bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic tools for reliable gene expression and recombineering in Pseudomonas putida
Authors: Cook Taylor B , Rand Jacqueline M , Nurani Wasti , Courtney Dylan K , Liu Sophia A , Pfleger Brian F
Published: January 2018

Pseudomonas putida is a promising bacterial host for producing natural products, such as polyketides and nonribosomal peptides. In these types of projects, researchers need a genetic toolbox consisting of plasmids, characterized promoters, and techniques for rapidly editing the genome. Past reports described constitutive promoter libraries, a suite of broad host range plasmids that replicate in P. putida, and genome-editing methods. To augment those tools, we have characterized a set of inducible promoters and discovered that IPTG-inducible promoter systems have poor dynamic range due to overexpression of the LacI repressor. By replacing the promoter driving lacI expression with weaker promoters, we increased the fold induction of an IPTG-inducible promoter in P. putida KT2440 to 80-fold. Upon discovering that gene expression from a plasmid was unpredictable when using a high-copy mutant of the BBR1 origin, we determined the copy numbers of several broad host range origins and found that plasmid copy numbers are significantly higher in P. putida KT2440 than in the synthetic biology workhorse, Escherichia coli. Lastly, we developed a λRed/Cas9 recombineering method in P. putida KT2440 using the genetic tools that we characterized. This method enabled the creation of scarless mutations without the need for performing classic two-step integration and marker removal protocols that depend on selection and counterselection genes. With the method, we generated four scarless deletions, three of which we were unable to create using a previously established genome-editing technique.
Efficacy in the use of local anesthesia in patients with surgical intervention for the resolution of anorectal pathologies
Authors: Dowling Victoria , Cortez Julio
Published: January 2018

A prospective, comparative, longitudinal study was conducted in the period from April 2016 to January 2017 in order to determine the efficacy of local anesthesia for the surgical resolution of anorectal pathologies in surgically operated patients who attended the General University Hospital “Luis Gomez Lopez. Thus, the population was composed of patients with anorectal pathologies of low complexity, with no previous anorectal surgical history (Hemorrhoids, anal fissure, perianal fistula, hypertrophic anal papilla, perianal condyloma acuminata), which were agreed to be included in this study, without contraindications for use of local anesthesia. A non-probabilistic, intentional sample was made up of 30 patients and the anesthetic protocol was administered following an anesthetic protocol of perianal local anesthesia using anesthetic mixture (70% of 2% lidocaine + 30% of 0.5% bupivacaine) quantifying pain tolerance during the intraoperative period on the first and fifth postoperative days, as well as any adverse effects. The results were expressed in absolute numbers and percentages; a good tolerance to pain was observed with some differences related to the sex of the individuals studied; no complications were observed.
Electro‐tactile stimulation (ETS) enhances cochlear‐implant Mandarin tone recognition
Authors: Huang Juan , Chang Janice , Zeng Fan‐Gang
Published: January 2018

Objective

Electro‐acoustic stimulation (EAS) is an effective method to enhance cochlear‐implant performance in individuals who have residual low‐frequency acoustic hearing. To help the majority of cochlear implant users who do not have any functional residual acoustic hearing, electro‐tactile stimulation (ETS) may be used because tactile sensation has a frequency range and perceptual capabilities similar to that produced by acoustic stimulation in the EAS users.

Methods

Following up the first ETS study showing enhanced English sentence recognition in noise,1 the present study evaluated the effect of ETS on Mandarin tone recognition in noise in two groups of adult Mandarin‐speaking individuals. The first group included 11 normal‐hearing individuals who listened to a 4‐channel, noise‐vocoded, cochlear‐implant simulation. The second group included 1 unilateral cochlear‐implant user and 2 bilateral users with each of their devices being tested independently. Both groups participated in a 4‐alternative, forced‐choice task, in which they had to identify a tone that was presented in noise at a 0‐dB signal‐to‐noise ratio via electric stimulation (actual or simulated cochlear implants), tactile stimulation or the combined ETS.

Results

While electric or tactile stimulation alone produced similar tone recognition (∼40% correct), the ETS enhanced the cochlear‐implant tone recognition by 17–18 percentage points. The size of the present ETS enhancement effect was similar to that of the previously reported EAS effect on Mandarin tone recognition. Psychophysical analysis on tactile sensation showed an important role of frequency discrimination in the ETS enhancement.

Conclusion

Tactile stimulation can potentially enhance Mandarin tone recognition in cochlear‐implant users who do not have usable residual acoustic hearing. To optimize this potential, high fundamental frequencies need to be transposed to a 100–200 Hz range.
“Disgusting Details Which Are Best Forgotten”: Disclosures of Child Sexual Abuse in Twentieth-Century Britain
Authors: Delap Lucy
Published: January 2018

For those who by the end of the twentieth century came to be termed “survivors” of child sexual abuse, different genres and forms have been available to narrate and evaluate that abuse. This article explores the reception and practical results of such disclosures: the unpredictable effects of telling, and the strategies of containment, silencing, or disbelief that greeted disclosures. I make note of the ethical challenges of writing the history of child sexual abuse and conclude that twenty-first-century observers have been too ready to perceive much of the previous century as a period of profound silence in relation to child sexual abuse. At the same time, historical and sociological accounts have also been too ready to claim the final third of the twentieth century as a period of compulsive disclosure and fluency in constructing sexual selves. The history of child sexual abuse reveals significant barriers to disclosure in the 1970s and 1980s, despite new visibility of child sexual abuse in the media and through feminist sexual politics. Attention to such obstacles suggests the need to rethink narratives of “permissive” sexual change to acknowledge more fully the ongoing inequities and hierarchies in sexual candor and voice.
The Divided Self
Authors: Laing R. D.
Published: January 2018

