bluuebunny/crossref_metadata_2025 huggingface dataset:
The Alk receptor tyrosine kinase regulates Sparkly, a novel activity regulating neuropeptide precursor in the Drosophila CNS
Authors: Sukumar Sanjay Kumar , Antonydhason Vimala , Molander Linnea , Sandakly Jawdat , Kleit Malak , Umapathy Ganesh , Mendoza-Garcia Patricia , Masudi Tafheem , Schlossser Andreas , Nässel Dick R. , Wegener Christian , Shirinian Margret , Palmer Ruth H.
Published: May 2024

Numerous roles for the Alk receptor tyrosine kinase have been described in
Drosophila
, including functions in the central nervous system (CNS), however the molecular details are poorly understood. To gain mechanistic insight, we employed Targeted DamID (TaDa) transcriptional profiling to identify targets of Alk signaling in the larval CNS. TaDa was employed in larval CNS tissues, while genetically manipulating Alk signaling output. The resulting TaDa data were analysed together with larval CNS scRNA-seq datasets performed under similar conditions, identifying a role for Alk in the transcriptional regulation of neuroendocrine gene expression. Further integration with bulk/scRNA-seq and protein datasets from larval brains in which Alk signaling was manipulated, identified a previously uncharacterized
Drosophila
neuropeptide precursor encoded by
CG4577
as an Alk signaling transcriptional target.
CG4577
, which we named
Sparkly (Spar),
is expressed in a subset of Alk-positive neuroendocrine cells in the developing larval CNS, including circadian clock neurons. In agreement with our TaDa analysis, overexpression of the
Drosophila
Alk ligand Jeb resulted in increased levels of Spar protein in the larval CNS. We show that Spar protein is expressed in circadian (Clock) neurons, and flies lacking Spar exhibit defects in sleep and circadian activity control. In summary, we report a novel activity regulating neuropeptide precursor gene that is regulated by Alk signaling in the
Drosophila
CNS.
When and why does motor preparation arise in recurrent neural network models of motor control?
Authors: Schimel Marine , Kao Ta-Chu , Hennequin Guillaume
Published: May 2024

During delayed ballistic reaches, motor areas consistently display movement-specific activity patterns prior to movement onset. It is unclear why these patterns arise: while they have been proposed to seed an initial neural state from which the movement unfolds, recent experiments have uncovered the presence and necessity of ongoing inputs during movement, which may lessen the need for careful initialization. Here, we modelled the motor cortex as an input-driven dynamical system, and we asked what the optimal way to control this system to perform fast delayed reaches is. We find that delay-period inputs consistently arise in an optimally controlled model of M1. By studying a variety of network architectures, we could dissect and predict the situations in which it is beneficial for a network to prepare. Finally, we show that optimal input-driven control of neural dynamics gives rise to multiple phases of preparation during reach sequences, providing a novel explanation for experimentally observed features of monkey M1 activity in double reaching.
Serotonergic and dopaminergic neurons in the dorsal raphe are differentially altered in a mouse model for parkinsonism
Authors: Boi Laura , Johansson Yvonne , Tonini Raffaella , Moratalla Rosario , Fisone Gilberto , Silberberg Gilad
Published: May 2024

Parkinson’s disease (PD) is characterized by motor impairments caused by degeneration of dopamine neurons in the substantia nigra pars compacta. In addition to these symptoms, PD patients often suffer from non-motor co-morbidities including sleep and psychiatric disturbances, which are thought to depend on concomitant alterations of serotonergic and noradrenergic transmission. A primary locus of serotonergic neurons is the dorsal raphe nucleus (DRN), providing brain-wide serotonergic input. Here, we identified electrophysiological and morphological parameters to classify serotonergic and dopaminergic neurons in the murine DRN under control conditions and in a PD model, following striatal injection of the catecholamine toxin, 6-hydroxydopamine (6-OHDA). Electrical and morphological properties of both neuronal populations were altered by 6-OHDA. In serotonergic neurons, most changes were reversed when 6-OHDA was injected in combination with desipramine, a noradrenaline reuptake inhibitor, protecting the noradrenergic terminals. Our results show that the depletion of both noradrenaline and dopamine in the 6-OHDA mouse model causes changes in the DRN neural circuitry.
The conserved genetic program of male germ cells uncovers ancient regulators of human spermatogenesis
Authors: Brattig Correia Rion , Almeida Joana M. , Wyrwoll Margot J. , Julca Irene , Sobral Daniel , Misra Chandra Shekhar , Di Persio Sara , Guilgur Leonardo G. , Schuppe Hans-Christian , Silva Neide , Prudêncio Pedro , Nóvoa Ana , Leocádio Ana S. , Bom Joana , Laurentino Sandra , Mallo Moisés , Kliesch Sabine , Mutwil Marek , Rocha Luis M. , Tüttelmann Frank , Becker Jörg D. , Navarro-Costa Paulo
Published: May 2024

Male germ cells share a common origin across animal species, therefore they likely retain a conserved genetic program that defines their cellular identity. However, the unique evolutionary dynamics of male germ cells coupled with their widespread leaky transcription pose significant obstacles to the identification of the core spermatogenic program. Through network analysis of the spermatocyte transcriptome of vertebrate and invertebrate species, we describe the conserved evolutionary origin of metazoan male germ cells at the molecular level. We estimate the average functional requirement of a metazoan male germ cell to correspond to the expression of approximately 10,000 protein-coding genes, a third of which defines a genetic scaffold of deeply conserved genes that has been retained throughout evolution. Such scaffold contains a set of 79 functional associations between 104 gene expression regulators that represent a core component of the conserved genetic program of metazoan spermatogenesis. By genetically interfering with the acquisition and maintenance of male germ cell identity, we uncover 161 previously unknown spermatogenesis genes and three new potential genetic causes of human infertility. These findings emphasize the importance of evolutionary history on human reproductive disease and establish a cross-species analytical pipeline that can be repurposed to other cell types and pathologies.
Neutralizing gut-derived lipopolysaccharide as a novel therapeutic strategy for severe leptospirosis
Authors: Xie Xufeng , Chen Xi , Zhang Shilei , Liu Jiuxi , Zhang Wenlong , Cao Yongguo
Published: May 2024

