bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving phosphorus use efficiency: a complex trait with emerging opportunities
Authors: Heuer Sigrid , Gaxiola Roberto , Schilling Rhiannon , Herrera‐Estrella Luis , López‐Arredondo Damar , Wissuwa Matthias , Delhaize Emmanuel , Rouached Hatem 
Published: November 2016

SummaryPhosphorus (P) is one of the essential nutrients for plants, and is indispensable for plant growth and development. P deficiency severely limits crop yield, and regular fertilizer applications are required to obtain high yields and to prevent soil degradation. To access P from the soil, plants have evolved high‐ and low‐affinity Pi transporters and the ability to induce root architectural changes to forage P. Also, adjustments of numerous cellular processes are triggered by the P starvation response, a tightly regulated process in plants. With the increasing demand for food as a result of a growing population, the demand for P fertilizer is steadily increasing. Given the high costs of fertilizers and in light of the fact that phosphate rock, the source of P fertilizer, is a finite natural resource, there is a need to enhance P fertilizer use efficiency in agricultural systems and to develop plants with enhanced Pi uptake and internal P‐use efficiency (PUE). In this review we will provide an overview of continuing relevant research and highlight different approaches towards developing crops with enhanced PUE. In this context, we will summarize our current understanding of root responses to low phosphorus conditions and will emphasize the importance of combining PUE with tolerance of other stresses, such as aluminum toxicity. Of the many genes associated with Pi deficiency, this review will focus on those that hold promise or are already at an advanced stage of testing (OsPSTOL1, AVP1, PHO1 and OsPHT1;6). Finally, an update is provided on the progress made exploring alternative technologies, such as phosphite fertilizer.
Copy number variations of CBF genes at the Fr‐A2 locus are essential components of winter hardiness in wheat
Authors: Würschum Tobias , Longin C. Friedrich H. , Hahn Volker , Tucker Matthew R. , Leiser Willmar L. 
Published: November 2016

SummaryWinter hardiness is important for the adaptation of wheat to the harsh winter conditions in temperate regions and is thus also an important breeding goal. Here, we employed a panel of 407 European winter wheat cultivars to dissect the genetic architecture of winter hardiness. We show that copy number variation (CNV) of CBF (C‐repeat Binding Factor) genes at the Fr‐A2 locus is the essential component for winter survival, with CBF‐A14 CNV being the most likely causal polymorphism, accounting for 24.3% of the genotypic variance. Genome‐wide association mapping identified several markers in the Fr‐A2 chromosomal region, which even after accounting for the effects of CBF‐A14 copy number explained approximately 15% of the genotypic variance. This suggests that additional, as yet undiscovered, polymorphisms are present at the Fr‐A2 locus. Furthermore, CNV of Vrn‐A1 explained an additional 3.0% of the genotypic variance. The allele frequencies of all loci associated with winter hardiness were found to show geographic patterns consistent with their role in adaptation. Collectively, our results from the candidate gene analysis, association mapping and genome‐wide prediction show that winter hardiness in wheat is a quantitative trait, but with a major contribution of the Fr‐A2 locus.
Calibration and Evaluation of Quantitative Antibody Titers for Measles Virus by Using the BioPlex 2200
Authors: Hatchette Todd F. , Scholz Heidi , Bolotin Shelly , Crowcroft Natasha S. , Jackson Colleen , McLachlan Elizabeth , Severini Alberto 
Published: November 2016

ABSTRACT
The BioPlex 2200 (Bio-Rad Laboratories, Hercules, CA) is a rapid, automated platform, which can screen large numbers of specimens for antibodies to measles, mumps, rubella, and varicella. Although approved for producing qualitative results, in this study we validated the test (off-label) to allow reporting of quantitative results. To do this, we used the third anti-measles World Health Organization standard to generate a calibration curve that allowed relative fluorescence intensity to be translated into quantitative antibody titer (antibody units [AU]/ml). The results from the BioPlex 2200 and the reference plaque reduction neutralization test (PRNT) exhibited a reasonable correlation following an exponential function, but correlation was poor in low-titer samples. Using a receiver operating characteristics analysis, an equivocal zone for the BioPlex 2200 was established between ≥0.13 and <1.10 AU/ml to achieve 100% specificity (95% confidence interval [CI] = 83.2 to 100%) and 100% sensitivity (95% CI = 93.5 to 100%) versus PRNT. By determining an equivocal range requiring confirmation by PRNT, we can avoid underestimating the levels of immunity through false-negative results and optimize methods for seroepidemiological studies.
Highly Multiplexed Proteomic Analysis of Quantiferon Supernatants To Identify Biomarkers of Latent Tuberculosis Infection
Authors: De Groote Mary Ann , Higgins Michael , Hraha Thomas , Wall Kirsten , Wilson Michael L. , Sterling David G. , Janjic Nebojsa , Reves Randall , Ochsner Urs A. , Belknap Robert 
Published: November 2016

