bluuebunny/crossref_metadata_2025 huggingface dataset:
A universal subcuticular bacterial symbiont of a coral predator, the crown-of-thorns starfish, in the Indo-Pacific
Authors: Wada Naohisa , Yuasa Hideaki , Kajitani Rei , Gotoh Yasuhiro , Ogura Yoshitoshi , Yoshimura Dai , Toyoda Atsushi , Tang Sen-Lin , Higashimura Yukio , Sweatman Hugh , Forsman Zac , Bronstein Omri , Eyal Gal , Thongtham Nalinee , Itoh Takehiko , Hayashi Tetsuya , Yasuda Nina
Published: February 2020

Background

Population outbreaks of the crown-of-thorns starfish (Acanthaster plancisensu lato; COTS), a primary predator of reef-building corals in the Indo-Pacific Ocean, are major concerns in coral reef management. While biological and ecological knowledge of COTS has been accumulating since the 1960s, little is known about its associated bacteria. The aim of this study was to provide fundamental information on dominant COTS-associated bacteria through a multifaceted molecular approach.

Methods

A total of 205 COTS individuals from 17 locations throughout the Indo-Pacific Ocean were examined for the presence of COTS-associated bacteria. We conducted 16S rRNA metabarcoding of COTS to determine the bacterial profiles of different parts of the body, and generated a full-length 16S rRNA gene sequence from a single dominant bacterium, which we designated COTS27. We performed phylogenetic analysis to determine the taxonomy, screening of COTS27 across the Indo-Pacific, FISH to visualize it within the COTS tissues, and reconstruction of the chromosome from the hologenome sequence data.

Results

We discovered that a single bacterium exists at high densities in the subcuticular space in COTS forming a biofilm-like structure between the cuticle and the epidermis. COTS27 belongs to a clade that presumably represents a distinct order (so-called marine spirochetes) in the phylumSpirochaetesand is universally present in COTS throughout the Indo-Pacific Ocean. The reconstructed genome of COTS27 includes some genetic traits that are probably linked to adaptation to marine environments and evolution as an extracellular endosymbiont in subcuticular spaces.

Conclusions

COTS27 can be found in three allopatrically speciated COTS species, ranging from northern Red Sea to the Pacific, implying that symbiotic relationship arose before the speciation (approximately 2 million years ago). The universal association of COTS27 with COTS and nearly mono-specific association at least with the Indo-Pacific COTS potentially provides a useful model system for studying symbiont-host interactions in marine invertebrates.
Live-cell single particle imaging reveals the role of RNA polymerase II in histone H2A.Z eviction
Authors: Ranjan Anand , Nguyen Vu Q. , Liu Sheng , Wisniewski Jan , Kim Jee Min , Tang Xiaona , Mizuguchi Gaku , Elalaoui Ejlal , Nickels Timothy J. , Jou Vivian , English Brian P. , Zheng Qinsi , Luk Ed , Lavis Luke D. , Lionnet Timothee , Wu Carl
Published: February 2020

The H2A.Z histone variant, a genome-wide hallmark of permissive chromatin, is enriched near transcription start sites in all eukaryotes. H2A.Z is deposited by the SWR1 chromatin remodeler and evicted by unclear mechanisms. We tracked H2A.Z in living yeast at single-molecule resolution, and found that H2A.Z eviction is dependent on RNA Polymerase II (Pol II) and the Kin28/Cdk7 kinase, which phosphorylates Serine 5 of heptapeptide repeats on the carboxy-terminal domain of the largest Pol II subunit Rpb1. These findings link H2A.Z eviction to transcription initiation, promoter escape and early elongation activities of Pol II. Because passage of Pol II through +1 nucleosomes genome-wide would obligate H2A.Z turnover, we propose that global transcription of noncoding RNAs prior to premature termination, in addition to transcription of mRNAs, are responsible for eviction of H2A.Z. Such usage of yeast Pol II suggests a general mechanism coupling eukaryotic transcription to erasure of the H2A.Z epigenetic signal.
Distinct chemotactic behavior in the originalEscherichia coliK-12 depending on forward-and-backward swimming, not on run-tumble movements
Authors: Kinosita Yoshiaki , Ishida Tsubasa , Yoshida Myu , Ito Rie , Morimoto Yusuke V. , Goto Kazuki , Berry Richard M. , Nishizaka Takayuki , Sowa Yoshiyuki
Published: February 2020

Most motile bacteria are propelled by rigid, helical, flagellar filaments and display distinct swimming patterns to explore their favorable environments.Escherichia colicells have a reversible rotary motor at the base of each filament. They exhibit a run-tumble swimming pattern, driven by switching of rotatory direction which causes polymorphic flagellar transformation. Here we report a novel swimming mode inE. coliATCC10798, which is one of the original K-12 clones. High-speed tracking of single ATCC10798 cells showed forward and backward swimming with an average turning angle of 150°. The flagellar helicity remained right-handed with a 1.3 μm pitch and 0.14 μm helix radius, which is assumed to be a curly type, regardless of motor switching; the flagella of ATCC10798 did not show polymorphic transformation. The torque and rotational switching of the motor was almost identical to theE. coliW3110 strain, which is a derivative of K-12 and a wild-type for chemotaxis. The single point mutation of N87K in FliC, one of the filament subunits, is critical to the change in flagellar morphology and swimming pattern, and lack of flagellar polymorphism.E. colicells expressing FliC(N87K) sensed ascending a chemotactic gradient in liquid but did not form rings on a semi-solid surface. Based on these findings, we propose a flagellar polymorphism-dependent migration mechanism in structured environments.
Interspike intervals within retinal spike bursts combinatorially encode multiple stimulus features
Authors: Ishii Toshiyuki , Hosoya Toshihiko
Published: February 2020

