bluuebunny/crossref_metadata_2025 huggingface dataset:
GeNOSA: inferring and experimentally supporting quantitative gene regulatory networks in prokaryotes
Authors: Chen Yi-Hsiung , Yang Chi-Dung , Tseng Ching-Ping , Huang Hsien-Da , Ho Shinn-Ying
Published: February 2015

Motivation: The establishment of quantitative gene regulatory networks (qGRNs) through existing network component analysis (NCA) approaches suffers from shortcomings such as usage limitations of problem constraints and the instability of inferred qGRNs. The proposed GeNOSA framework uses a global optimization algorithm (OptNCA) to cope with the stringent limitations of NCA approaches in large-scale qGRNs.

Results: OptNCA performs well against existing NCA-derived algorithms in terms of utilization of connectivity information and reconstruction accuracy of inferred GRNs using synthetic and real Escherichia coli datasets. For comparisons with other non-NCA-derived algorithms, OptNCA without using known qualitative regulations is also evaluated in terms of qualitative assessments using a synthetic Saccharomyces cerevisiae dataset of the DREAM3 challenges. We successfully demonstrate GeNOSA in several applications including deducing condition-dependent regulations, establishing high-consensus qGRNs and validating a sub-network experimentally for dose–response and time–course microarray data, and discovering and experimentally confirming a novel regulation of CRP on AscG.

Availability and implementation: All datasets and the GeNOSA framework are freely available from http://e045.life.nctu.edu.tw/GeNOSA.

Contact:  syho@mail.nctu.edu.tw

Supplementary information:  Supplementary data are available at Bioinformatics online.
Detection of significant protein coevolution
Authors: Ochoa David , Juan David , Valencia Alfonso , Pazos Florencio
Published: February 2015

Motivation: The evolution of proteins cannot be fully understood without taking into account the coevolutionary linkages entangling them. From a practical point of view, coevolution between protein families has been used as a way of detecting protein interactions and functional relationships from genomic information. The most common approach to inferring protein coevolution involves the quantification of phylogenetic tree similarity using a family of methodologies termed mirrortree. In spite of their success, a fundamental problem of these approaches is the lack of an adequate statistical framework to assess the significance of a given coevolutionary score (tree similarity). As a consequence, a number of ad hoc filters and arbitrary thresholds are required in an attempt to obtain a final set of confident coevolutionary signals.

Results: In this work, we developed a method for associating confidence estimators (P values) to the tree-similarity scores, using a null model specifically designed for the tree comparison problem. We show how this approach largely improves the quality and coverage (number of pairs that can be evaluated) of the detected coevolution in all the stages of the mirrortree workflow, independently of the starting genomic information. This not only leads to a better understanding of protein coevolution and its biological implications, but also to obtain a highly reliable and comprehensive network of predicted interactions, as well as information on the substructure of macromolecular complexes using only genomic information.

Availability and implementation: The software and datasets used in this work are freely available at: http://csbg.cnb.csic.es/pMT/.

Contact:  pazos@cnb.csic.es

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Gene-associated markers can assign origin in a weakly structured fish, Atlantic herring
Authors: Bekkevold Dorte , Helyar Sarah J. , Limborg Morten T. , Nielsen Einar E. , Hemmer-Hansen Jakob , Clausen Lotte A. W. , Carvalho Gary R.
Published: February 2015

Regulations on the exploitation of populations of commercially important fish species and the ensuing consumer interest in sustainable products have increased the need to accurately identify the population of origin of fish and fish products. Although genomics-based tools have proven highly useful, there are relatively few examples in marine fish displaying accurate origin assignment. We synthesize data for 156 single-nucleotide polymorphisms typed in 1039 herring, Clupea harengus L., spanning the Northeast Atlantic to develop a tool that allows assignment of individual herring to their regional origin. We show the method's suitability to address specific biological questions, as well as management applications. We analyse temporally replicated collections from two areas, the Skagerrak (n = 81, 84, 66) and the western Baltic (n = 52, 52). Both areas harbour heavily fished mixed-origin stocks, complicating management issues. We report novel genetic evidence that herring from the Baltic Sea contribute to catches in the North Sea, and find support that western Baltic feeding aggregations mainly constitute herring from the western Baltic with contributions from the Eastern Baltic. Our study describes a general approach and outlines a database allowing individual assignment and traceability of herring across a large part of its East Atlantic distribution.
Preparation of monoPEGylated Cyanovirin-N’s derivative and its anti-influenza A virus bioactivity in vitro and in vivo
Authors: Wu Chongchao , Chen Wei , Chen Jia , Han Bo , Peng Zhou , Ge Feng , Wei Bo , Liu Mingxian , Zhang Meiying , Qian Chuiwen , Hou Zhibo , Liu Ge , Guo Chaowan , Wang Yifei , Kitazato Kaio , Yu Guoying , Zou Chunbin , Xiong Sheng
Published: February 2015

