bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genotypic and Pathotypic Diversity of Xanthomonas oryzae pv. oryzae Strains in Taiwan
Authors: Deng Wen‐Ling , Lin Heng‐An , Shih Yu‐Cyuan , Kuo Chien‐Chih , Tzeng Jen‐Yu , Liu Li‐yu D. , Huang Shu‐Tzu , Huang Chi‐Ming , Chung Chia‐Lin 
Published: June 2016

AbstractRice bacterial leaf blight, caused by Xanthomonas oryzae pv. oryzae [(Ishiyama) Swings et al. 1990] (Xoo), is a major rice disease of the second crop season in Taiwan. A total of 88 Xoo strains collected from 10 major rice cultivating areas in Taiwan from 1986, 1997, 2000, 2004, and 2011 were characterized by repetitive‐element PCR (REP‐PCR) fingerprinting and virulence analyses. Among the five genetic clusters identified by the pJEL1/pJEL2 (IS1112‐based) and REP1R‐Dt/REP2‐D [repetitive extragenic palindromic (REP)‐based] primer sets, clusters A, C and D contained Xoo strains from geographically distant regions, which suggests a high frequency of Xoo dispersal in Taiwan. The 88 Xoo strains were evaluated by inoculations on IRBB near‐isogenic lines and five Taiwan rice cultivars. A subset of 45 moderately or highly virulent strains were classified into 15 pathotypes by their compatible or incompatible reactions on IR24 and 12 IRBB near‐isogenic lines, each containing a single resistance gene. Analysis of molecular haplotypes and pathotypes revealed a partial relationship. IRBB5, IRBB21 and IRBB4 were incompatible with 96%, 96% and 73% of the strains, so xa5, Xa21 and Xa4 can recognize most of the Xoo strains in Taiwan and elicit resistance. In contrast, IRBB3 (Xa3), IRBB8 (xa8), IRBB10 (Xa10), IRBB11 (Xa11), IRBB13 (xa13) and IRBB14 (Xa14) were susceptible to almost all of the 45 Xoo strains. Inoculation trials revealed significant differences in the susceptibility of five Taiwan cultivars to Xoo (from high to low susceptibility: Taichung Sen 10 > IR24, Taichung Native 1 > Taichung 192, Taikeng 9, Tainan 11). This study provides useful information for resistance breeding and the development of disease management strategies against bacterial blight disease of rice.
Understanding Maternal Support for Autonomy in Young Children with Down Syndrome
Authors: Gilmore Linda , Ryan Belinda , Cuskelly Monica , Gavidia‐Payne Susana 
Published: June 2016

AbstractPrior research has highlighted the importance of supporting the autonomy of children with Down syndrome from early childhood. There is some evidence to suggest that mothers of children with Down syndrome are more directive than those whose children are developing typically. However, the factors that contribute to maternal autonomy supportive vs. directive behaviors are not well understood. The current study aimed to explore the value and importance that mothers place upon their child's autonomy, as well as the specific factors that influence the support they provide. Interviews were conducted with 14 mothers of young children with Down syndrome. It was revealed that mothers held aspirations for their children's future that included autonomy and independence; however, their capacity to promote autonomy was sometimes constrained by a range of child and family factors, as well as by their focus on developing skills for independent functioning. Understanding the factors that may constrain support for autonomy represents an essential step in the process of designing interventions for promoting maternal support for autonomy in families of children with Down syndrome and other developmental disabilities.
Tree of life for the genera of Chinese vascular plants
Authors: Chen Zhi‐Duan , Yang Tuo , Lin Li , Lu Li‐Min , Li Hong‐Lei , Sun Miao , Liu Bing , Chen Min , Niu Yan‐Ting , Ye Jian‐Fei , Cao Zhi‐Yong , Liu Hong‐Mei , Wang Xiao‐Ming , Wang Wei , Zhang Jing‐Bo , Meng Zhen , Cao Wei , Li Jian‐Hui , Wu Sheng‐Dan , Zhao Hui‐Ling , Liu Zhong‐Jian , Du Zhi‐Yuan , Wang Qing‐Feng , Guo Jing , Tan Xin‐Xin , Su Jun‐Xia , Zhang Lin‐Jing , Yang Lei‐Lei , Liao Yi‐Ying , Li Ming‐He , Zhang Guo‐Qiang , Chung Shih‐Wen , Zhang Jian , Xiang Kun‐Li , Li Rui‐Qi , Soltis Douglas E. , Soltis Pamela S. , Zhou Shi‐Liang , Ran Jin‐Hua , Wang Xiao‐Quan , Jin Xiao‐Hua , Chen You‐Sheng , Gao Tian‐Gang , Li Jian‐Hua , Zhang Shou‐Zhou , Lu An‐Ming ,   China Phylogeny Consortium
Published: June 2016

