bluuebunny/crossref_metadata_2025 huggingface dataset:
The Gediz Supradetachment System (SW Turkey): Magmatism, Tectonics, and Sedimentation During Crustal Extension
Authors: Asti Riccardo , Faccenna Claudio , Rossetti Federico , Malusà Marco G. , Gliozzi Elsa , Faranda Costanza , Lirer Fabrizio , Cosentino Domenico
Published: March 2019

Unraveling the evolution of supradetachment basins developed in the hanging wall of low‐angle detachment faults may be an invaluable tool in reconstructing the tectonic evolution of highly extended terrains. These basins may record major regional tectonic events related to the exhumation of metamorphic core complexes, and the reconstruction of their evolution helps to quantify the amount of extension accommodated by such processes. Here we present stratigraphic and structural field evidence and micropaleontological constraints to the Neogene‐to‐Quaternary evolution of the supradetachment Gediz Graben that developed on top of the exhuming Central Menderes Massif (SW Turkey). This basin displays three different structural styles during its evolution: (i) it initiated as a ramp basin following the activation of the Gediz Detachment in the Middle Miocene, (ii) evolved as a half graben during the late Miocene following the activation of high‐angle brittle faults at its southern margin, and (iii) reached its final symmetric graben configuration in Late Pliocene (?)‐Quaternary times following the activation of its northern margin. New micropaleontological data document a short‐lived upper Tortonian marine episode in the basin, and major along‐strike variations in exhumation are documented on its southern margin. Our reconstruction shows how sedimentary basins originally formed in the hanging wall of detachment faults may eventually end up in tectonic contact with the mylonitic footwall. Finally, we highlight the importance of magmatism in localizing the deformation in highly extended terrains and in controlling the evolution of supradetachment systems.
Evidence for Multiple Ground‐Rupturing Earthquakes in the Past 4,000 Years Along the Pasuruan Fault, East Java, Indonesia: Documentation of Active Normal Faulting in the Javan Backarc
Authors: Marliyani G. I. , Arrowsmith J. R. , Helmi H.
Published: March 2019

Instrumental and historical records of earthquakes supplemented by paleoeseismic records reveal the earthquake potential of an area. The back‐arc region of the Javan subduction system has been considered to be inactive seismically and is identified as a region of low seismic hazard on the seismic hazard map of Indonesia. However, our study documents recent geological activity along Pasuruan Fault, a high‐angle normal fault located within this zone. The fault is expressed in the landscape as prominent ~13‐km‐long, 2‐ to 50‐m‐high scarps cutting Pleistocene sediments on the north coast of East Java. We excavated two fault‐perpendicular trenches across a relay ramp structure and documented evidence for past earthquakes in both trenches. Our preliminary age model, constrained by 23 radiocarbon dates on detrital charcoal, indicates that since 2006 ± 134 cal BCE, there have been at least six ground‐rupturing earthquakes along the fault at this location. The most recent is attributed to the 1852 Grati earthquake. Our modeled 95th percentile ranges for the next four earlier earthquakes (and their mean, in years CE) are 1786–1846(1816), 1666–1777(1721), 1086–1648(1367), and 726–1093(909). Using these events, we calculate a recurrence interval of 236 ± 46 years. The Pasuruan Fault is located near the western end of the Bali‐Flores back‐arc basin. The late Holocene activity along the fault shows that extensional faulting is ongoing though the mechanism causing this structure remains unclear. Although the fault is considered as a minor structure, its potential for producing large earthquakes may pose significant hazard to the densely populated region.
A 192,000-Year Record of Northwest African Fire History
Authors: Cook Terri
Published: March 2019

Biomarker analyses from an offshore sediment core suggest that increased fire occurrence around 55,000 years ago coincided with increased fuel loads and human settlement in this region.
Complementary Vantage Points: Integrating Hydrology and Economics for Sociohydrologic Knowledge Generation
Authors: Müller Marc F. , Levy Morgan C.
Published: March 2019

Because human and environmental systems in the Anthropocene are increasingly coupled, hydrologists and economists often find themselves studying the same systems from different vantage points. Here we argue that synthesis across economics and hydrology can help address two pressing sociohydrologic challenges: actionable prediction and the generation of transferable knowledge from place‐based studies. Specifically, we review (1) empirical methods and (2) theoretical approaches from economics and connect the two through a proposed iterative framework. First, we find that empirical methods for statistical analysis of natural and quasi‐experiments in economics can be leveraged to distinguish causal relations from mere correlations in complex and data scarce systems, which can help address the challenge of sociohydrologic prediction. Second, we find that economic theories based on rational choice can be used to decipher known paradoxes in water resources, which can help address the challenge of sociohydrologic knowledge generation. In both empirical and theoretical domains, specialized knowledge in hydrology remains critical to properly applying techniques from economics to coupled human‐water systems. We propose that linkages between the two fields highlight a large potential for interaction.
Spatially and spectrally resolved orbital angular momentum interactions in plasmonic vortex generators
Authors: Hachtel Jordan A. , Cho Sang-Yeon , Davidson Roderick B. , Feldman Matthew A. , Chisholm Matthew F. , Haglund Richard F. , Idrobo Juan Carlos , Pantelides Sokrates T. , Lawrie Benjamin J.
Published: March 2019

