bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluating the evolution of the Red River system based on in situ U‐Pb dating and Hf isotope analysis of zircons
Authors: van Hoang Long , Wu Fu‐Yuan , Clift Peter D. , Wysocka Anna , Swierczewska Anna
Published: November 2009

The Red River originates from SW China and SE Tibet and has a total length >1000 km. In this study, we present new U‐Pb dating and Hf isotopic analysis of zircon grains, from both modern and paleoriver sands in order to constrain the provenance of the modern river and to decipher drainage evolution through time. Our data show that the Yangtze and Songpan Garze blocks are the most important sources for sediment, although this material is mostly reworked via younger sedimentary rocks in the upper reaches of the Red River. Sands in the Da River and to a lesser extent the Lo River have zircon ages indicating that they are minor contributors to the net flow, consistent with rock uplift, which is strongest in the upper reaches of the Red River, rather than precipitation being the primary control on erosion. Sediments eroded from the metamorphic rocks along the Red River Fault Zone appear to have made a greater contribution during the Miocene. Zircon ages suggest that the Red River flowed north of the Day Nui Con Voi in the Middle‐Late Miocene. The Red River appears to have had a largely stable provenance since at least the Late Miocene. Upper Miocene sedimentary rocks NE of the Red River indicate the presence of a separate, large river in the Late Miocene. Hf isotope data indicate that the Irrawaddy River was never part of the Red River system. Although we do not exclude the Salween, Mekong, and Yangtze rivers from having been part of the Red River, any connection must have been pre‐Middle Miocene.
Climatology of gravity waves–induced electric fields in the equatorial E region
Authors: Aveiro H. C. , Denardini C. M. , Abdu M. A.
Published: November 2009

Equatorial electrojet (EEJ) observations using VHF radars show backscattered echoes from two types of electron density irregularities explained by the modified two‐stream (Type I) and the gradient drift (Type II) instabilities. From the Type II irregularity velocities obtained by a radar installed at São Luiz Space Observatory (2.58°S, 44.23°W, magnetic latitude 0.23°S) we have inferred the vertical electric fields (Ez). The Ez inference was based on geomagnetic field and atmospheric models. A harmonic analysis of these electric fields shows the presence of gravity waves (GW) induced oscillations in the EEJ. We calculated the ratio between GW‐related electric fields and the total Ez, which is an indicator of the efficiency in the production of an additional electric field due to a gravity wave neutral wind. In the present paper we describe the methodology of analysis and discuss some characteristics of the gravity waves that could modify the equatorial ionospheric electric fields.
Dependence of the quasi‐linear scattering rates on the wave normal distribution of chorus waves
Authors: Shprits Yuri Y. , Ni Binbin
Published: November 2009

The sensitivity of quasi‐linear scattering rates to the wave normal distribution of chorus waves is studied using the Full Diffusion Code newly developed at the University of California, Los Angeles. Scattering rates are computed for field‐aligned, oblique (∼20° wave normal angles), and highly oblique (∼40° wave normal angles) cases. For radiation belt electrons, scattering rates are relatively insensitive to the assumed distribution of wave normal angles at high energies; while when the energy is smaller, in the range of tens of keV, knowledge of the wave normal distribution becomes important. It is shown that Landau resonance becomes very important for the scattering of electrons with energies of tens of keV as waves become more oblique. Scattering rates for various order resonances and energies are presented. Our results show that, for a fixed ratio of plasma to gyrofrequency and fixed spectral properties of waves, scattering rates scale as an inverse of magnitude of the magnetic field. We also show that resonant scattering of 10 keV and 100 keV occurs within 10° and 20° latitude of the geomagnetic equator, respectively. At 1 MeV, dominant scattering occurs above 20° latitude. We also present local scattering rates as a function of energy and latitude. Implications of the presented results for the upcoming satellite mission's planning, future measurements, and radiation belt modeling are discussed.
Wind relaxations and poleward flow events in a coastal upwelling system on the central California coast
Authors: Melton Christopher , Washburn Libe , Gotschalk Chris
Published: November 2009

When upwelling favorable winds weaken or relax in coastal upwelling systems, prevailing equatorward currents often weaken and then reverse to form propagating poleward currents. Here the statistics of wind relaxations and poleward flow events along the south central California coast are derived using meteorological and oceanographic times series during 2000–2006. Over the 7‐year record, 169 wind relaxations were observed (about 1 every 2 weeks) and 127 of these were followed by poleward flow events. Thermistor moorings and current profilers along the 15 m isobath at Alegria, Point Arguello, Point Purisima, and Point Sal recorded the poleward flows. The poleward flows propagate northward at 10–30 km d−1 and appear as sequential temperature increases at the moorings. Wind relaxations occur throughout the year but are most frequent in September and least frequent in April when upwelling winds are strong and persistent. Poleward flows follow wind relaxations frequently during May through November and rarely in December and January. Sea level differences between Santa Monica and Port San Luis, California, decreased as winds relaxed, consistent with forcing by alongshore pressure gradients. Temperature distributions at Point Arguello, Point Purisima, and Point Sal were skewed toward higher values because of the poleward flows. The alongshore distance traveled by the poleward flows increased with duration of the wind relaxations and magnitudes of alongshore temperature and sea level differences prior to the relaxations.
T‐matrix studies of aerosol particle shape effects on IR resonance spectral line profiles and comparison with an experiment
Authors: Kleiber P. D. , Grassian V. H. , Young M. A. , Hudson Paula K.
Published: November 2009

