bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Politics of Teaching of Indigenous Traditions in Aotearoa/New Zealand
Authors: Wiseman Wendy A. 
Published: January 2015

AbstractReflecting on two study abroad trips to New Zealand in 2005 and 2007, I suggest in this essay that it is possible to mitigate the risk of (American or European) students recapitulating imperial attitudes through development of a rigorous curriculum focusing on the legacies of colonialism, institutional racism, and the somewhat dubious phenomenon of “post‐colonialism.” Readings, I argue, should be in continual play during cultural and social activities, operating in a dialectal move toward an “ethics of respect.” Such an ethics remains aporetic, or uncertain, insofar as no code of behavior can render us immune to the political and polemical effects of past and present forms of imperialism. However, a cultivated respect for distance and difference, including regarding questions of “authenticity,” can help to actualize the transformative promise of studying (indigenous) religion abroad. This essay is published alongside of six other essays, including a response from John Barbour, comprising a special section of the journal (see Teaching Theology and Religion 18:1, January 2015).
Finding Freedom Abroad: Working with Conservative Christian Students in Study Abroad Programs
Authors: Mercer Calvin 
Published: January 2015

AbstractConservative (fundamentalist, evangelical) Christian students present a general theological worldview that often correlates with significant anxiety. In a foreign setting, the anxiety of conservative students, removed from their supportive infrastructure, can be considerably heightened. This structure of thinking and emotion presents distinctive challenges and opportunities. Drawing upon my work as a clinician and as a religion professor who conducted study abroad programs, I make suggestions for working effectively with conservative Christian students in study abroad contexts. Suggestions include predeparture, in‐country, and post‐trip strategies. Specific examples of conversations with students are provided to illustrate the challenges and strategies. This essay is published alongside of seven other essays, including a response from John Barbour, comprising a special section of the journal (seeTeaching Theology and Religion18:1, January 2015).
Heart failure in sub‐Saharan Africa: review of the aetiology of heart failure and the role of point‐of‐care biomarker diagnostics
Authors: Glezeva Nadezhda , Gallagher Joe , Ledwidge Mark , O'Donoghue John , McDonald Kenneth , Chipolombwe John , Watson Chris 
Published: January 2015

SummaryWithin Africa, the burden of heart failure is significant. This arises from the increase in cardiovascular disease and associated risk factors such as hypertension and diabetes, as well as causes of heart failure which are particular to sub‐Saharan Africa, such as endomyocardial fibrosis. The lack of access to echocardiography and other imaging modalities, from a cost and technical perspective, combined with the predominantly rural nature of many countries with poor transport links, means that the vast majority of people never obtain an appropriate diagnosis. Similarly, research has been limited on the causes and treatment of heart failure in Africa and in particular endemic causes such as EMF and rheumatic heart disease. This review outlines the burden of heart failure in Africa and highlights the opportunity to expand diagnosis through the use of biomarkers, in particular natriuretic peptides. This builds on the success of point‐of‐care testing in human immunodeficiency virus and tuberculosis which have been extensively deployed in community settings in Africa.
The Curse of Being Landlocked: Institutions Rather than Trade
Authors: Carmignani Fabrizio 
Published: January 2015

AbstractThis article revisits the long‐term economic effects of being landlocked. The conventional wisdom, which also prevails in policy circles, is that landlockedness hurts development by reducing trade. Gravity models of bilateral trade seem to confirm this view. However, there is no evidence in cross‐country data of a systematic relationship between landlockedness and country's trade to GDP ratio. Drawing on this stylised fact, the paper explores the possibility that landlockedness might affect GDP independently from its effect on trade. Theoretical considerations suggest that institutional quality could be a relevant transmission mechanism. The estimation of a system of three equations confirms that landlockedness has a negative effect on GDP and that this negative effect is transmitted through institutions rather than trade. Moreover, after controlling for the transmission via institutions and trade, landlockedness has a further negative effect on GDP. These findings call for a review of the policy approach to the development of landlocked countries.
Biogeography of Heterotrophic Flagellate Populations Indicates the Presence of Generalist and Specialist Taxa in the Arctic Ocean
Authors: Thaler Mary , Lovejoy Connie 
Published: January 2015

