bluuebunny/crossref_metadata_2025_split huggingface dataset:
OsARF16, a transcription factor, is required for auxin and phosphate starvation response in rice (Oryza sativa L.)
Authors: SHEN CHENJIA , WANG SUIKANG , ZHANG SAINA , XU YANXIA , QIAN QIAN , QI YANHUA , JIANG DE AN 
Published: August 2012

ABSTRACTPlant responses to auxin and phosphate (Pi) starvation are closely linked. However, the underlying mechanisms connecting auxin to phosphate starvation (−Pi) responses are largely unclear. Here, we show that OsARF16, an auxin response factor, functions in both auxin and −Pi responses in rice (Oryza sativa L.). The knockout of OsARF16 led to primary roots (PR), lateral roots (LR) and root hair losing sensitivity to auxin and −Pi response. OsARF16 expression and OsARF16::GUS staining in PR and LR of rice Nipponbare (NIP) were induced by indole acetic acid and −Pi treatments. In −Pi conditions, the shoot biomass of osarf16 was slightly reduced, and neither root growth nor iron content was induced, indicating that the knockout of OsARF16 led to loss of response to Pi deficiency in rice. Six phosphate starvation‐induced genes (PSIs) were less induced by −Pi in osarf16 and these trends were similar to a knockdown mutant of OsPHR2 or AtPHR1, which was a key regulator under −Pi. These data first reveal the biological function of OsARF16, provide novel evidence of a linkage between auxin and −Pi responses and facilitate the development of new strategies for the efficient utilization of Pi in rice.
Metabolomics reveals herbivore‐induced metabolites of resistance and susceptibility in maize leaves and roots
Authors: MARTI GUILLAUME , ERB MATTHIAS , BOCCARD JULIEN , GLAUSER GAÉTAN , DOYEN GWLADYS R. , VILLARD NEIL , ROBERT CHRISTELLE A M. , TURLINGS TED C. J. , RUDAZ SERGE , WOLFENDER JEAN‐LUC 
Published: August 2012

ABSTRACTPlants respond to herbivory by reprogramming their metabolism. Most research in this context has focused on locally induced compounds that function as toxins or feeding deterrents. We developed an ultra‐high‐pressure liquid chromatography time‐of‐flight mass spectrometry (UHPLC‐TOF‐MS)‐based metabolomics approach to evaluate local and systemic herbivore‐induced changes in maize leaves, sap, roots and root exudates without any prior assumptions about their function. Thirty‐two differentially regulated compounds were identified from Spodoptera littoralis‐infested maize seedlings and isolated for structure assignment by microflow nuclear magnetic resonance (CapNMR). Nine compounds were quantified by a high throughput direct nano‐infusion tandem mass spectrometry/mass spectrometry (MS/MS) method. Leaf infestation led to a marked local increase of 1,3‐benzoxazin‐4‐ones, phospholipids, N‐hydroxycinnamoyltyramines, azealic acid and tryptophan. Only few changes were found in the root metabolome, but 1,3‐benzoxazin‐4‐ones increased in the vascular sap and root exudates. The role of N‐hydroxycinnamoyltyramines in plant–herbivore interactions is unknown, and we therefore tested the effect of the dominating p‐coumaroyltyramine on S. littoralis. Unexpectedly, p‐coumaroyltyramine was metabolized by the larvae and increased larval growth, possibly by providing additional nitrogen to the insect. Taken together, this study illustrates that herbivore attack leads to the induction of metabolites that can have contrasting effects on herbivore resistance in the leaves and roots.
Influence of imaging source and panel position uncertainties on the accuracy of 2D/3D image registration of cranial images
Authors: Warmerdam Guy , Steininger Philipp , Neuner Markus , Sharp Gregory , Winey Brian 
Published: August 2012

