bluuebunny/crossref_metadata_2025 huggingface dataset:
Direct observation of picosecond melting and disintegration of metallic nanoparticles
Authors: Ihm Yungok , Cho Do Hyung , Sung Daeho , Nam Daewoong , Jung Chulho , Sato Takahiro , Kim Sangsoo , Park Jaehyun , Kim Sunam , Gallagher-Jones Marcus , Kim Yoonhee , Xu Rui , Owada Shigeki , Shim Ji Hoon , Tono Kensuke , Yabashi Makina , Ishikawa Tetsuya , Miao Jianwei , Noh Do Young , Song Changyong
Published: June 2019

Despite more than a century of study, the fundamental mechanisms behind solid melting remain elusive at the nanoscale. Ultrafast phenomena in materials irradiated by intense femtosecond laser pulses have revived the interest in unveiling the puzzling processes of melting transitions. However, direct experimental validation of various microscopic models is limited due to the difficulty of imaging the internal structures of materials undergoing ultrafast and irreversible transitions. Here we overcome this challenge through time-resolved single-shot diffractive imaging using X-ray free electron laser pulses. Images of single Au nanoparticles show heterogeneous melting at the surface followed by density fluctuation deep inside the particle, which is directionally correlated to the polarization of the pumping laser. Observation of this directionality links the non-thermal electronic excitation to the thermal lattice melting, which is further verified by molecular dynamics simulations. This work provides direct evidence to the understanding of irreversible melting with an unprecedented spatiotemporal resolution.
Sialyl Lewisx-P-selectin cascade mediates tumor–mesothelial adhesion in ascitic fluid shear flow
Authors: Li Shan-Shan , Ip Carman K. M. , Tang Matthew Y. H. , Tang Maggie K. S. , Tong Yin , Zhang Jiangwen , Hassan Ayon Ahmed , Mak Abby S. C. , Yung Susan , Chan Tak-Mao , Ip Philip P. , Lee Cheuk Lun , Chiu Philip C. N. , Lee Leo Tsz On , Lai Hung-Cheng , Zeng Jin-Zhang , Shum Ho Cheung , Wong Alice S. T.
Published: June 2019

Organ-specific colonization suggests that specific cell–cell recognition is essential. Yet, very little is known about this particular interaction. Moreover, tumor cell lodgement requires binding under shear stress, but not static, conditions. Here, we successfully isolate the metastatic populations of cancer stem/tumor-initiating cells (M-CSCs). We show that the M-CSCs tether more and roll slower than the non-metastatic (NM)-CSCs, thus resulting in the preferential binding to the peritoneal mesothelium under ascitic fluid shear stress. Mechanistically, this interaction is mediated by P-selectin expressed by the peritoneal mesothelium. Insulin-like growth factor receptor-1 carrying an uncommon non-sulfated sialyl-Lewisx (sLex) epitope serves as a distinct P-selectin binding determinant. Several glycosyltransferases, particularly α1,3-fucosyltransferase with rate-limiting activity for sLex synthesis, are highly expressed in M-CSCs. Tumor xenografts and clinical samples corroborate the relevance of these findings. These data advance our understanding on the molecular regulation of peritoneal metastasis and support the therapeutic potential of targeting the sLex-P-selectin cascade.
Supramolecular peptide constructed by molecular Lego allowing programmable self-assembly for photodynamic therapy
Authors: Zhu Huangtianzhi , Wang Huanhuan , Shi Bingbing , Shangguan Liqing , Tong Weijun , Yu Guocan , Mao Zhengwei , Huang Feihe
Published: June 2019

Peptide self-assemblies with multiple nanostructures have great potentials in functional biomaterials, and yet the tedious and costly covalent peptide modification and the lack of facile controllability on self-assembly morphology retard the peptide-related exploration. Here we report a simple approach to fabricate a supramolecular peptide that shows programmable self-assembly with multiple morphologies and application in photodynamic therapy. Pillar[5]arene-based host−guest recognition is used to construct a supramolecular peptide, which simplify the peptide modification and promote the controllability of the self-assembly behavior. Due to the ERGDS sequences on the exterior surfaces and hydrophobic cores of self-assemblies, the nanoparticles formed from the supramolecular peptide are suitable vehicles to encapsulate a photosensitizer for photodynamic therapy. In vitro and in vivo studies demonstrate that the inherent targeting capability and supramolecular strategy greatly boost its photodynamic therapeutic efficiency. This supramolecular peptide holds promising potentials in precise cancer therapy and perspectives for the peptide modification.
Structural basis for the clamping and Ca2+ activation of SNARE-mediated fusion by synaptotagmin
Authors: Grushin Kirill , Wang Jing , Coleman Jeff , Rothman James E. , Sindelar Charles V. , Krishnakumar Shyam S.
Published: June 2019

Synapotagmin-1 (Syt1) interacts with both SNARE proteins and lipid membranes to synchronize neurotransmitter release to calcium (Ca2+) influx. Here we report the cryo-electron microscopy structure of the Syt1–SNARE complex on anionic-lipid containing membranes. Under resting conditions, the Syt1 C2 domains bind the membrane with a magnesium (Mg2+)-mediated partial insertion of the aliphatic loops, alongside weak interactions with the anionic lipid headgroups. The C2B domain concurrently interacts the SNARE bundle via the ‘primary’ interface and is positioned between the SNAREpins and the membrane. In this configuration, Syt1 is projected to sterically delay the complete assembly of the associated SNAREpins and thus, contribute to clamping fusion. This Syt1–SNARE organization is disrupted upon Ca2+-influx as Syt1 reorients into the membrane, likely displacing the attached SNAREpins and reversing the fusion clamp. We thus conclude that the cation (Mg2+/Ca2+) dependent membrane interaction is a key determinant of the dual clamp/activator function of Synaptotagmin-1.
Highly stacked 3D organic integrated circuits with via-hole-less multilevel metal interconnects
Authors: Yoo Hocheon , Park Hongkeun , Yoo Seunghyun , On Sungmin , Seong Hyejeong , Im Sung Gap , Kim Jae-Joon
Published: June 2019

