bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbiome changes through ontogeny of a tick pathogen vector
Authors: Zolnik Christine P. , Prill Robert J. , Falco Richard C. , Daniels Thomas J. , Kolokotronis Sergios‐Orestis 
Published: September 2016

AbstractBlacklegged ticks (Ixodes scapularis) are one of the most important pathogen vectors in the United States, responsible for transmitting Lyme disease and other tick‐borne diseases. The structure of a host's microbial community has the potential to affect the ecology and evolution of the host. We employed high‐throughput sequencing of the 16S rRNA gene V3‐V4 hypervariable regions in the first study to investigate the tick microbiome across all developmental stages (larvae, nymphs, adults). In addition to field‐collected life stages, newly hatched laboratory‐reared larvae were studied to determine the baseline microbial community structure and to assess transovarial transmission. We also targeted midguts and salivary glands due to their importance in pathogen maintenance and transmission. Over 100 000 sequences were produced per life stage replicate. Rickettsia was the most abundant bacterial genus across all sample types matching mostly the Ixodes rickettsial endosymbionts, and its proportion decreased as developmental stage progressed, with the exception of adult females that harboured a mean relative abundance of 97.9%. Laboratory‐reared larvae displayed the lowest bacterial diversity, containing almost exclusively Rickettsia. Many of the remaining bacteria included genera associated with soil, water and plants, suggesting environmental acquisition while off‐host. Female organs exhibited significantly different β‐diversity than the whole tick from which they were derived. Our results demonstrate clear differences in both α‐ and β‐diversity among tick developmental stages and between tick organs and the tick as a whole. Furthermore, field‐acquired bacteria appear to be very important to the overall internal bacterial community of this tick species, with influence from the host bloodmeal appearing limited.
Deep sequencing of mycovirus‐derived small RNAs from Botrytis species
Authors: Donaire Livia , Ayllón María A. 
Published: August 2016

SummaryRNA silencing is an ancient regulatory mechanism operating in all eukaryotic cells. In fungi, it was first discovered in Neurospora crassa, although its potential as a defence mechanism against mycoviruses was first reported in Cryphonectria parasitica and, later, in several fungal species. There is little evidence of the antiviral potential of RNA silencing in the phytopathogenic species of the fungal genus Botrytis. Moreover, little is known about the RNA silencing components in these fungi, although the analysis of public genome databases identified two Dicer‐like genes in B. cinerea, as in most of the ascomycetes sequenced to date. In this work, we used deep sequencing to study the virus‐derived small RNA (vsiRNA) populations from different mycoviruses infecting field isolates of Botrytis spp. The mycoviruses under study belong to different genera and species, and have different types of genome [double‐stranded RNA (dsRNA), (+)single‐stranded RNA (ssRNA) and (–)ssRNA]. In general, vsiRNAs derived from mycoviruses are mostly of 21, 20 and 22 nucleotides in length, possess sense or antisense orientation, either in a similar ratio or with a predominance of sense polarity depending on the virus species, have predominantly U at their 5′ end, and are unevenly distributed along the viral genome, showing conspicuous hotspots of vsiRNA accumulation. These characteristics reveal striking similarities with vsiRNAs produced by plant viruses, suggesting similar pathways of viral targeting in plants and fungi. We have shown that the fungal RNA silencing machinery acts against the mycoviruses used in this work in a similar manner independent of their viral or fungal origin.
Collapsing of Non‐centred Parameterized MCMC Algorithms with Applications to Epidemic Models
Authors: Neal Peter , Xiang Fei 
Published: September 2016

AbstractData augmentation is required for the implementation of many Markov chain Monte Carlo (MCMC) algorithms. The inclusion of augmented data can often lead to conditional distributions from well‐known probability distributions for some of the parameters in the model. In such cases, collapsing (integrating out parameters) has been shown to improve the performance of MCMC algorithms. We show how integrating out the infection rate parameter in epidemic models leads to efficient MCMC algorithms for two very different epidemic scenarios, final outcome data from a multitype SIR epidemic and longitudinal data from a spatial SI epidemic. The resulting MCMC algorithms give fresh insight into real‐life epidemic data sets.
Generation of chromosomal deletions in dicotyledonous plants employing a user‐friendly genome editing toolkit
Authors: Ordon Jana , Gantner Johannes , Kemna Jan , Schwalgun Lennart , Reschke Maik , Streubel Jana , Boch Jens , Stuttmann Johannes 
Published: August 2016