R. D. Laing was perhaps the most famous psychiatrist in the latter half of the 20th century. Yet today, for a man of such international repute, within his profession he has many detractors and few admirers. Despite his later writings on birth, his name and fame are inextricably linked with schizophrenia. For the vast majority of psychiatrists, the name of Laing today conjures up images of psychedelic irresponsibility in which parents were blamed and patients misled.
Gaze and Mutual Gaze
Authors: Argyle Michael , Cook Mark , Cramer Duncan
Published: January 2018

One of the first psychologists to investigate experimentally the role of gaze in human behaviour was Michael Argyle. In 1963 he set up a research group at Oxford with Ted Crossman and Adam Kendon, to study non-verbal communication in human social interaction, which included gaze as an important aspect of this behaviour. Shortly afterwards, Mark Cook joined this group which was funded until 1975, during which time considerable research on gaze had been carried out both at Oxford and elsewhere. This book summarises much of the work done in this field up until that time.
SHELTERING GOVERNMENT SUPPORT TO ‘GREEN’ ELECTRICITY: THE EUROPEAN UNION AND THE WORLD TRADE ORGANIZATION
Authors: Marín Durán Gracia
Published: January 2018

Since theCanada – Renewable Energy (2013)dispute at the World Trade Organization (WTO), the WTO Agreement on Subsidies and Countervailing Measures (SCM) has been the focal point of academic debate on the trade-environment interface, with a growing consensus that WTO subsidy rules need to be revisited with a view to securing ‘policy space’ for government support for renewable energy. This article explores whether, as suggested by some scholars, the European Union (EU)’s system of justifications for renewable energy aid could serve as a source of inspiration for the WTO. While this proposition may appear attractive at first sight, it is hardly conceivable, or even desirable, that the EU's approach to sheltering government support for renewable energy could be transposed to the WTO. This is because the two systems of subsidy control are fundamentally different in both substantive and procedural terms and, importantly, these differences reflect distinct objectives and political/institutional contexts. Nonetheless, this comparative analysis sheds light on where the key challenges lie for the WTO in ensuring that international trade rules and climate change mitigation objectives are mutually supportive. It is argued that the case for reviewing the SCM Agreement cannot be made by simply forging parallels with the EU's regulatory model, but needs to be carefully construed on the basis of a proper understanding of whether and how green policy space is actually constrained under the current WTO subsidy and trade remedy rules. However, this requires better information on existing WTO members’ practice in relation to renewable energy subsidies, as well as on their environmental effectiveness and possible trade-distortive impact. In this sense, the most valuable lesson that the WTO can draw from the EU's regulatory experience is the imperative of improving the transparency and knowledge-enhancing elements of its subsidy control system.
Crustacean prey in the diet of fishes from deep waters of the Eastern Ionian Sea
Authors: Anastasopoulou Aikaterini , Mytilineou Chryssi , Smith Christopher J. , Papadopoulou Konstantia N.
Published: January 2018

The gut analysis of 26 fish species caught in the deep waters of the Eastern Ionian Sea showed that crustaceans were a substantial resource for fish found in deep- water environments, comprising 37 crustacean taxa. Among all species examined, 77% included crustaceans in their guts. Dendrobranchiata/Caridea shrimps were the most frequent crustacean prey found in the guts of almost all examined fishes, with high values of relative abundance (N%). Season (summer, autumn) and fish behaviour (demersal, benthic) were not found to affect the diet of the examined fish species. Galeus melastomus could be considered to be a separate case showing the most diverse diet comprising all the crustacean groups. Differences in the proportion of the main crustacean categories consumed by the examined fish species were observed. The low richness and preference towards specific crustacean taxa or different crustacean species could be considered as an indication of interspecific competition for the same food resource in the oligotrophic waters of the Eastern Mediterranean. The occurrence of different crustacean taxa in the gut of some species through the analysed seasons, could be related to differences in prey availability or to selective preference for certain prey which in turn could be linked to different energetic requirements for growth and reproduction of predators.
Appellate Body Report onEU−Biodiesel: The Future of China's State Capitalism under the WTO Anti-Dumping Agreement
Authors: ZHOU WEIHUAN
Published: January 2018

China's unique economic system poses increasing challenges to the world trading system and attracts growing academic and policy debate. WTO members have frequently resorted to antidumping measures in dealing with price distortions caused by the Chinese government's influence on the economy. The Appellate Body's decision in the recentEU–Biodieseldispute starts to remove the flexibility of condemning state intervention and price distortions under the WTO Anti-Dumping Agreement through antidumping measures. This decision, read with the relevant WTO jurisprudence on the ‘ordinary course of trade’ test and subsidies, suggests that price distortions resulting from state intervention should be addressed under other WTO rules. Therefore, it is necessary for WTO members to shift their focus to, and explore the capacity of, the other rules to overcome the challenges arising from China's state capitalism.
The poverty of numbers: reflections on the legitimacy of global development indicators
Authors: Goodwin Morag
Published: January 2018

