bluuebunny/crossref_metadata_2025 huggingface dataset:
The effect of crack cocaine addiction and age on the microstructure and morphology of the human striatum and thalamus using shape analysis and fast diffusion kurtosis imaging
Authors: Garza-Villarreal Eduardo A , Mallar Chakravarty M , Hansen Brian , Eskildsen Simon F , Devenyi Gabriel A. , Castillo-Padilla Diana , Balducci Thania , Reyes-Zamorano Ernesto , Jespersen Sune N , Perez-Palacios Pamela , Patel Raihaan , Gonzalez-Olvera Jorge J
Published: July 2016

The striatum and thalamus are subcortical structures intimately involved in addiction. The morphology and microstructure of these have been studied in murine models of cocaine addiction, showing an effect of drug use, but also chronological age in morphology. Human studies using non-invasive MRI have shown inconsistencies in volume changes, and have also shown an age effect. In this exploratory study, we used MRI-based volumetric and novel shape analysis, as well as a novel fast diffusion kurtosis imaging sequence to study the morphology and microstructure of striatum and thalamus in crack cocaine addiction (CA) compared to matched healthy controls (HC), while investigating the effect of age and years of cocaine consumption. We did not find significant differences in volume and mean kurtosis (MKT) between groups. However, we found significant contraction of nucleus accumbens in CA compared to HC. We also found significant age related changes in volume and MKT of CA in striatum and thalamus that are different to those seen in normal aging. Interestingly, we found different effects and contributions of age and years of consumption in volume, displacement and MKT changes, suggesting each measure provides different but complementing information about morphological brain changes and that not all changes are related to the toxicity or the addiction to the drug. Our findings suggest that the use of finer methods and sequences provide complementing information about morphological and microstructural changes in cocaine addiction, and that brain alterations in cocaine addiction are related cocaine use and age differently.
Examining the occupancy-density relationship for a low density carnivore
Authors: Linden Daniel W. , Fuller Angela K. , Royle J. Andrew , Hare Matthew P.
Published: July 2016

The challenges associated with monitoring low-density carnivores across large landscapes have limited the ability to implement and evaluate conservation and management strategies for such species. Noninvasive sampling techniques and advanced statistical approaches have alleviated some of these challenges and can even allow for spatially explicit estimates of density, arguably the most valuable wildlife monitoring tool.

For some species, individual identification comes at no cost when unique attributes (e.g., pelage patterns) can be discerned with remote cameras, while other species require viable genetic material and expensive lab processing for individual assignment. Prohibitive costs may still force monitoring efforts to use species distribution or occupancy as a surrogate for density, which may not be appropriate under many conditions.

Here, we used a large-scale monitoring study of fisherPekania pennantito evaluate the effectiveness of occupancy as an approximation to density, particularly for informing harvest management decisions. We used a combination of remote cameras and baited hair snares during 2013–2015 to sample across a 70,096 km2region of western New York, USA. We fit occupancy and Royle-Nichols models to species detection-nondetection data collected by cameras, and spatial capture-recapture models to individual encounter data obtained by genotyped hair samples.

We found a close relationship between grid-cell estimates of fisher state variables from the models using detection-nondetection data and those from the SCR model, likely due to informative spatial covariates across a large landscape extent and a grid cell resolution that worked well with the movement ecology of the species. Spatially-explicit management recommendations for fisher were similar across models. We discuss design-based approaches to occupancy studies that can improve approximations to density.
Cross-scale dynamics and the evolutionary emergence of infectious diseases
Authors: Schreiber Sebastian J. , Ke Ruian , Loverdo Claude , Park Miran , Ahsan Prianna , Lloyd-Smith James O.
Published: July 2016

Abstract

When emerging pathogens encounter new host species for which they are poorly adapted, they must evolve to escape extinction. Pathogens experience selection on traits at multiple scales, including replication rates within host individuals and transmissibility between hosts. We analyze a stochastic model linking pathogen growth and competition within individuals to transmission between individuals. Our analysis reveals a new factor, the cross-scale reproductive number of a mutant virion, that quantifies how quickly mutant strains increase in frequency when they initially appear in the infected host population. This cross-scale reproductive number combines with viral mutation rates, single-strain reproductive numbers, and transmission bottleneck width to determine the likelihood of evolutionary emergence, and whether evolution occurs swiftly or gradually within chains of transmission. We find that wider transmission bottlenecks facilitate emergence of pathogens with short-term infections, but hinder emergence of pathogens exhibiting cross-scale selective conflict and long-term infections. Our results provide a framework to advance the integration of laboratory, clinical and field data in the context of evolutionary theory, laying the foundation for a new generation of evidence-based risk assessment of emergence threats.
Quantifying climate change impacts emphasises the importance of managing regional threats in the endangered Yellow-eyed penguin
Authors: Mattern Thomas , Meyer Stefan , Ellenberg Ursula , Houston David M. , Darby John T. , Young Melanie , van Heezik Yolanda , Seddon Philip J.
Published: July 2016

