bluuebunny/crossref_metadata_2025 huggingface dataset:
Differences in cognitive impairment between schizophrenia and bipolar disorder: Considering the role of heterogeneity
Authors: Bora Emre
Published: May 2016

Schizophrenia is associated with significant cognitive impairment. Bipolar disorder (BD) also presents with cognitive deficits that are similar to, albeit less severe, than those reported in schizophrenia. There has been controversy over whether selective deficits in social cognition or developmental trajectory of cognitive deficits can distinguish schizophrenia from BD. Also, available studies have not generally considered the potential effect of cognitive heterogeneity within the two disorders on between‐group differences. The current review examines the evidence on the specificity of social cognitive deficits and early neurocognitive impairment to schizophrenia and explores the overall outcome of studies investigating within and cross‐diagnosis cognitive heterogeneity in schizophrenia and BD. Current evidence does not support the specificity of social cognitive impairment to schizophrenia. Available studies also suggest that cognitive impairment in premorbid and early stages is evident not only in schizophrenia but also in many BD patients. Both schizophrenia and BD have a number of cognitive subgroups, including severe impairment, good functioning, and one or more selective or modest impairment clusters. While both disorders are represented in each cognitive subgroup, there are significant cross‐diagnostic differences regarding prevalences of individuals belonging to the severe impairment and good functioning subgroups. Individuals with schizophrenia are much more likely to exhibit severe cognitive impairment than individuals with BD and good cognitive functioning is more often observed in BD patients than schizophrenia patients. Further identification of the neurobiological and genetic characteristics of the cognitive subgroups in major psychoses can improve the validity of diagnostic systems and can advance the development of personalized management approaches, including cognitive remediation.
Pilot study on the feasibility of limited focused real‐time echocardiography during pediatric renal transplantation
Authors: Taylor Katherine , Lorenzo Armando , Mertens Luc , Dragulescu Andreea
Published: May 2016

Pediatric renal transplantation protocols describe supraphysiological blood pressure and CVP to optimize graft perfusion. Ideal CVP and blood pressure targets in children are uncertain and difficult to achieve and/or sustain without incurring morbidity. We correlated intra‐operative ECHO with standard monitoring to assess intravascular volume at critical intra‐operative stages. A feasibility pilot study of real‐time limited ECHO images during four critical stages of pediatric renal transplantation (baseline; venous and arterial clamps on; clamps off; 5–10 min post‐clamp release) was conducted. Simultaneous CVP, SBP and DBP measurements were obtained with ECHO images. A surgeon blinded to the ECHO study assessed the quality of graft perfusion. Thirteen patients (nine TTE and four TEE) were enrolled. The CI increased in all patients at vascular clamp removal and the post‐resuscitation period (average increase in CI 20%, range 8–49%). SBP, DBP and CVP were inconsistent. ECHO data confirmed an appropriate CI increase even when the targeted CVP and BP values described in protocols were not achieved. The surgeons were satisfied with graft perfusion in 12 of 13 cases, with one locally obstructed vessel. We suggested that aiming for fixed targets in CVP and BP is not necessary to augment CI and encourage good renal perfusion.
Survival of high‐risk pediatric neuroblastoma patients in a developing country
Authors: Easton Joseph C. , Gomez Sergio , Asdahl Peter H. , Conner J. Michael , Fynn Alcira B. , Ruiz Claudia , Ojha Rohit P.
Published: May 2016

Little information is available about survival of high‐risk pediatric neuroblastoma patients in developing countries. We aimed to assess survival among high‐risk pediatric neuroblastoma patients in La Plata, Argentina. Individuals eligible for our cohort were aged <20 yr when diagnosed with high‐risk neuroblastoma and received cancer‐directed therapy including stem cell transplantation at Hospital de Niños Sor Maria Ludovica between February 1999 and February 2015. We estimated overall survival probabilities using an extended Kaplan–Meier approach. Our study population comprised 39 high‐risk neuroblastoma patients, of whom 39% were aged >4 yr at diagnosis, 54% were male, and 62% had adrenal neuroblastoma. We observed 18 deaths, and the median survival time of our study population was 1.7 yr. The five‐yr overall survival probability was 24% (95% CL: 10%, 41%). In contrast, five‐yr survival of high‐risk neuroblastoma patients ranges between 23% and 76% in developed countries. Survival among high‐risk neuroblastoma patients is generally poor regardless of geographic location, but our results illustrate dramatically worse survival for patients in a developing country. We speculate that the observed survival differences could be attenuated or eliminated with improvements in treatment and supportive care, but addressing these issues will require creative solutions because of resource limitations.
Using International Videoconferencing to Extend the Global Reach of Community Health Nursing Education
Authors: Ziemba Rosemary , Sarkar Norma J. , Pickus Becca , Dallwig Amber , Wan Jiayi Angela , Alcindor Hilda
Published: May 2016

Travel abroad provides college students with a unique learning experience. When plans to take undergraduate community health nursing students from the United States to Haiti were cancelled due to health and safety concerns, faculty piloted international videoconferencing with a nursing program in Haiti as an alternative. During this semester‐long course, students in both countries assessed a local community using the Community as Partner framework and compared findings during videoconferences with their international peers. Despite communication challenges such as language barriers and limited internet access in Haiti, evaluative data suggests that all students valued learning with their nursing student peers in another country. For future international videoconferencing endeavors, especially with under‐resourced communities, we provide recommendations in the following categories: 1) Building relationships with a partner school, 2) Technology, 3) Pedagogy, and 4) Facilitating interactions between students.
New aphid vectors and efficiency of transmission of Potato virus A and strains of Potato virus Y in the UK
Authors: Fox A. , Collins L. E. , Macarthur R. , Blackburn L. F. , Northing P.
Published: May 2016

