bluuebunny/crossref_metadata_2025 huggingface dataset:
Frost halos from supercooled water droplets
Authors: Jung Stefan , Tiwari Manish K. , Poulikakos Dimos
Published: September 2012

Water freezing on solid surfaces is ubiquitous in nature. Even though icing/frosting impairs the performance and safety in many processes, its mechanism remains inadequately understood. Changing atmospheric conditions, surface properties, the complexity of icing physics, and the unorthodox behavior of water are the primary factors that make icing and frost formation intriguing and difficult to predict. In addition to its unquestioned scientific and practical importance, unraveling the frosting mechanism under different conditions is a prerequisite to develop “icephobic” surfaces, which may avoid ice formation and contamination. In this work we demonstrate that evaporation from a freezing supercooled sessile droplet, which starts explosively due to the sudden latent heat released upon recalescent freezing, generates a condensation halo around the droplet, which crystallizes and drastically affects the surface behavior. The process involves simultaneous multiple phase transitions and may also spread icing by initiating sequential freezing of neighboring droplets in the form of a domino effect and frost propagation. Experiments under controlled humidity conditions using substrates differing up to three orders of magnitude in thermal conductivity establish that a delicate balance between heat diffusion and vapor transport determines the final expanse of the frozen condensate halo, which, in turn, controls frost formation and propagation.
Suomi satellite brings to light a unique frontier of nighttime environmental sensing capabilities
Authors: Miller Steven D. , Mills Stephen P. , Elvidge Christopher D. , Lindsey Daniel T. , Lee Thomas F. , Hawkins Jeffrey D.
Published: September 2012

Most environmental satellite radiometers use solar reflectance information when it is available during the day but must resort at night to emission signals from infrared bands, which offer poor sensitivity to low-level clouds and surface features. A few sensors can take advantage of moonlight, but the inconsistent availability of the lunar source limits measurement utility. Here we show that the Day/Night Band (DNB) low-light visible sensor on the recently launched Suomi National Polar-orbiting Partnership (NPP) satellite has the unique ability to image cloud and surface features by way of reflected airglow, starlight, and zodiacal light illumination. Examples collected during new moon reveal not only meteorological and surface features, but also the direct emission of airglow structures in the mesosphere, including expansive regions of diffuse glow and wave patterns forced by tropospheric convection. The ability to leverage diffuse illumination sources for nocturnal environmental sensing applications extends the advantages of visible-light information to moonless nights.
Experimental results from a preclinical X-ray phase-contrast CT scanner
Authors: Tapfer Arne , Bech Martin , Velroyen Astrid , Meiser Jan , Mohr Jürgen , Walter Marco , Schulz Joachim , Pauwels Bart , Bruyndonckx Peter , Liu Xuan , Sasov Alexander , Pfeiffer Franz
Published: September 2012

To explore the future clinical potential of improved soft-tissue visibility with grating-based X-ray phase contrast (PC), we have developed a first preclinical computed tomography (CT) scanner featuring a rotating gantry. The main challenge in the transition from previous bench-top systems to a preclinical scanner are phase artifacts that are caused by minimal changes in the grating alignment during gantry rotation. In this paper, we present the first experimental results from the system together with an adaptive phase recovery method that corrects for these phase artifacts. Using this method, we show that the scanner can recover quantitatively accurate Hounsfield units in attenuation and phase. Moreover, we present a first tomography scan of biological tissue with complementary information in attenuation and phase contrast. The present study hence demonstrates the feasibility of grating-based phase contrast with a rotating gantry for the first time and paves the way for future in vivo studies on small animal disease models (in the mid-term future) and human diagnostics applications (in the long-term future).
cAMP response element-binding protein promotes gliomagenesis by modulating the expression of oncogenic microRNA-23a
Authors: Tan Xiaochao , Wang Shan , Zhu Liyuan , Wu Chao , Yin Bin , Zhao Jizong , Yuan Jiangang , Qiang Boqin , Peng Xiaozhong
Published: September 2012

Gliomas are the most common and deadly type of primary brain tumor. In this study, we showed that cAMP response element-binding protein (CREB), a proto-oncogenic transcription factor that is overexpressed in gliomas, can promote gliomagenesis by modulating the expression of oncogenic microRNA-23a (mir-23a). First, we found that CREB is highly expressed in glioma tissues and cell lines. CREB is also essential for glioma cell growth and cell survival in vitro and is critical for gliomagenesis in vivo. Second, microRNA microarray, ChIP-chip, ChIP-quantitative PCR, and luciferase reporter assays showed that CREB directly binds to the regulatory sequences of mir-23a and enhance the expression of mir-23a. Moreover, mir-23a was confirmed as a functional downstream target of CREB in glioma cell growth and cell survival. Finally, using computational prediction followed by experimental confirmation, we identified PTEN, which is frequently silenced in gliomas, as a downstream target of mir-23a. Taken together, we propose that CREB promotes gliomagenesis and acts as a modulator of oncogenic mir-23a, which represses the tumor suppressor PTEN.
Endochin-like quinolones are highly efficacious against acute and latent experimental toxoplasmosis
Authors: Doggett J. Stone , Nilsen Aaron , Forquer Isaac , Wegmann Keith W. , Jones-Brando Lorraine , Yolken Robert H. , Bordón Claudia , Charman Susan A. , Katneni Kasiram , Schultz Tracey , Burrows Jeremy N. , Hinrichs David J. , Meunier Brigitte , Carruthers Vern B. , Riscoe Michael K.
Published: September 2012

