bluuebunny/crossref_metadata_2025 huggingface dataset:
Winter severity determines functional trait composition of phytoplankton in seasonally ice‐covered lakes
Authors: Özkundakci Deniz , Gsell Alena S. , Hintze Thomas , Täuscher Helgard , Adrian Rita
Published: September 2015

How climate change will affect the community dynamics and functionality of lake ecosystems during winter is still little understood. This is also true for phytoplankton in seasonally ice‐covered temperate lakes which are particularly vulnerable to the presence or absence of ice. We examined changes in pelagic phytoplankton winter community structure in a north temperate lake (Müggelsee, Germany), covering 18 winters between 1995 and 2013. We tested how phytoplankton taxa composition varied along a winter‐severity gradient and to what extent winter severity shaped the functional trait composition of overwintering phytoplankton communities using multivariate statistical analyses and a functional trait‐based approach. We hypothesized that overwintering phytoplankton communities are dominated by taxa with trait combinations corresponding to the prevailing winter water column conditions, using ice thickness measurements as a winter‐severity indicator. Winter severity had little effect on univariate diversity indicators (taxon richness and evenness), but a strong relationship was found between the phytoplankton community structure and winter severity when taxon trait identity was taken into account. Species responses to winter severity were mediated by the key functional traits: motility, nutritional mode, and the ability to form resting stages. Accordingly, one or the other of two functional groups dominated the phytoplankton biomass during mild winters (i.e., thin or no ice cover; phototrophic taxa) or severe winters (i.e., thick ice cover; exclusively motile taxa). Based on predicted milder winters for temperate regions and a reduction in ice‐cover durations, phytoplankton communities during winter can be expected to comprise taxa that have a relative advantage when the water column is well mixed (i.e., need not be motile) and light is less limiting (i.e., need not be mixotrophic). A potential implication of this result is that winter severity promotes different communities at the vernal equinox, which may have different nutritional quality for the next trophic level and ecosystem‐scale effects.
Algorithm of medication review in frail older people: Focus on minimizing the use of high‐risk medications
Authors: Poudel Arjun , Ballokova Anna , Hubbard Ruth E , Gray Leonard C , Mitchell Charles A , Nissen Lisa M , Scott Ian A
Published: September 2015

Aim

Frail older people typically suffer several chronic diseases, receive multiple medications and are more likely to be institutionalized in residential aged care facilities. In such patients, optimizing prescribing and avoiding use of high‐risk medications might prevent adverse events. The present study aimed to develop a pragmatic, easily applied algorithm for medication review to help clinicians identify and discontinue potentially inappropriate high‐risk medications.

Methods

The literature was searched for robust evidence of the association of adverse effects related to potentially inappropriate medications in older patients to identify high‐risk medications. Prior research into the cessation of potentially inappropriate medications in older patients in different settings was synthesized into a four‐step algorithm for incorporation into clinical assessment protocols for patients, particularly those in residential aged care facilities.

Results

The algorithm comprises several steps leading to individualized prescribing recommendations: (i) identify a high‐risk medication; (ii) ascertain the current indications for the medication and assess their validity; (iii) assess if the drug is providing ongoing symptomatic benefit; and (iv) consider withdrawing, altering or continuing medications. Decision support resources were developed to complement the algorithm in ensuring a systematic and patient‐centered approach to medication discontinuation. These include a comprehensive list of high‐risk medications and the reasons for inappropriateness, lists of alternative treatments, and suggested medication withdrawal protocols.

Conclusions

The algorithm captures a range of different clinical scenarios in relation to potentially inappropriate medications, and offers an evidence‐based approach to identifying and, if appropriate, discontinuing such medications. Studies are required to evaluate algorithm effects on prescribing decisions and patient outcomes. Geriatr Gerontol Int 2016; 16: 1002–1013.
Estimating Aquifer Properties Using Derivative Analysis of Water Level Time Series from Active Well Fields
Authors: Lewis Alan R. , Ronayne Michael J. , Sale Thomas C.
Published: September 2015

Water level time series from groundwater production wells offer a transient dataset that can be used to estimate aquifer properties in areas with active groundwater development. This article describes a new parameter estimation method to infer aquifer properties from such datasets. Specifically, the method analyzes long‐term water level measurements from multiple, interacting groundwater production wells and relies on temporal water level derivatives to estimate the aquifer transmissivity and storativity. Analytically modeled derivatives are compared to derivatives calculated directly from the observed water level data; an optimization technique is used to identify best‐fitting transmissivity and storativity values that minimize the difference between modeled and observed derivatives. We demonstrate how the consideration of derivative (slope) behavior eliminates uncertainty associated with static water levels and well‐loss coefficients, enabling effective use of water level data from groundwater production wells. The method is applied to time‐series data collected over a period of 6 years from a municipal well field operating in the Denver Basin, Colorado (USA). The estimated aquifer properties are shown to be consistent with previously published values. The parameter estimation method is further tested using synthetic water level time series generated with a numerical model that incorporates the style of heterogeneity that occurs in the Denver Basin sandstone aquifers.
Comparative study of development parameters of four Ooencyrtus spp. (Hymenoptera: Encyrtidae) on natural and factitious hosts
Authors: Samra S. , Ghanim M. , Protasov A. , Mendel Z.
Published: September 2015

