bluuebunny/crossref_metadata_2025 huggingface dataset:
Global patterns and predictors of stem CO2 efflux in forest ecosystems
Authors: Yang Jinyan , He Yujie , Aubrey Doug P. , Zhuang Qianlai , Teskey Robert O.
Published: December 2015

Stem CO2 efflux (ES) plays an important role in the carbon balance of forest ecosystems. However, its primary controls at the global scale are poorly understood and observation‐based global estimates are lacking. We synthesized data from 121 published studies across global forest ecosystems and examined the relationships between annual ES and biotic and abiotic factors at individual, biome, and global scales, and developed a global gridded estimate of annual ES. We tested the following hypotheses: (1) Leaf area index (LAI) will be highly correlated with annual ES at biome and global scales; (2) there will be parallel patterns in stem and root CO2 effluxes (RA) in all forests; (3) annual ES will decline with forest age; and (4) LAI coupled with mean annual temperature (MAT) and mean annual precipitation (MAP) will be sufficient to predict annual ES across forests in different regions. Positive linear relationships were found between ES and LAI, as well as gross primary production (GPP), net primary production (NPP), wood NPP, soil CO2 efflux (RS), and RA. Annual ES was correlated with RA in temperate forests after controlling for GPP and MAT, suggesting other additional factors contributed to the relationship. Annual ES tended to decrease with stand age. Leaf area index, MAT and MAP, predicted 74% of variation in ES at global scales. Our statistical model estimated a global annual ES of 6.7 ± 1.1 Pg C yr−1 over the period of 2000–2012 with little interannual variability. Modeled mean annual ES was 71 ± 43, 270 ± 103, and 420 ± 134 g C m2 yr−1 for boreal, temperate, and tropical forests, respectively. We recommend that future studies report ES at a standardized constant temperature, incorporate more manipulative treatments, such as fertilization and drought, and whenever possible, simultaneously measure both aboveground and belowground CO2 fluxes.
Quantifying heterogeneous responses of fish community size structure using novel combined statistical techniques
Authors: Marshall Abigail M. , Bigg Grant R. , van Leeuwen Sonja M. , Pinnegar John K. , Wei Hua‐Liang , Webb Thomas J. , Blanchard Julia L.
Published: December 2015

To understand changes in ecosystems, the appropriate scale at which to study them must be determined. Large marine ecosystems (LMEs) cover thousands of square kilometres and are a useful classification scheme for ecosystem monitoring and assessment. However, averaging across LMEs may obscure intricate dynamics within. The purpose of this study is to mathematically determine local and regional patterns of ecological change within an LME using empirical orthogonal functions (EOFs). After using EOFs to define regions with distinct patterns of change, a statistical model originating from control theory is applied (Nonlinear AutoRegressive Moving Average with eXogenous input – NARMAX) to assess potential drivers of change within these regions. We have selected spatial data sets (0.5° latitude × 1°longitude) of fish abundance from North Sea fisheries research surveys (spanning 1980–2008) as well as of temperature, oxygen, net primary production and a fishing pressure proxy, to which we apply the EOF and NARMAX methods. Two regions showed significant changes since 1980: the central North Sea displayed a decrease in community size structure which the NARMAX model suggested was linked to changes in fishing; and the Norwegian trench region displayed an increase in community size structure which, as indicated by NARMAX results, was primarily linked to changes in sea‐bottom temperature. These regions were compared to an area of no change along the eastern Scottish coast where the model determined the community size structure was most strongly associated to net primary production. This study highlights the multifaceted effects of environmental change and fishing pressures in different regions of the North Sea. Furthermore, by highlighting this spatial heterogeneity in community size structure change, important local spatial dynamics are often overlooked when the North Sea is considered as a broad‐scale, homogeneous ecosystem (as normally is the case within the political Marine Strategy Framework Directive).
Powdered coconut water as a storage medium to preserve the viability of periodontal ligament cells: a laboratory study
Authors: Moura C. C. G. , Soares P. B. F. , Reis M. V. P. , Dechichi P. , Salgueiro C. C. M. , Sobral M. H. N. R. , Zanetta Barbosa D. , Soares C. J.
Published: December 2015

Aim

To investigate the ability of newly developed powdered coconut water formulas (ACP) with different osmolarities to maintain the viability of periodontal ligament (PDL) cells over time compared with other solutions.

Methodology

Dogs teeth were extracted and stored for two periods, 3 h or 24 h, in the following media: long‐shelf life CW (CW), pH‐adjusted long‐shelf life CW (pH‐CW) and powdered CW that was pH and osmolality adjusted (ACP‐404‐I, 250 mOsm kg−1 H2O; pH 7.0; ACP‐404‐II, 372 mOsm kg−1 H2O; pH 7.0; ACP‐404‐III, 300 mOsm kg−1 H2O; pH 7.4). The positive control group (Pc) corresponded to immediate measurement after tooth extraction, and two negative controls (Nc) corresponded to 3 h and 24 h of dry time. PDL cells were extracted, and cell viability analysed by Trypan blue exclusion. Data were analysed statistically using two‐way anova followed by the Tukey test and one‐way anova followed by the Dunnett test (P < 0.05).