Understanding the near-field electromagnetic interactions that produce optical orbital angular momentum (OAM) is crucial for integrating twisted light into nanotechnology. Here, we examine the cathodoluminescence (CL) of plasmonic vortices carrying OAM generated in spiral nanostructures. The nanospiral geometry defines a photonic local density of states that is sampled by the electron probe in a scanning transmission electron microscope (STEM), thus accessing the optical response of the plasmonic vortex with high spatial and spectral resolution. We map the full spectral dispersion of the plasmonic vortex in spiral structures designed to yield increasing topological charge. Additionally, we fabricate nested nanospirals and demonstrate that OAM from one nanospiral can be coupled to the nested nanospiral, resulting in enhanced luminescence in concentric spirals of like handedness with respect to concentric spirals of opposite handedness. The results illustrate the potential for generating and coupling plasmonic vortices in chiral nanostructures for sensitive detection and manipulation of optical OAM.
Diversity-disease relationships and shared species analyses for human microbiome-associated diseases
Authors: Ma Zhanshan (Sam) , Li Lianwei , Gotelli Nicholas J
Published: March 2019

Diversity indices have been routinely computed in the study of human microbiome-associated diseases (MADs). However, it is still unclear whether there is a consistent diversity-disease relationship (DDR) for the human MADs, and whether there are consistent differences in the taxonomic composition of microbiomes sampled from healthy versus diseased individuals. Here we reanalyzed raw data and used a meta-analysis to compare the microbiome diversity and composition of healthy versus diseased individuals in 41 comparisons extracted from 27 previously published studies of human MADs. In the DDR analysis, the average effect size across studies did not differ from zero for a comparison of healthy versus diseased individuals. In 30 of 41 comparisons (73%) there was no significant difference in microbiome diversity of healthy versus diseased individuals, or of different disease classes. For the species composition analysis (shared species analysis), the effect sizes were significantly different from zero. In 33 of 41 comparisons (80%), there were fewer OTUs (operational taxonomic units) shared between healthy and diseased individuals than expected by chance, but with 49% (20 of 41 comparisons) statistically significant. These results imply that the taxonomic composition of disease-associated microbiomes is often distinct from that of healthy individuals. Because species composition changes with disease state, some microbiome OTUs may serve as potential diagnostic indicators of disease. However, the overall species diversity of human microbiomes is not a reliable indicator of disease.
A modular atomic force microscopy approach reveals a large range of hydrophobic adhesion forces among bacterial members of the leaf microbiota
Authors: Mittelviefhaus Maximilian , Müller Daniel B , Zambelli Tomaso , Vorholt Julia A
Published: March 2019

Bacterial adhesion is the initial step in surface colonization and community formation. At the single-cell level, atomic force microscopy (AFM) techniques have enabled the quantification of adhesive forces between bacteria and substrata. However, conventional techniques depend on the irreversible immobilization of cells onto cantilevers, thus hampering throughput. Here, we developed a modular AFM method to reversibly immobilize functionalized beads as surface mimic and to probe adhesion of individual bacteria. We performed single-cell force spectroscopies with phylogenetically diverse leaf isolates of various size and morphology. Adhesion measurement of 28 bacterial strains revealed large differences in hydrophobic interactions of about three orders of magnitude. The highest adhesion forces of up to 50 nN were recorded for members of the Gammaproteobacteria. The hydrophobicity of the different isolates correlated positively with the retention of bacteria observed in planta and might provide a basis for successful leaf colonization and potentially disease outbreaks of pathogens.
Berberine downregulates CDC6 and inhibits proliferation via targeting JAK-STAT3 signaling in keratinocytes
Authors: Sun Shuna , Zhang Xiaojie , Xu Mengru , Zhang Fang , Tian Fei , Cui Jianfeng , Xia Yangyang , Liang Chenxi , Zhou Shujie , Wei Haifeng , Zhao Hui , Wu Guojing , Xu Bohan , Liu Xiaochen , Yang Guanqun , Wang Qinzhou , Zhang Lei , Gong Yaoqin , Shao Changshun , Zou Yongxin
Published: March 2019

Psoriasis is a chronic skin disease characterized by hyperproliferation and impaired differentiation of epidermal keratinocytes accompanied by increased inflammation, suggesting that molecules with antiproliferation and anti-inflammatory abilities may be effective for its treatment. One of the key steps in regulating cell proliferation is DNA replication initiation, which relies on prereplication complex (pre-RC) assembly on chromatin. CDC6 is an essential regulator of pre-RC assembly and DNA replication in eukaryotic cells, but its role in proliferation of keratinocytes and psoriasis is unknown. Here we examined CDC6 expression in psoriatic skin and evaluated its function in the proliferation of human keratinocytes. CDC6 expression is upregulated in epidermal cells in psoriatic lesions and it could be induced by IL-22/STAT3 signaling, a key signaling pathway involved in the pathogenesis of psoriasis, in keratinocytes. Depletion of CDC6 leads to decreased proliferation of keratinocytes. We also revealed that berberine (BBR) could inhibit CDK4/6-RB-CDC6 signaling in keratinocytes, leading to reduced proliferation of keratinocytes. The mechanism of antiproliferation effects of BBR is through the repression of JAK1, JAK2, and TYK2, which in turn inhibits activation of STAT3. Finally, we demonstrated that BBR could inhibit imiquimod-induced psoriasis-like skin lesions and upregulation of CDC6 and p-STAT3 in mice. Collectively, our findings indicate that BBR inhibits CDC6 expression and proliferation in human keratinocytes by interfering the JAK–STAT3 signaling pathway. Thus, BBR may serve as a potential therapeutic option for patients with psoriasis.
Flat-top TIRF illumination boosts DNA-PAINT imaging and quantification
Authors: Stehr Florian , Stein Johannes , Schueder Florian , Schwille Petra , Jungmann Ralf
Published: March 2019

