bluuebunny/crossref_metadata_2025 huggingface dataset:
Multiple phenotypes conferred by a single insect symbiont are independent
Authors: McLean A. H. C. , Hrček J. , Parker B. J. , Mathé-Hubert H. , Kaech H. , Paine C. , Godfray H. C. J.
Published: June 2020

Many microbial symbionts have multiple phenotypic consequences for their animal hosts. However, the ways in which different symbiont-mediated phenotypes combine to affect fitness are not well understood. We investigated whether there are correlations between different symbiont-mediated phenotypes. We used the symbiont
Spiroplasma
, a striking example of a bacterial symbiont conferring diverse phenotypes on insect hosts. We took 11 strains of
Spiroplasma
infecting pea aphids (
Acyrthosiphon pisum
) and assessed their ability to provide protection against the fungal pathogen
Pandora neoaphidis
and the parasitoids
Aphidius ervi
and
Praon volucre
. We also assessed effects on male offspring production for five of the
Spiroplasma
strains. All but one of the
Spiroplasma
strains provided very strong protection against the parasitoid
P. volucre
. As previously reported, variable protection against
P. neoaphidis
and
A. ervi
was also present; male-killing was likewise a variable phenotype. We find no evidence of any correlation, positive or negative, between the different phenotypes, nor was there any evidence of an effect of symbiont phylogeny on protective phenotype. We conclude that multiple symbiont-mediated phenotypes can evolve independently from one another without trade-offs between them.
Ammonium is the preferred source of nitrogen for planktonic foraminifer and their dinoflagellate symbionts
Authors: LeKieffre Charlotte , Spero Howard J. , Fehrenbacher Jennifer S. , Russell Ann D. , Ren Haojia , Geslin Emmanuelle , Meibom Anders
Published: June 2020

The symbiotic planktonic foraminiferaOrbulina universainhabits open ocean oligotrophic ecosystems where dissolved nutrients are scarce and often limit biological productivity. It has previously been proposed thatO. universameets its nitrogen (N) requirements by preying on zooplankton, and that its symbiotic dinoflagellates recycle metabolic ‘waste ammonium’ for their N pool. However, these conclusions were derived from bulk15N-enrichment experiments and model calculations, and our understanding of N assimilation and exchange between the foraminifer host cell and its symbiotic dinoflagellates remains poorly constrained. Here, we present data from pulse-chase experiments with13C-enriched inorganic carbon,15N-nitrate, and15N-ammonium, as well as a13C- and15N- enriched heterotrophic food source, followed by TEM (transmission electron microscopy) coupled to NanoSIMS (nanoscale secondary ion mass spectrometry) isotopic imaging to visualize and quantify C and N assimilation and translocation in the symbiotic system. High levels of15N-labelling were observed in the dinoflagellates and in foraminiferal organelles and cytoplasm after incubation with15N-ammonium, indicating efficient ammonium assimilation. Only weak15N-assimilation was observed after incubation with15N-nitrate. Feeding foraminifers with13C- and15N-labelled food resulted in dinoflagellates that were labelled with15N, thereby confirming the transfer of15N-compounds from the digestive vacuoles of the foraminifer to the symbiotic dinoflagellates, likely through recycling of ammonium. These observations are important for N isotope-based palaeoceanographic reconstructions, as they show that δ15N values recorded in the organic matrix in symbiotic species likely reflect ammonium recycling rather than alternative N sources, such as nitrates.
Ecological regime shift preserved in the Anthropocene stratigraphic record
Authors: Tomašových Adam , Albano Paolo G. , Fuksi Tomáš , Gallmetzer Ivo , Haselmair Alexandra , Kowalewski Michał , Nawrot Rafał , Nerlović Vedrana , Scarponi Daniele , Zuschin Martin
Published: June 2020

Palaeoecological data are unique historical archives that extend back far beyond the last several decades of ecological observations. However, the fossil record of continental shelves has been perceived as too coarse (with centennial-millennial resolution) and incomplete to detect processes occurring at yearly or decadal scales relevant to ecology and conservation. Here, we show that the youngest (Anthropocene) fossil record on the northern Adriatic continental shelf provides decadal-scale resolution that accurately documents an abrupt ecological change affecting benthic communities during the twentieth century. The magnitude and the duration of the twentieth century shift in body size of the bivalve
Corbula gibba
is unprecedented given that regional populations of this species were dominated by small-size classes throughout the Holocene. The shift coincided with compositional changes in benthic assemblages, driven by an increase from approximately 25% to approximately 70% in median per-assemblage abundance of
C. gibba
. This regime shift increase occurred preferentially at sites that experienced at least one hypoxic event per decade in the twentieth century. Larger size and higher abundance of
C. gibba
probably reflect ecological release as it coincides with an increase in the frequency of seasonal hypoxia that triggered mass mortality of competitors and predators. Higher frequency of hypoxic events is coupled with a decline in the depth of intense sediment mixing by burrowing benthic organisms from several decimetres to less than 20 cm, significantly improving the stratigraphic resolution of the Anthropocene fossil record and making it possible to detect sub-centennial ecological changes on continental shelves.
Herbaria macroalgae as a proxy for historical upwelling trends in Central California
Authors: Miller Emily A. , Lisin Susan E. , Smith Celia M. , Van Houtan Kyle S.
Published: June 2020

