bluuebunny/crossref_metadata_2025 huggingface dataset:
Voltage-dependent regulation of CaV2.2 channels by Gq-coupled receptor is facilitated by membrane-localized β subunit
Authors: Keum Dongil , Baek Christina , Kim Dong-Il , Kweon Hae-Jin , Suh Byung-Chang
Published: September 2014

G protein–coupled receptors (GPCRs) signal through molecular messengers, such as Gβγ, Ca2+, and phosphatidylinositol 4,5-bisphosphate (PIP2), to modulate N-type voltage-gated Ca2+ (CaV2.2) channels, playing a crucial role in regulating synaptic transmission. However, the cellular pathways through which GqPCRs inhibit CaV2.2 channel current are not completely understood. Here, we report that the location of CaV β subunits is key to determining the voltage dependence of CaV2.2 channel modulation by GqPCRs. Application of the muscarinic agonist oxotremorine-M to tsA-201 cells expressing M1 receptors, together with CaV N-type α1B, α2δ1, and membrane-localized β2a subunits, shifted the current-voltage relationship for CaV2.2 activation 5 mV to the right and slowed current activation. Muscarinic suppression of CaV2.2 activity was relieved by strong depolarizing prepulses. Moreover, when the C terminus of β-adrenergic receptor kinase (which binds Gβγ) was coexpressed with N-type channels, inhibition of CaV2.2 current after M1 receptor activation was markedly reduced and delayed, whereas the delay between PIP2 hydrolysis and inhibition of CaV2.2 current was decreased. When the Gβγ-insensitive CaV2.2 α1C-1B chimera was expressed, voltage-dependent inhibition of calcium current was virtually abolished, suggesting that M1 receptors act through Gβγ to inhibit CaV2.2 channels bearing membrane-localized CaV β2a subunits. Expression of cytosolic β subunits such as β2b and β3, as well as the palmitoylation-negative mutant β2a(C3,4S), reduced the voltage dependence of M1 muscarinic inhibition of CaV2.2 channels, whereas it increased inhibition mediated by PIP2 depletion. Together, our results indicate that, with membrane-localized CaV β subunits, CaV2.2 channels are subject to Gβγ-mediated voltage-dependent inhibition, whereas cytosol-localized β subunits confer more effective PIP2-mediated voltage-independent regulation. Thus, the voltage dependence of GqPCR regulation of calcium channels can be determined by the location of isotype-specific CaV β subunits.
A single amino acid substitution in CFTR converts ATP to an inhibitory ligand
Authors: Lin Wen-Ying , Jih Kang-Yang , Hwang Tzyh-Chang
Published: September 2014

Cystic fibrosis (CF), one of the most common lethal genetic diseases, is caused by loss-of-function mutations of the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which encodes a chloride channel that, when phosphorylated, is gated by ATP. The third most common pathogenic mutation, a glycine-to-aspartate mutation at position 551 or G551D, shows a significantly decreased open probability (Po) caused by failure of the mutant channel to respond to ATP. Recently, a CFTR-targeted drug, VX-770 (Ivacaftor), which potentiates G551D-CFTR function in vitro by boosting its Po, has been approved by the FDA to treat CF patients carrying this mutation. Here, we show that, in the presence of VX-770, G551D-CFTR becomes responsive to ATP, albeit with an unusual time course. In marked contrast to wild-type channels, which are stimulated by ATP, sudden removal of ATP in excised inside-out patches elicits an initial increase in macroscopic G551D-CFTR current followed by a slow decrease. Furthermore, decreasing [ATP] from 2 mM to 20 µM resulted in a paradoxical increase in G551D-CFTR current. These results suggest that the two ATP-binding sites in the G551D mutant mediate opposite effects on channel gating. We introduced mutations that specifically alter ATP-binding affinity in either nucleotide-binding domain (NBD1 or NBD2) into the G551D background and determined that this disease-associated mutation converts site 2, formed by the head subdomain of NBD2 and the tail subdomain of NBD1, into an inhibitory site, whereas site 1 remains stimulatory. G551E, but not G551K or G551S, exhibits a similar phenotype, indicating that electrostatic repulsion between the negatively charged side chain of aspartate and the γ-phosphate of ATP accounts for the observed mutational effects. Understanding the molecular mechanism of this gating defect lays a foundation for rational drug design for the treatment of CF.
GALAXY EMISSION LINE CLASSIFICATION USING THREE-DIMENSIONAL LINE RATIO DIAGRAMS
Authors: Vogt Frédéric P. A. , Dopita Michael A. , Kewley Lisa J. , Sutherland Ralph S. , Scharwächter Julia , Basurah Hassan M. , Ali Alaa , Amer Morsi A.
Published: September 2014

Two-dimensional (2D) line ratio diagnostic diagrams have become a key tool in understanding the excitation mechanisms of galaxies. The curves used to separate the different regions—H ii-like or excited by an active galactic nucleus (AGN)—have been refined over time but the core technique has not evolved significantly. However, the classification of galaxies based on their emission line ratios really is a multi-dimensional problem. Here we exploit recent software developments to explore the potential of three-dimensional (3D) line ratio diagnostic diagrams. We introduce the

diagrams, which are a specific set of 3D diagrams that separate the oxygen abundance and the ionization parameter of H ii region-like spectra and also enable us to probe the excitation mechanism of the gas. By examining these new 3D spaces interactively, we define the

diagnostics, a new set of 2D diagnostics that can provide the metallicity of objects excited by hot young stars and that cleanly separate H ii region-like objects from the different classes of AGNs. We show that these

diagnostics are consistent with the key log [N ii]/Hα versus log [O iii]/Hβ diagnostic currently used by the community. They also have the advantage of attaching a probability that a given object belongs to one class or the other. Finally, we discuss briefly why

diagrams can provide a new way to differentiate and study the different classes of AGNs in anticipation of a dedicated follow-up study.
Primary brain tumors and posterior reversible encephalopathy syndrome
Authors: Kamiya-Matsuoka Carlos , Cachia David , Olar Adriana , Armstrong Terri S. , Gilbert Mark R.
Published: September 2014

