bluuebunny/crossref_metadata_2025 huggingface dataset:
Social implications of bridging the gap through ‘caring for country’ in remote Indigenous communities of the Northern Territory, Australia
Authors: Gorman Julian , Vemuri Sivaram
Published: January 2012

‘Caring for country’ is a term used to describe the complex spiritual affiliation that encompasses the rights and responsibilities that Aboriginal Australians have with their land. It includes their custodial responsibilities for keeping the land healthy and its species abundant. This ontology and associated practice of ‘caring for country’ continues across large sections of the Northern Territory of Australia through customary practice and through the Indigenous Ranger Program. This Program has been described as a ‘two toolbox approach’, which combines traditional ecological knowledge with more conventional land management practice, to manage landscapes for their natural and cultural values. Since 2007 there have been several policy initiatives which have changed the dynamics in Aboriginal communities which in turn has affected the structure of the Indigenous Ranger Program. In response to the dire social conditions facing Aboriginal communities in the Northern Territory, the Commonwealth Government initiated the Northern Territory Emergency Response, which was a ‘top down’ approach with very little community engagement. At around the same time there was a shift in the way Indigenous Rangers jobs were funded. The unintended impact of this was a reduction in the number of Aboriginal people connected to the Ranger Program and potentially less input from culturally appropriate decision makers for land management. Another influencing policy change involved a shift in Commonwealth funding for land management from Natural Heritage Trust to Caring For Our Country funding. This new funding is more targeted and has changed the nature of the Ranger Program to being less ‘program based’ and more ‘outcome based’ by packaging many land management activities as ‘Fee for Service’ contracts. The transformation is taking place in a prescriptive manner. In this paper we advocate a more community-based approach which allows for greater community involvement in planning, decision making and governance.
Challenges to the effective delivery of health care to people with chronic hepatitis B in Australia
Authors: Wallace Jack , McNally Stephen , Richmond Jacqui , Hajarizadeh Behzad , Pitts Marian
Published: January 2012

Background
The complexity of the hepatitis B natural history and its prevalence in specific populations in Australia challenges the capacity of the health system to deliver health care effectively to affected people. This study explores the challenges in delivering health care to people with chronic hepatitis B (CHB) in Australia. Methods: We conducted a grounded theory based qualitative study in which data were gathered from 70 in-depth interviews with government program officers, clinicians and health and community workers across Australia, and four focus group discussions with 40 health and community workers from the communities most at risk of CHB. Results: A systematic approach to screening populations at risk, including people born in countries with intermediate or high prevalence of CHB; consensus on clinical guidelines; development of a shared care framework for CHB involving general practitioners; and effective communication between patients and health professionals were identified as essential. Workforce development, particularly for primary health care professionals, and developing the knowledge and capacity of health professionals to communicate effectively with people with HBV were described as other major factors in reducing the barriers to CHB treatment in Australia. Conclusion: To improve the clinical management of people with CHB in Australia, the health system needs to encourage the screening of people at risk, improve access to clinical services, and the knowledge and communication skills of primary health care and community health service providers. This study supported developing a shared care model and related infrastructures including training programs, referral pathways and clinical guidelines.
Managing the ranging behaviour of African wild dogs (Lycaon pictus) using translocated scent marks
Authors: Jackson Craig R. , McNutt J. Weldon , Apps Peter J.
Published: January 2012

Context
Conflict between large carnivores and livestock outside the boundaries of wildlife areas frequently results in losses to both livestock and predator populations. The endangered African wild dog (Lycaon pictus Temminck, 1820) is wide ranging and unrestricted by conventional fences, thereby posing a major challenge to conservation managers. Wild dogs are territorial and communicate residence using scent marks. Simulating the presence of other wild dogs using translocated foreign scent marks may therefore represent a means to manage wild dog ranging behaviour.

Aims
To investigate the effectiveness of using targeted scent-mark deployments to signal a wild dog pack to return to their frequented range within the safety of a protected area.

Methods
We report on the ranging behaviour of a wild dog pack reintroduced into a wildlife area in Botswana with no recent history of resident wild dogs. We describe daily movements by the free-ranging introduced pack and compare these to moves following targeted deployment of scent marks when the wild dog pack had ranged close to or outside the boundaries of the protected area.

Key results
Targeted foreign scent-mark exposure resulted in the pack moving closer to the geometric centre of its range. The mean distance travelled the day after exposure was significantly greater than the distance travelled the previous day and the mean daily distance moved during the study period.

Conclusions
Targeted exposure to foreign scent marks proved to be a viable alternative to recapturing dogs that had ranged beyond the boundaries of the wildlife area.

Implications
This novel approach to managing free-ranging carnivores utilises biologically relevant signals and holds potential not only for the conservation of African wild dogs, but also for other territorial species.
Habitat use, population dynamics and species identification of mulgara, Dasycercus blythi and D. cristicauda, in a zone of sympatry in central Australia
Authors: Pavey Chris R. , Nano Catherine E. M. , Cooper Steven J. B. , Cole Jeff R. , McDonald Peter J.
Published: January 2012

