bluuebunny/crossref_metadata_2025 huggingface dataset:
Principles of meiotic chromosome assembly revealed in S. cerevisiae
Authors: Schalbetter Stephanie A. , Fudenberg Geoffrey , Baxter Jonathan , Pollard Katherine S. , Neale Matthew J.
Published: October 2019

During meiotic prophase, chromosomes organise into a series of chromatin loops emanating from a proteinaceous axis, but the mechanisms of assembly remain unclear. Here we useSaccharomyces cerevisiaeto explore how this elaborate three-dimensional chromosome organisation is linked to genomic sequence. As cells enter meiosis, we observe that strong cohesin-dependent grid-like Hi-C interaction patterns emerge, reminiscent of mammalian interphase organisation, but with distinct regulation. Meiotic patterns agree with simulations of loop extrusion with growth limited by barriers, in which a heterogeneous population of expanding loops develop along the chromosome. Importantly, CTCF, the factor that imposes similar features in mammalian interphase, is absent inS. cerevisiae, suggesting alternative mechanisms of barrier formation. While grid-like interactions emerge independently of meiotic chromosome synapsis, synapsis itself generates additional compaction that matures differentially according to telomere proximity and chromosome size. Collectively, our results elucidate fundamental principles of chromosome assembly and demonstrate the essential role of cohesin within this evolutionarily conserved process.
Self-assembling peptides imaged by correlated liquid cell transmission electron microscopy and MALDI-imaging mass spectrometry
Authors: Touve Mollie A. , Carlini Andrea S. , Gianneschi Nathan C.
Published: October 2019

We describe the observation of stimuli-induced peptide-based nanoscale assemblies by liquid cell transmission electron microscopy (LCTEM). LCTEM offers the opportunity to directly image nanoscale materials in liquid. Despite broad interest in characterizing biological phenomena, electron beam-induced damage remains a significant problem. Concurrently, methods for verifying chemical structure during or following an LCTEM experiment have been few, with key examples limited to electron diffraction or elemental analysis of crystalline materials; this strategy is not translatable to biopolymers observed in nature. In this proof-of-concept study, oligomeric peptides are biologically or chemically stimulated within the liquid cell in a TEM to assemble into nanostructures. The resulting materials are analyzed by MALDI-imaging mass spectrometry (MALDI-IMS) to verify their identity. This approach confirms whether higher-order assemblies observed by LCTEM consist of intact peptides, verifying that observations made during the in situ experiment are because of those same peptides and not aberrant electron beam damage effects.
Cellular and synaptic phenotypes lead to disrupted information processing in Fmr1-KO mouse layer 4 barrel cortex
Authors: Domanski Aleksander P. F. , Booker Sam A. , Wyllie David J. A. , Isaac John T. R. , Kind Peter C.
Published: October 2019

Sensory hypersensitivity is a common and debilitating feature of neurodevelopmental disorders such as Fragile X Syndrome (FXS). How developmental changes in neuronal function culminate in network dysfunction that underlies sensory hypersensitivities is unknown. By systematically studying cellular and synaptic properties of layer 4 neurons combined with cellular and network simulations, we explored how the array of phenotypes in Fmr1-knockout (KO) mice produce circuit pathology during development. We show that many of the cellular and synaptic pathologies in Fmr1-KO mice are antagonistic, mitigating circuit dysfunction, and hence may be compensatory to the primary pathology. Overall, the layer 4 network in the Fmr1-KO exhibits significant alterations in spike output in response to thalamocortical input and distorted sensory encoding. This developmental loss of layer 4 sensory encoding precision would contribute to subsequent developmental alterations in layer 4-to-layer 2/3 connectivity and plasticity observed in Fmr1-KO mice, and circuit dysfunction underlying sensory hypersensitivity.
CRISPR-mediated gene silencing reveals involvement of the archaeal S-layer in cell division and virus infection
Authors: Zink Isabelle Anna , Pfeifer Kevin , Wimmer Erika , Sleytr Uwe B. , Schuster Bernhard , Schleper Christa
Published: October 2019

The S-layer is a proteinaceous surface lattice found in the cell envelope of bacteria and archaea. In most archaea, a glycosylated S-layer constitutes the sole cell wall and there is evidence that it contributes to cell shape maintenance and stress resilience. Here we use a gene-knockdown technology based on an endogenous CRISPR type III complex to gradually silence slaB, which encodes the S-layer membrane anchor in the hyperthermophilic archaeon Sulfolobus solfataricus. Silenced cells exhibit a reduced or peeled-off S-layer lattice, cell shape alterations and decreased surface glycosylation. These cells barely propagate but increase in diameter and DNA content, indicating impaired cell division; their phenotypes can be rescued through genetic complementation. Furthermore, S-layer depleted cells are less susceptible to infection with the virus SSV1. Our study highlights the usefulness of the CRISPR type III system for gene silencing in archaea, and supports that an intact S-layer is important for cell division and virus susceptibility.
Modeling and simulation of complex dynamic musculoskeletal architectures
Authors: Zhang Xiaotian , Chan Fan Kiat , Parthasarathy Tejaswin , Gazzola Mattia
Published: October 2019

