bluuebunny/crossref_metadata_2025 huggingface dataset:
Resonance of an imperfect joint of plates by the lowest-order symmetric Lamb mode
Authors: Mori Naoki , Biwa Shiro
Published: June 2015

Resonance behavior of an imperfect joint of elastic plates subjected to the incidence of the lowest-order symmetric (S0) Lamb mode is numerically analyzed in the frequency domain by the hybrid finite element method. To this purpose, the reflection and transmission characteristics of the S0 mode are calculated for the frequency range in which the S0 mode is the only symmetric mode that can propagate in the plates. The imperfect joint is modeled as a linear spring-type interface characterized by the normal and tangential stiffnesses. As a result, it is shown that the imperfect joint of plates has two resonance frequencies at which the out-of-plane displacement amplitudes at the joint are remarkably increased. One resonance frequency depends only on the normal stiffness, and the other only on the tangential stiffness. Each resonance frequency coincides with that of a free edge of a plate, and monotonically increases with the corresponding joint stiffness. Furthermore, it is also shown that the reflection and transmission behavior of the S0 mode at the imperfect joint of the plates can be well reproduced by the one-dimensional thin-plate approximation of extensional waves when the frequency is sufficiently small compared to the resonance frequencies.
Coral Mucus Is a Hot Spot for Viral Infections
Authors: Nguyen-Kim Hanh , Bettarel Yvan , Bouvier Thierry , Bouvier Corinne , Doan-Nhu Hai , Nguyen-Ngoc Lam , Nguyen-Thanh Thuy , Tran-Quang Huy , Brune Justine
Published: June 2015

There is increasing suspicion that viral communities play a pivotal role in maintaining coral health, yet their main ecological traits still remain poorly characterized. In this study, we examined the seasonal distribution and reproduction pathways of viruses inhabiting the mucus of the scleractinians
Fungia repanda
and
Acropora formosa
collected in Nha Trang Bay (Vietnam) during an 11-month survey. The strong coupling between epibiotic viral and bacterial abundance suggested that phages are dominant among coral-associated viral communities. Mucosal viruses also exhibited significant differences in their main features between the two coral species and were also remarkably contrasted with their planktonic counterparts. For example, their abundance (inferred from epifluorescence counts), lytic production rates (KCN incubations), and the proportion of lysogenic cells (mitomycin C inductions) were, respectively, 2.6-, 9.5-, and 2.2-fold higher in mucus than in the surrounding water. Both lytic and lysogenic indicators were tightly coupled with temperature and salinity, suggesting that the life strategy of viral epibionts is strongly dependent upon environmental circumstances. Finally, our results suggest that coral mucus may represent a highly favorable habitat for viral proliferation, promoting the development of both temperate and virulent phages. Here, we discuss how such an optimized viral arsenal could be crucial for coral viability by presumably forging complex links with both symbiotic and adjacent nonsymbiotic microorganisms.
Genetic Analysis of the Aspergillus flavus Vegetative Compatibility Group to Which a Biological Control Agent That Limits Aflatoxin Contamination in U.S. Crops Belongs
Authors: Grubisha Lisa C. , Cotty Peter J.
Published: June 2015

Some filamentous fungi inAspergillussectionFlaviproduce carcinogenic secondary compounds called aflatoxins. Aflatoxin contamination is routinely managed in commercial agriculture with strains ofAspergillus flavusthat do not produce aflatoxins. These non-aflatoxin-producing strains competitively exclude aflatoxin producers and reshape fungal communities so that strains with the aflatoxin-producing phenotype are less frequent. This study evaluated the genetic variation within naturally occurring atoxigenicA. flavusstrains from the endemic vegetative compatibility group (VCG) YV36. AF36 is a strain of VCG YV36 and was the first fungus used in agriculture for aflatoxin management. Genetic analyses based on mating-type loci, 21 microsatellite loci, and a single nucleotide polymorphism (SNP) in theaflCgene were applied to a set of 237 YV36 isolates collected from 1990 through 2005 from desert legumes and untreated fields and from fields previously treated with AF36 across the southern United States. One haplotype dominated across time and space. No recombination with strains belonging to VCGs other than YV36 was detected. All YV36 isolates carried the SNP inaflCthat prevents aflatoxin biosynthesis and themat1-2idiomorph at the mating-type locus. These results suggest that VCG YV36 has a clonal population structure maintained across both time and space. These results demonstrate the genetic stability of atoxigenic strains belonging to a broadly distributed endemic VCG in both untreated populations and populations where the short-term frequency of VCG YV36 has increased due to applications of a strain used to competitively exclude aflatoxin producers. This work supports the hypothesis that strains of this VCG are not involved in routine genetic exchange with aflatoxin-producing strains.
A Putative Type III Secretion System Effector Encoded by the
MA20_12780
Gene in Bradyrhizobium japonicum Is-34 Causes Incompatibility with
Rj
4
Genotype Soybeans
Authors: Tsurumaru Hirohito , Hashimoto Syougo , Okizaki Kouhei , Kanesaki Yu , Yoshikawa Hirofumi , Yamakawa Takeo
Published: June 2015

