bluuebunny/crossref_metadata_2025 huggingface dataset:
Bayesian Inventory Management with Potential Change‐Points in Demand
Authors: Wang Zhe (Frank) , Mersereau Adam J.
Published: September 2016

We consider the inventory management problem of a firm reacting to potential change points in demand, which we define as known epochs at which the demand distribution may (or may not) abruptly change. Motivating examples include global news events (e.g., the 9/11 terrorist attacks), local events (e.g., the opening of a nearby attraction), or internal events (e.g., a product redesign). In the periods following such a potential change point in demand, a manager is torn between using a possibly obsolete demand model estimated from a long data history and using a model estimated from a short, recent history. We formulate a Bayesian inventory problem just after a potential change point. We pursue heuristic policies coupled with cost lower bounds, including a new lower bounding approach to non‐perishable Bayesian inventory problems that relaxes the dependence between physical demand and demand signals and that can be applied for a broad set of belief and demand distributions. Our numerical studies reveal small gaps between the costs implied by our heuristic solutions and our lower bounds. We also provide analytical and numerical sensitivity results suggesting that a manager worried about downside profit risk should err on the side of underestimating demand at a potential change point.
Characterization of Cytospora isolates from wood cankers of declining grapevine in North America, with the descriptions of two new Cytospora species
Authors: Lawrence D. P. , Travadon R. , Pouzoulet J. , Rolshausen P. E. , Wilcox W. F. , Baumgartner K.
Published: September 2016

Cytospora species are ubiquitous pathogens of numerous woody plants, causing dieback and wood cankers in agronomic crops, timber trees and wildland trees (e.g. Prunus, Eucalyptus and Salix, respectively). Cytospora chrysosperma, C. cincta and C. leucostoma have been reported from grapevines in Iran showing symptoms of one or more recognized trunk diseases (esca, botryosphaeria‐, eutypa‐ and phomopsis diebacks); however, only C. chrysosperma was shown to be pathogenic to grapevine. To understand the potential role of Cytospora species in the grapevine trunk‐disease complex, 21 Cytospora isolates were examined that were recovered from dieback and wood cankers of Vitis vinifera and Vitis interspecific hybrids in seven northeastern U.S. states and two Canadian provinces. Phylogenetic analyses of ITS and translation elongation factor 1‐α identified two novel species: Cytospora vinacea sp. nov. and Cytospora viticola sp. nov. Differences in culture morphology and conidial dimensions also distinguished the species. When inoculated to the woody stems of potted V. vinifera ‘Thompson Seedless’ in the greenhouse, both species were pathogenic, based on development of wood lesions and fulfilment of Koch's postulates. Cytospora viticola was the most virulent based on lesion length at 12 months post‐inoculation. As cytospora canker shares some of the same general dieback‐type symptoms as botryosphaeria‐, eutypa‐ and phomopsis diebacks, it may be considered part of the grapevine trunk‐disease complex in eastern North America.
Life traits of four Botryosphaeriaceae species and molecular responses of different grapevine cultivars or hybrids
Authors: Bellée A. , Comont G. , Nivault A. , Abou‐Mansour E. , Coppin C. , Dufour M. C. , Corio‐Costet M. F.
Published: September 2016

Botryosphaeriaceae is a fungal family comprising many species involved in botryosphaeria dieback, a worldwide grapevine trunk disease. Currently, the interactions between Botryosphaeriaceae species and various grapevine cultivars are poorly understood and little data is available. This study investigated various life traits of five isolates belonging to four species of Botryosphaeriaceae found in French vineyards (Diplodia mutila, Diplodia seriata, Lasiodiplodia viticola and Neofusicoccum parvum). The two species N. parvum and L. viticola exhibited the highest optimal growth temperature and the best growth rates. They were also responsible for the most extensive necrosis and cankers in three Vitis vinifera cultivars (Cabernet Sauvignon, Merlot and Ugni‐Blanc) that differed in susceptibility to botryosphaeria dieback, and in two genotypes resistant to downy and powdery mildew (RV4 and RV5). Identification of the extracellular toxins produced by isolates in culture media showed that the N. parvum isolate had a different metabolite profile from the others, producing terremutin and salicylic acid derivatives, which are known to be compounds associated with virulence. In a second step, life traits were associated with nondestructive monitoring of gene expression involved in the defence mechanisms of five grapevine cultivars and genotypes after inoculation of wood cuttings with Botryosphaeriaceae. The transcript analyses were carried out at different times and were associated with principal component analysis (PCA). Each cultivar presented a specific transcript signature and several transcripts were correlated either with the size of necrosis/cankers or with symptom reduction, thus offering useful markers for breeding or estimating the defence status of plants.
Transcriptome analysis of the uniparous and multiparous goats ovaries
Authors: Wang LJ , Sun XW , Guo FY , Zhao YJ , Zhang JH , Zhao ZQ
Published: September 2016

