bluuebunny/crossref_metadata_2025 huggingface dataset:
Meteorite fusion crust variability
Authors: THAISEN Kevin G. , TAYLOR Lawrence A.
Published: January 2010

Abstract— Two assumptions commonly employed in meteorite interpretation are that fusion crust compositions represent the bulk‐rock chemistry of the interior meteorite and that the vesicles within the fusion crust result from the release of implanted solar wind volatiles. Electron microprobe analyses of thin sections from lunar meteorite Miller Range (MIL) 05035 and eucrite Bates Nunataks (BTN) 00300 were performed to determine if the chemical compositions of the fusion crust varied and/or represented the published bulk rock composition.

It was determined that fusion crust compositions are significantly influenced by the incorporation of fragments from the substrate, and by the composition and grain size of those minerals. Because of compositional heterogeneities throughout the meteorite, one cannot assume that fusion crust composition represents the bulk rock composition. If the compositional variability within the fusion crust and mineralogical differences among thin sections goes unnoticed, then the perceived composition and petrogenetic models of formation will be incorrect.

The formation of vesicles within these fusion crusts were also compared to current theories attributing vesicles to a solar wind origin. Previous work from the STONE‐5 experiment, where terrestrial rocks were exposed on the exterior of a spacecraft heatshield, produced a vesicular fusion crust without prolonged exposure to solar wind suggesting that the high temperatures experienced by a meteorite during passage through the Earth's atmosphere are sufficient to cause boiling of the melt. Therefore, the assumption that all vesicles found within a fusion crust are due to the release of implanted volatiles of solar wind may not be justified.
Organic matter from comet 81P/Wild 2, IDPs, and carbonaceous meteorites; similarities and differences
Authors: Wirick S. , Flynn G. J. , Keller L. P. , Nakamura‐Messenger K. , Peltzer C. , Jacobsen C. , Sandford S. , Zolensky M.
Published: January 2010

Abstract— During preliminary examination of 81P/Wild 2 particles collected by the NASA Stardust spacecraft, we analyzed seven, sulfur embedded and ultramicrotomed particles extracted from five different tracks. Sections were analyzed using a scanning transmission X‐ray microscope (SXTM) and carbon X‐ray absorption near edge structure (XANES) spectra were collected. We compared the carbon XANES spectra of these Wild 2 samples with a database of spectra on thirty‐four interplanetary dust particles (IDPs) and with several meteorites. Two of the particles analyzed are iron sulfides and there is evidence that an aliphatic compound associated with these particles can survive high temperatures. An iron sulfide from an IDP demonstrates the same phenomenon. Another, mostly carbon free containing particle radiation damaged, something we have not observed in any IDPs we have analyzed or any indigenous organic matter from the carbonaceous meteorites, Tagish Lake, Orgueil, Bells and Murchison. The carbonaceous material associated with this particle showed no mass loss during the initial analysis but chemically changed over a period of two months. The carbon XANES spectra of the other four particles varied more than spectra from IDPs and indigenous organic matter from meteorites. Comparison of the carbon XANES spectra from these particles with 1. the carbon XANES spectra from thirty‐four IDPs (<15 micron in size) and 2. the carbon XANES spectra from carbonaceous material from the Tagish Lake, Orgueil, Bells, and Murchison meteorites show that 81P/Wild 2 carbon XANES spectra are more similar to IDP carbon XANES spectra then to the carbon XANES spectra of meteorites.
Formation age of the lunar crater Giordano Bruno
Authors: Morota Tomokatsu , Haruyama Junichi , Miyamoto Hideaki , Honda Chikatoshi , Ohtake Makiko , Yokota Yasuhiro , Matsunaga Tsuneo , Hirata Naru , Demura Hirohide , Takeda Hiroshi , Ogawa Yoshiko , Kimura Jun
Published: January 2010

Abstract— Using the Terrain Camera onboard the Japanese lunar explorer, SELENE (Kaguya), we obtained new high‐resolution images of the 22‐kilometer‐diameter lunar crater Giordano Bruno. Based on crater size‐frequency measurements of small craters (<200 m in diameter) superposed on its continuous ejecta, the formation age of Giordano Bruno is estimated to be 1 to 10 Ma. This is constructive evidence against the crater's medieval age formation hypothesis.
Symmetric Inertial Confinement Fusion Implosions at Ultra-High Laser Energies
Authors: Glenzer S. H. , MacGowan B. J. , Michel P. , Meezan N. B. , Suter L. J. , Dixit S. N. , Kline J. L. , Kyrala G. A. , Bradley D. K. , Callahan D. A. , Dewald E. L. , Divol L. , Dzenitis E. , Edwards M. J. , Hamza A. V. , Haynam C. A. , Hinkel D. E. , Kalantar D. H. , Kilkenny J. D. , Landen O. L. , Lindl J. D. , LePape S. , Moody J. D. , Nikroo A. , Parham T. , Schneider M. B. , Town R. P. J. , Wegner P. , Widmann K. , Whitman P. , Young B. K. F. , Van Wonterghem B. , Atherton L. J. , Moses E. I.
Published: January 2010

Ignition Set to Go

One aim of the National Ignition Facility is to implode a capsule containing a deuterium-tritium fuel mix and initiate a fusion reaction. With 192 intense laser beams focused into a centimeter-scale cavity, a major challenge has been to create a symmetric implosion and the necessary temperatures within the cavity for ignition to be realized (see the Perspective by

Norreys

).

Glenzer
et al.

(p.
1228
, published online 28 January) now show that these conditions can be met, paving the way for the next step of igniting a fuel-filled capsule. Furthermore,

Li
et al.