It is no surprise that development institutions and actors have taken to indicators with such enthusiasm. Where indicators are both a form of knowledge production and simultaneously a technology of governance, they are a form of soft powers that allow such actors to set the standards for what it is to be developed in the twenty-first century. Such measures of civilisation have been dominant throughout a history of Global North–South encounters: measurement was central to the many forms of colonial control, from map-making to craniometry, to the global ‘discovery’ of poverty in the 1940s. This paper seeks to place development indicators in this colonial context by focusing on the issue of comparability or the global claim that underpins global development indicators.
Amiodaron-induzierte Schilddrüsenprobleme: optimales Management
Authors: Binz-Siegmann Katharina
Published: January 2018

Zusammenfassung. Amiodaron-induzierte Schilddrüsenfunktionsstörungen (Hypo- und Hyperthyreosen) sind häufig (14–18 % der behandelten Patienten). Oft werden sie spät erkannt und ungenügend behandelt. Eine ausführliche Anamnese und klinische Untersuchung kann Risikopatienten identifizieren. Die Hyperthyreose ist klinisch oft schwierig zu diagnostizieren, da Amiodaron beta-blockierende Aktivitäten aufweist und so die adrenergenen Symptome der Schilddrüsenüberfunktion maskiert. Regelmässige Laborkontrollen sind unerlässlich. Dabei gilt es zu berücksichtigen, dass Amiodaron den Schilddrüsenhormon-Metabolismus und damit die Schilddrüsenwerte beeinflusst. Während die Therapie der Hypothyreose einfach ist (Substitution), ist die Hyperthyreose oft schwieriger und langwieriger in der Behandlung (Thyreostatika, Kortikosteroide, gelegentlich Perchlorat oder sogar eine totale Thyroidektomie). Obwohl die Bedeutung des Amiodarons in der Behandlung der Rhythmusstörungen wegen neuerer Therapiestrategien abnimmt, ist die Kenntnis der potenziellen Nebenwirkungen (nicht nur der endokrinologischen) nach wie vor wichtig.
Fast intensity adaptation enhances the encoding of sound in Drosophila
Authors: Clemens Jan , Ozeri-Engelhard Nofar , Murthy Mala
Published: January 2018

To faithfully encode complex stimuli, sensory neurons should correct, via adaptation, for stimulus properties that corrupt pattern recognition. Here we investigate sound intensity adaptation in the Drosophila auditory system, which is largely devoted to processing courtship song. Mechanosensory neurons (JONs) in the antenna are sensitive not only to sound-induced antennal vibrations, but also to wind or gravity, which affect the antenna’s mean position. Song pattern recognition, therefore, requires adaptation to antennal position (stimulus mean) in addition to sound intensity (stimulus variance). We discover fast variance adaptation in Drosophila JONs, which corrects for background noise over the behaviorally relevant intensity range. We determine where mean and variance adaptation arises and how they interact. A computational model explains our results using a sequence of subtractive and divisive adaptation modules, interleaved by rectification. These results lay the foundation for identifying the molecular and biophysical implementation of adaptation to the statistics of natural sensory stimuli.
Mapping the microscale origins of magnetic resonance image contrast with subcellular diamond magnetometry
Authors: Davis Hunter C. , Ramesh Pradeep , Bhatnagar Aadyot , Lee-Gosselin Audrey , Barry John F. , Glenn David R. , Walsworth Ronald L. , Shapiro Mikhail G.
Published: January 2018

Magnetic resonance imaging (MRI) is a widely used biomedical imaging modality that derives much of its contrast from microscale magnetic field patterns in tissues. However, the connection between these patterns and the appearance of macroscale MR images has not been the subject of direct experimental study due to a lack of methods to map microscopic fields in biological samples. Here, we optically probe magnetic fields in mammalian cells and tissues with submicron resolution and nanotesla sensitivity using nitrogen-vacancy diamond magnetometry, and combine these measurements with simulations of nuclear spin precession to predict the corresponding MRI contrast. We demonstrate the utility of this technology in an in vitro model of macrophage iron uptake and histological samples from a mouse model of hepatic iron overload. In addition, we follow magnetic particle endocytosis in live cells. This approach bridges a fundamental gap between an MRI voxel and its microscopic constituents.
Unidirectional spin density wave state in metallic (Sr1−xLa
x
)2IrO4
Authors: Chen Xiang , Schmehr Julian L. , Islam Zahirul , Porter Zach , Zoghlin Eli , Finkelstein Kenneth , Ruff Jacob P. C. , Wilson Stephen D.
Published: January 2018

Materials that exhibit both strong spin–orbit coupling and electron correlation effects are predicted to host numerous new electronic states. One prominent example is the Jeff = 1/2 Mott state in Sr2IrO4, where introducing carriers is predicted to manifest high temperature superconductivity analogous to the S = 1/2 Mott state of La2CuO4. While bulk superconductivity currently remains elusive, anomalous quasiparticle behaviors paralleling those in the cuprates such as pseudogap formation and the formation of a d-wave gap are observed upon electron-doping Sr2IrO4. Here we establish a magnetic parallel between electron-doped Sr2IrO4 and hole-doped La2CuO4 by unveiling a spin density wave state in electron-doped Sr2IrO4. Our magnetic resonant X-ray scattering data reveal the presence of an incommensurate magnetic state reminiscent of the diagonal spin density wave state observed in the monolayer cuprate (La1−xSr
x
)2CuO4. This link supports the conjecture that the quenched Mott phases in electron-doped Sr2IrO4 and hole-doped La2CuO4 support common competing electronic phases.
Link between concentrations of sediment flux and deep crustal processes beneath the European Alps
Authors: Garefalakis Philippos , Schlunegger Fritz
Published: January 2018

