bluuebunny/crossref_metadata_2025 huggingface dataset:
Probing the ionotropic activity of the orphan glutamate delta 2 receptor with genetically-engineered photopharmacology
Authors: Lemoine Damien , Mondoloni Sarah , Tange Jérôme , Lambolez Bertrand , Faure Philippe , Taly Antoine , Tricoire Ludovic , Mourot Alexandre
Published: May 2020

Glutamate delta (GluD) receptors belong to the ionotropic glutamate receptor family, yet whether they actually form functional and physiologically-relevant ion channels in neurons remains a debated question. Here we used a chemo-genetic approach to engineer specific and photo-reversible pharmacology in the orphan GluD2 receptor. We incorporated a cysteine mutation in the cavity located above the putative ion channel pore, for site-specific conjugation with a photoswitchable ligand. We first showed that, in the constitutively-open GluD2 Lurcher mutant, current could be rapidly and reversibly decreased with light. We then transposed the cysteine mutation to the native receptor, to demonstrate with absolute pharmacological specificity that metabotropic glutamate receptor signaling opens the GluD2 ion channel in heterologous expression system. Our results assess the functional relevance of GluD2 ion channel and introduce an optogenetic tool that will provide a novel and powerful means for probing GluD2 ionotropic contribution to neuronal physiology.
Cingulin unfolds ZO-1 and organizes myosin-2B and γ-actin to mechanoregulate apical and tight junction membranes
Authors: Vasileva Ekaterina , Rouaud Florian , Spadaro Domenica , Huang Wenmao , Colom Adai , Flinois Arielle , Shah Jimit , Dugina Vera , Chaponnier Christine , Sluysmans Sophie , Méan Isabelle , Jond Lionel , Roux Aurélien , Yan Jie , Citi Sandra
Published: May 2020

How junctional proteins regulate the mechanics of the plasma membrane and how actin and myosin isoforms are selectively localized at epithelial cell-cell junctions is poorly understood. Here we show by atomic force indentation microscopy, immunofluorescence analysis and FLIM membrane tension imaging that the tight junction (TJ) protein cingulin maintains apical surface stiffness and TJ membrane tortuosity and down-regulates apico-lateral membrane tension in MDCK cells. KO of cingulin in MDCK, mCCD and Eph4 cells results in a decrease in the juxta-membrane accumulation of labeling for cytoplasmic myosin-2B (NM2B), γ-actin, phalloidin and ARHGEF18, but no detectable effect on myosin-2A (NM2A) and β-actin. Loss of paracingulin leads to weaker mechanical phenotypes in MDCK cells, correlating with no detectable effect on the junctional accumulation of myosins and actins. Cingulin and paracingulin form biomolecular condensates, bind to the ZU5 domain of ZO-1, and are recruited as clients into ZO-1 condensates in a ZU5-dependent manner. Cingulin binding to ZO-1 promotes the unfolding of ZO-1, as determined by interaction with DbpA in cells lacking ZO-2 and in vitro. Cingulin promotes the accumulation of a pool of ZO-1 at the TJ and is required in a ZU5-dependent manner for the recruitment of phalloidin-labelled actin filaments into ZO-1 condensates, suggesting that ZU5-cingulin interaction promotes ZO-1 interaction with actin filaments. Our results indicate that cingulin tethers the juxta-membrane and apical branched γ-actin-NM2B network to TJ to modulate ZO-1 conformation and the TJ assembly of a pool of ZO-1 and fine-tune the distribution of forces to apical and TJ membranes.
Need for speed: Examining protein behaviour during cryoEM grid preparation at different timescales
Authors: Klebl David P. , Gravett Molly S. C. , Kontziampasis Dimitrios , Wright David J. , Bon Robin S. , Monteiro Diana , Trebbin Martin , Sobott Frank , White Howard D. , Darrow Michele , Thompson Rebecca F. , Muench Stephen P.
Published: May 2020

A host of new technologies are under development to improve the quality and reproducibility of cryoEM grid preparation. Here we have systematically investigated the preparation of three macromolecular complexes using three different vitrification devices (Vitrobot™, chameleon and a time-resolved cryoEM device) on various timescales, including grids made within 6 ms, (the fastest reported to date), to interrogate particle behaviour at the air-water interface for different timepoints. Results demonstrate that different macromolecular complexes can respond to the thin film environment formed during cryoEM sample preparation in highly variable ways, shedding light on why cryoEM sample preparation can be difficult to optimise. We demonstrate that reducing time between sample application and vitrification is just one tool to improve cryoEM grid quality, but that it is unlikely to be a generic ‘silver bullet’ for improving the quality of every cryoEM sample preparation.
Conservation and host-specific expression of non-tandemly repeated heterogenous ribosome RNA gene in arbuscular mycorrhizal fungi
Authors: Maeda Taro , Kobayashi Yuuki , Nakagawa Tomomi , Ezawa Tatsuhiro , Yamaguchi Katsushi , Bino Takahiro , Nishimoto Yuki , Shigenobu Shuji , Kawaguchi Masayoshi
Published: May 2020