SummaryGenome editing facilitated by Cas9‐based RNA‐guided nucleases (RGNs) is becoming an increasingly important and popular technique for reverse genetics in both model and non‐model species. So far, RGNs were mainly applied for the induction of point mutations, and one major challenge consists in the detection of genome‐edited individuals from a mutagenized population. Also, point mutations are not appropriate for functional dissection of non‐coding DNA. Here, the multiplexing capacity of a newly developed genome editing toolkit was exploited for the induction of inheritable chromosomal deletions at six different loci in Nicotiana benthamiana and Arabidopsis. In both species, the preferential formation of small deletions was observed, suggesting reduced efficiency with increasing deletion size. Importantly, small deletions (<100 bp) were detected at high frequencies in N. benthamiana T0 and Arabidopsis T2 populations. Thus, targeting of small deletions by paired nucleases represents a simple approach for the generation of mutant alleles segregating as size polymorphisms in subsequent generations. Phenotypically selected deletions of up to 120 kb occurred at low frequencies in Arabidopsis, suggesting larger population sizes for the discovery of valuable alleles from addressing gene clusters or non‐coding DNA for deletion by programmable nucleases.
Cuerpos anfibios: metamorfosis y anfientidad sexual en XXY (2007) de Lucía Puenzo
Authors: Fradinger Moira 
Published: September 2016

<p>Analizo la película <em>XXY </em>de Lucía Puenzo (Argentina, 2007) desde el punto de vista de la relación entre la materia viviente de la zona costera uruguaya y la propuesta del film con respecto a la diversidad sexual. Sugiero la expresión “<em>anfientidad sexual”</em> para distinguir la manera en que el film representa la relación entre cuerpo, sexo y<em> </em>género al ficcionalizar un caso intersex a través de asociaciones entre los animales humanos y los anfibios y reptiles del ambiente costero, en especial las tortugas marinas que migran cruzando el Atlántico y que se encuentran en peligro de extinción. En tanto las tortugas determinan su sexo dependiendo de la temperatura del ambiente, representan un dinamismo relacional singular de la materia viviente, que corre peligro de extinguirse en nuestra era y que el film asocia con la variación sexual. </p>
Stuart Hall desde/en América Latina
Authors: Mato Daniel 
Published: September 2016

<p>Este artículo analiza cómo las ideas de Stuart Hall han sido adoptadas de manera rigurosa y crítica por los académicos e intelectuales latinoamericanos que pueden considerarse pioneros de los estudios culturales en América Latina y quienes los siguieron; por los que realizan estudios críticos, pero rechazan la etiqueta <em>estudios culturales</em>, y por aquellos cuyo trabajo puede claramente ubicarse dentro del campo de los estudios culturales, aun cuando hasta ahora no se ha asumido como tal. Este análisis lleva a la conclusión de que sería simplista limitar la discusión acerca de la importancia de las ideas de Hall en América Latina exclusivamente al campo de los llamados estudios culturales latinoamericanos y plantea, más bien, la necesidad de analizar su importancia de una manera más abarcante. </p>
Ultrasonographic diagnosis of stenosis of native arteriovenous fistulas in haemodialysis patients
Authors: Tirinescu Dacian Călin , Bondor Cosmina Ioana , Vlăduțiu Dan Ştefan , Pațiu Ioan Mihai , Moldovan Diana , Orășan Remus , Kacsó Ina Maria 
Published: August 2016

Aims: Ultrasound (US) examination is an important tool in the diagnosis of arteriovenous (AVF) stenoses; different US measures are available for assessing the severity of stenoses. The aim of our study was to analyse risk factors and consequences of AVF stenosis and its severity and to compare the usefulness of different US measures of stenoses’ severity. Material and methods: Ninety-seven prevalent patients from a single dialysis centre with patent AVF were included. We recorded history of disease, clinical and laboratory data. US was used to diagnosis the stenosis and to measure blood flow in the brachial artery, resistivity index (RI), and the diameter of the vessels (arteries, anastomosis, venous outflow). Results: Stenosis was present in 54.64% of the patients (59.6% juxtaanastomotic). Stenosis patients had higher age, lower diameter of the brachial artery, lower anastomosis diameter, and lower diastolic blood pressure (DBP). Atherosclerosis, delayed maturation of AVF, and statin treatment were more prominent in the stenosis group. Logistic regression disclosed delayed maturation, cholesterol, atherosclerosis, and DBP as significant predictors of stenosis. When severe stenosis was measured by the diameter reduction, stenosis patients had higher age, lower HDL cholesterol, and poorer dialysis efficacy. Flow in the brachial artery and RI were less useful for identifying risk factors or differences in outcome. Conclusions: Prevalence of stenosis was high in our cohort, more than half of the patients having some degree of stenosis. Risk factors for stenosis were related to atherosclerosis, low DBP, and delayed maturation of AVF. Diameter of stenosis is the most useful marker of severity.
Fast Mechanically Driven Daughter Cell Separation Is Widespread in
Actinobacteria
Authors: Zhou Xiaoxue , Halladin David K. , Theriot Julie A. 
Published: August 2016