Neurons in various regions of the brain generate spike bursts. While the number of spikes within a burst has been shown to carry information, information coding by interspike intervals (ISIs) is less well understood. In particular, a burst withkspikes hask−1 intraburst ISIs, and thesek−1 ISIs could theoretically encodek−1 independent values. In this study, we demonstrate that such combinatorial coding occurs for retinal bursts. By recording ganglion cell spikes from isolated salamander retinae, we found that intraburst ISIs encode oscillatory light sequences that are much faster than the light intensity modulation encoded by the number of spikes. When a burst has three spikes, the two intraburst ISIs combinatorially encode the amplitude and phase of the oscillatory sequence. Analysis of trial-to-trial variability suggested that intraburst ISIs are regulated by two independent mechanisms responding to orthogonal oscillatory components, one of which is common to bursts with different number of spikes. Therefore, the retina encodes multiple stimulus features by exploiting all degrees of freedom of burst spike patterns, i.e., the spike number and multiple intraburst ISIs.

Author Summary

Neurons in various regions of the brain generate spike bursts. Bursts are typically composed of a few spikes generated within dozens of milliseconds, and individual bursts are separated by much longer periods of silence (∼hundreds of milliseconds). Recent evidence indicates that the number of spikes in a burst, the interspike intervals (ISIs), and the overall duration of a burst, as well as the timing of burst onset, encode information. However, it remains unknown whether multiple ISIs within a single burst encode multiple independent information contents. Here we demonstrate that such combinatorial ISI coding occurs for spike bursts in the retina. We recorded ganglion cell spikes from isolated salamander retinae stimulated with computer-generated movies. Visual response analyses indicated that multiple ISIs within a single burst combinatorially encode the phase and amplitude of oscillatory light sequences, which are different from the stimulus feature encoded by the spike number. The result demonstrates that the retina encodes multiple stimulus features by exploiting all degrees of freedom of burst spike patterns, i.e., the spike number and multiple intraburst ISIs. Because synaptic transmission in the visual system is highly sensitive to ISIs, the combinatorial ISI coding must have a major impact on visual information processing.
Long-term changes in kelp forests in an inner basin of the Salish Sea
Authors: Berry Helen D. , Mumford Thomas F. , Christiaen Bart , Dowty Pete , Calloway Max , Ferrier Lisa , Grossman Eric E. , VanArendonk Nathan R.
Published: February 2020

Understanding the historical extent of biogenic habitats can provide insight into the nature of human impacts and inform restoration and conservation actions. Kelp forests form an important biogenic habitat that responds to natural and human drivers. Global concerns exist about threats to kelp forests, yet long term information is limited and research suggests that trends are geographically distinct. We examined distribution of the bull kelpNereocystis luetkeanaover 145 years in South Puget Sound (SPS), a semi-protected inner basin in a fjord estuary complex in the northeast Pacific Ocean. We synthesized 48 historical and modernNereocystissurveys and examined presence/absence within 1-km shoreline segments along 452 km of shoreline. Over the last 145 years,Nereocystishas been documented in 26% of the shoreline segments. Its extent decreased 62% basin-wide between the 1870s and 2017, with extreme losses in the two out of three sub-basins (96% in Central and 83% in West). In recent years, almost allNereocystisoccurred in the East sub-basin. In the majority of segments whereNereocystisdisappeared, the most recent observation was 4 decades ago, or earlier. Multiple natural and human factors that are known to impact kelp could have contributed to observed patterns, but limited data exist at the spatial and temporal scale of this study. In some areas, recent environmental conditions approached thresholds associated with decreased kelp performance. LongstandingNereocystislosses occurred exclusively in areas with relatively low current velocities. RemainingNereocystispredominantly occurred in areas where circulation is stronger. Exceptions to this pattern demonstrate that additional factors outside the scope of this study contributed to trajectories ofNereocystispersistence or loss.
Human hormone seasonality
Authors: Tendler Avichai , Bar Alon , Mendelsohn-Cohen Netta , Karin Omer , Korem Yael , Maimon Lior , Milo Tomer , Raz Moriya , Mayo Avi , Tanay Amos , Alon Uri
Published: February 2020