Purpose:To determine the effects of imager source and panel positioning uncertainties on the accuracy of dual intensity‐based 2D/3D image registration of cranial images.Methods:An open source 2D/3D image registration algorithm has been developed for registration of two orthogonal x‐rays to a 3D volumetric image. The initialization files of the algorithm allow for nine degrees of freedom system calibration includingx, y, z positions of the source and panel, and three rotational degrees of freedom of the panel about each of the three translational axes. A baseline system calibration was established and a baseline 2D/3D registration between two orthogonal x‐rays and the volumetric image was determined. The calibration file was manipulated to insert errors into each of the nine calibration variables of both imager geometries. Rigid six degrees of freedom registrations were iterated for each panel or source positional error over a range of predetermined calibration errors to determine the resulting error in the registration versus the baseline registration due to the manipulated error of the panel or source calibration.Results:Panel and source translational errors orthogonal to the imager/panel axis introduced the greatest errors in the registration accuracy (4.0 mm geometric error results in up to 2.7 mm registration error). Panel rotation about the imaging direction also resulted in errors of the registration (2.0° geometric error results in up to 1.7° registration error). Differences in magnification and panel tilt and roll, i.e., source and/or panel translation along the imaging direction and panel rotations about the orthogonal axes had minimal effects on the registration accuracy (below 0.3 mm and 0.2° registration error).Conclusions:While five of the nine imaging system variables were found to have a considerable effect on 2D/3D registration accuracy of cranial images, the other four variables showed minimal effects. Vendors typically provide simplified calibration procedures which aim to remove encountered geometric uncertainties by accounting for two panel translations. This study shows that at least the five relevant positional variables should be separately calibrated, if accurate alignment is required for 2D/3D registration.
Phase I Safety and Immunogenicity Evaluations of an Alphavirus Replicon HIV-1 Subtype CgagVaccine in Healthy HIV-1-Uninfected Adults
Authors: Wecker M. , Gilbert P. , Russell N. , Hural J. , Allen M. , Pensiero M. , Chulay J. , Chiu Ya-Lin , Abdool Karim S. S. , Burke D. S. 
Published: August 2012

ABSTRACTOn the basis of positive preclinical data, we evaluated the safety and immunogenicity of an alphavirus replicon HIV-1 subtype Cgagvaccine (AVX101), expressing a nonmyristoylated form of Gag, in two double-blind, randomized, placebo-controlled clinical trials in healthy HIV-1-uninfected adults. Escalating doses of AVX101 or placebo were administered subcutaneously to participants in the United States and Southern Africa. Because of vaccine stability issues, the first trial was halted prior to completion of all dose levels and a second trial was implemented. The second trial was also stopped prematurely due to documentation issues with the contract manufacturer. Safety and immunogenicity were evaluated through assessments of reactogenicity, reports of adverse events, and assessment of replication-competent and Venezuelan equine encephalitis (VEE) viremia. Immunogenicity was measured using the following assays: enzyme-linked immunosorbent assay (ELISA), chromium 51 (51Cr)-release cytotoxic T lymphocyte (CTL), gamma interferon (IFN-γ) ELISpot, intracellular cytokine staining (ICS), and lymphoproliferation assay (LPA). Anti-vector antibodies were also measured. AVX101 was well tolerated and exhibited only modest local reactogenicity. There were 5 serious adverse events reported during the trials; none were considered related to the study vaccine. In contrast to the preclinical data, immune responses in humans were limited. Only low levels of binding antibodies and T-cell responses were seen at the highest doses. This trial also highlighted the difficulties in developing a novel vector for HIV.
Reduced Frequency of Memory T Cells and Increased Th17 Responses in Patients with Active Tuberculosis
Authors: Marín Nancy D. , París Sara C. , Rojas Mauricio , García Luis F. 
Published: August 2012

