bluuebunny/crossref_metadata_2025 huggingface dataset:
Synaptic Zn2+potentiates the effects of cocaine on striatal dopamine neurotransmission and behavior
Authors: Gomez Juan L. , Bonaventura Jordi , Keighron Jacqueline , Wright Kelsey M. , Marable Dondre L. , Rodriguez Lionel A. , Lam Sherry , Carlton Meghan L. , Ellis Randall J. , Jordan Chloe , Bi Guo-hua , Solis Oscar , Pignatelli Marco , Bannon Michael J. , Xi Zheng-Xiong , Tanda Gianluigi , Michaelides Michael
Published: September 2020

Cocaine binds to the dopamine (DA) transporter (DAT) to regulate cocaine reward and seeking behavior. Zinc (Zn2+) also binds to the DAT, but thein vivorelevance of this interaction is unknown. We found that Zn2+concentrations in postmortem brain (caudate) tissue from humans who died of cocaine overdose were significantly lower than in control subjects. Moreover, the level of striatal Zn2+content in these subjects negatively correlated with plasma levels of benzoylecgonine, a cocaine metabolite indicative of recent use. In mice, repeated cocaine exposure increased synaptic Zn2+concentrations in the caudate putamen (CPu) and nucleus accumbens (NAc). Cocaine-induced increases in Zn2+were dependent on the Zn2+transporter 3 (ZnT3), a neuronal Zn2+transporter localized to synaptic vesicle membranes, as ZnT3 knockout (KO) mice were insensitive to cocaine-induced increases in striatal Zn2+. ZnT3 KO mice showed significantly lower electrically-evoked DA release and greater DA clearance when exposed to cocaine compared to controls. ZnT3 KO mice also displayed significant reductions in cocaine locomotor sensitization, conditioned place preference (CPP), self-administration, and reinstatement compared to control mice and were insensitive to cocaine-induced increases in striatal DAT binding. Finally, dietary Zn2+deficiency in mice resulted in decreased striatal Zn2+content, cocaine locomotor sensitization, CPP, and striatal DAT binding. These results indicate that cocaine increases synaptic Zn2+release and turnover/metabolism in the striatum, and that synaptically-released Zn2+potentiates the effects of cocaine on striatal DA neurotransmission and behavior and is required for cocaine-primed reinstatement. In sum, these findings reveal new insights into cocaine’s pharmacological mechanism of action and suggest that Zn2+may serve as an environmentally-derived regulator of DA neurotransmission, cocaine pharmacodynamics, and vulnerability to cocaine use disorders.
Morphological plasticity inChlamydomonas reinhardtiiand acclimation to micropollutant stress
Authors: Cheloni Giulia , Slaveykova Vera I.
Published: September 2020

Phytoplankton are characterized by a great phenotypic plasticity and amazing morphological variability, both playing a primary role in the acclimation to changing environments. However, there is a knowledge gap concerning the role of algal morphological plasticity in stress responses and acclimation to micropollutants. The present study aims examining the palmelloid colony formation of the green alga Chlamydomonas reinhardtii upon micropollutants exposure.

Cells were exposed to four micropollutants (MPs) with different modes of action (copper, cadmium, PFOS and paraquat) for a duration of 72h. Effects of MPs on palmelloid formation, growth and physiological traits (chlorophyll fluorescence, membrane integrity and oxidative stress) were monitored via flow cytometry and fluorescence microscopy. Palmelloid formation was observed upon treatment with the four micropollutants. Number of palmelloid colonies and their size were dependent on MP concentration and exposure duration. Cells reverted to their unicellular lifestyle when colonies were harvested and inoculated in fresh medium indicating that palmelloid formation is a plastic response to micropollutants. No physiological effects of these compounds were observed in cells forming palmelloids and palmelloid colonies accumulated lower Cd concentration than unicellularC. reinhardtiisuggesting that colony formation protects the cells form MPs exposure. The results show that colony formation inChlamydomonas reinhardtiiis a stress response strategy activated to face sub-lethal micropollutant concentrations.