Biological control approaches such as seeding and augmentation releases of populations of natural enemies mostly rely on the indoor production of predator or parasitoid species, often with the use of alternative prey/host species. In this study, we investigated several development parameters of four egg parasitoid species: Ooencyrtus fecundus, O. near fecundus, O. pityocampae and O. telenomicida, and compared their performance on their natural host, the variegated caper bug (CB) Stenozygum coloratum, and on an alternative, factitious host, the silk moth (SM) Bombyx mori. Survival was higher and development duration shorter in CB eggs, making the CB a better host for these congeners. However, adult longevity was generally longer for individuals that developed in SM eggs. Moreover, O. fecundus and O. pityocampae females that had developed in SM eggs displayed higher fecundity than all other female/host combinations. Survival also varied according to the age of the SM eggs: parasitoid survival rates were significantly higher in 9‐ to 12‐month‐old (post‐diapausing) eggs than in young (about 1 month old) ones. These results were probably influenced by differences among the egg sizes of the studied hosts. The number of non‐laying females and self‐superparasitism rates were exceptionally high in O. near fecundus. These findings suggest that SM eggs, and especially those which are being utilized after a long storage, could serve for mass rearing of the studied Ooencyrtus spp.
Driving with Mild Cognitive Impairment or Dementia: Cognitive Test Performance and Proxy Report of Daily Life Function in Older Women
Authors: Vaughan Leslie , Hogan Patricia E. , Rapp Stephen R. , Dugan Elizabeth , Marottoli Richard A. , Snively Beverly M. , Shumaker Sally A. , Sink Kaycee M.
Published: September 2015

Objectives

To investigate associations between proxy report of cognitive and functional limitations and cognitive performance and current or former driving status in older women with mild cognitive impairment (MCI) and all‐cause dementia.

Design

Cross‐sectional data analysis of retrospectively identified older women with adjudicated MCI and all‐cause dementia in the Women's Health Initiative Memory Study—Epidemiology of Cognitive Health Outcomes (WHIMS‐ECHO).

Setting

Academic medical center.

Participants

Women (mean age ± standard deviation 83.7 ± 3.5) adjudicated with MCI or dementia during Year 1, 2, 3, or 4 of the WHIMS‐ECHO follow‐up period (N = 385).

Measurements

The telephone‐administered cognitive battery included tests of attention, verbal learning and memory, verbal fluency, executive function, working memory, and global cognitive function plus self‐report measures of depressive symptomatology. The Dementia Questionnaire (DQ) was administered to a knowledgeable proxy (family member, friend).

Results

Sixty percent of women with MCI and 40% of those with dementia are current drivers. Proxy reports of functional limitations in instrumental activities of daily living (IADLs) are associated with current driving status in women with MCI, whereas performance‐based cognitive tests are not. In women with dementia, proxy reports of functional limitations in IADLs and performance‐based cognitive tests are associated with current driving status, as expected.

Conclusion

These findings have clinical implications for the importance of evaluating driving concurrently with other instrumental functional abilities in MCI and dementia. Additional work is needed to determine whether proxy report of cognitive and functional impairments should help guide referrals for driving assessment and rehabilitation or counseling for driving transition.
Long‐lasting effect of NMDA receptor antagonist memantine on ethanol‐cue association and relapse
Authors: Vengeliene Valentina , Olevska Anastasia , Spanagel Rainer
Published: September 2015

It is well known that the glutamatergic system plays a crucial role in alcohol addiction and especially in relapse‐like behaviour. However, results of clinical studies on compounds that influence the activity of the glutamatergic system have been disappointing so far. The aim of our study was to establish treatment conditions under which the N‐methyl‐d‐aspartate receptor (NMDAR) antagonist memantine may produce more reliable treatment effect with respect to alcohol relapse‐like behaviour. For this purpose, male Wistar rats were trained to associate several discrete stimuli with ethanol delivery. Thereafter, half of the animals received a brief memory reactivation session followed by two administrations of 20 mg/kg of memantine, while the other half received the same treatment without memory reactivation. Afterwards, a cue‐induced ethanol‐seeking behaviour test was performed followed by repeated extinction sessions and a reacquisition test. Our data show that administration of memantine reduced responding on the ethanol‐associated lever in a cue‐induced ethanol‐seeking test. This reduction did not depend on whether or not a memory reactivation session was introduced prior to memantine administration. Following extinction, however, reacquisition of ethanol self‐administration was only impaired in the group where memantine was given after a short memory reactivation session, showing that this schedule of drug administration produced a long‐lasting disruption of the association between the conditioned stimuli and the delivery of ethanol. In conclusion, we show that memantine disrupted the drug‐cue association, which consequently interfered with relapse‐like behaviour supporting the possibility that memantine is a treatment option for alcoholism.

image

Our data supports the possibility that memantine is a treatment option for alcoholism. However, the effectiveness of this drug seems to lie in its ability to disrupt conditioned behaviours and should be given in conjunction with exposure to conditioned drug stimuli.
Soluble amyloid precursor protein alpha inhibits tau phosphorylation through modulation of GSK3β signaling pathway
Authors: Deng Juan , Habib Ahsan , Obregon Demian F. , Barger Steven W. , Giunta Brian , Wang Yan‐Jiang , Hou Huayan , Sawmiller Darrell , Tan Jun
Published: September 2015

