bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating mechanisms of diversification in a Guineo‐Congolian tropical forest frog using demographic model selection
Authors: Portik Daniel M. , Leaché Adam D. , Rivera Danielle , Barej Michael F. , Burger Marius , Hirschfeld Mareike , Rödel Mark‐Oliver , Blackburn David C. , Fujita Matthew K. 
Published: July 2017

AbstractThe accumulation of biodiversity in tropical forests can occur through multiple allopatric and parapatric models of diversification, including forest refugia, riverine barriers and ecological gradients. Considerable debate surrounds the major diversification process, particularly in the West African Lower Guinea forests, which contain a complex geographic arrangement of topographic features and historical refugia. We used genomic data to investigate alternative mechanisms of diversification in the Gaboon forest frog, Scotobleps gabonicus, by first identifying population structure and then performing demographic model selection and spatially explicit analyses. We found that a majority of population divergences are best explained by allopatric models consistent with the forest refugia hypothesis and involve divergence in isolation with subsequent expansion and gene flow. These population divergences occurred simultaneously and conform to predictions based on climatically stable regions inferred through ecological niche modelling. Although forest refugia played a prominent role in the intraspecific diversification of S. gabonicus, we also find evidence for potential interactions between landscape features and historical refugia, including major rivers and elevational barriers such as the Cameroonian Volcanic Line. We outline the advantages of using genomewide variation in a model‐testing framework to distinguish between alternative allopatric hypotheses, and the pitfalls of limited geographic and molecular sampling. Although phylogeographic patterns are often species‐specific and related to life‐history traits, additional comparative studies incorporating genomic data are necessary for separating shared historical processes from idiosyncratic responses to environmental, climatic and geological influences on diversification.
Arbuscular mycorrhizal fungi alter the content and composition of secondary metabolites in Bituminaria bituminosa L.
Authors: Pistelli L. , Ulivieri V. , Giovanelli S. , Avio L. , Giovannetti M. , Pistelli L. 
Published: July 2017

Abstract

Secondary metabolites may be affected by arbuscular mycorrhizal fungi (AMF), which are beneficial symbionts associated with the roots of most plant species. Bituminaria bituminosa (L.) C.H.Stirt is known as a source of several phytochemicals and therefore used in folk medicine as a vulnerary, cicatrising, disinfectant agent. Characteristic metabolites found in B. bituminosa are furanocoumarins and pterocarpans, which are used in cosmetics and as chemotherapeutic agents. Here we address the question whether AMF inoculation might affect positively the synthesis of these phytochemicals.

B. bituminosa plants were inoculated with different AMF and several metabolites were assessed during full vegetative stage and flowering phase. Pigments (chlorophylls and carotenoids), polyphenols and flavonoids were spectrophotometrically determined; specific isoflavones (genistein), furanocoumarins (psoralene and angelicin), pterocarpans (bitucarpin A and erybraedin C) and plicatin B were assessed with HPLC; leaf volatile organic compounds were analysed using SPME and identified by GC‐MS.

During the vegetative stage, the inoculated plants had a high amount of furanocoumarins (angelicin and psoralen) and pterocarpans (erybraedin C and bitucarpin A). The analysis of volatile organic compounds of inoculated plants showed different chemical composition compared with non‐mycorrhizal plants.

Given the important potential role played by furanocoumarins and pterocarpans in the pharmaceutical industry, AMF inoculation of B. bituminosa plants may represent a suitable biotechnological tool to obtain higher amounts of such metabolites for pharmaceutical and medicinal purposes.
Small airway dysfunction in chronic hypersensitivity pneumonitis
Authors: Guerrero Zúñiga Selene , Sánchez Hernández Julia , Mateos Toledo Heidegger , Mejía Ávila Mayra , Gochicoa‐Rangel Laura , Miguel Reyes José Luis , Selman Moisés , Torre‐Bouscoulet Luis 
Published: July 2017