Contents

Transcriptome analysis of Inner Mongolia Cashmere goat and Dazu black goat generated 38,772,947 and 38,771,668 clean pair end reads, respectively, which were assembled into 72,422 and 80,069 unigenes by Trinity, respectively. For Inner Mongolia Cashmere goat, 26,051 and 10,100 unigenes were assigned to gene ontology (GO) categories and clusters of orthologous groups, respectively. A total of 32,772 unigenes can comment to SWISS‐Prot database, and the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG) mapped 24,420 unigenes. While annotating the unigenes about Dazu black goats, we found 29,444(45.42%), 11,271 (38.28%), 36,910(56.94%) and 27,766 (42.83%) unigenes were assigned to GO database, COG database, SWISS‐Prot database and KEGG database, respectively. In addition, we performed the bioinformatics analysis of gene expression profiling aimed at the ovarian transcriptome difference between Inner Mongolia Cashmere goat and Dazu black goat. We obtained a sequencing depth of over 5.5 million and 5.8 million tags. There were 1,133 DEGs between two species, of which 632 genes upregulated in the Dazu black goat and 501 genes downregulated compared with which in Inner Mongolia Cashmere goat. By annotating the 1,133 DEGs into KEGG database, we found 525 DEGs. And there were 68 DEGs annotated in metabolic pathways, 31 DEGs annotated in ribosome, 28 DEGs annotated in focal adhesion, 27 DEGs annotated in phagosome, 26 DEGs annotated in pathways in cancer, 25 DEGs annotated in ECM‐receptor interaction, 23 DEGs annotated in protein digestion and absorption, 20 DEGs annotated in oxidative phosphorylation, 17 DEGs annotated in lysosome, and 16 DEGs annotated in cell adhesion molecules.
Effect of short‐term exposure of cumulus–oocyte complex to 3‐morpholinosydnonimine on in vitro embryo development and gene expression in cattle
Authors: Loren P , Cheuquemán C , Sánchez E , Risopatrón J , Arias ME , Felmer R , Sánchez R
Published: September 2016

Contents

Short‐term exposure of gametes to different types of stress might induce stress tolerance in mammalian embryos. The aim of this study was to evaluate the effect of short‐term exposure of bovine mature cumulus–oocyte complex (COC) to 3‐morpholinosydnonimine (SIN‐1) on subsequent in vitro embryo development, embryo quality and relative gene expression. Matured COCs were incubated with SIN‐1 (0, 0.1, 1, 10 and 100 μM SIN‐1) for 1 hr before in vitro fertilization and zygotes were cultured until Day 7. The cleavage rate at 72 hr did not show any differences among groups. However, the blastocyst rate on Day 7 decreased with all treatments evaluated, with the embryos generated with 10 μM SIN‐1 showing the lowest embryo production rate. Embryo quality analysis did not show any differences in total cell number (TCN) or inner cell mass (ICM) among groups. Relative gene expression analysis showed a downregulation of eNOS expression and an upregulation of nNOS expression in all treatments evaluated compared to the control group. Also, a downregulation was observed in some treatments: SOD2 at 0.1 μM; SOD1 at 0.1 and 100 μM; PRDX5 at 0.1, 10 and 100 μM; and NANOG at 10 and 100 μM; and an upregulation of CDX2 expression was observed at 100 μM. The other genes (OCT4, HIF1A, HSPA1A, BCL2A and iNOS) did not show any differences in the relative gene expression. These results suggest that the short‐term exposure of mature bovine COCs to SIN‐1 does not induce stress tolerance and has no beneficial effect on bovine in vitro embryo production.
Toward the usable recognition of individual benefits and costs in regulatory analysis and governance
Authors: Cranor Carl F. , Finkel Adam M.
Published: September 2016

Regulatory agencies in the United States and Europe have well‐deserved reputations for fixating on the total benefits and costs of proposed and final regulatory actions, without doing any more than anecdotally mentioning the subpopulations and individuals who may bear disproportionate costs or reap disproportionate benefits. This is especially true on the “cost” side of the cost–benefit ledger, where analysts exert little effort to even inform decisionmakers and the public that the costs of regulations might be distributed either regressively or progressively. Many scholars and advocates have observed that regulation can increase the efficiency of market outcomes, but caution about its untoward (or suboptimal) effects on equity. Here, we argue that without considering distributional information about costs and benefits,regulatory policies in fact can also cause violence to notions of efficiency, for two reasons: (i) society cannot hope to approach Pareto‐efficient outcomes without identifying those who must lose so that others can gain more; and (ii) because the harm experienced by involuntary risks and by imposed regulatory costs is likely non‐linear in its magnitude (at the individual level), efficiency is, in fact, a strong function of the shape of the distribution of these effects. This article reviews evidence about the distribution of regulatory costs and benefits, describes how agencies fail to incorporate readily available distributional information, and sketches a vision for how they could analyze costs and benefits to promote more efficient regulatory choices and outcomes.
Effects of forage type and gibberellic acid on nitrate leaching losses
Authors: Woods R. R. , Cameron K. C. , Edwards G. R. , Di H. J. , Clough T. J.
Published: September 2016

Nitrogen (N) leaching from soil into water is a significant concern for intensively grazed forage‐based systems because it can cause a decline in water quality and is a risk to human health. Urine patches from grazing animals are the main source of this N. The objective of this study was to quantify the effect that forage type and gibberellic acid (GA) application had on N leaching and herbage N uptake from urine patches on perennial ryegrass–white clover (RGWC), Italian ryegrass and lucerne. A lysimeter study was conducted over 17 months to measure herbage growth, N uptake and N loss to water beneath each of the three forage types with the following treatments: control, urine (700 kg N/ha) and urine with GA (8 g GA active ingredient/ha). Compared with RGWC (205 kg N/ha), N leaching losses were 35.3% lower from Italian ryegrass (133 kg N/ha) and 98.5% higher from lucerne (407 kg N/ha). These differences in leaching loss are likely to be due to winter plant growth and N uptake. During the winter months, Italian ryegrass had higher N uptake, whereas lucerne had lower N uptake, compared with RGWC. The application of GA had no effect on N leaching losses, DM yield or N uptake of forage treated with 700 kg N/ha urine.
PILOT STUDY TO ASSESS MEAL PROGRESSION THROUGH THE GASTROINTESTINAL TRACT OF HABITUATED DOGS DETERMINED BY FLUOROSCOPIC IMAGING WITHOUT SEDATION OR PHYSICAL RESTRAINT
Authors: Wrigglesworth David J. , Bailey Michael Q. , Colyer Alison , Hughes Kevin R.
Published: September 2016

