bluuebunny/crossref_metadata_2025 huggingface dataset:
Behavioral performance requirements for division of labor influence adaptive brain mosaicism in a socially complex ant
Authors: Muratore I.B. , Fandozzi E.M. , Traniello J.F.A.
Published: July 2021

Brain evolution is hypothesized to be driven by neuroarchitectural requirements for behavioral performance. Assessments of such needs should be informed by the nature of sensory and motor processes underpinning behavior. We developed a novel metric to estimate the relative neuroanatomical investments required to perform tasks varying in sensorimotor and processing demands across polymorphic and polyethic workers of the leafcutter antAtta cephalotesand quantified brain size and structure to examine their correspondence with our computational approximations. Investment in multi-sensory integration and motor requirements for task performance was estimated to be greatest for media workers whose leaf-harvesting repertoire involves the most diverse and demanding sensory and motor processes, including plant discrimination, leaf cutting, and fragment transportation. Volumetric analysis of confocal brain images revealed that absolute brain size increased with worker size and compartmental scaling allometries among functionally specialized brain compartments differed among polymorphic workers. The mushroom bodies, centers of sensory integration and learning, and the antennal lobes, which process olfactory inputs, were significantly larger in medias than in minim workers (fungal gardeners) and major workers (“soldiers”), which had lower estimated task-related neural demands. Minims had a proportionally larger central complex, perhaps to control navigation in subterranean fungal garden chambers. These results indicate that variation in task performance requirements has selected for adaptive variation in brain size and mosaic scaling.
Multifaceted roles of SAMHD1 in cancer
Authors: McLaughlin Katie-May , Cinatl Jindrich , Wass Mark N. , Michaelis Martin
Published: July 2021

SAMHD1 is discussed as a tumour suppressor protein, but its potential role in cancer has only been investigated in very few cancer types. Here, we performed a systematic analysis of the TCGA (adult cancer) and TARGET (paediatric cancer) databases, the results of which did not suggest that SAMHD1 should be regarded as abona fidetumour suppressor. SAMHD1 mutations that interfere with SAMHD1 function were not associated with poor outcome, which would be expected for a tumour suppressor. High SAMHD1 tumour levels were associated with increased survival in some cancer entities and reduced survival in others. Moreover, the data suggested differences in the role of SAMHD1 between males and females and between different races. Often, there was no significant relationship between SAMHD1 levels and cancer outcome. Taken together, our results indicate that SAMHD1 may exert pro-or anti-tumourigenic effects and that SAMHD1 is involved in the oncogenic process in a minority of cancer cases. These findings seem to be in disaccord with a perception and narrative forming in the field suggesting that SAMHD1 is a tumour suppressor. A systematic literature review confirmed that most of the available scientific articles focus on a potential role of SAMHD1 as a tumour suppressor. The reasons for this remain unclear but may include confirmation bias and publication bias. Our findings emphasise that hypotheses, perceptions, and assumptions need to be continuously challenged by using all available data and evidence.
Three-dimensional drug screen identifies HDAC inhibitors as therapeutic agents in mTORC1-driven lymphangioleiomyomatosis
Authors: Pietrobon Adam , Yockell-Lelièvre Julien , Melong Nicole , Smith Laura J. , Delaney Sean P. , Azzam Nadine , Xue Chang , Merwin Nishanth , Lian Eric , Camacho-Magallanes Alberto , Doré Carole , Musso Gabriel , Julian Lisa M. , Kristof Arnold S. , Tam Roger Y. , Berman Jason N. , Shoichet Molly S. , Stanford William L.
Published: July 2021

Lymphangioleiomyomatosis (LAM) is a rare disease involving cystic lung destruction by invasive LAM cells. These cells harbor loss-of-function mutations in TSC2, conferring constitutive mTORC1 signaling. Rapamycin is the only clinically approved disease-modifying treatment, but its action is cytostatic and disease progresses upon its withdrawal. There is a critical need to identify novel agents that prevent the invasive phenotype and/or eradicate the neoplastic LAM cells. Here, we employed novel cellular and extracellular models to screen for candidate therapeutics in a physiologically relevant setting. We observed that lung-mimetic hydrogel culture of pluripotent stem cell-derived diseased cells more faithfully recapitulates human LAM biology compared to conventional culture on two-dimensional tissue culture plastic. Leveraging our culture system, we conducted a three-dimensional drug screen using a custom 800-compound library, tracking cytotoxicity and invasion modulation phenotypes at the single cell level. We identified histone deacetylase (HDAC) inhibitors as a group of anti-invasive agents that are also selectively cytotoxic towards TSC2-/- cells. Unexpectedly, we observed that next generation ATP-competitive mTORC1/2 inhibitors potentiate invasion. We determined anti-invasive effects of HDAC inhibitors to be independent of genotype, while selective cell death is mTORC1-dependent and mediated by apoptosis. Drug performance was subsequently evaluated at the single cell level in zebrafish xenografts. We observed consistent therapeutic efficacy in vivo at equivalent concentrations to those used in vitro, substantiating HDAC inhibitors as potential therapeutic candidates for pursuit in patients with LAM.