Results

At 3 h and 24 h, ACP‐404‐I had a performance similar to those of ACP‐404‐II and pH‐CW, with significantly higher (P = 0.004) percentages of viable cells than ACP‐404‐III and CW. The positive control group had a significantly higher (P = 0.002) percentage of viable cells than the negative control groups, CW and ACP‐404‐III, irrespective of the period evaluated.

Conclusion

Powdered coconut water formulas, ACP‐404‐I and ACP‐404‐II, preserved viability for up to 24 h.
Effects of pretreatment and drying methods on molecular structure, functional properties and thermal stability of fibre powder exhibiting colour from Centella asiatica L.
Authors: Ngamwonglumlert Luxsika , Devahastin Sakamon , Chiewchan Naphaporn
Published: December 2015

Effects of pretreatment and drying methods and particle size on characteristics of fibre powder from Centella asiatica L. leaves were investigated. Thermal stability of oil‐based colour solutions was also assessed. Steaming and combined steaming and alkaline soaking resulted in the powder with more greenness and higher chlorophylls contents, while combined steaming and acid soaking yielded dark yellow powder with lower chlorophylls contents. Chemical soaking led to the powder with decreased water holding capacity and solubility. Vacuum‐drying reduced chlorophylls degradation, hence retention of the greenness of the powder. Increased particle size resulted in decreased lightness of the powder, but in increased lightness of the solutions; water and oil holding capacities of the powder increased with the particle size. Fourier transform infrared (FTIR) spectra and X‐ray diffraction (XRD) patterns of the powder corresponded to its colour and functional property changes. Colour of the solutions changed only slightly upon heating at 80 and 180 °C for 1 h.
Cold, dry air is associated with influenza and pneumonia mortality in Auckland, New Zealand
Authors: Davis Robert E. , Dougherty Erin , McArthur Colin , Huang Qiu Sue , Baker Michael G.
Published: December 2015

The relationship between weather and influenza and pneumonia mortality was examined retrospectively using daily data from 1980 to 2009 in Auckland, New Zealand, a humid, subtropical location. Mortality events, defined when mortality exceeded 0·95 standard deviation above the mean, followed periods of anomalously cold air (ta.m. = −4·1, P < 0·01; tp.m. = −4·2, P < 0·01) and/or anomalously dry air (ta.m. = −4·1, P < 0·01; tp.m. = −3·8, P < 0·01) by up to 19 days. These results suggest that respiratory infection is enhanced during unusually cold conditions and during conditions with unusually low humidity, even in a subtropical location where humidity is typically high.
More Deaths Than Births: Subnational Natural Decrease in Europe and the United States
Authors: Johnson Kenneth M. , Field Layton M. , Poston Dudley L.
Published: December 2015

This article examines the prevalence and dynamics of natural decrease in the subnational populations of Europe and the United States. Natural decrease results from interactions between fertility, mortality, and migration over a protracted period. We document the greater incidence and degree of natural decrease in Europe. In the first decade of the twenty‐first century, natural decrease occurred in 58 percent of European NUTS 3 areas (“counties”) compared to only 28 percent of the US counties. Three critical demographic variables (proportion over 65, child‐women ratio, and proportion of women of childbearing age) each exert a significant and distinct impact on the likelihood of natural decrease. Our spatial regression models reflect remarkable consistency in the influence of each of these variables in Europe and in the US, demonstrating the similarity in the demographic processes that produce natural decrease.
Disruption of the chemical communication of the European agrobiont ground‐dwelling spider Pardosa agrestis by pesticides
Authors: Leccia F. , Kysilková K. , Kolářová M. , Hamouzová K. , Líznarová E. , Korenko S.
Published: December 2015

Lycosid spiders are among the most abundant and diverse insectivores occurring in all agroecosystems. Certain pest management practices, such as the application of pesticides, can disrupt their role in insect pest control. Therefore, understanding the effects of pesticides, including sublethal effects, is essential for the assessment of chemical effects on beneficial arthropods. We investigated the sexual chemical communication of the beneficial agrobiont spider Pardosa agrestis and its disruption by two widely used pesticides, the glyphosate‐based herbicide Roundup and the pyrethroïd‐based insecticide Nurelle D. A two‐choice olfactometer and Y‐maze were used to study the effectiveness of female airborne and dragline pheromone cues and the disruptive effect of the pesticides. Males of P. agrestis did not locate females via airborne cues, but were very receptive to female dragline silk and male dragline silk. When both female dragline silk and male dragline silk were provided at the same time, the males preferred female silk. Pesticide treatments significantly affected the male ability to follow female cues deposited on dragline silk. The 3‐h residues of both Roundup and Nurelle D significantly disrupted the male ability to follow female cues deposited on dragline silk. Treatment by 48‐h residues significantly disrupted the male ability only in the case of Nurelle D. Our results demonstrate that pesticides reduce the ability of male spiders to search for a mate due to the disruption of the male's ability to detect the silk cues of the female.
Fine‐tuning by strigolactones of root response to low phosphate
Authors: Kapulnik Yoram , Koltai Hinanit
Published: December 2015

