bluuebunny/crossref_metadata_2025 huggingface dataset:
Islands within islands: two montane palaeo‐endemic birds impacted by recent anthropogenic fragmentation
Authors: Robin V. V. , Gupta Pooja , Thatte Prachi , Ramakrishnan Uma
Published: July 2015

Anthropogenic habitat fragmentation of species that live in naturally patchy metapopulations such as mountaintops or sky islands experiences two levels of patchiness. Effects of such multilevel patchiness on species have rarely been examined. Metapopulation theory suggests that patchy habitats could have varied impacts on persistence, dependent on differential migration. It is not known whether montane endemic species, evolutionarily adapted to natural patchiness, are able to disperse between anthropogenic fragments at similar spatial scales as natural patches. We investigated historic and contemporary gene flow between natural and anthropogenic patches across the distribution range of a Western Ghats sky‐island‐endemic bird species complex. Data from 14 microsatellites for 218 individuals detected major genetic structuring by deep valleys, including one hitherto undescribed barrier. As expected, we found strong effects of historic genetic differentiation across natural patches, but not across anthropogenic fragments. Contrastingly, contemporary differentiation (DPS) was higher relative to historic differentiation (FST) in anthropogenic fragments, despite the species’ ability to historically traverse shallow valleys. Simulations of recent isolation resulted in high DPS/FST values, confirming recent isolation in Western Ghats anthropogenic fragments and also suggesting that this ratio can be used to identifying recent fragmentation in the context of historic connectedness. We suggest that in this landscape, in addition to natural patchiness affecting population connectivity, anthropogenic fragmentation additionally impacts connectivity, making anthropogenic fragments akin to islands within natural islands of montane habitat, a pattern that may be recovered in other sky‐island systems.
Association between left ventricular global longitudinal strain, health‐related quality of life and functional capacity in chronic kidney disease patients with preserved ejection fraction
Authors: Krishnasamy Rathika , Hawley Carmel M , Stanton Tony , Howden Erin J , Beetham Kassia S , Strand Haakan , Leano Rodel , Haluska Brian A , Coombes Jeff S , Isbel Nicole M
Published: July 2015

Aim

Patients with chronic kidney disease (CKD) have a significant burden of dyspnoea and fatigue in spite having normal left ventricular (LV) ejection fraction (EF). Global longitudinal strain (GLS) can detect subtle changes in LV function. This study aimed to evaluate the relationship between LV function, functional capacity and quality of life (QOL) in CKD patients with preserved EF.

Methods

A cross‐sectional study of patients with stage 3/4 CKD (n = 108). Clinical characteristics, biochemical data, functional capacity (6‐min walk test (6MWT), timed up and go (TUG) test) and QOL (short form‐12 (SF‐12v2™) ) were measured. Echocardiogram was used to assess GLS, EF and diastolic function (E/A, e' and E/e').

Results

The mean age was 58.1 ± 9.9 years, 55.6% were men, estimated glomerular filtration rate was 44.8 ± 10.6 mL/min/1.73 m2, GLS was −18.5 ± 3.6% and 19.4% had impaired GLS (>−16%). Patients with impaired GLS had a significantly shorter 6MWT and slower TUG test compared with patients with preserved GLS. Bivariate analysis showed GLS and E/e' correlated with distance walked in 6MWT (GLS (r = −0.24, P = 0.02); E/e'(r = −0.38, P = 0.002) ). Following adjustment for potential confounders, GLS remained independently associated with 6MWT (model R2 = 0.37, P < 0.001). Mean physical component summary scores (PCS) and mental component summary scores (MCS) were 43.0 ± 10.2 and 50.9 ± 9.5. There was no cardiac parameter that was independently associated with PCS. However women, lower systolic blood pressure and GLS was associated with lower MCS (model R2 = 0.30, P < 0.001).

Conclusion

GLS was associated with measures of functional capacity and QOL in CKD patients with preserved EF.
Novel Somatic Mutation in LEMD3 Splice Site Results in Buschke–Ollendorff Syndrome with Polyostotic Melorheostosis and Osteopoikilosis
Authors: Gutierrez Daniel , Cooper Kevin D. , Mitchell Anna L. , Cohn Heather I.
Published: July 2015

Buschke–Ollendorff syndrome is a rare autosomal dominant disorder caused by loss of function in LEMD3, resulting in connective tissue nevi and varying bone dysplasia. Although typically benign, we describe a novel LEMD3 splice site mutation (IVS12 + 1delG) in a 13‐year‐old boy with Buschke–Ollendorff syndrome presenting with severe skeletal deformities, polyostotic melorheostosis, and osteopoikilosis.
Physiological change and nutritional requirement of Pacific white shrimpLitopenaeus vannameiat low salinity
Authors: Li Erchao , Wang Xiaodan , Chen Ke , Xu Chang , Qin Jian G. , Chen Liqiao
Published: July 2015