The ribosomal RNA-encoding gene (rDNA) has a characteristic genomic nature: tens to thousands of copies in a genome, tandemly repeated structure, and intragenomic sequence homogeneity. These features contribute to ribosome productivity via physiological and evolutionary processes. We reported previously the exceptional absence of these features in the model arbuscular mycorrhizal (AM) fungusRhizophagus irregularis.Here we examine the phylogenetic distribution of the exceptional rDNA features in the genusRhizophagusvia improving the genome sequence ofR. clarus.Cross-species comparison indicated similarity of their rDNAs not only in the genomic features but also in the distribution of intragenomic polymorphic sites on the paralogs. Ribosomal RNA comprises multiple domains with different functions. The twoRhizophagusspecies commonly exhibited a variation enrichment site, ES27L, which is related to translational fidelity and antibiotic sensitivity. Variation enrichment on ES27L has not been observed in other organisms lacking the three rDNA features such as malaria parasites andCyanidioschyzon merolae.Expression profiling of rDNAs inR. irregularisrevealed that rDNA paralogs are expressed differently in association with host plant species. Our results suggest a broad distribution of the disarranged rDNA across AM fungi and its involvement in the successful association with the broad range of host species.
Eukaryotic cell biology is temporally coordinated to support the energetic demands of protein homeostasis
Authors: O’Neill John S. , Hoyle Nathaniel P. , Robertson J. Brian , Edgar Rachel S. , Beale Andrew D. , Peak-Chew Sew Y. , Day Jason , Costa Ana S. H. , Frezza Christian , Causton Helen C.
Published: May 2020

Every aspect of yeast physiology is subject to robust temporal regulation, this becomes apparent under nutrient-limiting conditions1-6and results in biological oscillations whose function and mechanism is poorly resolved7. These yeast metabolic oscillations share features with circadian rhythms and typically interact with, but are independent of, the cell division cycle. Here we show that these cellular rhythms act to minimise energy expenditure by temporally restricting protein synthesis until sufficient cellular resources are present, whilst maintaining osmotic homeostasis and protein quality control. Although nutrient supply is constant, cells initially ‘sequester and store’ metabolic resources such as carbohydrates, amino acids, K+and other osmolytes; which accumulateviaincreased synthesis, transport, autophagy and biomolecular condensation that is stimulated by low glucose and cytosolic acidification. Replete stores trigger increased H+export to elevate cytosolic pH, thereby stimulating TORC1 and liberating proteasomes, ribosomes, chaperones and metabolic enzymes from non-membrane bound compartments. This facilitates a burst of increased protein synthesis, the liquidation of storage carbohydrates to sustain higher respiration rates and increased ATP turnover, and the export of osmolytes to maintain osmotic potential. As the duration of translational bursting is determined by cell-intrinsic factors, the period of oscillation is determined by the time cells take to store sufficient resources to license passage through the pH-dependent metabolic checkpoint that initiates translational bursting. We propose that dynamic regulation of ion transport and metabolic plasticity are required to maintain osmotic and protein homeostasis during remodelling of eukaryotic proteomes, and that bioenergetic constraints have selected for temporal organisation that promotes oscillatory behaviour.
BAP31 regulated polarization of macrophages through C/EBP β in cutaneous wound healing
Authors: Yuan Qing , Zhao Bo , Cao Yu-hua , Yan Jia-cheng , Sun Li-jun , Liu Xia , Xu Yang , Wang Xiao-yu , Wang Bing
Published: May 2020

The functions carried out by macrophages are essential in the processes of repairing skin injury. However, the mechanism of the M2 macrophage and its role in cutaneous wound healing remain elusive. B cell receptor associated protein 31 (BAP31) plays an important role in the immune system, and its function in connection with macrophages has yet to be determined. The present study demonstrates that the process of cutaneous wound healing slowed down in bone marrow-specific BAP31 knock down Lyz2-cre-BAP31flox/floxmice. In addition, further studies show that various kinds of macrophage M2 polarization related factors were regulated by BAP31. Among these molecules C/EBP β was significantly affected. However, IL-4 but not IFN-γ, is able to recover the expression levels of C/EBP β and its downstream transcript factors induced by BAP31. Then, we demonstrated that BAP31 regulated macrophage M2 polarization by negative regulation of IL-4Rα and positive influence on Egr-2 to affect C/EBP β. Our findings reveal a novel mechanism of BAP31 in regulating M2 macrophage, and provide novel targets for the prevention and treatment of chronic wounds.
When effort matters: Expectations of reward and efficacy guide cognitive control allocation
Authors: Frömer R. , Lin H. , Dean Wolf C. K. , Inzlicht M. , Shenhav A.
Published: May 2020

The amount of mental effort we invest in a task is influenced by the reward we can expect if we perform that task well. However, some of the rewards that have the greatest potential for driving these efforts (e.g., jobs, grants) are partly determined by factors beyond one’s control. In such cases, effort has more limitedefficacyfor obtaining rewards. We have proposed that people integrate information about the expected reward and efficacy for effort to determine the expected value of control, and then adjust their control allocation (i.e. mental effort) accordingly. Here we test this theory’s key behavioral and neural predictions. We show that participants invest more control when this control is more rewarding and more efficacious, and that these incentive components separately modulate EEG signatures of incentive evaluation and proactive control allocation. Our findings support the prediction that people combine worth and worthwhileness to determine how much effort to invest.
RIPK2 Stabilizes c-Myc and is an Actionable Target for Inhibiting Prostate Cancer Metastasis
Authors: Yan Yiwu , Zhou Bo , Qian Chen , Vasquez Alex , Chatterjee Avradip , Yuan Xiaopu , Posadas Edwin , Kyprianou Natasha , Knudsen Beatrice S. , Murali Ramachandran , Gertych Arkadiusz , You Sungyong , Freeman Michael R. , Yang Wei
Published: May 2020