One Sentence Summary

We performed a drug screen in 3D and discovered HDAC inhibitors exhibit therapeutic efficacy in models of the lung disease lymphangioleiomyomatosis.
Mechanics defines the spatial pattern of compensatory proliferation
Authors: Kawaue Takumi , Yow Ivan , Le Anh Phuong , Lou Yuting , Loberas Mavis , Shagirov Murat , Prost Jacques , Hiraiwa Tetsuya , Ladoux Benoit , Toyama Yusuke
Published: July 2021

The number of cells in tissues is tightly controlled by cell division and cell death, and misregulation of cell numbers could lead to pathological conditions such as cancer. To maintain cell numbers in a tissue, a cell elimination process named programmed cell death or apoptosis, stimulates the proliferation of neighboring cells. This mechanism is called apoptosis-induced compensatory proliferation, which was originally reported more than 40 years ago. While only a limited number of the neigboring cells need to divide to compensate for apoptotic cell loss, the mechanisms that select cells for undergoing division remain an open question. Here we found that the spatial inhomogeneity in mechanotransduction through a growth-promoting transcription co-activator Yes-associated protein (YAP) in the neighboring tissue, accounts for the inhomogeneity of compensatory proliferation. Such inhomogeneous mechanotransduction arises from the combination of the non-uniform distribution of nuclear size, which is inherent in tissues, and the non-uniform pattern of mechanical force applied to the neighboring cells upon apoptosis. Our findings from a mechanical perspective complement the current biochemical understanding of compensatory growth and provide additional insights into cellular functions of how tissue precisely maintains its homeostasis.
Frequency-specific coactivation patterns in resting-state and their alterations in schizophrenia: an fMRI study
Authors: Yang Hang , Zhang Hong , Di Xin , Wang Shuai , Meng Chun , Tian Lin , Biswal Bharat
Published: July 2021

The resting-state human brain is a dynamic system that shows frequency-specific characteristics. Coactivation pattern (CAP) analysis has been recently used to identify recurring brain states sharing similar coactivation configurations. However, whether and how CAPs differ across different sub-frequency bands are unknown. In the current study, in addition to the typical low-frequency range (0.01 - 0.08 Hz), the spatial and temporal characteristics of CAPs in four sub-frequency bands, slow-5 (0.01 - 0.027 Hz), slow-4 (0.027 - 0.073 Hz), slow-3 (0.073 - 0.198 Hz), and slow-2 (0.198 - 0.25 Hz), were studied. Six CAP states were obtained for each band., The CAPs from the typical frequency range were spatially largely overlapped with those in slow-5, slow-4 and slow-3 but not with those in slow-2. With the increase of frequency, the CAP state became more unstable and resulted in an overall shorter persistence. The spatial and temporal characteristics of slow-4 and slow-5 were further compared, because they constitute most power of the resting-state fMRI signals. In general, slow-4 showed stronger coactivations or co-deactivations in subcortical regions, while slow-5 showed stronger coactivations or co-deactivations in large-scale cortical networks such as the dorsal attention network. Lastly, frequency-dependent dynamic alterations were also observed in schizophrenia patients. Combining the information obtained from both slow-5 and slow-4 increased the classification accuracy of schizophrenia patients than only using the typical range. In conclusion, our results revealed that the spatial and temporal characteristics of CAP state varied at different frequency bands, which could be helpful for identifying brain alterations in schizophrenia.
Convergent evolution of venom gland transcriptomes across Metazoa
Authors: Zancolli Giulia , Reijnders Maarten , Waterhouse Robert M. , Robinson-Rechavi Marc
Published: July 2021

Animals have repeatedly evolved specialized organs and anatomical structures to produce and deliver a cocktail of potent bioactive molecules to subdue prey or predators – venom. This makes it one of the most widespread convergent functions in the animal kingdom. Whether animals have adopted the same genetic toolkit to evolved venom systems is a fascinating question that still eludes us. Here, we performed the first comparative analysis of venom gland transcriptomes from 20 venomous species spanning the main Metazoan lineages, to test whether different animals have independently adopted similar molecular mechanisms to perform the same function. We found a strong convergence in gene expression profiles, with venom glands being more similar to each other than to any other tissue from the same species, and their differences closely mirroring the species phylogeny. Although venom glands secrete some of the fastest evolving molecules (toxins), their gene expression does not evolve faster than evolutionarily older tissues. We found 15 venom gland specific gene modules enriched in endoplasmic reticulum stress and unfolded protein response pathways, indicating that animals have independently adopted stress response mechanisms to cope with mass production of toxins. This, in turn, activates regulatory networks for epithelial development, cell turnover and maintenance which seem composed of both convergent and lineage-specific factors, possibly reflecting the different developmental origins of venom glands. This study represents the first step towards an understanding of the molecular mechanisms underlying the repeated evolution of one of the most successful adaptive traits in the animal kingdom.
Fly Cell Atlas: a single-cell transcriptomic atlas of the adult fruit fly
Authors: Li Hongjie , Janssens Jasper , De Waegeneer Maxime , Kolluru Sai Saroja , Davie Kristofer , Gardeux Vincent , Saelens Wouter , David Fabrice , Brbić Maria , Leskovec Jure , McLaughlin Colleen N. , Xie Qijing , Jones Robert C. , Brueckner Katja , Shim Jiwon , Tattikota Sudhir Gopal , Schnorrer Frank , Rust Katja , Nystul Todd G. , Carvalho-Santos Zita , Ribeiro Carlos , Pal Soumitra , Przytycka Teresa M. , Allen Aaron M. , Goodwin Stephen F. , Berry Cameron W. , Fuller Margaret T. , White-Cooper Helen , Matunis Erika L. , DiNardo Stephen , Galenza Anthony , O’Brien Lucy Erin , Dow Julian A. T. ,   FCA Consortium, Jasper Heinrich , Oliver Brian , Perrimon Norbert , Deplancke Bart , Quake Stephen R. , Luo Liqun , Aerts Stein
Published: July 2021