Large sediment fluxes from mountain belts have the potential to cause megafans to prograde into the neighbouring sedimentary basins. These mechanisms have been documented based from numerical modelling and stratigraphic records. However, little attention has been focused on inferring temporal changes in the concentrations of supplied sediment from coarse-grained deposits. Here, we extract changes of this variable in the field from a Late Oligocene, c. 4 km-thick suite of fluvial conglomerates situated in the North Alpine foreland basin, which evolved in response to the tectonic and erosional history of the Alps. We measure a decrease in channel depths from >2 m to <1 m and an increase in the largest grain sizes from <15 cm to >20 cm from the base to the top of the suite. These constraints are used to calculate an increase in fan surface slopes from <0.3° to >1.0° based on the Shields criteria for sediment entrainment. We combine slope and bulk grain size data with the Bagnold equation for sediment transport to infer higher concentrations of the supplied sediment. We use these shifts to propose a change towards faster erosion and a steeper landscape in the Alpine hinterland, driven by mantle-scale processes beneath the Alps.
Multiple mutations and overexpression of the MdaE7 carboxylesterase gene associated with male-linked malathion resistance in housefly, Musca domestica (Diptera: Muscidae)
Authors: Zhang Yi , Li Jing , Ma Zhuo , Shan Chao , Gao Xiwu
Published: January 2018

Two unique housefly strains, MSS and N-MRS, were selected and used to clarify mechanisms of sex-associated malathion resistance in the housefly, Musca domestica. Compared with the lab-susceptible CSS strain, susceptible females and resistant males were observed in the malathion-susceptible MSS strain, while the malathion-resistant near-isogenic line, N-MRS, achieved similar resistance level between genders. Significant synergistic effect of the esterase-inhibitor DEF on resistant houseflies pointed to the important involvement of esterase in this specific malathion resistance. Examination of the carboxylesterase gene MdαE7 in malathion resistant housefly populations found seven, non-synonymous SNP mutations (Ser250-Thr, Trp251-Ser, Met303-Ile, Leu354-Phe, Ser357-Leu, Trp378-Arg and Ser383-Thr), not found in susceptible houseflies, revealing a strong correlation between these mutations and the development of malathion resistance. Further genetic analysis conducted with bioassays by topical application and nucleotide polymorphism detection provided a first line of molecular evidence for a linkage between a male-determining factor and MdαE7 gene in the MSS and N-MRS males. This linkage results in a much higher level of malathion resistance for males than females in the MSS strain. Lastly, quantitative real-time PCR showed that MdαE7 was over expressed in the resistant strain due to the increased transcription level of mRNA rather than gene duplication.
Shrinkable silver diffraction grating fabricated inside a hydrogel using 522-nm femtosecond laser
Authors: Machida Manan , Nakajima Yasutaka , Torres-Mapa Maria Leilani , Heinemann Dag , Heisterkamp Alexander , Terakawa Mitsuhiro
Published: January 2018

The integration of metal microstructures and soft materials is promising for the realization of novel optical and biomedical devices owing to the flexibility and biocompatibility of the latter. Nevertheless, the fabrication of three-dimensional metal structures within a soft material is still challenging. In this study, we demonstrate the fabrication of a silver diffraction grating inside a biocompatible poly(ethylene glycol) diacrylate (PEGDA) hydrogel by using a 522-nm femtosecond laserviamulti-photon photoreduction of silver ions. The optical diffraction pattern obtained with the grating showed equally spaced diffraction spots, which indicated that a regular, periodic silver grating was formed. Notably, the distance between the diffraction spots changed when the water content in the hydrogel was reduced. The grating period decreased when the hydrogel shrank owing to the loss of water, but the straight shapes of the line structures were preserved, which demonstrated the optical tunability of the fabricated structure. Our results demonstrate the potential of the femtosecond laser-based photoreduction technique for the fabrication of novel tunable optical devices as well as highly precise structures.
A genome-wide association study identifies only two ancestry specific variants associated with spontaneous preterm birth
Authors: Rappoport Nadav , Toung Jonathan , Hadley Dexter , Wong Ronald J. , Fujioka Kazumichi , Reuter Jason , Abbott Charles W. , Oh Sam , Hu Donglei , Eng Celeste , Huntsman Scott , Bodian Dale L. , Niederhuber John E. , Hong Xiumei , Zhang Ge , Sikora-Wohfeld Weronika , Gignoux Christopher R. , Wang Hui , Oehlert John , Jelliffe-Pawlowski Laura L. , Gould Jeffrey B. , Darmstadt Gary L. , Wang Xiaobin , Bustamante Carlos D. , Snyder Michael P. , Ziv Elad , Patsopoulos Nikolaos A. , Muglia Louis J. , Burchard Esteban , Shaw Gary M. , O’Brodovich Hugh M. , Stevenson David K. , Butte Atul J. , Sirota Marina
Published: January 2018