The Pacific white shrimpLitopenaeus vannameiis a euryhaline species with optimal salinity of 20–25 practical salinity unit (psu) for growth and survival, but has been cultured in inland water with salinity <5 psu worldwide. In the past decade, much research progress has been made on the physiological and nutritional requirements of white shrimp at low salinity. This study reviews the recent findings in the aspects of growth, survival, energy metabolism, stress resistance and immunity of white shrimp at low salinity and synthesizes recent research outcomes in nutritional requirements in an attempt to improve the shrimp performance in aquaculture at low salinity. The white shrimp at low salinity usually show slow growth, low immunity, high susceptibility to pathogens and high energy demand. The diet containing 30–36% protein, 15–20% carbohydrate and supplementations of potassium, sodium, vitamin E and C, free amino acids (glycine, alanine, proline and taurine), antioxidants and probiotics can improve shrimp growth and immunity at low salinity. The white shrimp has demonstrated the ability to synthesizeDHAandEPAfromLNAat low ambient salinity, but further studies are needed to further confirm this finding. Future research should focus on the understanding of physiological mechanism and adaptation associated with salinity change and nutritional manipulation. The specific dietary requirements of essential fatty acids, essential amino acids, vitamins and minerals and the nutrition‐mediated immune response also warrant further study on shrimp at low salinity.
Minimal Modification to the Trerotola Backbleeding Technique Increases Its Effectiveness
Authors: Sequeira Adrian , Artikov Shukhrat
Published: July 2015

Thrombectomy of a clotted upper arm access may be complicated by brachial artery embolization. A number of techniques have been described to relieve the embolization that may not always be successful. Backbleeding is one such technique. We describe a minimal modification that makes backbleeding more effective.
Evaluation of the Impact of Codon Optimization and N-Linked Glycosylation on Functional Immunogenicity of Pfs25 DNA Vaccines Delivered by
In Vivo
Electroporation in Preclinical Studies in Mice
Authors: Datta Dibyadyuti , Bansal Geetha P. , Kumar Rajesh , Ellefsen Barry , Hannaman Drew , Kumar Nirbhay
Published: July 2015

Plasmodium falciparum
sexual stage surface antigen Pfs25 is a well-established candidate for malaria transmission-blocking vaccine development. Immunization with DNA vaccines encoding Pfs25 has been shown to elicit potent antibody responses in mice and nonhuman primates. Studies aimed at further optimization have revealed improved immunogenicity through the application of
in vivo
electroporation and by using a heterologous prime-boost approach. The goal of the studies reported here was to systematically evaluate the impact of codon optimization,
in vivo
electroporation, and N-linked glycosylation on the immunogenicity of Pfs25 encoded by DNA vaccines. The results from this study demonstrate that while codon optimization and
in vivo
electroporation greatly improved functional immunogenicity of Pfs25 DNA vaccines, the presence or absence of N-linked glycosylation did not significantly impact vaccine efficacy. These findings suggest that N-glycosylation of Pfs25 encoded by DNA vaccines is not detrimental to overall transmission-blocking efficacy.
Coinfection with “Rickettsia sibirica subsp. mongolotimonae” and Rickettsia conorii in a Human Patient: a Challenge for Molecular Diagnosis Tools
Authors: Nogueras María Mercedes , Roson Beatriz , Lario Sergio , Sanfeliu Isabel , Pons Immaculada , Anton Esperança , Casanovas Aurora , Segura Ferran
Published: July 2015

Rickettsioses are zoonoses transmitted by vectors. More than one agent can coexist in vectors. Although vectors may transmit more than one microorganism to humans, information on dual infections is scarce. We present a case of a patient with an atypical rickettsiosis diagnosis in whom two species of
Rickettsia
were detected.
Development and Validation of Two Screening Assays for the Hepatitis C Virus NS3 Q80K Polymorphism Associated with Reduced Response to Combination Treatment Regimens Containing Simeprevir
Authors: Chui C. K. S. , Dong W. W. Y. , Joy J. B. , Poon A. F. Y. , Dong W. Y. , Mo T. , Woods C. K. , Beatty C. , Hew H. , Harrigan P. R. , Brumme C. J.
Published: July 2015

Persons with hepatitis C virus (HCV) genotype 1a (GT1a) infections harboring a baseline Q80K polymorphism in nonstructural protein 3 (NS3) have a reduced virologic response to simeprevir in combination with pegylated interferon-alfa and ribavirin. We aimed to develop, validate, and freely disseminate an NS3 clinical sequencing assay to detect the Q80K polymorphism and potentially other HCV NS3 drug resistance mutations. HCV RNA was extracted from frozen plasma using a NucliSENS easyMAG automated nucleic acid extractor, amplified by nested reverse transcription-PCR, and sequenced using Sanger and/or next-generation (MiSeq) methods. Sanger chromatograms were analyzed using in-house software (RECall), and nucleotide mixtures were called automatically. MiSeq reads were iteratively mapped to the H77 reference genome, and consensus NS3 sequences were generated with nucleotides present at >20% called as mixtures. The accuracy, precision, and sensitivity for detecting the Q80K polymorphism were assessed in 70 samples previously sequenced by an external laboratory. A comparison of the sequences generated by the Sanger and MiSeq methods with those determined by an external lab revealed >98.5% nucleotide sequence concordance and zero discordant calls of the Q80K polymorphism. The results were both highly repeatable and reproducible (>99.7% nucleotide concordance and 100% Q80K concordance). The limits of detection (>2 and ∼5 log
10
IU/ml for the Sanger and MiSeq assays, respectively) are sufficiently low to allow genotyping in nearly all chronically infected treatment-naive persons. No systematic bias in the under- or overamplification of minority variants was observed. Coinfection with other viruses (e.g., HIV and hepatitis B virus [HBV]) did not affect the assay results. The two independent HCV NS3 sequencing assays with the automated analysis procedures described here are useful tools to screen for the Q80K polymorphism and other HCV protease inhibitor drug resistance mutations.
Antimicrobial Treatment Options for Granulomatous Mastitis Caused by Corynebacterium Species
Authors: Dobinson Hazel C. , Anderson Trevor P. , Chambers Stephen T. , Doogue Matthew P. , Seaward Lois , Werno Anja M.
Published: July 2015