We recently found that sAPPα decreases amyloid‐beta generation by directly associating with β‐site amyloid precursor protein (APP)‐converting enzyme 1 (BACE1), thereby modulating APP processing. Because inhibition of BACE1 decreases glycogen synthase kinase 3 beta (GSK3β)‐mediated Alzheimer's disease (AD)‐like tau phosphorylation in AD patient‐derived neurons, we determined whether sAPPα also reduces GSK3β‐mediated tau phosphorylation. We initially found increased levels of inhibitory phosphorylation of GSK3β (Ser9) in primary neurons from sAPPα over‐expressing mice. Further, recombinant human sAPPα evoked the same phenomenon in SH‐SY5Y cells. Further, in SH‐SY5Y cells over‐expressing BACE1, and HeLa cells over‐expressing human tau, sAPPα reduced GSK3β activity and tau phosphorylation. Importantly, the reductions in GSK3β activity and tau phosphorylation elicited by sAPPα were prevented by BACE1 but not γ‐secretase inhibition. In accord, AD mice over‐expressing human sAPPα had less GSK3β activity and tau phosphorylation compared with controls. These results implicate a direct relationship between APP β‐processing and GSK3β‐mediated tau phosphorylation and further define the central role of sAPPα in APP autoregulation and AD pathogenesis.

image

Hypothesized pathway for sAPPα‐mediated reduction of tau phosphorylation: Soluble amyloid precursor protein alpha (sAPPα) increases glycogen synthase kinase 3 beta (GSK3β) inhibitory phosphorylation by inhibiting β‐site APP‐converting enzyme 1 (BACE1) and followed by reduction of tau phosphorylation. BACE1 inhibition also results in a decrease of amyloid‐beta (Aβ) production. We believe these findings might provide a new strategy to use sAPPα, in treating both Aβ and tau pathology.
Deficiencies in Dermatologic Training in Pediatric Residency: Perspective of Pediatric Residency Program Directors
Authors: Khorsand Kate , Brandling‐Bennett Heather A.
Published: September 2015

Background/Objectives

Children with skin‐related problems commonly present to general pediatricians, and dermatology is among the top specialty areas that pediatricians have identified as having inadequate training to support their practice. This study was designed to document current opportunities for dermatologic training during pediatric residency and provides suggestions for improvement.

Methods

Pediatric residency program directors were contacted to participate in an online survey focusing on dermatologic training during pediatric residency. The survey was sent to 199 programs, from which 78 responses were received (response rate 39.2%). Required or elective rotations, other educational opportunities, and adequacy of dermatology training during pediatric residency were assessed and compared between institutions with zero, one, or two or more affiliated pediatric dermatologists.

Results

Eighty‐four percent of pediatric residency programs offer clinical training in dermatology. This training is required in only 19% of programs and is elective in 73%. Fewer than one‐quarter of eligible residents participate in the elective option. Didactic dermatology lectures are available at all of the programs. Overall, only 6% of residency program directors felt that their graduating residents received very adequate training in dermatology and 26% felt their residents received inadequate training.

Conclusions

Exposure to dermatology clinics was perceived to be the most desirable training modality for pediatric residents, but a minority of residents receive this exposure. Many pediatric residency program directors felt that residents receive inadequate dermatology training, which indicates a need to address educational deficiencies. Supporting a pediatric dermatologist on staff and requiring a rotation in pediatric dermatology could improve dermatologic curricula for pediatric residents.
Facing up to Ignorance and Privilege: Philosophy of Whiteness as Public Intellectualism
Authors: MacMullan Terrance
Published: September 2015

This article offers an overview on current trends and future research possibilities within the philosophy of whiteness. It examines the sub‐field of the philosophy of whiteness within the context of the larger field of the philosophy of race in order to assess the viability and relevance of this field of study. Some of the topics on whiteness examined in the article include the problems of white ignorance and privilege, the invisibility of white supremacist racism to white people, and how all these problems can be understood either as examples of epistemologies of ignorance or as unexamined habits in the sense used by pragmatist philosophy. The article argues that the current state of this field calls for a greater emphasis on public intellectualism on whiteness that would incorporate many ideas that are widely accepted by critical race scholars into the under‐informed public discourse on race and whiteness. It also argues that the increasing prevalence of negative liberty movements in the United States should be examined in light of established research on the philosophy of whiteness.
Sleeping arrangements and mass distribution of bed nets in six districts in central and northern Mozambique
Authors: Plucinski M. M. , Chicuecue S. , Macete E. , Chambe G. A. , Muguande O. , Matsinhe G. , Colborn J. , Yoon S. S. , Doyle T. J. , Kachur S. P. , Aide P. , Alonso P. L. , Guinovart C. , Morgan J.
Published: September 2015

Objective

Universal coverage with insecticide‐treated bed nets is a cornerstone of modern malaria control. Mozambique has developed a novel bed net allocation strategy, where the number of bed nets allocated per household is calculated on the basis of household composition and assumptions about who sleeps with whom. We set out to evaluate the performance of the novel allocation strategy.

Methods

A total of 1994 households were visited during household surveys following two universal coverage bed net distribution campaigns in Sofala and Nampula provinces in 2010–2013. Each sleeping space was observed for the presence of a bed net, and the sleeping patterns for each household were recorded. The observed coverage and efficiency were compared to a simulated coverage and efficiency had conventional allocation strategies been used. A composite indicator, the product of coverage and efficiency, was calculated. Observed sleeping patterns were compared with the sleeping pattern assumptions.

