bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental evolution of a pheromone signal
Authors: Blankers Thomas , Fruitet Elise , Burdfield-Steel Emily , Groot Astrid T.
Published: September 2021

Sexual signals are important in speciation, but understanding their evolution is complex as these signals are often composed of multiple, genetically interdependent components. To understand how signals evolve, we thus need to consider selection responses in multiple components and account for the genetic correlations among components. One intriguing possibility is that selection changes the genetic covariance structure of a multicomponent signal in a way that facilitates a response to selection. However, this hypothesis remains largely untested empirically. In this study, we investigate the evolutionary response of the multicomponent female sex pheromone blend of the moth Heliothis subflexa to 10 generations of artificial selection. We observed a selection response of about 3/4s of a phenotypic standard deviation in the components under selection. Interestingly, other pheromone components that are biochemically and genetically linked to the components under selection did not change. We also found that after the onset of selection, the genetic covariance structure diverged, resulting in the disassociation of components under selection and components not under selection across the first two genetic principle components. Our findings provide rare empirical support for an intriguing mechanism by which a sexual signal can respond to selection without possible constraints from indirect selection responses.
An unconventional GABAergic circuit differently controls pyramidal neuron activity in two visual cortical areas via endocannabinoids
Authors: Montmerle Martin , Koukouli Fani , Aguirre Andrea , Peixoto Jérémy , Choudhary Vikash , De Brito Van Velze Marcel , Varilh Marjorie , Julio-Kalajzic Francisca , Allene Camille , Mendéz Pablo , Marsicano Giovanni , Schlüter Oliver M. , Rebola Nelson , Bacci Alberto , Lourenço Joana
Published: September 2021

Perisomatic inhibition of neocortical pyramidal neurons (PNs) coordinates cortical network activity during sensory processing, and it has been mainly attributed to parvalbumin-expressing basket cells (BCs). However, cannabinoid receptor type 1 (CB1)-expressing interneurons also inhibit the perisomatic region of PNs but the connectivity and function of these elusive – yet prominent – neocortical GABAergic cells is unknown. We found that the connectivity pattern of CB1-positive BCs strongly differs between primary and high-order cortical visual areas. Moreover, persistently active CB1 signaling suppresses GABA release from CB1 BCs in the medial secondary visual cortex (V2M), but not in the primary (V1) visual area. Accordingly, in vivo, tonic CB1 signaling is responsible for higher but less coordinated PN activity in V2M than in V1. Our results indicate a differential CB1-mediated mechanism controlling PN activity, and suggest an alternative connectivity schemes of a specific GABAergic circuit in different cortical areas
Unscheduled DNA replication in G1 causes genome instability through head-to-tail replication fork collisions
Authors: Reusswig Karl-Uwe , Bittmann Julia , Peritore Martina , Wierer Michael , Mann Matthias , Pfander Boris
Published: September 2021

DNA replicates once per cell cycle. Interfering with the regulation of DNA replication initiation generates genome instability through over-replication and has been linked to early stages of cancer development. Here, we engineered genetic systems in budding yeast to induce unscheduled replication in the G1-phase of the cell cycle. Unscheduled G1 replication initiated at canonical S-phase origins across the genome. We quantified differences in replisomes in G1- and S-phase and identified firing factors, polymerase α, and histone supply as factors that limit replication outside S-phase. G1 replication per se did not trigger cellular checkpoints. Subsequent replication during S-phase, however, resulted in over-replication and led to chromosome breaks via head-to-tail replication fork collisions that are marked by chromosome-wide, strand-biased occurrence of RPA-bound single-stranded DNA. Low-level, sporadic induction of G1 replication induced an identical response, indicating findings from synthetic systems are applicable to naturally occurring scenarios of unscheduled replication initiation by G1/S deregulation.
Enzyme Catalysis Enhances Lateral Lipid Motility and Directional Particle Transport on Membranes
Authors: Somasundar Ambika , Mandal Niladri Sekhar , Sen Ayusman
Published: September 2021

The dynamic interplay between the composition of lipid membranes and the behavior of membrane-bound enzymes is critical to the understanding of cellular function and viability, and the design of membrane-based biosensing platforms. While there is a significant body of knowledge on how lipid composition and dynamics affect membrane-bound enzymes, little is known about how enzyme catalysis influences the motility and lateral transport in lipid membranes. Using enzymes-attached lipids in supported bilayers (SLB), we show catalysis-induced enhanced lateral diffusion of lipids in the bilayer. Enhancing the membrane viscosity by increasing the cholesterol content in the bilayer suppresses the overall diffusion but not the relative diffusion enhancement of the enzyme-attached lipids. We also provide direct evidence of catalysis-induced membrane fluctuations leading to the enhanced diffusion of passive tracers resting on the SLB. Additionally, by using active enzyme patches, we demonstrate the directional transport of tracers on SLBs. These are first steps in understanding diffusion and transport in lipid membranes due to active, out-of-equilibrium processes that are the hallmark of living systems. In general, our study demonstrates how active enzymes can be used to control diffusion and transport in confined 2-D environments.
tascCODA: Bayesian tree-aggregated analysis of compositional amplicon and single-cell data
Authors: Ostner Johannes , Carcy Salomé , Müller Christian L.
Published: September 2021