Strigolactones are plant hormones that regulate the development of different plant parts. In the shoot, they regulate axillary bud outgrowth and in the root, root architecture and root‐hair length and density. Strigolactones are also involved with communication in the rhizosphere, including enhancement of hyphal branching of arbuscular mycorrhizal fungi. Here we present the role and activity of strigolactones under conditions of phosphate deprivation. Under these conditions, their levels of biosynthesis and exudation increase, leading to changes in shoot and root development. At least for the latter, these changes are likely to be associated with alterations in auxin transport and sensitivity. On the other hand, strigolactones may positively affect plant–mycorrhiza interactions and thereby promote phosphate acquisition by the plant. Strigolactones may be a way for plants to fine‐tune their growth pattern under phosphate deprivation.
Stylistic and discursive functions of French negative particlenein an educational context
Authors: Mougeon Raymond , Rehner Katherine
Published: December 2015

This study examines use/non‐use of negative particleneby students and teachers in the high schools of four Ontario Francophone communities. The students were recorded in semi‐directed interviews and in the classroom. The teachers recorded themselves in the classroom. In the interviews,neuse is marginal and its non‐use ubiquitous and not influenced by social class, gender or topic formality. Overall, students do not usenesignificantly more in the classroom than in the interviews. These findings do not support the hypothesis in some studies thatneuse is a hyper‐stylistic variant, which hinged on the prescription ofneuse in writing. In the classroom, however, teachers display markedly different levels ofneuse/non‐use according to subject taught, speaker age, and addressee/discourse functions performed. Thus, there is some evidence thatneuse/non‐use is not entirely devoid of stylistic markedness, at least for teachers in the formal setting of the classroom. Finally, an examination ofneuse/non‐use co‐occurring with two phonological variants of post‐verbal negatorplusreveals findings that are germane to the debate concerning the possibility of analysing stylistic variation in spoken French as a form of diglossic code‐switching.
Is obesity associated with healing after non‐surgical periodontal therapy? A local vs. systemic evaluation
Authors: Duzagac E. , Cifcibasi E. , Erdem M. G. , Karabey V. , Kasali K. , Badur S. , Cintan S.
Published: December 2015

Background

We aimed to detect the role of obesity on the healing response to periodontal therapy in terms of serum lipids, C‐reactive protein (CRP) and both serum and gingival crevicular fluid adipocytokines.

Material and Methods

Thirty patients with periodontitis with (CPO) (n = 15) and without (n = 15) obesity and 15 healthy controls were included. Serum high‐density lipoprotein, low‐density lipoprotein, triglyceride, CRP levels and levels of adiponectin, interleukin (IL)‐6, tumor necrosis factor (TNF)‐α and IL‐10 were evaluated before and 3 mo after initial periodontal therapy. Clinical periodontal measurements were also recorded at baseline and 3 mo.

Results

Periodontal parameters improved significantly in both periodontitis groups with or without obesity (p < 0.05) with no significant difference in terms of gain clinical attachment level (p > 0.05) and change in numbers of sites with probing depth ≥ 4 mm. High‐density lipoprotein significantly increased in both groups (p > 0.05). CRP decreased significantly solely in the normal weight group. IL‐6, IL‐10 and TNF‐α levels in gingival crevicular fluid improved significantly based on therapy in both groups (p < 0.05). Only TNF‐α decreased significantly in the CPO, while adiponectin and IL‐10 in addition to TNF‐α improved significantly in the group of patients with periodontitis without obesity.

Conclusion

Patients with CPO respond to periodontal therapy as well as the non‐obese controls. This similar response is accompanied with consistent adipokine levels in gingival crevicular fluid. However, obesity affects the CRP and serum adipocytokine levels in response to therapy.
A Novel Method of Determining Wax Cohesiveness by Using A Texture Analyzer
Authors: Liu Lei , Wang Ning , Xu Lirong , Yu Xiuzhu , Zhang Rui , Wang Tong
Published: December 2015

In the current study, a new method for determining cohesiveness of waxes has been developed by using texture analyzer with blade probe. The texture analyzer was used to measure peak area from 0 to maximum force (rupture) during compression testing, which present the wax cohesiveness. When the handling temperature was 60C higher than the melting point of waxes, holding time was more than 6 h, the thickness of waxes was about 4 mm, the distant between two fulcrums was 20 mm (10 mm/10 mm), and the relative standard deviations of determinations were less than 10%. The analytical conditions were found to have no significant effect on the measurements. The peak area of waxes was correlated with the sensory evaluation; therefore, using a texture analyzer to determine wax cohesiveness is feasibility.

Practical Applications

Cohesiveness is an important parameter of wax texture properties. However, a standard method of determining wax cohesiveness is lacking. Texture analyzers are widely used to determine the cohesiveness of various foods, such as cheese, vegetables, meat, and so on. This article established a novel method to determine wax cohesiveness by using a texture analyzer with blade probe. It could provide guidance for the establishment of a standard method.
Streptococcus equi Detection Polymerase Chain Reaction Assay for Equine Nasopharyngeal and Guttural Pouch Wash Samples
Authors: Boyle A.G. , Rankin S.C. , Duffee L. , Boston R.C. , Wheeler‐Aceto H.
Published: December 2015

Background

Bacterial culture and polymerase chain reaction (PCR) assays for the detection of Streptococcus equi in nasopharyngeal washes (NPW) and guttural pouch lavage (GPL) samples have low sensitivity. In human diagnostics, processing of samples with flocked swabs has improved recovery rates of bacterial agents because of improved surface area and elution factors.

