bluuebunny/crossref_metadata_2025_split huggingface dataset:
phoD
Alkaline Phosphatase Gene Diversity in Soil
Authors: Ragot Sabine A. , Kertesz Michael A. , Bünemann Else K. 
Published: August 2015

ABSTRACT

Phosphatase enzymes are responsible for much of the recycling of organic phosphorus in soils. The PhoD alkaline phosphatase takes part in this process by hydrolyzing a range of organic phosphoesters. We analyzed the taxonomic and environmental distribution of
phoD
genes using whole-genome and metagenome databases.
phoD
alkaline phosphatase was found to be spread across 20 bacterial phyla and was ubiquitous in the environment, with the greatest abundance in soil. To study the great diversity of
phoD
, we developed a new set of primers which targets
phoD
genes in soil. The primer set was validated by 454 sequencing of six soils collected from two continents with different climates and soil properties and was compared to previously published primers. Up to 685 different
phoD
operational taxonomic units were found in each soil, which was 7 times higher than with previously published primers. The new primers amplified sequences belonging to 13 phyla, including 71 families. The most prevalent
phoD
genes identified in these soils were affiliated with the orders
Actinomycetales
(13 to 35%),
Bacillales
(1 to 29%),
Gloeobacterales
(1 to 18%),
Rhizobiales
(18 to 27%), and
Pseudomonadales
(0 to 22%). The primers also amplified
phoD
genes from additional orders, including
Burkholderiales
,
Caulobacterales
,
Deinococcales
,
Planctomycetales
, and
Xanthomonadales
, which represented the major differences in
phoD
composition between samples, highlighting the singularity of each community. Additionally, the
phoD
bacterial community structure was strongly related to soil pH, which varied between 4.2 and 6.8. These primers reveal the diversity of
phoD
in soil and represent a valuable tool for the study of
phoD
alkaline phosphatase in environmental samples.
Differences in Bacterial Community Structure in Two Color Morphs of the Hawaiian Reef Coral Montipora capitata
Authors: Shore-Maggio Amanda , Runyon Christina M. , Ushijima Blake , Aeby Greta S. , Callahan Sean M. 
Published: August 2015

ABSTRACT

Corals harbor diverse bacterial associations that contribute to the health of the host. Using 16S rRNA pyrosequencing, we compared the bacterial communities of red and orange morphs of the Hawaiian coral
Montipora capitata
. Although both color morphs shared dominant bacterial genera, weighted and unweighted UniFrac analyses showed distinct bacterial communities. A single operational taxonomic unit (OTU), classified as
Vibrio
, represented the largest driver of differences between the color morphs. This OTU comprised 35.4% (±5.5%) of the orange morph bacterial community yet comprised 1.1% (±0.6%) of the red morph bacterial community. Cultivable bacteria from the two color morphs were also compared and tested for antibacterial activity. Cultured isolates represented 14 genera (7% of the total genera identified from sequencing data), and all but two cultured isolates had a matching OTU from the sequencing data. Half of the isolates tested (8 out of 16) displayed antibacterial activity against other cultured isolates but not against two known bacterial pathogens of
M. capitata
. The results from this study demonstrate that the specificity of coral-bacterial associations extends beyond the level of coral species. In addition, culture-dependent methods captured bacterial diversity that was representative of both rare and abundant members of the associated bacterial community, as characterized by culture-independent methods.
Identification of Benzo[
a
]pyrene-Metabolizing Bacteria in Forest Soils by Using DNA-Based Stable-Isotope Probing
Authors: Song Mengke , Luo Chunling , Jiang Longfei , Zhang Dayi , Wang Yujie , Zhang Gan 
Published: August 2015

ABSTRACT

DNA-based stable-isotope probing (DNA-SIP) was used in this study to investigate the uncultivated bacteria with benzo[
a
]pyrene (BaP) metabolism capacities in two Chinese forest soils (Mt. Maoer in Heilongjiang Province and Mt. Baicaowa in Hubei Province). We characterized three different phylotypes with responsibility for BaP degradation, none of which were previously reported as BaP-degrading microorganisms by SIP. In Mt. Maoer soil microcosms, the putative BaP degraders were classified as belonging to the genus
Terrimonas
(family
Chitinophagaceae
, order
Sphingobacteriales
), whereas
Burkholderia
spp. were the key BaP degraders in Mt. Baicaowa soils. The addition of metabolic salicylate significantly increased BaP degradation efficiency in Mt. Maoer soils, and the BaP-metabolizing bacteria shifted to the microorganisms in the family
Oxalobacteraceae
(genus unclassified). Meanwhile, salicylate addition did not change either BaP degradation or putative BaP degraders in Mt. Baicaowa. Polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase (PAH-RHD) genes were amplified, sequenced, and quantified in the DNA-SIP
13
C heavy fraction to further confirm the BaP metabolism. By illuminating the microbial diversity and salicylate additive effects on BaP degradation across different soils, the results increased our understanding of BaP natural attenuation and provided a possible approach to enhance the bioremediation of BaP-contaminated soils.
Alcohol Selectivity in a Synthetic Thermophilic
n
-Butanol Pathway Is Driven by Biocatalytic and Thermostability Characteristics of Constituent Enzymes
Authors: Loder Andrew J. , Zeldes Benjamin M. , Garrison G. Dale , Lipscomb Gina L. , Adams Michael W. W. , Kelly Robert M. 
Published: August 2015

