bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reprogramming of plant cells by filamentous plant‐colonizing microbes
Authors: Doehlemann Gunther , Requena Natalia , Schaefer Patrick , Brunner Frederic , O'Connell Richard , Parker Jane E. 
Published: July 2014

SummaryAlthough phylogenetically unrelated, filamentous oomycetes and fungi establish similar structures to colonize plants and they represent economically the most important microbial threat to crop production. In mutualistic interactions established by root‐colonizing fungi, clear differences to pathogens can be seen, but there is mounting evidence that their infection strategies and molecular interactions have certain common features. To infect the host, fungi and oomycetes employ similar strategies to circumvent plant innate immunity. This process involves the suppression of basal defence responses which are triggered by the perception of conserved molecular patterns. To establish biotrophy, effector proteins are secreted from mutualistic and pathogenic microbes to the host tissue, where they play central roles in the modulation of host immunity and metabolic reprogramming of colonized host tissues. This review article discusses key effector mechanisms of filamentous pathogens and mutualists, how they modulate their host targets and the fundamental differences or parallels between these different interactions. The orchestration of effector actions during plant infection and the importance of their localization within host tissues are also discussed.
Evidence for biological denitrification inhibition (BDI) by plant secondary metabolites
Authors: Bardon Clément , Piola Florence , Bellvert Floriant , Haichar Feth el Zahar , Comte Gilles , Meiffren Guillaume , Pommier Thomas , Puijalon Sara , Tsafack Noelline , Poly Franck 
Published: July 2014

Summary

Previous studies on the effect of secondary metabolites on the functioning of rhizosphere microbial communities have often focused on aspects of the nitrogen (N) cycle but have overlooked biological denitrification inhibition (BDI), which can affect plant N‐nutrition. Here, we investigated the BDI by the compounds of Fallopia spp., an invasive weed shown to be associated with a low potential denitrification of the soil.

Fallopia spp. extracts were characterized by chromatographic analysis and were used to test the BDI effects on the metabolic and respiratory activities of denitrifying bacteria, under aerobic and anaerobic (denitrification) conditions. The BDI of Fallopia spp. extracts was tested on a complex soil community by measuring denitrification enzyme activity (DEA), substrate induced respiration (SIR), as well as abundances of denitrifiers and total bacteria.

In 15 strains of denitrifying bacteria, extracts led to a greater BDI (92%) than respiration inhibition (50%). Anaerobic metabolic activity reduction was correlated with catechin concentrations and the BDI was dose dependent. In soil, extracts reduced the DEA/SIR ratio without affecting the denitrifiers: total bacteria ratio.

We show that secondary metabolite(s) from Fallopia spp. inhibit denitrification. This provides new insight into plant–soil interactions and improves our understanding of a plant's ability to shape microbial soil functioning.
Hitchhiker's guide to multi‐dimensional plant pathology
Authors: Saunders Diane G. O. 
Published: July 2014

SummaryFilamentous pathogens pose a substantial threat to global food security. One central question in plant pathology is how pathogens cause infection and manage to evade or suppress plant immunity to promote disease. With many technological advances over the past decade, including DNA sequencing technology, an array of new tools has become embedded within the toolbox of next‐generation plant pathologists. By employing a multidisciplinary approach plant pathologists can fully leverage these technical advances to answer key questions in plant pathology, aimed at achieving global food security. This review discusses the impact of: cell biology and genetics on progressing our understanding of infection structure formation on the leaf surface; biochemical and molecular analysis to study how pathogens subdue plant immunity and manipulate plant processes through effectors; genomics and DNA sequencing technologies on all areas of plant pathology; and new forms of collaboration on accelerating exploitation of big data. As we embark on the next phase in plant pathology, the integration of systems biology promises to provide a holistic perspective of plant–pathogen interactions from big data and only once we fully appreciate these complexities can we design truly sustainable solutions to preserve our resources.
A Medicago truncatula rdr6 allele impairs transgene silencing and endogenous phased siRNA production but not development
Authors: Bustos‐Sanmamed Pilar , Hudik Elodie , Laffont Carole , Reynes Christelle , Sallet Erika , Wen Jiangqi , Mysore Kirankumar S. , Camproux Anne‐Claude , Hartmann Caroline , Gouzy Jérome , Frugier Florian , Crespi Martin , Lelandais‐Brière Christine 
Published: July 2014

