bluuebunny/crossref_metadata_2025 huggingface dataset:
Dual-level autoregulation of theE. coliDeaD RNA helicase via mRNA stability and Rho-dependent transcription termination
Authors: Ojha Sandeep , Jain Chaitanya
Published: April 2020

DEAD-box proteins (DBPs) are RNA remodeling factors associated with RNA helicase activity that are found in nearly all organisms. Despite extensive studies on the mechanisms used by DBPs to regulate RNA function, very little is known about how DBPs themselves are regulated. In this work, we have analyzed the expression and regulation of DeaD/CsdA, the largest of the DBPs inEscherichia coli(E. coli). We show thatdeaDtranscription initiates 838 nts upstream of the start of the coding region. We have also found that DeaD is autoregulated through a negative feedback mechanism that operates both at the level of mRNA stability and Rho-dependent transcription termination, and this regulation is dependent upon the 5’ untranslated region (5’ UTR). These findings suggest that DeaD might be regulating the conformation of its own mRNA through its RNA helicase activity to facilitate ribonuclease and Rho access to its 5’UTR.
In SilicoIdentification of Novel PrfA Inhibitors to Fight Listeriosis: A Virtual Screening and Molecular Dynamics Studies
Authors: Nizami Bilal , Tan Wen , Arias-Moreno Xabier
Published: April 2020

Listeria monocytogenesis considered to be one of the most dangerous foodborne pathogens as it can cause listeriosis, a life-threatening human disease. While the incidence of listeriosis is very low its fatality rate is exceptionally high. Because many multi-resistanceListeria monocytogenesstrains that do not respond to conventional antibiotic therapy have been recently described, development of new antimicrobials to fight listeriosis is necessary. The positive regulatory factor A (PrfA) is a key homodimeric transcription factor that modulates the transcription of multiple virulence factors which are ultimately responsible ofListeria monocytogenes’pathogenicity. In the present manuscript we describe several new potential PrfA inhibitors that were identified after performing ligand-based virtual screening followed by structure-based virtual screening against the wild-type PrfA structure. The three top-scored drug-likeness inhibitors bound to the wild-type PrfA structure were further assessed by Molecular Dynamics simulations. Besides, the three top-scored inhibitors were docked into a constitutive active apoPrfA mutant structure and the corresponding complexes were also simulated. According to the obtained data, PUBChem 87534955 (P875) and PUBChem 58473762 (P584) may not only bind and inhibit wild-type PrfA but the aforementioned apoPrfA mutant as well. Therefore, P875 and P584 might represent good starting points for the development of a completely new set of antimicrobial agents to treat listeriosis.
Reduction of Nemo-like kinase increases lysosome biogenesis and ameliorates TDP-43-related neurodegeneration
Authors: Tejwani Leon , Kokubu Hiroshi , Lee Paul J. , Xiang Yangfei , Luttik Kimberly , Soriano Armand , Yoon Jennifer , Park Junhyun , Ro Hannah , Ju Hyoungseok , Liao Clara , Tieze Sofia M. , Rigo Frank , Jafar-Nejad Paymaan , Lim Janghoo
Published: April 2020

Protein aggregation is a hallmark of many neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS). Although mutations in TARDBP, encoding TDP-43, account for less than 1% of all ALS cases, TDP-43-positive aggregates are present in nearly all ALS patients, including patients with sporadic ALS (sALS) or carrying other familial ALS (fALS)-causing mutations. Interestingly, TDP-43 inclusions are also present in subsets of patients with frontotemporal dementia, Alzheimer’s disease, and Parkinson’s disease; therefore, methods of activating intracellular protein quality control machinery capable of clearing toxic cytoplasmic TDP-43 species may alleviate disease-related phenotypes. Here, we identify a novel function of Nemo-like kinase (Nlk) as a negative regulator of lysosome biogenesis. Genetic or pharmacological reduction of Nlk increased lysosome formation and improved clearance of aggregated TDP-43. Furthermore, Nlk reduction ameliorated pathological, behavioral, and lifespan deficits in two distinct mouse models of TDP-43 proteinopathy. Because many toxic proteins can be cleared along the autophagy-lysosome axis, targeted reduction of Nlk represents a viable approach to therapy development for multiple neurodegenerative disorders.
Shape Analysis of the Human Association Pathways
Authors: Yeh Fang-Cheng
Published: April 2020

Shape analysis has been widely used in digital image processing and computer vision, but they have not been utilized to compare the structural characteristics of the human association pathways. Here we used shape analysis to derive length, area, volume, and shape metrics from diffusion MRI tractography and utilized them to study the morphology of human association pathways. The reliability analysis showed that shape descriptors achieved moderate to good test-retest reliability. Further analysis on association pathways showed left dominance in the arcuate fasciculus, cingulum, uncinate fasciculus, frontal aslant tract, and right dominance in the inferior fronto-occipital fasciculus and inferior longitudinal fasciculus. The superior longitudinal fasciculus has a mixed lateralization profile with different metrics showing either left or right dominance. The analysis of between-subject variations shows that the overall layout of the association pathways does not variate a lot across subjects, as shown by low between-subject variation in length, span, diameter, and radius. In contrast, the area of the pathway innervation region has a considerable between-subject variation. A follow-up analysis is warranted to thoroughly investigate the nature of population variations and their structure-function correlation.
TRIP6 is required for tension at adherens junctions
Authors: Venkatramanan Srividya , Ibar Consuelo , Irvine Kenneth D.
Published: April 2020