Toxoplasma gondii
is a widely distributed protozoan pathogen that causes devastating ocular and central nervous system disease. We show that the endochin-like quinolone (ELQ) class of compounds contains extremely potent inhibitors of
T. gondii
growth in vitro and is effective against acute and latent toxoplasmosis in mice. We screened 50 ELQs against
T. gondii
and selected two lead compounds, ELQ-271 and ELQ-316, for evaluation. ELQ-271 and ELQ-316, have in vitro IC
50
values of 0.1 nM and 0.007 nM, respectively. ELQ-271 and ELQ-316 have ED
50
values of 0.14 mg/kg and 0.08 mg/kg when administered orally to mice with acute toxoplasmosis. Moreover, ELQ-271 and ELQ-316 are highly active against the cyst form of
T. gondii
in mice at low doses, reducing cyst burden by 76–88% after 16 d of treatment. To investigate the ELQ mechanism of action against
T. gondii
, we demonstrate that endochin and ELQ-271 inhibit cytochrome
c
reduction by the
T. gondii
cytochrome
bc
1
complex at 8 nM and 31 nM, respectively. We also show that ELQ-271 inhibits the
Saccharomyces cerevisiae
cytochrome
bc
1
complex, and an M221Q amino acid substitution in the Q
i
site of the protein leads to >100-fold resistance. We conclude that ELQ-271 and ELQ-316 are orally bioavailable drugs that are effective against acute and latent toxoplasmosis, likely acting as inhibitors of the Q
i
site of the
T. gondii
cytochrome
bc
1
complex.
Pointillist structural color in
Pollia
fruit
Authors: Vignolini Silvia , Rudall Paula J. , Rowland Alice V. , Reed Alison , Moyroud Edwige , Faden Robert B. , Baumberg Jeremy J. , Glover Beverley J. , Steiner Ullrich
Published: September 2012

Biological communication by means of structural color has existed for at least 500 million years. Structural color is commonly observed in the animal kingdom, but has been little studied in plants. We present a striking example of multilayer-based strong iridescent coloration in plants, in the fruit of
Pollia condensata
. The color is caused by Bragg reflection of helicoidally stacked cellulose microfibrils that form multilayers in the cell walls of the epicarp. We demonstrate that animals and plants have convergently evolved multilayer-based photonic structures to generate colors using entirely distinct materials. The bright blue coloration of this fruit is more intense than that of any previously described biological material. Uniquely in nature, the reflected color differs from cell to cell, as the layer thicknesses in the multilayer stack vary, giving the fruit a striking pixelated or pointillist appearance. Because the multilayers form with both helicoidicities, optical characterization reveals that the reflected light from every epidermal cell is polarized circularly either to the left or to the right, a feature that has never previously been observed in a single tissue.
Activation of
Escherichia coli
antiterminator BglG requires its phosphorylation
Authors: Rothe Fabian M. , Bahr Thomas , Stülke Jörg , Rak Bodo , Görke Boris
Published: September 2012

Transcriptional antiterminator proteins of the BglG family control the expression of enzyme II (EII) carbohydrate transporters of the bacterial phosphotransferase system (PTS). In the PTS, phosphoryl groups are transferred from phosphoenolpyruvate (PEP) via the phosphotransferases enzyme I (EI) and HPr to the EIIs, which phosphorylate their substrates during transport. Activity of the antiterminators is negatively controlled by reversible phosphorylation catalyzed by the cognate EIIs in response to substrate availability and positively controlled by the PTS. For the
Escherichia coli
BglG antiterminator, two different mechanisms for activation by the PTS were proposed. According to the first model, BglG is activated by HPr-catalyzed phosphorylation at a site distinct from the EII-dependent phosphorylation site. According to the second model, BglG is not activated by phosphorylation, but solely through interaction with EI and HPr, which are localized at the cell pole. Subsequently BglG is released from the cell pole to the cytoplasm as an active dimer. Here we addressed this discrepancy and found that activation of BglG requires phosphorylatable HPr or the HPr homolog FruB in vivo. Further, we uniquely demonstrate that purified BglG protein becomes phosphorylated by FruB as well as by HPr in vitro. Histidine residue 208 in BglG is essential for this phosphorylation. These data suggest that BglG is in fact activated by phosphorylation and that there is no principal difference between the PTS-exerted mechanisms controlling the activities of BglG family proteins in Gram-positive and Gram-negative bacteria.
Dual modes of motility at the leading edge of migrating epithelial cell sheets
Authors: Klarlund Jes K.
Published: September 2012

Purse-string healing is driven by contraction of actin/myosin cables that span cells at wound edges, and it is the predominant mode of closing small round wounds in embryonic and some adult epithelia. Wounds can also heal by cell crawling, and my colleagues and I have shown previously that the presence of unconstrained, straight edges in sheets of epithelial cells is a sufficient signal to induce healing by crawling. Here, it is reported that the presence of highly concave edges, which are free or physically constrained by an inert material (agarose), is sufficient to induce formation of purse strings. It was determined that neither of the two types of healing required cell damage or other potential stimuli by using the particularly gentle procedure of introducing gaps by digesting agarose blocks imbedded in the cell sheets. Movement by crawling depends on signaling by the EGF receptor (EGFR); however, this was not required for purse-string contraction. A migrating epithelial cell sheet usually produces finger-like projections of crawling cells. The cells between fingers contain continuous actin cables, which were also determined to contain myosin IIA and exhibit additional characteristics of purse strings. When crawling was blocked by inhibition of EGFR signaling, the concave regions continued to move, suggesting that both mechanisms contribute to propel the sheets forward. Wounding epithelial cell sheets causes activation of the EGFR, which triggers movement by crawling. The EGFR was found to be activated only at straight and convex edges, which explains how both types of movement can coexist at leading epithelial edges.
Vacancy-stabilized crystalline order in hard cubes
Authors: Smallenburg Frank , Filion Laura , Marechal Matthieu , Dijkstra Marjolein
Published: September 2012