ABSTRACTThe tests for diagnosing latent tuberculosis infection (LTBI) are limited by a poor predictive value for identifying people at the highest risk for progressing to active tuberculosis (TB) and have various sensitivities and specificities in different populations. Identifying a more robust signature for LTBI is important for TB prevention and elimination. A pilot study was conducted with samples from immigrants to the United States that were screened for LTBI by the three commercially approved tests, namely, the tuberculin skin test (TST), the Quantiferon-TB Gold in-tube (QFT-GIT), and the T-SPOT.TB (T-SPOT). QFT-GIT supernatants from 13 people with concordant positive results and 26 people with concordant negative results were analyzed via the highly multiplexed SOMAscan proteomic assay. The proteins in the stimulated supernatants that distinguished LTBI from controls included interleukin-2 (IL-2), monocyte chemotactic protein 2 (MCP-2), interferon gamma inducible protein-10 (IP-10), interferon gamma (IFN-γ), tumor necrosis factor superfamily member 14 (TNFSF14, also known as LIGHT), monokine induced by gamma interferon (MIG), and granzyme B (P<0.00001). In addition, antigen stimulation increased the expression of heparin-binding EGF-like growth factor (HB-EGF) and activin AB in LTBI samples. In nil tubes, LIGHT was the most significant marker (P<0.0001) and was elevated in LTBI subjects. Other prominent markers in nonstimulated QFT-GIT supernatants were the complement-3 components C3b, iC3b, and C3d, which were upregulated in LTBI and markedly decreased upon stimulation. We found known and novel proteins that warrant further studies for developing improved tests for LTBI, for predicting progression to active disease, and for discriminating LTBI from active TB.
Rapid Identification of Measles Virus Vaccine Genotype by Real-Time PCR
Authors: Roy Felicia , Mendoza Lillian , Hiebert Joanne , McNall Rebecca J. , Bankamp Bettina , Connolly Sarah , Lüdde Amy , Friedrich Nicole , Mankertz Annette , Rota Paul A. , Severini Alberto 
Published: November 2016

ABSTRACT
During measles outbreaks, it is important to be able to rapidly distinguish between measles cases and vaccine reactions to avoid unnecessary outbreak response measures such as case isolation and contact investigations. We have developed a real-time reverse transcription-PCR (RT-PCR) method specific for genotype A measles virus (MeV) (MeVA RT-quantitative PCR [RT-qPCR]) that can identify measles vaccine strains rapidly, with high throughput, and without the need for sequencing to determine the genotype. We have evaluated the method independently in three measles reference laboratories using two platforms, the Roche LightCycler 480 system and the Applied Biosystems (ABI) 7500 real-time PCR system. In comparison to the standard real-time RT-PCR method, the MeVA RT-qPCR showed 99.5% specificity for genotype A and 94% sensitivity for both platforms. The new assay was able to detect RNA from five currently used vaccine strains, AIK-C, CAM-70, Edmonston-Zagreb, Moraten, and Shanghai-191. The MeVA RT-qPCR assay has been used successfully for measles surveillance in reference laboratories, and it could be readily deployed to national and subnational laboratories on a wide scale.
A Novel Selective Medium for Isolation of Bacteroides fragilis from Clinical Specimens
Authors: Ho Pak-Leung , Ho Lok-Yan , Yau Chong-Yee , Tong Man-Ki , Chow Kin-Hung 
Published: November 2016