Dasycercus cristicauda and Dasycercus blythi are significant mesopredators in arid Australia and both species are threatened nationally. We investigated size dimorphism, habitat use, and population dynamics of sympatric populations during a low rainfall period in central Australia and examined congruence between morphological and molecular methods of species identification. Our molecular analyses confirmed the presence of two Dasycercus species in sympatry and showed that the descriptions of Woolley (2005) allowed confident identification of the two species in the field. We captured 23 D. cristicauda and 55 D. blythi over 39 months on 20 monitoring plots and another 49 survey sites stratified across five habitat types within a 7000 km2 area. Both species showed sexual dimorphism in body mass with males being significantly heavier. The species typically occupied non-overlapping habitat; D. cristicauda was restricted to sandridges (n = 4 sites) with an understorey dominated by spinifex (Triodia), whereas D. blythi occupied sand plain and gibber plain, the latter being a new habitat for the species. Capture rate of D. cristicauda peaked in autumn-winter 2008 and winter 2009. D. blythi exhibited similar variability with peaks in winter 2009 and summer-autumn 2010. We consider that the relatively low abundance of each species during low rainfall periods makes them vulnerable to predation by feral house cats and European red foxes.
Plasma size scaling of avalanche-like heat transport in tokamaks
Authors: Jolliet S. , Idomura Y.
Published: February 2012

The influence of plasma size on global ion temperature gradient turbulence is studied with the full-f Eulerian code GT5D (Idomura et al
2009 Nucl. Fusion
49 065029). The gyrokinetic model includes a consistent neoclassical electric field as well as a fixed-power source operator, enabling long-time simulations with self-consistent turbulent transport and equilibrium profiles. The effects of plasma size (from ρ* = 1/100 to ρ* = 1/225) are studied by scaling the minor radius a and the input power. For the first time, worse-than-Bohm scaling is observed under experimentally realistic conditions. For all plasma sizes, avalanches propagate over significant radii but their propagation depends on the radial electric shear. It is found that this quantity does not scale with ρ* due to the building up of intrinsic momentum. Such a dependence can be inferred from a force balance relation, which remains approximately valid in nonlinear simulations. An adaptive parallel momentum source has been implemented in GT5D to damp the parallel momentum profile. The new scan then reveals that the radial electric shear scales with ρ* while the transport is globally higher. These simulations therefore suggest that intrinsic momentum reduces heat transport. This work also addresses another important issue in gyrokinetics: it is shown that for fixed initial physical parameters the turbulent quasi-steady-state is statistically independent of the initial conditions.
Chado Controller: advanced annotation management with a community annotation system
Authors: Guignon Valentin , Droc Gaëtan , Alaux Michael , Baurens Franc-Christophe , Garsmeur Olivier , Poiron Claire , Carver Tim , Rouard Mathieu , Bocs Stéphanie
Published: January 2012

Summary: We developed a controller that is compliant with the Chado database schema, GBrowse and genome annotation-editing tools such as Artemis and Apollo. It enables the management of public and private data, monitors manual annotation (with controlled vocabularies, structural and functional annotation controls) and stores versions of annotation for all modified features. The Chado controller uses PostgreSQL and Perl.

Availability: The Chado Controller package is available for download at http://www.gnpannot.org/content/chado-controller and runs on any Unix-like operating system, and documentation is available at http://www.gnpannot.org/content/chado-controller-doc

The system can be tested using the GNPAnnot Sandbox at http://www.gnpannot.org/content/gnpannot-sandbox-form

Contact:  valentin.guignon@cirad.fr; stephanie.sidibe-bocs@cirad.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Measurement of genome-wide RNA synthesis and decay rates with Dynamic Transcriptome Analysis (DTA)
Authors: Schwalb Björn , Schulz Daniel , Sun Mai , Zacher Benedikt , Dümcke Sebastian , Martin Dietmar E. , Cramer Patrick , Tresch Achim
Published: January 2012

Summary: Standard transcriptomics measures total cellular RNA levels. Our understanding of gene regulation would be greatly improved if we could measure RNA synthesis and decay rates on a genome-wide level. To that end, the Dynamic Transcriptome Analysis (DTA) method has been developed. DTA combines metabolic RNA labeling with standard transcriptomics to measure RNA synthesis and decay rates in a precise and non-perturbing manner. Here, we present the open source R/Bioconductor software package DTA. It implements all required bioinformatics steps that allow the accurate absolute quantification and comparison of RNA turnover.

Availability:  DTA is part of R/Bioconductor. To download and install DTA refer to http://bioconductor.org/packages/2.10/bioc/html/DTA.html

Contact:  schwalb@lmb.uni-muenchen.de
A new approach to bias correction in RNA-Seq
Authors: Jones Daniel C. , Ruzzo Walter L. , Peng Xinxia , Katze Michael G.
Published: January 2012

Motivation: Quantification of sequence abundance in RNA-Seq experiments is often conflated by protocol-specific sequence bias. The exact sources of the bias are unknown, but may be influenced by polymerase chain reaction amplification, or differing primer affinities and mixtures, for example. The result is decreased accuracy in many applications, such as de novo gene annotation and transcript quantification.

Results: We present a new method to measure and correct for these influences using a simple graphical model. Our model does not rely on existing gene annotations, and model selection is performed automatically making it applicable with few assumptions. We evaluate our method on several datasets, and by multiple criteria, demonstrating that it effectively decreases bias and increases uniformity. Additionally, we provide theoretical and empirical results showing that the method is unlikely to have any effect on unbiased data, suggesting it can be applied with little risk of spurious adjustment.