Planning for future ocean conditions requires historical data to establish more informed ecological baselines. To date, this process has been largely limited to instrument records and observations that begin around 1950. Here, we show how marine macroalgae specimens from herbaria repositories may document long-term ecosystem processes and extend historical information records into the nineteenth century. We tested the effect of drying and pressing six macroalgae species on amino acid, heavy metal and bulk stable isotope values over 1 year using modern and archived paper. We found historical paper composition did not consistently affect values. Certain species, however, had higher variability in particular metrics while others were more consistent. Multiple herbaria providedGelidium(Rhodophyta) samples collected in southern Monterey Bay from 1878 to 2018. We examined environmental relationships and foundδ15N correlated with the Bakun upwelling index, the productivity regime of this ecosystem, from 1946 to 2018. Then, we hindcasted the Bakun index using its derived relationship withGelidium δ15N from 1878 to 1945. This hindcast provided new information, observing an upwelling decrease mid-century leading up to the well-known sardine fishery crash. Our case study suggests marine macroalgae from herbaria are an underused resource of the marine environment that precedes modern scientific data streams.
Dietary antioxidants attenuate the endocrine stress response during long-duration flight of a migratory bird
Authors: Casagrande Stefania , DeMoranville Kristen J. , Trost Lisa , Pierce Barbara , Bryła Amadeusz , Dzialo Maciej , Sadowska Edyta T. , Bauchinger Ulf , McWilliams Scott R.
Published: June 2020

Glucocorticoids (GCs) are metabolic hormones that promote catabolic processes, which release stored energy and support high metabolic demands such as during prolonged flights of migrating birds. Dietary antioxidants (e.g. anthocyanins) support metabolism by quenching excess reactive oxygen species produced during aerobic metabolism and also by activating specific metabolic pathways. For example, similar to GCs' function, anthocyanins promote the release of stored energy, although the extent of complementarity between GCs and dietary antioxidants is not well known. If anthocyanins complement GCs functions, birds consuming anthocyanin-rich food can be expected to limit the secretion of GCs when coping with a metabolically challenging activity, avoiding the exposure to potential hormonal detrimental effects. We tested this hypothesis in European starlings (
Sturnus vulgaris
) flying in a wind tunnel. We compared levels of corticosterone, the main avian GC, immediately after a sustained flight and at rest for birds that were fed diets with or without an anthocyanin supplement. As predicted, we found (i) higher corticosterone after flight than at rest in both diet groups and (ii) anthocyanin-supplemented birds had less elevated corticosterone after flight than unsupplemented control birds. This provides novel evidence that dietary antioxidants attenuate the activation of the HPA axis (i.e. increased secretion of corticosterone) during long-duration flight.
Changes in taxonomic and phylogenetic diversity in the Anthropocene
Authors: Li Daijiang , Olden Julian D. , Lockwood Julie L. , Record Sydne , McKinney Michael L. , Baiser Benjamin
Published: June 2020

To better understand how ecosystems are changing, a multifaceted approach to measuring biodiversity that considers species richness (SR) and evolutionary history across spatial scales is needed. Here, we compiled 162 datasets for fish, bird and plant assemblages across the globe and measured how taxonomic and phylogenetic diversity changed at different spatial scales (within site
α
diversity and between sites spatial
β
diversity). Biodiversity change is measured from these datasets in three ways: across land use gradients, from species lists, and through sampling of the same locations across two time periods. We found that local SR and phylogenetic
α
diversity (Faith's PD (phylogenetic diversity)) increased for all taxonomic groups. However, when measured with a metric that is independent of SR (phylogenetic species variation, PSV), phylogenetic
α
diversity declined for all taxonomic groups. Land use datasets showed declines in SR, Faith's PD and PSV. For all taxonomic groups and data types, spatial taxonomic and phylogenetic
β
diversity decreased when measured with Sorensen dissimilarity and phylogenetic Sorensen dissimilarity, respectively, providing strong evidence of global biotic homogenization. The decoupling of
α
and
β
diversity, as well as taxonomic and phylogenetic diversity, highlights the need for a broader perspective on contemporary biodiversity changes. Conservation and environmental policy decisions thus need to consider biodiversity beyond local SR to protect biodiversity and ecosystem services.
The latitudinal diversity gradient of tetrapods across the Permo-Triassic mass extinction and recovery interval
Authors: Allen Bethany J. , Wignall Paul B. , Hill Daniel J. , Saupe Erin E. , Dunhill Alexander M.
Published: June 2020

The decline in species richness from the equator to the poles is referred to as the latitudinal diversity gradient (LDG). Higher equatorial diversity has been recognized for over 200 years, but the consistency of this pattern in deep time remains uncertain. Examination of spatial biodiversity patterns in the past across different global climate regimes and continental configurations can reveal how LDGs have varied over Earth history and potentially differentiate between suggested causal mechanisms. The Late Permian–Middle Triassic represents an ideal time interval for study, because it is characterized by large-scale volcanic episodes, extreme greenhouse temperatures and the most severe mass extinction event in Earth history. We examined terrestrial and marine tetrapod spatial biodiversity patterns using a database of global tetrapod occurrences. Terrestrial tetrapods exhibit a bimodal richness distribution throughout the Late Permian–Middle Triassic, with peaks in the northern low latitudes and southern mid-latitudes around 20–40° N and 60° S, respectively. Marine reptile fossils are known almost exclusively from the Northern Hemisphere in the Early and Middle Triassic, with highest diversity around 20° N. Reconstructed terrestrial LDGs contrast strongly with the generally unimodal gradients of today, potentially reflecting high global temperatures and prevailing Pangaean super-monsoonal climate system during the Permo-Triassic.
A treated case of rhinocerebral zygomycosis with aspergillosis: a case report from India
Authors: Malhothra Shalini , Mandal Sabyasachi , Meena Rajkumari , Patel Priti , Bhatia Nirmaljit Kaur , Duggal Nandini
Published: June 2020