HIGHLIGHTS

Sub-lethal concentrations of micropollutants (MPs) induce palmelloid formation inC. reinhardtii

Morphological changes are not associated to adverse effects on algal cells

Palmelloid formation is transitory, cells revert to unicellular lifestyle in the absence of MPs

Cells within large colonies experience lower Cd exposure than unicellularC. reinhardtii

Palmelloid formation is a morphological stress response that plays a role in cells acclimation to MPs
Programming cell growth into different cluster shapes using diffusible signals
Authors: Guo Yipei , Nitzan Mor , Brenner Michael P.
Published: September 2020

Recent advances in genetic engineering technologies has made it possible to construct artificial genetic circuits and use them to control how cells respond to their surroundings. This has been used to generate spatial patterns of differential gene expression. In addition to the spatial arrangement of different cell types, another important aspect of spatial structure lies in the overall shape of the group of cells. However, the question of how cells can be programmed, and how complex the rules need to be, to achieve a desired tissue morphology has received less attention. In this paper, we attempt to address these questions by developing a mathematical model to study how cells can use diffusion-mediated local rules to grow into clusters with different shapes. Within our model, cells are allowed to secrete diffusible chemicals which can either directly regulate the growth rate of cells (‘growth regulator’), or indirectly affect growth by changing the secretion rate or the effect of other growth regulators. We find that (1) a single growth inhibitor can be used to grow a rod-like structure, (2) multiple growth regulators are required to grow multiple protrusions, and (3) the length and shape of each protrusion can be controlled using growth-threshold regulators. Based on these regulatory schemes, we also postulate how the range of achievable structures scales with the number of signals: (A) the maximum possible number of protrusions increases exponentially with the number of growth inhibitors involved, and (B) to control the growth of each set of protrusions, it is necessary to have an independent threshold regulator. Together, these experimentally-testable findings illustrate how our approach can be used to guide the design of regulatory circuits for achieving a desired target structure.
DiffGR: Detecting Differentially Interacting Genomic Regions from Hi-C Contact Maps
Authors: Liu Huiling , Ma Wenxiu
Published: September 2020

Recent advances in Hi-C techniques have allowed us to map genome-wide chromatin interactions and uncover higher-order chromatin structures, thereby shedding light on the principles of genome architecture and functions. However, statistical methods for detecting changes in large-scale chromatin organization such as topologically-associating domains (TADs) are still lacking. We proposed a new statistical method, DiffGR, for detecting differentially interacting genomic regions at the TAD level between Hi-C contact maps. We utilized the stratum-adjusted correlation coefficient to measure similarity of local TAD regions. We then developed a non-parametric approach to identify statistically significant changes of genomic interacting regions. Through simulation studies, we demonstrated that DiffGR can robustly and effectively discover differential genomic regions under various conditions. Furthermore, we successfully revealed cell type-specific changes in genomic interacting regions in both human and mouse Hi-C datasets, and illustrated that DiffGR yielded consistent and advantageous results compared with state-of-the-art differential TAD detection methods. The DiffGR R code is published under the GNU GPL ≥ 2 license and is publicly available athttps://github.com/wmalab/DiffGR.
N-glucosyltransferase GbNGT1 fromGinkgocomplement auxin metabolic pathway
Authors: Yin Qinggang , Zhang Jing , Wang Shuhui , Cheng Jintang , Gao Han , Guo Cong , Ma Lianbao , Sun Limin , Chen Shilin , Liu An
Published: September 2020

As a group of the most important phytohormone, auxin homeostasis is regulated in a complex manner. Generally, auxin conjugations especially IAA glucosides are dominant on high auxin level conditions. Former terminal glucosylation researches mainly focus onO-position, while IAA-N-glucoside or IAA-Asp-N-glucoside has been neglected since their found in 2001. In our study, IAA-Asp-N-glucoside was firstly found specifically abundant (as high as 4.13 mg/g) in ginkgo seeds of 58 cultivars from Ginkgo Resource Nursery built in 1990. Furthermore, a novelN-glucosyltransferase GbNGT1, which could catalyze IAA-Asp and IAA to form their correspondingN-glucoside, was identified through differential transcriptome analysis andin vitroenzymatic test. The enzyme was demonstrated to possess specific catalyze capacity toward theN-position of IAA-amino acid or IAA among 52 substrates, and was typical of acid tolerance, metal ion independence and high temperature sensitivity. Docking and site-directed mutagenesis of this enzyme confirmed that E15G mutant could almost abolish enzyme catalytic activity towards IAA-Asp and IAAin vitroandin vivo. The IAA modification of GbNGT1 and GbGH3.5 was verified by transient expression assay inNicotiana benthamiana. In conclusion, our results complement the terminal metabolic pathway of auxin, and the specific catalytic function of GbNGT1 towards IAA-amino acid provide a new way to biosynthesis indole-amide compounds.