Accurate generative statistical modeling of count data is of critical relevance for the analysis of biological datasets from high-throughput sequencing technologies. Important instances include the modeling of microbiome compositions from amplicon sequencing surveys and the analysis of cell type compositions derived from single-cell RNA sequencing. Microbial and cell type abundance data share remarkably similar statistical features, including their inherent compositionality and a natural hierarchical ordering of the individual components from taxonomic or cell lineage tree information, respectively. To this end, we introduce a Bayesian model fortree-aggregatedamplicon andsingle-cellcompositionaldataanalysis (tascCODA) that seamlessly integrates hierarchical information and experimental covariate data into the generative modeling of compositional count data. By combining latent parameters based on the tree structure with spike-and-slab Lasso penalization,tascCODAcan determine covariate effects across different levels of the population hierarchy in a data-driven parsimonious way. In the context of differential abundance testing, we validatetascCODA’s excellent performance on a comprehensive set of synthetic benchmark scenarios. Our analyses on human single-cell RNA-seq data from ulcerative colitis patients and amplicon data from patients with irritable bowel syndrome, respectively, identified aggregated cell type and taxon compositional changes that were more predictive and parsimonious than those proposed by other schemes. We posit that tascCODA1constitutes a valuable addition to the growing statistical toolbox for generative modeling and analysis of compositional changes in microbial or cell population data.
Iron promotes Slc7a11-deficient valvular interstitial cell osteogenic differentiation: A possible mechanism by which ferroptosis participates in intraleaflet hemorrhage-induced calcification
Authors: Xu Ran , Zhu Dan , Guo Jianghong , Huang Ying
Published: September 2021

Background

Calcific aortic valve disease (CAVD) is the most frequent pathogeny of aortic valve replacement in developed countries. Iron deposits are found in the intraleaflet hemorrhage (IH) areas of calcific aortic valves. Ferroptosis is a form of regulated cell death that involves metabolic dysfunction resulting from iron overload-dependent excessive lipid peroxidation. In this research, we attempted to clarify the role of ferroptosis in CAVD.

Methods

The level of ferroptosis in tissue and valvular interstitial cells (VICs) was assessed by the contents of 4-HNE, NADPH, ROS, and GSH, lipid peroxidation and mitochondrial morphology. The levels of calcification, iron accumulation and Slc7a11 expression in surgical aortic valve specimens were detected by Alizarin red or Von Kossa, Perl’s blue and immunohistochemical staining. The osteogenic differentiation of VICs was assessed by PCR and western blot analyses. Furthermore, RNA sequencing was used to detect potential differentially expressed genes between normal and osteogenic medium-treated (OM-treated) VICs.

Results

Our experiments demonstrated that ferroptosis occurred in the IH areas of calcific aortic valves. We also found that Slc7a11 was expressed at low levels in OM-treated VICs and IH areas. Finally, we demonstrated that iron promoted Slc7a11-deficient VICs osteogenic differentiation by aggravating ferroptosis in vitro.

Conclusion

In conclusion, iron promotes Slc7a11-deficient VIC osteogenic differentiation by aggravating ferroptosis in vitro, thereby accelerating the progression of aortic valve calcification.

Statement

Statements and opinions expressed in the articles and communications herein are those of the author(s) and not necessarily those of the Editor(s), Society, or publisher, and the Editor(s), Society, and publisher disclaim any responsibility or liability for such material.

Brief Summary

In this work, two novel notions have been proposed. First, we reported that ferroptosis participated in the progression of CAVD. Second, this is the first cytology experiment of valvular interstitial cells (VICs) to clarify the mechanism by which intraleaflet hemorrhage aggravates calve calcification. This research provides new ideas and targets for alleviating the progression of CAVD, especially in patients who have calcified aortic valves without severe stenosis.
CRISPR/Cas9 mediated editing of the Quorn fungus Fusarium venenatum A3/5 by transient expression of Cas9 and sgRNAs targeting endogenous marker gene PKS12
Authors: Wilson Fiona M , Harrison Richard J
Published: September 2021

Background

Gene editing using CRISPR/Cas9 is a widely used tool for precise gene modification, modulating gene expression and introducing novel proteins, and its use has been reported in a number of filamentous fungi including the genus Fusarium. The aim of this study was to optimise gene editing efficiency using AMA1 replicator vectors for transient expression of CRISPR constituents in Fusarium venenatum (A3/5), used commercially in the production of mycoprotein (Quorn™).