A limiting factor of radiographic contrast studies is the requirement for restraint of the animal in order to reduce movement artifacts. To demonstrate that gastrointestinal transit can be analyzed by a barium meal in nonsedated and unrestrained dogs, a pilot study of six adult Labrador retriever dogs was undertaken. Study subjects were selected by convenience sampling from an available population of Labrador dogs and were trained to stand motionless during radiographic fluoroscopy. Following a meal containing 7% w/w powdered barium sulfate, radiographic images were generated using a digital fluoroscope C‐arm, at intervals of 5, 15, and 30 min, and at 1, 2, 3, 4, 5, 6, 7, and 8 h. A qualitative assessment of fill density using a 5‐point scale was made for the stomach, small intestine, and ascending, transverse, and descending regions of the colon at each timepoint. Gastric emptying half‐time occurred between 1 and 2 h postmeal. Mean fill density of the small intestine increased from 15 min postmeal and reached a peak at 3 h postmeal. Mean fill density of the proximal large intestine mirrored that of the small intestine. The distal large intestine remained empty for the first 2 h postmeal, then increased between hours 2 and 5 postmeal, and was subsequently at maximum fill density from hour 6 postmeal onwards. Fluoroscopic observation of a barium contrast meal provided an effective indication of the amount and progression of ingested food through the various regions of the gastrointestinal tract in habituated, fully conscious dogs.
Distribution of antimicrobial resistant Salmonella in an urban river that flows through the provincial city of Miyazaki, Japan
Authors: Suzuki Yoshihiro , Ushijima Masahiro
Published: September 2016

There is limited information regarding antimicrobial resistant Salmonella in the aquatic environment. In this study, we investigated the distribution of antimicrobial resistant Salmonella in the Yae River at sites upstream, midstream and downstream of the urban area of Miyazaki City, Japan. Pulsed field gel electrophoresis was performed to evaluate the genetic relationship among antimicrobial resistant Salmonella. The percentage of isolates that were resistant to at least one antimicrobial agent in upstream, midstream, and downstream sites was 23% (resistant isolates/total isolates = 11/44), 3% (1/34) and 32% (12/38), respectively. The 11 isolates of multidrug‐resistant Salmonella collected from downstream were classified to have a common genetic pattern belonging to the same cluster with a 100% similarity level. The multidrug‐resistant Salmonella were obtained from an identical source and were present in an urban river near human habitation.
Effects of recirculation rate of nitrified liquor and temperature on biological nitrification–denitrification process using a trickling filter
Authors: Kanda Ryo , Kishimoto Naoyuki , Hinobayashi Joji , Hashimoto Tsutomu
Published: September 2016

In the modified Ludzack–Ettinger process, high‐energy input is required in a nitrification tank. To address this issue, a new biological nitrification–denitrification system was constructed with a trickling filter for nitrification. The effects of recirculation rate of nitrified liquor and temperature through the treatment of municipal wastewater were evaluated. The highest DN removal efficiency was observed at 6.5 h of hydraulic retention in the denitrification tank and 350% of recirculation rate of nitrified liquid against the influent flow rate. The DN removal efficiencies did not reach theoretical values for all conditions tested because the COD/N ratios in the influent often decreased to less than 5 g‐COD/g‐N and temperatures dropped to less than 15°C in winter. The former inhibited the denitrification process and the latter significantly decreased the bioactivity of nitrifying bacteria. As such, this system is suitable in tropical and subtropical areas with annual minimum temperatures of over 15°C.
Exercise‐induced heat stress disrupts the shear–dilatory relationship
Authors: Ives Stephen J. , Lefferts Wesley K. , Wharton Margret , Fehling Patricia C. , Smith Denise L.
Published: September 2016

New Findings

What is the central question of this study?

Although heat stress is known to increase cardiovascular strain, no study, to date, had explored the potential impact of exercise‐induced heat stress on vascular function.

What is the main finding and its importance?

We found that acute exercise tended to reduce flow‐mediated dilatation (FMD), owing in part to reduced reactive hyperaemia/shear stimulus; thus, when FMD is normalized to shear no postexercise deficit exists. Exercise‐induced heat stress increased reactive hyperaemia, shear rate, coupled with a sustained FMD postexercise, suggests that exercise‐induced heat stress increases the amount of shear stimulus to elicit a similar response, indicating reduced vascular responsiveness, or reserve, which might increase cardiovascular susceptibility.

Heat stress increases cardiovascular strain and is of particular concern in occupations, such as firefighting, in which individuals are required to perform strenuous work while wearing personal protective equipment. Sudden cardiac events are associated with strenuous activity and are the leading cause of duty‐related death among firefighters, accounting for ∼50% of duty‐related fatalities per year. Understanding the acute effects of exercise‐induced heat stress (EIHS) on vascular endothelial function may provide insight into the mechanisms precipitating acute coronary events in firefighters. The purpose of this study, therefore, was to determine the effects of EIHS on vascular endothelial function. Using a balanced crossover design, 12 healthy men performed 100 min of moderate‐intensity, intermittent exercise with and without EIHS (personal protective equipment or cooling vest, respectively). Measurements of flow‐mediated dilatation (FMD), reactive hyperaemia and shear rate area under the curve (SRAUC) were performed pre‐ and postexercise. During EIHS, core temperature was significantly higher (38 ± 0.1 versus 37 ± 0.1°C). Postexercise FMD tended to be suppressed in both conditions, but was not different from pre‐exercise. Reactive hyperaemia was reduced after no‐EIHS but increased after EIHS. Thus, normalizing FMD to the shear stimulus (FMD/SRAUC) revealed a significant reduction in FMD after EIHS only (pre‐exercise 0.15 ± 0.04 and 0.13 ± 0.02 s−1 versus postexercise, 0.13 ± 0.02 and 0.06 ± 0.02 s−1, no‐EIHS and EIHS, respectively). We conclude that moderate heat stress superimposed on moderate‐intensity exercise resulted in reduced vascular endothelial function. This heat stress‐induced alteration in the shear–dilatory relationship may relate to the increased risk of acute coronary events associated with activities that combine physical exertion and heat stress (i.e. firefighting).
Inhibition linearizes firing rate responses in human motor units: implications for the role of persistent inward currents
Authors: Revill Ann L. , Fuglevand Andrew J.
Published: September 2016