The ability to obtain single cell transcriptomes for stable cell types and dynamic cell states is ushering in a new era for biology. We created the TabulaDrosophilae, a single cell atlas of the adult fruit fly which includes 580k cells from 15 individually dissected sexed tissues as well as the entire head and body. Over 100 researchers from the fly community contributed annotations to >250 distinct cell types across all tissues. We provide an in-depth analysis of cell type-related gene signatures and transcription factor markers, as well as sexual dimorphism, across the whole animal. Analysis of common cell types that are shared between tissues, such as blood and muscle cells, allowed the discovery of rare cell types and tissue-specific subtypes. This atlas provides a valuable resource for the entireDrosophilacommunity and serves as a comprehensive reference to study genetic perturbations and disease models at single cell resolution.
De novo human brain enhancers created by single nucleotide mutations
Authors: Li Shan , Hannenhalli Sridhar , Ovcharenko Ivan
Published: July 2021

Advanced human cognition is attributed to increased neocortex size and complexity, but the underlying gene regulatory mechanisms are unknown. Using deep learning model of embryonic neocortical enhancers, and human and macaque embryonic neocortex H3K27ac data, we identified ~4000 enhancers gained de novo in the human, largely attributable to single-nucleotide essential mutations. The genes near de novo gained enhancers exhibit increased expression in human embryonic neocortex relative to macaque, are involved in critical neural developmental processes, and are expressed specifically in the progenitor cells and interneurons. The gained enhancers, especially the essential mutations, are associated with central nervous system disorders/traits. Integrative computational analyses suggest that the essential mutations establish enhancer activities through affecting binding of key transcription factors of embryonic neocortex. Overall, our results suggest that non-coding mutations may have led to de novo enhancer gains in the embryonic human neocortex, that orchestrate the expression of genes involved in critical developmental processes associated with human cognition.
A New Likelihood-based Test for Natural Selection
Authors: Simon Helmut , Huttley Gavin
Published: July 2021

We present a new statistic for testing for neutral evolution from allele frequency data summarised as a site frequency spectrum, which we call the relative likelihood neutrality test orρ. Classical methods of testing for natural selection, such as Tajima’s D and its relatives, require the null model to have constant population size over time and therefore can confound demographic change with natural selection.ρcan directly incorporate a null hypothesis reflecting general demographic histories. It has a natural Bayesian interpretation as an approximation to the log-probability of the null model, given the data. We use simulations to show thatρhas greater power than Tajima’s D to detect departure from neutrality for a range of scenarios of positive and negative selection. We also show howρcan be adapted to account for sequencing error. Application to the ACKR1 (FYO) gene in humans supported previous studies inferring positive selection in sub-Saharan populations which were based on inter-population comparisons. However, we did not find the signal of selection to be maximal in the region of the FY*O or Duffy-null allele in these populations. We also appliedρto investigate in greater detail a region on the 2q11.1 band of the human genome that has previously been identified as showing evidence of selection. This was done for a range of populations: for the European populations we incorporated a demographic history with a bottleneck corresponding to the putative out of Africa event. We were able to localise signals of selection to some specific regions and genes. Overall, we suggest thatρwill be a useful tool for identifying genomic regions that may be subject to natural selection.
High Sensitivity and Low-Cost Flavin luciferase (FLUX)-based Reporter Gene for Mammalian Cell Expression
Authors: Phonbuppha Jittima , Tinikul Ruchanok , Ohmiya Yoshihiro , Chaiyen Pimchai
Published: July 2021

Luciferase-based gene reporters generating bioluminescence signals are important tools for biomedical research. Amongst the luciferases, flavin-dependent enzymes use the most common, and thus most economical chemicals. However, their applications in mammalian cells are limited due to their low signals compared to other systems. Here, we constructed Flavin Luciferase for Mammalian Cell Expression (FLUX) by engineering luciferase from Vibrio campbellii (the most thermostable bacterial luciferase reported to date) and optimizing its expression and reporter assays in mammalian cells. We found that the FLUX reporter gene can be overexpressed in various cell lines and showed outstanding signal-to-background in HepG2 cells, significantly higher than that of firefly luciferase (Fluc). The combined use of FLUX/Fluc as target/control vectors gave the most stable signals, better than the standard set of Fluc(target)/Rluc(control). We demonstrated that FLUX can be used for testing inhibitors of the NF-κB signaling pathway, validating FLUX applications for various assays in the future.
ProXs drive the formation of membraneless organelles in plants
Authors: Zhang Honghong , Peng Fangyu , Liu Yan , Deng Haiteng , Fang Xiaofeng
Published: July 2021