Multilevel metal interconnects are crucial for the development of large-scale organic integrated circuits. In particular, three-dimensional integrated circuits require a large number of vertical interconnects between layers. Here, we present a novel multilevel metal interconnect scheme that involves solvent-free patterning of insulator layers to form an interconnecting area that ensures a reliable electrical connection between two metals in different layers. Using a highly reliable interconnect method, the highest stacked organic transistors to date, a three-dimensional organic integrated circuits consisting of 5 transistors and 20 metal layers, is successfully fabricated in a solvent-free manner. All transistors exhibit outstanding device characteristics, including a high on/off current ratio of ~107, no hysteresis behavior, and excellent device-to-device uniformity. We also demonstrate two vertically-stacked complementary inverter circuits that use transistors on 4 different floors. All circuits show superb inverter characteristics with a 100% output voltage swing and gain up to 35 V per V.
Tumour-associated macrophages exhibit anti-tumoural properties in Sonic Hedgehog medulloblastoma
Authors: Maximov Victor , Chen Zhihong , Wei Yun , Robinson M. Hope , Herting Cameron J. , Shanmugam Nithya S. , Rudneva Vasilisa A. , Goldsmith Kelly C. , MacDonald Tobey J. , Northcott Paul A. , Hambardzumyan Dolores , Kenney Anna M.
Published: June 2019

Medulloblastoma, which is the most common malignant paediatric brain tumour, has a 70% survival rate, but standard treatments often lead to devastating life-long side effects and recurrence is fatal. One of the emerging strategies in the search for treatments is to determine the roles of tumour microenvironment cells in the growth and maintenance of tumours. The most attractive target is tumour-associated macrophages (TAMs), which are abundantly present in the Sonic Hedgehog (SHH) subgroup of medulloblastoma. Here, we report an unexpected beneficial role of TAMs in SHH medulloblastoma. In human patients, decreased macrophage number is correlated with significantly poorer outcome. We confirm macrophage anti-tumoural behaviour in both ex vivo and in vivo murine models of SHH medulloblastoma. Taken together, our findings suggest that macrophages play a positive role by impairing tumour growth in medulloblastoma, in contrast to the pro-tumoural role played by TAMs in glioblastoma, another common brain tumour.
Contact patterning by laser printing for flexible electronics on paper
Authors: Harper Angela F. , Diemer Peter J. , Jurchescu Oana D.
Published: June 2019

The desire for cost-effective strategies for producing organic electronic devices has led to many new methods for the organic semiconductor layer deposition; however, manufacturing contacts remains an expensive technique due to the high cost of both the materials used and the processing necessary for their patterning. In this work, we present a method for contact deposition and patterning, which overcomes these limitations and allows fabrication of all-printed organic thin-film transistors on paper. The method relies on depositing contacts using aerosol spray and patterning them with a digitally printed mask from an office laser printer, at ambient temperature and pressure. This technique, which we have denoted aerosol spray laser lithography, is cost-effective and extremely versatile in terms of material choice and electrode geometry. As the processing temperature does not exceed 155 °C, it is compatible with a variety of substrates, including plastic or paper. The success of this method marks an opportunity for a rapid, scalable, and low-cost alternative to current electrode-manufacturing techniques for development of flexible, large-area, electronic applications.
Suppression of olfactory signal transduction by insecticides
Authors: Takeuchi Hiroko , Kurahashi Takashi
Published: June 2019

2,4,6-Trichloroanisole (TCA) is a well-known, potent off-flavour compound present in various foods and beverages. TCA has been hypothesised to be a universal cause of flavour loss experienced in daily life. Here, however, we show that titres for the suppression of olfactory transducer channels caused by low-quality bananas are much higher than those for that caused by the TCA itself contained in the banana. We resurveyed other components of low-quality bananas and found that bananas also contain an insecticide (chlorpyrifos), and that it suppresses olfactory transducer channels. Other insecticides also suppressed olfactory transducer channels. Hence, even after passing safety examinations, certain insecticides may decrease the quality of foods and beverages by reducing their intrinsic scents.
HIV therapeutic vaccine enhances non-exhausted CD4+ T cells in a randomised phase 2 trial
Authors: Vieillard Vincent , Combadière Béhazine , Tubiana Roland , Launay Odile , Pialoux Gilles , Cotte Laurent , Girard Pierre-Marie , Simon Anne , Dudoit Yasmine , Reynes Jacques , Rockstroh Jürgen , Garcia Felipe , Gatell Jose , Devidas Alain , Yazdanpanah Yazdan , Weiss Laurence , Fätkenheuer Gerd , Autran Brigitte , Joyeux Delphine , Gharakhanian Shahin , Debré Patrice , Katlama Christine
Published: June 2019