Results

We present evidence of CRISPR/Cas9 mediated gene editing in Fusarium venenatum, by targeting the endogenous visible marker gene PKS12, which encodes a polyketide synthase responsible for the synthesis of the pigment aurofusarin. Constructs for expression of single guide RNAs (sgRNAs) were cloned into an AMA1 replicator vector incorporating a construct for constitutive expression of cas9 codon-optimised for Aspergillus niger or F. venenatum. Vectors were maintained under selection for transient expression of sgRNAs and cas9 in transformed protoplasts. 100% gene editing efficiency of protoplast-derived isolates was obtained using A. niger cas9 when sgRNA transcription was regulated by the F. venenatum 5SrRNA promoter. In comparison, expression of sgRNAs using a PgdpA-ribozyme construct was much less effective, generating mutant phenotypes in 0-40% of isolates, with evidence of off-target editing. Viable isolates were not obtained from protoplasts transformed with an AMA1 vector expressing cas9 codon-optimised for F. venenatum.

Conclusions

Using an AMA1 replicator vector for transient expression of A. niger cas9 and sgRNAs transcribed from the native 5SrRNA promoter, we demonstrate efficient gene editing of an endogenous marker gene in F. venenatum, resulting in knockout of gene function and a visible mutant phenotype in 100% of isolates. This establishes a platform for further development of CRISPR/Cas technology in F. venenatum, such as modulation of gene expression, gene insertion, base editing and prime editing. These tools will facilitate an understanding of the controls of secondary metabolism and hyphal development during fermentation of F. venenatum for mycoprotein production and may be used to validate prototypes of strains for improvement using classical means, enabling more cost-effective and sustainable production of this industrially important fungus.
Patterns of selection in the evolution of a transposable element
Authors: Dazenière Julie , Bousios Alexandros , Eyre-Walker Adam
Published: September 2021

Transposable elements (TEs) are a major component of most eukaryotic genomes. Here, we present a new approach which allows us to study patterns of natural selection in the evolution of TEs over short time scales. The method uses the alignment of all elements with intact gag/pol genes of a TE family from a single genome. We predict that the ratio of non-synonymous to synonymous variants (vN/vS) in the alignment should decrease as a function of the frequency of the variants, because elements with non-synonymous variants that reduce transposition will have fewer progeny. We apply our method to Sirevirus LTR retrotransposons that are abundant in maize and other plant species and show that vN/vS declines as variant frequency increases, indicating that negative selection is acting strongly on the Sirevirus genome. The asymptotic value of vN/vS suggests that at least 85% of all non-synonymous mutations in the TE reduce transposition. Crucially, these patterns in vN/vS are only predicted to occur if the gene products from a particular TE insertion preferentially promote the transposition of the same insertion. Overall, this study is the first to use large numbers of intact elements to shed new light on the selective processes that act on TEs.
Simulations on the efficacy of radiotherapy with different time schemes of antiangiogenic therapy
Authors: Tuzer Mert , Yilmaz Defne , Unlu Mehmet Burcin
Published: September 2021

The combination of radiotherapy and antiangiogenic agents has been suggested to be potent in tumor growth control compared to the application of antiangiogenic therapy or radiotherapy alone. Since radiotherapy is highly dependent on the oxygen level of the tumor area, antiangiogenic agents are utilized for the reoxygenation of tumor vasculature. We present a mathematical framework to investigate the efficacy of radiotherapy combined with antiangiogenic treatment. The framework consists of tumor cells, vasculature, and oxygenation levels evolving with time to mimic a tumor microenvironment. Non-linear partial differential equations (PDEs) are employed to simulate each component of the framework. Different treatment schemes are investigated to see the changes in tumor growth and oxygenation. To test combination schedules, radiation monotherapy, neoadjuvant, adjuvant, and concurrent cases are simulated. The efficiency of each therapy scheme on tumor growth control, the changes in tumor cell density, and oxygen levels shared by tumor cells are represented. The simulation results indicate that the application of radiotherapy after antiangiogenic treatment is more efficient in tumor growth control compared to other therapy schemes. The present study gives an insight into the possible interaction and timing of the combination of radiotherapy and antiangiogenic drug treatment.
A DCL3 dicing code within Pol IV-RDR2 transcripts diversifies the siRNA pool guiding RNA-directed DNA methylation
Authors: Loffer Andrew , Singh Jasleen , Fukudome Akihito , Mishra Vibhor , Wang Feng , Pikaard Craig S.
Published: September 2021

In plants, selfish genetic elements including retrotransposons and DNA viruses are transcriptionally silenced by RNA-directed DNA methylation. Guiding the process are short interfering RNAs (siRNAs) cut by DICER-LIKE 3 (DCL3) from double-stranded precursors of ∼30 bp synthesized by NUCLEAR RNA POLYMERASE IV (Pol IV) and RNA-DEPENDENT RNA POLYMERASE 2 (RDR2). We show that Pol IV initiating nucleotide choice, RDR2 initiation 1-2 nt internal to Pol IV transcript ends and RDR2 terminal transferase activity collectively yield a code that influences which end of the precursor is diced and whether 24 or 23 nt siRNAs are generated from the Pol IV or RDR2-transcribed strands. By diversifying the size, sequence, and strand polarity of siRNAs derived from a given precursor, alternative patterns of DCL3 dicing allow maximal siRNA coverage at methylated target loci.
Spatial modeling of extinct Southeast Asian Hobbit Homo floresiensis habitat suitability based on its diet availability and climatic parameters as a proxy
Authors: Wibowo Andri
Published: September 2021