Membraneless organelles (MLOs) are non-membranous structures inside cells that organize cellular space and processes. The recent discovery that MLOs can be assembled via liquid-liquid phase separation (LLPS) advanced our understanding of these structures. However, the proteins that are capable of forming MLOs are largely unknown, especially in plants. In this study, we developed a method to identify proteins that we referred as ProXs (Proteins enriched by b-isoX) in Arabidopsis. Heterologous expression in yeast cells showed that most ProXs were capable of forming MLOs autonomously. We applied this method to several model and crop species including early and higher plants. This allowed us to generate an atlas of ProXs for studying plant MLOs. Analysis of ProXs from different species revealed high degree of conservation, supporting that they play important roles in cellular functions and are positively selected during evolution. Our method will be a valuable tool to characterize novel MLOs from desired cells and the data generated in present study will be instrumental for the plant research community to investigate MLO biology.
A SUBTILISIN-LIKE SERINE PROTEASE1 (OsSUBSrP1), plays an important role in the wax and cutin pathway, is essential for panicle development in rice
Authors: Ali Asif , Wu Tingkai , Zhang Hongyu , Xu Peizhou , Zafar Syed Adeel , Liao Yongxiang , Chen Xiaoqiong , Liu Yutong , Wang Wenming , Wu Xianjun
Published: July 2021

Panicle degeneration is a severe physiological defect and causes reduction in grain yield. In this study, we characterized and presented the functional analysis of our previously reported mutant apa1331 (apical panicle abortion1331) that showed apical spikelet degeneration. The anthers from the apical spikelets of apa1331 were degenerated, pollen-less and showed lack of cuticle formation. Transverse sections showed normal meiosis till stage 5-6, however, defects in post-meiotic microspore development were found at stage 8-9 in apa1331. Measurement of wax and cutin analysis showed a significant reduction in anthers of apa1331 compared to Wildtype (WT). Quantification of H2O2 and MDA has indicated the excessive ROS (reactive oxygen species) in apa1331. Trypan blue staining, and TUNEL assay revealed cell death and excessive DNA fragmentation in apa1331. Map-based cloning and Mutmap analysis identified a candidate gene (LOC_Os04g40720) that is a SUBTILISIN-LIKE SERINE PROTEASE (OsSUBSrP1) which harbored an SNP (A>G) in apa1331. CRISPR-mediated knock-out lines of OsSUBSrP1 displayed spikelet degeneration comparable to apa1331. Global gene expression analysis revealed a significant downregulation of wax and cutin biosynthesis genes e.g., OsWDA1, OsMS2 and OsCER4 in apa1331. Our study reports the novel role of SUBSrP1 in ROS-mediated cell death in panicle development.

Highlights

1.

OsSUBSrP1 plays an important role in maintaining ROS-mediated programmed cell death.

2.

OsSUBSrP1 is essential for apical spikelet development.

3.

OsSUBSrP1 regulates the expression of wax and cutin biosynthesis pathway genes.
Global evolutionary dynamics and resistome analysis of Clostridioides difficile ribotype 017
Authors: Imwattana Korakrit , Putsathit Papanin , Collins Deirdre A , Leepattarakit Teera , Kiratisin Pattarachai , Riley Thomas V , Knight Daniel R
Published: July 2021

Clostridioides difficile PCR ribotype (RT) 017 ranks among the most successful strains of C. difficile in the world. In the past three decades, it has caused outbreaks on four continents, more than other “epidemic” strains, however, our understanding of the genomic epidemiology underpinning the spread of C. difficile RT 017 is limited. Here, we performed high-resolution phylogenomic and Bayesian evolutionary analyses on an updated and more representative dataset of 282 non-clonal C. difficile RT 017 isolates collected worldwide between 1981 and 2019. These analyses place an estimated time of global dissemination between 1953 and 1983 and identified the acquisition of the ermB-positive transposon Tn6194 as a key factor behind global emergence. This coincided with the introduction of clindamycin, a key inciter of C. difficile infection, into clinical practice in the 1960s. Based on the genomic data alone, the origin of C. difficile RT 017 could not be determined, however, geographical data and records of population movement suggest that C. difficile RT 017 had been moving between Asia and Europe since the Middle Ages and was later transported to North America around 1860 (95% CI: 1622 – 1954). A focused epidemiological study of 45 clinical C. difficile RT 017 genomes from a cluster in a tertiary hospital in Thailand revealed that the population consisted of two groups of multidrug-resistant (MDR) C. difficile RT 017 and a group of early, non-MDR C. difficile RT 017. The significant genomic diversity within each MDR group suggests that although they were all isolated from hospitalised patients, there was likely a reservoir of C. difficile RT 017 in the community that contributed to the spread of this pathogen.

