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The spouse has been identified as a primary source of support for patients in coping with cancer. Therefore, attention must be given to problems faced by the spouses. In this study, 120 spouses were asked to fill in the Hospital Anxiety and Depression Scale and a questionnaire containing 51 items. A response rate of 83% was obtained. Eighteen percent scored as cases on the anxiety dimension and 6% on the depression dimension. No differences were seen according to sex, age, patient's diagnosis, treatment and performance status. Significantly more spouses identified as cases regarding anxiety and depression had problems which they had never talked about, physics] symptoms, or feelings of anger. Generally, the level of contact with family and friends was maintained, but the perception of support from family and friends was Low. Only 23% sought professional support and only a fraction of the spouses identified as cases did so. Therefore the professional team must be aware of signals from spouses since help seeking does not seem to be part of their coping strategy. [ABSTRACT FROM AUTHOR]

Plant-derived phenolic acids are catabolized by soil microorganisms whose activity may enhance the decomposition of soil organic carbon (SOC). We characterized whether phenolic acid-degrading bacteria enhance SOC mineralization in forest soils when primed with 13 C-labeled p-hydroxybenzoic acid (pHB). We further tested whether pHB-induced priming could explain differences in SOC content among mono-specific tree plantations in a 70-year-old common garden experiment. pHB addition primed significant losses of SOC (3-13 µmols C g -1 dry wt soil over 7 days) compared to glucose, which reduced mineralization (-3 to -8 µmols C g -1 dry wt soil over 7 days). The principal degraders of pHB were Paraburkholderia and Caballeronia in all plantations regardless of tree species or soil type, with one predominant phylotype (RP11 ASV ) enriched 23-fold following peak pHB respiration. We isolated and confirmed the phenolic degrading activity of a strain matching this phylotype (RP11 T ), which encoded numerous oxidative enzymes, including secretion signal-bearing laccase, Dyp-type peroxidase and aryl-alcohol oxidase. Increased relative abundance of RP11 ASV corresponded with higher pHB respiration and expression of pHB monooxygenase (pobA), which was inversely proportional to SOC content among plantations. pobA expression proved a responsive measure of priming activity. We found that stimulating phenolic-acid degrading bacteria can prime decomposition and that this activity, corresponding with differences in tree species, is a potential mechanism in SOC cycling in forests. Overall, this study highlights the ecology and function of Paraburkholderia whose associations with plant roots and capacity to degrade phenolics suggest a role for specialized bacteria in the priming effect., (© 2021. The Author(s).)

Nitrous oxide (N 2 O) is a key climate change gas and nitrifying microbes living in terrestrial ecosystems contribute significantly to its formation. Many soils are acidic and global change will cause acidification of aquatic and terrestrial ecosystems, but the effect of decreasing pH on N 2 O formation by nitrifiers is poorly understood. Here, we used isotope-ratio mass spectrometry to investigate the effect of acidification on production of N 2 O by pure cultures of two ammonia-oxidizing archaea (AOA; Nitrosocosmicus oleophilus and Nitrosotenuis chungbukensis) and an ammonia-oxidizing bacterium (AOB; Nitrosomonas europaea). For all three strains acidification led to increased emission of N 2 O. However, changes of 15 N site preference (SP) values within the N 2 O molecule (as indicators of pathways for N 2 O formation), caused by decreasing pH, were highly different between the tested AOA and AOB. While acidification decreased the SP value in the AOB strain, SP values increased to a maximum value of 29‰ in N. oleophilus. In addition, 15 N-nitrite tracer experiments showed that acidification boosted nitrite transformation into N 2 O in all strains, but the incorporation rate was different for each ammonia oxidizer. Unexpectedly, for N. oleophilus more than 50% of the N 2 O produced at pH 5.5 had both nitrogen atoms from nitrite and we demonstrated that under these conditions expression of a putative cytochrome P450 NO reductase is strongly upregulated. Collectively, our results indicate that N. oleophilus might be able to enzymatically denitrify nitrite to N 2 O at low pH.

Following publication of the original article [1], the authors identified wrong citations in the maintext.

Background: Polynyas in the Southern Ocean are regions of intense primary production, mainly by Phaeocystis antarctica. Carbon fixed by phytoplankton in the water column is transferred to higher trophic levels, and finally, to the deep ocean. However, in the Amundsen Sea, most of this organic carbon does not reach the sediment but is degraded in the water column due to high bacterial heterotrophic activity., Results: We reconstructed 12 key bacterial genomes from different phases of bloom and analyzed the expression of genes involved in organic carbon remineralization. A high correlation of gene expression between the peak and decline phases was observed in an individual genome bin-based pairwise comparison of gene expression. Polaribacter belonging to Bacteroidetes was found to be dominant in the peak phase, and its transcriptional activity was high (48.9% of the total mRNA reads). Two dominant Polaribacter bins had the potential to utilize major polymers in P. antarctica, chrysolaminarin and xylan, with a distinct set of glycosyl hydrolases. In the decline phase, Gammaproteobacteria (Ant4D3, SUP05, and SAR92), with the potential to utilize low molecular weight-dissolved organic matter (LMW-DOM) including compatible solutes, was increased. The versatility of Gammaproteobacteria may contribute to their abundance in organic carbon-rich polynya waters, while the SAR11 clade was found to be predominant in the sea ice-covered oligotrophic ocean. SAR92 clade showed transcriptional activity for utilization of both polysaccharides and LMW-DOM; this may account for their abundance both in the peak and decline phases. Ant4D3 clade was dominant in all phases of the polynya bloom, implicating the crucial roles of this clade in LMW-DOM remineralization in the Antarctic polynyas., Conclusions: Genomic reconstruction and in situ gene expression analyses revealed the unique metabolic potential of dominant bacteria of the Antarctic polynya at a finer taxonomic level. The information can be used to predict temporal community succession linked to the availability of substrates derived from the P. antarctica bloom. Global warming has resulted in compositional changes in phytoplankton from P. antarctica to diatoms, and thus, repeated parallel studies in various polynyas are required to predict global warming-related changes in carbon remineralization.

Investigations of environmental microbial communities are crucial for the discovery of populations capable of degrading hazardous compounds and may lead to improved bioremediation strategies. The goal of this study was to identify microorganisms responsible for aerobic benzene degradation in coal tar-contaminated groundwater. Benzene degradation was monitored in laboratory incubations of well waters using gas chromatography mass spectrometry (GC-MS). Stable isotope probing (SIP) experiments using [ 13 C]benzene enabled us to obtain 13 C-labled community DNA. From this, 16S rRNA clone libraries identified Gammaproteobacteria and Betaproteobacteria as the active benzene-metabolizing microbial populations. Subsequent cultivation experiments yielded nine bacterial isolates that grew in the presence of benzene; five were confirmed in laboratory cultures to grow on benzene. The isolated benzene-degrading organisms were genotypically similar (>97% 16S rRNA gene nucleotide identities) to the organisms identified in SIP experiments. One isolate, Variovorax MAK3, was further investigated for the expression of a putative aromatic ring-hydroxylating dioxygenase (RHD) hypothesized to be involved in benzene degradation. Microcosm experiments using Variovorax MAK3 revealed a 10-fold increase in RHD (Vapar_5383) expression, establishing a link between this gene and benzene degradation. Furthermore, the addition of Variovorax MAK3 to microcosms prepared from site waters accelerated community benzene degradation and correspondingly increased RHD gene expression. In microcosms using uninoculated groundwater, quantitative (q)PCR assays (with 16S rRNA and RDH genes) showed that Variovorax was present and responsive to added benzene. These data demonstrate how the convergence of cultivation-dependent and -independent techniques can boost understandings of active populations and functional genes in complex benzene-degrading microbial communities., Importance: Benzene is a human carcinogen whose presence in contaminated groundwater drives environmental cleanup efforts. Although the aerobic biodegradation of benzene has long been established, knowledge of the identity of the microorganisms in complex naturally occurring microbial communities responsible for benzene biodegradation has evaded scientific inquiry for many decades. Here, we applied a molecular biology technique known as stable isotope probing (SIP) to the microbial communities residing in contaminated groundwater samples to identify the community members active in benzene biodegradation. We complemented this approach by isolating and growing in the laboratory a bacterium representative of the bacteria found using SIP. Further characterization of the isolated bacterium enabled us to track the expression of a key gene that attacks benzene both in pure cultures of the bacterium and in the naturally occurring groundwater microbial community. This work advances information regarding the documentation of microbial processes, especially the populations and genes that contribute to bioremediation., (Copyright © 2017 American Society for Microbiology.)