The nodulation of
Bradyrhizobium japonicum
Is-34 is restricted by
Rj
4
genotype soybeans (
Glycine max
). To identify the genes responsible for this incompatibility, Tn
5
mutants of
B. japonicum
Is-34 that were able to overcome this nodulation restriction were obtained. Analysis of the Tn
5
mutants revealed that Tn
5
was inserted into a region containing the
MA20_12780
gene. In addition, direct disruption of this gene using marker exchange overcame the nodulation restriction by
Rj
4
genotype soybeans. The
MA20_12780
gene has a
tts
box motif in its upstream region, indicating a possibility that this gene encodes a type III secretion system (T3SS) effector protein. Bioinformatic characterization revealed that the MA20_12780 protein contains the small ubiquitin-like modifier (SUMO) protease domain of the C48 peptidase (ubiquitin-like protease 1 [Ulp1]) family. The results of the present study indicate that a putative T3SS effector encoded by the
MA20_12780
gene causes the incompatibility with
Rj
4
genotype soybeans, and they suggest the possibility that the nodulation restriction of
B. japonicum
Is-34 may be due to
Rj
4
genotype soybeans recognizing the putative T3SS effector (MA20_12780 protein) as a virulence factor.
Indirect Immunodetection of Fungal Fragments by Field Emission Scanning Electron Microscopy
Authors: Afanou Komlavi Anani , Straumfors Anne , Skogstad Asbjørn , Nayak Ajay P. , Skaar Ida , Hjeljord Linda , Tronsmo Arne , Eduard Wijnand , Green Brett James
Published: June 2015

Submicronic fungal fragments have been observed in
in vitro
aerosolization experiments. The occurrence of these particles has therefore been suggested to contribute to respiratory health problems observed in mold-contaminated indoor environments. However, the role of submicronic fragments in exacerbating adverse health effects has remained unclear due to limitations associated with detection methods. In the present study, we report the development of an indirect immunodetection assay that utilizes chicken polyclonal antibodies developed against spores from
Aspergillus versicolor
and high-resolution field emission scanning electron microscopy (FESEM). Immunolabeling was performed with
A. versicolor
fragments immobilized and fixed onto poly-
l
-lysine-coated polycarbonate filters. Ninety percent of submicronic fragments and 1- to 2-μm fragments, compared to 100% of >2-μm fragments generated from pure freeze-dried mycelial fragments of
A. versicolor
, were positively labeled. In proof-of-concept experiments, air samples collected from moldy indoor environments were evaluated using the immunolabeling technique. Our results indicated that 13% of the total collected particles were derived from fungi. This fraction comprises 79% of the fragments that were detected by immunolabeling and 21% of the spore particles that were morphologically identified. The methods reported in this study enable the enumeration of fungal particles, including submicronic fragments, in a complex heterogeneous environmental sample.
Spatial Variation and Survival of Salmonella enterica Subspecies in a Population of Australian Sleepy Lizards (Tiliqua rugosa)
Authors: Parsons Sandra K. , Bull C. Michael , Gordon David M.
Published: June 2015

The life cycles of many enteric bacterial species require a transition between two very distinct environments. Their primary habitat is the gastrointestinal tract of the host, while their secondary habitat, during transmission from one host to another, consists of environments external to the host, such as soil, water, and sediments. Consequently, both host and environmental factors shape the genetic structure of enteric bacterial populations. This study examined the distribution of four
Salmonella enterica
subspecies in a population of sleepy lizards,
Tiliqua rugosa
, in a semiarid region of South Australia. The lizards living within the 1,920-m by 720-m study site were radio tracked, and their enteric bacteria were sampled at regular intervals throughout their active seasons in the years 2001, 2002, and 2006. Four of the six subspecies of
S. enterica
were present in this population and were nonrandomly distributed among the lizards. In particular,
S. enterica
subsp.
diarizonae
was restricted to lizards living in the most shaded parts of the study site with an overstorey of
Casuarina
trees. Experiments undertaken to investigate the survival of
S. enterica
cells under seminatural conditions revealed that cell survival decreased with increased exposure to elevated temperatures and UV light. Among the three
S. enterica
subspecies tested,
S. enterica
subsp.
diarizonae
consistently had an average expected life span that was shorter than that observed for the other two subspecies. There was no indication in the data that there was any competitive dominance hierarchy among the
S. enterica
subspecies within individual hosts. Thus, the nonrandom distribution of
S. enterica
subspecies in this population of lizards appears to be driven by their different survival characteristics in the external environment.
Flocculation of Escherichia coli Cells in Association with Enhanced Production of Outer Membrane Vesicles
Authors: Ojima Yoshihiro , Nguyen Minh Hong , Yajima Reiki , Taya Masahito
Published: June 2015

Microbial flocculation is a phenomenon of aggregation of dispersed bacterial cells in the form of flocs or flakes. In this study, the mechanism of spontaneous flocculation of
Escherichia coli
cells by overexpression of the
bcsB
gene was investigated. The flocculation induced by overexpression of
bcsB
was consistent among the various
E. coli
strains examined, including the K-12, B, and O strains, with flocs that resembled paper scraps in structure being about 1 to 2 mm. The distribution of green fluorescent protein-labeled
E. coli
cells within the floc structure was investigated by three-dimensional confocal laser scanning microscopy. Flocs were sensitive to proteinase K, indicating that the main component of the flocs was proteinous. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and nano-liquid chromatography tandem mass spectrometry analyses of the flocs strongly suggested the involvement of outer membrane vesicles (OMVs) in
E. coli
flocculation. The involvement of OMVs in flocculation was supported by transmission electron microscopy observation of flocs. Furthermore,
bcsB
-induced
E. coli
flocculation was greatly suppressed in strains with hypovesiculation phenotypes (Δ
dsbA
and Δ
dsbB
strains). Thus, our results demonstrate the strong correlation between spontaneous flocculation and enhanced OMV production of
E. coli
cells.
Identification and Heterologous Expression of the Chaxamycin Biosynthesis Gene Cluster from Streptomyces leeuwenhoekii
Authors: Castro Jean Franco , Razmilic Valeria , Gomez-Escribano Juan Pablo , Andrews Barbara , Asenjo Juan A. , Bibb Mervyn J.
Published: June 2015