Impact statement

This study utilises genomic sequence data from 282 non-clonal C. difficile ribotype (RT) 017 isolates collected from around the world to delineate the origin and spread of this epidemic lineage, as well as explore possible factors that have driven its success. It also reports a focused epidemiological investigation of a cluster of C. difficile RT 017 in a tertiary hospital in Thailand to identify possible sources of transmission in this specific setting.

Data summary

All new WGS data generated in this study has been submitted to the European Nucleotide Archive under the BioProject PRJEB44406 (sample accession ERS6268756 – ERS6268798). The complete genome of C. difficile MAR286 was submitted to GenBank under BioProject PRJNA679085 (accession CP072118). Details of all genomes included in the final analyses are available in the Supplementary Document, available at 10.6084/m9.figshare.14544792.
Model-informed target product profiles of long acting-injectables for use as seasonal malaria prevention
Authors: Burgert Lydia , Reiker Theresa , Golumbeanu Monica , Möhrle Jörg J. , Penny Melissa A.
Published: July 2021

1.

Seasonal malaria chemoprevention (SMC) has proven highly efficacious in reducing malaria incidence. However, the continued success of SMC is threatened by the spread of resistance against one of its main preventive ingredients, Sulfadoxine-Pyrimethamine(SP), operational challenges in delivery, and incomplete adherence to the regimens. Via a simulation study with an individual-based model of malaria dynamics, we provide quantitative evidence to assess long-acting injectables (LAIs) as potential alternatives to SMC. We explored the predicted impact of a range of novel preventive LAIs as a seasonal prevention tool in children aged three months to five years old during late-stage clinical trials and at implementation. LAIs were co-administered with a blood-stage clearing drug once at the beginning of the transmission season. We found the establishment of non-inferiority of LAIs to standard 3 or 4 rounds of SMC with SP-amodiaquine was challenging in clinical trial stages due to high intervention deployment coverage. However, our analysis of implementation settings where the achievable SMC coverage was much lower, LAIs with fewer visits per season are potential suitable replacements to SMC. Suitability as a replacement with higher impact is possible if the duration of protection of LAIs covered the duration of the transmission season. Furthermore, optimizing LAIs coverage and protective efficacy half-life via simulation analysis in settings with an SMC coverage of 60% revealed important trade-offs between protective efficacy decay and deployment coverage. Our analysis additionally highlights that for seasonal deployment for LAIs, it will be necessary to investigate the protective efficacy decay as early as possible during clinical development to ensure a well-informed candidate selection process.
Early life trauma leads to escalated aggressive behavior and its inheritance by impairing thyroid hormone availability in brain
Authors: Rawat Rohit Singh , Bhambri Aksheev , Pal Muneesh , Roy Avishek , Jain Suman , Pillai Beena , Konar Arpita
Published: July 2021

Escalated and inappropriate levels of aggressive behavior referred to as pathological in psychiatry can lead to violent outcomes with detrimental impact on health and society. Early life trauma triggers adulthood violence and criminality, though molecular mechanisms remain elusive. Here, we provide prefrontal cortex and hypothalamus specific transcriptome profiles of peripubertal stress (PPS) exposed Balb/c adult male mice exhibiting escalated aggression and adult female mice resilient to such aberrant behavioral responses. We identify transthyretin (TTR) as a key regulator of PPS induced escalated aggression and its intergenerational inheritance. TTR mediated long-term perturbation in hypothalamic thyroid hormone (TH) availability contributed to male aggressive behavior without affecting circulating hormone. Ttr gene ablation in hypothalamus impaired local TH signaling including levels of TH transporters (Mct8, Oatp1c1), deiodinase 2(DIO2) and TH responsive genes (Nrgn, Trh and Hr). Escalated aggressive behavior and impaired TTR-TH signaling was also inherited in F1 male progenies. Further, we deciphered Ttr promoter hyper methylation in hypothalamus of such abnormally aggressive males across generations. Interestingly prefrontal cortex showed opposite pattern of Ttr expression as well as long term epigenetic changes. Also, T4 increase by levothyroxine in PFC did not produce any behavioral changes. Our findings reveal that trauma during puberty trigger lasting escalated aggression by epigenetic programming of TTR and consequent impaired thyroid availability in brain. TTR-TH signaling in brain can serve as potential target in reversal of escalated aggression and related psychopathologies.
Polygenic routes lead to parallel altitudinal adaptation in Heliosperma pusillum (Caryophyllaceae)
Authors: Szukala Aglaia , Lovegrove-Walsh Jessica , Luqman Hirzi , Fior Simone , Wolfe Thomas , Frajman Božo , Schönswetter Peter , Paun Ovidiu
Published: July 2021

