bluuebunny/crossref_metadata_2025 huggingface dataset:
Can the metacommunity data matrix predict changes in species incidence and abundance?
Authors: Waller Donald M. , Mudrak Erika L. , Rogers David A.
Published: April 2016

Metacommunity matrices contain data on species incidence or abundance across sites, compactly portraying community composition and how it varies over sites. We constructed models based on an initial metacommunity matrix of either species incidence or abundance to test whether such data suffice to predict subsequent changes in incidence or abundance at each site. We then tested these models against extensive empirical data on vascular plant incidence and abundance collected from 156 forested sites in both the 1950s and 2000s. Predictions from these models parallel observed changes in species incidence and abundance in two distinctly different forest metacommunities and differ greatly from null model predictions. The abundance model shows greater power than the incidence model reflecting its higher information content. Predictions were more accurate for the more diverse forests of southern Wisconsin which are changing faster in response to succession and fragmentation. Simulations demonstrate that these results are fairly robust to variation in sampling intensity. These models, based only on the metacommunity matrix, do not require data on site conditions or species' characteristics. They thus provide a useful baseline for assessing more complex models incorporating data on species' functional traits, local site conditions, or landscape context. They may also prove useful to conservation biologists seeking to predict local population declines and extinction risks.
Physiological and biochemical changes associated with acute experimental dehydration in the desert adapted mouse,Peromyscus eremicus
Authors: Kordonowy Lauren , Lombardo Kaelina D. , Green Hannah L. , Dawson Molly , Bolton Evice A. , LaCourse Sarah , MacManes Matthew D.
Published: April 2016

Characterizing traits critical for adaptation to a given environment is an important first step in understanding how phenotypes evolve. How animals adapt to the extreme heat and aridity commonplace to deserts represents is an exceptionally interesting example of these processes, and has been the focus of study for decades. In contrast to those studies, where experiments are conducted on either wild animals or captive animals held in non-desert conditions, the study described here leverages a unique environmental chamber that replicates desert conditions for captivePeromyscus eremicus(cactus mouse). Here we establish baseline values for daily water intake and for serum electrolytes, as well as the response of these variables to experimental dehydration. In brief,P. eremicus’ daily water intake is very low. It’s serum electrolytes are distinct from many previously studied animals, and its response to acute dehydration is profound, though not suggestive of renal impairment, which is atypical of mammals.

Summary statement

The establishment of baseline values for serum electrolytes and water intake, as well as their response to acute dehydration is critical for characterizing the physiology necessary for desert survival.

Conflict of Interest Statement

The authors declare no conflict of interest.
Live Imaging of muscle histolysis inDrosophilametamorphosis
Authors: Kuleesha Yadav , Puah Wee Choo , Wasser Martin
Published: April 2016

Background:

The contribution of programmed cell death (PCD) to muscle wasting disorders remains a matter of debate.Drosophila melanogastermetamorphosis offers the opportunity to study muscle cell death in the context of development. Using live cell imaging of the abdomen, two groups of larval muscles can be observed, doomed muscles that undergo histolysis and persistent muscles that are remodelled and survive into adulthood.

Method:

To identify and characterize genes that control the decision between survival and cell death of muscles, we developed a method comprisingin vivoimaging, targeted gene perturbation and time-lapse image analysis. Our approach enabled us to study the cytological and temporal aspects of abnormal cell death phenotypes.

Results:

In a previous genetic screen for genes controlling muscle size and cell death in metamorphosis, we identified gene perturbations that induced cell death of persistent or inhibit histolysis of doomed larval muscles. RNA interference (RNAi) of the genes encoding the helicase Rm62 and the lysosomal Cathepsin-L homolog Cysteine proteinase 1 (Cp1) caused premature cell death of persistent muscle in early and mid-pupation, respectively. Silencing of the transcriptional co-repressorAtrophininhibited histolysis of doomed muscles. Overexpression of dominant-negative Target of Rapamycin (TOR) delayed the histolysis of a subset of doomed and induced ablation of all persistent muscles. RNAi ofAMPKα,which encodes a subunit of the AMPK protein complex that senses AMP and promotes ATP formation, led to loss of attachment and a spherical morphology. None of the perturbations affected the survival of newly formed adult muscles, suggesting that the method is useful to find genes that are crucial for the survival of metabolically challenged muscles, like those undergoing atrophy. The ablation of persistent muscles did not affect eclosion of adult flies.

Conclusions:

Live imaging is a versatile approach to uncover gene functions that are required for the survival of muscle undergoing remodelling, yet are dispensable for other adult muscles. Our approach promises to identify molecular mechanisms that can explain the resilience of muscles to PCD.
Fluorescence resonance energy transfer and protein-induced fluorescence enhancement as synergetic multi-scale molecular rulers
Authors: Ploetz Evelyn , Lerner Eitan , Husada Florence , Roelfs Martin , Chung SangYoon , Hohlbein Johannes , Weiss Shimon , Cordes Thorben
Published: April 2016