Climate change is a global issue with effects that are difficult to manage at a regional scale. Yet more often than not climate factors are just some of multiple stressors affecting species on a population level. Non-climatic factors - especially those of anthropogenic origins - may play equally important roles with regard to impacts on species and are often more feasible to address. Here we assess the influence of climate change on population trends of the endangered Yellow-eyed penguin (Megadyptes antipodes) over the last 30 years, using a Bayesian model. Sea surface temperature (SST) proved to be the dominating factor influencing survival of both adult birds and fledglings. Increasing SST since the mid-1990s was accompanied by a reduction in survival rates and population decline. The population model showed that 33% of the variation in population numbers could be explained by SST alone, significantly increasing pressure on the penguin population. Consequently, the population becomes less resilient to non-climate related impacts, such as fisheries interactions, habitat degradation and human disturbance. However, the extent of the contribution of these factors to declining population trends is extremely difficult to assess principally due to the absence of quantifiable data, creating a discussion bias towards climate variables, and effectively distracting from non-climate factors that can be managed on a regional scale to ensure the viability of the population.
Cohort Specific Effects of Cereal-bar Supplementation in Overweight Patients With or Without Type 2 Diabetes Mellitus
Authors: Jason Chou Chieh , Lauber Chris , Chakrabarti Anirikh , Siddharth Jay , Chalut-Carpentier Anne , Pataky Zoltan , Golay Alain , Parkinson Scott
Published: July 2016

The importance of gut microbes to metabolic health is becoming more evident and nutrition-based therapies to alter the composition of bacterial communities to manage metabolic disease are an attractive avenue to ameliorate some effects of Western diets. While the composition of gut microbial communities can vary significantly across disease states, it is not well known if these communities have common responses to nutritional interventions. To better understand fiber-bacterial community interactions, we collected biological parameters and fecal samples of overweight non-diabetic (OND) and diabetic (OD) individuals before and after daily supplementation of 2.8 g β-glucan on their habitual diet for 30 days. Fecal bacterial communities in an age-matched cohort were measured by sequencing partial 16S rRNA genes and imputed metagenomic content. Unexpectedly, we observed disconnected responses of biological measurements and the bacterial community. Based on average effect size, biological measurements were greater in the OND group while effects on the bacterial community were greatest on the OD cohort, and we suspect these observations are due to the significantly lower alpha diversity in the OD cohort. Our data indicate that responses to fiber supplementation are cohort specific and this should be considered when manipulating the microbiome via fiber supplementation.
Genetic diagnosis of Mendelian disorders via RNA sequencing
Authors: Kremer Laura S , Bader Daniel M , Mertes Christian , Kopajtich Robert , Pichler Garwin , Iuso Arcangela , Haack Tobias B , Graf Elisabeth , Schwarzmayr Thomas , Terrile Caterina , Koňařiková Eliška , Repp Birgit , Kastenmüller Gabi , Adamski Jerzy , Lichtner Peter , Leonhardt Christoph , Funalot Benoit , Donati Alice , Tiranti Valeria , Lombes Anne , Jardel Claude , Gläser Dieter , Taylor Robert W. , Ghezzi Daniele , Mayr Johannes A , Rötig Agnes , Freisinger Peter , Distelmaier Felix , Strom Tim M , Meitinger Thomas , Gagneur Julien , Prokisch Holger
Published: July 2016

Across a large variety of Mendelian disorders, ~50-75% of patients do not receive a genetic diagnosis by whole exome sequencing indicative of underlying disease-causing variants in non-coding regions. In contrast, whole genome sequencing facilitates the discovery of all genetic variants, but their sizeable number, coupled with a poor understanding of the non-coding genome, makes their prioritization challenging. Here, we demonstrate the power of transcriptome sequencing to provide a confirmed genetic diagnosis for 10% (5 of 48) of undiagnosed mitochondrial disease patients and identify strong candidate genes for patients remaining without diagnosis. We found a median of 1 aberrantly expressed gene, 5 aberrant splicing events, and 6 mono-allelically expressed rare variants in patient-derived fibroblasts and established disease-causing roles for each kind. Private exons often arose from sites that are weakly spliced in other individuals, providing an important clue for future variant prioritization. One such intronic exon-creating variant was found in three unrelated families in the complex I assembly factor TIMMDC1, which we consequently established as a novel disease-associated gene. In conclusion, our study expands the diagnostic tools for detecting non-exonic variants of Mendelian disorders and provides examples of intronic loss-of-function variants with pathological relevance.
Independent modes of ganglion cell translocation ensure correct lamination of the zebrafish retina
Authors: Icha Jaroslav , Grunert Christiane , Rocha-Martins Mauricio , Norden Caren
Published: July 2016

The arrangement of neurons into distinct layers is critical for neuronal connectivity and function of the nervous system. During development, most neurons move from their birthplace to the appropriate layer, where they polarize. However, kinetics and modes of many neuronal translocation events still await exploration. Here, we investigate ganglion cell (RGC) translocation across the embryonic zebrafish retina. After completing their translocation, RGCs establish the most basal retinal layer where they form the optic nerve. Usingin totolight sheet microscopy, we show that somal translocation of RGCs is a fast and directed event. It depends on basal process attachment and stabilized microtubules. Interestingly, interference with somal translocation induces a switch to multipolar migration. This multipolar mode is less efficient but still leads to successful RGC layer formation. When both modes are inhibited, RGCs that fail to translocate induce lamination defects, indicating that correct RGC translocation is crucial for subsequent retinal lamination.
Bright photoactivatable fluorophores for single-molecule imaging
Authors: Grimm Jonathan B. , English Brian P. , Muthusamy Anand K. , Mehl Brian P. , Dong Peng , Brown Timothy A. , Liu Zhe , Lionnet Timothée , Lavis Luke D.
Published: July 2016