Hypothesis

For S. equi subsp. equi (S. equi) detection in NPW and GPL samples we hypothesized that: direct‐PCR would be more reliable than flocked swab culture (FS culture); flocked swab PCR (FS‐PCR) would be equivalent to direct‐PCR; and FS culture would be more reliable than traditional culture.

Samples

A total of 193 samples (134 NPW and 59 GPL) from 113 horses with either suspected S. equi infection, convalescing from a known S. equi infection, or asymptomatic horses screened for S. equi.

Methods

Prospective study. Samples were submitted for S. equi direct‐PCR. Using logistic regression, direct‐PCR (gold standard) was compared to FS culture, traditional culture, and FS‐PCR also performed.

Results

Direct‐PCR was statistically more sensitive than FS‐PCR, FS culture, and traditional culture (P < .001). All methods had sensitivities <70% relative to the direct‐PCR. FS culture had a similar sensitivity relative to traditional culture. The odds of GPL samples being positive on direct‐PCR (P = .030) and FS‐PCR were greater than those for NPW samples (P = .021).

Conclusions and Clinical Importance

Use of flocked swabs during laboratory preprocessing did not improve detection of S. equi via either PCR or bacterial culture from samples. Direct‐PCR is the preferred method of detection of S. equi.
Multilocus phylogeography reveals nested endemism in a gecko across the monsoonal tropics of Australia
Authors: Moritz C. , Fujita M. K. , Rosauer D. , Agudo R. , Bourke G. , Doughty P. , Palmer R. , Pepper M. , Potter S. , Pratt R. , Scott M. , Tonione M. , Donnellan S.
Published: December 2015

Multilocus phylogeography can uncover taxonomically unrecognized lineage diversity across complex biomes. The Australian monsoonal tropics include vast, ecologically intact savanna‐woodland plains interspersed with ancient sandstone uplands. Although recognized in general for its high species richness and endemism, the biodiversity of the region remains underexplored due to its remoteness. This is despite a high rate of ongoing species discovery, especially in wetter regions and for rock‐restricted taxa. To provide a baseline for ongoing comparative analyses, we tested for phylogeographic structure in an ecologically generalized and widespread taxon, the gecko Heteronotia binoei. We apply coalescent analyses to multilocus sequence data (mitochondrial DNA and eight nuclear DNA introns) from individuals sampled extensively and at fine scale across the region. The results demonstrate surprisingly deep and geographically nested lineage diversity. Several intra‐specific clades previously shown to be endemic to the region were themselves found to contain multiple, short‐range lineages. To infer landscapes with concentrations of unique phylogeographic diversity, we probabilistically estimate the ranges of lineages from point data and then, combining these estimates with the nDNA species tree, estimate phyloendemism across the region. Highest levels of phyloendemism occur in northern Top End, especially on islands, across the topographically complex Arnhem escarpment, and across the sandstone ranges of the western Gulf region. These results drive home that deep phylogeographic structure is prevalent in tropical low‐dispersal taxa, even ones that are ubiquitous across geography and habitats.
Controlling false discoveries in genome scans for selection
Authors: François Olivier , Martins Helena , Caye Kevin , Schoville Sean D.
Published: December 2015

Population differentiation (PD) and ecological association (EA) tests have recently emerged as prominent statistical methods to investigate signatures of local adaptation using population genomic data. Based on statistical models, these genomewide testing procedures have attracted considerable attention as tools to identify loci potentially targeted by natural selection. An important issue with PD and EA tests is that incorrect model specification can generate large numbers of false‐positive associations. Spurious association may indeed arise when shared demographic history, patterns of isolation by distance, cryptic relatedness or genetic background are ignored. Recent works on PD and EA tests have widely focused on improvements of test corrections for those confounding effects. Despite significant algorithmic improvements, there is still a number of open questions on how to check that false discoveries are under control and implement test corrections, or how to combine statistical tests from multiple genome scan methods. This tutorial study provides a detailed answer to these questions. It clarifies the relationships between traditional methods based on allele frequency differentiation and EA methods and provides a unified framework for their underlying statistical tests. We demonstrate how techniques developed in the area of genomewide association studies, such as inflation factors and linear mixed models, benefit genome scan methods and provide guidelines for good practice while conducting statistical tests in landscape and population genomic applications. Finally, we highlight how the combination of several well‐calibrated statistical tests can increase the power to reject neutrality, improving our ability to infer patterns of local adaptation in large population genomic data sets.
A safety vs efficiency trade‐off identified in the hydraulic pathway of grass leaves is decoupled from photosynthesis, stomatal conductance and precipitation
Authors: Ocheltree Troy W. , Nippert Jesse B. , Prasad P. V. Vara
Published: December 2015

A common theme in plant physiological research is the trade‐off between stress tolerance and growth; an example of this trade‐off at the tissue level is the safety vs efficiency hypothesis, which suggests that plants with the greatest resistance to hydraulic failure should have low maximum hydraulic conductance.

Here, we quantified the leaf‐level drought tolerance of nine C4 grasses as the leaf water potential at which plants lost 50% (P50 × RR) of maximum leaf hydraulic conductance (Ksat), and compared this trait with other leaf‐level and whole‐plant functions.