Experimental infrared resonance absorption line profiles are compared with results from T‐matrix theory calculations for several mineral components of atmospheric dust (illite, kaolinite, montmorillonite, quartz, and calcite). The model results are used to infer general characteristics of the aerosol particle shape distribution. For the silicate clays the spectral line profiles are best fit by a shape distribution of highly eccentric oblate spheroids, consistent with the expected sheet‐like nature of the clay minerals. For quartz dust the spectral line profiles are best fit by a very broad distribution including both extreme oblate and prolate spheroids. For calcite a spheroid model with moderate shape parameters gives the best fit. Our results suggest that high‐resolution IR extinction measurements may offer useful insight into the shape distributions of atmospheric mineral dust.
Attitudes and beliefs about HIV/AIDS behaviour and education among Tanzanian youth
Authors: Maswanya Edward , Brown Graham , Merriman Gareth
Published: November 2009

Background:
Tanzania faced with an increasing problem from HIV sexual infection and vulnerability of students is a key concern. This paper explores beliefs, attitudes and behavioural perspectives on HIV/AIDS education among students in Tanzania as there has been few qualitative information on the subject.
Methods:
A total of 20 college students of both sexes were interviewed in a qualitative study. Health Belief Model and Social Cognitive Theory were used to guide the interview and constant comparative analysis on their attitudes, beliefs, behaviour and education towards HIV infection risks were utilised.
Results:
During the interview, the following topics emerged: misinformation and desire for HIV/AIDS education program in school curricula; perceptions of one’s own and peer’s susceptibility to HIV infection; social norms regarding sexual behaviour and perceptions regarding access to education and health services. Lack of accurate information and lack of education at home and at school further contributed to risk behaviour.
Conclusion:
The study highlighted important perspectives of students towards HIV infection, risk behaviours which are important for HIV prevention programs for students. Based on the findings, recommendations for improvement in prevention programs among college students within Tanzanian schools context are discussed.
Pilot study of Australian school-based sexual health education: parents' views
Authors: Macbeth Allison , Weerakoon Patricia , Sitharthan Gomathi
Published: November 2009

Background: Sexually transmissible infections (STIs) among young Australians increased dramatically between 1997 and 2007 with rates of chlamydia increasing by 528% and rates of gonorrhoea by 169% among 15–19 year olds. High notification rates of STIs and teenage pregnancy point to the need to investigate sexual health education (SHE) in Australian schools. This first quantitative study investigated the attitudes and experiences of parents to SHE in Australian schools. Methods: One hundred and seventeen (117) Australian parents were recruited through purposive sampling and snowballing methods to complete an online questionnaire in 2007. Results: Most respondents (97.4%) support SHE in schools and 95.7% advocate schools and parents sharing responsibility. A majority (82.9%) believe SHE should begin in primary school with discrepancy as to when specific topics should be introduced. There is consensus for a comprehensive curriculum, including topics potentially seen as controversial such as ‘masturbation’. ‘Abstinence’ was chosen by 15.4% of parents to not be included in SHE curricula. Most parents rate the SHE their children have received in school as ‘fair’ in quality, and want access to resources to help them educate their children, including workshops at schools, information about school SHE, literature, and trained sexual health educators. Conclusions: Parents generally support SHE in schools. They want programs to begin in primary school. They consider the current school programs to be ‘fair’ in quality. Parents also point out the need for a more comprehensive curriculum and they want to be involved with schools in the development and delivery of SHE.
Treatment of metronidazole-resistant Trichomonas vaginalis
Authors: Goldman Linda M. , Upcroft Jacqueline A. , Workowski Kimberly , Rapkin Andrea
Published: November 2009

A 58-year-old Caucasian woman presented with a 14-month history of persistent trichomoniasis not responsive to numerous courses of metronidazole and tinidazole. Vaginal secretion samples were obtained for sensitivity testing and treatment recommendations. In vitro susceptibility testing revealed the patient’s Trichomonas vaginalis isolate was highly resistant to both metronidazole and tinidazole. She was treated with topical furazolidone and experienced a complete symptomatic cure and culture remained negative 35 days post furazolidone treatment.
Genetic variation in human telomerase is associated with telomere length in Ashkenazi centenarians
Authors: Atzmon Gil , Cho Miook , Cawthon Richard M. , Budagov Temuri , Katz Micol , Yang Xiaoman , Siegel Glenn , Bergman Aviv , Huffman Derek M. , Schechter Clyde B. , Wright Woodring E. , Shay Jerry W. , Barzilai Nir , Govindaraju Diddahally R. , Suh Yousin
Published: November 2009

