bluuebunny/crossref_metadata_2025 huggingface dataset:
Chryseomicrobium amylolyticum sp. nov., isolated from a semi-arid tropical soil, and emended descriptions of the genus Chryseomicrobium and Chryseomicrobium imtechense
Authors: Raj P. Shalem , Sasikala Ch. , Ramaprasad E. V. V. , Subhash Y. , Busse H.-J. , Schumann P. , Ramana Ch. V.
Published: December 2012

A rod-shaped, non-motile, Gram-stain-positive, catalase-positive, starch-hydrolysing strain, JC16T, was isolated from a semi-arid tropical soil from India. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain JC16T clustered with the type species of the genus Chryseomicrobium, Chryseomicrobium imtechense MW 10T, a member of the family Planococcaceae within the phylum Firmicutes with 99.3 % sequence similarity. Major (>10 %) fatty acids of strain JC16T were iso-C15 : 0 and iso-C16 : 0. Minor (<10 and >1 %) amounts of C16 : 0, iso-C14 : 0, anteiso-C15 : 0, iso-C17 : 0, anteiso-C17 : 0, iso-C17 : 1ω10c and C16 : 1ω11c are present in strain JC16T. Polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phospholipids (PL2–4), aminolipids (AL1, 2) and an unknown lipid. Cell wall peptidoglycan was of the type l-Orn–d-Glu. The quinone system was composed of MK-7, MK-8 and MK-6. Genomic DNA G+C content of strain JC16T was 57.6 mol%. Distinct physiological, chemotaxonomic and genotypic differences (37 % reassociation based on DNA–DNA hybridization) from Chryseomicrobium imtechense MW 10T support the classification of strain JC16T as a representative of a novel species in the genus Chryseomicobium, for which the name Chryseomicrobium amylolyticum sp. nov. (type strain JC16T = DSM 23442T = NBRC 105215T) is proposed.
Gibbsiella papilionis sp. nov., isolated from the intestinal tract of the butterfly Mycalesis gotama, and emended description of the genus

Gibbsiella
Authors: Kim Pil Soo , Shin Na-Ri , Kim Joon Yong , Yun Ji-Hyun , Hyun Dong-Wook , Bae Jin-Woo
Published: December 2012

A novel Gram-negative, non-motile, facultative anaerobic and rod-shaped bacterium, designated strain LEN33T, was isolated from the intestinal tract of a butterfly (Mycalesis gotama). Strain LEN33T grew optimally at 37 °C in the presence of 1 % (w/v) NaCl and at pH 9. The novel strain was oxidase-negative and catalase-positive. The major cellular fatty acids were C14 : 0, C16 : 0 and cyclo-C17 : 0. Strain LEN33T contained two unidentified lipids, three unidentified amino-phospholipids, phosphatidylethanolamine (PE) and phosphatidylglycerol (PG). The major isoprenoid quinone was ubiquinone-8 (Q-8). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain LEN33T was most closely related to

Gibbsiella quercinecans

FRB 97T and

Gibbsiella dentisursi

NUM 1720T, with 98.7 % similarities. DNA–DNA hybridization experiments indicated less than 40.7±2 % relatedness to the closest phylogenetic species,

G. quercinecans

FRB 97T. The G+C content of genomic DNA was 58.7 mol%. Phenotypic, phylogenetic and genotypic analysis indicated that strain LEN33T represents a novel species within the genus

Gibbsiella

, for which the name Gibbsiella papilionis is proposed. The type strain is referred to as LEN33T ( = KACC 16707T = JCM 18389T). An emended description of the genus Gibbsiella is also proposed.
Azospirillum humicireducens sp. nov., a nitrogen-fixing bacterium isolated from a microbial fuel cell
Authors: Zhou Shungui , Han Luchao , Wang Yueqiang , Yang Guiqin , Zhuang Li , Hu Pei
Published: December 2012

A Gram-negative, facultative anaerobic, motile, spiral, straight-to-slightly curved rod-shaped and nitrogen-fixing strain, designated SgZ-5T, was isolated from a microbial fuel cell (MFC) and was characterized by means of a polyphasic approach. Growth occurred with 0–1 % (w/v) NaCl (optimum 1 %) and at pH 5.5–8.5 (optimum pH 7.2) and at 25–37 °C (optimum 30 °C) in nutrient broth (NB). The strain had the ability to grow under anaerobic conditions via the oxidation of various organic compounds coupled to the reduction of anthraquione-2,6-disulfonate (AQDS). Chemotaxonomic characteristics (main ubiquinone Q-10, major fatty acid C18 : 1ω7c/C18 : 1ω6c and DNA G+C content 67.7 mol%) were similar to those of members of the genus

Azospirillum

. According to the results of phylogenetic analyses, strain SgZ-5T belonged to the genus

Azospirillum

within the family

Rhodospirillaceae

of the class

Alphaproteobacteria

, and was related most closely to the type strains of

Azospirillum lipoferum

,

Azospirillum thiophilum

and

Azospirillum oryzae

(98.0, 97.6 and 97.1 % 16S rRNA gene sequence similarity, respectively). DNA–DNA pairing studies showed that the unidentified organism displayed reassociation values of 36.7±3.7, 24.1±2.2 and 22.3±2.4 % to the type strains of

A. lipoferum

,

A. thiophilum

and

A. oryzae

, respectively. Similarities between nifH gene sequences of strain SgZ-5T and members of the genus