Small molecule fluorophores are important tools for advanced imaging experiments. The development of self-labeling protein tags such as the HaloTag and SNAP-tag has expanded the utility of chemical dyes in live-cell microscopy. We recently described a general method for improving the brightness and photostability of small, cell-permeable fluorophores, resulting in the azetidine-containing “Janelia Fluor” (JF) dyes. Here, we refine and extend the utility of the JF dyes by synthesizing photoactivatable derivatives that are compatible with established live-cell labeling strategies. These compounds retain the superior brightness of the JF dyes but their facile photoactivation enables improved single-particle tracking and localization microscopy experiments.
Inconsistencies inC. elegansbehavioural annotation
Authors: Szigeti Balázs , Stone Thomas , Webb Barbara
Published: July 2016

High quality behavioural annotation is a key component to link genes to behaviour, yet relatively little attention has been paid to check the consistency of various automated methods and expert judgement. In this paper we investigate the consistency of annotation for the ‘Omega turn’ ofC. elegans, which is a frequently used behavioural assay for this animal. First the output of four Omega detection algorithms are examined for the same data set, and shown to have relative low consistency, with F-scores around 0.5. Consistency of expert annotation is then analysed, based on an online survey combining two methods: participants judged a fixed set of predetermined clips; and an adaptive psychophysical procedure was used to estimate individual’s threshold for Omega turn detection. This survey also revealed a substantial lack of consistency in decisions and thresholds. Such inconsistency makes cross-publication comparison difficult and raises issues of reproducibility.
A statistical definition for reproducibility and replicability
Authors: Patil Prasad , Peng Roger D. , Leek Jeffrey T.
Published: July 2016

Everyone agrees that reproducibility and replicability are fundamental characteristics of scientific studies. These topics are attracting increasing attention, scrutiny, and debate both in the popular press and the scientific literature. But there are no formal statistical definitions for these concepts, which leads to confusion since the same words are used for different concepts by different people in different fields. We provide formal and informal definitions of scientific studies, reproducibility, and replicability that can be used to clarify discussions around these concepts in the scientific and popular press.
Temporal Stability and Molecular Persistence of the Bone Marrow Plasma Cell Antibody Repertoire
Authors: Wu Gabriel C. , Cheung Nai-Kong V. , Georgiou George , Marcotte Edward M. , Ippolito Gregory C.
Published: July 2016

Plasma cells in human bone marrow (BM PCs) are thought to be intrinsically long-lived and to be responsible for sustaining lifelong immunity through the constitutive secretion of antibody—but the underlying basis for this serological memory remains controversial. Here, we analyzed the molecular persistence of serological immunity by an examination of BM PC immunoglobulin heavy-chain (IGH) transcripts derived from serial bone marrow specimens obtained during a span of several years. Using high-throughput sequence analysis of the same individual for 6.5 years, we show that the BM PC repertoire is remarkably stable over time. We find that the bias in IGH V, D, and J individual gene usage and also the combinatorial V–D, V–J, D–J, and V-D-J usage across time to be nearly static. When compared to a second donor with time points 2 years apart, these overall patterns are preserved, and surprisingly, we find high correlation of gene usage between the two donors. Lastly, we report the persistence of numerous BM PC clonal clusters (~2%) identifiable across 6.5 years at all time points assayed, supporting a model of serological memory based, at least in part, upon intrinsic longevity of human PCs. We anticipate that this longitudinal study will facilitate the ability to differentiate between healthy and diseased antibody repertoire states, by serving as a point of comparison with future deep-sequencing studies involving immune intervention.
Rapid Germination of a Barley Mutant Is Correlated with a Rapid Turnover of Abscisic Acid Outside the Embryo
Authors: Visser K. , Vissers APA. , Cagirgan M. I. , Kijne J. W. , Wang M.
Published: August 2016

In our study of the role of abscisic acid (ABA) in controlling the germination of barley grains, we tested a barley mutant line with a gigantum appearance (Hordeum distichum cv Quantum) for an ABA-insensitive phenotype by assaying germination in the presence of 10–4 M ABA. Dissected embryos of the mutant germinated at least 10 h earlier than did those of the wild type. The half-maximal concentrations of ABA inhibitory for germination were determined to be 5 x 10–4 M for the mutant and 10–6 M for the wild type. Expression of an ABA-induced Rab gene was studied to determine ABA responsiveness. The ABA concentration required for a half-maximal induction of Rab gene expression was 4 x 10–6 M in isolated embryos of both the mutant and wild type. This result suggests that ABA signal transduction pathways were not affected in the mutant. When isolated embryos were allowed to imbibe in water, ABA was released from the mutant and wild-type embryos at the same rate. However, the free ABA level in the incubation medium of the mutant showed a much faster decrease than that of the wild type, as demonstrated by two independent ABA assay methods (high-performance liquid chromatography and enzyme-linked immunosorbent assay). Our results suggest that turnover of ABA outside the embryo is a determining factor in the germination of barley seeds.
Improving relations between users and libraries: a survey of Chinese academic libraries
Authors: Zhai Xiaojuan , Wang Jingjing
Published: August 2016

Purpose

This study aims to investigate the effectiveness of library services according to user experiences (UXs). The study discusses underlying internal problems existing in libraries that affect user satisfaction. Furthermore, it seeks to identify ways to improve the UX.

