted into the supernatant of KSHV-infected PEL cells. Deletion studies of the regulatory region revealed that the region encompassing nucleotides −143 to −125 of the
ANGPT-1
-regulating sequence was responsible for this upregulation. Moreover, an electrophoretic mobility shift assay and chromatin immunoprecipitation, followed by quantitative PCR, suggested that some KSHV-infected PEL cell line-specific DNA-binding factors, such as OCT-1, should be involved in the upregulation of
ANGPT-1
in a sequence-dependent manner.

IMPORTANCE
We confirmed that ANGPT-1 was expressed in and secreted from KSHV-infected PEL cells and that the transcriptional activity of
ANGPT-1
was upregulated. A 19-bp fragment was identified as the region responsible for
ANGPT-1
upregulation through binding with OCT-1 as a core factor in PEL cells. This study suggests that ANGPT-1 is overproduced in KSHV-infected PEL cells, which could affect the pathophysiology of AIDS patients with PEL.
Species-Specific Transmission of Novel Picornaviruses in Lemurs
Authors: Lim Efrem S. , Deem Sharon L. , Porton Ingrid J. , Cao Song , Wang David
Published: January 2015

The roles of host genetics versus exposure and contact frequency in driving cross-species transmission remain the subject of debate. Here, we used a multitaxon lemur collection at the Saint Louis Zoo in the United States as a model to gain insight into viral transmission in a setting of high interspecies contact. Lemurs are a diverse and understudied group of primates that are highly endangered. The speciation of lemurs, which are endemic to the island of Madagascar, occurred in geographic isolation apart from that of continental African primates. Although evidence of endogenized viruses in lemur genomes exists, no exogenous viruses of lemurs have been described to date. Here we identified two novel picornaviruses in fecal specimens of ring-tailed lemurs (
Lemur catta
) and black-and-white ruffed lemurs (
Varecia variegata
). We found that the viruses were transmitted in a species-specific manner (lesavirus 1 was detected only in ring-tailed lemurs, while lesavirus 2 was detected only in black-and-white ruffed lemurs). Longitudinal sampling over a 1-year interval demonstrated ongoing infection in the collection. This was supported by evidence of viral clearance in some animals and new infections in previously uninfected animals, including a set of newly born triplets that acquired the infection. While the two virus strains were found to be cocirculating in a mixed-species exhibit of ring-tailed lemurs, black-and-white ruffed lemurs, and black lemurs, there was no evidence of cross-species transmission. This suggests that despite high-intensity contact, host species barriers can prevent cross-species transmissions of these viruses.

IMPORTANCE
Up to 75% of emerging infectious diseases in humans today are the result of zoonotic transmission. However, a challenge in understanding transmission dynamics has been the limited models of cross-species transmission. Zoos provide a unique opportunity to explore parameters defining viral transmission. We demonstrated that ongoing virus transmission in a mixed lemur species exhibit was species specific. This suggests that despite high contact intensity, host species barriers contribute to protection from cross-species transmission of these viruses. While the combinations of species might differ, most zoological parks worldwide commonly feature mixed-species exhibits. Collectively, this report demonstrates a widely applicable approach toward understanding infectious disease transmission.
HeLa Nucleic Acid Contamination in The Cancer Genome Atlas Leads to the Misidentification of Human Papillomavirus 18
Authors: Cantalupo Paul G. , Katz Joshua P. , Pipas James M.
Published: January 2015

We searched The Cancer Genome Atlas (TCGA) database for viruses by comparing non-human reads present in transcriptome sequencing (RNA-Seq) and whole-exome sequencing (WXS) data to viral sequence databases. Human papillomavirus 18 (HPV18) is an etiologic agent of cervical cancer, and as expected, we found robust expression of HPV18 genes in cervical cancer samples. In agreement with previous studies, we also found HPV18 transcripts in non-cervical cancer samples, including those from the colon, rectum, and normal kidney. However, in each of these cases, HPV18 gene expression was low, and single-nucleotide variants and positions of genomic alignments matched the integrated portion of HPV18 present in HeLa cells. Chimeric reads that match a known virus-cell junction of HPV18 integrated in HeLa cells were also present in some samples. We hypothesize that HPV18 sequences in these non-cervical samples are due to nucleic acid contamination from HeLa cells. This finding highlights the problems that contamination presents in computational virus detection pipelines.