Influenza A virus (IAV) has been raising public health and safety concerns worldwide. Cyanovirin-N (CVN) is a prominent anti-IAV candidate, but both cytotoxicity and immunogenicity have hindered the development of this protein as a viable therapy. In this article, linker-CVN (LCVN) with a flexible and hydrophilic polypeptide at the N-terminus was efficiently produced from the cytoplasm of Escherichia coli at a >15-l scale. PEGylation at the N-terminal α-amine of LCVN was also reformed as 20 kDa PEGylated linkered Cyanovirin-N (PEG20k–LCVN). The 50% effective concentrations of PEG20k–LCVN were 0.43 ± 0.11 µM for influenza A/HK/8/68 (H3N2) and 0.04 ± 0.02 µM for A/Swan/Hokkaido/51/96 (H5N3), dramatically lower than that of the positive control, Ribavirin (2.88 ± 0.66 × 103 µM and 1.79 ± 0.62 × 103 µM, respectively). A total of 12.5 µM PEG20k–LCVN effectively inactivate the propagation of H3N2 in chicken embryos. About 2.0 mg/kg/day PEG20k–LCVN increased double the survival rate (66.67%, P = 0.0378) of H3N2 infected mice, prolonged the median survival period, downregulated the mRNA level of viral nuclear protein and decreased (attenuated) the pathology lesion in mice lung. A novel PEGylated CVN derivative, PEG20k–LCVN, exhibited potent and strain-dependent anti-IAV activity in nanomolar concentrations in vitro, as well as in micromolar concentration in vivo.
A Continuous-Time, Latent-Variable Model of Time Series Data
Authors: Tahk Alexander M.
Published: February 2015

Many types of time series data in political science, including polling data and events data, exhibit important features'such as irregular spacing, noninstantaneous observation, overlapping observation times, and sampling or other measurement error'that are ignored in most statistical analyses because of model limitations. Ignoring these properties can lead not only to biased coefficients but also to incorrect inference about the direction of causality. This article develops a continuous-time model to overcome these limitations. This new model treats observations as noisy samples collected over an interval of time and can be viewed as a generalization of the vector autoregressive model. Monte Carlo simulations and two empirical examples demonstrate the importance of modeling these features of the data.
Effectiveness of Single-Digit IOP Targets on Decreasing Global and Localized Visual Field Progression After Filtration Surgery in Eyes With Progressive Normal-Tension Glaucoma
Authors: Iverson Shawn M. , Schultz Scott K. , Shi Wei , Feuer William J. , Greenfield David S.
Published: February 2015

Purpose:

To examine the effectiveness of achieving single-digit intraocular pressure (IOP) targets with filtration surgery on decreasing global and localized visual field (VF) progression in eyes with progressive normal-tension glaucoma (NTG).

Methods:

A retrospective chart review was conducted to identify NTG patients who underwent trabeculectomy with mitomycin C between 2006 and 2010 for progressive VF loss with preoperative IOP≤15 mm Hg during the 12 months before surgery. All eyes had glaucomatous optic neuropathy and progressive VF loss, uncontrolled IOP on maximum therapy, and a minimum of 2 baseline preoperative and 4 postoperative VF examinations. VF progression was assessed using Guided Progression Analysis (GPA) and Progressor software.

Results:

Fifteen eyes of 14 patients (mean age 71.8±7.5 y) were enrolled with mean follow-up of 71±26 months. Mean postoperative IOP (8.5±3.5 mm Hg) was significantly (P<0.001) reduced compared with preoperatively (13.1±1.5 mm Hg). The probability of achieving an IOP goal ≤10 mm Hg was 66% at 4 years’ follow-up. The overall rate of postoperative VF progression using any method was 13.3% (1 eye using Progressor; 1 eye using GPA and Progressor). Average postoperative slope of MD (−0.25±0.86 dB/y) and pattern SD (0.49±0.83 dB/y) were improved (P=0.05 and 0.07) compared with the preoperative slopes (−1.05±0.66 and 1.21±0.71 dB/y).

Conclusions:

Achieving single-digit IOP targets with filtration surgery has a beneficial effect on reducing global and localized rates of VF progression in NTG eyes with progression at low IOP.
Clinical Outcomes of Ahmed Glaucoma Valve Implantation With or Without Intravitreal Bevacizumab Pretreatment for Neovascular Glaucoma: A Systematic Review and Meta-Analysis
Authors: Zhou Minwen , Xu Xun , Zhang Xiulan , Sun Xiaodong
Published: February 2015

Purpose:

To evaluate the efficacy and tolerability of Ahmed glaucoma valve (AGV) implantation with intravitreal bevacizumab injection (IVB) pretreatment in the treatment of neovascular glaucoma (NVG).

Methods:

A comprehensive literature search was performed according to the Cochrane collaboration methodology to identify controlled clinical trials comparing AGV implantation with (IVB group) or without IVB (control group) pretreatment for NVG. The main outcome measures were the weighted mean differences (WMDs) for intraocular pressure reduction, a reduction in glaucoma medications, odds ratio (OR) for complete success rates, and qualified success rates. Tolerability estimates were measured by OR for adverse events.

Results:

The WMD of the intraocular pressure reduction when comparing the IVB group with the control group was 3.30 (−1.21 to 7.80). The IVB group was associated with numerically greater but nonsignificant IOP lowering efficacy compared with the control group (P=0.152). Both groups were comparable in the reduction of glaucoma medication, with a WMD of 0.28 (−0.03 to 0.59) at the follow-up endpoint (P=0.077). The IVB group was associated with significant greater complete success rates compared with the control group, with a pooled OR of 3.18 (1.41 to 7.19). However, it did not show a significant difference for the qualified success rate between them, with a pooled OR of 2.00 (0.95 to 4.21). The IVB group was associated with a significantly lower frequency of hyphema than the control group, with a pooled OR of 0.15 (0.07 to 0.32).