Super-resolution (SR) techniques have extended the optical resolution down to a few nanometers. However, quantitative treatment of SR data remains challenging due to its complex dependence on a manifold of experimental parameters. Among the different SR variants, DNA-PAINT is relatively straightforward to implement, since it achieves the necessary ‘blinking’ without the use of rather complex optical or chemical activation schemes. However, it still suffers from image and quantification artifacts caused by inhomogeneous optical excitation. Here we demonstrate that several experimental challenges can be alleviated by introducing a segment-wise analysis approach and ultimately overcome by implementing a flat-top illumination profile for TIRF microscopy using a commercially-available beam-shaping device. The improvements with regards to homogeneous spatial resolution and precise kinetic information over the whole field-of-view were quantitatively assayed using DNA origami and cell samples. Our findings open the door to high-throughput DNA-PAINT studies with thus far unprecedented accuracy for quantitative data interpretation.
Sperm-inherited H3K27me3 impacts offspring transcription and development in C. elegans
Authors: Kaneshiro Kiyomi Raye , Rechtsteiner Andreas , Strome Susan
Published: March 2019

Paternal epigenetic inheritance is gaining attention for its growing medical relevance. However, the form in which paternal epigenetic information is transmitted to offspring and how it influences offspring development remain poorly understood. Here we show that in C. elegans, sperm-inherited chromatin states transmitted to the primordial germ cells in offspring influence germline transcription and development. We show that sperm chromosomes inherited lacking the repressive histone modification H3K27me3 are maintained in that state by H3K36me3 antagonism. Inheritance of H3K27me3-lacking sperm chromosomes results in derepression in the germline of somatic genes, especially neuronal genes, predominantly from sperm-inherited alleles. This results in germ cells primed for losing their germ cell identity and adopting a neuronal fate. These data demonstrate that histone modifications are one mechanism through which epigenetic information from a father can shape offspring gene expression and development.
Reversible histone glycation is associated with disease-related changes in chromatin architecture
Authors: Zheng Qingfei , Omans Nathaniel D. , Leicher Rachel , Osunsade Adewola , Agustinus Albert S. , Finkin-Groner Efrat , D’Ambrosio Hannah , Liu Bo , Chandarlapaty Sarat , Liu Shixin , David Yael
Published: March 2019

Cellular proteins continuously undergo non-enzymatic covalent modifications (NECMs) that accumulate under normal physiological conditions and are stimulated by changes in the cellular microenvironment. Glycation, the hallmark of diabetes, is a prevalent NECM associated with an array of pathologies. Histone proteins are particularly susceptible to NECMs due to their long half-lives and nucleophilic disordered tails that undergo extensive regulatory modifications; however, histone NECMs remain poorly understood. Here we perform a detailed analysis of histone glycation in vitro and in vivo and find it has global ramifications on histone enzymatic PTMs, the assembly and stability of nucleosomes, and chromatin architecture. Importantly, we identify a physiologic regulation mechanism, the enzyme DJ-1, which functions as a potent histone deglycase. Finally, we detect intense histone glycation and DJ-1 overexpression in breast cancer tumors. Collectively, our results suggest an additional mechanism for cellular metabolic damage through epigenetic perturbation, with implications in pathogenesis.
Memory phototransistors based on exponential-association photoelectric conversion law
Authors: Shao Zhibin , Jiang Tianhao , Zhang Xiujuan , Zhang Xiaohong , Wu Xiaofeng , Xia Feifei , Xiong Shiyun , Lee Shuit-Tong , Jie Jiansheng
Published: March 2019

Ultraweak light detectors have wide-ranging important applications such as astronomical observation, remote sensing, laser ranging, and night vision. Current commercial ultraweak light detectors are commonly based on a photomultiplier tube or an avalanche photodiode, and they are incompatible with microelectronic devices for digital imaging applications, because of their high operating voltage and bulky size. Herein, we develop a memory phototransistor for ultraweak light detection, by exploiting the charge-storage accumulative effect in CdS nanoribbon. The memory phototransistors break the power law of traditional photodetectors and follow a time-dependent exponential-association photoelectric conversion law. Significantly, the memory phototransistors exhibit ultrahigh responsivity of 3.8 × 109 A W−1 and detectivity of 7.7 × 1022 Jones. As a result, the memory phototransistors are able to detect ultraweak light of 6 nW cm−2 with an extremely high sensitivity of 4 × 107. The proposed memory phototransistors offer a design concept for ultraweak light sensing devices.
Growth strategy of microbes on mixed carbon sources
Authors: Wang Xin , Xia Kang , Yang Xiaojing , Tang Chao
Published: March 2019