Availability: The method is implemented in the seqbias R/Bioconductor package, available freely under the LGPL license from http://bioconductor.org

Contact:  dcjones@cs.washington.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
The Transcriptome Analysis and Comparison Explorer—T-ACE: a platform-independent, graphical tool to process large RNAseq datasets of non-model organisms
Authors: Philipp E. E. R. , Kraemer L. , Mountfort D. , Schilhabel M. , Schreiber S. , Rosenstiel P.
Published: January 2012

Motivation: Next generation sequencing (NGS) technologies allow a rapid and cost-effective compilation of large RNA sequence datasets in model and non-model organisms. However, the storage and analysis of transcriptome information from different NGS platforms is still a significant bottleneck, leading to a delay in data dissemination and subsequent biological understanding. Especially database interfaces with transcriptome analysis modules going beyond mere read counts are missing. Here, we present the Transcriptome Analysis and Comparison Explorer (T-ACE), a tool designed for the organization and analysis of large sequence datasets, and especially suited for transcriptome projects of non-model organisms with little or no a priori sequence information. T-ACE offers a TCL-based interface, which accesses a PostgreSQL database via a php-script. Within T-ACE, information belonging to single sequences or contigs, such as annotation or read coverage, is linked to the respective sequence and immediately accessible. Sequences and assigned information can be searched via keyword- or BLAST-search. Additionally, T-ACE provides within and between transcriptome analysis modules on the level of expression, GO terms, KEGG pathways and protein domains. Results are visualized and can be easily exported for external analysis. We developed T-ACE for laboratory environments, which have only a limited amount of bioinformatics support, and for collaborative projects in which different partners work on the same dataset from different locations or platforms (Windows/Linux/MacOS). For laboratories with some experience in bioinformatics and programming, the low complexity of the database structure and open-source code provides a framework that can be customized according to the different needs of the user and transcriptome project.

Contact:  e.philipp@ikmb.uni-kiel.de; l.kraemer@ikmb.uni_kiel.de; p.rosenstiel@mucosa.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
A co-module approach for elucidating drug–disease associations and revealing their molecular basis
Authors: Zhao Shiwen , Li Shao
Published: January 2012

Motivation: Understanding how drugs and diseases are associated in the molecular level is of critical importance to unveil disease mechanisms and treatments. Until recently, few studies attempt end to discover important gene modules shared by both drugs and diseases.

Results: Here, we propose a novel presentation of drug–gene–disease relationship, a ‘co-module’, which is characterized by closely related drugs, diseases and genes. We first define a network-based gene closeness profile to relate drug to disease. Then, we develop a Bayesian partition method to identify drug–gene–disease co-modules underlying the gene closeness data. Genes share similar notable patterns with respect not only to the drugs but also the diseases within a co-module. Simulations show that our method, comCIPHER, achieves a better performance compared with a popular co-module detection method, PPA. We apply comCIPHER to a set consisting of 723 drugs, 275 diseases and 1442 genes and demonstrate that our co-module approach is able to identify new drug–disease associations and highlight their molecular basis. Disease co-morbidity emerges as well. Three co-modules are further illustrated in which new drug applications, including the anti-cancer metastasis activity of an anti-asthma drug Pranlukast, and a cardiovascular stress-testing agent Arbutamine for obesity, as well as potential side-effects, e.g. hypotension for Triamterene, are computationally identified.

Availability: The compiled version of comCIPHER can be found at http://bioinfo.au.tsinghua.edu.cn/comCIPHER/. The 86 co-modules can be downloaded from http://bioinfo.au.tsinghua.edu.cn/comCIPHER/Co_Module_Results.zip.

Contact:  shaoli@mail.tsinghua.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction
Authors: Westesson Oscar , Barquist Lars , Holmes Ian
Published: January 2012

Summary: We describe handalign, a software package for Bayesian reconstruction of phylogenetic history. The underlying model of sequence evolution describes indels and substitutions. Alignments, trees and model parameters are all treated as jointly dependent random variables and sampled via Metropolis–Hastings Markov chain Monte Carlo (MCMC), enabling systematic statistical parameter inference and hypothesis testing. handalign implements several different MCMC proposal kernels, allows sampling from arbitrary target distributions via Hastings ratios, and uses standard file formats for trees, alignments and models.

Availability and Implementation: Installation and usage instructions are at http://biowiki.org/HandAlign

Contact:  ihh@berkeley.edu

Supplementary information:Supplementary material is available at Bioinformatics online.
SOAP3: ultra-fast GPU-based parallel alignment tool for short reads
Authors: Liu Chi-Man , Wong Thomas , Wu Edward , Luo Ruibang , Yiu Siu-Ming , Li Yingrui , Wang Bingqiang , Yu Chang , Chu Xiaowen , Zhao Kaiyong , Li Ruiqiang , Lam Tak-Wah
Published: January 2012

Summary: SOAP3 is the first short read alignment tool that leverages the multi-processors in a graphic processing unit (GPU) to achieve a drastic improvement in speed. We adapted the compressed full-text index (BWT) used by SOAP2 in view of the advantages and disadvantages of GPU. When tested with millions of Illumina Hiseq 2000 length-100 bp reads, SOAP3 takes < 30 s to align a million read pairs onto the human reference genome and is at least 7.5 and 20 times faster than BWA and Bowtie, respectively. For aligning reads with up to four mismatches, SOAP3 aligns slightly more reads than BWA and Bowtie; this is because SOAP3, unlike BWA and Bowtie, is not heuristic-based and always reports all answers.

Availability: SOAP3 is available at: http://www.cs.hku.hk/2bwt-tools/soap3; http://soap.genomics.org.cn/soap3.html.