Design/methodology/approach

The methodology comprised a questionnaire administered at Nanjing University Library, China. The survey examined users’ satisfaction with the online public access catalogue, locating books on the shelves, and users’ participation in the organization of library resources. This study used the annual reading quantity of users system, a new system of measurement that distinguishes between informal and avid library users.

Findings

The data analysis indicated poor user satisfaction. The problems were mainly associated with the libraries’ resource organization, such as descriptive cataloguing, subject headings and classification, which is controlled by library administration. Moreover, users’ feedback is not integrated within the library system. Because of the process-oriented architecture of the current integrated library system, librarians and users do not communicate effectively. These barriers between users and the library staff members are difficult to overcome.

Originality/value

The study describes that the results relate to user satisfaction with searching and locating books based on the patron’s reading level. Differences were observed between light and avid readers in terms of satisfaction with the ease of searching and finding books. This demonstrates the internal connections of these results with library procedures. Furthermore, this study identifies improvement measures to resolve these problems.
What might Evans‐Pritchard have made of two degrees?
Authors: Rayner Steve
Published: August 2016

To what extent is the December 2015 Paris Agreement on climate change based on magical thinking?
Prevalence of halitosis in elderly living in nursing homes
Authors: Zellmer M , Gahnberg L , Ramberg P
Published: August 2016

Objectives

Halitosis is a concern for many people, but has sparsely been studied in elderly living in nursing homes. The aim of this investigation was to study the prevalence of halitosis in this particular group and factors that could be associated with this condition.

Method and materials

One hundred and twenty‐four residents at three different nursing homes were included in the study. The level of halitosis was assessed using an organoleptic method based on a 6‐graded scale. Oral status, including registrations of plaque, gingivitis and assessment of hyposalivation, was performed by two investigators who both examined all patients. Medical history, that is medication, neurological conditions, diabetes, cardiovascular disease, chronic obstructive pulmonary disease (COPD)/asthma, dementia and mental illness, was obtained from the patient files. Registrations of the use of oral hygiene aids, ADL (Activity of Daily Life) and the frequency of contact with dental services were included in the clinical examination.

Results

Halitosis occurred in over 50% of residents living in nursing homes and was found to be associated with the presence of hyposalivation, periodontal disease, calculus, fixed prosthodontics and dementia.

Conclusion

Halitosis was a common finding in the elderly living in Swedish nursing homes.
Encumbered by vulnerability and temporality – the meanings of trigger situations when learning to live with diabetes
Authors: Kneck Åsa , Eriksson Lars E , Lundman Berit , Fagerberg Ingegerd
Published: August 2016

Aims and objectives

The aim of the study was to illuminate the meanings of trigger situations experienced in everyday life when learning to live with diabetes.

Background

Adults become active learners when faced with situations they do not know how to manage, triggering a need to understand something in a different way than before. Knowing more about experiential learning for persons living with diabetes is important for understanding how learning can be supported by health care.

Design

A life‐world approach with a phenomenological hermeneutical method, inspired by the philosophy of Paul Ricoeur.

Methods

This method was used for interpreting transcriptions of interviews and consists of three stages: naïve understanding, structural analysis and a comprehensive understanding. Participants (n = 13), with either type I or type II diabetes, were interviewed on three different occasions over a three‐year period after being diagnosed with diabetes.

Results

When learning to live with diabetes, the meanings of trigger situations were described as ‘the unpredictable body heightens insecurity with awareness of one's own dependability’, ‘losing control in unsustainable situations’ and ‘encumbered by vulnerability and temporality in earlier familiar situations’.

Conclusion

The meanings of trigger situations were to lose the smooth, unreflected way of managing an everyday life situation, interlaced with feelings of lost control of how to live with new insights of being vulnerable. Trigger situations meant an opportunity for learning, as well as being demanding, unplanned and with limited freedom of choice. Trigger situations presented life and body as unpredictable.