ABSTRACT

A novel
Bacteroides fragilis
selective (BFS) medium, consisting of a brain heart infusion agar base supplemented with yeast extract, cysteine hydrochloride, bile salts, vitamin K, hemin, glucose, esculin, ferric ammonium citrate, bromothymol blue, gentamicin, kanamycin, and novobiocin, was evaluated. When BFS agar was tested with a collection of 303 bacteria of different genera, it allowed the growth of
B. fragilis
as large yellow colonies, with blackening of the medium after 48 h of anaerobic incubation, while the growth of most other anaerobes, facultative anaerobes, and aerobes was inhibited. In a prospective comparison of BFS agar with a routinely used medium (neomycin blood agar) in 1,209 clinical specimens, 60
B. fragilis
bacteria were detected on BFS agar while 46 were detected on the routine agar (McNemar's test,
P
= 0.008). In conclusion, this novel medium may be added to improve the recovery of
B. fragilis
in clinical specimens and to facilitate surveillance of antimicrobial-resistant strains.
Ablation of Programmed −1 Ribosomal Frameshifting in Venezuelan Equine Encephalitis Virus Results in Attenuated Neuropathogenicity
Authors: Kendra Joseph A. , de la Fuente Cynthia , Brahms Ashwini , Woodson Caitlin , Bell Todd M. , Chen Bin , Khan Yousuf A. , Jacobs Jonathan L. , Kehn-Hall Kylene , Dinman Jonathan D. 
Published: November 2016

ABSTRACT

The alphaviruses Venezuelan equine encephalitis virus (VEEV), eastern equine encephalitis virus (EEEV), and western equine encephalitis virus (WEEV) are arthropod-borne positive-strand RNA viruses that are capable of causing acute and fatal encephalitis in many mammals, including humans. VEEV was weaponized during the Cold War and is recognized as a select agent. Currently, there are no FDA-approved vaccines or therapeutics for these viruses. The spread of VEEV and other members of this family due to climate change-mediated vector range expansion underscores the need for research aimed at developing medical countermeasures. These viruses utilize programmed −1 ribosomal frameshifting (−1 PRF) to synthesize the viral
trans
-frame (TF) protein, which has previously been shown to be important for neuropathogenesis in the related Sindbis virus. Here, the alphavirus −1 PRF signals were characterized, revealing novel −1 PRF stimulatory structures. −1 PRF attenuation mildly affected the kinetics of VEEV accumulation in cultured cells but strongly inhibited its pathogenesis in an aerosol infection mouse model. Importantly, the decreased viral titers in the brains of mice infected with the mutant virus suggest that the alphavirus TF protein is important for passage through the blood-brain barrier and/or for neuroinvasiveness. These findings suggest a novel approach to the development of safe and effective live attenuated vaccines directed against VEEV and perhaps other closely related −1 PRF-utilizing viruses.

IMPORTANCE
Venezuelan equine encephalitis virus (VEEV) is a select agent that has been weaponized. This arthropod-borne positive-strand RNA virus causes acute and fatal encephalitis in many mammals, including humans. There is no vaccine or other approved therapeutic. VEEV and related alphaviruses utilize programmed −1 ribosomal frameshifting (−1 PRF) to synthesize the viral
trans
-frame (TF) protein, which is important for neuropathogenesis. −1 PRF attenuation strongly inhibited VEEV pathogenesis in mice, and viral replication analyses suggest that the TF protein is critical for neurological disease. These findings suggest a new approach to the development of safe and effective live attenuated vaccines directed against VEEV and other related viruses.
Mapping of Functional Subdomains in the Terminal Protein Domain of Hepatitis B Virus Polymerase
Authors: Clark Daniel N. , Flanagan John M. , Hu Jianming 
Published: November 2016

ABSTRACT
Hepatitis B virus (HBV) encodes a multifunction reverse transcriptase or polymerase (P), which is composed of several domains. The terminal protein (TP) domain is unique to HBV and related hepadnaviruses and is required for specifically binding to the viral pregenomic RNA (pgRNA). Subsequently, the TP domain is necessary for pgRNA packaging into viral nucleocapsids and the initiation of viral reverse transcription for conversion of the pgRNA to viral DNA. Uniquely, the HBV P protein initiates reverse transcription via a protein priming mechanism using the TP domain as a primer. No structural homologs or high-resolution structure exists for the TP domain. Secondary structure prediction identified three disordered loops in TP with highly conserved sequences. A meta-analysis of mutagenesis studies indicated these predicted loops are almost exclusively where functionally important residues are located. Newly constructed TP mutations revealed a priming loop in TP which plays a specific role in protein-primed DNA synthesis beyond simply harboring the site of priming. Substitutions of potential sites of phosphorylation surrounding the priming site demonstrated that these residues are involved in interactions critical for priming but are unlikely to be phosphorylated during viral replication. Furthermore, the first 13 and 66 TP residues were shown to be dispensable for protein priming and pgRNA binding, respectively. Combining current and previous mutagenesis work with sequence analysis has increased our understanding of TP structure and functions by mapping specific functions to distinct predicted secondary structures and will facilitate antiviral targeting of this unique domain.