The discovery of a new prehistoric species of the genus Homo remains a significant matter of intense interest. One of significant discovery recently is the Homo floresiensis, representing a small-bodied and small-brained hominin, excavated, and found in Liang Bua Cave in Flores Island, East Nusa Tenggara, Indonesia. This species height was only about 106 cm (3’6“) and the weight was 30-40 kg (66-86 lbs). H. floresiensis was known consumed extant murine rodents as its diets as this was evidence found in Liang Bua Cave. Then this study aims to model the H. floresiensis suitable habitat using maximum entropy method and 2 extant murine rodents, Rattus exulans and R. rattus as a proxy. The results show that the most suitable habitats for H. floresiensis indicated by suitable habitat values close to 1 were concentrated in the central of Flores Island that was overlapped with mountainous areas with elevation ranging from 1500 to 2000 m. These suitable habitats were also overlapped with dense vegetation covers, volcanic rock, and Kiro rock formation. Climatic parameters that limit the distributions of H. floresiensis were annual mean temperature, isothermality, minimum temperature of coldest period, and precipitation seasonality. Parts of Flores Island with the low temperature below 20 °C were favorable for H. floresiensis while an increase in isothermality limits the H. floresiensis distributions.
Reduced metabolic activity in established Gardnerella spp. biofilms contributes to protection from the bactericidal effects of metronidazole
Authors: Khan Salahuddin , Hill Janet E.
Published: September 2021

Gardnerella spp. can form biofilm and it has been suggested that failure of antibiotic treatment of bacterial vaginosis and recurrent vaginosis are linked to this property, however no specific mechanisms have been identified. Here, we performed broth microdilution assays to measure the minimum inhibitory concentration (MIC) of metronidazole for thirty-five Gardnerella isolates in one medium in which Gardnerella spp. grow primarily as biofilm and another in which growth is primarily planktonic. The MIC of isolates in the two conditions were highly correlated (R2= 0.69, p <0.001). No significant reduction in viable cell count of 7/9 isolates was observed when established biofilms were exposed to metronidazole at levels double the MIC. Subsequent measurements of metabolic activity in established biofilms formed by a larger collection of 31 isolates showed reduced metabolic activity following treatment with 128 μg/ml of metronidazole relative to untreated controls in 27/31 cases. The amount of biofilm produced by Gardnerella isolates was not enhanced by metronidazole exposure, even at sub-MIC levels. Our results suggest that reduced metabolic activity in Gardnerella spp. growing in established biofilms may be a mechanism of protection from the bactericidal effects of metronidazole.
A supervised learning algorithm to evaluate occurrence records in virtual species
Authors: Rios Richard , Noguera-Urbano Elkin A. , Espinosa Jairo , Ochoa Jose Manuel
Published: September 2021

Digital and open access of occurrence data have encouraged the development of tools to improve biodiversity conservation and management. In this study, we proposed a methodology to evaluate point-occurrence records based on expert knowledge. We firstly generated virtual data to test our methodology without confounding factors by simulating geographical distributions, virtual sampling, and expert checking of occurrence records. We used a set of non-linear bioclimatic variables and principal component analysis (PCA) to define a duality function between niche and biotope spaces. Subsequently, a supervised-learning model was fit to classify records between true and doubtful presence based on the virtual expert checking. We then tested our methodology using three virtual species and 10-fold cross validation. Also, we evaluated the prediction performance of the supervise model compared with the virtual observer using a virtual external database of occurrence data.
PHIST: fast and accurate prediction of prokaryotic hosts from metagenomic viral sequences
Authors: Zielezinski Andrzej , Deorowicz Sebastian , Gudyś Adam
Published: September 2021

PHIST (Phage-Host Interaction Search Tool) predicts prokaryotic hosts of viruses from their genomic sequences. It improves host prediction accuracy at species level over current alignment-based tools (on average by 3 percentage points) as well as alignment-free and CRISPR-based tools (by 14–20 percentage points). PHIST is also two orders of magnitude faster than alignment-based tools making it suitable for metagenomics studies.