A wide diversity of ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaeota exists and plays a key role in the N cycle in a variety of habitats. In this study, we isolated and characterized an ammonia-oxidizing archaeon, strain MY3, from a coal tar-contaminated sediment. Phylogenetically, strain MY3 falls in clade 'Nitrosocosmicus' of the thaumarchaeotal group I.1b. The cells of strain MY3 are large 'walnut-like' cocci, divide by binary fission along a central cingulum, and form aggregates. Strain MY3 is mesophilic and neutrophilic. An assay of 13 C-bicarbonate incorporation into archaeal membrane lipids indicated that strain MY3 is capable of autotrophy. In contrast to some other AOA, TCA cycle intermediates, i.e. pruvate, oxaloacetate and α-ketoglutarate, did not affect the growth rates and yields of strain MY3. The attachment of cells of strain MY3 to XAD-7 hydrophobic beads and to the adsorbent vermiculite demonstrated the potential of strain MY3 to form biofilms. The cell surface was confirmed to be hydrophobic by the extraction of strain MY3 from an aqueous medium with p-xylene. Our finding of a strong potential for surface attachment by strain MY3 may reflect an adaptation to the selective pressures in hydrophobic terrestrial environments., (© 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Ammonia-oxidizing archaea (AOA), that is, members of the Thaumarchaeota phylum, occur ubiquitously in the environment and are of major significance for global nitrogen cycling. However, controls on cell growth and organic carbon assimilation by AOA are poorly understood. We isolated an ammonia-oxidizing archaeon (designated strain DDS1) from seawater and used this organism to study the physiology of ammonia oxidation. These findings were confirmed using four additional Thaumarchaeota strains from both marine and terrestrial habitats. Ammonia oxidation by strain DDS1 was enhanced in coculture with other bacteria, as well as in artificial seawater media supplemented with α-keto acids (e.g., pyruvate, oxaloacetate). α-Keto acid-enhanced activity of AOA has previously been interpreted as evidence of mixotrophy. However, assays for heterotrophic growth indicated that incorporation of pyruvate into archaeal membrane lipids was negligible. Lipid carbon atoms were, instead, derived from dissolved inorganic carbon, indicating strict autotrophic growth. α-Keto acids spontaneously detoxify H2O2 via a nonenzymatic decarboxylation reaction, suggesting a role of α-keto acids as H2O2 scavengers. Indeed, agents that also scavenge H2O2, such as dimethylthiourea and catalase, replaced the α-keto acid requirement, enhancing growth of strain DDS1. In fact, in the absence of α-keto acids, strain DDS1 and other AOA isolates were shown to endogenously produce H2O2 (up to ∼4.5 μM), which was inhibitory to growth. Genomic analyses indicated catalase genes are largely absent in the AOA. Our results indicate that AOA broadly feature strict autotrophic nutrition and implicate H2O2 as an important factor determining the activity, evolution, and community ecology of AOA ecotypes.

The glyoxylate shunt (GS) is a two-step metabolic pathway (isocitrate lyase, aceA; and malate synthase, glcB) that serves as an alternative to the tricarboxylic acid cycle. The GS bypasses the carbon dioxide-producing steps of the tricarboxylic acid cycle and is essential for acetate and fatty acid metabolism in bacteria. GS can be up-regulated under conditions of oxidative stress, antibiotic stress, and host infection, which implies that it plays important but poorly explored roles in stress defense and pathogenesis. In many bacterial species, including Pseudomonas aeruginosa, aceA and glcB are not in an operon, unlike in Escherichia coli In P. aeruginosa, we explored relationships between GS genes and growth, transcription profiles, and biofilm formation. Contrary to our expectations, deletion of aceA in P. aeruginosa improved cell growth under conditions of oxidative and antibiotic stress. Transcriptome data suggested that aceA mutants underwent a metabolic shift toward aerobic denitrification; this was supported by additional evidence, including up-regulation of denitrification-related genes, decreased oxygen consumption without lowering ATP yield, increased production of denitrification intermediates (NO and N2O), and increased cyanide resistance. The aceA mutants also produced a thicker exopolysaccharide layer; that is, a phenotype consistent with aerobic denitrification. A bioinformatic survey across known bacterial genomes showed that only microorganisms capable of aerobic metabolism possess the glyoxylate shunt. This trend is consistent with the hypothesis that the GS plays a previously unrecognized role in allowing bacteria to tolerate oxidative stress., (© 2016 by The American Society for Biochemistry and Molecular Biology, Inc.)

A genome-wide transcriptional analysis of Alteromonas naphthalenivorans SN2 was performed to investigate its ecophysiological behavior in contaminated tidal flats and seawater. The experimental design mimicked these habitats that either added naphthalene or pyruvate; tidal flat-naphthalene (TF-N), tidal flat-pyruvate (TF-P), seawater-naphthalene (SW-N), and seawater-pyruvate (SW-P). The transcriptional profiles clustered by habitat (TF-N/TF-P and SW-N/SW-P), rather than carbon source, suggesting that the former may exert a greater influence on genome-wide expression in strain SN2 than the latter. Metabolic mapping of cDNA reads from strain SN2 based on KEGG pathway showed that metabolic and regulatory genes associated with energy metabolism, translation, and cell motility were highly expressed in all four test conditions, probably highlighting the copiotrophic properties of strain SN2 as an opportunistic marine r-strategist. Differential gene expression analysis revealed that strain SN2 displayed specific cellular responses to environmental variables (tidal flat, seawater, naphthalene, and pyruvate) and exhibited certain ecological fitness traits -- its notable PAH degradation capability in seasonally cold tidal flat might be reflected in elevated expression of stress response and chaperone proteins, while fast growth in nitrogen-deficient and aerobic seawater probably correlated with high expression of glutamine synthetase, enzymes utilizing nitrite/nitrate, and those involved in the removal of reactive oxygen species.

The communities and abundances of methanotrophs and methanogens, along with the oxygen, methane, and total organic carbon (TOC) concentrations, were investigated along a depth gradient in a flooded rice paddy. Broad patterns in vertical profiles of oxygen, methane, TOC, and microbial abundances were similar in the bulk and rhizosphere soils, though methane and TOC concentrations and 16S rRNA gene copies were clearly higher in the rhizosphere soil than in the bulk soil. Oxygen concentrations decreased sharply to below detection limits at 8 mm depth. Pyrosequencing of 16S rRNA genes showed that bacterial and archaeal communities varied according to the oxic, oxic-anoxic, and anoxic zones, indicating that oxygen is a determining factor for the distribution of bacterial and archaeal communities. Aerobic methanotrophs were maximally observed near the oxic-anoxic interface, while methane, TOC, and methanogens were highest in the rhizosphere soil at 30-200 mm depth, suggesting that methane is produced mainly from organic carbon derived from rice plants and is metabolized aerobically. The relative abundances of type I methanotrophs such as Methylococcus, Methylomonas, and Methylocaldum decreased more drastically than those of type II methanotrophs (such as Methylocystis and Methylosinus) with increasing depth. Methanosaeta and Methanoregula were predominant methanogens at all depths, and the relative abundances of Methanosaeta, Methanoregula, and Methanosphaerula, and GOM_Arc_I increased with increasing depth. Based on contrasts between absolute abundances of methanogens and methanotrophs at depths sampled across rhizosphere and bulk soils (especially millimeter-scale slices at the surface), we have identified populations of methanogens (Methanosaeta, Methanoregula, Methanocella, Methanobacterium, and Methanosphaerula), and methanotrophs (Methylosarcina, Methylococcus, Methylosinus, and unclassified Methylocystaceae) that are likely physiologically active in situ.