VAC-3S is a therapeutic vaccine comprising a highly conserved HIV-gp41 motif coupled with the CRM197 carrier protein. High levels of anti-3S antibodies (Abs) have been associated with improved protection of CD4+ T-cell survival. A previous phase 1 study demonstrated the safety of VAC-3S. This multicentre, randomised, double-blind, placebo-controlled phase 2 clinical trial enroled between January 2014 and March 2015 HIV-1-infected patients under ART with plasma HIV RNA levels below 50 copies/mL and CD4 counts between 200 and 500 cells/μL. Participants were immunised with 16, 32, or 64 μg of VAC-3S, and compared to placebo. The primary outcome was immunogenicity assessed by changes from baseline of anti-3S Abs levels at week 12. Secondary outcomes included adverse events and the course of plasma HIV RNA level, CD4 count, CD4/CD8 ratio, inflammation and immune checkpoints from week 0 to week 48. Vaccination was well tolerated with no serious adverse events and induced a significant increase in anti-3S Ab response in vaccinated patients (p < 0.0001), compared to placebo. In high responders, the robust increased of CD4 count was associated with a significant and sustained reduction of PD-1 expression on CD4+ T cells through week 48 (variance p = 0.0017). PD-1 expression was correlated with level of anti-3S Abs (p = 0.0092, r = −0.68) and expression of NKp44L (p < 0.0001; r = 0.54) in CD4+ T cells. Our findings regarding the increase of non-exhausted CD4+ T cells have potentially important application in personalised HIV vaccination for HIV-infected patients with high level of PD-1 to improve their T-cell immune function.
Synergistic effect of band convergence and carrier transport on enhancing the thermoelectric performance of Ga doped Cu2Te at medium temperatures
Authors: Sarkar Sayan , Sarswat Prashant K. , Saini Shrikant , Mele Paolo , Free Michael L.
Published: June 2019

Recent advances in high performance thermoelectric materials have garnered unprecedented attention owing to their capability of direct transformation of heat energy to useful electricity. Copper Telluride (Cu2Te), a member of the chalcogenide family has emerged as a state-of-the-art thermoelectric material with low thermal conductivity and high thermoelectric (TE) performance, however, this material exhibits exceptional transport properties only at very high temperatures. In this study, we have investigated the synergistic effects of Ga doping on the TE performance by first principles calculations along with experimental validations. The DFT (Density Functional Theory) calculations predicted that Ga doping, within considerable limits enhanced the electrical conductivity and Seebeck coefficients in Cu2Te. This proof of concept was validated by experimental synthesis of Ga doped Cu2Te by simple direct annealing for shorter durations of 48 hours at 1120 ºC  (~1/4th) than in previous work and subsequent thermoelectric characterization. The enhanced electrical conductivity, thermopower, and moderate thermal conductivities led to the optimized TE performance in 3 atomic % Ga doping (Cu1.97Ga0.03Te), exhibiting a ZT value of 0.46 at 600 K, almost three times that of pristine Cu2Te in this temperature range. This comprehensive study provides the platform for developing new low-cost and energy efficient TE materials with enhanced ZT performance in medium temperature applications.
Fast eating is a strong risk factor for new-onset diabetes among the Japanese general population
Authors: Kudo Akihiro , Asahi Koichi , Satoh Hiroaki , Iseki Kunitoshi , Moriyama Toshiki , Yamagata Kunihiro , Tsuruya Kazuhiko , Fujimoto Shouichi , Narita Ichiei , Konta Tsuneo , Kondo Masahide , Shibagaki Yugo , Kasahara Masato , Watanabe Tsuyoshi , Shimabukuro Michio
Published: June 2019

Although many studies that have examined the relationship of type and amount of food and the frequency of eating with new onset of diabetes, there are few reports on the relationship between how meals are eaten, such as skipping breakfast, snacking or food ingestion speed, and the onset of diabetes. We investigated the relationship between eating speed, as well as other eating habits such as snacking and skip breakfast, and new onset of diabetes in a nation-wide Japanese cohort. We obtained data from the nation-wide annual health check program in Japan. In 197,825 participants without diabetes in 2008, questionnaires recorded data on the diet habits (eating speed, snack after supper or before sleep, and skipping breakfast) and unadjusted and multivariable-adjusted logistic regression models were used to measure the odds ratio of new-onset diabetes mellitus in a 3-year follow up. The proportion of fast eaters, those who snack after supper, snack before sleep, and skip breakfast was higher in the new-onset diabetes group than in the group who did not develop diabetes mellitus. As compared with the non-fast eater group, fast eaters were generally younger, had higher BMI, had more weight gain from 20 years onwards, and experienced frequent weight fluctuations of ≥3 kg within 1 year. The risk of fast eaters developing diabetes mellitus remained even after correction for multiple factors including age, body weight, rate of weight change, blood pressure, smoking, and alcohol consumption. No other eating habits were independent predictors for onset of diabetes mellitus. Results show that fast eating is a sole predisposing factor among eating habits for new-onset diabetes. Future studies were warranted to evaluate whether avoidance of fast eating is beneficial for prevention of diabetes mellitus.
Non-Invasive Photodynamic Therapy against -Periodontitis-causing Bacteria
Authors: Park Danbi , Choi Eun Joo , Weon Kwon-Yeon , Lee Wan , Lee Seoung Hoon , Choi Joon-Seok , Park Gyu Hwan , Lee Bada , Byun Mi Ran , Baek Kyunghwa , Choi Jin Woo
Published: June 2019