AbstractWe reconstructed a phylogenetic tree of Chinese vascular plants (Tracheophyta) using sequences of the chloroplast genes atpB, matK, ndhF, and rbcL and mitochondrial matR. We produced a matrix comprising 6098 species and including 13 695 DNA sequences, of which 1803 were newly generated. Our taxonomic sampling spanned 3114 genera representing 323 families of Chinese vascular plants, covering more than 93% of all genera known from China. The comprehensive large phylogeny supports most relationships among and within families recognized by recent molecular phylogenetic studies for lycophytes, ferns (monilophytes), gymnosperms, and angiosperms. For angiosperms, most families in Angiosperm Phylogeny Group IV are supported as monophyletic, except for a paraphyletic Dipterocarpaceae and Santalaceae. The infrafamilial relationships of several large families and monophyly of some large genera are well supported by our dense taxonomic sampling. Our results showed that two species of Eberhardtia are sister to a clade formed by all other taxa of Sapotaceae, except Sarcosperma. We have made our phylogeny of Chinese vascular plants publically available for the creation of subtrees via SoTree (http://www.darwintree.cn/flora/index.shtml), an automated phylogeny assembly tool for ecologists.
Acceleration‐Based Automated Vehicle Classification on Mobile Bridges
Authors: Yeum Chul Min , Dyke Shirley J. , Basora Rovira Ricardo E. , Silva Christian , Demo Jeff 
Published: June 2016

AbstractMobile bridges have been used for a broad range of applications including military transportation or disaster restoration. Because mobile bridges are rapidly deployed under a wide variety of conditions, often remaining in place for just minutes to hours, and have irregular usage patterns, a detailed record of usage history is important for ensuring structural safety. To facilitate usage data collection in mobile bridges, a new acceleration‐based vehicle classification technique is proposed to automatically identify the class of each vehicle. Herein we present a new technique that is based on the premise that each class of vehicles produces distinctive dynamic patterns while crossing this mobile bridge, and those patterns can be extracted from the system's acceleration responses. Measured acceleration signals are converted to time–frequency images to extract two‐dimensional patterns. The Viola–Jones object detection algorithm is applied here to extract and classify those patterns. The effectiveness of the technique is investigated and demonstrated using laboratory and full‐scale mobile bridges by simulating realistic scenarios.
Modeling and Validation of the Ecological Behavior of Wild-Type Listeria monocytogenes and Stress-Resistant Variants
Authors: Metselaar Karin I. , Abee Tjakko , Zwietering Marcel H. , den Besten Heidy M. W. 
Published: June 2016

ABSTRACT

Listeria monocytogenes
exhibits a heterogeneous response upon stress exposure which can be partially attributed to the presence of stable stress-resistant variants. This study aimed to evaluate the impact of the presence of stress-resistant variants of
Listeria monocytogenes
and their corresponding trade-offs on population composition under different environmental conditions. A set of stress robustness and growth parameters of the wild type (WT) and an
rpsU
deletion variant was obtained and used to model their growth behavior under combined mild stress conditions and to model their kinetics under single- and mixed-strain conditions in a simulated food chain. Growth predictions for the WT and the
rpsU
deletion variant matched the experimental data generally well, although some deviations from the predictions were observed. The data highlighted the influence of the environmental conditions on the ratio between the WT and variant. Prediction of performance in the simulated food chain proved to be challenging. The trend of faster growth and lower stress robustness for the WT than for the
rpsU
variant in the different steps of the chain was confirmed, but especially for the inactivation steps and the time needed to resume growth after an inactivation step, the experimental data deviated from the model predictions. This report provides insights into the conditions which can select for stress-resistant variants in industrial settings and discusses their potential persistence in food processing environments.