It is difficult to gauge the success of programmatic efforts to reduce unmet need for contraception without knowing whether individual women have had their need met and adopted contraception. However, the number of true longitudinal datasets tracking the transition of panels of individual women in and out of states of contraceptive use is limited. This study analyses changes in contraceptive use states using Demographic and Health Survey data for 22 sub-Saharan African countries. A cohort approach, tracking representative samples of five-year age groups longitudinally across surveys, as well as period-based techniques, are applied to indicate whether new users of contraception have been drawn from women who previously had no need and/or those who had unmet need for family planning. The results suggest that a greater proportion of increases in contraceptive use in recent years can be attributed to decreases in the percentage of women with no need, especially among younger women, than to decreases in the proportion with unmet need.

Deciphering the in situ activities of microorganisms is essential for understanding the biogeochemical processes occurring in complex environments. Here, we used environmental metaproteomics to obtain information about the identity of subsurface microbial populations in coal tar-contaminated groundwater and the metabolic processes they catalyze. Metaproteomic libraries (two shotgun and seven slices from one SDS-PAGE gel) were generated from replicate samples of microbial biomass. Peptide fragment analysis using nano-liquid chromatography (LC)-mass spectrometry (MS)/MS of the three protein pools generated a total of 95,725 mass spectra. When analyzed using mascot v.2.3.02 and searched against the NCBInr bacterial database [confidence interval 99% (P < 0.01)], a total of 1,270 proteins had at least two peptide matches. Replication of identified proteins across the three libraries was low (3.3%); however, in each library, the most frequently identified protein host was Candidatus Methylomirabilis oxyfera (15, 12 and 62 proteins for each shotgun and the gel-slice library respectively). Remarkably, eight of the nine proteins in the nitrite-dependent anaerobic methane oxidation pathway were found. Additionally, 39 proteins were matched to known anammox bacteria including hydroxylamine and hydrazine oxidase. Metaproteomics thus revealed a microbial population, closely related to Ca. Methylomirabilis oxyfera, actively engaged in nitrite-dependent anaerobic methane oxidation and likely competing for nitrite with anammox bacteria., (© 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Non-culture-based procedures were used to investigate plasmids showing ampicillin resistance properties in two different environments: remote mountain soil (Mt. Jeombong) and sludge (Tancheon wastewater treatment plant). Total DNA extracted from the environmental samples was directly transformed into Escherichia coli TOP10, and a single and three different plasmids were obtained from the mountain soil and sludge samples, respectively. Interestingly, the restriction fragment length polymorphism pattern of the plasmid from the mountain soil sample, designated pEMB1, was identical to the pattern of one of the three plasmids from the sludge sample. Complete DNA sequencing of plasmid pEMB1 (8,744 bp) showed the presence of six open reading frames, including a β-lactamase gene. Using BLASTX, the orf5 and orf6 genes were suggested to encode a CopG family transcriptional regulator and a plasmid stabilization system, respectively. Functional characterization of these genes using a knockout orf5 plasmid (pEMB1ΔparD) and the cloning and expression of orf6 (pET21bparE) indicated that these genes were antitoxin (parD) and toxin (parE) genes. Plasmid stability tests using pEMB1 and pEMB1ΔparDE in E. coli revealed that the orf5 and orf6 genes enhanced plasmid maintenance in the absence of ampicillin. Using a PCR-based survey, pEMB1-like plasmids were additionally detected in samples from other human-impacted sites (sludge samples) and two other remote mountain soil samples, suggesting that plasmids harboring a β-lactamase gene with a ParD-ParE toxin-antitoxin system occurs broadly in the environment. This study extends knowledge about the dissemination and persistence of antibiotic resistance genes in naturally occurring microbial populations., (Copyright © 2015, American Society for Microbiology. All Rights Reserved.)

Tissue-mimicking phantoms and software for quantifying the ability of human observers to detect small low-echo spheres as a function of depth have been developed. Detectability is related to the imager's ability to delineate the boundary of a 3-D object such as a spiculated tumor. The phantoms accommodate a broad range of transducer shapes and sizes. Three phantoms are described: one with 2-mm-diameter spheres (for higher frequencies), one with 3.2-mm-diameter spheres (for lower frequencies) and one with 4-mm-diameter spheres (for lower frequencies). The spheres are randomly distributed in each phantom. The attenuation coefficients of spheres and surroundings are nearly identical; thus, compromising shadowing or enhancement distal to spheres does not occur. Reproducibility results are given for pairs of independent data sets involving eight different combinations of scanner, transducer and console settings. The following comparison results are also reported: (i) only the selected frequency differs; (ii) transducers and scan parameters are nearly the same but manufacturers differ; (iii) ordinary B-scanning, spatial compounding and tissue harmonic imaging are addressed. The phantoms and software promise to be valuable tools for scanning system and setup comparisons and for acceptance testing., (Copyright © 2014 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.)

Anaerobic digesters rely on the diversity and distribution of parallel metabolic pathways mediated by complex syntrophic microbial communities to maintain robust and optimal performance. Using mesophilic swine waste digesters, we experimented with increased ammonia loading to induce a shift from aceticlastic methanogenesis to an alternative acetate-consuming pathway of syntrophic acetate oxidation. In comparison with control digesters, we observed shifts in bacterial 16S rRNA gene content and in functional gene repertoires over the course of the digesters' 3-year operating period. During the first year, under identical startup conditions, all bioreactors mirrored each other closely in terms of bacterial phylotype content, phylogenetic structure, and evenness. When we perturbed the digesters by increasing the ammonia concentration or temperature, the distribution of bacterial phylotypes became more uneven, followed by a return to more even communities once syntrophic acetate oxidation had allowed the experimental bioreactors to regain stable operation. The emergence of syntrophic acetate oxidation coincided with a partial shift from aceticlastic to hydrogenotrophic methanogens. Our 16S rRNA gene analysis also revealed that acetate-fed enrichment experiments resulted in communities that did not represent the bioreactor community. Analysis of shotgun sequencing of community DNA suggests that syntrophic acetate oxidation was carried out by a heterogeneous community rather than by a specific keystone population with representatives of enriched cultures with this metabolic capacity.

Ammonia-oxidizing archaea (AOA) are ubiquitous and abundant and contribute significantly to the carbon and nitrogen cycles in the ocean. In this study, we assembled AOA draft genomes from two deep marine sediments from Donghae, South Korea, and Svalbard, Arctic region, by sequencing the enriched metagenomes. Three major microorganism clusters belonging to Thaumarchaeota, Epsilonproteobacteria, and Gammaproteobacteria were deduced from their 16S rRNA genes, GC contents, and oligonucleotide frequencies. Three archaeal genomes were identified, two of which were distinct and were designated Ca. "Nitrosopumilus koreensis" AR1 and "Nitrosopumilus sediminis" AR2. AR1 and AR2 exhibited average nucleotide identities of 85.2% and 79.5% to N. maritimus, respectively. The AR1 and AR2 genomes contained genes pertaining to energy metabolism and carbon fixation as conserved in other AOA, but, conversely, had fewer heme-containing proteins and more copper-containing proteins than other AOA. Most of the distinctive AR1 and AR2 genes were located in genomic islands (GIs) that were not present in other AOA genomes or in a reference water-column metagenome from the Sargasso Sea. A putative gene cluster involved in urea utilization was found in the AR2 genome, but not the AR1 genome, suggesting niche specialization in marine AOA. Co-cultured bacterial genome analysis suggested that bacterial sulfur and nitrogen metabolism could be involved in interactions with AOA. Our results provide fundamental information concerning the metabolic potential of deep marine sedimentary AOA.