Leptospirosis is an emerging infectious disease caused by pathogenic
Leptospira
spp. Humans and some mammals can develop severe forms of leptospirosis accompanied by a dysregulated inflammatory response, which often results in death. The gut microbiota has been increasingly recognized as a vital element in systemic health. However, the precise role of the gut microbiota in severe leptospirosis is still unknown. Here, we aimed to explore the function and potential mechanisms of the gut microbiota in a hamster model of severe leptospirosis. Our study showed that leptospires were able to multiply in the intestine, cause pathological injury, and induce intestinal and systemic inflammatory responses. 16S rRNA gene sequencing analysis revealed that
Leptospira
infection changed the composition of the gut microbiota of hamsters with an expansion of Proteobacteria. In addition, gut barrier permeability was increased after infection, as reflected by a decrease in the expression of tight junctions. Translocated Proteobacteria were found in the intestinal epithelium of moribund hamsters, as determined by fluorescence in situ hybridization, with elevated LPS levels in the serum. Moreover, gut microbiota depletion reduced the survival time, increased the leptospiral load, and promoted the expression of proinflammatory cytokines after
Leptospira
infection. Intriguingly, fecal filtration and serum from moribund hamsters both increased the transcription of
TNF-α
,
IL-1β
,
IL-10
, and
TLR4
in macrophages compared with those from uninfected hamsters. These stimulating activities were inhibited by LPS neutralization using polymyxin B. Based on our findings, we identified an LPS neutralization therapy that significantly improved the survival rates in severe leptospirosis when used in combination with antibiotic therapy or polyclonal antibody therapy. In conclusion, our study not only uncovers the role of the gut microbiota in severe leptospirosis but also provides a therapeutic strategy for severe leptospirosis.
Clearance of protein aggregates during cell division
Authors: Du Shoukang , Wang Yuhan , Chen Bowen , Xie Shuangshuang , Chan Kuan Yoow , Hay David C. , Chew Ting Gang
Published: May 2024

Protein aggregates are spatially organized and regulated in cells to prevent deleterious effects of proteostatic stress. Misfolding of proteins in the ER result in aggregate formation, but how the aggregates are processed especially during cell division is not well understood. Here, we induced proteostatic stress and protein aggregation using a proteostasis reporter, which is prone to misfolding and aggregation in the ER. Unexpectedly, we detected solid-like protein aggregates deposited mainly in the nucleus and surrounded by the ER membrane. The membrane-bound aggregates were then cleared as cells progressed through mitosis and cytokinesis. Aggregate clearance was depended on Hsp70 family chaperones in the ER, particularly BiP, and proteasomal activity. The clearance culminates at mitotic exit and required cyclin-dependent kinase 1 (Cdk1) inactivation but was independent of the anaphase-promoting complex (APC/C). Thus, dividing cells have the capacity to clear protein aggregates to maintain proteostasis in the newly divided cells, which could have implications for human disease development and aging.
A ventral hippocampal-lateral septum pathway regulates social novelty preference
Authors: Rashid Maha , Thomas Sarah , Isaac Jennifer , Karkare Sonia , Klein Hannah , Murugan Malavika
Published: May 2024

The ability to distinguish strangers from familiar individuals is crucial for the survival of most mammalian species. In humans, an inability to recognize kin and familiar individuals and engage in appropriate behaviors is associated with several types of dementia, including Alzheimer’s disease. Mice preferentially spend more time investigating a novel individual relative to a familiar individual. Yet, how social novelty related information drives increased investigation of the novel animal remains poorly understood. Recent evidence has implicated the ventral hippocampus (vHPC) as a key node in encoding information about conspecific identity. Of particular interest are vHPC projections to the lateral septum (LS), a region that has been implicated in driving a wide range of motivated social behaviors. In this study using chemogenetics, optogenetics and monosynaptic rabies tracing, we identified a novel vHPC-LS-ventral tegmental area (VTA) pathway that is necessary for mice to preferentially investigate novel conspecifics. Using monosynaptic rabies tracing, we established that LS neurons make direct monosynaptic connections onto dopaminergic neurons in the VTA. Thus, we have identified a potential pathway via which conspecific identity could be transformed to drive motivated social behaviors.
Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data
Authors: Hall Michael B. , Wick Ryan R. , Judd Louise M. , Nguyen An N. T. , Steinig Eike J. , Xie Ouli , Davies Mark R. , Seemann Torsten , Stinear Timothy P. , Coin Lachlan J. M.
Published: May 2024