Background

Posterior reversible encephalopathy syndrome (PRES) is a neurotoxic encephalopathic state associated with reversible cerebral vasogenic edema. It is an increasingly recognized occurrence in the oncology population. However, it is very uncommon in patients with primary brain tumors (PBTs). The aim of this study was to analyze the clinicoradiological features and report the clinical outcomes of PRES in PBT patients.

Methods

We identified 4 cases with PBT who developed PRES at MD Anderson Cancer Center (MDACC) between 2012 and 2014. Clinical and radiological data were abstracted from their records. In addition, we also solicited 8 cases from the literature.

Results

The median age at PRES onset was 19 years, male-to-female ratio was 1:1, and the syndrome occurred in patients with ependymoma (n = 4), glioblastoma (n = 3), diffuse intrinsic pontine glioma (DIPG; n = 3), juvenile pilocytic astrocytoma (n = 1), and atypical meningioma (n = 1). Two glioblastomas and 2 DIPG cases received bevacizumab and vandetanib before the onset of symptoms, respectively. The most common clinical presentation was seizures (n = 7). Three MDACC patients recovered completely in 3–4 weeks after the onset of symptoms. One patient died due to active cancer and several comorbidities including PRES.

Conclusions

Hypertension seems to be the most important coexisting risk factor for development of PRES; however, the potential effects of chemotherapeutic agents in the pathogenesis of PRES should also be examined. The clinicoradiological course of PRES in PBT patients did not vary from the classical descriptions of PRES found in other causes. PRES must be considered as part of the differential diagnosis in patients with PBTs presenting with seizures or acute encephalopathy.
First Report of Bacterial Blight of Pomegranate Caused by Xanthomonas axonopodis pv. punicae in Turkey
Authors: Icoz S. M. , Polat I. , Sulu G. , Yilmaz M. , Unlu A. , Soylu S. , Bozkurt I. A. , Baysal Ö.
Published: September 2014

Pomegranate (Punica granatum L.) is an increasingly important fruit crop that is widely cultivated in Turkey. Typical bacterial blight symptoms were observed since spring of 2011 in pomegranate orchards located in Antalya Province. Symptoms were characterized by dark brown, angular to irregularly shaped spots on leaves and fruit; cankers on stems, branches, and trunks; and split trunks. The pathogen was isolated from leaf spots on naturally infected plants showing typical symptoms onto yeast dextrose chalk agar. Bright yellow bacterial colonies were consistently isolated. Bacterial strains were characterized as gram negative, oxidase negative, catalase positive, tobacco hypersensitivity positive, and able to produce acid from L-arabinose, D-galactose, D-glucose, and D-mannitol but not from D-xylose. Pathogenicity of the representative bacterial strain Serik-4 was performed on 2-year-old pomegranate plants cv. Hicaz. Leaves were sprayed until runoff with bacterial cell suspensions containing 107 CFU/ml. Inoculated plants were covered with transparent plastic bags to maintain moisture for 48 h. Negative control plants were inoculated with sterile distilled water. Plants were then incubated in a greenhouse at 30°C for 14 days. Symptoms on leaves included dark brown, angular to irregularly shaped water soaked lesions along the veins of the inoculated plants 10 days after inoculation. No lesions developed on the control plants. The symptoms on inoculated plants were similar to those on naturally infected plants. Yellow bacterial colonies were re-isolated from the inoculated plants and identified as the same as the original strain by conventional tests and FAME analysis, thus fulfilling Koch's postulates. Fatty acid methyl ester profiling of the representative strain Serik-4 using GC-MIDI (Microbial Identification Inc, Newark, DE) identified the genus of the bacterium as Xanthomonas. The identity of Serik-4 was further confirmed by amplifying the 16S rRNA gene with the universal primers 27F and 1492R (3) and sequence analysis (GenBank Accession No. KM007073). The 16S rRNA gene sequences of Serik-4 was 99% identical to the corresponding gene sequences of the Xanthomonas axonopodis pv. punicae strain present in the NCBI database (JQ067629.1). High incidence of bacterial blight caused by X. axonopodis pv. punicae on pomegranate has been previously reported in India (2), Pakistan (1), and South Africa (4). To our knowledge, this is the first report of bacterial blight on pomegranate caused by X. axonopodis pv. punicae in Turkey.