Telomere length in humans is emerging as a biomarker of aging because its shortening is associated with aging-related diseases and early mortality. However, genetic mechanisms responsible for these associations are not known. Here, in a cohort of Ashkenazi Jewish centenarians, their offspring, and offspring-matched controls, we studied the inheritance and maintenance of telomere length and variations in two major genes associated with telomerase enzyme activity,
hTERT
and
hTERC
. We demonstrated that centenarians and their offspring maintain longer telomeres compared with controls with advancing age and that longer telomeres are associated with protection from age-related diseases, better cognitive function, and lipid profiles of healthy aging. Sequence analysis of
hTERT
and
hTERC
showed overrepresentation of synonymous and intronic mutations among centenarians relative to controls. Moreover, we identified a common
hTERT
haplotype that is associated with both exceptional longevity and longer telomere length. Thus, variations in human telomerase gene that are associated with better maintenance of telomere length may confer healthy aging and exceptional longevity in humans.
RNA recognition by the embryonic cell fate determinant and germline totipotency factor MEX-3
Authors: Pagano John M. , Farley Brian M. , Essien Kingsley I. , Ryder Sean P.
Published: November 2009

Totipotent stem cells have the potential to differentiate into every cell type. Renewal of totipotent stem cells in the germline and cellular differentiation during early embryogenesis rely upon posttranscriptional regulatory mechanisms. The
Caenorhabditis elegans
RNA binding protein, MEX-3, plays a key role in both processes. MEX-3 is a maternally-supplied factor that controls the RNA metabolism of transcripts encoding critical cell fate determinants. However, the nucleotide sequence specificity and requirements of MEX-3 mRNA recognition remain unclear. Only a few candidate regulatory targets have been identified, and the full extent of the network of MEX-3 targets is not known. Here, we define the consensus sequence required for MEX-3 RNA recognition and demonstrate that this element is required for MEX-3 dependent regulation of gene expression in live worms. Based on this work, we identify several candidate MEX-3 targets that help explain its dual role in regulating germline stem cell totipotency and embryonic cell fate specification.
Bioengineered corporal tissue for structural and functional restoration of the penis
Authors: Chen Kuo-Liang , Eberli Daniel , Yoo James J. , Atala Anthony
Published: November 2009

Various reconstructive procedures have been attempted to restore a cosmetically acceptable phallus that would allow normal reproductive, sexual, and urinary function in patients requiring penile reconstruction. However, these procedures are limited by a shortage of native penile tissue. We previously demonstrated that a short segment of the penile corporal body can be replaced using naturally derived collagen matrices with autologous cells. In the current study, we examined the feasibility of engineering the entire pendular penile corporal bodies in a rabbit model. Neocorpora were engineered from cavernosal collagen matrices seeded with autologous cells using a multistep static/dynamic procedure, and these were implanted to replace the excised corpora. The bioengineered corpora demonstrated structural and functional parameters similar to native tissue and male rabbits receiving the bilateral implants were able to successfully impregnate females. This study demonstrates that neocorpora can be engineered for total pendular penile corporal body replacement. This technology has considerable potential for patients requiring penile reconstruction.
A double-hexameric MCM2-7 complex is loaded onto origin DNA during licensing of eukaryotic DNA replication
Authors: Evrin Cecile , Clarke Pippa , Zech Juergen , Lurz Rudi , Sun Jingchuan , Uhle Stefan , Li Huilin , Stillman Bruce , Speck Christian
Published: November 2009

During pre-replication complex (pre-RC) formation, origin recognition complex (ORC), Cdc6, and Cdt1 cooperatively load the 6-subunit mini chromosome maintenance (MCM2-7) complex onto DNA. Loading of MCM2-7 is a prerequisite for DNA licensing that restricts DNA replication to once per cell cycle. During S phase MCM2-7 functions as part of the replicative helicase but within the pre-RC MCM2-7 is inactive. The organization of replicative DNA helicases before and after loading onto DNA has been studied in bacteria and viruses but not eukaryotes and is of major importance for understanding the MCM2-7 loading mechanism and replisome assembly. Lack of an efficient reconstituted pre-RC system has hindered the detailed mechanistic and structural analysis of MCM2-7 loading for a long time. We have reconstituted
Saccharomyces cerevisiae
pre-RC formation with purified proteins and showed efficient loading of MCM2-7 onto origin DNA in vitro. MCM2-7 loading was found to be dependent on the presence of all pre-RC proteins, origin DNA, and ATP hydrolysis. The quaternary structure of MCM2-7 changes during pre-RC formation: MCM2-7 before loading is a single hexamer in solution but is transformed into a double-hexamer during pre-RC formation. Using electron microscopy (EM), we observed that loaded MCM2-7 encircles DNA. The loaded MCM2-7 complex can slide on DNA, and sliding is not directional. Our results provide key insights into mechanisms of pre-RC formation and have important implications for understanding the role of the MCM2-7 in establishment of bidirectional replication forks.
Mindfulness Meditation for Substance Use Disorders: A Systematic Review
Authors: Zgierska Aleksandra , Rabago David , Chawla Neharika , Kushner Kenneth , Koehler Robert , Marlatt Alan
Published: November 2009