Natural creatures, from fish and cephalopods to snakes and birds, combine neural control, sensory feedback and compliant mechanics to effectively operate across dynamic, uncertain environments. In order to facilitate the understanding of the biophysical mechanisms at play and to streamline their potential use in engineering applications, we present here a versatile numerical approach to the simulation of musculoskeletal architectures. It relies on the assembly of heterogenous, active and passive Cosserat rods into dynamic structures that model bones, tendons, ligaments, fibers and muscle connectivity. We demonstrate its utility in a range of problems involving biological and soft robotic scenarios across scales and environments: from the engineering of millimeter-long bio-hybrid robots to the synthesis and reconstruction of complex musculoskeletal systems. The versatility of this methodology offers a framework to aid forward and inverse bioengineering designs as well as fundamental discovery in the functioning of living organisms.
A mutualistic interaction between Streptomyces bacteria, strawberry plants and pollinating bees
Authors: Kim Da-Ran , Cho Gyeongjun , Jeon Chang-Wook , Weller David M. , Thomashow Linda S. , Paulitz Timothy C. , Kwak Youn-Sig
Published: October 2019

Microbes can establish mutualistic interactions with plants and insects. Here we track the movement of an endophytic strain of Streptomyces bacteria throughout a managed strawberry ecosystem. We show that a Streptomyces isolate found in the rhizosphere and on flowers protects both the plant and pollinating honeybees from pathogens (phytopathogenic fungus Botrytis cinerea and pathogenic bacteria, respectively). The pollinators can transfer the Streptomyces bacteria among flowers and plants, and Streptomyces can move into the plant vascular bundle from the flowers and from the rhizosphere. Our results present a tripartite mutualism between Streptomyces, plant and pollinator partners.
Maternal insulin resistance multigenerationally impairs synaptic plasticity and memory via gametic mechanisms
Authors: Fusco Salvatore , Spinelli Matteo , Cocco Sara , Ripoli Cristian , Mastrodonato Alessia , Natale Francesca , Rinaudo Marco , Livrizzi Giulia , Grassi Claudio
Published: October 2019

Metabolic diseases harm brain health and cognitive functions, but whether maternal metabolic unbalance may affect brain plasticity of next generations is still unclear. Here, we demonstrate that maternal high fat diet (HFD)-dependent insulin resistance multigenerationally impairs synaptic plasticity, learning and memory. HFD downregulates BDNF and insulin signaling in maternal tissues and epigenetically inhibits BDNF expression in both germline and hippocampus of progeny. Notably, exposure of the HFD offspring to novel enriched environment restores Bdnf epigenetic activation in the male germline and counteracts the transmission of cognitive impairment to the next generations. BDNF administration to HFD-fed mothers or preserved insulin sensitivity in HFD-fed p66Shc KO mice also prevents the intergenerational transmission of brain damage to the progeny. Collectively, our data suggest that maternal diet multigenerationally impacts on descendants’ brain health via gametic mechanisms susceptible to lifestyle.
A secreted microRNA disrupts autophagy in distinct tissues of Caenorhabditis elegans upon ageing
Authors: Zhou Yifei , Wang Xueqing , Song Mengjiao , He Zhidong , Cui Guizhong , Peng Guangdun , Dieterich Christoph , Antebi Adam , Jing Naihe , Shen Yidong
Published: October 2019

Macroautophagy, a key player in protein quality control, is proposed to be systematically impaired in distinct tissues and causes coordinated disruption of protein homeostasis and ageing throughout the body. Although tissue-specific changes in autophagy and ageing have been extensively explored, the mechanism underlying the inter-tissue regulation of autophagy with ageing is poorly understood. Here, we show that a secreted microRNA, mir-83/miR-29, controls the age-related decrease in macroautophagy across tissues in Caenorhabditis elegans. Upregulated in the intestine by hsf-1/HSF1 with age, mir-83 is transported across tissues potentially via extracellular vesicles and disrupts macroautophagy by suppressing CUP-5/MCOLN, a vital autophagy regulator, autonomously in the intestine as well as non-autonomously in body wall muscle. Mutating mir-83 thereby enhances macroautophagy in different tissues, promoting protein homeostasis and longevity. These findings thus identify a microRNA-based mechanism to coordinate the decreasing macroautophagy in various tissues with age.
Giant anisotropic thermal expansion actuated by thermodynamically assisted reorientation of imidazoliums in a single crystal
Authors: Yao Zi-Shuo , Guan Hanxi , Shiota Yoshihito , He Chun-Ting , Wang Xiao-Lei , Wu Shu-Qi , Zheng Xiaoyan , Su Sheng-Qun , Yoshizawa Kazunari , Kong Xueqian , Sato Osamu , Tao Jun
Published: October 2019

Materials demonstrating unusual large positive and negative thermal expansion are fascinating for their potential applications as high-precision microscale actuators and thermal expansion compensators for normal solids. However, manipulating molecular motion to execute huge thermal expansion of materials remains a formidable challenge. Here, we report a single-crystal Cu(II) complex exhibiting giant thermal expansion actuated by collective reorientation of imidazoliums. The circular molecular cations, which are rotationally disordered at a high temperature and statically ordered at a low temperature, demonstrate significant reorientation in the molecular planes. Such atypical molecular motion, revealed by variable-temperature single crystal X-ray diffraction and solid-state NMR analyses, drives an exceptionally large positive thermal expansion and a negative thermal expansion in a perpendicular direction of the crystal. The consequent large shape change (~10%) of bulk material, with remarkable durability, suggests that this complex is a strong candidate as a microscale thermal actuating material.
Tracking vegetation phenology across diverse biomes using Version 2.0 of the PhenoCam Dataset
Authors: Seyednasrollah Bijan , Young Adam M. , Hufkens Koen , Milliman Tom , Friedl Mark A. , Frolking Steve , Richardson Andrew D.
Published: October 2019