Streptomyces leeuwenhoekii
, isolated from the hyperarid Atacama Desert, produces the new ansamycin-like compounds chaxamycins A to D, which possess potent antibacterial activity and moderate antiproliferative activity. We report the development of genetic tools to manipulate
S. leeuwenhoekii
and the identification and partial characterization of the 80.2-kb chaxamycin biosynthesis gene cluster, which was achieved by both mutational analysis in the natural producer and heterologous expression in
Streptomyces coelicolor
A3(2) strain M1152. Restoration of chaxamycin production in a nonproducing Δ
cxmK
mutant (
cxmK
encodes 3-amino-5-hydroxybenzoic acid [AHBA] synthase) was achieved by supplementing the growth medium with AHBA, suggesting that mutasynthesis may be a viable approach for the generation of novel chaxamycin derivatives.
Pyrobaculum yellowstonensis Strain WP30 Respires on Elemental Sulfur and/or Arsenate in Circumneutral Sulfidic Geothermal Sediments of Yellowstone National Park
Authors: Jay Z. J. , Beam J. P. , Dohnalkova A. , Lohmayer R. , Bodle B. , Planer-Friedrich B. , Romine M. , Inskeep W. P.
Published: June 2015

Thermoproteales
(phylum
Crenarchaeota
) populations are abundant in high-temperature (>70°C) environments of Yellowstone National Park (YNP) and are important in mediating the biogeochemical cycles of sulfur, arsenic, and carbon. The objectives of this study were to determine the specific physiological attributes of the isolate
Pyrobaculum yellowstonensis
strain WP30, which was obtained from an elemental sulfur sediment (Joseph's Coat Hot Spring [JCHS], 80°C, pH 6.1, 135 μM As) and relate this organism to geochemical processes occurring
in situ
. Strain WP30 is a chemoorganoheterotroph and requires elemental sulfur and/or arsenate as an electron acceptor. Growth in the presence of elemental sulfur and arsenate resulted in the formation of thioarsenates and polysulfides. The complete genome of this organism was sequenced (1.99 Mb, 58% G+C content), revealing numerous metabolic pathways for the degradation of carbohydrates, amino acids, and lipids. Multiple dimethyl sulfoxide-molybdopterin (DMSO-MPT) oxidoreductase genes, which are implicated in the reduction of sulfur and arsenic, were identified. Pathways for the
de novo
synthesis of nearly all required cofactors and metabolites were identified. The comparative genomics of
P. yellowstonensis
and the assembled metagenome sequence from JCHS showed that this organism is highly related (∼95% average nucleotide sequence identity) to
in situ
populations. The physiological attributes and metabolic capabilities of
P. yellowstonensis
provide an important foundation for developing an understanding of the distribution and function of these populations in YNP.
Nitrite-Oxidizing Bacterium Nitrobacter winogradskyi Produces
N
-Acyl-Homoserine Lactone Autoinducers
Authors: Mellbye Brett L. , Bottomley Peter J. , Sayavedra-Soto Luis A.
Published: June 2015

Nitrobacter winogradskyi
is a chemolithotrophic bacterium that plays a role in the nitrogen cycle by oxidizing nitrite to nitrate. Here, we demonstrate a functional
N
-acyl-homoserine lactone (acyl-HSL) synthase in this bacterium. The
N. winogradskyi
genome contains genes encoding a putative acyl-HSL autoinducer synthase (nwi0626,
nwiI
) and a putative acyl-HSL autoinducer receptor (nwi0627,
nwiR
) with amino acid sequences 38 to 78% identical to those in
Rhodopseudomonas palustris
and other
Rhizobiales
. Expression of
nwiI
and
nwiR
correlated with acyl-HSL production during culture.
N. winogradskyi
produces two distinct acyl-HSLs,
N
-decanoyl-
l
-homoserine lactone (C
10
-HSL) and a monounsaturated acyl-HSL (C
10:1
-HSL), in a cell-density- and growth phase-dependent manner, during batch and chemostat culture. The acyl-HSLs were detected by bioassay and identified by ultraperformance liquid chromatography with information-dependent acquisition mass spectrometry (UPLC-IDA-MS). The C=C bond in C
10:1
-HSL was confirmed by conversion into bromohydrin and detection by UPLC-IDA-MS.
The United States Culture Collection Network (USCCN): Enhancing Microbial Genomics Research through Living Microbe Culture Collections
Authors: Boundy-Mills Kyria , Hess Matthias , Bennett A. Rick , Ryan Matthew , Kang Seogchan , Nobles David , Eisen Jonathan A. , Inderbitzin Patrik , Sitepu Irnayuli R. , Torok Tamas , Brown Daniel R. , Cho Juliana , Wertz John E. , Mukherjee Supratim , Cady Sherry L. , McCluskey Kevin
Published: June 2015

