bluuebunny/crossref_metadata_2025 huggingface dataset:
SARS-CoV-2 ribosomal frameshifting pseudoknot: Improved secondary structure prediction and detection of inter-viral structural similarity
Authors: Trinity Luke , Lansing Lance , Jabbari Hosna , Stege Ulrike
Published: September 2020

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to the COVID-19 pandemic; a pandemic of a scale that has not been seen in the modern era. Despite over 29 million reported cases and over 900, 000 deaths worldwide as of September 2020, herd immunity and widespread vaccination efforts by many experts are expected to be insufficient in addressing this crisis for the foreseeable future. Thus, there is an urgent need for treatments that can lessen the effects of SARS-CoV-2 in patients who become seriously affected. Many viruses including HIV, the common cold, SARS-CoV and SARS-CoV-2 use a unique mechanism known as −1 programmed ribosomal frameshifting (−1 PRF) to successfully replicate and infect cells in the human host. SARS-CoV (the coronavirus responsible for SARS) and SARS-CoV-2 possess a unique RNA structure, a three-stemmed pseudoknot, that stimulates −1 PRF. Recent experiments identified that small molecules can be introduced as antiviral agents to bind with the pseudoknot and disrupt its stimulation of −1 PRF. If successfully developed, small molecule therapy that targets −1 PRF in SARS-CoV-2 is an excellent strategy to improve patients’ prognoses. Crucial to developing these successful therapies is modeling the structure of the SARS-CoV-2 −1 PRF pseudoknot. Following a structural alignment approach, we identify similarities in the −1 PRF pseudoknots of the novel coronavirus SARS-CoV-2, the original SARS-CoV, as well as a third coronavirus: MERS-CoV, the coronavirus responsible for Middle East Respiratory Syndrome (MERS). In addition, we provide a better understanding of the SARS-CoV-2 −1 PRF pseudoknot by comprehensively investigating the structural landscape using a hierarchical folding approach. Since understanding the impact of mutations is vital to long-term success of treatments that are based on predicted RNA functional structures, we provide insight on SARS-CoV-2 −1 PRF pseudoknot sequence mutations and their effect on the resulting structure and its function.
Single individual structural variant detection uncovers widespread hemizygosity in molluscs
Authors: Calcino Andrew D , Kenny Nathan J , Gerdol Marco
Published: September 2020

The advent of complete genomic sequencing has opened a window into genomic phenomena obscured by fragmented assemblies. A good example of these is the existence of hemizygous regions of autosomal chromosomes, which can result in marked differences in gene content between individuals within species. While these hemizygous regions, and presence/absence variation of genes that can result, are well known in plants, firm evidence has only recently emerged for their existence in metazoans.

Here we use recently published, complete genomes from wild-caught molluscs to investigate the prevalence of hemizygosity and pan-genomes across a well-known and ecologically important clade. We show that hemizygous regions are widespread in mollusc genomes, not clustered in individual chromosomes, and often contain genes linked to transposition, DNA repair and stress response. With targeted investigations of HSP70-12 and C1qDC, we also show how individual gene families are distributed within pan-genomes.

This work suggests that pan-genomes are widespread across the conchiferan Mollusca, and represent useful tools for genomic evolution, allowing the maintenance of additional genetic diversity within the population. As genomic sequencing and re-sequencing becomes more routine, the prevalence of hemizygosity, and its impact on selection and adaptation, are key targets for research across the tree of life.
A homologue of the mammalian tumour suppressor protein PTEN is a functional lipid phosphatase and required for chemotaxis in filamentous fungi
Authors: Hassing Berit , Candy Alyesha , Eaton Carla J. , Fernandes Tania R. , Mesarich Carl H. , Di Pietro Antonio , Scott Barry
Published: September 2020

Phosphoinositides (PI) are essential components of eukaryotic membranes and function in a large number of signalling processes. While lipid second messengers are well studied in mammals and yeast, their role in filamentous fungi is poorly understood. We used fluorescent PI-binding molecular probes to localise the phosphorylated phosphatidylinositol species PI[3]P, PI[3,5]P2, PI[4]P and PI[4,5]P2 in hyphae of the endophyte Epichloë festucae in axenic culture and during interaction with its grass host Lolium perenne. We also analysed the roles of the phosphatidylinositol-4-phosphate 5-kinase MssD and the predicted phosphatidylinositol-3,4,5-triphosphate 3-phosphatase TepA, a homologue of the mammalian tumour suppressor protein PTEN. Deletion of tepA in E. festucae and in the root-infecting tomato pathogen Fusarium oxysporum had no impact on growth in culture or the host interaction phenotype. However, this mutation did uncover the presence of PI[3,4,5]P3 in septa of E. festucae and showed that TepA is required for chemotropism in F. oxysporum. The identification of PI[3,4,5]P3 in septa of ΔtepA strains suggests that filamentous fungi are able to generate PI[3,4,5]P3 using an alternative biosynthetic pathway and that fungal PTEN homologues are functional lipid phosphatases. The F. oxysporum chemotropism defect demonstrates a conserved role of PTEN homologues in chemotaxis across protists, fungi and mammals.
Latency and amplitude of the stop-signal P3 event-related potential are related to inhibitory GABAaactivity in primary motor cortex
Authors: Hynd Megan , Soh Cheol , Rangel Benjamin O. , Wessel Jan R.
Published: September 2020