ABSTRACT

Dividing cells of the coccoid Gram-positive bacterium
Staphylococcus aureus
undergo extremely rapid (millisecond) daughter cell separation (DCS) driven by mechanical crack propagation, a strategy that is very distinct from the gradual, enzymatically driven cell wall remodeling process that has been well described in several rod-shaped model bacteria. To determine if other bacteria, especially those in the same phylum (
Firmicutes
) or with similar coccoid shapes as
S. aureus
, might use a similar mechanically driven strategy for DCS, we used high-resolution video microscopy to examine cytokinesis in a phylogenetically wide range of species with various cell shapes and sizes. We found that fast mechanically driven DCS is rather rare in the
Firmicutes
(low G+C Gram positives), observed only in
Staphylococcus
and its closest coccoid relatives in the
Macrococcus
genus, and we did not observe this division strategy among the Gram-negative
Proteobacteria
. In contrast, several members of the high-G+C Gram-positive phylum
Actinobacteria
(
Micrococcus luteus
,
Brachybacterium faecium
,
Corynebacterium glutamicum
, and
Mycobacterium smegmatis
) with diverse shapes ranging from coccoid to rod all undergo fast mechanical DCS during cell division. Most intriguingly, similar fast mechanical DCS was also observed during the sporulation of the actinobacterium
Streptomyces venezuelae
.

IMPORTANCE
Much of our knowledge on bacterial cytokinesis comes from studying rod-shaped model organisms such as
Escherichia coli
and
Bacillus subtilis
. Less is known about variations in this process among different bacterial species. While cell division in many bacteria has been characterized to some extent genetically or biochemically, few species have been examined using video microscopy to uncover the kinetics of cytokinesis and daughter cell separation (DCS). In this work, we found that fast (millisecond) DCS is exhibited by species in two independent clades of Gram-positive bacteria and is particularly prevalent among the
Actinobacteria
, a diverse group that includes significant pathogens as well as bacteria that generate medically important antibiotics.
Colistin- and Carbapenem-Resistant Escherichia coli Harboring
mcr-1
and
bla
NDM-5
, Causing a Complicated Urinary Tract Infection in a Patient from the United States
Authors: Mediavilla José R. , Patrawalla Amee , Chen Liang , Chavda Kalyan D. , Mathema Barun , Vinnard Christopher , Dever Lisa L. , Kreiswirth Barry N. 
Published: August 2016

ABSTRACT

Colistin is increasingly used as an antibiotic of last resort for the treatment of carbapenem-resistant Gram-negative infections. The plasmid-borne colistin resistance gene
mcr-1
was initially identified in animal and clinical samples from China and subsequently reported worldwide, including in the United States. Of particular concern is the spread of
mcr-1
into carbapenem-resistant bacteria, thereby creating strains that approach pan-resistance. While several reports of
mcr-1
have involved carbapenem-resistant strains, no such isolates have been described in the United States. Here, we report the isolation and identification of an
Escherichia coli
strain harboring both
mcr-1
and carbapenemase gene
bla
NDM-5
from a urine sample in a patient without recent travel outside the United States. The isolate exhibited resistance to both colistin and carbapenems, but was susceptible to amikacin, aztreonam, gentamicin, nitrofurantoin, tigecycline, and trimethoprim-sulfamethoxazole. The
mcr-1
- and
bla
NDM-5
-harboring plasmids were completely sequenced and shown to be highly similar to plasmids previously reported from China. The strain in this report was first isolated in August 2014, highlighting an earlier presence of
mcr-1
within the United States than previously recognized.