We examine the effect of vacancies on the phase behavior and structure of systems consisting of hard cubes using event-driven molecular dynamics and Monte Carlo simulations. We find a first-order phase transition between a fluid and a simple cubic crystal phase that is stabilized by a surprisingly large number of vacancies, reaching a net vacancy concentration of approximately 6.4% near bulk coexistence. Remarkably, we find that vacancies increase the positional order in the system. Finally, we show that the vacancies are delocalized and therefore hard to detect.
Testis tissue explantation cures spermatogenic failure in c-Kit ligand mutant mice
Authors: Sato Takuya , Yokonishi Tetsuhiro , Komeya Mitsuru , Katagiri Kumiko , Kubota Yoshinobu , Matoba Shogo , Ogonuki Narumi , Ogura Atsuo , Yoshida Shosei , Ogawa Takehiko
Published: September 2012

Male infertility is most commonly caused by spermatogenic defects or insufficiencies, the majority of which are as yet cureless. Recently, we succeeded in cultivating mouse testicular tissues for producing fertile sperm from spermatogonial stem cells. Here, we show that one of the most severe types of spermatogenic defect mutant can be treated by the culture method without any genetic manipulations. The
Sl/Sl

d

mouse is used as a model of such male infertility. The testis of the
Sl/Sl

d

mouse has only primitive spermatogonia as germ cells, lacking any sign of spermatogenesis owing to mutations of the c-kit ligand (KITL) gene that cause the loss of membrane-bound-type KITL from the surface of Sertoli cells. To compensate for the deficit, we cultured testis tissues of
Sl/Sl

d

mice with a medium containing recombinant KITL and found that it induced the differentiation of spermatogonia up to the end of meiosis. We further discovered that colony stimulating factor-1 (CSF-1) enhances the effect of KITL and promotes spermatogenesis up to the production of sperm. Microinsemination of haploid cells resulted in delivery of healthy offspring. This study demonstrated that spermatogenic impairments can be treated in vitro with the supplementation of certain factors or substances that are insufficient in the original testes.
Allometric scaling of population variance with mean body size is predicted from Taylor’s law and density-mass allometry
Authors: Cohen Joel E. , Xu Meng , Schuster William S. F.
Published: September 2012

Two widely tested empirical patterns in ecology are combined here to predict how the variation of population density relates to the average body size of organisms. Taylor’s law (TL) asserts that the variance of the population density of a set of populations is a power-law function of the mean population density. Density–mass allometry (DMA) asserts that the mean population density of a set of populations is a power-law function of the mean individual body mass. Combined, DMA and TL predict that the variance of the population density is a power-law function of mean individual body mass. We call this relationship “variance–mass allometry” (VMA). We confirmed the theoretically predicted power-law form and the theoretically predicted parameters of VMA, using detailed data on individual oak trees (
Quercus
spp.) of Black Rock Forest, Cornwall, New York. These results connect the variability of population density to the mean body mass of individuals.
Genetic composition of yield heterosis in an elite rice hybrid
Authors: Zhou Gang , Chen Ying , Yao Wen , Zhang Chengjun , Xie Weibo , Hua Jinping , Xing Yongzhong , Xiao Jinghua , Zhang Qifa
Published: September 2012

Heterosis refers to the superior performance of hybrids relative to the parents. Utilization of heterosis has contributed tremendously to the increased productivity in many crops for decades. Although there have been a range of studies on various aspects of heterosis, the key to understanding the biological mechanisms of heterotic performance in crop hybrids is the genetic basis, much of which is still uncharacterized. In this study, we dissected the genetic composition of yield and yield component traits using data of replicated field trials of an “immortalized F2” population derived from an elite rice hybrid. On the basis of an ultrahigh-density SNP bin map constructed with population sequencing, we calculated single-locus and epistatic genetic effects in the whole genome and identified components pertaining to heterosis of the hybrid. The results showed that the relative contributions of the genetic components varied with traits. Overdominance/pseudo-overdominance is the most important contributor to heterosis of yield, number of grains per panicle, and grain weight. Dominance × dominance interaction is important for heterosis of tillers per plant and grain weight and has roles in yield and grain number. Single-locus dominance has relatively small contributions in all of the traits. The results suggest that cumulative effects of these components may adequately explain the genetic basis of heterosis in the hybrid.
Mood and the DRM paradigm: An investigation of the effects of valence and arousal on false memory
Authors: Van Damme Ilse
Published: September 2012