Understanding how organisms adapt to the environment is a major goal of modern biology. Parallel evolution - the independent evolution of similar phenotypes in different populations - provides a powerful framework to investigate the evolutionary potential of populations, the constraints of evolution, its repeatability and therefore its predictability. Here, we quantified the degree of gene expression and functional parallelism across replicated ecotype formation in Heliosperma pusillum (Caryophyllaceae), and gained insights into the architecture of adaptive traits. Population structure analyses and demographic modelling support a previously formulated hypothesis of parallel polytopic divergence of montane and alpine ecotypes. We detect a large proportion of differentially expressed genes (DEGs) underlying divergence within each replicate ecotype pair, with a strikingly low amount of shared DEGs across pairs. Functional enrichment of DEGs reveals that the traits affected by significant expression divergence are largely consistent across ecotype pairs, in strong contrast to the non-shared genetic basis. The remarkable redundancy of differential gene expression indicates a polygenic architecture for the diverged adaptive traits. We conclude that polygenic traits appear key to opening multiple routes for adaptation, widening the adaptive potential of organisms.
circFL-seq reveals full-length circular RNAs with rolling circular reverse transcription and nanopore sequencing
Authors: Liu Zelin , Tao Changyu , Li Shiwei , Du Minghao , Bai Yongtai , Hu Xueyan , Li Yu , Chen Jian , Yang Ence
Published: July 2021

Circular RNAs (circRNAs) act through multiple mechanisms with their sequence features to fine-tune gene expression networks. Due to overlapping sequences with linear cognates, identifying internal sequences of circRNAs remains a great challenge, which hinders comprehensive understanding of circRNA functions and mechanisms. Here, based on rolling circular reverse transcription (RCRT) and nanopore sequencing, we developed circFL-seq, a full-length circRNA sequencing method, to profile circRNA at the isoform level. With a customized computational pipeline circfull to directly identify full-length sequences from rolling circular reads, we reconstructed 77,606 high-quality circRNAs from seven human cell lines and two human tissues. Benefiting from rolling circles and long-read sequencing, circFL-seq showed more than tenfold enrichment of circRNA reads and advantages for both detection and quantification at the isoform level compared to short-read RNA sequencing. The concordance of RT-qPCR and circFL-seq results for the identification of differential alternative splicing suggested wide application prospects for functional studies of internal variants in circRNAs. Moreover, the detection of cancer-related fusion circRNAs at the omics scale may further expand the application of circFL-seq. Together, the accurate identification and quantification of full-length circRNAs make circFL-seq a potential tool for large-scale screening of functional circRNAs.
Novel microbial syntrophies identified by longitudinal metagenomics
Authors: Raguideau Sebastien , Trego Anna , Farrell Fred , Collins Gavin , Quince Christopher , Soyer Orkun S
Published: July 2021

Identifying species interactions in a microbial community and how this relates to community function is a key challenge. Towards addressing this challenge, we present here an extensive genome-resolved, longitudinal dataset and associated metadata. We collected weekly samples of microbial communities and recorded operating conditions from industrial methane producing anaerobic digestion reactors for a year. This allowed us to recover 2240 dereplicated metagenome assembled genomes (dMAGs), together with their coverage dynamics and functional annotations from which functional traits were inferred. Of these dMAGs, 1910 were novel species, with 22 representing novel orders and classes. Methanogenic communities are expected to be strongly structured by syntrophic and other associations between the methanogens and syntrophs that produce their substrates. We identified 450 potential syntrophic dMAGs by searching for pairs of methanogenic and non-methanogenic dMAGs that had highly correlated time-series. Genomes of potential syntrophs were enriched for oxidoreductases and sugar transport genes and there was a strong taxonomic signal in their associations with methanogens. Of particular note, we found that Bathyarchaeiea associated specifically with methanogens from the Thermoplasmata, and Thermococci classes. Same syntrophic associations were only rarely observed across multiple reactors, suggesting that syntrophies might be facultative, with particular strains within a species forming syntrophic associations only sometimes and not necessarily always with the same methanogenic partner. The presented results show that longitudinal metagenomics is a highly valuable approach for identifying species and their interactions in microbial communities.

One Sentence Summary

Longitudinal study of microbial communities identifies novel species and predicts their interactions and role in community function.
Structural relationships among transformational leadership, affective organizational commitment, and job performance: the mediating role of employee engagement
Authors: Park Jiwon , Han Soo Jeoung , Kim Jiyoung , Kim Woocheol
Published: July 2021

Purpose

The purpose of this paper is to investigate the structural relationships among transformational leadership, affective organizational commitment and job performance, as well as the mediating effect of employee engagement on their relationships.

Design/methodology/approach

To examine the structural relationships among the research variables, structural equation modeling analysis and bootstrap estimates were performed using the data of 600 full-time employees working in Korean private organizations.

Findings

The results of the data analysis suggest that transformational leadership had a significant impact on employee affective organizational commitment and job performance through employee engagement as a mediator. Specifically, employee engagement partially mediated the mechanism in which transformational leadership affects employee affective organizational commitment, whereas there existed a full mediation of the association between transformational leadership and job performance.

Practical implications

The study finding suggested that transformational leadership was the key catalyst in both encouraging affective organizational commitment and task performance of employees throughout the mediator, employee engagement. Thus, organizations need to create a safe and positive environment that promotes employee engagement and should offer interventions for leaders to build skill sets of transformational leadership.