ABSTRACT

n
-Butanol is generated as a natural product of metabolism by several microorganisms, but almost all grow at mesophilic temperatures. A synthetic pathway for
n
-butanol production from acetyl coenzyme A (acetyl-CoA) that functioned at 70°C was assembled
in vitro
from enzymes recruited from thermophilic bacteria to inform efforts for engineering butanol production into thermophilic hosts. Recombinant versions of eight thermophilic enzymes (β-ketothiolase [Thl], 3-hydroxybutyryl-CoA dehydrogenase [Hbd], and 3-hydroxybutyryl-CoA dehydratase [Crt] from
Caldanaerobacter subterraneus
subsp.
tengcongensis
;
trans
-2-enoyl-CoA reductase [Ter] from
Spirochaeta thermophila
; bifunctional acetaldehyde dehydrogenase/alcohol dehydrogenase [AdhE] from
Clostridium thermocellum
; and AdhE, aldehyde dehydrogenase [Bad], and butanol dehydrogenase [Bdh] from
Thermoanaerobacter
sp. strain X514) were utilized to examine three possible pathways for
n
-butanol. These pathways differed in the two steps required to convert butyryl-CoA to
n
-butanol: Thl-Hbd-Crt-Ter-AdhE (
C. thermocellum
), Thl-Hbd-Crt-Ter-AdhE (
Thermoanaerobacter
X514), and Thl-Hbd-Crt-Ter-Bad-Bdh.
n
-Butanol was produced at 70°C, but with different amounts of ethanol as a coproduct, because of the broad substrate specificities of AdhE, Bad, and Bdh. A reaction kinetics model, validated via comparison to
in vitro
experiments, was used to determine relative enzyme ratios needed to maximize
n
-butanol production. By using large relative amounts of Thl and Hbd and small amounts of Bad and Bdh, >70% conversion to
n
-butanol was observed
in vitro
, but with a 60% decrease in the predicted pathway flux. With more-selective hypothetical versions of Bad and Bdh, >70% conversion to
n
-butanol is predicted, with a 19% increase in pathway flux. Thus, more-selective thermophilic versions of Bad, Bdh, and AdhE are needed to fully exploit biocatalytic
n
-butanol production at elevated temperatures.
Deciphering the Diversities of Astroviruses and Noroviruses in Wastewater Treatment Plant Effluents by a High-Throughput Sequencing Method
Authors: Prevost B. , Lucas F. S. , Ambert-Balay K. , Pothier P. , Moulin L. , Wurtzer S. 
Published: August 2015

ABSTRACT
Although clinical epidemiology lists human enteric viruses to be among the primary causes of acute gastroenteritis in the human population, their circulation in the environment remains poorly investigated. These viruses are excreted by the human population into sewers and may be released into rivers through the effluents of wastewater treatment plants (WWTPs). In order to evaluate the viral diversity and loads in WWTP effluents of the Paris, France, urban area, which includes about 9 million inhabitants (approximately 15% of the French population), the seasonal occurrence of astroviruses and noroviruses in 100 WWTP effluent samples was investigated over 1 year. The coupling of these measurements with a high-throughput sequencing approach allowed the specific estimation of the diversity of human astroviruses (human astrovirus genotype 1 [HAstV-1], HAstV-2, HAstV-5, and HAstV-6), 7 genotypes of noroviruses (NoVs) of genogroup I (NoV GI.1 to NoV GI.6 and NoV GI.8), and 16 genotypes of NoVs of genogroup II (NoV GII.1 to NoV GII.7, NoV GII.9, NoV GII.12 to NoV GII.17, NoV GII.20, and NoV GII.21) in effluent samples. Comparison of the viral diversity in WWTP effluents to the viral diversity found by analysis of clinical data obtained throughout France underlined the consistency between the identified genotypes. However, some genotypes were locally present in effluents and were not found in the analysis of the clinical data. These findings could highlight an underestimation of the diversity of enteric viruses circulating in the human population. Consequently, analysis of WWTP effluents could allow the exploration of viral diversity not only in environmental waters but also in a human population linked to a sewerage network in order to better comprehend viral epidemiology and to forecast seasonal outbreaks.
A Genomic View of Lactobacilli and Pediococci Demonstrates that Phylogeny Matches Ecology and Physiology
Authors: Zheng Jinshui , Ruan Lifang , Sun Ming , Gänzle Michael 
Published: August 2015