ABSTRACTBackground and objectiveLung biopsies from patients with hypersensitivity pneumonitis (HP) have demonstrated small airway (SA) involvement, but there is no information concerning SA function in HP, and it is unknown whether pharmacological treatment could modify its function. SA function in patients with chronic HP using ultrasonic pneumography (UPG) and impulse oscillometry (IOS) was explored. We also compared initial results with those obtained after 4 weeks of standardized treatment with azathioprine and prednisone.MethodsThe study group consisted of adults with recent diagnoses of HP. All patients completed UPG, IOS, spirometry, body plethysmography, single‐breath carbon monoxide diffusing capacity (DLCO) and the 6‐min walk test (6MWT). The fraction of exhaled nitric oxide (FENO) was obtained to assess eosinophilic airway inflammation. Measurements were taken at diagnosis and after 4 weeks of treatment.ResultsA total of 20 consecutive patients (16 women) with chronic HP participated in the study. Median age was 50 years (interquartile range (IQR): 42–54). At diagnosis, the UPG phase 3 slope was abnormally high, consistent with maldistribution of ventilation. For IOS, all patients had low reactance at 5 Hz (X5) and elevated reactance area (AX) reflecting low compliance, and only eight (40%) patients had elevated R5 (resistance at 5 Hz (total)) and R5–20 (resistance at 5 Hz–resistance at 20 Hz (peripheral)) attributed to SA resistance. In contrast, FENO parameters were within normal limits. After treatment, forced vital capacity (FVC), the 6‐min walk distance and the distribution of ventilation showed significant improvement, although DLCO did not.ConclusionPatients with chronic HP have SA abnormalities that are partially revealed by the UPG and IOS tests. Lung volumes, but not gas exchange, improved after treatment with azathioprine and prednisone.
The association of non‐alcoholic fatty liver disease with lung function: A survey design analysis using propensity score
Authors: Kwak Min‐Sun , Kim Eunyoung , Jang Eun Jin , Lee Chang‐Hoon 
Published: July 2017

ABSTRACTBackground and objectiveAlthough both non‐alcoholic fatty liver disease (NAFLD) and lung function are known to be associated with metabolic syndromes, few studies have evaluated the relationship between NAFLD and lung function. Our population‐based study was conducted to investigate whether NAFLD, diagnosed by elevation of liver enzymes without other chronic liver disease or heavy alcohol drinking, is associated with lung function.MethodsA survey design analysis was performed using national representative data of health and nutritional status of civilians in Korea (Korean National Health and Nutrition Examination Survey, KNHANES) between 2010 and 2012. The criteria for NAFLD diagnosis was elevated serum alanine aminotransferase (ALT) without other chronic liver disease or heavy alcohol drinking. Covariate‐adjusted linear regression analyses and post‐stratification adjustments to the survey weights based on the propensity scores (PS) were conducted to evaluate the association of NAFLD and lung function, including the forced expiratory volume in 1 s (FEV1) and forced vital capacity (FVC).ResultsA total of 7417 subjects were included in this analysis. NAFLD was significantly associated with a lower FVC among males as determined by both the covariate‐adjusted linear regression analysis (P < 0.01 in all multivariable models) and PS analysis (P = 0.007). In the PS analysis, NAFLD was significantly associated with lower FEV1 (P = 0.044) among males. Among females, NAFLD was associated with a lower FVC according to the linear regression analysis; this finding was not verified with the PS analysis.ConclusionNAFLD was significantly associated with lower lung function and this relationship was more prominent among males.
Investigation of Respiratory Syncytial Virus Outbreak on an Adult Stem Cell Transplant Unit by Use of Whole-Genome Sequencing
Authors: Zhu Yijun , Zembower Teresa R. , Metzger Kristen E. , Lei Zhengdeng , Green Stefan J. , Qi Chao 
Published: July 2017