Key points

Motor neurons are the output neurons of the central nervous system and are responsible for controlling muscle contraction.

When initially activated during voluntary contraction, firing rates of motor neurons increase steeply but then level out at modest rates.

Activation of an intrinsic source of excitatory current at recruitment onset may underlie the initial steep increase in firing rate in motor neurons.

We attempted to disable this intrinsic excitatory current by artificially activating an inhibitory reflex.

When motor neuron activity was recorded while the inhibitory reflex was engaged, firing rates no longer increased steeply, suggesting that the intrinsic excitatory current was probably responsible for the initial sharp rise in motor neuron firing rate.

During graded isometric contractions, motor unit (MU) firing rates increase steeply upon recruitment but then level off at modest rates even though muscle force continues to increase. The mechanisms underlying such firing behaviour are not known although activation of persistent inward currents (PICs) might be involved. PICs are intrinsic, voltage‐dependent currents that activate strongly when motor neurons (MNs) are first recruited. Such activation might cause a sharp escalation in depolarizing current and underlie the steep initial rise in MU firing rate. Because PICs can be disabled with synaptic inhibition, we hypothesized that artificial activation of an inhibitory pathway might curb this initial steep rise in firing rate. To test this, human subjects performed slow triangular ramp contractions of the ankle dorsiflexors in the absence and presence of tonic synaptic inhibition delivered to tibialis anterior (TA) MNs by sural nerve stimulation. Firing rate profiles (expressed as a function of contraction force) of TA MUs recorded during these tasks were compared for control and stimulation conditions. Under control conditions, during the ascending phase of the triangular contractions, 93% of the firing rate profiles were best fitted by rising exponential functions. With stimulation, however, firing rate profiles were best fitted with linear functions or with less steeply rising exponentials. Firing rate profiles for the descending phases of the contractions were best fitted with linear functions for both control and stimulation conditions. These results seem consistent with the idea that PICs contribute to non‐linear firing rate profiles during ascending but not descending phases of contractions.
The complementary and divergent roles of uncoupling proteins 1 and 3 in thermoregulation
Authors: Riley Christopher L. , Dao Christine , Kenaston M. Alexander , Muto Luigina , Kohno Shohei , Nowinski Sara M. , Solmonson Ashley D. , Pfeiffer Matthew , Sack Michael N. , Lu Zhongping , Fiermonte Giuseppe , Sprague Jon E. , Mills Edward M.
Published: September 2016

Key points

Both uncoupling protein 1 (UCP1) and UCP3 are important for mammalian thermoregulation.

UCP1 and UCP3 in brown adipose tissue mediate early and late phases of sympathomimetic thermogenesis, respectively.

Lipopolysaccharide thermogenesis requires skeletal muscle UCP3 but not UCP1.

Acute noradrenaline‐induced hyperthermia requires UCP1 but not UCP3.

Loss of both UCP1 and UCP3 accelerate the loss of body temperature compared to UCP1KO alone during acute cold exposure.

Uncoupling protein 1 (UCP1) is the established mediator of brown adipose tissue‐dependent thermogenesis. In contrast, the role of UCP3, expressed in both skeletal muscle and brown adipose tissue, in thermoregulatory physiology is less well understood. Here, we show that mice lacking UCP3 (UCP3KO) have impaired sympathomimetic (methamphetamine) and completely abrogated lipopolysaccharide (LPS) thermogenesis, but a normal response to noradrenaline. By comparison, UCP1 knockout (UCP1KO) mice exhibit blunted methamphetamine and fully inhibited noradrenaline thermogenesis, but an increased febrile response to LPS. We further establish that mice lacking both UCP1 and 3 (UCPDK) fail to show methamphetamine‐induced hyperthermia, and have a markedly accelerated loss of body temperature and survival after cold exposure compared to UCP1KO mice. Finally, we show that skeletal muscle‐specific human UCP3 expression is able to significantly rescue LPS, but not sympathomimetic thermogenesis blunted in UCP3KO mice. These studies identify UCP3 as an important mediator of physiological thermogenesis and support a renewed focus on targeting UCP3 in metabolic physiology.
Gallium arsenide (GaAs) (001) after sublimation of arsenic (As) thin-film cap, by XPS
Authors: Engelhard Mark H. , Lyubinetsky Andre , Baer Don R.
Published: September 2016

Survey and high-energy-resolution spectra are reported for MBEgrownGaAs (001) that had been capped with As. The As cap was removed by heating in situ prior to analysis. The current data expands upon the spectral regions previously reported in Surface Science Spectra. High energy resolution spectral features reported include: 2p, 3s, 3p, 3d, and L3M4,5M4,5 peaks for As; 2p, 3s, 3p, 3d, and L3M4,5M4,5 peaks for Ga; and the valence band region.
Saltational evolution of the heterotrimeric G protein signaling mechanisms in the plant kingdom
Authors: Urano Daisuke , Maruta Natsumi , Trusov Yuri , Stoian Richard , Wu Qingyu , Liang Ying , Jaiswal Dinesh Kumar , Thung Leena , Jackson David , Botella José Ramón , Jones Alan M.
Published: September 2016