By stopping actions even after their initiation, humans can adapt their ongoing behavior rapidly to changing environmental circumstances. The neural processes underlying the implementation of rapid action-stopping are still controversially discussed. In the early 1990s, a fronto-central P3 event-related potential (ERP) was identified in the human EEG response following stop-signals in the classic stop-signal task, accompanied by the proposal that this ERP reflects the “inhibitory” side of the purported horse-race underlying successful action-stopping. Later studies have lent support to this interpretation by finding that the amplitude and onset of the stop-signal P3 relate to both overt behavior and to movement-related EEG activity in ways predicted by the race model. However, such studies are limited by the ability of EEG to allow direct inferences about the presence (or absence) of true, physiologically inhibitory signaling at the neuronal level. To address this, we here present a cross-modal individual differences investigation of the relationship between the features stop-signal P3 ERP and GABAergic neurotransmission in primary motor cortex (M1, as measured by paired-pulse transcranial magnetic stimulation). Following recent work, we measured short-interval intracortical inhibition (SICI), a marker of inhibitory GABAaactivity in M1, in a group of 41 human participants who also performed the stop-signal task while undergoing EEG recordings. In line with the P3-inhibition hypothesis, we found that subjects with stronger inhibitory GABA activity in M1 also showed both faster onsets and larger amplitudes of the stop-signal P3. This provides direct evidence linking the properties of this ERP to a true physiological index of motor system inhibition. We discuss these findings in the context of recent theoretical developments and empirical findings regarding the neural implementation of inhibitory control during action-stopping.
Proteomic analysis of metabolic pathways supports chloroplast-mitochondria cross-talk in a Cu-limited diatom
Authors: Hippmann Anna A. , Schuback Nina , Moon Kyung-Mee , McCrow John P. , Allen Andrew E. , Foster Leonard F. , Green Beverley R. , Maldonado Maria T.
Published: September 2020

Diatoms are one of the most successful phytoplankton groups in our oceans, being responsible for over 20% of the Earth’s photosynthetic productivity. Their chimeric genomes have genes derived from red algae, green algae, bacteria and heterotrophs, resulting in multiple isoenzymes targeted to different cellular compartments with the potential for differential regulation under nutrient limitation. The resulting interactions between metabolic pathways are not yet fully understood.

We previously showed how acclimation to Cu limitation enhanced susceptibility to overreduction of the photosynthetic electron transport chain and its reorganization to favor photoprotection over light-harvesting in the oceanic diatomThalassiosira oceanica(Hippmann et al., 2017). In order to gain a better understanding of the overall metabolic changes that help alleviate the stress of Cu limitation, we have further analyzed the comprehensive proteomic datasets generated in that study to identify differentially expressed proteins involved in carbon, nitrogen and oxidative stress-related metabolic pathways.

Metabolic pathway analysis showed integrated responses to Cu limitation. The up-regulation of ferredoxin (Fdx) was correlated with up-regulation of plastidial Fdx-dependent isoenzymes involved in nitrogen assimilation as well as enzymes involved in glutathione synthesis, thus integrating nitrogen uptake and metabolism with photosynthesis and oxidative stress resistance. The differential expression of glycolytic isoenzymes located in the chloroplast and mitochondria may enable them to channel both excess electrons and/or ATP between these compartments. Additional evidence for chloroplast-mitochondrial cross-talk is the increased expression of chloroplast and mitochondrial proteins involved in the proposed malate shunt under Cu limitation.

One sentence summary

Diatoms adapt to Cu limitation by regulating their large repertoire of isoenzymes to channel electrons away from the chloroplast, enhance nitrogen uptake, and integrate the oxidative stress response.123
Impact of temporal pH fluctuations on the coexistence of nasal bacteria
Authors: Dedrick Sandra , Akbari M. Javad , Dyckman Samantha , Zhao Nannan , Liu Yang-Yu , Momeni Babak
Published: September 2020

To manipulate nasal microbiota for respiratory health, we need to better understand how this microbial community is assembled and maintained. Previous work has demonstrated that the pH in the nasal passage experiences temporal fluctuations. Yet, the impact of such pH fluctuations on nasal microbiota is not fully understood. Here, we examine how temporal fluctuations in pH might affect the coexistence of nasal bacteria. We take advantage of the cultivability of nasal bacteria to experimentally assess their responses to pH. Based on experimentally observed responses, we formulate a mathematical model to numerically investigate the impact of temporal pH fluctuations on species coexistence. Through extensive numerical simulations, we find that the composition of nasal communities is robust against pH fluctuations. Our results suggest that nasal microbiota could be more robust than expected against environmental fluctuations.
Single-Cell RNA Sequencing of Batch Chlamydomonas Cultures Reveals Heterogeneity in their Diurnal Cycle Phase
Authors: Ma Feiyang , Salomé Patrice A. , Merchant Sabeeha S. , Pellegrini Matteo
Published: September 2020