ABSTRACT

Heterotrophic marine flagellates (HF) are ubiquitous in the world's oceans and represented in nearly all branches of the domain Eukaryota. However, the factors determining distributions of major taxonomic groups are poorly known. The Arctic Ocean is a good model environment for examining the distribution of functionally similar but phylogenetically diverse HF because the physical oceanography and annual ice cycles result in distinct environments that could select for microbial communities or favor specific taxa. We reanalyzed new and previously published high-throughput sequencing data from multiple studies in the Arctic Ocean to identify broad patterns in the distribution of individual taxa. HF accounted for fewer than 2% to over one-half of the reads from the water column and for up to 60% of reads from ice, which was dominated by
Cryothecomonas
. In the water column, many HF phylotypes belonging to Telonemia and Picozoa, uncultured marine stramenopiles (MAST), and choanoflagellates were geographically widely distributed. However, for two groups in particular, Telonemia and
Cryothecomonas
, some species level taxa showed more restricted distributions. For example, several phylotypes of Telonemia favored open waters with lower nutrients such as the Canada Basin and offshore of the Mackenzie Shelf. In summary, we found that while some Arctic HF were successful over a range of conditions, others could be specialists that occur under particular conditions. We conclude that tracking species level diversity in HF not only is feasible but also provides a potential tool for understanding the responses of marine microbial ecosystems to rapidly changing ice regimes.
Counting Viruses and Bacteria in Photosynthetic Microbial Mats
Authors: Carreira Cátia , Staal Marc , Middelboe Mathias , Brussaard Corina P. D. 
Published: January 2015

ABSTRACT

Viral abundances in benthic environments are the highest found in aquatic systems. Photosynthetic microbial mats represent benthic environments with high microbial activity and possibly high viral densities, yet viral abundances have not been examined in such systems. Existing extraction procedures typically used in benthic viral ecology were applied to the complex matrix of microbial mats but were found to inefficiently extract viruses. Here, we present a method for extraction and quantification of viruses from photosynthetic microbial mats using epifluorescence microscopy (EFM) and flow cytometry (FCM). A combination of EDTA addition, probe sonication, and enzyme treatment applied to a glutaraldehyde-fixed sample resulted in a substantially higher viral (5- to 33-fold) extraction efficiency and reduced background noise compared to previously published methods. Using this method, it was found that in general, intertidal photosynthetic microbial mats harbor very high viral abundances (2.8 × 10
10
± 0.3 × 10
10
g
−1
) compared with benthic habitats (10
7
to 10
9
g
−1
). This procedure also showed 4.5- and 4-fold-increased efficacies of extraction of viruses and bacteria, respectively, from intertidal sediments, allowing a single method to be used for the microbial mat and underlying sediment.
Xylan Utilization Regulon in Xanthomonas citri pv. citri Strain 306: Gene Expression and Utilization of Oligoxylosides
Authors: Chow V. , Shantharaj D. , Guo Y. , Nong G. , Minsavage G. V. , Jones J. B. , Preston J. F. 
Published: January 2015

ABSTRACT

Xanthomonas citri
pv. citri strain 306 (
Xcc
306), a causative agent of citrus canker, produces endoxylanases that catalyze the depolymerization of cell wall-associated xylans. In the sequenced genomes of all plant-pathogenic xanthomonads, genes encoding xylanolytic enzymes are clustered in three adjacent operons. In
Xcc
306, these consecutive operons contain genes encoding the glycoside hydrolase family 10 (GH10) endoxylanases Xyn10A and Xyn10C, the
agu67
gene, encoding a GH67 α-glucuronidase (Agu67), the
xyn43E
gene, encoding a putative GH43 α-
l
-arabinofuranosidase, and the
xyn43F
gene, encoding a putative β-xylosidase. Recombinant Xyn10A and Xyn10C convert polymeric 4-
O
-methylglucuronoxylan (MeGX

n

) to oligoxylosides methylglucuronoxylotriose (MeGX
3
), xylotriose (X
3
), and xylobiose (X
2
).
Xcc
306 completely utilizes MeGX

n

predigested with Xyn10A or Xyn10C but shows little utilization of MeGX

n

.
Xcc
306 with a deletion in the gene encoding α-glucuronidase (
Xcc
306 Δ
agu67
) will not utilize MeGX
3
for growth, demonstrating the role of Agu67 in the complete utilization of GH10-digested MeGX