Monitoring vegetation phenology is critical for quantifying climate change impacts on ecosystems. We present an extensive dataset of 1783 site-years of phenological data derived from PhenoCam network imagery from 393 digital cameras, situated from tropics to tundra across a wide range of plant functional types, biomes, and climates. Most cameras are located in North America. Every half hour, cameras upload images to the PhenoCam server. Images are displayed in near-real time and provisional data products, including timeseries of the Green Chromatic Coordinate (Gcc), are made publicly available through the project web page (https://phenocam.sr.unh.edu/webcam/gallery/). Processing is conducted separately for each plant functional type in the camera field of view. The PhenoCam Dataset v2.0, described here, has been fully processed and curated, including outlier detection and expert inspection, to ensure high quality data. This dataset can be used to validate satellite data products, to evaluate predictions of land surface models, to interpret the seasonality of ecosystem-scale CO2 and H2O flux data, and to study climate change impacts on the terrestrial biosphere.
16S rDNA based skin microbiome data of healthy individuals and leprosy patients from India
Authors: Bayal Nitin , Nagpal Sunil , Haque Mohammed Monzoorul , Patole Milind S. , Valluri Vijayalakshmi , Suryavanshi Rohini , Mande Sharmila S. , Mande Shekhar C.
Published: October 2019

Leprosy is an infectious disease that has predilection in skin and peripheral nerves. Skin has its own microbiome, however it is not extensively studied in Indian leprosy patients. Here, by using next-generation 16S rDNA sequencing, we have attempted to assess the skin associated microbial diversity pertaining to affected and unaffected skin of Indian leprosy patients. A total of 90 skin swab samples were collected from 60 individuals (30 healthy controls, 30 patients) residing in Hyderabad and Miraj, two distinct geographical locations in India to assess the homo/heterogeneity of skin microbial signatures. While a large increase in genus Methylobacterium and Pseudomonas was seen in patients from Miraj and Hyderabad respectively, a considerable decrease in genus Staphylococcus in the leprosy patients (as compared to controls) from both geographical locations was also observed. We expect that, these datasets can not-only provide further interesting insights, but will also help to observe dynamics of microbiome in the diseased state and generate hypotheses to test for skin microbiome transplantation studies in leprosy.
Satellite-based time-series of sea-surface temperature since 1981 for climate applications
Authors: Merchant Christopher J. , Embury Owen , Bulgin Claire E. , Block Thomas , Corlett Gary K. , Fiedler Emma , Good Simon A. , Mittaz Jonathan , Rayner Nick A. , Berry David , Eastwood Steinar , Taylor Michael , Tsushima Yoko , Waterfall Alison , Wilson Ruth , Donlon Craig
Published: October 2019

A climate data record of global sea surface temperature (SST) spanning 1981–2016 has been developed from 4 × 1012 satellite measurements of thermal infra-red radiance. The spatial area represented by pixel SST estimates is between 1 km2 and 45 km2. The mean density of good-quality observations is 13 km−2 yr−1. SST uncertainty is evaluated per datum, the median uncertainty for pixel SSTs being 0.18 K. Multi-annual observational stability relative to drifting buoy measurements is within 0.003 K yr−1 of zero with high confidence, despite maximal independence from in situ SSTs over the latter two decades of the record. Data are provided at native resolution, gridded at 0.05° latitude-longitude resolution (individual sensors), and aggregated and gap-filled on a daily 0.05° grid. Skin SSTs, depth-adjusted SSTs de-aliased with respect to the diurnal cycle, and SST anomalies are provided. Target applications of the dataset include: climate and ocean model evaluation; quantification of marine change and variability (including marine heatwaves); climate and ocean-atmosphere processes; and specific applications in ocean ecology, oceanography and geophysics.
Mithramycin A Inhibits Colorectal Cancer Growth by Targeting Cancer Stem Cells
Authors: Quarni Waise , Dutta Rinku , Green Ryan , Katiri Sandhyabanu , Patel Bhaumik , Mohapatra Shyam S. , Mohapatra Subhra
Published: October 2019

The pivotal role of cancer initiating stem cells (CSCs) in tumor initiation, growth, metastasis and drug resistance has led to the postulation of a ‘total cancer therapy’ paradigm, which involves targeting both cancer cells and CSCs for effective therapy. However, the progress in identifying drugs for total cancer therapy has been limited. Herein, we show for the first time that mithramycin A (Mit-A) can successfully inhibit CSC proliferation, in addition to inhibiting bulk cancer cells in a model of colorectal cancer (CRC), the second leading cause of death among men and women in the United States. To this end, a polymeric nanofiber scaffold culture system was established to develop 3D tumor organoids (tumoroids) from CRC cell lines such as HT29, HCT116, KM12, CT26 and MC38 as well as ex vivo mouse tumors. These tumoroids possessed increased expression of CSC markers and transcription factors, expanded the number of CSCs in culture and increased CSC functional properties measured by aldehyde dehydrogenase activity. Screening of an NCI library of FDA approved drugs led to the identification of Mit-A as a potential total cancer therapy drug. In both sphere and tumoroid culture, Mit-A inhibits cancer growth by reducing the expression of cancer stemness markers. In addition, Mit-A inhibits the expression of SP1, a previously known target in CRCs. Moreover, Mit-A significantly reduces growth of tumoroids in ex vivo cultures and CRC tumor growth in vivo. Finally, a dose-dependent treatment on CRC cells indicate that Mit-A significantly induces the cell death and PARP-cleavage of both CSC and non-CSC cells. Taken together the results of these in vitro, ex vivo and in vivo studies lead to the inference that Mit-A is a promising drug candidate for total cancer therapy of CRCs.
Structural analysis of biological targets by host:guest crystal lattice engineering
Authors: Ernst Patrick , Plückthun Andreas , Mittl Peer R. E.
Published: October 2019