IMPORTANCE
HBV is a major cause of viral hepatitis, liver cirrhosis, and hepatocellular carcinoma. One important feature of this virus is its polymerase, the enzyme used to create the DNA genome from a specific viral RNA by reverse transcription. One region of this polymerase, the TP domain, is required for association with the viral RNA and production of the DNA genome. Targeting the TP domain for antiviral development is difficult due to the lack of homology to other proteins and high-resolution structure. This study mapped the TP functions according to predicted secondary structure, where it folds into alpha helices or unstructured loops. Three predicted loops were found to be the most important regions functionally and the most conserved evolutionarily. Identification of these functional subdomains in TP will facilitate its targeting for antiviral development.
A Novel Rabies Vaccine Expressing CXCL13 Enhances Humoral Immunity by Recruiting both T Follicular Helper and Germinal Center B Cells
Authors: Wang Zhao , Li Mingming , Zhou Ming , Zhang Yajing , Yang Jie , Cao Yandi , Wang Kunlun , Cui Min , Chen Huanchun , Fu Zhen F. , Zhao Ling 
Published: November 2016

ABSTRACT
Rabies remains a public health threat in most parts of the world, and approximately 99% of the cases are transmitted by dogs. There is an urgent need to develop an efficacious and affordable vaccine to control canine-transmitted rabies in developing countries. Our previous studies demonstrate that overexpression of chemokines/cytokines such as CCL-3 (MIP-1α) and granulocyte-macrophage colony-stimulating factor (GM-CSF) can enhance the immunogenicity of rabies vaccines. In the present study, the chemokine CXCL13 was inserted into the genome of the recombinant rabies virus (rRABV) strain LBNSE, and the effect of the chemokine CXCL13 on the immunogenicity of RABV was investigated. It was found that LBNSE-CXCL13 recruited follicular helper T (Tfh) and germinal center (GC) B cells, promoted the formation of GCs, and increased the population of plasma cells in immunized mice. Further studies showed that mice immunized with LBNSE-CXCL13 produced more rabies virus-neutralizing antibodies (VNAs) and developed better protection than those immunized with the parent virus LBNSE or the GM-CSF-expressing RABV (LBNSE-GM-CSF). Collectively, these findings provide a better understanding of the role of CXCL13 expression in the immunogenicity of the RABV, which may help in designing more-efficacious rabies vaccines.

IMPORTANCE
Rabies is endemic in most parts of the world, and more effort is needed to develop affordable and effective vaccines to control or eliminate this disease. The chemokine CXCL13 recruits both Tfh and B cells, which is essential for the homing of Tfh cells and the development of B cell follicles. In this study, the effect of the overexpression of CXCL13 on the immunogenicity of the RABV was evaluated in a mouse model. We found that CXCL13 expression promoted humoral immunity by recruiting Tfh and GC B cells, facilitating the formation of GCs, and increasing the number of plasma cells. As expected, the overexpression of CXCL13 resulted in enhanced virus-neutralizing antibody (VNA) production and protection against a virulent RABV challenge. These findings provide a better understanding of the role of CXCL13 in RABV-induced immune responses, which will help in designing more efficacious rabies vaccines.
Palmitoylation of Sindbis Virus TF Protein Regulates Its Plasma Membrane Localization and Subsequent Incorporation into Virions
Authors: Ramsey Jolene , Renzi Emily C. , Arnold Randy J. , Trinidad Jonathan C. , Mukhopadhyay Suchetana 
Published: November 2016