Contact:  liruiqiang@gmail.com, twlam@cs.hku.hk
First Report of a Ceratobasidium sp. Causing Root Rot on Canola in Washington State
Authors: Schroeder K. L. , Paulitz T. C.
Published: February 2012

Rhizoctonia root rot occurs commonly on canola (Brassica napus L.) in Washington State. Recently, isolates of an additional pathogen were found to be involved in this disease complex. Isolates of an AG-I-like Ceratobasidium sp. were collected from roots and root zone soil in central Washington near Ritzville. Identity of selected isolates was verified by sequencing the internal transcribed spacer (ITS) region of the rDNA (GenBank Accession Nos. JQ247570, JQ247571, and JQ247572), with a 90 to 93% identity to AG-I. All isolates also amplified with AG-I-like specific primers (1). Six isolates were included in pathogenicity assays conducted in the greenhouse. There were five replicates of three plants for each treatment and the experiment was conducted twice. Pasteurized soil was infested with ground oat inoculum (1%) and placed into containers (3.8 × 21 cm). Infested soils were seeded with canola, chickpea (Cicer arietinum L.), lentil (Lens culinaris Medik.), pea (Pisum sativum L.), barley (Hordeum vulgare L.), or wheat (Triticum aestivum L.). After 3 weeks of incubation at 15°C, the plants were destructively harvested. The emergence of canola was consistently reduced in soil infested with a Ceratobasidium sp., with reductions of 0 to 23% (average 11%). There was no postemergence damping-off, a symptom commonly associated with AG-2-1 (2). Plant height and top dry weights were significantly reduced for canola seeded into infested soil. Heights of plants growing in infested soil was reduced by 25 to 53% (average 42%) and top dry weight was reduced by 37 to 81% (average 61%) compared with the noninfested control. The legume hosts tested in this study were also affected by this Ceratobasidium sp., but to a lesser extent. Compared with the noninfested controls, there was evidence of preemergence damping-off in chickpea (0 to 27%, average 13%) and pea plants were consistently stunted (5 to 23%, average 12%). Chickpea and pea plants grown in infested soil also had reduced top dry weights of 9 to 28% (average 17%) and 13 to 35% (average 21%), respectively. The roots of all infected hosts had a characteristic brown discoloration with tapered, rotted root tips (spear tips). There was no reduction in emergence or plant height of wheat and barley; there was inconsistent reduction in dry weight of these plants. To our knowledge, this is the first report of a Ceratobasidium sp. causing disease on canola in Washington State.

References: (1) P. A. Okubara et al. Phytopathology 98:837, 2008. (2) T. C. Paulitz et al. Plant Dis. 90:829, 2006.
On the application of mixed hidden Markov models to multiple behavioural time series
Authors: Schliehe-Diecks S. , Kappeler P. M. , Langrock R.
Published: February 2012

Analysing behavioural sequences and quantifying the likelihood of occurrences of different behaviours is a difficult task as motivational states are not observable. Furthermore, it is ecologically highly relevant and yet more complicated to scale an appropriate model for one individual up to the population level. In this manuscript (mixed) hidden Markov models (HMMs) are used to model the feeding behaviour of 54 subadult grey mouse lemurs (Microcebus murinus), small nocturnal primates endemic to Madagascar that forage solitarily. Our primary aim is to introduce ecologists and other users to various HMM methods, many of which have been developed only recently, and which in this form have not previously been synthesized in the ecological literature. Our specific application of mixed HMMs aims at gaining a better understanding of mouse lemur behaviour, in particular concerning sex-specific differences. The model we consider incorporates random effects for accommodating heterogeneity across animals, i.e. accounts for different personalities of the animals. Additional subject- and time-specific covariates in the model describe the influence of sex, body mass and time of night.
Three-dimensional periodic complex structures in soft matter: investigation using scattering methods
Authors: Impéror-Clerc Marianne
Published: February 2012

Three-dimensional periodic complex structures are encountered in various soft matter systems such as liquid crystals, block-copolymer phases and the related nano-structured materials. Here, we review several well-defined topologies: two-dimensional hexagonal phase, three-dimensional packing of spheres, tetrahedral close packing (
tcp
) bi-continuous and tri-continuous cubic phases. We illustrate how small-angle X-ray scattering experiments help us to investigate these different structures and introduce the main available structural models based on both direct and inverse methods.
Hydrodynamics of the double-wave structure of insect spermatozoa flagella
Authors: Pak On Shun , Spagnolie Saverio E. , Lauga Eric
Published: February 2012

In addition to conventional planar and helical flagellar waves, insect sperm flagella have also been observed to display a double-wave structure characterized by the presence of two superimposed helical waves. In this paper, we present a hydrodynamic investigation of the locomotion of insect spermatozoa exhibiting the double-wave structure, idealized here as superhelical waves. Resolving the hydrodynamic interactions with a non-local slender body theory, we predict the swimming kinematics of these superhelical swimmers based on experimentally collected geometric and kinematic data. Our consideration provides insight into the relative contributions of the major and minor helical waves to swimming; namely, propulsion is owing primarily to the minor wave, with negligible contribution from the major wave. We also explore the dependence of the propulsion speed on geometric and kinematic parameters, revealing counterintuitive results, particularly for the case when the minor and major helical structures are of opposite chirality.
Haemocompatibility and ion exchange capability of nanocellulose polypyrrole membranes intended for blood purification
Authors: Ferraz Natalia , Carlsson Daniel O. , Hong Jaan , Larsson Rolf , Fellström Bengt , Nyholm Leif , Strømme Maria , Mihranyan Albert
Published: February 2012