Relevance to clinical practice

If healthcare professionals can identify the worries and questions raised in trigger situations, knowledge gaps can be identified and reflected on to stimulate learning.
Wide recognition of Culex pipiens and lack of detection of Culex torrentium through biomolecular differentiation of mosquitoes in the Emilia‐Romagna region, Northern Italy
Authors: CALZOLARI M. , BONILAURI P. , BELLINI R. , BECKER S. , DOTTORI M.
Published: August 2016

The Culex pipiens complex includes species with reported differences in vector competence for arthropod‐borne viruses, many of which are of significant importance to human health such as the West Nile virus and the Sindbis virus. This group of mosquitoes is difficult to distinguish morphologically; particularly as adult females. In Europe, the two species of the complex, Culex pipiens Linnaeus 1758 and Culex torrentium Martini 1925, are often found sympatrically. With the aim to characterize the presence and spread of both species in the Emilia‐Romagna region, Northern Italy, mosquitoes of the complex – collected during the West Nile virus surveillance plans – were tested by multiplex real‐time PCR for the detection of the two species Cx. pipiens and Cx. torrentium. A total of 24 165 mosquitoes, collected between 2012 and 2014 from 105 sites, and sorted in 204 pools, were tested. All tested pools were found to be composed of Cx. pipiens, whereas Cx. torrentium was not detected. These results indicate a likely absence of Cx. torrentium mosquitoes within the surveyed territory, whereas Cx. pipiens is widely distributed in the area mentioned. This is in line with previous reports, which describe a pre‐alpine distribution of Cx. torrentium in Italy.
Effects of neratinib and combination with irradiation and chemotherapy in head and neck cancer cells
Authors: Schneider S , Thurnher D , Kadletz L , Seemann R , Brunner M , Kotowski U , Schmid R , Lill C , Heiduschka G
Published: August 2016

Objective

Prognosis of patients with head and neck squamous cell carcinoma (HNSCC) is still poor. Novel therapeutic approaches are of great interest to improve the effects of radiochemotherapy. We evaluated the effects of tyrosine kinase inhibitor neratinib on HNSCC cell lines CAL27, SCC25 and FaDu as a single agent and in combination with irradiation and chemotherapy.

Methods

Effects of neratinib were evaluated in HNSCC cell lines CAL27, SCC25 and FaDu. Effect on cell viability of neratinib and combination with cisplatin and irradiation was measured using CCK‐8 assays and clonogenic assays. Western blot analysis was performed to distinguish the effect on epithelial growth factor receptor and HER2 expression. Apoptosis was evaluated by flow cytometry analysis.

Results

Growth inhibition was achieved in all cell lines, whereas combination of cisplatin and neratinib showed greater inhibition than each agent alone. Apoptosis was induced in all cell lines. Combination of neratinib with irradiation or cisplatin showed significantly increased apoptosis. In clonogenic assays, significant growth inhibition was observed in all investigated cell lines.

Conclusion

Neratinib, as a single agent or in combination with chemo‐irradiation, may be a promising treatment option for patients with head and neck cancer.
Detection of plant pathogens using real‐time PCR: how reliable are late Ct values?
Authors: Grosdidier M. , Aguayo J. , Marçais B. , Ioos R.
Published: August 2016

Effective detection of pathogens from complex substrates is a challenging task. Molecular approaches such as real‐time PCR can detect pathogens present even in low quantities. However, weak real‐time PCR signals, as represented by high cycle threshold (Ct) values, may be questionable. Therefore, setting a reliable Ct threshold to declare a positive reaction is important for specific detection. In this study, five methods were assessed for their performance in determining a Ct cut‐off value. These methods were based on the widely used probability of detection (POD) or receiver‐operating characteristic (ROC) approaches. Two important forest pathogens, Hymenoscyphus fraxineus and Fusarium circinatum, were used to set up three experimental frameworks that combined two types of substrates (seed lots and spore traps) and different PCR machines. The ROC‐based method emerged as the most complete and flexible method under various experimental conditions. It was demonstrated that the ROC method leads to a cut‐off value below which late Ct results can reliably be considered indicative of positive test results. This cut‐off value must be determined for each experimental approach used. The method based on the distribution of a previously determined set of Ct values corresponding to false‐positives appeared to be better adapted to detecting false‐negative results, and thus useful for testing potentially invasive pathogens.
Sound localization in the presence of multiple reflections using a binaurally integrated cross-correlation/auto-correlation mechanism
Authors: Braasch Jonas
Published: July 2016

A precedence effect model is described that can use a binaural signal to robustly localize a sound source in the presence of multiple reflections for the frontal horizontal plane. The model also estimates a room impulse response from a running binaural signal and determines the spatial locations and delays of early reflections, without any prior or additional knowledge of the source. A dual-layer cross-correlation/auto-correlation algorithm is used to determine the interaural time difference of the direct sound source component and to estimate a binaural activity pattern.
Claisen thermally rearranged (CTR) polymers
Authors: Tena Alberto , Rangou Sofia , Shishatskiy Sergey , Filiz Volkan , Abetz Volker
Published: July 2016

Second generation of thermally rearranged polymers presents low temperatures for a complete rearrangement.
Epigenetics and aging
Authors: Pal Sangita , Tyler Jessica K.
Published: July 2016

Researchers review how random changes and our environment (for example, diet) determines our life span.
HU multimerization shift controls nucleoid compaction
Authors: Hammel Michal , Amlanjyoti Dhar , Reyes Francis E. , Chen Jian-Hua , Parpana Rochelle , Tang Henry Y. H. , Larabell Carolyn A. , Tainer John A. , Adhya Sankar
Published: July 2016