The mission of the United States Culture Collection Network (USCCN;
http://usccn.org
) is “to facilitate the safe and responsible utilization of microbial resources for research, education, industry, medicine, and agriculture for the betterment of human kind.” Microbial culture collections are a key component of life science research, biotechnology, and emerging global biobased economies. Representatives and users of several microbial culture collections from the United States and Europe gathered at the University of California, Davis, to discuss how collections of microorganisms can better serve users and stakeholders and to showcase existing resources available in public culture collections.
Identification of a Novel Dye-Decolorizing Peroxidase, EfeB, Translocated by a Twin-Arginine Translocation System in Streptococcus thermophilus CGMCC 7.179
Authors: Zhang Chenchen , Xin Yongping , Wang Yue , Guo Tingting , Lu Shiyi , Kong Jian
Published: June 2015

Streptococcus thermophilus
is a facultative anaerobic bacterium that has the ability to grow and survive in aerobic environments, but the mechanism for this remains unclear. In this study, the
efeB
gene, encoding a dye-decolorizing peroxidase, was identified in the genome of
Streptococcus thermophilus
CGMCC 7.179, and purified EfeB was able to decolorize reactive blue 5. Strikingly, genes encoding two components (TatA and TatC) of the twin-arginine translocation (TAT) system were also found in the same operon with the
efeB
gene. Knocking out
efeB
or
tatC
resulted in decreased growth of the strain under aerobic conditions, and complementation of the
efeB
-deficient strains with the
efeB
gene enhanced the biomass of the hosts only in the presence of the
tatC
gene. Moreover, it was proved for both
S. thermophilus
CGMCC 7.179 and
Escherichia coli
DE3 that EfeB could be translocated by the TAT system of
S. thermophilus
. In addition, the transcriptional levels of
efeB
and
tatC
increased when the strain was cultured under aerobic conditions. Overall, these results provide the first evidence that EfeB plays a role in protecting cells of
S. thermophilus
from oxidative stress, with the assistance of the TAT system.
New Insight into Microbial Iron Oxidation as Revealed by the Proteomic Profile of an Obligate Iron-Oxidizing Chemolithoautotroph
Authors: Barco Roman A. , Emerson David , Sylvan Jason B. , Orcutt Beth N. , Jacobson Meyers Myrna E. , Ramírez Gustavo A. , Zhong John D. , Edwards Katrina J.
Published: June 2015

Microaerophilic, neutrophilic, iron-oxidizing bacteria (FeOB) grow via the oxidation of reduced Fe(II) at or near neutral pH, in the presence of oxygen, making them relevant in numerous environments with elevated Fe(II) concentrations. However, the biochemical mechanisms for Fe(II) oxidation by these neutrophilic FeOB are unknown, and genetic markers for this process are unavailable. In the ocean, microaerophilic microorganisms in the genus
Mariprofundus
of the class
Zetaproteobacteria
are the only organisms known to chemolithoautotrophically oxidize Fe and concurrently biomineralize it in the form of twisted stalks of iron oxyhydroxides. The aim of this study was to identify highly expressed proteins associated with the electron transport chain of microaerophilic, neutrophilic FeOB. To this end,
Mariprofundus ferrooxydans
PV-1 was cultivated, and its proteins were extracted, assayed for redox activity, and analyzed via liquid chromatography-tandem mass spectrometry for identification of peptides. The results indicate that a cytochrome
c
4
,
cbb
3
-type cytochrome oxidase subunits, and an outer membrane cytochrome
c
were among the most highly expressed proteins and suggest an involvement in the process of aerobic, neutrophilic bacterial Fe oxidation. Proteins associated with alternative complex III, phosphate transport, carbon fixation, and biofilm formation were abundant, consistent with the lifestyle of
Mariprofundus
.
Microbial Community Composition, Functions, and Activities in the Gulf of Mexico 1 Year after the Deepwater Horizon Accident
Authors: Yergeau Etienne , Maynard Christine , Sanschagrin Sylvie , Champagne Julie , Juck David , Lee Kenneth , Greer Charles W.
Published: June 2015

Several studies have assessed the effects of the released oil on microbes, either during or immediately after the Deepwater Horizon accident. However, little is known about the potential longer-term persistent effects on microbial communities and their functions. In this study, one water column station near the wellhead (3.78 km southwest of the wellhead), one water column reference station outside the affected area (37.77 km southeast of the wellhead), and deep-sea sediments near the wellhead (3.66 km southeast of the wellhead) were sampled 1 year after the capping of the well. In order to analyze microbial community composition, function, and activity, we used metagenomics, metatranscriptomics, and mineralization assays. Mineralization of hexadecane was significantly higher at the wellhead station at a depth of ∼1,200 m than at the reference station. Community composition based on taxonomical or functional data showed that the samples taken at a depth of ∼1,200 m were significantly more dissimilar between the stations than at other depths (surface, 100 m, 750 m, and >1,500 m). Both
Bacteria
and
Archaea
showed reduced activity at depths of ∼1,200 m when the wellhead station was compared to the reference station, and their activity was significantly higher in surficial sediments than in 10-cm sediments. Surficial sediments also harbored significantly different active genera than did 5- and 10-cm sediments. For the remaining microbial parameters assessed, no significant differences could be observed between the wellhead and reference stations and between surface and 5- to 10-cm-deep sediments.
Ectomycorrhizal Communities on the Roots of Two Beech (Fagus sylvatica) Populations from Contrasting Climates Differ in Nitrogen Acquisition in a Common Environment
Authors: Leberecht Martin , Dannenmann Michael , Gschwendtner Silvia , Bilela Silvija , Meier Rudolf , Simon Judy , Rennenberg Heinz , Schloter Michael , Polle Andrea
Published: June 2015