Originality/value

Because previous studies had explored the impacts of transformational leadership on employee positive attitude and job performance separately, there is little known about how these three constructs correlate. By investigating the impacts of transformational leadership on attitude and performance simultaneously in this study, this study expanded to the extant literature by providing better understanding of transformational leadership. Moreover, given that articles on transformational leadership have been limited in the HRD literature, findings of this study can offer trustworthy information for HRD practice and encourage HRD scholars to explore transformational leadership-related research.
Human rights violations, detention conditions and the invisible nature of women in European immigration detention: a legal realist account
Authors: Van Hout Marie Claire
Published: July 2021

Purpose

The purpose of this paper was to conduct a legal realist assessment of women’s situation in European immigration detention which focuses on relevant international and European human rights instruments applicable to conditions and health rights in detention settings, academic literature and relevant European Court of Human Rights (ECtHR) jurisprudence since 2010.

Design/methodology/approach

In spite of the United Nations human rights frameworks and European Union (EU) standards, conditions in European immigration detention settings continue to pose a health risk to those detained. Migrant health rights when detained are intertwined with the right not to be subjected to arbitrary detention, detention in conditions compatible for respect for human dignity and right to medical assistance. Migrant women are particularly vulnerable requiring special consideration (pregnant and lactating women; single women travelling alone or with children; adolescent girls; early-married children, including with newborn infants) in immigration detention settings.

Findings

The situation of women in immigration detention is patchy in EU policy, academic literature and ECtHR jurisprudence. Where referred to, they are at best confined to their positionality as pregnant women or as mothers, with their unique gendered health needs ill-resourced. ECtHR jurisprudence is largely from male applicants. Where women are applicants, cases centre on dire conditions of detention, extreme vulnerability of children accompanying their mother and arbitrary or unlawful detention of these women (with child).

Originality/value

Concerns have been raised by the European Parliament around immigration detention of women including those travelling with their children. There is a continued failure to maintain minimum and equivalent standards of care for women in European immigration detention settings.
Examination of social workers' attitudes towards sustainable development and environment in the focus of the COVID-19 pandemic
Authors: Yildirim Filiz , Öztürk Hatice , Abukan Bilge
Published: July 2021

Purpose

The purpose of this paper is to assess the views of social workers concerning theoretical and practical courses covering their professional responsibilities, focussing on sustainable development and the natural environment. It also investigates the impact on their attitudes towards sustainable development referencing their adoption of ecocentric or anthropocentric attitudes during the COVID-19 pandemic.

Design/methodology/approach

This study used a structural equation model to answer six research questions, while the descriptive statistics answered one of the research questions through an online survey conducted with 315 social workers.

Findings

This study demonstrated the need to consider attitudes to sustainable development focussing on the ecocentric and anthropocentric attitudes, as well as the current COVID-19 global pandemic.

Originality/value

This study is the first initiative to examine attitudes towards sustainable development and the natural environment from a social work perspective focussed on the COVID-19 pandemic. In addition, it is the first to emphasise the responsibilities of social workers in relation to micro, meso and macro level interventions during and after the global pandemic.
Financial abuse, statutory provisions and the courts: adequacy and analysis of enduring and lasting powers of attorney
Authors: O'Sullivan Owen P.
Published: July 2021

Purpose

Financial abuse can be difficult to detect, and it is deemed to have the same potential to cause distress as other forms of abuse. The delegation of financial affairs brings with it the scope for degrees of exploitation. This study aims to assess the adequacy of the statutory provisions and courts in England and Wales at protecting at risk older people from the harm of financial abuse.

Design/methodology/approach

This review focuses on the enduring power of attorney and the lasting power of attorney provisions. Cases discussed were selected based on their judgments’ significance in relation to these powers, the range of issues illustrated and the extent of associated commentary and attention received in the literature. This piece is presented as a narrative review, and as such, references to case law and associated commentary are non-exhaustive.

Findings

Shortcomings and vulnerabilities are identified and explored with respect to both provisions. These are contrasted and contextualised in view of the broader challenges and complexities associated with preventing financial abuse within society. Key consideration is given to powers of creation, registration, supervision, objection and revocation in addition to the role and powers of both the Office of the Public Guardian and the Court of Protection.

Originality/value

Given these powers of attorney are exercised during a donor’s lifetime, they will directly experience their effects. This review illustrates there remains scope for further reform to introduce new safeguards and bolster existing ones to mitigate the risk of financial exploitation and to support people to plan and safeguard their financial future with increased confidence and security.
A new fuzzy FUCOM-QFD approach for evaluating strategies to enhance the resilience of the healthcare sector to combat the COVID-19 pandemic
Authors: Khan Feroz , Ali Yousaf , Pamucar Dragan
Published: July 2021

Purpose

The coronavirus disease 2019 (COVID-19) pandemic has subjected a considerable strain on the healthcare (HC) systems around the world. The most affected countries are developing countries because of their weak HC infrastructure and meagre resources. Hence, building the resilience of the HC system of such countries becomes essential. Therefore, this study aims to build a resilience-based model on the HC sector of Pakistan to combat the COVID-19 and future pandemics in the country.