Results

In households reached by the campaign, 93% (95% CI: 93–94%) of sleeping spaces in Sofala and 84% (82–86%) in Nampula were covered by campaign bed nets. The achieved efficiency was high, with 92% (91–93%) of distributed bed nets in Sofala and 93% (91–95%) in Nampula covering a sleeping space. Using the composite indicator, the novel allocation strategy outperformed all conventional strategies in Sofala and was tied for best in Nampula. The sleeping pattern assumptions were completely satisfied in 66% of households in Sofala and 56% of households in Nampula. The most common violation of the sleeping pattern assumptions was that male children 3–10 years of age tended not to share sleeping spaces with female children 3–10 or 10–16 years of age.

Conclusions

The sleeping pattern assumptions underlying the novel bed net allocation strategy are generally valid, and net allocation using these assumptions can achieve high coverage and compare favourably with conventional allocation strategies.
Dual effects of atmospheric pressure plasma jet on skin wound healing of mice
Authors: Xu Gui‐Min , Shi Xing‐Min , Cai Jing‐Fen , Chen Si‐Le , Li Ping , Yao Cong‐Wei , Chang Zheng‐Shi , Zhang Guan‐Jun
Published: September 2015

Cold plasma has become an attractive tool for promoting wound healing and treating skin diseases. This article presents an atmospheric pressure plasma jet (APPJ) generated in argon gas through dielectric barrier discharge, which was applied to superficial skin wounds in BALB/c mice. The mice (n = 50) were assigned randomly into five groups (named A, B, C, D, E) with 10 animals in each group. Natural wound healing was compared with stimulated wound healing treated daily with APPJ for different time spans (10, 20, 30, 40, and 50 seconds) on 14 consecutive days. APPJ emission spectra, morphological changes in animal wounds, and tissue histological parameters were analyzed. Statistical results revealed that wound size changed over the duration of the experimental period and there was a significant interaction between experimental day and group. Differences between group C and other groups at day 7 were statistically significant (p < 0.05). All groups had nearly achieved closure of the untreated control wounds at day 14. The wounds treated with APPJ for 10, 20, 30, and 40 seconds showed significantly enhanced daily improvement compared with the control and almost complete closure at day 12, 10, 7, and 13, respectively. The optimal results of epidermal cell regeneration, granulation tissue hyperplasia, and collagen deposition in histological aspect were observed at day 7. However, the wounds treated for 50 seconds were less well healed at day 14 than those of the control. It was concluded that appropriate doses of cold plasma could inactivate bacteria around the wound, activate fibroblast proliferation in wound tissue, and eventually promote wound healing. Whereas, over doses of plasma suppressed wound healing due to causing cell death by apoptosis or necrosis. Both positive and negative effects may be related to the existence of reactive oxygen and nitrogen species (ROS and RNS) in APPJ.
Inhibition of Pseudomonas aeruginosa biofilm formation on wound dressings
Authors: Brandenburg Kenneth S. , Calderon Diego F. , Kierski Patricia R. , Brown Amanda L. , Shah Nihar M. , Abbott Nicholas L. , Schurr Michael J. , Murphy Christopher J. , McAnulty Jonathan F. , Czuprynski Charles J.
Published: September 2015

Chronic nonhealing skin wounds often contain bacterial biofilms that prevent normal wound healing and closure and present challenges to the use of conventional wound dressings. We investigated inhibition of Pseudomonas aeruginosa biofilm formation, a common pathogen of chronic skin wounds, on a commercially available biological wound dressing. Building on prior reports, we examined whether the amino acid tryptophan would inhibit P. aeruginosa biofilm formation on the three‐dimensional surface of the biological dressing. Bacterial biomass and biofilm polysaccharides were quantified using crystal violet staining or an enzyme linked lectin, respectively. Bacterial cells and biofilm matrix adherent to the wound dressing were visualized through scanning electron microscopy. d‐/l‐tryptophan inhibited P. aeruginosa biofilm formation on the wound dressing in a dose dependent manner and was not directly cytotoxic to immortalized human keratinocytes although there was some reduction in cellular metabolism or enzymatic activity. More importantly, d‐/l‐tryptophan did not impair wound healing in a splinted skin wound murine model. Furthermore, wound closure was improved when d‐/l‐tryptophan treated wound dressing with P. aeruginosa biofilms were compared with untreated dressings. These findings indicate that tryptophan may prove useful for integration into wound dressings to inhibit biofilm formation and promote wound healing.
Long‐lasting effects of dexamethasone on immune cells and wound healing in the zebrafish
Authors: Sharif Faiza , Steenbergen Peter J. , Metz Juriaan R. , Champagne Danielle L.
Published: September 2015

This study assessed the lasting impact of dexamethasone (DEX) exposure during early development on tissue repair capacity at later life stages (5, 14, and 24 days post fertilization [dpf]) in zebrafish larvae. Using the caudal fin amputation model, we show that prior exposure to DEX significantly delays but does not prevent wound healing at all life stages studied. DEX‐induced impairments on wound healing were fully restored to normal levels with longer post amputation recovery time. Further analyses revealed that DEX mainly exerted its detrimental effects in the early phase (0–5 hours) of wound‐healing process. Specifically, we observed the following events: (1) massive amount of cell death both by necrosis and apoptosis; (2) significant reduction in the number as well as misplacement of macrophages at the wound site; (3) aberrant migration and misplacement of neutrophils and macrophages at the wound site. These events were accompanied by significant (likely compensatory) changes in the expression of genes involved in tissue patterning, including up‐regulation of FKBP5 6 hours post DEX exposure and that of Wnt3a and RARγ at 24 hours post amputation. Taken together, this study provides evidence that DEX exposure during early sensitive periods of development appears to cause permanent alterations in the cellular/molecular immune processes that are involved in the early phase of wound healing in zebrafish. These findings are consistent with previous studies showing that antenatal course of DEX is associated with immediate and lasting alterations of the immune system in rodent models and humans. Therefore, the current findings support the use of the larval zebrafish model to study the impact of stress and stress hormone exposure in immature organisms on health risks in later life.
Rationally designed graphene-nanotube 3D architectures with a seamless nodal junction for efficient energy conversion and storage
Authors: Xue Yuhua , Ding Yong , Niu Jianbing , Xia Zhenhai , Roy Ajit , Chen Hao , Qu Jia , Wang Zhong Lin , Dai Liming
Published: September 2015