To overcome the laborious identification of crystallisation conditions for protein X-ray crystallography, we developed a method where the examined protein is immobilised as a guest molecule in a universal host lattice. We applied crystal engineering to create a generic crystalline host lattice under reproducible, predefined conditions and analysed the structures of target guest molecules of different size, namely two 15-mer peptides and green fluorescent protein (sfGFP). A fusion protein with an N-terminal endo-α-N-acetylgalactosaminidase (EngBF) domain and a C-terminal designed ankyrin repeat protein (DARPin) domain establishes the crystal lattice. The target is recruited into the host lattice, always in the same crystal form, through binding to the DARPin. The target structures can be determined rapidly from difference Fourier maps, whose quality depends on the size of the target and the orientation of the DARPin.
Identification of microRNAs and relative target genes in Moringa oleifera leaf and callus
Authors: Pirrò Stefano , Matic Ivana , Guidi Arianna , Zanella Letizia , Gismondi Angelo , Cicconi Rosella , Bernardini Roberta , Colizzi Vittorio , Canini Antonella , Mattei Maurizio , Galgani Andrea
Published: October 2019

MicroRNAs, a class of small, non-coding RNAs, play important roles in plant growth, development and stress response by negatively regulating gene expression. Moringa oleifera Lam. plant has many medical and nutritional uses; however, little attention has been dedicated to its potential for the bio production of active compounds. In this study, 431 conserved and 392 novel microRNA families were identified and 9 novel small RNA libraries constructed from leaf, and cold stress treated callus, using high-throughput sequencing technology. Based on the M. oleifera genome, the microRNA repertoire of the seed was re-evaluated. qRT-PCR analysis confirmed the expression pattern of 11 conserved microRNAs in all groups. MicroRNA159 was found to be the most abundant conserved microRNA in leaf and callus, while microRNA393 was most abundantly expressed in the seed. The majority of predicted microRNA target genes were transcriptional factors involved in plant reproduction, growth/development and abiotic/biotic stress response. In conclusion, this is the first comprehensive analysis of microRNAs in M. oleifera leaf and callus which represents an important addition to the existing M. oleifera seed microRNA database and allows for possible exploitation of plant microRNAs induced with abiotic stress, as a tool for bio-enrichment with pharmacologically important phytochemicals.
Regulatory Crosstalk of Doxorubicin, Estradiol and TNFα Combined Treatment in Breast Cancer-derived Cell Lines
Authors: Nassiri Isar , Inga Alberto , Meškytė Erna Marija , Alessandrini Federica , Ciribilli Yari , Priami Corrado
Published: October 2019

We present a new model of ESR1 network regulation based on analysis of Doxorubicin, Estradiol, and TNFα combination treatment in MCF-7. We used Doxorubicin as a therapeutic agent, TNFα as marker and mediator of an inflammatory microenvironment and 17β-Estradiol (E2) as an agonist of Estrogen Receptors, known predisposing factor for hormone-driven breast cancer, whose pharmacological inhibition reduces the risk of breast cancer recurrence. Based on the results of transcriptomics analysis, we found 71 differentially expressed genes that are specific for the combination treatment with Doxorubicin + Estradiol + TNFα in comparison with single or double treatments. The responsiveness to the triple treatment was examined for seven genes by qPCR, of which six were validated, and then extended to four additional cell lines differing for p53 and/or ER status. The results of differential regulation enrichment analysis highlight the role of the ESR1 network that included 36 of 71 specific differentially expressed genes. We propose that the combined activation of p53 and NF-kB transcription factors significantly influences ligand-dependent, ER-driven transcriptional responses, also of the ESR1 gene itself. These results provide a model of coordinated interaction of TFs to explain the Doxorubicin, E2 and TNFα induced repression mechanisms.
Deep learning-based optical field screening for robust optical diffraction tomography
Authors: Ryu DongHun , Jo YoungJu , Yoo Jihyeong , Chang Taean , Ahn Daewoong , Kim Young Seo , Kim Geon , Min Hyun-Seok , Park YongKeun
Published: October 2019

In tomographic reconstruction, the image quality of the reconstructed images can be significantly degraded by defects in the measured two-dimensional (2D) raw image data. Despite the importance of screening defective 2D images for robust tomographic reconstruction, manual inspection and rule-based automation suffer from low-throughput and insufficient accuracy, respectively. Here, we present deep learning-enabled quality control for holographic data to produce robust and high-throughput optical diffraction tomography (ODT). The key idea is to distil the knowledge of an expert into a deep convolutional neural network. We built an extensive database of optical field images with clean/noisy annotations, and then trained a binary-classification network based upon the data. The trained network outperformed visual inspection by non-expert users and a widely used rule-based algorithm, with >90% test accuracy. Subsequently, we confirmed that the superior screening performance significantly improved the tomogram quality. To further confirm the trained model’s performance and generalisability, we evaluated it on unseen biological cell data obtained with a setup that was not used to generate the training dataset. Lastly, we interpreted the trained model using various visualisation techniques that provided the saliency map underlying each model inference. We envision the proposed network would a powerful lightweight module in the tomographic reconstruction pipeline.
Intranasal oxytocin selectively modulates the behavior of rhesus monkeys in an expression matching task
Authors: Taubert Jessica , Flessert Molly , Liu Ning , Ungerleider Leslie G.
Published: October 2019