The aphid‐transmitted viruses Potato virus Y (PVY) and Potato virus A (PVA) commonly affect seed potatoes in the UK. The transmission efficiency for aphid species is used to calculate a potential transmission risk and is expressed as a relative efficiency factor (REF). These REFs have not previously been calculated for UK strains of viruses or aphid clones. Using a previously published method, REFs have been calculated for the aphid species and viruses commonly occurring in UK potatoes. The efficiency of transmission of Myzus persicae is nominally set to a REF of 1 and REFs for other species are calculated relative to this. These data represent the first set of REFs calculated for PVA transmission. Macrosiphum euphorbiae (REF 0.91) was almost as efficient as M. persicae at PVA transmission. The data were further analysed to compare transmission rates of PVY and PVA using a binomial (logit) generalized mixed model to take into account the potential influence of variation in virus titre between leaves. This approach found that there is little variation between the efficiency of transmission between clones of each aphid species or between strains within a virus species. This is a first report that Aphis fabae, Metopolophium dirhodum, Sitobion avenae, Acyrthosiphon pisum and Cavariella aegopodii have the ability to vector PVA. This study also represents a first report that C. aegopodii has the ability to vector PVY and confirms the potential of S. avenae, A. fabae, M. euphorbiae and Rhopalosiphum padi as important PVY vectors.
Nighttime evaporative demand induces plasticity in leaf and root hydraulic traits
Authors: Claverie Elodie , Schoppach Rémy , Sadok Walid
Published: May 2016

Increasing evidence suggests that nocturnal transpiration rate (TRN) is a non‐negligible contributor to global water cycles. Short‐term variation in nocturnal vapor pressure deficit (VPDN) has been suggested to be a key environmental variable influencing TRN. However, the long‐term effects of VPDN on plant growth and development remain unknown, despite recent evidence documenting long‐term effects of daytime VPD on plant anatomy, growth and productivity. Here we hypothesized that plant anatomical and functional traits influencing leaf and root hydraulics could be influenced by long‐term exposure to VPDN. A total of 23 leaf and root traits were examined on four wheat (Triticum aestivum) genotypes, which were subjected to two long‐term (30 day long) growth experiments where daytime VPD and daytime/nighttime temperature regimes were kept identical, with variation only stemming from VPDN, imposed at two levels (0.4 and 1.4 kPa). The VPDN treatment did not influence phenology, leaf areas, dry weights, number of tillers or their dry weights, consistently with a drought and temperature‐independent treatment. In contrast, vein densities, adaxial stomata densities, TRN and cuticular TR, were strongly increased following exposure to high VPDN. Simultaneously, whole‐root system xylem sap exudation and seminal root endodermis thickness were decreased, hypothetically indicating a change in root hydraulic properties. Overall these results suggest that plants ‘sense’ and adapt to variations in VPDN conditions over developmental scales by optimizing both leaf and root hydraulics.
All 17 S‐locus F‐box proteins of the S2‐ and S3‐haplotypes of Petunia inflata are assembled into similar SCF complexes with a specific function in self‐incompatibility
Authors: Li Shu , Williams Justin S. , Sun Penglin , Kao Teh‐hui
Published: May 2016

The collaborative non‐self‐recognition model for S‐RNase‐based self‐incompatibility predicts that multiple S‐locus F‐box proteins (SLFs) produced by pollen of a given S‐haplotype collectively mediate ubiquitination and degradation of all non‐self S‐RNases, but not self S‐RNases, in the pollen tube, thereby resulting in cross‐compatible pollination but self‐incompatible pollination. We had previously used pollen extracts containing GFP‐fused S2‐SLF1 (SLF1 with an S2‐haplotype) of Petunia inflata for co‐immunoprecipitation (Co‐IP) and mass spectrometry (MS), and identified PiCUL1‐P (a pollen‐specific Cullin1), PiSSK1 (a pollen‐specific Skp1‐like protein) and PiRBX1 (a conventional Rbx1) as components of the SCFS2–SLF1 complex. Using pollen extracts containing PiSSK1:FLAG:GFP for Co‐IP/MS, we identified two additional SLFs (SLF4 and SLF13) that were assembled into SCFSLF complexes. As 17 SLF genes (SLF1 to SLF17) have been identified in S2 and S3 pollen, here we examined whether all 17 SLFs are assembled into similar complexes and, if so, whether these complexes are unique to SLFs. We modified the previous Co‐IP/MS procedure, including the addition of style extracts from four different S‐genotypes to pollen extracts containing PiSSK1:FLAG:GFP, to perform four separate experiments. The results taken together show that all 17 SLFs and an SLF‐like protein, SLFLike1 (encoded by an S‐locus‐linked gene), co‐immunoprecipitated with PiSSK1:FLAG:GFP. Moreover, of the 179 other F‐box proteins predicted by S2 and S3 pollen transcriptomes, only a pair with 94.9% identity and another pair with 99.7% identity co‐immunoprecipitated with PiSSK1:FLAG:GFP. These results suggest that SCFSLF complexes have evolved specifically to function in self‐incompatibility.
Multi‐level regulation of the chloroplast ATP synthase: the chloroplast NADPH thioredoxin reductase C (NTRC) is required for redox modulation specifically under low irradiance
Authors: Carrillo L. Ruby , Froehlich John E. , Cruz Jeffrey A. , Savage Linda J. , Kramer David M.
Published: May 2016