Conclusion:

The use of IVB pretreatment for NVG is a safe and effective additional step during AGV implantation surgery.
Sex-dependent effects of nutrition on telomere dynamics in zebra finches (Taeniopygia guttata)
Authors: Noguera Jose C. , Metcalfe Neil B. , Boner Winnie , Monaghan Pat
Published: February 2015

At a cellular level, oxidative stress is known to increase telomere attrition, and hence cellular senescence and risk of disease. It has been proposed that dietary micronutrients play an important role in telomere protection due to their antioxidant properties. We experimentally manipulated dietary micronutrients during early life in zebra finches (Taeniopygia guttata). We found no effects of micronutrient intake on telomere loss during chick growth. However, females given a diet high in micronutrients during sexual maturation showed reduced telomere loss; there was no such effect in males. These results suggest that micronutrients may influence rates of cellular senescence, but differences in micronutrient requirement and allocation strategies, probably linked to the development of sexual coloration, may underlie sex differences in response.
Socioecological variables predict telomere length in wild spotted hyenas
Authors: Lewin Nora , Treidel Lisa A. , Holekamp Kay E. , Place Ned J. , Haussmann Mark F.
Published: February 2015

Telomeres are regarded as important biomarkers of ageing and serve as useful tools in revealing how stress acts at the cellular level. However, the effects of social and ecological factors on telomere length remain poorly understood, particularly in free-ranging mammals. Here, we investigated the influences of within-group dominance rank and group membership on telomere length in wild adult spotted hyenas (
Crocuta crocuta
). We found large effects of both factors; high-ranking hyenas exhibited significantly greater mean telomere length than did subordinate animals, and group membership significantly predicted mean telomere length within high-ranking females. We further inquired whether prey availability mediates the observed effect of group membership on telomere length, but this hypothesis was not supported. Interestingly, adult telomere length was not predicted by age. Our work shows for the first time, to the best of our knowledge, the effects of social rank on telomere length in a wild mammal and enhances our understanding of how social and ecological variables may contribute to organismal senescence.
James Gregory, the University observatory and the early acquisition of scientific instruments at the University of St Andrews
Authors: Rawson Helen C.
Published: February 2015

James Gregory, inventor of the reflecting telescope and Fellow of the Royal Society, was the first Regius Professor of Mathematics of the University of St Andrews, 1668–74. He attempted to establish in St Andrews what would, if completed, have been the first purpose-built observatory in the British Isles. He travelled to London in 1673 to purchase instruments for equipping the observatory and improving the teaching and study of natural philosophy and mathematics in the university, seeking the advice of John Flamsteed, later the first Astronomer Royal. This paper considers the observatory initiative and the early acquisition of instruments at the University of St Andrews, with reference to Gregory's correspondence, inventories made
ca.
1699–
ca.
1718 and extant instruments themselves, some of which predate Gregory's time. It examines the structure and fate of the university observatory, the legacy of Gregory's teaching and endeavours, and the meridian line laid down in 1748 in the University Library.
Renormalized Mori–Zwanzig-reduced models for systems without scale separation
Authors: Stinis Panos
Published: February 2015

Model reduction for complex systems is a rather active area of research. For many real-world systems, constructing an accurate reduced model is prohibitively expensive. The main difficulty stems from the tremendous range of spatial and temporal scales present in the solution of such systems. This leads to the need to develop reduced models where, inevitably, the resolved variables donotexhibit (spatial and/or temporal) scale separation from the unresolved ones. We present a brief survey of recent results on the construction of Mori–Zwanzig-reduced models for such systems. The construction is inspired by the concepts of scale dependence and renormalization which first appeared in the context of high-energy and statistical physics.
Iterative Potts and Blake–Zisserman minimization for the recovery of functions with discontinuities from indirect measurements
Authors: Weinmann Andreas , Storath Martin
Published: February 2015

Signals with discontinuities appear in many problems in the applied sciences ranging from mechanics, electrical engineering to biology and medicine. The concrete data acquired are typically discrete, indirect and noisy measurements of some quantities describing the signal under consideration. The task is to restore the signal and, in particular, the discontinuities. In this respect, classical methods perform rather poor, whereas non-convex non-smooth variational methods seem to be the correct choice. Examples are methods based on Mumford–Shah and piecewise constant Mumford–Shah functionals and discretized versions which are known as Blake–Zisserman and Potts functionals. Owing to their non-convexity, minimization of such functionals is challenging. In this paper, we propose a new iterative minimization strategy for Blake–Zisserman as well as Potts functionals and a related jump-sparsity problem dealing with indirect, noisy measurements. We provide a convergence analysis and underpin our findings with numerical experiments.
The motion of point vortices on closed surfaces
Authors: Dritschel D. G. , Boatto S.
Published: February 2015

We develop a mathematical framework for the dynamics of a set of point vortices on a class of differentiable surfaces conformal to the unit sphere. When the sum of the vortex circulations is non-zero, a compensating uniform vorticity field is required to satisfy the Gauss condition (that the integral of the Laplace–Beltrami operator must vanish). On variable Gaussian curvature surfaces, this results in self-induced vortex motion, a feature entirely absent on the plane, the sphere or the hyperboloid. We derive explicit equations of motion for vortices on surfaces of revolution and compute their solutions for a variety of surfaces. We also apply these equations to study the linear stability of a ring of vortices on any surface of revolution. On an ellipsoid of revolution, as few as two vortices can be unstable on oblate surfaces or sufficiently prolate ones. This extends known results for the plane, where seven vortices are marginally unstable (Thomson 1883
A treatise on the motion of vortex rings
, pp. 94–108; Dritschel 1985
J. Fluid Mech.
157
, 95–134 (
doi:10.1017/S0022112088003088
)), and the sphere, where four vortices may be unstable if sufficiently close to the equator (Polvani & Dritschel 1993
J. Fluid Mech.
255
, 35–64 (
doi:10.1017/S0022112093002381
)).
Adaptation to enemy shifts: rapid resistance evolution to local
Vibrio
spp. in invasive Pacific oysters
Authors: Wendling Carolin C. , Wegner K. Mathias
Published: February 2015