Relapse is common in substance use disorders (SUDs), even among treated individuals. The goal of this article was to systematically review the existing evidence on mindfulness meditation-based interventions (MM) for SUDs. The comprehensive search for and review of literature found over 2000 abstracts and resulted in 25 eligible manuscripts (22 published, 3 unpublished: 8 randomized controlled trials, 7 controlled nonrandomized, 6 noncontrolled prospective, and 2 qualitative studies, and 1 case report). When appropriate, methodological quality, absolute risk reduction, number needed to treat, and effect size were assessed. Overall, although preliminary evidence suggests MM efficacy and safety, conclusive data for MM as a treatment of SUDs are lacking. Significant methodological limitations exist in most studies. Further, it is unclear which persons with SUDs might benefit most from MM. Future trials must be of sufficient sample size to answer a specific clinical question and should target both assessment of effect size and mechanisms of action.
Transitional Process of Ploy(N-isopropylacrylamide) in Deuterated Solution
Authors: Zhang Shao-hua , Chen Yang , Li Heng , Weng Yu-xiang
Published: November 2009

The fast phase-transitional process of ploy(N-isopropylacrylamide) (PNIPAM) in deuterated solution was studied by laser induced temperature jump technique combined with time-resolved mid-infrared absorbance difference spectroscopy on nanosecond level. The multi-peaks of amide I' band of PNIPAM among the energy range of 15651700 cm-1 was experimentally resolved to three groups (i, ii, iii) for the first time, while the distinct three-stage procedure in the phase transitional process of long-chain PNIPAM was observed firstly too. Furthermore, proper assignments were also made for the three group peaks in amide I' band and the three steps in the kinetics process of long-chain PNIPAM.
Simulation Study on the Structure and Dynamics of Water in Sodium Tetrafluoroborate/Water
Authors: Tian Guo-cai , Li Jian , Hua Yi-xin
Published: November 2009

The microstructure, IR spectrum, as well as rotation dynamics of water molecule in sodium tetrafluoroborate (NaBF4)/water mixture at room temperatures were studied with molecular dynamics simulation. Different concentrations of water (6.25%, 25.0%, 50.0%, 75.0%, 90.0%, and 99.6%) in NaBF4/water mixture were simulated to understand the structure and dynamics. It was shown that water molecules tend to be isolated from each other in mixtures with more ions than water molecules in both liquids. With increase of the molar fraction of water in the mixture, the rotation bands and the bending bands of water display red shift whereas the OH stretch bands show blue shift, and the decay of the reorientation correlation function becomes slower. This suggests that the molecules are hindered and their motions are difficult and slow, due to the hydrogen-bond interactions and the inharmonic interactions between the inter- or intra-molecular modes.
First-principles Band Structures Calculation of Tin-phthalocyanine
Authors: Yang Yan-ting , Wu Fu-gen , Wei Zhi-gang
Published: November 2009

We adopt the density function theory with generalized approximation by the Beeke exchange plus Lee-Yang-Parr correlation functional to calculate the electronic first-principles band structure of tin-phthalocyanine (SnPc). The intermolecular interaction related to transport behavior was analyzed from the -point wave function as well as from the bandwidths and band gaps. From the calculated bandwidths of the frontier bands as well as the effective masses of the electron and hole, it can be concluded that the mobility of the electron is about two times larger than that of the hole. Furthermore, when several bands near the Fermi surface are taken into account, we find that the interband gaps within the unoccupied bands are generally smaller than those of the occupied bands, indicating that the electron can hop from one band to another which is much easier than the hole. This may happen through electron-phonon coupling for instance, thus effectively yielding an even larger mobility for the electron than for the hole. These facts indicate that in SnPc the electrons are the dominant carriers in transport, in contrast to most organic materials.
Mobility, Microtubule Nucleation and Structure of Microtubule-organizing Centers in Multinucleated Hyphae ofAshbya gossypii
Authors: Lang Claudia , Grava Sandrine , van den Hoorn Tineke , Trimble Rhonda , Philippsen Peter , Jaspersen Sue L.
Published: November 2009

We investigated the migration of multiple nuclei in hyphae of the filamentous fungus Ashbya gossypii. Three types of cytoplasmic microtubule (cMT)-dependent nuclear movements were characterized using live cell imaging: short-range oscillations (up to 4.5 μm/min), rotations (up to 180° in 30 s), and long-range nuclear bypassing (up to 9 μm/min). These movements were superimposed on a cMT-independent mode of nuclear migration, cotransport with the cytoplasmic stream. This latter mode is sufficient to support wild-type-like hyphal growth speeds. cMT-dependent nuclear movements were led by a nuclear-associated microtubule-organizing center, the spindle pole body (SPB), which is the sole site of microtubule nucleation in A. gossypii. Analysis of A. gossypii SPBs by electron microscopy revealed an overall laminar structure similar to the budding yeast SPB but with distinct differences at the cytoplasmic side. Up to six perpendicular and tangential cMTs emanated from a more spherical outer plaque. The perpendicular and tangential cMTs most likely correspond to short, often cortex-associated cMTs and to long, hyphal growth-axis–oriented cMTs, respectively, seen by in vivo imaging. Each SPB nucleates its own array of cMTs, and the lack of overlapping cMT arrays between neighboring nuclei explains the autonomous nuclear oscillations and bypassing observed in A. gossypii hyphae.
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
Authors: Robinson Mark D. , McCarthy Davis J. , Smyth Gordon K.
Published: November 2009

Summary: It is expected that emerging digital gene expression (DGE) technologies will overtake microarray technologies in the near future for many functional genomics applications. One of the fundamental data analysis tasks, especially for gene expression studies, involves determining whether there is evidence that counts for a transcript or exon are significantly different across experimental conditions. edgeR is a Bioconductor software package for examining differential expression of replicated count data. An overdispersed Poisson model is used to account for both biological and technical variability. Empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference. The methodology can be used even with the most minimal levels of replication, provided at least one phenotype or experimental condition is replicated. The software may have other applications beyond sequencing data, such as proteome peptide count data.