Advanced microscopy methods allow obtaining information on (dynamic) conformational changes in biomolecules via measuring a single molecular distance in the structure. It is, however, extremely challenging to capture the full depth of a three-dimensional biochemical state, binding-related structural changes or conformational cross-talk in multi-protein complexes using one-dimensional assays. In this paper we address this fundamental problem by extending the standard molecular ruler based on Förster resonance energy transfer (FRET) into a two-dimensional assay via its combination with protein-induced fluorescence enhancement (PIFE). We show that donor brightness (viaPIFE) and energy transfer efficiency (viaFRET) can simultaneously report on e.g., the conformational state of dsDNA following its interaction with unlabelled proteins (BamHI, EcoRV, T7 DNA polymerase gp5/trx). The PIFE-FRET assay uses established labelling protocols and single molecule fluorescence detection schemes (alternating-laser excitation, ALEX). Besides quantitative studies of PIFE and FRET ruler characteristics, we outline possible applications of ALEX-based PIFE-FRET for single-molecule studies with diffusing and immobilized molecules. Finally, we study transcription initiation and scrunching ofE. coliRNA-polymerase with PIFE-FRET and provide direct evidence for the physical presence and vicinity of the polymerase that causes structural changes and scrunching of the transcriptional DNA bubble.
Negotiators’ emotion perception and value-claiming under different incentives
Authors: Kong Dejun Tony , Bottom William P. , Konczak Lee J.
Published: April 2016

Purpose

The purpose of this paper is to examine how negotiators’ self-evaluated emotion perception is related to value claiming under two incentive schemes. Adopting an ability-motivation interaction perspective, the authors hypothesize that the relationship will be stronger in the contingent (upon value-claiming performance) versus fixed (non-contingent upon value-claiming performance) pay condition.

Design/methodology/approach

Multi-level analysis of data (120 participants, 60 dyads) from a laboratory study provided evidence supporting the hypothesis proposed in this paper.

Findings

Emotional perception was indeed more strongly related to value claiming in the contingent pay condition than in the fixed pay condition. Negotiators’ emotion perception also had a direct, positive linkage with relationship satisfaction, regardless of the incentive scheme.

Research limitations/implications

The limitations of the current paper include self-report measures of emotion perception, a US student sample and a focus on value claiming as the instrumental outcome. The authors urge future research to address these limitations in replicating and extending the current findings.

Originality/value

The present paper is the first to explicitly test the moderating role of incentive schemes on the linkage between negotiators’ emotion perception and performance. The findings not only show the context-dependent predictive value of negotiators’ emotion perception but also shed light on both negotiation and emotional intelligence (EI) research.
Does ethnic conflict impede or enable employee innovation behavior?
Authors: Reade Carol , Lee Hyun-Jung
Published: April 2016

Purpose

The purpose of this study is to investigate whether a societal context of ethnic conflict influences employee innovation behavior in the work domain and whether a collaborative conflict management style adopted by supervisors plays a moderating role.

Design/methodology/approach

Drawing on the conflict, organizational behavior and innovation literature, the study examines the main and interaction effects of employee sensitivity to ethnic conflict, organizational frustration and collaborative conflict management style of supervisors on employee engagement with colleagues to innovate products, services and job processes. Hypotheses are tested using hierarchical regression analysis, controlling for ethnic diversity in workgroups.

Findings

Employee innovation behavior is greatest when employee sensitivity to ethnic conflict is high, organizational frustration is low and when supervisors are perceived to be highly collaborative in managing conflict, regardless of whether the workgroup is ethnically homogenous or diverse.

Research limitations/implications

The study findings expand our knowledge of the effects of sociopolitical conflict on employee behavior and the role of collaborative conflict management. Future research can address limitations including self-reports, cross-sectional design and single country setting.

Practical implications

The findings of this study suggest that employee innovation behavior can be enhanced through developing collaborative conflict management skills of those in leadership positions.

Originality/value

This is the first study to empirically examine the influence of ethnic conflict on employee innovation behavior and is of value to businesses operating in conflict settings.
Work relationships: counteracting the negative effects of conflict
Authors: Jungst Martijn , Blumberg Boris
Published: April 2016

Purpose

Guided by social resource theory, this study aims to examine the influence of conflict (i.e. task and relationship) on performance. The authors investigated whether job engagement mediates this relationship and whether social network quality moderates the relationship between conflict, job engagement and performance.

Design/methodology/approach

The authors built and tested a moderated mediation model, using data from 217 graduate students.

Findings

Results showed that job engagement operates as a mediating mechanism between task conflict and performance. The authors also found that the indirect effect of job engagement depended upon the quality of the social networks. When the quality of the social network was high, both the task and relationship conflict did not negatively influence the association between job engagement and performance.

Research limitations/implications

These findings provide new insights into how social embeddedness in the form of social network quality can create a social context in which conflict works out less detrimental.

Practical implications

Given that employees are interdependent and coworkers are likely to differ in their personal values and opinions, the authors conclude that managers should facilitate the development of meaningful relationships at work.