(p.
1231
, published online 28 January) show how charged particles can be used to characterize and measure the conditions within the imploding capsule. The high energies and temperature realized can also be used to model astrophysical and other extreme energy processes in a laboratory settings.
Expansion of Genetic Diversity in Randomly Mating Founder Populations ofAlternaria brassicicolaInfectingCakile maritimain Australia
Authors: Linde C. C. , Liles J. A. , Thrall P. H.
Published: January 2010

Founder populations of fungal plant pathogens are expected to have low levels of genetic diversity coupled with further genetic drift due to, e.g., limited host availability, which should result in additional population bottlenecks. This study used microsatellite markers in the interaction betweenCakile maritimaand the fungal pathogenAlternaria brassicicolato explore genetic expectations associated with such situations. The host,C. maritima, was introduced into Australia approximately 100 years ago, but it is unknown whether the pathogen was already present in Australia, as it has a wide occurrence, or whether it was introduced to Australia on brassicaceous hosts. ElevenA. brassicicolapopulations were studied, and all showed moderate levels of gene and genotypic diversity. Chi-square tests of the frequencies of mating type alleles, a large number of genotypes, and linkage equilibrium among microsatellite loci all suggestA. brassicicolareproduces sexually. Significant genetic differentiation was found among populations, but there was no evidence for isolation by distance effects. Bayesian analyses identified eight clusters where the inferred clusters did not represent geographical populations but instead consisted of individuals admixed from all populations. Further analysis indicated that fungal populations were more likely to have experienced a recent population expansion than a population bottleneck. It is suggested thatA. brassicicolahas been introduced into Australia multiple times, potentially increasing the diversity and size of anyA. brassicolapopulations already present there. Combined with its ability to reproduce sexually, such processes appear to have increased the evolutionary potential of the pathogen through recent population expansions.
Girdling Affects Ectomycorrhizal Fungal (EMF) Diversity and Reveals Functional Differences in EMF Community Composition in a Beech Forest
Authors: Pena Rodica , Offermann Christine , Simon Judy , Naumann Pascale Sarah , Geßler Arthur , Holst Jutta , Dannenmann Michael , Mayer Helmut , Kögel-Knabner Ingrid , Rennenberg Heinz , Polle Andrea
Published: January 2010

The relationships between plant carbon resources, soil carbon and nitrogen content, and ectomycorrhizal fungal (EMF) diversity in a monospecific, old-growth beech (
Fagus sylvatica
) forest were investigated by manipulating carbon flux by girdling. We hypothesized that disruption of the carbon supply would not affect diversity and EMF species numbers if EM fungi can be supplied by plant internal carbohydrate resources or would result in selective disappearance of EMF taxa because of differences in carbon demand of different fungi. Tree carbohydrate status, root demography, EMF colonization, and EMF taxon abundance were measured repeatedly during 1 year after girdling. Girdling did not affect root colonization but decreased EMF species richness of an estimated 79 to 90 taxa to about 40 taxa.
Cenococcum geophilum
,
Lactarius blennius
, and
Tomentella lapida
were dominant, colonizing about 70% of the root tips, and remained unaffected by girdling. Mainly cryptic EMF species disappeared. Therefore, the Shannon-Wiener index (
H
′) decreased but evenness was unaffected.
H
′ was positively correlated with glucose, fructose, and starch concentrations of fine roots and also with the ratio of dissolved organic carbon to dissolved organic nitrogen (DOC/DON), suggesting that both
H
′ and DOC/DON were governed by changes in belowground carbon allocation. Our results suggest that beech maintains numerous rare EMF species by recent photosynthate. These EM fungi may constitute biological insurance for adaptation to changing environmental conditions. The preservation of taxa previously not known to colonize beech may, thus, form an important reservoir for future forest development.
Agreement, Precision, and Accuracy of Epifluorescence Microscopy Methods for Enumeration of Total Bacterial Numbers
Authors: Seo Eun-Young , Ahn Tae-Seok , Zo Young-Gun
Published: January 2010

To assess interchangeability of estimates of bacterial abundance by different epifluorescence microscopy methods, total bacterial numbers (TBNs) determined by most widely accepted protocols were statistically compared. Bacteria in a set of distinctive samples were stained with acridine orange (AO), 4′-6-diamidino-2-phenylindole (DAPI), and BacLight and enumerated by visual counting (VC) and supervised image analysis (IA). Model II regression and Bland-Altman analysis proved general agreements between IA and VC methods, although IA counts tended to be lower than VC counts by 7% on a logarithmic scale. Distributions of cells and latex beads on polycarbonate filters were best fitted to negative binomial models rather than to Poisson or log-normal models. The fitted models revealed higher precisions of TBNs by the IA method than those by the VC method. In pairwise comparisons of the staining methods, TBNs by AO and BacLight staining showed good agreement with each other, but DAPI staining had tendencies of underestimation. Although precisions of the three staining methods were comparable to one another (intraclass correlation coefficients, 0.97 to 0.98), accuracy of the DAPI staining method was rebutted by disproportionateness of TBNs between pairs of samples that carried 2-fold different volumes of identical cell suspensions. It was concluded that the TBN values estimated by AO and BacLight staining are relatively accurate and interchangeable for quantitative interpretation and that IA provides better precision than does VC. As a prudent measure, it is suggested to avoid use of DAPI staining for comparative studies investigating accuracy of novel cell-counting methods.
Expanded Multilocus Sequence Typing and Comparative Genomic Hybridization of
Campylobacter coli
Isolates from Multiple Hosts
Authors: Lang Ping , Lefebure Tristan , Wang Wei , Pavinski Bitar Paulina , Meinersmann Richard J. , Kaya Katherine , Stanhope Michael J.
Published: January 2010