Azospirillum

ranged from 94.0 to 97.0 %. A combination of phenotypic, chemotaxonomic, phylogenetic and genotypic data clearly indicated that strain SgZ-5T represents a novel species, for which the name Azospirillum humicireducens sp. nov. is proposed. The type strain is SgZ-5T ( = CCTCC AB 2012021T = KACC 16605T).
Novosphingobium
aquaticum sp. nov., isolated from the humic-matter-rich bog lake Grosse Fuchskuhle
Authors: Glaeser Stefanie P. , Bolte Kathrin , Busse Hans-Jürgen , Kämpfer Peter , Grossart Hans-Peter , Glaeser Jens
Published: December 2012

A yellow‐pigmented, Gram-negative rod, designated FNE08-86T, was isolated from subsurface water of the humic-matter-rich and almost-neutral north-east basin of the experimentally divided bog lake Grosse Fuchskuhle (Brandenburg, Germany). Analysis of the nearly full-length 16S rRNA gene sequence showed the highest 16S rRNA gene sequence similarity with

Novosphingobium rosa

IAM 14222T (96.3 %). Sequence similarities with all other members of the genus

Novosphingobium

species were <96 %, but phylogenetic tree construction clearly showed the placement of strain FNE08-86T within the genus

Novosphingobium

. The predominant fatty acids were C18 : 1ω7c and C16 : 0, and only a single 2-hydroxy fatty acid, C14 : 0 2-OH, was detected. The polar lipid profile revealed phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine as major compounds, with smaller amounts of sphingoglycolipid, phosphatidylmonomethylethanolamine, diphosphatidylglycerol and several unidentified lipids. In the quinone system ubiquinone Q-10 was predominant and in the polyamine pattern spermidine was predominant. Characterization by genotypic, chemotaxonomic and phenotypic analysis indicated that strain FNE08-86T represents a novel species of the genus

Novosphingobium

, for which we propose the name Novosphingobium aquaticum sp. nov. (type strain FNE08-86T  = DSM 25088T  = CCM 7983T).
Microbacterium lemovicicum sp. nov., a bacterium isolated from a natural uranium-rich soil
Authors: Mondani Laure , Piette Laurie , Christen Richard , Bachar Dipankar , Berthomieu Catherine , Chapon Virginie
Published: December 2012

An actinobacterial strain, designated ViU22T, was isolated from a natural uranium-rich soil and was studied using a polyphasic approach. Cells formed orange-pigmented colonies, were rod-shaped, Gram-positive (non-staining method), non-motile and non-spore-forming. This organism grew in 0–4.5 % (w/v) NaCl and at 15–37 °C, with optimal growth occurring in 0.5 % (w/v) NaCl and at 30 °C. Comparative 16S rRNA gene sequence analysis revealed that the strain ViU22T belonged to the genus

Microbacterium

. It exhibited highest 16S rRNA gene sequence similarity with the type strains of

Microbacterium testaceum

(98.14 %) and

Microbacterium binotii

(98.02 %). The DNA–DNA relatedness of strains ViU22T with the most closely related type strains

Microbacterium testaceum

and

Microbacterium binotii

DSM 19164T was 20.10 % (±0.70) and 28.05 % (±0.35), respectively. Strain ViU22T possessed a type B2β peptidoglycan with partial substitution of glutamic acid by 3-hydroxy glutamic acid. The major menaquinones were MK-11 and MK-12. Major polar lipids detected in the strain ViU22T were diphosphatidylglycerol, phosphatidylglycerol, an unknown phospholipid and unknown glycolipids. The predominant fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0, a pattern reported for other

Microbacterium

species. The major cell-wall sugars were galactose, xylose and mannose and the DNA G+C content was 71 mol%. Together, the DNA–DNA hybridization results and the differentiating phenotypic characteristics, showed that strain ViU22T should be classified as the type strain of a novel species within the genus

Microbacterium

, for which the name

Microbacterium

lemovicicum sp. nov. is proposed. The type strain is ViU22T ( = ATCC BAA-2396T = CCUG 62198T = DSM 25044T).
Wickerhamomyces mori sp. nov., an anamorphic yeast species found in the guts of wood-boring insect larvae
Authors: Hui Feng-Li , Chen Liang , Chu Xue-Ying , Niu Qiu-Hong , Ke Tao
Published: December 2012

A novel anamorphic yeast species is described to accommodate three isolates recovered from the guts of three different wood-boring insect larvae collected in Henan, central China. On the basis of sequence analyses of the D1/D2 domains of the large-subunit rRNA gene and the internal transcribed spacer regions, the three strains are assigned to a novel species of the genus Wickerhamomyces, although the formation of ascospores was not observed. These strains also exhibited a number of distinct morphological and physiological characteristics that clearly differentiated them from Wickerhamomyces mucosus, Candida odintsovae and Wickerhamomyces rabaulensis, the most closely related species. In view of the phenotypic differences and unique rRNA gene sequences, we consider that these three isolates represent a novel species of the genus Wickerhamomyces, Wickerhamomyces mori sp. nov. The type strain is NYNU 1216T ( = CICC 1983T  = CBS 12678T).
Genotype analysis of Porphyromonas gingivalis fimA in Korean adults using new primers
Authors: Moon Ji-Hoi , Herr Yeek , Lee Hyeon-Woo , Shin Seung-Il , Kim Cheul , Amano Atsuo , Lee Jin-Yong
Published: December 2012