Originality/value

Whereas prior research has found conflict (i.e. task and relationship) to negatively associate with performance, the authors show that social networks do affect the strength of the relationship between conflict (i.e. task and relationship) and performance.
Initiation strategies for simultaneous control of antiphase domains and stacking faults in GaAs solar cells on Ge
Authors: Faucher Joseph , Masuda Taizo , Lee Minjoo Larry
Published: April 2016

Incorporating a Ge junction into a lattice-matched GaInP/GaAs/GaInNAsSb triple-junction cell grown by molecular beam epitaxy (MBE) could enable concentrated efficiencies of ∼50%. Epitaxial integration allows lift-off and wafer bonding steps to be avoided, but growth of III–Vs on Ge by MBE can lead to antiphase domains (APD) and stacking fault pyramids (SFP), both of which diminish solar cell performance. Initiating growth by migration-enhanced epitaxy (MEE) is typically cited as necessary to obtain high-quality III–Vs on Ge. In this work, the authors show that typical MEE growth conditions force a compromise between APD height (hAPD) and SFP density (ρSFP). As APDs can readily self-terminate while SFPs cannot, a two-step initiation strategy was employed, where MEE is performed under conditions that minimize ρSFP followed by low-temperature MBE conditions that encourage APD termination. By doing so, the authors obtained ρSFP < 104 cm−2 with hAPD ≤ 57 nm. The authors also demonstrated that high-quality GaAs on Ge can be grown without MEE initiation using conventional MBE conditions, though with taller APDs. Both the two-step initiation and conventional MBE initiation yield GaAs cells with high open-circuit voltage and internal quantum efficiency, demonstrating promising paths toward epitaxial integration of high-efficiency solar cells on Ge.
Nonlinear acoustic propagation in bubbly liquids: Multiple scattering, softening and hardening phenomena
Authors: Doc Jean-Baptiste , Conoir Jean-Marc , Marchiano Régis , Fuster Daniel
Published: April 2016

The weakly nonlinear propagation of acoustic waves in monodisperse bubbly liquids is investigated numerically. A hydrodynamic model based on the averaged two-phase fluid equations is coupled with the Rayleigh-Plesset equation to model the dynamics of bubbles at the local scale. The present model is validated in the linear regime by comparing with the Foldy approximation. The analysis of the pressure signals in the linear regime highlights two resonance frequencies: the Minnaert frequency and a multiple scattering resonance that strongly depends on the bubble concentration. For weakly nonlinear regimes, the generation of higher harmonics is observed only for the Minnaert frequency. Linear combinations between the Minnaert harmonics and the multiple scattering resonance are also observed. However, the most significant effect observed is the appearance of softening-hardening effects that share some similarities with those observed for sandstones or cracked materials. These effects are related to the multiple scattering resonance. Downward or upward resonance frequency shifts can be observed depending on the characteristic of the incident wave when increasing the excitation amplitude. It is shown that the frequency shift can be explained assuming that the acoustic wave velocity depends on a law different from those usually encountered for sandstones or cracked materials.
Audiovisual speech perception development at varying levels of perceptual processing
Authors: Lalonde Kaylah , Holt Rachael Frush
Published: April 2016

This study used the auditory evaluation framework [Erber (1982). Auditory Training (Alexander Graham Bell Association, Washington, DC)] to characterize the influence of visual speech on audiovisual (AV) speech perception in adults and children at multiple levels of perceptual processing. Six- to eight-year-old children and adults completed auditory and AV speech perception tasks at three levels of perceptual processing (detection, discrimination, and recognition). The tasks differed in the level of perceptual processing required to complete them. Adults and children demonstrated visual speech influence at all levels of perceptual processing. Whereas children demonstrated the same visual speech influence at each level of perceptual processing, adults demonstrated greater visual speech influence on tasks requiring higher levels of perceptual processing. These results support previous research demonstrating multiple mechanisms of AV speech processing (general perceptual and speech-specific mechanisms) with independent maturational time courses. The results suggest that adults rely on both general perceptual mechanisms that apply to all levels of perceptual processing and speech-specific mechanisms that apply when making phonetic decisions and/or accessing the lexicon. Six- to eight-year-old children seem to rely only on general perceptual mechanisms across levels. As expected, developmental differences in AV benefit on this and other recognition tasks likely reflect immature speech-specific mechanisms and phonetic processing in children.
The crystal structure of human dopamine β-hydroxylase at 2.9 Å resolution
Authors: Vendelboe Trine V. , Harris Pernille , Zhao Yuguang , Walter Thomas S. , Harlos Karl , El Omari Kamel , Christensen Hans E. M.
Published: April 2016

This first structure of the enzyme converting dopamine to norepinephrine provides new perspectives on numerous disorders.
Hanbury Brown and Twiss interferometry with twisted light
Authors: Magaña-Loaiza Omar S. , Mirhosseini Mohammad , Cross Robert M. , Rafsanjani Seyed Mohammad Hashemi , Boyd Robert W.
Published: April 2016

Fluctuations of twisted beams of random light, such as sunlight, lead to an angular Hanbury Brown–Twiss effect.
Agrobacterium tumefaciens Zur Regulates the High-Affinity Zinc Uptake System TroCBA and the Putative Metal Chaperone YciC, along with ZinT and ZnuABC, for Survival under Zinc-Limiting Conditions
Authors: Chaoprasid Paweena , Dokpikul Thanittra , Johnrod Jaruwan , Sirirakphaisarn Sirin , Nookabkaew Sumontha , Sukchawalit Rojana , Mongkolsuk Skorn
Published: April 2016