Zygomycosis and aspergillosis are two serious fungal infections that are commonly seen in immunocompromised patients. Since both of these infections involve fungi that invade vessels of the arterial system, an early and rapid diagnosis by direct examination of KOH mounts of the relevant clinical sample can clinch the diagnosis. Here, we present a case of a 60-year-old diabetic patient who presented with swelling and pain over the nose and left eye for 7 days with loss of vision in the left eye. After investigation, the patient was diagnosed as having rhinocerebral mucormycosis and aspergillosis, and was initially treated with amphotericin B (1 mg kg−1 day−1 intravenously), followed by endoscopic debridement under general anaesthesia. The patient gradually improved after surgery, and treatment with intravenous amphotericin B was continued along with the addition of 200 mg oral voriconazole twice daily (for the aspergillosis). With prompt diagnosis and treatment, the patient survived these fatal fungal co-infections and finally was discharged.
First isolation and whole-genome characterization of a G9P[14] rotavirus strain from a diarrheic child in Egypt
Authors: Shoeib Ashraf , Velasquez Portocarrero Daniel E. , Wang Yuhuan , Jiang Baoming
Published: June 2020

An unusual group A rotavirus (RVA) strain (RVA/Human-tc/EGY/AS997/2012/G9[14]) was isolated for the first time in a faecal sample from a 6-month-old child who was hospitalized for treatment of acute gastroenteritis in Egypt in 2012. Whole-genome analysis showed that the strain AS997 had a unique genotype constellation: G9-P[14]-I2-R2-C2-M2-A11-N2-T1-E2-H1. Phylogenetic analysis indicated that the strain AS997 had the consensus P[14] genotype constellation with the G9, T1 and H1 reassortment. This suggests either a mixed gene configuration originated from a human Wa-like strain and a P[14]-containing animal virus, or that this P[14] could have been acquired via reassortment of human strains only. The study shows the possible roles of interspecies transmission and multiple reassortment events leading to the generation of novel rotavirus genotypes and underlines the importance of whole-genome characterization of rotavirus strains in surveillance studies.
Genomic sequence analysis of Dissulfurirhabdus thermomarina SH388 and proposed reassignment to Dissulfurirhabdaceae fam. nov.
Authors: Ward Lewis M. , Bertran Emma , Johnston David T.
Published: June 2020

Here, we report the draft genome sequence of

Dissulfurirhabdus thermomarina

SH388. Improved phylogenetic and taxonomic analysis of this organism using genome-level analyses supports assignment of this organism to a novel family within the phylum Desulfobacterota. Additionally, comparative genomic and phylogenetic analyses contextualize the convergent evolution of sulfur disproportionation and potential extracellular electron transfer in this organism relative to other members of the Desulfobacterota.
Genomic modeling as an approach to identify surrogates for use in experimental validation of SARS-CoV-2 and HuNoVs inactivation by UV-C treatment
Authors: Pendyala Brahmaiah , Patras Ankit , D’Souza Doris
Published: June 2020

Severe Acute Respiratory Syndrome coronavirus-2 (SARS-CoV-2) is responsible for the COVID-19 pandemic that continues to pose significant public health concerns. While research to deliver vaccines and antivirals are being pursued, various effective technologies to control its environmental spread are also being targeted. Ultraviolet light (UV-C) technologies are effective against a broad spectrum of microorganisms when used even on large surface areas. In this study, we developed a pyrimidine dinucleotide frequency based genomic model to predict the sensitivity of select enveloped and non-enveloped viruses to UV-C treatments in order to identify potential SARS-CoV-2 and human noroviruses surrogates. The results revealed that this model was best fitted using linear regression with r2=0.90. The predicted UV-C sensitivity (D90- dose for 90% inactivation) for SARS-CoV-2 and MERS-CoV was found to be 21 and 28 J/m2, respectively (with an estimated 18 J/m2as published for SARS-CoV-1), suggesting that coronaviruses are highly sensitive to UV-C light compared to other ssRNA viruses used in this modeling study. Murine hepatitis virus (MHV) A59 strain with a D90of 21 J/m2close to that of SARS-CoV-2 was identified as a suitable surrogate to validate SARS-CoV-2 inactivation by UV-C treatment. Furthermore, the non-enveloped human noroviruses (HuNoVs), had predicted D90values of 69.1, 89 and 77.6 J/m2for genogroups GI, GII and GIV, respectively. Murine norovirus (MNV-1) of GV with a D90= 100 J/m2was identified as a potential conservative surrogate for UV-C inactivation of these HuNoVs. This study provides useful insights for the identification of potential nonpathogenic surrogates to understand inactivation kinetics and their use in experimental validation of UV-C disinfection systems. This approach can be used to narrow the number of surrogates used in testing UV-C inactivation of other human and animal ssRNA viral pathogens for experimental validation that can save cost, labor and time.
Granger-Causal Testing for Irregularly Sampled Time Series with Application to Nitrogen Signaling in Arabidopsis
Authors: Heerah Sachin , Molinari Roberto , Guerrier Stéphane , Marshall-Colon Amy
Published: June 2020