SummaryRNA‐dependent RNA polymerase 6 (RDR6) and suppressor of gene silencing 3 (SGS3) act together in post‐transcriptional transgene silencing mediated by small interfering RNAs (siRNAs) and in biogenesis of various endogenous siRNAs including the tasiARFs, known regulators of auxin responses and plant development. Legumes, the third major crop family worldwide, has been widely improved through transgenic approaches. Here, we isolated rdr6 and sgs3 mutants in the model legume Medicago truncatula. Two sgs3 and one rdr6 alleles led to strong developmental defects and impaired biogenesis of tasiARFs. In contrast, the rdr6.1 homozygous plants produced sufficient amounts of tasiARFs to ensure proper development. High throughput sequencing of small RNAs from this specific mutant identified 354 potential MtRDR6 substrates, for which siRNA production was significantly reduced in the mutant. Among them, we found a large variety of novel phased loci corresponding to protein‐encoding genes or transposable elements. Interestingly, measurement of GFP expression revealed that post‐transcriptional transgene silencing was reduced in rdr6.1 roots. Hence, this novel mis‐sense mutation, affecting a highly conserved amino acid residue in plant RDR6s, may be an interesting tool both to analyse endogenous pha‐siRNA functions and to improve transgene expression, at least in legume species.
Pre‐flight assessment in patients with obesity hypoventilation syndrome
Authors: Ali Masood , Smith Ian E. , Gulati Atul , Shneerson John M. 
Published: July 2014

AbstractBackground and objectiveReduced atmospheric pressure during air travel can cause significant hypoxaemia in some patients with respiratory disease. Our aims were to investigate the degree of hypoxaemia in patients with obesity hypoventilation syndrome (OHS) during hypoxic challenge test (HCT), and to identify any predictors of a positive HCT.MethodsThirteen patients underwent assessment, including HCT, lung function and incremental shuttle walk test. All had OHS well controlled with long‐term nocturnal non‐invasive ventilation (NIV). Patients with chronic obstructive pulmonary disease were excluded. A positive HCT was defined according to the British Thoracic Society (BTS) recommendation as arterial oxygen tension (PaO2) <6.6 kPa and/or oxygen saturation <85%.ResultsMean age was 57 (± 11) years. Mean body mass index was 51.7 (± 12) kg/m2. Mean baseline PaO2 and arterial carbon dioxide tension (PaCO2) were 10.2 (9.5–11.3) kPa and 5.2 (3.7–6.8) kPa, respectively. Seven patients (54%) had a positive HCT. The correlation between baseline PaO2 and PaO2 at the end of the HCT was not statistically significant (r = 0.433, P = 0.184). A negative correlation was observed between baseline PaCO2 and PaO2 at the end of the HCT (r = −0.793, P = 0.004). A positive correlation was observed between the distance walked and the PaO2 at the end of the HCT (r = 0.608, P = 0.047).ConclusionsOHS is a risk factor for severe hypoxaemia during air travel even if the ventilatory failure is well controlled. An HCT before air travel is advisable in all OHS patients. Those with positive HCT may use NIV or have oxygen on‐board as per BTS recommendation.
The Requirements Entropy Framework in Systems Engineering
Authors: Grenn Michael W. , Sarkani Shahram , Mazzuchi Thomas 
Published: July 2014