Stable isotope probing (SIP) is a cultivation-free methodology that provides information about the identity of microorganisms participating in assimilatory processes in complex communities. In this study, a Herminiimonas-related bacterium was identified as the dominant member of a denitrifying microcosm fed [(13)C]toluene. The genome of the uncultivated toluene-degrading bacterium was obtained by applying pyrosequencing to the heavy DNA fraction. The draft genome comprised ~3.8 Mb, in 131 assembled contigs. Metabolic reconstruction of aromatic hydrocarbon (toluene, benzoate, p-cresol, 4-hydroxybenzoate, phenylacetate, and cyclohexane carboxylate) degradation indicated that the bacterium might specialize in anaerobic hydrocarbon degradation. This characteristic is novel for the order Burkholderiales within the class Betaproteobacteria. Under aerobic conditions, the benzoate oxidation gene cluster (BOX) system is likely involved in the degradation of benzoate via benzoyl coenzyme A. Many putative genes for aromatic hydrocarbon degradation were closely related to those in the Rhodocyclaceae (particularly Aromatoleum aromaticum EbN1) with respect to organization and sequence similarity. Putative mobile genetic elements associated with these catabolic genes were highly abundant, suggesting gene acquisition by Herminiimonas via horizontal gene transfer.

Methane emissions, along with methanotrophs and methanogens and soil chemical properties, were investigated in a flooded rice ecosystem. Methane emission increased after rice transplantation (from 7.2 to 552 mg day(-1) m(-2) ) and was positively and significantly correlated with transcripts of pmoA and mcrA genes, transcript/gene ratios of mcrA, temperature and total organic carbon. Methane flux was negatively correlated with sulfate concentration. Methanotrophs represented only a small proportion (0.79-1.75%) of the total bacterial 16S rRNA gene reads: Methylocystis (type II methanotroph) decreased rapidly after rice transplantation, while Methylosinus and unclassified Methylocystaceae (type II) were relatively constant throughout rice cultivation. Methylocaldum, Methylobacter, Methylomonas and Methylosarcina (type I) were sparse during the early period, but they increased after 60 days, and their maximum abundances were observed at 90-120 days. Of 33 218 archaeal reads, 68.3-86.6% were classified as methanogens. Methanosaeta, Methanocella, Methanosarcina and Methanobacterium were dominant methanogens, and their maximum abundances were observed at days 60-90. Only four reads were characteristic of anaerobic methanotrophs, suggesting that anaerobic methane metabolism is negligible in this rice paddy system. After completing a multivariate canonical correspondence analysis of our integrated data set, we found normalized mcrA/pmoA transcript ratios to be a promising parameter for predicting net methane fluxes emitted from rice paddy soils., (© 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.)

Our goal is to strengthen the foundations of metaproteomics as a microbial community analysis tool that links the functional identity of actively expressed gene products with host phylogeny. We used shotgun metaproteomics to survey waters in six disparate aquatic habitats (Cayuga Lake, NY; Oneida Lake, NY; Gulf of Maine; Chesapeake Bay, MD; Gulf of Mexico; and the South Pacific). Peptide pools prepared from filter-gathered microbial biomass, analyzed by nano-liquid chromatography-mass spectrometry (MS/MS) generating 9,693 ± 1,073 mass spectra identified 326 ± 107 bacterial proteins per sample. Distribution of proteobacterial (Alpha and Beta) and cyanobacterial (Prochlorococcus and Synechococcus spp.) protein hosts across all six samples was consistent with the previously published biogeography for these microorganisms. Marine samples were enriched in transport proteins (TRAP-type for dicarboxylates and ATP binding cassette (ABC)-type for amino acids and carbohydrates) compared with the freshwater samples. We were able to match in situ expression of many key proteins catalyzing C-, N-, and S-cycle processes with their bacterial hosts across all six habitats. Pelagibacter was identified as the host of ABC-type sugar-, organic polyanion-, and glycine betaine-transport proteins; this extends previously published studies of Pelagibacter's in situ biogeochemical role in marine C- and N-metabolism. Proteins matched to Ruegeria confirmed these organism's role in marine waters oxidizing both carbon monoxide and sulfide. By documenting both processes expressed in situ and the identity of host cells, metaproteomics tested several existing hypotheses about ecophysiological processes and provided fodder for new ones.

Purpose: Quantitative ultrasound based approaches such as attenuation slope estimation can be used to determine underlying tissue properties and eventually used as a supplemental diagnostic technique to B-mode imaging. The authors investigate the impact of backscatter intensity and frequency dependence variations on the attenuation slope estimation accuracy., Methods: The authors compare three frequency domain based attenuation slope estimation algorithms, namely, a spectral difference method, the reference phantom method, and two spectral shift methods: a hybrid method and centroid downshift method. Both the reference phantom and hybrid method use a tissue-mimicking phantom with well-defined acoustic properties to reduce system dependencies and diffraction effects. The normalized power spectral ratio obtained is then filtered by a Gaussian filter centered at the transmit center frequency in the hybrid method. A spectral shift method is then used to estimate the attenuation coefficient from the normalized and filtered spectrum. The centroid downshift method utilizes the shift in power spectrum toward lower frequencies with depth. Numerical phantoms that incorporate variations in the backscatter intensity from -3 to 3 dB, by varying the scatterer number density and variations in the scatterer diameters ranging from 10 to 100 μm are simulated. Experimental tissue mimicking phantoms with three different scatterer diameter ranges (5-40, 75-90, and 125-150 μm) are also used to evaluate the accuracy of the estimation methods., Results: The reference phantom method provided accurate results when the acoustical properties of the reference and the sample are well matched. Underestimation occurs when the reference phantom possessed a higher sound speed than the sample, and overestimation occurs when the reference phantom had a lower sound speed than the sample. The centroid downshift method depends significantly on the bandwidth of the power spectrum, which in turn depends on the frequency dependence of the backscattering. The hybrid method was the least susceptible to changes in the sample's acoustic properties and provided the lowest standard deviation in the numerical simulations and experimental evaluations., Conclusions: No significant variations in the estimation accuracy of the attenuation coefficient were observed with an increase in the scatterer number density in the simulated numerical phantoms for the three methods. Changes in the scatterer diameters, which result in different frequency dependence of backscatter, do not significantly affect attenuation slope estimation with the reference phantom and hybrid approaches. The centroid method is sensitive to variations in the scatterer diameter due to the frequency shift introduced in the power spectrum.

Microbial processes that eliminate organic environmental contamination are important. Progress in the biotechnology of biodegradation relies upon the underlying sciences of environmental microbiology and analytical geochemistry. Recent key discoveries advancing knowledge of biodegradation (in general) and the aromatic-hydrocarbon biodegradation (in particular) have relied upon characterization of microorganisms: pure-culture isolates, laboratory enrichment cultures, and in contaminated field sites. New analytical and molecular tools (ranging from sequencing the DNA of biodegrading microorganisms to assessing changes in the isotopic ratios of 13C to 12C and 2H to 1H in contaminant pools in field sites) have deepened our insights into the mechanisms (how), the occurrence (what), and the identity (who) of active players that effect biodegradation of organic environmental pollutants., (Copyright © 2012. Published by Elsevier Ltd.)