Although the neuropeptide oxytocin (OT) is thought to regulate prosocial behavior in mammals, there is considerable debate as to how intranasal OT influences primate behavior. The aim of this study was to determine whether intranasal OT has a general anxiolytic effect on the performance of rhesus monkeys tasked with matching face stimuli, or a more selective effect on their behavior towards aversive facial expressions. To this end, we developed an innovative delayed match-to-sample task where the exact same trials could be used to assess either a monkey’s ability to match facial expressions or facial identities. If OT has a general affect on behavior, then performance in both tasks should be altered by the administration of OT. We tested four male rhesus monkeys (Macaca mulatta) in both the expression and identity task after the intranasal administration of either OT or saline in a within-subjects design. We found that OT inhalation selectively reduced a selection bias against negatively valenced expressions. Based on the same visual input, performance in the identity task was also unaffected by OT. This dissociation provides evidence that intranasal OT affects primate behavior under very particular circumstances, rather than acting as a general anxiolytic, in a highly translatable nonhuman model, the rhesus monkey.
Antiviral interferons induced by Newcastle disease virus (NDV) drive a tumor-selective apoptosis
Authors: Ginting Teridah Ernala , Christian Salomo , Larasati Young Othiwi , Suryatenggara Jeremiah , Suriapranata Ivet Marita , Mathew George
Published: October 2019

Newcastle disease virus (NDV) strongly induces both type I and III antiviral interferons (IFNs-α/-β and IFN-λ, respectively) in tumor cells while it induces mainly type III IFN in normal cells. Impairment of antiviral type I IFN signaling in tumor cells is thought to be the reason for effective oncolysis. However, there is lack of clarity why lentogenic strain NDV can also induce oncolysis. NDV infection caused apoptosis in normal and tumor cells as demonstrated with the caspase-3 enzyme activation and annexin-V detection. The apoptosis response was inhibited by B18R protein (a type I IFN inhibitor) in tumor cells i.e. A549 and U87MG, and not in normal cells i.e. NB1RGB and HEK293. Similarly, UV-inactivated medium from NDV infection was shown to induce apoptosis in corresponding cells and the response was inhibited in A549 and U87MG cells with the addition of B18R protein. Treatment with combination of IFNs-α/-β/-λ or IFNs-α/-β or IFN-λ in NB1RGB, HEK293, A549 and U87MG showed that caspase activity in IFNs-α/-β/-λ group was the highest, followed with IFN-α/-β group and IFN-λ group. This suggests that tumor-selectivity of NDV is mainly because of the cumulative effect of type I and III in tumor cells that lead to higher apoptotic effect.
Rapid human-driven undermining of atoll island capacity to adjust to ocean climate-related pressures
Authors: Duvat Virginie K. E. , Magnan Alexandre K.
Published: October 2019

Most studies addressing the future of atoll islands focused on ocean-climate drivers of risk, especially sea-level rise, and disregarded the role of local human disturbances. However, the future habitability of these countries will critically depend on the response of inhabited and exploited islands to ocean-climate pressures. Here, using the Maldives as a case study and based on a database including 608 islands (representing 56.8% and 86.0% of the country’s land area and population, respectively), we assess the influence of human disturbances on island natural response capacity over the last decade. We show that over the last decade, island change was rapid and primarily controlled by anthropogenic drivers. The great majority of inhabited and exploited islands now exhibit an altered-to-annihilated capacity to respond to ocean-climate pressures, which has major implications for future research and adaptation strategies. First, future studies should consider not only climate, but also anthropogenic tipping points (in contrast to climate tipping points). Second, adaptation strategies must be implemented without delay, despite climate uncertainties, in order to contain any additional detrimental path-dependency effects. This study provides critical information for better addressing the attribution issue under climate change, and a replicable rapid assessment frame.
Diat.barcode, an open-access curated barcode library for diatoms
Authors: Rimet Frédéric , Gusev Evgenuy , Kahlert Maria , Kelly Martyn G. , Kulikovskiy Maxim , Maltsev Yevhen , Mann David G. , Pfannkuchen Martin , Trobajo Rosa , Vasselon Valentin , Zimmermann Jonas , Bouchez Agnès
Published: October 2019