The purpose of this work was to evaluate the evolutionary history of
Campylobacter coli
isolates derived from multiple host sources and to use microarray comparative genomic hybridization to assess whether there are particular genes comprising the dispensable portion of the genome that are more commonly associated with certain host species. Genotyping and ClonalFrame analyses of an expanded 16-gene multilocus sequence typing (MLST) data set involving 85 isolates from 4 different hosts species tentatively supported the development of
C. coli
host-preferred groups and suggested that recombination has played various roles in their diversification; however, geography could not be excluded as a contributing factor underlying the history of some of the groups. Population genetic analyses of the
C. coli
pubMLST database by use of STRUCTURE suggested that isolates from swine form a relatively homogeneous genetic group, that chicken and human isolates show considerable genetic overlap, that isolates from ducks and wild birds have similarity with environmental water samples and that turkey isolates have a connection with human infection similar to that observed for chickens. Analysis of molecular variance (AMOVA) was performed on these same data and suggested that host species was a significant factor in explaining genetic variation and that macrogeography (North America, Europe, and the United Kingdom) was not. The microarray comparative genomic hybridization data suggested that there were combinations of genes more commonly associated with isolates derived from particular hosts and, combined with the results on evolutionary history, suggest that this is due to a combination of common ancestry in some cases and lateral gene transfer in others.
Quantitative Assessment of Ammonia-Oxidizing Bacterial Communities in the Epiphyton of Submerged Macrophytes in Shallow Lakes
Authors: Coci M. , Nicol G. W. , Pilloni G. N. , Schmid M. , Kamst-van Agterveld M. P. , Bodelier P. L. E. , Laanbroek H. J.
Published: January 2010

In addition to the benthic and pelagic habitats, the epiphytic compartment of submerged macrophytes in shallow freshwater lakes offers a niche to bacterial ammonia-oxidizing communities. However, the diversity, numbers, and activity of epiphytic ammonia-oxidizing bacteria have long been overlooked. In the present study, we analyzed quantitatively the epiphytic communities of three shallow lakes by a potential nitrification assay and by quantitative PCR of 16S rRNA genes. On the basis of the m
2
of the lake surface, the gene copy numbers of epiphytic ammonia oxidizers were not significantly different from those in the benthic and pelagic compartments. The potential ammonia-oxidizing activities measured in the epiphytic compartment were also not significantly different from the activities determined in the benthic compartment. No potential ammonia-oxidizing activities were observed in the pelagic compartment. No activity was detected in the epiphyton of
Chara aspera
, the dominant submerged macrophyte in Lake Nuldernauw in The Netherlands. The presence of ammonia-oxidizing bacterial cells in the epiphyton of
Potamogeton pectinatus
was also demonstrated by fluorescent
in situ
hybridization microscopy images. By comparing the community composition as assessed by the 16S rRNA gene PCR-denaturing gradient gel electrophoresis approach, it was concluded that the epiphytic ammonia-oxidizing communities consisted of cells that were also present in the benthic and pelagic compartments. Of the environmental parameters examined, only the water retention time, the Kjeldahl nitrogen content, and the total phosphorus content correlated with potential ammonia-oxidizing activities. None of these parameters correlated with the numbers of gene copies related to ammonia-oxidizing betaproteobacteria.
Inhibition of the Early Stage of
Salmonella enterica
Serovar Enteritidis Biofilm Development on Stainless Steel by Cell-Free Supernatant of a
Hafnia alvei
Culture
Authors: Chorianopoulos Nikos G. , Giaouris Efstathios D. , Kourkoutas Yiannis , Nychas George-John E.
Published: January 2010

Compounds present in
Hafnia alvei
cell-free culture supernatant cumulatively negatively influence the early stage of biofilm development by
Salmonella enterica
serovar Enteritidis on stainless steel while they also reduce the overall metabolic activity of
S
. Enteritidis planktonic cells. Although acylhomoserine lactones (AHLs) were detected among these compounds, the use of several synthetic AHLs was not able to affect the initial stage of biofilm formation by this pathogen.
Bacterial Symbionts of the Brown Planthopper,Nilaparvata lugens(Homoptera: Delphacidae)
Authors: Tang Ming , Lv Lu , Jing Shengli , Zhu Lili , He Guangcun
Published: January 2010

The brown planthopper (Nilaparvata lugensStål), the most destructive pest of rice, has been identified, including biotypes with high virulence towards previously resistant rice varieties. There have also been many reports of a yeast-like symbiont ofN. lugens, but little is known about the bacterial microbes. In this study, we examined the bacterial microbes inN. lugensand identified a total of 18 operational taxonomic units (OTUs) representing four phyla (Proteobacteria,Firmicutes,Actinobacteria, andBacteroidetes) by sequencing and analyzing 16S rRNA gene libraries obtained from three populations ofN. lugens, which were maintained on the rice varieties TN1, Mudgo, and ASD7. Several of the OTUs were similar to previously reported secondary symbionts of other insects, including an endosymbiont of the psyllidGlycapsis brimblecombei, anAsaiasp. found in the mosquitoAnopheles stephensi, andWolbachia, found in the miteMetaseiulus occidentalis. However, the species and numbers of the detected OTUs differed substantially among theN. lugenspopulations. Further,in situhybridization analysis using digoxigenin-labeled probes indicated that OTU 1 was located in hypogastrium tissues near the ovipositor and ovary in biotype 1 insects, while OTU 2 was located in the front of the ovipositor sheath in biotype 2 insects. In addition, masses of bacterium-like organisms were observed in the tubes of salivary sheaths in rice plant tissues that the insects had fed upon. The results provide indications of the diversity of the bacterial microbes harbored by the brown planthopper and of possible associations between specific bacterial microbes and biotypes ofN. lugens.
Significance of Wall Structure, Macromolecular Composition, and Surface Polymers to the Survival and Transport of
Cryptosporidium parvum
Oocysts
Authors: Jenkins Michael B. , Eaglesham Barbara S. , Anthony Larry C. , Kachlany Scott C. , Bowman Dwight D. , Ghiorse William C.
Published: January 2010