Beech (
Fagus sylvatica
), a dominant forest species in Central Europe, competes for nitrogen with soil microbes and suffers from N limitation under dry conditions. We hypothesized that ectomycorrhizal communities and the free-living rhizosphere microbes from beech trees from sites with two contrasting climatic conditions exhibit differences in N acquisition that contribute to differences in host N uptake and are related to differences in host belowground carbon allocation. To test these hypotheses, young trees from the natural regeneration of two genetically similar populations, one from dryer conditions (located in an area with a southwest exposure [SW trees]) and the other from a cooler, moist climate (located in an area with a northeast exposure [NE trees]), were transplanted into a homogeneous substrate in the same environment and labeled with
13
CO
2
and
15
NH
4
+
. Free-living rhizosphere microbes were characterized by marker genes for the N cycle, but no differences between the rhizospheres of SW or NE trees were found. Lower
15
N enrichment was found in the ectomycorrhizal communities of the NE tree communities than the SW tree communities, whereas no significant differences in
15
N enrichment were observed for nonmycorrhizal root tips of SW and NE trees. Neither the ectomycorrhizal communities nor the nonmycorrhizal root tips originating from NE and SW trees showed differences in
13
C signatures. Because the level of
15
N accumulation in fine roots and the amount transferred to leaves were lower in NE trees than SW trees, our data support the suggestion that the ectomycorrhizal community influences N transfer to its host and demonstrate that the fungal community from the dry condition was more efficient in N acquisition when environmental constraints were relieved. These findings highlight the importance of adapted ectomycorrhizal communities for forest nutrition in a changing climate.
Methanotrophic and Methanogenic Communities in Swiss Alpine Fens Dominated by Carex rostrata and Eriophorum angustifolium
Authors: Cheema Simrita , Zeyer Josef , Henneberger Ruth
Published: June 2015

Vascular plants play a key role in controlling CH
4
emissions from natural wetlands, because they influence CH
4
production, oxidation, and transport to the atmosphere. Here we investigated differences in the abundance and composition of methanotrophic and methanogenic communities in three Swiss alpine fens dominated by different vascular plant species under natural conditions. The sampling locations either were situated at geographically distinct sites with different physicochemical properties but the same dominant plant species (
Carex rostrata
) or were located within the same site, showing comparable physicochemical pore water properties, but had different plant species (
C. rostrata
or
Eriophorum angustifolium
). All three locations were permanently submerged and showed high levels of CH
4
emissions (80.3 to 184.4 mg CH
4
m
−2
day
−1
). Soil samples were collected from three different depths with different pore water CH
4
and O
2
concentrations and were analyzed for
pmoA
and
mcrA
gene and transcript abundance and community composition, as well as soil structure. The dominant plant species appeared to have a significant influence on the composition of the active methanotrophic communities (transcript level), while the methanogenic communities differed significantly only at the gene level. Yet no plant species-specific microbial taxa were discerned. Moreover, for all communities, differences in composition were more pronounced with the site (i.e., with different physicochemical properties) than with the plant species. Moreover, depth significantly influenced the composition of the active methanotrophic communities. Differences in abundance were generally low, and active methanotrophs and methanogens coexisted at all three locations and depths independently of CH
4
and O
2
concentrations or plant species.
Development and Evaluation of Three Real-Time PCR Assays for Genotyping and Source Tracking Cryptosporidium spp. in Water
Authors: Li Na , Neumann Norman F. , Ruecker Norma , Alderisio Kerri A. , Sturbaum Gregory D. , Villegas Eric N. , Chalmers Rachel , Monis Paul , Feng Yaoyu , Xiao Lihua
Published: June 2015

The occurrence of
Cryptosporidium
oocysts in drinking source water can present a serious public health risk. To rapidly and effectively assess the source and human-infective potential of
Cryptosporidium
oocysts in water, sensitive detection and correct identification of oocysts to the species level (genotyping) are essential. In this study, we developed three real-time PCR genotyping assays, two targeting the small-subunit (SSU) rRNA gene (18S-LC1 and 18S-LC2 assays) and one targeting the 90-kDa heat shock protein (hsp90) gene (hsp90 assay), and evaluated the sensitivity and
Cryptosporidium
species detection range of these assays. Using fluorescence resonance energy transfer probes and melt curve analysis, the 18S-LC1 and hsp90 assays could differentiate common human-pathogenic species (
C. parvum
,
C. hominis
, and
C. meleagridis
), while the 18S-LC2 assay was able to differentiate nonpathogenic species (such as
C. andersoni
) from human-pathogenic ones commonly found in source water. In sensitivity evaluations, the 18S-LC2 and hsp90 genotyping assays could detect as few as 1
Cryptosporidium
oocyst per sample. Thus, the 18S-LC2 and hsp90 genotyping assays might be used in environmental monitoring, whereas the 18S-LC1 genotyping assay could be useful for genotyping
Cryptosporidium
spp. in clinical specimens or wastewater samples.
CO Metabolism in the Acetogen Acetobacterium woodii
Authors: Bertsch Johannes , Müller Volker
Published: June 2015