ABSTRACTPhenotypic and functional alterations inMycobacterium tuberculosisT cell subsets have been reported in patients with active tuberculosis. A better understanding of these alterations will increase the knowledge about immunopathogenesis and also may contribute to the development of new diagnostics and prophylactic strategies. Here, theex vivophenotype of CD4+and CD8+T cells and the frequency and phenotype of gamma interferon (IFN-γ)- and interleukin 17 (IL-17)-producing cells elicited in short-term and long-term cultures following CFP-10 and purified protein derivative (PPD) stimulation were determined in noninfected persons (non-TBi), latently infected persons (LTBi), and patients with active tuberculosis (ATB). Phenotypic characterization of T cells was done based on the expression of CD45RO and CD27. Results show that ATB had a reduced frequency of circulating CD4+CD45RO+CD27+T cells and an increased frequency of CD4+CD45RO−CD27+T cells. ATB also had a higher frequency of circulating IL-17-producing CD4+T cells than did LTBi after PPD stimulation, whereas LTBi had more IFN-γ-producing CD4+T cells than did non-TBi. The phenotype of IFN-γ-producing cells at 24 h differs from the phenotype of IL-17-producing cells with no differences between LTBi and ATB. At 144 h, IFN-γ- and IL-17-producing cells were mainly CD45RO+CD27+T cells and they were more frequent in ATB. These results suggest thatM. tuberculosisinfection induces alterations in T cells which interfere with an adequate specific immune response.
Comparative Whole-Genome Mapping To Determine Staphylococcus aureus Genome Size, Virulence Motifs, and Clonality
Authors: Shukla Sanjay K. , Pantrang Madhulatha , Stahl Buffy , Briska Adam M. , Stemper Mary E. , Wagner Trevor K. , Zentz Emily B. , Callister Steven M. , Lovrich Steven D. , Henkhaus John K. , Dykes Colin W. 
Published: August 2012

ABSTRACT

Despite being a clonal pathogen,
Staphylococcus aureus
continues to acquire virulence and antibiotic-resistant genes located on mobile genetic elements such as genomic islands, prophages, pathogenicity islands, and the staphylococcal chromosomal cassette
mec
(SCC
mec
) by horizontal gene transfer from other staphylococci. The potential virulence of a
S. aureus
strain is often determined by comparing its pulsed-field gel electrophoresis (PFGE) or multilocus sequence typing profiles to that of known epidemic or virulent clones and by PCR of the toxin genes. Whole-genome mapping (formerly optical mapping), which is a high-resolution ordered restriction mapping of a bacterial genome, is a relatively new genomic tool that allows comparative analysis across entire bacterial genomes to identify regions of genomic similarities and dissimilarities, including small and large insertions and deletions. We explored whether whole-genome maps (WGMs) of methicillin-resistant
S. aureus
(MRSA) could be used to predict the presence of methicillin resistance, SCC
mec
type, and Panton-Valentine leukocidin (PVL)-producing genes on an
S. aureus
genome. We determined the WGMs of 47 diverse clinical isolates of
S. aureus
, including well-characterized reference MRSA strains, and annotated the signature restriction pattern in SCC
mec
types, arginine catabolic mobile element (ACME), and PVL-carrying prophage, PhiSa2 or PhiSa2-like regions on the genome. WGMs of these isolates accurately characterized them as MRSA or methicillin-sensitive
S. aureus
based on the presence or absence of the SCC
mec
motif, ACME and the unique signature pattern for the prophage insertion that harbored the PVL genes. Susceptibility to methicillin resistance and the presence of
mecA
, SCC
mec
types, and PVL genes were confirmed by PCR. A WGM clustering approach was further able to discriminate isolates within the same PFGE clonal group. These results showed that WGMs could be used not only to genotype
S. aureus
but also to identify genetic motifs in MRSA that may predict virulence.
Clinical and Microbiological Differences between Mycobacterium abscessus and Mycobacterium massiliense Lung Diseases
Authors: Harada Toshiyuki , Akiyama Yasushi , Kurashima Atsuyuki , Nagai Hideaki , Tsuyuguchi Kazunari , Fujii Takashi , Yano Syuichi , Shigeto Eriko , Kuraoka Toshihiko , Kajiki Akira , Kobashi Yoshihiro , Kokubu Fumio , Sato Atsuo , Yoshida Shiomi , Iwamoto Tomotada , Saito Hajime 
Published: August 2012