Agrobacterium tumefaciens
has a cluster of genes (Atu3178, Atu3179, and Atu3180) encoding an ABC-type transporter, here named
troA
,
troB
, and
troC
, respectively, which is shown here to be a zinc-specific uptake system. Reverse transcription (RT)-PCR analysis confirmed that
troA
,
troB
, and
troC
are cotranscribed, with
troC
as the first gene of the operon. The
yciC
(Atu3181) gene is transcribed in the opposite orientation to that of the
troCBA
operon and belongs to a metal-binding GTPase family. Expression of
troCBA
and
yciC
was inducible under zinc-limiting conditions and was controlled by the zinc uptake regulator, Zur. Compared to the wild type, the mutant strain lacking
troC
was hypersensitive to a metal chelator, EDTA, and the phenotype could be rescued by the addition of zinc, while the strain with a single
yciC
mutation showed no phenotype. However,
yciC
was important for survival under zinc limitation when either
troC
or
zinT
was inactivated. The periplasmic zinc-binding protein, ZinT, could not function when TroC was inactivated, suggesting that ZinT may interact with TroCBA in zinc uptake. Unlike many other bacteria, the ABC-type transporter ZnuABC was not the major zinc uptake system in
A. tumefaciens
. However, the important role of
A. tumefaciens
ZnuABC was revealed when TroCBA was impaired. The strain containing double mutations in the
znuA
and
troC
genes exhibited a growth defect in minimal medium.
A. tumefaciens
requires cooperation of zinc uptake systems and zinc chaperones, including TroCBA, ZnuABC, ZinT, and YciC, for survival under a wide range of zinc-limiting conditions.

IMPORTANCE
Both host and pathogen battle over access to essential metals, including zinc. In low-zinc environments, physiological responses that make it possible to acquire enough zinc are important for bacterial survival and could determine the outcome of host-pathogen interactions.
A. tumefaciens
was found to operate a novel pathway for zinc uptake in which ZinT functions in concert with the high-affinity zinc importer TroCBA.
Genomic Resolution of Outbreak-Associated Legionella pneumophila Serogroup 1 Isolates from New York State
Authors: Raphael Brian H. , Baker Deborah J. , Nazarian Elizabeth , Lapierre Pascal , Bopp Dianna , Kozak-Muiznieks Natalia A. , Morrison Shatavia S. , Lucas Claressa E. , Mercante Jeffrey W. , Musser Kimberlee A. , Winchell Jonas M.
Published: April 2016

A total of 30
Legionella pneumophila
serogroup 1 isolates representing 10 separate legionellosis laboratory investigations (“outbreaks”) that occurred in New York State between 2004 and 2012 were selected for evaluation of whole-genome sequencing (WGS) approaches for molecular subtyping of this organism. Clinical and environmental isolates were available for each outbreak and were initially examined by pulsed-field gel electrophoresis (PFGE). Sequence-based typing alleles were extracted from WGS data yielding complete sequence types (ST) for isolates representing 8 out of the 10 outbreaks evaluated in this study. Isolates from separate outbreaks sharing the same ST also contained the fewest differences in core genome single nucleotide polymorphisms (SNPs) and the greatest proportion of identical allele sequences in a whole-genome multilocus sequence typing (wgMLST) scheme. Both core SNP and wgMLST analyses distinguished isolates from separate outbreaks, including those from two outbreaks sharing indistinguishable PFGE profiles. Isolates from a hospital-associated outbreak spanning multiple years shared indistinguishable PFGE profiles but displayed differences in their genome sequences, suggesting the presence of multiple environmental sources. Finally, the
rtx
gene demonstrated differences in the repeat region sequence among ST1 isolates from different outbreaks, suggesting that variation in this gene may be useful for targeted molecular subtyping approaches for
L. pneumophila
. This study demonstrates the utility of various genome sequence analysis approaches for
L. pneumophila
for environmental source attribution studies while furthering the understanding of
Legionella
ecology.

IMPORTANCE
We demonstrate that whole-genome sequencing helps to improve resolution of
Legionella pneumophila
isolated during laboratory investigations of legionellosis compared to traditional subtyping methods. These data can be important in confirming the environmental sources of legionellosis outbreaks. Moreover, we evaluated various methods to analyze genome sequence data to help resolve outbreak-related isolates.
Species Diversity of Environmental GIM-1-Producing Bacteria Collected during a Long-Term Outbreak
Authors: Wendel Andreas F. , Ressina Sofija , Kolbe-Busch Susanne , Pfeffer Klaus , MacKenzie Colin R.
Published: April 2016

Reports of outbreaks concerning carbapenemase-producing Gram-negative bacteria in which the main source of transmission is the hospital environment are increasing. This study describes the results of environmental sampling in a protracted polyspecies metallo-beta-lactamase GIM-1 outbreak driven by plasmids and bacterial clones of
Enterobacter cloacae
and
Pseudomonas aeruginosa
in a tertiary care center. Environmental sampling targeting wet locations (especially sinks) was carried out on a surgical intensive care unit and on a medical ward on several occasions in 2012 and 2013. We were able to demonstrate 43
bla
GIM-1
-carrying bacteria (mainly nonfermenters but also
Enterobacteriaceae
) that were either related or unrelated to clinical strains in 30 sinks and one hair washbasin. GIM-1 was found in 12 different species, some of which are described here as carriers of GIM-1. Forty out of 43 bacteria displayed resistance to carbapenems and, in addition, to various non-beta-lactam antibiotics. Colistin resistance was observed in two
E. cloacae
isolates with MICs above 256 mg/liter. The
bla
GIM-1
gene was harbored in 12 different class 1 integrons, some without the typical 3′ end. The
bla
GIM-1
gene was localized on plasmids in five isolates.
In vitro
plasmid transfer by conjugation was successful in one isolate. The environment, with putatively multispecies biofilms, seems to be an important biological niche for multidrug-resistant bacteria and resistance genes. Biofilms may serve as a “melting pot” for horizontal gene transfer, for dissemination into new species, and as a reservoir to propagate future hospital outbreaks.