IMPORTANCE
Colistin has become the last line of defense for the treatment of infections caused by Gram-negative bacteria resistant to multiple classes of antibiotics, in particular carbapenem-resistant
Enterobacteriaceae
(CRE). Resistance to colistin, encoded by the plasmid-borne gene
mcr-1
, was first identified in animal and clinical samples from China in November 2015 and has subsequently been reported from numerous other countries. In April 2016,
mcr-1
was identified in a carbapenem-susceptible
Escherichia coli
strain from a clinical sample in the United States, followed by a second report from a carbapenem-susceptible
E. coli
strain originally isolated in May 2015. We report the isolation and identification of an
E. coli
strain harboring both colistin (
mcr-1
) and carbapenem (
bla
NDM-5
) resistance genes, originally isolated in August 2014 from urine of a patient with recurrent urinary tract infections. To our knowledge, this is the first report in the United States of a clinical bacterial isolate with both colistin and carbapenem resistance, highlighting the importance of active surveillance efforts for colistin- and carbapenem-resistant organisms.
The Nucleoid Binding Protein H-NS Biases Genome-Wide Transposon Insertion Landscapes
Authors: Kimura Satoshi , Hubbard Troy P. , Davis Brigid M. , Waldor Matthew K. 
Published: August 2016

ABSTRACT

Transposon insertion sequencing (TIS; also known as TnSeq) is a potent approach commonly used to comprehensively define the genetic loci that contribute to bacterial fitness in diverse environments. A key presumption underlying analyses of TIS datasets is that loci with a low frequency of transposon insertions contribute to fitness. However, it is not known whether factors such as nucleoid binding proteins can alter the frequency of transposon insertion and thus whether TIS output may systematically reflect factors that are independent of the role of the loci in fitness. Here, we investigated whether the histone-like nucleoid structuring (H-NS) protein, which preferentially associates with AT-rich sequences, modulates the frequency of Mariner transposon insertion in the
Vibrio cholerae
genome, using comparative analysis of TIS results from wild-type (wt) and
Δhns V. cholerae
strains. These analyses were overlaid on gene classification based on GC content as well as on extant genome-wide identification of H-NS binding loci. Our analyses revealed a significant dearth of insertions within AT-rich loci in wt
V. cholerae
that was not apparent in the
Δhns
insertion library. Additionally, we observed a striking correlation between genetic loci that are overrepresented in the
Δhns
insertion library relative to their insertion frequency in wt
V. cholerae
and loci previously found to physically interact with H-NS. Collectively, our findings reveal that factors other than genetic fitness can systematically modulate the frequency of transposon insertions in TIS studies and add a cautionary note to interpretation of TIS data, particularly for AT-rich sequences.

IMPORTANCE
Transposon insertion sequencing (TIS) is often used to assess the relative frequency with which genetic loci can be disrupted, which is taken as an indicator of their importance for bacterial fitness. Here, we report that biological factors other than the relative levels of fitness of insertion mutants can influence TIS output. We found that the presence of the DNA binding protein H-NS, which preferentially recognizes AT-rich sequences, is linked to significant underrepresentation of mutations within AT-rich loci in transposon insertion libraries. Furthermore, there is a marked correspondence between loci bound by H-NS and loci with an increased frequency of disruption in a Δ
hns
insertion library relative to a wt library. Our data suggest that factors other than genetic fitness (e.g., DNA binding proteins such as H-NS) can systematically modulate the frequency of transposon insertions in TIS studies and add a note of caution for interpretation of TIS data.
Sleeping Beauty and the Story of the Bacille Calmette-Guérin Vaccine
Authors: Fletcher Helen A. 
Published: August 2016

ABSTRACT

Mycobacterium bovis
BCG is the only available vaccine for protection against tuberculosis (TB). While BCG protects children from severe disease, it has little impact on pulmonary disease in adults. A recombinant BCG vaccine BCG Δ
ureC
::
hly
(strain VPM1002) is in advanced clinical trials and shows promise for improved vaccine safety but little change in efficacy in animal models. A second-generation recombinant BCG vaccine with an additional deletion of the
nuoG
gene (BCG Δ
ureC
::
hly
Δ
nuoG
) shows improved efficacy in a mouse model compared to that of VPM1002. BCG was first used in humans in 1921 and, like Sleeping Beauty pricked by the spinning wheel, we have slept for 100 years, showing a reluctance to invest in clinical development or in biomanufacturing capacity for TB vaccines. The advance of recombinant BCGs should awaken us from our sleep and call us to invest in new-generation TB vaccines and to protect the biomanufacture of our current BCG vaccine.
Predicting mortality in patients treated differently: updating and external validation of a prediction model for nursing home residents with dementia and lower respiratory infections
Authors: Rauh Simone P , Heymans Martijn W , Mehr David R , Kruse Robin L , Lane Patricia , Kowall Neil W , Volicer Ladislav , van der Steen Jenny T 
Published: August 2016

