bluuebunny/crossref_metadata_2025 huggingface dataset:
The Preoperative Sexual Functioning and Quality of Sexual Life in Colorectal Cancer: A Study among Patients and Their Partners
Authors: Traa Marjan Johanna , De Vries Jolanda , Roukema Jan Anne , Den Oudsten Brenda Leontine
Published: September 2012

Introduction

Even though the body of literature on sexual functioning is growing, information on the preoperative sexual functioning and the quality of sexual life after colorectal cancer is lacking. Research focusing on female patients and on partners is also rather scarce.

Aim

This cross-sectional study aimed to describe the preoperative sexual functioning, quality of sexual life, and relationship functioning for male and female colorectal cancer patients and their partners. In addition, the mean scores of the patients and partners were compared with mean norm scores.

Methods

Patients diagnosed with colorectal cancer (N = 136) and their partners (N = 106) were recruited before surgical treatment in six Dutch hospitals.

Main Outcome Measures

Men completed the International Index of Erectile Functioning, while women completed the Female Sexual Function Index. All partnered participants completed the Golombok-Rust Inventory of Sexual Satisfaction and the Maudsley Marital Questionnaire. The mean scores were compared with mean norm scores derived from the manuals of the questionnaires.

Results

All participants were in a heterosexual relationship. Female patients reported a lower quality of sexual life compared with male patients. Male partners reported a lower sexual functioning and a lower quality of sexual life compared with male patients. Colorectal cancer patients and partners (both sexes) reported a lower sexual functioning and a lower quality of sexual life compared with norm populations but scored similar on relationship functioning.

Conclusion

A lower sexual functioning and a lower quality of sexual life are already reported preoperatively; however, relationship functioning was comparable with a norm population. Therefore, all the impairment seen after treatment should not be solely attributed to the effects of treatment.
Impact of the invasion of the imported fire ant
Authors: Vinson S. Bradleigh
Published: September 2012

The impact of the imported fire ant (IFA) is complex, in large part, because several very different species of “Fire Ants” have invaded and one of these has two forms, all of which are hard to separate by the public, as well as, some investigators not focused on the ant. Each of these different “IFA” species and forms differ in their impact. Further, these ants impact a number of “things” ranging from the environment and wildlife (plants and animals) as well as people, their environment and infrastructure. In addition, they can not only lead to death of living things (including people), but they can destroy many aspects of our environment and infrastructure at the cost of millions of dollars. But there are some beneficial aspects and some people can make many thousands of dollars due to their presence. This is an attempt to look at these issues.
Ischemic Bowel Disease and Risk of Stroke: A One-Year Follow-up Study
Authors: Kang Jiunn-Horng , Keller Joseph J. , Lin Herng-Ching
Published: September 2012

Background

Ischemic bowel disease and stroke have been noted to have shared pathomechanisms. However, data regarding the stroke occurrence following ischemic bowel disease are still lacking.

Aim

The aim of this study is to explore the risk of stroke in patients with ischemic bowel disease during a one-year follow-up period in Taiwan.

Methods

Data used in this study were retrieved from the ‘Longitudinal Health Insurance Database 2000. Five hundred sixty-nine patients hospitalized with ischemic bowel disease were included as the study group, and 3414 subjects, matched by age and gender, were randomly extracted as a comparison group. Cox proportional hazards regression analysis was performed to test the relationship of ischemic bowel disease and subsequent stroke during the one-year follow-up period.

Results

The incidence rate of stroke among the sampled subjects during the 30-day, 90-day, and 365-day follow-up period was 1·24, 0·76, and 0·43 per 10 person-years. The adjusted hazard ratio for stroke for those patients with ischemic bowel disease within 30-, 90-, and 365-day follow-up periods was found to be 3·71 (95% confidence interval = 1·89–7·27), 2·11 (95% confidence interval = 1·22–3·66), and 1·70 (95% confidence interval = 1·14–2·52) times that of matched comparisons, respectively. The adjusted hazard ratio of ischemic stroke for patients with ischemic bowel disease was found to be 5·29 during the 30-day follow-up period than comparisons.

Conclusions

We found ischemic bowel disease to be significantly associated with stroke occurrence.
Thromboelastography in Patients with Acute Ischemic Stroke
Authors: Elliott Andrea , Wetzel Jeremy , Roper Tiffany , Pivalizza Evan , McCarthy James , Wallace Cristina , Hess Mary Jane , Peng Hui , Rahbar Mohammad H. , Sangha Navdeep , Grotta James C.
Published: September 2012

Background

Thromboelastography measures the dynamics of coagulation. There are limited data about thromboelastography in acute ischemic stroke other than a single study from 1974 suggesting that acute ischemic stroke patients are hypercoagulable. There have been no studies of thromboelastography in the thrombolytic era despite its potential usefulness as a measure of clot lysis. This study was designed to provide initial thromboelastography data in stroke patients before and after tissue plasminogen activator therapy and to provide the necessary preliminary data for further study of thromboelastography's ability to identify clot subtype and predict response to tissue plasminogen activator therapy.

Methods

All acute ischemic stroke patients presenting between 11/2009 and 2/2011 eligible for tissue plasminogen activator therapy were screened and 56 enrolled. Blood was drawn before (52 patients) and 10 mins after tissue plasminogen activator bolus (30 patients). Demographics, vitals, labs, 24 h National Institutes of Health Stroke Scale, and computed tomography scan results were collected. Patients were compared with normal controls.