IMPORTANCE
In Gram-negative bacteria, resistance to the clinically relevant broad-spectrum carbapenem antibiotics is a major public health concern. Major reservoirs for these resistant organisms are not only the gastrointestinal tracts of animals and humans but also the (hospital) environment. Due to the difficulty in eradicating biofilm formation in the latter, a sustained dissemination of multidrug-resistant bacteria from the environment can occur. In addition, horizontal transfer of resistance genes on mobile genetic elements within biofilms adds to the total “resistance gene pool” in the environment. To gain insight into the transmission pathways of a rare and locally restricted carbapenemases resistance gene (
bla
GIM-1
), we analyzed the genetic background of the
bla
GIM-1
gene in environmental bacteria during a long-term polyspecies outbreak in a German hospital.
Measles in the United States since the Millennium: Perils and Progress in the Postelimination Era
Authors: Schuchat Anne , Fiebelkorn Amy Parker , Bellini William
Published: April 2016

This article describes measles and measles vaccination, along with the challenges, successes, and progress in the postelimination era.
The Role of Bacterial Spores in Metal Cycling and Their Potential Application in Metal Contaminant Bioremediation
Authors: Butterfield Cristina N. , Lee Sung-Woo , Tebo Bradley M.
Published: April 2016

Bacteria are one of the premier biological forces that, in combination with chemical and physical forces, drive metal availability in the environment. Bacterial spores, when found in the environment, are often considered to be dormant and metabolically inactive, in a resting state waiting for favorable conditions for them to germinate. However, this is a highly oversimplified view of spores in the environment. The surface of bacterial spores represents a potential site for chemical reactions to occur. Additionally, proteins in the outer layers (spore coats or exosporium) may also have more specific catalytic activity. As a consequence, bacterial spores can play a role in geochemical processes and may indeed find uses in various biotechnological applications. The aim of this review is to introduce the role of bacteria and bacterial spores in biogeochemical cycles and their potential use as toxic metal bioremediation agents.
Population Phylogenomics of Extraintestinal PathogenicEscherichia coli
Authors: Tourret Jérôme , Denamur Erick
Published: April 2016

The emergence of genomics over the last 10 years has provided new insights into the evolution and virulence of extraintestinalEscherichia coli. By combining population genetics and phylogenetic approaches to analyze whole-genome sequences, it became possible to link genomic features to specific phenotypes, such as the ability to cause urinary tract infections. AnE. colichromosome can vary extensively in length, ranging from 4.3 to 6.2 Mb, encoding 4,084 to 6,453 proteins. This huge diversity is structured as a set of less than 2,000 genes (core genome) that are conserved between all the strains and a set of variable genes. Based on the core genome, the history of the species can be reliably reconstructed, revealing the recent emergence of phylogenetic groups A and B1 and the more ancient groups B2, F, and D. Urovirulence is most often observed in B2/F/D group strains and is a multigenic process involving numerous combinations of genes and specific alleles with epistatic interactions, all leading down multiple evolutionary paths. The genes involved mainly code for adhesins, toxins, iron capture systems, and protectins, as well as metabolic pathways and mutation-rate-control systems. However, the barrier between commensal and uropathogenicE. colistrains is difficult to draw as the factors that are responsible for virulence have probably also been selected to allow survival ofE. colias a commensal in the intestinal tract. Genomic studies have also demonstrated that infections are not the result of a unique and stable isolate, but rather often involve several isolates with variable levels of diversity that dynamically changes over time.
Contrasting Lifestyles Within the Host Cell
Authors: Case Elizabeth Di Russo , Samuel James E.
Published: April 2016

Intracellular bacterial pathogens have evolved to exploit the protected niche provided within the boundaries of a eukaryotic host cell. Upon entering a host cell, some bacteria can evade the adaptive immune response of its host and replicate in a relatively nutrient-rich environment devoid of competition from other host flora. Growth within a host cell is not without their hazards, however. Many pathogens enter their hosts through receptor-mediated endocytosis or phagocytosis, two intracellular trafficking pathways that terminate in a highly degradative organelle, the phagolysosome. This usually deadly compartment is maintained at a low pH and contains degradative enzymes and reactive oxygen species, resulting in an environment to which few bacterial species are adapted. Some intracellular pathogens, such asShigella,Listeria,Francisella, andRickettsia, escape the phagosome to replicate within the cytosol of the host cell. Bacteria that remain within a vacuole either alter the trafficking of their initial phagosomal compartment or adapt to survive within the harsh environment it will soon become. In this chapter, we focus on the mechanisms by which different vacuolar pathogens either evade lysosomal fusion, as in the case ofMycobacteriumandChlamydia, or allow interaction with lysosomes to varying degrees, such asBrucellaandCoxiella, and their specific adaptations to inhabit a replicative niche.
Staying Alive:
Vibrio cholerae
’s Cycle of Environmental Survival, Transmission, and Dissemination
Authors: Conner Jenna G. , Teschler Jennifer K. , Jones Christopher J. , Yildiz Fitnat H.
Published: April 2016