Preterm birth (PTB), or the delivery prior to 37 weeks of gestation, is a significant cause of infant morbidity and mortality. Although twin studies estimate that maternal genetic contributions account for approximately 30% of the incidence of PTB, and other studies reported fetal gene polymorphism association, to date no consistent associations have been identified. In this study, we performed the largest reported genome-wide association study analysis on 1,349 cases of PTB and 12,595 ancestry-matched controls from the focusing on genomic fetal signals. We tested over 2 million single nucleotide polymorphisms (SNPs) for associations with PTB across five subpopulations: African (AFR), the Americas (AMR), European, South Asian, and East Asian. We identified only two intergenic loci associated with PTB at a genome-wide level of significance: rs17591250 (P = 4.55E-09) on chromosome 1 in the AFR population and rs1979081 (P = 3.72E-08) on chromosome 8 in the AMR group. We have queried several existing replication cohorts and found no support of these associations. We conclude that the fetal genetic contribution to PTB is unlikely due to single common genetic variant, but could be explained by interactions of multiple common variants, or of rare variants affected by environmental influences, all not detectable using a GWAS alone.
Unraveling Individual Differences In The HIV-1 Transgenic Rat: Therapeutic Efficacy Of Methylphenidate
Authors: McLaurin Kristen A. , Li Hailong , Booze Rosemarie M. , Fairchild Amanda J. , Mactutus Charles F.
Published: January 2018

Despite the heterogeneity of HIV-1 associated neurocognitive disorders (HAND), assignment of categorical diagnoses based on the level of impairment (e.g., Frascati criteria) obfuscates the well-acknowledged variability observed within the population of HIV-1+ individuals. The present study sought to elucidate the natural heterogeneity in adult HIV-1 transgenic (Tg) rats using three interrelated aims. First, heterogeneity of the HIV-1 transgene was examined using a pretest-posttest design to assess therapeutic efficacy of oral self-administration (OSA) of methylphenidate (MPH; 2.4 ± 0.2 mg/kg), targeting neurotransmitter alterations in HIV-1, on temporal processing. Approximately 42% of HIV-1 Tg animals displayed an improvement in temporal processing following OSA of MPH. Second, repeated OSA of MPH (22–27 days) altered dendritic spine morphology in layer II-III pyramidal neurons in the medial prefrontal cortex. HIV-1 Tg animals exhibited a population shift towards longer spines with decreased head diameter on lower order branches; a shift associated with temporal processing impairment. Third, in HIV-1 Tg animals, dendritic spine backbone length (µm) was associated with temporal processing impairment; a brain/behavior relationship not observed in control animals. Assessing the therapeutic efficacy of MPH revealed heterogeneity in the neural mechanisms underlying neurocognitive impairments, providing a key target for individualized therapeutic and diagnostic approaches for HAND.
Predicting inhibitory and activatory drug targets by chemically and genetically perturbed transcriptome signatures
Authors: Sawada Ryusuke , Iwata Michio , Tabei Yasuo , Yamato Haruka , Yamanishi Yoshihiro
Published: January 2018

Genome-wide identification of all target proteins of drug candidate compounds is a challenging issue in drug discovery. Moreover, emerging phenotypic effects, including therapeutic and adverse effects, are heavily dependent on the inhibition or activation of target proteins. Here we propose a novel computational method for predicting inhibitory and activatory targets of drug candidate compounds. Specifically, we integrated chemically-induced and genetically-perturbed gene expression profiles in human cell lines, which avoided dependence on chemical structures of compounds or proteins. Predictive models for individual target proteins were simultaneously constructed by the joint learning algorithm based on transcriptomic changes in global patterns of gene expression profiles following chemical treatments, and following knock-down and over-expression of proteins. This method discriminates between inhibitory and activatory targets and enables accurate identification of therapeutic effects. Herein, we comprehensively predicted drug–target–disease association networks for 1,124 drugs, 829 target proteins, and 365 human diseases, and validated some of these predictionsin vitro. The proposed method is expected to facilitate identification of new drug indications and potential adverse effects.
Alterations in the properties of the cell membrane due to glycosphingolipid accumulation in a model of Gaucher disease
Authors: Batta Gyula , Soltész Lilla , Kovács Tamás , Bozó Tamás , Mészár Zoltán , Kellermayer Miklós , Szöllősi János , Nagy Peter
Published: January 2018

Gaucher disease is a lysosomal storage disease characterized by the malfunction of glucocerebrosidase resulting in the accumulation of glucosylceramide and other sphingolipids in certain cells. Although the disease symptoms are usually attributed to the storage of undigested substrate in lysosomes, here we show that glycosphingolipids accumulating in the plasma membrane cause profound changes in the properties of the membrane. The fluidity of the sphingolipid-enriched membrane decreased accompanied by the enlargement of raft-like ordered membrane domains. The mobility of non-raft proteins and lipids was severely restricted, while raft-resident components were only mildly affected. The rate of endocytosis of transferrin receptor, a non-raft protein, was significantly retarded in Gaucher cells, while the endocytosis of the raft-associated GM1 ganglioside was unaffected. Interferon-γ-induced STAT1 phosphorylation was also significantly inhibited in Gaucher cells. Atomic force microscopy revealed that sphingolipid accumulation was associated with a more compliant membrane capable of producing an increased number of nanotubes. The results imply that glycosphingolipid accumulation in the plasma membrane has significant effects on membrane properties, which may be important in the pathogenesis of Gaucher disease.
Bacterial community assembly from cow teat skin to ripened cheeses is influenced by grazing systems
Authors: Frétin Marie , Martin Bruno , Rifa Etienne , Isabelle Verdier-Metz , Pomiès Dominique , Ferlay Anne , Montel Marie-Christine , Delbès Céline
Published: January 2018