Corynebacterium
species are increasingly recognized as important pathogens in granulomatous mastitis. Currently, there are no published treatment protocols for
Corynebacterium
breast infections. This study describes antimicrobial treatment options in the context of other management strategies used for granulomatous mastitis.
Corynebacterium
spp. isolated from breast tissue and aspirate samples stored from 2002 to 2013 were identified and determined to the species level using matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS), 16S RNA sequencing, and
rpoB
gene targets. The MICs for 12 antimicrobials were performed using Etest for each isolate. Correlations of these with antimicrobial characteristics, choice of antimicrobial, and disease outcome were evaluated.
Corynebacterium
spp. from breast tissue and aspirate samples were confirmed in 17 isolates from 16 patients. Based on EUCAST breakpoints,
Corynebacterium kroppenstedtii
isolates (
n
= 11) were susceptible to seven antibiotic classes but resistant to β-lactam antibiotics.
Corynebacterium tuberculostearicum
isolates (
n
= 4) were multidrug resistant. Two nonlipophilic species were isolated,
Corynebacterium glucuronolyticum
and
Corynebacterium freneyi
, both of which have various susceptibilities to antimicrobial agents. Short-course antimicrobial therapy was common (median, 6 courses per subject; range, 1 to 9 courses). Patients with
C. kroppenstedtii
presented with a hot painful breast mass and underwent multiple surgical procedures (median, 4 procedures; range, 2 to 6 procedures). The management of
Corynebacterium
breast infections requires a multidisciplinary approach and includes culture and appropriate sensitivity testing to guide antimicrobial therapy. Established infections have a poor outcome, possibly because adequate concentrations of some drugs will be difficult to achieve in lipophilic granulomata. Lipophilic antimicrobial therapy may offer a therapeutic advantage. The role of immunotherapy has not been defined.
Comparison between Salmonella enterica Serotype Enteritidis Genotyping Methods and Phage Type
Authors: De Cesare Alessandra , Krishnamani Keshav , Parisi Antonio , Ricci Antonia , Luzzi Ida , Barco Lisa , Lucchi Alex , Miccolupo Angela , Manfreda Gerardo
Published: July 2015

A quantitative comparison between discriminatory indexes and concordance among multilocus variable-number tandem-repeat analysis (MLVA), pulsed-field gel electrophoresis (PFGE), automated ribotyping, and phage typing has been performed, testing 238
Salmonella enterica
serotype Enteritidis isolates not epidemiologically correlated. The results show that MLVA is the best choice, but each typing method provides a piece of information for establishing clonal relationships between the isolates.
Emergence of Serotype IV Group B Streptococcus Adult Invasive Disease in Manitoba and Saskatchewan, Canada, Is Driven by Clonal Sequence Type 459 Strains
Authors: Teatero Sarah , Athey Taryn B. T. , Van Caeseele Paul , Horsman Greg , Alexander David C. , Melano Roberto G. , Li Aimin , Flores Anthony R. , Shelburne Samuel A. , McGeer Allison , Demczuk Walter , Martin Irene , Fittipaldi Nahuel
Published: July 2015

Serotype IV group B
Streptococcus
(GBS) is emerging in Canada and the United States with rates as high as 5% of the total burden of adult invasive GBS disease. To understand this emergence, we studied the population structure and assessed the antimicrobial susceptibility of serotype IV isolates causing adult invasive infection in Manitoba and Saskatchewan, Canada, between 2010 and 2014. Whole-genome sequencing was used to determine multilocus sequence typing information and identify genes encoding antimicrobial resistance in 85 invasive serotype IV GBS strains. Antimicrobial susceptibility testing was performed by standard methods. Strain divergence was assessed using genome-wide single-nucleotide polymorphism analysis. Serotype IV strains were responsible for 16.9% of adult invasive GBS infections in Manitoba and Saskatchewan during the period. The majority of serotype IV isolates (89%) were clonally related, tetracycline-, erythromycin-, and clindamycin-resistant sequence type 459 (ST459) strains that possessed genes
tetM
and
ermTR
. Genome comparisons between ST459 and serotype V ST1 GBS identified several areas of recombination in an overall similar genomic background. Serotype IV ST459 GBS strains are expanding and causing a substantial percentage of adult invasive GBS disease. This emergence may be linked to the acquisition of resistance to tetracycline, macrolides, and lincosamides.
Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Whole-Genome Sequence-Based Typing of Listeria monocytogenes
Authors: Ruppitsch Werner , Pietzka Ariane , Prior Karola , Bletz Stefan , Fernandez Haizpea Lasa , Allerberger Franz , Harmsen Dag , Mellmann Alexander
Published: July 2015