Variant calling is fundamental in bacterial genomics, underpinning the identification of disease transmission clusters, the construction of phylogenetic trees, and antimicrobial resistance prediction. This study presents a comprehensive benchmarking of SNP and indel variant calling accuracy across 14 diverse bacterial species using Oxford Nanopore Technologies (ONT) and Illumina sequencing. We generate gold standard reference genomes and project variations from closelyrelated strains onto them, creating biologically realistic distributions of SNPs and indels.Our results demonstrate that ONT variant calls from deep learning-based tools delivered higher SNP and indel accuracy than traditional methods and Illumina, with Clair3 providing the most accurate results overall. We investigate the causes of missed and false calls, highlighting the limitations inherent in short reads and discover that ONT’s traditional limitations with homopolymerinduced indel errors are absent with high-accuracy basecalling models and deep learning-based variant calls. Furthermore, our findings on the impact of read depth on variant calling offer valuable insights for sequencing projects with limited resources, showing that 10x depth is sufficient to achieve variant calls that match or exceed Illumina.In conclusion, our research highlights the superior accuracy of deep learning tools in SNP and indel detection with ONT sequencing, challenging the primacy of short-read sequencing. The reduction of systematic errors and the ability to attain high accuracy at lower read depths enhance the viability of ONT for widespread use in clinical and public health bacterial genomics.
USP22 as a key regulator of glycolysis pathway in osteosarcoma: insights from bioinformatics and experimental approaches
Authors: Zhang Qiao , Zhu Jinwei , Xie Jian , Gu Yurong , Chen Lu
Published: May 2024

Background

Osteosarcoma is the most common primary malignant bone tumor, but its pathogenesis remains unclear. Ubiquitin-specific processing peptidase 22 (USP22) is reported to be highly expressed and associated with tumor malignancy and prognosis in cancers. However, the role and mechanism of USP22 in osteosarcoma is not fully understood. This study aims to investigate the function and potential mechanism of USP22 in osteosarcoma using bioinformatics analysis combined with experimental validation.

Methods

We first integrated transcriptomic datasets and clinical information of osteosarcoma from GEO and TCGA databases to assess the expression and prognostic value of USP22 in osteosarcoma. Then, differential expression analysis and weighted gene co-expression network analysis (WGCNA) were conducted to identify USP22-related co-expressed genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to explore the biological functions and signaling pathways of USP22 co-expressed genes. To validate the accuracy of bioinformatics analyses, we downregulated USP22 expression in osteosarcoma cell line Sao-2 using siRNA and assessed its effect on cell proliferation, migration, invasion, apoptosis, and regulation of key signaling pathways.

Results

We found that USP22 was highly expressed in osteosarcoma tissues and correlated with poor prognosis in osteosarcoma patients. USP22 also showed potential as a diagnostic marker for osteosarcoma. In addition, 344 USP22-related co-expressed genes were identified, mainly involved in signaling pathways such as glycolysis, oxidative phosphorylation, spliceosome, thermogenesis, and cell cycle. The in vitro experiments confirmed the accuracy and reliability of bioinformatics analyses. We found that downregulation of USP22 could inhibit Sao-2 cell proliferation, migration, invasion, and induce apoptosis. Furthermore, downregulation of USP22 significantly reduced aerobic glycolysis levels in Sao-2 cells and inhibited the expression of key enzymes and transporters in aerobic glycolysis pathways such as HK2, PKM2, and GLUT1.

Conclusions

USP22 plays a critical role in the occurrence, development, and prognosis of osteosarcoma. USP22 could influence Sao-2 cell proliferation, apoptosis, migration, and invasion by regulating the glycolysis pathway, thereby promoting osteosarcoma progression. Therefore, USP22 may be a potential therapeutic target for the treatment of osteosarcoma.
CONSUMERS’ OPINIONS ON THE USEFULNESS, UNDERSTANDABILITY, AND RELIABILITY OF PRODUCT CLAIMS ON NATURAL COSMETICS PACKAGING
Authors: KOZIK Natalia , CHOLEWA-WÓJCIK Agnieszka , JAROSSOVÁ Małgorzata
Published: May 2024

Packaging and its integral elements can be among the carriers of product claims, which often encourage consumers to purchase cosmetics, and many make purchasing decisions based on them. There is, therefore, a tendency to put an increasing number of claims on packaging; these, according to requirements, should be useful, understandable, and reliable. This article aims to determine the importance of information placed on packaging during the purchase of natural cosmetics in comparison with other packaging elements, and to assess the usefulness, understandability, and reliability of selected groups of product claims placed on natural cosmetics packaging. The results confirm that the information placed on the packaging of natural cosmetics is an important element to which consumers pay attention. The most useful, understandable, and reliable claims are performance claims, ingredient-related claims, and environmental claims.
The first observation of 1J(SnC) coupling constants in tin–carbon double‐bond compounds
Authors: Mizuhata Yoshiyuki , Tokitoh Norihiro
Published: November 2010

The 1J(SnC)s in the tin–carbon double‐bond systems were determined for the first time. These results were supported by theoretical calculations, showing the high s‐character of the SnC double bonds. The new findings obtained will be of great use in the development of tin‐containing functionalized materials. Copyright © 2010 John Wiley & Sons, Ltd.
Novel low‐dielectric‐constant copolyimide thin films composed with SiO2 hollow spheres
Authors: Yuan Yuan , Lin Bao‐Ping , Sun Yue‐ming
Published: November 2010

A series of copolyimide/SiO2 hollow sphere thin films were prepared successfully based on bis[3,5‐dimethyl‐4‐(4‐aminophenoxy)phenyl]methane and 9,9‐bis(4‐(4‐aminophenoxy)phenyl)fluorene (molar ratio = 3 : 1) as diamine, and 4,4′‐(4,4′‐isopropylidenediphenoxy)bis(phthalic anhydride) as dianhydride, with different wt % SiO2 hollow sphere powder with particle size 500 nm. Some films possessed excellent dielectric properties, with ultralow dielectric constants of 1.8 at 1 MHz. The structures and properties of the thin films were measured with Fourier transform infrared spectra, scanning electron microscope, thermogravimetric analysis, and dynamic mechanical thermal analysis. The polyimide (PI) films exhibited glass‐transition temperatures in the range of 209– 273°C and possessed initial thermal decomposition temperature reaching up to 413–477°C in air and 418–472°C in nitrogen. Meanwhile, the composite films were also exhibited good mechanical properties. © 2010 Wiley Periodicals, Inc. J Appl Polym Sci, 2011
Solid State Electrochemical Study of Oxygen Nonstoichiometry and Transport in Superconducting Ceramics
Authors: Schoch B. , Weppner W.
Published: November 2010