ABSTRACT

In recent years, many novel nontuberculous mycobacterial species have been discovered through genetic analysis.
Mycobacterium massiliense
and
M. bolletii
have recently been identified as species separate from
M. abscessus
. However, little is known regarding their clinical and microbiological differences in Japan. We performed a molecular identification of stored
M. abscessus
clinical isolates for further identification. We compared clinical characteristics, radiological findings, microbiological findings, and treatment outcomes among patients with
M. abscessus
and
M. massiliense
lung diseases. An analysis of 102 previous isolates of
M. abscessus
identified 72 (71%)
M. abscessus
, 27 (26%)
M. massiliense
, and 3 (3%)
M. bolletii
isolates. Clinical and radiological findings were indistinguishable between the
M. abscessus
and
M. massiliense
groups. Forty-two (58%) patients with
M. abscessus
and 20 (74%) patients with
M. massiliense
infections received antimicrobial treatment. Both the
M. abscessus
and
M. massiliense
groups showed a high level of resistance to all antimicrobials, except for clarithromycin, kanamycin, and amikacin. However, resistance to clarithromycin was more frequently observed in the
M. abscessus
than in the
M. massiliense
group (16% and 4%, respectively;
P
= 0.145). Moreover, the level of resistance to imipenem was significantly lower in
M. abscessus
isolates than in
M. massiliense
isolates (19% and 48%, respectively;
P
= 0.007). The proportions of radiological improvement, sputum smear conversion to negativity, and negative culture conversion during the follow-up period were higher in patients with
M. massiliense
infections than in those with
M. abscessus
infections. Patients with
M. massiliense
infections responded more favorably to antimicrobial therapy than those with
M. abscessus
infections.
Direct Blood PCR in Combination with Nucleic Acid Lateral Flow Immunoassay for Detection of Plasmodium Species in Settings Where Malaria Is Endemic
Authors: Mens P. F. , de Bes H. M. , Sondo P. , Laochan N. , Keereecharoen L. , van Amerongen A. , Flint J. , Sak J. R. S. , Proux S. , Tinto H. , Schallig H. D. F. H. 
Published: August 2012

ABSTRACTDeclining malaria transmission and known difficulties with current diagnostic tools for malaria, such as microscopy and rapid diagnostic tests (RDTs) in particular at low parasite densities, still warrant the search for sensitive diagnostic tests. Molecular tests need substantial simplification before implementation in clinical settings in countries where malaria is endemic. Direct blood PCR (db-PCR), circumventing DNA extraction, to detectPlasmodiumwas developed and adapted to be visualized by nucleic acid lateral flow immunoassay (NALFIA). The assay was evaluated in the laboratory against samples from confirmed Sudanese patients (n= 51), returning travelers (n= 214), samples from the Dutch Blood Bank (n= 100), and in the field in Burkina Faso (n= 283) and Thailand (n= 381) on suspected malaria cases and compared to RDT and microscopy. The sensitivity and specificity of db-PCR-NALFIA compared to the initial diagnosis in the laboratory were 94.4% (95% confidence interval [CI] = 0.909 to 0.969) and 97.4% (95% CI = 0.909 to 0.969), respectively. In Burkina Faso, the sensitivity was 94.8% (95% CI = 0.88.7 to 97.9%), and the specificity was 82.4% (95% CI = 75.4 to 87.7%) compared to microscopy and 93.3% (95% CI = 87.4 to 96.7%) and 91.4% (95% CI = 85.2 to 95.3%) compared to RDT. In Thailand, the sensitivity and specificity were 93.4% (CI = 86.4 to 97.1%) and 90.9 (95% CI = 86.7 to 93.9%), respectively, compared to microscopy and 95.6% (95% CI = 88.5 to 98.6%) and 87.1% (95% CI = 82.5 to 90.6) compared to RDT. db-PCR-NALFIA is highly sensitive and specific for easy and rapid detection ofPlasmodiumparasites and can be easily used in countries where malaria is endemic. The inability of the device to discriminatePlasmodiumspecies requires further investigation.
Association of Campylobacter upsaliensis with Persistent Bloody Diarrhea
Authors: Couturier Brianne A. , Hale DeVon C. , Couturier Marc Roger 
Published: August 2012