One hypothesis for the success of invasive species is reduced pathogen burden, resulting from a release from infections or high immunological fitness of invaders. Despite strong selection exerted on the host, the evolutionary response of invaders to newly acquired pathogens has rarely been considered. The two independent and genetically distinct invasions of the Pacific oyster
Crassostrea gigas
into the North Sea represent an ideal model system to study fast evolutionary responses of invasive populations. By exposing both invasion sources to ubiquitous and phylogenetically diverse pathogens (
Vibrio
spp.), we demonstrate that within a few generations hosts adapted to newly encountered pathogen communities. However, local adaptation only became apparent in selective environments, i.e. at elevated temperatures reflecting patterns of disease outbreaks in natural populations. Resistance against sympatric and allopatric
Vibrio
spp. strains was dominantly inherited in crosses between both invasion sources, resulting in an overall higher resistance of admixed individuals than pure lines. Therefore, we suggest that a simple genetic resistance mechanism of the host is matched to a common virulence mechanism shared by local
Vibrio
strains. This combination might have facilitated a fast evolutionary response that can explain another dimension of why invasive species can be so successful in newly invaded ranges.
Bypass of genetic constraints during mutator evolution to antibiotic resistance
Authors: Couce Alejandro , Rodríguez-Rojas Alexandro , Blázquez Jesús
Published: February 2015

Genetic constraints can block many mutational pathways to optimal genotypes in real fitness landscapes, yet the extent to which this can limit evolution remains to be determined. Interestingly, mutator bacteria elevate only specific types of mutations, and therefore could be very sensitive to genetic constraints. Testing this possibility is not only clinically relevant, but can also inform about the general impact of genetic constraints in adaptation. Here, we evolved 576 populations of two mutator and one wild-typeEscherichia colito doubling concentrations of the antibiotic cefotaxime. All strains carried TEM-1, a β-lactamase enzyme well known by its low availability of mutational pathways. Crucially, one of the mutators does not elevate any of the relevant first-step mutations known to improve cefatoximase activity. Despite this, both mutators displayed a similar ability to evolve more than 1000-fold resistance. Initial adaptation proceeded in parallel through general multi-drug resistance mechanisms. High-level resistance, in contrast, was achieved through divergent paths; with thea prioriinferior mutator exploiting alternative mutational pathways in PBP3, the target of the antibiotic. These results have implications for mutator management in clinical infections and, more generally, illustrate that limits to natural selection in real organisms are alleviated by the existence of multiple loci contributing to fitness.
The mechanics and physics of fracturing: application to thermal aspects of crack propagation and to fracking
Authors: Cherepanov Genady P.
Published: February 2015

By way of introduction, the general invariant integral (GI) based on the energy conservation law is presented, with mention of cosmic, gravitational, mass, elastic, thermal and electromagnetic energy of matter application to demonstrate the approach, including Coulomb's Law generalized for moving electric charges, Newton's Law generalized for coupled gravitational/cosmic field, the new Archimedes’ Law accounting for gravitational and surface energy, and others. Then using this approach the temperature track behind a moving crack is found, and the coupling of elastic and thermal energies is set up in fracturing. For porous materials saturated with a fluid or gas, the notion of binary continuum is used to introduce the corresponding GIs. As applied to the horizontal drilling and fracturing of boreholes, the field of pressure and flow rate as well as the fluid output from both a horizontal borehole and a fracture are derived in the fluid extraction regime. The theory of fracking in shale gas reservoirs is suggested for three basic regimes of the drill mud permeation, with calculating the shape and volume of the local region of the multiply fractured rock in terms of the pressures of rock, drill mud and shale gas.
Dynamic fracture of inorganic glasses by hard spherical and conical projectiles
Authors: Chaudhri M. Munawar
Published: February 2015

In this article, high-speed photographic investigations of the dynamic crack initiation and propagation in several inorganic glasses by the impact of small spherical and conical projectiles are described. These were carried out at speeds of up to approximately 2×106frames s−1. The glasses were fused silica, ‘Pyrex’ (a borosilicate glass), soda lime and B2O3. The projectiles were 0.8–2 mm diameter spheres of steel, glass, sapphire and tungsten carbide, and their velocities were up to 340 m s−1. In fused silica and Pyrex, spherical projectiles' impact produced Hertzian cone cracks travelling at terminal crack velocities, whereas in soda-lime glass fast splinter cracks were generated. No crack bifurcation was observed, which has been explained by the nature of the stress intensity factor of the particle-impact-generated cracks, which leads to a stable crack growth. Crack bifurcation was, however, observed in thermally tempered glass; this bifurcation has been explained by the tensile residual stress and the associated unstable crack growth. A new explanation has been proposed for the decrease of the included angle of the Hertzian cone cracks with increasing impact velocity. B2O3glass showed dynamic compaction and plasticity owing to impact with steel spheres. Other observations, such as total contact time, crack lengths and response to oblique impacts, have also been explained.
Cleaving the Halqeh-ye-nur diamonds: a dynamic fracture analysis
Authors: Atkinson Colin , Martineau Philip M. , Khan Rizwan U. A. , Field John E. , Fisher David , Davies Nick M. , Samartseva Julia V. , Putterman Seth J. , Hird Jonathan R.
Published: February 2015