HU networks control chromatin-like DNA compaction to synchronize bacterial responses for pathogenesis and changing environments.
Self-optimized superconductivity attainable by interlayer phase separation at cuprate interfaces
Authors: Misawa Takahiro , Nomura Yusuke , Biermann Silke , Imada Masatoshi
Published: July 2016

Resolving how and why maximized superconducting amplitude can be self-organized at interfaces opens perspectives for design.
Physiological and Proteomic Responses of Continuous Cultures of Microcystis aeruginosa PCC 7806 to Changes in Iron Bioavailability and Growth Rate
Authors: Yeung Anna C. Y. , D'Agostino Paul M. , Poljak Anne , McDonald James , Bligh Mark W. , Waite T. David , Neilan Brett A.
Published: July 2016

The hepatotoxin microcystin (MCYST) is produced by a variety of freshwater cyanobacterial species, including
Microcystis aeruginosa
. Interestingly, MCYST-producing
M. aeruginosa
strains have been shown to outcompete their nontoxic counterparts under iron-limiting conditions. However, the reasons for this are unclear. Here we examined the proteomic response of
M. aeruginosa
PCC 7806 continuous cultures under different iron and growth regimes. Iron limitation was correlated with a global reduction in levels of proteins associated with energy metabolism and photosynthesis. These proteomic changes were consistent with physiological observations, including reduced chlorophyll
a
content and reduced cell size. While levels of MCYST biosynthesis proteins did not fluctuate during the study period, both intra- and extracellular toxin quotas were significantly higher under iron-limiting conditions. Our results support the hypothesis that intracellular MCYST plays a role in protecting the cell against oxidative stress. Further, we propose that extracellular MCYST may act as a signaling molecule, stimulating MCYST production under conditions of iron limitation and enhancing the fitness of bloom populations.

IMPORTANCE
Microcystin production in water supply reservoirs is a global public health problem. Understanding the ecophysiology of hepatotoxic cyanobacteria, including their responses to the presence of key micronutrient metals such as iron, is central to managing harmful blooms. To our knowledge, this was the first study to examine proteomic and physiological changes occurring in
M. aeruginosa
continuous cultures under conditions of iron limitation at different growth rates.
Transcriptional Control in Marine Copiotrophic and Oligotrophic Bacteria with Streamlined Genomes
Authors: Cottrell Matthew T. , Kirchman David L.
Published: July 2016

Bacteria often respond to environmental stimuli using transcriptional control, but this may not be the case for marine bacteria such as “CandidatusPelagibacter ubique,” a cultivated representative of the SAR11 clade, the most abundant organism in the ocean. This bacterium has a small, streamlined genome and an unusually low number of transcriptional regulators, suggesting that transcriptional control is low inPelagibacterand limits its response to environmental conditions. Transcriptome sequencing during batch culture growth revealed that only 0.1% of protein-encoding genes appear to be under transcriptional control inPelagibacterand in another oligotroph (SAR92) whereas >10% of genes were under transcriptional control in the copiotrophsPolaribactersp. strain MED152 andRuegeria pomeroyi. When growth levels changed, transcript levels remained steady inPelagibacterand SAR92 but shifted in MED152 andR. pomeroyi. Transcript abundances per cell, determined using an internal RNA sequencing standard, were low (<1 transcript per cell) for all but a few of the most highly transcribed genes in all four taxa, and there was no correlation between transcript abundances per cell and shifts in the levels of transcription. These results suggest that low transcriptional control contributes to the success ofPelagibacterand possibly other oligotrophic microbes that dominate microbial communities in the oceans.

IMPORTANCEDiverse heterotrophic bacteria drive biogeochemical cycling in the ocean. The most abundant types of marine bacteria are oligotrophs with small, streamlined genomes. The metabolic controls that regulate the response of oligotrophic bacteria to environmental conditions remain unclear. Our results reveal that transcriptional control is lower in marine oligotrophic bacteria than in marine copiotrophic bacteria. Although responses of bacteria to environmental conditions are commonly regulated at the level of transcription, metabolism in the most abundant bacteria in the ocean appears to be regulated by other mechanisms.
An Ecotype of Neorickettsia risticii Causing Potomac Horse Fever in Canada
Authors: Xiong Qingming , Bekebrede Hannah , Sharma Pratibha , Arroyo Luis G. , Baird John D. , Rikihisa Yasuko
Published: July 2016

Neorickettsia
(formerly
Ehrlichia
)
risticii
is an obligatory intracellular bacterium of digenetic trematodes. When a horse accidentally ingests aquatic insects containing encysted trematodes infected with
N. risticii
, the bacterium is transmitted from trematodes to horse cells and causes an acute and often fatal disease called Potomac horse fever (PHF). Since the discovery of
N. risticii
in the United States in 1984, using immunofluorescence and PCR assays, PHF has been increasingly recognized throughout North America and South America. However, so far, there exist only a few stable
N. risticii
culture isolates, all of which are from horses within the United States, and the strain diversity and environmental spreading and distribution of pathogenic
N. risticii
strains remain poorly understood. This paper reports the isolation of
N. risticii
from the blood of a horse with acute PHF in Ontario, Canada. Intracellular
N. risticii
colonies were detected in P388D
1
cells after 47 days of culturing and 8 days after the addition of rapamycin. Molecular phylogenetic analysis based on amino acid sequences of major surface proteins P51 and Ssa1 showed that this isolate is distinct from any previously sequenced strains but closely related to midwestern U.S. strains. This is the first Canadian strain cultured, and a new method was developed to reactivate dormant
N. risticii
to improve culture isolation.