Hippo signaling mediates influences of cytoskeletal tension on organ growth. TRIP6 and LIMD1 have each been identified as being required for tension-dependent inhibition of the Hippo pathway LATS kinases and their recruitment to adherens junctions, but the relationship between TRIP6 and LIMD1 was unknown. Using siRNA-mediated gene knockdown we show that TRIP6 is required for LIMD1 localization to adherens junctions, whereas LIMD1 is not required for TRIP6 localization. TRIP6, but not LIMD1, is also required for recruitment of Vinculin and VASP to adherens junctions. Knockdown of TRIP6 or Vinculin, but not of LIMD1, also influences the localization of phosphorylated myosin light chain and F-actin. In TRIP6 knockdown cells actin stress fibers are lost apically but increased basally, and there is a corresponding increase in recruitment of Vinculin and VASP to basal focal adhesions. These observations identify a role for TRIP6 in organizing F-actin and maintaining tension at adherens junctions that could account for its influence on LIMD1 and LATS. They also suggest that focal adhesions and adherens junctions compete for key proteins needed to maintain attachments to contractile F-actin.
Targeting subtype-specific metabolic preferences in nucleotide biosynthesis inhibits tumor growth in a breast cancer model
Authors: Ogrodzinski Martin P. , Teoh Shao Thing , Lunt Sophia Y.
Published: April 2020

Investigating metabolic rewiring in cancer can lead to the discovery of new treatment strategies for breast cancer subtypes that currently lack targeted therapies. Using MMTV-Myc driven tumors to model breast cancer heterogeneity, we investigated metabolic differences between two histological subtypes, the epithelial-mesenchymal transition (EMT) and the papillary subtypes, using a combination of genomic and metabolomic techniques. We identified differences in nucleotide metabolism between EMT and papillary subtypes: EMT tumors preferentially use the nucleotide salvage pathway, while papillary tumors preferde novonucleotide biosynthesis. Using CRISPR/Cas9 gene editing and mass spectrometry-based methods, we determined that targeting the preferred pathway in each subtype resulted in greater metabolic impact than targeting the non-preferred pathway. We further show that knocking out the preferred nucleotide pathway in each subtype has a deleterious effect onin vivotumor growth. In contrast, knocking out the non-preferred pathway has a lesser effect or results in increased tumor growth.
Identifying regulatory and spatial genomic architectural elements using cell type independent machine and deep learning models
Authors: Martens Laura D. , Faust Oisín , Pirvan Liviu , Bihary Dóra , Samarajiwa Shamith A.
Published: April 2020

Chromosome conformation capture methods such as Hi-C enables mapping of genome-wide chromatin interactions and is a promising technology to understand the role of spatial chromatin organisation in gene regulation. However, the generation and analysis of these data sets at high resolutions remain technically challenging and costly. We developed a machine and deep learning approach to predict functionally important, highly interacting chromatin regions (HICR) and topologically associated domain (TAD) boundaries independent of Hi-C data in both normal physiological states and pathological conditions such as cancer. This approach utilises gradient boosted trees and convolutional neural networks trained on both Hi-C and histone modification epigenomic data from three different cell types. Given only epigenomic modification data these models are able to predict chromatin interactions and TAD boundaries with high accuracy. We demonstrate that our models are transferable across cell types, indicating that combinatorial histone mark signatures may be universal predictors for highly interacting chromatin regions and spatial chromatin architecture elements.
Enhancement of motor performance by a training method combining motor imagery and neurofeedback
Authors: Sha Chosei , Tamura Kaori , Okamoto Tsuyoshi
Published: April 2020

Motor imagery and neurofeedback have been proposed as motor training approaches, but their effects on the enhancement of motor performance are still controversial. This study aimed to enhance motor performance using a training protocol combining motor imagery and neurofeedback. Seventeen participants were randomly assigned to the training or control group. The training group received real-time electroencephalography activity feedback relative to the motor imagery of the motor action. The control group reiterated the motor imagery of the intended motor action without feedback. The motor performance of the training group was enhanced significantly more than that of the control group. Subsequently, the proposed training protocol was tested in five elite male tennis players to investigate its applicability to sports activities. The motor performance was enhanced in three of these five professional tennis players. Using our training protocol, which combined motor imagery and neurofeedback training, we achieved enhanced motor performance. Furthermore, we could suggest the applicability to sports from the results with world-level tennis players.
The effect of Dicer knockout on RNA interference using various Dicer substrate interfering RNA structures
Authors: Song Min-Sun , Rossi John J
Published: April 2020