Infectious diseases kill nearly 9 million people annually. Bacterial pathogens are responsible for a large proportion of these diseases, and the bacterial agents of pneumonia, diarrhea, and tuberculosis are leading causes of death and disability worldwide. Increasingly, the crucial role of nonhost environments in the life cycle of bacterial pathogens is being recognized. Heightened scrutiny has been given to the biological processes impacting pathogen dissemination and survival in the natural environment, because these processes are essential for the transmission of pathogenic bacteria to new hosts. This chapter focuses on the model environmental pathogen
Vibrio cholerae
to describe recent advances in our understanding of how pathogens survive between hosts and to highlight the processes necessary to support the cycle of environmental survival, transmission, and dissemination. We describe the physiological and molecular responses of
V. cholerae
to changing environmental conditions, focusing on its survival in aquatic reservoirs between hosts and its entry into and exit from human hosts.
Evolution of Bacterial Pathogens Within the Human Host
Authors: Bliven Kimberly A. , Maurelli Anthony T.
Published: April 2016

Selective pressures within the human host, including interactions with innate and adaptive immune responses, exposure to medical interventions such as antibiotics, and competition with commensal microbiota all facilitate the evolution of bacterial pathogens. In this chapter, we present examples of pathogen strategies that emerged as a result of selective pressures within the human host niche and discuss the resulting coevolutionary “arms race” between these organisms. In bacterial pathogens, many of the genes responsible for these strategies are encoded on mobile pathogenicity islands or plasmids, underscoring the importance of horizontal gene transfer in the emergence of virulent microbial species.
Microbial Endocrinology in the Pathogenesis of Infectious Disease
Authors: Lyte Mark
Published: April 2016

Microbial endocrinology represents the intersection of two seemingly disparate fields, microbiology and neurobiology, and is based on the shared presence of neurochemicals that are exactly the same in host as well as in the microorganism. The ability of microorganisms to not only respond to, but also produce, many of the same neurochemicals that are produced by the host, such as during periods of stress, has led to the introduction of this evolutionary-based mechanism which has a role in the pathogenesis of infectious disease. The consideration of microbial endocrinology–based mechanisms has demonstrated, for example, that the prevalent use of catecholamine-based synthetic drugs in the clinical setting contributes to the formation of biofilms in indwelling medical devices. Production of neurochemicals by microorganisms most often employs the same biosynthetic pathways as those utilized by the host, indicating that acquisition of host neurochemical-based signaling system in the host may have been acquired due to lateral gene transfer from microorganisms. That both host and microorganism produce and respond to the very same neurochemicals means that there is bidirectionality contained with the theoretical underpinnings of microbial endocrinology. This can be seen in the role of microbial endocrinology in the microbiota-gut-brain axis and its relevance to infectious disease. Such shared pathways argue for a role of microorganism-neurochemical interactions in infectious disease.
The Staphylococcal Biofilm: Adhesins, Regulation, and Host Response
Authors: Paharik Alexandra E. , Horswill Alexander R.
Published: April 2016

The staphylococci comprise a diverse genus of Gram-positive, nonmotile commensal organisms that inhabit the skin and mucous membranes of humans and other mammals. In general, staphylococci are benign members of the natural flora, but many species have the capacity to be opportunistic pathogens, mainly infecting individuals who have medical device implants or are otherwise immunocompromised.Staphylococcus aureusandStaphylococcus epidermidisare major sources of hospital-acquired infections and are the most common causes of surgical site infections and medical device-associated bloodstream infections. The ability of staphylococci to form biofilmsin vivomakes them highly resistant to chemotherapeutics and leads to chronic diseases. These biofilm infections include osteomyelitis, endocarditis, medical device infections, and persistence in the cystic fibrosis lung. Here, we provide a comprehensive analysis of our current understanding of staphylococcal biofilm formation, with an emphasis on adhesins and regulation, while also addressing how staphylococcal biofilms interact with the immune system. On the whole, this review will provide a thorough picture of biofilm formation of the staphylococcus genus and how this mode of growth impacts the host.
Organ manifestations and long-term outcome of Fabry disease in patients with the GLA haplotype D313Y
Authors: Oder Daniel , Üçeyler Nurcan , Liu Dan , Hu Kai , Petritsch Bernhard , Sommer Claudia , Ertl Georg , Wanner Christoph , Nordbeck Peter
Published: April 2016

Objectives

The severity of Fabry disease is dependent on the type of mutation in the α-galactosidase A (AgalA) encoding gene (GLA). This study focused on the impact of the GLA haplotype D313Y on long-term organ involvement and function.

Setting and participants

In this monocentric study, all participants presenting with the D313Y haplotype between 2001 and 2015 were comprehensively clinically investigated at baseline and during a 4-year follow-up if available. Five females and one male were included.

Primary and secondary outcome measures

Cardiac, nephrological, neurological, laboratory and quality of life data.

Results

AgalA enzyme activity in leucocytes (0.3±0.9 nmol/min/mg protein (mean±SD)) and serum lyso-Gb3 (0.6±0.3 ng/mL at baseline) were in normal range in all patients. Cardiac morphology and function were normal (left-ventricular (LV) ejection fraction 66±8%; interventricular septum 7.7±1.4 mm; LV posterior wall 7.5±1.4 mm; normalised LV mass in MRI 52±9 g/m2; LV global longitudinal strain −21.6±1.9%) and there were no signs of myocardial fibrosis in cardiac MRI. Cardiospecific biomarkers were also in normal range. Renal function was not impaired (estimated glomerular filtration rate MDRD 103±15 mL/min; serum-creatinine 0.75±0.07 mg/dL; cystatin-c 0.71±0.12 mg/L). One female patient (also carrying a Factor V Leiden mutation) had a transitory ischaemic attack. One patient showed white matter lesions in brain MRI, but none had Fabry-associated pain attacks, pain crises, evoked pain or permanent pain. Health-related quality of life analysis revealed a reduction in individual well-being. At long-term follow-up after 4 years, no significant change was seen in any parameter.