Rapid diversification of the XLG family of Gα proteins may have enabled plants to adapt to the variable land environment.
Feast and famine, sickness and health
Authors: Mushegian Alexandra A.
Published: September 2016

Glucose metabolism differentially affects tissue responses to inflammation in viral and bacterial disease.
Paper of note in
Science
Authors: VanHook Annalisa M.
Published: September 2016

This week’s article highlights a mechanism by which bacterial virulence factors influence gut epithelial cells.
In Vitro
and
In Vivo
Activities of a Bi-Aryl Oxazolidinone, RBx 11760, against Gram-Positive Bacteria
Authors: Barman Tarani Kanta , Kumar Manoj , Mathur Tarun , Chaira Tridib , Ramkumar G. , Kalia Vandana , Rao Madhvi , Pandya Manisha , Yadav Ajay Singh , Das Biswajit , Upadhyay Dilip J. , Hamidullah  , Konwar Rituraj , Raj V. Samuel , Singh Harpal
Published: September 2016

RBx 11760, a bi-aryl oxazolidinone, was investigated for antibacterial activity against Gram-positive bacteria. The MIC
90
s of RBx 11760 and linezolid against
Staphylococcus aureus
were 2 and 4 mg/liter, against
Staphylococcus epidermidis
were 0.5 and 2 mg/liter, and against
Enterococcus
were 1 and 4 mg/liter, respectively. Similarly, against
Streptococcus pneumoniae
the MIC
90
s of RBx 11760 and linezolid were 0.5 and 2 mg/liter, respectively. In time-kill studies, RBx 11760, tedizolid, and linezolid exhibited bacteriostatic effect against all tested strains except
S. pneumoniae
. RBx 11760 showed 2-log
10
kill at 4× MIC while tedizolid and linezolid showed 2-log
10
and 1.4-log
10
kill at 16× MIC, respectively, against methicillin-resistant
S. aureus
(MRSA) H-29. Against
S. pneumoniae
5051, RBx 11760 showed bactericidal activity, with 4.6-log
10
kill at 4× MIC compared to 2.42-log
10
and 1.95-log
10
kill for tedizolid and linezolid, respectively, at 16× MIC. RBx 11760 showed postantibiotic effects (PAE) at 3 h at 4 mg/liter against MRSA H-29, and linezolid showed the same effect at 16 mg/liter. RBx 11760 inhibited biofilm production against methicillin-resistant
S. epidermidis
(MRSE) ATCC 35984 in a concentration-dependent manner. In a foreign-body model, linezolid and rifampin resulted in no advantage over stasis, while the same dose of RBx 11760 demonstrated a significant killing compared to the initial control against
S. aureus
(
P
< 0.05) and MRSE (
P
< 0.01). The difference in killing was statistically significant for the lower dose of RBx 11760 (
P
< 0.05) versus the higher dose of linezolid (
P
> 0.05 [not significant]) in a groin abscess model. In neutropenic mouse thigh infection, RBx 11760 showed stasis at 20 mg/kg of body weight, whereas tedizolid showed the same effect at 40 mg/kg. These data support RBx 11760 as a promising investigational candidate.
The Celecoxib Derivative AR-12 Has Broad-Spectrum Antifungal Activity
In Vitro
and Improves the Activity of Fluconazole in a Murine Model of Cryptococcosis
Authors: Koselny Kristy , Green Julianne , DiDone Louis , Halterman Justin P. , Fothergill Annette W. , Wiederhold Nathan P. , Patterson Thomas F. , Cushion Melanie T. , Rappelye Chad , Wellington Melanie , Krysan Damian J.
Published: September 2016

Only one new class of antifungal drugs has been introduced into clinical practice in the last 30 years, and thus the identification of small molecules with novel mechanisms of action is an important goal of current anti-infective research. Here, we describe the characterization of the spectrum of
in vitro
activity and
in vivo
activity of AR-12, a celecoxib derivative which has been tested in a phase I clinical trial as an anticancer agent. AR-12 inhibits fungal acetyl coenzyme A (acetyl-CoA) synthetase
in vitro
and is fungicidal at concentrations similar to those achieved in human plasma. AR-12 has a broad spectrum of activity, including activity against yeasts (e.g.,
Candida albicans
, non-
albicans Candida
spp.,
Cryptococcus neoformans
), molds (e.g.,
Fusarium
,
Mucor
), and dimorphic fungi (
Blastomyces
,
Histoplasma
, and
Coccidioides
) with MICs of 2 to 4 μg/ml. AR-12 is also active against azole- and echinocandin-resistant
Candida
isolates, and subinhibitory AR-12 concentrations increase the susceptibility of fluconazole- and echinocandin-resistant
Candida
isolates. Finally, AR-12 also increases the activity of fluconazole in a murine model of cryptococcosis. Taken together, these data indicate that AR-12 represents a promising class of small molecules with broad-spectrum antifungal activity.
Nationwide Surveillance of Novel Oxazolidinone Resistance Gene
optrA
in Enterococcus Isolates in China from 2004 to 2014
Authors: Cui Lanqing , Wang Yang , Lv Yuan , Wang Shan , Song Yunjia , Li Yun , Liu Jian , Xue Feng , Yang Weiwei , Zhang Jia
Published: September 2016