Seamlessly joint graphene-nanotube 3D architectures were created by one-step CVD for efficient energy conversion and storage.
Detection of single amino acid mutation in human breast cancer by disordered plasmonic self-similar chain
Authors: Coluccio Maria Laura , Gentile Francesco , Das Gobind , Nicastri Annalisa , Perri Angela Mena , Candeloro Patrizio , Perozziello Gerardo , Proietti Zaccaria Remo , Gongora Juan Sebastian Totero , Alrasheed Salma , Fratalocchi Andrea , Limongi Tania , Cuda Giovanni , Di Fabrizio Enzo
Published: September 2015

Novel nanoarray for single molecule detection from peptide mixture.
Nanoarchaeota, Their Sulfolobales Host, and Nanoarchaeota Virus Distribution across Yellowstone National Park Hot Springs
Authors: Munson-McGee Jacob H. , Field Erin K. , Bateson Mary , Rooney Colleen , Stepanauskas Ramunas , Young Mark J.
Published: September 2015

Nanoarchaeota
are obligate symbionts with reduced genomes first described from marine thermal vent environments. Here, both community metagenomics and single-cell analysis revealed the presence of
Nanoarchaeota
in high-temperature (∼90°C), acidic (pH ≈ 2.5 to 3.0) hot springs in Yellowstone National Park (YNP) (United States). Single-cell genome analysis of two cells resulted in two nearly identical genomes, with an estimated full length of 650 kbp. Genome comparison showed that these two cells are more closely related to the recently proposed
Nanobsidianus stetteri
from a more neutral YNP hot spring than to the marine
Nanoarchaeum equitans
. Single-cell and catalyzed reporter deposition-fluorescence
in situ
hybridization (CARD-FISH) analysis of environmental hot spring samples identified the host of the YNP
Nanoarchaeota
as a
Sulfolobales
species known to inhabit the hot springs. Furthermore, we demonstrate that
Nanoarchaeota
are widespread in acidic to near neutral hot springs in YNP. An integrated viral sequence was also found within one
Nanoarchaeota
single-cell genome and further analysis of the purified viral fraction from environmental samples indicates that this is likely a virus replicating within the YNP
Nanoarchaeota
.
Eradication of Methicillin-Resistant Staphylococcus aureus and of Enterobacteriaceae Expressing Extended-Spectrum Beta-Lactamases on a Model Pig Farm
Authors: Schmithausen Ricarda Maria , Kellner Sophia Ricarda , Schulze-Geisthoevel Sophia Veronika , Hack Sylvia , Engelhart Steffen , Bodenstein Isabel , Al-Sabti Nahed , Reif Marion , Fimmers Rolf , Körber-Irrgang Barbara , Harlizius Jürgen , Hoerauf Achim , Exner Martin , Bierbaum Gabriele , Petersen Brigitte , Bekeredjian-Ding Isabelle
Published: September 2015

Colonization of livestock with bacteria resistant to antibiotics is considered a risk for the entry of drug-resistant pathogens into the food chain. For this reason, there is a need for novel concepts to address the eradication of drug-resistant commensals on farms. In the present report, we evaluated the decontamination measures taken on a farm contaminated with methicillin-resistant
Staphylococcus aureus
(MRSA) and
Enterobacteriaceae
expressing extended-spectrum β-lactamases (ESBL-E). The decontamination process preceded the conversion from piglet breeding to gilt production. Microbiological surveillance showed that the decontamination measures eliminated the MRSA and ESBL-E strains that were detected on the farm before the complete removal of pigs, cleaning and disinfection of the stable, and construction of an additional stable meeting high-quality standards. After pig production was restarted, ESBL-E remained undetectable over 12 months, but MRSA was recovered from pigs and the environment within the first 2 days. However,
spa
(
Staphylococcus aureus
protein A gene) typing revealed acquisition of an MRSA strain (type t034) that had not been detected before decontamination. Interestingly, we observed that a farmworker who had been colonized with the prior MRSA strain (t2011) acquired the new strain (t034) after 2 months. In summary, this report demonstrates that decontamination protocols similar to those used here can lead to successful elimination of contaminating MRSA and ESBL-E in pigs and the stable environment. Nevertheless, decontamination protocols do not prevent the acquisition of new MRSA strains.
Geogenic Factors as Drivers of Microbial Community Diversity in Soils Overlying Polymetallic Deposits
Authors: Reith Frank , Zammit Carla M. , Pohrib Rebecca , Gregg Adrienne L. , Wakelin Steven A.
Published: September 2015