Periodontitis is initiated by causative bacteria in the gingival sulcus. However, as the lesion is often deep and out of circulation system and biofilm is frequently formed on the bacteria cluster, use of antibacterial agents has been limited and the invasive method such as curettage is thought as an only treatment. Here we designed non-invasive photodynamic therapy (PDT), with the ointment which leads a photosensitizer deliverable into gingival sulcus. We assessed whether 650 nm light-emitting-diode (LED) penetrates the 3-mm soft tissue and effectively activates a photosensitizer toluidine-blue-O (TBO) through the thickness to remove Porphyromonas gingivalis and Fusobacterium nucleatum species. The oral ointment formulation was optimized to efficiently deliver the photosensitizer into gingival sulcus and its efficacy of PDT was evaluated in in vitro and in vivo models. Four weeks of TBO-formulation mediated-PDT treatment significantly attenuated periodontitis-induced alveolar bone loss and inflammatory cytokines production in rats. These results confirm that a 650 nm LED indeed penetrates the gingiva and activates our TBO formulation which is sufficiently delivered to, and retained within, the gingival sulcus; thus, it effectively kills the bacteria that reside around the gingival sulcus. Collectively, TBO-mediated PDT using LED irradiation has potential as a safe adjunctive procedure for periodontitis treatment.
Disrupted Maturation of the Microbiota and Metabolome among Extremely Preterm Infants with Postnatal Growth Failure
Authors: Younge Noelle E. , Newgard Christopher B. , Cotten C. Michael , Goldberg Ronald N. , Muehlbauer Michael J. , Bain James R. , Stevens Robert D. , O’Connell Thomas M. , Rawls John F. , Seed Patrick C. , Ashley Patricia L.
Published: June 2019

Growth failure during infancy is a major global problem that has adverse effects on long-term health and neurodevelopment. Preterm infants are disproportionately affected by growth failure and its effects. Herein we found that extremely preterm infants with postnatal growth failure have disrupted maturation of the intestinal microbiota, characterized by persistently low diversity, dominance of pathogenic bacteria within the Enterobacteriaceae family, and a paucity of strictly anaerobic taxa including Veillonella relative to infants with appropriate postnatal growth. Metabolomic profiling of infants with growth failure demonstrated elevated serum acylcarnitines, fatty acids, and other byproducts of lipolysis and fatty acid oxidation. Machine learning algorithms for normal maturation of the microbiota and metabolome among infants with appropriate growth revealed a pattern of delayed maturation of the microbiota and metabolome among infants with growth failure. Collectively, we identified novel microbial and metabolic features of growth failure in preterm infants and potentially modifiable targets for intervention.
Functional characterisation of a novel class of in-frame insertion variants of KRAS and HRAS
Authors: Eijkelenboom Astrid , van Schaik Frederik M. A. , van Es Robert M. , Ten Broek Roel W. , Rinne Tuula , van der Vleuten Carine , Flucke Uta , Ligtenberg Marjolijn J. L. , Rehmann Holger
Published: June 2019

Mutations in the RAS genes are identified in a variety of clinical settings, ranging from somatic mutations in oncology to germline mutations in developmental disorders, also known as ‘RASopathies’, and vascular malformations/overgrowth syndromes. Generally single amino acid substitutions are identified, that result in an increase of the GTP bound fraction of the RAS proteins causing constitutive signalling. Here, a series of 7 in-frame insertions and duplications in HRAS (n = 5) and KRAS (n = 2) is presented, resulting in the insertion of 7–10 amino acids residues in the switch II region. These variants were identified in routine diagnostic screening of 299 samples for somatic mutations in vascular malformations/overgrowth syndromes (n = 6) and in germline analyses for RASopathies (n = 1). Biophysical characterization shows the inability of Guanine Nucleotide Exchange Factors to induce GTP loading and reduced intrinsic and GAP-stimulated GTP hydrolysis. As a consequence of these opposing effects, increased RAS signalling is detected in a cellular model system. Therefore these in-frame insertions represent a new class of weakly activating clinically relevant RAS variants.
Microfluidic Collective Cell Migration Assay for Study of Endothelial Cell Proliferation and Migration under Combinations of Oxygen Gradients, Tensions, and Drug Treatments
Authors: Shih Hsiu-Chen , Lee Tse-Ang , Wu Hsiao-Mei , Ko Ping-Liang , Liao Wei-Hao , Tung Yi-Chung
Published: June 2019

Proliferation and migration of endothelial cells play an important role in many biological activities, and they can be regulated by various microenvironmental factors. In this paper, a novel microfluidic collective cell migration assay is developed to study endothelial cell migration and proliferation under combinations of three oxygen conditions: normoxia, oxygen gradient, and hypoxia and three medium compositions: normal growth medium, the medium with cytochalasin-D for actin polymerization inhibition, and with YC-1 for hypoxia-inducible factor (HIF) inhibition. The microfluidic device designed in the paper allows cell patterns formed with consistent dimensions using laminar flow patterning. In addition, stable oxygen gradients can be generated within the device by a spatially confined chemical reaction method. The device can be operated in conventional cell incubators with minimal chemical reagents and instrumentation for practical applications. The results show directional collective cell migration of the endothelial cells under the oxygen gradients for all the medium compositions. The directional behavior has never been discussed before, and indicates critical roles of oxygen gradients in guiding endothelial cell migration during various biological activities. The developed assay provides a practical yet powerful tool for further in vitro study of endothelial cell behaviors under various physiological microenvironments.
A critical analysis of Powell’s results on the interdivision time distribution
Authors: Quedeville Vincent , Morchain Jérôme , Villedieu Philippe , Fox Rodney O.
Published: June 2019