The Wood-Ljungdahl pathway allows acetogenic bacteria to grow on a number of one-carbon substrates, such as carbon dioxide, formate, methyl groups, or even carbon monoxide. Since carbon monoxide alone or in combination with hydrogen and carbon dioxide (synthesis gas) is an increasingly important feedstock for third-generation biotechnology, we studied CO metabolism in the model acetogen
Acetobacterium woodii
. When cells grew on H
2
-CO
2
, addition of 5 to 15% CO led to higher final optical densities, indicating the utilization of CO as a cosubstrate. However, the growth rate was decreased by the presence of small amounts of CO, which correlated with an inhibition of H
2
consumption. Experiments with resting cells revealed that the degree of inhibition of H
2
consumption was a function of the CO concentration. Since the hydrogen-dependent CO
2
reductase (HDCR) of
A. woodii
is known to be very sensitive to CO, we speculated that cells may be more tolerant toward CO when growing on formate, the product of the HDCR reaction. Indeed, addition of up to 25% CO did not influence growth rates on formate, while the final optical densities and the production of acetate increased. Higher concentrations (75 and 100%) led to a slight inhibition of growth and to decreasing rates of formate and CO consumption. Experiments with resting cells revealed that the HDCR is a site of CO inhibition. In contrast,
A. woodii
was not able to grow on CO as a sole carbon and energy source, and growth on fructose-CO or methanol-CO was not observed.
Secretion of Polypeptide Crystals from Tetrahymena thermophila Secretory Organelles (Mucocysts) Depends on Processing by a Cysteine Cathepsin, Cth4p
Authors: Kumar Santosh , Briguglio Joseph S. , Turkewitz Aaron P.
Published: June 2015

In many organisms, sophisticated mechanisms facilitate release of peptides in response to extracellular stimuli. In the ciliate
Tetrahymena thermophila
, efficient peptide secretion depends on specialized vesicles called mucocysts that contain dense crystalline cores that expand rapidly during exocytosis. Core assembly depends of endoproteolytic cleavage of mucocyst proproteins by an aspartyl protease, cathepsin 3 (
CTH3
). Here, we show that a second enzyme identified by expression profiling, Cth4p, is also required for processing of proGrl proteins and for assembly of functional mucocysts. Cth4p is a cysteine cathepsin that localizes partially to endolysosomal structures and appears to act downstream of, and may be activated by, Cth3p. Disruption of
CTH4
results in cells (Δ
cth4
) that show aberrant trimming of Grl proproteins, as well as grossly aberrant mucocyst exocytosis. Surprisingly, Δ
cth4
cells succeed in assembling crystalline mucocyst cores. However, those cores do not undergo normal directional expansion during exocytosis, and they thus fail to efficiently extrude from the cells. We could phenocopy the Δ
cth4
defects by mutating conserved catalytic residues, indicating that the
in vivo
function of Cth4p is enzymatic. Our results indicate that as for canonical proteins packaged in animal secretory granules, the maturation of mucocyst proproteins involves sequential processing steps. The Δ
cth4
defects uncouple, in an unanticipated way, the assembly of mucocyst cores and their subsequent expansion and thereby reveal a previously unsuspected aspect of polypeptide secretion in ciliates.
Acetylcholine Protects against Candida albicans Infection by Inhibiting Biofilm Formation and Promoting Hemocyte Function in a Galleria mellonella Infection Model
Authors: Rajendran Ranjith , Borghi Elisa , Falleni Monica , Perdoni Federica , Tosi Delfina , Lappin David F. , O'Donnell Lindsay , Greetham Darren , Ramage Gordon , Nile Christopher
Published: June 2015

Both neuronal acetylcholine and nonneuronal acetylcholine have been demonstrated to modulate inflammatory responses. Studies investigating the role of acetylcholine in the pathogenesis of bacterial infections have revealed contradictory findings with regard to disease outcome. At present, the role of acetylcholine in the pathogenesis of fungal infections is unknown. Therefore, the aim of this study was to determine whether acetylcholine plays a role in fungal biofilm formation and the pathogenesis of
Candida albicans
infection. The effect of acetylcholine on
C. albicans
biofilm formation and metabolism
in vitro
was assessed using a crystal violet assay and phenotypic microarray analysis. Its effect on the outcome of a
C. albicans
infection, fungal burden, and biofilm formation were investigated
in vivo
using a
Galleria mellonella
infection model. In addition, its effect on modulation of host immunity to
C. albicans
infection was also determined
in vivo
using hemocyte counts, cytospin analysis, larval histology, lysozyme assays, hemolytic assays, and real-time PCR. Acetylcholine was shown to have the ability to inhibit
C. albicans
biofilm formation
in vitro
and
in vivo
. In addition, acetylcholine protected
G. mellonella
larvae from
C. albicans
infection mortality. The
in vivo
protection occurred through acetylcholine enhancing the function of hemocytes while at the same time inhibiting
C. albicans
biofilm formation. Furthermore, acetylcholine also inhibited inflammation-induced damage to internal organs. This is the first demonstration of a role for acetylcholine in protection against fungal infections, in addition to being the first report that this molecule can inhibit
C. albicans
biofilm formation. Therefore, acetylcholine has the capacity to modulate complex host-fungal interactions and plays a role in dictating the pathogenesis of fungal infections.
Developmental Coordination of Gamete Differentiation with Programmed Cell Death in Sporulating Yeast
Authors: Eastwood Michael D. , Meneghini Marc D.
Published: June 2015