Availability and implementation

GNU-licensed C++ code wrapped in Python API available at:https://github.com/refresh-bio/phist

Contact

andrzej.zielezinski@amu.edu.pl,adam.gudys@polsl.pl

Supplementary information

Supplementary data are available at publisher Web site.
Effects of acute and repeated administration of the selective M4 PAM VU0152099 on cocaine vs. food choice in male rats
Authors: Thomsen Morgane , Crittenden Jill R. , Lindsley Craig W. , Graybiel Ann M.
Published: September 2021

Abstract

Ligands that stimulate muscarinic acetylcholine receptors 1 and 4 (M1, M4) have shown promising effects as putative pharmacotherapy for cocaine use disorder in rodent assays. We have previously shown reductions in cocaine effects with acute M4 stimulation, as well as long-lasting, delayed, reductions in cocaine taking and cocaine seeking with combined M1/M4 receptor stimulation or with M1 stimulation alone. M4 stimulation opposes dopaminergic signaling acutely, but direct dopamine receptor antagonists have proved unhelpful in managing cocaine use disorder because they lose efficacy with long-term administration. It is therefore critical to determine whether M4 approaches themselves can remain effective with repeated or chronic dosing. We assessed the effects of repeated administration of the M4 positive allosteric modulator (PAM) VU0152099 in rats trained to choose between intravenous cocaine and a liquid food reinforcer, to obtain quantitative measurement of whether M4 stimulation could produce delayed and lasting reduction in cocaine taking. VU0152099 produced progressively augmenting suppression of cocaine choice and cocaine intake, but produced neither rebound nor lasting effects after treatment ended. To compare and contrast effects of M1 vs. M4 stimulation, we tested whether the M4 PAM VU0152100 suppressed cocaine self-administration in mice lacking CalDAG-GEFI signaling factor, required for M1-mediated suppression of cocaine self-administration. CalDAG-GEFI ablation had no effect on M4-mediated suppression of cocaine self-administration. These findings support the potential usefulness of M4 PAMs as pharmacotherapy to manage cocaine use disorder, alone or in combination with M1-selective ligands, and show that M1 and M4 stimulation modulate cocaine-taking behavior by distinct mechanisms.
The 14-3-3 Proteins Bmh1 and Bmh2 Are Key Regulators of Meiotic Commitment
Authors: Gavade Janardan N. , Puccia Chris , Herod S. Grace , Trinidad Jonathan C. , Berchowitz Luke E. , Lacefield Soni
Published: September 2021

Induction of meiosis requires exogenous signals that activate internal gene regulatory networks. Meiotic commitment ensures the irreversible continuation of meiosis, even upon withdrawal of the meiosis inducing signals. Budding yeast cells have a unique property in that cells enter meiosis when starved, but if given nutrient-rich medium prior to the commitment point, they exit meiosis and enter mitosis. After the meiotic commitment point in prometaphase I, cells remain in meiosis even with addition of nutrients. Despite the importance of meiotic commitment in ensuring the production of gametes, only a few genes involved in the commitment process are known. We performed a genome-scale screen in budding yeast and discovered new regulators of meiotic commitment including Bcy1, which is involved in nutrient sensing, the meiosis-specific kinase Ime2, Polo kinase Cdc5, and the 14-3-3 proteins Bmh1 and Bmh2. Importantly, we found that Bmh1 and Bmh2 are involved in multiple processes throughout meiosis including the maintenance of the middle meiosis transcription factor Ndt80, activation of Cdc5, and interaction with an RNA-binding protein Pes4, which is important for regulating the timing of translation of several mRNAs in meiosis II. This study identifies a meiotic commitment regulatory network with the 14-3-3 proteins functioning as central regulators.
Metabolic and functional connectivity provide unique and complementary insights into cognition-connectome relationships
Authors: Voigt Katharina , Liang Emma X. , Misic Bratislav , Ward Phillip G.D. , Egan Gary F. , Jamadar Sharna D.
Published: September 2021

A major challenge in current cognitive neuroscience is how functional brain connectivity gives rise to human cognition. Functional magnetic resonance imaging (fMRI) describes brain connectivity based on cerebral oxygenation dynamics (hemodynamic connectivity), whereas [18 F]-fluorodeoxyglucose functional positron emission tomography (FDG-fPET) describes brain connectivity based on cerebral glucose uptake (metabolic connectivity), each providing a unique characterisation of the human brain. How these two modalities differ in their contribution to cognition and behaviour is unclear. We used simultaneous resting-state FDG-fPET/fMRI to investigate how hemodynamic connectivity and metabolic connectivity relate to cognitive function by applying partial least squares analyses. Results revealed that while for both modalities the frontoparietal anatomical subdivisions related the strongest to cognition, using hemodynamic measures this network expressed executive functioning, episodic memory, and depression, while for metabolic measures this network exclusively expressed executive functioning. These findings demonstrate the unique advantages that simultaneous FDG-PET/fMRI has to provide a comprehensive understanding of the neural mechanisms that underpin cognition and highlights the importance of multimodality imaging in cognitive neuroscience research.
Entrectinib - a SARS-CoV-2 inhibitor in Human Lung Tissue (HLT) cells
Authors: Peralta-Garcia Alejandro , Torrens-Fontanals Mariona , Stepniewski Tomasz Maciej , Grau-Expósito Judit , Perea David , Ayinampudi Vikram , Waldhoer Maria , Zimmermann Mirjam , Buzón Maria J. , Genescà Meritxell , Selent Jana
Published: September 2021

