bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of Elecsys Syphilis Assay for Routine and Blood Screening and Detection of Early Infection
Authors: Kremastinou J. , Polymerou V. , Lavranos D. , Aranda Arrufat A. , Harwood J. , Martínez Lorenzo M. J. , Ng K. P. , Queiros L. , Vereb I. , Cusini M. 
Published: June 2016

ABSTRACT

Treponema pallidum
infections can have severe complications if not diagnosed and treated at an early stage. Screening and diagnosis of syphilis require assays with high specificity and sensitivity. The Elecsys Syphilis assay is an automated treponemal immunoassay for the detection of antibodies against
T. pallidum
. The performance of this assay was investigated previously in a multicenter study. The current study expands on that evaluation in a variety of diagnostic settings and patient populations, at seven independent laboratories. The samples included routine diagnostic samples, blood donation samples, samples from patients with confirmed HIV infections, samples from living organ or bone marrow donors, and banked samples, including samples previously confirmed as syphilis positive. This study also investigated the seroconversion sensitivity of the assay. With a total of 1,965 syphilis-negative routine diagnostic samples and 5,792 syphilis-negative samples collected from blood donations, the Elecsys Syphilis assay had specificity values of 99.85% and 99.86%, respectively. With 333 samples previously identified as syphilis positive, the sensitivity was 100% regardless of disease stage. The assay also showed 100% sensitivity and specificity with samples from 69 patients coinfected with HIV. The Elecsys Syphilis assay detected infection in the same bleed or earlier, compared with comparator assays, in a set of sequential samples from a patient with primary syphilis. In archived serial blood samples collected from 14 patients with direct diagnoses of primary syphilis, the Elecsys Syphilis assay detected
T. pallidum
antibodies for 3 patients for whom antibodies were not detected with the Architect Syphilis TP assay, indicating a trend for earlier detection of infection, which may have the potential to shorten the time between infection and reactive screening test results.
Development of Potent Antiviral Drugs Inspired by Viral Hexameric DNA-Packaging Motors with Revolving Mechanism
Authors: Pi Fengmei , Zhao Zhengyi , Chelikani Venkata , Yoder Kristine , Kvaratskhelia Mamuka , Guo Peixuan 
Published: June 2016

ABSTRACT

The intracellular parasitic nature of viruses and the emergence of antiviral drug resistance necessitate the development of new potent antiviral drugs. Recently, a method for developing potent inhibitory drugs by targeting biological machines with high stoichiometry and a sequential-action mechanism was described. Inspired by this finding, we reviewed the development of antiviral drugs targeting viral DNA-packaging motors. Inhibiting multisubunit targets with sequential actions resembles breaking one bulb in a series of Christmas lights, which turns off the entire string. Indeed, studies on viral DNA packaging might lead to the development of new antiviral drugs. Recent elucidation of the mechanism of the viral double-stranded DNA (dsDNA)-packaging motor with sequential one-way revolving motion will promote the development of potent antiviral drugs with high specificity and efficiency. Traditionally, biomotors have been classified into two categories: linear and rotation motors. Recently discovered was a third type of biomotor, including the viral DNA-packaging motor, beside the bacterial DNA translocases, that uses a revolving mechanism without rotation. By analogy, rotation resembles the Earth's rotation on its own axis, while revolving resembles the Earth's revolving around the Sun (see animations at
http://rnanano.osu.edu/movie.html
). Herein, we review the structures of viral dsDNA-packaging motors, the stoichiometries of motor components, and the motion mechanisms of the motors. All viral dsDNA-packaging motors, including those of dsDNA/dsRNA bacteriophages, adenoviruses, poxviruses, herpesviruses, mimiviruses, megaviruses, pandoraviruses, and pithoviruses, contain a high-stoichiometry machine composed of multiple components that work cooperatively and sequentially. Thus, it is an ideal target for potent drug development based on the power function of the stoichiometries of target complexes that work sequentially.
Establishment and Reversal of HIV-1 Latency in Naive and Central Memory CD4+T CellsIn Vitro
Authors: Zerbato Jennifer M. , Serrao Erik , Lenzi Gina , Kim Baek , Ambrose Zandrea , Watkins Simon C. , Engelman Alan N. , Sluis-Cremer Nicolas 
Published: June 2016