Results

Acute ischemic stroke patients had shorter R (4·8 ± 1·5 vs. 6·0 ± 1·7 min, P = 0·0004), greater a Angle (65·0 ± 7·6 vs. 61·5 ± 5·9°, P = 0·01), and shorter K (1·7 ± 0·7 vs. 2·1 ± 0·7 min, P = 0·002) indicating faster clotting. Additionally, a subset formed clots with stronger platelet-fibrin matrices. Treatment with tissue plasminogen activator resulted in reduction in all indices of clot strength (LY30 = 0 (0–0·4) vs. 94·4 (15·2–95·3) P < 0·0001); however, there was considerable variability in response.

Conclusions

Thromboelastography demonstrates that many acute ischemic stroke patients are hypercoaguable. Thromboelastography values reflect variable clot subtype and response to tissue plasminogen activator. Further study based on these data will determine if thromboelastography is useful for measuring the dynamic aspects of clot formation and monitoring lytic therapy.
Sedimentary Crust and Metallogeny of Granitoid Affinity: Implications from the Geotectonic Histories of the Circum‐Japan Sea Region, Central Andes and Southeastern Australia
Authors: Sato Kohei
Published: September 2012

Metallogeny of granitoid affinity was reviewed from the aspect of geotectonic history of the continental crust, particularly of the genesis of sedimentary crust involved in magmatism. The redox state of granitoids and related mineralization shows a remarkable contrast between the east and west sides of the Pacific Rim, but if examined closely, the reduced‐type and oxidized‐type granitoid provinces are juxtaposed in three regions: the circum‐Japan Sea region, the central Andes, and the Lachlan Fold Belt in southeastern Australia. Comparative study of these regions revealed that the reduced‐type magmatism associated with Sn mineralization generated in thick sedimentary crust which formed in three geotectonic environments: (i) accretionary terrane along a subduction zone (e.g. Jurassic East Asia), (ii) continental rift (e.g. Early Paleozoic Andes), and (iii) mega‐fan (e.g. Early Paleozoic southeastern Australia). A collisional orogen can provide large amounts of clastic sediment to these environments. The age gap between the magmatism and sedimentation varies depending on the tectonic evolution of individual regions. Thin sedimentary crust may not play an essential role for the reduced‐type magmatism. The oxidized‐type magmatism associated with porphyry Cu and other mineralization generated in the crust which was initially carbon‐free igneous crust or modified from sedimentary crust by magmatism. Subduction‐related basaltic magmas are relatively oxidized, and may enhance fO2 conditions of granitoid activity. Repeated magmatism in a monotonous convergent margin may be favorable for porphyry Cu mineralization as exemplified in the eastern Pacific Rim.
Forensic expertise and judicial practice: evidence or proof?
Authors: Apostolov Aleksandar
Published: September 2012

Rationale, aims and objectives

This study presents for discussion the possibility of adopting a hypothesis of absolute truth in forensic serology and DNA testing of biological traces, taking into account identification probability, which is usually assumed to be greater than 95%. Can this be so? Established identity and mathematically calculated probability below this rate is not false because it depends on the sensitivity of the method, the possible number of variations and theoretical combinations. The result from a study can be considered a 100% identification result only if this study takes account of absolutely all quantitative criteria that characterize it.

Methods

Under the conditions of continually evolving theory and practice, and the introduction of modified and expanded methods for analysis of biological materials, it may therefore be asked which method considers ‘everything’. Although this finding is nihilistic, it reflects a truth, which we can define as absolute. In forensic practice, research methods assumed to be orientation ones and others identified as evidence for the presence of biological traces on objects carriers, are routinely employed.

Results

Based on several groups of forensic cases, the question of the limits of precision and relevance of the results to the categories of evidence and proof is formulated and discussed. Three groups of expertise cases are presented, which warrant discussion: (i) a study of condoms with genetic material on both sides: female DNA on the outer surface and male DNA on the inner. What is this evidence for or what does it prove?; (ii) a study of cigarette butts found at a crime scene with deposited cellular material from the offender. Is this evidence or proof?; (iii) the DNA expertise in the case of controversial parental origin or the vasectomy of the man referred to as the father.

Conclusions

What will the court choose as proof or is it a case of mutually exclusive evidence? Such considerations lead to the dilemma: ‘evidence or proof'?
Everolimus is associated with a reduced incidence of cytomegalovirus infection following de novo cardiac transplantation
Authors: Kobashigawa J. , Ross H. , Bara C. , Delgado J.F. , Dengler T. , Lehmkuhl H.B. , Wang S.‐S. , Dong G. , Witte S. , Junge G. , Potena L.
Published: September 2012

Background

Cytomegalovirus (CMV) causes several complications following cardiac transplantation including cardiac allograft vasculopathy. Previous studies suggested that immunosuppressive treatment based on everolimus might reduce CMV infection. Aiming to better characterize the action of everolimus on CMV and its interplay with patient/recipient serology and anti‐CMV prophylaxis, we analyzed data from 3 large randomized studies comparing various everolimus regimens with azathioprine (AZA)‐ and mycophenolate mofetil (MMF)‐based regimens.