ABSTRACT
A viral whole-genome sequencing (WGS) strategy, based on PCR amplification followed by next-generation sequencing, was used to investigate a nosocomial respiratory syncytial virus-B (RSV-B) outbreak in a hematology-oncology and stem cell transplant unit. RSV-B genomes from 16 patients and health care workers (HCWs) suspected to be involved in the outbreak were compared to RSV-B genomes that were acquired from outpatients during the same time period but epidemiologically unrelated to the outbreak. Phylogenetic analysis of the whole genome identified a cluster of 11 patients and HCWs who had an identical RSV-B strain which was clearly distinct from strains recovered from individuals unrelated to the outbreak. Sequence variation of the glycoprotein (G) gene alone was insufficient to distinguish the outbreak strains from the outbreak-unrelated strains, thereby demonstrating that WGS is valuable for local outbreak investigation.
Rapid Detection of Bacillus anthracis Bloodstream Infections by Use of a Novel Assay in the GeneXpert System
Authors: Banada Padmapriya P. , Deshpande Srinidhi , Russo Riccardo , Singleton Eric , Shah Darshini , Patel Bhavana , Burday Michele , Koshy Ranie , Wang Qing , Jones Martin , Gall Alexander , Lokhov Sergey , Kwiatkowski Robert , Persing David , Connell Nancy , Alland David 
Published: July 2017

ABSTRACT

Bacillus anthracis
is a tier 1 select agent with the potential to quickly cause severe disease. Rapid identification of this pathogen may accelerate treatment and reduce mortality in the event of a bioterrorism attack. We developed a rapid and sensitive assay to detect
B. anthracis
bacteremia using a system that is suitable for point-of-care testing. A filter-based cartridge that included both sample processing and PCR amplification functions was loaded with all reagents needed for sample processing and multiplex nested PCR. The assay limit of detection (LOD) and dynamic range were determined by spiking
B. anthracis
DNA into individual PCR mixtures and
B. anthracis
CFU into human blood. One-milliliter blood samples were added to the filter-based detection cartridge and tested for
B. anthracis
on a GeneXpert instrument. Assay specificity was determined by testing blood spiked with non-anthrax bacterial isolates or by testing blood samples drawn from patients with concurrent non-
B. anthracis
bacteremia or nonbacteremic controls. The assay LODs were 5 genome equivalents per reaction and 10 CFU/ml blood for both the
B. anthracis
Sterne and V1B strains. There was a 6-log
10
dynamic range. Assay specificity was 100% for tests of non-
B. anthracis
bacterial isolates and patient blood samples. Assay time was less than 90 min. This automated system suitable for point-of-care detection rapidly identifies
B. anthracis
directly from blood with high sensitivity. This assay might lead to early detection and more rapid therapy in the event of a bioterrorism attack.
Genetic Stability of Parainfluenza Virus 5-Vectored Human Respiratory Syncytial Virus Vaccine Candidates after
In Vitro
and
In Vivo
Passage
Authors: Phan Shannon I. , Adam Carolyn M. , Chen Zhenhai , Citron Michael , Liang Xiaoping , Espeseth Amy S. , Wang Dai , He Biao 
Published: July 2017

ABSTRACT

Human respiratory syncytial virus (RSV) is the leading etiologic agent of lower respiratory tract infections in children, but no licensed vaccine exists. Previously, we developed two parainfluenza virus 5 (PIV5)-based RSV vaccine candidates that protect mice against RSV challenge. PIV5 was engineered to express either the RSV fusion protein (F) or the RSV major attachment glycoprotein (G) between the hemagglutinin-neuraminidase (HN) and RNA-dependent RNA polymerase (L) genes of the PIV5 genome [PIV5-RSV-F (HN-L) and PIV5-RSV-G (HN-L), respectively]. To investigate the stability of the vaccine candidates
in vitro
, they were passaged in Vero cells at high and low multiplicities of infection (MOIs) for 11 generations and the genome sequences, growth kinetics, and protein expression of the resulting viruses were compared with those of the parent viruses. Sporadic mutations were detected in the consensus sequences of the viruses after high-MOI passages, and mutation rates increased under low-MOI-passage conditions. None of the mutations abolished antigen expression. Increased numbers of mutations correlated with increased growth rates
in vitro
, indicating that the viruses evolved through the course of serial passages. We also examined the
in vivo
stability of the vaccine candidates after a single passage in African green monkeys. No mutations were detected in the consensus sequences of viruses collected from the bronchoalveolar lavage (BAL) fluid of the animals.
In vivo
, mutations in RSV G and PIV5 L were found in individual isolates of PIV5-RSV-G (HN-L), but plaque isolates of PIV5-RSV-F (HN-L) had no mutations. To improve upon the PIV5-RSV-F (HN-L) candidate, additional vaccine candidates were generated in which the gene for RSV F was inserted into earlier positions in the PIV5 genome. These insertions did not negatively impact the sequence stability of the vaccine candidates. The results suggest that the RSV F and G gene insertions are stable in the PIV5 genome. However, the function of the foreign gene insertion may need to be considered when designing PIV5-based vaccines.