ABSTRACT

Lactobacilli are used widely in food, feed, and health applications. The taxonomy of the genus
Lactobacillus
, however, is confounded by the apparent lack of physiological markers for phylogenetic groups of lactobacilli and the unclear relationships between the diverse phylogenetic groups. This study used the core and pan-genomes of 174 type strains of
Lactobacillus
and
Pediococcus
to establish phylogenetic relationships and to identify metabolic properties differentiating phylogenetic groups. The core genome phylogenetic tree separated homofermentative lactobacilli and pediococci from heterofermentative lactobacilli. Aldolase and phosphofructokinase were generally present in homofermentative but not in heterofermentative lactobacilli; a two-domain alcohol dehydrogenase and mannitol dehydrogenase were present in most heterofermentative lactobacilli but absent in most homofermentative organisms. Other genes were predominantly present in homofermentative lactobacilli (pyruvate formate lyase) or heterofermentative lactobacilli (lactaldehyde dehydrogenase and glycerol dehydratase). Cluster analysis of the phylogenomic tree and the average nucleotide identity grouped the genus
Lactobacillus sensu lato
into 24 phylogenetic groups, including pediococci, with stable intra- and intergroup relationships. Individual groups may be differentiated by characteristic metabolic properties. The link between phylogeny and physiology that is proposed in this study facilitates future studies on the ecology, physiology, and industrial applications of lactobacilli.
Efficient Production of Lumichrome by Microbacterium sp. Strain TPU 3598
Authors: Yamamoto Kazunori , Asano Yasuhisa 
Published: August 2015

ABSTRACT

Lumichrome is a photodegradation product of riboflavin and is available as a photosensitizer and fluorescent dye. To develop new efficient methods of lumichrome production, we isolated bacterial strains with high lumichrome productivity from soil. The strain with highest productivity was identified as
Microbacterium
sp. strain TPU 3598. Since this strain inductively produced lumichrome when cultivated with riboflavin, we developed two different methods, a cultivation method and a resting cell method, for the production of large amounts of lumichrome using the strain. In the cultivation method, 2.4 g (9.9 mmol) of lumichrome was produced from 3.8 g (10.1 mmol) of riboflavin at the 500-ml scale (98% yield). The strain also produced 4.7 g (19.4 mmol) of lumichrome from 7.6 g (20.2 mmol) of riboflavin (96% yield) by addition of riboflavin during cultivation at the 500-ml scale. In the resting cell method, 20 g of cells (wet weight) in 100 ml of potassium phosphate buffer, pH 7.0, produced 2.4 g of lumichrome from 3.8 g of riboflavin (98% yield). Since the lumichrome production by these methods was carried out in suspension, the resulting lumichrome was easily purified from the cultivation medium or reaction mixture by centrifugation and crystallization. Thus, the biochemical methods we describe here are a significant improvement in terms of simplicity and yield over the existing chemical, photolytic, and other biochemical methods of lumichrome production.
Circulation of Coxiella burnetii in a Naturally Infected Flock of Dairy Sheep: Shedding Dynamics, Environmental Contamination, and Genotype Diversity
Authors: Joulié A. , Laroucau K. , Bailly X. , Prigent M. , Gasqui P. , Lepetitcolin E. , Blanchard B. , Rousset E. , Sidi-Boumedine K. , Jourdain E. 
Published: August 2015