Dicer-substrate siRNA (DsiRNA) was a useful tool for sequence-specific gene silencing. DsiRNA was proposed to have increased efficacy via RNAi gene silencing, but the molecular mechanism underlying the increased efficacy is not precise. We designed the tetra-looped DsiRNA as the tetra-looped RNAs have been reported more stable structure and increased binding efficiency with RNA and protein. To gain a deeper understanding of the Dicer function of DsiRNA, we knocked out Dicer in the HCT116 cell line and analyzed the efficacy of various Dicer substrates on RNAi gene silencing activity. Tetra-looped DsiRNA demonstrated increased efficacy of gene silencing Dicer expressing cells with activity favoring the guide strand. The gene silencing activity of all DsiRNAs was reduced in Dicer knockout cells. Thus, this study allows us to understand the Dicer function of key RNAi silencing and provides valuable resources for RNAi research and applications.
Global analysis of protein stability by temperature and chemical denaturation
Authors: Hamborg Louise , Horsted Emma Wenzel , Johansson Kristoffer Enøe , Willemoës Martin , Lindorff-Larsen Kresten , Teilum Kaare
Published: April 2020

The stability of a protein is a fundamental property that determines under which conditions, the protein is functional. Equilibrium unfolding with denaturants requires preparation of several samples and only provides the free energy of folding when performed at a single temperature. The typical sample requirement is around 0.5 – 1 mg of protein. If the stability of many proteins or protein variants needs to be determined, substantial protein production may be needed. Here we have determined the stability of acyl-coenzyme A binding protein at pH 5.3 and chymotrypsin inhibitor 2 at pH 3 and pH 6.25 by combined temperature and denaturant unfolding. We used a setup where tryptophan fluorescence is measured in quartz capillaries where only 10 μl is needed. Temperature unfolding of a series of 15 samples at increasing denaturant concentrations provided accurate and precise thermodynamic parameters. We find that the number of samples may be further reduced and less than 10 μg of protein in total are needed for reliable stability measurements. For assessment of stability of protein purified in small scale e.g. in micro plate format, our method will be highly applicable. The routine for fitting the experimental data is made available as a python notebook.
Virtual EEG-electrodes: Convolutional neural networks as a method for upsampling or restoring channels
Authors: Svantesson Mats , Olausson Håkan , Eklund Anders , Thordstein Magnus
Published: April 2020

Background

In clinical practice, EEGs are assessed visually. For practical reasons, recordings often need to be performed with a reduced number of electrodes and artifacts make assessment difficult. To circumvent these obstacles, different interpolation techniques can be utilized. These techniques usually perform better for higher electrode densities and values interpolated at areas far from electrodes can be unreliable. Using a method that learns the statistical distribution of the cortical electrical fields and predicts values may yield better results.

New Method

Generative networks based on convolutional layers were trained to upsample from 4 or 14 channels or to dynamically restore single missing channels to recreate 21 channel EEGs. 5,144 hours of data from 1,385 subjects of the Temple University Hospital EEG database were used for training and evaluating the networks.

Comparison with Existing Method

The results were compared to spherical spline interpolation. Several statistical measures were used as well as a visual evaluation by board certified clinical neurophysiologists. Overall, the generative networks performed significantly better. There was no difference between real and network generated data in the number of examples assessed as artificial by experienced EEG interpreters whereas for data generated by interpolation, the number was significantly higher. In addition, network performance improved with increasing number of included subjects, with the greatest effect seen in the range 5 – 100 subjects.

Conclusions

Using neural networks to restore or upsample EEG signals is a viable alternative to interpolation methods.
Tmed2regulates Smoothened trafficking and Hedgehog signalling
Authors: Di Minin Giulio , Dumeau Charles E. , Grison Alice , Chan Wesley , Monfort Asun , Jerome-Majewska Loydie A. , Wutz Anton
Published: April 2020

Hedgehog (HH) signalling plays a key role in embryonic pattering and stem cell differentiation. Compounds that selectively bind Smoothened (SMO) can induce cell death in mouse embryonic stem cells (ESCs). Here we perform a genetic screen in haploid ESCs and discover that SMO inhibits a cell death pathway that resembles dissociation induced death of human ESCs and Anoikis. In mouse ESCs, SMO acts through a G-protein coupled mechanism that is independent of GLI activation. Our screen also identifies the Golgi proteins Tmed2 and Tmed10. We show that TMED2 binds SMO and controls its abundance at the plasma membrane. In neural differentiation and neural tube pattering Tmed2 acts as a repressor of HH signalling strength. We demonstrate that the interaction between SMO and TMED2 is regulated by HH signalling suggesting SMO release form the ER-Golgi is critical for controlling G-protein and GLI mediated functions of mammalian HH signalling.
A comprehensive toolkit for quick and easy visualization of marker proteins, protein-protein interactions and cell morphology inMarchantia polymorpha
Authors: Westermann Jens , Koebke Eva , Lentz Roswitha , Hülskamp Martin , Boisson-Dernier Aurélien
Published: April 2020