Conclusions

The results of the current study suggest that the D313Y genotype does not lead to severe organ manifestations as seen in genotypes known to be causal for classical FD.
Socioeconomic differences in the benefits of structured physical activity compared with health education on the prevention of major mobility disability in older adults: the LIFE study
Authors: Bann David , Chen Haiying , Bonell Chris , Glynn Nancy W , Fielding Roger A , Manini Todd , King Abby C , Pahor Marco , Mihalko Shannon L , Gill Thomas M
Published: April 2016

Background

Evidence is lacking on whether health-benefiting community-based interventions differ in their effectiveness according to socioeconomic characteristics. We evaluated whether the benefit of a structured physical activity intervention on reducing mobility disability in older adults differs by education or income.

Methods

The Lifestyle Interventions and Independence for Elders (LIFE) study was a multicentre, randomised trial that compared a structured physical activity programme with a health education programme on the incidence of mobility disability among at-risk community-living older adults (aged 70–89 years; average follow-up of 2.6 years). Education (≤ high school (0–12 years), college (13–17 years) or postgraduate) and annual household income were self-reported (<$24 999, $25 000 to $49 999 and ≥$50 000). The risk of disability (objectively defined as loss of ability to walk 400 m) was compared between the 2 treatment groups using Cox regression, separately by socioeconomic group. Socioeconomic group×intervention interaction terms were tested.

Results

The effect of reducing the incidence of mobility disability was larger for those with postgraduate education (0.72, 0.51 to 1.03; N=411) compared with lower education (high school or less (0.93, 0.70 to 1.24; N=536). However, the education group×intervention interaction term was not statistically significant (p=0.54). Findings were in the same direction yet less pronounced when household income was used as the socioeconomic indicator.

Conclusions

In the largest and longest running trial of physical activity amongst at-risk older adults, intervention effect sizes were largest among those with higher education or income, yet tests of statistical interactions were non-significant, likely due to inadequate power.

Trial registration number

NCT01072500.
The history of pulse therapy in lupus nephritis (1976–2016)
Authors: Scheinberg Morton
Published: April 2016

Pulse therapy with methylprednisolone became standard of care for the treatment of worsening lupus nephritis since its introduction in 1976. Even today, 40 years since its introduction, it is still a gold standard for this clinical condition. In this communication, we have reviewed the events that surrounded the use of this therapy by one of the authors of the original paper published inLancet40 years ago.
Concomitant origin of the anterior or posterior spinal artery with the feeder of a spinal dural arteriovenous fistula (SDAVF)
Authors: Adrianto Yudhi , Yang Ku Hyun , Koo Hae-Won , Park Wonhyoung , Jung Sung Chul , Park Jie Eun , Kim Kwang-Kuk , Jeon Sang Ryong , Suh Dae Chul
Published: April 2016

Background/objective

The concomitant origin of the anterior spinal artery (ASA) or the posterior spinal artery (PSA) from the feeder of a spinal dural arteriovenous fistula (SDAVF) is rare and the exact incidence is not known. We present our experience with the management of SDAVFs in such cases.

Methods

In 63 patients with SDAVF between 1993 and 2015, the feeder origin of the SDAVF was evaluated to determine whether it was concomitant with the origin of the ASA or PSA. Embolization was attempted when the patient did not want open surgery and an endovascular approach was regarded as safe and possible. The outcome of the procedure was evaluated as complete, partial, or no obliteration. The clinical outcome was evaluated by Aminoff–Logue (ALS) gait and micturition scale scores.

Results

Nine patients (14%) had a concomitant origin of the ASA or PSA with the feeder. There were two cervical, five thoracic, and two lumbar level SDAVFs. A concomitant origin of the feeder was identified with the ASA (n=7) and PSA (n=2). Embolization was performed in four patients and open surgery was performed in five. Embolization resulted in complete obliteration in three patients and partial obliteration in one. Using the ALS gait and micturition scale, the final outcome improved in six while three cases remained in an unchanged condition over 2–148 months.

Conclusions

The concomitant origin of the ASA or PSA with the feeder occurs occasionally. Complete obliteration of the fistula can be achieved either by embolization or open surgery. Embolization can be carefully performed in selected patients who are in a poor condition and do not want to undergo open surgery.
A single Mediterranean meal does not impair postprandial flow-mediated dilatation in healthy men with subclinical metabolic dysregulations
Authors: Lacroix Sébastien , Des Rosiers Christine , Gayda Mathieu , Nozza Anna , Thorin Éric , Tardif Jean-Claude , Nigam Anil
Published: April 2016