Strains of Porphyromonas gingivalis, a periodontopathic bacterium, are classified into six genotypic variants based on nucleotide sequence differences in the fimA gene encoding FimA. A PCR assay using primer sets specific for each genotype has demonstrated that the most predominant fimA genotype in periodontitis patients is type II, which is now commonly referred to as the periodontitis-associated fimA genotype of P. gingivalis. However, the potential for false type II fimA positives caused by cross-hybridization of type II fimA-specific primers with type Ib fimA has complicated the genotyping. A previous study developed new primers that specifically amplified only the DNA fragment of type II fimA. The aim of the present study was to assess the prevalence of P. gingivalis fimA genotypes in Korean adults and to reconfirm the relationship between type II fimA and periodontitis using the new primers. Among 412 Korean adults, P. gingivalis was detected in 97.5 % of patients and 57.8 % of healthy subjects. Type II fimA was the most widely distributed type among healthy and periodontitis subjects. Organisms with types II, Ib and IV fimA had a significant frequency of occurrence in periodontitis subjects. Statistical analysis, however, revealed that a more significant correlation was found between periodontitis and the occurrence of type Ib fimA.
Appetitive Pavlovian goal-tracking memories reconsolidate only under specific conditions
Authors: Reichelt Amy C. , Lee Jonathan L.C.
Published: December 2012

Despite extensive evidence that appetitive memories undergo reconsolidation, two notable failures to observe reconsolidation have been reported: instrumental responding and goal-tracking. However, these studies do not provide conclusive evidence for a lack of memory reconsolidation due to the numerous boundary conditions that dictate whether a memory will undergo reconsolidation. In this study we sought to reexamine reconsolidation in an appetitive, Pavlovian conditioned approach procedure and the behavioral boundary conditions within which memories are destabilized and reconsolidated. This study demonstrated that a Pavlovian goal-tracking memory, previously thought to be resistant to destabilization, will undergo memory reconsolidation under discrete conditions that favor reconsolidation as opposed to extinction, and that this is dependent on the amount of training rats received. With restricted training, systemic administration of MK-801 impaired memory extinction. In contrast, with more extended training, MK-801 administration impaired memory reconsolidation. We also demonstrate that behavioral boundary conditions that exist for appetitive memory reconsolidation are much more complex than simple parametric calculations. Moreover, extinction per se is not a boundary on reconsolidation, in that MK-801 also has no behavioral effect under some conditions.
Rice GLYCOSYLTRANSFERASE1 Encodes a Glycosyltransferase Essential for Pollen Wall Formation
Authors: Moon Sunok , Kim Sung-Ryul , Zhao Guochao , Yi Jakyung , Yoo Youngchul , Jin Ping , Lee Sang-Won , Jung Ki-hong , Zhang Dabing , An Gynheung
Published: December 2012

The pollen wall consists of an exine and an intine. The mechanism underlying its formation is not well understood. Glycosyltransferases catalyze the modification of biological molecules by attaching a single or multiple sugars and play key roles in a wide range of biological processes. We examined the role of GLYCOSYLTRANSFERASE1 (OsGT1) in pollen wall development in rice (Oryza sativa). This gene is highly expressed in mature pollen, and plants containing alleles caused by transfer DNA insertion do not produce homozygous progeny. Reciprocal crosses between OsGT1/osgt1 and the wild type indicated that the mutation leads to a male gametophyte defect. Microscopic analyses revealed that osgt1 pollen developed normally to the pollen mitosis stage but failed to produce mature grains. In osgt1 pollen, intine structure was disrupted. In addition, starch and protein levels were much lower in the mutant grains. Recombinant OsGT1 transferred glucose from UDP-glucose to the third and seventh positions of quercetin, a universal substrate of glycosyltransferases. Consistent with the role of OsGT1, an OsGT1-green fluorescent protein fusion protein was localized to the Golgi apparatus. Taken together, our results suggest that OsGT1 is a Golgi-localized glycosyltransferase essential for intine construction and pollen maturation, providing new insight into male reproductive development.
Acquisition, Conservation, and Loss of Dual-Targeted Proteins in Land Plants
Authors: Xu Lin , Carrie Chris , Law Simon R. , Murcha Monika W. , Whelan James
Published: December 2012

The dual-targeting ability of a variety of proteins from Physcomitrella patens, rice (Oryza sativa), and Arabidopsis (Arabidopsis thaliana) was tested to determine when dual targeting arose and to what extent it was conserved in land plants. Overall, the targeting ability of over 80 different proteins from rice and P. patens, representing 42 dual-targeted proteins in Arabidopsis, was tested. We found that dual targeting arose early in land plant evolution, as it was evident in many cases with P. patens proteins that were conserved in rice and Arabidopsis. Furthermore, we found that the acquisition of dual-targeting ability is still occurring, evident in P. patens as well as rice and Arabidopsis. The loss of dual-targeting ability appears to be rare, but does occur. Ascorbate peroxidase represents such an example. After gene duplication in rice, individual genes encode proteins that are targeted to a single organelle. Although we found that dual targeting was generally conserved, the ability to detect dual-targeted proteins differed depending on the cell types used. Furthermore, it appears that small changes in the targeting signal can result in a loss (or gain) of dual-targeting ability. Overall, examination of the targeting signals within this study did not reveal any clear patterns that would predict dual-targeting ability. The acquisition of dual-targeting ability also appears to be coordinated between proteins. Mitochondrial intermembrane space import and assembly protein40, a protein involved in oxidative folding in mitochondria and peroxisomes, provides an example where acquisition of dual targeting is accompanied by the dual targeting of substrate proteins.
Trafficking of Vacuolar Proteins: The Crucial Role of Arabidopsis Vacuolar Protein Sorting 29 in Recycling Vacuolar Sorting Receptor
Authors: Kang Hyangju , Kim Soo Youn , Song Kyungyoung , Sohn Eun Ju , Lee Yongjik , Lee Dong Wook , Hara-Nishimura Ikuko , Hwang Inhwan
Published: December 2012