Hormones control the major biological functions of stress response, growth, metabolism and reproduction. In animals these hormones show pronounced seasonality, with different set-points for different seasons. In humans, the seasonality of these hormones remains unclear, due to a lack of datasets large enough to discern common patterns and cover all hormones. Here, we analyze an Israeli health record on 46 million person-years, including millions of hormone blood tests. We find clear seasonal patterns: the effector hormones peak in winter-spring, whereas most of their upstream regulating pituitary hormones peak only months later, in summer. This delay of months is unexpected because known delays in the hormone circuits last hours. We explain the precise delays and amplitudes by proposing and testing a mechanism for the circannual clock: the gland masses grow with a timescale of months due to trophic effects of the hormones, generating a feedback circuit with a natural frequency of about a year that can entrain to the seasons. Thus, humans may show coordinated seasonal set-points with a winter-spring peak in the growth, stress, metabolism and reproduction axes.
Effects of MP2RAGE B1+sensitivity on inter-site T1reproducibility and morphometry at 7T
Authors: Haast Roy AM , Lau Jonathan C , Ivanov Dimo , Menon Ravi S , Uludağ Kâmil , Khan Ali R
Published: February 2020

Most neuroanatomical studies are based on MR images, whose intensity profiles are not solely determined by the tissue’s longitudinal relaxation times (T1) but also affected by varying non-T1contributions, hampering data reproducibility. In contrast, quantitative imaging using the MP2RAGE sequence, for example, allows direct characterization of the brain based on the tissue property of interest. Combined with 7 Tesla (7T) MRI, this offers unique opportunities to obtain robust high-resolution brain data characterized by a high reproducibility, sensitivity and specificity. However, specific MP2RAGE parameters choices – e.g., to emphasize intracortical myelin-dependent contrast variations – can substantially impact image quality and cortical analyses through remnants of B1+-related intensity variations, as illustrated in our previous work. To follow up on this: we (1) validate this protocol effect using a dataset acquired with a particularly B1+insensitive set of MP2RAGE parameters combined with parallel transmission excitation; and (2) extend our analyses to evaluate the effects on hippocampal and subcortical morphometry. The latter remained unexplored initially but will provide important insights related to generalizability and reproducibility of neurodegenerative research using 7T MRI. We confirm that B1+inhomogeneities have a considerably variable effect on cortical T1and thickness estimates, as well as on hippocampal and subcortical morphometry depending on MP2RAGE setup. While T1differed substantially across datasets initially, we show inter-site T1comparability improves after correcting for the spatially varying B1+field using a separately acquired Sa2RAGE B1+map. Finally, as for cortical thickness, removal of B1+residuals affects hippocampal and subcortical volumetry and boundary definitions, particularly near structures characterized by strong intensity changes (e.g. cerebral spinal fluid and arteries). Taken together, we show that the choice of MP2RAGE parameters can impact T1comparability across sites and present evidence that hippocampal and subcortical segmentation results are modulated by B1+inhomogeneities. This calls for careful (1) consideration of sequence parameters when setting acquisition protocols; as well as (2) interpretation of results focused on neuroanatomical changes due to disease.

Highlights

Previously observed effects of B1+inhomogeneities on cortical T1and thickness depend strongly on MP2RAGE parameters

Inter-site comparability of cortical T1and thickness greatly improves after removal of B1+residuals

Post-hoc MP2RAGE B1+correction affects hippocampal (and subcortical) size and shape analyses

Neuroradiological research would benefit from careful examination of imaging protocols and their impact on results, especially when B1+maps are not acquired
Altered parasitism of a butterfly assemblage associated with a range-expanding species
Authors: Audusseau H. , Ryrholm N. , Stefanescu C. , Tharel S. , Jansson C. , Champeaux L. , Shaw M. R. , Raper C. , Lewis O. T. , Janz N. , Schmucki R.
Published: February 2020

Aim

Biotic interactions are an important factor structuring ecological communities but data scarcity limits our understanding of the impact of their response to climate and land use changes on communities. We studied the impact of a change in species assemblage on biotic interactions in a community of closely-related butterflies. Specifically, we examined the impact of the recent range expansion ofAraschnia levanaon the resident species, with a particular focus on natural enemies, parasitoids, shared with other butterfly species in the assemblage.

Location

Sweden.

Time period

Two years (2017-2018).

Major taxa studied

Nettle-feeding butterflies (Aglais urticae, Aglais io, Araschnia levana, andVanessa atalanta) and their parasitoids.

Methods

We assessed parasitism in 6777 butterfly larvae sampled in the field from 19 sites distributed along a 500 km latitudinal gradient, and every two weeks throughout species’ reproductive seasons. We identified the parasitoid complex of each butterfly species and their overlap, and analysed how parasitism rates were affected by species assemblage, variations in abundance, time, and the arrival ofA. levana.

Results

Parasitoids caused high mortality, with substantial overlap across the four host species. The composition of the host community influenced parasitism rates and this effect was specific to each species. In particular, the rate of parasitism in resident species was comparatively higher at sites whereA. levanahas been established for longer.