IMPORTANCE
The genetic stability of live viral vaccines is important for safety and efficacy. PIV5 is a promising live viral vector and has been used to develop vaccines. In this work, we examined the genetic stability of a PIV5-based RSV vaccine
in vitro
and
in vivo
. We found that insertions of foreign genes, such as the RSV F and G genes, were stably maintained in the PIV5 genome and there was no mutation that abolished the expression of RSV F or G. Interestingly, the function of the inserted gene may have an impact on PIV5 genome stability.
A Domain of Herpes Simplex Virus pU
L
33 Required To Release Monomeric Viral Genomes from Cleaved Concatemeric DNA
Authors: Yang Kui , Dang Xiaoqun , Baines Joel D. 
Published: July 2017

ABSTRACT

Monomeric herpesvirus DNA is cleaved from concatemers and inserted into preformed capsids through the actions of the viral terminase. The terminase of herpes simplex virus (HSV) is composed of three subunits encoded by U
L
15, U
L
28, and U
L
33. The U
L
33-encoded protein (pU
L
33) interacts with pU
L
28, but its precise role in the DNA cleavage and packaging reaction is unclear. To investigate the function of pU
L
33, we generated a panel of recombinant viruses with either deletions or substitutions in the most conserved regions of U
L
33 using a bacterial artificial chromosome system. Deletion of 11 amino acids (residues 50 to 60 or residues 110 to 120) precluded viral replication, whereas the truncation of the last 10 amino acids from the pU
L
33 C terminus did not affect viral replication or the interaction of pU
L
33 with pU
L
28. Mutations that replaced the lysine at codon 110 and the arginine at codon 111 with alanine codons failed to replicate, and the pU
L
33 mutant interacted with pU
L
28 less efficiently. Interestingly, genomic termini of the large (L) and small (S) components were detected readily in cells infected with these mutants, indicating that concatemeric DNA was cleaved efficiently. However, the release of monomeric genomes as assessed by pulsed-field gel electrophoresis was greatly diminished, and DNA-containing capsids were not observed. These results suggest that pU
L
33 is necessary for one of the two viral DNA cleavage events required to release individual genomes from concatemeric viral DNA.

IMPORTANCE
This paper shows a role for pU
L
33 in one of the two DNA cleavage events required to release monomeric genomes from concatemeric viral DNA. This is the first time that such a phenotype has been observed and is the first identification of a function of this protein relevant to DNA packaging other than its interaction with other terminase components.
Roles of Cellular NSF Protein in Entry and Nuclear Egress of Budded Virions of Autographa californica Multiple Nucleopolyhedrovirus
Authors: Guo Ya , Yue Qi , Gao Jinli , Wang Zhe , Chen Yun-Ru , Blissard Gary W. , Liu Tong-Xian , Li Zhaofei 
Published: July 2017