We found a clear trade‐off between Ksat and P50 × RR when Ksat was normalized by leaf area and mass (P = 0.05 and 0.01, respectively). However, no trade‐off existed between P50 × RR and gas‐exchange rates; rather, there was a positive relationship between P50 × RR and photosynthesis (P = 0.08). P50 × RR was not correlated with species distributions based on precipitation (P = 0.70), but was correlated with temperature during the wettest quarter of the year (P < 0.01).

These results suggest a trade‐off between safety and efficiency in the hydraulic system of grass leaves, which can be decoupled from other leaf‐level functions. The unique physiology of C4 plants and adaptations to pulse‐driven systems may provide mechanisms that could decouple hydraulic conductance from other plant functions.
Elucidation of the first committed step in betalain biosynthesis enables the heterologous engineering of betalain pigments in plants
Authors: Polturak Guy , Breitel Dario , Grossman Noam , Sarrion‐Perdigones Alejandro , Weithorn Efrat , Pliner Margarita , Orzaez Diego , Granell Antonio , Rogachev Ilana , Aharoni Asaph
Published: December 2015

Betalains are tyrosine‐derived red‐violet and yellow pigments, found in plants only of the Caryophyllales order. Although much progress has been made in recent years in the understanding of the betalain biosynthetic process, many questions remain open with regards to several of the proposed steps in the pathway. Most conspicuous by its absence is the characterization of the first committed step in the pathway, namely the 3‐hydroxylation of tyrosine to form l‐3,4‐dihydroxyphenylalanine (l‐DOPA).

We used transcriptome analysis of the betalain‐producing plants red beet (Beta vulgaris) and four o'clocks (Mirabilis jalapa) to identify a novel, betalain‐related cytochrome P450‐type gene, CYP76AD6, and carried out gene silencing and recombinant expression assays in Nicotiana benthamiana and yeast cells to examine its functionality.

l‐DOPA formation in red beet was found to be redundantly catalyzed by CYP76AD6 together with a known betalain‐related enzyme, CYP76AD1, which was previously thought to only catalyze a succeeding step in the pathway. While CYP76AD1 catalyzes both l‐DOPA formation and its subsequent conversion to cyclo‐DOPA, CYP76AD6 uniquely exhibits only tyrosine hydroxylase activity.

The new findings enabled us to metabolically engineer entirely red‐pigmented tobacco plants through heterologous expression of three genes taking part in the fully decoded betalain biosynthetic pathway.
A first report of leptospirosis after liver transplantation
Authors: Song A.T.W. , Abas L. , Andrade L.C. , Andraus W. , D'Albuquerque L.A.C. , Abdala E.
Published: December 2015

Leptospirosis has been rarely reported in solid organ transplant recipients. We report the first case to our knowledge of leptospirosis in a liver transplant recipient who developed jaundice and renal insufficiency. We describe his favorable clinical progression and discuss the possible mechanisms involved in the more benign disease course. We also review the previously published cases of leptospirosis in solid organ transplant recipients. Although this disease does not appear to present any particularities in this context, we highlight the importance of clinical suspicion in this setting, particularly after liver transplantation.
Good families of Drinfeld modular curves
Authors: Bassa Alp , Beelen Peter , Nguyen Nhut
Published: December 2015

In this paper, we investigate examples of good and optimal Drinfeld modular towers of function fields. Surprisingly, the optimality of these towers has not been investigated in full detail in the literature. We also give an algorithmic approach for obtaining explicit defining equations for some of these towers and, in particular, give a new explicit example of an optimal tower over a quadratic finite field.
Orthogonal matching pursuit applied to the deconvolution approach for the mapping of acoustic sources inverse problem
Authors: Padois Thomas , Berry Alain
Published: December 2015

Microphone arrays and beamforming have become a standard method to localize aeroacoustic sources. Deconvolution techniques have been developed to improve spatial resolution of beamforming maps. The deconvolution approach for the mapping of acoustic sources (DAMAS) is a standard deconvolution technique, which has been enhanced via a sparsity approach called sparsity constrained deconvolution approach for the mapping of acoustic sources (SC-DAMAS). In this paper, the DAMAS inverse problem is solved using the orthogonal matching pursuit (OMP) and compared with beamforming and SC-DAMAS. The resulting noise source maps show that OMP-DAMAS is an efficient source localization technique in the case of uncorrelated or correlated acoustic sources. Moreover, the computation time is clearly reduced as compared to SC-DAMAS.
Imipenem Treatment Induces Expression of Important Genes and Phenotypes in a Resistant Acinetobacter baumannii Isolate
Authors: Dhabaan Ghulam Nasser , AbuBakar Sazaly , Cerqueira Gustavo Maia , Al-Haroni Mohammed , Pang Sui Ping , Hassan Hamimah
Published: December 2015