The cell-age and interdivision-time probability density functions (PDFs) have been extensively investigated since the 1940s due to their fundamental role in cell growth. The pioneering work of Powell established the first relationship between the interdivision-time and cell-age PDFs. In the literature, two definitions for the interdivision-time PDF have been proposed. One stands for the age-at-rupture PDF and is experimentally observable, whereas the other is the probability density that a cell divides at a certain age and is unobservable. From Powell’s results pertaining to the unobservable interdivision-time PDF, Painter and Marr derived an inequality that is true but is incorrectly used by experimentalists to analyse single-cell data. Unfortunately, the confusion between these two PDFs persists. To dissipate this confusion, exact relationships between the cell-age and the interdivision-time PDFs are derived in this work from an age-structured model, which can be used by experimentalists to analyse cell growth in batch and continuous culture modes.
Dietary Patterns and Age-Related Macular Degeneration in Korea: The Korea National Health and Nutrition Examination Survey 2010–2011
Authors: Kang Kyung Tae , Kim Yu Cheol
Published: June 2019

This study was performed to reveal dietary patterns and age-related macular degeneration risk association in general Korean population. A retrospective cross-sectional database analysis using the data collected from January 2010 to December 2011 at a Korea nationwide survey was conducted. The present analysis was performed from December 2016 to November 2017. Detailed grading with fundus photographs was performed by observers blinded to the patient characteristics. The current study focused on subjects forty year and older who had fundus photographs that is assessable from at least one eye (7,899 participants). Participants were excluded if they reported extreme energy intake (142 participants) or if they were likely to have changed dietary behavior (1,171 participants), or with missing data (n = 764). After exclusion, 5,843 participants data were analyzed in the current study. As the result, 6.8% of the participants exhibited early stages of age-related macular degeneration and 0.6% exhibited late stages. Furthermore, relatively more frequent fish consumption was associated reduced odds of early age-related macular degeneration when comparing the third quartile with the first quartile groups, however, relatively more frequent legume consumption was associated with reduced odds of late age-related macular degeneration when comparing the third quartile with the first quartile groups. In conclusion, the current study insists that the diet pattern rich in fish and legume might have protective effect against age-related macular degeneration in Korean population.
Chronic synaptic insulin resistance after traumatic brain injury abolishes insulin protection from amyloid beta and tau oligomer-induced synaptic dysfunction
Authors: Franklin Whitney , Krishnan Balaji , Taglialatela Giulio
Published: June 2019

Traumatic brain injury (TBI) is a risk factor for Alzheimer’s disease (AD), although the mechanisms contributing to this increased risk are unknown. Insulin resistance is an additional risk factor for AD whereby decreased insulin signaling increases synaptic sensitivity to amyloid beta (Aβ) and tau. Considering this, we used rats that underwent a lateral fluid percussion injury at acute and chronic time-points to investigate whether decreased insulin responsiveness in TBI animals is playing a role in synaptic vulnerability to AD pathology. We detected acute and chronic decreases in insulin responsiveness in isolated hippocampal synaptosomes after TBI. In addition to assessing both Aβ and tau binding on synaptosomes, we performed electrophysiology to assess the dysfunctional impact of Aβ and tau oligomers as well as the protective effect of insulin. While we saw no difference in binding or degree of LTP inhibition by either Aβ or tau oligomers between sham and TBI animals, we found that insulin treatment was able to block oligomer-induced LTP inhibition in sham but not in TBI animals. Since insulin treatment has been discussed as a therapy for AD, this gives valuable insight into therapeutic implications of treating AD patients based on one’s history of associated risk factors.
Transcriptomic analysis of resistant and susceptible banana corms in response to infection by Fusarium oxysporum f. sp. cubense tropical race 4
Authors: Zhang Lei , Cenci Alberto , Rouard Mathieu , Zhang Dong , Wang Yunyue , Tang Weihua , Zheng Si-Jun
Published: June 2019

Fusarium wilt disease, caused by Fusarium oxysporum f. sp. cubense, especially by tropical race 4 (Foc TR4), is threatening the global banana industry. Musa acuminata Pahang, a wild diploid banana that displays strong resistance to Foc TR4, holds great potential to understand the underlying resistance mechanisms. Microscopic examination reports that, in a wounding inoculation system, the Foc TR4 infection processes in roots of Pahang (resistant) and a triploid cultivar Brazilian (susceptible) were similar by 7 days post inoculation (dpi), but significant differences were observed in corms of both genotypes at 14 dpi. We compare transcriptomic responses in the corms of Pahang and Brazilian, and show that Pahang exhibited constitutive defense responses before Foc TR4 infection and inducible defense responses prior to Brazilian at the initial Foc TR4 infection stage. Most key enzymatic genes in the phenylalanine metabolism pathway were up-regulated in Brazilian, suggesting that lignin and phytotoxin may be triggered during later stages of Foc TR4 infection. This study unravels a few potential resistance candidate genes whose expression patterns were assessed by RT-qPCR assay and improves our understanding the defense mechanisms of Pahang response to Foc TR4.
Genome-Wide DNA from Degraded Petrous Bones and the Assessment of Sex and Probable Geographic Origins of Forensic Cases
Authors: Gaudio Daniel , Fernandes Daniel M. , Schmidt Ryan , Cheronet Olivia , Mazzarelli Debora , Mattia Mirko , O’Keeffe Tadhg , Feeney Robin N. M. , Cattaneo Cristina , Pinhasi Ron
Published: June 2019