Composites of nanocellulose and the conductive polymer polypyrrole (PPy) are presented as candidates for a new generation of haemodialysis membranes. The composites may combine active ion exchange with passive ultrafiltration, and the large surface area (about 80 m2g−1) could potentially provide compact dialysers. Herein, the haemocompatibility of the novel membranes and the feasibility of effectively removing small uraemic toxins by potential-controlled ion exchange were studied. The thrombogenic properties of the composites were improved by applying a stable heparin coating. In terms of platelet adhesion and thrombin generation, the composites were comparable with haemocompatible polymer polysulphone, and regarding complement activation, the composites were more biocompatible than commercially available membranes. It was possible to extract phosphate and oxalate ions from solutions with physiological pH and the same tonicity as that of the blood. The exchange capacity of the materials was found to be 600 ± 26 and 706 ± 31 μmol g−1in a 0.1 M solution (pH 7.4) and in an isotonic solution of phosphate, respectively. The corresponding values with oxalate were 523 ± 5 in a 0.1 M solution (pH 7.4) and 610 ± 1 μmol g−1in an isotonic solution. The heparinized PPy–cellulose composite is consequently a promising haemodialysis material, with respect to both potential-controlled extraction of small uraemic toxins and haemocompatibility.
Estimates of generalized Stieltjes constants with a quasi-geometric rate of decay
Authors: Adell José A.
Published: February 2012

We approximate each generalized Stieltjes constant
γ

n

(
a
) by means of a finite sum involving Bernoulli numbers. Such an approximation has a quasi-geometric rate of convergence, which improves as Re(
a
) increases. A more detailed analysis, including numerical computations, is carried out for the constants
γ
0
(1) and
γ
1
(1). The key point in the proof is a probabilistic representation of the aforementioned constants, obtained as a consequence of a differential calculus concerning the gamma process.
Double twinning mechanisms in magnesium alloys via dissociation of lattice dislocations
Authors: Beyerlein I. J. , Wang J. , Barnett M. R. , Tomé C. N.
Published: February 2012

In this work, we propose dislocation mechanisms for the formation of

double twin structures in hexagonal close packed (HCP) crystals through the nucleation of secondary twins within primary twin domains. The model considers that secondary twins associated with the most commonly observed double twin variants (i.e. type 1 and type 2) nucleate and thicken by a sequence of three distinct dissociation reactions of mixed basal dislocations. Provided that the less frequently observed double twin variants (i.e. type 3 and type 4) also form by a dislocation-based mechanism, we show that their development must proceed by a separate set of dissociation reactions involving pyramidal 〈c+a〉 slip dislocations. Mechanistic, crystallographic and energetic considerations indicate that the type 1 variant should be the most prevalent. The mechanisms proposed here would also apply to the analysis of

compound twins and HCP metals other than Mg that exhibit double twinning, such as titanium.
Orbital prefrontal cortex volume predicts social network size: an imaging study of individual differences in humans
Authors: Powell Joanne , Lewis Penelope A. , Roberts Neil , García-Fiñana Marta , Dunbar R. I. M.
Published: February 2012

The social brain hypothesis, an explanation for the unusually large brains of primates, posits that the size of social group typical of a species is directly related to the volume of its neocortex. To test whether this hypothesis also applies at the within-species level, we applied the Cavalieri method of stereology in conjunction with point counting on magnetic resonance images to determine the volume of prefrontal cortex (PFC) subfields, including dorsal and orbital regions. Path analysis in a sample of 40 healthy adult humans revealed a significant linear relationship between orbital (but not dorsal) PFC volume and the size of subjects' social networks that was mediated by individual intentionality (mentalizing) competences. The results support the social brain hypothesis by indicating a relationship between PFC volume and social network size that applies within species, and, more importantly, indicates that the relationship is mediated by social cognitive skills.
Rhodovulum tesquicola sp. nov., a haloalkaliphilic purple non-sulfur bacterium from brackish steppe soda lakes
Authors: Kompantseva Elena I. , Komova Anastasia V. , Novikov Andrey A. , Kostrikina Nadezhda A.
Published: January 2012

Two strains of purple non-sulfur bacteria (A-36sTand A-51s) were isolated from brackish steppe soda lakes of southern Siberia. Genetically, the isolates were related most closely to the type strains ofRhodovulum steppenseandRhodovulum strictum,from which they differed at the species level (98.5 % 16S rRNA gene sequence similarity, 40–53 % DNA–DNA relatedness). Cells of the two strains were ovoid to rod-shaped, 0.4–0.8 µm wide and 1.0–2.5 µm long, and motile by means of a polar flagellum. They contained internal photosynthetic membranes of vesicular type and photosynthetic pigments (bacteriochlorophyllaand carotenoids of the spheroidene series). The strains were obligate haloalkaliphiles, growing over wide ranges of salinity (0.3–10.0 % NaCl) and pH (7.5–10.0), with growth optima at 1.0–3.0 % NaCl and pH 8.5–9.0. Photoheterotrophic and chemoheterotrophic growth occurred with a number of organic compounds and biotin,p-aminobenzoate, thiamine and niacin as growth factors. No anaerobic respiration on nitrite, nitrate or fumarate and no fermentation were demonstrated. The strains grew photolithoautotrophically and chemolithoautotrophically with sulfide, sulfur and thiosulfate, oxidizing them to sulfate. Sulfide was oxidized via deposition of extracellular elemental sulfur. No growth with H2as the electron donor was observed. The major fatty acid was C18 : 1(78 %). The major quinone was ubiquinone Q-10. The DNA G+C content of strain A-36sTwas 65.4 mol% (Tm). According to genotypic and phenotypic characteristics, the investigated strains were assigned to a novel species of the genusRhodovulum, for which the nameRhodovulum tesquicolasp. nov. is proposed. The type strain is A-36sT( = VKM B-2491T = ATCC BAA-1573T), which was isolated from steppe soda lake Sul’fatnoe (Zabaikal’skii Krai, southern Siberia, Russia).
Micromonospora cremea sp. nov. and Micromonospora zamorensis sp. nov., isolated from the rhizosphere of Pisum sativum
Authors: Carro Lorena , Pukall Rüdiger , Spröer Cathrin , Kroppenstedt Reiner M. , Trujillo Martha E.
Published: January 2012