Acinetobacter baumannii
has emerged as a notorious multidrug-resistant pathogen, and development of novel control measures is of the utmost importance. Understanding the factors that play a role in drug resistance may contribute to the identification of novel therapeutic targets. Pili are essential for
A. baumannii
adherence to and biofilm formation on abiotic surfaces as well as virulence. In the present study, we found that biofilm formation was significantly induced in an imipenem-resistant (Imp
r
) strain treated with a subinhibitory concentration of antibiotic compared to that in an untreated control and an imipenem-susceptible (Imp
s
) isolate. Using microarray and quantitative PCR analyses, we observed that several genes responsible for the synthesis of type IV pili were significantly upregulated in the Imp
r
but not in the Imp
s
isolate. Notably, this finding is corroborated by an increase in the motility of the Imp
r
strain. Our results suggest that the ability to overproduce colonization factors in response to imipenem treatment confers biological advantage to
A. baumannii
and may contribute to clinical success.
The Toxicity of a Novel Antifungal Compound Is Modulated by Endoplasmic Reticulum-Associated Protein Degradation Components
Authors: Raj Shriya , Krishnan Karthik , Askew David S. , Helynck Olivier , Suzanne Peggy , Lesnard Aurélien , Rault Sylvain , Zeidler Ute , d'Enfert Christophe , Latgé Jean-Paul , Munier-Lehmann Hélène , Saveanu Cosmin
Published: December 2015

In a search for new antifungal compounds, we screened a library of 4,454 chemicals for toxicity against the human fungal pathogen
Aspergillus fumigatus
. We identified sr7575, a molecule that inhibits growth of the evolutionary distant fungi
A. fumigatus
,
Cryptococcus neoformans
,
Candida albicans
, and
Saccharomyces cerevisiae
but lacks acute toxicity for mammalian cells. To gain insight into the mode of inhibition, sr7575 was screened against 4,885
S. cerevisiae
mutants from the systematic collection of haploid deletion strains and 977 barcoded haploid DAmP (decreased abundance by mRNA perturbation) strains in which the function of essential genes was perturbed by the introduction of a drug resistance cassette downstream of the coding sequence region. Comparisons with previously published chemogenomic screens revealed that the set of mutants conferring sensitivity to sr7575 was strikingly narrow, affecting components of the endoplasmic reticulum-associated protein degradation (ERAD) stress response and the ER membrane protein complex (EMC). ERAD-deficient mutants were hypersensitive to sr7575 in both
S. cerevisiae
and
A. fumigatus
, indicating a conserved mechanism of growth inhibition between yeast and filamentous fungi. Although the unfolded protein response (UPR) is linked to ERAD regulation, sr7575 did not trigger the UPR in
A. fumigatus
and UPR mutants showed no enhanced sensitivity to the compound. The data from this chemogenomic analysis demonstrate that sr7575 exerts its antifungal activity by disrupting ER protein quality control in a manner that requires ERAD intervention but bypasses the need for the canonical UPR. ER protein quality control is thus a specific vulnerability of fungal organisms that might be exploited for antifungal drug development.
Evolution of AbGRI2-0, the Progenitor of the AbGRI2 Resistance Island in Global Clone 2 of Acinetobacter baumannii
Authors: Blackwell Grace A. , Nigro Steven J. , Hall Ruth M.
Published: December 2015

A320, isolated in the Netherlands in 1982 and also known as RUH134, is the earliest available multiply antibiotic-resistant (MAR)
Acinetobacter baumannii
isolate belonging to global clone 2 (GC2) and is the reference strain for this clone. The draft genome sequence of A320 was used to investigate the original location and configuration of the IS
26
-bounded AbGRI2 resistance island found in current GC2 isolates. PCR mapping and sequencing were used to order contigs composing the resistance islands. A320 contains two IS
26
-bounded resistance islands, AbGRI2-0a and AbGRI2-0b, of 7.8 kb and 25.4 kb, respectively. Together they contain
bla
TEM
,
aacC1
,
aadA1
,
sul1
,
catA1
, and
aphA1b
genes, which confer resistance to antibiotics used clinically in the 1970s, as well as an incomplete mercury resistance module. Tracking the continuity of the chromosome and the target site duplications revealed that the two resistance islands were originally together as AbGRI2-0, an island of 32.4 kb, and were subsequently separated via an IS
26
-mediated intramolecular inversion that reversed the orientation of 1.54 Mb of the chromosome and duplicated an IS
26
. A320 contains an ancestral form of AbGRI2, and the original insertion site of the AbGRI2 island was identified. Many of the AbGRI2 versions present in the completed GC2 genomes can be derived from it via the variant AbGRI2-1. IS
26
-mediated inversions have also played a part in forming AbGRI2-0, and, upon reversal, large regions of AbGRI2-0 are identical to parts of AbaR0, the ancestral version of the AbaR islands present in GC1 isolates. This indicates a common source.
Complete Genome Sequence of Streptococcus anginosus J4211, a Clinical Isolate
Authors: Rahman Maliha , Nguyen Scott V. , McCullor Kimberly A. , King Catherine J. , Jorgensen James H. , McShan W. Michael
Published: December 2015

Streptococcus anginosus
is an opportunistic human pathogen that causes abscesses of the brain, liver, and other organs. Here, we announce the complete genome sequence of a clinically isolated strain of
S. anginosus
J4211. The genome sequence contains two prophages and multiple mobile genetic elements.
Complete Genome Sequence of the Porcine Epidemic Diarrhea Virus Variant CH/HNYF/2014
Authors: Li Renfeng , Tian Xiangqin , Qiao Songlin , Guo Junqing , Xie Weitao , Zhang Gaiping
Published: December 2015