The chloroplast ATP synthase is known to be regulated by redox modulation of a disulfide bridge on the γ‐subunit through the ferredoxin–thioredoxin regulatory system. We show that a second enzyme, the recently identified chloroplast NADPH thioredoxin reductase C (NTRC), plays a role specifically at low irradiance. Arabidopsis mutants lacking NTRC (ntrc) displayed a striking photosynthetic phenotype in which feedback regulation of the light reactions was strongly activated at low light, but returned to wild‐type levels as irradiance was increased. This effect was caused by an altered redox state of the γ‐subunit under low, but not high, light. The low light‐specific decrease in ATP synthase activity in ntrc resulted in a buildup of the thylakoid proton motive force with subsequent activation of non‐photochemical quenching and downregulation of linear electron flow. We conclude that NTRC provides redox modulation at low light using the relatively oxidizing substrate NADPH, whereas the canonical ferredoxin–thioredoxin system can take over at higher light, when reduced ferredoxin can accumulate. Based on these results, we reassess previous models for ATP synthase regulation and propose that NTRC is most likely regulated by light. We also find that ntrc is highly sensitive to rapidly changing light intensities that probably do not involve the chloroplast ATP synthase, implicating this system in multiple photosynthetic processes, particularly under fluctuating environmental conditions.
High‐Level Ciprofloxacin‐Resistant Campylobacter jejuni Isolates Circulating in Humans and Animals in Incheon, Republic of Korea
Authors: Kim J. S. , Lee M. Y. , Kim S. J. , Jeon S.‐E. , Cha I. , Hong S. , Chung G. T. , Huh M.‐J. , Kang Y.‐H. , Yoo C.‐K. , Kim J.
Published: May 2016

Campylobacter jejuni is one of the major causative pathogens of outbreaks or sporadic cases of diarrhoeal diseases worldwide. In this study, we compared the phenotypic and genetic characteristics of C. jejuni isolates of human and food‐producing animal origins in Korea and examined the genetic relatedness between these two groups of isolates. Regardless of isolation source, all C. jejuni isolates harboured four virulence genes, cadF, cdtB, ciaB and racR, whereas the wlaN and virB11 genes were more frequently observed in human isolates. Antimicrobial susceptibility testing showed that the majority of C. jejuni isolates displayed high‐level resistance to fluoroquinolone (95.2%) or tetracycline (76.2%) antibiotics, and 12.4% of isolates exhibited multidrug resistance (more than three classes of antibiotics tested). Pulsed‐field gel electrophoresis (PFGE) of all Campylobacter isolates revealed 51 different SmaI‐PFGE patterns and six major clusters containing both human and animal isolates. These results indicate that genetically diverse strains of C. jejuni with antimicrobial drug‐resistance and virulence properties have prevailed in Incheon. Nevertheless, some particular populations continue to circulate within the community, providing the evidence for an epidemiological link of C. jejuni infections between humans and food‐producing animals. Therefore, the continued monitoring and surveillance of C. jejuni isolates of human and food‐producing animal origins are required for public health and food safety.
Genomic and transcriptomic predictors of response levels to endurance exercise training
Authors: Sarzynski Mark A. , Ghosh Sujoy , Bouchard Claude
Published: May 2016

Predicting the responsiveness to regular exercise is a topic of great relevance due to its potential role in personalized exercise medicine applications. The present review focuses on cardiorespiratory fitness (commonly measured by maximal oxygen uptake, ), a trait with wide‐ranging impact on health and performance indicators. Gains in demonstrate large inter‐individual variation even in response to standardized exercise training programmes. The estimated heritability of 47% suggests that genomic‐based predictors alone are insufficient to account for the total trainability variance. Candidate gene and genome‐wide linkage studies have not significantly contributed to our understanding of the molecular basis of trainability. A genome‐wide association study suggested that trainability is influenced by multiple genes of small effects, but these findings still await rigorous replication. Valuable evidence, however, has been obtained by combining skeletal muscle transcript abundance profiles with common DNA variants for the prediction of the response to exercise training. Although the physiological determinants of measured at a given time are largely enunciated, what is poorly understood are the details of tissue‐specific molecular mechanisms that limit and related signalling pathways in response to exercise training. Bioinformatics explorations based on thousands of variants have been used to interrogate pathways and systems instead of single variants and genes, and the main findings, along with those from exercise experimental studies, have been summarized here in a working model of trainability.

image
Mutation at a distance caused by homopolymeric guanine repeats in
Saccharomyces cerevisiae
Authors: McDonald Michael J. , Yu Yen-Hsin , Guo Jheng-Fen , Chong Shin Yen , Kao Cheng-Fu , Leu Jun-Yi
Published: May 2016

Short guanine repeats cause a
REV1
-dependent 4- to 18-fold increase in the substitution rate of the surrounding DNA sequence.
Structural basis of Dscam1 homodimerization: Insights into context constraint for protein recognition
Authors: Li Shu-Ang , Cheng Linna , Yu Yamei , Wang Jia-huai , Chen Qiang
Published: May 2016