n

. Preferential growth on oligoxylosides compared to growth on polymeric MeGX

n

indicates that GH10 xylanases, either secreted by
Xcc
306
in planta
or produced by the plant host, generate oligoxylosides that are processed by Xyn10 xylanases and Agu67 residing in the periplasm. Coordinate induction by oligoxylosides of
xyn10
,
agu67
,
cirA
, the
tonB
receptor, and other genes within these three operons indicates that they constitute a regulon that is responsive to the oligoxylosides generated by the action of
Xcc
306 GH10 xylanases on MeGX

n

. The combined expression of genes in this regulon may allow scavenging of oligoxylosides derived from cell wall deconstruction, thereby contributing to the tissue colonization and/or survival of
Xcc
306 and, ultimately, to plant disease.
Metabolic Engineering of Corynebacterium glutamicum for Methanol Metabolism
Authors: Witthoff Sabrina , Schmitz Katja , Niedenführ Sebastian , Nöh Katharina , Noack Stephan , Bott Michael , Marienhagen Jan 
Published: January 2015

ABSTRACT

Methanol is already an important carbon feedstock in the chemical industry, but it has found only limited application in biotechnological production processes. This can be mostly attributed to the inability of most microbial platform organisms to utilize methanol as a carbon and energy source. With the aim to turn methanol into a suitable feedstock for microbial production processes, we engineered the industrially important but nonmethylotrophic bacterium
Corynebacterium glutamicum
toward the utilization of methanol as an auxiliary carbon source in a sugar-based medium. Initial oxidation of methanol to formaldehyde was achieved by heterologous expression of a methanol dehydrogenase from
Bacillus methanolicus
, whereas assimilation of formaldehyde was realized by implementing the two key enzymes of the ribulose monophosphate pathway of
Bacillus subtilis
: 3-hexulose-6-phosphate synthase and 6-phospho-3-hexuloisomerase. The recombinant
C. glutamicum
strain showed an average methanol consumption rate of 1.7 ± 0.3 mM/h (mean ± standard deviation) in a glucose-methanol medium, and the culture grew to a higher cell density than in medium without methanol. In addition, [
13
C]methanol-labeling experiments revealed labeling fractions of 3 to 10% in the m + 1 mass isotopomers of various intracellular metabolites. In the background of a
C. glutamicum
Δ
ald
Δ
adhE
mutant being strongly impaired in its ability to oxidize formaldehyde to CO
2
, the m + 1 labeling of these intermediates was increased (8 to 25%), pointing toward higher formaldehyde assimilation capabilities of this strain. The engineered
C. glutamicum
strains represent a promising starting point for the development of sugar-based biotechnological production processes using methanol as an auxiliary substrate.
Listeria Phage and Phage Tail Induction Triggered by Components of Bacterial Growth Media (Phosphate, LiCl, Nalidixic Acid, and Acriflavine)
Authors: Lemaître Jean-Paul , Duroux Amandine , Pimpie Romain , Duez Jean-Marie , Milat Marie-Louise 
Published: January 2015

ABSTRACT

The detection of
Listeria monocytogenes
from food is currently carried out using a double enrichment. For the ISO methodology, this double enrichment is performed using half-Fraser and Fraser broths, in which the overgrowth of
L. innocua
can occur in samples where both species are present. In this study, we analyzed the induction of phages and phage tails of
Listeria
spp. in these media and in two brain heart infusion (BHI) broths (BHIM [bioMérieux] and BHIK [Biokar]) to identify putative effectors. It appears that Na
2
HPO
4
at concentrations ranging from 1 to 40 g/liter with an initial pH of 7.5 can induce phage or phage tail production of
Listeria
spp., especially with 10 g/liter of Na
2
HPO
4
and a pH of 7.5, conditions present in half-Fraser and Fraser broths. Exposure to LiCl in BHIM (18 to 21 g/liter) can also induce phage and phage tail release, but in half-Fraser and Fraser broths, the concentration of LiCl is much lower (3 g/liter). Low phage titers were induced by acriflavine and/or nalidixic acid. We also show that the production of phages and phage tails can occur in half-Fraser and Fraser broths. This study points out that induction of phages and phage tails could be triggered by compounds present in enrichment media. This could lead to a false-negative result for the detection of
L. monocytogenes
in food products.
Identification and Characterization of Carboxyl Esterases of Gill Chamber-Associated Microbiota in the Deep-Sea Shrimp Rimicaris exoculata by Using Functional Metagenomics
Authors: Alcaide María , Tchigvintsev Anatoli , Martínez-Martínez Mónica , Popovic Ana , Reva Oleg N. , Lafraya Álvaro , Bargiela Rafael , Nechitaylo Taras Y. , Matesanz Ruth , Cambon-Bonavita Marie-Anne , Jebbar Mohamed , Yakimov Michail M. , Savchenko Alexei , Golyshina Olga V. , Yakunin Alexander F. , Golyshin Peter N. , Ferrer Manuel 
Published: January 2015