The structure and composition of the oocyst wall are primary factors determining the survival and hydrologic transport of
Cryptosporidium parvum
oocysts outside the host. Microscopic and biochemical analyses of whole oocysts and purified oocyst walls were undertaken to better understand the inactivation kinetics and hydrologic transport of oocysts in terrestrial and aquatic environments. Results of microscopy showed an outer electron-dense layer, a translucent middle layer, two inner electron-dense layers, and a suture structure embedded in the inner electron-dense layers. Freeze-substitution showed an expanded glycocalyx layer external to the outer bilayer, and Alcian Blue staining confirmed its presence on some but not all oocysts. Biochemical analyses of purified oocyst walls revealed carbohydrate components, medium- and long-chain fatty acids, and aliphatic hydrocarbons. Purified walls contained 7.5% total protein (by the Lowry assay), with five major bands in SDS-PAGE gels. Staining of purified oocyst walls with magnesium anilinonaphthalene-8-sulfonic acid indicated the presence of hydrophobic proteins. These structural and biochemical analyses support a model of the oocyst wall that is variably impermeable and resistant to many environmental pressures. The strength and flexibility of oocyst walls appear to depend on an inner layer of glycoprotein. The temperature-dependent permeability of oocyst walls may be associated with waxy hydrocarbons in the electron-translucent layer. The complex chemistry of these layers may explain the known acid-fast staining properties of oocysts, as well as some of the survival characteristics of oocysts in terrestrial and aquatic environments. The outer glycocalyx surface layer provides immunogenicity and attachment possibilities, and its ephemeral nature may explain the variable surface properties noted in oocyst hydrologic transport studies.
Effects of Trp- and Arg-Containing Antimicrobial-Peptide Structure on Inhibition of
Escherichia coli
Planktonic Growth and Biofilm Formation
Authors: Hou Shuyu , Liu Zhigang , Young Anne W. , Mark Sheron L. , Kallenbach Neville R. , Ren Dacheng
Published: January 2010

Biofilms are sessile microbial communities that cause serious chronic infections with high morbidity and mortality. In order to develop more effective approaches for biofilm control, a series of linear cationic antimicrobial peptides (AMPs) with various arginine (Arg or R) and tryptophan (Trp or W) repeats [(RW)

n

-NH
2
, where
n
= 2, 3, or 4] were rigorously compared to correlate their structures with antimicrobial activities affecting the planktonic growth and biofilm formation of
Escherichia coli
. The chain length of AMPs appears to be important for inhibition of bacterial planktonic growth, since the hexameric and octameric peptides significantly inhibited
E. coli
growth, while tetrameric peptide did not cause noticeable inhibition. In addition, all AMPs except the tetrameric peptide significantly reduced
E. coli
biofilm surface coverage and the viability of biofilm cells, when added at inoculation. In addition to inhibition of biofilm formation, significant killing of biofilm cells was observed after a 3-hour treatment of preformed biofilms with hexameric peptide. Interestingly, treatment with the octameric peptide caused significant biofilm dispersion without apparent killing of biofilm cells that remained on the surface; e.g., the surface coverage was reduced by 91.5 ± 3.5% by 200 μM octameric peptide. The detached biofilm cells, however, were effectively killed by this peptide. Overall, these results suggest that hexameric and octameric peptides are potent inhibitors of both bacterial planktonic growth and biofilm formation, while the octameric peptide can also disperse existing biofilms and kill the detached cells. These results are helpful for designing novel biofilm inhibitors and developing more effective therapeutic methods.
Anaerobic Digestion of Renewable Biomass: Thermophilic Temperature Governs Methanogen Population Dynamics
Authors: Krakat Niclas , Westphal A. , Schmidt S. , Scherer P.
Published: January 2010

Beet silage and beet juice were digested continuously as representative energy crops in a thermophilic biogas fermentor for more than 7 years. Fluorescence microscopy of 15 samples covering a period of 650 days revealed that a decrease in temperature from 60°C to 55°C converted a morphologically uniform archaeal population (rods) into a population of methanogens exhibiting different cellular morphologies (rods and coccoid cells). A subsequent temperature increase back to 60°C reestablished the uniform morphology of methanogens observed in the previous 60°C period. In order to verify these observations, representative samples were investigated by amplified rRNA gene restriction analysis (ARDRA) and fluorescence in situ hybridization (FISH). Both methods confirmed the temperature-dependent population shift observed by fluorescence microscopy. Moreover, all samples investigated demonstrated that hydrogenotrophic
Methanobacteriales
dominated in the fermentor, as 29 of 34 identified operational taxonomic units (OTUs) were assigned to this order. This apparent discrimination of acetoclastic methanogens contradicts common models for anaerobic digestion processes, such as anaerobic digestion model 1 (ADM1), which describes the acetotrophic
Euryarchaeota
as predominant organisms.
Microbial Community Analysis of Anodes from Sediment Microbial Fuel Cells Powered by Rhizodeposits of Living Rice Plants
Authors: De Schamphelaire Liesje , Cabezas Angela , Marzorati Massimo , Friedrich Michael W. , Boon Nico , Verstraete Willy
Published: January 2010