Availability: The package is freely available under the LGPL licence from the Bioconductor web site (http://bioconductor.org).

Contact:  mrobinson@wehi.edu.au
Co-expression networks: graph properties and topological comparisons
Authors: Xulvi-Brunet Ramon , Li Hongzhe
Published: November 2009

Motivation: Microarray-based gene expression data have been generated widely to study different biological processes and systems. Gene co-expression networks are often used to extract information about groups of genes that are ‘functionally’ related or co-regulated. However, the structural properties of such co-expression networks have not been rigorously studied and fully compared with known biological networks. In this article, we aim at investigating the structural properties of co-expression networks inferred for the species Saccharomyces Cerevisiae and comparing them with the topological properties of the known, well-established transcriptional network, MIPS physical network and protein–protein interaction (PPI) network of yeast.

Results: These topological comparisons indicate that co-expression networks are not distinctly related with either the PPI or the MIPS physical interaction networks, showing important structural differences between them. When focusing on a more literal comparison, vertex by vertex and edge by edge, the conclusion is the same: the fact that two genes exhibit a high gene expression correlation degree does not seem to obviously correlate with the existence of a physical binding between the proteins produced by these genes or the existence of a MIPS physical interaction between the genes. The comparison of the yeast regulatory network with inferred yeast co-expression networks would suggest, however, that they could somehow be related.

Conclusions: We conclude that the gene expression-based co-expression networks reflect more on the gene regulatory networks but less on the PPI or MIPS physical interaction networks.

Contact:  hongzhe@mail.med.upenn.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Identification of substrates for Ser/Thr kinases using residue-based statistical pair potentials
Authors: Kumar Narendra , Mohanty Debasisa
Published: November 2009

Motivation:  In silico methods are being widely used for identifying substrates for various kinases and deciphering cell signaling networks. However, most of the available phosphorylation site prediction methods use motifs or profiles derived from a known data set of kinase substrates and hence, their applicability is limited to only those kinase families for which experimental substrate data is available. This prompted us to develop a novel multi-scale structure-based approach which does not require training using experimental substrate data.

Results:In this work, for the first time, we have used residue-based statistical pair potentials for scoring the binding energy of various substrate peptides in complex with kinases. Extensive benchmarking on Phospho.ELM data set indicate that our method outperforms other structure-based methods and has a prediction accuracy comparable to available sequence-based methods. We also demonstrate that the rank of the true substrate can be further improved, if the high-scoring candidate substrates that are short-listed based on pair potential score, are modeled using all atom forcefield and MM/PBSA approach.

Contact:  deb@nii.res.in

Supplementary information:  Supplementary data are available at Bioinformatics Online.
PerturbationAnalyzer: a tool for investigating the effects of concentration perturbation on protein interaction networks
Authors: Li Fei , Li Peng , Xu Wenjian , Peng Yuxing , Bo Xiaochen , Wang Shengqi
Published: November 2009

Summary:The propagation of perturbations in protein concentration through a protein interaction network (PIN) can shed light on network dynamics and function. In order to facilitate this type of study, PerturbationAnalyzer, which is an open source plugin for Cytoscape, has been developed. PerturbationAnalyzer can be used in manual mode for simulating user-defined perturbations, as well as in batch mode for evaluating network robustness and identifying significant proteins that cause large propagation effects in the PINs when their concentrations are perturbed. Results from PerturbationAnalyzer can be represented in an intuitive and customizable way and can also be exported for further exploration. PerturbationAnalyzer has great potential in mining the design principles of protein networks, and may be a useful tool for identifying drug targets.

Availability:PerturbationAnalyzer can be accessed from the Cytoscape web site http://www.cytoscape.org/plugins/index.php or http://biotech.bmi.ac.cn/PerturbationAnalyzer.

Contact:  boxc@bmi.ac.cn; sqwang@bmi.ac.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
PyNAST: a flexible tool for aligning sequences to a template alignment
Authors: Caporaso J. Gregory , Bittinger Kyle , Bushman Frederic D. , DeSantis Todd Z. , Andersen Gary L. , Knight Rob
Published: November 2009

Motivation: The Nearest Alignment Space Termination (NAST) tool is commonly used in sequence-based microbial ecology community analysis, but due to the limited portability of the original implementation, it has not been as widely adopted as possible. Python Nearest Alignment Space Termination (PyNAST) is a complete reimplementation of NAST, which includes three convenient interfaces: a Mac OS X GUI, a command-line interface and a simple application programming interface (API).