Motivation

Identification of system-wide causal relationships can contribute to our understanding of long-distance, intercellular signaling in biological organisms. Dynamic transcriptome analysis holds great potential to uncover coordinated biological processes between organs. However, many existing dynamic transcriptome studies are characterized by sparse and often unevenly spaced time points that make the identification of causal relationships across organs analytically challenging. Application of existing statistical models, designed for regular time series with abundant time points, to sparse data may fail to reveal biologically significant, causal relationships. With increasing research interest in biological time series data, there is a need for new statistical methods that are able to determine causality within and between time series data sets. Here, a statistical framework was developed to identify (Granger) causal gene-gene relationships of unevenly spaced, multivariate time series data from two different tissues ofArabidopsis thalianain response to a nitrogen signal.

Results

This work delivers a statistical approach for modelling irregularly sampled bivariate signals which embeds functions from the domain of engineering that allow to adapt the model’s dependence structure to the specific sampling time. Using Maximum-Likelihood to estimate the parameters of this model for each bivariate time series, it is then possible to use bootstrap procedures for small samples (or asymptotics for large samples) in order to test for Granger-Causality. When applied to theArabidopsis thalianadata, the proposed approach produced 3,078 significant interactions, in which 2,012 interactions have root causal genes and 1,066 interactions have shoot causal genes. Many of the predicted causal and target genes are known players in local and long-distance nitrogen signaling, including genes encoding transcription factors, hormones, and signaling peptides. Of the 1,007 total causal genes (either organ), 384 are either known or predicted mobile transcripts, suggesting that the identified causal genes may be directly involved in long-distance nitrogen signaling through intercellular interactions. The model predictions and subsequent network analysis identified nitrogen-responsive genes that can be further tested for their specific roles in long-distance nitrogen signaling.

Availability

The method was developed with the R statistical software and is made available thorugh the R package “irg” hosted on the GitHub repositoryhttps://github.com/SMAC-Group/irg. A sample data set is made available as an example to apply the method and the completeArabidopsis thalianadata can be found at:https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97500.

Contact

amymc@illinois.edu
Quorum sensing-induced phenotypic switching as a regulatory nutritional stress response in a competitive two-species biofilm: An individual-based cellular automata model
Authors: Chirathanamettu Tejesh Reddy , Pawar Parag D.
Published: June 2020

Competition for nutrients in a polymicrobial biofilm may lead to susceptible species being subjected to nutritional stress. The influence of bacterial growth rates and interspecies interactions on their susceptibility and response to nutritional stress is not well understood.Pseudomonas aeruginosaandStaphylococcus aureusare two prevalent causative pathogens that coexist in biofilm-associated infections. Despite being the slower-growing species,P. aeruginosadominates in a two-species biofilm by inducing phenotypic switching ofS. aureusto a metabolically-challenged small colony variant (SCV) via the release of 2-heptyl-4-hydroxyquinoline N-oxide (HQNO). We hypothesize thatP. aeruginosaexperiences nutritional stress in competition withS. aureus, and that the release of HQNO is an adaptive response to nutritional stress. We present an individual-based two-species biofilm model in which interactions between entities induce emergent properties. As the biofilm matured, the difference in growth rates of the two species caused a non-uniform distribution of nutrients leading to nutritional stress forP. aeruginosaand a concurrent increase in the proportion ofS. aureussubpopulation. The latter resulted in increased release of autoinducer, and subsequently the upregulation ofP. aeruginosacells via quorum sensing. UpregulatedP. aeruginosacells released HQNO at enhanced rates, thereby inducing phenotypic switching ofS. aureusto SCVs which consume nutrient at a reduced rate. This shifted the nutrient distribution back in favor ofP. aeruginosa, thereby relieving nutritional stress. Increase in nutritional stress potentiated the transformation ofS. aureusinto SCVs. HQNO production decreased once nutritional stress was relieved, indicating that phenotypic switching acts as a regulatory stress-adaptive response.
Cell entry of SARS-CoV-2 conferred by angiotensin-converting enzyme 2 (ACE2) of different species
Authors: Tang Yan-Dong , Li Yu-Ming , Sun Jing , Zhang Hong-Liang , Wang Tong-Yun , Sun Ming-Xia , Yang Yue-Lin , Hu Xiao-Liang , Zhao Jincun , Cai Xui-Hui
Published: June 2020

The outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a huge threat to many countries around the world. However, where is it origin and which animals are sensitive to cross-species transmission is unclear. The interaction of virus and cell receptor is a key determinant of host range for the novel coronavirus. Angiotensin-converting enzyme 2 (ACE2) is demonstrated as the primary entry receptor for SARS-CoV-2. In this study, we evaluated the SARS-CoV-2 entry mediated by ACE2 of 11 different species of animals, and discovered that ACE2 ofRhinolophus sinicus(Chinese horseshoe bat),Felis catus(domestic cat),Canis lupus familiaris(dog),Sus scrofa(pig),Capra hircus(goat) and especiallyManis javanica(Malayan pangolin) were able to render SARS-CoV-2 entry in non-susceptible cells. This is the first report that ACE2 of Pangolin could mediate SARS-CoV-2 entry which increases the presume that SARS-CoV-2 may have a pangolin origin. However, none of the ACE2 proteins fromRhinolophus ferrumequinum(greater horseshoe bat),Gallus gallus(chicken),Notechis scutatus(mainland tiger snake),Mus musculus(house mouse) rendered SARS-CoV-2 entry. Specifically, a natural isoform ofMacaca mulatta(Rhesus monkey) ACE2 with a mutation of Y217N was resistance to infection, which rises the possible impact of this type of ACE2 during monkey studies of SARS-CoV-2. Overall, these results clarify that SARS-CoV-2 could engage receptors of multiple species of animals and it is a perplexed work to track SARS-CoV-2 origin and its intermediate hosts.

IMPORTANCE

In this study, we illustrated that SARS-CoV-2 is able to engage receptors of multiple species of animals. This indicated that it may be a perplexed work to track SARS-CoV-2 origin and discover its intermediate hosts. This feature of virus is considered to potentiate its diverse cross-species transmissibility. Of note, here is the first report that ACE2 of Pangolin could mediate SARS-CoV-2 entry which increases the possibility that SARS-CoV-2 may have a pangolin origin. And we also demonstrated that not all species of bat were sensitive to SARS-CoV-2 infection. At last, it is also important to detect the expression ratio of the Y217N ACE2 to the prototype in Rhesus monkeys to be recruited for studies on SARS-CoV-2 infection.
Cdc48 regulates intranuclear quality control sequestration of the Hsh155 splicing factor
Authors: Mathew Veena , Kumar Arun , Jiang Yangyang K. , West Kyra , Tam Annie S. , Stirling Peter C.
Published: June 2020

Cdc48/VCP is a highly conserved ATPase chaperone that plays an essential role in the assembly or disassembly of protein-DNA complexes and in degradation of misfolded proteins. We find that Cdc48 accumulates during cellular stress at intranuclear protein quality control (INQ) sites. Cdc48 function is required to suppress INQ formation under non-stress conditions and to promote recovery following genotoxic stress. Cdc48 physically associates with the INQ substrate and splicing factor Hsh155 and regulates its assembly with partner proteins. Accordingly,cdc48mutants have defects in splicing and show spontaneous distribution of Hsh155 to INQ aggregates where it is stabilized. Overall, this study shows that Cdc48 regulates deposition of proteins at INQ and suggests a previously unknown role for Cdc48 in the regulation or stability of splicing subcomplexes.
Broad gene expression throughout the mouse and marmoset brain after intravenous delivery of engineered AAV capsids
Authors: Flytzanis Nicholas C. , Goeden Nick , Goertsen David , Cummins Alexander , Pickel James , Gradinaru Viviana
Published: June 2020

Genetic intervention is increasingly explored as a therapeutic option for debilitating disorders of the central nervous system. The safety and efficacy of gene therapies relies upon expressing a transgene in affected cells while minimizing off-target expression. To achieve organ/cell-type specific targeting after intravenous delivery of viral vectors, we employed a Cre-transgenic-based screening platform for fast and efficient capsid selection, paired with sequential engineering of multiple surface-exposed loops. We identified capsid variants that are enriched in the brain and detargeted from the liver in mice. The improved enrichment in the brain extends to non-human primates, enabling robust, non-invasive gene delivery to the marmoset brain following IV administration. Importantly, the capsids identified display non-overlapping cell-type tropisms within the brain, with one exhibiting high specificity to neurons. The ability to cross the blood–brain barrier with cell-type specificity in rodents and non-human primates enables new avenues for basic research and potential therapeutic interventions unattainable with naturally occurring serotypes.
ER – lysosome contacts at a pre-axonal region regulate axonal lysosome availability
Authors: Özkan Nazmiye , Koppers Max , van Soest Inge , van Harten Alexandra , Liv Nalan , Klumperman Judith , Hoogenraad Casper C. , Farías Ginny G.
Published: June 2020

Neuronal function relies on careful coordination of organelle organization and transport. Kinesin-1 mediates transport of the ER and lysosomes into the axon and it is increasingly recognized that contacts between the ER and lysosomes influence organelle organization. However, it is unclear how organelle organization, inter-organelle communication and transport are linked and how this contributes to local organelle availability in neurons. Here, we show that somatic ER tubules are required for proper lysosome transport into the axon. Somatic ER tubule disruption causes accumulation of enlarged and less motile lysosomes at the soma. ER tubules regulate lysosome size and axonal translocation by promoting lysosome homo-fission. ER tubule – lysosome contacts often occur at a somatic pre-axonal region, where the kinesin-1-binding ER-protein P180 binds microtubules to promote kinesin-1-powered lysosome fission and subsequent axonal translocation. We propose that ER tubule – lysosome contacts at a pre-axonal region finely orchestrate axonal lysosome availability for proper neuronal function.
Polygenic local adaptation in metapopulations: a stochastic eco-evolutionary model
Authors: Szép Enikő , Sachdeva Himani , Barton Nick
Published: June 2020