The retromer is involved in recycling lysosomal sorting receptors in mammals. A component of the retromer complex in Arabidopsis thaliana, vacuolar protein sorting 29 (VPS29), plays a crucial role in trafficking storage proteins to protein storage vacuoles. However, it is not known whether or how vacuolar sorting receptors (VSRs) are recycled from the prevacuolar compartment (PVC) to the trans-Golgi network (TGN) during trafficking to the lytic vacuole (LV). Here, we report that VPS29 plays an essential role in the trafficking of soluble proteins to the LV from the TGN to the PVC. maigo1-1 (mag1-1) mutants, which harbor a knockdown mutation in VPS29, were defective in trafficking of two soluble proteins, Arabidopsis aleurain-like protein (AALP):green fluorescent protein (GFP) and sporamin:GFP, to the LV but not in trafficking membrane proteins to the LV or plasma membrane or via the secretory pathway. AALP:GFP and sporamin:GFP in mag1-1 protoplasts accumulated in the TGN but were also secreted into the medium. In mag1-1 mutants, VSR1 failed to recycle from the PVC to the TGN; rather, a significant proportion was transported to the LV; VSR1 overexpression rescued this defect. Moreover, endogenous VSRs were expressed at higher levels in mag1-1 plants. Based on these results, we propose that VPS29 plays a crucial role in recycling VSRs from the PVC to the TGN during the trafficking of soluble proteins to the LV.
REVIEW: The role of ecosystems and their management in regulating climate, and soil, water and air quality
Authors: Smith Pete , Ashmore Mike R. , Black Helaina I. J. , Burgess Paul J. , Evans Chris D. , Quine Timothy A. , Thomson Amanda M. , Hicks Kevin , Orr Harriet G.
Published: December 2012

Ecosystems have a critical role in regulating climate, and soil, water and air quality, but management to change an ecosystem process in support of one regulating ecosystem service can either provide co‐benefits to other services or can result in trade‐offs.

We examine the role of ecosystems in delivering these regulating ecosystem services, using the UK as our case study region. We identify some of the main co‐benefits and trade‐offs of ecosystem management within, and across, the regulating services of climate regulation, and soil, water and air quality regulation, and where relevant, we also describe interactions with other ecosystem services. Our analysis clearly identifies the many important linkages between these different ecosystem services.

However, soil, water and air quality regulation are often governed by different legislation or are under the jurisdiction of different regulators, which can make optimal management difficult to identify and to implement. Policies and legislation addressing air, water and soil are sometimes disconnected, with no integrated overview of how these policies interact. This can lead to conflicting messages regarding the use and management of soil, water and air. Similarly, climate change legislation is separate from that aiming to protect and enhance soil, water and air quality, leading to further potential for policy conflict.

All regulating services, even if they are synergistic, may trade off against other ecosystem services. At a policy level, this may well be the biggest conflict. The fact that even individual regulating services comprise multiple and contrasting indicators (e.g. the various components of water quality such as nutrient levels, acidity, pathogens and sediments), adds to the complexity of the challenge.

Synthesis and applications. We conclude that although there are some good examples of integrated ecosystem management, some aspects of ecosystem management could be better coordinated to deliver multiple ecosystem services, and that an ecosystem services framework to assess co‐benefits and trade‐offs would help regulators, policy‐makers and ecosystem managers to deliver more coherent ecosystem management strategies. In this way, an ecosystem services framework may improve the regulation of climate, and soil, water and air quality, even in the absence of economic valuation of the individual services.
Functional diversity in a large river floodplain: anticipating the response of native and alien macroinvertebrates to the restoration of hydrological connectivity
Authors: Paillex Amael , Dolédec Sylvain , Castella Emmanuel , Mérigoux Sylvie , Aldridge David C.
Published: December 2012

Rivers and floodplains are among the most threatened ecosystems. Hydroelectric power plants and embankments have reduced the hydrological connectivity between rivers and their floodplain channels, leading to loss of freshwater habitats and biological communities. To prevent and reverse such loss, numerous restoration programmes have aimed at rejuvenating the lateral hydrological connectivity between rivers and floodplain channels. Despite considerable global attention, we know remarkably little about the ecological benefits of floodplain restoration programmes.

We analysed the functional diversity of different macroinvertebrate groups (natives and aliens) along a gradient of lateral hydrological connectivity on the Rhône river in France. We used 36 sampling sites to describe the functional diversity (Rao's quadratic entropy) before and after the enhancement of the lateral hydrological connectivity by restoration. The effects of restoration on functional diversity were tested for each macroinvertebrate group and at multiple spatial levels (alpha and beta).

Before restoration, alpha functional diversity of the entire macroinvertebrate community peaked in sites with a high lateral connectivity. The contribution of the native groups to functional diversity was higher than that of the alien group. The latter was not constrained by high values of lateral hydrological connectivity and reached a maximum in highly connected sites.