By placing the anode of a sediment microbial fuel cell (SMFC) in the rhizosphere of a rice plant, root-excreted rhizodeposits can be microbially oxidized with concomitant current generation. Here, various molecular techniques were used to characterize the composition of bacterial and archaeal communities on such anodes, as influenced by electrical circuitry, sediment matrix, and the presence of plants. Closed-circuit anodes in potting soil were enriched with
Desulfobulbus
-like species, members of the family
Geobacteraceae
, and as yet uncultured representatives of the domain
Archaea
.
The Carnivorous Pale Pitcher Plant Harbors Diverse, Distinct, and Time-Dependent Bacterial Communities
Authors: Koopman Margaret M. , Fuselier Danielle M. , Hird Sarah , Carstens Bryan C.
Published: January 2010

The ability of American carnivorous pitcher plants (
Sarracenia
) to digest insect prey is facilitated by microbial associations. Knowledge of the details surrounding this interaction has been limited by our capability to characterize bacterial diversity in this system. To describe microbial diversity within and between pitchers of one species,
Sarracenia alata
, and to explore how these communities change over time as pitchers accumulate and digest insect prey, we collected and analyzed environmental sequence tag (454 pyrosequencing) and genomic fingerprint (automated ribosomal intergenic spacer analysis and terminal restriction fragment length polymorphism) data. Microbial richness associated with pitcher plant fluid is high; more than 1,000 unique phylogroups were identified across at least seven phyla and 50 families. We documented an increase in bacterial diversity and abundance with time and observed repeated changes in bacterial community composition. Pitchers from different plants harbored significantly more similar bacterial communities at a given time point than communities coming from the same genetic host over time. The microbial communities in pitcher plant fluid also differ significantly from those present in the surrounding soil. These findings indicate that the bacteria associated with pitcher plant leaves are far from random assemblages and represent an important step toward understanding this unique plant-microbe interaction.
Use of Fatty Acid Methyl Ester Profiles for Discrimination ofBacillus cereusT-Strain Spores Grown on Different Media
Authors: Ehrhardt Christopher J. , Chu Vivian , Brown TeeCie , Simmons Terrie L. , Swan Brandon K. , Bannan Jason , Robertson James M.
Published: January 2010

The goal of this study was to determine if cellular fatty acid methyl ester (FAME) profiling could be used to distinguish among spore samples from a single species (Bacillus cereusT strain) that were prepared on 10 different medium formulations. To analyze profile differences and identify FAME biomarkers diagnostic for the chemical constituents in each sporulation medium, a variety of statistical techniques were used, including nonmetric multidimensional scaling (nMDS), analysis of similarities (ANOSIM), and discriminant function analysis (DFA). The results showed that one FAME biomarker, oleic acid (18:1 ω9c), was exclusively associated with spores grown on Columbia agar supplemented with sheep blood and was indicative of blood supplements that were present in the sporulation medium. For spores grown in other formulations, multivariate comparisons across several FAME biomarkers were required to discern profile differences. Clustering patterns in nMDS plots andRvalues from ANOSIM revealed that dissimilarities among FAME profiles were most pronounced when spores grown with disparate sources of complex additives or protein supplements were compared (R> 0.8), although other factors also contributed to FAME differences. DFA indicated that differentiation could be maximized with a targeted subset of FAME variables, and the relative contributions of branched FAME biomarkers to group dissimilarities changed when different media were compared. When taken together, these analyses indicate thatB. cereusspore samples grown in different media can be resolved with FAME profiling and that this may be a useful technique for providing intelligence about the production methods ofBacillusorganisms in a forensic investigation.
Rapid Assessment of the Viability of
Mycobacterium avium
subsp.
paratuberculosis
Cells after Heat Treatment, Using an Optimized Phage Amplification Assay
Authors: Foddai Antonio , Elliott Christopher T. , Grant Irene R.
Published: January 2010

Thermal inactivation experiments were carried out to assess the utility of a recently optimized phage amplification assay to accurately enumerate viable
Mycobacterium avium
subsp.
paratuberculosis
cells in milk. Ultra-heat-treated (UHT) whole milk was spiked with large numbers of
M. avium
subsp.
paratuberculosis
organisms (10
6
to 10
7
CFU/ml) and dispensed in 100-μl aliquots in thin-walled 200-μl PCR tubes. A Primus 96 advanced thermal cycler (Peqlab, Erlangen, Germany) was used to achieve the following time and temperature treatments: (i) 63°C for 3, 6, and 9 min; (ii) 68°C for 20, 40, and 60 s; and (iii) 72°C for 5, 10, 15, and 25 s. After thermal stress, the number of surviving
M. avium
subsp.
paratuberculosis
cells was assessed by both phage amplification assay and culture on Herrold's egg yolk medium (HEYM). A high correlation between PFU/ml and CFU/ml counts was observed for both unheated (
r
2
= 0.943) and heated (
r
2
= 0.971)
M. avium
subsp.
paratuberculosis
cells.
D
and
z
values obtained using the two types of counts were not significantly different (
P
> 0.05). The
D
68°C
, mean
D
63°C
, and
D
72°C
for four
M. avium
subsp.
paratuberculosis
strains were 81.8, 9.8, and 4.2 s, respectively, yielding a mean
z
value of 6.9°C. Complete inactivation of 10
6
to 10
7
CFU of
M. avium
subsp.
paratuberculosis
/ml milk was not observed for any of the time-temperature combinations studied; 5.2- to 6.6-log
10
reductions in numbers were achieved depending on the temperature and time. Nonlinear thermal inactivation kinetics were consistently observed for this bacterium. This study confirms that the optimized phage assay can be employed in place of conventional culture on HEYM to speed up the acquisition of results (48 h instead of a minimum of 6 weeks) for inactivation experiments involving
M. avium
subsp.
paratuberculosis
-spiked samples.
Development and Application of a PCR-Targeted Gene Disruption Method for Studying CelR Function in
Thermobifida fusca
Authors: Deng Yu , Fong Stephen S.
Published: January 2010