Zirconia based solid oxygen ion conductors were employed to control the oxygen content and activity of YBa2Cu3O6+x at elevated temperatures at which the material is commonly prepared and the superconducting properties are adjusted. Experimental problems of the reactivity between the electrolyte and the sample and the exchange of oxygen with the surrounding gas phase due to the high oxygen equilibrium partial pressure became eliminated. The lowest oxygen concentration appears at the composition YBa2Cu3O6 which corresponds at the same time to the ideal stoichiometry. The oxygen activity increases rapidly for small oxygen excess concentrations and turns finally into a very slow increase at large stoichiometric deviations; this is related to a semiconductor‐metal transition. The maximum oxygen concentration is limited to 60% of the structurally expected amount. The Wagner factor drops from nearly 200 at ideal stoichiometry to a value close to 1 at large oxygen excess indicating the increasing role of screening effects by large hole concentrations which are generated to compensate the negative charge of the oxygen ions. Accordingly, the chemical diffusion coefficient of YBa2Cu3O6%plus;x drops rapidly with increasing deviation from the ideal stoichiometry from about to 10−9.8 to 10−12.3 cm2 at 700°C. The diffusivity is less stoichiometry dependent, but still decreases with increasing oxygen content. The partial ionic (minority) conductivity is several orders of magnitude lower than in ceramic solid electrolytes.
Focused Directed Evolution of Pentaerythritol Tetranitrate Reductase by Using Automated Anaerobic Kinetic Screening of Site‐Saturated Libraries
Authors: Hulley Martyn E. , Toogood Helen S. , Fryszkowska Anna , Mansell David , Stephens Gill M. , Gardiner John M. , Scrutton Nigel S.
Published: November 2010

This work describes the development of an automated robotic platform for the rapid screening of enzyme variants generated from directed evolution studies of pentraerythritol tetranitrate (PETN) reductase, a target for industrial biocatalysis. By using a 96‐well format, near pure enzyme was recovered and was suitable for high throughput kinetic assays; this enabled rapid screening for improved and new activities from libraries of enzyme variants. Initial characterisation of several single site‐saturation libraries targeted at active site residues of PETN reductase, are described. Two mutants (T26S and W102F) were shown to have switched in substrate enantiopreference against substrates (E)‐2‐aryl‐1‐nitropropene and α‐methyl‐trans‐cinnamaldehyde, respectively, with an increase in ee (62 % (R) for W102F). In addition, the detection of mutants with weak activity against α,β‐unsaturated carboxylic acid substrates showed progress in the expansion of the substrate range of PETN reductase. These methods can readily be adapted for rapid evolution of enzyme variants with other oxidoreductase enzymes.
Catalyst Characterization with O2‐TPD, N2 ‐,Kr‐sorption and SEM Using the Example of the Epoxidation of 1,3‐Butadiene
Authors: Otto T. N. , Dinjus E. , Hagen V. , Puls A.
Published: November 2010

Die temperaturprogrammierte O2‐Desorption (O2‐TPD), die N2‐ und Kr‐ Gassorption sowie die Raster‐Elektronen‐Mikroskopie (REM) sind bedeutende Analysemethoden in der Katalysechemie. Am Beispiel eines korund‐ und eines calciumhexaaluminathaltigen Trägermaterials werden die Methoden angewendet und das Potenzial der eingesetzten Katalysatoren hinsichtlich der Oberflächeneigenschaften und der damit verbundenen Aktivität aufgezeigt. Welches der beiden geträgerten Katalysatorsysteme für die Ag‐katalysierte Epoxidierung von 1,3‐Butadien zu 3,4‐Epoxy‐1‐buten vorteilhafter ist, wird im Rohrreaktor getestet.
Fitting Solid Sponges into a Reactor Tube Concerning the Partial Oxidation of o‐Xylene as an Example
Authors: Mülheims Philip , Marz Stefan , Müller Steffen Peter , Kraushaar‐Czarnetzki Bettina
Published: November 2010

Der Einsatz fester, offenporiger Schwämme in verfahrenstechnischen Anwendungen verspricht viele Vorteile. Bedingt durch ihre Struktureigenschaften weisen sie einen geringen Druckverlust und einen verbesserten Wärme‐ und Stofftransport im Vergleich zu herkömmlichen Partikelschüttungen auf. So wurde in den vergangenen Jahren in zahlreichen Studien das Potenzial dieser neuen Struktur aufgezeigt. In den wenigsten Veröffentlichungen wird jedoch auf die Art der Einpassung fester Schwämme in ihre Umgebung eingegangen. Im Rahmen dieser Arbeit wird anhand des Einsatzes keramischer Schwämme als Katalysatorträger in der partiellen Oxidation von o‐Xylol gezeigt, welche Bedeutung die Einpassung in Bezug auf das Prozess‐, das Umsatzverhalten und den Wärmetransport hat.
Stochastic model for living radical polymerisation of styrene initiated by epoxide radical ring opening
Authors: Al‐Harthi Mamdouh
Published: November 2010