Results: The availability of PyNAST will make the popular NAST algorithm more portable and thereby applicable to datasets orders of magnitude larger by allowing users to install PyNAST on their own hardware. Additionally because users can align to arbitrary template alignments, a feature not available via the original NAST web interface, the NAST algorithm will be readily applicable to novel tasks outside of microbial community analysis.

Availability: PyNAST is available at http://pynast.sourceforge.net.

Contact:  rob.knight@colorado.edu
The analysis of echotrace obtained by a split-beam echosounder to observe the tilt-angle dependence of fish target strength in situ
Authors: Furusawa Masahiko , Amakasu Kazuo
Published: November 2009

Furusawa, M., and Amakusu, K. 2010. The analysis of echotrace obtained by a split-beam echosounder to observe the tilt-angle dependence of fish target strength in situ. – ICES Journal of Marine Science, 67: 215–230. A method of echotrace analysis (ETA), proposed by Furusawa and Miyanohana in 1988 utilizes successive echodata from an individual fish to obtain the target-strength (TS) pattern as a function of fish tilt angle and behaviour. The method can be applied to data from an echosounder with any beam configuration, single-, dual-, and split-beam. However, the method has not been applied rigorously to split-beam sounder data, which provide most comprehensive and accurate information. The aim of this work is to establish an accurate and practical ETA method for split-beam echosounder data. Although the basic theory had already been developed, some theoretical and practical enhancement was needed; smoothing of an echotrack by linear and quadratic regressions, correction for transducer motion, and comparison of an observed TS pattern with a prolate-spheroid theoretical model. The analysis starts from careful selection of a single echotrace on an echogram and ends with a composite display of results including a three-dimensional fish track and a TS pattern as a function of the tilt angle of the fish. The method was applied to typical echotrace examples, and utility and practicality were confirmed. A means of increasing the number of applicable echotraces is discussed.
Remote sensing of underwater vegetation using single-beam acoustics
Authors: Quintino Victor , Freitas Rosa , Mamede Renato , Ricardo Fernando , Rodrigues Ana Maria , Mota Jorge , Pérez-Ruzafa Ángel , Marcos Concepción
Published: November 2009

Quintino, V., Freitas, R., Mamede, R., Ricardo, F., Rodrigues, A. M., Mota, J., Pérez-Ruzafa, Á., and Marcos, C. 2010. Remote sensing of underwater vegetation using single-beam acoustics. – ICES Journal of Marine Science, 67: 594–605. A single-beam, acoustic, ground-discrimination system (QTC VIEW, Series V) was used to study the distribution of underwater macrophytes in a shallow-water coastal system, employing frequencies of 50 and 200 kHz. The study was conducted in Mar Menor, SE Spain, where the expansion of Caulerpa prolifera has contributed to the silting up of the superficial sediments. A direct relationship was identified between algal biomass and sediment-fines content. Acoustic information on sediment grain size and data on algal biomass were obtained in muddy and sandy sediments, including vegetated and non-vegetated seabed. Non-vegetated muddy areas were created by diving and handpicking the algae. The multivariate acoustic data were analysed under the null hypotheses that there were no acoustic differences between bare seabeds with contrasting superficial sediment types or among low, medium, and high algal-biomass areas, having in mind that grain size can act as a confounding factor. Both null hypotheses were rejected, and the results showed that 200 kHz was better than 50 kHz in distinguishing cover levels of algal biomass. The relationship between the 200-kHz acoustic data and algal biomass suggests utility in modelling the latter using the former.
Immediate maximum economic yield; a realistic fisheries economic reference point
Authors: Lleonart Jordi , Merino Gorka
Published: November 2009

Lleonart, J., and Merino, G. 2010. Immediate maximum economic yield; a realistic fisheries economic reference point. – ICES Journal of Marine Science, 67: 577–582. Unregulated or poorly managed fisheries tend towards overexploitation, but fisheries rent does not completely dissipate when immediate rent maximization is sought. The principle of immediate economic rent maximization is the basis of the derivation of a classic model and has led to the definition of a relationship in a catch-and-effort diagram termed the dynamic immediate maximum economic yield (DIMEY) curve. For any initial biomass, if the economic rent in the immediate fishing season is maximized, then the fishing effort and catch strategy that follows will be located on the DIMEY curve. The DIMEY curve is not only used for dynamic simulation but also used to identify a new reference point, the immediate maximum economic yield (IMEY), which is proposed as more realistic than the classic open-access solution for unregulated fisheries. IMEY is proposed as an asymptotic outcome for unregulated or poorly managed fisheries when short-term economic objectives drive fleet activities. IMEY properties are described and compared with traditional fisheries reference points in the yield-and-effort diagram. Theoretical conclusions are compared with empirical evidence provided by the red shrimp fishery off Blanes, Spain (NW Mediterranean). Observed catch-and-effort records are plotted and were positively correlated with the DIMEY curve and IMEY.
Role of host cell polarity and leading edge properties in Pseudomonas type III secretion
Authors: Bridge Dacie R. , Novotny Matthew J. , Moore Elizabeth R. , Olson Joan C.
Published: November 2009