Despite advances in diagnosis and treatment, metastatic prostate cancer remains incurable and is associated with high mortality rates. Thus, novel actionable drug targets are urgently needed for therapeutic interventions in advanced prostate cancer. Here we report receptor-interacting protein kinase 2 (RIPK2) as an actionable drug target for suppressing prostate cancer metastasis. RIPK2 is frequently amplified in lethal prostate cancers and its overexpression is associated with disease progression and aggressiveness. Genetic and pharmacological inhibition of RIPK2 significantly suppressed prostate cancer progressionin vitroand metastasisin vivo.Multi-level proteomic analysis revealed that RIPK2 strongly regulates c-Myc protein stability and activity, largely by activating the MKK7/JNK/c-Myc phosphorylation pathway—a novel, non-canonical RIPK2 signaling pathway. Targeting RIPK2 inhibits this phosphorylation pathway, and thus promotes the degradation of c-Myc—a potent oncoprotein for which no drugs have been approved for clinical use yet. These results support targeting RIPK2 for personalized therapy in prostate cancer patients towards improving survival.
Improved RAD51 binders through motif shuffling based on the modularity of BRC repeats
Authors: Lindenburg Laurens H. , Pantelejevs Teodors , Gielen Fabrice , Zuazua-Villar Pedro , Butz Maren , Rees Eric , Kaminski Clemens F. , Downs Jessica A. , Hyvönen Marko , Hollfelder Florian
Published: May 2020

Exchanges of protein sequence modules support leaps in function unavailable through point mutations during evolution. Here we study the role of the two RAD51-interacting modules within the eight binding BRC repeats of BRCA2. We created 64 chimeric repeats by shuffling these modules and measured their binding to RAD51. We found that certain shuffled repeats were stronger than any of the natural repeats, suggesting balancing of relative properties in BRC repeats. Surprisingly, the contribution from the two modules was poorly correlated with affinities of natural repeats, with weak BRC8 repeat containing the most effective N-terminal module. The binding of the strongest chimera, BRC8-2, to RAD51 was improved by −2.44 kCal/mol compared to the strongest natural repeat, BRC4. Crystal structure of RAD51:BRC8-2 complex shows an improved interface fit and an extended β-hairpin in this repeat. BRC8-2 was shown to function in human cells, preventing the formation of nuclear foci after ionizing radiation.
Reducing visible aerosol generation during phacoemulsification in the era of Covid-19
Authors: Darcy Kieren , Elhaddad Omar , Achiron Asaf , Keller Johannes , Leadbetter Duncan , Tole Derek , Liyanage Sidath E
Published: May 2020

Objective: To assess potential methods of reducing visible aerosol generation during clear corneal phacoemulsification surgery in the era of Covid-19.
Methods: Aerosol generation during phacoemulsification was assessed using a model comprising a human cadaveric corneoscleral rim mounted on an artificial anterior chamber. Typical phacoemulsification settings were used and visible aerosol production was recorded using high speed 4K camera. Aerosolisation was evaluated under various experimental settings: Two different phacoemulsification tip sizes (2.2mm, 2.75mm), varying levels of corneal moisture, the use of suction and blowing air in the surgical field, the use of hydroxypropyl methylcellulose (HPMC) coating of the cornea with a static and moving tip.
Results: This model demonstrates visible aerosol generation during phacoemulsification with a 2.75mm phacoemulsification tip. No visible aerosol was noted with a 2.2mm tip. The presence of visible aerosol is unrelated to corneal wetting. Suction in close proximity to the aerosol plume did not impact on its dispersion. Blowing air redirected the aerosol plume towards the ocular surface. Visible aerosol production was abolished when HPMC was used to coat the cornea. This effect lasted for an average of 67±8 seconds in the static model. Visible aerosol generation was discerned during movement of the 2.2mm tip towards the corneal wound.
Conclusions: We demonstrate visible aerosol production in the setting of a model of a clear cornea phacoemulsification. Visible aerosol can be reduced using a 2.2mm phacoemulsification tip and reapplying HPMC every minute during phacoemulsification.
Similar masking effects of natural backgrounds on detection performances in humans, macaques, and macaque-V1 population responses
Authors: Bai Yoon , Chen Spencer , Chen Yuzhi , Geisler Wilson S. , Seidemann Eyal
Published: May 2020

Visual systems evolve to process the stimuli that arise in the organism’s natural environment and hence to fully understand the neural computations in the visual system it is important to measure behavioral and neural responses to natural visual stimuli. Here we measured psychometric and neurometric functions and thresholds in the macaque monkey for detection of a windowed sine-wave target in uniform backgrounds and in natural backgrounds of various contrasts. The neurometric functions and neurometric thresholds were obtained by near-optimal decoding of voltage-sensitive-dye-imaging (VSDI) responses at the retinotopic scale in primary visual cortex (V1). The results were compared with previous human psychophysical measurements made under the same conditions. We found that human and macaque behavioral thresholds followed the generalized Weber’s law as function of contrast, and that both the slopes and the intercepts of the threshold functions match each other up to a single scale factor. We also found that the neurometric thresholds followed the generalized Weber’s law and that the neurometric slopes and intercepts matched the behavioral slopes and intercepts up to a single scale factor. We conclude that human and macaque ability to detect targets in natural backgrounds are affected in the same way by background contrast, that these effects are consistent with population decoding at the retinotopic scale by down-stream circuits, and that the macaque monkey is an appropriate animal model for gaining an understanding of the neural mechanisms in humans for detecting targets in natural backgrounds. Finally, we discuss limitations of the current study and potential next steps.