The photosynthetic unicellular alga Chlamydomonas (Chlamydomonas reinhardtii) is a versatile reference for algal biology because of the facility with which it can be cultured in the laboratory. Genomic and systems biology approaches have previously been used to describe how the transcriptome responds to environmental changes, but this analysis has been limited to bulk data, representing the average behavior from pools of cells. Here, we apply single-cell RNA sequencing (scRNA-seq) to probe the heterogeneity of Chlamydomonas cell populations under three environments and in two genotypes differing in the presence of a cell wall. First, we determined that RNA can be extracted from single algal cells with or without a cell wall, offering the possibility to sample algae communities in the wild. Second, scRNA-seq successfully separated single cells into non-overlapping cell clusters according to their growth conditions. Cells exposed to iron or nitrogen deficiency were easily distinguished despite a shared tendency to arrest cell division to economize resources. Notably, these groups of cells recapitulated known patterns observed with bulk RNA-seq, but also revealed their inherent heterogeneity. A substantial source of variation between cells originated from their endogenous diurnal phase, although cultures were grown in constant light. We exploited this result to show that circadian iron responses may be conserved from algae to land plants. We propose that bulk RNA-seq data represent an average of varied cell states that hides underappreciated heterogeneity.

One-sentence summary

We show that single-cell RNA-seq (scRNA-seq) can be applied to Chlamydomonas cultures to reveal the that heterogenity in bulk cultures is largely driven by diurnal cycle phases

The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantcell.org) is: Matteo Pellegrini (matteop@mcdb.ucla.edu)
Calcium imaging and the curse of negativity
Authors: Vanwalleghem Gilles , Constantin Lena , Scott Ethan K.
Published: September 2020

The imaging of neuronal activity using calcium indicators has become a staple of modern neuroscience. However, without ground truths, there is a real risk of missing a significant portion of the real responses. Here, we show that a common assumption, the non-negativity of the neuronal responses as detected by calcium indicators, biases all levels of the frequently used analytical methods for these data. From the extraction of meaningful fluorescence changes to spike inference and the analysis of inferred spikes, each step risks missing real responses because of the assumption of non-negativity. We first show that negative deviations from baseline can exist in calcium imaging of neuronal activity. Then, we use simulated data to test three popular algorithms for image analysis, finding that suite2p may be the best suited to large datasets. Spike inference algorithms also showed their limitations in dealing with inhibited neurons, and new approaches may be needed to address this problem. We further suggest avoiding data analysis approaches that may ignore inhibited responses in favor of a first exploratory step to ensure that none are present. Taking these steps will ensure that inhibition, as well as excitation, is detected in calcium imaging datasets.
X chromosome-dependent disruption of placental regulatory networks in hybrid dwarf hamsters
Authors: Brekke Thomas D. , Moore Emily C. , Campbell-Staton Shane C. , Callahan Colin M. , Cheviron Zachary A. , Good Jeffrey M.
Published: September 2020

Embryonic development in mammals is highly sensitive to changes in gene expression within the placenta. The placenta is also highly enriched for genes showing parent-of-origin or imprinted expression, which is predicted to evolve rapidly in response to parental conflict. However, little is known about the evolution of placental gene expression, or if divergence of placental gene expression plays an important role in mammalian speciation. We used crosses between two species of dwarf hamsters (Phodopus sungorusandP. campbelli) to examine the genetic and regulatory underpinnings of severe placental overgrowth in their hybrids. Using quantitative genetic mapping and mitochondrial substitution lines, we show that overgrowth of hybrid placentas was primarily caused by genetic differences on the maternally inheritedP. sungorusX chromosome. Mitochondrial interactions did not contribute to abnormal hybrid placental development, and there was only weak correspondence between placental disruption and embryonic growth. Genome-wide analyses of placental transcriptomes from the parental species and first and second-generation hybrids revealed a central group of co-expressed X-linked and autosomal genes that were highly enriched for maternally-biased expression. Expression of this gene network was strongly correlated with placental size and showed widespread misexpression dependent on epistatic interactions with X-linked hybrid incompatibilities. Collectively, our results indicate that the X chromosome is likely to play a prominent role in the evolution of placental gene expression and the accumulation of hybrid developmental barriers between mammalian species.
Cenote-Taker 2 Democratizes Virus Discovery and Sequence Annotation
Authors: Tisza Michael J. , Belford Anna K. , Dominguez-Huerta Guillermo , Bolduc Benjamin , Sullivan Matthew B. , Buck Christopher B.
Published: September 2020