Main conclusions

Parasitoid pressure is a significant source of mortality in the nettle-feeding butterfly community studied. Variations in butterfly species assemblages are associated with substantial variations in rates of parasitism. This is likely to affect the population dynamics of their butterfly host species, and, potentially, the larger number of species with which they interact.
Mitochondrial CaMKII causes metabolic reprogramming, energetic insufficiency, and dilated cardiomyopathy
Authors: Luczak Elizabeth D. , Wu Yuejin , Granger Jonathan M. , Joiner Mei-ling A. , Wilson Nicholas R. , Gupta Ashish , Umapathi Priya , Murphy Kevin R. , Reyes Gaido Oscar E. , Sabet Amin , Corradini Eleonora , Wang Yibin , Heck Albert J.R. , Wei An-Chi , Weiss Robert G. , Anderson Mark E.
Published: February 2020

Despite the clear association between myocardial injury, heart failure and depressed myocardial energetics, little is known about upstream signals responsible for remodeling myocardial metabolism after pathological stress. We found increased mitochondrial calmodulin kinase II (CaMKII) activation and left ventricular dilation in mice one week after myocardial infarction (MI) surgery. In contrast, mice with genetic mitochondrial CaMKII inhibition were protected from left ventricular dilation and dysfunction after MI. Mice with myocardial and mitochondrial CaMKII over-expression (mtCaMKII) had severe dilated cardiomyopathy and decreased ATP that caused elevated cytoplasmic resting (diastolic) Ca2+concentration and reduced mechanical performance. We mapped a metabolic pathway that allowed us to rescue disease phenotypes in mtCaMKII mice, providing new insights into physiological and pathological metabolic consequences of CaMKII signaling in mitochondria. Our findings suggest myocardial dilation, a disease phenotype lacking specific therapies, can be prevented by targeted replacement of mitochondrial creatine kinase, or mitochondrial-targeted CaMKII inhibition.
A trans-eQTL network regulates osteoclast multinucleation and bone mass
Authors: Pereira Marie , Ko Jeong-Hun , Logan John , Protheroe Hayley , Kim Kee-Beom , Tan Amelia Li Min , Park Kwon-Sik , Rotival Maxime , Petretto Enrico , Bassett J. H. Duncan , Williams Graham R. , Behmoaras Jacques
Published: February 2020

Functional characterisation of cell-type specific regulatory networks is key to establish a causal link between genetic variation and phenotype. The osteoclast offers a unique model for interrogating the contribution of co-regulated genes toin vivophenotype as its multinucleation and resorption activities determine quantifiable skeletal traits. Here we took advantage of atrans-regulated gene network (MMnet, macrophage multinucleation network) which we found to be significantly enriched for GWAS variants associated with bone-related phenotypes. We found that the network hub geneBcat1and seven other co-regulated MMnet genes out of 13, regulate bone function. Specifically, global (Pik3cb−/−,Atp8b2+/−,Igsf8−/−,Eml1−/−,Appl2−/−,Deptor−/−) and myeloid-specificSlc40a1ΔLysMCreknockout mice displayed abnormal bone phenotypes. We report antagonizing effects of MMnet genes on bone mass in mice and osteoclast multinucleation/resorption in humans with strong correlation between the two. These results identify MMnet as a functionally conserved network that regulates osteoclast fusion and bone mass.

Impact statement

We took advantage of the osteoclast whose multinucleation properties correlate with bone mass. We show that atrans-regulated gene network (MMnet) controls skeletal homeostasis through osteoclast multinucleation and function.
New functional identity of the essential inner membrane protein YejM: the cardiolipin translocator is also a metalloenzyme
Authors: Gabale Uma , Peña Palomino Perla A. , Kim HyunAh , Chen Wenya , Ressl Susanne
Published: February 2020

Recent recurrent outbreaks of Gram-negative bacteria show the critical need to target essential bacterial mechanisms to fight the increase of antibiotic resistance. Pathogenic Gram-negative bacteria have developed several strategies to protect themselves against the host immune response and antibiotics. One strategy is to remodel the outer membrane where several genes are involved.yejMwas discovered as an essential gene inE. coliandS. typhimuriumthat plays a critical role in their virulence by changing the outer membrane permeability by translocating and increasing the cardiolipin lipid concentration. How the inner membrane protein YejM with its periplasmic domain acts as a cardiolipin translocator remains unknown. Despite overwhelming structural similarity of the periplasmic domains of two YejM homologues with hydrolases like arylsulfatases, no enzymatic activity has been reported for YejM. Our studies reveal an intact active site with bound metal ions in the structure of YejM periplasmic domain. Furthermore, we show that YejM has a phosphatase activity that is dependent on the presence of magnesium ions and is linked to its cardiolipin translocation properties. Understanding the molecular mechanism by which YejM is involved in OM remodeling will help to identify a new drug target in the fight against the increased antibiotic resistance.
Delay-period activity in frontal, parietal, and occipital cortex tracks different attractor dynamics in visual working memory
Authors: Yu Qing , Panichello Matthew F. , Cai Ying , Postle Bradley R. , Buschman Timothy J.
Published: February 2020