ABSTRACTThis paper introduces a requirements entropy framework (REF) for measuring requirements trends and estimating engineering effort during system development. The REF treats the requirements engineering process as an open system in which the total number of requirements R transition from initial states of high requirements entropy HR, disorder and uncertainty toward the desired end state of as R increase in quality. The cumulative requirements quality Q reflects the meaning of the requirements information in the context of the SE problem. The distribution of R among N discrete quality levels is determined by the number of quality attributes accumulated by R at any given time in the process. The number of possibilities P reflects the uncertainty of the requirements information relative to . The HR is measured or estimated using R, N and P by extending principles of information theory and statistical mechanics to the requirements engineering process. The requirements information I increases as HR and uncertainty decrease, and ΔI is the additional information necessary to achieve the desired state from the perspective of the receiver. The HR may increase, decrease or remain steady depending on the degree to which additions, deletions and revisions impact the distribution of R among the quality levels. Current requirements volatility metrics generally treat additions, deletions and revisions the same and simply measure the quantity of these changes over time. The REF measures the quantity of requirements changes over time, distinguishes between their positive and negative effects in terms of , and ΔI, and forecasts when a specified desired state of requirements quality will be reached, enabling more accurate assessment of the status and progress of the engineering effort. Results from random variable simulations suggest the REF is an improved leading indicator of requirements trends that can be readily combined with current methods. The additional engineering effort ΔE needed to transition R from their current state to the desired state can also be estimated. Simulation results are compared with measured engineering effort data for Department of Defense programs, and the results suggest the REF is a promising new method for estimating engineering effort for a wide range of system development programs.
The role of microRNA‐15b in the impaired angiogenesis in diabetic wounds
Authors: Xu Junwang , Zgheib Carlos , Hu Junyi , Wu Wenjie , Zhang Liping , Liechty Kenneth W. 
Published: July 2014

AbstractThe impairment in diabetic wound healing represents a significant clinical problem. Decreased angiogenesis is thought to play a central role in the pathogenesis of this impairment. We have previously shown that treatment of diabetic murine wounds with mesenchymal stem cells can improve healing, but the mechanisms are not completely defined. MicroRNA‐15b (miR‐15b) has been implicated in the regulation of the angiogenic response. We hypothesized that abnormal miR‐15b expression may contribute to the impaired angiogenesis observed in impaired diabetic wound healing. To test this hypothesis, we examined the expression of miR‐15b and its target genes in diabetic and nondiabetic mice before and after injury. MiR‐15b expression was significantly up‐regulated in diabetic mouse wounds during the wound healing response. Increased miR‐15b levels also closely correlated with decreased gene expression of its proangiogenic target genes. Furthermore, the correction of the diabetic wound healing impairment with mesenchymal stem cell treatment was associated with a significant decrease in miR‐15b expression level and increased gene expression of its proangiogenic target genes. These results provide the first evidence that increased expression of miR‐15b in diabetic wounds in response to injury may, in part, be responsible for the abnormal angiogenic response seen in diabetic wounds and may contribute to the observed wound healing impairment.
Hepatitis B Virus Antibody Levels 7 to 9 Years after Booster Vaccination in Alaska Native Persons
Authors: Keck James W. , Bulkow Lisa R. , Raczniak Gregory A. , Negus Susan E. , Zanis Carolyn L. , Bruce Michael G. , Spradling Philip R. , Teshale Eyasu H. , McMahon Brian J. 
Published: July 2014

ABSTRACTHepatitis B antibody persistence was assessed in individuals who had previously received a vaccine booster. We measured hepatitis B surface antigen antibody (anti-HBs) levels 7 to 9 years post-hepatitis B booster in individuals with primary vaccination at birth. While 95 (91.3%) of 104 participants had detectable anti-HBs (minimum, 0.1 mIU/ml; maximum, 1,029 mIU/ml), only 43 (41%) had protective levels of ≥10 mIU/ml. Pre- and week 4 postbooster anti-HBs levels were significant predictors of hepatitis B immunity at follow-up (P< 0.001). Almost all participants had detectable anti-HBs 7 to 9 years after the hepatitis B vaccine booster, but less than half had levels ≥10 mIU/ml.
A New Modified Live Porcine Reproductive and Respiratory Syndrome Vaccine Improves Growth Performance in Pigs under Field Conditions
Authors: Park Changhoon , Seo Hwi Won , Kang Ikjae , Jeong Jiwoon , Choi Kyuhyung , Chae Chanhee 
Published: July 2014