Viruses, despite their great abundance and significance in biological systems, remain largely mysterious. Indeed, the vast majority of the perhaps hundreds of millions of viral species on the planet remain undiscovered. Additionally, many viruses deposited in central databases like GenBank and RefSeq are littered with genes annotated as “hypothetical protein” or the equivalent. Cenote-Taker2, a virus discovery and annotation tool available on command line and with a graphical user interface with free high-performance computation access, utilizes highly sensitive models of hallmark virus genes to discover familiar or divergent viral sequences from user-input contigs. Additionally, Cenote-Taker2 uses a flexible set of modules to automatically annotate the sequence features of contigs, providing more gene information than comparable tools. The outputs include readable and interactive genome maps, virome summary tables, and files that can be directly submitted to GenBank. We expect Cenote-Taker2 to facilitate virus discovery, annotation, and expansion of the known virome.
Molecular basis for cysteine oxidation by Plant Cysteine Oxidases fromArabidopsis thaliana
Authors: Guo Qiong , Chen Zhenzhen , Wu Gao , Wen Jie , Liao Shanhui , Xu Chao
Published: September 2020

Plant Cysteine Oxidases (PCOs) play important roles in controlling the stability of Group VII ethylene response factors (ERF-VIIs) via N-Arg/degron pathway through catalyzing the oxidation of their N-Cys for subsequent Arginyl-tRNA--protein transferase 1 (ATE1) mediated arginine installation. Here we presented structures of PCO2, PCO4, and PCO5 fromArabidopsis thaliana(AtPCOs) and examined theirin vitroactivity by MS. On the basis of Tris-boundAtPCO2, we modelled the Cys-boundAtPCO2 structure and identified key residues involved in N-Cys oxidation. Alanine substitution of potential N-Cys interaction residues impaired the activity ofAtPCO5 remarkably. The structural research, complemented by mutagenesis and mass spectrometry experiments, not only uncovers the substrate recognition and catalytic mode byAtPCOs, but also sheds light on the future design of potent inhibitors for plant cysteine oxidases.
Comprehensive characterization of tissue-specific chromatin accessibility in L2Caenorhabditis elegansnematodes
Authors: Durham Timothy J. , Daza Riza M. , Gevirtzman Louis , Cusanovich Darren A. , Noble William Stafford , Shendure Jay , Waterston Robert H.
Published: September 2020

Recently developed single cell technologies allow researchers to characterize cell states at ever greater resolution and scale.C. elegansis a particularly tractable system for studying development, and recent single cell RNA-seq studies characterized the gene expression patterns for nearly every cell type in the embryo and at the second larval stage (L2). Gene expression patterns are useful for learning about gene function and give insight into the biochemical state of different cell types; however, in order to understand these cell types, we must also determine how these gene expression levels are regulated. We present the first single cell ATAC-seq study inC. elegans. We collected data in L2 larvae to match the available single cell RNA-seq data set, and we identify tissue-specific chromatin accessibility patterns that align well with existing data, including the L2 single cell RNA-seq results. Using a novel implementation of the latent Dirichlet allocation algorithm, we leverage the single-cell resolution of the sci-ATAC-seq data to identify accessible loci at the level of individual cell types, providing new maps of putative cell type-specific gene regulatory sites, with promise for better understanding of cellular differentiation and gene regulation in the worm.
Characterization of the habitat- and season-independent increase in fungal biomass induced by the invasive giant goldenrod and its impact on the fungivorous nematode community
Authors: Harkes Paula , van Heumen Lisa J.M. , van den Elsen Sven J.J. , Mooijman Paul J.W. , Quist Casper W. , Vervoort Mariëtte T. W. , Gort Gerrit , Holterman Martijn H.M. , van Steenbrugge Joris J.M. , Helder Johannes
Published: September 2020

Outside its native range, the invasive plant species giant goldenrod (Solidago gigantea) has been shown to increase belowground fungal biomass. This non-obvious effect is poorly characterized; we don’t know whether it is plant developmental stage-dependent, which fractions of the fungal community are affected, and whether it is reflected in the next trophic level. To address the questions, fungal assemblages in soil samples collected from invaded and non-invaded plots in two soil types were compared. Whereas ergosterol as a marker for fungal biomass demonstrated a significant increase in fungal biomass, specific qPCR assays did not point at a quantitative shift. MiSeq-based characterization of the belowground effects of giant goldenrod revealed a local increase of mainly Cladosporiaceae and Glomeraceae. This asymmetric boost in the fungal community was reflected in a specific shift in the fungivorous nematode community. Our findings provide insight in the potential impact of invasive plants on local fungal communities.
A torsion-based rheometer for measuring viscoelastic material properties
Authors: Jutzeler Elise , Asp Merrill , Kerr Katherine , Song Dawei , Patteson Alison
Published: September 2020

Rheology and the study of viscoelastic materials is an integral part of engineering and the study of biophysical systems however the cost of a rheometer is only feasible for colleges, universities and research laboratories. Even if a rheometer can be purchased it is bulky and delicately calibrated limiting its usefulness to the laboratory itself. The design presented here is less than a tenth of the cost of a professional rheometer and portable making it the ideal solution for high school students as a way to introduce viscoelasticity at a younger age as well as for use in the field for obtaining preliminary rheological data.
Mean-field modeling of brain-scale dynamics for the evaluation of EEG source-space networks
Authors: Allouch Sahar , Yochum Maxime , Kabbara Aya , Duprez Joan , Khalil Mohamad , Wendling Fabrice , Hassan Mahmoud , Modolo Julien
Published: September 2020