ObjectiveTo evaluate whether a model that was previously developed to predict 14-day mortality for nursing home residents with dementia and lower respiratory tract infection who received antibiotics could be applied to residents who were not treated with antibiotics. Specifically, in this same data set, to update the model using recalibration methods; and subsequently examine the historical, geographical, methodological and spectrum transportability through external validation of the updated model.Design1 cohort study was used to develop the prediction model, and 4 cohort studies from 2 countries were used for the external validation of the model.SettingNursing homes in the Netherlands and the USA.Participants157 untreated residents were included in the development of the model; 239 untreated residents were included in the external validation cohorts.OutcomeModel performance was evaluated by assessing discrimination: area under the receiver operating characteristic curves; and calibration: Hosmer and Lemeshow goodness-of-fit statistics and calibration graphs. Further, reclassification tables allowed for a comparison of patient classifications between models.ResultsThe original prediction model applied to the untreated residents, who were sicker, showed excellent discrimination but poor calibration, underestimating mortality. Adjusting the intercept improved calibration. Recalibrating the slope did not substantially improve the performance of the model. Applying the updated model to the other 4 data sets resulted in acceptable discrimination. Calibration was inadequate only in one data set that differed substantially from the other data sets in case-mix. Adjusting the intercept for this population again improved calibration.ConclusionsThe discriminative performance of the model seems robust for differences between settings. To improve calibration, we recommend adjusting the intercept when applying the model in settings where different mortality rates are expected. An impact study may evaluate the usefulness of the two prediction models for treated and untreated residents and whether it supports decision-making in clinical practice.
Is poor oral health a risk marker for incident cardiovascular disease hospitalisation and all-cause mortality? Findings from 172 630 participants from the prospective 45 and Up Study
Authors: Joshy Grace , Arora Manish , Korda Rosemary J , Chalmers John , Banks Emily 
Published: August 2016

ObjectiveTo investigate the relationship between oral health and incident hospitalisation for ischaemic heart disease (IHD), heart failure (HF), ischaemic stroke and peripheral vascular disease (PVD) and all-cause mortality.DesignProspective population-based study of Australian men and women aged 45 years or older, who were recruited to the 45 and Up Study between January 2006 and April 2009; baseline questionnaire data were linked to hospitalisations and deaths up to December 2011. Study exposures include tooth loss and self-rated health of teeth and gums at baseline.SettingNew South Wales, Australia.ParticipantsIndividuals aged 45–75 years, excluding those with a history of cancer/cardiovascular disease (CVD) at baseline; n=172 630.Primary outcomesIncident hospitalisation for IHD, HF, ischaemic stroke and PVD and all-cause mortality.ResultsDuring a median follow-up of 3.9 years, 3239 incident hospitalisations for IHD, 212 for HF, 283 for ischaemic stroke and 359 for PVD, and 1908 deaths, were observed. Cox proportional hazards models examined the relationship between oral health indicators and incident hospitalisation for CVD and all-cause mortality, adjusting for potential confounding factors. All-cause mortality and incident CVD hospitalisation risk increased significantly with increasing tooth loss for all outcomes except ischaemic stroke (ptrend<0.05). In those reporting no teeth versus ≥20 teeth left, risks were increased for HF (HR, 95% CI 1.97, 1.27 to 3.07), PVD (2.53, 1.81 to 3.52) and all-cause mortality (1.60, 1.37 to 1.87). The risk of IHD, PVD and all-cause mortality (but not HF or ischaemic stroke) increased significantly with worsening self-rated health of teeth and gums (ptrend<0.05). In those reporting poor versus very good health of teeth and gums, risks were increased for IHD (1.19, 1.03 to 1.38), PVD (1.66, 1.13 to 2.43) and all-cause mortality (1.76, 1.50 to 2.08).ConclusionsTooth loss and, to a lesser extent, self-rated health of teeth and gums, are markers for increased risk of IHD, PVD and all-cause mortality. Tooth loss is also a marker for increased risk of HF.