ABSTRACTThe change in growth performance resulting from a new modified live porcine reproductive and respiratory syndrome (PRRS) vaccine was evaluated under field conditions for registration with the government as guided by the Republic of Korea's Animal and Plant Quarantine Agency. Three farms were selected based on their history of PRRS-associated respiratory diseases. On each farm, a total of 45 3-week-old pigs were randomly allocated to one of two treatment groups, (i) vaccinated (n= 25) or (ii) control (n= 20) animals. A new modified live PRRSV vaccine increased market weight by 1.26 kg/pig (104.71 kg versus 103.45 kg;P< 0.05) and decreased mortality by 17% (1.33% versus 18.33%;P< 0.05). Pathological examination indicated that vaccination effectively reduced microscopic lung lesions compared with control animals on the 3 farms. Thus, the new modified live PRRS vaccine improved growth performance and decreased mortality and lung lesions when evaluated under field conditions.
Genome Sequencing of Mycobacterium abscessus Isolates from Patients in the United States and Comparisons to Globally Diverse Clinical Strains
Authors: Davidson Rebecca M. , Hasan Nabeeh A. , Reynolds Paul R. , Totten Sarah , Garcia Benjamin , Levin Adrah , Ramamoorthy Preveen , Heifets Leonid , Daley Charles L. , Strong Michael 
Published: July 2014

ABSTRACT

Nontuberculous mycobacterial infections caused by
Mycobacterium abscessus
are responsible for a range of disease manifestations from pulmonary to skin infections and are notoriously difficult to treat, due to innate resistance to many antibiotics. Previous population studies of clinical
M. abscessus
isolates utilized multilocus sequence typing or pulsed-field gel electrophoresis, but high-resolution examinations of genetic diversity at the whole-genome level have not been well characterized, particularly among clinical isolates derived in the United States. We performed whole-genome sequencing of 11 clinical
M. abscessus
isolates derived from eight U.S. patients with pulmonary nontuberculous mycobacterial infections, compared them to 30 globally diverse clinical isolates, and investigated intrapatient genomic diversity and evolution. Phylogenomic analyses revealed a cluster of closely related U.S. and Western European M.
abscessus
subsp.
abscessus
isolates that are genetically distinct from other European isolates and all Asian isolates. Large-scale variation analyses suggested genome content differences of 0.3 to 8.3%, relative to the reference strain ATCC 19977
T
. Longitudinally sampled isolates showed very few single-nucleotide polymorphisms and correlated genomic deletion patterns, suggesting homogeneous infection populations. Our study explores the genomic diversity of clinical
M. abscessus
strains from multiple continents and provides insight into the genome plasticity of an opportunistic pathogen.
Evaluation of 16S rRNA Gene PCR Sensitivity and Specificity for Diagnosis of Prosthetic Joint Infection: a Prospective Multicenter Cross-Sectional Study
Authors: Bémer Pascale , Plouzeau Chloé , Tande Didier , Léger Julie , Giraudeau Bruno , Valentin Anne Sophie , Jolivet-Gougeon Anne , Vincent Pascal , Corvec Stéphane , Gibaud Sophie , Juvin Marie Emmanuelle , Héry-Arnaud Genevieve , Lemarié Carole , Kempf Marie , Bret Laurent , Quentin Roland , Coffre Carine , de Pinieux Gonzague , Bernard Louis , Burucoa Christophe 
Published: July 2014

ABSTRACT

There is no standard method for the diagnosis of prosthetic joint infection (PJI). The contribution of 16S rRNA gene PCR sequencing on a routine basis remains to be defined. We performed a prospective multicenter study to assess the contributions of 16S rRNA gene assays in PJI diagnosis. Over a 2-year period, all patients suspected to have PJIs and a few uninfected patients undergoing primary arthroplasty (control group) were included. Five perioperative samples per patient were collected for culture and 16S rRNA gene PCR sequencing and one for histological examination. Three multicenter quality control assays were performed with both DNA extracts and crushed samples. The diagnosis of PJI was based on clinical, bacteriological, and histological criteria, according to Infectious Diseases Society of America guidelines. A molecular diagnosis was modeled on the bacteriological criterion (≥1 positive sample for strict pathogens and ≥2 for commensal skin flora). Molecular data were analyzed according to the diagnosis of PJI. Between December 2010 and March 2012, 264 suspected cases of PJI and 35 control cases were included. PJI was confirmed in 215/264 suspected cases, 192 (89%) with a bacteriological criterion. The PJIs were monomicrobial (163 cases [85%]; staphylococci,
n
= 108; streptococci,
n
= 22; Gram-negative bacilli,
n
= 16; anaerobes,
n
= 13; others,
n
= 4) or polymicrobial (29 cases [15%]). The molecular diagnosis was positive in 151/215 confirmed cases of PJI (143 cases with bacteriological PJI documentation and 8 treated cases without bacteriological documentation) and in 2/49 cases without confirmed PJI (sensitivity, 73.3%; specificity, 95.5%). The 16S rRNA gene PCR assay showed a lack of sensitivity in the diagnosis of PJI on a multicenter routine basis.
Interspecies Transfer of
bla
IMP-4
in a Patient with Prolonged Colonization by IMP-4-Producing Enterobacteriaceae
Authors: Sidjabat Hanna E. , Heney Claire , George Narelle M. , Nimmo Graeme R. , Paterson David L. 
Published: July 2014