ABSTRACT

Q fever is a worldwide zoonosis caused by
Coxiella burnetii
. Domestic ruminants are considered to be the main reservoir. Sheep, in particular, may frequently cause outbreaks in humans. Because within-flock circulation data are essential to implementing optimal management strategies, we performed a follow-up study of a naturally infected flock of dairy sheep. We aimed to (i) describe
C. burnetii
shedding dynamics by sampling vaginal mucus, feces, and milk, (ii) assess circulating strain diversity, and (iii) quantify barn environmental contamination. For 8 months, we sampled vaginal mucus and feces every 3 weeks from aborting and nonaborting ewes (
n
= 11 and
n
= 26, respectively); for lactating females, milk was obtained as well. We also sampled vaginal mucus from nine ewe lambs. Dust and air samples were collected every 3 and 6 weeks, respectively. All samples were screened using real-time PCR, and strongly positive samples were further analyzed using quantitative PCR. Vaginal and fecal samples with sufficient bacterial burdens were then genotyped by multiple-locus variable-number tandem-repeat analysis (MLVA) using 17 markers.
C. burnetii
burdens were higher in vaginal mucus and feces than in milk, and they peaked in the first 3 weeks postabortion or postpartum. Primiparous females and aborting females tended to shed
C. burnetii
longer and have higher bacterial burdens than nonaborting and multiparous females. Six genotype clusters were identified; they were independent of abortion status, and within-individual genotype diversity was observed.
C. burnetii
was also detected in air and dust samples. Further studies should determine whether the within-flock circulation dynamics observed here are generalizable.
Resistance of Aerosolized Bacterial Viruses to Relative Humidity and Temperature
Authors: Verreault Daniel , Marcoux-Voiselle Mélissa , Turgeon Nathalie , Moineau Sylvain , Duchaine Caroline 
Published: August 2015

ABSTRACT
The use of aerosolized bacteriophages as surrogates for hazardous viruses might simplify and accelerate the discovery of links between viral components and their persistence in the airborne state under diverse environmental conditions. In this study, four structurally distinct lytic phages, MS2 (single-stranded RNA [ssRNA]), ϕ6 (double-stranded RNA [dsRNA]), ϕX174 (single-stranded DNA [ssDNA]), and PR772 (double-stranded DNA [dsDNA]), were nebulized into a rotating chamber and exposed to various levels of relative humidity (RH) and temperature as well as to germicidal UV radiation. The aerosolized viral particles were allowed to remain airborne for up to 14 h before being sampled for analysis by plaque assays and quantitative PCRs. Phages ϕ6 and MS2 were the most resistant at low levels of relative humidity, while ϕX174 was more resistant at 80% RH. Phage ϕ6 lost its infectivity immediately after exposure to 30°C and 80% RH. The infectivity of all tested phages rapidly declined as a function of the exposure time to UVC radiation, phage MS2 being the most resistant. Taken altogether, our data indicate that these aerosolized phages behave differently under various environmental conditions and highlight the necessity of carefully selecting viral simulants in bioaerosol studies.
Evasion of the Innate Immune Type I Interferon System by Monkeypox Virus
Authors: Arndt William D. , Cotsmire Samantha , Trainor Kelly , Harrington Heather , Hauns Kevin , Kibler Karen V. , Huynh Trung P. , Jacobs Bertram L. 
Published: August 2015

ABSTRACT
The vaccinia virus (VACV) E3 protein has been shown to be important for blocking activation of the cellular innate immune system and allowing viral replication to occur unhindered. Mutation or deletion of E3L severely affects viral host range and pathogenesis. While the monkeypox virus (MPXV) genome encodes a homologue of the VACV E3 protein, encoded by the F3L gene, the MPXV gene is predicted to encode a protein with a truncation of 37 N-terminal amino acids. VACV with a genome encoding a similarly truncated E3L protein (VACV-E3LΔ37N) has been shown to be attenuated in mouse models, and infection with VACV-E3LΔ37N has been shown to lead to activation of the host antiviral protein kinase R pathway. In this report, we present data demonstrating that, despite containing a truncated E3 homologue, MPXV phenotypically resembles a wild-type (wt) VACV rather than VACV-E3LΔ37N. Thus, MPXV appears to contain a gene or genes that can suppress the phenotypes associated with an N-terminal truncation in E3. The suppression maps to sequences outside F3L, suggesting that the suppression is extragenic in nature. Thus, MPXV appears to have evolved mechanisms to minimize the effects of partial inactivation of its E3 homologue.