After restoration, within‐site functional diversity (alpha FD) declined linearly following the enhancement of lateral hydrological connectivity. The restoration operations increased the contribution of the aliens to functional diversity and reduced the contribution of a group of native taxa. In addition, among‐sites functional diversity (beta FD) was successfully enlarged by restoration.

Synthesis and applications. The lateral hydrological connectivity (LHC) represents a key parameter for explaining the functional diversity (FD) of macroinvertebrates in a floodplain ecosystem. Our results demonstrate that restoration‐induced changes to functional diversity can be predicted. Controversially, restoration‐induced enhancement of lateral hydrological connectivity increased the functional diversity of the alien macroinvertebrates. However, these species contributed only to a small part of the total macroinvertebrate functional diversity. We recommend that restoration programmes diversify the levels of lateral hydrological connectivity among the channels to ensure an optimal functional diversity at the floodplain scale.
Invasive species management restores a plant–pollinator mutualism in Hawaii
Authors: Hanna Cause , Foote David , Kremen Claire
Published: December 2012

The management and removal of invasive species may give rise to unanticipated changes in plant–pollinator mutualisms because they can alter the composition and functioning of plant–pollinator interactions in a variety of ways. To utilize a functional approach for invasive species management, we examined the restoration of plant–pollinator mutualisms following the large‐scale removal of an invasive nectar thief and arthropod predator, Vespula pensylvanica.

We reduced V. pensylvanica populations in large plots managed over multiple years to examine the response of plant–pollinator mutualisms and the fruit production of a functionally important endemic Hawaiian tree species, Metrosideros polymorpha. To integrate knowledge of the invader's behaviour and the plant's mating system, we determined the efficacy of V. pensylvanica as a pollinator of M. polymorpha and quantified the dependence of M. polymorpha on animal pollination (e.g. level of self‐compatibility and pollen limitation).

The reduction of V. pensylvanica in managed sites, when compared to unmanaged sites, resulted in a significant increase in the visitation rates of effective bee pollinators (e.g. introduced Apis mellifera and native Hylaeus spp.) and in the fruit production of M. polymorpha.

Apis mellifera, following the management of V. pensylvanica, appears to be acting as a substitute pollinator for M. polymorpha, replacing extinct or threatened bird and bee species in our study system.

Synthesis and applications. Fruit production of the native M. polymorpha was increased after management of the invasive pollinator predator V. pensylvanica; however, the main pollinators were no longer native but introduced. This research thus demonstrates the diverse impacts of introduced species on ecological function and the ambiguous role they play in restoration. We recommend incorporating ecological function and context into invasive species management as this approach may enable conservation managers to simultaneously minimize the negative and maximize the positive impacts (e.g. taxon substitution) of introduced species. Such novel restoration approaches are needed, especially in highly degraded ecosystems.
New Zealand occupational therapists' views on evidence‐based practice: A replicated survey of attitudes, confidence and behaviours
Authors: Graham Fiona , Robertson Linda , Anderson Jane
Published: December 2012

Background/aim

Evidence‐based practice is internationally recognised as an essential component of contemporary occupational therapy, and as being critical to the future of the profession. However, its uptake by therapists has been modest with barriers such as therapists attitudes, skills and organisational support frequently cited. This study explored New Zealand therapists' perceptions of their behaviours, skills and attitudes regarding evidence‐based practice.

Method

A survey comprising open and closed questions was emailed to all therapists holding practicing certificates who had consented to be contacted about research (n = 1587) with 30% (n = 473) of surveys returned. Therapists' evidence‐based practice attitudes, skills and behaviours were examined using descriptive statistics. Relationships between therapists' perceptions of evidence‐based practice and demographic characteristics of therapists were explored using Chi‐square analysis. Text responses were analysed using content analysis.

Results

New Zealand therapists have a positive attitude towards evidence‐based practice (84%), but report moderate reference to research literature (56%) during clinical decision‐making and moderate (66%) to low (35%) levels of confidence in research‐related skills. Therapists with training in evidence‐based practice had higher levels of confidence, perceived research as more relevant to practice and reported less barriers to implementing evidence‐based practice than other therapists. A perception that evidence‐based practice is separate to clinical reasoning was widely held.

Conclusion

New Zealand therapists' evidence‐based practice behaviours, skills and attitudes are largely consistent with international comparisons. However, if New Zealand therapists are to enact the ideal of being ‘evidence‐based’ then accessible training in evidence‐based practice‐related skills is indicated and should include education of what evidence‐based practice means.
High and stable substrate specificities of microorganisms in enhanced biological phosphorus removal plants
Authors: Kindaichi Tomonori , Nierychlo Marta , Kragelund Caroline , Nielsen Jeppe Lund , Nielsen Per Halkjær
Published: December 2012