Understanding the dynamics of brain-scale functional networks at rest and during cognitive tasks is the subject of intense research efforts to unveil fundamental principles of brain functions. To estimate these large-scale brain networks, the emergent method called “electroencephalography (EEG) source connectivity” has generated increasing interest in the network neuroscience community, due to its ability to identify cortical brain networks with satisfactory spatio-temporal resolution, while reducing mixing and volume conduction effects. However, no consensus has been reached yet regarding a unified EEG source connectivity pipeline, and several methodological issues have to be carefully accounted for to avoid pitfalls. Thus, a validation toolbox that provides flexible “ground truth” models is needed for an objective methods/parameters evaluation and, thereby an optimization of the EEG source connectivity pipeline. In this paper, we show how a recently developed large-scale model of brain-scale activity, named COALIA, can provide to some extent such ground truth by providing realistic simulations of source-level and scalp-level activity. Using a bottom-up approach, the model bridges cortical micro-circuitry and large-scale network dynamics. Here, we provide an example of the potential use of COALIA to analyze, in the context of epileptiform activity, the effect of three key factors involved in the “EEG source connectivity” pipeline: (i) EEG sensors density, (ii) algorithm used to solve the inverse problem, and (iii) functional connectivity measure. Results showed that a high electrode density (at least 64 channels) is required to accurately estimate cortical networks. Regarding the inverse solution/connectivity measure combination, the best performance at high electrode density was obtained using the weighted minimum norm estimate (wMNE) combined with the weighted phase lag index (wPLI). Although those results are specific to the considered aforementioned context (epileptiform activity), we believe that this model-based approach can be successfully applied to other experimental questions/contexts. We aim at presenting a proof-of-concept of the interest of COALIA in the network neuroscience field, and its potential use in optimizing the EEG source-space network estimation pipeline.
Mimicry is associated with procedural learning, not social bonding, neural systems in autism
Authors: Tunçgenç Bahar , Koch Carolyn , Herstic Amira , Eigsti Inge-Marie , Mostofsky Stewart
Published: September 2020

Mimicry facilitates social bonding throughout the lifespan. Mimicry impairments in autism spectrum conditions (ASC) are widely reported, including differentiation of the brain networks associated with its social bonding and learning functions. This study examined associations between volumes of brain regions associated withsocial bondingversusprocedural skill learning, and mimicry of gestures during a naturalistic interaction in ASC and neurotypical (NT) children. Consistent with predictions, results revealed reduced mimicry in ASC relative to the NT children. Mimicry frequency was negatively associated with autism symptom severity. Mimicry was predicted predominantly by the volume of procedural skill learning regions in ASC, and by bonding regions in NT. Further, bonding regions contributed significantly less to mimicry in ASC than in NT, while the contribution of learning regions was not different across groups. These findings suggest that associating mimicry with skill learning, rather than social bonding, may partially explain observed communication difficulties in ASC.
Wing Geometry and Genetic Analyses Reveal Contrasting Spatial Structures between Male and FemaleAedes aegyptiPopulations in Metropolitan Manila, Philippines
Authors: Carvajal Thaddeus M. , Amalin Divina M. , Watanabe Kozo
Published: September 2020

Background

Many important arboviral diseases (e.g. dengue, chikungunya) are transmitted by the bite of a female mosquito vector,Aedes aegypti. Hence, the population genetic structure of the mosquito has been studied in order to understand its role as an efficient vector. Several studies utilized an integrative approach; to combine genetic and phenotypic data to determine the population structure ofAe. aegyptibut these studies have only focused on female populations. To address this particular gap, our study compared the population variability and structuring between male and femaleAe. aegyptipopulations using phenotypic (wing geometry) and genetic (microsatellites) data from a highly-urbanized and dengue-endemic region of the Philippines, Metropolitan Manila.

Methods

Five mosquito populations comprised of female (n = 137) and male (n = 49) adultAe. aegyptimosquitoes were used in this study. All mosquito individuals underwent geometric morphometric (26 landmarks), and genetic (11 microsatellite loci) analyses.

Results

Results revealed thatFSTestimates (genetic) were 0.055 and 0.009 whileQSTestimates (phenotypic) were 0.318 and 0.309 in in male and female populations, respectively. Wing shape variation plots showed that male populations were distinctly separated from each other while female populations overlapped. Similarly, discriminant analysis of principal components using genetic data revealed that male populations were also distinctly separated from each other while female populations showed near-overlapping populations. Genetic and phenetic dendrograms showed the formation of two groups in male populations but no groups in female populations. Further analysis indicated a significant correlation(r= 0.68,p= 0.02) between the genetic and phenetic distances of male populations. Bayesian analysis using genetic data also detected multiple clusters in male (K = 3) and female (K = 2) populations, while no clusters were detected using the phenotypic data from both sexes.