This paper analyses the conditions for local adaptation in a metapopulation with infinitely many islands under a model of hard selection, where population size depends on local fitness. Each island belongs to one of two distinct ecological niches or habitats. Fitness is influenced by an additive trait which is under habitat-dependent directional selection. Our analysis is based on the diffusion approximation and accounts for both genetic drift and demographic stochasticity. By neglecting linkage disequilibria, it yields the joint distribution of allele frequencies and population size on each island. We find that under hard selection, the conditions for local adaptation in a rare habitat are more restrictive for more polygenic traits: even moderate migration load per locus at very many loci is sufficient for population sizes to decline. This further reduces the efficacy of selection at individual loci due to increased drift and because smaller populations are more prone to swamping due to migration, causing a positive feedback between increasing maladaptation and declining population sizes. Our analysis also highlights the importance of demographic stochasticity, which exacerbates the decline in numbers of maladapted populations, leading to population collapse in the rare habitat at significantly lower migration than predicted by deterministic arguments.
The Effect of Choline Alphoscerate on Non spatial memory and Neurogenesis in a Rat Model of Dual Stress
Authors: Yu Hyo Jeong , Kim Min Jung , Park Jung Mee , Park So Young , Park Shi Nae , Yang Dong Won
Published: June 2020

Choline alphoscerate (α-GPC) is a choline-based compound and acetylcholine precursor commonly found in the brain; it has been known to be effective in treating neuronal injury and increasing the levels of acetylcholine (Ach) and brain-derived neurotrophic factor (BDNF) which in turn enhances memory and cognitive function. This study was designed to establish rat models of dual stress using noise and restraint in order to investigate the effect of α-GPC on cognitive function and neurogenesis after dual stress. The rats were randomly divided into four groups as follows: a control group (CG), a control with α-GPC group (CDG), a noise-restraint stress group (NRSG), and a noise-restraint stress with α-GPC group (NRSDG). Two experimental groups were exposed to the double stress stimuli of noise and restraint, which involved 110dB sound pressure level (SPL) white band noise and restraint at the same time for 3 hours/day for 7 days. While the CG and NRSG received saline, the CDG and NRSDG received α-GPC (400mg/kg) orally after stress exposure. The α-GPC–treated group showed increased memory function compared to the dual stress group in the novel object recognition test. In analysis of the hippocampus, the α-GPC–treated group showed greater Choline acetyltransferase (ChAT) and BDNF expression compared to the dual stress group. The α-GPC–treated group showed significantly increased neuroblast expression compared to the dual stress group, which suggests that α-GPC enhances BDNF expression and protects the activity of the immature cells at the dentate gyrus. Our results suggest that α-GPC treatment can protect cognitive function and neurogenesis in a dual stress model.
Nitric oxide coordinates histone acetylation and expression of genes involved in growth/development and stress response
Authors: Ageeva-Kieferle Alexandra , Georgii Elisabeth , Winkler Barbro , Ghirardo Andrea , Albert Andreas , Hüther Patrick , Mengel Alexander , Becker Claude , Schnitzler Jörg-Peter , Durner Jörg , Lindermayr Christian
Published: June 2020

Nitric oxide (NO) is a signaling molecule with multiple regulatory functions in plant physiology and stress response. Besides direct effects on the transcriptional machinery, NO can fulfill its signaling function via epigenetic mechanisms.

We report that light intensity-dependent changes in NO correlate with changes in global histone acetylation (H3, H3K9 and H3K9/K14) inArabidopsis thalianawild-type leaves and that this correlation depends on S-nitrosoglutathione reductase and histone deacetylase 6. The activity of histone deacetylase 6 was sensitive to NO, which demonstrates that NO participates in regulation of histone acetylation. ChIP-seq and RNA-seq analyses revealed that NO is involved in the metabolic switch from growth and development to stress response. This coordinating function of NO might be of special importance in adaptation to a changing environment and could therefore be a promising starting point to mitigating the negative effects of climate change on plant productivity.
Microtubule poleward flux in human cells is driven by the coordinated action of four kinesins
Authors: Steblyanko Yulia , Rajendraprasad Girish , Osswald Mariana , Eibes Susana , Geley Stephan , Pereira António J. , Maiato Helder , Barisic Marin
Published: June 2020

Mitotic spindle microtubules (MTs) undergo continuous poleward flux, whose driving force and function in humans remain unclear. Here, we combined loss-of-function screenings with analysis of MT dynamics in human cells to investigate the molecular mechanisms underlying MT-flux. We report that kinesin-7/CENP-E at kinetochores (KTs) is the predominant driver of MT-flux in early prometaphase, while kinesin-4/KIF4A on chromosome arms facilitates MT-flux during late prometaphase and metaphase. We show that both of these activities work in coordination with MT-crosslinking motors kinesin-5/EG5 and kinesin-12/KIF15. Our data further indicate that MT-flux driving force is transmitted from non-KT MTs to KT-MTs via MT-coupling by HSET and NuMA. Moreover, we found that MT-flux rate correlates with spindle size and this correlation depends on the establishment of stable end-on KT-MT attachments. Strikingly, we revealed that flux is required to counteract the kinesin 13/MCAK-dependent MT-depolymerization to regulate spindle length. Thus, our study demonstrates that MT-flux in human cells is driven by the coordinated action of four kinesins, and is required to regulate mitotic spindle size in response to MCAK-mediated MT-depolymerizing activity at KTs.
Language impairment with a partial duplication of DOCK8
Authors: Benítez-Burraco Antonio , Fernández-Urquiza Maite , Jiménez-Romero Mª Salud
Published: June 2020