Whole-genome sequencing (WGS) has emerged today as an ultimate typing tool to characterize
Listeria monocytogenes
outbreaks. However, data analysis and interlaboratory comparability of WGS data are still challenging for most public health laboratories. Therefore, we have developed and evaluated a new
L. monocytogenes
typing scheme based on genome-wide gene-by-gene comparisons (core genome multilocus the sequence typing [cgMLST]) to allow for a unique typing nomenclature. Initially, we determined the breadth of the
L. monocytogenes
population based on MLST data with a Bayesian approach. Based on the genome sequence data of representative isolates for the whole population, cgMLST target genes were defined and reappraised with 67
L. monocytogenes
isolates from two outbreaks and serotype reference strains. The Bayesian population analysis generated five
L. monocytogenes
groups. Using all available NCBI RefSeq genomes (
n
= 36) and six additionally sequenced strains, all genetic groups were covered. Pairwise comparisons of these 42 genome sequences resulted in 1,701 cgMLST targets present in all 42 genomes with 100% overlap and ≥90% sequence similarity. Overall, ≥99.1% of the cgMLST targets were present in 67 outbreak and serotype reference strains, underlining the representativeness of the cgMLST scheme. Moreover, cgMLST enabled clustering of outbreak isolates with ≤10 alleles difference and unambiguous separation from unrelated outgroup isolates. In conclusion, the novel cgMLST scheme not only improves outbreak investigations but also enables, due to the availability of the automatically curated cgMLST nomenclature, interlaboratory exchange of data that are crucial, especially for rapid responses during transsectorial outbreaks.
Molecular Epidemiology of Novel Pathogen “Brachyspira hampsonii” Reveals Relationships between Diverse Genetic Groups, Regions, Host Species, and Other Pathogenic and Commensal Brachyspira Species
Authors: Mirajkar Nandita S. , Bekele Aschalew Z. , Chander Yogesh Y. , Gebhart Connie J.
Published: July 2015

Outbreaks of bloody diarrhea in swine herds in the late 2000s signaled the reemergence of an economically significant disease, swine dysentery, in the United States. Investigations confirmed the emergence of a novel spirochete in swine, provisionally designated “
Brachyspira hampsonii
,” with two genetically distinct clades. Although it has since been detected in swine and migratory birds in Europe and North America, little is known about its genetic diversity or its relationships with other
Brachyspira
species. This study characterizes
B. hampsonii
using a newly developed multilocus sequence typing (MLST) approach and elucidates the diversity, distribution, population structure, and genetic relationships of this pathogen from diverse epidemiological sources globally. Genetic characterization of 81
B. hampsonii
isolates, originating from six countries, with our newly established MLST scheme identified a total of 20 sequence types (STs) belonging to three clonal complexes (CCs).
B. hampsonii
showed a heterogeneous population structure with evidence of microevolution locally in swine production systems, while its clustering patterns showed associations with its epidemiological origins (country, swine production system, and host species). The close genetic relatedness of
B. hampsonii
isolates from different countries and host species highlights the importance of strict biosecurity control measures. A comparative analysis of 430 isolates representing seven
Brachyspira
species (pathogens and commensals) from 19 countries and 10 host species depicted clustering by microbial species. It revealed the close genetic relatedness of
B. hampsonii
with commensal
Brachyspira
species and also provided support for the two clades of
B. hampsonii
to be considered a single species.
An Aptamer against the Matrix Binding Domain on the Hepatitis B Virus Capsid Impairs Virion Formation
Authors: Orabi Ahmed , Bieringer Maria , Geerlof Arie , Bruss Volker
Published: July 2015

The hepatitis B virus (HBV) particle is an icosahedral nucleocapsid surrounded by a lipid envelope containing viral surface proteins. A small domain (matrix domain [MD]) in the large surface protein L and a narrow region (matrix binding domain [MBD]) including isoleucine 126 on the capsid surface have been mapped, in which point mutations such as core I126A specifically blocked nucleocapsid envelopment. It is possible that the two domains interact with each other during virion morphogenesis. By the systematic evolution of ligands by exponential enrichment (SELEX) method, we evolved DNA aptamers from an oligonucleotide library binding to purified recombinant capsids but not binding to the corresponding I126A mutant capsids. Aptamers bound to capsids were separated from unbound molecules by filtration. After 13 rounds of selections and amplifications, 16 different aptamers were found among 73 clones. The four most frequent aptamers represented more than 50% of the clones. The main aptamer, AO-01 (13 clones, 18%), showed the lowest dissociation constant (

K
d

) of 180 ± 82 nM for capsid binding among the four molecules. Its

K
d

for I126A capsids was 1,306 ± 503 nM. Cotransfection of Huh7 cells with AO-01 and an HBV genomic construct resulted in 47% inhibition of virion production at 3 days posttransfection, but there was no inhibition by cotransfection of an aptamer with a random sequence. The half-life of AO-01 in cells was 2 h, which might explain the incomplete inhibition. The results support the importance of the MBD for nucleocapsid envelopment. Inhibiting the MD-MBD interaction with a low-molecular-weight substance might represent a new approach for an antiviral therapy.