References: (1) M. A. Akhtar and M. H. R. Bhatti. Pakistan J. Agric. Res. 13:95, 1992. (2) R. Chand and R. Kishun. Indian Phytopathol. 44:370, 1991. (3) D. J. Lane. Page 115 in: Nucleic Acid Techniques in Bacterial Systematics, 1991. (4) Y. Petersen et al. Australas. Plant Pathol. 39:544, 2010.
Acquired Resistance to Mefenoxam in Sensitive Isolates ofPhytophthora infestans
Authors: Childers Richard , Danies Giovanna , Myers Kevin , Fei Zhangjun , Small Ian M. , Fry William E.
Published: September 2014

The systemic fungicide mefenoxam has been important in the control of late blight disease caused by Phytophthora infestans. This phenylamide fungicide has a negative effect on the synthesis of ribosomal RNA; however, the genetic basis for inherited field resistance is still not completely clear. We recently observed that a sensitive isolate became tolerant after a single passage on mefenoxam-containing medium. Further analyses revealed that all sensitive isolates tested (in three diverse genotypes) acquired this resistance equally quickly. In contrast, isolates that were “resistant” to mefenoxam in the initial assessment (stably resistant) did not increase in resistance upon further exposure. However, there appeared to be a cost associated with acquired resistance in the initially sensitive isolates, in that isolates with acquired resistance grew more slowly on mefenoxam-free medium than did the same isolates that had never been exposed to mefenoxam. The acquired resistance of the sensitive isolates declined slightly with subsequent culturing on medium free of mefenoxam. To investigate the mechanism of acquired resistance, we employed strand-specific RNA sequencing. Many differentially expressed genes were genotype specific, but one set of genes was differentially expressed in all genotypes. Among these were several genes (a phospholipase “Pi-PLD-like-3,” two ATP-binding cassette superfamily [ABC] transporters, and a mannitol dehydrogenase) that were up-regulated and whose function might contribute to a resistance phenotype.
Resistance to QoI Fungicides Is Widespread in Brazilian Populations of the Wheat Blast Pathogen Magnaporthe oryzae
Authors: Castroagudín Vanina L. , Ceresini Paulo C. , de Oliveira Samanta C. , Reges Juliana T. A. , Maciel João L. N. , Bonato Ana L. V. , Dorigan Adriano F. , McDonald Bruce A.
Published: September 2014

Wheat blast, caused by Magnaporthe oryzae, is an important disease across central and southern Brazil. Control has relied mainly on strobilurin fungicides (quinone-outside inhibitors [QoIs]). Here, we report the widespread distribution of QoI resistance in M. oryzae populations sampled from wheat fields and poaceous hosts across central and southern Brazil and the evolution of the cytochrome b (cyt b) gene. Sequence analysis of the cyt b gene distinguished nine haplotypes, with four haplotypes carrying the G143A mutation associated with QoI resistance and two haplotypes shared between isolates sampled from wheat and other poaceous hosts. The frequency of the G143A mutation in the wheat-infecting population increased from 36% in 2005 to 90% in 2012. The G143A mutation was found in many different nuclear genetic backgrounds of M. oryzae. Our findings indicate an urgent need to reexamine the use of strobilurins to manage fungal wheat diseases in Brazil.
Simultaneous Detection of Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola in Rice Seed Using a Padlock Probe-Based Assay
Authors: Tian Yanli , Zhao Yuqiang , Xu Rui , Liu Fengquan , Hu Baishi , Walcott R. R.
Published: September 2014

Based on 16S-23S internal transcribed spacer ribosomal DNA sequence data, two padlock probes (PLPs), P-Xoo and P-Xoc, were designed and tested to detect Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola, respectively. These PLPs were combined with dot-blot hybridization to detect X. oryzae pv. oryzae and X. oryzae pv. oryzicola individually in rice seed. Using this technique, a detection sensitivity of 1 pg of X. oryzae pv. oryzae genomic DNA was observed. The technique also facilitated the detection of X. oryzae pv. oryzae in rice seedlots with 2% artificially infested seed. With regards to X. oryzae pv. oryzicola a detection threshold of 1 pg genomic DNA was observed and the pathogen was successful detected in rice seedlots with 0.2% artificially infested seed. The PLP assays detected X. oryzae pv. oryzae and X. oryzae pv. oryzicola in 39.3% (13 of 33) and 21.3% (10 of 47) of naturally infested commercial rice seedlots, respectively. In contrast, conventional polymerase chain reaction using OSF1/OSR1 and XoocF/XoocR primers sets detected X. oryzae pv. oryzae and X. oryzae pv. oryzicola in 9.1% (3 of 33) and 8.5% (4 of 47) of the same rice seedlots, respectively. We also detected both pathogens simultaneously in two seedlots, which successfully proved that PLPs (P-Xoo and P-Xoc) combined with reverse dotblot hybridization can be used to simultaneously detect multiple pathogens in naturally infested commercial rice seedlots. This approach has the potential to be an important tool for detecting multiple pathogens in seed and thereby preventing the spread of important pathogens.
Hollow Prosthetic Eyes
Authors: Worrell Emma
Published: September 2014

A new technique to produce hollow prostheses is presented. A small case series of patients utilized standard methods to fabricate hollow ocular prostheses where rehabilitation had proved difficult. This article describes the fabrication and results of hollow ocular prostheses. Each hollow eye was significantly reduced in weight, one-third lighter than the original weight, with the exact size, shape, and volume of the existing solid prosthesis. This simple design significantly reduced the weight of these eyes and revolutionized these patients’ rehabilitation. Previously the solid prostheses overburdened the lower eyelids, causing discomfort, irritation, discharge, and reddening, whereas the new lightweight prostheses are unobtrusive, comfortable, and good aesthetically.
What do we know about gliotransmitter release from astrocytes?
Authors: Sahlender Daniela A. , Savtchouk Iaroslav , Volterra Andrea
Published: September 2014