Barcode-based 16S rRNA gene pyrosequencing showed that the kimchi microbiome was dominated by six lactic acid bacteria (LAB), Leuconostoc (Lc.) mesenteroides, Lactobacillus (Lb.) sakei, Weissella (W.) koreensis, Lc. gelidum, Lc. carnosum, and Lc. gasicomitatum. Therefore, we used completed genome sequences of representatives of these bacteria to investigate metatranscriptomic gene-expression profiles during kimchi fermentation. Total mRNA was extracted from kimchi samples taken at five time points during a 29 day-fermentation. Nearly all (97.7%) of the metagenome sequences that were recruited on all LAB genomes of GenBank mapped onto the six LAB strains; this high coverage rate indicated that this approach for assessing processes carried out by the kimchi microbiome was valid. Expressed mRNA sequences (as cDNA) were determined using Illumina GA IIx. Assignment of mRNA sequences to metabolic genes using MG-RAST revealed the prevalence of carbohydrate metabolism and lactic acid fermentation. The mRNA sequencing reads were mapped onto genomes of the six LAB strains, which showed that Lc. mesenteroides was most active during the early-stage fermentation, whereas gene expression by Lb. sakei and W. koreensis was high during later stages. However, gene expression by Lb. sakei decreased rapidly at 25 days of fermentation, which was possibly caused by bacteriophage infection of the Lactobacillus species. Many genes related to carbohydrate transport and hydrolysis and lactate fermentation were actively expressed, which indicated typical heterolactic acid fermentation. Mannitol dehydrogenase-encoding genes (mdh) were identified from all Leuconostoc species and especially Lc. mesenteroides, which harbored three copies (two copies on chromosome and one copy on plasmid) of mdh with different expression patterns. These results contribute to knowledge of the active populations and gene expression in the LAB community responsible for an important fermentation process., (Copyright © 2013 Elsevier B.V. All rights reserved.)

Pseudoxanthomonas spadix BD-a59, isolated from gasoline-contaminated soil, has the ability to degrade all six BTEX (benzene, toluene, ethylbenzene, and o-, m-, and p-xylene) compounds. The genomic features of strain BD-a59 were analyzed bioinformatically and compared with those of another fully sequenced Pseudoxanthomonas strain, P. suwonensis 11-1, which was isolated from cotton waste compost. The genome of strain BD-a59 differed from that of strain 11-1 in many characteristics, including the number of rRNA operons, dioxygenases, monooxygenases, genomic islands (GIs), and heavy metal resistance genes. A high abundance of phage integrases and GIs and the patterns in several other genetic measures (e.g., GC content, GC skew, Karlin signature, and clustered regularly interspaced short palindromic repeat [CRISPR] gene homology) indicated that strain BD-a59's genomic architecture may have been altered through horizontal gene transfers (HGT), phage attack, and genetic reshuffling during its evolutionary history. The genes for benzene/toluene, ethylbenzene, and xylene degradations were encoded on GI-9, -13, and -21, respectively, which suggests that they may have been acquired by HGT. We used bioinformatics to predict the biodegradation pathways of the six BTEX compounds, and these pathways were proved experimentally through the analysis of the intermediates of each BTEX compound using a gas chromatograph and mass spectrometry (GC-MS). The elevated abundances of dioxygenases, monooxygenases, and rRNA operons in strain BD-a59 (relative to strain 11-1), as well as other genomic characteristics, likely confer traits that enhance ecological fitness by enabling strain BD-a59 to degrade hydrocarbons in the soil environment.

Backscatter and attenuation coefficient estimates are needed in many quantitative ultrasound strategies. In clinical applications, these parameters may not be easily obtained because of variations in scattering by tissues overlying a region of interest (ROI). The goal of this study is to assess the accuracy of backscatter and attenuation estimates for regions distal to nonuniform layers of tissue-mimicking materials. In addition, this work compares results of these estimates for "layered" phantoms scanned using different clinical ultrasound machines. Two tissue-mimicking phantoms were constructed, each exhibiting depth-dependent variations in attenuation or backscatter. The phantoms were scanned with three ultrasound imaging systems, acquiring radio frequency echo data for offline analysis. The attenuation coefficient and the backscatter coefficient (BSC) for sections of the phantoms were estimated using the reference phantom method. Properties of each layer were also measured with laboratory techniques on test samples manufactured during the construction of the phantom. Estimates of the attenuation coefficient versus frequency slope, α(0), using backscatter data from the different systems agreed to within 0.24 dB/cm-MHz. Bias in the α(0) estimates varied with the location of the ROI. BSC estimates for phantom sections whose locations ranged from 0 to 7 cm from the transducer agreed among the different systems and with theoretical predictions, with a mean bias error of 1.01 dB over the used bandwidths. This study demonstrates that attenuation and BSCs can be accurately estimated in layered inhomogeneous media using pulse-echo data from clinical imaging systems.

A key step toward implementing quantitative ultrasound techniques in a clinical setting is demonstrating that parameters such as the ultrasonic backscatter coefficient (BSC) can be accurately estimated independent of the clinical imaging system used. In previous studies, agreement in BSC estimates for well characterized phantoms was demonstrated across different laboratory systems. The goal of this study was to compare the BSC estimates of a tissue mimicking sample measured using four clinical scanners, each providing RF echo data in the 1-15 MHz frequency range. The sample was previously described and characterized with single-element transducer systems. Using a reference phantom for analysis, excellent quantitative agreement was observed across the four array-based imaging systems for BSC estimates. Additionally, the estimates from data acquired with the clinical systems agreed with theoretical predictions and with estimates from laboratory measurements using single-element transducers.

Pyrosequencing of 16S rRNA genes (targeting Bacteria and Archaea) and (1)H nuclear magnetic resonance were applied to investigate the rumen microbiota and metabolites of Hanwoo steers in the growth stage (HGS), Hanwoo steers in the late fattening stage (HFS), Holstein-Friesian dairy cattle (HDC), and Korean native goats (KNG) in the late fattening stage. This was a two-part investigation. We began by comparing metabolites and microbiota of Hanwoo steers at two stages of husbandry. Statistical comparisons of metabolites and microbial communities showed no significant differences between HFS and HGS (differing by a dietary shift at 24 months and age [67 months versus 12 months]). We then augmented the study by extending the investigation to HDC and KNG. Overall, pyrosequencing of 16S rRNA genes showed that the rumens had highly diverse microbial communities containing many previously undescribed microorganisms. Bioinformatic analysis revealed that the bacterial sequences were predominantly affiliated with four phyla-Bacteroidetes, Firmicutes, Fibrobacteres, and Proteobacteria-in all ruminants. However, interestingly, the bacterial reads belonging to Fibrobacteres were present at a very low abundance (<0.1%) in KNG. Archaeal community analysis showed that almost all of these reads fell into a clade related to, but distinct from, known cultivated methanogens. Statistical analyses showed that the microbial communities and metabolites of KNG were clearly distinct from those of other ruminants. In addition, bacterial communities and metabolite profiles of HGS and HDC, fed similar diets, were distinctive. Our data indicate that bovine host breeds override diet as the key factor that determines bacterial community and metabolite profiles in the rumen.

The strain image contrast of some in vivo breast lesions changes with increasing applied load. This change is attributed to differences in the nonlinear elastic properties of the constituent tissues suggesting some potential to help classify breast diseases by their nonlinear elastic properties. A phantom with inclusions and long-term stability is desired to serve as a test bed for nonlinear elasticity imaging method development, testing, etc. This study reports a phantom designed to investigate nonlinear elastic properties with ultrasound elastographic techniques. The phantom contains four spherical inclusions and was manufactured from a mixture of gelatin, agar and oil. The phantom background and each of the inclusions have distinct Young's modulus and nonlinear mechanical behavior. This phantom was subjected to large deformations (up to 20%) while scanning with ultrasound, and changes in strain image contrast and contrast-to-noise ratio between inclusion and background, as a function of applied deformation, were investigated. The changes in contrast over a large deformation range predicted by the finite element analysis (FEA) were consistent with those experimentally observed. Therefore, the paper reports a procedure for making phantoms with predictable nonlinear behavior, based on independent measurements of the constituent materials, and shows that the resulting strain images (e.g., strain contrast) agree with that predicted with nonlinear FEA.