A total of 2,201 nonduplicate enterococcal isolates collected from 29 hospitals in 23 cities in China between 2004 and 2014 were screened for the oxazolidinone resistance gene
optrA
; 45 isolates (2.0%) were
optrA
positive with 11 OptrA variants identified. The positive rate of
optrA
increased from 0.4% to 3.9% during the 10-year surveillance period. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence type (MLST) analysis revealed that 37
optrA
-positive
Enterococcus faecalis
isolates clustered into 25 PFGE patterns and 21 sequence types, while 6
Enterococcus faecium
isolates represented 6 PFGE patterns and 6 sequence types. The present study underscores the importance of routine and persistent monitoring of oxazolidinone resistance and
optrA
gene.
Potential Use of Dimethyl Sulfoxide in Treatment of Infections Caused by Pseudomonas aeruginosa
Authors: Guo Qiao , Wu Qiaolian , Bai Dangdang , Liu Yang , Chen Lin , Jin Sheng , Wu Yuting , Duan Kangmin
Published: September 2016

Dimethyl sulfoxide (DMSO) is commonly used as a solvent to dissolve water-insoluble drugs or other test samples in both
in vivo
and
in vitro
experiments. It was observed during our experiment that DMSO at noninhibitory concentrations could significantly inhibit pyocyanin production in the human pathogen
Pseudomonas aeruginosa
. Pyocyanin is an important pathogenic factor whose production is controlled by a cell density-dependent quorum-sensing (QS) system. Investigation of the effect of DMSO on QS showed that DMSO has significant QS antagonistic activities and concentrations of DMSO in the micromolar range attenuated a battery of QS-controlled virulence factors, including rhamnolipid, elastase, and LasA protease production and biofilm formation. Further study indicated that DMSO inhibition of biofilm formation and pyocyanin production was attained by reducing the level of production of an autoinducer molecule of the
rhl
QS system,
N
-butanoyl-
l
-homoserine lactone (C
4
-HSL). In a mouse model of a burn wound infection with
P. aeruginosa
, treatment with DMSO significantly decreased mouse mortality compared with that for mice in the control group. The capacity of DMSO to attenuate the pathogenicity of
P. aeruginosa
points to the potential use of DMSO as an antipathogenic agent for the treatment of
P. aeruginosa
infection. As a commonly used solvent, however, DMSO's impact on bacterial virulence calls for cautionary attention in its usage in biological, medicinal, and clinical studies.
Moxifloxacin Is a Potent
In Vitro
Inhibitor of OCT- and MATE-Mediated Transport of Metformin and Ethambutol
Authors: te Brake Lindsey H. M. , van den Heuvel Jeroen J. M. W. , Buaben Aaron O. , van Crevel Reinout , Bilos Albert , Russel Frans G. , Aarnoutse Rob E. , Koenderink Jan B.
Published: September 2016

It is largely unknown if simultaneous administration of tuberculosis (TB) drugs and metformin leads to drug-drug interactions (DDIs). Disposition of metformin is determined by organic cation transporters (OCTs) and multidrug and toxin extrusion proteins (MATEs). Thus, any DDIs would primarily be mediated via these transporters. This study aimed to assess the
in vitro
inhibitory effects of TB drugs (rifampin, isoniazid, pyrazinamide, ethambutol, amikacin, moxifloxacin, and linezolid) on metformin transport and whether TB drugs are also substrates themselves of OCTs and MATEs. HEK293 cells overexpressing OCT1, OCT2, OCT3, MATE1, and MATE2K were used to study TB drug-mediated inhibition of [
14
C]metformin uptake and to test if TB drugs are transporter substrates. Metformin uptake was determined by quantifying [
14
C]metformin radioactivity, and TB drug uptake was analyzed using liquid chromatography-tandem mass spectrometry. DDI indices were calculated (plasma maximum concentrations [
C
max
]/50% inhibitory concentrations [IC
50
]), and based on the literature, a cutoff of >0.1 was assumed to warrant further
in vivo
investigation. Moxifloxacin was the only TB drug identified as a potent inhibitor (DDI index of >0.1) of MATE1- and MATE2K-mediated metformin transport, with IC
50
s of 12 μM (95% confidence intervals [CI], 5.1 to 29 μM) and 7.6 μM (95% CI, 0.2 to 242 μM), respectively. Of all TB drugs, only ethambutol appeared to be a substrate of OCT1, OCT2, OCT3, MATE1, and MATE2K. MATE1-mediated ethambutol uptake was inhibited strongly (DDI index of >0.1) by moxifloxacin (IC
50
, 12 μM [95% CI, 3.4 to 43 μM]). Our findings provide a mechanistic basis for DDI predictions concerning ethambutol. According to international guidelines, an
in vivo
interaction study is warranted for the observed
in vitro
interaction between ethambutol and moxifloxacin.
The Expression of Antibiotic Resistance Methyltransferase Correlates with mRNA Stability Independently of Ribosome Stalling
Authors: Dzyubak Ekaterina , Yap Mee-Ngan F.
Published: September 2016