ABSTRACTThe latent HIV-1 reservoir primarily resides in resting CD4+T cells which are a heterogeneous population composed of both naive (TN) and memory cells. In HIV-1-infected individuals, viral DNA has been detected in both naive and memory CD4+T cell subsets although the frequency of HIV-1 DNA is typically higher in memory cells, particularly in the central memory (TCM) cell subset. TNand TCMcells are distinct cell populations distinguished by many phenotypic and physiological differences. In this study, we used a primary cell model of HIV-1 latency that utilizes direct infection of highly purified TNand TCMcells to address differences in the establishment and reversal of HIV-1 latency. Consistent with what is seenin vivo, we found that HIV-1 infected TNcells less efficiently than TCMcells. However, when the infected TNcells were treated with latency-reversing agents, including anti-CD3/CD28 antibodies, phorbol myristate acetate/phytohemagglutinin, and prostratin, as much (if not more) extracellular virion-associated HIV-1 RNA was produced per infected TNcell as per infected TCMcell. There were no major differences in the genomic distribution of HIV-1 integration sites between TNand TCMcells that accounted for these observed differences. We observed decay of the latent HIV-1 cells in both T cell subsets after exposure to each of the latency-reversing agents. Collectively, these data highlight significant differences in the establishment and reversal of HIV-1 latency in TNand TCMCD4+T cells and suggest that each subset should be independently studied in preclinical and clinical studies.IMPORTANCEThe latent HIV-1 reservoir is frequently described as residing within resting memory CD4+T cells. This is largely due to the consistent finding that memory CD4+T cells, specifically the central (TCM) and transitional memory compartments, harbor the highest levels of HIV-1 DNA in individuals on suppressive therapy. This has yielded little research into the contribution of CD4+naive T (TN) cells to the latent reservoir. In this study, we show that although TNcells harbor significantly lower levels of HIV-1 DNA, following latency reversal, they produced as many virions as did the TCMcells (if not more virions). This suggests that latently infected TNcells may be a major source of virus following treatment interruption or failure. These findings highlight the need for a better understanding of the establishment and reversal of HIV-1 latency in TNcells in evaluating therapeutic approaches to eliminate the latent reservoir.
Distinct Particle Morphologies Revealed through Comparative Parallel Analyses of Retrovirus-Like Particles
Authors: Martin Jessica L. , Cao Sheng , Maldonado Jose O. , Zhang Wei , Mansky Louis M. 
Published: June 2016

ABSTRACTThe Gag protein is the main retroviral structural protein, and its expression alone is usually sufficient for production of virus-like particles (VLPs). In this study, we sought to investigate—in parallel comparative analyses—Gag cellular distribution, VLP size, and basic morphological features using Gag expression constructs (Gag or Gag-YFP, where YFP is yellow fluorescent protein) created from all representative retroviral genera:Alpharetrovirus,Betaretrovirus,Deltaretrovirus,Epsilonretrovirus,Gammaretrovirus,Lentivirus, andSpumavirus. We analyzed Gag cellular distribution by confocal microscopy, VLP budding by thin-section transmission electron microscopy (TEM), and general morphological features of the VLPs by cryogenic transmission electron microscopy (cryo-TEM). Punctate Gag was observed near the plasma membrane for all Gag constructs tested except for the representativeBeta- andEpsilonretrovirusGag proteins. This is the first report ofEpsilonretrovirusGag localizing to the nucleus of HeLa cells. While VLPs were not produced by the representativeBeta- andEpsilonretrovirusGag proteins, the other Gag proteins produced VLPs as confirmed by TEM, and morphological differences were observed by cryo-TEM. In particular, we observedDeltaretrovirus-like particles with flat regions of electron density that did not follow viral membrane curvature,Lentivirus-like particles with a narrow range and consistent electron density, suggesting a tightly packed Gag lattice, andSpumavirus-like particles with large envelope protein spikes and no visible electron density associated with a Gag lattice. Taken together, these parallel comparative analyses demonstrate for the first time the distinct morphological features that exist among retrovirus-like particles. Investigation of these differences will provide greater insights into the retroviral assembly pathway.IMPORTANCEComparative analysis among retroviruses has been critically important in enhancing our understanding of retroviral replication and pathogenesis, including that of important human pathogens such as human T-cell leukemia virus type 1 (HTLV-1) and HIV-1. In this study, parallel comparative analyses have been used to study Gag expression and virus-like particle morphology among representative retroviruses in the known retroviral genera. Distinct differences were observed, which enhances current knowledge of the retroviral assembly pathway.
Structure-Function Analysis of the ϕX174 DNA-Piloting Protein Using Length-Altering Mutations
Authors: Roznowski Aaron P. , Fane Bentley A. 
Published: June 2016