This study shows that the geogenic factors landform, lithology, and underlying mineral deposits (expressed by elevated metal concentrations in overlying soils) are key drivers of microbial community diversity in naturally metal-rich Australian soils with different land uses, i.e., agriculture versus natural bushland. One hundred sixty-eight soil samples were obtained from two metal-rich provinces in Australia, i.e., the Fifield Au-Pt field (New South Wales) and the Hillside Cu-Au-U rare-earth-element (REE) deposit (South Australia). Soils were analyzed using three-domain multiplex terminal-restriction-fragment-length-polymorphism (M-TRFLP) and PhyloChip microarrays. Geogenic factors were determined using field-mapping techniques and analyses of >50 geochemical parameters. At Fifield, microbial communities differed significantly with geogenic factors and equally with land use (
P
< 0.05). At Hillside, communities in surface soils (0.03- to 0.2-m depth) differed significantly with landform and land use (
P
< 0.05). Communities in deeper soils (>0.2 m) differed significantly with lithology and mineral deposit (
P
< 0.05). Across both sites, elevated metal contents in soils overlying mineral deposits were selective for a range of bacterial taxa, most importantly
Acidobacteria
,
Bacilli
,
Betaproteobacteria
, and
Epsilonproteobacteria
. In conclusion, long-term geogenic factors can be just as important as land use in determining soil microbial community diversity.
Positive Regulation of Staphylococcal Enterotoxin H by Rot (Repressor of Toxin) Protein and Its Importance in Clonal Complex 81 Subtype 1 Lineage-Related Food Poisoning
Authors: Sato'o Yusuke , Hisatsune Junzo , Nagasako Yuria , Ono Hisaya K. , Omoe Katsuhiko , Sugai Motoyuki
Published: September 2015

We previously demonstrated the clonal complex 81 (CC81) subtype 1 lineage is the major staphylococcal food poisoning (SFP)-associated lineage in Japan (Y. Sato'o et al., J Clin Microbiol
52:
2637–2640, 2014,
http://dx.doi.org/10.1128/JCM.00661-14
). Strains of this lineage produce staphylococcal enterotoxin H (SEH) in addition to SEA. However, an evaluation of the risk for the recently reported SEH has not been sufficiently conducted. We first searched for staphylococcal enterotoxin (SE) genes and SE proteins in milk samples that caused a large SFP outbreak in Japan. Only SEA and SEH were detected, while there were several SE genes detected in the samples. We next designed an experimental model using a meat product to assess the productivity of SEs and found that only SEA and SEH were detectably produced
in situ
. Therefore, we investigated the regulation of SEH production using a CC81 subtype 1 isolate. Through mutant analysis of global regulators, we found the repressor of toxin (Rot) functioned oppositely as a stimulator of SEH production. SEA production was not affected by Rot.
seh
mRNA expression correlated with
rot
both in media and on the meat product, and the Rot protein was shown to directly bind to the
seh
promoter. The
seh
promoter sequence was predicted to form a loop structure and to hide the RNA polymerase binding sequences. We propose Rot binds to the promoter sequence of
seh
and unfolds the secondary structure that may lead the RNA polymerase to bind the promoter, and then
seh
mRNA transcription begins. This alternative Rot regulation for SEH may contribute to sufficient toxin production by the CC81 subtype 1 lineage in foods to induce SFP.
Fungal Community Shifts in Structure and Function across a Boreal Forest Fire Chronosequence
Authors: Sun Hui , Santalahti Minna , Pumpanen Jukka , Köster Kajar , Berninger Frank , Raffaello Tommaso , Jumpponen Ari , Asiegbu Fred O. , Heinonsalo Jussi
Published: September 2015

Forest fires are a common natural disturbance in forested ecosystems and have a large impact on the microbial communities in forest soils. The response of soil fungal communities to forest fire is poorly documented. Here, we investigated fungal community structure and function across a 152-year boreal forest fire chronosequence using high-throughput sequencing of the internal transcribed spacer 2 (ITS2) region and a functional gene array (GeoChip). Our results demonstrate that the boreal forest soil fungal community was most diverse soon after a fire disturbance and declined over time. The differences in the fungal communities were explained by changes in the abundance of basidiomycetes and ascomycetes. Ectomycorrhizal (ECM) fungi contributed to the increase in basidiomycete abundance over time, with the operational taxonomic units (OTUs) representing the generaCortinariusandPilodermadominating in abundance. Hierarchical cluster analysis by using gene signal intensity revealed that the sites with different fire histories formed separate clusters, suggesting differences in the potential to maintain essential biogeochemical soil processes. The site with the greatest biological diversity had also the most diverse genes. The genes involved in organic matter degradation in the mature forest, in which ECM fungi were the most abundant, were as common in the youngest site, in which saprotrophic fungi had a relatively higher abundance. This study provides insight into the impact of fire disturbance on soil fungal community dynamics.
High-Level Heterologous Production of
d
-Cycloserine by Escherichia coli
Authors: Kumagai Takanori , Ozawa Tomoki , Tanimoto Momoko , Noda Masafumi , Matoba Yasuyuki , Sugiyama Masanori
Published: September 2015