The acquisition of biological information and assessment of the most probable geographic origin of unidentified individuals for obtaining positive identification is central in forensic sciences. Identification based on forensic DNA, however, varies greatly in relation to degradation of DNA. Our primary aim is to assess the applicability of a petrous bone sampling method in combination with Next Generation Sequencing to evaluate the quality and quantity of DNA in taphonomically degraded petrous bones from forensic and cemetery cases. A related aim is to analyse the genomic data to obtain the molecular sex of each individual, and their most probable geographic origin. Six of seven subjects were previously identified and used for comparison with the results. To analyse their probable geographic origin, samples were genotyped for the 627.719 SNP positions. Results show that the inner ear cochlear region of the petrous bone provides good percentages of endogenous DNA (14.61–66.89%), even in the case of burnt bodies. All comparisons between forensic records and genetic results agree (sex) and are compatible (geographic origin). The application of the proposed methodology may be a powerful tool for use in forensic scenarios, ranging from missing persons to unidentified migrants who perish when crossing borders.
Automated detection of the HER2 gene amplification status in Fluorescence in situ hybridization images for the diagnostics of cancer tissues
Authors: Zakrzewski Falk , de Back Walter , Weigert Martin , Wenke Torsten , Zeugner Silke , Mantey Robert , Sperling Christian , Friedrich Katrin , Roeder Ingo , Aust Daniela , Baretton Gustavo , Hönscheid Pia
Published: June 2019

The human epidermal growth factor receptor 2 (HER2) gene amplification status is a crucial marker for evaluating clinical therapies of breast or gastric cancer. We propose a deep learning-based pipeline for the detection, localization and classification of interphase nuclei depending on their HER2 gene amplification state in Fluorescence in situ hybridization (FISH) images. Our pipeline combines two RetinaNet-based object localization networks which are trained (1) to detect and classify interphase nuclei into distinct classes normal, low-grade and high-grade and (2) to detect and classify FISH signals into distinct classes HER2 or centromere of chromosome 17 (CEN17). By independently classifying each nucleus twice, the two-step pipeline provides both robustness and interpretability for the automated detection of the HER2 amplification status. The accuracy of our deep learning-based pipeline is on par with that of three pathologists and a set of 57 validation images containing several hundreds of nuclei are accurately classified. The automatic pipeline is a first step towards assisting pathologists in evaluating the HER2 status of tumors using FISH images, for analyzing FISH images in retrospective studies, and for optimizing the documentation of each tumor sample by automatically annotating and reporting of the HER2 gene amplification specificities.
First report of community dynamics of arbuscular mycorrhizal fungi in radiocesium degradation lands after the Fukushima-Daiichi Nuclear disaster in Japan
Authors: Higo Masao , Kang Dong-Jin , Isobe Katsunori
Published: June 2019

Arbuscular mycorrhizal fungi (AMF) can be beneficial for improving restoration of radioactive-cesium (137Cs)-contaminated soils through soil remediation. However, there has been no information on species diversity and the composition of AMF communities in137Cs-contaminated soil after the Fukushima-Daiichi Nuclear Power Plant (NPP) disaster. We examined the community dynamics of indigenous AMF colonizing roots of napiergrass (Pennisetum purpureum) in two different137Cs-contaminated land-use fields (grassland and paddy field) by an Illumina MiSeq sequencing investigation within a 30-km radius around the Fukushima-Daiichi NPP in 2013 (sampling year 1) and 2014 (sampling year 2). We found nine AMF families, including Glomeraceae, Gigasporaceae, Paraglomeraceae, Claroideoglomeraceae, Acaulosporaceae, Archeosporaceae, Ambisporaceae, Diversisporaceae and uncultured Glomeromycotina in roots. Glomeraceae was the most abundant in both grassland and paddy field, followed by Paraglomeraceae. The diversity of AMF in grassland and paddy field was higher in 2014 than in 2013. Furthermore, the AMF community structure was impacted by sampling year and land-use type. The AMF community structures colonizing napiergrass roots were also significantly impacted by land-use type and year throughout the 2-year investigation. To our knowledge, our results are the first report to reveal the community dynamics of indigenous AMF in the137Cs-contaminated fields around NPP.
Gene expression profiles during subclinical Mycobacterium avium subspecies paratuberculosis infection in sheep can predict disease outcome
Authors: Purdie Auriol C. , Plain Karren M. , Begg Douglas J. , de Silva Kumudika , Whittington Richard J.
Published: June 2019

Paratuberculosis in ruminants is caused by infection withMycobacterium aviumsubspeciesparatuberculosis(MAP) however exposure does not predetermine progression to clinical disease. The pathogenesis incorporates a subclinical phase during which MAP is capable of evading host immune responses through adaptation of host cellular immune mechanisms. Presented are results of transcriptomic analysis of Merino sheep experimentally exposed to MAP and repeatedly sampled over the subclinical phase, identifying genes consistently changed over time in comparison to unexposed controls and associated with different disease outcomes. MAP exposed sheep were classified as diseased 45% (n = 9) or resilient 55% (n = 11). Significant gene expression changes were identified in the white blood cells of paucibacillary (n = 116), multibacillary (n = 98) and resilient cohorts (n = 53) compared to controls. Members of several gene families were differentially regulated, including S100 calcium binding, lysozyme function, MHC class I and class II, T cell receptor and transcription factors. The microarray findings were validated by qPCR. These differentially regulated genes are presented as putative biomarkers of MAP exposure, or of the specified disease or resilience outcomes. Further,in silicofunctional analysis of genes suggests that experimental MAP exposure in Merino sheep results in adaptations to cellular growth, proliferation and lipid metabolism.
Incidence, predictors, and prognosis of premature discontinuation or switch of prasugrel or ticagrelor: the ATLANTIS - SWITCH study
Authors: Winter Max-Paul , von Lewinski Dirk , Wallner Markus , Prüller Florian , Kolesnik Ewald , Hengstenberg Christian , Siller-Matula Jolanta M.
Published: June 2019