Three actinobacterial strains, CR30T, CR36 and CR38T, were isolated from rhizosphere soil ofPisum sativumplants collected in Spain. The strains were filamentous, Gram-stain-positive and produced single spores. Phylogenetic, chemotaxonomic and morphological analyses confirmed that the three strains belonged to the genusMicromonospora. 16S rRNA gene sequence analysis of strains CR30Tand CR36 showed a close relationship toMicromonospora coriariaeNAR01T(99.3 % similarity) while strain CR38Thad a similarity of 99.0 % withMicromonospora saelicesensisLupac 09T. In addition,gyrBgene phylogeny clearly differentiated the novel isolates from recognizedMicromonosporaspecies. DNA–DNA hybridization, BOX-PCR and ARDRA profiles confirmed that these strains represent novel genomic species. The cell-wall peptidoglycan of strains CR30Tand CR38Tcontainedmeso-diaminopimelic acid. Both strains had MK-10(H4) as the main menaquinone and a phospholipid type II pattern. An array of physiological tests also differentiated the isolates from their closest neighbours. Considering all the data obtained, it is proposed that strains CR30Tand CR36 represent a novel species under the nameMicromonospora cremeasp. nov. (type strain CR30T = CECT 7891T = DSM 45599T), whereas CR38Trepresents a second novel species, for which the nameMicromonospora zamorensissp. nov. is proposed, with CR38T( = CECT 7892T = DSM 45600T) as the type strain.
Mycetocola manganoxydans sp. nov., an actinobacterium isolated from the Taklamakan desert
Authors: Luo Xuesong , Wang Jun , Zeng Xian-Chun , Wang Yaqiong , Zhou Lingli , Nie Yao , Dai Jun , Fang Chengxiang
Published: January 2012

Two Gram-staining-positive, aerobic, non-sporulating bacteria forming short rods and cocci, designated MB1-7 and MB1-14T, were isolated from the Taklamakan desert. The isolates could oxidize manganese (II) ions. The isolates shared 95.4–98.0 % 16S rRNA gene sequence similarity with members of the genus

Mycetocola

. Although the isolates possessed chemotaxonomic properties similar to those of

Mycetocola reblochoni

, they were readily distinguished from this taxon by DNA–DNA relatedness and phenotypic characters. According to morphological and chemotaxonomic characteristics, as well as phylogenetic analysis and DNA–DNA relatedness, the two isolates represent a novel species of the genus

Mycetocola

, for which the name Mycetocola manganoxydans sp. nov. is proposed. The type strain is MB1-14T ( = CCTCC AB 209002T  = KCTC 19753T).
Legionella cardiaca sp. nov., isolated from a case of native valve endocarditis in a human heart
Authors: Pearce Meghan M. , Theodoropoulos Nicole , Mandel Mark J. , Brown Ellen , Reed Kurt D. , Cianciotto Nicholas P.
Published: January 2012

A Gram-negative, rod-shaped bacterium, designated H63T, was isolated from aortic valve tissue of a patient with native valve endocarditis. 16S rRNA gene sequencing revealed that H63T belongs to the genus

Legionella

, with its closest neighbours being the type strains of

Legionella brunensis

(98.8 % similarity),

L. londiniensis

(97.0 %),

L. jordanis

(96.8 %),

L. erythra

(96.2 %),

L. dresdenensis

(96.0 %) and

L. rubrilucens

,

L. feeleii

,

L. pneumophila

and

L. birminghamensis

(95.7 %). DNA–DNA hybridization studies yielded values of <70 % relatedness between strain H63T and its nearest neighbours in terms of 16S rRNA gene sequence similarity, indicating that the strain represents a novel species. Phylogenetic analysis of the 16S rRNA, macrophage infectivity potentiator (mip) and RNase P (rnpB) genes confirmed that H63T represents a distinct species, with

L. brunensis

being its closest sister taxon. Fatty acid composition and biochemical traits, such as the inability to ferment glucose and reduce nitrate, supported the affiliation of H63T to the genus

Legionella

. H63T was distinguishable from its neighbours based on it being positive for hippurate hydrolysis. H63T was further differentiated by its inability to grow on BCYE agar at 17 °C, its poor growth on low-iron medium and the absence of sliding motility. Also, H63T did not react with antisera generated from type strains of

Legionella

species. H63T replicated within macrophages. It also grew in mouse lungs, inducing histopathological evidence of pneumonia and dissemination to the spleen. Together, these results confirm that H63T represents a novel, pathogenic