Since the start of the COVID-19 outbreak, pharmaceutical companies and research groups have focused on the development of vaccines and antiviral drugs against SARS-CoV-2. Here, we apply a drug repurposing strategy to identify potential drug candidates that are able to block the entrance of the virus into human cells. By combining virtual screening with in vitro pseudovirus assays and antiviral assays in Human Lung Tissue (HLT) cells, we identify entrectinib as a promising antiviral drug. We found that part of the antiviral action of entrectinib is mediated by a non-specific mechanism, likely occurring at the viral membrane level. Such a profile could provide entrectinib with protection against the development of drug resistance by emerging SARS-CoV-2 variants.
A copper switch for inducing CRISPR/Cas9-based transcriptional activation tightly regulates gene expression in Nicotiana benthamiana
Authors: Garcia-Perez Elena , Diego-Martin Borja , Quijano-Rubio Alfredo , Moreno-Gimenez Elena , Orzaez Diego , Vazquez-Vilar Marta
Published: September 2021

CRISPR-based programmable transcriptional activators (PTAs) are used in plants for rewiring gene networks. Better tuning of their activity in a time and dose-dependent manner should allow precise control of gene expression. Here, we report the optimization of a Copper Inducible system called CI-switch for conditional gene activation in Nicotiana benthamiana. In the presence of copper, the copper-responsive factor CUP2 undergoes a conformational change and binds a DNA motif named copper-binding site (CBS). In this study, we tested several activation domains fused to CUP2 and found that the non-viral Gal4 domain results in strong activation of a reporter gene equipped with a minimal promoter, offering advantages over previous designs. To connect copper regulation with downstream programable elements, several copper-dependent configurations of the strong dCasEV2.1 PTA were assayed, aiming at maximizing activation range, while minimizing undesired background expression. The best configuration involved a dual copper regulation of the two protein components of the PTA, namely dCas9:EDLL and MS2:VPR, and a constitutive RNA pol III-driven expression of the third component, a guide RNA with anchoring sites for the MS2 RNA-binding domain. With these optimizations in place, the CI/dCasEV2.1 system resulted in copper-dependent activation rates of 2,600-fold for the endogenous N. benthamiana DFR gene, with negligible expression in the absence of the trigger. The tight regulation of copper over CI/dCasEV2.1 makes this system ideal for the conditional production of plant-derived metabolites and recombinant proteins in the field.
Electric shock causes a fear-like persistent behavioral response in the nematode Caenorhabditis elegans
Authors: Tee Ling Fei , Young Jared J. , Suzuki Ryoga , Maruyama Keisuke , Endo Yuto , Kimura Koutarou D.
Published: September 2021

Behavioral persistency reflects internal brain states, which are the foundations of multiple brain functions. However, experimental paradigms that enable genetic analyses of behavioral persistency and its associated brain functions have been limited. Here we report novel persistent behavioral responses caused by electric stimuli in the nematode Caenorhabditis elegans. When the animals on bacterial food are stimulated by alternating current, their movement speed suddenly increases more than 2-fold, which persists for minutes even after the electric stimulation is terminated. Genetic analyses reveal that multiple types of voltage-gated channels are required for the response, possibly as the sensors, and neuropeptide signaling regulates the duration of the persistent response. Additional behavioral analyses indicate that the animal’s response to electric shock is scalable and has a negative valence. These properties, along with persistence, have been recently regarded as essential features of emotion, suggesting that the animal’s response to electric shock may express a form of emotion, such as fear.
Fuzzy Integral With Particle Swarm Optimization for CNN-Based Motor-Imagery EEG Classification
Authors: Huang Jian-Xue , Huang Ya-Lin , Hsieh Chia-Ying , Wei Chun-Shu
Published: September 2021

Recently, decoding human electroencephalographic (EEG) data using convolutional neural network (CNN) has driven the state-of-the-art recognition of motor-imagery EEG patterns for brain-computer interfacing (BCI). While a variety of CNN models have been used to classify motor-imagery EEG data, it is unclear if aggregating an ensemble of heterogeneous CNN models could further enhance the classification performance. To integrate the outputs of ensemble classifiers, this work utilizes fuzzy integral with particle swarm optimization (PSO) to estimate optimal confidence levels assigned to classifiers. The proposed frame-work aggregates CNN classifiers and fuzzy integral with PSO, achieving robust performance in single-trial classification of motor-imagery EEG data across various CNN model training schemes depending on the scenarios of BCI usage. This proof-of-concept study demonstrates the feasibility of applying fuzzy fusion techniques to enhance CNN-based EEG decoding and benefit practical applications of BCI.
Hi-C Contacts Encode Heterogeneity in Sub-diffusive Motion of E. coli Chromosomal Loci
Authors: Bera Palash , Wasim Abdul , Mondal Jagannath
Published: September 2021