Comparison of Dscam1 structures reveals the detailed mechanism of Dscam1 isoform-specific recognition.
Ricci curvature: An economic indicator for market fragility and systemic risk
Authors: Sandhu Romeil S. , Georgiou Tryphon T. , Tannenbaum Allen R.
Published: May 2016

Researchers introduce the geometric concept of curvature toward the application of uncovering systemic risk and market fragility.
Ecosystem context and historical contingency in apex predator recoveries
Authors: Stier Adrian C. , Samhouri Jameal F. , Novak Mark , Marshall Kristin N. , Ward Eric J. , Holt Robert D. , Levin Phillip S.
Published: May 2016

Variable life histories, species interactions, and historical contingency underlie why some predators recover and others do not.
Synchronization of optical photons for quantum information processing
Authors: Makino Kenzo , Hashimoto Yosuke , Yoshikawa Jun-ichi , Ohdan Hideaki , Toyama Takeshi , van Loock Peter , Furusawa Akira
Published: May 2016

We observe the Hong-Ou-Mandel interference via homodyne tomography on two photons extracted from two quantum memories.
Hydrogen atoms can be located accurately and precisely by x-ray crystallography
Authors: Woińska Magdalena , Grabowsky Simon , Dominiak Paulina M. , Woźniak Krzysztof , Jayatilaka Dylan
Published: May 2016

Hydrogen atoms cannot hide from x-rays anymore but can instead be detected very reliably in routine measurements.
Fundamentals of cancer metabolism
Authors: DeBerardinis Ralph J. , Chandel Navdeep S.
Published: May 2016

Researchers provide a conceptual framework to understand current knowledge of the fundamentals of cancer metabolism.
Structural basis for regulation of human calcium-sensing receptor by magnesium ions and an unexpected tryptophan derivative co-agonist
Authors: Zhang Chen , Zhang Tuo , Zou Juan , Miller Cassandra Lynn , Gorkhali Rakshya , Yang Jeong-Yeh , Schilmiller Anthony , Wang Shuo , Huang Kenneth , Brown Edward M. , Moremen Kelley W. , Hu Jian , Yang Jenny J.
Published: May 2016

Structural and functional characterization of the extracellular domain of the human CaSR with bound Mg
2+
and a tryptophan derivative.
Prebiotic chemicals—amino acid and phosphorus—in the coma of comet 67P/Churyumov-Gerasimenko
Authors: Altwegg Kathrin , Balsiger Hans , Bar-Nun Akiva , Berthelier Jean-Jacques , Bieler Andre , Bochsler Peter , Briois Christelle , Calmonte Ursina , Combi Michael R. , Cottin Hervé , De Keyser Johan , Dhooghe Frederik , Fiethe Bjorn , Fuselier Stephen A. , Gasc Sébastien , Gombosi Tamas I. , Hansen Kenneth C. , Haessig Myrtha , Jäckel Annette , Kopp Ernest , Korth Axel , Le Roy Lena , Mall Urs , Marty Bernard , Mousis Olivier , Owen Tobias , Rème Henri , Rubin Martin , Sémon Thierry , Tzou Chia-Yu , Hunter Waite James , Wurz Peter
Published: May 2016

The detection of glycine and phosphorus in the coma of 67P shows that comets contain all ingredients to help spark life on Earth.
Oxyhalides: A new class of high-
T

C

multiferroic materials
Authors: Zhao Li , Fernández-Díaz Maria Teresa , Tjeng Liu Hao , Komarek Alexander C.
Published: May 2016

Researchers discover a new class of magnetoelectric multiferroics with high critical temperature.
Encapsulation-free controlled release: Electrostatic adsorption eliminates the need for protein encapsulation in PLGA nanoparticles
Authors: Pakulska Malgosia M. , Elliott Donaghue Irja , Obermeyer Jaclyn M. , Tuladhar Anup , McLaughlin Christopher K. , Shendruk Tyler N. , Shoichet Molly S.
Published: May 2016

Researchers demonstrate that encapsulation is not necessary to achieve controlled, long-term protein release.
How To Live with Phosphorus Scarcity in Soil and Sediment: Lessons from Bacteria
Authors: Tapia-Torres Yunuen , Rodríguez-Torres Maria Dolores , Elser James J. , Islas Africa , Souza Valeria , García-Oliva Felipe , Olmedo-Álvarez Gabriela
Published: May 2016

Phosphorus (P) plays a fundamental role in the physiology and biochemistry of all living things. Recent evidence indicates that organisms in the oceans can break down and use P forms in different oxidation states (e.g., +5, +3, +1, and −3); however, information is lacking for organisms from soil and sediment. The Cuatro Ciénegas Basin (CCB), Mexico, is an oligotrophic ecosystem with acute P limitation, providing a great opportunity to assess the various strategies that bacteria from soil and sediment use to obtain P. We measured the activities in sediment and soil of different exoenzymes involved in P recycling and evaluated 1,163 bacterial isolates (mainly
Bacillus
spp.) for their ability to use six different P substrates. DNA turned out to be a preferred substrate, comparable to a more bioavailable P source, potassium phosphate. Phosphodiesterase activity, required for DNA degradation, was observed consistently in the sampled-soil and sediment communities. A capability to use phosphite (PO
3
3−
) and calcium phosphate was observed mainly in sediment isolates. Phosphonates were used at a lower frequency by both soil and sediment isolates, and phosphonatase activity was detected only in soil communities. Our results revealed that soil and sediment bacteria are able to break down and use P forms in different oxidation states and contribute to ecosystem P cycling. Different strategies for P utilization were distributed between and within the different taxonomic lineages analyzed, suggesting a dynamic movement of P utilization traits among bacteria in microbial communities.