Microbial communities are typically characterized by conditions of nutrient limitation so the availability of the resources is likely a key factor in the niche differentiation across all species and in the regulation of the community structure. In this study we have investigated whether four species exhibit anyin situshort‐term changes in substrate uptake pattern when exposed to variations in substrate and growth conditions. Microautoradiography was combined with fluorescencein situhybridization to investigatein situcell‐specific substrate uptake profiles of four probe‐defined coexisting species in a wastewater treatment plant with enhanced biological phosphorus removal. These were the filamentous ‘CandidatusMicrothrix’ andCaldilinea(type 0803), the polyphosphate‐accumulating organism ‘Candidatus Accumulibacter’, and the denitrifyingAzoarcus. The experimental conditions mimicked the conditions potentially encountered in the respective environment (starvation, high/low substrate concentration, induction with specific substrates, and single/multiple substrates). The results showed that each probe‐defined species exhibited very distinct and constant substrate uptake profile in time and space, which hardly changed under any of the conditions tested. Such niche partitioning implies that a significant change in substrate composition will be reflected in a changed community structure rather than the substrate uptake response from the different species.
The making of public health emergencies: West Nile virus in New York City
Authors: McCormick Sabrina , Whitney Kristoffer
Published: December 2012

In this article we use the case of the West Nile virus (WNV) to investigate the social construction of public health emergencies (PHEs) and the subsequent changes in public health governance that they instigate. Informed by medical sociological literature on the social construction of illness, science and technology studies, and risk and disaster literature, we create a conceptual framework for connecting health and crisis. Our investigation of the WNV analyses PHEs as brief, but vitally important, moments in which a ‘crisis’ is co‐constructed between states, affected populations and disease vectors. In these moments of crisis new interventions are enacted, which have long‐term effects for institutional structures and disease management. Using extensive qualitative data collection, we conceptualise two mechanisms that underlie the declaration of PHEs and the expansion of related ‘emergencies’ across space and time: (i) crisis interventions that have the potential to marginalise the interaction of citizens with state institutions and (ii) institutional rearrangement of state agencies stemming from the original crisis issue, resulting in altered networks and institutional practices and drawing heavily upon the crisis as a symbol of similar, future public health threats.
The importance of father’s and own education for self‐assessed health across Europe: an East–West divide?
Authors: Monden Christiaan W.S. , de Graaf Nan Dirk
Published: December 2012

How are one’s own education, father’s education, and especially the combination of the two, related to self‐assessed health across European societies? In this study, we test hypotheses about differences in self‐assessed health between 16 post‐socialist countries in Central and Eastern Europe and 17 Western European countries. We find substantial cross‐national variation in the (relative) importance of own and father’s education for self‐assessed health. Over 65 per cent of this cross‐national variation is accounted for by the East–West divide. This simple dichotomy explains cross‐national differences better than gross domestic product or income inequality. An individual’s father’s education is more important, both in absolute and relative terms, for self‐assessed heath in Eastern Europe than in Western Europe. Intergenerational mobility moderates the relative effects of one’s own and one’s father’s education. In Eastern Europe the relative importance of one’s father’s education is greater than it is in Western Europe – particularly for those who are downwardly mobile and have a father with tertiary education. The results are sometimes contradictory to initial expectations; the theoretical implications are discussed.
Introduction: why a Sociology of Pandemics?
Authors: Dingwall Robert , Hoffman Lily M. , Staniland Karen
Published: December 2012

Infectious disease has re‐emerged as a public health threat in an increasingly globalised era, adding trans‐national actors to traditional national and local government actors. This special issue showcases new sociological work in response to this challenge. The contributors have investigated the social construction of new and re‐emerging diseases; the development of surveillance systems, public health governance; the impact of scientific/technical modalities on uncertainty and risk, the interplay of infectious disease, public health and national security concerns, and public and media responses. The case studies range broadly across North America, Europe and Asia and define new agendas for medical sociologists and public health policymakers.
The ‘window of opportunity’ for death after severe brain injury: family experiences
Authors: Kitzinger Jenny , Kitzinger Celia
Published: December 2012

This article builds on and develops the emerging bioethics literature on the ‘window of opportunity’ for allowing death by withholding or withdrawing treatment. Our findings are drawn from in‐depth interviews with 26 people (from 14 different families) with severely brain injured relatives. These interviews were specifically selected from a larger study on the basis of interviewees’ reports that their relatives would not have wanted to be kept alive in their current condition (e.g. in vegetative or minimally conscious states). Our analysis tracks the decision‐making processes that have led to the situation in which life‐sustaining treatments continue to be delivered to these patients – maintaining them in a state that some families describe as a ‘fate worse than death’. We show how the medico‐legal ‘window of opportunity’ for allowing the patient to die structures family experience and fails to deliver optimal outcomes for patients. We end with some suggestions for change.
Charismatic authority in modern healthcare: the case of the ‘diabetes specialist podiatrist’
Authors: Bacon Dawn , Borthwick Alan M.
Published: December 2012

Professional specialisation is broadly considered to result from increased complexity in professional knowledge and to be linked to specialist education, formalised credentials and registration. However, the degree of formal organisation may vary across professions. In healthcare, although medical specialisation is linked to rigorous selection criteria, formal training programmes and specialist registration, some forms of specialisation in the allied health professions are much less formal. Drawing on Weber’s concept of charismatic authority, the establishment of a specialist role in podiatry, the ‘diabetes specialist podiatrist’, in the absence of codified or credentialed authority, is explored. ‘Charismatic’ leaders in podiatry, having attracted a following of practitioners, were able to constitute a speciality area of practice in the absence of established career pathways and acquire a degree of legitimacy in the medical field of diabetology.
Antibacterial activity of zinc oxide nanoparticle suspensions on food‐borne pathogens
Authors: Mirhosseini Mahboubeh , Firouzabadi Fatemeh B
Published: December 2012