Astrocytes participate in information processing by actively modulating synaptic properties via gliotransmitter release. Various mechanisms of astrocytic release have been reported, including release from storage organelles via exocytosis and release from the cytosol via plasma membrane ion channels and pumps. It is still not fully clear which mechanisms operate under which conditions, but some of them, being Ca
2+
-regulated, may be physiologically relevant. The properties of Ca
2+
-dependent transmitter release via exocytosis or via ion channels are different and expected to produce different extracellular transmitter concentrations over time and to have distinct functional consequences. The molecular aspects of these two release pathways are still under active investigation. Here, we discuss the existing morphological and functional evidence in support of either of them. Transgenic mouse models, specific antagonists and localization studies have provided insight into regulated exocytosis, albeit not in a systematic fashion. Even more remains to be uncovered about the details of channel-mediated release. Better functional tools and improved ultrastructural approaches are needed in order fully to define specific modalities and effects of astrocytic gliotransmitter release pathways.
Dissecting tripartite synapses with STED microscopy
Authors: Panatier Aude , Arizono Misa , Nägerl U. Valentin
Published: September 2014

The concept of the tripartite synapse reflects the important role that astrocytic processes are thought to play in the function and regulation of neuronal synapses in the mammalian nervous system. However, many basic aspects regarding the dynamic interplay between pre- and postsynaptic neuronal structures and their astrocytic partners remain to be explored. A major experimental hurdle has been the small physical size of the relevant glial and synaptic structures, leaving them largely out of reach for conventional light microscopic approaches such as confocal and two-photon microscopy. Hence, most of what we know about the organization of the tripartite synapse is based on electron microscopy, which does not lend itself to investigating dynamic events and which cannot be carried out in parallel with functional assays. The development and application of superresolution microscopy for neuron–glia research is opening up exciting experimental opportunities in this regard. In this paper, we provide a basic explanation of the theory and operation of stimulated emission depletion (STED) microscopy, outlining the potential of this recent superresolution imaging modality for advancing our understanding of the morpho-functional interactions between astrocytes and neurons that regulate synaptic physiology.
Hyaluronan-based extracellular matrix under conditions of homeostatic plasticity
Authors: Valenzuela Juan Carlos , Heise Christopher , Franken Gilbert , Singh Jeet , Schweitzer Barbara , Seidenbecher Constanze I. , Frischknecht Renato
Published: September 2014

Neuronal networks are balanced by mechanisms of homeostatic plasticity, which adjusts synaptic strength via molecular and morphological changes in the pre- and post-synapse. Here, we wondered whether the hyaluronic acid-based extracellular matrix (ECM) of the brain is involved in mechanisms of homeostatic plasticity. We hypothesized that the ECM, being rich in chondroitin sulfate proteoglycans such as brevican, which are suggested to stabilize synapses by their inhibitory effect on structural plasticity, must be remodelled to allow for structural and molecular changes during conditions of homeostatic plasticity. We found a high abundance of cleaved brevican fragments throughout the hippocampus and cortex and in neuronal cultures, with the strongest labelling in perineuronal nets on parvalbumin-positive interneurons. Using an antibody specific for a brevican fragment cleaved by the matrix metalloprotease ADAMTS4, we identified the enzyme as the main brevican-processing protease. Interestingly, we found ADAMTS4 largely associated with synapses. After inducing homeostatic plasticity in neuronal cell cultures by prolonged network inactivation, we found increased brevican processing at inhibitory as well as excitatory synapses, which is in line with the ADAMTS4 subcellular localization. Thus, the ECM is remodelled in conditions of homeostatic plasticity, which may liberate synapses to allow for a higher degree of structural plasticity.
GABAergic interneuron to astrocyte signalling: a neglected form of cell communication in the brain
Authors: Losi Gabriele , Mariotti Letizia , Carmignoto Giorgio
Published: September 2014

GABAergic interneurons represent a minority of all cortical neurons and yet they efficiently control neural network activities in all brain areas. In parallel, glial cell astrocytes exert a broad control of brain tissue homeostasis and metabolism, modulate synaptic transmission and contribute to brain information processing in a dynamic interaction with neurons that is finely regulated in time and space. As most studies have focused on glutamatergic neurons and excitatory transmission, our knowledge of functional interactions between GABAergic interneurons and astrocytes is largely defective. Here, we critically discuss the currently available literature that hints at a potential relevance of this specific signalling in brain function. Astrocytes can respond to GABA through different mechanisms that include GABA receptors and transporters. GABA-activated astrocytes can, in turn, modulate local neuronal activity by releasing gliotransmitters including glutamate and ATP. In addition, astrocyte activation by different signals can modulate GABAergic neurotransmission. Full clarification of the reciprocal signalling between different GABAergic interneurons and astrocytes will improve our understanding of brain network complexity and has the potential to unveil novel therapeutic strategies for brain disorders.
Nesterenkonia rhizosphaerae sp. nov., an alkaliphilic actinobacterium isolated from rhizosphere soil in a saline-alkaline desert
Authors: Wang Hong-Fei , Zhang Yong-Guang , Chen Ji-Yue , Hozzein Wael N. , Li Li , Wadaan Mohammed A. M. , Zhang Yuan-Ming , Li Wen-Jun
Published: September 2014

An alkaliphilic actinobacterial strain, designated EGI 80099T, was isolated from a rhizosphere soil sample of Reaumuria soongorica found in the desert soils of Fukang, Xinjiang, north-west China. Cells of strain EGI 80099T were Gram-stain-positive, non-motile, non-endospore-forming cocci. The predominant menaquinones were MK-7, MK-8 and MK-9. The major cellular fatty acids (>10 %) were anteiso-C15 : 0 and anteiso-C17 : 0. Analysis of the cell wall showed the presence of peptidoglycan of the type l-Lys–Gly–l-Glu, variation A4α. Cells of the isolate contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, an unknown phospholipid and an unidentified glycolipid as polar lipids. The genomic DNA G+C content was 63.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain EGI 80099T belongs to the genus