ABSTRACTCampylobacter upsaliensisis a zoonotic, emerging pathogen that is not readily recovered in traditional stool culture. This case represents the first report of persistent bloody diarrhea withC. upsaliensisthat was confirmed by filtration culture, PCR, and sequencing.
Localization of a Region in the Fusion Protein of Avian Metapneumovirus That Modulates Cell-Cell Fusion
Authors: Wei Yongwei , Feng Kurtis , Yao Xiangjie , Cai Hui , Li Junan , Mirza Anne M. , Iorio Ronald M. , Li Jianrong 
Published: August 2012

ABSTRACT

The genus
Metapneumovirus
within the subfamily
Pneumovirinae
of the family
Paramyxoviridae
includes two members, human metapneumovirus (hMPV) and avian metapneumovirus (aMPV), causing respiratory tract infections in humans and birds, respectively. Paramyxoviruses enter host cells by fusing the viral envelope with a host cell membrane. Membrane fusion of hMPV appears to be unique, in that fusion of some hMPV strains requires low pH. Here, we show that the fusion (F) proteins of aMPV promote fusion in the absence of the attachment protein and low pH is not required. Furthermore, there are notable differences in cell-cell fusion among aMPV subtypes. Trypsin was required for cell-cell fusion induced by subtype B but not subtypes A and C. The F protein of aMPV subtype A was highly fusogenic, whereas those from subtypes B and C were not. By construction and evaluation of chimeric F proteins composed of domains from the F proteins of subtypes A and B, we localized a region composed of amino acid residues 170 to 338 in the F protein that is responsible for the hyperfusogenic phenotype of the F from subtype A. Further mutagenesis analysis revealed that residues R295, G297, and K323 in this region collectively contributed to the hyperfusogenicity. Taken together, we have identified a region in the aMPV F protein that modulates the extent of membrane fusion. A model for fusion consistent with these data is presented.
High-Resolution Functional Profiling of the Norovirus Genome
Authors: Thorne Lucy , Bailey Dalan , Goodfellow Ian 
Published: August 2012

ABSTRACT
Human noroviruses (HuNoV) are a major cause of nonbacterial gastroenteritis worldwide, yet details of the life cycle and replication of HuNoV are relatively unknown due to the lack of an efficient cell culture system. Studies with murine norovirus (MNV), which can be propagated in permissive cells, have begun to probe different aspects of the norovirus life cycle; however, our understanding of the specific functions of the viral proteins lags far behind that of other RNA viruses. Genome-wide functional profiling by insertional mutagenesis can reveal protein domains essential for replication and can lead to generation of tagged viruses, which has not yet been achieved for noroviruses. Here, transposon-mediated insertional mutagenesis was used to create 5 libraries of mutagenized MNV infectious clones, each containing a 15-nucleotide sequence randomly inserted within a defined region of the genome. Infectious virus was recovered from each library and was subsequently passaged in cell culture to determine the effect of each insertion by insertion-specific fluorescent PCR profiling. Genome-wide profiling of over 2,000 insertions revealed essential protein domains and confirmed known functional motifs. As validation, several insertion sites were introduced into a wild-type clone, successfully allowing the recovery of infectious virus. Screening of a number of reporter proteins and epitope tags led to the generation of the first infectious epitope-tagged noroviruses carrying the FLAG epitope tag in either NS4 or VP2. Subsequent work confirmed that epitope-tagged fully infectious noroviruses may be of use in the dissection of the molecular interactions that occur within the viral replication complex.
Flavivirus Replication Complex Assembly Revealed by DNAJC14 Functional Mapping
Authors: Yi Zhigang , Yuan Zhenghong , Rice Charles M. , MacDonald Margaret R. 
Published: August 2012