IMPORTANCE
Listeria monocytogenes
exhibits a heterogeneous stress response which can partially be attributed to the presence of genetic variants. These stress-resistant variants survive better under severe conditions but have, on the other hand, a reduced growth rate. To date, the ecological behavior and potential impact of the presence of stress-resistant variants is not fully understood. In this study, we quantitatively assessed growth and inactivation behavior of wild-type
L. monocytogenes
and its stress-resistant variants. Predictions were validated under different conditions, as well as along a model food chain. This work illustrates the effects of environmental factors on population dynamics of
L. monocytogenes
and is a first step in evaluating the impact of population diversity on food safety.
The Microbiota of Breast Tissue and Its Association with Breast Cancer
Authors: Urbaniak Camilla , Gloor Gregory B. , Brackstone Muriel , Scott Leslie , Tangney Mark , Reid Gregor 
Published: June 2016

ABSTRACT

In the United States, 1 in 8 women will be diagnosed with breast cancer in her lifetime. Along with genetics, the environment contributes to disease development, but what these exact environmental factors are remains unknown. We have previously shown that breast tissue is not sterile but contains a diverse population of bacteria. We thus believe that the host's local microbiome could be modulating the risk of breast cancer development. Using 16S rRNA amplicon sequencing, we show that bacterial profiles differ between normal adjacent tissue from women with breast cancer and tissue from healthy controls. Women with breast cancer had higher relative abundances of
Bacillus
,
Enterobacteriaceae
and
Staphylococcus
.
Escherichia coli
(a member of the
Enterobacteriaceae
family) and
Staphylococcus epidermidis
, isolated from breast cancer patients, were shown to induce DNA double-stranded breaks in HeLa cells using the histone-2AX (H2AX) phosphorylation (γ-H2AX) assay. We also found that microbial profiles are similar between normal adjacent tissue and tissue sampled directly from the tumor. This study raises important questions as to what role the breast microbiome plays in disease development or progression and how we can manipulate this for possible therapeutics or prevention.

IMPORTANCE
This study shows that different bacterial profiles in breast tissue exist between healthy women and those with breast cancer. Higher relative abundances of bacteria that had the ability to cause DNA damage
in vitro
were detected in breast cancer patients, as was a decrease in some lactic acid bacteria, known for their beneficial health effects, including anticarcinogenic properties. This study raises important questions as to the role of the mammary microbiome in modulating the risk of breast cancer development.
LsbB Bacteriocin Interacts with the Third Transmembrane Domain of the YvjB Receptor
Authors: Miljkovic Marija , Uzelac Gordana , Mirkovic Nemanja , Devescovi Giulia , Diep Dzung B. , Venturi Vittorio , Kojic Milan 
Published: June 2016

ABSTRACT

The Zn-dependent membrane-located protease YvjB has previously been shown to serve as a target receptor for LsbB, a class II leaderless lactococcal bacteriocin. Although
yvjB
is highly conserved in the genus
Lactococcus
, the bacteriocin appears to be active only against the subspecies
L. lactis
subsp.
lactis
. Comparative analysis of the YvjB proteins of a sensitive strain (YvjB
MN
) and a resistant strain (YvjB
MG
) showed that they differ from each other in 31 positions. In this study, we applied site-directed mutagenesis and performed directed binding studies to provide biochemical evidence that LsbB interacts with the third transmembrane helix of YvjB in susceptible cells. The site-directed mutagenesis of LsbB and YvjB proteins showed that certain amino acids and the length of LsbB are responsible for the bacteriocin activity, most probably through adequate interaction of these two proteins; the essential amino acids in LsbB responsible for the activity are tryptophan (Trp
25
) and terminal alanine (Ala
30
). It was also shown that the distance between Trp
25
and terminal alanine is crucial for LsbB activity. The crucial region in YvjB for the interaction with LsbB is the beginning of the third transmembrane helix, particularly amino acids tyrosine (Tyr
356
) and alanine (Ala
353
).
In vitro
experiments showed that LsbB could interact with both YvjB
MN
and YvjB
MG
, but the strength of interaction is significantly less with YvjB
MG
.
In vivo
experiments with immunofluorescently labeled antibody demonstrated that LsbB specifically interacts only with cells carrying YvjB
MN
.