Nesterenkonia

, sharing 95.68–97.37 % sequence similarities with the type strains of recognized species within this genus. DNA–DNA hybridization of strain EGI 80099T with the type strains of species that showed the highest sequence similarities,

Nesterenkonia aethiopica

DSM 17733T (97.37 %),

Nesterenkonia flava

CAAS 251T (97.23 %) and

Nesterenkonia xinjiangensis

YIM 70097T (97.02 %), gave relatedness values of 8.7–62.2 %. Data from DNA–DNA hybridizations and physiological and biochemical tests indicated that strain EGI 80099T represents a novel species of the genus

Nesterenkonia

, for which the name Nesterenkonia
rhizosphaerae sp. nov. is proposed. The type strain is EGI 80099T ( = BCRC 16947T = JCM 19129T).
Transcriptional regulation of the Aggregatibacter actinomycetemcomitans ygiW–qseBC operon by QseB and integration host factor proteins
Authors: Juárez-Rodríguez María Dolores , Torres-Escobar Ascención , Demuth Donald R.
Published: September 2014

The QseBC two-component system plays a pivotal role in regulating virulence and biofilm growth of the oral pathogen Aggregatibacter actinomycetemcomitans. We previously showed that QseBC autoregulates the ygiW–qseBC operon. In this study, we characterized the promoter that drives ygiW–qseBC expression. Using lacZ transcriptional fusion constructs and 5′-rapid amplification of cDNA ends, we showed that ygiW–qseBC expression is driven by a promoter that initiates transcription 53 bases upstream of ygiW and identified putative cis-acting promoter elements, whose function was confirmed using site-specific mutagenesis. Using electrophoretic mobility shift assays, two trans-acting proteins were shown to interact with the ygiW–qseBC promoter. The QseB response regulator bound to probes containing the direct repeat sequence CTTAA-N6-CTTAA, where the CTTAA repeats flank the −35 element of the promoter. The ygiW–qseBC expression could not be detected in A. actinomycetemcomitans ΔqseB or ΔqseBC strains, but was restored to WT levels in the ΔqseBC mutant when complemented by single copy chromosomal insertion of qseBC. Interestingly, qseB partially complemented the ΔqseBC strain, suggesting that QseB could be activated in the absence of QseC. QseB activation required its phosphorylation since complementation did not occur using qseB
pho−, encoding a protein with the active site aspartate substituted with alanine. These results suggest that QseB is a strong positive regulator of ygiW–qseBC expression. In addition, integration host factor (IHF) bound to two sites in the promoter region and an additional site near the 5′ end of the ygiW ORF. The expression of ygiW–qseBC was increased by twofold in ΔihfA and ΔihfB strains of A. actinomycetemcomitans, suggesting that IHF is a negative regulator of the ygiW–qseBC operon.
Interpretable per Case Weighted Ensemble Method for Cancer Associations
Authors: Jalali Adrin , Pfeifer Nico
Published: September 2014

Motivation

Molecular measurements from cancer patients such as gene expression and DNA methylation are usually very noisy. Further-more, cancer types can be very heterogeneous. Therefore, one of the main assumptions for machine learning, that the underlying unknown distribution is the same for all samples, might not be completely fullfilled. We introduce a method, that can estimate this bias on a per-feature level and incorporate calculated feature confidences into a weighted combination of classifiers with disjoint feature sets.

Results

The new method achieves state-of-the-art performance on many different cancer data sets with measured DNA methylation or gene expression. Moreover, we show how to visualize the learned classifiers to find interesting associations with the target label. Applied to a leukemia data set we find several ribosomal proteins associated with leukemia's risk group that might be interesting targets for follow-up studies and support the hypothesis that the ribosomes are a new frontier in gene regulation.Availability:The method is available under GPLv3+ License athttps://github.com/adrinjalali/Network-Classifier.
Drosophila TRF2 is a preferential core promoter regulator
Authors: Kedmi Adi , Zehavi Yonathan , Glick Yair , Orenstein Yaron , Ideses Diana , Wachtel Chaim , Doniger Tirza , Waldman Ben-Asher Hiba , Muster Nemone , Thompson James , Anderson Scott , Avrahami Dorit , Yates John R. , Shamir Ron , Gerber Doron , Juven-Gershon Tamar
Published: September 2014

Transcription of protein-coding genes is highly dependent on the RNA polymerase II core promoter. Core promoters, generally defined as the regions that direct transcription initiation, consist of functional core promoter motifs (such as the TATA-box, initiator [Inr], and downstream core promoter element [DPE]) that confer specific properties to the core promoter. The known basal transcription factors that support TATA-dependent transcription are insufficient for in vitro transcription of DPE-dependent promoters. In search of a transcription factor that supports DPE-dependent transcription, we used a biochemical complementation approach and identified the Drosophila TBP (TATA-box-binding protein)-related factor 2 (TRF2) as an enriched factor in the fractions that support DPE-dependent transcription. We demonstrate that the short TRF2 isoform preferentially activates DPE-dependent promoters. DNA microarray analysis reveals the enrichment of DPE promoters among short TRF2 up-regulated genes. Using primer extension analysis and reporter assays, we show the importance of the DPE in transcriptional regulation of TRF2 target genes. It was previously shown that, unlike TBP, TRF2 fails to bind DNA containing TATA-boxes. Using microfluidic affinity analysis, we discovered that short TRF2-bound DNA oligos are enriched for Inr and DPE motifs. Taken together, our findings highlight the role of short TRF2 as a preferential core promoter regulator.
Repression of the soma-specific transcriptome by Polycomb-repressive complex 2 promotes male germ cell development
Authors: Mu Weipeng , Starmer Joshua , Fedoriw Andrew M. , Yee Della , Magnuson Terry
Published: September 2014