A stochastic model was developed to simulate the polymerisation kinetics and the detailed microstructure of the resulting polymers made by the living radical polymerisation of styrene initiated by epoxide radical ring opening. The model was used to predict monomer conversion, average molecular weight, polydispersity index, and molecular weight distribution as a function of polymerisation time. Simulations were used to explore the effects of rate constant values on chain microstructures and polymer properties and validated with experimental data published in the literature. It was found that some parameters, such as the exchange rate constant, have no significant effect on the polymerisation kinetics, whereas major effects were observed when other rate constants, such as the reduction rate constant, were changed.
Crystallization‐Driven Asymmetric Synthesis of Pyridine‐β‐nitroalcohols via Discovery‐Oriented Self‐Resolution of a Dynamic System (Eur. J. Org. Chem. 33/2010)
Authors: Angelin Marcus , Vongvilai Pornrapee , Fischer Andreas , Ramström Olof
Published: November 2010

The cover picture shows how diastereoselective crystallization selects and amplifies a certain pyridine‐nitroalcohol from a dynamic system of chemical compounds (symbolized by puzzle pieces). This serendipitous finding demonstrates the potential of working with dynamic systems for discovery purposes in general and provides an effective asymmetric synthesis protocol for pyridine‐nitroalcohols in particular. Details are discussed in the Short Communication by O. Ramström et al. on p. 6315 ff.
Performance of La2–xSrxCo0.5Ni0.5O4±δ as an Oxygen Electrode for Solid Oxide Reversible Cells
Authors: Laguna‐Bercero M. A. , Kinadjan N. , Sayers R. , El Shinawi H. , Greaves C. , Skinner S. J.
Published: November 2010

La2 – xSrxCo0.5Ni0.5O4 ± δ (LSCN) is presented as a novel electrode for both solid oxide fuel cells (SOFCs) and solid oxide electrolysis cells (SOECs). LSCN/10Sc1CeSZ (scandia and ceria stabilised zirconia)/LSCN symmetrical cells were fabricated and characterised by AC impedance spectroscopy under different oxygen partial pressures at temperatures of up to 900 °C. At 850 °C polarisation resistances of 5.15 and 5.74 Ω cm2 were found applying air and oxygen, respectively. Electrolysis and fuel cell j–V experiments were also performed at temperatures between 700 and 850 °C using a LSCN/10Sc1CeSZ/Ni‐YSZ. Electrochemical results showed that the cell performs equally in both SOFC and SOEC modes. Detailed results in terms of performance are presented and discussed. LSCN is presented as a good candidate for both SOFC and SOEC. The similar performance obtained for j–V (current density–voltage) curves in electrolysis and fuel cell operation mode is thought to be related to the flexible oxygen non‐stoichiometry of the LSCN (K2NiF4‐type structure).
Finding maximal transcriptome differences between reprotoxic and non‐reprotoxic phthalate responses in rat testis
Authors: Yuan Xiaolian , Jonker Martijs J. , de Wilde Jillian , Verhoef Aart , Wittink Floyd R.A. , van Benthem Jan , Bessems Jos G. , Hakkert Betty C. , Kuiper Raoul V. , van Steeg Harry , Breit Timo M. , Luijten Mirjam
Published: November 2010

The chemical legislation of the EU, Registration, Evaluation, and Authorization of Chemicals (REACH), stipulates that about 30 000 chemical substances are to be assessed on their possible risks. Toxicological evaluation of these compounds will at least partly be based on animal testing. In particular, the assessment of reproductive toxicity is a very complicated, time‐consuming and animal‐demanding process. Introducing microarray‐based technologies can potentially refine in vivo toxicity testing. If compounds of a distinct chemical class induce reproducible gene‐expression responses with a recognizable overlap, these gene‐expression signatures may indicate intrinsic features of certain compounds, including specific toxicity. In the present study, we have set out the first steps towards this approach for the reproductive toxicity of phthalates. Male rats were treated with a single dose of either reprotoxic or non‐reprotoxic phthalates, and were analyzed 24 h afterwards. Subsequently, histopathological and gene‐expression profiling analyses were performed. Despite ambiguous histopathological observations, we were able to identify genes with differential expression profiles between the reprotoxic phthalates and the non‐reprotoxic counterparts. This shows that differences in gene‐expression profiles, indicative of the type of exposure, may be detected earlier, or at lower doses, than classical pathological endpoints. These findings are promising for ‘early warning’ biomarker analyses and for using toxicogenomics in a category approach. Ultimately, this could lead to a more cost‐effective approach for prioritizing the toxicity testing of large numbers of chemicals in a short period of time in hazard assessment of chemicals, which is one of the objectives of the REACH chemical legislation. Copyright © 2010 John Wiley & Sons, Ltd.
Sciatic nerve repair by reinforced nerve conduits made of gelatin–tricalcium phosphate composites
Authors: Yang Yi‐Chin , Shen Chiung‐Chyi , Cheng Hsu‐Chen , Liu Bai‐Shuan
Published: November 2010

This study proposes a biodegradable GGT composite nerve guide conduit containing genipin–cross‐linked gelatin and tricalcium phosphate (TCP) ceramic particles in peripheral nerve regeneration. The proposed genipin–cross‐linked gelatin annexed with TCP ceramic particles (GGT) conduit was dark bluish and round with a rough and compact surface. Water uptake and swelling tests indicated that the hydrated GGT conduit exhibited increased stability with not collapsing or stenosis. The GGT conduit had higher mechanical properties than the genipin–cross‐linked gelatin without TCP ceramic particles (GG) conduit and served as a better nerve guide conduit. Cytotoxicity tests revealed that the GGT conduit was not toxic and that it promoted the viability and growth of neural stem cells. The experiments in this study confirmed the effectiveness of the GGT conduit as a guidance channel for repairing a 10‐mm gap in rat sciatic nerve. Walking track analysis showed a significantly higher sciatic function index score and better toe spreading development in the GGT group than in the silicone group 8 weeks after implantation. Gross examination revealed that the diameter of the intratubular newly formed nerve fibers in GGT conduits exceeded those in silicone tubes after the implantation period. Histological observations revealed that the morphology and distribution patterns of nerve fibers in the GGT conduits at 8 weeks after implantation were similar to those of normal nerves. The quantitative results indicated the superiority of the conduits over the silicone tubes. Motor functional and histomorphometric assessments demonstrate that the proposed GGT conduit is a suitable candidate for peripheral nerve repair. © 2010 Wiley Periodicals, Inc. J Biomed Mater Res Part A, 2011.
Genipin‐crosslinked microcarriers mediating hepatocellular aggregates formation and functionalities
Authors: Lau Ting Ting , Wang Chunming , Png Sze Wei , Su Kai , Wang Dong‐An
Published: November 2010