Sow's milk is a potential route for the vertical transmission of porcine epidemic diarrhea virus (PEDV) from sow to suckling piglet. We report here the complete genome sequence of PEDV strain CH/HNYF/2014, which was isolated from milk samples
.
This information provides further understanding of the transmission mechanisms and genetic diversity of PEDV.
Complete Genome Sequences of Two Shiga Toxin-Producing Escherichia coli Strains from Serotypes O119:H4 and O165:H25
Authors: Lindsey Rebecca L. , Knipe Kristen , Rowe Lori , Garcia-Toledo Lisley , Loparev Vladimir , Juieng Phalasy , Trees Eija , Strockbine Nancy , Stripling Devon , Gerner-Smidt Peter
Published: December 2015

Shiga toxin-producing
Escherichia coli
(STEC) is an important foodborne pathogen. Here, we report complete whole-genome sequences for two STEC strains of serotypes O119:H4 and O165:H25 isolated from clinical cases in the United States.
A Coming of Age Story: Chlamydia in the Post-Genetic Era
Authors: Hooppaw Anna J. , Fisher Derek J.
Published: December 2015

Chlamydia
spp. are ubiquitous, obligate, intracellular Gram-negative bacterial pathogens that undergo a unique biphasic developmental cycle transitioning between the infectious, extracellular elementary body and the replicative, intracellular reticulate body. The primary
Chlamydia
species associated with human disease are
C. trachomatis
, which is the leading cause of both reportable bacterial sexually transmitted infections and preventable blindness, and
C. pneumoniae
, which infects the respiratory tract and is associated with cardiovascular disease. Collectively, these pathogens are a significant source of morbidity and pose a substantial financial burden on the global economy. Past efforts to elucidate virulence mechanisms of these unique and important pathogens were largely hindered by an absence of genetic methods. Watershed studies in 2011 and 2012 demonstrated that forward and reverse genetic approaches were feasible with
Chlamydia
and that shuttle vectors could be selected and maintained within the bacterium. While these breakthroughs have led to a steady expansion of the chlamydial genetic tool kit, there are still roads left to be traveled. This minireview provides a synopsis of the currently available genetic methods for
Chlamydia
along with a comparison to the methods used in other obligate intracellular bacteria. Limitations and advantages of these techniques will be discussed with an eye toward the methods still needed, and how the current state of the art for genetics in obligate intracellular bacteria could direct future technological advances for
Chlamydia
.
Acinetobacter baumannii Is Dependent on the Type II Secretion System and Its Substrate LipA for Lipid Utilization and
In Vivo
Fitness
Authors: Johnson Tanya L. , Waack Ursula , Smith Sara , Mobley Harry , Sandkvist Maria
Published: December 2015

Gram-negative bacteria express a number of sophisticated secretion systems to transport virulence factors across the cell envelope, including the type II secretion (T2S) system. Genes for the T2S components GspC through GspN and PilD are conserved among isolates of
Acinetobacter baumannii
, an increasingly common nosocomial pathogen that is developing multidrug resistance at an alarming rate. In contrast to most species, however, the T2S genes are dispersed throughout the genome rather than linked into one or two operons. Despite this unique genetic organization, we show here that the
A. baumannii
T2S system is functional. Deletion of
gspD
or
gspE
in
A. baumannii
ATCC 17978 results in loss of secretion of LipA, a lipase that breaks down long-chain fatty acids. Due to a lack of extracellular lipase, the
gspD
mutant, the
gspE
mutant, and a
lipA
deletion strain are incapable of growth on long-chain fatty acids as a sole source of carbon, while their growth characteristics are indistinguishable from those of the wild-type strain in nutrient-rich broth. Genetic inactivation of the T2S system and its substrate, LipA, also has a negative impact on
in vivo
fitness in a neutropenic murine model for bacteremia. Both the
gspD
and
lipA
mutants are outcompeted by the wild-type strain as judged by their reduced numbers in spleen and liver following intravenous coinoculation. Collectively, our findings suggest that the T2S system plays a hitherto-unrecognized role in
in vivo
survival of
A. baumannii
by transporting a lipase that may contribute to fatty acid metabolism.

IMPORTANCE
Infections by multidrug-resistant
Acinetobacter baumannii
are a growing health concern worldwide, underscoring the need for a better understanding of the molecular mechanisms by which this pathogen causes disease. In this study, we demonstrated that
A. baumannii
expresses a functional type II secretion (T2S) system that is responsible for secretion of LipA, an extracellular lipase required for utilization of exogenously added lipids. The T2S system and the secreted lipase support
in vivo
colonization and thus contribute to the pathogenic potential of
A. baumannii
.
Pathogenicity Island Cross Talk Mediated by Recombination Directionality Factors Facilitates Excision from the Chromosome
Authors: Carpenter Megan R. , Rozovsky Sharon , Boyd E. Fidelma
Published: December 2015

Pathogenicity islands (PAIs) are mobile integrated genetic elements (MIGEs) that contain a diverse range of virulence factors and are essential in the evolution of pathogenic bacteria. PAIs are widespread among bacteria and integrate into the host genome, commonly at a tRNA locus, via integrase-mediated site-specific recombination. The excision of PAIs is the first step in the horizontal transfer of these elements and is not well understood. In this study, we examined the role of recombination directionality factors (RDFs) and their relationship with integrases in the excision of two PAIs essential forVibrio choleraehost colonization:Vibriopathogenicity island 1 (VPI-1) and VPI-2. VPI-1 does not contain an RDF, which allowed us to answer the question of whether RDFs are an absolute requirement for excision. We found that an RDF was required for efficient excision of VPI-2 but not VPI-1 and that RDFs can induce excision of both islands. Expression data revealed that the RDFs act as transcriptional repressors to both VPI-1- and VPI-2-encoded integrases. We demonstrated that the RDFsVibrioexcision factor A (VefA) and VefB bind at the attachment sites (overlapping theintpromoter region) of VPI-1 and VPI-2, thus supporting this mode of integrase repression. In addition,V. choleraeRDFs are promiscuous due to their dual functions of promoting excision of both VPI-1 and VPI-2 and acting as negative transcriptional regulators of the integrases. This is the first demonstration of cross talk between PAIs mediated via RDFs which reveals the complex interactions that occur between separately acquired MIGEs.