Polycomb-repressive complex 2 (PRC2) catalyzes the methylation of histone H3 Lys27 (H3K27) and functions as a critical epigenetic regulator of both stem cell pluripotency and somatic differentiation, but its role in male germ cell development is unknown. Using conditional mutagenesis to remove the core PRC2 subunits EED and SUZ12 during male germ cell development, we identified a requirement for PRC2 in both mitotic and meiotic germ cells. We observed a paucity of mutant spermatogonial stem cells (SSCs), which appears independent of repression of the known cell cycle inhibitors Ink4a/Ink4b/Arf. Moreover, mutant spermatocytes exhibited ectopic expression of somatic lamins and an abnormal distribution of SUN1 proteins on the nuclear envelope. These defects were coincident with abnormal chromosome dynamics, affecting homologous chromosome pairing and synapsis. We observed acquisition of H3K27me3 on stage-specific genes during meiotic progression, indicating a requirement for PRC2 in regulating the meiotic transcriptional program. Together, these data demonstrate that transcriptional repression of soma-specific genes by PRC2 facilitates homeostasis and differentiation during mammalian spermatogenesis.
Drosophila TAP/p32 is a core histone chaperone that cooperates with NAP-1, NLP, and nucleophosmin in sperm chromatin remodeling during fertilization
Authors: Emelyanov Alexander V. , Rabbani Joshua , Mehta Monika , Vershilova Elena , Keogh Michael C. , Fyodorov Dmitry V.
Published: September 2014

Nuclear DNA in the male gamete of sexually reproducing animals is organized as sperm chromatin compacted primarily by sperm-specific protamines. Fertilization leads to sperm chromatin remodeling, during which protamines are expelled and replaced by histones. Despite our increased understanding of the factors that mediate nucleosome assembly in the nascent male pronucleus, the machinery for protamine removal remains largely unknown. Here we identify four Drosophila protamine chaperones that mediate the dissociation of protamine–DNA complexes: NAP-1, NLP, and nucleophosmin are previously characterized histone chaperones, and TAP/p32 has no known function in chromatin metabolism. We show that TAP/p32 is required for the removal of Drosophila protamine B in vitro, whereas NAP-1, NLP, and Nph share roles in the removal of protamine A. Embryos from P32-null females show defective formation of the male pronucleus in vivo. TAP/p32, similar to NAP-1, NLP, and Nph, facilitates nucleosome assembly in vitro and is therefore a histone chaperone. Furthermore, mutants of P32, Nlp, and Nph exhibit synthetic-lethal genetic interactions. In summary, we identified factors mediating protamine removal from DNA and reconstituted in a defined system the process of sperm chromatin remodeling that exchanges protamines for histones to form the nucleosome-based chromatin characteristic of somatic cells.
Population and single-cell genomics reveal the Aire dependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia
Authors: Sansom Stephen N. , Shikama-Dorn Noriko , Zhanybekova Saule , Nusspaumer Gretel , Macaulay Iain C. , Deadman Mary E. , Heger Andreas , Ponting Chris P. , Holländer Georg A.
Published: September 2014

Promiscuous gene expression (PGE) by thymic epithelial cells (TEC) is essential for generating a diverse T cell antigen receptor repertoire tolerant to self-antigens, and thus for avoiding autoimmunity. Nevertheless, the extent and nature of this unusual expression program within TEC populations and single cells are unknown. Using deep transcriptome sequencing of carefully identified mouse TEC subpopulations, we discovered a program of PGE that is common between medullary (m) and cortical TEC, further elaborated in mTEC, and completed in mature mTEC expressing the autoimmune regulator gene (Aire). TEC populations are capable of expressing up to 19,293 protein-coding genes, the highest number of genes known to be expressed in any cell type. Remarkably, in mouse mTEC, Aire expression alone positively regulates 3980 tissue-restricted genes. Notably, the tissue specificities of these genes include known targets of autoimmunity in human AIRE deficiency. Led by the observation that genes induced by Aire expression are generally characterized by a repressive chromatin state in somatic tissues, we found these genes to be strongly associated with H3K27me3 marks in mTEC. Our findings are consistent with AIRE targeting and inducing the promiscuous expression of genes previously epigenetically silenced by Polycomb group proteins. Comparison of the transcriptomes of 174 single mTEC indicates that genes induced by Aire expression are transcribed stochastically at low cell frequency. Furthermore, when present, Aire expression-dependent transcript levels were 16-fold higher, on average, in individual TEC than in the mTEC population.
Functional neuroanatomy of Drosophila olfactory memory formation
Authors: Guven-Ozkan Tugba , Davis Ronald L.
Published: September 2014

New approaches, techniques and tools invented over the last decade and a half have revolutionized the functional dissection of neural circuitry underlying Drosophila learning. The new methodologies have been used aggressively by researchers attempting to answer three critical questions about olfactory memories formed with appetitive and aversive reinforcers: (1) Which neurons within the olfactory nervous system mediate the acquisition of memory? (2) What is the complete neural circuitry extending from the site(s) of acquisition to the site(s) controlling memory expression? (3) How is information processed across this circuit to consolidate early-forming, disruptable memories to stable, late memories? Much progress has been made and a few strong conclusions have emerged: (1) Acquisition occurs at multiple sites within the olfactory nervous system but is mediated predominantly by the γ mushroom body neurons. (2) The expression of long-term memory is completely dependent on the synaptic output of α/β mushroom body neurons. (3) Consolidation occurs, in part, through circuit interactions between mushroom body and dorsal paired medial neurons. Despite this progress, a complete and unified model that details the pathway from acquisition to memory expression remains elusive.
Crystal structure of 2-(1,3,7,9-tetramethyl-2,4,6,8-tetraoxo-1,2,3,4,6,7,8,9-octahydropyrido[2,3-d:6,5-d′]dipyrimidin-5-yl)benzamide dimethylformamide hemisolvate
Authors: Ayvazyan Armen
Published: September 2014