New & Noteworthy

We measured macaque detection performance in natural images and compared their performance to the detection sensitivity of neurophysiological responses recorded in the primary visual cortex (V1), and to the performance of human subjects. We found that (i) human and macaque behavioral performances are in quantitative agreement, (ii) are consistent with near-optimal decoding of V1 population responses.

Significance

Natural selection guarantees that neural computations will be matched to the task-relevant natural stimuli in the organism’s environment, and thus it is crucial to measure behavioral and neural responses to natural stimuli. We measured the ability of macaque monkeys to detect targets in natural images and compared their performance to neurophysiological responses recorded in the macaque’s primary visual cortex (V1), and to the performance of humans under the same conditions. We found that (i) human and macaque behavioral performance are in quantitative agreement, (ii) are consistent with near-optimal population decoding of V1 neural responses, and (iii) that the macaque monkey is an appropriate animal model for gaining understanding of the neural mechanisms in humans for detecting targets in natural backgrounds.
SpacePHARER: Sensitive identification of phages from CRISPR spacers in prokaryotic hosts
Authors: Zhang R. , Mirdita M. , Karin E. Levy , Norroy C. , Galiez C. , Söding J.
Published: May 2020

SpacePHARER (CRISPR Spacer Phage-Host Pair Finder) is a sensitive and fast tool forde novoprediction of phage-host relationships via identifying phage genomes that match CRISPR spacers in genomic or metagenomic data. SpacePHARER gains sensitivity by comparing spacers and phages at the protein level, optimizing its scores for matching very short sequences, and combining evidence from multiple matches, while controlling for false positives. We demonstrate SpacePHARER by searching a comprehensive spacer list against all complete phage genomes.
Electromembrane extraction and mass spectrometry for liver organoid drug metabolism studies
Authors: Skottvoll Frøydis Sved , Hansen Frederik , Harrison Sean , Boger Ida Sneis , Mrsa Ago , Restan Magnus Saed , Stein Matthias , Lundanes Elsa , Pedersen-Bjergaard Stig , Aizenshtadt Aleksandra , Krauss Stefan , Sullivan Gareth , Bogen Inger Lise , Wilson Steven Ray
Published: May 2020

Liver organoids are emerging tools for precision drug development and toxicity screening. We demonstrate that electromembrane extraction (EME) based on electrophoresis across an oil membrane is suited for segregating selected organoid-derived drug metabolites prior to mass spectrometry (MS)-based measurements. EME, allowed drugs and drug metabolites to be separated from cell medium components (albumin, etc.) that could interfere with subsequent measurements. Multi-well EME (Parallel-EME) holding 100 μL solutions allowed for simple and repeatable monitoring of heroin phase I metabolism kinetics. Organoid Parallel-EME extracts were compatible with ultrahigh-performance liquid chromatography (UHPLC) used to separate the analytes prior to detection. Taken together, liver organoids are well-matched with EME followed by MS-based measurements.
Structure and function of stator units of the bacterial flagellar motor
Authors: Santiveri Mònica , Roa-Eguiara Aritz , Kühne Caroline , Wadhwa Navish , Berg Howard C. , Erhardt Marc , Taylor Nicholas M. I.
Published: May 2020

Many bacteria use the flagellum for locomotion and chemotaxis. Its bi-directional rotation is driven by the membrane-embedded motor, which uses energy from the transmembrane ion gradient to generate torque at the interface between stator units and rotor. The structural organization of the stator unit (MotAB), its conformational changes upon ion transport and how these changes power rotation of the flagellum, remain unknown. Here we present ~3 Å-resolution cryo-electron microscopy reconstructions of the stator unit in different functional states. We show that the stator unit consists of a dimer of MotB surrounded by a pentamer of MotA. Combining structural data with mutagenesis and functional studies, we identify key residues involved in torque generation and present a mechanistic model for motor function and switching of rotational direction.

One Sentence Summary

Structural basis of torque generation in the bidirectional bacterial flagellar motor
A vector system for fast-forwardin vivostudies of the ZAR1 resistosome in the model plantNicotiana benthamiana
Authors: Harant Adeline , Sakai Toshiyuki , Kamoun Sophien , Adachi Hiroaki
Published: May 2020

Nicotiana benthamianahas emerged as a complementary experimental system to Arabidopsis. It enables fast-forwardin vivoanalyses primarily through transient gene expression and is particularly popular in the study of plant immunity. Recently, our understanding of NLR plant immune receptors has greatly advanced following the discovery of Arabidopsis ZAR1 resistosome. Here, we describe a novel vector system of 52 plasmids that enables functional studies of the ZAR1 resistosome inN. benthamiana. We showed that ZAR1 stands out among the coiled coil class of NLRs for being highly conserved across distantly related dicot plant species and confirmed NbZAR1 as theN. benthamianaortholog of Arabidopsis ZAR1. NbZAR1 triggers autoimmune cell death inN. benthamianaand this activity is dependent on a functional N-terminal α1 helix. C-terminally tagged NbZAR1 remains functional inN. benthamianathus enabling cell biology and biochemical studies in this plant system. We conclude that the NbZAR1 open source plasmids form an additional experimental system to Arabidopsis forin plantaresistosome studies.
Alpha-, beta-, and gamma-diversity of bacteria varies across global habitats
Authors: Walters Kendra E. , Martiny Jennifer B.H.
Published: May 2020