The gametogenesis program of the budding yeast
Saccharomyces cerevisiae
, also known as sporulation, employs unusual internal meiotic divisions, after which all four meiotic products differentiate within the parental cell. We showed previously that sporulation is typically accompanied by the destruction of discarded immature meiotic products through their exposure to proteases released from the mother cell vacuole, which undergoes an apparent programmed rupture. Here we demonstrate that vacuolar rupture contributes to
de facto
programmed cell death (PCD) of the meiotic mother cell itself. Meiotic mother cell PCD is accompanied by an accumulation of depolarized mitochondria, organelle swelling, altered plasma membrane characteristics, and cytoplasmic clearance. To ensure that the gametes survive the destructive consequences of developing within a cell that is executing PCD, we hypothesized that PCD is restrained from occurring until spores have attained a threshold degree of differentiation. Consistent with this hypothesis, gene deletions that perturb all but the most terminal postmeiotic spore developmental stages are associated with altered PCD. In these mutants, meiotic mother cells exhibit a delay in vacuolar rupture and then appear to undergo an alternative form of PCD associated with catastrophic consequences for the underdeveloped spores. Our findings reveal yeast sporulation as a context of bona fide PCD that is developmentally coordinated with gamete differentiation.
A patient-initiated voluntary online survey of adverse medical events: the perspective of 696 injured patients and families
Authors: Southwick Frederick S , Cranley Nicole M , Hallisy Julia A
Published: June 2015

Background

Preventable medical errors continue to be a major cause of death in the USA and throughout the world. Many patients have written about their experiences on websites and in published books.

Methods

As patients and family members who have experienced medical harm, we have created a nationwide voluntary survey in order to more broadly and systematically capture the perspective of patients and patient families experiencing adverse medical events and have used quantitative and qualitative analysis to summarise the responses of 696 patients and their families.

Results

Harm was most commonly associated with diagnostic and therapeutic errors, followed by surgical or procedural complications, hospital-associated infections and medication errors, and our quantitative results match those of previous provider-initiated patient surveys. Qualitative analysis of 450 narratives revealed a lack of perceived provider and system accountability, deficient and disrespectful communication and a failure of providers to listen as major themes. The consequences of adverse events included death, post-traumatic stress, financial hardship and permanent disability. These conditions and consequences led to a loss of patients’ trust in both the health system and providers. Patients and family members offered suggestions for preventing future adverse events and emphasised the importance of shared decision-making.

Conclusions

This large voluntary survey of medical harm highlights the potential efficacy of patient-initiated surveys for providing meaningful feedback and for guiding improvements in patient care.
Waiting time reduction in intravitreal clinics by optimization of appointment scheduling: balancing demand and supply
Authors: Ugarte Marta
Published: June 2015

This study was designed guided by the Model for Improvement framework to reduce waiting times and visit duration in the intravitreal therapy clinic, while improving patient and staff experience. In our aim to provide good quality, patient-centred care and constantly improve, we optimised the appointment profile and patient flow.

We involved a multidisciplinary team (one consultant, junior doctors, staff nurses, technicians, and receptionist), as well as patients and relatives, to try to understand the main delays in the clinic. Process mapping, a fishbone diagram, run charts, together with feedback from patients and staff, provided an insight on the possible roots of the delays experienced by our patients. The results of the inquiry led us to take actions focused on optimising appointment scheduling.

After implementing the new scheduling profile (with a gap in the middle of the session), various cycles of plan-do-study-act and a comparative, qualitative study by interviewing 10 patients demonstrated that the waiting times decreased, and patients and staff experience improved.
Evaluation of cell-line-derived xenograft tumours as controls for immunohistochemical testing for ER and PR
Authors: Hasan Tahrim , Carter Beverley , Denic Nash , Gai Luis , Power Jennifer , Voisey Kim , Kao K R
Published: June 2015

Quality control (QC) for immunohistochemistry (IHC) analysis routinely incorporates archived specimens for on-slide control material. We have assessed the utility of cell-line-derived xenograft (CDX) tumours for QC in breast estrogen receptor (ER) and progesterone receptor (PR) biomarker testing. Immunoblot and IHC analyses were used to select cell lines with different steady-state levels of ER and PR expression. CDX tumours all demonstrated consistent and comparable expression of ER and PR with corresponding cell lines from which they were derived. Three pathologists experienced in breast biomarker reporting scored tumours from different locations on mammary fat pads to determine reproducibility. Tumours from different locations were consistently scored as identical, and the CDX tumours representing different levels of biomarker expression were similar to patient-derived controls. Pathologists could not consistently distinguish CDX tumours from patient-derived controls, suggesting that within the appropriate quality management setting, CDX tumours may serve as control material for reporting purposes.
Does feeding zone influence egg size in slow-breeding seabirds?
Authors: Dobson F. Stephen , Jouventin Pierre
Published: June 2015