The degree of surface roughness and clarity with which a surface in a brittle material can be formed via fracture is known to be related to the speed of the propagating crack. Cracks traversing a brittle material at low speed produce very smooth surfaces, while those propagating faster create less reflective and rough surfaces (Buehler MJ, Gao H. 2006
Nature
439
, 307–310 (
doi:10.1038/nature04408
)). The elastic wave speeds (
c
l
≈18 000 m s
−1
,
c

s

≈11 750 m s
−1
) in diamond are fast (Willmott GR, Field JE. 2006
Phil. Mag.
86
, 4305–4318 (
doi:10.1080/14786430500482336
)) and present a particular problem in creating smooth surfaces during the cleaving of diamond—a routine operation in the fashioning of diamonds for gemstone purposes—as the waves are reflected from the boundaries of the material and can add a tensile component to the propagating crack tip causing the well-known cleavage steps observed on diamond surfaces (Field JE. 1971
Contemp. Phys.
12
, 1–31 (
doi:10.1080/00107517108205103
); Field JE. 1979
Properties of diamond
, 1st edn, Academic Press; Wilks EM. 1958
Phil. Mag.
3
, 1074–1080 (
doi:10.1080/14786435808237036
)). Here we report an analysis of two diamonds, having large dimensions and high aspect ratio, which from a gemological analysis are shown to have been cleaved from the same 200 carat specimen. A methodology for their manufacture is calculated by an analysis of a model problem. This takes into account the effect of multiple reflections from the sample boundaries. It is suggested that the lapidary had an intuitive guide to how to apply the cleavage force in order to control the crack speed. In particular, it is shown that it is likely that this technique caused the fracture to propagate at a lower speed. The sacrifice of a large diamond with the intention of creating thin plates, rather than a faceted gemstone, demonstrates how symbolism and beliefs associated with gemstones have changed over the centuries (Harlow GE. 1998
The nature of diamonds
, Cambridge University Press). The scientific insights gained by studying these gemstones suggest a method of producing macroscale atomically flat and stress-free surfaces on other brittle materials.
Fracturing across the multi-scales of diverse materials
Authors: Armstrong R. W. , Antolovich S. D. , Griffiths J. R. , Knott J. F.
Published: February 2015

Everyone has to deal with fracturing of materials at one level or another, beginning from normal household chores and extending to the largest scale of observations reported for catastrophic events occurring on a geological level or even expanded to events in outer space. Such wide perspective is introduced in the current introduction of this theme issue. The follow-on organization of technical articles provides a flavour of the range in size scales at which fracturing occurs in a wide diversity of materials—from ‘fracking’ oil extraction and earth moving to laboratory testing of rock material and extending to the cracking of tooth enamel. Of important scientific interest are observations made and analysed at the smallest dimensions corresponding to the mechanisms by which fracture is either enhanced or hindered by permanent deformation or other processes. Such events are irrevocably linked to the atomic structure in all engineering materials, a sampling of which is presented, including results for crystalline and amorphous materials. Hooray for the broad subject description that is hoped to be appealing to the interested reader.
Anaerosolibacter carboniphilus gen. nov., sp. nov., a strictly anaerobic iron-reducing bacterium isolated from coal-contaminated soil
Authors: Hong Heeji , Kim So-Jeong , Min Ui-Gi , Lee Yong-Jae , Kim Song-Gun , Roh Seong Woon , Kim Jong-Geol , Na Jeong-Geol , Rhee Sung-Keun
Published: February 2015

A strictly anaerobic, mesophilic, iron-reducing bacterial strain, IRF19T, was isolated from coal-contaminated soil in the Republic of Korea. IRF19T cells were straight, rod-shaped, Gram-staining-negative and motile by means of flagella. The optimum pH and temperature for their growth were determined to be pH 7.5–8.0 and 40 °C, while the optimum range was pH 6.5–10.0 and 20–45 °C, respectively. Strain IRF19T did not require NaCl for growth but it tolerated up to 2 % (w/v). Growth was observed with yeast extract, d-glucose, d-fructose, d-ribose, d-mannitol, d-mannose, l-serine, l-alanine and l-isoleucine. Fe(III), elemental sulfur, thiosulfate and sulfate were used as electron acceptors. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain IRF19T is affiliated to the family

Clostridiaceae

and is most closely related to

Salimesophilobacter vulgaris

Zn2T (93.5 % similarity),

Geosporobacter subterraneus

VNs68T (93.2 %) and

Thermotalea metallivorans

B2-1T (92.3 %). The major cellular fatty acids of strain IRF19T were C14 : 0, iso-C15 : 0 and C16 : 0, and the profile was distinct from those of the closely related species. The major respiratory quinone of strain IRF19T was menaquinone MK-5 (V-H2). The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unknown phospholipid and two unknown polar lipids. The G+C content of the genomic DNA of strain IRF19T was determined to be 37.4 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic results, strain IRF19T is considered to represent a novel species of a novel genus of the family

Clostridiaceae

, for which we propose the name Anaerosolibacter carboniphilus gen. nov., sp. nov., with the type strain IRF19T ( = KCTC 15396T = JCM 19988T).
Alteromonas gracilis sp. nov., a marine polysaccharide-producing bacterium
Authors: Matsuyama Hidetoshi , Minami Hideki , Sakaki Takeshi , Kasahara Hirokazu , Baba Shotaro , Ishimaru Shota , Hirota Kikue , Yumoto Isao
Published: February 2015