In engineered regenerative medicine, various types of scaffolds have been customized to pursue the optimal environment for different types of therapeutic cells. In liver therapeutic research, hepatocytes require attachment to solid anchors for survival and proliferation before they could grow into cellular aggregates with enhanced functionalities. Among the various biomaterials scaffolds and vehicles, microspherical cell carriers are suited to these requirements. Individual spheres may provide two‐dimensional (2D) cell‐affinitive surfaces for cell adhesion and spreading; whereas multiple microcarriers may form three‐dimensional (3D) matrices with inter‐spherical space for cell expansion and multicellular aggregation. In this study, we culture human liver carcinoma cell line (HepG2) cells on genipin‐crosslinked gelatin microspheres of two different sizes. Results suggest that both microcarriers support cell adhesion, proliferation, and spontaneous formation of hepatocellular aggregates, among which the spheres with bigger size (200–300 μm) seem more favorable than the smaller ones in terms of aggregate formation and liver specific functionalities. These findings suggest that the genipin‐crosslinked microcarrier is a competent vehicle for liver cell delivery. © 2010 Wiley Periodicals, Inc. J Biomed Mater Res Part A, 2010.
Hamel‐isomorphic images of the unit ball
Authors: Cichoń Jacek , Szczepaniak Przemysław
Published: November 2010

In this article we consider linear isomorphisms over the field of rational numbers between the linear spaces ℝ2 and ℝ. We prove that if f is such an isomorphism, then the image by f of the unit disk is a strictly nonmeasurable subset of the real line, which has different properties than classical non‐measurable subsets of reals. We shall also consider the question whether all images of bounded measurable subsets of the plane via a such mapping are non‐measurable (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Pulse radiolysis studies of 2‐ and 3‐hydroxybenzyl alcohols: inhibition of dehydration of ·OH‐(hydroxybenzyl alcohols) adducts by H2PO4− ions
Authors: Dhiman Surajdevprakash B. , Naik Devidas B.
Published: November 2010

Reactions of ·OH/O.− radicals and H‐atoms as well as specific oxidants such as Cl2.− and N3· radicals have been studied with 2‐ and 3‐hydroxybenzyl alcohols (2‐ and 3‐HBA) at various pH using pulse radiolysis technique. At pH 6.8, ·OH radicals were found to react quite fast with both the HBAs (k = 7.8 × 109 dm3 mol−1 s−1 with 2‐HBA and 2 × 109 dm3 mol−1 s−1 with 3‐HBA) mainly by adduct formation and to a minor extent by H‐abstraction from CH2OH groups. ·OH‐(HBA) adduct were found to undergo decay to give phenoxyl type radicals in a pH dependent way and it was also very much dependent on buffer‐ion concentrations. It was seen that ·OH‐(2‐HBA) and ·OH‐(3‐HBA) adducts react with HPO42− ions (k = 2.1 × 107 and 2.8 × 107 dm3 mol−1 s−1 at pH 6.8, respectively) giving the phenoxyl type radicals of HBAs. At the same time, this reaction is very much hindered in the presence of H2PO ions indicating the role of phosphate ion concentration in determining the reaction pathway of ·OH adduct decay to final stable product. In the acidic region adducts were found to react with H+ ions. At pH 1, reaction of ·OH radicals with HBAs gave exclusively phenoxyl type radicals. Proportion of the reducing radicals formed by H‐abstraction pathway in ·OH/O
.− reactions with HBAs was determined following electron transfer to methyl viologen. H‐atom abstraction is the major pathway in O
.− reaction with HBAs compared to ·OH radical reaction. H‐atom reaction with 2‐ and 3‐HBA gave transient species which were found to transfer electron to methyl viologen quantitatively. Copyright © 2010 John Wiley & Sons, Ltd.
Structural, electronic, and optical properties of doubly ortho‐linked quinoxaline/diphenylfluorene hybrids
Authors: Ran Xue‐Qin , Feng Ji‐Kang , Zou Lu‐Yi , Ren Ai‐Min , Sun Chia‐Chung
Published: November 2010