Bacteria are essential parts of ecosystems and are the most abundant organisms on the planet. Yet, we still do not know which habitats support the highest diversity of bacteria across multiple scales. We analyzed alpha-, beta-, and gamma-diversity of bacterial assemblages using 11,680 samples compiled by the Earth Microbiome Project. We found that soils contained the highest bacterial richness within a single sample (alpha-diversity), but sediment assemblages were the most diverse at a global scale (gamma-diversity). Sediment, biofilms/mats, and inland water exhibited the most variation in community composition among geographic locations (beta-diversity). Within soils, agricultural lands, hot deserts, grasslands, and shrublands contained the highest richness, while forests, cold deserts, and tundra biomes consistently harbored fewer bacterial species. Surprisingly, agricultural soils encompassed similar levels of beta-diversity as other soil biomes. These patterns were robust to the alpha- and beta-diversity metrics used and the taxonomic binning approach. Overall, the results support the idea that spatial environmental heterogeneity is an important driver of bacterial diversity.
Supramammillary neurons projecting to the septum regulate dopamine and motivation for environmental interaction
Authors: Kesner Andrew J. , Shin Rick , Calva Coleman B. , Don Reuben F. , Junn Sue , Potter Christian T. , Ramsey Leslie A. , Abou-Elnaga Ahmed F. , Cover Christopher G. , Wang Dong V. , Lu Hanbing , Yang Yihong , Ikemoto Satoshi
Published: May 2020

The supramammillary region (SuM) is a posterior hypothalamic structure, known to regulate hippocampal theta oscillations and arousal. However, recent studies reported that the stimulation of SuM neurons with neuroactive chemicals, including substances of abuse, is reinforcing. We conducted experiments to illuminate how SuM neurons mediate such effects. The excitation of SuM glutamatergic (GLU) neurons was reinforcing in mice; this effect was relayed by the projections to septal GLU neurons. SuM neurons were active during exploration and approach behavior and diminished activity during sucrose consumption. Consistently, inhibition of SuM neurons disrupted approach responses, but not sucrose consumption. Such functions are similar to those of mesolimbic dopamine neurons. Indeed, the stimulation of SuM-to-septum GLU neurons and septum-to-ventral tegmental area (VTA) GLU neurons activated mesolimbic dopamine neurons. We propose that the supramammillo-septo-VTA pathway is important in reinforcement and approach motivation and may play an important role in mood and substance-use disorders.
Cooperation increases robustness to ecological disturbance in microbial cross-feeding networks
Authors: Oña Leonardo , Kost Christian
Published: May 2020

Microorganisms mainly exist within complex networks of ecological interactions. Given that the growth and survival of community members frequently depend on an obligate exchange of essential metabolites, it is generally unclear how such communities can persist despite the destabilizing force of ecological disturbance. Here we address this issue using a population dynamics model. In contrast to previous work that suggests the potential for obligate interaction networks to evolve is limited, we find the opposite pattern: natural selection in the form of ecological disturbance favors both specific network topologies and cooperative cross-feeding among community members. These results establish environmental selection as a key driver shaping the architecture of microbial interaction networks.
Proteasome-mediated regulation of Cdhr1a by Siah1 modulates photoreceptor development and survival in zebrafish
Authors: Piedade Warlen P. , Titialii-Torres Kayla , Morris Ann , Famulski Jakub
Published: May 2020

Congenital retinal dystrophies are a major cause of unpreventable and incurable blindness worldwide. Mutations in CDHR1, a retina specific cadherin, are associated with cone-rod dystrophy. The ubiquitin proteasome system (UPS) is responsible for mediating orderly and precise targeting of protein degradation to maintain biological homeostasis and coordinate proper development, including retinal development. Recently, our lab uncovered that the seven in absentia (Siah) family of E3 ubiquitin ligases play a role in optic fissure fusion, and identified Cdhr1a as a potential target of Siah. Using two-color whole mountin situhybridization and immunohistochemistry, we detectedsiah1andcdhr1aco-expression as well as protein co-localization in the retinal outer nuclear layer (ONL), and more precisely in the connecting cilium of rods and cones between 3-5 days post fertilization (dpf). We confirmed that Siah1 targets Cdhr1a for proteasomal degradation by co-transfection and co-immunoprecipitation in cell culture. To analyze the functional importance of this interaction, we created two transgenic zebrafish lines that expresssiah1or an inactivesiah1(siah1ΔRING) under the control of the heat shock promoter to modulate Siah activity during photoreceptor development. Overexpression ofsiah1, but notsiah1ΔRING, resulted in a decrease in the number of rods and cones at 72 hours post fertilization (hpf). The number of retinal ganglion cells, amacrine and bipolar was not affected by Siah1 overexpression, and there was no significant reduction of proliferating cells in the Siah1 overexpressing retina. We did however detect increased cell death, confirmed by an increase in the number of TUNEL+ cells in the ONL, which was proteasome-dependent, as MG132 treatment rescued the cell death phenotype. Lastly, reduction in rods and cones resulting from increased Siah1 expression was rescued by injection ofcdhr1mRNA, and to an even greater extent by injection of a Siah1-insensitivecdhr1avariant mRNA. Taken together, our work provides the first evidence that Cdhr1a plays a role during early photoreceptor development and that Cdhr1a is regulated by Siah1 via the UPS. This work provides new avenues for investigation into the roles of CDHR1, and now also Siah1, in the predisposition and pathogenesis of inherited cone-rod dystrophy.
The impact of genetic background and gender on the increase in mitotic index in response to mating ofDrosophila melanogaster
Authors: Malpe Manashree , Schulz Cordula
Published: May 2020