Cardiovascular risk factors are known to exacerbate high-saturated fatty acid meal (HSFAM)-induced endothelial dysfunction, but the influence of subclinical metabolic dysregulations and the acute impact of a single mixed Mediterranean-type meal (MMM) remains unknown. Thus, this study has the objective to evaluate the metabolic and vascular effect of such meals in healthy subjects with or without subclinical fasting metabolic dysregulations. Twenty-eight healthy males without overt cardiovascular risk factors randomly ingested 1 of 2 isocaloric meals on separate days. Plasma metabolic markers, fatty acid (FA) profile, and endothelial function (flow-mediated dilatation; FMD) were assessed at baseline and 2 and 4 h after meal ingestion. Unsupervised hierarchical clustering identified 2 subgroups of participants (n = 11 and 17) differing by their baseline metabolic profiles. The MMM did not significantly alter postprandial endothelial function in all subjects, irrespective of baseline metabolic parameters. In contrast, the HSFAM induced postprandial endothelial dysfunction (Δ%FMDabsolute = −5.28 ± 2.54, p < 0.01 vs. MMM) in a subgroup of individuals with significantly greater body mass index, fasting insulinemia, and lipid parameters (n = 11). Finally, the postprandial plasma FA profiles were differentially enriched by the HSFAM and MMM, notably with saturated FAs and omega-3 polyunsaturated FAs, respectively. Collectively, our results highlight the detrimental impact of a single HSFAM on endothelial function in healthy individuals displaying subclinical fasting metabolic dysregulations. Such individuals could benefit from MMM, demonstrated herein to be without any acute detriment to endothelial function.
Effects of obesity and mild hypohydration on local sweating and cutaneous vascular responses during passive heat stress in females
Authors: Moyen Nicole E. , Burchfield Jenna M. , Butts Cory L. , Glenn Jordan M. , Tucker Matthew A. , Treece Keeley , Smith Amber J. , McDermott Brendon P. , Ganio Matthew S.
Published: April 2016

The purpose of this study was to evaluate the effect of obesity and mild hypohydration on local sweating (LSR) and cutaneous vascular conductance (CVC) responses during passive heat stress in females. Thirteen obese (age, 24 ± 4 years; 45.4% ± 5.2% body fat) and 12 nonobese (age, 22 ± 2 years; 25.1% ± 3.9% body fat) females were passively heated (1.0 °C rectal temperature increase) while either euhydrated (EUHY) or mildly hypohydrated (HYPO; via fluid restriction). Chest and forearm LSR (ventilated capsule) and CVC (Laser Doppler flowmetry) onset, sensitivity, and plateau/steady state were recorded as mean body temperature increased (ΔTb). Participants began trials EUHY (urine specific gravity, Usg = 1.009 ± 0.006) or HYPO (Usg = 1.025 ± 0.004; p < 0.05), and remained EUHY or HYPO. Independent of obesity, HYPO decreased sweat sensitivity at the chest (HYPO = 0.79 ± 0.35, EUHY = 0.95 ± 0.39 Δmg·min−1·cm−2/°C ΔTb) and forearm (HYPO = 0.82 ± 0.39, EUHY = 1.06 ± 0.34 Δmg·min−1·cm−2/°C ΔTb); forearm LSR plateau was also decreased (HYPO = 0.66 ± 0.19, EUHY = 0.78 ± 0.23 mg·min−1·cm−2; all p < 0.05). Overall, obese females had lower chest-sweat sensitivity (0.72 ± 0.35 vs. 1.01 ± 0.33 Δmg·min−1·cm−2/°C ΔTb) and plateau (0.55 ± 0.27 vs. 0.80 ± 0.25 mg·min−1·cm−2; p < 0.05). While hypohydrated, obese females had a lower chest LSR (p < 0.05) versus nonobese females midway (0.45 ± 0.26 vs. 0.73 ± 0.23 mg·min−1·cm−2) and at the end (0.53 ± 0.27 vs. 0.81 ± 0.24 mg·min−1·cm−2) of heating. Furthermore, HYPO (relative to the EUHY trials) led to a greater decrease in CVC sensitivity in obese (–28 ± 27 Δ% maximal CVC/°C ΔTb) versus nonobese females (+9.2 ± 33 Δ% maximal CVC/°C ΔTb; p < 0.05). In conclusion, mild hypohydration impairs females’ sweating responses during passive heat stress, and this effect is exacerbated when obese.
New transient method for determining soil hydraulic conductivity function
Authors: Leung A.K. , Coo J.L. , Ng C.W.W. , Chen R.
Published: April 2016

The instantaneous profile method (IPM) is a transient method for measuring a soil’s hydraulic conductivity function (SHCF), which relates soil hydraulic conductivity with suction. In the existing interpretation method of the IPM, boundary flux during testing must be known to integrate instantaneous profiles of water content for obtaining the water flow rate. However, it is usually difficult and expensive to measure a boundary flux and if not known, assumptions that may not be easily justified (especially in the field condition) have to be made. In this study, a new method is proposed so that boundary flux does not need to be measured, controlled or assumed during a test. The new method is evaluated through (i) hypothetical column tests using transient seepage analyses and (ii) five case studies. The new method is capable of determining an SHCF with good accuracy. Normalized root-mean-square deviation (NRMSD) for the old and new methods is less than 5% and 10%, respectively. The accuracy of the new method can be increased substantially (i.e., NRMSD <5%) when the spacing of sensors installed along a soil column is reduced. Closer sensor spacing reduces error propagation due to numerical differentiation of instantaneous profiles of hydraulic head for determining hydraulic gradient.