Nanoparticles (NPs) are increasingly recognised for their utility in biological applications including nanomedicine and food safety. The present study investigated the antibacterial activity of zinc oxide (ZnO) when tested against the Gram‐negative bacteria Escherichia coli as well as the Gram‐positive bacterium Staphylococcus aureus, and the effect was more pronounced with the Gram‐positive than with the Gram‐negative bacteria. ZnO NPs also exhibited a preferential ability to suppress growth of E. coli and S. aureus in milk. This study suggested that the application of ZnO NPs as antibacterial agents in food systems and medicine may be effective at inhibiting certain pathogens.
Protective Effects of Merlot Red Wine Extract and its Major Polyphenols in Pc12 Cells under Oxidative Stress Conditions
Authors: Martín Sara , González‐Burgos Elena , Carretero M. Emilia , Gómez‐Serranillos M. Pilar
Published: December 2012

Abstract:  The potential effect of the extracts from free‐run and pressed Merlot red wine has been evaluated in PC12 cells under oxidative stress situation. Comparing both vinification process, pressed Merlot red wine extract possessed higher neuroprotective activity than the free run wine, possibly attributed to the major content in all global polyphenolic families. High performance liquid chromatography determination of individual polyphenols showed that the major compounds found in Merlot red wine extract were quercetin, catechin, epicatechin, tyrosol, gallic acid, and procyanidins. Pretreatments with these polyphenolic compounds (0.25 mM and 0.1 mM, 24 h) significantly increased cell viability of H2O2 and Fenton reaction treated cells. Moreover, these polyphenols attenuated ROS production and decreased the Redox Index of glutathione (RI = GSSG/GSH + GSSG) in cells treated only with Fenton reaction. Furthermore, some polyphenols induced antioxidant enzymes activity and protein expression. Quercetin was the most active. These results support the beneficial effects of red wine extracts and some of its polyphenols under oxidative stress conditions.

Practical Application:  This research provides evidences of the preventive properties of wine extracts and its major polyphenols under oxidative stress conditions.
Proanthocyanidin Oligomers Isolated from Salacia reticulata leaves potently Inhibit Pancreatic Lipase Activity
Authors: Koga K. , Hisamura M. , Kanetaka T. , Yoshino K. , Matsuo Y. , Tanaka T.
Published: December 2012

Abstract:  The pancreatic lipase inhibitory (PLI) activity of leaf extracts (aqueous, 60 and 99.8 (v/v)% EtOH) of Salacia reticulata Wight, referred to “Kothala himbutu” (KT) in Singhalese, was compared with that of KT stem extracts. Evaporated residue contents and PLI activity of each leaf extract were higher than those of each stem extract, respectively. Among the extracts, the 60% EtOH leaf extract showed the most potent PLI activity. The 60% EtOH leaf extract was separated by a Diaion HP20/water‐acetone system and furthermore the most potent fraction by a Sephadex LH20/water‐ethanol‐acetone system. The 60% acetone fraction from the LH20/water‐ethanol‐acetone system had the most potent PLI activity (IC50 value; 15 ppm).

The active compounds in the active fraction of KT leaves were most likely a polyphenol, as assessed by the Folin–Ciocalteu method. Based on these spectroscopic and chemical examinations, the active fraction was shown to be proanthocyanidin oligomers composed of epigallocatechin, epicathechin, and epiafzelechin as main constituents. The degree of polymerization was estimated to be about 5 from the ratio of the peak area of the thio ethers/flavan‐3‐ols at 230 nm. This was consistent with the results of matrix‐assisted laser desorption ionization time‐of‐flight (MALDI‐TOF) MS, which showed the [M+Na]+ peaks corresponding to trimers—octamers. From the average molecular weight and IC50 value of the active compounds estimated on these results, the active compounds from the KT leaf extract were one of the stronger effective lipid‐lowering therapeutic agent, of which PLI activity (μM/L) was almost the same as epigallocatechin gallate.

Practical Application:  Proanthocyanidin oligomers isolated from Salacia reticulata, referred to “Kothala himbutu” (KT) in Singhalese, leaves was proved to potently inhibit pancreatic lipase activity. After confirming in vivo examination, healthy foods, teas, and liquors containing the extracts of KT leaves are expected to be on market.
Comparative randomized study on efficacy of losartan versus propranolol in lowering portal pressure in decompensated chronic liver disease
Authors: Agasti Ananta Kumar , Mahajan Ajay U. , Phadke Aniruddha Y. , Nathani Pratap J. , Sawant Prabha
Published: December 2012

Objective

This study aimed to compare the efficacy of losartan, an angiotensin II receptor antagonist, with propranolol on portal hypertension in patients with decompensated chronic liver disease.

Methods

In all, 30 patients with Child–Pugh B cirrhosis and large varices without any prior therapy for portal hypertension were randomized to either losartan (n = 15) or propranolol (n = 15). Clinical, biochemical and hemodynamic parameters including hepatic venous pressure gradient (HVPG), wedged hepatic venous pressure (WHVP), mean arterial blood pressure (MABP) and free hepatic venous pressure (FHVP) were measured at baseline and after 4‐week therapy. Patients with HVPG < 12 mmHg were regarded as responders.

Results

An equal number of responders were seen in both groups (6/15, 40.0%). The reduction of WHVP and HVPG was greater in the losartan group than in the propranolol group, although no significant differences between them were found. Heart rate decreased more in the propranolol arm than in the losartan arm (P < 0.01); however, no correlation between the decrease of heart rate and the reduction of HVPG was observed. One patient in the losartan group, although a responder, had gastrointestinal bleeding 2 months after the drug administration, but the varices were small under endoscopy and did not require definitive therapy. The fall of MABP was greater with losartan, with no statistical difference between the two groups.