Copy-number variations of the distal region of the short arm of chromosome 9 are associated with learning disabilities and behavioral disturbances. Deletions of the 9p are more frequent than duplications. We report in detail on the cognitive and language features of a child with a duplication in the 9p24.3 region (arr[hg19] 9p24.3(266,045-459,076)x3). He exhibits marked expressive and receptive problems, which affect to both structural aspects of language (notably, inflectional morphology, complex syntax, and sentence semantics), and to functional aspects (pragmatics). These problems might result from a severe underlying deficit in working memory. Regarding the molecular causes of the observed symptoms, they might result from the altered expression of selected genes involved in procedural learning, particularly, some of components of the SLIT/ROBO/FOXP2 network, strongly related to the development and evolution of language. Dysregulation of specific components of this network can result in turn from an altered interaction between DOCK8, affected by the microduplication in 9p24.3 borne by our proband, and CDC42, acting as the hub component of the network encompassing language-related genes. Still, some genes found strongly upregulated in the subject and not related to these genes, particularly NRCAM, can contribute to the observed problems in the language domain, as well as to specific features of the proband, particularly, his impulsivity.
Personalized vagino-cervical microbiome dynamics after oral probiotics
Authors: Chen Chen , Hao Lilan , Tian Liu , Song Liju , Zhang Xiaowei , Jie Zhuye , Tong Xin , Xiao Liang , Zhang Tao , Jin Xin , Xu Xun , Yang Huanming , Wang Jian , Kristiansen Karsten , Jia Huijue
Published: June 2020

The vaginal microbiota is presumably much simpler than the gut microbiome, and oral probiotics appear as a promising means to modulate its homeostasis in the general population. Here, 60 women were followed for over a year before, during and after a probiotic containingLactobacillus rhamnosusGR-1 andL. reuteriRC-14. Shotgun metagenomic data of 1334 samples from multiple body sites did not support colonization of the probiotics to the vagino-cervical microbiome, yet the microbiome was stable in those dominated by Lactobacilli and some individuals have likely benefited from this medication-free intervention.
A new modulated crystal structure of the ANS complex of the St John's wort Hyp-1 protein with 36 protein molecules in the asymmetric unit of the supercell
Authors: Smietanska Joanna , Sliwiak Joanna , Gilski Miroslaw , Dauter Zbigniew , Strzalka Radoslaw , Wolny Janusz , Jaskolski Mariusz
Published: June 2020

Superstructure modulation, with violation of the strict short-range periodic order of consecutive crystal unit cells, is well known in small-molecule crystallography but is rarely reported for macromolecular crystals. To date, one modulated macromolecular crystal structure has been successfully determined and refined for a pathogenesis-related class 10 protein fromHypericum perforatum(Hyp-1) crystallized as a complex with 8-anilinonaphthalene-1-sulfonate (ANS) [Sliwiaket al.(2015),Acta Cryst.D71, 829–843]. The commensurate modulation in that case was interpreted in a supercell with sevenfold expansion alongc. When crystallized in the additional presence of melatonin, the Hyp-1–ANS complex formed crystals with a different pattern of structure modulation, in which the supercell shows a ninefold expansion ofc, manifested in the diffraction pattern by a wave of reflection-intensity modulation with crests atl= 9nandl= 9n± 4. Despite complicated tetartohedral twinning, the structure has been successfully determined and refined to 2.3 Å resolution using a description in a ninefold-expanded supercell, with 36 independent Hyp-1 chains and 156 ANS ligands populating the three internal (95 ligands) and five interstitial (61 ligands) binding sites. The commensurate superstructures and ligand-binding sites of the two crystal structures are compared, with a discussion of the effect of melatonin on the co-crystallization process.
Two particle-picking procedures for filamentous proteins: SPHIRE-crYOLO filament mode and SPHIRE-STRIPER
Authors: Wagner Thorsten , Lusnig Luca , Pospich Sabrina , Stabrin Markus , Schönfeld Fabian , Raunser Stefan
Published: June 2020

Structure determination of filamentous molecular complexes involves the selection of filaments from cryo-EM micrographs. The automatic selection of helical specimens is particularly difficult, and thus many challenging samples with issues such as contamination or aggregation are still manually picked. Here, two approaches for selecting filamentous complexes are presented: one uses a trained deep neural network to identify the filaments and is integrated in SPHIRE-crYOLO, while the other, called SPHIRE-STRIPER, is based on a classical line-detection approach. The advantage of the crYOLO-based procedure is that it performs accurately on very challenging data sets and selects filaments with high accuracy. Although STRIPER is less precise, the user benefits from less intervention, since in contrast to crYOLO, STRIPER does not require training. The performance of both procedures on Tobacco mosaic virus and filamentous F-actin data sets is described to demonstrate the robustness of each method.
Symmetry and Painlevé analysis for the extended Sakovich equation
Authors: Wang Gangwei , Wazwaz Abdul-Majid
Published: June 2020

Purpose

The purpose of this paper is to concern with introducing symmetry analysis to the extended Sakovich equation.

Design/methodology/approach

The newly developed Sakovich equation has been handled by using the Lie symmetries via using the Lie group method.