IMPORTANCE
Neorickettsia risticii
is an environmental bacterium that lives inside flukes that are parasitic to aquatic snails, insects, and bats. When a horse accidentally ingests insects harboring flukes infected with
N. risticii
, the bacterium is transmitted to the horse and causes an acute and often fatal disease called Potomac horse fever. Although the disease has been increasingly recognized throughout North and South America,
N. risticii
has not been cultured outside the United States. This paper reports the first Canadian strain cultured and a new method to effectively culture isolate
N. risticii
from the horse blood sample. Molecular analysis showed that the genotype of this Canadian strain is distinct from previously sequenced strains but closely related to midwestern U.S. strains. Culture isolation of
N. risticii
strains would confirm the geographic presence of pathogenic
N. risticii
, help elucidate
N. risticii
strain diversity and environmental spreading and distribution, and improve diagnosis and development of vaccines for this dreadful disease.
Inclusion of Konjac Flour in the Gestation Diet Changes the Gut Microbiota, Alleviates Oxidative Stress, and Improves Insulin Sensitivity in Sows
Authors: Tan Chengquan , Wei Hongkui , Ao Jiangtao , Long Guang , Peng Jian
Published: July 2016

Although dietary fibers contribute to health and physiology primarily via the fermentative actions of the gut microbiota of the hosts, few studies have focused on how these interactions influence the metabolic status of sows. Here, the effects of inclusion of konjac flour (KF) in a gestation diet on oxidative stress status, insulin sensitivity, and gut microbiota were investigated to elucidate the correlation between the microbiota and metabolic changes in sows. Sows were assigned to either control or 2.2% KF dietary treatment during gestation. The gut microbiota population in sows during gestation and lactation was assessed by 16S rRNA gene sequencing. The oxidative stress parameters, homeostasis model assessment (HOMA) values, and fatty acids in the blood of sows were also assessed. Compared to the control diet group, KF significantly reduced the serum levels of reactive oxygen species (ROS) and 8-hydroxy-deoxyguanosine (8-OHdG) but increased the serum concentrations of glutathione peroxidase (GSH-Px) in sows on day 1 in lactation. Additionally, sows in the KF group had a lower HOMA insulin resistance value but a higher HOMA insulin sensitivity (HOMA-IS) value. KF induced changes in the gut microbial composition at the phylum and genus levels. The increased relative abundances of
Akkermansia
and
Roseburia
in the KF group were positively correlated with the HOMA-IS. Overall, dietary KF alleviated oxidative stress and improved insulin sensitivity of sows, and the changes in the gut microbiota in response to KF may have been correlated with the host metabolism response.

IMPORTANCE
To date, the effect of dietary fiber on metabolism responses and gut microbiota in sows has not been investigated. Here, KF supplementation of a gestation diet in sows was found to alleviate oxidative stress and to improve insulin sensitivity. Pyrosequencing analysis revealed that KF treatment induces changes in the gut microbiota composition at the phylum and genus levels. Moreover, the changes of gut microbiota in response to KF may be correlated with the host metabolism response.
Use of a Bacterial Luciferase Monitoring System To Estimate Real-Time Dynamics of Intracellular Metabolism in Escherichia coli
Authors: Shimada Tomohiro , Tanaka Kan
Published: July 2016

Regulation of central carbon metabolism has long been an important research subject in every organism. While the dynamics of metabolic flows during changes in available carbon sources have been estimated based on changes in metabolism-related gene expression, as well as on changes in the metabolome, the flux change itself has scarcely been measured because of technical difficulty, which has made conclusions elusive in many cases. Here, we used a monitoring system employing
Vibrio fischeri
luciferase to probe the intracellular metabolic condition in
Escherichia coli
. Using a batch culture provided with a limited amount of glucose, we performed a time course analysis, where the predominant carbon source shifts from glucose to acetate, and identified a series of sequential peaks in the luciferase activity (peaks 1 to 4). Two major peaks, peaks 1 and 3, were considered to correspond to the glucose and acetate consuming phases, respectively, based on the glucose, acetate, and dissolved oxygen concentrations in the medium. The pattern of these peaks was changed by the addition of a different carbon source or by an increasing concentration of glucose, which was consistent with the present model. Genetically, mutations involved in glycolysis or the tricarboxylic acid (TCA) cycle/gluconeogenesis specifically affected peak 1 or peak 3, respectively, as expected from the corresponding metabolic phase. Intriguingly, mutants for the acetate excretion pathway showed a phenotype of extended peak 2 and delayed transition to the TCA cycle/gluconeogenesis phase, which suggests that peak 2 represents the metabolic transition phase. These results indicate that the bacterial luciferase monitoring system is useful to understand the real-time dynamics of metabolism in living bacterial cells.