Conclusions

Our results revealed contrasting phenotypic and genetic patterns between male and femaleAe. aegypti, indicating that male populations were more spatially structured than female populations. Although genetic markers demonstrated higher sensitivity in detecting population structures than phenotypic markers, correlating patterns of population structure were still observed between the two markers.
Scarcity of scale-free topology is universal across biochemical networks
Authors: Smith Harrison B. , Kim Hyunju , Walker Sara I.
Published: September 2020

Biochemical reactions underlie all living processes. Like many biological and technological systems, their complex web of interactions is difficult to fully capture and quantify with simple mathematical objects. Nonetheless, a huge volume of research has suggested many real-world biological and technological systems – including biochemical systems – can be described rather simply as ‘scale-free’ networks, characterized by a power-law degree distribution. More recently, rigorous statistical analyses across a variety of systems have upended this view, suggesting truly scale-free networks may be rare. We provide a first application of these newer methods across two distinct levels of biological organization: analyzing a large ensemble of biochemical networks generated from the reactions encoded in 785 ecosystem-level metagenomes and 1082 individual-level genomes (representing all three domains of life). Our results confirm only a few percent of individual and ecosystem-level biochemical networks meet the criteria necessary to be anything more than super-weakly scale-free. Leveraging the simultaneous analysis of the multiple coarse-grained projections of biochemistry, we perform distinguishability tests across properties of individual and ecosystem-level biochemical networks to determine whether or not they share common structure, indicative of common generative mechanisms across levels. Our results indicate there is no sharp transition in the organization of biochemistry across distinct levels of the biological hierarchy - a result that holds across different network projections. This suggests the existence of common organizing principles operating across different levels of organization in biochemical networks, independent of the project chosen.

Author Summary

Fully characterizing living systems requires rigorous analysis of the complex webs of interactions governing living processes. Here we apply statistical approaches to analyze a large data set of biochemical networks across two levels of organization: individuals and ecosystems. We find that independent of level of organization, the standard ‘scale-free’ model is not a good description of the data. Interestingly, there is no sharp transition in the shape of degree distributions for biochemical networks when comparing those of individuals to ecosystems. This suggests the existence of common organizing principles operating across different levels of biochemical organization that are revealed across different network projections.
Privacy preserving storage of sequenced genomic data
Authors: Hekel Rastislav , Budis Jaroslav , Kucharik Marcel , Radvanszky Jan , Pös Zuzana , Szemes Tomas
Published: September 2020

Introduction

Current and future applications of genomic data may raise ethical and privacy concerns. Processing and storing these data introduces a risk of abuse by a potential adversary since a human genome contains sensitive personal information. For this reason, we developed a privacy preserving method, called Varlock, for secure storage of sequenced genomic data.

Materials and methods

We used a public set of population allele frequencies to mask personal alleles detected in genomic reads. Each personal allele described by the public set is masked by a randomly selected population allele with respect to its frequency. Masked alleles are preserved in an encrypted confidential file that can be shared, in whole or in part, using public-key cryptography.

Results

Our method masked personal variants and introduced new variants detected in a personal masked genome. Alternative alleles with lower population frequency were masked and introduced more often. We performed a joint PCA analysis of personal and masked VCFs, showing that the VCFs between the two groups can not be trivially mapped. Moreover, the method is reversible and personal alleles can be unmasked in specific genomic regions on demand.

Conclusion

Our method masks personal alleles within genomic reads while preserving valuable non-sensitive properties of sequenced DNA fragments for further research. Personal alleles may be restored in desired genomic regions and shared with patients, clinics, and researchers. We suggest that the method can provide an additional layer of security for storing and sharing the raw aligned reads.
Recessive effects in cancer predisposition exposed by genome-wide and proteome-wide association studies
Authors: Brandes Nadav , Linial Nathan , Linial Michal
Published: September 2020

The characterization of germline genetic variation affecting cancer risk, known as cancer predisposition, is fundamental to preventive and personalized medicine. Current attempts to detect cancer predisposition genomic regions are typically based on small-scale familial studies or genome-wide association studies (GWAS) over dedicated case-control cohorts. In this study, we utilized the UK Biobank as a large-scale prospective cohort to conduct a comprehensive analysis of cancer predisposition using both GWAS and proteome-wide association study (PWAS), a method that highlights genetic associations mediated by functional alterations to protein-coding genes. We discovered 137 unique genomic loci implicated with cancer risk in the white British population across nine cancer types and pan-cancer. While most of these genomic regions are supported by external evidence, our results highlight novel loci as well. We performed a comparative analysis of cancer predisposition between cancer types, finding that most of the implicated regions are cancer-type specific. We further analyzed the role of recessive genetic effects in cancer predisposition. We found that 30 of the 137 cancer regions were recovered only by a recessive model, highlighting the importance of recessive inheritance outside of familial studies. Finally, we show that many of the cancer associations exert substantial cancer risk in the studied cohort, suggesting their clinical relevance.
A DNA Methylation Reader–Chaperone Regulator–Transcription Factor Complex Activates OsHKT1;5 Expression during Salinity Stress
Authors: Wang Jie , Nan Nan , Li Ning , Liu Yutong , Wang Tian-Jing , Hwang Inhwan , Liu Bao , Xu Zheng-Yi
Published: September 2020