IMPORTANCE
The antimicrobial activity of LsbB bacteriocin depends on the correct interaction with the corresponding receptor in the bacterial membrane of sensitive cells. Membrane-located bacteriocin receptors have essential primary functions, such as cell wall synthesis or sugar transport, and it seems that interaction with bacteriocins is suicidal for cells. This study showed that the C-terminal part of LsbB is crucial for the bacteriocin activity, most probably through adequate interaction with the third transmembrane domain of the YvjB receptor. The conserved Tyr
356
and Ala
353
residues of YvjB are essential for the function of this Zn-dependent membrane-located protease as a bacteriocin receptor.
Elucidation of Taste- and Odor-Producing Bacteria and Toxigenic Cyanobacteria in a Midwestern Drinking Water Supply Reservoir by Shotgun Metagenomic Analysis
Authors: Otten Timothy G. , Graham Jennifer L. , Harris Theodore D. , Dreher Theo W. 
Published: June 2016

ABSTRACT

While commonplace in clinical settings, DNA-based assays for identification or enumeration of drinking water pathogens and other biological contaminants remain widely unadopted by the monitoring community. In this study, shotgun metagenomics was used to identify taste-and-odor producers and toxin-producing cyanobacteria over a 2-year period in a drinking water reservoir. The sequencing data implicated several cyanobacteria, including
Anabaena
spp.,
Microcystis
spp., and an unresolved member of the order
Oscillatoriales
as the likely principal producers of geosmin, microcystin, and 2-methylisoborneol (MIB), respectively. To further demonstrate this, quantitative PCR (qPCR) assays targeting geosmin-producing
Anabaena
and microcystin-producing
Microcystis
were utilized, and these data were fitted using generalized linear models and compared with routine monitoring data, including microscopic cell counts, sonde-based physicochemical analyses, and assays of all inorganic and organic nitrogen and phosphorus forms and fractions. The qPCR assays explained the greatest variation in observed geosmin (adjusted
R
2
= 0.71) and microcystin (adjusted
R
2
= 0.84) concentrations over the study period, highlighting their potential for routine monitoring applications. The origin of the monoterpene cyclase required for MIB biosynthesis was putatively linked to a periphytic cyanobacterial mat attached to the concrete drinking water inflow structure. We conclude that shotgun metagenomics can be used to identify microbial agents involved in water quality deterioration and to guide PCR assay selection or design for routine monitoring purposes. Finally, we offer estimates of microbial diversity and metagenomic coverage of our data sets for reference to others wishing to apply shotgun metagenomics to other lacustrine systems.

IMPORTANCE
Cyanobacterial toxins and microbial taste-and-odor compounds are a growing concern for drinking water utilities reliant upon surface water resources. Specific identification of the microorganism(s) responsible for water quality degradation is often complicated by the presence of co-occurring taxa capable of producing these undesirable metabolites. Here we present a framework for how shotgun metagenomics can be used to definitively identify problematic microorganisms and how these data can guide the development of rapid genetic assays for routine monitoring purposes.
Survival, Biofilm Formation, and Growth Potential of Environmental and Enteric Escherichia coli Strains in Drinking Water Microcosms
Authors: Abberton Cathy L. , Bereschenko Ludmila , van der Wielen Paul W. J. J. , Smith Cindy J. 
Published: June 2016