Thermobifida fusca
is a high-G+C-content, thermophilic, Gram-positive soil actinobacterium with high cellulolytic activity. In
T. fusca
, CelR is thought to act as the primary regulator of cellulase gene expression by binding to a 14-bp inverted repeat [5′-(T)GGGAGCGCTCCC(A)] that is upstream of many known cellulase genes. Previously, the ability to study the roles and regulation of cellulase genes in
T. fusca
has been limited largely by a lack of established genetic engineering methods for
T. fusca
. In this study, we developed an efficient procedure for creating precise chromosomal gene disruptions and demonstrated this procedure by generating a
celR
deletion strain. The
celR
deletion strain was then characterized using measurements for growth behavior, cellulase activity, and gene expression. The
celR
deletion strain of
T. fusca
exhibited a severely crippled growth phenotype with a prolonged lag phase and decreased cell yields for growth on both glucose and cellobiose. While the maximum endoglucanase activity and cellulase activity were not significantly changed, the endoglucanase activity and cellulase activity per cell were highly elevated. Measurements of mRNA transcript levels in both the
celR
deletion strain and the wild-type strain indicated that the CelR protein potentially acts as a repressor for some genes and as an activator for other genes. Overall, we established and demonstrated a method for manipulating chromosomal DNA in
T. fusca
that can be used to study the cellulolytic capabilities of this organism. Components of this method may be useful in developing genetic engineering methods for other currently intractable organisms.
Improved Strains and Plasmid Vectors for Conditional Overexpression of His-Tagged Proteins in
Haloferax volcanii
Authors: Allers Thorsten , Barak Shahar , Liddell Susan , Wardell Kayleigh , Mevarech Moshe
Published: January 2010

Research into archaea will not achieve its full potential until systems are in place to carry out genetics and biochemistry in the same species.
Haloferax volcanii
is widely regarded as the best-equipped organism for archaeal genetics, but the development of tools for the expression and purification of
H. volcanii
proteins has been neglected. We have developed a series of plasmid vectors and host strains for conditional overexpression of halophilic proteins in
H. volcanii
. The plasmids feature the tryptophan-inducible p.
tnaA
promoter and a 6×His tag for protein purification by metal affinity chromatography. Purification is facilitated by host strains, where
pitA
is replaced by the ortholog from
Natronomonas pharaonis
. The latter lacks the histidine-rich linker region found in
H. volcanii
PitA and does not copurify with His-tagged recombinant proteins. We also deleted the
mrr
restriction endonuclease gene, thereby allowing direct transformation without the need to passage DNA through an
Escherichia coli dam
mutant.
Dependence of Continuous-Flow Biofilm Formation by
Listeria monocytogenes
EGD-e on SOS Response Factor YneA
Authors: van der Veen Stijn , Abee Tjakko
Published: January 2010

Listeria monocytogenes
was previously shown to form biofilms composed of a network of knitted chains under continuous-flow conditions. Here we show that the SOS response is activated under these conditions and that deletion of its regulon member
yneA
results in diminished biofilm formation under continuous-flow conditions.
d
-Xylose as a Repressor or Inducer of Xylanase Expression in
Hypocrea jecorina
(
Trichoderma reesei
)
Authors: Mach-Aigner Astrid R. , Pucher Marion E. , Mach Robert L.
Published: January 2010

For
Hypocrea jecorina
(anamorph
Trichoderma reesei
), a filamentous fungus used for hydrolase production in different industries, it has been a long-term practice to use
d
-xylose as an inducing substance. We demonstrate in this study that the degree of xylanase-encoding gene induction strictly depends on the concentration of
d
-xylose, which was found to be optimal from 0.5 to 1 mM for 3 h of cultivation. At higher concentrations of
d
-xylose, a reduced level of xylanase gene expression was observed. In the present study, we also provide evidence that the
d
-xylose concentration-dependent induction is antagonized by carbon catabolite repressor 1. This repressor mediates its influence on
d
-xylose indirectly, by reducing the expression of xylanase regulator 1, the main activator of most hydrolase-encoding genes. Additionally, a direct influence of the repressor on xylanase 1 expression in the presence of
d
-xylose was found. Furthermore, we show that
d
-xylose reductase 1 is needed to metabolize
d
-xylose to achieve full induction of xylanase expression. Finally, a strain which expresses xylanase regulator 1 at a constant level was used to partially overcome the negative influence exerted by carbon catabolite repressor 1 on
d
-xylose.
Molecular Characterization of Sewage-Borne Pathogens and Detection of Sewage Markers in an Urban Stream in Caracas, Venezuela
Authors: Betancourt W. Q. , Querales L. , Sulbaran Y. F. , Rodriguez-Diaz J. , Caraballo L. , Pujol F. H.
Published: January 2010