ABSTRACT
Although the ϕX174 H protein is monomeric during procapsid morphogenesis, 10 proteins oligomerize to form a DNA translocating conduit (H-tube) for penetration. However, the timing and location of H-tube formation are unknown. The H-tube's highly repetitive primary and quaternary structures made it amenable to a genetic analysis using in-frame insertions and deletions. Length-altered proteins were characterized for the ability to perform the protein's three known functions: participation in particle assembly, genome translocation, and stimulation of viral protein synthesis. Insertion mutants were viable. Theoretically, these proteins would produce an assembled tube exceeding the capsid's internal diameter, suggesting that virions do not contain a fully assembled tube. Lengthened proteins were also used to test the biological significance of the crystal structure. Particles containing H proteins of two different lengths were significantly less infectious than both parents, indicating an inability to pilot DNA. Shortened H proteins were not fully functional. Although they could still stimulate viral protein synthesis, they either were not incorporated into virions or, if incorporated, failed to pilot the genome. Mutant proteins that failed to incorporate contained deletions within an 85-amino-acid segment, suggesting the existence of an incorporation domain. The revertants of shortened H protein mutants fell into two classes. The first class duplicated sequences neighboring the deletion, restoring wild-type length but not wild-type sequence. The second class suppressed an incorporation defect, allowing the use of the shortened protein.

IMPORTANCE
The H-tube crystal structure represents the first high-resolution structure of a virally encoded DNA-translocating conduit. It has similarities with other viral proteins through which DNA must travel, such as the α-helical barrel domains of P22 portal proteins and T7 proteins that form tail tube extensions during infection. Thus, the H protein serves as a paradigm for the assembly and function of long α-helical supramolecular structures and nanotubes. Highly repetitive in primary and quaternary structure, they are amenable to structure-function analyses using in-frame insertions and deletions as presented herein.
The Evolutionary Histories of Antiretroviral Proteins SERINC3 and SERINC5 Do Not Support an Evolutionary Arms Race in Primates
Authors: Murrell Ben , Vollbrecht Thomas , Guatelli John , Wertheim Joel O. 
Published: June 2016

ABSTRACT
Molecular evolutionary arms races between viruses and their hosts are important drivers of adaptation. These Red Queen dynamics have been frequently observed in primate retroviruses and their antagonists, host restriction factor genes, such as APOBEC3F/G, TRIM5-α, SAMHD1, and BST-2. Host restriction factors have experienced some of the most intense and pervasive adaptive evolution documented in primates. Recently, two novel host factors, SERINC3 and SERINC5, were identified as the targets of HIV-1 Nef, a protein crucial for the optimal infectivity of virus particles. Here, we compared the evolutionary fingerprints of SERINC3 and SERINC5 to those of other primate restriction factors and to a set of other genes with diverse functions. SERINC genes evolved in a manner distinct from the canonical arms race dynamics seen in the other restriction factors. Despite their antiviral activity against HIV-1 and other retroviruses, SERINC3 and SERINC5 have a relatively uneventful evolutionary history in primates.

IMPORTANCE
Restriction factors are host proteins that block viral infection and replication. Many viruses, like HIV-1 and related retroviruses, evolved accessory proteins to counteract these restriction factors. The importance of these interactions is evidenced by the intense adaptive selection pressures that dominate the evolutionary histories of both the host and viral genes involved in this so-called arms race. The dynamics of these arms races can point to mechanisms by which these viral infections can be prevented. Two human genes, SERINC3 and SERINC5, were recently identified as targets of an HIV-1 accessory protein important for viral infectivity. Unexpectedly, we found that these SERINC genes, unlike other host restriction factor genes, show no evidence of a recent evolutionary arms race with viral pathogens.
Flow Cytometric and Cytokine ELISpot Approaches To Characterize the Cell-Mediated Immune Response in Ferrets following Influenza Virus Infection
Authors: DiPiazza Anthony , Richards Katherine , Batarse Frances , Lockard Laura , Zeng Hui , García-Sastre Adolfo , Albrecht Randy A. , Sant Andrea J. 
Published: June 2016