Underneath its apparently simple architecture, the circular chromosome of E. coli is known for displaying complex dynamics in its cytoplasm. Recent experiments have hinted at an inherently heterogeneous dynamics of chromosomal loci, the origin of which has largely been elusive. In this regard, here we investigate the loci dynamics of E. coli chromosome in a minimally growing condition at 30°C by integrating the experimentally derived Hi-C interaction matrix within a computer model. Our quantitative analysis demonstrates that, while the dynamics of the chromosome is sub-diffusive in a viscoelastic media in general, the diffusion constants and the diffusive exponents are strongly dependent on the spatial coordinates of chromosomal loci. In particular, the loci in Ter Macro-domain display slower mobility compared to the others. The result is found to be robust even in the presence of active noise. Interestingly, a series of control investigations reveal that the absence of Hi-C interactions in the model would have abolished the heterogeneity in loci diffusion, indicating that the observed coordinate-dependent chromosome dynamics is heavily dictated via Hi-C-guided longrange inter-loci communications. Overall, the study underscores the key role of Hi-C interactions in guiding the inter-loci encounter and in modulating the underlying heterogeneity of the loci diffusion.
Food insecurity, food waste, food behaviours and cooking confidence of UK citizens at the start of the COVID-19 lockdown
Authors: Armstrong Beth , Reynolds Christian , Martins Carla Adriano , Frankowska Angelina , Levy Renata Bertazzi , Rauber Fernanda , Osei-Kwasi Hibbah A. , Vega Marcelo , Cediel Gustavo , Schmidt Ximena , Kluczkovski Alana , Akparibo Robert , Auma Carolyn L. , Defeyter Margaret Anne A. , Tereza da Silva Jacqueline , Bridge Gemma
Published: September 2021

Purpose

The current pilot study explored food insecurity, food waste, food related behaviours and cooking confidence of UK consumers following the COVID-19 lockdown.

Design/methodology/approach

Data were collected from 473 UK-based consumers (63% female) in March 2020. A cross-sectional online survey measured variables including food insecurity prevalence, self-reported food waste, food management behaviours, confidence and frequency of use of a range of cooking methods, type of food eaten (ultra-processed, semi-finished, unprocessed) and packaging type foods are purchased in.

Findings

39% of participants have experienced some food insecurity in the last 12 months. Being younger, having a greater BMI and living in a smaller household were associated with food insecurity. Green leaves, carrots, potatoes and sliced bread are the most wasted of purchased foods. Polenta, green leaves and white rice are the most wasted cooked foods. Food secure participants reported wasting a smaller percentage of purchased and cooked foods compared to food insecure participants. Overall, participants were most confident about boiling, microwaving and stir-frying and least confident with using a pressure cooker or sous vide. Food secure participants were more confident with boiling, stir-frying, grilling and roasting than insecure food participants.

Practical implications

This has implications for post lockdown policy, including food policies and guidance for public-facing communications.

Originality/value

We identified novel differences in self-report food waste behaviours and cooking confidence between the food secure and insecure consumers and observed demographics associated with food insecurity.
Understanding the key takeaway of construction robots towards construction automation
Authors: Huang Zhu , Mao Chao , Wang Jun , Sadick Abdul-Manan
Published: September 2021

Purpose

The construction industry is the major sector in China but it has been exposed to a series of problems including low productivity and workforce shortage. However, construction robots as an effective and sustainable approach to overcome the difficulties in construction industry have not been widely adopted. Few studies attempted to investigate on the adoption of construction robots in China. In order to fill this gap, this study aim to address the barriers to the adoption of construction robots in China.

Design/methodology/approach

Through literature review, semi-structured interview 24 factors hindering the adoption of construction robots are summarized. Next, a total of valid 150 questionnaires delivered to the 7 stakeholders were collected. Ranking analysis was used to identify 21 critical factors was determined by the mean score analysis and factor analysis extracted 21 critical factors into 5 clusters.

Findings

Results indicate that the “technological performance and management” cluster is the most dominant of the 5 clusters. The most important barrier is “Limited research and design input”, followed by “High purchase cost” and “Unstructured construction environment”. Construction robots are still under R&D have had limited field applications in the production and construction process.

Originality/value

The research findings provide a useful reference for different stakeholders to identify the critical factors appropriate strategies to promote the adoption of construction robots. Furthermore, this study provides recommendations to promote adoption of construction robots.
Anticipated positive evaluation of social media posts: social return, revisit intention, recommend intention and mediating role of memorable tourism experience
Authors: Mittal Amit , Bhandari Harveen , Chand Pawan Kumar
Published: September 2021

Purpose

The purpose of this study is to examine how the anticipated positive evaluation of a tourist’s social media posts by significant others, known as social return (SR), impacts the memorable tourism experience (MTE) and how this evaluation influences the revisit intention and recommend intention (operationalized dimensions of behavioral intention-BI).

Design/methodology/approach

The relationship among SR, MTE and BI was measured using established scales that were assessed for reliability and validity. Structural equation modeling was applied to the data collected from 316 respondents who had visited a heritage site.

Findings

The findings indicate that SR significantly impacts MTE and BI and MTE partially mediates the relationship between SR and BI. However, the impact of SR on revisit intention is weak despite being statistically significant.