Diatoms (Bacillariophyta) are ubiquitous microalgae which produce a siliceous exoskeleton and which make a major contribution to the productivity of oceans and freshwaters. They display a huge diversity, which makes them excellent ecological indicators of aquatic ecosystems. Usually, diatoms are identified using characteristics of their exoskeleton morphology. DNA-barcoding is an alternative to this and the use of High-Throughput-Sequencing enables the rapid analysis of many environmental samples at a lower cost than analyses under microscope. However, to identify environmental sequences correctly, an expertly curated reference library is needed. Several curated libraries for protists exists; none, however are dedicated to diatoms. Diat.barcode is an open-access library dedicated to diatoms which has been maintained since 2012. Data come from two sources (1) the NCBI nucleotide database and (2) unpublished sequencing data of culture collections. Since 2017, several experts have collaborated to curate this library forrbcL, a chloroplast marker suitable for species-level identification of diatoms. For the latest version of the database (version 7), 605 of the 3482 taxonomical names originally assigned by the authors of therbcL sequences were modified after curation. The database is accessible athttps://www6.inra.fr/carrtel-collection_eng/Barcoding-database.
Impact of UV sterilization and short term storage on the in vitro release kinetics and bioactivity of biomolecules from electrospun scaffolds
Authors: Evrova Olivera , Kellenberger Damian , Scalera Chiara , Calcagni Maurizio , Giovanoli Pietro , Vogel Viola , Buschmann Johanna
Published: October 2019

To effectively translate bioactive scaffolds into a preclinical setting, proper sterilization techniques and storage conditions need to be carefully considered, as the chosen sterilization technique and storage condition might affect the structural and mechanical properties of the scaffolds, as well as the bioactivity and release kinetics of the incorporated biomolecules. Since rarely tested or quantified, we show here in a proof-of-concept study how these parameters are affected by UV sterilization and one week storage at different temperatures using bioactive electrospun DegraPol scaffolds that were specifically designed for application in the field of tendon rupture repair. Even though UV sterilization and the different storage conditions did not impact the morphology or the physicochemical properties of the bioactive scaffolds, UV sterilization caused significant attenuation of the growth factor release kinetics, here platelet derived growth factor (PDGF-BB) release (by approx. 85%) and slight decrease in ascorbic acid release (by approx. 20%). In contrast, 4 °C and −20 °C storage did not have a major effect on the release kinetics of PDGF-BB, while storage at room temperature caused increase in PDGF-BB released. All storage conditions had little effect on ascorbic acid release. Equally important, neither UV sterilization nor storage affected the bioactivity of the released PDGF-BB, suggesting stability of the bioactive scaffolds for at least one week and showing potential for bioactive DegraPol scaffolds to be translated into an off-the-shelf available product. These parameters are expected to be scaffold and protein-dependent.
The geographical and seasonal mosaic in a plant-herbivore interaction: patterns of defences and herbivory by a specialist and a non-specialist
Authors: Verçosa Diomar , Cogni Rodrigo , Alves Marcos Nopper , Trigo José Roberto
Published: October 2019

In order to evaluate the geographic mosaic theory of coevolution, it is crucial to investigate geographical variation on the outcome of ecological interactions and the functional traits which dictate these outcomes. Plant populations are attacked by specialist and non-specialist herbivores and may have different types of chemical and biotic defences. We investigated geographical and seasonal variation in the interaction between the plantCrotalaria pallidaand its two major herbivores (the specialistUtetheisa ornatrixand the non-specialistEtiella zinckenella). We first showed that attack by the two herbivores and a chemical and a biotic defence vary greatly in time and space. Second, we performed a common garden experiment that revealed genetic variation among populations in herbivore resistance and a chemical defence, but no genetic variation in a biotic defence. Third, we sampled 20 populations on a much larger geographical scale and showed great variation in attack rates by the two herbivores and a chemical defence. Finally, we showed that herbivory is not correlated with a chemical defence in the 20 field populations. Our study shows that to understand the evolution of ecological interactions it is crucial to investigate how the outcome of the interaction and the important species traits vary geographically and seasonally.
Pleione: A tool for statistical and multi-objective calibration of Rule-based models
Authors: Santibáñez Rodrigo , Garrido Daniel , Martin Alberto J. M.
Published: October 2019

Mathematical models based on Ordinary Differential Equations (ODEs) are frequently used to describe and simulate biological systems. Nevertheless, such models are often difficult to understand. Unlike ODE models, Rule-Based Models (RBMs) utilise formal language to describe reactions as a cumulative number of statements that are easier to understand and correct. They are also gaining popularity because of their conciseness and simulation flexibility. However, RBMs generally lack tools to perform further analysis that requires simulation. This situation arises because exact and approximate simulations are computationally intensive. Translating RBMs into ODEs is commonly used to reduce simulation time, but this technique may be prohibitive due to combinatorial explosion. Here, we present the software called Pleione to calibrate RBMs. Parameter calibration is essential given the incomplete experimental determination of reaction rates and the goal of using models to reproduce experimental data. The software distributes stochastic simulations and calculations and incorporates equivalence tests to determine the fitness of RBMs compared with data. The primary features of Pleione were thoroughly tested on a model of gene regulation in Escherichia coli. Pleione yielded satisfactory results regarding calculation time and error reduction for multiple simulators, models, parameter search strategies, and computing infrastructures.
Malaria risk assessment and mapping using satellite imagery and boosted regression trees in the Peruvian Amazon
Authors: Solano-Villarreal Elisa , Valdivia Walter , Pearcy Morgan , Linard Catherine , Pasapera-Gonzales José , Moreno-Gutierrez Diamantina , Lejeune Philippe , Llanos-Cuentas Alejandro , Speybroeck Niko , Hayette Marie-Pierre , Rosas-Aguirre Angel
Published: October 2019