Even though stable genomic transformation of sporelings and thalli ofMarchantia polymorphais comparatively straightforward and efficient, numerous problems can arise during critical phases of the process such as efficient spore production, poor selection capacity of antibiotics or low transformation efficiency. It is therefore also desirable to establish quick methods not relying on stable transgenics to analyze the localization, interactions and functions of proteins of interest. The introduction of foreign DNA into living cells via biolistic mechanisms has been first reported roughly 30 years ago and has been commonly exploited in established plant model species such asArabidopsis thalianaorNicotiana benthamiana. Here we report the fast and reliable transient biolistic transformation of Marchantia thallus epidermal cells using fluorescent protein fusions. We present a catalogue of fluorescent markers which can be readily used for tagging of a variety of subcellular compartments. Moreover, we report the functionality of the bimolecular fluorescence complementation (BiFC) inM. polymorphawith the example of the p-body markers MpDCP1/2. Finally, we provide standard staining procedures for live cell imaging inM. polymorpha, applicable to visualize cell boundaries or cellular structures, to complement or support protein localizations and to understand how results gained by transient transformations can be embedded in cell architecture and dynamics. Taken together, we offer a set of easy and quick tools for experiments that aim at understanding subcellular localization, protein-protein interactions and thus functions of proteins of interest in the emerging early diverging land plant modelM. polymorpha.
One-shot analysis of translated mammalian lncRNAs with AHARIBO
Authors: Minati Luca , Firrito Claudia , Piano Alessia Del , Peretti Alberto , Sidoli Simone , Peroni Daniele , Belli Romina , Gandolfi Francesco , Romanel Alessandro , Bernabò Paola , Zasso Jacopo , Quattrone Alessandro , Guella Graziano , Lauria Fabio , Viero Gabriella , Clamer Massimiliano
Published: April 2020

A vast portion of the mammalian genome is transcribed as long non-coding RNAs (lncRNAs) acting in the cytoplasm with largely unknown functions. Surprisingly, lncRNAs have been shown to interact with ribosomes, encode uncharacterized proteins, or act as ribosome sponges. These functions still remain mostly undetected and understudied owing to the lack of efficient tools for genome-wide simultaneous identification of ribosome-associated lncRNAs and peptide-producing lncRNAs.

Here we present AHARIBO, a method for the detection of lncRNAs either untranslated, but associated with ribosomes, or encoding small peptides. Using AHARIBO in mouse embryonic stem cells during neuronal differentiation, we isolated ribosome-protected RNA fragments, translated RNAs and correspondingde novosynthesized polypeptides. Besides identifying mRNAs under active translation and associated ribosomes, we found and distinguished lncRNAs acting as ribosome sponges or encoding micropeptides, laying the ground for a better functional understanding of hundreds lncRNAs.
Deregulation of the histone H3K9 di-methylation landscape suppresses canonical Wnt signaling in embryonal rhabdomyosarcoma
Authors: Pal Ananya , Leung Jia Yu , Ang Gareth Chin Khye , Rao Vinay Kumar , Pignata Luca , Lim Huey Jin , Hebrard Maxime , Chang Kenneth T , Lee Victor KM , Guccione Ernesto , Taneja Reshma
Published: April 2020

The Wnt signaling pathway is down-regulated in embryonal rhabdomyosarcoma (ERMS) and contributes to the block of myogenic differentiation. Epigenetic mechanisms leading to its suppression are unknown and could pave the way towards novel therapeutic modalities. In this study, we demonstrate that the H3K9 lysine methyltransferase G9a suppresses canonical Wnt signaling by activating expression of the Wnt antagonistDKK1. Inhibition of G9a expression or activity reducedDKK1expression and elevated canonical Wnt signaling resulting in myogenic differentiationin vitroandin vivo. Mechanistically, G9a impacted Sp1 and p300 enrichment at theDKK1promoter in a methylation-dependent manner. The reduced tumor growth upon G9a deficiency was reversed by recombinant DKK1 or LGK974, which also inhibits Wnt signaling. Consistently, among thirteen drugs targeting chromatin modifiers, G9a inhibitors were highly effective in reducing ERMS cell viability. Together, our study demonstrates that ERMS cells are vulnerable to G9a inhibitors and suggest that targeting the G9a-DKK1-β-catenin node holds promise for differentiation therapy.
The Coevolution of Promoters and Transcription Factors in Animal and Plant Cells
Authors: Zhang Jingsong , Yu Xiangtian , Su Zhixi , He Shutao , Zhou Yiwei , Dai Hao , Hao Xiaohu , Zeng Tao , Wang Wen , Chen Luonan
Published: April 2020

Coevolution has been acknowledged to play a significant role in driving the evolution of molecules and species. Promoters and transcription factors (TFs), especially their interactions, are key determinants for the regulation of gene expression. However, the evolutionary processes and mechanisms of promoter and TF interactions are still poorly understood. Here we conduct extensive physicochemical analyses of multi-omics sequences in 440 animal species and 223 plant species which span nearly one billion years of phylogeny. We demonstrate that promoters and TFs obey antagonistic coevolution in the animal kingdom while follow mutualistic coevolution in the plant kingdom. Furthermore, we reveal that such two coevolutionary strategies result in different evolutionary transitions of transcriptional networks in the two kingdoms. These results suggest that the two distinct coevolutionary mechanisms are likely to be major drivers of far greater genetic divergence between animals and plants, and open a new door to understanding the roles of promoters and TFs in tumor initiation and progression, and human ageing as well in molecular interactions and evolution.
Contrasting stripes are a widespread feature of group living in birds, mammals and fishes
Authors: Negro Juan J. , Doña Jorge , Blázquez M. del Carmen , Rodríguez Airam , Herbert-Read James E. , Brooke M. de L.
Published: April 2020