The replenishment of specialized cells depends on the activity of stem cells. Recent advances in stem cell research have shown that the germline stem cells (GSCs) inDrosophila melanogastercan increase their mitotic activity in response to mating. Here, we show that this ability to respond to mating is eliminated if the males are mutant for the ABC transporter, White, the genetic background for a plethora of fly lines. Furthermore, we were not able to reproduce previous findings that female flies increase their GSC numbers and mitotic activity upon mating. Our findings underline the importance of careful experimental design and control specimen.
SARS-CoV2 (COVID-19) Structural/Evolution Dynamicome: Insights into functional evolution and human genomics
Authors: Gupta Ruchir , Charron Jacob , Stenger Cynthia L , Painter Jared , Steward Hunter , Cook Taylor W , Faber William , Frisch Austin , Lind Eric , Bauss Jacob , Li Xiaopeng , Sirpilla Olivia , Soehnlen Xavier , Underwood Adam , Hinds David , Morris Michele , Lamb Neil , Carcillo Joseph A , Bupp Caleb , Uhal Bruce D , Rajasekaran Surender , Prokop Jeremy W
Published: May 2020

The SARS-CoV-2 pandemic, starting in 2019, has challenged the speed at which labs perform science, ranging from discoveries of the viral composition to handling health outcomes in humans. The small ~30kb single-stranded RNA genome of Coronaviruses makes them adept at cross species spread and drift, increasing their probability to cause pandemics. However, this small genome also allows for a robust understanding of all proteins coded by the virus. We employed protein modeling, molecular dynamic simulations, evolutionary mapping, and 3D printing to gain a full proteome and dynamicome understanding of SARS-CoV-2. The Viral Integrated Structural Evolution Dynamic Database (VIStEDD) has been established (prokoplab.com/vistedd), opening future discoveries and educational usage. In this paper, we highlight VIStEDD usage for nsp6, Nucleocapsid (N), and Spike (S) surface glycoprotein. For both nsp6 and N we reveal highly conserved surface amino acids that likely drive protein-protein interactions. In characterizing viral S protein, we have developed a quantitative dynamics cross correlation matrix insight into interaction with the ACE2/SLC6A19 dimer complex. From this quantitative matrix, we elucidated 47 potential functional missense variants from population genomic databases within ACE2/SLC6A19/TMPRSS2, warranting genomic enrichment analyses in SARS-CoV-2 patients. Moreover, these variants have ultralow frequency, but can exist as hemizygous in males for ACE2, which falls on the X-chromosome. Two noncoding variants (rs4646118 and rs143185769) found in ~9% of African descent individuals for ACE2 may regulate expression and be related to increased susceptibility of African Americans to SARS-CoV-2. This powerful database of SARS-CoV-2 can aid in research progress in the ongoing pandemic.
Robust computational design and evaluation of peptide vaccines for cellular immunity with application to SARS-CoV-2
Authors: Liu Ge , Carter Brandon , Bricken Trenton , Jain Siddhartha , Viard Mathias , Carrington Mary , Gifford David K.
Published: May 2020

We present a combinatorial machine learning method to evaluate and optimize peptide vaccine formulations, and we find for SARS-CoV-2 that it provides superior predicted display of viral epitopes by MHC class I and MHC class II molecules over populations when compared to other candidate vaccines. Our method is robust to idiosyncratic errors in the prediction of MHC peptide display and considers target population HLA haplotype frequencies during optimization. To minimize clinical development time our methods validate vaccines with multiple peptide presentation algorithms to increase the probability that a vaccine will be effective. We optimize an objective function that is based on the presentation likelihood of a diverse set of vaccine peptides conditioned on a target population HLA haplotype distribution and expected epitope drift. We produce separate peptide formulations for MHC class I loci (HLA-A, HLA-B, and HLA-C) and class II loci (HLA-DP, HLA-DQ, and HLA-DR) to permit signal sequence based cell compartment targeting using nucleic acid based vaccine platforms. Our SARS-CoV-2 MHC class I vaccine formulations provide 93.21% predicted population coverage with at least five vaccine peptide-HLA hits on average in an individual (≥ 1 peptide 99.91%) with all vaccine peptides perfectly conserved across 4,690 geographically sampled SARS-CoV-2 genomes. Our MHC class II vaccine formulations provide 90.17% predicted coverage with at least five vaccine peptide-HLA hits on average in an individual with all peptides having observed mutation probability ≤ 0.001. We evaluate 29 previously published peptide vaccine designs with our evaluation tool with the requirement of having at least five vaccine peptide-HLA hits per individual, and they have a predicted maximum of 58.51% MHC class I coverage and 71.65% MHC class II coverage given haplotype based analysis. We provide an open source implementation of our design methods (OptiVax), vaccine evaluation tool (EvalVax), as well as the data used in our design efforts.
SARS-CoV-2 amino acid substitutions widely spread in the human population are mainly located in highly conserved segments of the structural proteins
Authors: Cortey Martí , Li Yanli , Díaz Ivan , Clilverd Hepzibar , Darwich Laila , Mateu Enric
Published: May 2020