Recent studies regarding the effect of mood on the DRM (Deese–Roediger–McDermott) illusion have not been able to clearly establish yet whether valence or arousal is most critical in determining susceptibility to false memories, nor what the underlying processes are. In three experiments, both the valence and the level of arousal of participants' mood were manipulated. Six conditions were used: positive mood with high/low arousal, negative mood with high/low arousal, neutral mood, and a control condition. Memory was tested by means of immediate and delayed recognition and immediate free recall. The mood induction procedure was effective. For recognition memory, there was an effect of arousal on the endorsement of critical lures. Low-arousal moods elicited more false recognition than high-arousal moods, regardless of valence. Based on signal detection analyses, the effect was attributed to more liberal response criteria with low arousal, in combination with a tendency towards improved item-specific memory with high arousal.
Dynein light chain 1 and a spindle-associated adaptor promote dynein asymmetry and spindle orientation
Authors: Dunsch Anja K. , Hammond Dean , Lloyd Jennifer , Schermelleh Lothar , Gruneberg Ulrike , Barr Francis A.
Published: September 2012

The cytoplasmic dynein motor generates pulling forces to center and orient the mitotic spindle within the cell. During this positioning process, dynein oscillates from one pole of the cell cortex to the other but only accumulates at the pole farthest from the spindle. Here, we show that dynein light chain 1 (DYNLL1) is required for this asymmetric cortical localization of dynein and has a specific function defining spindle orientation. DYNLL1 interacted with a spindle-microtubule–associated adaptor formed by CHICA and HMMR via TQT motifs in CHICA. In cells depleted of CHICA or HMMR, the mitotic spindle failed to orient correctly in relation to the growth surface. Furthermore, CHICA TQT motif mutants localized to the mitotic spindle but failed to recruit DYNLL1 to spindle microtubules and did not correct the spindle orientation or dynein localization defects. These findings support a model where DYNLL1 and CHICA-HMMR form part of the regulatory system feeding back spindle position to dynein at the cell cortex.
Neuropilin 1 is expressed on thymus-derived natural regulatory T cells, but not mucosa-generated induced Foxp3+ T reg cells
Authors: Weiss Jonathan M. , Bilate Angelina M. , Gobert Michael , Ding Yi , Curotto de Lafaille Maria A. , Parkhurst Christopher N. , Xiong Huizhong , Dolpady Jayashree , Frey Alan B. , Ruocco Maria Grazia , Yang Yi , Floess Stefan , Huehn Jochen , Oh Soyoung , Li Ming O. , Niec Rachel E. , Rudensky Alexander Y. , Dustin Michael L. , Littman Dan R. , Lafaille Juan J.
Published: September 2012

Foxp3 activity is essential for the normal function of the immune system. Two types of regulatory T (T reg) cells express Foxp3, thymus-generated natural T reg (nT reg) cells, and peripherally generated adaptive T reg (iT reg) cells. These cell types have complementary functions. Until now, it has not been possible to distinguish iT reg from nT reg cells in vivo based solely on surface markers. We report here that Neuropilin 1 (Nrp1) is expressed at high levels by most nT reg cells; in contrast, mucosa-generated iT reg and other noninflammatory iT reg cells express low levels of Nrp1. We found that Nrp1 expression is under the control of TGF-β. By tracing nT reg and iT reg cells, we could establish that some tumors have a very large proportion of infiltrating iT reg cells. iT reg cells obtained from highly inflammatory environments, such as the spinal cords of mice with spontaneous autoimmune encephalomyelitis (EAE) and the lungs of mice with chronic asthma, express Nrp1. In the same animals, iT reg cells in secondary lymphoid organs remain Nrp1low. We also determined that, in spontaneous EAE, iT reg cells help to establish a chronic phase of the disease.
Nonintegral stoichiometry in CFTR gating revealed by a pore-lining mutation
Authors: Jih Kang-Yang , Sohma Yoshiro , Hwang Tzyh-Chang
Published: September 2012

Cystic fibrosis transmembrane conductance regulator (CFTR) is a unique member of the ATP-binding cassette (ABC) protein superfamily. Unlike most other ABC proteins that function as active transporters, CFTR is an ATP-gated chloride channel. The opening of CFTR’s gate is associated with ATP-induced dimerization of its two nucleotide-binding domains (NBD1 and NBD2), whereas gate closure is facilitated by ATP hydrolysis-triggered partial separation of the NBDs. This generally held theme of CFTR gating—a strict coupling between the ATP hydrolysis cycle and the gating cycle—is put to the test by our recent finding of a short-lived, post-hydrolytic state that can bind ATP and reenter the ATP-induced original open state. We accidentally found a mutant CFTR channel that exhibits two distinct open conductance states, the smaller O1 state and the larger O2 state. In the presence of ATP, the transition between the two states follows a preferred O1→O2 order, a telltale sign of a violation of microscopic reversibility, hence demanding an external energy input likely from ATP hydrolysis, as such preferred gating transition was abolished in a hydrolysis-deficient mutant. Interestingly, we also observed a considerable amount of opening events that contain more than one O1→O2 transition, indicating that more than one ATP molecule may be hydrolyzed within an opening burst. We thus conclude a nonintegral stoichiometry between the gating cycle and ATP consumption. Our results lead to a six-state gating model conforming to the classical allosteric mechanism: both NBDs and transmembrane domains hold a certain degree of autonomy, whereas the conformational change in one domain will facilitate the conformational change in the other domain.
Pythoscape: a framework for generation of large protein similarity networks
Authors: Barber Alan E. , Babbitt Patricia C.
Published: September 2012

Pythoscape is a framework implemented in Python for processing large protein similarity networks for visualization in other software packages. Protein similarity networks are graphical representations of sequence, structural and other similarities among proteins for which pairwise all-by-all similarity connections have been calculated. Mapping of biological and other information to network nodes or edges enables hypothesis creation about sequence–structure–function relationships across sets of related proteins. Pythoscape provides several options to calculate pairwise similarities for input sequences or structures, applies filters to network edges and defines sets of similar nodes and their associated data as single nodes (termed representative nodes) for compression of network information and output data or formatted files for visualization.