Methods

CMV data were analyzed from 1009 patients in 3 trials of de novo cardiac transplant recipients who were randomized to everolimus 1.5 mg/day, everolimus 3 mg/day, or AZA 1–3 mg/kg/day, plus standard‐dose (SD) cyclosporine (CsA; study B253, n = 634); everolimus 1.5 mg/day plus SD‐ or reduced‐dose (RD)‐CsA (study A2403, n = 199); and everolimus 1.5 mg/day plus RD‐CsA or MMF plus SD‐CsA (study A2411, n = 176).

Results

In study B253, patients allocated to everolimus experienced almost a 70% reduction in odds of experiencing CMV infection compared with AZA (P < 0.001). In study A2403, CMV infection was low in both everolimus arms, irrespective of CsA dosing, and in study A2411, patients allocated to everolimus experienced an 80% reduction in odds of experiencing CMV infection, compared with MMF (P < 0.001). CMV syndrome/disease was rare and less frequent in everolimus‐treated patients. Subgroup analyses showed that the benefit everolimus provides, in terms of CMV events, is retained in CMV‐naïve recipients and is independent of anti‐CMV prophylaxis or preemptive approaches.

Conclusions

Everolimus is associated with a lower incidence of CMV infection compared with AZA and MMF, which combined with its immunosuppressive efficacy and antiproliferative effects may positively impact long‐term outcomes.
Persistent Rhodococcus equi infection in a renal transplant patient: case report and review of the literature
Authors: Menon V. , Gottlieb T. , Gallagher M. , Cheong E.L.
Published: September 2012

Rhodococcus equi is a pathogen that mainly causes infection in immunocompromised hosts. We report a case of relapsing R. equi pulmonary infection in a 57‐year‐old male renal transplant recipient who was treated with 12 months of antibiotics, adjunctive surgery, and a reduction in his immunosuppression. He suffered from relapsing disease, treatment‐related complications, and ultimately died of Pneumocystis pneumonia. Case reports in the literature portray a good cure rate for transplant‐related R. equi infections, with shorter durations of antibiotics. The case illustrates the difficulties in the management of R. equi infections. Forty cases from the literature were reviewed and compared in terms of epidemiology, location of infection, transplant type, immunosuppression used, treatment used, outcomes, and possible exposures.
A Model for Feeder-Extruder Interactions
Authors: Conner J. H. , Bigio D. I.
Published: September 2012

In the field of plastic extrusion, the accurate feeding of materials to the extrusion process is an important issue. The end product quality is partially dependent upon the extruder receiving feed materials in the correct proportions. Therefore, the understanding of the relationship between the feeder and the extruder is very important. This paper presents and analyzes this relationship. The feeder is usually a separate and distinct item from the extruder. The feed materials and the environmental conditions may affect the flow rate of the reaction or blending process of the extrusion process. The variation of this feed material may cause the quality of the overall product to be beyond an acceptable quality. This paper shows that two feeder parameters, the period and amplitude of the feeder error, affect the composition of the materials throughout the extrusion process. Understanding the effect of these parameters will allow for the overall improvement in product quality. This paper also shows that the extrusion process is able to dampen the error of the feeder. In other words, by mixing a fluid element the average fluid composition will tend towards a nominal value. The fluid composition error associated with the fluid element will decay exponentially. This paper presents two models to describe phenomena described above. The first model is a theoretical description of an idealized mixing process with a time varying feeder error. The second model is an iterative mass transfer model representing a nonintermeshing twin screw extrusion process. An analysis of each of these models will demonstrate how the error of fluid composition reduces as a function of the amount of mixing.
A Method for Estimating and Compensating Quasistatic Errors of Machine Tools
Authors: Ferreira P. M. , Liu C. Richard
Published: September 2012

Quasistatic errors are the major contributors to positioning inaccuracies of machine tools. These errors, estimated to account for 70 percent of the errors of the machine, have been observed to be as high as 70 to 120 μm for production class machining centers. In this paper, a model for these errors is developed. Further, it is shown that the parameters for this model can be estimated by the observation of a few (nine) error vectors in the machine’s workspace. These two results form the basis for a viable error compensation scheme; the model for error compensation and the parameter estimation for updating the model. Experimental results verify the validity of the approach. An order-of-magnitude improvement in the accuracy of the machine, with respect to a calibration frame, was observed.
Pharmacogenomics and Patient Care: One Size Does Not Fit All
Authors: Giacomini Kathleen M. , Yee Sook Wah , Ratain Mark J. , Weinshilboum Richard M. , Kamatani Naoyuki , Nakamura Yusuke
Published: September 2012

Pharmacogenomics research provides insights into a personalized approach to prescribing and dosing medications.
Biomaterial-Associated Infection: Locating the Finish Line in the Race for the Surface
Authors: Busscher Henk J. , van der Mei Henny C. , Subbiahdoss Guruprakash , Jutte Paul C. , van den Dungen Jan J. A. M. , Zaat Sebastian A. J. , Schultz Marcus J. , Grainger David W.
Published: September 2012

This Review discusses approaches to developing infection-reducing biomaterials that strike a balance between host tissue integration and prevention of microbial attachment.
Effect of pH on the Electrophoretic Mobility of Spores of Bacillus anthracis and Its Surrogates in Aqueous Solutions
Authors: White Colin P. , Popovici Jonathan , Lytle Darren A. , Adcock Noreen J. , Rice Eugene W.
Published: September 2012