Following the 2007 oil spill in South Korean tidal flats, we sought to identify microbial players influencing the environmental fate of released polycyclic aromatic hydrocarbons (PAHs). Two years of monitoring showed that PAH concentrations in sediments declined substantially. Enrichment cultures were established using seawater and modified minimal media containing naphthalene as sole carbon source. The enriched microbial community was characterized by 16S rRNA-based DGGE profiling; sequencing selected bands indicated Alteromonas (among others) were active. Alteromonas sp. SN2 was isolated and was able to degrade naphthalene, phenanthrene, anthracene, and pyrene in laboratory-incubated microcosm assays. PCR-based analysis of DNA extracted from the sediments revealed naphthalene dioxygenase (NDO) genes of only two bacterial groups: Alteromonas and Cycloclasticus, having gentisate and catechol metabolic pathways, respectively. However, reverse transcriptase PCR-based analysis of field-fixed mRNA revealed in situ expression of only the Alteromonas-associated NDO genes; in laboratory microcosms these NDO genes were markedly induced by naphthalene addition. Analysis by GC/MS showed that naphthalene in tidal-flat samples was metabolized predominantly via the gentisate pathway; this signature metabolite was detected (0.04 μM) in contaminated field sediment. A quantitative PCR-based two-year data set monitoring Alteromonas-specific 16S rRNA genes and NDO transcripts in sea-tidal flat field samples showed that the abundance of bacteria related to strain SN2 during the winter season was 20-fold higher than in the summer season. Based on the above data, we conclude that strain SN2 and its relatives are site natives--key players in PAH degradation and adapted to winter conditions in these contaminated sea-tidal-flat sediments.

Nitrification of excess ammonia in soil causes eutrophication of water resources and emission of atmospheric N(2) O gas. The first step of nitrification, ammonia oxidation, is mediated by Archaea as well as Bacteria. The physiological reactions mediated by ammonia-oxidizing archaea (AOA) and their contribution to soil nitrification are still unclear. Results of non-culture-based studies have shown the thaumarchaeotal group I.1b lineage of AOA to be dominant over both AOA of group I.1a and ammonia-oxidizing bacteria in various soils. We obtained from an agricultural soil a highly enriched ammonia-oxidizing culture dominated by a single archaeal population [c. 90% of total cells, as determined microscopically (by fluorescence in situ hybridization) and by quantitative PCR of its 16S rRNA gene]. The archaeon (termed 'strain JG1') fell within thaumarchaeotal group I.1b and was related to the moderately thermophilic archaeon, Candidatus Nitrososphaera gargensis, and the mesophilic archaeon, Ca. Nitrososphaera viennensis with 97.0% and 99.1% 16S rRNA gene sequence similarity respectively. Strain JG1 was neutrophilic (growth range pH 6.0-8.0) and mesophilic (growth range temperature 25-40°C). The optimum temperature of strain JG1 (35-40°C) is > 10°C higher than that of ammonia-oxidizing bacteria (AOB). Membrane analysis showed that strain JG1 contained a glycerol dialkyl glycerol tetraether, GDGT-4, and its regioisomer as major core lipids; this crenarchaeol regioisomer was previously detected in similar abundance in the thermophile, Ca. N. gargensis and has been frequently observed in tropical soils. Substrate uptake assays showed that the affinity of strain JG1 for ammonia and oxygen was much higher than those of AOB. These traits may give a competitive advantage to AOA related to strain JG1 in oligotrophic environments. (13) C-bicarbonate incorporation into archaeal lipids of strain JG1 established its ability to grow autotrophically. Strain JG1 produced a significant amount of N(2) O gas - implicating AOA as a possible source of N(2) O emission from soils. Sequences of archaeal amoA and 16S rRNA genes closely related to those of strain JG1 have been retrieved from various terrestrial environments in which lineage of strain JG1 is likely engaged in autotrophic nitrification., (© 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.)

Alteromonas species are globally distributed copiotrophic bacteria in marine habitats. Among these, sea-tidal flats are distinctive: undergoing seasonal temperature and oxygen-tension changes, plus periodic exposure to petroleum hydrocarbons. Strain SN2 of the genus Alteromonas was isolated from hydrocarbon-contaminated sea-tidal flat sediment and has been shown to metabolize aromatic hydrocarbons there. Strain SN2's genomic features were analyzed bioinformatically and compared to those of Alteromonas macleodii ecotypes: AltDE and ATCC 27126. Strain SN2's genome differs from that of the other two strains in: size, average nucleotide identity value, tRNA genes, noncoding RNAs, dioxygenase gene content, signal transduction genes, and the degree to which genes collected during the Global Ocean Sampling project are represented. Patterns in genetic characteristics (e.g., GC content, GC skew, Karlin signature, CRISPR gene homology) indicate that strain SN2's genome architecture has been altered via horizontal gene transfer (HGT). Experiments proved that strain SN2 was far more cold tolerant, especially at 5°C, than the other two strains. Consistent with the HGT hypothesis, a total of 15 genomic islands in strain SN2 likely confer ecological fitness traits (especially membrane transport, aromatic hydrocarbon metabolism, and fatty acid biosynthesis) specific to the adaptation of strain SN2 to its seasonally cold sea-tidal flat habitat.

Soil nitrification is an important process for agricultural productivity and environmental pollution. Though one cultivated representative of ammonia-oxidizing Archaea from soil has been described, additional representatives warrant characterization. We describe an ammonia-oxidizing archaeon (strain MY1) in a highly enriched culture derived from agricultural soil. Fluorescence in situ hybridization microscopy showed that, after 2 years of enrichment, the culture was composed of >90% archaeal cells. Clone libraries of both 16S rRNA and archaeal amoA genes featured a single sequence each. No bacterial amoA genes could be detected by PCR. A [¹³C]bicarbonate assimilation assay showed stoichiometric incorporation of ¹³C into Archaea-specific glycerol dialkyl glycerol tetraethers. Strain MY1 falls phylogenetically within crenarchaeal group I.1a; sequence comparisons to "Candidatus Nitrosopumilus maritimus" revealed 96.9% 16S rRNA and 89.2% amoA gene similarities. Completed growth assays showed strain MY1 to be chemoautotrophic, mesophilic (optimum at 25°C), neutrophilic (optimum at pH 6.5 to 7.0), and nonhalophilic (optimum at 0.2 to 0.4% salinity). Kinetic respirometry assays showed that strain MY1's affinities for ammonia and oxygen were much higher than those of ammonia-oxidizing bacteria (AOB). The yield of the greenhouse gas N₂O in the strain MY1 culture was lower but comparable to that of soil AOB. We propose that this new soil ammonia-oxidizing archaeon be designated "Candidatus Nitrosoarchaeum koreensis."

Purpose: Features extracted from axial-shear strain images of breast masses have been previously utilized to differentiate and classify benign from malignant breast masses. In this paper, we compare shear strain patterns exhibited by both the full-shear (axial and lateral component) versus only the axial-shear strain component for differentiating between bound masses (malignant) when compared to unbound masses (benign)., Methods: We examine different breast mass characteristics such as mass shape, asymmetric location of masses, stiffness variations, and mass bonding characteristics to background tissue to assess their impact on shear strain patterns generated due to a uniaxial applied deformation. Two-dimensional finite element simulations of both circular and elliptical inclusions embedded within a uniform background were utilized. Different degrees of bonding were characterized using friction coefficient values ranging from 0.01 to 100 denoting loosely bound to firmly bound masses. Single-inclusion tissue-mimicking phantoms mimicking firmly bound and loosely bound ellipsoidal masses oriented at four different angles to the applied deformation were studied to corroborate the mass differentiation performance., Results: Our results indicate that the normalized axial-shear strain and full-shear strain area features are larger for bound when compared to unbound masses. A higher stiffness ratio or contrast between the inclusion and background also improves differentiation. Larger applied deformations reduce the discrimination performance for masses with friction coefficients lower than 0.4, due to increased mass slippage with applied deformations. Potential errors with the use of these features would occur for unbound inclusions at larger applied deformations and for asymmetric mass positions within the background normal tissue., Conclusions: Finite element and tissue-mimicking phantom results demonstrate the feasibility of utilizing both the normalized axial-shear and full-shear strain area features to classify breast masses. Differentiation between bound or unbound masses was not affected by the mass size or shape for masses where the applied deformation is normal to the mass surface. Shear strain patterns vary significantly especially within unbound masses, when the mass surface is not normal to the applied deformation. Discrimination performance for unbound masses was improved by utilizing only the normalized shear strain area patterns located outside the mass as illustrated in this paper.