IMPORTANCEDeciphering the mechanisms of pathogenicity island excision is necessary for understanding the evolution and spread of these elements to their nonpathogenic counterparts. Such mechanistic insight would assist in predicting the mobility of uncharacterized genetic elements. This study identified extensive RDF-mediated cross talk between two nonhomologous VPIs and demonstrated the dual functionality of RDF proteins: (i) inducing PAI excision and (ii) acting as transcriptional regulators. Findings from this study may be implicated in determining the mobilome contribution of other bacteria with multiple MIGEs.
Reexamining the Germination Phenotypes of Several Clostridium difficile Strains Suggests Another Role for the CspC Germinant Receptor
Authors: Bhattacharjee Disha , Francis Michael B. , Ding Xicheng , McAllister Kathleen N. , Shrestha Ritu , Sorg Joseph A.
Published: December 2015

Clostridium difficile
spore germination is essential for colonization and disease. The signals that initiate
C. difficile
spore germination are a combination of taurocholic acid (a bile acid) and glycine. Interestingly, the chenodeoxycholic acid class (CDCA) bile acids competitively inhibit taurocholic acid-mediated germination, suggesting that compounds that inhibit spore germination could be developed into drugs that prophylactically prevent
C. difficile
infection or reduce recurring disease. However, a recent report called into question the utility of such a strategy to prevent infection by describing
C. difficile
strains that germinated in the apparent absence of bile acids or germinated in the presence of the CDCA inhibitor. Because the mechanisms of
C. difficile
spore germination are beginning to be elucidated, the mechanism of germination in these particular strains could yield important information on how
C. difficile
spores initiate germination. Therefore, we quantified the interaction of these strains with taurocholic acid and CDCA, the rates of spore germination, the release of DPA from the spore core, and the abundance of the germinant receptor complex (CspC, CspB, and SleC). We found that strains previously observed to germinate in the absence of taurocholic acid correspond to more potent 50% effective concentrations (EC
50
values; the concentrations that achieve a half-maximum germination rate) of the germinant and are still inhibited by CDCA, possibly explaining the previous observations. By comparing the germination kinetics and the abundance of proteins in the germinant receptor complex, we revised our original model for CspC-mediated activation of spore germination and propose that CspC may activate spore germination and then inhibit downstream processes.

IMPORTANCE
Clostridium difficile
forms metabolically dormant spores that persist in the health care environment. In susceptible hosts,
C. difficile
spores germinate in response to certain bile acids and glycine. Blocking germination by
C. difficile
spores is an attractive strategy to prevent the initiation of disease or to block recurring infection. However, certain
C. difficile
strains have been identified whose spores germinate in the absence of bile acids or are not blocked by known inhibitors of
C. difficile
spore germination (calling into question the utility of such strategies). Here, we further investigate these strains and reestablish that bile acid activators and inhibitors of germination affect these strains and use these data to suggest another role for the
C. difficile
bile acid germinant receptor.
New Choices in Undergraduate Biology Course Designs, but Use the
Vision and Change
ModelReview of:
Building a Pathway for Student Learning: A How-to Guide to Course Design
; Steven Jones, Robert Noyd, and Kenneth Sagendorf; (2014). Stylus Publishing, Sterling, VA. 139 pages.
Authors: Horak Rachel E. A.
Published: December 2015

Review of: Building a Pathway for Student Learning: A How-to Guide to Course Design; Steven Jones, Robert Noyd, and Kenneth Sagendorf; (2014). Stylus Publishing, Sterling, VA. 139 pages.
Journal Watch
Authors: Herzog Jennifer A.
Published: December 2015

In this section, I provide articles on recent developments and new technology used in microbiology and related fields. I also post articles that may help you bring new information or techniques into your laboratory or classroom via case studies or lab exercises. I hope you find this information useful, and I encourage you to send suggestions, questions, or comments to me at herzogja@herkimer.edu. I look forward to hearing from you!
A Simulation of Communicable Disease and Herd Immunity for the Microbiology Classroom or Laboratory
Authors: Wiles Jeff
Published: December 2015

Modern medicine has reduced the incidence of communicable disease, but humanity continues to suffer from a wide variety of ailments caused by infectious microorganisms. Modelling this transmission allows for a greater awareness of the various mechanisms through which disease can spread. This procedure allows students to participate in a completely safe, real-time exercise that demonstrates the ease at which a susceptible population can become infected. In addition, this exercise allows for a demonstration of the efficacy of herd immunity. An easily-prepared set of cards takes the place of actual microorganisms.