IMPORTANCE
Approximately 240 million people are persistently infected with HBV. To date, antiviral therapies depend on a single target, the viral reverse transcriptase. Future additional targets could be viral protein-protein interactions. We selected a 55-base-long single-stranded DNA molecule (aptamer) which binds with relatively high affinity to a region on the HBV capsid interacting with viral envelope proteins during budding. This aptamer inhibits virion formation in cell culture. The results substantiate the current model for HBV morphogenesis and show that the capsid envelope interaction is a potential antiviral target.
Host Cell Plasma Membrane Phosphatidylserine Regulates the Assembly and Budding of Ebola Virus
Authors: Adu-Gyamfi Emmanuel , Johnson Kristen A. , Fraser Mark E. , Scott Jordan L. , Soni Smita P. , Jones Keaton R. , Digman Michelle A. , Gratton Enrico , Tessier Charles R. , Stahelin Robert V.
Published: July 2015

Lipid-enveloped viruses replicate and bud from the host cell where they acquire their lipid coat. Ebola virus, which buds from the plasma membrane of the host cell, causes viral hemorrhagic fever and has a high fatality rate. To date, little has been known about how budding and egress of Ebola virus are mediated at the plasma membrane. We have found that the lipid phosphatidylserine (PS) regulates the assembly of Ebola virus matrix protein VP40. VP40 binds PS-containing membranes with nanomolar affinity, and binding of PS regulates VP40 localization and oligomerization on the plasma membrane inner leaflet. Further, alteration of PS levels in mammalian cells inhibits assembly and egress of VP40. Notably, interactions of VP40 with the plasma membrane induced exposure of PS on the outer leaflet of the plasma membrane at sites of egress, whereas PS is typically found only on the inner leaflet. Taking the data together, we present a model accounting for the role of plasma membrane PS in assembly of Ebola virus-like particles.

IMPORTANCE
The lipid-enveloped Ebola virus causes severe infection with a high mortality rate and currently lacks FDA-approved therapeutics or vaccines. Ebola virus harbors just seven genes in its genome, and there is a critical requirement for acquisition of its lipid envelope from the plasma membrane of the human cell that it infects during the replication process. There is, however, a dearth of information available on the required contents of this envelope for egress and subsequent attachment and entry. Here we demonstrate that plasma membrane phosphatidylserine is critical for Ebola virus budding from the host cell plasma membrane. This report, to our knowledge, is the first to highlight the role of lipids in human cell membranes in the Ebola virus replication cycle and draws a clear link between selective binding and transport of a lipid across the membrane of the human cell and use of that lipid for subsequent viral entry.
Longitudinal Detection of Prion Shedding in Saliva and Urine by Chronic Wasting Disease-Infected Deer by Real-Time Quaking-Induced Conversion
Authors: Henderson Davin M. , Denkers Nathaniel D. , Hoover Clare E. , Garbino Nina , Mathiason Candace K. , Hoover Edward A.
Published: July 2015

Chronic wasting disease (CWD) is an emergent, rapidly spreading prion disease of cervids. Shedding of infectious prions in saliva and urine is thought to be an important factor in CWD transmission. To help to elucidate this issue, we applied an
in vitro
amplification assay to determine the onset, duration, and magnitude of prion shedding in longitudinally collected saliva and urine samples from CWD-exposed white-tailed deer. We detected prion shedding as early as 3 months after CWD exposure and sustained shedding throughout the disease course. We estimated that the 50% lethal dose (LD
50
) for cervidized transgenic mice would be contained in 1 ml of infected deer saliva or 10 ml of urine. Given the average course of infection and daily production of these body fluids, an infected deer would shed thousands of prion infectious doses over the course of CWD infection. The direct and indirect environmental impacts of this magnitude of prion shedding on cervid and noncervid species are surely significant.

IMPORTANCE
Chronic wasting disease (CWD) is an emerging and uniformly fatal prion disease affecting free-ranging deer and elk and is now recognized in 22 U.S. states and 2 Canadian provinces. It is unique among prion diseases in that it is transmitted naturally through wild populations. A major hypothesis to explain CWD's florid spread is that prions are shed in excreta and transmitted via direct or indirect environmental contact. Here we use a rapid
in vitro
assay to show that infectious doses of CWD prions are in fact shed throughout the multiyear disease course in deer. This finding is an important advance in assessing the risks posed by shed CWD prions to animals as well as humans.
The Intracellular Domain of the Coxsackievirus and Adenovirus Receptor Differentially Influences Adenovirus Entry
Authors: Loustalot Fabien , Kremer Eric J. , Salinas Sara
Published: July 2015

The coxsackievirus and adenovirus receptor (CAR) is a cell adhesion molecule used as a docking molecule by some adenoviruses (AdVs) and group B coxsackieviruses. We previously proposed that the preferential transduction of neurons by canine adenovirus type 2 (CAV-2) is due to CAR-mediated internalization. Our proposed pathway of CAV-2 entry is in contrast to that of human AdV type 5 (HAdV-C5) in nonneuronal cells, where internalization is mediated by auxiliary receptors such as integrins. We therefore asked if in fibroblast-like cells the intracellular domain (ICD) of CAR plays a role in the internalization of the CAV-2 fiber knob (FK
CAV
), CAV-2, or HAdV-C5 when the capsid cannot engage integrins. Here, we show that in fibroblast-like cells, the CAR ICD is needed for FK
CAV
entry and efficient CAV-2 transduction but dispensable for HAdV-C5 and an HAdV-C5 capsid lacking the RGD sequence (an integrin-interacting motif) in the penton. Moreover, the deletion of the CAR ICD further impacts CAV-2 intracellular trafficking, highlighting the crucial role of CAR in CAV-2 intracellular dynamics. These data demonstrate that the CAR ICD contains sequences important for the recruitment of the endocytic machinery that differentially influences AdV cell entry.