ABSTRACT
DNAJC14 is an Hsp40 family member that broadly modulates flavivirus replication. The mechanism by which DNAJC14 stoichiometrically participates in flavivirus replication complex (RC) formation is unknown; both reduced and elevated levels result in replication inhibition. Using yellow fever virus (YFV), we demonstrate that DNAJC14 redistributes and clusters with YFV nonstructural proteins via a transmembrane domain and a newly identified membrane-binding domain (MBD), which both mediate targeting to detergent-resistant membranes. Furthermore, the RC and DNAJC14 reside as part of a protein interaction network that remains after 1% Triton solubilization. Mutagenesis studies demonstrate that entry into this protein interaction network requires the DNAJC14 C-terminal self-interaction domain. Fusion of the DNAJC14 MBD and self-interaction domain with another Hsp40 family protein is sufficient to confer YFV-inhibitory activity. Our findings support a novel model of DNAJC14 action that includes specific membrane targeting of both DNAJC14 and YFV replication proteins, the formation of protein interactions, and a microdomain-specific chaperone event leading to RC formation. This process alters the properties of the RC membrane and results in the formation of a protein scaffold that maintains the RC.
Glycan-Dependent Immunogenicity of Recombinant Soluble Trimeric Hemagglutinin
Authors: de Vries Robert P. , Smit Cornelis H. , de Bruin Erwin , Rigter Alan , de Vries Erik , Cornelissen Lisette A. H. M. , Eggink Dirk , Chung Nancy P. Y. , Moore John P. , Sanders Rogier W. , Hokke Cornelis H. , Koopmans Marion , Rottier Peter J. M. , de Haan Cornelis A. M. 
Published: August 2012

ABSTRACT

Recombinant soluble trimeric influenza A virus (IAV) hemagglutinin (sHA
3
) has proven an effective vaccine antigen against IAV. Here, we investigate to what extent the glycosylation status of the sHA
3
glycoprotein affects its immunogenicity. Different glycosylation forms of subtype H5 trimeric HA protein (sH5
3
) were produced by expression in insect cells and different mammalian cells in the absence and presence of inhibitors of N-glycan-modifying enzymes or by enzymatic removal of the oligosaccharides. The following sH5
3
preparations were evaluated: (i) HA proteins carrying complex glycans produced in HEK293T cells; (ii) HA proteins carrying Man
9
GlcNAc
2
moieties, expressed in HEK293T cells treated with kifunensine; (iii) HA proteins containing Man
5
GlcNAc
2
moieties derived from HEK293S GnTI(−) cells; (iv) insect cell-produced HA proteins carrying paucimannosidic N-glycans; and (v) HEK293S GnTI(−) cell-produced HA proteins treated with endoglycosidase H, thus carrying side chains composed of only a single
N
-acetylglucosamine each. The different HA glycosylation states were confirmed by comparative electrophoretic analysis and by mass spectrometric analysis of released glycans. The immunogenicity of the HA preparations was studied in chickens and mice. The results demonstrate that HA proteins carrying terminal mannose moieties induce significantly lower hemagglutination inhibition antibody titers than HA proteins carrying complex glycans or single
N
-acetylglucosamine side chains. However, the glycosylation state of the HA proteins did not affect the breadth of the antibody response as measured by an HA1 antigen microarray. We conclude that the glycosylation state of recombinant antigens is a factor of significant importance when developing glycoprotein-based vaccines, such as recombinant HA proteins.