ABSTRACTThe shrimpRimicaris exoculatadominates the fauna in deep-sea hydrothermal vent sites along the Mid-Atlantic Ridge (depth, 2,320 m). Here, we identified and biochemically characterized three carboxyl esterases from microbial communities inhabiting theR. exoculatagill that were isolated by naive screens of a gill chamber metagenomic library. These proteins exhibit low to moderate identity to known esterase sequences (≤52%) and to each other (11.9 to 63.7%) and appear to have originated from unknown species or from genera ofProteobacteriarelated toThiothrix/Leucothrix(MGS-RG1/RG2) and to theRhodobacteraceaegroup (MGS-RG3). A library of 131 esters and 31 additional esterase/lipase preparations was used to evaluate the activity profiles of these enzymes. All 3 of these enzymes had greater esterase than lipase activity and exhibited specific activities with ester substrates (≤356 U mg−1) in the range of similar enzymes. MGS-RG3 was inhibited by salts and pressure and had a low optimal temperature (30°C), and its substrate profile clustered within a group of low-activity and substrate-restricted marine enzymes. In contrast, MGS-RG1 and MGS-RG2 were most active at 45 to 50°C and were salt activated and barotolerant. They also exhibited wider substrate profiles that were close to those of highly active promiscuous enzymes from a marine hydrothermal vent (MGS-RG2) and from a cold brackish lake (MGS-RG1). The data presented are discussed in the context of promoting the examination of enzyme activities of taxa found in habitats that have been neglected for enzyme prospecting; the enzymes found in these taxa may reflect distinct habitat-specific adaptations and may constitute new sources of rare reaction specificities.
Bacteriophage PBC1 and Its Endolysin as an Antimicrobial Agent against Bacillus cereus
Authors: Kong Minsuk , Ryu Sangryeol 
Published: January 2015

ABSTRACT

Bacillus cereus
is an opportunistic human pathogen responsible for food poisoning and other, nongastrointestinal infections. Due to the emergence of multidrug-resistant
B. cereus
strains, the demand for alternative therapeutic options is increasing. To address these problems, we isolated and characterized a
Siphoviridae
virulent phage, PBC1, and its lytic enzymes. PBC1 showed a very narrow host range, infecting only 1 of 22
B. cereus
strains. Phylogenetic analysis based on the major capsid protein revealed that PBC1 is more closely related to the
Bacillus clarkii
phage BCJA1c and phages of lactic acid bacteria than to the phages infecting
B. cereus
. Whole-genome comparison showed that the late-gene region, including the terminase gene, structural genes, and holin gene of PBC1, is similar to that from
B. cereus
temperate phage 250, whereas their endolysins are different. Compared to the extreme host specificity of PBC1, its endolysin, LysPBC1, showed a much broader lytic spectrum, albeit limited to the genus
Bacillus
. The catalytic domain of LysPBC1 when expressed alone also showed
Bacillus
-specific lytic activity, which was lower against the
B. cereus
group but higher against the
Bacillus subtilis
group than the full-length protein. Taken together, these results suggest that the virulent phage PBC1 is a useful component of a phage cocktail to control
B. cereus
, even with its exceptionally narrow host range, as it can kill a strain of
B. cereus
that is not killed by other phages, and that LysPBC1 is an alternative biocontrol agent against
B. cereus
.
Effects of Norspermidine and Spermidine on Biofilm Formation by Potentially Pathogenic Escherichia coli and Salmonella enterica Wild-Type Strains
Authors: Nesse Live L. , Berg Kristin , Vestby Lene K. 
Published: January 2015