Molecular characterization of two sewage-borne pathogens identified hepatitis A virus (HAV) subgenotype IA and
Giardia duodenalis
assemblages A and B as predominant genotypes circulating in an urban area of Venezuela. This study reveals epidemiological features of human pathogens of worldwide distribution and the efficacy of molecular methods for accurate assessment of sewage pollution.
Polymorphic Mutation Frequencies of Clinical and Environmental
Stenotrophomonas maltophilia
Populations
Authors: Turrientes María Carmen , Baquero María Rosario , Sánchez María Blanca , Valdezate Sylvia , Escudero Esther , Berg Gabrielle , Cantón Rafael , Baquero Fernando , Galán Juan Carlos , Martínez José Luis
Published: January 2010

Mutation frequencies were studied in 174
Stenotrophomonas maltophilia
isolates from clinical and nonclinical environments by detecting spontaneous rifampin-resistant mutants in otherwise-susceptible populations. The distribution of mutation frequencies followed a pattern similar to that found for other bacterial species, with a modal value of 1 × 10
−8
. Nevertheless, the proportion of isolates showing mutation frequencies below the modal value (hypomutators) was significantly higher for
S. maltophilia
than those so far reported in other organisms. Low mutation frequencies were particularly frequent among environmental
S. maltophilia
strains (58.3%), whereas strong mutators were found only among isolates with a clinical origin. These results indicate that clinical environments might select bacterial populations with high mutation frequencies, likely by second-order selection processes. In several of the strong-mutator isolates, functional-complementation assays with a wild-type allele of the
mutS
gene demonstrated that the mutator phenotype was due to the impairment of MutS activity.
In silico
analysis of the amino acid changes present in the MutS proteins of these hypermutator strains in comparison with the normomutator isolates suggests that the cause of the defect in MutS might be a H683P amino acid change.
Characterization of Wet-Heat Inactivation of Single Spores of
Bacillus
Species by Dual-Trap Raman Spectroscopy and Elastic Light Scattering
Authors: Zhang Pengfei , Kong Lingbo , Setlow Peter , Li Yong-qing
Published: January 2010

Dual-trap laser tweezers Raman spectroscopy (LTRS) and elastic light scattering (ELS) were used to investigate dynamic processes during high-temperature treatment of individual spores of
Bacillus cereus
,
Bacillus megaterium
, and
Bacillus subtilis
in water. Major conclusions from these studies included the following. (i) After spores of all three species were added to water at 80 to 90°C, the level of the 1:1 complex of Ca
2+
and dipicolinic acid (CaDPA; ∼25% of the dry weight of the spore core) in individual spores remained relatively constant during a highly variable lag time (
T
lag
), and then CaDPA was released within 1 to 2 min. (ii) The
T
lag
values prior to rapid CaDPA release and thus the times for wet-heat killing of individual spores of all three species were very heterogeneous. (iii) The heterogeneity in kinetics of wet-heat killing of individual spores was not due to differences in the microscopic physical environments during heat treatment. (iv) During the wet-heat treatment of spores of all three species, spore protein denaturation largely but not completely accompanied rapid CaDPA release, as some changes in protein structure preceded rapid CaDPA release. (v) Changes in the ELS from individual spores of all three species were strongly correlated with the release of CaDPA. The ELS intensities of
B. cereus
and
B. megaterium
spores decreased gradually and reached minima at
T
1
when ∼80% of spore CaDPA was released, then increased rapidly until
T
2
when full CaDPA release was complete, and then remained nearly constant. The ELS intensity of
B. subtilis
spores showed similar features, although the intensity changed minimally, if at all, prior to
T
1
. (vi) Carotenoids in
B. megaterium
spores' inner membranes exhibited two changes during heat treatment. First, the carotenoid's two Raman bands at 1,155 and 1,516 cm
−1
decreased rapidly to a low value and to zero, respectively, well before
T
lag
, and then the residual 1,155-cm
−1
band disappeared, in parallel with the rapid CaDPA release beginning at
T
lag
.
Membrane Topology of Outer Membrane Protein AlgE, Which Is Required for Alginate Production in
Pseudomonas aeruginosa
Authors: Hay Iain D. , Rehman Zahid U. , Rehm Bernd H. A.
Published: January 2010

The ubiquitous opportunistic human pathogen
Pseudomonas aeruginosa
secretes a viscous extracellular polysaccharide, called alginate, as a virulence factor during chronic infection of patients with cystic fibrosis. In the present study, it was demonstrated that the outer membrane protein AlgE is required for the production of alginate in
P. aeruginosa
. An isogenic marker-free
algE
deletion mutant was constructed. This strain was incapable of producing alginate but did secrete alginate degradation products, indicating that polymerization occurs but that the alginate chain is subsequently degraded during transit through the periplasm. Alginate production was restored by introducing the
algE
gene. The membrane topology of the outer membrane protein AlgE was assessed by site-specific insertions of FLAG epitopes into predicted extracellular loop regions.
Wide Dispersal and Possible Multiple Origins of Low-Copy-Number Plasmids inRickettsiaSpecies Associated with Blood-Feeding Arthropods
Authors: Baldridge Gerald D. , Burkhardt Nicole Y. , Labruna Marcelo B. , Pacheco Richard C. , Paddock Christopher D. , Williamson Philip C. , Billingsley Peggy M. , Felsheim Roderick F. , Kurtti Timothy J. , Munderloh Ulrike G.
Published: January 2010