IMPORTANCE
Poxviruses have evolved to have many mechanisms to evade host antiviral innate immunity; these mechanisms may allow these viruses to cause disease. Within the family of poxviruses, variola virus (which causes smallpox) is the most pathogenic, while monkeypox virus is intermediate in pathogenicity between vaccinia virus and variola virus. Understanding the mechanisms of monkeypox virus innate immune evasion will help us to understand the evolution of poxvirus innate immune evasion capabilities, providing a better understanding of how poxviruses cause disease.
Murine Antibody Responses to Cleaved Soluble HIV-1 Envelope Trimers Are Highly Restricted in Specificity
Authors: Hu Joyce K. , Crampton Jordan C. , Cupo Albert , Ketas Thomas , van Gils Marit J. , Sliepen Kwinten , de Taeye Steven W. , Sok Devin , Ozorowski Gabriel , Deresa Isaiah , Stanfield Robyn , Ward Andrew B. , Burton Dennis R. , Klasse Per Johan , Sanders Rogier W. , Moore John P. , Crotty Shane 
Published: August 2015

ABSTRACTGenerating neutralizing antibodies (nAbs) is a major goal of many current HIV-1 vaccine efforts. To be of practical value, these nAbs must be both potent and cross-reactive in order to be capable of preventing the transmission of the highly diverse and generally neutralization resistant (Tier-2) HIV-1 strains that are in circulation. The HIV-1 envelope glycoprotein (Env) spike is the only target for nAbs. To explore whether Tier-2 nAbs can be induced by Env proteins, we immunized conventional mice with soluble BG505 SOSIP.664 trimers that mimic the native Env spike. Here, we report that it is extremely difficult for murine B cells to recognize the Env epitopes necessary for inducing Tier-2 nAbs. Thus, while trimer-immunized mice raised Env-binding IgG Abs and had high-quality T follicular helper (Tfh) cell and germinal center (GC) responses, they did not make BG505.T332N nAbs. Epitope mapping studies showed that Ab responses in mice were specific to areas near the base of the soluble trimer. These areas are not well shielded by glycans and likely are occluded on virions, which is consistent with the lack of BG505.T332N nAbs. These data inform immunogen design and suggest that it is useful to obscure nonneutralizing epitopes presented on the base of soluble Env trimers and that the glycan shield of well-formed HIV Env trimers is virtually impenetrable for murine B cell receptors (BCRs).IMPORTANCEHuman HIV vaccine efficacy trials have not generated meaningful neutralizing antibodies to circulating HIV strains. One possible hindrance has been the lack of immunogens that properly mimic the native conformation of the HIV envelope trimer protein. Here, we tested the first generation of soluble, native-like envelope trimer immunogens in a conventional mouse model. We attempted to generate neutralizing antibodies to neutralization-resistant circulating HIV strains. Various vaccine strategies failed to induce neutralizing antibodies to a neutralization-resistant HIV strain. Further analysis revealed that mouse antibodies targeted areas near the bottom of the soluble envelope trimers. These areas are not easily accessible on the HIV virion due to occlusion by the viral membrane and may have resulted from an absence of glycan shielding. Our results suggest that obscuring the bottom of soluble envelope trimers is a useful strategy to reduce antibody responses to epitopes that are not useful for virus neutralization.
A qualitative cancer screening study with childhood sexual abuse survivors: experiences, perspectives and compassionate care
Authors: Gesink Dionne , Nattel Lilian 
Published: August 2015

ObjectiveThe childhood sexual abuse (CSA) survivor population is substantial and survivors have been identified as part of the population who were under-screened or never-screened for breast, cervical and colon cancer. Our objective was to learn CSA survivor perspectives on, and experiences with, breast, cervical and colon cancer screening with the intention of generating recommendations to help healthcare providers improve cancer screening participation.DesignA pragmatic constructivist qualitative study involving individual, semistructured, in-depth interviews was conducted in January 2014. Thematic analysis was used to describe CSA survivor perspectives on cancer screening and identify potential facilitators for screening.ParticipantsA diverse purposive sample of adult female CSA survivors was recruited. The inclusion criteria were: being a CSA survivor, being in a stable living situation, where stable meant able to meet one's financial needs independently, able to maintain supportive relationships, having participated in therapy to recover from past abuse, and living in a safe environment. 12 survivors were interviewed whose ages ranged from the early 40s to mid-70s. Descriptive saturation was reached after 10 interviews.SettingInterviews were conducted over the phone or Internet. CSA survivors were primarily from urban and rural Ontario, but some resided elsewhere in Canada and the USA.ResultsThe core concept that emerged was that compassionate care at every level of the healthcare experience could improve cancer screening participation. Main themes included: desire for holistic care; unique needs of patients with dissociative identity disorder; the patient-healthcare provider relationship; appointment interactions; the cancer screening environment; and provider assumptions about patients.ConclusionsCompassionate care can be delivered by: building a relationship; practising respect; focusing attention on the patient; not rushing the appointment; keeping the environment positive and comfortable; maintaining patient dignity; sharing control whenever possible; explaining procedures; and using laughter to reduce power imbalance through shared humanity.