Contact:  babbitt@cgl.ucsf.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
ImgLib2—generic image processing in Java
Authors: Pietzsch Tobias , Preibisch Stephan , Tomančák Pavel , Saalfeld Stephan
Published: September 2012

Summary: ImgLib2 is an open-source Java library for n-dimensional data representation and manipulation with focus on image processing. It aims at minimizing code duplication by cleanly separating pixel-algebra, data access and data representation in memory. Algorithms can be implemented for classes of pixel types and generic access patterns by which they become independent of the specific dimensionality, pixel type and data representation. ImgLib2 illustrates that an elegant high-level programming interface can be achieved without sacrificing performance. It provides efficient implementations of common data types, storage layouts and algorithms. It is the data model underlying ImageJ2, the KNIME Image Processing toolbox and an increasing number of Fiji-Plugins.

Availability: ImgLib2 is licensed under BSD. Documentation and source code are available at http://imglib2.net and in a public repository at https://github.com/imagej/imglib.

Supplementary Information:  Supplementary data are available at Bioinformatics Online.

Contact: saalfeld@mpi-cbg.de
GREVE: Genomic Recurrent Event ViEwer to assist the identification of patterns across individual cancer samples
Authors: Cazier Jean-Baptiste , Holmes Chris C. , Broxholme John
Published: September 2012

Summary: GREVE has been developed to assist with the identification of recurrent genomic aberrations across cancer samples. The exact characterization of such aberrations remains a challenge despite the availability of increasing amount of data, from SNParray to next-generation sequencing. Furthermore, genomic aberrations in cancer are especially difficult to handle because they are, by nature, unique to the patients. However, their recurrence in specific regions of the genome has been shown to reflect their relevance in the development of tumors. GREVE makes use of previously characterized events to identify such regions and focus any further analysis.

Availability: GREVE is available through a web interface and open-source application (http://www.well.ox.ac.uk/GREVE).
FetalQuant: deducing fractional fetal DNA concentration from massively parallel sequencing of DNA in maternal plasma
Authors: Jiang Peiyong , Chan K. C. Allen , Liao Gary J. W. , Zheng Yama W. L. , Leung Tak Y. , Chiu Rossa W. K. , Lo Yuk Ming Dennis , Sun Hao
Published: September 2012

Motivation: The fractional fetal DNA concentration is one of the critical parameters for non-invasive prenatal diagnosis based on the analysis of DNA in maternal plasma. Massively parallel sequencing (MPS) of DNA in maternal plasma has been demonstrated to be a powerful tool for the non-invasive prenatal diagnosis of fetal chromosomal aneuploidies. With the rapid advance of MPS technologies, the sequencing cost per base is dramatically reducing, especially when using targeted MPS. Even though several approaches have been developed for deducing the fractional fetal DNA concentration, none of them can be used to deduce the fractional fetal DNA concentration directly from the sequencing data without prior genotype information.

Result: In this study, we implement a statistical mixture model, named FetalQuant, which utilizes the maximum likelihood to estimate the fractional fetal DNA concentration directly from targeted MPS of DNA in maternal plasma. This method allows the improved deduction of the fractional fetal DNA concentration, obviating the need of genotype information without loss of accuracy. Furthermore, by using Bayes’ rule, this method can distinguish the informative single-nucleotide polymorphism loci where the mother is homozygous and the fetus is heterozygous. We believe that FetalQuant can help expand the spectrum of diagnostic applications using MPS on DNA in maternal plasma.

Availability: Software and simulation data are available at http://sourceforge.net/projects/fetalquant/

Contact:  haosun@cuhk.edu.hk

Supplementary Information:  Supplementary data are available at Bioinformatics online.
RAPHAEL: recognition, periodicity and insertion assignment of solenoid protein structures
Authors: Walsh Ian , Sirocco Francesco G. , Minervini Giovanni , Di Domenico Tomás , Ferrari Carlo , Tosatto Silvio C. E.
Published: September 2012

Motivation: Repeat proteins form a distinct class of structures where folding is greatly simplified. Several classes have been defined, with solenoid repeats of periodicity between ca. 5 and 40 being the most challenging to detect. Such proteins evolve quickly and their periodicity may be rapidly hidden at sequence level. From a structural point of view, finding solenoids may be complicated by the presence of insertions or multiple domains. To the best of our knowledge, no automated methods are available to characterize solenoid repeats from structure.

Results: Here we introduce RAPHAEL, a novel method for the detection of solenoids in protein structures. It reliably solves three problems of increasing difficulty: (1) recognition of solenoid domains, (2) determination of their periodicity and (3) assignment of insertions. RAPHAEL uses a geometric approach mimicking manual classification, producing several numeric parameters that are optimized for maximum performance. The resulting method is very accurate, with 89.5% of solenoid proteins and 97.2% of non-solenoid proteins correctly classified. RAPHAEL periodicities have a Spearman correlation coefficient of 0.877 against the manually established ones. A baseline algorithm for insertion detection in identified solenoids has a Q2 value of 79.8%, suggesting room for further improvement. RAPHAEL finds 1931 highly confident repeat structures not previously annotated as solenoids in the Protein Data Bank records.