A classic problem in microbiology is that bacteria display two types of growth behavior when cultured on a mixture of two carbon sources: the two sources are sequentially consumed one after another (diauxie) or they are simultaneously consumed (co-utilization). The search for the molecular mechanism of diauxie led to the discovery of the lac operon. However, questions remain as why microbes would bother to have different strategies of taking up nutrients. Here we show that diauxie versus co-utilization can be understood from the topological features of the metabolic network. A model of optimal allocation of protein resources quantitatively explains why and how the cell makes the choice. In case of co-utilization, the model predicts the percentage of each carbon source in supplying the amino acid pools, which is quantitatively verified by experiments. Our work solves a long-standing puzzle and provides a quantitative framework for the carbon source utilization of microbes.
Converse flexoelectricity yields large piezoresponse force microscopy signals in non-piezoelectric materials
Authors: Abdollahi Amir , Domingo Neus , Arias Irene , Catalan Gustau
Published: March 2019

Converse flexoelectricity is a mechanical stress induced by an electric polarization gradient. It can appear in any material, irrespective of symmetry, whenever there is an inhomogeneous electric field distribution. This situation invariably happens in piezoresponse force microscopy (PFM), which is a technique whereby a voltage is delivered to the tip of an atomic force microscope in order to stimulate and probe piezoelectricity at the nanoscale. While PFM is the premier technique for studying ferroelectricity and piezoelectricity at the nanoscale, here we show, theoretically and experimentally, that large effective piezoelectric coefficients can be measured in non-piezoelectric dielectrics due to converse flexoelectricity.
Twenty-eight-day mortality in lung cancer patients with metastasis who initiated mechanical ventilation in the emergency department
Authors: Shin Sun Hye , Lee Hyun , Kang Hyung Koo , Park Joo Hyun
Published: March 2019

Few data are available regarding treatment outcomes in lung cancer patients with metastasis who initiated mechanical ventilation in the emergency department (ED). We aimed to evaluate 28-day mortality in lung cancer patients with metastasis who initiated mechanical ventilation in the ED. Patients with solid malignancy who initiated mechanical ventilation in the ED of a tertiary hospital were retrospectively identified and stratified into four groups according to the presence of lung cancer and metastasis. Among 212 included patients, the mortality rates by the 28th hospital day were as follows: 44.2% (19/43) in non-lung cancer patients without metastasis, 63.2% (43/68) in non-lung cancer patients with metastasis, 52.4% (11/21) in lung cancer patients without metastasis, and 66.2% (53/80) in lung cancer patients with metastasis. In multivariable analysis, lung cancer patients with metastasis had significantly higher odds ratio for 28-day mortality than non-lung cancer patients without metastasis (adjusted odds ratio [OR] = 7.17, 95% confidence interval [CI] = 2.14–24.01). Sepsis-related respiratory failure (adjusted OR = 2.60, 95% CI = 1.16–5.84) and cardiopulmonary resuscitation (adjusted OR = 13.34, 95% CI = 4.45–39.95) over respiratory failure without sepsis and acute organ dysfunction process measured by sequential organ failure assessment (SOFA) score (adjusted OR = 1.15, 95% CI = 1.05–12.6) were independently associated with an increase in mortality rate. In conclusion, the treatment outcomes in lung cancer patients with metastasis who initiated mechanical ventilation in the ED were poor. Aggressive resuscitation versus end-of-life care in advance of an unexpected medical crisis should be considered in lung cancer patients with metastasis via a multidisciplinary approach with a consideration of underlying comorbid illnesses in the acute organ dysfunction processes.
X-Ray Fluorescence Ionomics of Herbarium Collections
Authors: van der Ent Antony , Echevarria Guillaume , Pollard A. Joseph , Erskine Peter D.
Published: March 2019

Global herbaria are the greatest repositories of information on the plant kingdom. Discoveries of trace element hyperaccumulator plants have historically required time-consuming destructive chemical analysis of fragments from herbarium specimens, which severely constrains the collection of large datasets. Recent advances in handheld X-Ray Fluorescence spectroscopy (XRF) systems have enabled non-destructive analysis of plant samples and here we propose a new method, which we term “Herbarium XRF Ionomics”, to extract elemental data from herbarium specimens. We present two case studies from major tropical herbaria where Herbarium XRF Ionomics has led to the discovery of new hyperaccumulator plants and provided valuable insights into phylogenetic patterns of trace element hyperaccumulation. Herbarium XRF Ionomics is a new value proposition for continued funding and retention of herbarium specimens globally.
Forceful mastication activates osteocytes and builds a stout jawbone
Authors: Inoue Masamu , Ono Takehito , Kameo Yoshitaka , Sasaki Fumiyuki , Ono Takashi , Adachi Taiji , Nakashima Tomoki
Published: March 2019

Bone undergoes a constant reconstruction process of resorption and formation called bone remodeling, so that it can endure mechanical loading. During food ingestion, masticatory muscles generate the required masticatory force. The magnitude of applied masticatory force has long been believed to be closely correlated with the shape of the jawbone. However, both the mechanism underlying this correlation and evidence of causation remain largely to be determined. Here, we established a novel mouse model of increased mastication in which mice were fed with a hard diet (HD) to elicit greater masticatory force. A novel in silico computer simulation indicated that the masticatory load onto the jawbone leads to the typical bone profile seen in the individuals with strong masticatory force, which was confirmed by in vivo micro-computed tomography (micro-CT) analyses. Mechanistically, increased mastication induced Insulin–like growth factor (IGF)-1 and suppressed sclerostin in osteocytes. IGF-1 enhanced osteoblastogenesis of the cells derived from tendon. Together, these findings indicate that the osteocytes balance the cytokine expression upon the mechanical loading of increased mastication, in order to enhance bone formation. This bone formation leads to morphological change in the jawbone, so that the bone adapts to the mechanical environment to which it is exposed.
Modelling viscous boundary layer dissipation effects in liquid surrounding individual solid nano and micro-particles in an ultrasonic field
Authors: Forrester Derek Michael , Huang Jinrui , Pinfield Valerie J.
Published: March 2019