IMPORTANCE
Understanding how viruses interact with the host cell surface and reach the intracellular space is of crucial importance for applied and fundamental virology. Here, we compare the role of a cell adhesion molecule (CAR) in the internalization of adenoviruses that naturally infect humans and Canidae. We show that the intracellular domain of CAR differentially regulates AdV entry and trafficking. Our study highlights the mechanistic differences that a receptor can have for two viruses from the same family.
Plasmid-Mediated Quinolone Resistance
Authors: Jacoby George A. , Strahilevitz Jacob , Hooper David C.
Published: July 2015

Three mechanisms for plasmid-mediated quinolone resistance (PMQR) have been discovered since 1998. Plasmid genesqnrA, qnrB, qnrC, qnrD, qnrS,andqnrVCcode for proteins of the pentapeptide repeat family that protects DNA gyrase and topoisomerase IV from quinolone inhibition. Theqnrgenes appear to have been acquired from chromosomal genes in aquatic bacteria, are usually associated with mobilizing or transposable elements on plasmids, and are often incorporated into sul1-type integrons. The second plasmid-mediated mechanism involves acetylation of quinolones with an appropriate amino nitrogen target by a variant of the common aminoglycoside acetyltransferase AAC(6′)-Ib. The third mechanism is enhanced efflux produced by plasmid genes for pumps QepAB and OqxAB. PMQR has been found in clinical and environmental isolates around the world and appears to be spreading. The plasmid-mediated mechanisms provide only low-level resistance that by itself does not exceed the clinical breakpoint for susceptibility but nonetheless facilitates selection of higher-level resistance and makes infection by pathogens containing PMQR harder to treat.
Conditional Activation of Toxin-Antitoxin Systems: Postsegregational Killing and Beyond
Authors: Hernández-Arriaga Ana María , Chan Wai Ting , Espinosa Manuel , Díaz-Orejas Ramón
Published: July 2015

Toxin-antitoxin (TA) systems are small genetic modules formed by a stable toxin and an unstable antitoxin that are widely present in plasmids and in chromosomes of Bacteria and Archaea. Toxins can interfere with cell growth or viability, targeting a variety of key processes. Antitoxin inhibits expression of the toxin, interacts with it, and neutralizes its effect. In a plasmid context, toxins are kept silent by the continuous synthesis of the unstable antitoxins; in plasmid-free cells (segregants), toxins can be activated owing to the faster decay of the antitoxin, and this results in the elimination of these cells from the population (
p
ost
s
egregational
k
illing [PSK]) and in an increase of plasmid-containing cells in a growing culture. Chromosomal TA systems can also be activated in particular circumstances, and the interference with cell growth and viability that ensues contributes in different ways to the physiology of the cell. In this article, we review the conditional activation of TAs in selected plasmidic and chromosomal TA pairs and the implications of this activation. On the whole, the analysis underscores TA interactions involved in PSK and points to the effective contribution of TA systems to the physiology of the cell.
DNA Assembly Tools and Strategies for the Generation of Plasmids
Authors: Baek Chang-Ho , Liss Michael , Clancy Kevin , Chesnut Jonathan , Katzen Federico
Published: July 2015

Since the discovery of restriction enzymes and the generation of the first recombinant DNA molecule over 40 years ago, molecular biology has evolved into a multidisciplinary field that has democratized the conversion of a digitized DNA sequence stored in a computer into its biological counterpart, usually as a plasmid, stored in a living cell. In this article, we summarize the most relevant tools that allow the swift assembly of DNA sequences into useful plasmids for biotechnological purposes. We cover the main components and stages in a typical DNA assembly workflow, namely
in silico
design,
de novo
gene synthesis, and
in vitro
and
in vivo
sequence assembly methodologies.
Plasmid-Mediated Antimicrobial Resistance in Staphylococci and Other
Firmicutes
Authors: Schwarz Stefan , Shen Jianzhong , Wendlandt Sarah , Feßler Andrea T. , Wang Yang , Kadlec Kristina , Wu Cong-Ming
Published: July 2015

In staphylococci and other
Firmicutes
, resistance to numerous classes of antimicrobial agents, which are commonly used in human and veterinary medicine, is mediated by genes that are associated with mobile genetic elements. The gene products of some of these antimicrobial resistance genes confer resistance to only specific members of a certain class of antimicrobial agents, whereas others confer resistance to the entire class or even to members of different classes of antimicrobial agents. The resistance mechanisms specified by the resistance genes fall into any of three major categories: active efflux, enzymatic inactivation, and modification/replacement/protection of the target sites of the antimicrobial agents. Among the mobile genetic elements that carry such resistance genes, plasmids play an important role as carriers of primarily plasmid-borne resistance genes, but also as vectors for nonconjugative and conjugative transposons that harbor resistance genes. Plasmids can be exchanged by horizontal gene transfer between members of the same species but also between bacteria belonging to different species and genera. Plasmids are highly flexible elements, and various mechanisms exist by which plasmids can recombine, form cointegrates, or become integrated in part or
in toto
into the chromosomal DNA or into other plasmids. As such, plasmids play a key role in the dissemination of antimicrobial resistance genes within the gene pool to which staphylococci and other
Firmicutes
have access. This chapter is intended to provide an overview of the current knowledge of plasmid-mediated antimicrobial resistance in staphylococci and other
Firmicutes
.
Resolution of Multimeric Forms of Circular Plasmids and Chromosomes
Authors: Crozat Estelle , Fournes Florian , Cornet François , Hallet Bernard , Rousseau Philippe
Published: July 2015