Availability: The RAPHAEL web server is available with additional data at http://protein.bio.unipd.it/raphael/

Contact:  silvio.tosatto@unipd.it

Supplementary information:  Supplementary data are available at Bioinformatics online
ChemBioServer: a web-based pipeline for filtering, clustering and visualization of chemical compounds used in drug discovery
Authors: Athanasiadis Emmanouil , Cournia Zoe , Spyrou George
Published: September 2012

Summary: ChemBioServer is a publicly available web application for effectively mining and filtering chemical compounds used in drug discovery. It provides researchers with the ability to (i) browse and visualize compounds along with their properties, (ii) filter chemical compounds for a variety of properties such as steric clashes and toxicity, (iii) apply perfect match substructure search, (iv) cluster compounds according to their physicochemical properties providing representative compounds for each cluster, (v) build custom compound mining pipelines and (vi) quantify through property graphs the top ranking compounds in drug discovery procedures. ChemBioServer allows for pre-processing of compounds prior to an in silico screen, as well as for post-processing of top-ranked molecules resulting from a docking exercise with the aim to increase the efficiency and the quality of compound selection that will pass to the experimental test phase.

Availability: The ChemBioServer web application is available at: http://bioserver-3.bioacademy.gr/Bioserver/ChemBioServer/.

Contact:  gspyrou@bioacademy.gr
Comparing clustering and pre-processing in taxonomy analysis
Authors: Bonder Marc J. , Abeln Sanne , Zaura Egija , Brandt Bernd W.
Published: September 2012

Motivation: Massively parallel sequencing allows for rapid sequencing of large numbers of sequences in just a single run. Thus, 16S ribosomal RNA (rRNA) amplicon sequencing of complex microbial communities has become possible. The sequenced 16S rRNA fragments (reads) are clustered into operational taxonomic units and taxonomic categories are assigned. Recent reports suggest that data pre-processing should be performed before clustering. We assessed combinations of data pre-processing steps and clustering algorithms on cluster accuracy for oral microbial sequence data.

Results: The number of clusters varied up to two orders of magnitude depending on pre-processing. Pre-processing using both denoising and chimera checking resulted in a number of clusters that was closest to the number of species in the mock dataset (25 versus 15). Based on run time, purity and normalized mutual information, we could not identify a single best clustering algorithm. The differences in clustering accuracy among the algorithms after the same pre-processing were minor compared with the differences in accuracy among different pre-processing steps.

Supplementary information:  Supplementary data are available at Bioinformatics online.

Contact:  bonder.m.j@gmail.com or b.brandt@acta.nl
The origins of formal education in sub-Saharan Africa: was British rule more benign?
Authors: Frankema Ewout H.P.
Published: September 2012

British colonial rule has often been praised for its comparatively benign features, such as its support of local educational development. This study argues that the impact of British educational policies and investments on the supply of schooling in British Africa should not be overstated. Until 1940, mission schools, mainly run by African converts, provided the bulk of education at extremely low costs. Given the limited financial capacity of missionary societies, the Africanization of the mission was a prerequisite for rising enrolment rates and this only occurred in areas where the demand for Western education was high. The British happened to control most of these “fertile” areas.
Utility of lung ultrasound in predicting pulmonary and cardiac pressures
Authors: Platz Elke , Lattanzi AnnMarie , Agbo Chioma , Takeuchi Madoka , Resnic Frederic S. , Solomon Scott D. , Desai Akshay S.
Published: September 2012

Aims

Quantification of linear lung ultrasound (LUS) artefacts (B‐lines) represents a novel, non‐invasive approach to assess pulmonary congestion. We investigated the relationship between the number of B‐lines (vertical artefacts arising from the pleural line) and intracardiac pressures.

Methods and results

Prior to scheduled right heart catheterization (RHC), 100 subjects underwent LUS of eight zones. A reviewer blinded to the haemodynamic data quantified the number of sonographic B‐lines. Of 92 subjects who completed RHC, 79 had adequate LUS data of all zones [median age 61 years, 26 women, median left ventricular ejection fraction (LVEF) 58%, 35 with history of heart failure; 22 postcardiac transplantation]. The number of B‐lines correlated with measured right atrial (r = 0.32), pulmonary artery diastolic (PADP) (r = 0.34), mean pulmonary artery (mPAP) (r = 0.43), pulmonary artery systolic (PASP) (r = 0.48) pressures, and pulmonary vascular resistance (PVR) (r = 0.51) (P < 0.005 for all), but not with pulmonary capillary wedge pressure. There was a graded association between tertiles of B‐line number and increasing PADP, mPAP, PASP, and PVR (P for trend ≤0.001 for all). Each additional B‐line was associated with an increase in PASP of 1 mmHg and an increase in PVR of 0.1 Wood units. These associations remained robust after multivariable adjustment (P = 0.002). Assessment of two inferior lateral zones resulted in similar correlations to the eight‐zone method.