Findings

The developed extended Sakovich model exhibit symmetries and invariant solutions.

Research limitations/implications

The present study is to address the two main motivations: the study of symmetry analysis and the study of soliton solutions of the extended Sakovich equation.

Practical implications

The work introduces symmetry analysis to the Painlevé-integrable extended Sakovich equation.

Social implications

The work presents useful symmetry algorithms for handling new integrable equations.

Originality/value

The paper presents an original work with symmetry analysis and shows useful findings.
Thermal effect on stability and minimum oil film thickness of a deep/shallow pockets conical bearing
Authors: Wu Ningning , Guo Hong , Yang Shuai , Zhang Shaolin
Published: June 2020

Purpose

This paper aims to study the influence of thermal effect on the performance for a high-speed conical hybrid bearing including stability and minimum oil film thickness.

Design/methodology/approach

A thermal hydrodynamic (THD) model and dynamic model of single mass rigid rotor system were established by taking conical hybrid bearing with shallow and deep pockets as the research object, dynamic coefficient and stability parameters of bearing-rotor system were obtained by using finite element method (FEM) and finite difference method (FDM) to solve computational models of Reynolds equation, energy equation and viscosity-temperature equation. Minimum oil film thickness was obtained based on bearing force balance. Dynamic coefficient was compared with previous findings.

Findings

After considering thermal effect, the dimensionless critical mass decreases, a significant decrease in the instability speed, and the stability of the system decreases greatly; the minimum oil film thickness decreases because of thermal effect.

Originality/value

The thermal effect is combined with dynamic characteristics to analyze stability of the rotor system for a conical hybrid bearing. Influence of thermal effect on minimum oil film thickness is studied.

Peer review

The peer review history for this article is available at:https://publons.com/publon/10.1108/ILT-12-2019-0542/
How does mobile social media affect knowledge sharing under the “Guanxi” system?
Authors: Zhang Xi , Tang Jiaxin , Wei Xin , Yi Minghui , Ordóñez de Pablos Patricia
Published: June 2020

Purpose

The purpose of this paper is to explore the impact of mobile social media functions on explicit and implicit knowledge sharing under the “Guanxi” system based on the framework of stimulus–organism–response (SOR).

Design/methodology/approach

Combined with Guanxi theory, this paper designs an experiment to collect data from the new product development (NPD) teams.

Findings

Interestingly, the results show that the effect of social media communication function on employees is greater than the impact of collaboration on employees. Specifically, on the one hand, the more employees communicate in social media, the better their feelings will be, the less they will share knowledge. On the other hand, the collaboration function has a significantly negative impact on the psychological factors of employees. Excessively close cooperation and contact may instead create a contradiction between the employees, which is not conducive to the occurrence of knowledge sharing.

Originality/value

This paper extends SOR framework by combining Guanxi theory to examine the relationship between social media functions and knowledge sharing behavior (KSB). In practical, companies should pay attention to the frequency of employee using social media when it is introduced for NPD teams to control the negative influence of social media functions on employee KSB.
Correlation of anthropometric indices with lipid profile indices among Malay obese and non-obese subjects in Malaysia
Authors: Nadeem Muhammad Ilyas , Abu Bakar Yasrul Izad , Akram Sana , Baig Atif Amin
Published: June 2020

Purpose

This study aims to determine the correlation of anthropometric measurements with serum lipid profile among Malay subjects in Kuala Terengganu, Malaysia.

Design/methodology/approach

This cross-sectional study was conducted in Kuala Terengganu on a total of 193 individuals aged 18-60 years. Subjects were recruited via direct interview as per inclusion criteria and anthropometric measurements, i.e. body mass index (BMI), waist circumference (WC), hip circumference (HC), waist-to-hip ratio (WHR), waist-to-height ratio, abdominal volume index and conicity index, were taken using International Standards for Anthropometric Assessment Guidelines. Fasting blood samples were collected for serum lipid profile analysis that measures triglyceride (TG), total cholesterol (TC), high-density lipoproteins (HDL), low-density lipoproteins (LDL), TG/HDL, TC/HDL and LDL/HDL. Besides socio-demographic characteristics, means and association of anthropometric parameters with lipid profiles were performed using simple linear regression and multivariate-adjusted regression analysis.

Findings

The mean age of obese (male [39.2 ± 8.7] and female [41.1 ± 1.0]) and non-obese (male [29.8 ± 1.3] and female [33.3 ± 1.3]) respondents was compared. Means of anthropometric indices and lipid profile were significantly (p< 0.001) higher in obese than in non-obese group. Multivariate-adjusted regression showed that weight and BMI increased risks for prevalent high TC, TG, LDL, TC/HDL, TG/HDL, LDL/HDL, hypercholesterolemia, hypertriglyceridemia and dyslipidemia. Regardless of sex, age and prevalent obese status, WHR increased risks for high prevalence of TC, TG, LDL, TC/HDL and LDL/HDL, and presents an independent risk factor for hypercholesterolemia and dyslipidemia. WC was highly associated with TG, while HC was associated with atherogenic lipid profile ratios: TC/HDL, TG/HDL and LDL/HDL.

Originality/value

In conclusion, the lipid profile (TC, TG and TG/HDL) of triglyceridemia and hypercholesteremia is highly correlated with anthropometric measurements (BMI, WC and WHR) of central obesity that predict obesity-associated cardiac risks.