One of the disadvantages of circular plasmids and chromosomes is their high sensitivity to rearrangements caused by homologous recombination. Odd numbers of crossing-over occurring during or after replication of a circular replicon result in the formation of a dimeric molecule in which the two copies of the replicon are fused. If they are not converted back to monomers, the dimers of replicons may fail to correctly segregate at the time of cell division. Resolution of multimeric forms of circular plasmids and chromosomes is mediated by site-specific recombination, and the enzymes that catalyze this type of reaction fall into two families of proteins: the serine and tyrosine recombinase families. Here we give an overview of the variety of site-specific resolution systems found on circular plasmids and chromosomes.
Using Plasmids as DNA Vaccines for Infectious Diseases
Authors: Tregoning John S. , Kinnear Ekaterina
Published: July 2015

DNA plasmids can be used to induce a protective (or therapeutic) immune response by delivering genes encoding vaccine antigens. That naked DNA (without the refinement of coat proteins or host evasion systems) can cross from outside the cell into the nucleus and be expressed is particularly remarkable given the sophistication of the immune system in preventing infection by pathogens. As a result of the ease, low cost, and speed of custom gene synthesis, DNA vaccines dangle a tantalizing prospect of the next wave of vaccine technology, promising individual designer vaccines for cancer or mass vaccines with a rapid response time to emerging pandemics. There is considerable enthusiasm for the use of DNA vaccination as an approach, but this enthusiasm should be tempered by the successive failures in clinical trials to induce a potent immune response. The technology is evolving with the development of improved delivery systems that increase expression levels, particularly electroporation and the incorporation of genetically encoded adjuvants. This review will introduce some key concepts in the use of DNA plasmids as vaccines, including how the DNA enters the cell and is expressed, how it induces an immune response, and a summary of clinical trials with DNA vaccines. The review also explores the advances being made in vector design, delivery, formulation, and adjuvants to try to realize the promise of this technology for new vaccines. If the immunogenicity and expression barriers can be cracked, then DNA vaccines may offer a step change in mass vaccination.
Pontine abscess with initial treatment failure following infectious endocarditis withStreptococcus salivarius
Authors: Knudtzen Fredrikke Christie , Lynge Maja , Gaini Shahin
Published: July 2015

We present a case report of a 65-year-old man admitted to the department of infectious diseases on suspicion of meningitis with headache, fever and double vision. A cerebral MRI revealed a 17×30 mm pontine abscess with surrounding oedema. The patient had, 2 months prior to admission, been treated forStreptococcus salivariusaortic valve endocarditis. The abscess was not suitable for surgery, and the patient received multidrug antibiotic treatment for 4 weeks. The patient initially responded well clinically, but was readmitted 4 weeks after discontinuation of treatment, with headache and dizziness. A new cerebral MRI showed progression of the abscess. He received an additional 8 weeks of broad spectrum antibiotic treatment, followed by 12 weeks of oral treatment with pivampicillin. His symptoms resolved and a cerebral MRI at discontinuation of treatment showed regression of the abscess to 7.5 mm.
Crystals seen on CSF microscopy in a case of suspected subarachnoid haemorrhage
Authors: Weiand Daniel , Hanning Ian , Mouhamadou Moussa , Wearmouth Debbie
Published: July 2015

Although crystals are rarely identified on cerebrospinal fluid (CSF) microscopy, their presence can be of significant diagnostic value. We report a case of oxalate crystals seen on CSF microscopy of a 43-year-old woman. The patient presented with headaches, nausea and vomiting. CT of the head showed a small focus of hyper-density, suspicious of haemorrhage, in the right side of the pontine cistern. CSF cell count was within the normal range. Although no organisms were seen on microscopy, copious oxalate crystals were seen. The same crystals were seen on microscopy of CSF collected in a fluoride oxalate container used for glucose analysis. A follow-up contrast-enhanced CT angiogram did not demonstrate any abnormalities. It transpired that excess CSF had been collected into a fluoride oxalate container. This had subsequently been decanted into a plain container for microbiological analysis. Correct specimen collection should be emphasised when teaching lumbar puncture technique.
Status postpneumonectomy for pulmonary artery sarcoma
Authors: Siordia Juan A , Garlish Amanda , Truong Huong
Published: July 2015

Primary pulmonary artery sarcoma is a rare disease that has a poor survival prognosis due to misdiagnosis with pulmonary thromboembolism or metastatic embolisation, detailed image findings and complicated surgical procedures. Surgical procedures established for treatment include pneumonectomy and pulmonary endarterectomy. Survival after surgery still remains at 1 year survival of 50%. The following case report demonstrates a patient's status postpneumonectomy for pulmonary artery sarcoma that presented with no complications after 1.5-year follow-up.
Intercostal neuralgia as a symptom of an osteoblastoma in thoracic spine
Authors: Kobayashi Hiroshi , Shinoda Yusuke , Ohki Takahiro , Kawano Hirotaka
Published: July 2015