The electrophoretic mobility (EPM) of endospores of
Bacillus anthracis
and surrogates was measured in aqueous solution across a broad pH range and several ionic strengths. EPM values trended around phylogenetic clustering based on the 16S rRNA gene. Measurements reported here provide new insight for
Bacillus anthracis
surrogate selection and for attachment/detachment and transport studies.
Identification and Distribution of High-Abundance Proteins in the Octopus Spring Microbial Mat Community
Authors: Schaffert Courtney S. , Klatt Christian G. , Ward David M. , Pauley Mark , Steinke Laurey
Published: September 2012

A shotgun metaproteomics approach was employed to identify proteins in a hot spring microbial mat community. We identified 202 proteins encompassing 19 known functions from 12 known phyla. Importantly, we identified two key enzymes involved in the 3-hydroxypropionate CO
2
fixation pathway in uncultivated
Roseiflexus
spp., which are known photoheterotrophs.
Characterizing Pneumocystis in the Lungs of Bats: Understanding Pneumocystis Evolution and the Spread of Pneumocystis Organisms in Mammal Populations
Authors: Akbar Haroon , Pinçon Claire , Aliouat-Denis Cecile-Marie , Derouiche Sandra , Taylor Maria-Lucia , Pottier Muriel , Carreto-Binaghi Laura-Helena , González-González Antonio E. , Courpon Aurore , Barriel Véronique , Guillot Jacques , Chabé Magali , Suarez-Alvarez Roberto O. , Aliouat El Moukhtar , Dei-Cas Eduardo , Demanche Christine
Published: September 2012

Bats belong to a wide variety of species and occupy diversified habitats, from cities to the countryside. Their different diets (i.e., nectarivore, frugivore, insectivore, hematophage) lead Chiroptera to colonize a range of ecological niches. These flying mammals exert an undisputable impact on both ecosystems and circulation of pathogens that they harbor.Pneumocystisspecies are recognized as major opportunistic fungal pathogens which cause life-threatening pneumonia in severely immunocompromised or weakened mammals.Pneumocystisconsists of a heterogeneous group of highly adapted host-specific fungal parasites that colonize a wide range of mammalian hosts. In the present study, 216 lungs of 19 bat species, sampled from diverse biotopes in the New and Old Worlds, were examined. Each bat species may be harboring a specificPneumocystisspecies. We report 32.9% ofPneumocystiscarriage in wild bats (41.9% in Microchiroptera). Ecological and behavioral factors (elevation, crowding, migration) seemed to influence thePneumocystiscarriage. This study suggests thatPneumocystis-host association may yield much information onPneumocystistransmission, phylogeny, and biology in mammals. Moreover, the link between genetic variability ofPneumocystisisolated from populations of the same bat species and their geographic area could be exploited in terms of phylogeography.
Breaking the Silence: Protein Stabilization Uncovers Silenced Biosynthetic Gene Clusters in the Fungus Aspergillus nidulans
Authors: Gerke Jennifer , Bayram Özgür , Feussner Kirstin , Landesfeind Manuel , Shelest Ekaterina , Feussner Ivo , Braus Gerhard H.
Published: September 2012

The genomes of filamentous fungi comprise numerous putative gene clusters coding for the biosynthesis of chemically and structurally diverse secondary metabolites (SMs), which are rarely expressed under laboratory conditions. Previous approaches to activate these genes were based primarily on artificially targeting the cellular protein synthesis apparatus. Here, we applied an alternative approach of genetically impairing the protein degradation apparatus of the model fungus
Aspergillus nidulans
by deleting the conserved eukaryotic
csnE/CSN5
deneddylase subunit of the COP9 signalosome. This defect in protein degradation results in the activation of a previously silenced gene cluster comprising a polyketide synthase gene producing the antibiotic 2,4-dihydroxy-3-methyl-6-(2-oxopropyl)benzaldehyde (DHMBA). The
csnE/CSN5
gene is highly conserved in fungi, and therefore, the deletion is a feasible approach for the identification of new SMs.
Comparison of the Levels of Bacterial Diversity in Freshwater, Intertidal Wetland, and Marine Sediments by Using Millions of Illumina Tags
Authors: Wang Yu , Sheng Hua-Fang , He Yan , Wu Jin-Ya , Jiang Yun-Xia , Tam Nora Fung-Yee , Zhou Hong-Wei
Published: September 2012

Sediment, a special realm in aquatic environments, has high microbial diversity. While there are numerous reports about the microbial community in marine sediment, freshwater and intertidal sediment communities have been overlooked. The present study determined millions of Illumina reads for a comparison of bacterial communities in freshwater, intertidal wetland, and marine sediments along Pearl River, China, using a technically consistent approach. Our results show that both taxon richness and evenness were the highest in freshwater sediment, medium in intertidal sediment, and lowest in marine sediment. The high number of sequences allowed the determination of a wide variety of bacterial lineages in all sediments for reliable statistical analyses. Principal component analysis showed that the three types of communities could be well separated from phylum to operational taxonomy unit (OTU) levels, and the OTUs from abundant to rare showed satisfactory resolutions. Statistical analysis (LEfSe) demonstrated that the freshwater sediment was enriched with
Acidobacteria
,
Nitrospira
,
Verrucomicrobia
,
Alphaproteobacteria
, and
Betaproteobacteria
. The intertidal sediment had a unique community with diverse primary producers (such as
Chloroflexi
,
Bacillariophyta
,
Gammaproteobacteria
, and
Epsilonproteobacteria
) as well as saprophytic microbes (such as
Actinomycetales
,
Bacteroidetes
, and
Firmicutes
). The marine sediment had a higher abundance of
Gammaproteobacteria
and
Deltaproteobacteria
, which were mainly involved in sulfate reduction in anaerobic conditions. These results are helpful for a systematic understanding of bacterial communities in natural sediment environments.
Genetic Barcodes for Improved Environmental Tracking of an Anthrax Simulant
Authors: Buckley Patricia , Rivers Bryan , Katoski Sarah , Kim Michael H. , Kragl F. Joseph , Broomall Stacey , Krepps Michael , Skowronski Evan W. , Rosenzweig C. Nicole , Paikoff Sari , Emanuel Peter , Gibbons Henry S.
Published: September 2012