One important neural hallmark of working memory is persistent elevated delay-period activity in frontal and parietal cortex. In human fMRI, delay-period BOLD activity in frontal and parietal cortex increases monotonically with memory load and asymptotes at an individual’s capacity. Previous work has demonstrated that frontal and parietal delay-period activity correlates with the decline in behavioral memory precision observed with increasing memory load. However, because memory precision can be influenced by a variety of factors, it remains unclear what cognitive processes underlie persistent activity in frontal and parietal cortex. Recent psychophysical work has shown that attractor dynamics bias memory representations toward a few stable representations and reduce the effects of internal noise. From this perspective, imprecision in memory results from both drift towards stable attractor states and random diffusion. Here we asked whether delay-period BOLD activity in frontal and parietal cortex might be explained, in part, by these attractor dynamics. We analyzed data from an existing experiment in which subjects performed delayed recall for line orientation, at different loads, during fMRI scanning. We modeled subjects’ behavior using a discrete attractor model, and calculated within-subject correlation between frontal and parietal delay-period activity and estimated sources of memory error (drift and diffusion). We found that although increases in frontal and parietal activity were associated with increases in both diffusion and drift, diffusion explained the most variance in frontal and parietal delay-period activity. In comparison, a subsequent whole-brain regression analysis showed that drift rather than diffusion explained the most variance in delay-period activity in lateral occipital cortex. These results provide a new interpretation for the function of frontal, parietal, and occipital delay-period activity in working memory.
Gene tree discord, simplex plots, and statistical tests under the coalescent
Authors: Allman Elizabeth S. , Mitchell Jonathan D. , Rhodes John A.
Published: February 2020

Abstract

A simple graphical device, the simplex plot of quartet concordance factors, is introduced to aid in the exploration of a collection of gene trees on a common set of taxa. A single plot summarizes all gene tree discord, and allows for visual comparison to the expected discord from the multispecies coalescent model (MSC) of incomplete lineage sorting on a species tree. A formal statistical procedure is described that can quantify the deviation from expectation for each subset of four taxa, suggesting when the data is not in accord with the MSC, and thus either gene tree inference error is substantial or a more complex model such as that on a network may be required. If the collection of gene trees appears to be in accord with the MSC, the plots may reveal when substantial incomplete lineage sorting is present and coalescent based species tree inference is preferred over concatenation approaches. Applications to both simulated and empirical multilocus data sets illustrate the insights provided.
Increased metal tolerance and bioaccumulation of zinc and cadmium in Chlamydomonas reinhardtii expressing a AtHMA4 C-terminal domain protein
Authors: Ibuot Aniefon , Webster Rachel E. , Williams Lorraine E. , Pittman Jon K.
Published: February 2020

The use of microalgal biomass for metal pollutant bioremediation might be improved by genetic engineering to modify the selectivity or capacity of metal biosorption. A plant cadmium (Cd) and zinc (Zn) transporter (AtHMA4) was used as a transgene to increase the ability of Chlamydomonas reinhardtii to tolerate 0.2 mM Cd and 0.3 mM Zn exposure. The transgenic cells showed increased accumulation and internalisation of both metals compared to wild type. AtHMA4 was expressed either as the full-length protein or just the C-terminal tail, which is known to have metal binding sites. Similar Cd and Zn tolerance and accumulation was observed with expression of either the full-length protein or C-terminal domain, suggesting that enhanced metal tolerance was mainly due to increased metal binding rather than metal transport. The effectiveness of the transgenic cells was further examined by immobilisation in calcium alginate to generate microalgal beads that could be added to a metal contaminated solution. Immobilisation maintained metal tolerance, while AtHMA4-expressing cells in alginate showed a concentration-dependent increase in metal biosorption that was significantly greater than alginate beads composed of wild type cells. This demonstrates that expressing AtHMA4 full-length or C-terminus has great potential as a strategy for bioremediation using microalgal biomass.
Comparison of protein and peptide fractionation approaches in protein identification and quantification fromSaccharomyces cerevisiae
Authors: Deng Liting , Handler David C. L. , Multari Dylan , Haynes Paul A.
Published: February 2020

Proteomics, as a high-throughput technology, has been developed with the aim of investigating the maximum number of proteins in cells. However, protein discovery and data generation vary in depth and coverage when different technical strategies are used. In this study, four different sample preparation, and peptide or protein fractionation, methods were applied to identify and quantify proteins from log-phase yeast lysate: sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE); gas phase fractionation (GPF); filter-aided sample preparation (FASP)- GPF; and FASP-high pH reversed phase fractionation (HpH). Fractionated samples were initially analyzed and compared using nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) employing data dependent acquisition on a linear ion trap instrument. The number of fractions and replicates was adjusted so that each experiment used a similar amount of mass spectrometric instrument time, approximately 16 hours. A second set of experiments was performed using a Q Exactive Orbitrap instrument, comparing FASP-GPF, SDS-PAGE and FASP-HpH. Compared with results from the linear ion trap mass spectrometer, the use of a Q Exactive Orbitrap mass spectrometer enabled a small increase in protein identifications using SDS-PAGE and FASP-GPF methods, and a large increase using FASP-HpH. A big advantage of using the higher resolution instrument found in this study was the substantially increased peptide identifications which enhance the proteome coverage. A total of 1035, 1357 and 2134 proteins were separately identified by FASP-GPF, SDS-PAGE and FASP-HpH. Combining results from the Orbitrap experiments, there were a total of 2269 proteins found, with 94% of them identified using the FASP-HpH method. Therefore, the FASP-HpH method is the optimal choice among these approaches when using a high resolution spectrometer, when applied to this type of sample.
In situstructural analysis of the flagellum attachment zone inTrypanosoma bruceiusing cryo-scanning transmission electron tomography
Authors: Trépout Sylvain
Published: February 2020