IMPORTANCE
Viruses associated with cancer can be detected by searching tumor sequence databases. Several studies involving searches of the TCGA database have reported the presence of HPV18, a known cause of cervical cancer, in a small number of additional cancers, including those of the rectum, kidney, and colon. We have determined that the sequences related to HPV18 in non-cervical samples are due to nucleic acid contamination from HeLa cells. To our knowledge, this is the first report of the misidentification of viruses in next-generation sequencing data of tumors due to contamination with a cancer cell line. These results raise awareness of the difficulty of accurately identifying viruses in human sequence databases.
The Endoplasmic Reticulum Membrane J Protein C18 Executes a Distinct Role in Promoting Simian Virus 40 Membrane Penetration
Authors: Bagchi Parikshit , Walczak Christopher Paul , Tsai Billy
Published: January 2015

The nonenveloped simian virus 40 (SV40) hijacks the three endoplasmic reticulum (ER) membrane-bound J proteins B12, B14, and C18 to escape from the ER into the cytosol en route to successful infection. How C18 controls SV40 ER-to-cytosol membrane penetration is the least understood of these processes. We previously found that SV40 triggers B12 and B14 to reorganize into discrete puncta in the ER membrane called foci, structures postulated to represent the cytosol entry site (C. P. Walczak, M. S. Ravindran, T. Inoue, and B. Tsai, PLoS Pathog
10:
e1004007, 2014). We now find that SV40 also recruits C18 to the virus-induced B12/B14 foci. Importantly, the C18 foci harbor membrane penetration-competent SV40, further implicating this structure as the membrane penetration site. Consistent with this, a mutant SV40 that cannot penetrate the ER membrane and promote infection fails to induce C18 foci. C18 also regulates the recruitment of B12/B14 into the foci. In contrast to B14, C18's cytosolic Hsc70-binding J domain, but not the lumenal domain, is essential for its targeting to the foci; this J domain likewise is necessary to support SV40 infection. Knockdown-rescue experiments reveal that C18 executes a role that is not redundant with those of B12/B14 during SV40 infection. Collectively, our data illuminate C18's contribution to SV40 ER membrane penetration, strengthening the idea that SV40-triggered foci are critical for cytosol entry.

IMPORTANCE
Polyomaviruses (PyVs) cause devastating human diseases, particularly in immunocompromised patients. As this virus family continues to be a significant human pathogen, clarifying the molecular basis of their cellular entry pathway remains a high priority. To infect cells, PyV traffics from the cell surface to the ER, where it penetrates the ER membrane to reach the cytosol. In the cytosol, the virus moves to the nucleus to cause infection. ER-to-cytosol membrane penetration is a critical yet mysterious infection step. In this study, we clarify the role of an ER membrane protein called C18 in mobilizing the simian PyV SV40, a PyV archetype, from the ER into the cytosol. Our findings also support the hypothesis that SV40 induces the formation of punctate structures in the ER membrane, called foci, that serve as the portal for cytosol entry of the virus.
Clathrin Mediates Infectious Hepatitis C Virus Particle Egress
Authors: Benedicto Ignacio , Gondar Virgínia , Molina-Jiménez Francisca , García-Buey Luisa , López-Cabrera Manuel , Gastaminza Pablo , Majano Pedro L.
Published: January 2015