Irrigated lands are increasingly salinized, which adversely affects agricultural productivity. To respond to high sodium (Na+) concentrations, plants harbor multiple Na+ transport systems. Rice (Oryza sativa) HIGH-AFFINITY POTASSIUM (K+) TRANSPORTER1;5 (OsHKT1;5), a Na+-selective transporter, maintains K+/Na+ homeostasis under salt stress. However, the mechanism regulating OsHKT1;5 expression remains unknown. Here, we present evidence that a protein complex consisting of rice BCL-2-ASSOCIATED ATHANOGENE4 (OsBAG4), OsMYB106, and OsSUVH7 regulates OsHKT1;5 expression in response to salt stress. We isolated a salt stress–sensitive mutant, osbag4-1, that showed significantly reduced OsHKT1;5 expression and reduced K+ and elevated Na+ levels in shoots. Using comparative interactomics, we isolate0d two OsBAG4-interacting proteins, OsMYB106 (a MYB transcription factor) and OsSUVH7 (a DNA methylation reader), that were crucial for OsHKT1;5 expression. OsMYB106 and OsSUVH7 bound to the MYB binding cis-element (MYBE) and the miniature inverted-repeat transposable element (MITE) upstream of the MYBE, respectively, in the OsHKT1;5 promoter. OsBAG4 functioned as a bridge between OsSUVH7 and OsMYB106 to facilitate OsMYB106 binding to the consensus MYBE in the OsHKT1;5 promoter, thereby activating the OsHKT1;5 expression. Elimination of the MITE or knockout of OsMYB106 or OsSUVH7 decreased OsHKT1;5 expression and increased salt sensitivity. Our findings reveal a transcriptional complex, consisting of a DNA methylation reader, a chaperone regulator, and a transcription factor, that collaboratively regulate OsHKT1;5 expression during salinity stress.
Vascular Bundles Mediate Systemic Reactive Oxygen Signaling during Light Stress
Authors: Zandalinas Sara I. , Fichman Yosef , Mittler Ron
Published: September 2020

Systemic signaling and systemic acquired acclimation (SAA) are essential for plant survival during episodes of environmental stress. Recent studies highlighted a key role for reactive oxygen species (ROS) signaling in mediating systemic responses and SAA during light stress in Arabidopsis (Arabidopsis thaliana). These studies further identified the RESPIRATORY BURST OXIDASE HOMOLOG D (RBOHD) protein as a key player in mediating rapid systemic ROS responses. Here, we report that tissue-specific expression of RBOHD in phloem or xylem parenchyma cells of the rbohD mutant restores systemic ROS signaling, systemic stress-response transcript expression, and SAA to a local treatment of light stress. We further demonstrate that RBOHD and RBOHF are both required for local and systemic ROS signaling at the vascular bundles of Arabidopsis. Taken together, our findings highlight a key role for RBOHD-driven ROS production at the vascular bundles of Arabidopsis in mediating light stress–induced systemic signaling and SAA. In addition, they suggest that the integration of ROS, calcium, electric, and hydraulic signals, during systemic signaling, occurs at the vascular bundles.
Trust me, I am the social media manager! Public sector communication's trust work in municipality social media channels
Authors: Lovari Alessandro , Materassi Letizia
Published: September 2020

Purpose

The study aims at investigating the role of social media managers (SMMs) as trust mediators and access points in the context of local government. Little empirical work is devoted to this issue and the purpose of the paper is to provide a better understanding of the trust work routines.

Design/methodology/approach

This paper presents the results of a pilot study. Authors adopt a qualitative approach, using semi-structured in-depth interviews with a selected panel of PR professionals, managing social media channels on behalf of eleven Italian municipalities.

Findings

SMMs are aware of having a key-role in nurturing trust, and trust is a design value of their work. This article shows many “signs of trust” that SMMs perceive as important to foster trust in the digital environment and in relations with citizens within the municipal context.

Research limitations/implications

This pilot study draws upon a small sample and a single country-focus.

Practical implications

The detected “signs of trust” can be useful for further investigations and provide SMMs with practical suggestions to integrate into their strategies.

Originality/value

Two main fields – the use of social media and the impact on public sector communication and the institution/citizen trust relationships – are connected to the specific role played by SMMs: an emerging figure as yet little analyzed by scholars.
Smart factories for single-family wooden houses – a practitioner’s perspective
Authors: Vestin Alexander , Säfsten Kristina , Löfving Malin
Published: September 2020

Purpose

The meaning of Industry 4.0 has started to be outlined for the construction industry, but there is still limited knowledge on the implications for the single-family wooden house building industry. The purpose of this paper is to expand the understanding of what the fourth industrial revolution implies for the single-family wooden house industry. The paper contributes with practitioners’ view of the content and meaning of a smart single-family wooden house factory.