The development of realistic risk models that predict the dissemination, dispersion and persistence of potential biothreat agents have utilized nonpathogenic surrogate organisms such as
Bacillus atrophaeus
subsp.
globigii
or commercial products such as
Bacillus thuringiensis
subsp.
kurstaki
. Comparison of results from outdoor tests under different conditions requires the use of genetically identical strains; however, the requirement for isogenic strains limits the ability to compare other desirable properties, such as the behavior in the environment of the same strain prepared using different methods. Finally, current methods do not allow long-term studies of persistence or reaerosolization in test sites where simulants are heavily used or in areas where
B. thuringiensis
subsp.
kurstaki
is applied as a biopesticide. To create a set of genetically heterogeneous yet phenotypically indistinguishable strains so that variables intrinsic to simulations (e.g., sample preparation) can be varied and the strains can be tested under otherwise identical conditions, we have developed a strategy of introducing small genetic signatures (“barcodes”) into neutral regions of the genome. The barcodes are stable over 300 generations and do not impact
in vitro
growth or sporulation. Each barcode contains common and specific tags that allow differentiation of marked strains from wild-type strains and from each other. Each tag is paired with specific real-time PCR assays that facilitate discrimination of barcoded strains from wild-type strains and from each other. These uniquely barcoded strains will be valuable tools for research into the environmental fate of released organisms by providing specific artificial detection signatures.
Effects of Iron and Nitrogen Limitation on Sulfur Isotope Fractionation during Microbial Sulfate Reduction
Authors: Sim Min Sub , Ono Shuhei , Bosak Tanja
Published: September 2012

Sulfate-reducing microbes utilize sulfate as an electron acceptor and produce sulfide that is depleted in heavy isotopes of sulfur relative to sulfate. Thus, the distribution of sulfur isotopes in sediments can trace microbial sulfate reduction (MSR), and it also has the potential to reflect the physiology of sulfate-reducing microbes. This study investigates the relationship between the availability of iron and reduced nitrogen and the magnitude of S-isotope fractionation during MSR by a marine sulfate-reducing bacterium, DMSS-1, a
Desulfovibrio
species, isolated from salt marsh in Cape Cod, MA. Submicromolar levels of iron increase sulfur isotope fractionation by about 50% relative to iron-replete cultures of DMSS-1. Iron-limited cultures also exhibit decreased cytochrome
c
-to-total protein ratios and cell-specific sulfate reduction rates (csSRR), implying changes in the electron transport chain that couples carbon and sulfur metabolisms. When DMSS-1 fixes nitrogen in ammonium-deficient medium, it also produces larger fractionation, but it occurs at faster csSRRs than in the ammonium-replete control cultures. The energy and reducing power required for nitrogen fixation may be responsible for the reverse trend between S-isotope fractionation and csSRR in this case. Iron deficiency and nitrogen fixation by sulfate-reducing microbes may lead to the large observed S-isotope effects in some euxinic basins and various anoxic sediments.
Heterotrophic Archaea Contribute to Carbon Cycling in Low-pH, Suboxic Biofilm Communities
Authors: Justice Nicholas B. , Pan Chongle , Mueller Ryan , Spaulding Susan E. , Shah Vega , Sun Christine L. , Yelton Alexis P. , Miller Christopher S. , Thomas Brian C. , Shah Manesh , VerBerkmoes Nathan , Hettich Robert , Banfield Jillian F.
Published: September 2012

Archaea are widely distributed and yet are most often not the most abundant members of microbial communities. Here, we document a transition from
Bacteria
- to
Archaea
-dominated communities in microbial biofilms sampled from the Richmond Mine acid mine drainage (AMD) system (∼pH 1.0, ∼38°C) and in laboratory-cultivated biofilms. This transition occurs when chemoautotrophic microbial communities that develop at the air-solution interface sink to the sediment-solution interface and degrade under microaerobic and anaerobic conditions. The archaea identified in these sunken biofilms are from the class
Thermoplasmata
, and in some cases, the highly divergent ARMAN nanoarchaeal lineage. In several of the sunken biofilms, nanoarchaea comprise 10 to 25% of the community, based on fluorescent
in situ
hybridization and metagenomic analyses. Comparative community proteomic analyses show a persistence of bacterial proteins in sunken biofilms, but there is clear evidence for amino acid modifications due to acid hydrolysis. Given the low representation of bacterial cells in sunken biofilms based on microscopy, we infer that hydrolysis reflects proteins derived from lysed cells. For archaea, we detected ∼2,400 distinct proteins, including a subset involved in proteolysis and peptide uptake. Laboratory cultivation experiments using complex carbon substrates demonstrated anaerobic enrichment of
Ferroplasma
and Aplasma coupled to the reduction of ferric iron. These findings indicate dominance of acidophilic archaea in degrading biofilms and suggest that they play roles in anaerobic nutrient cycling at low pH.
Choline and
N
,
N
-Dimethylethanolamine as Direct Substrates for Methanogens
Authors: Watkins Andrew J. , Roussel Erwan G. , Webster Gordon , Parkes R. John , Sass Henrik
Published: September 2012