Although it is well established that hepatitis C virus (HCV) entry into hepatocytes depends on clathrin-mediated endocytosis, the possible roles of clathrin in other steps of the viral cycle remain unexplored. Thus, we studied whether cell culture-derived HCV (HCVcc) exocytosis was altered after clathrin interference. Knockdown of clathrin or the clathrin adaptor AP-1 in HCVcc-infected human hepatoma cell cultures impaired viral secretion without altering intracellular HCVcc levels or apolipoprotein B (apoB) and apoE exocytosis. Similar reductions in HCVcc secretion were observed after treatment with specific clathrin and dynamin inhibitors. Furthermore, detergent-free immunoprecipitation assays, neutralization experiments, and immunofluorescence analyses suggested that whereas apoE associated with infectious intracellular HCV precursors in endoplasmic reticulum (ER)-related structures, AP-1 participated in HCVcc egress in a post-ER compartment. Finally, we observed that clathrin and AP-1 knockdown altered the endosomal distribution of HCV core, reducing and increasing its colocalization with early endosome and lysosome markers, respectively. Our data support a model in which nascent HCV particles associate with apoE in the ER and exit cells following a clathrin-dependent transendosomal secretory route.

IMPORTANCE
HCV entry into hepatocytes depends on clathrin-mediated endocytosis. Here we demonstrate for the first time that clathrin also participates in HCV exit from infected cells. Our data uncover important features of HCV egress, which may lead to the development of new therapeutic interventions. Interestingly, we show that secretion of the very-low-density lipoprotein (VLDL) components apoB and apoE is not impaired after clathrin interference. This is a significant finding, since, to date, it has been proposed that HCV and VLDL follow similar exocytic routes. Given that lipid metabolism recently emerged as a potential target for therapies against HCV infection, our data may help in the design of new strategies to interfere specifically with HCV exocytosis without perturbing cellular lipid homeostasis, with the aim of achieving more efficient, selective, and safe antivirals.
Identification of Three Redundant Segments Responsible for Herpes Simplex Virus 1 ICP0 To Fuse with ND10 Nuclear Bodies
Authors: Zheng Yi , Gu Haidong
Published: January 2015

Infected cell protein 0 (ICP0) of herpes simplex virus 1 (HSV-1) is a key regulator in both lytic and latent infections. In lytic infection, an important early event is the colocalization of ICP0 to nuclear domain 10 (ND10), the discrete nuclear bodies that impose restrictions on viral expression. ICP0 contains an E3 ubiquitin ligase that degrades promyelocytic leukemia protein (PML) and Sp100, two major components of ND10, and disperses ND10 to alleviate repression. We previously reported that the association between ICP0 and ND10 is a dynamic process that includes three steps: adhesion, fusion, and retention. ICP0 residues 245 to 474, defined as ND10 entry signal (ND10-ES), is a region required for the fusion step. Without ND10-ES, ICP0 adheres at the ND10 surface but fails to enter. In the present study, we focus on characterizing ND10-ES. Here we report the following. (i) Fusion of ICP0 with ND10 relies on specific sequences located within ND10-ES. Replacement of ND10-ES by the corresponding region from ORF61 of varicella-zoster virus did not rescue ND10 fusion. (ii) Three tandem ND10 fusion segments (ND10-FS1, ND10-FS2, and ND10-FS3), encompassing 200 amino acids within ND10-ES, redundantly facilitate fusion. Each of the three segments is sufficient to independently drive the fusion process, but none of the segments by themselves are necessary for ND10 fusion. Only when all three segments are deleted is fusion blocked. (iii) The SUMO interaction motif located within ND10-FS2 is not required for ND10 fusion but is required for the complete degradation of PML, suggesting that PML degradation and ND10 fusion are regulated by different molecular mechanisms.

IMPORTANCE
ND10 nuclear bodies are part of the cell-intrinsic antiviral defenses that restrict viral gene expression upon virus infection. As a countermeasure, infected cell protein 0 (ICP0) of herpes simplex virus 1 (HSV-1) localizes to ND10s, degrades the ND10 organizer, and disperses ND10 components in order to alleviate repression. We studied the ICP0-ND10 association to delineate elements important for this dynamic interaction and to understand its role in viral replication and host defense. In this work, we show that ICP0 contains three redundant segments to ensure an effective mergence of ICP0 with ND10 nuclear bodies. This is the first study to systematically investigate ICP0 elements that are important for ICP0-ND10 fusion.
The Clostridium Sporulation Programs: Diversity and Preservation of Endospore Differentiation
Authors: Al-Hinai Mohab A. , Jones Shawn W. , Papoutsakis Eleftherios T.
Published: January 2015