Ultrasonic attenuation may be measured accurately with clinical systems and array transducers by using reference phantom methods (RPM) to account for diffraction and other system dependencies on echo signals. Assumptions with the RPM are that the speeds of sound in the sample (c(sam)) and in the reference medium (c(ref)) are the same and that they match the speed assumed in the system beamformer (c(bf)). This work assesses the accuracy of attenuation measurements by the RPM when these assumptions are not met. Attenuation was measured for two homogeneous phantoms, one with a speed of sound of 1500 m/s and the other with a sound speed of 1580 m/s. Both have an attenuation coefficient approximately equal to that of the reference, in which the speed of sound is 1540 m/s. Echo signals from the samples and the reference were acquired from a Siemens S2000 scanner with a 9L4 linear array transducer. Separate acquisitions were obtained with c(bf) at its default value of 1540 m/s and when it was set at values matching the speeds of sound of the phantoms. Simulations were also performed using conditions matching those of the experiment. RPM-measured attenuation coefficients exhibited spatially-dependent biases when c(sam) differed from c(df) and c(ref). Mean errors of 19% were seen for simulated data, with the maximum errors in attenuation measurements occurring for regions of interest near the transmit focus. Biases were minimized (mean error with simulated data was 5.6%) using c(bf) that matched c(sam) and assuring that power spectra used for attenuation computations in the sample are from precisely the same depth as those from the reference. Setting the transmit focus well beyond the depth range used to compute attenuation values minimized the bias.

In vivo estimations of the frequency-dependent acoustic attenuation (alpha) and backscatter (eta) coefficients using radiofrequency (rf) echoes acquired with clinical ultrasound systems must be independent of the data acquisition setup and the estimation procedures. In a recent in vivo assessment of these parameters in rodent mammary tumors, overall agreement was observed among alpha and eta estimates using data from four clinical imaging systems. In some cases, particularly in highly-attenuating heterogeneous tumors, multisystem variability was observed. This paper compares alpha and eta estimates of a well-characterized rodent-tumor-mimicking homogeneous phantom scanned using seven transducers with the same four clinical imaging systems: a Siemens Acuson S2000, an Ultrasonix RP, a Zonare Z.one and a VisualSonics Vevo2100. alpha and eta estimates of lesion-mimicking spheres in the phantom were independently assessed by three research groups, who analyzed their system's rf echo signals. Imaging-system-based estimates of alpha and eta of both lesion-mimicking spheres were comparable to through-transmission laboratory estimates and to predictions using Faran's theory, respectively. A few notable variations in results among the clinical systems were observed but the average and maximum percent difference between alpha estimates and laboratory-assessed values was 11% and 29%, respectively. Excluding a single outlier dataset, the average and maximum average difference between eta estimates for the clinical systems and values predicted from scattering theory was 16% and 33%, respectively. These results were an improvement over previous interlaboratory comparisons of attenuation and backscatter estimates. Although the standardization of our estimation methodologies can be further improved, this study validates our results from previous rodent breast-tumor model studies.

The comparative genomics of Acinetobacter oleivorans DR1 assayed with A. baylyi ADP1, A. calcoaceticus PHEA-2, and A. baumannii ATCC 17978 revealed that the incorporation of phage-related genomic regions and the absence of transposable elements have contributed to the large size (4.15 Mb) of the DR1 genome. A horizontally transferred genomic region and a higher proportion of transcriptional regulator- and signal peptide-coding genes were identified as characteristics of the DR1 genome. Incomplete glucose metabolism, metabolic pathways of aromatic compounds, biofilm formation, antibiotics and metal resistance, and natural competence genes were conserved in four compared genomes. Interestingly, only strain DR1 possesses gentisate 1,2-dioxygenase (nagI) and grows on gentisate, whereas other species cannot. Expression of the nagI gene was upregulated during gentisate utilization, and four downstream open reading frames (ORFs) were cotranscribed, supporting the notion that gentisate metabolism is a unique characteristic of strain DR1. The genomic analysis of strain DR1 provides additional insights into the function, ecology, and evolution of Acinetobacter species.

Polaromonas naphthalenivorans strain CJ2 metabolizes naphthalene via the gentisate pathway and has recently been shown to carry a third copy of gentisate 1,2-dioxygenase (GDO), encoded by nagI3, within a previously uncharacterized naphthalene catabolic gene cluster. The role of this cluster (especially nagI3) in naphthalene metabolism of strain CJ2 was investigated by documenting patterns in regulation, transcription and enzyme activity. Transcriptional analysis of wild-type cells showed the third cluster to be polycistronic and that nagI3 was expressed at a relatively high level. Individual knockout mutants of all three nagI genes were constructed and their influence on both GDO activity and cell growth was evaluated. Of the three knockout strains, CJ2ΔnagI3 showed severely diminished GDO activity and grew slowest on aromatic substrates. These observations are consistent with the hypothesis that nagI3 may prevent toxic intracellular levels of gentisate from accumulating in CJ2 cells. All three nagI genes from strain CJ2 were cloned into Escherichia coli: the nagI2 and nagI3 genes were successfully overexpressed. The subunit mass of the GDOs were ~36-39 kDa, and their structures were deduced to be dimeric. The K(m) values of NagI2 and NagI3 were 31 and 10 µM, respectively, indicating that the higher affinity of NagI3 for gentisate may protect the wild-type cells from gentisate toxicity. These results provide clues for explaining why the third gene cluster, particularly the nagI3 gene, is important in strain CJ2. The organization of genes in the third gene cluster matched that of clusters in Polaromonas sp. JS666 and Leptothrix cholodnii SP-6. While horizontal gene transfer (HGT) is one hypothesis for explaining this genetic motif, gene duplication within the ancestral lineage is equally valid. The HGT hypothesis was discounted by noting that the nagI3 allele of strain CJ2 did not share high sequence identity with its homologues in Polaromonas sp. JS666 and L. cholodnii SP-6.

Absolute backscatter coefficients in tissue-mimicking phantoms were experimentally determined in the 5-50 MHz frequency range using a broadband technique. A focused broadband transducer from a commercial research system, the VisualSonics Vevo 770, was used with two tissue-mimicking phantoms. The phantoms differed regarding the thin layers covering their surfaces to prevent desiccation and regarding glass bead concentrations and diameter distributions. Ultrasound scanning of these phantoms was performed through the thin layer. To avoid signal saturation, the power spectra obtained from the backscattered radio frequency signals were calibrated by using the signal from a liquid planar reflector, a water-brominated hydrocarbon interface with acoustic impedance close to that of water. Experimental values of absolute backscatter coefficients were compared with those predicted by the Faran scattering model over the frequency range 5-50 MHz. The mean percent difference and standard deviation was 54% ± 45% for the phantom with a mean glass bead diameter of 5.40 μm and was 47% ± 28% for the phantom with 5.16 μm mean diameter beads.

Quantitative ultrasound (QUS) has been used to characterize soft tissues at ordinary abdominal ultrasound frequencies (2 to 15 MHz) and is beginning application at high frequencies (20 to 70 MHz). For example, backscatter and attenuation coefficients can be estimated in vivo using a reference phantom. At high frequencies, it is crucial that reverberations do not compromise the measurements. Such reverberations can occur between the phantom's scanning window and transducer components as well as within the scanning window between its surfaces. Transducers are designed to minimize reverberations between the transducer and soft tissue. Thus, the acoustic impedance of a phantom scanning window should be tissuelike; polymethylpentene (TPX) is commonly used because of its tissuelike acoustic impedance. For QUS, it is also crucial to correct for the transmission coefficient of the scanning window. Computation of the latter requires knowledge of the ultrasonic properties, viz, density, speed and attenuation coefficients. This work reports values for the ultrasonic properties of two versions of TPX over the high-frequency range. One form (TPX film) is used as a scanning window on high-frequency phantoms, and at 40 MHz and 22°C was found to have an attenuation coefficient of 120 dB/cm and a propagation speed of 2093 m/s., (Copyright © 2011 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.)