IMPORTANCE
Phosphorus (P) is an essential element for life found in molecules, such as DNA, cell walls, and in molecules for energy transfer, such as ATP. The Valley of Cuatro Ciénegas, Coahuila (Mexico), is a unique desert characterized by an extreme limitation of P and a great diversity of microbial life. How do bacteria in this valley manage to obtain P? We measured the availability of P and the enzymatic activity associated with P release in soil and sediment. Our results revealed that soil and sediment bacteria can break down and use P forms in different oxidation states and contribute to ecosystem P cycling. Even genetically related bacterial isolates exhibited different preferences for molecules, such as DNA, calcium phosphate, phosphite, and phosphonates, as substrates to obtain P, evidencing a distribution of roles for P utilization and suggesting a dynamic movement of P utilization traits among bacteria in microbial communities.
Effects of Oxygen Availability on Acetic Acid Tolerance and Intracellular pH in Dekkera bruxellensis
Authors: Capusoni Claudia , Arioli Stefania , Zambelli Paolo , Moktaduzzaman M. , Mora Diego , Compagno Concetta
Published: May 2016

The yeast
Dekkera bruxellensis
, associated with wine and beer production, has recently received attention, because its high ethanol and acid tolerance enables it to compete with
Saccharomyces cerevisiae
in distilleries that produce fuel ethanol. We investigated how different cultivation conditions affect the acetic acid tolerance of
D. bruxellensis
. We analyzed the ability of two strains (CBS 98 and CBS 4482) exhibiting different degrees of tolerance to grow in the presence of acetic acid under aerobic and oxygen-limited conditions. We found that the concomitant presence of acetic acid and oxygen had a negative effect on
D. bruxellensis
growth. In contrast, incubation under oxygen-limited conditions resulted in reproducible growth kinetics that exhibited a shorter adaptive phase and higher growth rates than those with cultivation under aerobic conditions. This positive effect was more pronounced in CBS 98, the more-sensitive strain. Cultivation of CBS 98 cells under oxygen-limited conditions improved their ability to restore their intracellular pH upon acetic acid exposure and to reduce the oxidative damage to intracellular macromolecules caused by the presence of acetic acid. This study reveals an important role of oxidative stress in acetic acid tolerance in
D. bruxellensis
, indicating that reduced oxygen availability can protect against the damage caused by the presence of acetic acid. This aspect is important for optimizing industrial processes performed in the presence of acetic acid.

IMPORTANCE
This study reveals an important role of oxidative stress in acetic acid tolerance in
D. bruxellensis
, indicating that reduced oxygen availability can have a protective role against the damage caused by the presence of acetic acid. This aspect is important for the optimization of industrial processes performed in the presence of acetic acid.
Environmental Sequencing Provides Reasonable Estimates of the Relative Abundance of Specific Picoeukaryotes
Authors: Giner Caterina R. , Forn Irene , Romac Sarah , Logares Ramiro , de Vargas Colomban , Massana Ramon
Published: May 2016

High-throughput sequencing (HTS) is revolutionizing environmental surveys of microbial diversity in the three domains of life by providing detailed information on which taxa are present in microbial assemblages. However, it is still unclear how the relative abundance of specific taxa gathered by HTS correlates with cell abundances. Here, we quantified the relative cell abundance of 6 picoeukaryotic taxa in 13 planktonic samples from 6 European coastal sites using epifluorescence microscopy on tyramide signal amplification-fluorescence
in situ
hybridization preparations. These relative abundance values were then compared with HTS data obtained in three separate molecular surveys: 454 sequencing of the V4 region of the 18S ribosomal DNA (rDNA) using DNA and RNA extracts (DNA-V4 and cDNA-V4) and Illumina sequencing of the V9 region (cDNA-V9). The microscopic and molecular signals were generally correlated, indicating that a relative increase in specific 18S rDNA was the result of a large proportion of cells in the given taxa. Despite these positive correlations, the slopes often deviated from 1, precluding a direct translation of sequences to cells. Our data highlighted clear differences depending on the nucleic acid template or the 18S rDNA region targeted. Thus, the molecular signal obtained using cDNA templates was always closer to relative cell abundances, while the V4 and V9 regions gave better results depending on the taxa. Our data support the quantitative use of HTS data but warn about considering it as a direct proxy of cell abundances.

IMPORTANCE
Direct studies on marine picoeukaryotes by epifluorescence microscopy are problematic due to the lack of morphological features and due to the limited number and poor resolution of specific phylogenetic probes used in fluorescence
in situ
hybridization (FISH) routines. As a consequence, there is an increasing use of molecular methods, including high-throughput sequencing (HTS), to study marine microbial diversity. HTS can provide a detailed picture of the taxa present in a community and can reveal diversity not evident using other methods, but it is still unclear what the meaning of the sequence abundance in a given taxon is. Our aim is to investigate the correspondence between the relative HTS signal and relative cell abundances in selected picoeukaryotic taxa. Environmental sequencing provides reasonable estimates of the relative abundance of specific taxa. Better results are obtained when using RNA extracts as the templates, while the region of 18S ribosomal DNA had different influences depending on the taxa assayed.
Population Genetic Structure of Listeria monocytogenes Strains as Determined by Pulsed-Field Gel Electrophoresis and Multilocus Sequence Typing
Authors: Henri Clémentine , Félix Benjamin , Guillier Laurent , Leekitcharoenphon Pimlapas , Michelon Damien , Mariet Jean-François , Aarestrup Frank M. , Mistou Michel-Yves , Hendriksen René S. , Roussel Sophie
Published: May 2016