Type III secretion (T3S) functions in establishing infections in a large number of Gram-negative bacteria, yet little is known about how host cell properties might function in this process. We used the opportunistic pathogenPseudomonas aeruginosaand the ability to alter host cell sensitivity toPseudomonasT3S to explore this problem. HT-29 epithelial cells were used to study cellular changes associated with loss of T3S sensitivity, which could be induced by treatment with methyl-beta-cyclodextrin or perfringolysin O. HL-60 promyelocytic cells are innately resistant toPseudomonasT3S and were used to study cellular changes occurring in response to induction of T3S sensitivity, which occurred following treatment with phorbol esters. Using both cell models, a positive correlation was observed between eukaryotic cell adherence to tissue culture wells and T3S sensitivity. In examining the type of adhesion process linked to T3S sensitivity in HT-29 cells, a hierarchical order of protein involvement was identified that paralleled the architecture of leading edge (LE) focal complexes. Conversely, in HL-60 cells, induction of T3S sensitivity coincided with the onset of LE properties and the development of actin-rich projections associated with polarized cell migration. When LE architecture was examined by immunofluorescent staining for actin, Rac1, IQ-motif-containing GTPase-activating protein 1 (IQGAP1) and phosphatidylinositol 3 kinase (PI3 kinase), intact LE structure was found to closely correlate with host cell sensitivity toP. aeruginosaT3S. Our model for host cell involvement inPseudomonasT3S proposes that cortical actin polymerization at the LE alters membrane properties to favour T3S translocon function and the establishment of infections, which is consistent withPseudomonasinfections targeting wounded epithelial barriers undergoing cell migration.
Autophagy is involved in starvation response and cell death in Blastocystis
Authors: Yin Jing , Ye Angeline J. J. , Tan Kevin S. W.
Published: November 2009

Previous studies have demonstrated that colony forms ofBlastocystisundergo cell death with numerous membrane-bound vesicles containing organelles located within the central vacuole, resembling morphological features of autophagy. In this study, we investigated whetherBlastocystisunderwent autophagy upon amino acid starvation and rapamycin treatment. Concurrently, we provide new insight into a possible function of the central vacuole. The use of the autophagy marker monodansylcadaverine, and the autophagy inhibitors3-methyladenine and wortmannin, showed the existence of autophagy in amino-acid-starved and rapamycin-treatedBlastocystis. Confocal microscopy and transmission electron microscopy studies also showed morphological changes that were suggestive of autophagy. The unusually large size of the autophagic compartments within the parasite central vacuole was found to be unique inBlastocystis. In addition, autophagy was found to be triggered when cells were exposed to the cytotoxic antibody mAb 1D5, and autophagy was intensified in the presence of the caspase inhibitor zVAD.fmk. Taken together, our results suggest that the core machinery for autophagy is conserved inBlastocystis, and that it plays an important role in the starvation response and cell death of the parasite.
Analysis of adherence, biofilm formation and cytotoxicity suggests a greater virulence potential of Gardnerella vaginalis relative to other bacterial-vaginosis-associated anaerobes
Authors: Patterson Jennifer L. , Stull-Lane Annica , Girerd Philippe H. , Jefferson Kimberly K.
Published: November 2009

Worldwide, bacterial vaginosis (BV) is the most common vaginal disorder in women of childbearing age. BV is characterized by a dramatic shift in the vaginal microflora, involving a relative decrease in lactobacilli, and a proliferation of anaerobes. In most cases of BV, the predominant bacterial species found is Gardnerella vaginalis. However, pure cultures of G. vaginalis do not always result in BV, and asymptomatic women are sometimes colonized with low numbers of G. vaginalis. Thus, there is controversy about whether G. vaginalis is an opportunistic pathogen and the causative agent of many cases of BV, or whether BV is a polymicrobial condition caused by the collective effects of an altered microbial flora. Recent studies of the biofilm-forming potential and cytotoxic activity of G. vaginalis have renewed interest in the virulence potential of this organism. In an effort to tease apart the aetiology of this disorder, we utilized in vitro assays to compare three virulence properties of G. vaginalis relative to other BV-associated anaerobes. We designed a viable assay to analyse bacterial adherence to vaginal epithelial cells, we compared biofilm-producing capacities, and we assessed cytotoxic activity. Of the BV-associated anaerobes tested, only G. vaginalis demonstrated all three virulence properties combined. This study suggests that G. vaginalis is more virulent than other BV-associated anaerobes, and that many of the bacterial species frequently isolated from BV may be relatively avirulent opportunists that colonize the vagina after G. vaginalis has initiated an infection.
Integrating multiple ‘omics’ analysis for microbial biology: application and methodologies
Authors: Zhang Weiwen , Li Feng , Nie Lei
Published: November 2009