Members of the Erm methyltransferase family modify 23S rRNA of the bacterial ribosome and render cross-resistance to macrolides and multiple distantly related antibiotics. Previous studies have shown that the expression of
erm
is activated when a macrolide-bound ribosome stalls the translation of the leader peptide preceding the cotranscribed
erm
. Ribosome stalling is thought to destabilize the inhibitory stem-loop mRNA structure and exposes the
erm
Shine-Dalgarno (SD) sequence for translational initiation. Paradoxically, mutations that abolish ribosome stalling are routinely found in hyper-resistant clinical isolates; however, the significance of the stalling-dead leader sequence is largely unknown. Here, we show that nonsense mutations in the
Staphylococcus aureus
ErmB leader peptide (ErmBL) lead to high basal and induced expression of downstream ErmB in the absence or presence of macrolide concomitantly with elevated ribosome methylation and resistance. The overexpression of ErmB is associated with the reduced turnover of the
ermBL-ermB
transcript, and the macrolide appears to mitigate mRNA cleavage at a site immediately downstream of the
ermBL
SD sequence. The stabilizing effect of antibiotics on mRNA is not limited to
ermBL-ermB
; cationic antibiotics representing a ribosome-stalling inducer and a noninducer increase the half-life of specific transcripts. These data unveil a new layer of
ermB
regulation and imply that ErmBL translation or ribosome stalling serves as a “tuner” to suppress aberrant production of ErmB because methylated ribosome may impose a fitness cost on the bacterium as a result of misregulated translation.
Filifactor alocis Promotes Neutrophil Degranulation and Chemotactic Activity
Authors: Armstrong Cortney L. , Miralda Irina , Neff Adam C. , Tian Shifu , Vashishta Aruna , Perez Lisandra , Le Junyi , Lamont Richard J. , Uriarte Silvia M.
Published: September 2016

Filifactor alocisis a recently recognized periodontal pathogen; however, little is known regarding its interactions with the immune system. As the first-responder phagocytic cells, neutrophils are recruited in large numbers to the periodontal pocket, where they play a crucial role in the innate defense of the periodontium. Thus, in order to colonize, successful periodontal pathogens must devise means to interfere with neutrophil chemotaxis and activation. In this study, we assessed major neutrophil functions, including degranulation and cell migration, associated with the p38 mitogen-activated protein kinase (MAPK) signaling pathway upon challenge withF. alocis.Under conditions lacking a chemotactic gradient,F. alocis-challenged neutrophils had increased migration compared to uninfected cells, indicating thatF. alocisincreases chemokinesis in human neutrophils. In addition, neutrophil chemotaxis induced by interleukin-8 was significantly enhanced when cells were challenged withF. alocis, compared to noninfected cells. Similar to live bacteria, heat-killedF. alocisinduced both random and directed migration of human neutrophils. The interaction ofF. alociswith Toll-like receptor 2 induced granule exocytosis along with a transient ERK1/2 and sustained p38 MAPK activation. Moreover,F. alocis-induced secretory vesicle and specific granule exocytosis were p38 MAPK dependent. Blocking neutrophil degranulation with TAT-SNAP23 fusion protein significantly reduced the chemotactic and random migration induced byF. alocis. Therefore, we propose that induction of random migration byF. alociswill prolong neutrophil traffic time in the gingival tissue, and subsequent degranulation will contribute to tissue damage.
Thermal Unfolding of the Pertussis Toxin S1 Subunit Facilitates Toxin Translocation to the Cytosol by the Mechanism of Endoplasmic Reticulum-Associated Degradation
Authors: Banerjee Tuhina , Cilenti Lucia , Taylor Michael , Showman Adrienne , Tatulian Suren A. , Teter Ken
Published: September 2016

Pertussis toxin (PT) moves from the host cell surface to the endoplasmic reticulum (ER) by retrograde vesicular transport. The catalytic PTS1 subunit dissociates from the rest of the toxin in the ER and then shifts to a disordered conformation which may trigger its export to the cytosol through the quality control mechanism of ER-associated degradation (ERAD). Functional roles for toxin instability and ERAD in PTS1 translocation have not been established. We addressed these issues with the use of a surface plasmon resonance system to quantify the cytosolic pool of PTS1 from intoxicated cells. Only 3% of surface-associated PTS1 reached the host cytosol after 3 h of toxin exposure. This represented, on average, 38,000 molecules of cytosolic PTS1 per cell. Cells treated with a proteasome inhibitor contained larger quantities of cytosolic PTS1. Stabilization of the dissociated PTS1 subunit with chemical chaperones inhibited toxin export to the cytosol and blocked PT intoxication. ERAD-defective cell lines likewise exhibited reduced quantities of cytosolic PTS1 and PT resistance. These observations identify the unfolding of dissociated PTS1 as a trigger for its ERAD-mediated translocation to the cytosol.
The Helical Shape of Campylobacter jejuni Promotes
In Vivo
Pathogenesis by Aiding Transit through Intestinal Mucus and Colonization of Crypts
Authors: Stahl Martin , Frirdich Emilisa , Vermeulen Jenny , Badayeva Yuliya , Li Xiaoxia , Vallance Bruce A. , Gaynor Erin C.
Published: September 2016

Campylobacter jejuni
is a helix-shaped enteric bacterial pathogen and a common cause of gastroenteritis. We recently developed a mouse model for this human pathogen utilizing the SIGIRR-deficient mouse strain, which exhibits significant intestinal inflammation in response to intestinal
C. jejuni
infection. In the current study, this mouse model was used to define whether
C. jejuni
's characteristic helical shape plays a role in its ability to colonize and elicit inflammation in the mouse intestine. Mice were infected with the previously characterized straight-rod Δ
pgp1
and Δ
pgp2
mutant strains, along with a newly characterized curved-rod Δ
1228
mutant strain. We also compared the resultant infections and pathology to those elicited by the helix-shaped wild-type
C. jejuni
and complemented strains. Despite displaying wild-type colonization of the intestinal lumen, the straight-rod Δ
pgp1
and Δ
pgp2
mutants were essentially nonpathogenic, while all strains with a curved or helical shape retained their expected virulence. Furthermore, analysis of
C. jejuni
localization within the ceca of infected mice determined that the primary difference between the rod-shaped, nonpathogenic mutants and the helix-shaped, pathogenic strains was the ability to colonize intestinal crypts. Rod-shaped mutants appeared unable to colonize intestinal crypts due to an inability to pass through the intestinal mucus layer to directly contact the epithelium. Together, these results support a critical role for
C. jejuni
's helical morphology in enabling it to traverse and colonize the mucus-filled intestinal crypts of their host, a necessary step required to trigger intestinal inflammation in response to
C. jejuni
.
The Topology of the
l
-Arginine Exporter ArgO Conforms to an N
in
-C
out
Configuration in Escherichia coli: Requirement for the Cytoplasmic N-Terminal Domain, Functional Helical Interactions, and an Aspartate Pair for ArgO Function
Authors: Pathania Amit , Gupta Arvind Kumar , Dubey Swati , Gopal Balasubramanian , Sardesai Abhijit A.
Published: September 2016