Grouping is a widespread form of predator defense, with individuals in groups often performing evasive collective movements in response to predators’ attacks. Individuals in these groups use behavioral rules to coordinate their movements, with visual cues about neighbors’ positions and orientations informing movement decisions. Although the exact visual cues individuals use to coordinate their movements with neighbors have not yet been decoded, some studies have suggested that stripes, lines or other body patterns may act as conspicuous conveyors of movement information that could promote coordinated group movement, or promote dazzle camouflage, thereby confusing predators. We used phylogenetic logistic regressions to test whether the contrasting achromatic stripes present in four different taxa vulnerable to predation, including species within two orders of birds (Anseriformes and Charadriiformes), a suborder of Artiodactyla (the ruminants) and several orders of marine fish (predominantly Perciformes) were associated with group living. Contrasting patterns were significantly more prevalent in social species, and tended to be absent in solitary species or species less vulnerable to predation. We suggest that stripes taking the form of light-colored lines on dark backgrounds, orvice versa, provide a widespread mechanism across taxa that serves either to inform conspecifics of neighbors’ directional movement, or to confuse predators, when moving in groups. Detection and processing of patterns and of motion in the visual channel is essentially colourblind. That diverse animal taxa with widely different vision systems (including di-, tri- and tetrachromats) appear to have converged on a similar use of achromatic patterns is therefore expected given signal-detection theory. This hypothesis would explain the convergent evolution of conspicuous achromatic patterns as an antipredator mechanism in numerous vertebrate species.
Learned SPARCOM: Unfolded Deep Super-Resolution Microscopy
Authors: Dardikman-Yoffe Gili , Eldar Yonina C.
Published: April 2020

The use of photo-activated fluorescent molecules to create long sequences of low emitter-density diffraction-limited images enables high-precision emitter localization. However, this is achieved at the cost of lengthy imaging times, limiting temporal resolution. In recent years, a variety of approaches have been suggested to reduce imaging times, ranging from classical optimization and statistical algorithms to deep learning methods. Classical methods often rely on prior knowledge of the optical system and require heuristic adjustment of parameters or do not lead to good enough performance. Deep learning methods proposed to date tend to suffer from poor generalization ability outside the specific distribution they were trained on, and require learning of many parameters. They also tend to lead to black-box solutions that are hard to interpret. In this paper, we suggest combining a recent high-performing classical method, SPARCOM, with model-based deep learning, using the algorithm unfolding approach which relies on an iterative algorithm to design a compact neural network considering domain knowledge. We show that the resulting network, Learned SPARCOM (LSPARCOM), requires far fewer layers and parameters, and can be trained on a single field of view. Nonetheless it yields comparable or superior results to those obtained by SPARCOM with no heuristic parameter determination or explicit knowledge of the point spread function, and is able to generalize better than standard deep learning techniques. It even allows producing a high-quality reconstruction from as few as 25 frames. This is due to a significantly smaller network, which also contributes to fast performance - 5× improvement in execution time relative to SPARCOM, and a full order of magnitudes improvement relative to a leading competing deep learning method (Deep-STORM) when implemented serially. Our results show that we can obtain super-resolution imaging from a small number of high emitter density frames without knowledge of the optical system and across different test sets. Thus, we believe LSPARCOM will find broad use in single molecule localization microscopy of biological structures, and pave the way to interpretable, efficient live-cell imaging in a broad range of settings.
Multiple paths to cold tolerance: the role of environmental cues, morphological traits and the circadian clock genevrille
Authors: Poikela Noora , Tyukmaeva Venera , Hoikkala Anneli , Kankare Maaria
Published: April 2020

Background

Tracing the association between insect cold tolerance and latitudinally and locally varying environmental conditions, as well as key morphological traits and molecular mechanisms, is essential for understanding the processes involved in adaptation. We explored these issues in two closely-related species,Drosophila montanaandDrosophila flavomontana, originating from diverse climatic locations across several latitudes on the coastal and mountainous regions of North America. We also investigated the association between sequence variation in one of the key circadian clock genes,vrille, and cold tolerance in both species. Finally, we studied the impact ofvrilleon fly cold tolerance and cold acclimation ability by silencing it with RNA interference inD. montana.

Results

We performed a principal component analysis (PCA) on variables representing bioclimatic conditions on the study sites and used latitude as a proxy of photoperiod. PC1 separated the mountainous continental sites from the coastal ones based on temperature variability and precipitation, while PC2 arranged the sites based on summer and annual mean temperatures. Cold tolerance tests showedD. montanato be more cold-tolerant thanD. flavomontanaand chill coma resistance (CTmin) of this species showed an association with PC2. Chill coma recovery time (CCRT) of both species improved towards northern latitudes, and inD. flavomontanathis trait was also associated with PC1.D. flavomontanaflies were darkest in the coast and in the northern mountainous populations, but coloration showed no linkage with cold tolerance. Body size decreased towards cold environments in both species, but only withinD. montanapopulations largest flies showed fastest recovery from cold. Finally, both the sequence analysis and RNAi study onvrillesuggested this gene to play an essential role inD. montanacold resistance and acclimation, but not in recovery time.