Design/methodology/approach

An exploratory multiple case study was carried out at two Swedish single-family wooden house builders, combined with a traditional literature review.

Findings

As a result of a multiple case studies, the content and meaning of a smart single-family wooden house factory was elaborated on. In total, 15 components of a smart single-family wooden house factory were identified, of which 8 corresponded to the components of Industry 4.0 as described in other sectors.

Research limitations/implications

The study can be expanded to also include multi-family wooden house builders and other branches of the offsite wooden building industry.

Practical implications

Managers in the house-building industry who want to improve and strive for a smart single-family wooden house factory can learn from this study, get an insight of what other companies consider as important and how it relates to Industry 4.0.

Originality/value

To the best of the authors’ knowledge, this study is a first attempt to understand what Industry 4.0 mean and how it can be accomplished for the single-family wooden house offsite manufacturing industry.
An extended car-following model integrating average speed and electronic throttle dynamics of multiple preceding vehicles
Authors: Li Shihao , Cheng Rongjun , Ge Hongxia , Zheng Pengjun
Published: September 2020

Purpose

The purpose of this study is to explore the influence of the electronic throttle (ET) dynamics and the average speed of multiple preceding vehicles on the stability of traffic flow.

Design/methodology/approach

An extended car-following model integrating the ET dynamics and the average speed of multiple preceding vehicles is presented in this paper. The novel model’s stability conditions are obtained by using the thought of control theory, and the modified Korteweg–de Vries equation is inferred in terms of the nonlinear analysis method. In addition, some simulation experiments are implemented to explore the properties of traffic flow, and the results of these experiments confirm the correctness of theoretical analysis.

Findings

In view of the results of theoretical analysis and numerical simulation, traffic flow will become more stable when the average speed and ET dynamics of multiple preceding vehicles are considered, and the stability of traffic flow will also be enhanced by increasing the number of preceding vehicles considered.

Research limitations/implications

This study leaves the factors such as the mixed traffic flow, the multilane and so on out of account in real road environment, which more or less influences the traffic flow’s stability, so the real traffic environment is not fully reflected.

Originality/value

There is little research integrating ET dynamics and the average velocity of multiple preceding vehicles to study the properties of traffic flow. The enhanced model constructed in this study can better reflect the real traffic, which can also give some theoretical reference for the development of connected and autonomous vehicles.
Designing healthy workspaces: results from Australian certified open-plan offices
Authors: Candido Christhina , Marzban Samin , Haddad Shamila , Mackey Martin , Loder Angela
Published: September 2020

Purpose

From poor indoor environmental quality conditions to musculoskeletal discomfort, the interior design of workspaces has the potential to negatively affect human health. One of the key responses from industry has been the rise of health-related guidelines, certification and rating tools. Despite the rapid adoption of such tools by the Australian high-end corporate real estate, there is a scarcity of empirical evidence arising from such premises. This study aims to compare results from certified premises against other open-plan offices to understand differences arising from occupants’ satisfaction, perceived productivity and health.

Design/methodology/approach

A total of 1,121 post-occupancy evaluation (POE) surveys conducted in 9 offices were analyzed. All these premises hold a certification from the Green Building Council of Australia and two achieved a WELL rating. The analysis is performed in three parts: comparing WELL-certified (2 cases) and non-WELL certified (7 cases) offices along with comparison with a benchmark of 9,794 POE surveys from the BOSSA database, comparing activity-based working (ABW) (5 cases) and traditional (4 cases) offices along with comparison with BOSSA database and qualitative study of the similar design features in all 9 offices accompanied with an in-depth analysis of the health-related issues that might have occurred because of poor ergonomic design. For the first two parts, several t-tests are performed.

Findings

Highest scores for overall satisfaction, workability, perceived productivity and health were reported on WELL-rated premises. Offices incorporating active design principles outperformed others on workability, satisfaction with work area, collaboration, unwanted interruptions, perceived productivity and health. ABW environments outperformed the traditional offices on spatial comfort, thermal comfort, noise and privacy, personal control, comfort of furnishing, adjustability of the work area and space to collaborate. People using sit–stand workstations reported spending significantly less time seated and female workers were more prone to reporting pain over the past 12 months. The best-performing offices implemented active and biophilic design, prioritized overall ergonomics and different spaces designed to support a variety of work-related activities.

Originality/value

This research conducts a comparison between certified premises against other offices in terms of occupants’ satisfaction, perceived productivity and health. A qualitative analysis is also conducted to investigate personal and physical environmental aspects. The way of working (ABW or traditional), implementation of active design features, self-reported musculoskeletal discomfort and physical activity were also investigated. The study has taken a holistic approach to investigate many health-related physical, environmental and emotional aspects in certified workspaces.