Legionella

species, for which the name Legionella cardiaca sp. nov. is proposed. The type strain is H63T ( = ATCC BAA-2315T  = DSM 25049T  = JCM 17854T).
A monocarboxylate transporter required for hepatocyte secretion of ketone bodies during fasting
Authors: Hugo Sarah E. , Cruz-Garcia Lourdes , Karanth Santhosh , Anderson Ryan M. , Stainier Didier Y.R. , Schlegel Amnon
Published: February 2012

To find new genes that influence liver lipid mass, we performed a genetic screen for zebrafish mutants with hepatic steatosis, a pathological accumulation of fat. The red moon (rmn) mutant develops hepatic steatosis as maternally deposited yolk is depleted. Conversely, hepatic steatosis is suppressed in rmn mutants by adequate nutrition. Adult rmn mutants show increased liver neutral lipids and induction of hepatic lipid biosynthetic genes when fasted. Positional cloning of the rmn locus reveals a loss-of-function mutation in slc16a6a (solute carrier family 16a, member 6a), a gene that we show encodes a transporter of the major ketone body β-hydroxybutyrate. Restoring wild-type zebrafish slc16a6a expression or introducing human SLC16A6 in rmn mutant livers rescues the mutant phenotype. Radiotracer analysis confirms that loss of Slc16a6a function causes diversion of liver-trapped ketogenic precursors into triacylglycerol. Underscoring the importance of Slc16a6a to normal fasting physiology, previously fed rmn mutants are more sensitive to death by starvation than are wild-type larvae. Our unbiased, forward genetic approach has found a heretofore unrecognized critical step in fasting energy metabolism: hepatic ketone body transport. Since β-hydroxybutyrate is both a major fuel and a signaling molecule in fasting, the discovery of this transporter provides a new direction for modulating circulating levels of ketone bodies in metabolic diseases.
The Gal3p transducer of the GAL regulon interacts with the Gal80p repressor in its ligand-induced closed conformation
Authors: Lavy Tali , Kumar P. Rajesh , He Hongzhen , Joshua-Tor Leemor
Published: February 2012

A wealth of genetic information and some biochemical analysis have made the GAL regulon of the yeast Saccharomyces cerevisiae a classic model system for studying transcriptional activation in eukaryotes. Galactose induces this transcriptional switch, which is regulated by three proteins: the transcriptional activator Gal4p, bound to DNA; the repressor Gal80p; and the transducer Gal3p. We showed previously that NADP appears to act as a trigger to kick the repressor off the activator. Sustained activation involves a complex of the transducer Gal3p and Gal80p mediated by galactose and ATP. We solved the crystal structure of the complex of Gal3p–Gal80p with α-D-galactose and ATP to 2.1 Å resolution. The interaction between the proteins occurs only when Gal3p is in a “closed” state induced by ligand binding. The structure of the complex provides a rationale for the phenotypes of several well-known Gal80p and Gal3p mutants as well as the lack of galactokinase activity of Gal3p.
Microevolution of extensively drug-resistant tuberculosis in Russia
Authors: Casali Nicola , Nikolayevskyy Vladyslav , Balabanova Yanina , Ignatyeva Olga , Kontsevaya Irina , Harris Simon R. , Bentley Stephen D. , Parkhill Julian , Nejentsev Sergey , Hoffner Sven E. , Horstmann Rolf D. , Brown Timothy , Drobniewski Francis
Published: February 2012

Extensively drug-resistant (XDR) tuberculosis (TB), which is resistant to both first- and second-line antibiotics, is an escalating problem, particularly in the Russian Federation. Molecular fingerprinting of 2348 Mycobacterium tuberculosis isolates collected in Samara Oblast, Russia, revealed that 72% belonged to the Beijing lineage, a genotype associated with enhanced acquisition of drug resistance and increased virulence. Whole-genome sequencing of 34 Samaran isolates, plus 25 isolates representing global M. tuberculosis complex diversity, revealed that Beijing isolates originating in Eastern Europe formed a monophyletic group. Homoplasic polymorphisms within this clade were almost invariably associated with antibiotic resistance, indicating that the evolution of this population is primarily driven by drug therapy. Resistance genotypes showed a strong correlation with drug susceptibility phenotypes. A novel homoplasic mutation in rpoC, found only in isolates carrying a common rpoB rifampicin-resistance mutation, may play a role in fitness compensation. Most multidrug-resistant (MDR) isolates also had mutations in the promoter of a virulence gene, eis, which increase its expression and confer kanamycin resistance. Kanamycin therapy may thus select for mutants with increased virulence, helping preserve bacterial fitness and promoting transmission of drug-resistant TB strains. The East European clade was dominated by two MDR clusters, each disseminated across Samara. Polymorphisms conferring fluoroquinolone resistance were independently acquired multiple times within each cluster, indicating that XDR TB is currently not widely transmitted.
A multiplicity of factors contributes to selective RNA polymerase III occupancy of a subset of RNA polymerase III genes in mouse liver
Authors: Canella Donatella , Bernasconi David , Gilardi Federica , LeMartelot Gwendal , Migliavacca Eugenia , Praz Viviane , Cousin Pascal , Delorenzi Mauro , Hernandez Nouria ,   The CycliX Consortium
Published: January 2012