Upon application of ultrasonic waves to a suspension of solid particles in liquid, multiple scattering occurs at the particle/liquid interfaces leading to attenuation. It was recently shown through experimental verification that multiple scattering theory must include shear wave influences at the boundary between the liquid and solid particles in a nanofluid when the concentration of the scatterers is even as low as a few percent by volume. Herein, we consider silica spheres of 50–450 nm diameter in the long-wavelength regime to elucidate the form of the shear decay fields at the liquid/solid interface for individual particles. This is important because the overlap of these fields ultimately leads to the conversion of a compressional wave to shear waves and back into the compressional wave, the effect originating due to the density contrast between the particle and the liquid. Therefore, we examine in detail the velocity, vorticity and viscous dissipation in the shear wave field and around the silica spheres using finite element modelling, giving clarity to the viscous boundary effects. We also compare the numerical modelling to semi-analytical results.
Identification of new DNA-associated proteins from Waddlia chondrophila
Authors: de Barsy Marie , Herrgott Lucas , Martin Virginie , Pillonel Trestan , Viollier Patrick H. , Greub Gilbert
Published: March 2019

Transcriptional regulation in Chlamydiae is still poorly understood. The absence until recently of genetic tools is the main cause of this gap. We discovered three new potential DNA-associated proteins of Waddlia chondrophila, a Chlamydia-related bacterium, using heparin chromatography coupled to mass spectrometry (Wcw_0377, Wcw_1456, and Wcw_1460). By ChIP-seq analysis, we determined the regulatory landscape of these three proteins and we showed that Wcw_0377 binds all along the genome whereas Wcw_1456 and _1460 possess a wide regulon with a large number of co-regulated genes. Wcw_1456 and Wcw_1460 interact with RpoD (σ66), emerging as potential RpoD regulators. On the other hand, Wcw_0377 is able to reach the host nucleus, where it might interact with eukaryotic histones through its putative chromatin-remodelling SWIB/MDM2 domain.
Revealing Dissociable Attention Biases in Chronic Smokers Through an Individual-Differences Approach
Authors: Della Libera Chiara , Zandonai Thomas , Zamboni Lorenzo , Santandrea Elisa , Sandri Marco , Lugoboni Fabio , Chiamulera Cristiano , Chelazzi Leonardo
Published: March 2019

Addiction is accompanied by attentional biases (AB), wherein drug-related cues grab attention independently of their perceptual salience. AB have emerged in different flavours depending on the experimental approach, and their clinical relevance is still debated. In chronic smokers we sought evidence for dissociable attention abnormalities that may play distinct roles in the clinical manifestations of the disorder. Fifty smokers performed a modified visual probe-task measuring two forms of AB and their temporal dynamics, and data on their personality traits and smoking history/status were collected. Two fully dissociable AB effects were found: A Global effect, reflecting the overall impact of smoke cues on attention, and a Location-specific effect, indexing the impact of smoke cues on visuospatial orienting. Importantly, the two effects could be neatly separated from one another as they: (i) unfolded with dissimilar temporal dynamics, (ii) were accounted for by different sets of predictors associated with personality traits and smoking history and (iii) were not correlated with one another. Importantly, the relevance of each of these two components in the single individual depends on a complex blend of personality traits and smoking habits, a result that future efforts addressing the clinical relevance of addiction-related AB should take into careful consideration.
RNAi Screening-based Identification of USP10 as a Novel Regulator of Paraptosis
Authors: Kim Jin Yeop , Lee Dong Min , Woo Hyun Goo , Kim Ki Deok , Lee Hong Jae , Kwon Yong-Jun , Choi Kyeong Sook
Published: March 2019

Accumulating reports demonstrate that apoptosis does not explain all the effects of cancer therapy due to the innate and acquired apoptotic resistance of malignant cancer cells. Recently, paraptosis, a type of programmed cell death accompanied by dilation of mitochondria and/or the endoplasmic reticulum (ER), has garnered interest in cancer research as an alternative way to kill apoptosis-resistant cancers. We describe here the adaptation and validation of a high-content cell-based assay to screen and identify novel paraptotic regulators employing the malignant breast cancer cells undergoing curcumin-induced paraptosis. We used YFP-Mito cells, which express fluorescence selectively in mitochondria, to select paraptosis-related genes whose corresponding siRNAs appeared to modulate mitochondrial dilation, a morphological feature of paraptosis. From the selected 38 candidate genes, we chose ubiquitin specific peptidase 10 (USP10), a ubiquitin specific protease, as a strongly active candidate that warranted further evaluation of its involvement in paraptosis. We found that both siRNA-mediated knockdown of USP10 and treatment with the USP10 inhibitor, spautin-1, effectively attenuated curcumin-induced paraptosis. This systematic assay, in which a siRNA library is screened for the ability to ameliorate paraptotic changes in mitochondria, may enable researchers to identify potent regulators of paraptosis and new candidate genes/drugs to combat malignant breast cancer.
Simple Tyrosine Derivatives Act as Low Molecular Weight Organogelators
Authors: Aykent Güzide , Zeytun Cansu , Marion Antoine , Özçubukçu Salih
Published: March 2019