Aim of the present study was to investigate the frequency and predictors of premature discontinuation or switch of ADP receptor blockers and its association with serious adverse events. For this purpose 571 consecutive ACS patients receiving ticagrelor (n = 258, 45%) or prasugrel (n = 313, 55%) undergoing PCI were enrolled in this prospective, observational, multicenter ATLANTIS-SWITCH substudy. Predictors of premature discontinuation or switch of antiplatelet therapy and their association with major adverse cardiovascular events and TIMI bleeding events were evaluated. Premature stop/switch was found in 72 (12.6%) patients: 34 (5.9%) stopped and 38 (6.7%) switched the ADP blocker. Ticagrelor treated patients were significantly more likely to stop/switch therapy as compared to prasugrel (15.9% vs. 9.2%, p = 0.016). We identified 4 independent predictors for stop/switch of ADP blocker: major surgery, need for oral anticoagulation (OAC), TIMI major bleeding and drug intolerance. TIMI major bleeding was a driver of stop/switch actions and occurred in 4.3% vs 0.2% in patients with vs without stop/switch (p = 0.001). The majority of stop/switch actions (75%) were physicians driven decisions. Importantly, stop/switch of therapy was not associated with increased risk of MACE (p = 0.936). In conclusion premature switch/stop of ADP blockers appears to be safe when mainly driven by physician’s decision and clinical indication.
Relationship between ETS Transcription Factor ETV1 and TGF-β-regulated SMAD Proteins in Prostate Cancer
Authors: Oh Sangphil , Shin Sook , Song Hoogeun , Grande Joseph P. , Janknecht Ralf
Published: June 2019

The ETS transcription factor ETV1 is frequently overexpressed in aggressive prostate cancer, which is one underlying cause of this disease. Accordingly, transgenic mice that prostate-specifically overexpress ETV1 develop prostatic intraepithelial neoplasia. However, progression to the adenocarcinoma stage is stifled in these mice, suggesting that inhibitory pathways possibly preclude ETV1 from exerting its full oncogenic potential. Here we provide evidence that TGF-β/SMAD signaling represents such an inhibitory pathway. First, we discovered that ETV1 forms complexes with SMAD4. Second, SMAD2, SMAD3 and SMAD4 overexpression impaired ETV1’s ability to stimulate gene transcription. Third, TGF-β1 inhibited ETV1-induced invasion by benign RWPE-1 prostate cells. Fourth, increased expression of SMAD3 and SMAD4 was observable in prostates of ETV1 transgenic mice. Conversely, we found that ETV1 may enhance TGF-β signaling in PC3 prostate cancer cells, revealing a different facet of the ETV1/TGF-β interplay. Altogether, these data provide more insights into the regulation and action of ETV1 and additionally suggest that TGF-β/SMAD signaling exerts its tumor suppressive activity, at least in part, by curtailing the oncogenic potential of ETV1 in prostatic lesions.
Hair Cortisol Measurement by an Automated Method
Authors: Gonzalez Diego , Jacobsen Dario , Ibar Carolina , Pavan Carlos , Monti José , Fernandez Machulsky Nahuel , Balbi Ayelen , Fritzler Analy , Jamardo Juan , Repetto Esteban M. , Berg Gabriela , Fabre Bibiana
Published: June 2019

We present the development of the first procedure for hair cortisol measurement through an automated method. Hair samples were obtained from 286 individuals. After cortisol extraction, samples were measured in a Siemens Immulite 2000 (Gwynedd, UK) automated chemoluminiscent immunoassay analyzer. Normal reference values were obtained from hair cortisol levels measured in 213 healthy individuals with low levels of stress. Hair cortisol concentration median was 55 pg/mg hair (2.5–97.5 percentile (40–128)) in healthy individuals with low levels of stress and 250 pg/mg hair (range 182–520) in stressed individuals. No significant differences were observed in hair cortisol levels between subjects with and without dye (40 (40–107) and 40 (40–155) pg/mg hair, respectively; p = 0.128). The novel procedure presented here shows an adequate analytical performance.
Influence of Initial Residual Stress on Growth and Pattern Creation for a Layered Aorta
Authors: Du Yangkun , Lü Chaofeng , Destrade Michel , Chen Weiqiu
Published: June 2019

Residual stress is ubiquitous and indispensable in most biological and artificial materials, where it sustains and optimizes many biological and functional mechanisms. The theory of volume growth, starting from a stress-free initial state, is widely used to explain the creation and evolution of growth-induced residual stress and the resulting changes in shape, and to model how growing bio-tissues such as arteries and solid tumors develop a strategy of pattern creation according to geometrical and material parameters. This modelling provides promising avenues for designing and directing some appropriate morphology of a given tissue or organ and achieve some targeted biomedical function. In this paper, we rely on a modified, augmented theory to reveal how we can obtain growth-induced residual stress and pattern evolution of a layered artery by starting from an existing, non-zero initial residual stress state. We use experimentally determined residual stress distributions of aged bi-layered human aortas and quantify their influence by a magnitude factor. Our results show that initial residual stress has a more significant impact on residual stress accumulation and the subsequent evolution of patterns than geometry and material parameters. Additionally, we provide an essential explanation for growth-induced patterns driven by differential growth coupled to an initial residual stress. Finally, we show that initial residual stress is a readily available way to control growth-induced pattern creation for tissues and thus may provide a promising inspiration for biomedical engineering.
Characterization of mouse ocular response to a 35-day spaceflight mission: Evidence of blood-retinal barrier disruption and ocular adaptations
Authors: Mao Xiao W. , Nishiyama Nina C. , Byrum Stephanie D. , Stanbouly Seta , Jones Tamako , Drew Alyson , Sridharan Vijayalakshmi , Boerma Marjan , Tackett Alan J. , Zawieja David , Willey Jeffrey S. , Delp Michael , Pecaut Michael J.
Published: June 2019