The title compound, C20H18N6O5·0.5C3H7NO, crystallized as a dimethylformamide (DMF) solvate. In the main molecule, the dihedral angle between the pyridodipyrimidine fused-ring system and the benzamide substituent is 82.26 (11)°. In the crystal, the benzamide molecules are linked by N—H...O hydrogen bonds to generate tetramers with an approximate square-prismatic shape, which appears to correlate with the tetragonal crystal symmetry. The DMF molecule is disordered about a crystallographic twofold axis and accepts a C—H...O interaction from the benzamide molecule.
Crystal structure of anhydrous poly[bis(μ2-sarcosinato-κ3O,N:O′)copper(II)]
Authors: Butcher Ray J. , Brewer Greg , Zemba Matthew
Published: September 2014

The title compound, [Cu(C3H6NO2)2]n, is a bis-complex of the anion of sarcosine (N-methylglycine). The asymmetric unit consists of a copper(II) ion, located on a center of inversion, and one molecule of the uninegative sarcosinate anion. The copper(II) ion exhibits a typical Jahn–Teller distorted [4 + 2] coordination geometry. The four shorter equatorial bonds are to the nitrogen and carboxylate O atoms of two sarcosinate anions, and the longer axial bonds are to carboxylate O atoms of neighboring complexes. The overall structure is made up from two chains formed by these longer axial Cu—O bonds, one extending parallel to [011] and the other parallel to [0-11]. Each one-dimensional array is connected by the equatorial bridging moieties to the chains on either side, creating an extended two-dimensional framework parallel to (100). There is a single intermolecular hydrogen-bonding interaction within the sheets between the amino NH group and an O atom of an adjacent molecule.
Crystal structure of flufenoxuron: a benzoylurea pesticide
Authors: Jeon Youngeun , Kang Gihaeng , Lee Sangjin , Kim Tae Ho
Published: September 2014

The title compound, C21H11ClF6N2O3(systematic name: 1-{4-[2-chloro-4-(trifluoromethyl)phenoxy]-2-fluorophenyl}-3-(2,6-difluorobenzoyl)urea), is a benzoylurea pesticide. The dihedral angles between the central fluorobenzene ring and the terminal difluorophenyl ring and chlorophenyl ring system are 62.15 (5) and 88.03 (5)°, respectively. In the crystal, N—H...O hydrogen bonds link adjacent molecules, formingR22(8) inversion dimers that pack into loop chains along thea-axis direction by short F...F contacts [2.729 (2) Å]. In addition, the chains are linked by weak C—H...π and π–π interactions [inter-centroid distances = 3.661 (2) and 3.535 (12) Å], resulting in a three-dimensional architecture.
An imported case of cutaneous leishmaniasis caused by Leishmania (Leishmania) donovani in Japan
Authors: Ito Kotaro , Takahara Masakazu , Ito Makoto , Oshiro Minoru , Takahashi Kenzo , Uezato Hiroshi , Imafuku Shinichi
Published: September 2014

Leishmaniasis is a major world health problem, and 12 million people are estimated to be infected in 88 countries. There have been few reports of leishmaniasis in Japan and all were of foreign origin; therefore diagnosis is difficult for Japanese physicians. There are 21 different pathogenic Leishmania species, and identification is obtained by polymerase chain reaction (PCR). Here we report an imported case of leishmaniasis by Leishmania (Leishmania) donovani infection from Sri Lanka. L. (L.) donovani usually causes visceral leishmaniasis, but in this case, the patient manifested cutaneous leishmaniasis. The identification of Leishmania species by PCR and investigation of the patient's background such as nationality and disease endemicity are important for diagnosis and treatment. This is the first report of cutaneous leishmaniasis by L. (L.) donovani in Japan.
Tissue factor expression on the surface of monocytes from a patient with hereditary angioedema
Authors: Iwamoto Kazumasa , Morioke Satoshi , Yanase Yuhki , Uchida Kazue , Hide Michihiro
Published: September 2014

Hereditary angioedema (HAE) presents as severe angioedema, which is mostly due to the C1 inhibitor (C1‐INH) gene mutations. Environmental factors, minor trauma and oral contraceptives have been reported to induce angioedema attack, but the trigger may often be uncertain. Activated factor XII controlled by C1‐INH facilitates bradykinin generation and also regulates coagulation cascade, but the relationship between edema formation and coagulation is still unclear. We have described a 35‐year‐old female patient with HAE, presenting with frequent angioedema attacks in the absence of an apparent triggering factor. She showed higher levels of FDP and D‐dimer during angioedema than those in remission. In addition, tissue factor (TF), an initiator of the extrinsic coagulation cascade, was expressed on the surface of monocytes. It was significantly higher than that of monocytes from healthy controls and tends to further increase during attacks. The expression of TF on monocytes may play a role in the induction of angioedema attacks in HAE by activating the coagulation pathway in association with reduced functions of C1‐INH.
Untangling the influence of phylogeny, soil and climate on leaf element concentrations in a biodiversity hotspot
Authors: Hao Zhuan , Kuang Yuanwen , Kang Ming
Published: September 2014

Plant elemental properties are fundamentally important for physiology and biogeochemical cycling in ecosystems. No study has examined foliar elements and their interaction with soil and climate conditions at large geographic scales in Karst areas of China, a biodiversity hotspot in the world. Yet such information is important for understanding the functional diversity of nutrient strategies and the physiological adaptations of plants to climatic and edaphic heterogeneity.