The gelation of L-Tyr(tBu)-OH in tetrahydrofuran (THF) was discovered serendipitously. It was noted that this tremendously low molecular weight (LMW) compound has the ability to gel a wide variety of organic solvents (e.g., N,N-Dimetylformamide (DMF), THF, butanol, toluene), even in very low concentrations (i.e., 0.1 wt/v% in DMF). Addition of bases such as NaOH and piperidine enhanced the gel property. By changing the side-chain protecting group to tert-butyldimethylsilyl (TBDMS), a fluoride ion-responsive organogel was also acquired. This new organogelator responded fluoride ion concentration as low as 0.2 ppm. Characterization of microstructures and gel behaviours were studied by powder X-Ray diffraction spectroscopy (XRD), transmission electron microscopy (TEM), rheological measurements and molecular dynamics (MD) simulations. Experimental observations and theoretical simulations consistently show a fibre-like structure of the gel, in which the organogelator molecules are held together via a dense network of hydrogen bonds, and via van der Waals interactions between hydrophobic groups.
Structure and Diversity of Soil Bacterial Communities in Offshore Islands
Authors: Lin Yu-Te , Lin Yu-Fei , Tsai Isheng J. , Chang Ed-Haun , Jien Shih-Hao , Lin Yen-Ju , Chiu Chih-Yu
Published: March 2019

The effects of biogeographical separation and parent material differences in soil bacterial structure and diversity in offshore islands remain poorly understood. In the current study, we used next-generation sequencing to characterize the differences in soil bacterial communities in five offshore subtropical granite islands (Matsu Islets, MI) of mainland China and two offshore tropical andesite islands (Orchid [OI] and Green Islands [GI]) of Taiwan. The soils of OI and GI were more acidic and had higher organic carbon and total nitrogen content than MI soils. The bacterial communities were dominated by Acidobacteria and Proteobacteria but had different relative abundance because soils were derived from different parent material and because of geographic distance. Non-metric multi-dimensional scaling revealed that the communities formed different clusters among different parent material and geographically distributed soils. The alpha-diversity in bacterial communities was higher in tropical than subtropical soils. Mantel test and redundancy analysis indicated that bacterial diversity and compositions of OI and GI soils, respectively, were positively correlated with soil pH, organic carbon, total nitrogen, microbial biomass carbon and nitrogen. These results suggest that variations in soil properties of offshore islands could result from differences in soil parent material. Distinct soils derived from different parent material and geographic distance could in turn alter the bacterial communities.
Detecting changes in facial temperature induced by a sudden auditory stimulus based on deep learning-assisted face tracking
Authors: Sonkusare Saurabh , Ahmedt-Aristizabal David , Aburn Matthew J. , Nguyen Vinh Thai , Pang Tianji , Frydman Sascha , Denman Simon , Fookes Clinton , Breakspear Michael , Guo Christine C.
Published: March 2019

Thermal Imaging (Infrared-Imaging-IRI) is a promising new technique for psychophysiological research and application. Unlike traditional physiological measures (like skin conductance and heart rate), it is uniquely contact-free, substantially enhancing its ecological validity. Investigating facial regions and subsequent reliable signal extraction from IRI data is challenging due to head motion artefacts. Exploiting its potential thus depends on advances in analytical methods. Here, we developed a novel semi-automated thermal signal extraction method employing deep learning algorithms for facial landmark identification. We applied this method to physiological responses elicited by a sudden auditory stimulus, to determine if facial temperature changes induced by a stimulus of a loud sound can be detected. We compared thermal responses with psycho-physiological sensor-based tools of galvanic skin response (GSR) and electrocardiography (ECG). We found that the temperatures of selected facial regions, particularly the nose tip, significantly decreased after the auditory stimulus. Additionally, this response was quite rapid at around 4–5 seconds, starting less than 2 seconds following the GSR changes. These results demonstrate that our methodology offers a sensitive and robust tool to capture facial physiological changes with minimal manual intervention and manual pre-processing of signals. Newer methodological developments for reliable temperature extraction promise to boost IRI use as an ecologically-valid technique in social and affective neuroscience.
A dispersal of Homo sapiens from southern to eastern Africa immediately preceded the out-of-Africa migration
Authors: Rito Teresa , Vieira Daniel , Silva Marina , Conde-Sousa Eduardo , Pereira Luísa , Mellars Paul , Richards Martin B. , Soares Pedro
Published: March 2019

Africa was the birth-place ofHomo sapiensand has the earliest evidence for symbolic behaviour and complex technologies. The best-attested early flowering of these distinctive features was in a glacial refuge zone on the southern coast 100–70 ka, with fewer indications in eastern Africa until after 70 ka. Yet it was eastern Africa, not the south, that witnessed the first major demographic expansion, ~70–60 ka, which led to the peopling of the rest of the world. One possible explanation is that important cultural traits were transmitted from south to east at this time. Here we identify a mitochondrial signal of such a dispersal soon after ~70 ka – the only time in the last 200,000 years that humid climate conditions encompassed southern and tropical Africa. This dispersal immediately preceded the out-of-Africa expansions, potentially providing the trigger for these expansions by transmitting significant cultural elements from the southern African refuge.
Calcium electroporation and electrochemotherapy for cancer treatment: Importance of cell membrane composition investigated by lipidomics, calorimetry and in vitro efficacy
Authors: Hoejholt K. L. , Mužić T. , Jensen S. D. , Dalgaard L. T. , Bilgin M. , Nylandsted J. , Heimburg T. , Frandsen S. K. , Gehl J.
Published: March 2019