Choline (
N
,
N
,
N
-trimethylethanolamine), which is widely distributed in membrane lipids and is a component of sediment biota, has been shown to be utilized anaerobically by mixed prokaryote cultures to produce methane but not by pure cultures of methanogens. Here, we show that five recently isolated
Methanococcoides
strains from a range of sediments (Aarhus Bay, Denmark; Severn Estuary mudflats at Portishead, United Kingdom; Darwin Mud Volcano, Gulf of Cadiz; Napoli mud volcano, eastern Mediterranean) can directly utilize choline for methanogenesis producing ethanolamine, which is not further metabolized. Di- and monomethylethanolamine are metabolic intermediates that temporarily accumulate. Consistent with this, dimethylethanolamine was shown to be another new growth substrate, but monomethylethanolamine was not. The specific methanogen inhibitor 2-bromoethanesulfonate (BES) inhibited methane production from choline. When choline and trimethylamine are provided together, diauxic growth occurs, with trimethylamine being utilized first, and then after a lag (∼7 days) choline is metabolized. Three type strains of
Methanococcoides
(
M. methylutens
,
M. burtonii
, and
M. alaskense
), in contrast, did not utilize choline. However, two of them (
M. methylutens
and
M. burtonii
) did metabolize dimethylethanolamine. These results extend the known substrates that can be directly utilized by some methanogens, giving them the advantage that they would not be reliant on bacterial syntrophs for their substrate supply.
Prevalence and Diversity of Viruses in the Entomopathogenic Fungus Beauveria bassiana
Authors: Herrero Noemí , Dueñas Encarna , Quesada-Moraga Enrique , Zabalgogeazcoa Iñigo
Published: September 2012

Viruses have been discovered in numerous fungal species, but unlike most known animal or plant viruses, they are rarely associated with deleterious effects on their hosts. The knowledge about viruses among entomopathogenic fungi is very limited, although their existence is suspected because of the presence of virus-like double-stranded RNA (dsRNA) in isolates of several species.
Beauveria bassiana
is one of the most-studied species of entomopathogenic fungi; it has a cosmopolitan distribution and is used as a biological control agent against invertebrates in agriculture. We analyzed a collection of 73 isolates obtained at different locations and from different habitats in Spain and Portugal, searching for dsRNA elements indicative of viral infections. The results revealed that the prevalence of viral infections is high; 54.8% of the isolates contained dsRNA elements with viral characteristics. The dsRNA electropherotypes of infected isolates indicated that virus diversity was high in the collection analyzed and that mixed virus infections occurred in fungal isolates. However, a hybridization experiment indicated that dsRNA bands that are similar in size do not always have similar sequences. Particular virus species or dsRNA profiles were not associated with locations or types of habitats, probably because of the ubiquity and efficient dispersion of this fungus as an airborne species. The sequence of one of the most common dsRNA elements corresponded to the 5.2-kbp genome of a previously undescribed member of the
Totiviridae
family, termed
B. bassiana
RNA virus 1 (BbRV1).
Biosynthesis of
cis
,
cis
-Muconic Acid and Its Aromatic Precursors, Catechol and Protocatechuic Acid, from Renewable Feedstocks by Saccharomyces cerevisiae
Authors: Weber Christian , Brückner Christine , Weinreb Sheila , Lehr Claudia , Essl Christine , Boles Eckhard
Published: September 2012

Adipic acid is a high-value compound used primarily as a precursor for the synthesis of nylon, coatings, and plastics. Today it is produced mainly in chemical processes from petrochemicals like benzene. Because of the strong environmental impact of the production processes and the dependence on fossil resources, biotechnological production processes would provide an interesting alternative. Here we describe the first engineered
Saccharomyces cerevisiae
strain expressing a heterologous biosynthetic pathway converting the intermediate 3-dehydroshikimate of the aromatic amino acid biosynthesis pathway via protocatechuic acid and catechol into
cis
,
cis
-muconic acid, which can be chemically dehydrogenated to adipic acid. The pathway consists of three heterologous microbial enzymes, 3-dehydroshikimate dehydratase, protocatechuic acid decarboxylase composed of three different subunits, and catechol 1,2-dioxygenase. For each heterologous reaction step, we analyzed several potential candidates for their expression and activity in yeast to compose a functional
cis
,
cis
-muconic acid synthesis pathway. Carbon flow into the heterologous pathway was optimized by increasing the flux through selected steps of the common aromatic amino acid biosynthesis pathway and by blocking the conversion of 3-dehydroshikimate into shikimate. The recombinant yeast cells finally produced about 1.56 mg/liter
cis
,
cis
-muconic acid.
Detection and Tracking of a Novel Genetically Tagged Biological Simulant in the Environment
Authors: Emanuel Peter A. , Buckley Patricia E. , Sutton Tiffany A. , Edmonds Jason M. , Bailey Andrew M. , Rivers Bryan A. , Kim Michael H. , Ginley William J. , Keiser Christopher C. , Doherty Robert W. , Kragl F. Joseph , Narayanan Fiona E. , Katoski Sarah E. , Paikoff Sari , Leppert Samuel P. , Strawbridge John B. , VanReenen Daniel R. , Biberos Sally S. , Moore Douglas , Phillips Douglas W. , Mingioni Lisa R. , Melles Ogba , Ondercin Daniel G. , Hirsh Beth , Bieschke Kendall M. , Harris Crystal L. , Omberg Kristin M. , Rastogi Vipin K. , Van Cuyk Sheila , Gibbons Henry S.
Published: September 2012