TheSevere acute respiratory syndrome coronavirus 2(SARS-CoV-2) pandemic offers a unique opportunity to study the introduction and evolution of a pathogen into a completely naïve human population. We identified and analysed the amino acid mutations that gained prominence worldwide in the early months of the pandemic. Eight mutations have been identified along the viral genome, mostly located in conserved segments of the structural proteins and showing low variability among coronavirus, which indicated that they might have a functional impact. At the moment of writing this paper, these mutations present a varied success in the SARS-CoV-2 virus population; ranging from a change in the spike protein that becomes absolutely prevalent, two mutations in the nucleocapsid protein showing frequencies around 25%, to a mutation in the matrix protein that nearly fades out after reaching a frequency of 20%.
Prophage exotoxins enhance colonization fitness in epidemic scarlet fever-causingStreptococcus pyogenes
Authors: Brouwer Stephan , Barnett Timothy C. , Ly Diane , Kasper Katherine J. , De Oliveira David M.P. , Rivera-Hernandez Tania , Cork Amanda J. , McIntyre Liam , Jespersen Magnus G. , Richter Johanna , Schulz Benjamin L. , Dougan Gordon , Nizet Victor , Yuen Kwok-Yung , You Yuanhai , McCormick John K. , Sanderson-Smith Martina L. , Davies Mark R. , Walker Mark J.
Published: May 2020

The re-emergence of scarlet fever poses a new global public health threat. The capacity of North-East Asian serotype M12 (emm12)Streptococcus pyogenes(group AStreptococcus, GAS) to cause scarlet fever has been linked epidemiologically to the presence of novel prophages, including prophage ΦHKU.vir encoding the secreted superantigens SSA and SpeC and the DNase Spd1. Here we report the comprehensive molecular characterization of ΦHKU.vir-encoded exotoxins. We demonstrate that streptolysin O (SLO)-induced glutathione efflux from host cellular stores is a previously unappreciated GAS virulence mechanism that promotes SSA release and activity, representing the first description of a thiol-activated bacterial superantigen. Spd1 is required for optimal growth in human blood, confers resistance to neutrophil killing, and degrades neutrophil extracellular traps (NETs). Investigating single, double and triple isogenic knockout mutants of the ΦHKU.vir-encoded exotoxins, we find that SpeC and Spd1 act synergistically to facilitate nasopharyngeal colonization in a mouse model. These results offer insight into the etiology and pathogenesis of scarlet fever-causing GAS mediated by phage ΦHKU.vir exotoxins.
Contesting digital finance for the poor
Authors: Ozili Peterson K.
Published: May 2020

Purpose

This paper aims to critically assess digital finance as a pro-poor intervention in the development finance space.

Design/methodology/approach

Using critical policy discourse analysis, this paper explains the turn from microfinance to digital finance, and thereafter discusses four issues: the lack of evidence that digital finance for poor people actually promotes socioeconomic development; the risks that poor people are exposed to, which arises from their exposure to digital finance technology; the lack of evidence that digital finance actually brings poor people immediate benefits; and the weak business rationale for digital finance.

Findings

The expectation for digital finance serving as a major pro-poor private sector intervention lacks justification.

Originality/value

The paper reflects on the effect of digital finance for poor people.
Investigation of magnetohydrodynamics in Ag-TiO2/water hybrid nanofluid in a Shamse knot shaped cavity
Authors: Ma Yuan , Rashidi Mohammad Mehdi , Mohebbi Rasul , Yang Zhigang
Published: May 2020

Purpose

The nanofluid natural convection heat transfer in a hollow complex enclosure, which is named as Shamse knot shape, is studied numerically. This paper aims to present how the Rayleigh number, nanoparticle volume fraction, Hartmann number and hollow side length affect the fluid flow and heat transfer characteristics.

Design/methodology/approach

The continuity, momentum and energy equations have been solved using lattice Boltzmann method (LBM). Numerical simulation has been obtained for a wide range of Rayleigh number (103 ≤ Ra ≤ 106), nanoparticle volume fraction (0 ≤ ϕ 0.05) and Hartmann number (0 ≤ Ha ≤ 60) to analyze the fluid flow pattern and heat transfer characteristics. Moreover, the effect of hollow side length (D) on flow field and thermal performance is studied.

Findings

The results showed that the magnetic field has a negative effect on the thermal performance and the average Nusselt number decreases by increasing the Hartmann number. Because of the high conduction heat transfer coefficient of nanoparticles, the average Nusselt number increases by rising the nanoparticle volume fraction. The effect of adding nanoparticles on heat transfer is more effective at low nanoparticle volume fraction (0 ≤ ϕ ≤ 0.01). It was also found that at Ra = 106, when the hollow side length increases to 3, the flow pattern becomes different due to the small gap. The averaged Nu is an increasing function of D at low Ra and an opposite trend occurs at high Rayleigh number.