Conclusions

Our study demonstrates the complexity of insect cold tolerance and emphasizes the need to trace its association with multiple environmental variables and morphological traits to identify potential agents of natural selection. It also shows that a circadian clock genevrilleis essential both for short- and long-term cold acclimation, potentially elucidating the connection between circadian clock system and cold tolerance.
An open-sourced bioinformatic pipeline for the processing of Next-Generation Sequencing derived nucleotide reads: Identification and authentication of ancient metagenomic DNA
Authors: Collin Thomas C. , Drosou Konstantina , O’Riordan Jeremiah Daniel , Meshveliani Tengiz , Pinhasi Ron , Feeney Robin N. M.
Published: April 2020

Bioinformatic pipelines optimised for the processing and assessment of metagenomic ancient DNA (aDNA) are needed for studies that do not make use of high yielding DNA capture techniques. These bioinformatic pipelines are traditionally optimised for broad aDNA purposes, are contingent on selection biases and are associated with high costs. Here we present a bioinformatic pipeline optimised for the identification and assessment of ancient metagenomic DNA without the use of expensive DNA capture techniques. Our pipeline actively conserves aDNA reads, allowing the application of a bioinformatic approach by identifying the shortest reads possible for analysis (22-28bp). The time required for processing is drastically reduced through the use of a 10% segmented non-redundant sequence file (229 hours to 53). Processing speed is improved through the optimisation of BLAST parameters (53 hours to 48). Additionally, the use of multi-alignment authentication in the identification of taxa increases overall confidence of metagenomic results. DNA yields are further increased through the use of an optimal MAPQ setting (MAPQ 25) and the optimisation of the duplicate removal process using multiple sequence identifiers (a 4.35-6.88% better retention). Moreover, characteristic aDNA damage patterns are used to bioinformatically assess ancient vs. modern DNA origin throughout pipeline development. Of additional value, this pipeline uses open-source technologies, which increases its accessibility to the scientific community.
Endophilin A2 regulates B cell protein trafficking and humoral responses
Authors: Malinova Dessislava , Wasim Laabiah , Engels Niklas , Tolar Pavel
Published: April 2020

Antigen-specific B cell responses require endosomal trafficking to regulate antigen uptake and presentation to helper T cells, and to control expression and signaling of immune receptors. However, the molecular composition of B cell endosomal trafficking pathways and their specific roles in B cell responses have not been systematically investigated. Here we report high-throughput identification of genes regulating B cell receptor (BCR)-mediated antigen internalization using genome-wide functional screens. We show that antigen internalization depends both on clathrin-coated pits and on clathrin-independent endocytosis mediated by endophilin A2. Although endophilin A2 is dispensable for presentation of the endocytosed antigen, it is required for metabolic support of germinal center (GC) B cell proliferation, in part through regulation of iron uptake. Consequently, endophilin A2 deficient mice show selective defects in GC B cell responses and production of high-affinity IgG. The requirement for endophilin A2 highlights a unique importance of clathrin-independent intracellular trafficking in GC B cell clonal expansion and antibody responses.

HIGHLIGHTS

Genome-wide CRISPR screens comprehensively identify genes regulating antigen uptake in B cells

B cell receptor-mediated antigen internalization is mediated by both epsin1- dependent clathrin-coated pits and a novel fast endophilin A2-mediated endocytosis.

Endophilin A2 is required for peripheral B cell development, antigen-specific germinal center responses and high-affinity IgG production.

Endophilin A2 is broadly essential for B cell intracellular trafficking pathways providing metabolic support of germinal center B cell proliferation, in part through regulation of iron uptake.
Desert Hedgehog-driven endothelium integrity is enhanced by Gas1 but negatively regulated by Cdon
Authors: Chapouly Candice , Hollier Pierre-Louis , Guimbal Sarah , Cornuault Lauriane , Gadeau Alain-Pierre , Renault Marie-Ange
Published: April 2020

Evidences accumulated within the past decades, identified Hedgehog (Hh) signaling as a new regulator of micro-vessel integrity. More specifically, we recently identified Desert Hedgehog (Dhh) as a downstream effector of Klf2 in endothelial cells (ECs).

Objective

The purpose of this study is to investigate whether Hh co-receptors Gas1 and Cdon may be used as therapeutic targets to modulate Dhh signaling in ECs.

Methods and results

We demonstrated that both Gas1 and Cdon are expressed in adult ECs and relied on either siRNAs or EC specific conditional KO mice to investigate their role. We found that Gas1 deficiency mainly photocopies Dhh deficiency especially by inducing VCAM-1 and ICAM-1 overexpression while Cdon deficiency has opposite effects by promoting endothelial junction integrity. At a molecular level, Cdon prevents Dhh binding to Ptch1 and thus acts a decoy receptor for Dhh, while Gas1 promotes Dhh binding to Smo and as a result potentiates Dhh effects. Since Cdon is overexpressed in ECs treated by inflammatory cytokines including TNFα and Il1β, we then tested whether Cdon inhibition would promote endothelium integrity in acute inflammatory conditions and found that both fibrinogen and IgG extravasation were decreased in association with an increased Cdh5 expression in the brain cortex of EC specific Cdon KO mice administered locally with Il1β.