Listeria monocytogenes
is a ubiquitous bacterium that may cause the foodborne illness listeriosis. Only a small amount of data about the population genetic structure of strains isolated from food is available. This study aimed to provide an accurate view of the
L. monocytogenes
food strain population in France. From 1999 to 2014, 1,894
L. monocytogenes
strains were isolated from food at the French National Reference Laboratory for
L. monocytogenes
and classified according to the five risk food matrices defined by the European Food Safety Authority (EFSA). A total of 396 strains were selected on the basis of different pulsed-field gel electrophoresis (PFGE) clusters, serotypes, and strain origins and typed by multilocus sequence typing (MLST), and the MLST results were supplemented with MLST data available from Institut Pasteur, representing human and additional food strains from France. The distribution of sequence types (STs) was compared between food and clinical strains on a panel of 675 strains. High congruence between PFGE and MLST was found. Out of 73 PFGE clusters, the two most prevalent corresponded to ST9 and ST121. Using original statistical analysis, we demonstrated that (i) there was not a clear association between ST9 and ST121 and the food matrices, (ii) serotype IIc, ST8, and ST4 were associated with meat products, and (iii) ST13 was associated with dairy products. Of the two major STs, ST121 was the ST that included the fewest clinical strains, which might indicate lower virulence. This observation may be directly relevant for refining risk analysis models for the better management of food safety.

IMPORTANCE
This study showed a very useful backward compatibility between PFGE and MLST for surveillance. The results enabled better understanding of the population structure of
L. monocytogenes
strains isolated from food and management of the health risks associated with
L. monocytogenes
food strains. Moreover, this work provided an accurate view of
L. monocytogenes
strain populations associated with specific food matrices. We clearly showed that some STs were associated with food matrices, such as meat, meat products, and dairy products. We opened the way to source attribution modeling in order to quantify the relative importance of the main food matrices.
Genome Evolution and Nitrogen Fixation in Bacterial Ectosymbionts of a Protist Inhabiting Wood-Feeding Cockroaches
Authors: Tai Vera , Carpenter Kevin J. , Weber Peter K. , Nalepa Christine A. , Perlman Steve J. , Keeling Patrick J.
Published: May 2016

By combining genomics and isotope imaging analysis using high-resolution secondary ion mass spectrometry (NanoSIMS), we examined the function and evolution ofBacteroidalesectosymbionts of the protistBarbulanymphafrom the hindguts of the wood-eating cockroachCryptocercus punctulatus. In particular, we investigated the structure of ectosymbiont genomes, which, in contrast to those of endosymbionts, has been little studied to date, and tested the hypothesis that these ectosymbionts fix nitrogen. Unlike with most obligate endosymbionts, genome reduction has not played a major role in the evolution of theBarbulanymphaectosymbionts. Instead, interaction with the external environment has remained important for this symbiont as genes for synthesis of transporters, outer membrane proteins, lipopolysaccharides, and lipoproteins have been retained. The ectosymbiont genome carried two complete operons for nitrogen fixation, a urea transporter, and a urease, indicating the availability of nitrogen as a driving force behind the symbiosis. NanoSIMS analysis ofC. punctulatushindgut symbionts exposedin vivoto15N2supports the hypothesis thatBarbulanymphaectosymbionts are capable of nitrogen fixation. This genomic andin vivofunctional investigation of protist ectosymbionts highlights the diversity of evolutionary forces and trajectories that shape symbiotic interactions.

IMPORTANCEThe ecological and evolutionary importance of symbioses is increasingly clear, but the overall diversity of symbiotic interactions remains poorly explored. In this study, we investigated the evolution and nitrogen fixation capabilities of ectosymbionts attached to the protistBarbulanymphafrom the hindgut of the wood-eating cockroachCryptocercus punctulatus. In addressing genome evolution of protist ectosymbionts, our data suggest that the ecological pressures influencing the evolution of extracellular symbionts clearly differ from intracellular symbionts and organelles. Using NanoSIMS analysis, we also obtained direct imaging evidence of a specific hindgut microbe playing a role in nitrogen fixation. These results demonstrate the power of combining NanoSIMS and genomics tools for investigating the biology of uncultivable microbes. This investigation paves the way for a more precise understanding of microbial interactions in the hindguts of wood-eating insects and further exploration of the diversity and ecological significance of symbiosis between microbes.
Shape Changes and Interaction Mechanism of Escherichia coli Cells Treated with Sericin and Use of a Sericin-Based Hydrogel for Wound Healing
Authors: Xue Rui , Liu Yalong , Zhang Qingsong , Liang Congcong , Qin Huazhen , Liu Pengfei , Wang Ke , Zhang Xiaoyong , Chen Li , Wei Yen
Published: May 2016