ArgO and LysE are members of the LysE family of exporter proteins and ordinarily mediate the export of
l
-arginine (Arg) in
Escherichia coli
and
l
-lysine (Lys) and Arg in
Corynebacterium glutamicum
, respectively. Under certain conditions, ArgO also mediates Lys export. To delineate the arrangement of ArgO in the cytoplasmic membrane of
E. coli
, we have employed a combination of cysteine accessibility
in situ
, alkaline phosphatase fusion reporters, and protein modeling to arrive at a topological model of ArgO. Our studies indicate that ArgO assumes an N
in
-C
out
configuration, potentially forming a five-transmembrane helix bundle flanked by a cytoplasmic N-terminal domain (NTD) comprising roughly its first 38 to 43 amino acyl residues and a short periplasmic C-terminal region (CTR). Mutagenesis studies indicate that the CTR, but not the NTD, is dispensable for ArgO function
in vivo
and that a pair of conserved aspartate residues, located near the opposing edges of the cytoplasmic membrane, may play a pivotal role in facilitating transmembrane Arg flux. Additional studies on amino acid substitutions that impair ArgO function
in vivo
and their derivatives bearing compensatory amino acid alterations indicate a role for intramolecular interactions in the Arg export mechanism, and some interactions are corroborated by normal-mode analyses. Lastly, our studies suggest that ArgO may exist as a monomer
in vivo
, thus highlighting the requirement for intramolecular interactions in ArgO, as opposed to interactions across multiple ArgO monomers, in the formation of an Arg-translocating conduit.

IMPORTANCE
The orthologous proteins LysE of
C. glutamicum
and ArgO of
E. coli
function as exporters of the basic amino acids
l
-arginine and
l
-lysine and the basic amino acid
l
-arginine, respectively, and LysE can functionally substitute for ArgO when expressed in
E. coli
. Notwithstanding this functional equivalence, studies reported here show that ArgO possesses a membrane topology that is distinct from that reported for LysE, with substantial variation in the topological arrangement of the proximal one-third portions of the two exporters. Additional genetic and
in silico
studies reveal the importance of (i) the cytoplasmic N-terminal domain, (ii) a pair of conserved aspartate residues, and (iii) potential intramolecular interactions in ArgO function and indicate that an Arg-translocating conduit is formed by a monomer of ArgO.
Changes in Bacillus Spore Small Molecules, rRNA, Germination, and Outgrowth after Extended Sublethal Exposure to Various Temperatures: Evidence that Protein Synthesis Is Not Essential for Spore Germination
Authors: Korza George , Setlow Barbara , Rao Lei , Li Qiao , Setlow Peter
Published: September 2016

rRNAs of dormant spores of
Bacillus subtilis
were >95% degraded during extended incubation at 50°C, as reported previously (E. Segev, Y. Smith, and S. Ben-Yehuda, Cell 148:139–114, 2012, doi:
http://dx.doi.org/10.1016/j.cell.2011.11.059
), and this was also true of spores of
Bacillus megaterium
. Incubation of spores of these two species for ∼20 h at 75 to 80°C also resulted in the degradation of all or the great majority of the 23S and 16S rRNAs, although this rRNA degradation was slower than nonenzymatic hydrolysis of purified rRNAs at these temperatures. This rRNA degradation at high temperature generated almost exclusively oligonucleotides with minimal levels of mononucleotides. RNase Y, suggested to be involved in rRNA hydrolysis during
B. subtilis
spore incubation at 50°C, did not play a role in
B. subtilis
spore rRNA breakdown at 80°C. Twenty hours of incubation of
Bacillus
spores at 70°C also decreased the already minimal levels of ATP in dormant spores 10- to 30-fold, to ≤0.01% of the total free adenine nucleotide levels. Spores depleted of rRNA were viable and germinated relatively normally, often even faster than starting spores. Their return to vegetative growth was also similar to that of untreated spores for
B. megaterium
spores and slower for heat-treated
B. subtilis
spores; accumulation of rRNA took place only after completion of spore germination. These findings thus strongly suggest that protein synthesis is not essential for
Bacillus
spore germination.

IMPORTANCE
A recent report (L. Sinai, A. Rosenberg, Y. Smith, E. Segev, and S. Ben-Yehuda, Mol Cell 57:3486–3495, 2015, doi:
http://dx.doi.org/10.1016/j.molcel.2014.12.019
) suggested that protein synthesis is essential for early steps in the germination of dormant spores of
Bacillus subtilis
. If true, this would be a paradigm shift in our understanding of spore germination. We now show that essentially all of the rRNA can be eliminated from spores of
Bacillus megaterium
or
B. subtilis
, and these rRNA-depleted spores are viable and germinate as well as or better than spores with normal rRNA levels. Thus, protein synthesis is not required in the process of spore germination.