Calcium electroporation is a novel anti-cancer treatment investigated in clinical trials. We explored cell sensitivity to calcium electroporation and electroporation with bleomycin, using viability assays at different time and temperature points, as well as heat calorimetry, lipidomics, and flow cytometry. Three cell lines: HT29 (colon cancer), MDA-MB231 (breast cancer), and HDF-n (normal fibroblasts) were investigated for; (a) cell survival dependent on time of addition of drug relative to electroporation (1.2 kV/cm, 8 pulses, 99 µs, 1 Hz), at different temperatures (37 °C, 27 °C, 17 °C); (b) heat capacity profiles obtained by differential scanning calorimetry without added calcium; (c) lipid composition by mass spectrometry; (d) phosphatidylserine in the plasma membrane outer leaflet using flow cytometry. Temperature as well as time of drug administration affected treatment efficacy in HT29 and HDF-n cells, but not MDA-MB231 cells. Interestingly the HT29 cell line displayed a higher phase transition temperature (approximately 20 °C) versus 14 °C (HDF-n) and 15 °C (MDA-MB231). Furthermore the HT29 cell membranes had a higher ratio of ethers to esters, and a higher expression of phosphatidylserine in the outer leaflet. In conclusion, lipid composition and heat capacity of the membrane might influence permeabilisation of cells and thereby the effect of calcium electroporation and electrochemotherapy.
Interspecific gamete compatibility and hybrid larval fitness in reef-building corals: Implications for coral reef restoration
Authors: Chan Wing Yan , Peplow Lesa M. , van Oppen Madeleine J. H.
Published: March 2019

Climate warming is a major cause of the global decline of coral reefs. Active reef restoration, although still in its infancy, is one of several possible ways to help restore coral cover and reef ecosystem function. The deployment of mature coral larvae onto depauperate reef substratum has been shown to significantly increase larval recruitment, providing a novel option for the delivery of ex situ bred coral stock to the reef for restoration purposes. The success of such reef restoration approaches may be improved by the use of coral larval stock augmented for climate resilience. Here we explore whether coral climate resilience can be enhanced via interspecific hybridization through hybrid vigour. Firstly, we assessed cross-fertility of four pairs of Acropora species from the Great Barrier Reef. Temporal isolation in gamete release between the Acropora species was limited, but gametic incompatibility was present with varying strength between species pairs and depending on the direction of the hybrid crosses. We subsequently examined the fitness of hybrid and purebred larvae under heat stress by comparing their survival and settlement success throughout 10 days of exposure to 28 °C, 29.5 °C and 31 °C. Fitness of the majority of Acropora hybrid larvae was similar to that of the purebred larvae of both parental species, and in some instances it was higher than that of the purebred larvae of one of the parental species. Lower hybrid fertilization success did not affect larval fitness. These findings indicate that high hybrid fitness can be achieved after overcoming partial prezygotic barriers, and that interspecific hybridization may be a tool to enhance coral recruitment and climate resilience.
Satellite-based indicator of zooplankton distribution for global monitoring
Authors: Druon Jean-Noël , Hélaouët Pierre , Beaugrand Grégory , Fromentin Jean-Marc , Palialexis Andreas , Hoepffner Nicolas
Published: March 2019

This study investigates the association between an index of mesozooplankton biomass, derived from the Continuous Plankton Recorder survey and satellite-derived productivity fronts in the North Atlantic. While chlorophyll-a content (CHL) is commonly described as a proxy for phytoplankton biomass, the size of productivity fronts estimated from the horizontal gradient of CHL appears to be directly linked to mesozooplankton biomass. Our results suggest that the lifespan of productivity fronts, which ranges from weeks to months, meets the time requirement of mesozooplankton to develop. The proposed indicator describes the daily distribution of mesozooplankton’s suitable feeding habitat. It also provides a coherent interpretation of the productivity front development with respect to phytoplankton activity (CHL values) and potential predation by higher trophic levels. Since mesozooplankton are essential for feeding at higher trophic levels, this satellite-derived indicator delivers essential information for research and policy. An unanticipated positive trend of the indicator from 2003 to 2017 is observed at a basin scale under the current effects of climate change, with regional peaks in relatively poorly productive areas. Such monitoring indicator is potentially important to advances in marine food web modelling, fisheries science and the dynamic management of oceans towards sustainability.
Optimization and evaluation of a non-invasive tool for peste des petits ruminants surveillance and control
Authors: Bataille Arnaud , Kwiatek Olivier , Belfkhi Salima , Mounier Lucile , Parida Satya , Mahapatra Mana , Caron Alexandre , Chubwa Chobi Clement , Keyyu Julius , Kock Richard , Jones Bryony A. , Libeau Geneviève
Published: March 2019