ABSTRACT

In eukaryotic cells, the
s
oluble
N
-ethylmaleimide-
s
ensitive
f
actor (NSF)
a
ttachment protein
re
ceptor (SNARE) proteins comprise the minimal machinery that triggers fusion of transport vesicles with their target membranes. Comparative studies revealed that genes encoding the components of the SNARE system are highly conserved in yeast, insect, and human genomes. Upon infection of insect cells by the virus Autographa californica multiple nucleopolyhedrovirus (AcMNPV), the transcript levels of most SNARE genes initially were upregulated. We found that overexpression of dominant-negative (DN) forms of NSF or knockdown of the expression of NSF, the key regulator of the SNARE system, significantly affected infectious AcMNPV production. In cells expressing DN NSF, entering virions were trapped in the cytoplasm or transported to the nucleus with low efficiency. The presence of DN NSF also moderately reduced trafficking of the viral envelope glycoprotein GP64 to the plasma membrane but dramatically inhibited production of infectious budded virions (BV). Transmission electron microscopy analysis of infections in cells expressing DN NSF revealed that progeny nucleocapsids were retained in a perinuclear space surrounded by inner and outer nuclear membranes. Several baculovirus conserved (core) proteins (Ac76, Ac78, GP41, Ac93, and Ac103) that are important for infectious budded virion production were found to associate with NSF, and NSF was detected within the assembled BV. Together, these data indicate that the cellular SNARE system is involved in AcMNPV infection and that NSF is required for efficient entry and nuclear egress of budded virions of AcMNPV.

IMPORTANCE
Little is known regarding the complex interplay between cellular factors and baculoviruses during viral entry and egress. Here, we examined the cellular SNARE system, which mediates the fusion of vesicles in healthy cells, and its relation to baculovirus infection. Using a DN approach and RNA interference knockdown, we demonstrated that a general disruption of the SNARE machinery significantly inhibited the production of infectious BV of AcMNPV. The presence of a DN NSF protein resulted in low-efficiency entry of BV and the retention of progeny nucleocapsids in the perinuclear space during egress. Combined with these effects, we also found that several conserved (core) baculovirus proteins closely associate with NSF, and these results suggest their involvement in the egress of BV. Our findings are the first to demonstrate that the SNARE system is required for efficient entry of BV and nuclear egress of progeny nucleocapsids of baculoviruses.
Targeted Genome Sequencing Reveals Varicella-Zoster Virus Open Reading Frame 12 Deletion
Authors: Cohrs Randall J. , Lee Katherine S. , Beach Addilynn , Sanford Bridget , Baird Nicholas L. , Como Christina , Graybill Chiharu , Jones Dallas , Tekeste Eden , Ballard Mitchell , Chen Xiaomi , Yalacki David , Frietze Seth , Jones Kenneth , Lenac Rovis Tihana , Jonjić Stipan , Haas Jürgen , Gilden Don 
Published: July 2017

ABSTRACTThe neurotropic herpesvirus varicella-zoster virus (VZV) establishes a lifelong latent infection in humans following primary infection. The low abundance of VZV nucleic acids in human neurons has hindered an understanding of the mechanisms that regulate viral gene transcription during latency. To overcome this critical barrier, we optimized a targeted capture protocol to enrich VZV DNA and cDNA prior to whole-genome/transcriptome sequence analysis. Since the VZV genome is remarkably stable, it was surprising to detect that VZV32, a VZV laboratory strain with no discernible growth defect in tissue culture, contained a 2,158-bp deletion in open reading frame (ORF) 12. Consequently, ORF 12 and 13 protein expression was abolished and Akt phosphorylation was inhibited. The discovery of the ORF 12 deletion, revealed through targeted genome sequencing analysis, points to the need to authenticate the VZV genome when the virus is propagated in tissue culture.IMPORTANCEViruses isolated from clinical samples often undergo genetic modifications when cultured in the laboratory. Historically, VZV is among the most genetically stable herpesviruses, a notion supported by more than 60 complete genome sequences from multiple isolates and following multiplein vitropassages. However, application of enrichment protocols to targeted genome sequencing revealed the unexpected deletion of a significant portion of VZV ORF 12 following propagation in cultured human fibroblast cells. While the enrichment protocol did not introduce bias in either the virus genome or transcriptome, the findings indicate the need for authentication of VZV by sequencing when the virus is propagated in tissue culture.