This is the first study to assess the risk of co-endemic Plasmodium vivax and Plasmodium falciparum transmission in the Peruvian Amazon using boosted regression tree (BRT) models based on social and environmental predictors derived from satellite imagery and data. Yearly cross-validated BRT models were created to discriminate high-risk (annual parasite index API > 10 cases/1000 people) and very-high-risk for malaria (API > 50 cases/1000 people) in 2766 georeferenced villages of Loreto department, between 2010–2017 as other parts in the article (graphs, tables, and texts). Predictors were cumulative annual rainfall, forest coverage, annual forest loss, annual mean land surface temperature, normalized difference vegetation index (NDVI), normalized difference water index (NDWI), shortest distance to rivers, time to populated villages, and population density. BRT models built with predictor data of a given year efficiently discriminated the malaria risk for that year in villages (area under the ROC curve (AUC) > 0.80), and most models also effectively predicted malaria risk in the following year. Cumulative rainfall, population density and time to populated villages were consistently the top three predictors for both P. vivax and P. falciparum incidence. Maps created using the BRT models characterize the spatial distribution of the malaria incidence in Loreto and should contribute to malaria-related decision making in the area.
Patterns of human social contact and contact with animals in Shanghai, China
Authors: Zhang Juanjuan , Klepac Petra , Read Jonathan M. , Rosello Alicia , Wang Xiling , Lai Shengjie , Li Meng , Song Yujian , Wei Qingzhen , Jiang Hao , Yang Juan , Lynn Henry , Flasche Stefan , Jit Mark , Yu Hongjie
Published: October 2019

East Asia is as a principal hotspot for emerging zoonotic infections. Understanding the likely pathways for their emergence and spread requires knowledge on human-human and human-animal contacts, but such studies are rare. We used self-completed and interviewer-completed contact diaries to quantify patterns of these contacts for 965 individuals in 2017/2018 in a high-income densely-populated area of China, Shanghai City. Interviewer-completed diaries recorded more social contacts (19.3 vs. 18.0) and longer social contact duration (35.0 vs. 29.1 hours) than self-reporting. Strong age-assortativity was observed in all age groups especially among young participants (aged 7–20) and middle aged participants (25–55 years). 17.7% of participants reported touching animals (15.3% (pets), 0.0% (poultry) and 0.1% (livestock)). Human-human contact was very frequent but contact with animals (especially poultry) was rare although associated with frequent human-human contact. Hence, this densely populated area is more likely to act as an accelerator for human-human spread but less likely to be at the source of a zoonosis outbreak. We also propose that telephone interview at the end of reporting day is a potential improvement of the design of future contact surveys.
Morphological prediction of glaucoma by quantitative analyses of ocular shape and volume using 3-dimensional T2-weighted MR images
Authors: Tatewaki Yasuko , Mutoh Tatsushi , Omodaka Kazuko , Thyreau Benjamin , Matsudaira Izumi , Furukawa Hiroaki , Yamada Keiji , Kunitoki Keiko , Kawashima Ryuta , Nakazawa Toru , Taki Yasuyuki
Published: October 2019

Elongated axial length of the eye increases the morbidity of glaucoma. Myopia also associates with elongated axial length, and such ellipsoid shape of the eyeball strongly contributes its pathogenesis. Morphological features of the eyeballs, which could be important factors for developing glaucoma, have not been well described. The aim of this study was to investigate the three-dimensional (3D) topographic features of glaucomatous eyeballs with/without myopia to evaluate the potential of those features for predicting glaucoma. Using a 3.0-tesla MRI, volume-isotropic turbo-spin-echo acquisition T2-weighted images were obtained from 55 patients with glaucoma and 22 controls to delineate the eyeballs. Eyeball volumes, axial lengths and transverse lengths were semi-automatically calculated and compared between four groups: normal, myopia, glaucoma, and glaucoma with myopia. Both glaucoma and myopia increased the eyeball volume compared to the normal eyes. An increased anisotropy ratio (axial/transversus length) was observed in myopic eyes compared to normal, whereas in the glaucomatous eyes, with or without myopia, no increase in anisotropy ratio was observed. Increasing volume of eyes can be caused by myopia and glaucoma. Myopic eyes were ellipsoid in shape, but there was less anisotropy and a near-spherical shape in glaucomatous eyes, even in glaucomatous myopic eyes.
A versatile microfluidic device for highly inclined thin illumination microscopy in the moss Physcomitrella patens
Authors: Kozgunova Elena , Goshima Gohta
Published: October 2019

High-resolution microscopy is a valuable tool for studying cellular processes, such as signalling, membrane trafficking, or cytoskeleton remodelling. Several techniques of inclined illumination microscopy allow imaging at a near single molecular level; however, the application of these methods to plant cells is limited, owing to thick cell walls as well as the necessity to excise a part of the tissue for sample preparation. In this study, we utilised a simple, easy-to-use microfluidic device for highly inclined and laminated optical sheet (HILO) microscopy using a model plant Physcomitrella patens. We demonstrated that the shallow microfluidic device can be used for long-term culture of living cells and enables high-resolution HILO imaging of microtubules without perturbing their dynamics. In addition, our microdevice allows the supply and robust washout of compounds during HILO microscopy imaging, for example, to perform a microtubule regrowth assay. Furthermore, we tested long-term (48 h) HILO imaging using a microdevice and visualised the developmental changes in the microtubule dynamics during tissue regeneration. These novel applications of the microfluidic device provide a valuable resource for studying molecular dynamics in living plant cells.
Corroboration and efficacy of Magneto-Fluorescent (NiZnFe/CdS) Nanostructures Prepared using Differently Processed Core
Authors: Rawat Dipti , Barman P. B. , Singh Ragini Raj
Published: October 2019