Previously, we successfully cloned a
d
-cycloserine (
d
-CS) biosynthetic gene cluster consisting of 10 open reading frames (designated
dcsA
to
dcsJ
) from
d
-CS-producing
Streptomyces lavendulae
ATCC 11924. In this study, we put four
d
-CS biosynthetic genes (
dcsC
,
dcsD
,
dcsE
, and
dcsG
) in tandem under the control of the T7 promoter in an
Escherichia coli
host. SDS-PAGE analysis demonstrated that the 4 gene products were simultaneously expressed in host cells. When
l
-serine and hydroxyurea (HU), the precursors of
d
-CS, were incubated together with the
E. coli
resting cell suspension, the cells produced significant amounts of
d
-CS (350 ± 20 μM). To increase the productivity of
d
-CS, the
dcsJ
gene, which might be responsible for the
d
-CS excretion, was connected downstream of the four genes. The
E. coli
resting cells harboring the five genes produced
d
-CS at 660 ± 31 μM. The
dcsD
gene product, DcsD, forms
O
-ureido-
l
-serine from
O
-acetyl-
l
-serine (OAS) and HU, which are intermediates in
d
-CS biosynthesis. DcsD also catalyzes the formation of
l
-cysteine from OAS and H
2
S. To repress the side catalytic activity of DcsD, the
E. coli
chromosomal
cysJ
and
cysK
genes, encoding the sulfite reductase α subunit and OAS sulfhydrylase, respectively, were disrupted. When resting cells of the double-knockout mutant harboring the four
d
-CS biosynthetic genes, together with
dcsJ
, were incubated with
l
-serine and HU, the
d
-CS production was 980 ± 57 μM, which is comparable to that of
d
-CS-producing
S. lavendulae
ATCC 11924 (930 ± 36 μM).
Coexistence of Lactic Acid Bacteria and Potential Spoilage Microbiota in a Dairy Processing Environment
Authors: Stellato Giuseppina , De Filippis Francesca , La Storia Antonietta , Ercolini Danilo
Published: September 2015

Microbial contamination in food processing plants can play a fundamental role in food quality and safety. In this study, the microbiota in a dairy plant was studied by both 16S rRNA- and 26S rRNA-based culture-independent high-throughput amplicon sequencing. Environmental samples from surfaces and tools were studied along with the different types of cheese produced in the same plant. The microbiota of environmental swabs was very complex, including more than 200 operational taxonomic units with extremely variable relative abundances (0.01 to 99%) depending on the species and sample. A core microbiota shared by 70% of the samples indicated a coexistence of lactic acid bacteria with a remarkable level of
Streptococcus thermophilus
and possible spoilage-associated bacteria, including
Pseudomonas
,
Acinetobacter
, and
Psychrobacter
, with a relative abundance above 50%. The most abundant yeasts were
Kluyveromyces marxianus
,
Yamadazyma triangularis
,
Trichosporon faecale
, and
Debaryomyces hansenii
. Beta-diversity analyses showed a clear separation of environmental and cheese samples based on both yeast and bacterial community structure. In addition, predicted metagenomes also indicated differential distribution of metabolic pathways between the two categories of samples. Cooccurrence and coexclusion pattern analyses indicated that the occurrence of potential spoilers was excluded by lactic acid bacteria. In addition, their persistence in the environment can be helpful to counter the development of potential spoilers that may contaminate the cheeses, with possible negative effects on their microbiological quality.
Impact of Environmental Factors on Bacteriocin Promoter Activity in Gut-Derived Lactobacillus salivarius
Authors: Guinane Caitriona M. , Piper Clare , Draper Lorraine A. , O'Connor Paula M. , Hill Colin , Ross R. Paul , Cotter Paul D.
Published: September 2015

Bacteriocin production is regarded as a desirable probiotic trait that aids in colonization and persistence in the gastrointestinal tract (GIT). Strains of
Lactobacillus salivarius
, a species associated with the GIT, are regarded as promising probiotic candidates and have a number of associated bacteriocins documented to date. These include multiple class IIb bacteriocins (salivaricin T, salivaricin P, and ABP-118) and the class IId bacteriocin bactofencin A, which show activity against medically important pathogens. However, the production of a bacteriocin in laboratory media does not ensure production under stressful environmental conditions, such as those encountered within the GIT. To allow this issue to be addressed, the promoter regions located upstream of the structural genes encoding the
L. salivarius
bacteriocins mentioned above were fused to a number of reporter proteins (green fluorescent protein [GFP], red fluorescent protein [RFP], and luciferase [Lux]). Of these, only transcriptional fusions to GFP generated signals of sufficient strength to enable the study of promoter activity in
L. salivarius
. While analysis of the class IIb bacteriocin promoter regions indicated relatively weak GFP expression, assessment of the promoter of the antistaphylococcal bacteriocin bactofencin A revealed a strong promoter that is most active in the absence of the antimicrobial peptide and is positively induced in the presence of mild environmental stresses, including simulated gastric fluid. Taken together, these data provide information on factors that influence bacteriocin production, which will assist in the development of strategies to optimize
in vivo
and
in vitro
production of these antimicrobials.
A Ferrous Iron Exporter Mediates Iron Resistance in Shewanella oneidensis MR-1
Authors: Bennett Brittany D. , Brutinel Evan D. , Gralnick Jeffrey A.
Published: September 2015