A variant of
Bacillus thuringiensis
subsp.
kurstaki
containing a single, stable copy of a uniquely amplifiable DNA oligomer integrated into the genome for tracking the fate of biological agents in the environment was developed. The use of genetically tagged spores overcomes the ambiguity of discerning the test material from pre-existing environmental microflora or from previously released background material. In this study, we demonstrate the utility of the genetically “barcoded” simulant in a controlled indoor setting and in an outdoor release. In an ambient breeze tunnel test, spores deposited on tiles were reaerosolized and detected by real-time PCR at distances of 30 m from the point of deposition. Real-time PCR signals were inversely correlated with distance from the seeded tiles. An outdoor release of powdered spore simulant at Aberdeen Proving Ground, Edgewood, MD, was monitored from a distance by a light detection and ranging (LIDAR) laser. Over a 2-week period, an array of air sampling units collected samples were analyzed for the presence of viable spores and using barcode-specific real-time PCR assays. Barcoded
B. thuringiensis
subsp.
kurstaki
spores were unambiguously identified on the day of the release, and viable material was recovered in a pattern consistent with the cloud track predicted by prevailing winds and by data tracks provided by the LIDAR system. Finally, the real-time PCR assays successfully differentiated barcoded
B. thuringiensis
subsp.
kurstaki
spores from wild-type spores under field conditions.
Inactivation of Salmonella enterica by UV-C Light Alone and in Combination with Mild Temperatures
Authors: Gayán E. , Serrano M. J. , Raso J. , Álvarez I. , Condón S.
Published: September 2012

The aim of this investigation was to study the efficacy of the combined processes of UV light and mild temperatures for the inactivation of
Salmonella enterica
subsp.
enterica
and to explore the mechanism of inactivation. The doses to inactivate the 99.99% (4D) of the initial population ranged from 18.03 (
Salmonella enterica
serovar Typhimurium STCC 878) to 12.75 J ml
−1
(
Salmonella enterica
serovar Enteritidis ATCC 13076). The pH and water activity of the treatment medium did not change the UV tolerance, but it decreased exponentially by increasing the absorption coefficient. An inactivating synergistic effect was observed by applying simultaneous UV light and heat treatment (UV-H). A less synergistic effect was observed by applying UV light first and heat subsequently. UV did not damage cell envelopes, but the number of injured cells was higher after a UV-H treatment than after heating. The synergistic effect observed by combining simultaneous UV and heat treatment opens the possibility to design combined treatments for pasteurization of liquid food with high UV absorptivity, such as fruit juices.
Seasonal Variations of Indoor Microbial Exposures and Their Relation to Temperature, Relative Humidity, and Air Exchange Rate
Authors: Frankel Mika , Bekö Gabriel , Timm Michael , Gustavsen Sine , Hansen Erik Wind , Madsen Anne Mette
Published: September 2012

Indoor microbial exposure has been related to adverse pulmonary health effects. Exposure assessment is not standardized, and various factors may affect the measured exposure. The aim of this study was to investigate the seasonal variation of selected microbial exposures and their associations with temperature, relative humidity, and air exchange rates in Danish homes. Airborne inhalable dust was sampled in five Danish homes throughout the four seasons of 1 year (indoors,
n
= 127; outdoors,
n
= 37). Measurements included culturable fungi and bacteria, endotoxin,
N
-acetyl-beta-
d
-glucosaminidase, total inflammatory potential, particles (0.75 to 15 μm), temperature, relative humidity, and air exchange rates. Significant seasonal variation was found for all indoor microbial exposures, excluding endotoxin. Indoor fungi peaked in summer (median, 235 CFU/m
3
) and were lowest in winter (median, 26 CFU/m
3
). Indoor bacteria peaked in spring (median, 2,165 CFU/m
3
) and were lowest in summer (median, 240 CFU/m
3
). Concentrations of fungi were predominately higher outdoors than indoors, whereas bacteria, endotoxin, and inhalable dust concentrations were highest indoors. Bacteria and endotoxin correlated with the mass of inhalable dust and number of particles. Temperature and air exchange rates were positively associated with fungi and
N
-acetyl-beta-
d
-glucosaminidase and negatively with bacteria and the total inflammatory potential. Although temperature, relative humidity, and air exchange rates were significantly associated with several indoor microbial exposures, they could not fully explain the observed seasonal variations when tested in a mixed statistical model. In conclusion, the season significantly affects indoor microbial exposures, which are influenced by temperature, relative humidity, and air exchange rates.
Fate of Bacillus thuringiensis subsp. israelensis in the Field: Evidence for Spore Recycling and Differential Persistence of Toxins in Leaf Litter
Authors: Tetreau Guillaume , Alessi Mattia , Veyrenc Sylvie , Périgon Sophie , David Jean-Philippe , Reynaud Stéphane , Després Laurence
Published: September 2012