The optical and electronic properties of spiro‐fluorene‐dibenzosuberene[d](1,4‐bis(4‐t‐butylphenyl)quinoxaline) 1a, spiro‐fluorene‐dibenzosuberene[d](1,4‐bis(4‐methoxyphenyl)quinoxaline) 1b, spiro‐fluorene‐dibenzosuberene[d](1‐(4‐(N,N‐diphenylamino)‐phenyl)‐quinoxaline) 1c, spiro‐fluorene‐dibenzosuberene[d](1,4‐bis(methylphenylamino)quinoxaline) 1d, spiro‐fluorene‐dibenzosuberene[d](1,4‐bis(methyl‐(4‐methylphenyl)amino)quinoxaline) 1e, spiro‐fluorene‐dibenzosuberene[d](1,4‐bis(methyl‐(4‐methoxyphenyl)amino)quinoxaline) 1f, 5,8‐bis‐(4‐methoxy‐phenyl)‐2,3‐diphenyl‐quinoxaline 1, and N,N,N',N'‐tetraphenyl‐ 5h‐dibenzo[a,d]cycloheptene‐3,7‐diamine 2 were investigated theoretically in this paper. The doubly ortho‐linked quinoxaline/diphenylfluorene hybrids 1a–1f show great potential as bipolar materials for the design of optimized organic light‐emitting diodes (OLEDs). Density functional theory (DFT) and ab initio HF were employed to study the geometric and electronic structures of these molecules in the ground state, and ab initio CIS were used to investigate the lowest singlet excited states. The radiative lifetime (τ) and the maximal absorption/emission wavelength of these molecules were calculated within time‐dependent DFT (TDDFT). The results show that the LUMO energies of the bipolar molecules 1a–1d are all lower than those of 1 and 2, consequently, the electron‐accepting abilities of 1a–1d are greatly improved. The HOMO energies of 1c–1f are all higher than those of 1 and 2, suggesting that the hole‐creating abilities of 1c–1f become better. Also, the results reveal that the HOMO and LUMO energies, energy gaps, IP, EA, as well as the maximal absorption/emission spectra can be tuned feasibly by changing the C5‐ and C8‐substituents in the quinoxaline backbone of these molecules. As expected, these materials show different emission spectra varying from 436.11 to 715.47 nm. Copyright © 2010 John Wiley & Sons, Ltd.
A study of the surface characteristics of homemade ultrasound phantoms
Authors: Althoff Seth , Sudhir Amita , Woods William A.
Published: November 2010

Objectives

Expertise in the utilization of procedure-guided ultrasonography has become increasingly important within the field of Emergency Medicine. Consequently, ultrasound phantoms have been implemented as simulation tools in introductory courses. This study of the surface behavior of gelatin blocks was performed to describe the behaviors of phantoms for ultrasound training.

Methods

Gelatin blocks of varying preparation techniques and component concentrations were tested on exposed and latex-coated surfaces to determine the variation in surface disruption and force–displacement characteristics of each of the surfaces tested.

Results

Gelatin blocks made at a cooler temperature than current recommendations have a more durable surface. Latex-coated blocks have the most durable surface.

Conclusions

Gelatin blocks made at a lower temperature than current recommendations result in a more desirable phantom. A re-usable latex coating can add to the durability of the phantom.
The DNA methylome
Authors: Pelizzola Mattia , Ecker Joseph R.
Published: November 2010

Complete DNA methylomes for several organisms are now available, helping clarify the evolutionary story of this epigenetic mark and its distribution in key genomic elements. Nonetheless, a complete understanding of its role, the mechanisms responsible for its establishment and maintenance, and its cross talk with other components of cellular machinery remains elusive.
Fucosidosis in a domestic shorthair cat
Authors: Arrol Lorna P. , Kerrins Annette M. , Yamakawa Yoshika , Smith Peter M.
Published: November 2010

This paper documents the first reported case of fucosidosis in a cat. The cat presented with signs of forebrain and cerebellar dysfunction and a magnetic resonance imaging scan of the brain suggested a degenerative or metabolic disease process. A fine needle aspirate of grossly normal lymph nodes revealed vacuolated lymphocytes and a renal biopsy of an irregular shaped kidney identified vacuolated tubular epithelial cells. A white cell lysosomal enzyme screen revealed negligible α-fucosidase activity. Fucosidosis should be considered in the differential diagnosis of young cats with cerebellar dysfunction and must be added to the list of lysosomal storage diseases affecting the cat.
Ecosystems and Biogeochemical Cycling in a Changing Ocean: Fifth Annual Ocean Carbon and Biogeochemistry Summer Workshop; La Jolla, California, 19–22 July 2010
Authors: Benway Heather M. , Doney Scott C.
Published: November 2010

The Ocean Carbon and Biogeochemistry (OCB) program is a coordinating body for the U.S. research community that focuses on the ocean's role as a component of the global Earth system, bringing together research in geochemistry, ocean physics, and ecology. The fifth annual Ocean Carbon and Biogeochemistry summer workshop, sponsored by the U.S. National Science Foundation, NASA, and the National Oceanic and Atmospheric Administration, convened 107 participants at the Scripps Institution of Oceanography, in California.
Honors
Authors: Anonymous
Published: November 2010

During the height of the Deepwater Horizon oil spill disaster, I joined a group of engineers and other scientists to discuss the evidence for an oil plume, at least 22 miles long and about a mile wide, floating 3000 feet beneath the surface of the Gulf of Mexico.

As the chemist in the group, I wondered aloud about how we could exploit the aqueous solubilities of the petroleum hydrocarbons, benzene, toluene, ethylbenzene, and total xylenes to understand plume formation. I suspected the key to knowledge lay in the plume's chemical properties.
Discussing Progress in Understanding Ice Sheet—Ocean Interactions: Advanced Climate Dynamics Course 2010: Ice Sheet—Ocean Interactions; Lyngen, Norway, 8–19 June 2010
Authors: Borreguero Laura Herraiz , Mottram Ruth , Cvijanovic Ivana
Published: November 2010

Sea level rise is one of many expected consequences of climate change, with accompanying complex social and economic challenges. Major uncertainties in sea level rise projections relate to the response of ice sheets to sea level rise and the key role that interactions with the ocean may play. Recognizing that probably no comprehensive curriculum currently exists at any single university that covers this novel and interdisciplinary subject, the Advanced Climate Dynamics Courses (ACDC) team brought together a group of 40 international students, postdocs, and lecturers from diverse backgrounds to provide an overview and discussion of state‐of‐the‐art research into ocean—ice sheet interactions and to propose research priorities for the next decade.