Plasmids are mobile genetic elements of bacteria that can impart important adaptive traits, such as increased virulence or antibiotic resistance. We report the existence of plasmids inRickettsia(Rickettsiales;Rickettsiaceae) species, includingRickettsia akari, “CandidatusRickettsia amblyommii,”R. bellii,R. rhipicephali, and REIS, the rickettsial endosymbiont ofIxodes scapularis. All of the rickettsiae were isolated from humans or North and South American ticks.R. parkeriisolates from both continents did not possess plasmids. We have now demonstrated plasmids in nearly allRickettsiaspecies that we have surveyed from three continents, which represent three of the four major proposed phylogenetic groups associated with blood-feeding arthropods. Gel-based evidence consistent with the existence of multiple plasmids in some species was confirmed by cloning plasmids with very different sequences from each of two “Ca. Rickettsia amblyommii” isolates. Phylogenetic analysis of rickettsial ParA plasmid partitioning proteins indicated multipleparAgene origins and plasmid incompatibility groups, consistent with possible multiple plasmid origins. Phylogenetic analysis of potentially host-adaptive rickettsial small heat shock proteins showed thathsp2genes were plasmid specific and thathsp1genes, found only on plasmids of “Ca. Rickettsia amblyommii,”R. felis,R. monacensis, andR. peacockii, were probably acquired independently of thehsp2genes. Plasmid copy numbers in sevenRickettsiaspecies ranged from 2.4 to 9.2 per chromosomal equivalent, as determined by real-time quantitative PCR. Plasmids may be of significance in rickettsial evolution and epidemiology by conferring genetic plasticity and host-adaptive traits via horizontal gene transfer that counteracts the reductive genome evolution typical of obligate intracellular bacteria.
Streptomyces coelicolor
A3(2) CYP102 Protein, a Novel Fatty Acid Hydroxylase Encoded as a Heme Domain without an N-Terminal Redox Partner
Authors: Lamb David C. , Lei Li , Zhao Bin , Yuan Hang , Jackson Colin J. , Warrilow Andrew G. S. , Skaug Tove , Dyson Paul J. , Dawson Eric S. , Kelly Steven L. , Hachey David L. , Waterman Michael R.
Published: January 2010

The gene from
Streptomyces coelicolor
A3(2) encoding CYP102B1, a recently discovered CYP102 subfamily which exists solely as a single P450 heme domain, has been cloned, expressed in
Escherichia coli
, purified, characterized, and compared to its fusion protein family members. Purified reconstitution metabolism experiments with spinach ferredoxin, ferredoxin reductase, and NADPH revealed differences in the regio- and stereoselective metabolism of arachidonic acid compared to that of CYP102A1, exclusively producing 11,12-epoxyeicosa-5,8,14-trienoic acid in addition to the shared metabolites 18-hydroxy arachidonic acid and 14,15-epoxyeicosa-5,8,11-trienoic acid. Consequently, in order to elucidate the physiological function of
CYP102B1
, transposon mutagenesis was used to generate an
S. coelicolor
A3(2) strain lacking CYP102B1 activity and the phenotype was assessed.
Effect of Starvation on the Endocytic Pathway in Dictyostelium Cells
Authors: Smith Ewan W. , Lima Wanessa C. , Charette Steve J. , Cosson Pierre
Published: January 2010

Dictyostelium discoideum
amoebae have been used extensively to study the structure and dynamics of the endocytic pathway. Here, we show that while the general structure of the endocytic pathway is maintained in starved cells, its dynamics rapidly slow down. In addition, analysis of
apm3
and
lvsB
mutants reveals that the functional organization of the endocytic pathway is profoundly modified upon starvation. Indeed, in these mutant cells, some of the defects observed in rich medium persist in starved cells, notably an abnormally slow transfer of endocytosed material between endocytic compartments. Other parameters, such as endocytosis of the fluid phase or the rate of fusion of postlysosomes to the cell surface, vary dramatically upon starvation. Studying the endocytic pathway in starved cells can provide a different perspective, allowing the primary (invariant) defects resulting from specific mutations to be distinguished from their secondary (conditional) consequences.
Comparative Transcriptome Analysis Reveals Novel Roles of the Ras and Cyclic AMP Signaling Pathways in Environmental Stress Response and Antifungal Drug Sensitivity in Cryptococcus neoformans
Authors: Maeng Shinae , Ko Young-Joon , Kim Gyu-Bum , Jung Kwang-Woo , Floyd Anna , Heitman Joseph , Bahn Yong-Sun
Published: January 2010

The cyclic AMP (cAMP) pathway plays a central role in the growth, differentiation, and virulence of pathogenic fungi, including
Cryptococcus neoformans
. Three upstream signaling regulators of adenylyl cyclase (Cac1), Ras, Aca1, and Gpa1, have been demonstrated to control the cAMP pathway in
C. neoformans
, but their functional relationship remains elusive. We performed a genome-wide transcriptome analysis with a DNA microarray using the
ras1
Δ,
gpa1
Δ,
cac1
Δ,
aca1
Δ, and
pka1
Δ
pka2
Δ mutants. The
aca1
Δ,
gpa1
Δ,
cac1
Δ, and
pka1
Δ
pka2
Δ mutants displayed similar transcriptome patterns, whereas the
ras1
Δ mutant exhibited transcriptome patterns distinct from those of the wild type and the cAMP mutants. Interestingly, a number of environmental stress response genes are modulated differentially in the
ras1
Δ and cAMP mutants. In fact, the Ras signaling pathway was found to be involved in osmotic and genotoxic stress responses and the maintenance of cell wall integrity via the Cdc24-dependent signaling pathway. Notably, the Ras and cAMP mutants exhibited hypersensitivity to a polyene drug, amphotericin B, without showing effects on ergosterol biosynthesis, which suggested a novel method of antifungal combination therapy. Among the cAMP-dependent gene products that we characterized, two small heat shock proteins, Hsp12 and Hsp122, were found to be involved in the polyene antifungal drug susceptibility of
C. neoformans
.