Bacillus thuringiensis
subsp.
israelensis
is a bioinsecticide increasingly used worldwide for mosquito control. Despite its apparent low level of persistence in the field due to the rapid loss of its insecticidal activity, an increasing number of studies suggested that the recycling of
B. thuringiensis
subsp.
israelensis
can occur under specific, unknown conditions. Decaying leaf litters sampled in mosquito breeding sites in the French Rhône-Alpes region several months after a treatment were shown to exhibit a high level of larval toxicity and contained large amounts of spores. In the present article, we show that the high concentration of toxins found in these litters is consistent with spore recycling in the field, which gave rise to the production of new crystal toxins. Furthermore, in these toxic leaf litter samples, Cry4Aa and Cry4Ba toxins became the major toxins instead of Cyt1Aa in the commercial mixture. In a microcosm experiment performed in the laboratory, we also demonstrated that the toxins, when added in their crystal form to nontoxic leaf litter, exhibited patterns of differential persistence consistent with the proportions of toxins observed in the field-collected toxic leaf litter samples (Cry4 > Cry11 > Cyt). These results give strong evidence that
B. thuringiensis
subsp.
israelensis
recycled in specific breeding sites containing leaf litters, and one would be justified in asking whether mosquitoes can become resistant when exposed to field-persistent
B. thuringiensis
subsp.
israelensis
for several generations.
Homologous Alkalophilic and Acidophilic
l
-Arabinose Isomerases Reveal Region-Specific Contributions to the pH Dependence of Activity and Stability
Authors: Lee Sang-Jae , Lee Sang Jun , Lee Yong-Jik , Kim Seong-Bo , Kim Sung-Kun , Lee Dong-Woo
Published: September 2012

To study the pH dependence of
l
-arabinose isomerase (AI) activity and stability, we compared homologous AIs with their chimeras. This study demonstrated that an ionizable amino acid near the catalytic site determines the optimal pH (pH
opt
) for activity, whereas the N-terminal surface R residues play an important role in determining the pH
opt
for stability.
Quantitative Analysis of the Modes of Growth Inhibition by Weak Organic Acids in Saccharomyces cerevisiae
Authors: Ullah Azmat , Orij Rick , Brul Stanley , Smits Gertien J.
Published: September 2012

Weak organic acids are naturally occurring compounds that are commercially used as preservatives in the food and beverage industries. They extend the shelf life of food products by inhibiting microbial growth. There are a number of theories that explain the antifungal properties of these weak acids, but the exact mechanism is still unknown. We set out to quantitatively determine the contributions of various mechanisms of antifungal activity of these weak acids, as well as the mechanisms that yeast uses to counteract their effects. We analyzed the effects of four weak organic acids differing in lipophilicity (sorbic, benzoic, propionic, and acetic acids) on growth and intracellular pH (pH
i
) in
Saccharomyces cerevisiae
. Although lipophilicity of the acids correlated with the rate of acidification of the cytosol, our data confirmed that not initial acidification, but rather the cell's ability to restore pH
i
, was a determinant for growth inhibition. This pH
i
recovery in turn depended on the nature of the organic anion. We identified long-term acidification as the major cause of growth inhibition under acetic acid stress. Restoration of pH
i
, and consequently growth rate, in the presence of this weak acid required the full activity of the plasma membrane ATPase Pma1p. Surprisingly, the proposed anion export pump Pdr12p was shown to play an important role in the ability of yeast cells to restore the pH
i
upon lipophilic (sorbic and benzoic) acid stress, probably through a charge interaction of anion and proton transport.
Role of
rpoS
in Escherichia coli O157:H7 Strain H32 Biofilm Development and Survival
Authors: Sheldon Jessica R. , Yim Mi-Sung , Saliba Jessica H. , Chung Wai-Hong , Wong Kwok-Yin , Leung Kam Tin
Published: September 2012

The protein RpoS is responsible for mediating cell survival during the stationary phase by conferring cell resistance to various stressors and has been linked to biofilm formation. In this study, the role of the
rpoS
gene in
Escherichia coli
O157:H7 biofilm formation and survival in water was investigated. Confocal scanning laser microscopy of biofilms established on coverslips revealed a nutrient-dependent role of
rpoS
in biofilm formation, where the biofilm biomass volume of the
rpoS
mutant was 2.4- to 7.5-fold the size of its
rpoS
+
wild-type counterpart in minimal growth medium. The enhanced biofilm formation of the
rpoS
mutant did not, however, translate to increased survival in sterile double-distilled water (ddH
2
O), filter-sterilized lake water, or unfiltered lake water. The
rpoS
mutant had an overall reduction of 3.10 and 5.30 log
10
in sterile ddH
2
O and filter-sterilized lake water, respectively, while only minor reductions of 0.53 and 0.61 log
10
in viable counts were observed for the wild-type form in the two media over a 13-day period, respectively. However, the survival rates of the detached biofilm-derived
rpoS
+
and
rpoS
mutant cells were comparable. Under the competitive stress conditions of unfiltered lake water, the advantage conferred by the presence of
rpoS
was lost, and both the wild-type and knockout forms displayed similar declines in viable counts. These results suggest that
rpoS
does have an influence on both biofilm formation and survival of
E. coli
O157:H7 and that the advantage conferred by
rpoS
is contingent on the environmental conditions.