ABSTRACT

A patient was colonized by IMP-4-producing
Enterobacter cloacae
and
Escherichia coli
strains for 7 months. IMP-4-producing
E. cloacae
strains were first and last isolated at day 33 and at 8 months after admission, respectively. IMP-4-producing
E. coli
strains were first and last isolated at days 88 and 181 after admission, respectively. The
E. cloacae
and
E. coli
isolates shared identical genetic features in terms of
bla
IMP-4
,
bla
TEM-1
,
qnrB2
,
aacA4
, HI2 plasmids, and IS
CR1
. This study shows the first prolonged colonization with
in vivo
interspecies transfer of
bla
IMP-4
.
Molecular Characterization of a Lizard Adenovirus Reveals the First Atadenovirus with Two Fiber Genes and the First Adenovirus with Either One Short or Three Long Fibers per Penton
Authors: Pénzes Judit J. , Menéndez-Conejero Rosa , Condezo Gabriela N. , Ball Inna , Papp Tibor , Doszpoly Andor , Paradela Alberto , Pérez-Berná Ana J. , López-Sanz María , Nguyen Thanh H. , van Raaij Mark J. , Marschang Rachel E. , Harrach Balázs , Benkő Mária , San Martín Carmen 
Published: July 2014

ABSTRACT

Although adenoviruses (AdVs) have been found in a wide variety of reptiles, including numerous squamate species, turtles, and crocodiles, the number of reptilian adenovirus isolates is still scarce. The only fully sequenced reptilian adenovirus, snake adenovirus 1 (SnAdV-1), belongs to the
Atadenovirus
genus. Recently, two new atadenoviruses were isolated from a captive Gila monster (
Heloderma suspectum
) and Mexican beaded lizards (
Heloderma horridum
). Here we report the full genomic and proteomic characterization of the latter, designated lizard adenovirus 2 (LAdV-2). The double-stranded DNA (dsDNA) genome of LAdV-2 is 32,965 bp long, with an average G+C content of 44.16%. The overall arrangement and gene content of the LAdV-2 genome were largely concordant with those in other atadenoviruses, except for four novel open reading frames (ORFs) at the right end of the genome. Phylogeny reconstructions and plesiomorphic traits shared with SnAdV-1 further supported the assignment of LAdV-2 to the
Atadenovirus
genus. Surprisingly, two fiber genes were found for the first time in an atadenovirus. After optimizing the production of LAdV-2 in cell culture, we determined the protein compositions of the virions. The two fiber genes produce two fiber proteins of different sizes that are incorporated into the viral particles. Interestingly, the two different fiber proteins assemble as either one short or three long fiber projections per vertex. Stoichiometry estimations indicate that the long fiber triplet is present at only one or two vertices per virion. Neither triple fibers nor a mixed number of fibers per vertex had previously been reported for adenoviruses or any other virus.

IMPORTANCE
Here we show that a lizard adenovirus, LAdV-2, has a penton architecture never observed before. LAdV-2 expresses two fiber proteins—one short and one long. In the virion, most vertices have one short fiber, but a few of them have three long fibers attached to the same penton base. This observation raises new intriguing questions on virus structure. How can the triple fiber attach to a pentameric vertex? What determines the number and location of each vertex type in the icosahedral particle? Since fibers are responsible for primary attachment to the host, this novel architecture also suggests a novel mode of cell entry for LAdV-2. Adenoviruses have a recognized potential in nanobiomedicine, but only a few of the more than 200 types found so far in nature have been characterized in detail. Exploring the taxonomic wealth of adenoviruses should improve our chances to successfully use them as therapeutic tools.