Conclusions

Easily obtainable, LUS may be useful in the estimation of right‐sided cardiac pressures and PVR. Further evaluation of lung ultrasound as an adjunct to heart failure diagnosis, monitoring, and prognosis is warranted.
The p35 human invariant chain in transgenic mice restores mature B cells in the absence of endogenous CD74
Authors: Genève Laetitia , Ménard Catherine , Labrecque Nathalie , Thibodeau Jacques
Published: September 2012

The invariant chain (Ii; CD74) has pleiotropic functions and Ii-deficient mice show defects in MHC class II (MHC II) transport and B cell maturation. In humans, but not in mice, a minor Iip35 isoform of unknown function includes an endoplasmic reticulum-retention motif that is masked upon binding of MHC II molecules. To gain further insight into the roles of Ii in B cell homeostasis, we generated Iip35 transgenic mice (Tgp35) and bred these with mice deficient for Ii (Tgp35/mIiKO). Iip35 was shown to compete with mIi for the binding to I-Ab . In addition, classical endosomal degradation products (p20/p10) and the class II-associated invariant chain peptide (CLIP) fragment were detected. Moreover, Iip35 favored the formation of compact peptide–MHC II complexes in the Tgp35/mIiKO mice. I-Ab levels were restored at the plasma membrane of mature B cells but Iip35 affected the fine conformation of MHC II molecules as judged by the increased reactivity of the AF6-120.1 antibody in permeabilized cells. However, the human Iip35 cannot fully replace the endogenous Ii. Indeed, most immature B cells in the bone marrow and spleen of transgenic mice had reduced surface expression of MHC II molecules, demonstrating a dominant-negative effect of Iip35 in Tgp35 mice. Interestingly, while maturation to follicular B cells was normal, Iip35 expression appeared to reduce the proportions of marginal zone B cells. These results emphasize the importance of Ii in B cell homeostasis and suggest that Iip35 could have regulatory functions.
Regulation of intestinal homeostasis by innate and adaptive immunity
Authors: Kayama Hisako , Takeda Kiyoshi
Published: September 2012

The intestine is a unique tissue where an elaborate balance is maintained between tolerance and immune responses against a variety of environmental factors such as food and the microflora. In a healthy individual, the microflora stimulates innate and adaptive immune systems to maintain gut homeostasis. However, the interaction of environmental factors with particular genetic backgrounds can lead to dramatic changes in the composition of the microflora (i.e. dysbiosis). Many of the specific commensal-bacterial products and the signaling pathways they trigger have been characterized. The role of T h 1, T h 2 and T h 17 cells in inflammatory bowel disease has been widely investigated, as has the contribution of epithelial cells and subsets of dendritic cells and macrophages. To date, multiple regulatory cells in adaptive immunity, such as regulatory T cells and regulatory B cells, have been shown to maintain gut homeostasis by preventing inappropriate innate and adaptive immune responses to commensal bacteria. Additionally, regulatory myeloid cells have recently been identified that prevent intestinal inflammation by inhibiting T-cell proliferation. An increasing body of evidence has shown that multiple regulatory mechanisms contribute to the maintenance of gut homeostasis.
Chitinophaga cymbidii sp. nov., isolated from Cymbidium goeringii roots
Authors: Li Lubin , Sun Lei , Shi Nan , Liu Lin , Guo Huijuan , Xu Aifang , Zhang Xiaoxia , Yao Na
Published: September 2012

Two Gram-staining-negative, aerobic, non-spore-forming rod-shaped, non-motile bacteria, designated strains R156-2T and T58-2 were isolated from the roots of Cymbidium goeringii. The colonies were yellow-pigmented. On the basis of 16S rRNA gene sequence similarity, strains R156-2T and T58-2 were shown to be members of the genus

Chitinophaga

. Strains R156-2T and T58-2 showed the greatest level of sequence similarity with

Chitinophaga niabensis

(96.0–96.3 %). The major menaquinone was MK-7. The main cellular fatty acids were iso-C15 : 0, C16 : 1ω5c and iso-C17 : 0 3-OH. Phenotypic and genotypic analyses indicated that strains R156-2T and T58-2 could not be assigned to any recognized species. Therefore, strains R156-2T and T58-2 represent a novel species of the genus

Chitinophaga

, for which the name Chitinophaga cymbidii sp. nov. is proposed. The type strain is R156-2T ( = ACCC 05363T = KCTC 23738T). The DNA G+C content of this strain is 51.9 mol%.
Pseudoalteromonas arabiensis sp. nov., a marine polysaccharide-producing bacterium
Authors: Matsuyama Hidetoshi , Minami Hideki , Kasahara Hirokazu , Kato Yoshihisa , Murayama Masafumi , Yumoto Isao
Published: September 2012

A novel exopolysaccharide-producing bacterium, designated strain k53T, was isolated from sediment from the Arabia Sea, Indian Ocean. The strain was Gram-negative, motile, strictly aerobic, oxidase-positive and catalase-positive, and required Na+ for growth. Its major isoprenoid quinone was ubiquinone-8 (Q-8), and its cellular fatty acid profile mainly consisted of C16 : 1ω7c, C16 : 0 and C18 : 1ω7c. The DNA G+C content was 43 mol%. 16S rRNA gene sequence analysis suggested that strain k53T is a member of the genus

Pseudoalteromonas

. Strain k53T exhibited close phylogenetic affinity to

Pseudoalteromonas lipolytica

LMEB 39T (98.0% 16S rRNA gene sequence similarity) and
Pseudoalteromonas donghaensis
HJ51T (97.3 %).The DNA–DNA reassociation values between strain k53T and