ABSTRACT

Escherichia coli
is the most commonly used indicator for fecal contamination in drinking water distribution systems (WDS). The assumption is that
E. coli
bacteria are of enteric origin and cannot persist for long outside their host and therefore act as indicators of recent contamination events. This study investigates the fate of
E. coli
in drinking water, specifically addressing survival, biofilm formation under shear stress, and regrowth in a series of laboratory-controlled experiments. We show the extended persistence of three
E. coli
strains (two enteric isolates and one soil isolate) in sterile and nonsterile drinking water microcosms at 8 and 17°C, with
T
90
(time taken for a reduction in cell number of 1 log
10
unit) values ranging from 17.4 ± 1.8 to 149 ± 67.7 days, using standard plate counts and a series of (reverse transcription-)quantitative PCR [(RT-)Q-PCR] assays targeting 16S rRNA,
tuf
,
uidA
, and
rodA
genes and transcripts. Furthermore, each strain was capable of attaching to a surface and replicating to form biofilm in the presence of nutrients under a range of shear stress values (0.6, 2.0, and 4.4 dynes [dyn] cm
−2
; BioFlux system; Fluxion); however, cell numbers did not increase when drinking water flowed over the biofilm (
P
> 0.05 by
t
test). Finally,
E. coli
regrowth within drinking water microcosms containing polyethylene PE-100 pipe wall material was not observed in the biofilm or water phase using a combination of culturing and Q-PCR methods for
E. coli
. The results of this work highlight that when
E. coli
enters drinking water it has the potential to survive and attach to surfaces but that regrowth within drinking water or biofilm is unlikely.

IMPORTANCE
The provision of clean, safe drinking water is fundamental to society. WDS deliver water to consumers via a vast network of pipes
. E. coli
is used as an indicator organism for recent contamination events based on the premise that it cannot survive for long outside its host. A key public health concern therefore arises around the fate of
E. coli
on entering a WDS; its survival, ability to form a biofilm, and potential for regrowth. In particular, if
E. coli
bacteria have the ability to incorporate and regrow within the pipe wall biofilm of a WDS, they could reinoculate the water at a later stage. This study sheds light on the fate of environmental and enteric strains of
E. coli
in drinking water showing extended survival, the potential for biofilm formation under shear stress, and importantly, that regrowth in the presence of an indigenous microbial community is unlikely.
Yersinia enterocolitica-Specific Infection by Bacteriophages TG1 and ϕR1-RT Is Dependent on Temperature-Regulated Expression of the Phage Host Receptor OmpF
Authors: Leon-Velarde Carlos G. , Happonen Lotta , Pajunen Maria , Leskinen Katarzyna , Kropinski Andrew M. , Mattinen Laura , Rajtor Monika , Zur Joanna , Smith Darren , Chen Shu , Nawaz Ayesha , Johnson Roger P. , Odumeru Joseph A. , Griffiths Mansel W. , Skurnik Mikael 
Published: June 2016

ABSTRACT

Bacteriophages present huge potential both as a resource for developing novel tools for bacterial diagnostics and for use in phage therapy. This potential is also valid for bacteriophages specific for
Yersinia enterocolitica
. To increase our knowledge of
Y. enterocolitica
-specific phages, we characterized two novel yersiniophages. The genomes of the bacteriophages vB_YenM_TG1 (TG1) and vB_YenM_ϕR1-RT (ϕR1-RT), isolated from pig manure in Canada and from sewage in Finland, consist of linear double-stranded DNA of 162,101 and 168,809 bp, respectively. Their genomes comprise 262 putative coding sequences and 4 tRNA genes and share 91% overall nucleotide identity. Based on phylogenetic analyses of their whole-genome sequences and large terminase subunit protein sequences, a genus named
Tg1virus
within the family
Myoviridae
is proposed, with TG1 and ϕR1-RT (R1RT in the ICTV database) as member species. These bacteriophages exhibit a host range restricted to
Y. enterocolitica
and display lytic activity against the epidemiologically significant serotypes O:3, O:5,27, and O:9 at and below 25°C. Adsorption analyses of lipopolysaccharide (LPS) and OmpF mutants demonstrate that these phages use both the LPS inner core heptosyl residues and the outer membrane protein OmpF as phage receptors. Based on RNA sequencing and quantitative proteomics, we also demonstrate that temperature-dependent infection is due to strong repression of OmpF at 37°C. In addition, ϕR1-RT was shown to be able to enter into a pseudolysogenic state. Together, this work provides further insight into phage-host cell interactions by highlighting the importance of understanding underlying factors which may affect the abundance of phage host receptors on the cell surface.

IMPORTANCE
Only a small number of bacteriophages infecting
Y. enterocolitica
, the predominant causative agent of yersiniosis, have been previously described. Here, two newly isolated
Y. enterocolitica
phages were studied in detail, with the aim of elucidating the host cell receptors required for infection. Our research further expands the repertoire of phages available for consideration as potential antimicrobial agents or as diagnostic tools for this important bacterial pathogen.