Design/methodology/approach

The study uses a novel hybrid approach to formulate a model based on resilient attributes (RAs) and resilient strategies (RSs). In the first step, the multi-criteria decision-making (MCDM) technique, i.e. full consistency method (FUCOM) is used to prioritize the RAs. Whereas, the fuzzy quality function deployment (QFD) is used to rank the RSs.

Findings

The findings suggest “leadership and governance capacity” to be the topmost RA. Whereas “building the operational capacity of the management”, “resilience education” and “Strengthening laboratories and diagnostic systems” are ranked to be the top three RSs, respectively.

Practical implications

The model developed in this study and the prioritization RAs and RSs will help build resilience in the HC sector of Pakistan. The policymakers and the government can take help from the prioritized RAs and RSs developed in this study to help make the current HC system more resilient towards the current COVID-19 and future pandemics in the country.

Originality/value

A new model has been developed to present a sound mathematical model for building resilience in the HC sector consisting of FUCOM and fuzzy QFD methods. The main contribution of the paper is the presentation of a comprehensive and more robust model that will help to make the current HC system of Pakistan more resilient.
Information content of order flows in the FX market: importance of nonfundamental factors
Authors: Hammami Yacine , Kharrat Sabrine
Published: July 2021

Purpose

The purpose of the paper is to show that order flows determine exchange rate dynamics because they carry information about nonfundamental factors besides macroeconomic fundamentals.

Design/methodology/approach

To understand the role of nonfundamental factors in driving order flows, this study uses two approaches. Initially, Evans and Rime (2016) VAR framework is followed to study the incremental information transmitted by order flow compared to macroeconomic variables. Then, the study uses the settings in which Rime et al. (2010) conduct their empirical work, which gives the researcher more latitude in specifying the identity of the factors that drive order flows.

Findings

The findings evidence that order flows explain the dynamics of the TND/USD exchange rate. The results highlight that order flows convey information about technical strategies, the currency systematic factors and political risk. This study also documents the presence of a Ramadan effect in exchange rates and order flows.

Originality/value

This study makes four contributions to the literature. First, it complements the literature on the FX microstructure of emerging markets. The study investigates the information content carried by order flows, while the previous literature has focused solely on examining the explanatory power of order flows to explain exchange rates in emerging countries. The second contribution is that the study demonstrates formally that order flows determine exchange rates because they transmit information about nonfundamental factors. Third, this study is the first to examine whether order flows convey information about technical analysis. Four, the study relates order flow to nontraditional factors that are relevant to the Tunisian FX market.
Cross-sector dialogue for sustainability: to partner or not to partner?
Authors: Louche Celine , Young Suzanne , Fougère Martin
Published: July 2021

Purpose

The purpose of this paper is to introduce the topic and review the contributions of the special issue papers on cross-sector dialogue for sustainability. The paper also presents avenues for further research.

Design/methodology/approach

The paper is based on a review of the current literature on cross-sector partnership and dialogue. It explores the current issues in cross-sector partnerships through a discussion of the papers accepted for the special issue, their focus, findings and key contributions.

Findings

It highlights three main key research themes and learnings from the special issue papers: a high level of “hybridity” of collaboration forms, which involve important tensions; a need to understand partnership in its context and the importance of the individual level in cross-sector collaboration.

Practical implications

The authors call for attention to be paid to two forms of myopia: a tendency to view partnerships primarily from a resource-based view (without much attempt to measure societal impact) and a reluctance to be explicitly critical (despite empirical evidence of some suboptimal aspects of partnerships).

Social implications

The authors call for researchers to move away from a resource-based approach to one that is situated in exploring the value derived from partnerships in the broader societal context. The authors suggest some avenues for further research to move the discussion beyond the partnership imperative.

Originality/value

The paper outlines the need to critically revisit the very essence of what real partnership means and whether dialogue is really taking place.
Exploring remote and onsite employees’ preferred appreciation languages prior to COVID-19 and during COVID-19
Authors: White Paul
Published: July 2021

Purpose

Communicating appreciation to employees has been shown to be an important factor in contributing to employee engagement and making workplaces more effective. Research has shown that employees differ in how they desire to be shown appreciation. The purpose of this paper is to examine how working remotely (vs onsite), the experience of the COVID-19 pandemic and employees’ age group impacted the ways employees want to be shown appreciation at work.

Design/methodology/approach

Using the five Languages of Appreciation as a framework (Chapman and White, 2019), over 200,000 individuals’ results from the Motivating By Appreciation Inventory were compared across various groups. The dependent variable: (Primary Language of Appreciation) was examined in light of three independent variables: work setting (onsite vs remote), timeframe (pre-COVID-19 vs during COVID-19) and age range of the employee.

Findings

Preferences for how to be shown appreciation were quite stable across work setting, timeframe and age range, suggesting that one’s preferred ways of being shown appreciation is largely an internal characteristic that is only mildly influenced by external factors. Minor trends were found when comparing various age groups and remote vs onsite employees.

Originality/value

Understanding the impact of the COVID-19 pandemic on employees’ desires for appreciation is critical for organizational leaders. With vast numbers of new remote employees in the workforce, understanding how they are similar to and vary from onsite employees is paramount for addressing the needs of all team members. This study provides valuable information on both topics, as well as differences across age groups.