P. lipolytica

JCM 15903T and

P. donghaensis

LMG 24469T were 17 % and 12 %, respectively. Owing to the significant differences in phenotypic and chemotaxonomic characteristics, and phylogenetic analysis based on the 16S rRNA gene sequence and DNA–DNA relatedness data, the isolate merits classification as a representative of a novel species, for which the name Pseudoalteromonas arabiensis is proposed. The type strain of this species is k53T ( = JCM 17292T = NCIMB 14688T).
Dyadobacter jejuensis sp. nov., isolated from seawater
Authors: Chun Jeesun , Kang Ji Young , Joung Yochan , Kim Haneul , Joh Kiseong , Jahng Kwang Yeop
Published: September 2012

A taxonomic study was carried out on a novel bacterial strain, designated AM1R11T, which was isolated from seawater of Jeju Island in Korea. Cells of the isolate were found to be Gram-negative, rod-shaped and non-motile. Comparison of the 16S rRNA gene sequences indicated that the isolate belonged to the family

Cytophagaceae

, with

Dyadobacter ginsengisoli

Gsoil 043T as its closest relative, with a similarity of 96.6 %. It contained summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c, 36.9 %), iso-C15 : 0 (16.5 %) and C16 : 1ω5c (16.3 %) as the major fatty acids and MK-7 as the predominant menaquinone. The polar lipid profile of strain AM1R11T revealed the presence of phosphatidylethanolamine, one aminolipid and four unidentified lipids (L1, L2, L3 and L4). The DNA G+C content of strain AM1R11T was 45.1 mol%. On the basis of the evidence presented, it is concluded that strain AM1R11T represents a novel species of the genus

Dyadobacter

, for which the name Dyadobacter jejuensis sp. nov. is proposed. The type strain is AM1R11T ( = KACC 16446T = JCM 17918T).
Winogradskyella litorisediminis sp. nov., isolated from coastal sediment
Authors: Kang Chul-Hyung , Lee Soo-Young , Yoon Jung-Hoon
Published: September 2012

A Gram-staining-negative, non-flagellated, non-gliding, aerobic, rod-shaped bacterium, designated DPS-8T, was isolated from coastal sediment of Geoje island in the South Sea, South Korea, and subjected to a polyphasic study. Strain DPS-8T grew optimally at 30 °C, at pH 7.0–7.5 and in the presence of 2 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain DPS-8T joined the clade comprising the type strains of

Winogradskyella

species with a high bootstrap resampling value of 93.5 %. Phylogenetic trees constructed using maximum-likelihood and maximum-parsimony algorithms revealed that strain DPS-8T belonged to the genus

Winogradskyella

. Strain DPS-8T exhibited 94.1–96.5 % 16S rRNA gene sequence similarity to the type strains of species of the genus

Winogradskyella

. Strain DPS-8T contained MK-6 as the predominant menaquinone and iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 0 3-OH and C16 : 1ω7c and/or iso-C15 : 0 2-OH as the major fatty acids. The major polar lipids of strain DPS-8T were phosphatidylethanolamine and two unidentified lipids. The DNA G+C content of strain DPS-8T was 34.7 mol%. Differential phenotypic properties, together with its phylogenetic distinctiveness, revealed that strain DPS-8T is separate from recognized species of the genus

Winogradskyella

. On the basis of the data presented, strain DPS-8T is considered to represent a novel species of the genus

Winogradskyella

, for which the name Winogradskyella litorisediminis sp. nov. is proposed. The type strain is DPS-8T ( = KCTC 32110T = CCUG 62215T).
Characterization of a Viral Synergism in the MonocotBrachypodium distachyonReveals Distinctly Altered Host Molecular Processes Associated with Disease
Authors: Mandadi Kranthi K. , Scholthof Karen-Beth G.
Published: September 2012

Panicum mosaic virus (PMV) and its satellite virus (SPMV) together infect several small grain crops, biofuel, and forage and turf grasses. Here, we establish the emerging monocot model Brachypodium (Brachypodium distachyon) as an alternate host to study PMV- and SPMV-host interactions and viral synergism. Infection of Brachypodium with PMV+SPMV induced chlorosis and necrosis of leaves, reduced seed set, caused stunting, and lowered biomass, more than PMV alone. Toward gaining a molecular understanding of PMV- and SPMV-affected host processes, we used a custom-designed microarray and analyzed global changes in gene expression of PMV- and PMV+SPMV-infected plants. PMV infection by itself modulated expression of putative genes functioning in carbon metabolism, photosynthesis, metabolite transport, protein modification, cell wall remodeling, and cell death. Many of these genes were additively altered in a coinfection with PMV+SPMV and correlated to the exacerbated symptoms of PMV+SPMV coinfected plants. PMV+SPMV coinfection also uniquely altered expression of certain genes, including transcription and splicing factors. Among the host defenses commonly affected in PMV and PMV+SPMV coinfections, expression of an antiviral RNA silencing component, SILENCING DEFECTIVE3, was suppressed. Several salicylic acid signaling components, such as pathogenesis-related genes and WRKY transcription factors, were up-regulated. By contrast, several genes in jasmonic acid and ethylene responses were down-regulated. Strikingly, numerous protein kinases, including several classes of receptor-like kinases, were misexpressed. Taken together, our results identified distinctly altered immune responses in monocot antiviral defenses and provide insights into monocot viral synergism.