The health risks associated with spaceflight-induced ocular structural and functional damage has become a recent concern for NASA. The goal of the present study was to characterize the effects of spaceflight and reentry to 1 g on the structure and integrity of the retina and blood-retinal barrier (BRB) in the eye. To investigate possible mechanisms, changes in protein expression profiles were examined in mouse ocular tissue after spaceflight. Ten week old male C57BL/6 mice were launched to the International Space Station (ISS) on Space-X 12 at the Kennedy Space Center (KSC) on August, 2017. After a 35-day mission, mice were returned to Earth alive. Within 38 +/− 4 hours of splashdown, mice were euthanized and ocular tissues were collected for analysis. Ground control (GC) and vivarium control mice were maintained on Earth in flight hardware or normal vivarium cages respectively. Repeated intraocular pressure (IOP) measurements were performed before the flight launch and re-measured before the mice were euthanized after splashdown. IOP was significantly lower in post-flight measurements compared to that of pre-flight (14.4–19.3 mmHg vs 16.3–20.3 mmHg) (p < 0.05) for the left eye. Flight group had significant apoptosis in the retina and retinal vascular endothelial cells compared to control groups (p < 0.05). Immunohistochemical analysis of the retina revealed that an increased expression of aquaporin-4 (AQP-4) in the flight mice compared to controls gave strong indication of disturbance of BRB integrity. There were also a significant increase in the expression of platelet endothelial cell adhesion molecule-1 (PECAM-1) and a decrease in the expression of the BRB-related tight junction protein, Zonula occludens-1 (ZO-1). Proteomic analysis showed that many key proteins and pathways responsible for cell death, cell cycle, immune response, mitochondrial function and metabolic stress were significantly altered in the flight mice compared to ground control animals. These data indicate a complex cellular response that may alter retina structure and BRB integrity following long-term spaceflight.
Heterogenising study samples across testing time improves reproducibility of behavioural data
Authors: Bodden Carina , von Kortzfleisch Vanessa Tabea , Karwinkel Fabian , Kaiser Sylvia , Sachser Norbert , Richter S. Helene
Published: June 2019

The ongoing debate on the reproducibility crisis in the life sciences highlights the need for a rethinking of current methodologies. Since the trend towards ever more standardised experiments is at risk of causing highly idiosyncratic results, an alternative approach has been suggested to improve the robustness of findings, particularly from animal experiments. This concept, referred to as “systematic heterogenisation”, postulates increased external validity and hence, improved reproducibility by introducing variation systematically into a single experiment. However, the implementation of this concept in practice requires the identification of suitable heterogenisation factors. Here we show that the time of day at which experiments are conducted has a significant impact on the reproducibility of behavioural differences between two mouse strains, C57BL/6J and DBA/2N. Specifically, we found remarkably varying strain effects on anxiety, exploration, and learning, depending on the testing time, i.e. morning, noon or afternoon. In a follow-up simulation approach, we demonstrate that the systematic inclusion of two different testing times significantly improved reproducibility between replicate experiments. Our results emphasise the potential of time as an effective and easy-to-handle heterogenisation factor for single-laboratory studies. Its systematic variation likely improves reproducibility of research findings and hence contributes to a fundamental issue of experimental design and conduct in laboratory animal science.
A novel endogenous selection marker for the diatom Phaeodactylum tricornutum based on a unique mutation in phytoene desaturase 1
Authors: Taparia Yogesh , Zarka Aliza , Leu Stefan , Zarivach Raz , Boussiba Sammy , Khozin-Goldberg Inna
Published: June 2019

Phaeodactylum tricornutumis a well-developed model diatom for both marine ecology and microalgal biotechnology, which has been enabled by the sequenced genome and the availability of gene delivery tools, such as biolistic transformation andE.coli-mediated conjugation. Till now, these tools have mainly relied on two selectable markers of bacterial origin which confer resistance to antibiotics Zeocin and nourseothricin. An alternative cost-effective and preferably endogenous selectable marker would facilitate gene stacking efforts through successive transformation or conjugation. We performed UV-mutagenesis ofP.tricornutumto obtain mutations in the phytoene desaturase (PDS) gene, conferring resistance to the bleaching herbicide norflurazon. Two mutants displaying high tolerance to norflurazon and carrying unique mutations in PtPDS1 (PHATRDRAFT_45735) were selected. These mutants revealed novel point mutations at a conserved residue Gly290 to Ser/Arg. Homology-based structural modeling of mutated PDS1, over a resolved crystallographic model of rice PDS1 complexed with norflurazon, suggests steric hindrance by bulkier residue substitution may confer herbicide resistance. We report the characterization of PtPDS1 mutants and the development of the first endogenous selectable marker in diatoms suitable for industrial strain development, with the added benefit of biocontainment. The plasmid carrying the mutated PDS1 as a selection marker and eGFP as a reporter was created. An optimized biolistic transformation system is reported which allowed the isolation of positive transgenic events at the rate of 96.7%. Additionally, the ease ofin vivoUV-mutagenesis may be employed as a strategy to create PDS-norflurazon-based selectable markers for other diatoms.