Conclusion

The effect of losartan was comparable to propranolol in reducing portal pressure in decompensated Child–Pugh B chronic liver disease.
LbNrt RNA silencing in the mycorrhizal symbiont Laccaria bicolor reveals a nitrate‐independent regulatory role for a eukaryotic NRT2‐type nitrate transporter
Authors: Kemppainen Minna J. , Pardo Alejandro G.
Published: December 2012

Fungal nitrogen metabolism plays a fundamental role in function of mycorrhizal symbiosis and consequently in nutrient cycling of terrestrial ecosystems. Despite its global ecological relevance the information on control and molecular regulation of nitrogen utilization in mycorrhizal fungi is very limited. We have extended the nitrate utilization RNA silencing studies of the model mycorrhizal basidiomycete, Laccaria bicolor, by altering the expression of LbNrt, the sole nitrate transporter‐encoding gene of the fungus. Here we report the first nutrient transporter mutants for mycorrhizal fungi. Silencing of LbNrt results in fungal strains with minimal detectable LbNrt transcript levels, significantly reduced growth capacity on nitrate and altered symbiotic interaction with poplar. Transporter silencing also creates marked co‐downregulation of whole Laccaria fHANT‐AC (fungal high‐affinity nitrate assimilation cluster). Most importantly, this effect on the nitrate utilization pathway appears independent of extracellular nitrate or nitrogen status of the fungus. Our results indicate a novel and central nitrate uptake‐independent regulatory role for a eukaryotic nitrate transporter. The possible cellular mechanisms behind this regulation mode are discussed in the light of current knowledge on NRT2‐type nitrate transporters in different eukaryotes.
Harmonizing, annotating and sharing data in biodiversity–ecosystem functioning research
Authors: Nadrowski Karin , Ratcliffe Sophia , Bönisch Gerhard , Bruelheide Helge , Kattge Jens , Liu Xiaojuan , Maicher Lutz , Mi Xiangcheng , Prilop Michael , Seifarth Daniel , Welter Karl , Windisch Sven , Wirth Christian
Published: December 2012

The integrative research field of biodiversity–ecosystem functioning (BEF) requires close collaboration between researchers from different disciplines working on different scales in time, space as well as taxon resolution. Data can describe anything from abiotic ecosystem components, to organisms, parts of organisms, genetic information or element stocks and flows. Researchers prefer the convenience of spreadsheets for data preparation, which can lead to isolated data sets that are diverse in structure and follow diverging naming conventions.

BEFdata (https://github.com/befdata/befdata) is a new, open source web platform for the upload, validation and storage of data from a formatted Excel workbook. Metadata can be downloaded in Ecological Metadata Language (EML). BEFdata allows the harmonization of naming conventions by generating category lists from the primary data, which can be reviewed and managed via the Excel workbook or directly on the platform. BEFdata provides a secure environment during ongoing analysis; project members can only access primary data from other researchers after the acceptance of a data request.

Due to its generic database schema, BEFdata platforms can be used for any research domain working with tabular data. It supports the compilation of coherent data sets at the level of the primary data, allowing researchers to explicitly model correlation structures across data sets for synthesis. The EML export enables efficient publishing of data in global repositories.
Comparing parent–offspring regression with frequentist and Bayesian animal models to estimate heritability in wild populations: a simulation study for Gaussian and binary traits
Authors: de Villemereuil Pierre , Gimenez Olivier , Doligez Blandine
Published: December 2012

Estimating heritability of traits in wild populations is a major prerequisite to understand their evolution. Until recently, most heritability estimates had been obtained using parent‐offspring regressions. However, the popularity of animal models, that is, (generalized) linear mixed models assessing the genetic variance component based on population pedigree information, has markedly increased in the past few years. Animal models are claimed to perform better than parent–offspring regressions mainly because they use full between‐individual relatedness information and they allow explicit modelling of the environmental effects shared by individuals. However, the differences between heritability estimates obtained using both approaches are not straight forward, and the factors influencing these differences remain unclear.

We performed a simulation study to evaluate and compare the accuracy and precision of estimates obtained from parent–offspring regressions and animal models using both Frequentist (REML, PQL) and Bayesian (MCMC) estimation methods. We explored the influence of (i) the presence and type of shared environmental effects (non‐transgenerational or transgenerational), (ii) the distribution of the phenotypic trait considered (Gaussian or binary trait) and (iii) data quantity and quality (sample size, pedigree connectivity) on heritability estimates obtained from the two approaches for different levels of true heritability.

In the absence of shared environmental effects, the animal model using the REML method performed best for a Gaussian trait, while the animal model using MCMC was more appropriate for a binary trait. For low quantity and quality data, and a binary trait, the parent–offspring regression yielded very imprecise estimates.

Estimates from the parent–offspring regression were not influenced by a non‐transgenerational shared environmental effect, whereas estimates from animal models in which environmental effects are ignored were affected by both non‐transgenerational and transgenerational effects.

We discuss the relevance of each approach and estimation method for estimating heritability in wild populations. Importantly, because most effects fitted in animal models are, in fact, non‐transgenerational (including environmental maternal effects), we advocate a systematic comparison between parent–offspring regression and animal model estimates to detect potentially missing non‐transgenerational environmental effects.