Peste des petits ruminants (PPR) is a highly contagious and devastating viral disease affecting mainly sheep and goats, but also a large number of wild species within the order Artiodactyla. A better understanding of PPR transmission dynamics in multi-host systems is necessary to efficiently control the disease, in particular where wildlife and livestock co-occur. Notably, the role of wildlife in PPR epidemiology is still not clearly understood. Non-invasive strategies to detect PPR infection without the need for animal handling could greatly facilitate research on PPR epidemiology and management of the disease in atypical hosts and in complex field situations. Here, we describe optimized methods for the direct detection of PPR virus genetic material and antigen in fecal samples. We use these methods to determine the detection window of PPR in fecal samples, and compare the sensitivity of these methods to standard invasive sampling and PPR diagnostic methods using field samples collected at a wildlife-livestock interface in Africa. Our results show that quantitative reverse transcription PCR (RT-QPCR) amplification of PPRV from fecal swabs has good sensitivity in comparison to ocular swabs. Animals infected by PPRV could be identified relatively early on and during the whole course of infection based on fecal samples using RT-QPCR. Partial gene sequences could also be retrieved in some cases, from both fecal and ocular samples, providing important information about virus origin and relatedness to other PPRV strains. Non-invasive strategies for PPRV surveillance could provide important data to fill major gaps in our knowledge of the multi-host PPR epidemiology.
Honey bee colony performance and health are enhanced by apiary proximity to US Conservation Reserve Program (CRP) lands
Authors: Ricigliano Vincent A. , Mott Brendon M. , Maes Patrick W. , Floyd Amy S. , Fitz William , Copeland Duan C. , Meikle William G. , Anderson Kirk E.
Published: March 2019

Honey bee colony performance and health are intimately linked to the foraging environment. Recent evidence suggests that the US Conservation Reserve Program (CRP) has a positive impact on environmental suitability for supporting honey bee apiaries. However, relatively little is known about the influence of habitat conservation efforts on honey bee colony health. Identifying specific factors that influence bee health at the colony level incorporates longitudinal monitoring of physiology across diverse environments. Using a pooled-sampling method to overcome individual variation, we monitored colony-level molecular biomarkers during critical pre- and post-winter time points. Major categories of colony health (nutrition, oxidative stress resistance, and immunity) were impacted by apiary site. In general, apiaries within foraging distance of CRP lands showed improved performance and higher gene expression of vitellogenin (vg), a nutritionally regulated protein with central storage and regulatory functions. Mirroring vg levels, gene transcripts encoding antioxidant enzymes and immune-related proteins were typically higher in colonies exposed to CRP environments. Our study highlights the potential of CRP lands to improve pollinator health and the utility of colony-level molecular diagnostics to assess environmental suitability for honey bees.
An engineered GH1 β-glucosidase displays enhanced glucose tolerance and increased sugar release from lignocellulosic materials
Authors: Santos Clelton A. , Morais Mariana A. B. , Terrett Oliver M. , Lyczakowski Jan J. , Zanphorlin Letícia M. , Ferreira-Filho Jaire A. , Tonoli Celisa C. C. , Murakami Mario T. , Dupree Paul , Souza Anete P.
Published: March 2019

β-glucosidases play a critical role among the enzymes in enzymatic cocktails designed for plant biomass deconstruction. By catalysing the breakdown of β-1, 4-glycosidic linkages, β-glucosidases produce free fermentable glucose and alleviate the inhibition of other cellulases by cellobiose during saccharification. Despite this benefit, most characterised fungal β-glucosidases show weak activity at high glucose concentrations, limiting enzymatic hydrolysis of plant biomass in industrial settings. In this study, structural analyses combined with site-directed mutagenesis efficiently improved the functional properties of a GH1 β-glucosidase highly expressed by Trichoderma harzianum (ThBgl) under biomass degradation conditions. The tailored enzyme displayed high glucose tolerance levels, confirming that glucose tolerance can be achieved by the substitution of two amino acids that act as gatekeepers, changing active-site accessibility and preventing product inhibition. Furthermore, the enhanced efficiency of the engineered enzyme in terms of the amount of glucose released and ethanol yield was confirmed by saccharification and simultaneous saccharification and fermentation experiments using a wide range of plant biomass feedstocks. Our results not only experimentally confirm the structural basis of glucose tolerance in GH1 β-glucosidases but also demonstrate a strategy to improve technologies for bioethanol production based on enzymatic hydrolysis.
Involvement of the RND efflux pump transporter SmeH in the acquisition of resistance to ceftazidime in Stenotrophomonas maltophilia
Authors: Blanco Paula , Corona Fernando , Martínez José Luis
Published: March 2019

The emergence of antibiotic resistant Gram-negative bacteria has become a serious global health issue. In this study, we have employed the intrinsically resistant opportunistic pathogen Stenotrophomonas maltophilia as a model to study the mechanisms involved in the acquisition of mutation-driven resistance to antibiotics. To this aim, laboratory experimental evolution studies, followed by whole-genome sequencing, were performed in the presence of the third-generation cephalosporin ceftazidime. Using this approach, we determined that exposure to increasing concentrations of ceftazidime selects high-level resistance in S. maltophilia through a novel mechanism: amino acid substitutions in SmeH, the transporter protein of the SmeGH RND efflux pump. The recreation of these mutants in a wild-type background demonstrated that, in addition to ceftazidime, the existence of these substitutions provides bacteria with cross-resistance to other beta-lactam drugs. This acquired resistance does not impose relevant fitness costs when bacteria grow in the absence of antibiotics. Structural prediction of both amino acid residues points that the observed resistance phenotype could be driven by changes in substrate access and recognition.