IMPORTANCE
Intracellular metabolic flows dynamically change during shifts in available carbon sources. However, because of technical difficulty, the flux change has scarcely been measured in living cells. Here, we used a
Vibrio fischeri
luciferase monitoring system to probe the intracellular metabolic condition in
Escherichia coli
. Using a limited amount of glucose batch culture, a series of sequential peaks (peaks 1 to 4) in the luciferase activity was observed. Changes in the pattern of these peaks by the addition of extra carbon sources and in mutant strains involved in glycolysis or the TCA cycle/gluconeogenesis gene assigned the metabolic phase corresponding to peak 1 as the glycolysis phase and peak 3 as the TCA cycle/gluconeogenesis phase. Intriguingly, the acetate excretion pathway engaged in peak 2 represents the metabolic transition phase. These results indicate that the bacterial luciferase monitoring system is useful to understand the real-time dynamics of metabolism in living bacterial cells.
Ultrastructure Variability of the Exosporium Layer of Clostridium difficile Spores from Sporulating Cultures and Biofilms
Authors: Pizarro-Guajardo Marjorie , Calderón-Romero Paulina , Paredes-Sabja Daniel
Published: July 2016

The anaerobic sporeformer
Clostridium difficile
is the leading cause of nosocomial antibiotic-associated diarrhea in developed and developing countries. The metabolically dormant spore form is considered the morphotype responsible for transmission, infection, and persistence, and the outermost exosporium layer is likely to play a major role in spore-host interactions during recurrent infections, contributing to the persistence of the spore in the host. A recent study (M. Pizarro-Guajardo, P. Calderón-Romero, P. Castro-Córdova, P. Mora-Uribe, and D. Paredes-Sabja, Appl Environ Microbiol 82:2202–2209, 2016,
http://dx.doi.org/10.1128/AEM.03410-15
) demonstrated by transmission electron microscopy the presence of two ultrastructural morphotypes of the exosporium layer in spores formed from the same sporulating culture. However, whether these distinct morphotypes appeared due to purification techniques and whether they appeared during biofilm development remain unclear. In this communication, we demonstrate through transmission electron microscopy that these two exosporium morphotypes are formed under sporulation conditions and are also present in spores formed during biofilm development. In summary, this work provides definitive evidence that in a population of sporulating cells, spores with a thick outermost exosporium layer and spores with a thin outermost exosporium layer are formed.

IMPORTANCE
Clostridium difficile
spores are recognized as the morphotype of persistence and transmission of
C. difficile
infections. Spores of
C. difficile
are intrinsically resistant to all known antibiotic therapies. Development of spore-based removal strategies requires a detailed knowledge of the spore surface for proper antigen selection. In this context, in this work we provide definitive evidence that two types of spores, those with a thick outermost exosporium layer and those with a thin outermost exosporium layer, are formed in the same
C. difficile
sporulating culture or during biofilm development.
Transmission of Staphylococcus aureus from Humans to Green Monkeys in The Gambia as Revealed by Whole-Genome Sequencing
Authors: Senghore Madikay , Bayliss Sion C. , Kwambana-Adams Brenda A. , Foster-Nyarko Ebenezer , Manneh Jainaba , Dione Michel , Badji Henry , Ebruke Chinelo , Doughty Emma L. , Thorpe Harry A. , Jasinska Anna J. , Schmitt Christopher A. , Cramer Jennifer D. , Turner Trudy R. , Weinstock George , Freimer Nelson B. , Pallen Mark J. , Feil Edward J. , Antonio Martin
Published: July 2016

Staphylococcus aureus
is an important pathogen of humans and animals. We genome sequenced 90
S. aureus
isolates from The Gambia: 46 isolates from invasive disease in humans, 13 human carriage isolates, and 31 monkey carriage isolates. We inferred multiple anthroponotic transmissions of
S. aureus
from humans to green monkeys (
Chlorocebus sabaeus
) in The Gambia over different time scales. We report a novel monkey-associated clade of
S. aureus
that emerged from a human-to-monkey switch estimated to have occurred 2,700 years ago. Adaptation of this lineage to the monkey host is accompanied by the loss of phage-carrying genes that are known to play an important role in human colonization. We also report recent anthroponotic transmission of the well-characterized human lineages sequence type 6 (ST6) and ST15 to monkeys, probably because of steadily increasing encroachment of humans into the monkeys' habitat. Although we have found no evidence of transmission of
S. aureus
from monkeys to humans, as the two species come into ever-closer contact, there might be an increased risk of additional interspecies exchanges of potential pathogens.

IMPORTANCE
The population structures of
Staphylococcus aureus
in humans and monkeys in sub-Saharan Africa have been previously described using multilocus sequence typing (MLST). However, these data lack the power to accurately infer details regarding the origin and maintenance of new adaptive lineages. Here, we describe the use of whole-genome sequencing to detect transmission of
S. aureus
between humans and nonhuman primates and to document the genetic changes accompanying host adaptation. We note that human-to-monkey switches tend to be more common than the reverse and that a novel monkey-associated clade is likely to have emerged from such a switch approximately 2,700 years ago. Moreover, analysis of the accessory genome provides important clues as to the genetic changes underpinning host adaptation and, in particular, shows that human-to-monkey switches tend to be associated with the loss of genes known to confer adaptation to the human host.