Biogeochemistry is the discipline that strives to understand intricate processes, often microbially mediated ones, that transform and recycle both organic and inorganic substances in soils, sediments, and waters. These processes, manifestations of diverse and highly evolved cellular mechanisms catalyzed by Bacteria and Archaea, maintain the biosphere. Progress in biogeochemistry relies upon the underlying science of environmental microbiology. Over the last 2 years, important discoveries have advanced the ecological, physiological, biochemical, and genomic bases for a variety of microbiological processes including anaerobic methane oxidation, photosynthesis, phosphorous uptake, biodegradation of organic pollutants, and numerous aspects of the nitrogen and sulfur cycles. Here recent literature is assessed and placed within a five-stage paradigm for making scientific progress in environmental microbiology, biogeochemistry, and biotechnology., (Copyright © 2011 Elsevier Ltd. All rights reserved.)

Kimchi, a traditional food in the Korean culture, is made from vegetables by fermentation. In this study, metagenomic approaches were used to monitor changes in bacterial populations, metabolic potential, and overall genetic features of the microbial community during the 29-day fermentation process. Metagenomic DNA was extracted from kimchi samples obtained periodically and was sequenced using a 454 GS FLX Titanium system, which yielded a total of 701,556 reads, with an average read length of 438 bp. Phylogenetic analysis based on 16S rRNA genes from the metagenome indicated that the kimchi microbiome was dominated by members of three genera: Leuconostoc, Lactobacillus, and Weissella. Assignment of metagenomic sequences to SEED categories of the Metagenome Rapid Annotation using Subsystem Technology (MG-RAST) server revealed a genetic profile characteristic of heterotrophic lactic acid fermentation of carbohydrates, which was supported by the detection of mannitol, lactate, acetate, and ethanol as fermentation products. When the metagenomic reads were mapped onto the database of completed genomes, the Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 and Lactobacillus sakei subsp. sakei 23K genomes were highly represented. These same two genera were confirmed to be important in kimchi fermentation when the majority of kimchi metagenomic sequences showed very high identity to Leuconostoc mesenteroides and Lactobacillus genes. Besides microbial genome sequences, a surprisingly large number of phage DNA sequences were identified from the cellular fractions, possibly indicating that a high proportion of cells were infected by bacteriophages during fermentation. Overall, these results provide insights into the kimchi microbial community and also shed light on fermentation processes carried out broadly by complex microbial communities.

This paper presents a new shear wave velocity imaging technique to monitor radio-frequency and microwave ablation procedures, coined electrode vibration elastography. A piezoelectric actuator attached to an ablation needle is transiently vibrated to generate shear waves that are tracked at high frame rates. The time-to-peak algorithm is used to reconstruct the shear wave velocity and thereby the shear modulus variations. The feasibility of electrode vibration elastography is demonstrated using finite element models and ultrasound simulations, tissue-mimicking phantoms simulating fully (phantom 1) and partially ablated (phantom 2) regions, and an ex vivo bovine liver ablation experiment. In phantom experiments, good boundary delineation was observed. Shear wave velocity estimates were within 7% of mechanical measurements in phantom 1 and within 17% in phantom 2. Good boundary delineation was also demonstrated in the ex vivo experiment. The shear wave velocity estimates inside the ablated region were higher than mechanical testing estimates, but estimates in the untreated tissue were within 20% of mechanical measurements. A comparison of electrode vibration elastography and electrode displacement elastography showed the complementary information that they can provide. Electrode vibration elastography shows promise as an imaging modality that provides ablation boundary delineation and quantitative information during ablation procedures.

The prognosis of ipsilateral supraclavicular lymph node recurrence after early breast cancer appears to be worse than for other loco-regional recurrences, but better than for distant metastases. The purpose of the present study was to investigate the relationship between different types of salvage treatment and primary patient characteristics, treatment response, and survival after supraclavicular recurrence (SR) in a large patient population. From the Danish Breast Cancer Cooperative Group treatment database 1977-2003, 305 patients were identified with SR without distant disease as site of first recurrence. Salvage treatment types as well as other factors were related to response and survival. The median follow-up time for progression after SR was 25 months. Complete remission was 76% among patients receiving excision surgery, 67% with combined loco-regional and systemic therapy, and 48% with systemic therapy alone. Median progression-free survival (PFS) and overall survival was 18 and 29 months, respectively. The 5-year PFS probability was 15%. In univariate analysis, combination salvage therapy, negative nodal status and low malignancy grade were related to longer PFS. In multivariate analysis, salvage therapy and malignancy grade remained independent factors for survival. In conclusion, the prognosis of SR is generally poor. However, it appears to be a curable condition. An independent marker of improved outcome is local and systemic combination salvage treatment, which can be considered.

Applicability of ultrasound phantoms to biological tissue has been limited because most phantoms have generally used strong scatterers. The objective was to develop very weakly scattering phantoms, whose acoustic scattering properties are likely closer to those of tissues and then compare theoretical simulations and experimental backscatter coefficient (BSC) results. The phantoms consisted of agar spheres of various diameters (nominally between 90 and 212 microm), containing ultrafiltered milk, suspended in an agar background. BSC estimates were performed at two institutions over the frequency range 1-13 MHz, and compared to three models. Excellent agreement was shown between the two laboratory results as well as with the three models.

Perfluorooctanoic acid (PFOA) is an industrial chemical that has become disseminated globally in aquatic and terrestrial habitats, humans, and wildlife. Understanding PFOA's biodegradability (susceptibility to microbial metabolic attack) is a crucial element in developing an informed strategy for predicting and managing this compound's environmental fate. Reasoning that PFOA might be susceptible to reductive defluorination by anaerobic microbial communities, we embarked on a 2-phase experimental approach examining the potential of five different microbial communities (from a municipal waste-water treatment plant, industrial site sediment, an agricultural soil, and soils from two fire training areas) to alter PFOA's molecular structure. A series of primarily anaerobic incubations (up to 259d in duration) were established with acetate, lactate, ethanol, and/or hydrogen gas as electron donors and PFOA (at concentrations of 100 ppm and 100 ppb) as the electron acceptor. Cometabolism of PFOA during reductive dechlorination of trichloroethene (TCE) and during reduction of nitrate, iron, sulfate, and methanogenesis were also examined. Endpoints of potential PFOA transformation included release of fluoride and detection of potential transformation products by LC/Orbitrap MS and LC/accurate radioisotope counting in a (14)C radiotracer study. The strongest indication of PFOA transformation occurred during its potential cometabolism at the 100 ppb concentration during reductive dechlorination of TCE. Despite an extensive search for transformation products to corroborate potential cometabolism of PFOA, we were unable to document any alteration of PFOA's chemical structure. We conclude that, under conditions examined, PFOA is microbiologically inert, hence environmentally persistent., (Copyright (c) 2010 Elsevier Ltd. All rights reserved.)

The development of phantom materials for elasticity imaging is reported in this paper. These materials were specifically designed to provide nonlinear stress/strain relationship that can be controlled independently of the small strain shear modulus of the material. The materials are mixtures of agar and gelatin gels. Oil droplet dispersions in these materials provide further control of the small strain shear modulus and the nonlinear parameter of the material. Since these materials are mostly water, they are assumed to be incompressible under typical experimental conditions in elasticity imaging. The Veronda-Westman model for strain energy density provided a good fit to all materials used in this study. Materials with a constant gelatin concentration (3.0% dry weight) but varying agar concentration (0.6-2.8% dry weight) demonstrated the same power law relationship between elastic modulus and agar concentration found for pure agar (1.89 +/- 0.02), consistent with percolation theory, and provided a consistent nonlinearity parameter of 4.5 +/- 0.3. The insights provided by this study will form the basis for stable elastography phantoms with stiffness and nonlinear stress/strain relationships in the background that differ from those in the target.