To verify the interaction mechanism between sericin and
Escherichia coli
, especially the morphological and structural changes in the bacterial cells, the antimicrobial activity of sericin against
E. coli
as a model for Gram-negative bacteria was investigated. The antibacterial activity of sericin on
E. coli
and the interaction mechanism were investigated in this study by analyzing the growth, integrity, and morphology of the bacterial cells following treatment with sericin. The changes in morphology and cellular compositions of bacterial cells treated with sericin were observed by an inverted fluorescence microscope, scanning electron microscopy, and transmission electron microscopy. Changes in electrical conductivity, total sugar concentration of the broth for the bacteria, and protein expression of the bacteria were determined to investigate the permeability of the cell membrane. A sericin-based hydrogel was prepared for an
in vivo
study of wound dressing. The results showed that the antibacterial activity of the hydrogel increased with the increase in the concentration of sericin from 10 g/liter to 40 g/liter. The introduction of sericin induces membrane blebbing of
E. coli
cells caused by antibiotic action on the cell membrane. The cytoplasm shrinkage phenomenon was accompanied by blurring of the membrane wall boundaries. When
E. coli
cells were treated with sericin, release of intracellular components quickly increased. The electrical conductivity assay indicated that the charged ions are reduced after exposure to sericin so that the integrity of the cell membrane is weakened and metabolism is blocked. In addition, sodium dodecyl sulfate-polyacrylamide gel electrophoresis demonstrated that sericin hinders the expression of bacterial protein. Sericin may damage the integrity of the bacterial cell membrane, thereby eventually inhibiting the growth and reproduction of
E. coli
. Compared to sterile gauze, the sericin-based hydrogel promoted fibroblast cell proliferation and accelerated the formation of granulation tissues and neovessels.

IMPORTANCE
The specific relationship and interaction mechanism between sericin and
E. coli
cells were investigated and elucidated. The results show that after 12 h of treatment, sericin molecules induce membrane blebbing of
E. coli
cells, and the bacteria show decreases in liquidity and permeability of biological membrane, resulting in alterations in the conductivity of the culture medium and the integrity of the outer membrane. The subsequent
in vivo
results demonstrate that the sericin-poly(
N
-isopropylacrylamide-
N
,
N
′-methylene-bis-acrylamide [NIPAm-MBA]) hydrogel accelerated wound healing compared to that with sterile gauze, which is a beneficial result for future applications in clinical medicine and the textile, food, and coating industries.
Hyperconcentrated Sweet Whey, a New Culture Medium That Enhances Propionibacterium freudenreichii Stress Tolerance
Authors: Huang Song , Rabah Houem , Jardin Julien , Briard-Bion Valérie , Parayre Sandrine , Maillard Marie-Bernadette , Le Loir Yves , Chen Xiao Dong , Schuck Pierre , Jeantet Romain , Jan Gwénaël
Published: May 2016

Propionibacterium freudenreichii
is used as a cheese-ripening starter and as a probiotic. Its reported physiological effects at the gut level, including modulation of bifidobacteria, colon epithelial cell proliferation and apoptosis, and intestinal inflammation, rely on active metabolism
in situ
. Survival and activity are thus key factors determining its efficacy, creating stress adaptation and tolerance bottlenecks for probiotic applications. Growth media and growth conditions determine tolerance acquisition. We investigated the possibility of using sweet whey, a dairy by-product, to sustain
P. freudenreichii
growth. It was used at different concentrations (dry matter) as a culture medium. Using hyperconcentrated sweet whey led to enhanced multistress tolerance acquisition, overexpression of key stress proteins, and accumulation of intracellular storage molecules and compatible solutes, as well as enhanced survival upon spray drying. A simplified process from growth to spray drying of propionibacteria was developed using sweet whey as a 2-in-1 medium to both culture
P. freudenreichii
and protect it from heat and osmotic injury without harvesting and washing steps. As spray drying is far cheaper and more energy efficient than freeze-drying, this work opens new perspectives for the sustainable development of new starter and probiotic preparations with enhanced robustness.

IMPORTANCE
In this study, we demonstrate that sweet whey, a dairy industry by-product, not only allows the growth of probiotic dairy propionibacteria, but also triggers a multitolerance response through osmoadaptation and general stress response. We also show that propionibacteria accumulate compatible solutes under these culture conditions, which might account for the limited loss of viability after spray drying. This work opens new perspectives for more energy-efficient production of dairy starters and probiotics.
Detection of Antibiotic Resistance Genes in Source and Drinking Water Samples from a First Nations Community in Canada
Authors: Fernando Dinesh M. , Tun Hein Min , Poole Jenna , Patidar Rakesh , Li Ru , Mi Ruidong , Amarawansha Geethani E. A. , Fernando W. G. Dilantha , Khafipour Ehsan , Farenhorst Annemieke , Kumar Ayush
Published: May 2016

Access to safe drinking water is now recognized as a human right by the United Nations. In developed countries like Canada, access to clean water is generally not a matter of concern. However, one in every five First Nations reserves is under a drinking water advisory, often due to unacceptable microbiological quality. In this study, we analyzed source and potable water from a First Nations community for the presence of coliform bacteria as well as various antibiotic resistance genes. Samples, including those from drinking water sources, were found to be positive for various antibiotic resistance genes, namely,
ampC
,
tet
(A),
mecA
, β-lactamase genes (SHV-type, TEM-type, CTX-M-type, OXA-1, and CMY-2-type), and carbapenemase genes (KPC, IMP, VIM, NDM, GES, and OXA-48 genes). Not surprisingly, substantial numbers of total coliforms, including
Escherichia coli
, were recovered from these samples, and this result was also confirmed using Illumina sequencing of the 16S rRNA gene. These findings deserve further attention, as the presence of coliforms and antibiotic resistance genes potentially puts the health of the community members at risk.