ABSTRACTInfluenza virus infections represent a significant socioeconomic and public health burden worldwide. Although ferrets are considered by many to be ideal for modeling human responses to influenza infection and vaccination, efforts to understand the cellular immune response have been severely hampered by a paucity of standardized procedures and reagents. In this study, we developed flow cytometric and T cell enzyme-linked immunosorbent spot (ELISpot) approaches to characterize the leukocyte composition and antigen-specific T cell response within key lymphoid tissues following influenza virus infection in ferrets. Through a newly designed and implemented set of serological reagents, we used multiparameter flow cytometry to directly quantify the frequency of CD4+and CD8+T cells, Ig+B cells, CD11b+myeloid-derived cells, and major histocompatibility complex (MHC) class II-positive antigen-presenting cells (APCs) both prior to and after intranasal infection with A/California/04/09 (H1N1). We found that the leukocyte composition was altered at 10 days postinfection, with notable gains in the frequency of T cells and myeloid cells within the draining lymph node. Furthermore, these studies revealed that the antigen specificity of influenza virus-reactive CD4 and CD8 T cells was very broad, with recognition of the viral HA, NA, M1, NS1, and NP proteins, and that total reactivity to influenza virus postinfection represented approximately 0.1% of the circulating peripheral blood mononuclear cells (PBMC). Finally, we observed distinct patterns of reactivity between individual animals, suggesting heterogeneity at the MHC locus in ferrets within commercial populations, a finding of considerable interest in efforts to move the ferret model forward for influenza vaccine and challenge studies.IMPORTANCEFerrets are an ideal animal model to study transmission, diseases, and vaccine efficacies of respiratory viruses because of their close anatomical and physiological resemblances to humans. However, a lack of reagents has limited our understanding of the cell-mediated immune response following infection and vaccination. In this study, we used cross-reactive and ferret-specific antibodies to study the leukocyte composition and antigen-specific CD4 and CD8 T cell responses following influenza A/California/04/09 (H1N1) virus infection. These studies revealed strikingly distinct patterns of reactivity between CD4 and CD8 T cells, which were overlaid with differences in protein-specific responses between individual animals. Our results provide a first, in-depth look at the T cell repertoire in response to influenza infection and suggest that there is considerable heterogeneity at the MHC locus, which is akin to that in humans and an area of intense research interest.
Major Histocompatibility Complex Class II HLA-DRα Is Downregulated by Kaposi's Sarcoma-Associated Herpesvirus-Encoded Lytic Transactivator RTA and MARCH8
Authors: Sun Zhiguo , Jha Hem Chandra , Pei Yong-gang , Robertson Erle S. 
Published: June 2016

ABSTRACT
Kaposi's sarcoma-associated herpesvirus (KSHV) maintains two modes of life cycle, the latent and lytic phases. To evade the attack of the cell host's immune system, KSHV switches from the lytic to the latent phase, a phase in which only a few of viral proteins are expressed. The mechanism by which KSHV evades the attack of the immune system and establishes latency has not been fully understood. Major histocompatibility complex class II (MHC-II) molecules are key components of the immune system defense mechanism against viral infections. Here we report that HLA-DRα, a member of the MHC-II molecules, was downregulated by the replication and transcription activator (RTA) protein encoded by KSHV ORF50, an important regulator of the viral life cycle. RTA not only downregulated HLA-DRα at the protein level through direct binding and degradation through the proteasome pathway but also indirectly downregulated the protein level of HLA-DRα by enhancing the expression of MARCH8, a member of the membrane-associated RING-CH (MARCH) proteins. Our findings indicate that KSHV RTA facilitates evasion of the virus from the immune system through manipulation of HLA-DRα.