Originality/value

For the first time, the effects of magnetic field, Rayleigh number, nanoparticle volume fraction and hollow side length on natural convection heat transfer of hybrid nanofluid (Ag-TiO2/water) is investigated in a complicated cavity.
Effect of supply chain strategic collaboration announcements on shareholder value: an empirical investigation from China
Authors: Liu Weihua , Wei Wanying , Si Cheng , Xie Dong , Chen Lujie
Published: May 2020

Purpose

This study empirically examines the impact of announcements on supply chain strategic collaboration (SCSC) on companies' shareholder value.

Design/methodology/approach

This study analyzes changes in shareholder value of companies listed in China based on data of 208 SCSC announcements. The signaling theory is applied to determine correlation among SCSC announcements and the market. An event study is used to estimate the stock market reaction to SCSC announcements. The common market model estimates stock abnormal returns after the event. The least squares method and regression model calculate the model parameter value.

Findings

There is a positive and statistically significant relationship between SCSC announcement and shareholder value. Market reaction to product development collaboration is significantly higher than to technology-sharing collaboration, market collaboration, and other SCSC types. The market reacts more positively to suppliers and companies with greater supply chain control power than to buyers and companies with lower control power. Announcements from the service supply chain can lead to stronger market reactions than those from manufacturing supply chains.

Practical implications

The findings provide a systematic assessment of how SCSC announcements contribute to firms' shareholder value. The result provides a benchmark of value promotion that can be expected from SCSC announcements.

Originality/value

This study fills the research gap that using secondary data to assess changes in companies’ shareholder value caused by SCSC announcements and firstly examines these changes by constructing the signaler–signal–receiver progress based on signaling theory. The research results provide a new reference and inspiration for deeper understanding of the impact mechanism of SCSC. Furthermore, this study contributes to the development of the signaling theory using an empirical study in an emerging market, China.
Investigating the environmental behavior of business and accounting university students
Authors: Kyriakopoulos Grigorios , Ntanos Stamatios , Asonitou Sofia
Published: May 2020

Purpose

The purpose of this study is to explore the underlying dimensions of environmental behavior (EB) and examine how environmental education (EE) and ecological sensitivity (ES) motivate the EB of Business Administration and Accounting students (BAS).

Design/methodology/approach

A questionnaire survey was conducted and a sample of 190 BAS was randomly selected from the departments of Business Administration and Accounting and Finance at the University of West Attica (UNIWA), Greece.

Findings

The analysis was structured upon four underlying components under the EB of the sample: information seeking, recycling, green consuming and active participation. A positive relationship between EB and EE was revealed, while EB and ES were moderately interrelated. An important result was the hesitation of students to convert EE and ES to active participation and green consuming behavior, thus reaffirming similar results from other studies.

Research limitations/implications

The findings should be further developed using larger samples among other higher education institutions. Future research could be extended to students who reside at sub-urban or rural regions or students who are educated upon diverse academic disciplines. The basket of questions can be enriched with issues of immediate concern among future business executives such as the “ethical” role of accountants or the value creation for local societies.

Originality/value

The significance of this study lies on associating students’ EB with formal EE with personality characteristics such as ES. Educational policy-makers can enrich the curricula of BAS with environmentally oriented courses and teaching methods that can increase the active participation of students.
Workaholism and organizational citizenship behaviors: exploring gender role beliefs
Authors: Aziz Shahnaz , Pittman Christina , Wuensch Karl
Published: May 2020

Purpose

The purpose of the current study was to examine the relationships among workaholism, organizational citizenship behaviors (OCBs) and gender role beliefs.

Design/methodology/approach

Data were collected, through administration of an online survey, from 409 faculty and staff at a large Southeastern university.

Findings

Workaholism and OCBs were negatively related. Additionally, both feminine and masculine role beliefs were associated with OCBs.

Research limitations/implications

Future researchers may benefit from examining a sample outside an educational institution.

Social implications

As our society continues to change, gender role beliefs will become less restricted to our biological genders and it will become essential for organizations to understand how they relate to work behavior (e.g. OCBs). Namely, androgyny may be a desirable trait for employees.

Originality/value

This is the first study to investigate the relationships among workaholism, OCBs and gender role beliefs.
“Real-world:” preservice teachers' research competence and research difficulties in action research
Authors: Toquero Cathy Mae Dabi
Published: May 2020

Purpose

The purpose of this study is to provide an analysis of the teacher education program focused on the development of the research competence of the preservice teachers, difficulties they encountered in conducting action research and the need to provide them with realistic research opportunities.

Design/methodology/approach

This qualitative study made use of data sources taken from observations, feedback sessions, presentations and follow-up written interview of 133 randomly selected preservice teachers.

Findings

Findings reported that the multicultural preservice teachers have novice research skills and that the real-world application of their research skills developed their research competence. However, they encountered difficulties creating their action research, such as in the literature review and the research conceptualization.

Research limitations/implications

Aside from the self-reported experiences of the students, the training on the action research mainly focused on the conceptualization, design formulation of interventions and proposal writing stage but were not implemented due to course constraints.

Practical implications

This study can assist policymakers to integrate a mandatory research course as part of the curricular offerings and for the university to create space for students to practice their research skills based on real-life problems in the basic level institutions.

Social implications

Understanding the challenges, difficulties, and basic competence in the research development of the preservice teachers would strengthen the research practice of the future teachers for evidence-based teaching in the schools.

Originality/value

The limited literature focus on the development of research competence on teacher education students using action research, including the difficulties that university students experience in doing research based on a societal context.