Among the key issues addressed were small‐scale processes near the Antarctic ice shelves and Greenland outlet glaciers. These are fast changing components in the climate system, often related to large‐scale forcings (atmospheric teleconnections and oceanic circulation). Progress in understanding and modeling is hampered by the range of scales involved, the lack of observations, and the difficulties in constraining, initializing, and providing adequate boundary conditions for ice sheet and ocean models.
AGU Blogosphere: A New Community of Earth and Space Science Blogs
Authors: Viñas Maria‐José
Published: November 2010

Less than a year ago, AGU had yet to explore the world of science blogging. Now AGU not only has three blogs of its own but also has launched the AGU Blogosphere, a network of independent Earth and space science blogs hosted under the Union's umbrella. The new network of blogs, composed of seven external blogs written by scientists and covering topics including planetary exploration, landslides, Washington, D.C.—area geology, volcanoes, climate change, and more, can now be found together with the in‐house blogs at http://blogs.agu.org.

It's been a fast, exciting immersion into the blogosphere for AGU. Efforts began with the 2009 Fall Meeting blog, run by AGU staff with the invaluable help of science writing students at University of California, Santa Cruz and New York's Columbia University. This successful experience inspired AGU outreach staff to make a permanent meetings blog, which regularly covers the science presented at AGU meetings.
New AGU Journal Editors Appointed
Authors: Major Barbara
Published: November 2010

New editors have been appointed for Geophysical Research Letters, Global Biogeochemical Cycles, JGR‐Oceans, JGR‐Planets, and JGR‐Earth Surface.

Geophysical Research Letters welcomes Benoît Lavraud (Centre d'Etude Spatiale des Rayonnements, Toulouse, France) and Peter Strutton (University of Tasmania, Hobart, Australia). Lavraud's area of expertise is space sciences, and Strutton's is ocean sciences.
The dynamic consequences of invasion: negative plant-soil feedbacks on natives increase ver the time course of invasion
Authors: Schultheis Elizabeth , Lau Jennifer
Published: November 2010

Background/Questions/Methods

*Exotic species can negatively impact native community members, directly through interference competition, or indirectly by altering interactions between native species and other species such as pathogens and mutualists. Soil microbial communities have been shown to respond to invasive species, yet are relatively stable and may take time to respond to perturbations. For this reason, microbe-mediated effects of invasives on natives may take time to develop and may change throughout the invasion process. Few studies have investigated how species interactions between natives and exotics change during invasions.Acer platanoides was introduced into the US from Europe in 1756 and has since invaded intact forests, lowering understory diversity and inhibiting native tree species regeneration. We hypothesize that A. platanoides invasion will decrease seedling survival in the native A. saccharum by changing the soil microbial community through plant-soil feedbacks (PSF), and this relationship will intensify over the course of an invasion. We collected soil samples from beneath the canopies of both species co-occurring in Michigan forests that had been invaded by A. platanoides for varying time periods. In the greenhouse, we inoculated seedlings of both species with the microbial communities to determine how the soil community affects seedling survival and growth.*b)

Results/Conclusion

*The microbe-mediated negative effects of A. platanoides on survival of the native congener A. saccharum increased with increasing invasion age (negative correlation between invasion age and A. saccharum survival; r = -0.806, R^2^ = 0.65, p = 0.032). This result was not related to A. platanoides density, suggesting that age of invasion drives this pattern. Contrastingly, invasion age did not significantly influence survival of A. platanoides seedlings, indicating that A. platanoides’ PSF impacts native species but not on conspecific regeneration. Overall, A. platanoides seedlings had increased growth (more and larger leaves) when grown in soil communities collected from the native A. saccharum, but A. saccharum seedlings had reduced growth when grown in conspecific soil (p = 0.044). These results suggest that invasive species may have increased performance in exotic ranges by their ability to modify the soil microbial community in a manner that suppresses the growth of native species.We show the microbial community cultivated by an invader alters the performance of a native plant species, and this effect increases over the course of an invasion. In future work, we plan to identify changes in microbial community composition and the relative abundances of mutualists versus antagonists in response to invasion to identify potential mechanisms.
Coexistence of grazed and grazing excluded patches increases plant and invertebrate diversity in a Mediterranean oak woodland
Authors: Bugalho Miguel , Xavier Lecomte , Caldeira Maria , Gonçalves Merícia , Branco Manuela
Published: November 2010

Grazing is a global, dominant land use affecting biodiversity and ecosystem processes. In Mediterranean ecosystems grazing is a major ecological and evolutionary driver but, surprisingly, there is little information on the use of grazing as a tool to manage biodiversity in these ecosystems. We conducted an experiment to assess if the coexistence of grazing and grazing-excluded patches would increase plant and invertebrate diversity in a Mediterranean evergreen oak woodland. Plant community traits were different between treatments. Plant and litter biomass was higher, and the proportion of bare ground was lower, in grazing-excluded plots. Grazing affected functional diversity with legumes, invertebrate detritivores and sup sucking insects being more abundant in ungrazed plots. There were no differences between treatments in the number of species but there were plant species and invertebrate taxa recorded in grazed or grazing excluded plots, only. Ant communities were functionally different between treatments. Honeydew ant eaters were associated with ungrazed and higher plant biomass plots, and seed-eater as well as aggressive predator ant species were associated with grazed, more open habitat, plots. Management practices aiming to maintain grazing and grazing-excluded patches can increase habitat heterogeneity and promote diversity at the estate level.