Research limitations/implications

This paper seeks to extend the SR concept introduced in tourism and hospitality literature in 2018. This study validated the scale in a new context while retaining the inviolability of the scale by including a world heritage site. This study used an extended version of the MTE scale and an adapted version of the BI scale. The use of these three scales together is an attempt to examine the symbolic nature of social media posts that can generate perceptions regarding the memorability of the tourist’s visit.

Originality/value

SR is a relatively new construct and has been very sparsely studied with no known study linking SR, MTE and BI.
Does gender matter for the unemployment hysteresis effect among Asian countries?
Authors: Li Zheng-Zheng , Su Chi Wei , Tao Ran
Published: September 2021

Purpose

This study aims to examine the unemployment hysteresis effects from the perspective of the heterogeneity of genders within Asian countries.

Design/methodology/approach

The authors use the annual unemployment rate dataset of 12 Asian countries ranging from 1991–2020. Traditional unit root tests are initially employed to investigate the unemployment hysteresis effect. Considering the structural break and cross-section dependence problems, the sequential panel selection method (SPSM) and the Kapetanios–Snell–Shin (KSS) panel unit root test with Fourier functions have proven to be more applicable.

Findings

The empirical results indicate that the unemployment rate is stationary in most Asian regions for both females and males, which confirms the mean reversion process of the natural unemployment hypothesis. This suggests that these countries' unemployment rates are flexible to quickly revert to its long-run equilibrium determined by the labor markets. However, only the female unemployment rate in Pakistan and Nepal and adult female unemployment rates in these two economies present non-stationary series. In line with the unemployment hysteresis effect, it means shocks will leave a permanent impact on their labor market.

Practical implications

On the one hand, in most of the Asian countries, it can be inferred that the trade-off between inflation and unemployment is temporary because the natural unemployment hypothesis holds. Therefore, policymakers may consider using monetary policy as a tool to control inflation and stimulate growth during a recession. Such policy measures should not have a long-run impact on unemployment or cause a permanent shift in the natural unemployment rate. On the other hand, the government should implement active labor protective programs such as education or training schemes, job search assistance programs and maternity protection, especially for female adults, to reduce the negative shocks in the economic downturn, which is beneficial for them away from being long-term unemployed. It is also necessary to improve the labor unions to reduce the discrimination between female and male labors.

Originality/value

This paper innovatively concentrates on the heterogeneity performances between genders about the unemployment hysteresis effect within Asian countries. Furthermore, taking into account the age-specific characteristics, the youth and adult unemployment rates have been investigated. Additionally, the approximation of bootstrap distribution and the advanced panel KSS unit root test with a Fourier function are employed. Thereby, targeted policies for the government can be applied to reduce the discrimination and negative shocks on female adults in the labor market.
No expatriate is an island: the role of salient stakeholders' support in international assignments
Authors: Chan Hak Liong , Zawawi Dahlia , Ng Siew Imm , Nipo Debbra Toria Anak
Published: September 2021

Purpose

International assignments are an effective tool to develop employees' cultural competencies, yet expatriate failure rates remain high. This paper aims to examine salient stakeholders' (i.e. organisations, host country nationals (HCNs) and spouses) support as antecedents of expatriates' work adjustment and task performance. It also explores work adjustment as a mediator between support and task performance.

Design/methodology/approach

Adopting the quantitative approach, survey data were collected from 112 expatriates who were married and based in organisations in Malaysia. Partial least squares-structural equation modelling was employed to analyse the data.

Findings

The findings validate the direct influences of perceived organisational support (POS) on work adjustment, HCN support on work adjustment, and spousal support on task performance. The indirect effect of HCN support on task performance through work adjustment was also established. When expatriates' work adjustment improves as a result of receiving HCN support, their task performance is enhanced.

Practical implications

This study evidences that expatriate-hiring firms should provide suitable support for expatriates when they work overseas. Local employees and spouses should likewise be tasked to help expatriates maximise their full potential in achieving successful performance in their assignments.

Originality/value

The contribution of this study is the exploration of the relationships between support, work adjustment and task performance among expatriates. It also adds to the limited knowledge on the role of specific stakeholders in the expatriate context.
A lifecycle cost model considering both component and system burn-in for operationally unrepairable systems
Authors: Teo Kah How , Tai Kang , Schena Vincenzo , Simonini Luca
Published: September 2021

Purpose

This study presents a lifecycle cost model considering multi-level burn-in for operationally unrepairable systems including assembly and warranty costs. A numerical method to obtain system reliability under component replacement during burn-in is also presented with derived error bounds.

Design/methodology/approach

The final system reliability after component and system burn-in is obtained and warranty costs are computed. On failure during operation, the system is replaced with another that undergoes an identical burn-in procedure. Cost behaviours for a small and large system are shown in a numerical example.

Findings

There are more cost savings when system burn-in is conducted for a large system whereas a strategy focusing on component burn-in only can also result in cost savings for small systems. In addition, a minimum system burn-in duration is required before cost savings are achieved for these operationally unrepairable systems.

Originality/value

The operationally unrepairable system is a niche class of systems which small satellites fall under and no such study has been conducted before. The authors present a different approach towards the testing of small satellites for a constellation mission.