The flagellum ofTrypanosoma bruceiis a 20 µm-long organelle responsible for locomotion and cell morphogenesis. The flagellum attachment zone (FAZ) is a multi-protein complex whose function is to attach the flagellum to the cell body but also to guide cytokinesis. Cryo-transmission electron microscopy is a tool of choice to access the structure of the FAZ in a close-to-native state. However, because of the large dimension of the cell body, the whole FAZ cannot be structurally studiedin situat high resolution in 3D using classical transmission electron microscopy approaches. In the present work, cryo-scanning transmission electron tomography, a new method capable of investigating cryo-fixed thick biological samples, has been used to study wholeT. bruceicells at the bloodstream stage. The method has been used to visualise and characterise the structure and organisation of the FAZ filament. It is composed of an array of cytoplasmic stick-like structures. These sticks are heterogeneously distributed between the posterior part and the anterior tip of the cell. This cryo-STET investigation provides new insights in the structure the FAZ filament. In combination with protein structure predictions, this work proposes a new model for the elongation of the FAZ.

Highlights

Flagellar and cellular membranes are in close contact next to the FAZ filament

Sticks are heterogeneously distributed along the FAZ filament length

Thin appendages are present between the FAZ filament sticks to neighbouring microtubules

FAZ elongation could originate from the force exerted by dynein motors on subpellicular microtubules
Improved discrimination of asymmetric and symmetric arginine dimethylation by optimization of the normalized collision energy in LC-MS proteomics
Authors: Hartel Nicolas G. , Liu Christopher Z. , Graham Nicholas A.
Published: February 2020

Protein arginine methylation regulates diverse biological processes including signaling, metabolism, splicing, and transcription. Despite its important biological roles, arginine methylation remains an understudied post-translational modification. Partly, this is because the two forms of arginine dimethylation, asymmetric dimethylarginine (ADMA) and symmetric dimethylarginine (SDMA), are isobaric and therefore indistinguishable by traditional mass spectrometry techniques. Thus, there exists a need for methods that can differentiate these two modifications. Recently, it has been shown that the ADMA and SDMA can be distinguished by the characteristic neutral loss (NL) of dimethylamine and methylamine, respectively. However, the utility of this method is limited because the vast majority of dimethylarginine peptides do not generate measurable NL ions. Here, we report that increasing the normalized collision energy (NCE) in a higher-energy collisional dissociation (HCD) cell increases the generation of the characteristic NL that distinguish ADMA and SDMA. By analyzing both synthetic and endogenous methyl-peptides, we identify an optimal NCE value that maximizes NL generation and simultaneously improves methyl-peptide identification. Using two orthogonal methyl peptide enrichment strategies, high pH strong cation exchange (SCX) and immunoaffinity purification (IAP), we demonstrate that the optimal NCE increases improves NL-based ADMA and SDMA annotation and methyl peptide identifications by 125% and 17%, respectively, compared to the standard NCE. This simple parameter change will greatly facilitate the identification and annotation of ADMA and SDMA in mass spectrometry-based methyl-proteomics to improve our understanding of how these modifications differentially regulate protein function.
Psychological contract violation and patient’s antisocial behaviour
Authors: Chang Po-Chien , Wu Ting , Du Juan
Published: February 2020

Purpose

The purpose of this study is to examine the dual effects of the violation of psychological contract on patient’s antisocial behaviour via the mediator of patient trust and the role of doctor-patient communication as a critical contingent variable in the psychological contract violation of patient’s antisocial behaviour relationship.

Design/methodology/approach

The data were collected from 483 hospitalized patients distributed in Shanxi province, China by using a self-administered survey.

Findings

The results indicated that psychological contract violation is positively associated with patient antisocial behaviour via patient trust. Moreover, the study found that doctor-patient communication moderates the mediated effects of psychological contract violation on patient’s antisocial behaviour through patient trust; that is, the mediated effect on antisocial behaviour is weaker when both doctor and patients have more communication.

Research limitations/implications

Due to a cross-sectional design in nature, the causal relationship cannot be developed based on the results. Despite the limitation, the present study provides insights for improving doctor-patient relationship by emphasizing the importance of increasing patient trust and doctor-patient communication.

Practical implications

To improve the quality of doctor-patient relationship, this study addresses the significance of properly showing understandings and care to regain mutual trust and reducing the likelihood of patient’s antisocial behaviour.

Social implications

The research findings have implications for both the health system and medical schools in China to reinforce the professional ethics and improve their medical humanities as the main concerns to generate a more sustainable doctor–patient relationship.

Originality/value

This study includes patient trust as a mediator and doctor-patient communication as a moderator to investigate the moderated mediation relationship among patients and medical professionals. By further examining the doctor-patient relationship, the results may not only help improve the efficient implementation of medical practices but also support the institutes and develop medical professionals for more positive doctor-patient relationships.
Cultural equity: knowledge and outcomes aspects
Authors: Torelli Carlos J. , Oh Hyewon , Stoner Jennifer L.
Published: February 2020

Purpose

The purpose of this paper is to propose cultural equity as a construct to better understand the characteristics that define a culturally symbolic brand and the downstream consequences for consumer behavior and nation branding in the era of globalization.