A novel exopolysaccharide-producing bacterium, designated strain 9a2T, was isolated from Pacific Ocean sediment. The strain was Gram-stain-negative, motile, strictly aerobic, oxidase- and catalase-positive, and required NaCl for growth. Its major isoprenoid quinone was ubiquinone-8 (Q-8), and its cellular fatty acid profile consisted mainly of C16 : 1ω7c, C18 : 1ω9cand C16 : 0. The DNA G+C content was 46.6 mol%. 16S rRNA gene sequence analysis suggested that strain 9a2Tis a member of the genusAlteromonas. Strain 9a2Texhibited closest phylogenetic affinity toAlteromonas macleodiiNBRC 102226T(99.3 % 16S rRNA gene sequence similarity),A. marinaSW-47T(99.3 %),A. litoreaTF-22T(99.0 %),A. australicaH17T(98.7 %),A. simiduiiBCRC 17572T(98.5 %),A. stellipolarisLMG 21861T(98.3 %) andA. hispanicaF-32T(98.2 %). The DNA–DNA reassociation values between strain 9a2TandA. macleodiiJCM 20772T,A. marinaJCM 11804T,A. litoreaJCM 12188T,A. australicaCIP 109921T,A. simiduiiJCM 13896T,A. stellipolarisLMG 21861TandA. hispanicaLMG 22958Twere below 70 %. Strain 9a2Tcontained phosphatidylethanolamine, phosphatidylglycerol and an unidentified polar lipid. Owing to differences in phenotypic and chemotaxonomic characteristics, phylogenetic analysis based on 16S rRNA gene sequences and DNA–DNA relatedness data, the isolate merits classification as representing a novel species, for which the nameAlteromonasgracilissp. nov. is proposed. The type strain of this species is 9a2T( = JCM 30236T = NCIMB 14947T).
Sulfuriferula multivorans gen. nov., sp. nov., isolated from a freshwater lake, reclassification of ‘Thiobacillus plumbophilus’ as Sulfuriferula plumbophilus sp. nov., and description of Sulfuricellaceae fam. nov. and Sulfuricellales ord. nov.
Authors: Watanabe Tomohiro , Kojima Hisaya , Fukui Manabu
Published: February 2015

A sulfur-oxidizing bacterium, strain TTNT, was isolated from a

Thioploca

sample obtained from a freshwater lake in Japan. The isolate shared 97.1 % 16S rRNA gene sequence similarity with an obligately aerobic chemolithoautotroph, ‘Thiobacillus plumbophilus’ Gro7T. Cells were rods, motile, and Gram-stain-negative. The G+C content of the genomic DNA was approximately 66 mol%. Strain TTNT grew over a temperature range of 8–32 °C (optimum 22–25 °C), an NaCl concentration range of 0–133.3 mM (optimum 0–3.3 mM) and a pH range of 5.3–8.6 (optimum pH 6.4–7.0). Strain TTNT was facultatively anaerobic and could utilize nitrate as an electron acceptor. The isolate oxidized tetrathionate, thiosulfate and elemental sulfur as the sole energy sources for autotrophic growth, and could also grow heterotrophically on a number of organic substrates. Based on its phylogenetic and phenotypic properties, strain TTNT represents a novel species of a novel genus, for which the name Sulfuriferula multivorans gen. nov., sp. nov. is proposed. The type strain is TTNT ( = NBRC 110683T = DSM 29343T). Along with this, the reclassification of ‘Thiobacillus plumbophilus’ as Sulfuriferula plumbophilus sp. nov. (type strain Gro7T = NBRC 107929T = DSM 6690T) is proposed. Based on the data obtained in this study, we describe the designations Sulfuricellaceae fam. nov. and Sulfuricellales ord. nov.
Marinomonas mangrovi sp. nov., isolated from mangrove sediment
Authors: Zhang De-Chao , Margesin Rosa
Published: February 2015

A Gram-stain-negative, Na+-requiring bacterial strain, designated B20-1T, was isolated from soil of the root system of mangrove forest. Cells were curved rods and motile by means of a polar flagellum. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain B20-1T belonged to the genus

Marinomonas

, sharing highest sequence similarities with

Marinomonas rhizomae

IVIA-Po-145T (97.6 %),

Marinomonas dokdonensis

DSW10-10T (97.0 %) and

Marinomonas foliarum

IVIA-Po-155T (96.9 %). The predominant cellular fatty acids of strain B20-1T were C10 : 0 3-OH, C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C16 : 0. Phosphatidylethanolamine and phosphatidylglycerol were identified as the predominant phospholipids. The predominant ubiquinone was Q-8. The genomic DNA G+C content of strain B20-1T was 46.6 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness, a novel species, Marinomonas mangrovi sp. nov., is proposed with B20-1T ( = DSM 28136T = LMG 28077T) as the type strain.
Rufibacter roseus sp. nov., isolated from radiation-polluted soil
Authors: Zhang Zhi-Dong , Gu Mei-Ying , Zhu Jing , Li Shan-Hui , Zhang Li-Juan , Xie Yu-Qing , Shi Yu-Hu , Wang Wei , Li Wen-Jun
Published: February 2015

A rose, Gram-stain-negative, aerobic, rod-shaped bacterium that was motile by gliding, and designated strain H359T, was isolated from radiation-polluted soil (with high Cs137) from the Xinjiang Uygur Autonomous Region of PR China and subjected to a polyphasic taxonomic analysis. The isolate grew optimally at 30 °C and pH 7.0. It grew with NaCl up to 4 % (w/v). 16S rRNA gene sequence analysis indicated that strain H359T belonged to the genus

Rufibacter

, a member of the family

Cytophagaceae

, with

Rufibacter tibetensis

CCTCC AB 208084T as its closest phylogenetic relative, having 96.1 % 16S rRNA gene sequence similarity to the type strain. Strain H359T contained menaquinone-7 (MK-7) as the predominant menaquinone, and the major fatty acids were iso-C15 : 0, summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 1ω5c. The polar lipid profile had phosphatidylethanolamine as the major component. The DNA G+C content was 43.9 mol%. Based on phenotypic, genotypic and phylogenetic evidence, strain H359T represents a novel species of the genus