The genomic loci occupied by RNA polymerase (RNAP) III have been characterized in human culture cells by genome-wide chromatin immunoprecipitations, followed by deep sequencing (ChIP-seq). These studies have shown that only ∼40% of the annotated 622 human tRNA genes and pseudogenes are occupied by RNAP-III, and that these genes are often in open chromatin regions rich in active RNAP-II transcription units. We have used ChIP-seq to characterize RNAP-III-occupied loci in a differentiated tissue, the mouse liver. Our studies define the mouse liver RNAP-III-occupied loci including a conserved mammalian interspersed repeat (MIR) as a potential regulator of an RNAP-III subunit-encoding gene. They reveal that synteny relationships can be established between a number of human and mouse RNAP-III genes, and that the expression levels of these genes are significantly linked. They establish that variations within the A and B promoter boxes, as well as the strength of the terminator sequence, can strongly affect RNAP-III occupancy of tRNA genes. They reveal correlations with various genomic features that explain the observed variation of 81% of tRNA scores. In mouse liver, loci represented in the NCBI37/mm9 genome assembly that are clearly occupied by RNAP-III comprise 50Rn5s(5S RNA) genes, 14 known non-tRNA RNAP-III genes, nineRn4.5s(4.5S RNA) genes, and 29 SINEs. Moreover, out of the 433 annotated tRNA genes, half are occupied by RNAP-III. Transfer RNA gene expression levels reflect both an underlying genomic organization conserved in dividing human culture cells and resting mouse liver cells, and the particular promoter and terminator strengths of individual genes.
Retrotransposon profiling of RNA polymerase III initiation sites
Authors: Qi Xiaojie , Daily Kenneth , Nguyen Kim , Wang Haoyi , Mayhew David , Rigor Paul , Forouzan Sholeh , Johnston Mark , Mitra Robi David , Baldi Pierre , Sandmeyer Suzanne
Published: January 2012

Although retroviruses are relatively promiscuous in choice of integration sites, retrotransposons can display marked integration specificity. In yeast and slime mold, some retrotransposons are associated with tRNA genes (tDNAs). In the Saccharomyces cerevisiae genome, the long terminal repeat retrotransposon Ty3 is found at RNA polymerase III (Pol III) transcription start sites of tDNAs. Ty1, 2, and 4 elements also cluster in the upstream regions of these genes. To determine the extent to which other Pol III–transcribed genes serve as genomic targets for Ty3, a set of 10,000 Ty3 genomic retrotranspositions were mapped using high-throughput DNA sequencing. Integrations occurred at all known tDNAs, two tDNA relics (iYGR033c and ZOD1), and six non-tDNA, Pol III–transcribed types of genes (RDN5, SNR6, SNR52, RPR1, RNA170, and SCR1). Previous work in vitro demonstrated that the Pol III transcription factor (TF) IIIB is important for Ty3 targeting. However, seven loci that bind the TFIIIB loader, TFIIIC, were not targeted, underscoring the unexplained absence of TFIIIB at those sites. Ty3 integrations also occurred in two open reading frames not previously associated with Pol III transcription, suggesting the existence of a small number of additional sites in the yeast genome that interact with Pol III transcription complexes.
Evolutionary rate covariation reveals shared functionality and coexpression of genes
Authors: Clark Nathan L. , Alani Eric , Aquadro Charles F.
Published: January 2012

Evolutionary rate covariation (ERC) is a phylogenetic signature that reflects the covariation of a pair of proteins over evolutionary time. ERC is typically elevated between interacting proteins and so is a promising signature to characterize molecular and functional interactions across the genome. ERC is often assumed to result from compensatory changes at interaction interfaces (i.e., intermolecular coevolution); however, its origin is still unclear and is likely to be complex. Here, we determine the biological factors responsible for ERC in a proteome-wide data set of 4459 proteins in 18 budding yeast species. We show that direct physical interaction is not required to produce ERC, because we observe strong correlations between noninteracting but cofunctional enzymes. We also demonstrate that ERC is uniformly distributed along the protein primary sequence, suggesting that intermolecular coevolution is not generally responsible for ERC between physically interacting proteins. Using multivariate analysis, we show that a pair of proteins is likely to exhibit ERC if they share a biological function or if their expression levels coevolve between species. Thus, ERC indicates shared function and coexpression of protein pairs and not necessarily coevolution between sites, as has been assumed in previous studies. This full interpretation of ERC now provides us with a powerful tool to assign uncharacterized proteins to functional groups and to determine the interconnectedness between entire genetic pathways.
Ectocarpus: A Model Organism for the Brown Algae
Authors: Coelho Susana M. , Scornet Delphine , Rousvoal Sylvie , Peters Nick T. , Dartevelle Laurence , Peters Akira F. , Cock J. Mark
Published: February 2012

The brown algae are an interesting group of organisms from several points of view. They are the dominant organisms in many coastal ecosystems, where they often form large, underwater forests. They also have an unusual evolutionary history, being members of the stramenopiles, which are very distantly related to well-studied animal and green plant models. As a consequence of this history, brown algae have evolved many novel features, for example in terms of their cell biology and metabolic pathways. They are also one of only a small number of eukaryotic groups to have independently evolved complex multicellularity. Despite these interesting features, the brown algae have remained a relatively poorly studied group. This situation has started to change over the last few years, however, with the emergence of the filamentous brown alga Ectocarpus as a model system that is amenable to the genomic and genetic approaches that have proved to be so powerful in more classical model organisms such as Drosophila and Arabidopsis.