IMPORTANCE
In this study, we highlight the poor microbiological quality of drinking water in a First Nations community in Canada. We examined the coliform load as well as the presence of antibiotic resistance genes in these samples. This study examined the presence of antibiotic-resistant genes in drinking water samples from a First Nations Community in Canada. We believe that our findings are of considerable significance, since the issue of poor water quality in First Nations communities in Canada is often ignored, and our findings will help shed some light on this important issue.
Anaplasma marginale Actively Modulates Vacuolar Maturation during Intracellular Infection of Its Tick Vector, Dermacentor andersoni
Authors: Magunda Forgivemore , Thompson Chelsea Wright , Schneider David A. , Noh Susan M.
Published: May 2016

Tick-borne transmission of bacterial pathogens in the orderRickettsialesis responsible for diverse infectious diseases, many of them severe, in humans and animals. Transmission dynamics differ among these pathogens and are reflected in the pathogen-vector interaction.Anaplasma marginalehas been shown to establish and maintain infectivity withinDermacentorspp. for weeks to months while escaping the complex network of vacuolar peptidases that are responsible for digestion of the tick blood meal. How this prolonged maintenance of infectivity in a potentially hostile environment is achieved has been unknown. Using the natural vectorDermacentor andersoni, we demonstrated thatA. marginale-infected tick vacuoles (AmVs) concurrently recruit markers of the early endosome (Rab5), recycling endosome (Rab4 and Rab11), and late endosome (Rab7), are maintained near neutral pH, do not fuse with lysosomes, exclude the protease cathepsin L, and engage the endoplasmic reticulum and Golgi apparatus for up to 21 days postinfection. Maintenance of this safe vacuolar niche requires activeA. marginaleprotein synthesis; in its absence, the AmVs mature into acidic, protease-active phagolysosomes. Identification of this bacterially directed modeling of the tick midgut endosome provides a mechanistic basis for examination of the differences in transmission efficiency observed amongA. marginalestrains and among vector populations.

IMPORTANCETicks transmit a variety of intracellular bacterial pathogens that cause significant diseases in humans and animals. For successful transmission, these bacterial pathogens must first gain entry into the tick midgut digestive cells, avoid digestion, and establish a replicative niche without harming the tick vector. Little is known about how this replicative niche is established and maintained. Using the ruminant pathogenA. marginaleand its natural tick vector,D. andersoni, this study characterized the features of theA. marginaleniche in the tick midgut and demonstrates thatA. marginaleprotein synthesis is required for the maintenance of this niche. This work opens a new line of inquiry about the pathogen effectors and their targets within the tick that mediate tick-pathogen interactions and ultimately serve as the determinants of pathogen success.
Vibrio anguillarum Is Genetically and Phenotypically Unaffected by Long-Term Continuous Exposure to the Antibacterial Compound Tropodithietic Acid
Authors: Rasmussen Bastian Barker , Grotkjær Torben , D'Alvise Paul W. , Yin Guangliang , Zhang Faxing , Bunk Boyke , Spröer Cathrin , Bentzon-Tilia Mikkel , Gram Lone
Published: May 2016

Minimizing the use of antibiotics in the food production chain is essential for limiting the development and spread of antibiotic-resistant bacteria. One alternative intervention strategy is the use of probiotic bacteria, and bacteria of the marine
Roseobacter
clade are capable of antagonizing fish-pathogenic vibrios in fish larvae and live feed cultures for fish larvae. The antibacterial compound tropodithietic acid (TDA), an antiporter that disrupts the proton motive force, is key in the antibacterial activity of several roseobacters. Introducing probiotics on a larger scale requires understanding of any potential side effects of long-term exposure of the pathogen to the probionts or any compounds they produce. Here we exposed the fish pathogen
Vibrio anguillarum
to TDA for several hundred generations in an adaptive evolution experiment. No tolerance or resistance arose during the 90 days of exposure, and whole-genome sequencing of TDA-exposed lineages and clones revealed few mutational changes, compared to lineages grown without TDA. Amino acid-changing mutations were found in two to six different genes per clone; however, no mutations appeared unique to the TDA-exposed lineages or clones. None of the virulence genes of
V. anguillarum
was affected, and infectivity assays using fish cell lines indicated that the TDA-exposed lineages and clones were less invasive than the wild-type strain. Thus, long-term TDA exposure does not appear to result in TDA resistance and the physiology of
V. anguillarum
appears unaffected, supporting the application of TDA-producing roseobacters as probiotics in aquaculture.

IMPORTANCE
It is important to limit the use of antibiotics in our food production, to reduce the risk of bacteria developing antibiotic resistance. We showed previously that marine bacteria of the
Roseobacter
clade can prevent or reduce bacterial diseases in fish larvae, acting as probiotics. Roseobacters produce the antimicrobial compound tropodithietic acid (TDA), and we were concerned regarding whether long-term exposure to this compound could induce resistance or affect the disease-causing ability of the fish pathogen. Therefore, we exposed the fish pathogen
Vibrio anguillarum
to increasing TDA concentrations over 3 months. We did not see the development of any resistance to TDA, and subsequent infection assays revealed that none of the TDA-exposed clones had increased virulence toward fish cells. Hence, this study supports the use of roseobacters as a non-risk-based disease control measure in aquaculture.