Rufibacter

, for which the name Rufibacter roseus sp. nov. is proposed. The type strain is H359T ( = CPCC 100615T = KCTC 42217T).
Glycomyces tarimensis sp. nov., an actinomycete isolated from a saline-alkali habitat
Authors: Lv Ling-Ling , Zhang Yue-Feng , Zhang Li-Li
Published: February 2015

A novel actinomycete strain, designated TRM 45387T, was isolated from a saline-alkali soil in Xinjiang Province (40° 22′ N 79° 08′ E), north-west China. The isolate was characterized using a polyphasic approach. 16S rRNA gene sequence analysis indicated that strain TRM 45387T belonged to the genus

Glycomyces

and was closely related to

Glycomyces arizonensis

DSM 44726T (96.59 % 16S rRNA gene sequence similarity). The G+C content of the DNA was 71.26 mol%. The isolate contained meso-diaminopimelic acid as the diagnostic diamino acid, and xylose, glucose, galactose, arabinose and ribose as the major whole-cell sugars. The diagnostic phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositolmannosides. The predominant menaquinone was MK-10(H6). The major fatty acids were iso-C16 : 0, anteiso-C17 : 0 and anteiso-C15 : 0. On the basis of the evidence from this polyphasic study, a novel species, Glycomyces tarimensis sp. nov., is proposed. The type strain of Glycomyces tarimensis is TRM 45387T ( = CCTCC AA 2014007T = JCM 30184T).
Prauserella isguenensis sp. nov., a halophilic actinomycete isolated from desert soil
Authors: Saker Rafika , Bouras Noureddine , Meklat Atika , Zitouni Abdelghani , Schumann Peter , Spröer Cathrin , Sabaou Nasserdine , Klenk Hans-Peter
Published: February 2015

Two actinomycete strains, designated H225T and H137, were isolated from two soil samples collected from the arid region of Ahbas at Béni-Isguen (Mzab), located in the Algerian Sahara. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the novel strains should be assigned to the genus

Prauserella

of the family

Pseudonocardiaceae

, and they were therefore subjected to a polyphasic taxonomic study. These two strains contained meso-diaminopimelic acid as the diagnostic diamino acid and arabinose and galactose as major whole-cell sugars. The diagnostic phospholipid was phosphatidylethanolamine. The predominant menaquinone was MK-9(H4), and the major fatty acid was iso-C16 : 0. DNA–DNA hybridization values between strain H225T and its closest phylogenetic neighbours, namely

Prauserella flava

DSM 45265T,

Prauserella alba

DSM 44590T,

Prauserella aidingensis

DSM 45266T,

Prauserella salsuginis

DSM 45264T and

Prauserella sediminis

DSM 45267T, were clearly below the 70 % threshold used for species delineation. The genomic DNA G+C content of strains H225T and H137 was 70.4 mol%. On the basis of phenotypic and genotypic data, strains H225T and H137T are considered to represent a novel species of the genus

Prauserella

, for which the name Prauserella isguenensis sp. nov. is proposed. The type strain is H225T ( = DSM 46664T = CECT 8577T).
Belliella aquatica sp. nov., isolated from a saline lake
Authors: Zhong Zhi-Ping , Liu Ying , Hou Ting-Ting , Zhou Yu-Guang , Liu Hong-Can , Liu Zhi-Pei
Published: February 2015

A Gram-staining-negative bacterium, strain TS-T86T, was isolated from Lake Tuosu, a saline lake (salinity 5.4 %, w/w) in Qaidam basin, China. Its taxonomic position was determined by using a polyphasic approach. Strain TS-T86T was strictly heterotrophic, aerobic and catalase- and oxidase-positive. Cells were non-spore-forming, non-motile rods, 0.4–0.6 µm wide and 1.2–2.3 µm long. Growth was observed in the presence of 0–9.0 % (w/v) NaCl (optimum, 2.0 %), at 4–35 °C (optimum, 25 °C) and at pH 7.0–10.5 (optimum, pH 8.5–9.0). Strain TS-T86T contained MK-7 as the predominant respiratory quinone. The major fatty acids (>10 %) were iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 1ω9c, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The polar lipids consisted of phosphatidylethanolamine, an unknown phospholipid, six unidentified aminolipids and two uncharacterized lipids. The DNA G+C content was 35 mol% (T
m). Phylogenetic trees based on 16S rRNA gene sequences showed that strain TS-T86T was associated with the genus

Belliella

, and showed the highest sequence similarity to

Belliella baltica

BA134T (98.5 %) and then to

Belliella kenyensis

No.164T (95.7 %) and

Belliella pelovolcani

CC-SAL-25T (95.3 %). DNA–DNA relatedness of strain TS-T86T to

Belliella baltica

DSM 15883T was 32±3 %. It is concluded that strain TS-T86T represents a novel species of the genus

Belliella

, for which the name Belliella aquatica sp. nov. is proposed. The type strain is TS-T86T ( = CGMCC 1.12479T = JCM 19468T).
Exiguobacterium enclense sp. nov., isolated from sediment
Authors: Dastager Syed G. , Mawlankar Rahul , Sonalkar Vidya V. , Thorat Meghana N. , Mual Poonam , Verma Ashish , Krishnamurthi Srinivasan , Tang Shan-Kun , Li Wen-Jun
Published: February 2015