Design/methodology/approach

This paper is an empirical investigation of the knowledge and outcome aspects of cultural equity with a total of 1,771 consumers located in three different countries/continents, 77 different brands as stimuli, and using a variety of measures, surveys, lab experiments, procedures and consumer contexts.

Findings

Cultural equity is the facet of brand equity attributed to the brand's cultural symbolism or the favorable responses by consumers to the cultural symbolism of a brand. A brand has cultural equity if it has a distinctive cultural symbolism in consumers' minds (brand knowledge aspect of cultural equity: association with the central concept that defines the culture, embodiment of culturally relevant values and embeddedness in a cultural knowledge network), and such symbolism elicits a favorable consumer response to the marketing of the brand (outcome aspect of cultural equity: favorable evaluations and strong self-brand connections).

Practical implications

This paper offers a framework that allows marketers to develop cultural positioning strategies in hyper-competitive and globalized markets and identify ways for building and protecting their brands' cultural equity.

Originality/value

This paper advances our understanding of brands as cultural symbols by introducing cultural equity and integrates prior research on brand equity, cross-cultural differences in consumer behavior, country-of-origin effects and nation branding.
Tracing the evolution of the literature on knowledge management in inter-organizational contexts: a bibliometric analysis
Authors: Agostini Lara , Nosella Anna , Sarala Riikka , Spender J.-C. , Wegner Douglas
Published: February 2020

Purpose

Based on the growing interest devoted to knowledge management (KM) in inter-organizational contexts, the purpose of this paper is to systematize existing literature and understand how it developed over time, thus tracing its roots and evolution to unveil gaps and suggest new promising areas for future research.

Design/methodology/approach

This study used bibliographic techniques to analyze a sample of 85 studies along three main periods (1998-2010, 2011-2014 and 2015-2019). In particular, this study focused on co-occurrences of keywords to identify the most dominant themes, as well as connections among these themes.

Findings

Overall, the review shows the main outlets that have published papers on the topic of KM in inter-organizational contexts, as well as the theoretical background this research builds on. The temporal analysis exhibits the core topics that have persisted and grown consistently over time as the links between KM, innovation and networks. In addition, the review highlights new emerging themes, such as the human and social side of KM, and new interesting contexts of study (e.g. coopetition and open/user innovation), which opens exciting avenues for new research opportunities.

Originality/value

This study illustrates the conceptual structure of the field in three distinct periods and contributes to a more nuanced understanding of the key topics and their interrelatedness within the area of KM in inter-organizational contexts. Both researchers and practitioners can profit from the study because it reveals consolidated topics while identifying areas that still need to be investigated to foster KM in inter-organizational settings.
Legal challenges and opportunities of blockchain technology in the real estate sector
Authors: Garcia-Teruel Rosa M.
Published: February 2020

Purpose

Blockchain, which was originally created to enable peer-to-peer digital payment systems (bitcoin), is considered to have several benefits for different sectors, such as the real estate one. In a standard European-wide real estate transaction, several intermediaries are involved. As a consequence, these agreements are usually time-consuming and involve extra difficulties to cross-border operations. As blockchain, combined with smart contracts, may have an important role in these transactions, this paper aims to explore its prospective challenges, limitations and opportunities in the real estate sector and discover how the traditional intermediaries have to face a possible implementation of this technology.

Design/methodology/approach

This paper analyses the current intermediaries in the real estate sector in European Union (EU), their functions and how can blockchain strengthen the security of these transactions while reducing their time. The author uses a legal methodology to approach it.

Findings

Blockchain, combined with smart contracts, has both challenges and opportunities for the real estate sector. On the one hand, it may improve procedures, allow EU transactions and the interconnection between public administration. However, to not reduce parties rights, this blockchain should have some special features, such as the possibility of being amended.

Originality/value

This paper provides a valuable overview of all the intermediaries that could be affected by blockchain protocols. It is of interest of blockchain developers, public administrations and researchers who are working on blockchain and property conveyancing.
Connecting business and sustainable development goals in Spain
Authors: Lopez Belen
Published: February 2020

Purpose

This article aims to analyze the Corporate Social Responsibility (CSR) strategy of Spanish MNCs and how the firms integrate the Sustainable Development Goals (SDGs) in their reports and communication messages.

Design/methodology/approach

The analysis is based on cases studies with data collected through the corporate websites of Spanish MNCs listed in the Dow Jones Sustainability Index.

Findings

The findings tend to indicate that the stakeholder theory and creating shared value are both useful in the analysis of CSR business goals linked to the sustainable development goals of MNCs. However, companies generate little engagement with their stakeholders.

Research limitations/implications

The results of this article resulted from an in-depth analysis of case studies with data collected from a selected sample of MNCs. The qualitative analysis allows us to understand how SDGs are integrated in the CSR activities. But there is a lack of global indicators to measure the impacts of business through the SDGs.