The objectives of this study were to explore bacterial community assembly from cow teat skin to raw milk cheeses and to evaluate the role of farming systems on this assembly using 16S rRNA gene high-throughput sequencing. The two grazing systems studied (extensive vs. semi-extensive) had a greater effect on the microbiota of cow teat skin than on that of raw milks and cheeses. On teat skin, the relative abundance of several taxa at different taxonomic levels (Coriobacteriia, Bifidobacteriales, Corynebacteriales, Lachnospiraceae, Atopobium, and Clostridium) varied depending on the grazing system and the period (early or late summer). In cheese, the abundance of sub-dominant lactic acid bacteria (LAB) varied depending on the grazing system. Overall, 85% of OTUs detected in raw milks and 27% of OTUs detected in ripened cheeses were also found on cow teat skin. Several shared OTUs were assigned to taxa known to be involved in the development of cheese sensory characteristics, such as Micrococcales, Staphylococcaceae, and LAB. Our results highlight the key role of cow teat skin as a reservoir of microbial diversity for raw milk, and for the first time, that cow teat skin serves as a potential source of microorganisms found in raw-milk cheeses.
Comparative Analysis of Gene Expression Profiles of Human Dental Fluorosis and Kashin-Beck Disease
Authors: Zhang Qiang , Ma Jing , Liu Haiqing , He Duolong , Chen Lilin , Wu Haikun , Jiang Hong , Lu Qing , Bai Shenglu
Published: January 2018

To explore the pathologies of Kashin-Beck disease (KBD) and KBD accompanied with dental fluorosis (DF), we conducted a comparative analysis of gene expression profiles. 12 subjects were recruited, including 4 KBD patients, 4 patients with KBD and DF and 4 healthy subjects. Genome-wide expression profiles from their peripheral blood mononuclear cells were evaluated by customized oligonucleotide microarray. R programming software was used for the microarray data analysis followed by functional enrichment analysis through KOBAS. Several potential biomarkers were identified, and quantitative real-time reverse transcription–polymerase chain reaction (qRT-PCR) was used for their validation. In this study, 28 genes and 8 genes were found to be up- and down-regulated respectively in KBD patients compared with health subjects. In patients with KBD and DF, we obtained 10 up-regulated and 3 down-regulated genes compared with health controls. Strikingly, no differential expression gene (DEG) was identified between the two groups of patients. A total of 10 overlaps (DUSP2, KLRF1, SRP19, KLRC3, CD69, SIK1, ITGA4, ID3, HSPA1A, GPR18) were obtained between DEGs of patients with KBD and patients with KBD and DF. They play important roles in metabolism, differentiation, apoptosis and bone-development. The relative abundance of 8 DEGs, i.e. FCRL6, KLRC3, CXCR4, CD93, CLK1, GPR18, SRP19 and KLRF1, were further confirmed by qRT-PCR analysis.
Surveillance of vector-borne pathogens under imperfect detection: lessons from Chagas disease risk (mis)measurement
Authors: Minuzzi-Souza Thaís Tâmara Castro , Nitz Nadjar , Cuba César Augusto Cuba , Hagström Luciana , Hecht Mariana Machado , Santana Camila , Ribeiro Marcelle , Vital Tamires Emanuele , Santalucia Marcelo , Knox Monique , Obara Marcos Takashi , Abad-Franch Fernando , Gurgel-Gonçalves Rodrigo
Published: January 2018

Vector-borne pathogens threaten human health worldwide. Despite their critical role in disease prevention, routine surveillance systems often rely on low-complexity pathogen detection tests of uncertain accuracy. In Chagas disease surveillance, optical microscopy (OM) is routinely used for detecting Trypanosoma cruzi in its vectors. Here, we use replicate T. cruzi detection data and hierarchical site-occupancy models to assess the reliability of OM-based T. cruzi surveillance while explicitly accounting for false-negative and false-positive results. We investigated 841 triatomines with OM slides (1194 fresh, 1192 Giemsa-stained) plus conventional (cPCR, 841 assays) and quantitative PCR (qPCR, 1682 assays). Detections were considered unambiguous only when parasitologists unmistakably identified T. cruzi in Giemsa-stained slides. qPCR was >99% sensitive and specific, whereas cPCR was ~100% specific but only ~55% sensitive. In routine surveillance, examination of a single OM slide per vector missed ~50–75% of infections and wrongly scored as infected ~7% of the bugs. qPCR-based and model-based infection frequency estimates were nearly three times higher, on average, than OM-based indices. We conclude that the risk of vector-borne Chagas disease may be substantially higher than routine surveillance data suggest. The hierarchical modelling approach we illustrate can help enhance vector-borne disease surveillance systems when pathogen detection is imperfect.
Inflammatory Proteomic Network Analysis of Statin-treated and Lipopolysaccharide-activated Macrophages
Authors: Kamal Abu Hena M. , Chakrabarty Jayanta K. , Udden S. M. Nashir , Zaki Md. Hasan , Chowdhury Saiful M.
Published: January 2018