We assessed the influence of phylogeny, soil type and the climate on leaf element concentrations in a clade of taxonomically diverse Karst plants from the subfamily Didymocarpoideae under an explicit phylogenetic framework. We measured leaf concentrations of seven elements and evaluated soil properties for 422 populations of 177 Didymocarpoideae species. The phylogenetic signals present in the leaf element concentrations and in soil and climatic variables were quantified at both the subfamily (Didymocarpoideae) and genus (Primulina) levels. The correlations between leaf elements and soil and climate conditions were analysed at these two phylogenetic scales.

The Didymocarpoideae subfamily is generally characterized by higher Ca and Mg contents relative to other plants in China. Across the subfamily, a strong phylogenetic signal is detected for all of the leaf elements analysed as well as for most soil and climate variables, whereas the genus Primulina exhibits no significant phylogenetic signal in leaf elements or in most soil variables.

We detected an influence of both soil and climatic conditions on leaf element concentrations. However, the patterns of the relationships between leaf elements and soil and climate variables vary at the subfamily and genus levels. The phylogeny has a stronger effect than soil and climatic factors on leaf element concentrations at the subfamily level, while the leaf element contents within the genus Primulina are mostly influenced by environmental conditions. We conclude that the influences of taxonomy, soil and climate on leaf element concentrations are dependent on the phylogenetic scale of analysis.
Soil biota enhance agricultural sustainability by improving crop yield, nutrient uptake and reducing nitrogen leaching losses
Authors: Bender S. Franz , van der Heijden Marcel G.A.
Published: September 2014

Efficient resource use is a key factor for sustainable production and a necessity for meeting future global food demands. However, the factors that control resource use efficiency in agro‐ecosystems are only partly understood.

We investigated the influence of soil biota on nutrient leaching, nutrient‐use efficiency and plant performance in outdoor, open‐top lysimeters comprising a volume of 230 L. The lysimeters were filled with sterilized soil in two horizons and inoculated with a reduced soil‐life inoculum (soil biota ≤11 μm, microbially dominated) and an enriched soil‐life inoculum [soil organisms ≤2 mm, also containing arbuscular mycorrhizal fungi (AMF)]. A crop rotation was planted, and nutrient leaching losses, plant biomass and nutrient contents were assessed over a period of almost 2 years.

In the first year of the experiment, enriched soil life increased crop yield (+22%), N uptake (+29%) and P uptake (+110%) of maize and strongly reduced leaching losses of N (−51%, corresponding to a reduction of 76 kg N ha−1). In the second year, wheat biomass (+17%) and P contents (+80%) were significantly increased by enriched soil life, but the differences were lower than in the first year.

Enriched soil life also increased P mobilization from soil (+112%) and significantly reduced relative P leaching losses (−25%), defined as g P leached per kg P plant uptake, as well as relative N leaching losses (−36%), defined as kg N leached per kg N plant uptake, demonstrating that nutrient‐use efficiency was increased in the enriched soil‐life treatment.

Synthesis and applications. Soil biota are a key factor determining resource efficiency in agriculture. The results suggest that applying farming practices, which favour a rich and abundant soil life (e.g. reduced tillage, organic farming, crop rotation), can reduce environmental impacts, enhance crop yield and result in a more sustainable agricultural system. However, this needs to be confirmed in field situations. Enhanced nutrient‐use efficiency obtained through farming practices which exert positive effects on soil biota could result in reduced amounts of fertilisers needed for agricultural production and reduced nutrient losses to the environment, providing benefits of such practices beyond positive effects on biodiversity.
l‐arginine and aminoguanidine reduce colonic damage of acetic acid‐induced colitis in rats: Potential modulation of nuclear factor‐κB/p65
Authors: Farghaly Hanan SM , Thabit Romany H
Published: September 2014

The transcription factor, nuclear factor‐κB (NF‐κB) is a key inducer of inducible nitric oxide synthase (iNOS) gene expression. The aim of the present study was to investigate the potential protective effect of l‐arginine (Arg; nitric oxide precursor) and aminoguanidine (inducible nitric oxide synthase inhibitor) against acetic acid (AA)‐induced colitis in rats, and the potential role of NF‐κB. Colitis was induced by intrarectal inoculation of rats with 4% acetic acid for three consecutive days. The effect of Arg and aminoguanidine on nitric oxide levels was assessed by Greiss assay and protein expression of NF‐κB/p65, and inducible nitric oxide synthase was also investigated by immunohistochemistry. Slides were examined using ImageJ, and results reported as the percent area positive for each marker. Intrarectal AA caused a significant increase in bodyweight loss and colon weights. Arg at 100 mg/day for 7 days before induction of colitis diminished the changes in both bodyweight loss and colon weights. Furthermore, Arg attenuated the colonic tissues macroscopic and microscopic damage induced by acetic acid. In addition, i.p. AG 100 mg/kg given during and after induction of colitis recovered the colonic ulcerative lesion induced by AA. Arg can protect against colonic inflammation; an effect that probably be attributed to its nitric oxide‐donating property, resulting in modulatory effects on the expression of NF‐κB/p65 in the colon tissues. The results suggested that Arg might reduce the inflammation associated with colitis as confirmed by histopathological investigations. Arg might inhibit AA‐induced colitis through the NF‐κB/nitric oxide pathway.