Practical implications

MNCs with a CSR strategy report the information connected with SDGs. However, there is a need of metrics to better understand the contribution of companies for sustainable development and then to clearly know the contribution of business in sustainable development.

Social implications

Create shared value means that companies integrate SDGs in their CSR activities and, as a result, they can create different impacts in economic, social, and environmental issues. If companies communicate these activities and engage the stakeholders the social impact may be even greater.

Originality/value

The stakeholders theory serves to explain that companies can make a real contribution to society in their relationship with stakeholders. In addition, the creation of shared value is applicable to the integration of SDGs in companies within the CSR strategy.
Identification and validation of key genes with prognostic value in non‐small‐cell lung cancer via integrated bioinformatics analysis
Authors: Wang Li , Qu Jialin , Liang Yu , Zhao Deze , Rehman Faisal UL , Qin Kang , Zhang Xiaochun
Published: February 2020

Background

Lung cancer is the most common cause of cancer‐related death among all human cancers and the five‐year survival rates are only 23%. The precise molecular mechanisms of non‐small cell lung cancer (NSCLC) are still unknown. The aim of this study was to identify and validate the key genes with prognostic value in lung tumorigenesis.

Methods

Four GEO datasets were obtained from the Gene Expression Omnibus (GEO) database. Common differentially expressed genes (DEGs) were selected for Kyoto Encyclopedia of Genes and Genomes pathway analysis and Gene Ontology enrichment analysis. Protein‐protein interaction (PPI) networks were constructed using the STRING database and visualized by Cytoscape software and Molecular Complex Detection (MCODE) were utilized to PPI network to pick out meaningful DEGs. Hub genes, filtered from the CytoHubba, were validated using the Gene Expression Profiling Interactive Analysis database. The expressions and prognostic values of hub genes were carried out through Gene Expression Profiling Interactive Analysis (GEPIA) and Kaplan‐Meier plotter. Finally, quantitative PCR and the Oncomine database were used to verify the differences in the expression of hub genes in lung cancer cells and tissues.

Results

A total of 121 DEGs (49 upregulated and 72 downregulated) were identified from four datasets. The PPI network was established with 121 nodes and 588 protein pairs. Finally, AURKA, KIAA0101, CDC20, MKI67, CHEK1, HJURP, and OIP5 were selected by Cytohubba, and they all correlated with worse overall survival (OS) in NSCLC.

Conclusion

The results showed that AURKA, KIAA0101, CDC20, MKI67, CHEK1, HJURP, and OIP5 may be critical genes in the development and prognosis of NSCLC.

Key points

Our results indicated that AURKA, KIAA0101, CDC20, MKI67, CHEK1, HJURP, and OIP5 may be critical genes in the development and prognosis of NSCLC. Our methods showed a new way to explore the key genes in cancer development.
Timing Eclipses Amount: The Critical Importance of Intermittency in Alcohol Exposure Effects
Authors: Spear Linda Patia
Published: February 2020

Frequency and duration of ethanol (EtOH) exposures influence the consequences of those experiences, with evidence building from basic science studies in rats and mice that intermittent alcohol access (IAA) typically produces a greater escalation of EtOH intake than more continuous alcohol access (CAA). IAA also better simulates human use patterns where alcohol levels typically clear from the body between periods of use. A variety of mechanisms have been proposed to contribute to the enhanced intake of EtOH induced by IAA, including a possible attenuation in the aversive effects of EtOH, although further studies are needed to address this and other possibilities. Neural differences include indications of an IAA‐associated increase in NR2B receptors that is not evident with CAA; although little studied, alterations in other neural and neurotransmitter systems are evident as well. Many gaps in understanding of IAA/CAA effects remain. Further work is needed to characterize neural mechanisms underlying these effects, consequences of IAA/CAA on EtOH effects beyond intake, and the impact of stress and environmental variables on these differences. IAA/CAA studies to date have also largely been limited to males and to adult animals, and hence, more studies examining IAA/CAA across sex and age are needed. Such additional work is essential to determine unique contributors to IAA‐induced elevations in EtOH intake that may provide important insights for the development of new prevention/intervention strategies for heavy alcohol use and abuse.
The effects of gendered information in stories on preschool children’s development of gender stereotypes
Authors: Seitz Maximilian , Lenhart Jan , Rübsam Nina
Published: February 2020

Social‐cognitive theory posits that children learn gender stereotypes through gendered information. The present study examined whether children learn new gender stereotypes from stories when unknown words are linked to a gendered protagonist or context information. In Experiment 1, 40 3‐ to 6‐year‐old preschoolers were read stories with either a gendered protagonist embedded within a non‐gendered context, or a non‐gendered protagonist embedded within a gendered context. In Experiment 2, the same sample of children were read stories with the protagonist and the context displaying congruent or incongruent gender information. Each story featured an unknown activity linked with the stereotypical content. Both experiments indicate that the children rated the activity according to both the gender of the context and of the protagonist; however, the effect of the latter was stronger. In addition, children showed higher interest in the unknown activity if the protagonist’s gender matched their own sex. Thus, gender information in stories influences how children perceive unknown words.