A Gram-stain-positive bacterium, designated strain NIO-1109T, was isolated from a marine sediment sample from Chorao Island, Goa, India. Phenotypic and chemotaxonomic characteristics and data from phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NIO-1109T was related to the genus

Exiguobacterium

. Strain NIO-1109T exhibited >98.0 % 16S rRNA gene sequence similarity with respect to

Exiguobacterium indicum

HHS 31T (99.5 %) and

Exiguobacterium acetylicum

NCIMB 9889T (99.1 %); the type strains of other species showed <98 % similarity. Levels of DNA–DNA relatedness between strain NIO-1109T and

E. acetylicum

DSM 20416T and

E. indicum

LMG 23471T were less than 70 % (33.0±2.0 and 37±3.2 %, respectively). Strain NIO-1109T also differed from these two closely related species in a number of phenotypic traits. Based on phenotypic, chemotaxonomic and phylogenetic data, strain NIO-1109T is considered to represent a novel species of the genus

Exiguobacterium

, for which the name Exiguobacterium enclense sp. nov. is proposed. The type strain is NIO-1109T ( = NCIM 5457T = DSM 25128T = CCTCC AB 2011124T).
Identification of RNA helicases in human immunodeficiency virus 1 (HIV-1) replication – a targeted small interfering RNA library screen using pseudotyped and WT HIV-1
Authors: Williams Claire A. , Abbink Truus E. M. , Jeang Kuan-Teh , Lever Andrew M. L.
Published: February 2015

Central to the development of new treatments for human immunodeficiency virus 1 (HIV-1) is a more thorough understanding of the viral life cycle and the cellular cofactors upon which this depends. Targeting cellular proteins and their interaction with HIV-1 has the potential to reduce the problem of emerging viral resistance to drugs as mutational escape is more difficult. We performed a short interfering RNA (siRNA) library screen targeting 59 cellular RNA helicases, assessing the effect on both viral capsid protein production and infectious virion formation. Five RNA helicases were identified which, when knocked down, reproducibly decreased infectious particle production: DDX5, DDX10, DDX17, DDX28 and DDX52. Two of these proteins (DDX5 and DDX17) have known roles in HIV-1 replication. A further helicase (DDX10) was a positive hit from a previous genome-wide siRNA screen; however, DDX28 and DDX52 have not previously been implicated as essential cofactors for HIV-1.
Exome Sequencing and Prediction of Long-Term Kidney Allograft Function
Authors: Mesnard L. , Muthukumar T. , Burbach M. , Li C. , Shang H. , Dadhania D. , Lee J. R , Sharma V. K. , Xiang J. , Suberbielle C. , Carmagnat M. , Ouali N. , Rondeau E. , Friedewald J. J. , Abecassis M. M. , Suthanthiran M. , Campagne F.
Published: February 2015

Current strategies to improve graft outcome following kidney transplantation consider information at the HLA loci. Here, we used exome sequencing of DNA from ABO compatible kidney graft recipients and their living donors to determine recipient and donor mismatches at the amino acid level over entire exomes. We estimated the number of amino acid mismatches in transmembrane proteins, more likely to be seen as foreign by the recipient’s immune system, and designated this tally as the allogenomics mismatch score (AMS). The AMS can be measured prior to transplantation with DNA for potential donor and recipient pairs. We examined the degree of relationship between the AMS and post-transplantation kidney allograft function by linear regression. In a discovery cohort, we found a significant inverse correlation between the AMS and kidney graft function at 36 months post-transplantation (n=10 recipient/donor pairs; 20 exomes) (r2>=0.57, P<0.05). The predictive ability of the AMS persists when the score is restricted to regions outside of the HLA loci. This relationship was validated using an independent cohort of 24 recipient donor pairs (n=48 exomes) (r2>=0.39, P<0.005). In an additional cohort of living and mostly intra-familial recipient/donor pairs (n=19, 38 exomes), we validated the association after controlling for donor age at time of transplantation. Finally, a model that controls for donor age, HLA mismatches and time post-transplantation yields a consistent AMS effect across these three independent cohorts (P<0.05). Taken together, these results show that the AMS is a strong predictor of long-term graft function in kidney transplant recipients.

One Sentence Summary

Prediction of long-term kidney graft function with exome sequencing
Protein Domain Hotspots Reveal Functional Mutations across Genes in Cancer
Authors: Miller Martin L. , Reznik Ed , Gauthier Nicholas P. , Aksoy Bülent Arman , Korkut Anil , Gao Jianjion , Ciriello Giovanni , Schultz Nikolaus , Sander Chris
Published: February 2015

In cancer genomics, frequent recurrence of mutations in independent tumor samples is a strong indication of functional impact. However, rare functional mutations can escape detection by recurrence analysis for lack of statistical power. We address this problem by extending the notion of recurrence of mutations from single genes to gene families that share homologous protein domains. In addition to lowering the threshold of detection, this sharpens the functional interpretation of the impact of mutations, as protein domains more succinctly embody function than entire genes. Mapping mutations in 22 different tumor types to equivalent positions in multiple sequence alignments of protein domains, we confirm well-known functional mutation hotspots and make two types of discoveries: 1) identification and functional interpretation of uncharacterized rare variants in one gene that are equivalent to well-characterized mutations in canonical cancer genes, such as uncharacterizedERBB4(S303F) mutations that are analogous to canonicalERRB2(S310F) mutations in the furin-like domain, and 2) detection of previously unknown mutation hotspots with novel functional implications. With the rapid expansion of cancer genomics projects, protein domain hotspot analysis is likely to provide many more leads linking mutations in proteins to the cancer phenotype.