Conclusion

Altogether these results demonstrate that Gas1 is a positive regulator of Dhh in ECs while Cdon is a negative regulator. Interestingly Cdon blocking molecules may then be used to promote endothelium integrity at least in inflammatory conditions.
Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis
Authors: Hsiao Chiaowen Joyce , Tung PoYuan , Blischak John D. , Burnett Jonathan E. , Barr Kenneth A. , Dey Kushal K. , Stephens Matthew , Gilad Yoav
Published: April 2020

Cellular heterogeneity in gene expression is driven by cellular processes, such as cell cycle and cell-type identity, and cellular environment such as spatial location. The cell cycle, in particular, is thought to be a key driver of cell-to-cell heterogeneity in gene expression, even in otherwise homogeneous cell populations. Recent advances in single-cell RNA-sequencing (scRNA-seq) facilitate detailed characterization of gene expression heterogeneity and can thus shed new light on the processes driving heterogeneity. Here, we combined fluorescence imaging with scRNA-seq to measure cell cycle phase and gene expression levels in human induced pluripotent stem cells (iPSCs). By using these data, we developed a novel approach to characterize cell cycle progression. Although standard methods assign cells to discrete cell cycle stages, our method goes beyond this and quantifies cell cycle progression on a continuum. We found that, on average, scRNA-seq data from only five genes predicted a cell's position on the cell cycle continuum to within 14% of the entire cycle and that using more genes did not improve this accuracy. Our data and predictor of cell cycle phase can directly help future studies to account for cell cycle–related heterogeneity in iPSCs. Our results and methods also provide a foundation for future work to characterize the effects of the cell cycle on expression heterogeneity in other cell types.
Electron diffraction study of the space group of Bi5Ti3FeO15 multiferroic ceramic
Authors: Zheng Ying , Wu Xinyan , Zhang Yongcheng , Shao Weiquan , Ye Wanneng
Published: April 2020

Bi5Ti3FeO15 (pentabismuth trititanium iron pentadecaoxide), which is a multiferroic four-layer Aurivillius phase compound, has received much attention in recent years. However, three mutually inconsistent orthorhombic space groups, i.e. A21
am, Fmm2 and Pnn2, have been reported for the room-temperature phase of Bi5Ti3FeO15 by X-ray and neutron diffraction investigations. Here, electron diffraction results are presented and discussed for the first time to unambiguously clarify the room-temperature space group of ceramic Bi5Ti3FeO15. It has been found that all the observed reflections from the ceramic agree with those expected in A21
am, while the observed reflections 011, 013 and 015 should be forbidden in the case of Fmm2, and no 107 and 109 reflections were observed although allowed for Pnn2. The present study has demonstrated that the space group of Bi5Ti3FeO15 ceramic is A21
am rather than Fmm2 or Pnn2, an identification that proved to be a challenge for X-ray diffraction. On the basis of the space group A21
am, the lattice parameters of the Bi5Ti3FeO15 ceramic were calculated from its X-ray diffraction data.
Earnings persistence, institutional investors monitoring and types of political connections
Authors: Tee Chwee Ming , Rasiah Puspavathy
Published: April 2020

Purpose

The purpose of this study is to examine whether institutional investors monitoring attenuate (exacerbate) weaker earnings persistence in politically connected firms (PCFs). In addition, it investigates whether earnings persistence do vary according to different types of political connections.

Design/methodology/approach

This study employs earnings persistence as measure of earnings quality and ordinary least squares (OLS) model to examine: (1) the moderating effect of institutional investors’ ownership on the association between earnings persistence and PCFs and (2) the association between different types of political connections and earnings persistence.

Findings

This study finds that institutional investors' ownership attenuates weaker earnings quality in PCFs, indicating effective monitoring. However, stronger earnings persistence is associated with PCFs with longer political ties, audited by big four audit firm and with higher CEO power.

Originality/value

This study reveals the lower earnings persistence in PCFs can be attenuated by institutional investors monitoring. However, findings also suggest that earnings persistence in PCFs is affected by duration of political ties, big four audit firm and CEO power. This suggests that PCFs should not be viewed as a homogeneous group of firms.
To be or not to be in the sample? On using manipulation checks in experimental accounting research
Authors: Kotzian Peter , Stoeber Thomas , Hoos Florian , Weissenberger Barbara E.
Published: April 2020

Purpose

Manipulation checks are a recommended for experimental accounting research. Usage of information gained by manipulation checks varies. In some studies, participants who failed the manipulation check are removed from the sample. Other studies report the results of the manipulation checks but still use the full sample. Some authors recommend removing participants who failed the manipulation check as a means to increase the power of the statistical analysis. Others warn that removing these participants endangers the randomization as a crucial precondition for gaining valid insights from experimental research. Until now, there is little research on how sensitive results react to exclusion of participants. The purpose of this paper is to study the effects of removing participants failing the manipulation checks on the evaluation of a hypothesis and the development of alternative usages of the information gained from manipulation checks.

Design/methodology/approach

Based on an analytical model and a simulation, the authors show how removing participants who fail the manipulation check affects experimental findings.