IMPORTANCE
Kaposi's sarcoma-associated herpesvirus (KSHV) has a causal role in a number of human cancers, and its persistence in infected cells is controlled by the host's immune system. The mechanism by which KSHV evades an attack by the immune system has not been well understood. This work represents studies which identify a novel mechanism by which the virus can facilitate evasion of an immune system. We now show that RTA, the replication and transcription activator encoded by KSHV (ORF50), can function as an E3 ligase to degrade HLA-DRα. It can directly bind and induce degradation of HLA-DRα through the ubiquitin-proteasome degradation pathway. In addition to the direct regulation of HLA-DRα, RTA can also indirectly downregulate the level of HLA-DRα protein by upregulating transcription of MARCH8. Increased MARCH8 results in the downregulation of HLA-DRα. Furthermore, we also demonstrate that expression of HLA-DRα was impaired in KSHV
de novo
infection.
Asymmetric exhumation of the Mount Everest region: Implications for the tectono-topographic evolution of the Himalaya
Authors: Carrapa B. , Robert X. , DeCelles P.G. , Orme D.A. , Thomson S.N. , Schoenbohm L.M. 
Published: June 2016

Abstract
The tectonic and topographic history of the Himalaya-Tibet orogenic system remains controversial, with several competing models that predict different exhumation histories. Here, we present new low-temperature thermochronological data from the Mount Everest region, which, combined with thermal-kinematic landscape evolution modeling, indicate asymmetric exhumation of Mount Everest consistent with a scenario in which the southern edge of the Tibetan Plateau was located &gt;100 km farther south during the mid-Miocene. Northward plateau retreat was caused by erosional incision during the Pliocene. Our results suggest that the South Tibetan Detachment was a localized structure and that no coupling between precipitation and erosion is required for Miocene exhumation of Greater Himalayan Sequence rocks on Mount Everest.
Sedimentary record of plate coupling and decoupling during growth of the Andes
Authors: Horton Brian K. , Fuentes Facundo 
Published: June 2016

Abstract
Geochronologic, provenance, and sediment accumulation records from the long-lived (&gt;100 m.y.) retroarc basin at the transition from the central to southern Andes provide improved resolution to examine the duration and controls on mixed-mode deformation and an enigmatic foreland depositional hiatus. Detrital zircon U-Pb ages for the Malargüe and Neuquén basin systems of western Argentina reveal shifts in exhumation and accumulation compatible with magmatic-arc and thrust-belt sources during unsteady Cretaceous–Neogene deformation. Fully developed foreland basin conditions were only achieved during separate periods of Late Cretaceous and Neogene shortening contemporaneous with possible episodes of enhanced coupling between a westward-advancing South American plate and the subducting Nazca slab. Separating these two contractional episodes is a 20–40 m.y. phase of reduced sedimentation and unconformity development, potentially signifying a neutral to extensional mode across the retroarc hinterland to forearc region during diminished plate coupling. We propose that the Andean orogen and its foreland and forearc basins have always been sensitive to variations in subduction dynamics, such that regional shifts in slab buoyancy and subduction geometry (particularly slab dip) superimposed on plate-scale shifts in convergence have governed mechanical coupling along the plate boundary and resulting fluctuations among contractional, extensional, and neutral tectonic regimes.
Evidence for Cretaceous-Paleogene boundary bolide “impact winter” conditions from New Jersey, USA
Authors: Vellekoop Johan , Esmeray-Senlet Selen , Miller Kenneth G. , Browning James V. , Sluijs Appy , van de Schootbrugge Bas , Sinninghe Damsté Jaap S. , Brinkhuis Henk 
Published: June 2016

Abstract
Abrupt and short-lived “impact winter” conditions have commonly been implicated as the main mechanism leading to the mass extinction at the Cretaceous-Paleogene (K-Pg) boundary (ca. 66 Ma), marking the end of the reign of the non-avian dinosaurs. However, so far only limited evidence has been available for such a climatic perturbation. Here we perform high-resolution TEX86 organic paleothermometry on three shallow cores from the New Jersey paleoshelf, (northeastern USA) to assess the impact-provoked climatic perturbations immediately following the K-Pg impact and to place these short-term events in the context of long-term climate evolution. We provide evidence of impact-provoked, severe climatic cooling immediately following the K-Pg impact. This so-called “impact winter” occurred superimposed on a long-term cooling trend that followed a warm phase in the latest Cretaceous.