A significant component of immune biology research is the investigation of protein encoding genes that play central roles in contributing inflammatory response. A gel-free quantitative bottom-up proteomics study was performed on immune cell macrophages after the combined treatment of lipopolysaccharide (LPS) and statin drugs using mass spectrometry and a detailed bioinformatics analyses were conducted. Systematic bioinformatics analysis was applied for discovering novel relationships among proteins and effects of statin and lipopolysaccharide in macrophage cells. Based on gene ontology, majority of protein encoding genes was involved in metabolic and cellular processes and are actively associated with binding, structural molecular, and catalytic activity. Notably, proteomic data analyzed by Ingenuity Pathway Analysis (IPA), discovered the plectin and prohibitin 2 protein interactions network and inflammatory-disease based protein networks. Two up-regulated proteins, plectin and prohibitin 2, were further validated by immunoblotting. Plectin was also cross-validated by immunocytochemistry, since its expression was highly modulated by statin but inhibited during LPS-stimulation. Collectively, the significant up-regulation of plectin due to the treatment of statin, suggests that statin has a significant impact on the cytoskeletal networks of cells. Plectin might have a significant role in the intermediate filament assembly and dynamics, and possibly stabilizing and crosslinking intermediate filament networks.
Comparison of changes in mitochondrial bioenergetics between keratinocytes in human external auditory canal skin and cholesteatomas from normoxia to hypoxia
Authors: Shih Cheng-Ping , Lee Jen-Tin , Chen Hang-Kang , Lin Yi-Chun , Chen Hsin-Chien , Lin Yuan-Yung , Kuo Chao-Yin , Chen Yu-Ting , Wang Chih-Hung
Published: January 2018

Cholesteatoma has attracted many studies seeking to uncover its nature and the pathogenesis of related diseases. However, no researchers have explored the mitochondrial bioenergetics of cholesteatoma. The aim of this study was to investigate the energy demand and differential mitochondrial respiration profiles between keratinocytes in external auditory canal (EAC) skin and cholesteatoma samples cultured in normoxic (20% O2) and hypoxic (5% O2) conditions. Enhanced cellular proliferation of both types of keratinocytes was found in hypoxia compared to normoxia. In 20% O2conditions, cholesteatoma keratinocytes exhibited less mitochondrial mass, lower ATP levels, and significantly lower basal oxygen consumption rate (OCR) and reserve capacity compared to normal skin keratinocytes. In contrast, in hypoxic conditions, cholesteatoma keratinocytes showed markedly higher levels in maximal OCR and reserve capacity, as well as lower proton leak OCRs, compared to normal skin keratinocytes. Hypoxia induced the reverse mitochondrial bioenergy profile from that in normoxia between these two types of keratinocytes, implying that an adaptive change of mitochondrial respiration to oxygen fluctuations may develop in cases of cholesteatoma. Such adaptation in response to hypoxic conditions may play a role in explaining the pathogenesis of acquired cholesteatoma.
Modeling tumor immunity of mouse glioblastoma by exhausted CD8+ T cells
Authors: Nakashima Hiroshi , Alayo Quazim A. , Penaloza-MacMaster Pablo , Freeman Gordon J. , Kuchroo Vijay K. , Reardon David A. , Fernandez Soledad , Caligiuri Michael , Chiocca E. Antonio
Published: January 2018

T cell exhaustion occurs during chronic infection and cancers. Programmed cell death protein-1 (PD-1) is a major inhibitory checkpoint receptor involved in T cell exhaustion. Blocking antibodies (Abs) against PD-1 or its ligand, PD-L1, have been shown to reverse T cell exhaustion during chronic infection and cancers, leading to improved control of persistent antigen. However, modeling tumor-specific T cell responses in mouse has been difficult due to the lack of reagents to detect and phenotype tumor-specific immune responses. We developed a novel mouse glioma model expressing a viral epitope derived from lymphocytic choriomeningitis virus (LCMV), which allowed monitoring of tumor-specific CD8 T-cell responses. These CD8 T cells express high levels of PD-1 and are unable to reject tumors, but this can be reversed by anti-PD-1 treatment. These results suggest the efficacy of PD-1 blockade as a treatment for glioblastoma, an aggressive tumor that results in a uniformly lethal outcome. Importantly, this new syngeneic tumor model may also provide further opportunities to characterize anti-tumor T cell exhaustion and develop novel cancer immunotherapies.
Protein tyrosine kinase, PtkA, is required for Mycobacterium tuberculosis growth in macrophages
Authors: Wong Dennis , Li Wu , Chao Joseph D. , Zhou Peifu , Narula Gagandeep , Tsui Clement , Ko Mary , Xie Jianping , Martinez-Frailes Carlos , Av-Gay Yossef
Published: January 2018

Protein phosphorylation plays a key role in Mycobacterium tuberculosis (Mtb) physiology and pathogenesis. We have previously shown that a secreted protein tyrosine phosphatase, PtpA, is essential for Mtb inhibition of host macrophage acidification and maturation, and is a substrate of the protein tyrosine kinase, PtkA, encoded in the same operon. In this study, we constructed a ∆ptkA deletion mutant in Mtb and found that the mutant exhibited impaired intracellular survival in the THP-1 macrophage infection model, correlated with the strain’s inability to inhibit macrophage phagosome acidification. By contrast, the mutant displayed increased resistance to oxidative stress in vitro. Proteomic and transcriptional analyses revealed upregulation of ptpA, and increased secretion of TrxB2, in the ΔptkA mutant. Kinase and protein-protein interaction studies demonstrated that TrxB2 is a substrate of PtkA phosphorylation. Taken together these studies establish a central role for the ptkA-ptpA operon in Mtb pathogenesis.
Zircon evidence for incorporation of terrigenous sediments into the magma source of continental basalts
Authors: Xu Zheng , Zheng Yong-Fei , Zhao Zi-Fu
Published: January 2018