In several bird species, mothers that endow their eggs with additional resources benefit from more rapid development and more robust offspring. We examined egg size and associated life-history traits in 44 species of the slow-breeding procellariiform seabirds (albatrosses and petrels). The far distant foraging of some of the species should subject them to difficult ecological conditions and perhaps delays in return to the nest. Such delays might lead to poorer egg care by the remaining parent. To compensate, we predicted a positive association of egg size with foraging zone (offshore, near pelagic, far pelagic), and both with the length of incubation shifts. We tested this hypothesis and also examined egg size and fitness-related reproductive traits. Egg size scaled significantly and tightly with female body mass (β = 0.72, R2= 0.98). After influences of both size and phylogeny were removed, however, egg size was positively and significantly associated with both mean length of incubation shift and feeding zone (r = 0.45 and 0.46, respectively), perhaps indicating a life-history syndrome of egg size, incubation, and distance that species go to forage during the breeding season, and supporting the compensation hypothesis.
Ideas for Citizen Science in Astronomy
Authors: Marshall Philip J. , Lintott Chris J. , Fletcher Leigh N.
Published: June 2015

We review the expanding, internet-enabled, and rapidly evolving field of citizen astronomy, focusing on research projects in stellar, extragalactic, and planetary science that have benefited from the participation of members of the public. These volunteers contribute in various ways: making and analyzing new observations, visually classifying features in images and light curves, exploring models constrained by astronomical data sets, and initiating new scientific enquiries. The most productive citizen astronomy projects involve close collaboration between the professionals and amateurs involved and occupy scientific niches not easily filled by great observatories or machine learning methods: Citizen astronomers are motivated by being of service to science, as well as by their interest in the subject. We expect participation and productivity in citizen astronomy to increase, as data sets get larger and citizen science platforms become more efficient. Opportunities include engaging citizens in ever-more advanced analyses and facilitating citizen-led enquiry through professional tools designed with citizens in mind.
The Occurrence and Architecture of Exoplanetary Systems
Authors: Winn Joshua N. , Fabrycky Daniel C.
Published: June 2015

The basic geometry of the Solar System—the shapes, spacings, and orientations of the planetary orbits—has long been a subject of fascination as well as inspiration for planet-formation theories. For exoplanetary systems, those same properties have only recently come into focus. Here we review our current knowledge of the occurrence of planets around other stars, their orbital distances and eccentricities, the orbital spacings and mutual inclinations in multiplanet systems, the orientation of the host star's rotation axis, and the properties of planets in binary-star systems.
Revisiting the Unified Model of Active Galactic Nuclei
Authors: Netzer Hagai
Published: June 2015

This review describes recent developments related to the unified model of active galactic nuclei (AGNs). It focuses on new ideas about the origin and properties of the central obscurer (torus) and the connection to its surroundings. The review does not address radio unification. AGN tori must be clumpy but uncertainties about their properties persist. Today's most promising models involve disk winds of various types and hydrodynamic simulations that link the large-scale galactic disk to the inner accretion flow. Infrared (IR) studies greatly improved our understanding of the spectral energy distribution of AGNs, but they are hindered by various selection effects. X-ray samples are more complete. The dependence of the covering factor of the torus on luminosity is a basic relationship that remains unexplained. There is also much confusion regarding real type-II AGNs, which do not fit into a simple unification scheme. The most impressive recent results are due to IR interferometry, which is not in accord with most torus models, and the accurate mapping of central ionization cones. AGN unification may not apply to merging systems and is possibly restricted to secularly evolving galaxies.
Grid-Based Hydrodynamics in Astrophysical Fluid Flows
Authors: Teyssier Romain
Published: June 2015

In this review, the equations of hydrodynamics, magnetohydrodynamics, and radiation hydrodynamics are presented, together with their corresponding nonideal source terms. I overview the current landscape of modern grid-based numerical techniques with an emphasis on numerical diffusion, which plays a fundamental role in stabilizing the solution but is also the main source of errors associated with these numerical techniques. I discuss in great detail the inclusion of additional important source terms, such as cooling and gravity. I also show how to modify classic operator-splitting techniques to avoid undesirable numerical errors associated with these additional source terms, in particular in the presence of highly supersonic flows. I finally present various mesh adaptation strategies that can be used to minimize these numerical errors. To conclude, I review existing astrophysical software that is publicly available to perform simulations for such astrophysical fluids.
Visible/Infrared Imaging Spectroscopy and Energy-Resolving Detectors
Authors: Eisenhauer Frank , Raab Walfried
Published: June 2015

Imaging spectroscopy has seen rapid progress over the past 25 years, leading to breakthroughs in many fields of astronomy that would not have been otherwise possible. This review overviews the visible/infrared imaging spectroscopy techniques as well as energy-resolving detectors. We introduce the working principle of scanning Fabry-Perot and Fourier transform spectrometers and explain the most common integral field concepts based on mirror slicers, lenslet arrays, and fibers. The main advantage of integral field spectrographs is the simultaneous measurement of spatial and spectral information. Although Fabry-Perot and Fourier transform spectrometers can provide a larger field of view, it is ultimately the higher sensitivity of integral field units that make them the technique of choice. This is arguably the case for image slicers, which make the most efficient use of the available detector pixels and have equal or higher transmission than lenslet arrays and fiber integral field units, respectively. We also address the more specific issues of large étendue operation, focal ratio degradation, anamorphic magnification, and diffraction-limited operation. This review also covers the emerging technology of energy-resolving detectors, which promise very simple and efficient instrument designs. These energy-resolving detectors are based on superconducting thin film technology and exploit either the very small superconducting energy to count the number of quasi-particles excited in the absorption of the photon or the extremely steep phase transition between the normal- and superconducting phase to measure a temperature increase. We have put special emphasis on an overview of the underlying physical phenomena as well as on the recent technological progress and astronomical path finder experiments.