Findings

Simulations show that statistical results and conclusions drawn from an experiment differ substantially, depending on whether participants who failed the manipulation check are removed from the sample. As the participants who are removed are no random sub-sample, but share a certain property, the experimental results react strongly, typically showing significant results, where there are actually none.

Originality/value

This paper is, to the best of the authors’ knowledge, the first to address the sensitivity of experimental results to removing participants who fail the manipulation check from the sample and the implications for the validity of conclusions drawn from experimental accounting research. This paper’s contribution is a better way of using information gained in the manipulation check in the statistical analysis of the experimental data.
An entrepreneurial view of universal work-integrated learning
Authors: Dorland AnneMarie , Finch David J. , Levallet Nadège , Raby Simon , Ross Stephanie , Swiston Alexandra
Published: April 2020

Purpose

Work-integrated learning (WIL) has emerged as a leading pedagogy that blends theory with application. In recent years, policymakers, educators and practitioners have called for a significant expansion of WIL, one which would enable every undergraduate student has at least one WIL experience during their program of study. Despite these appeals, there remains a significant divide between the aspiration of universality and the realities. Consequently, the study asks the following question: How can post-secondary institutions expand their WIL initiatives to universal levels that deliver transformative learning?

Design/methodology/approach

In this exploratory study, the authors leverage research from entrepreneurship and management to develop a conceptual model of universal work-integrated learning (UWIL). Entrepreneurship and management research is relevant in this context, as the rapid introduction of a UWIL has transformative implications at the level of the individual (e.g. students, faculty), organization (e.g. processes) and the learning ecosystem (e.g. partners, policymakers) — issues at the core of research in entrepreneurship and management over the past two decades.

Findings

At the core of the authors’ proposal is the contention that the high-impact talent challenge and the delivery of UWIL must be reframed as not simply a challenge facing educators, but as a challenge facing the broader ecosystem of the workforce and the larger community. The authors propose the implementation of UWIL through an open innovation framework based on five strategic pillars.

Originality/value

Ultimately, the findings the authors present here can be leveraged by all members of the learning ecosystem, including administrators, faculty, policymakers, accreditation bodies and community partners, as a framework for operationalizing a UWIL strategy. The study’s model challenges all members of this learning ecosystem to operationalize a UWIL strategy. This entrepreneurial reframing introduces the potential for innovating the delivery of UWIL by leveraging the broader learning ecosystem to drive efficiencies and transformative learning.
Peacemaking at work and at home
Authors: Zhang Xiaolei , Bollen Katalien , Euwema Martin
Published: April 2020

Purpose

The purpose of this paper is to explore the relations between peacemaking at work and peacemaking at home. Peacemaking is defined as voluntarily helping behavior in interpersonal conflict, by a person who has no formal authority over the conflicting parties, acts impartial and works with either one or more parties to solve the conflict constructively (Zhang et al., 2018).

Design/methodology/approach

In total, 639 participants engaged in a survey to measure their peacemaking behavior at work and at home. First, the peacemaking scale is validated using factor analysis. To test the hypotheses regression analysis is conducted.

Findings

Results show that peacemaking at work and at home are positively-related. Further, compared to peacemaking at work, people tend to be more often engaged in peacemaking at home; are more focused on settling the issues, provide more emotional support and use more humor, however, are less multi-partial.

Research limitations/implications

Although based on self-reports, the results regarding the positive relation between peacemaking at work and at home may be enlightening in human resource management such as personnel selection.

Originality/value

The study provides the first theory-based instrument to measure peacemaking as informal helping behavior in interpersonal conflict, at work and at home. Five components are measured, namely, peacemaking in general, multi-partiality, settlement-oriented, emotion-oriented and humorous peacemaking behaviors.
Institutional environment and internationalization of franchise chains: a regional and global analysis
Authors: Lanfranchi Andrea , Melo Pedro Lucas de Resende , Borini Felipe Mendes , Telles Renato
Published: April 2020

Purpose

In this study, the authors identify how formal institutional environments in destination countries matter to franchise chains as they internationalize. The institutional environment of the destination countries of franchise chains is characterized according to three institutional dimensions necessary to attract international investment – public governance, ease of doing business and legal processes – and analyzed in the context of regional and global franchise expansion.

Design/methodology/approach

The descriptive quantitative study involved 625 franchise chains from Australia, Brazil, Germany, India, Russia, South Africa and the United States, with a total of 2,939 observations.

Findings

Results suggest that franchise chains from emerging markets are guided by the institutional conditions of ease of doing business and the quality of legal processes in global expansion and guided by ease of doing business, quality of legal processes and governance in regional expansion. On the other hand, franchise chains from developed markets are guided by the ease of doing business, quality of legal processes and governance in global expansion and governance and ease of doing business in regional expansion.

Research limitations/implications

The sample included only franchise chains associated with organizations that represent franchises in their countries of origin, and the study does not analyze the effect of institutional distance between countries of origin and destination.

Originality/value

This study identifies the formal institutional characteristics that explain selection and commitment in international markets by franchise chains from different countries. The contribution is in analyzing the phenomenon through the lens of institutional theory and showing, through a global sample, that institutions matter to franchise chains from different types of countries (developed and emerging) and with different strategies for internationalization (global and regional).