ABSTRACT

Polyamines are present in all living cells. In bacteria, polyamines are involved in a variety of functions, including biofilm formation, thus indicating that polyamines may have potential in the control of unwanted biofilm. In the present study, the effects of the polyamines norspermidine and spermidine on biofilms of 10 potentially pathogenic wild-type strains of
Escherichia coli
serotype O103:H2,
Salmonella enterica
subsp.
enterica
serovar Typhimurium, and
S. enterica
serovar Agona were investigated. We found that exogenously supplied norspermidine and spermidine did not mediate disassembly of preformed biofilm of any of the
E. coli
and
S. enterica
strains. However, the polyamines did affect biofilm production. Interestingly, the two species reacted differently to the polyamines. Both polyamines reduced the amount of biofilm formed by
E. coli
but tended to increase biofilm formation by
S. enterica
. Whether the effects observed were due to the polyamines specifically targeting biofilm formation, being toxic for the cells, or maybe a combination of the two, is not known. However, there were no indications that the effect was mediated through binding to exopolysaccharides, as earlier suggested for
E. coli
. Our results indicate that norspermidine and spermidine do not have potential as inhibitors of
S. enterica
biofilm. Furthermore, we found that the commercial polyamines used contributed to the higher pH of the test medium. Failure to acknowledge and control this important phenomenon may lead to misinterpretation of the results.
Retention in Treated Wastewater Affects Survival and Deposition of Staphylococcus aureus and Escherichia coli in Sand Columns
Authors: Li Jiuyi , Zhao Xiaokang , Tian Xiujun , Li Jin , Sjollema Jelmer , Wang Aimin 
Published: January 2015

ABSTRACT

The fate and transport of pathogenic bacteria from wastewater treatment facilities in the Earth's subsurface have attracted extensive concern over recent decades, while the impact of treated-wastewater chemistry on bacterial viability and transport behavior remains unclear. The influence of retention time in effluent from a full-scale municipal wastewater treatment plant on the survival and deposition of
Staphylococcus aureus
and
Escherichia coli
strains in sand columns was investigated in this paper. In comparison to the bacteria cultivated in nutrient-rich growth media, retention in treated wastewater significantly reduced the viability of all strains. Bacterial surface properties, e.g., zeta potential, hydrophobicity, and surface charges, varied dramatically in treated wastewater, though no universal trend was found for different strains. Retention in treated wastewater effluent resulted in changes in bacterial deposition in sand columns. Longer retention periods in treated wastewater decreased bacterial deposition rates for the strains evaluated and elevated the transport potential in sand columns. We suggest that the wastewater quality should be taken into account in estimating the fate of pathogenic bacteria discharged from wastewater treatment facilities and the risks they pose in the aquatic environment.
Involvement of the Cytochrome P450 System EthBAD in the
N
-Deethoxymethylation of Acetochlor by Rhodococcus sp. Strain T3-1
Authors: Wang Fei , Zhou Jie , Li Zhoukun , Dong Weiliang , Hou Ying , Huang Yan , Cui Zhongli 
Published: January 2015

ABSTRACT

Acetochlor [2-chloro-
N
-(ethoxymethyl)-
N
-(2-ethyl-6-methylphenyl)-acetamide] is a widely applied herbicide with potential carcinogenic properties.
N
-Deethoxymethylation is the key step in acetochlor biodegradation.
N
-Deethoxymethylase is a multicomponent enzyme that catalyzes the conversion of acetochlor to 2′-methyl-6′-ethyl-2-chloroacetanilide (CMEPA). Fast detection of CMEPA by a two-enzyme (
N
-deethoxymethylase–amide hydrolase) system was established in this research. Based on the fast detection method, a three-component enzyme was purified from
Rhodococcus
sp. strain T3-1 using ammonium sulfate precipitation and hydrophobic interaction chromatography. The molecular masses of the components of the purified enzyme were estimated to be 45, 43, and 11 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Based on the results of peptide mass fingerprint analysis, acetochlor
N
-deethoxymethylase was identified as a cytochrome P450 system, composed of a cytochrome P450 oxygenase (43-kDa component; EthB), a ferredoxin (45 kDa; EthA), and a reductase (11 kDa; EthD), that is involved in the degradation of methyl
tert
-butyl ether. The gene cluster
ethABCD
was cloned by PCR amplification and expressed in
Escherichia coli
BL21(DE3). Resting cells of a recombinant
E. coli
strain showed deethoxymethylation activity against acetochlor. Subcloning of
ethABCD
showed that
ethABD
expressed in
E. coli
BL21(DE3) has the activity of acetochlor
N
-deethoxymethylase and is capable of converting acetochlor to CMEPA.