Crustal components may be incorporated into continental basalts by either shallow contamination or deep mixing. While the former proceeds at crustal depths with common preservation of refractory minerals, the latter occurs at mantle depths with rare survival of relict minerals. Discrimination between the two mechanisms has great bearing to subcontinental mantle geochemistry. Here we report the occurrence of relict zircons in Cenozoic continental basalts from eastern China. A combined study of zircon U-Pb ages and geochemistry indicates that detrital zircons were carried by terrigenous sediments into a subcontinental subduction zone, where the zircon were transferred by fluids into the magma sources of continental basalts. The basalts were sampled from three petrotectonic units with distinct differences in their magmatic and metamorphic ages, making the crustal contamination discernible. The terrigenous sediments were carried by the subducting oceanic crust into the asthenospheric mantle, producing both soluble and insoluble materials at the slab-mantle interface. These materials were served as metasomatic agents to react with the overlying mantle wedge peridotite, generating a kind of ultramafic metasomatites that contain the relict zircons. Therefore, the occurrence of relict zircons in continental basalts indicates that this refractory mineral can survive extreme temperature-pressure conditions in the asthenospheric mantle.
Controlled Alternate Quantum Walks based Quantum Hash Function
Authors: Li Dan , Yang Yu-Guang , Bi Jing-Lin , Yuan Jia-Bin , Xu Juan
Published: January 2018

Through introducing controlled alternate quantum walks, we present controlled alternate quantum walks (CAQW) based quantum hash function. CAQW based quantum hash function have excellent security, outstanding statistical performance and splendid expansibility. Furthermore, due to the structure of alternate quantum walks, implementing CAQW based quantum hash function significantly reduces the resources necessary for its feasible experimental realization than implementing other quantum hash functions.
HybTrack: A hybrid single particle tracking software using manual and automatic detection of dim signals
Authors: Lee Byung Hun , Park Hye Yoon
Published: January 2018

Single particle tracking is a compelling technique for investigating the dynamics of nanoparticles and biological molecules in a broad range of research fields. In particular, recent advances in fluorescence microscopy have made single molecule tracking a prevalent method for studying biomolecules with a high spatial and temporal precision. Particle tracking algorithms have matured over the past three decades into more easily accessible platforms. However, there is an inherent difficulty in tracing particles that have a low signal-to-noise ratio and/or heterogeneous subpopulations. Here, we present a new MATLAB based tracking program which combines the benefits of manual and automatic tracking methods. The program prompts the user to manually locate a particle when an ambiguous situation occurs during automatic tracking. We demonstrate the utility of this program by tracking the movement of β-actin mRNA in the dendrites of cultured hippocampal neurons. We show that the diffusion coefficient of β-actin mRNA decreases upon neuronal stimulation by bicuculline treatment. This tracking method enables an efficient dissection of the dynamic regulation of biological molecules in highly complex intracellular environments.
Ultrafast syn-eruptive degassing and ascent trigger high-energy basic eruptions
Authors: Giuffrida Marisa , Viccaro Marco , Ottolini Luisa
Published: January 2018

Lithium gradients in plagioclase are capable of recording extremely short-lived processes associated with gas loss from magmas prior to extrusion at the surface. We present SIMS profiles of the 7Li/30Si ion ratio in plagioclase crystals from products of the paroxysmal sequence that occurred in the period 2011–2013 at Mt. Etna (Italy) in an attempt to constrain the final ascent and degassing processes leading to these powerful eruptions involving basic magma. The observed Li concentrations reflect cycles of Li addition to the melt through gas flushing, and a syn-eruptive stage of magma degassing driven by decompression that finally produce significant Li depletion from the melt. Modeling the decreases in Li concentration in plagioclase by diffusion allowed determination of magma ascent timescales that are on the order of minutes or less. Knowledge of the storage depth beneath the volcano has led to the quantification of a mean magma ascent velocity of ~43 m/s for paroxysmal eruptions at Etna. The importance of these results relies on the application of methods, recently used exclusively for closed-system volcanoes producing violent eruptions, to open-conduit systems that have generally quiet eruptive periods of activity sometimes interrupted by sudden re-awakening and the production of anomalously energetic eruptions.
Increased Abundance of Clostridium and Fusobacterium in Gastric Microbiota of Patients with Gastric Cancer in Taiwan
Authors: Hsieh Yung-Yu , Tung Shui-Yi , Pan Hung-Yu , Yen Chih-Wei , Xu Huang-Wei , Lin Ying-Jhen , Deng Yi-Fang , Hsu Wan-Ting , Wu Cheng-Shyong , Li Chin
Published: January 2018

Helicobacter pylori is recognised as a main risk factor for gastric cancer. However, approximately half of the patients with gastritis are negative for H. pylori infection, and the abundance of H. pylori decreases in patients with cancer. In the current study, we profiled gastric epithelium-associated bacterial species in patients with gastritis, intestinal metaplasia, and gastric cancer to identify additional potential pathogenic bacteria. The overall composition of the microbiota was similar between the patients with gastritis and those with intestinal metaplasia. H. pylori was present in half of the non-cancer group, and the dominant bacterial species in the H. pylori-negative patients were Burkholderia, Enterobacter, and Leclercia. The abundance of those bacteria was similar between the cancer and non-cancer groups, whereas the frequency and abundance of H. pylori were significantly lower in the cancer group. Instead, Clostridium, Fusobacterium, and Lactobacillus species were frequently abundant in patients with gastric cancer, demonstrating a gastric cancer-specific bacterial signature. A receiver operating characteristic curve analysis showed that Clostridium colicanis and Fusobacterium nucleatum exhibited a diagnostic ability for gastric cancer. Our findings indicate that the gastric microenvironment is frequently colonised by Clostridium and Fusobacterium in patients with gastric cancer.