ABSTRACT
Palmitoylation is a reversible, posttranslational modification that helps target proteins to cellular membranes. The alphavirus small membrane proteins 6K and TF have been reported to be palmitoylated and to positively regulate budding. 6K and TF are isoforms that are identical in their N termini but unique in their C termini due to a −1 ribosomal frameshift during translation. In this study, we used cysteine (Cys) mutants to test differential palmitoylation of the Sindbis virus 6K and TF proteins. We modularly mutated the five Cys residues in the identical N termini of 6K and TF, the four additional Cys residues in TF's unique C terminus, or all nine Cys residues in TF. Using these mutants, we determined that TF palmitoylation occurs primarily in the N terminus. In contrast, 6K is not palmitoylated, even on these shared residues. In the C-terminal Cys mutant, TF protein levels increase both in the cell and in the released virion compared to the wild type. In viruses with the N-terminal Cys residues mutated, TF is much less efficiently localized to the plasma membrane, and it is not incorporated into the virion. The three Cys mutants have minor defects in cell culture growth but a high incidence of abnormal particle morphologies compared to the wild-type virus as determined by transmission electron microscopy. We propose a model where the C terminus of TF modulates the palmitoylation of TF at the N terminus, and palmitoylated TF is preferentially trafficked to the plasma membrane for virus budding.

IMPORTANCE
Alphaviruses are a reemerging viral cause of arthritogenic disease. Recently, the small 6K and TF proteins of alphaviruses were shown to contribute to virulence
in vivo
. Nevertheless, a clear understanding of the molecular mechanisms by which either protein acts to promote virus infection is missing. The TF protein is a component of budded virions, and optimal levels of TF correlate positively with wild-type-like particle morphology. In this study, we show that the palmitoylation of TF regulates its localization to the plasma membrane, which is the site of alphavirus budding. Mutants in which TF is not palmitoylated display drastically reduced plasma membrane localization, which effectively prevents TF from participating in budding or being incorporated into virus particles. Investigation of the regulation of TF will aid current efforts in the alphavirus field searching for approaches to mitigate alphaviral disease in humans.
Kaposi's Sarcoma-Associated Herpesvirus MicroRNAs Target GADD45B To Protect Infected Cells from Cell Cycle Arrest and Apoptosis
Authors: Liu Xiaoyan , Happel Christine , Ziegelbauer Joseph M. 
Published: November 2016

ABSTRACT

Kaposi's sarcoma is one of the most common malignancies in HIV-infected individuals. The responsible agent, Kaposi's sarcoma-associated herpesvirus (KSHV; HHV8), expresses multiple microRNAs (miRNAs), but the targets and functions of these miRNAs are not completely understood. After infection in primary endothelial cells with KSHV,
growth arrest DNA damage-inducible gene 45 beta
(
GADD45B
) is one of the most repressed genes using genomic expression profiling.
GADD45B
was also repressed in mRNA expression profiling experiments when KSHV miRNAs were introduced to uninfected cells. We hypothesized that KSHV miRNAs target human
GADD45B
to protect cells from consequences of DNA damage, which can be triggered by viral infection. Expression of GADD45B protein is induced by the p53 activator, Nutlin-3, and KSHV miRNA-K9 inhibits this induction. In addition, Nutlin-3 increased apoptosis and cell cycle arrest based on flow cytometry assays. KSHV miR-K9 protected primary endothelial cells from apoptosis and cell cycle arrest following Nutlin-3 treatment. Similar protective phenotypes were seen for targeting GADD45B with short interfering RNAs (siRNAs), as with miR-K9. KSHV miR-K9 also decreased the protein levels of cleaved caspase-3, cleaved caspase-7, and cleaved poly(ADP-ribose) polymerase (PARP). In B lymphocytes latently infected with KSHV, specific inhibitors of KSHV miR-K9 led to increased GADD45B expression and apoptosis, indicating that miR-K9 is important for reducing apoptosis in infected cells. Furthermore, ectopic expression of GADD45B in KSHV-infected cells promoted apoptosis. Together, these results identify a new miRNA target and demonstrate that KSHV miRNAs are important for protecting infected cells from DNA damage responses.

IMPORTANCE
Kaposi's sarcoma-associated herpesvirus is a leading cause of cancers in individuals with AIDS. Promoting survival of infected cells is essential for maintaining viral infections. A virus needs to combat various cellular defense mechanisms designed to eradicate the viral infection. One such response can include DNA damage response factors, which can promote an arrest in cell growth and trigger cell death. We used a new approach to search for human genes repressed by small nucleic acids (microRNAs) expressed by a gammaherpesvirus (KSHV), which identified a gene called
GADD45B
as a target of microRNAs. Repression of GADD45B, which is expressed in response to DNA damage, benefited survival of infected cells in response to a DNA damage response. This information could be used to design new treatments for herpesvirus infections.