Recent advances in various ‘omics’ technologies enable quantitative monitoring of the abundance of various biological molecules in a high-throughput manner, and thus allow determination of their variation between different biological states on a genomic scale. Several popular ‘omics’ platforms that have been used in microbial systems biology include transcriptomics, which measures mRNA transcript levels; proteomics, which quantifies protein abundance; metabolomics, which determines abundance of small cellular metabolites; interactomics, which resolves the whole set of molecular interactions in cells; and fluxomics, which establishes dynamic changes of molecules within a cell over time. However, no single ‘omics’ analysis can fully unravel the complexities of fundamental microbial biology. Therefore, integration of multiple layers of information, the multi-‘omics’ approach, is required to acquire a precise picture of living micro-organisms. In spite of this being a challenging task, some attempts have been made recently to integrate heterogeneous ‘omics’ datasets in various microbial systems and the results have demonstrated that the multi-‘omics’ approach is a powerful tool for understanding the functional principles and dynamics of total cellular systems. This article reviews some basic concepts of various experimental ‘omics’ approaches, recent application of the integrated ‘omics’ for exploring metabolic and regulatory mechanisms in microbes, and advances in computational and statistical methodologies associated with integrated ‘omics’ analyses. Online databases and bioinformatic infrastructure available for integrated ‘omics’ analyses are also briefly discussed.
PAP1 [poly(A) polymerase 1] homozygosity and hyperadenylation are major determinants of increased mRNA stability of CDR1 in azole-resistant clinical isolates of Candida albicans
Authors: Manoharlal Raman , Gorantala Jyotsna , Sharma Monika , Sanglard Dominique , Prasad Rajendra
Published: November 2009

Using genetically matched azole-susceptible (AS) and azole-resistant (AR) clinical isolates ofCandida albicans, we recently demonstrated thatCDR1overexpression in AR isolates is due to its enhanced transcriptional activation and mRNA stability. This study examines the molecular mechanisms underlying enhancedCDR1mRNA stability in AR isolates. Mapping of the 3′ untranslated region (3′ UTR) ofCDR1revealed that it was rich in adenylate/uridylate (AU) elements, possessed heterogeneous polyadenylation sites, and had putative consensus sequences for RNA-binding proteins. Swapping of heterologous and chimericlacZ–CDR13′ UTR transcriptional reporter fusion constructs did not alter the reporter activity in AS and AR isolates, indicating thatcis-acting sequences within theCDR13′ UTR itself are not sufficient to confer the observed differential mRNA decay. Interestingly, the poly(A) tail of theCDR1mRNA of AR isolates was ∼35–50 % hyperadenylated as compared with AS isolates.C. albicanspoly(A) polymerase (PAP1), responsible for mRNA adenylation, resides on chromosome 5 in close proximity to the mating type-like (MTL) locus. Two differentPAP1alleles,PAP1-a/PAP1-α, were recovered from AS (MTL-a/MTL-α), while a single type ofPAP1allele (PAP1-α) was recovered from AR isolates (MTL-α/MTL-α). Among the heterozygous deletions ofPAP1-a(Δpap1-a/PAP1-α) andPAP1-α(PAP1-a/Δpap1-α), only the former led to relatively enhanced drug resistance, to polyadenylation and to transcript stability ofCDR1in the AS isolate. This suggests a dominant negative role ofPAP1-ainCDR1transcript polyadenylation and stability. Taken together, our study provides the first evidence, to our knowledge, that loss of heterozygosity at thePAP1locus is linked to hyperadenylation and subsequent increased stability ofCDR1transcripts, thus contributing to enhanced drug resistance.
A Virus-Induced Gene Silencing Screen Identifies a Role for Thylakoid Formation1 in Pseudomonas syringae pv tomato Symptom Development in Tomato and Arabidopsis
Authors: Wangdi Tamding , Uppalapati Srinivasa Rao , Nagaraj Satish , Ryu Choong-Min , Bender Carol L. , Mysore Kirankumar S.
Published: November 2009

Pseudomonas syringae pv tomato DC3000 (Pst DC3000), which causes disease in tomato (Solanum lycopersicum) and Arabidopsis (Arabidopsis thaliana), produces coronatine (COR), a non-host-specific phytotoxin. COR, which functions as a jasmonate mimic, is required for full virulence of Pst DC3000 and for the induction of chlorosis in host plants. Previous genetic screens based on insensitivity to COR and/or methyl jasmonate identified several potential targets for COR and methyl jasmonate. In this study, we utilized Nicotianabenthamiana and virus-induced gene silencing to individually reduce the expression of over 4,000 genes. The silenced lines of N. benthamiana were then screened for altered responses to purified COR. Using this forward genetics approach, several genes were identified with altered responses to COR. These were designated as ALC (for altered COR response) genes. When silenced, one of the identified genes, ALC1, produced a hypersensitive/necrosis-like phenotype upon COR application in a Coronatine-Insensitive1 (COI1)-dependent manner. To understand the involvement of ALC1 during the Pst DC3000-host interaction, we used the nucleotide sequence of ALC1 and identified its ortholog in Arabidopsis (Thylakoid Formation1 [THF1]) and tomato (SlALC1). In pathogenicity assays performed on Arabidopsis thf1 mutant and SlALC1-silenced tomato plants, Pst DC3000 induced accelerated coalescing necrotic lesions. Furthermore, we showed that COR affects ALC1 localization in chloroplasts in a COI1-dependent manner. In conclusion, our results show that the virus-induced gene silencing-based forward genetic screen has the potential to identify new players in COR signaling and disease-associated necrotic cell death.