An osteoblastoma is a benign bone lesion most commonly affecting the spine; it is frequently found in the posterior elements of the vertebra. When an osteoblastoma originates in the spine, it usually causes dull and localised dorsal pain, but the period between symptom development and diagnosis can be long. MRI shows intense peritumoural oedema accompanying the osteoblastoma. We present a case of a 15-year-old boy with osteoblastoma at the level of the T8–9 left laminae causing intercostal neuralgia without direct invasion to the intercostal nerve. Immediately after surgery, intercostal neuralgia was diminished. To our knowledge, this is the first case of an osteoblastoma with intercostal neuralgia, which is possibly the key symptom for diagnosing an osteoblastoma in the thoracic spine.
Exercise during pregnancy. A narrative review asking: what do we know?
Authors: Barakat Ruben , Perales María , Garatachea Nuria , Ruiz Jonatan R , Lucia Alejandro
Published: July 2015

Although there is no consensus as to whether exercise is beneficial during pregnancy, most studies report it poses no risk to either the mother or the fetus, and many suggest it to be beneficial to both. This review, which examines the evidence available, also reveals the many differences in study design followed, the type of exercise undertaken and the variables measured, which make it difficult to compare results. Advances in our understanding of the effects of exercise during pregnancy might best be made by undertaking randomised clinical trials with standardised protocols. However, most of the studies examining the relationship between exercise and pregnancy report no complications on maternal or fetal well-being. This is also in line with recent review studies advising that the pregnant population without obstetric contraindications should be encouraged to exercise during pregnancy. Therefore, the results of the present review stimulate those responsible for the healthcare of the pregnant woman to recommend moderate exercise throughout pregnancy without risk to maternal and fetal health.
Rationale and design of three observational, prospective cohort studies including biobanking to evaluate and improve diagnostics, management strategies and risk stratification in venous thromboembolism: theVTEval Project
Authors: Frank Bernd , Ariza Liana , Lamparter Heidrun , Grossmann Vera , Prochaska Jürgen H , Ullmann Alexander , Kindler Florentina , Weisser Gerhard , Walter Ulrich , Lackner Karl J , Espinola-Klein Christine , Münzel Thomas , Konstantinides Stavros V , Wild Philipp S
Published: July 2015

Introduction

Venous thromboembolism (VTE) with its two manifestations deep vein thrombosis (DVT) and pulmonary embolism (PE) is a major public health problem. TheVTEval Projectaims to investigate numerous research questions on diagnosis, clinical management, treatment and prognosis of VTE, which have remained uncertain to date.

Methods and analysis

TheVTEval Projectconsists of three observational, prospective cohort studies on VTE comprising cohorts of individuals with a clinical suspicion of acute PE (with or without DVT), with a clinical suspicion of acute DVT (without symptomatic PE) and with an incidental diagnosis of VTE (PE or DVT). TheVTEval Projectexpects to enrol a total of approximately 2000 individuals with subsequent active and passive follow-up investigations over a time period of 5 years per participant. Time points for active follow-up investigations are at months 3, 6, 12, 24 and 36 after diagnosis (depending on the disease cohort); passive follow-up investigations via registry offices and the cancer registry are performed 48 and 60 months after diagnosis for all participants. Primary short-term outcome is defined by overall mortality (PE-related death and all other causes of death), primary long-term outcome by symptomatic VTE (PE-related death, recurrence of non-fatal PE or DVT). TheVTEval Projectincludes three ‘all-comer’ studies and involves the standardised acquisition of high-quality data, covering the systematic assessment of VTE including symptoms, risk profile, psychosocial, environmental and lifestyle factors as well as clinical and subclinical disease, and it builds up a large state-of-the-art biorepository containing various materials from serial blood samplings.

Ethics and dissemination

TheVTEval Projecthas been approved by the local data safety commissioner and the responsible ethics committee (reference no. 837.320.12 (8421-F)). Trial results will be published in peer-reviewed journals and presented at national and international scientific meetings.

Trial registration number

NCT02156401.
Reliable EGFR mutation testing in ultrasound-guided supraclavicular lymph node fine-needle aspirates: a cohort study with diagnostic performance analysis
Authors: Awwad Amir , Tiwari Sandeep , Sovani Vishakha , Baldwin David R , Kumaran Maruti
Published: July 2015

Introduction

15–30% of patients with lung cancer will have supraclavicular and cervical lymphadenopathy (SCLN). Ultrasound (US)-guided fine-needle aspiration (FNA) cytology is regarded as an effective diagnostic tool in small size lymph nodes (LNs) and impalpable positron emission tomography detected nodes. We evaluated our diagnostic service performance in relation to the adequacy of samples for epidermal growth factor receptor (EGFR) mutation.

Methods

Retrospective data analysis from electronic records, searching for all suspected lung cancer referrals that underwent US of the neck±FNA, over a continuous period of 4 years.

Results

Of 306 cases with suspected lung cancer referred to our department for US FNA of SCLN, 228 patients underwent the procedure. Of the remaining 78 patients, LNs were not detected in 52 cases and appeared benign in 26. Cytological diagnosis was established in 171 patients (75%) for treatment decisions without further investigations. The remaining 57 patients had further investigations; 45 reconfirmed the US-guided FNA diagnosis. The average LN size was 12.9 mm, and positive cytology was obtained in LNs ranging from 3 to 45 mm. Of 57 adenocarcinoma cases, 34 were tested for EGFR confirming 4 positive, 25 negative and 5 insufficient samples. No complications were recorded.

Conclusions

US-guided FNA of SCLN remains an important diagnostic tool in lung cancer. Adequate tissue can be obtained for reliable diagnosis from LNs and for EGFR mutational analysis, without the need for more invasive and expensive investigations in more than 80% of cases.