The selected and controlled preparation of core@shell nanostructures, which unite the multiple functions of ferromagnetic Ni-Zn ferrite core and CdS shell in a single material with tuneable fluorescence and magnetic properties, have been proposed by the seed mediated aqueous growth process. The shell particle thickness and core of nanostructures were precisely tuned. Current work exhibits the comparative study of core@shell multifunctional nanostructures where core being annealed at two different temperatures. The core@shell nanostructure formation was confirmed by complementary structural, elemental, optical, magnetic and IR measurements. Optical and magnetic characterizations were performed to study elaborative effects of different structural combinations of core@shell nanostructures to achieve best configuration with high-luminescence and magnetic outcomes. The interface of magnetic/nonmagnetic NiZnFe2O4/CdS nanostructures was inspected. Unexpectedly, in some of the core@shell nanostructures presence of substantial exchange-bias was observed in spite of the non-magnetic nature of CdS QDs which is clearly an “optically-active” and “magnetically-inactive” material. Presence of “exchange-bias” was confirmed by the change in “magnetic-anisotropy” as well as shift in susceptibility derivative. Finally, successful formulation of stable and efficient core@shell nanostructures achieved, which shows no exchange-bias and shift. Current findings suggest that these magneto-fluorescent nanostructures can be used in spintronics; and drug delivery-diagnosis-imaging applications in nanomedicine field.
Need for speed: Short lifespan selects for increased learning ability
Authors: Liedtke Jannis , Fromhage Lutz
Published: October 2019

It is generally assumed that an investment into cognitive abilities and their associated cost is particularly beneficial for long-lived species, as a prolonged lifespan allows to recoup the initial investment. However, ephemeral organisms possess astonishing cognitive abilities too. Invertebrates, for example, are capable of simple associative learning, reversal learning, and planning. How can this discrepancy between theory and evidence be explained? Using a simulation, we show that short lives can actually select for an increase in learning abilities. The rationale behind this is that when learning is needed to exploit otherwise inaccessible resources, one needs to learn fast in order to utilize the resources when constrained by short lifespans. And thus, increased cognitive abilities may evolve, not despite short lifespan, but because of it.
Dietary protein restriction throughout intrauterine and postnatal life results in potentially beneficial myocardial tissue remodeling in the adult mouse heart
Authors: Hennig Maria , Ewering Lea , Pyschny Simon , Shimoyama Shinya , Olecka Maja , Ewald Dominik , Magarin Manuela , Uebing Anselm , Thierfelder Ludwig , Jux Christian , Drenckhahn Jörg-Detlef
Published: October 2019

Diet composition impacts metabolic and cardiovascular health with high caloric diets contributing to obesity related disorders. Dietary interventions such as caloric restriction exert beneficial effects in the cardiovascular system, but alteration of which specific nutrient is responsible is less clear. This study investigates the effects of a low protein diet (LPD) on morphology, tissue composition and function of the neonatal and adult mouse heart. Mice were subjected to LPD (8.8% protein) or standard protein diet (SPD, 22% protein) throughout intrauterine and postnatal life. At birth LPD female but not male offspring exhibit reduced body weight whereas heart weight was unchanged in both sexes. Cardiomyocyte cross sectional area was increased in newborn LPD females compared to SPD, whereas proliferation, cellular tissue composition and vascularization were unaffected. Adult female mice on LPD exhibit reduced body weight but normal heart weight compared to SPD controls. Echocardiography revealed normal left ventricular contractility in LPD animals. Histology showed reduced interstitial fibrosis, lower cardiomyocyte volume and elevated numbers of cardiomyocyte and non-myocyte nuclei per tissue area in adult LPD versus SPD myocardium. Furthermore, capillary density was increased in LPD hearts. In conclusion, pre- and postnatal dietary protein restriction in mice causes a potentially beneficial myocardial remodeling.
Relationship of the blood metabolome to subsequent carcass traits at slaughter in feedlot Wagyu crossbred steers
Authors: Connolly Samantha , Dona Anthony , Wilkinson-White Lorna , Hamblin Darren , D’Occhio Michael , González Luciano A.
Published: October 2019

The aim of the present study was to determine the relationships between the blood metabolome and (1) carcass traits with a focus on intramuscular fat (marbling), and (2) the length of time cattle consumed a high-starch diet in feedlot cattle. Blood samples were obtained from 181 Wagyu-crossbred steers between 300–400 days before slaughter when carcass data was collected. 1H NMR spectroscopy identified 35 metabolites with 7 positively associated with marbling (3-hydroxybutyrate, propionate, acetate, creatine, histidine, valine, and isoleucine; P ≤ 0.05). Subcutaneous rump fat thickness was positively associated with glucose, leucine and lipids (P ≤ 0.05) and negatively associated with anserine and arabinose (P ≤ 0.05). Carcass weight and growth rate were negatively associated with 3-hydroxybutyrate (P < 0.05), and growth rate was negatively associated with creatine (P < 0.05) and positively associated with aspartate (P < 0.05). Glucose and arginine showed a significant interaction between marbling and number of days animals consumed a high-starch diet (P < 0.05). Sire was the single variable with the largest effect on the relative concentration of metabolites and carcass and production traits. Blood metabolomics helps understand fat and muscle metabolism, and is associated with genotype, and carcass and production traits in cattle offering potential biomarkers suitable to select animals for management and genetic improvement.