Bacillus
and
Clostridium
organisms initiate the sporulation process when unfavorable conditions are detected. The sporulation process is a carefully orchestrated cascade of events at both the transcriptional and posttranslational levels involving a multitude of sigma factors, transcription factors, proteases, and phosphatases. Like
Bacillus
genomes, sequenced
Clostridium
genomes contain genes for all major sporulation-specific transcription and sigma factors (
spo0A
,
sigH
,
sigF
,
sigE
,
sigG
, and
sigK
) that orchestrate the sporulation program. However, recent studies have shown that there are substantial differences in the sporulation programs between the two genera as well as among different
Clostridium
species. First, in the absence of a
Bacillus
-like phosphorelay system, activation of Spo0A in
Clostridium
organisms is carried out by a number of orphan histidine kinases. Second, downstream of Spo0A, the transcriptional and posttranslational regulation of the canonical set of four sporulation-specific sigma factors (σ
F
, σ
E
, σ
G
, and σ
K
) display different patterns, not only compared to
Bacillus
but also among
Clostridium
organisms. Finally, recent studies demonstrated that σ
K
, the last sigma factor to be activated according to the
Bacillus subtilis
model, is involved in the very early stages of sporulation in
Clostridium acetobutylicum
,
C. perfringens
, and
C. botulinum
as well as in the very late stages of spore maturation in
C. acetobutylicum
. Despite profound differences in initiation, propagation, and orchestration of expression of spore morphogenetic components, these findings demonstrate not only the robustness of the endospore sporulation program but also the plasticity of the program to generate different complex phenotypes, some apparently regulated at the epigenetic level.
Atropine sulfate for treatment of bradycardia in a patient with morbid obesity: what may happen when you least expect it
Authors: Carron Michele , Veronese Stefano
Published: January 2015

A 74-year-old morbidly obese man was scheduled for surgical repair of an incisional ventral hernia. Anaesthesia was induced with propofol and fentanyl, and maintained with desflurane. A second dose of fentanyl 0.2 mg, given before starting surgery, resulted in sinus bradycardia and mild decrease of arterial blood pressure. Atropine sulfate 0.5 mg was administered. One minute later, the ECG rhythm on the monitor changed to third degree atrioventricular block with a ventricular response rate of 40 beats/min associated with marked hypotension. Isoproterenol 0.02 mg reverted the atrioventricular block to sinus rhythm. Cardiac enzymes and ECG ruled out acute myocardial ischaemia. The surgical procedure and the recovery from anaesthesia were uneventful. The patient was discharged from the hospital on the fifth postoperative day. For the treatment of bradycardia atropine sulfate should be adjusted at least to lean body weight in order to avoid paradoxical heart rate response in patients with obesity.
Distal renal tubular acidosis in primary hyperparathyroidism
Authors: Lo Tom Edward Ngo , Tan Iris Thiele Isip
Published: January 2015

Primary hyperparathyroidism manifests biochemically as a disturbance in serum calcium homeostasis. The kidney appears to be the central organ that sets the serum calcium level. Hyperchloraemia, defective urinary acidification and renal tubular acidosis have been reported to be associated with primary hyperparathyroidism. Distal renal tubular acidosis due to primary hyperparathyroidism is rarely reported. Renal tubular dysfunction due to significant hypercalciuria appears to be one of the proposed mechanisms. This case report will highlight a case of primary hyperparathyroidism in a 26-year old Filipino man due to a solitary functioning parathyroid adenoma presenting with recurrent nephrolithiasis leading to distal renal tubular acidosis manifesting with hypokalaemia and hypomagnesaemia. The patient underwent a minimally invasive selective parathyroidectomy that resulted in full reversal of hypercalcaemia and hyperparathyroidism together with the features of distal renal tubular acidosis. He is currently on frequent follow-up for monitoring of electrolyte abnormalities and gradual resolution of nephrocalcinosis.