Shewanella oneidensis
strain MR-1 is a dissimilatory metal-reducing bacterium frequently found in aquatic sediments. In the absence of oxygen,
S. oneidensis
can respire extracellular, insoluble oxidized metals, such as iron (hydr)oxides, making it intimately involved in environmental metal and nutrient cycling. The reduction of ferric iron (Fe
3+
) results in the production of ferrous iron (Fe
2+
) ions, which remain soluble under certain conditions and are toxic to cells at higher concentrations. We have identified an inner membrane protein in
S. oneidensis
, encoded by the gene SO_4475 and here called FeoE, which is important for survival during anaerobic iron respiration. FeoE, a member of the cation diffusion facilitator (CDF) protein family, functions to export excess Fe
2+
from the MR-1 cytoplasm. Mutants lacking
feoE
exhibit an increased sensitivity to Fe
2+
. The export function of FeoE is specific for Fe
2+
, as an
feoE
mutant is equally sensitive to other metal ions known to be substrates of other CDF proteins (Cd
2+
, Co
2+
, Cu
2+
, Mn
2+
, Ni
2+
, or Zn
2+
). The substrate specificity of FeoE differs from that of FieF, the
Escherichia coli
homolog of FeoE, which has been reported to be a Cd
2+
/Zn
2+
or Fe
2+
/Zn
2+
exporter. A complemented
feoE
mutant has an increased growth rate in the presence of excess Fe
2+
compared to that of the Δ
feoE
mutant complemented with
fieF
. It is possible that FeoE has evolved to become an efficient and specific Fe
2+
exporter in response to the high levels of iron often present in the types of environmental niches in which
Shewanella
species can be found.
A Novel Type Pathway-Specific Regulator and Dynamic Genome Environments of a Solanapyrone Biosynthesis Gene Cluster in the Fungus Ascochyta rabiei
Authors: Kim Wonyong , Park Jeong-Jin , Gang David R. , Peever Tobin L. , Chen Weidong
Published: September 2015

Secondary metabolite genes are often clustered together and situated in particular genomic regions, like the subtelomere, that can facilitate niche adaptation in fungi. Solanapyrones are toxic secondary metabolites produced by fungi occupying different ecological niches. Full-genome sequencing of the ascomycete
Ascochyta rabiei
revealed a solanapyrone biosynthesis gene cluster embedded in an AT-rich region proximal to a telomere end and surrounded by
Tc1/Mariner
-type transposable elements. The highly AT-rich environment of the solanapyrone cluster is likely the product of repeat-induced point mutations. Several secondary metabolism-related genes were found in the flanking regions of the solanapyrone cluster. Although the solanapyrone cluster appears to be resistant to repeat-induced point mutations, a
P450
monooxygenase gene adjacent to the cluster has been degraded by such mutations. Among the six solanapyrone cluster genes (
sol1
to
sol6
),
sol4
encodes a novel type of Zn(II)2Cys6 zinc cluster transcription factor. Deletion of
sol4
resulted in the complete loss of solanapyrone production but did not compromise growth, sporulation, or virulence. Gene expression studies with the
sol4
deletion and
sol4
-overexpressing mutants delimited the boundaries of the solanapyrone gene cluster and revealed that
sol4
is likely a specific regulator of solanapyrone biosynthesis and appears to be necessary and sufficient for induction of the solanapyrone cluster genes. Despite the dynamic surrounding genomic regions, the solanapyrone gene cluster has maintained its integrity, suggesting important roles of solanapyrones in fungal biology.
Function and Regulation of Cph2 in Candida albicans
Authors: Lane Shelley , Di Lena Pietro , Tormanen Kati , Baldi Pierre , Liu Haoping
Published: September 2015

Candida albicans
is associated with humans as both a harmless commensal organism and a pathogen. Cph2 is a transcription factor whose DNA binding domain is similar to that of mammalian sterol response element binding proteins (SREBPs). SREBPs are master regulators of cellular cholesterol levels and are highly conserved from fungi to mammals. However, ergosterol biosynthesis is regulated by the zinc finger transcription factor Upc2 in
C. albicans
and several other yeasts. Cph2 is not necessary for ergosterol biosynthesis but is important for colonization in the murine gastrointestinal (GI) tract. Here we demonstrate that Cph2 is a membrane-associated transcription factor that is processed to release the N-terminal DNA binding domain like SREBPs, but its cleavage is not regulated by cellular levels of ergosterol or oxygen. Chromatin immunoprecipitation sequencing (ChIP-seq) shows that Cph2 binds to the promoters of
HMS1
and other components of the regulatory circuit for GI tract colonization. In addition, 50% of Cph2 targets are also bound by Hms1 and other factors of the regulatory circuit. Several common targets function at the head of the glycolysis pathway. Thus, Cph2 is an integral part of the regulatory circuit for GI colonization that regulates glycolytic flux. Transcriptome sequencing (RNA-seq) shows a significant overlap in genes differentially regulated by Cph2 and hypoxia, and Cph2 is important for optimal expression of some hypoxia-responsive genes in glycolysis and the citric acid cycle. We suggest that Cph2 and Upc2 regulate hypoxia-responsive expression in different pathways, consistent with a synthetic lethal defect of the
cph2 upc2
double mutant in hypoxia.
Origin and Dissemination of Antimicrobial Resistance among Uropathogenic
Escherichia coli
Authors: Nolan Lisa K. , Li Ganwu , Logue Catherine M.
Published: September 2015

Antimicrobial agents of various types have important bearing on the outcomes of microbial infections. These agents may be bacteriostatic or –cidal, exert their impact via various means, originate from a living organism or a laboratory, and appropriately be used in or on living tissue or not. Though the primary focus of this chapter is on resistance to the antimicrobial agents used to treat uropathogenic
Escherichia coli
(UPEC)-caused urinary tract infections (UTIs), some attention will be given to UPEC’s resistance to silver-containing antiseptics, which may be incorporated into catheters to prevent foreign body-associated UTIs.