Highlight

The N-glucosylation of IAA or IAA-amino acids in auxin metabolism had been neglected over decades, our work for GbNGT1 redeems the missing chain of auxin metabolic pathway.
Advanced eMAGE for highly efficient combinatorial editing of a stable genome
Authors: Liang Zhuobin , Metzner Eli , Isaacs Farren J.
Published: September 2020

Eukaryotic multiplex genome engineering (eMAGE) offers a powerful tool to generate precise combinatorial genome modifications inSaccharomyces cerevisiae. We optimize the design of synthetic oligonucleotides and enrichment of edited populations to increase editing frequencies up to 90%, reduce workflow time by 40%, and engineer a tunable mismatch repair system to lower the rate of spontaneous mutations ∼17-fold. These advances transiently evade genome maintenance to introduce multiple edits at high efficiencies in a stable genetic background, expanding utility of eMAGE in eukaryotic cells.
Multi-regional module-based signal transmission in mouse visual cortex
Authors: Jia Xiaoxuan , Siegle Joshua H. , Durand Séverine , Heller Greggory , Ramirez Tamina , Koch Christof , Olsen Shawn R.
Published: September 2020

The visual cortex is organized hierarchically, but the presence of extensive recurrent and parallel pathways make it challenging to decipher how signals flow between neuronal populations. Here, we tracked the flow of spiking activity recorded from six interconnected levels of the mouse visual hierarchy. By analyzing leading and lagging spike-timing relationships among pairs of simultaneously recorded neurons, we created a cellular-scale directed network graph. Using a module-detection algorithm to cluster neurons based on shared connectivity patterns, we uncovered two multi-regional communication modules distributed across the hierarchy. The direction of signal flow between and within these modules, differences in layer and area distributions, and distinct temporal dynamics suggest that one module is positioned to transmit feedforward sensory signals, whereas the other integrates inputs for recurrent processing. These results suggest that multi-regional functional modules may be a fundamental feature of organization beyond cortical areas that supports signal propagation across hierarchical recurrent networks.
Low cost conservation: Fishing gear threats to marine species
Authors: Cashion Tim , Tai Travis C. , Lam Vicky W.Y. , Pauly Daniel , Sumaila U. Rashid
Published: September 2020

Understanding conflicts between objectives of fisheries and conservation is the key to finding win-win situations for marine biodiversity and fishers. Many marine species are threatened by harmful interactions with fisheries, but the threats they face are associated with the fishing gear used. Here, we undertake a novel analysis of marine species and their gear-specific threats to evaluate conservation-fisheries trade-offs to identify areas with high competing goals. Our analysis suggests that gillnet and longline fisheries pose the greatest risk to marine species yet deliver relatively low profits, emphasizing the inefficiencies of these gears. We find that the majority of the high seas has low economic fisheries benefits with over 25% of the high seas categorized as areas of ‘conservation prioritisation’ over fisheries.
Ebselen derivatives are very potent dual inhibitors of SARS-CoV-2 proteases - PLproand Mproin in vitro studies
Authors: Zmudzinski Mikolaj , Rut Wioletta , Olech Kamila , Granda Jarosław , Giurg Mirosław , Burda-Grabowska Małgorzata , Zhang Linlin , Sun Xinyuanyuan , Lv Zongyang , Nayak Digant , Kesik-Brodacka Malgorzata , Olsen Shaun K. , Hilgenfeld Rolf , Drag Marcin
Published: September 2020

Proteases encoded by SARS-CoV-2 constitute a promising target for new therapies against COVID-19. SARS-CoV-2 main protease (Mpro, 3CLpro) and papain-like protease (PLpro) are responsible for viral polyprotein cleavage - a process crucial for viral survival and replication. Recently it was shown that 2-phenylbenzisoselenazol-3(2H)-one (ebselen), an organoselenium anti-inflammatory small-molecule drug, is a potent, covalent inhibitor of both the proteases and its potency was evaluated in enzymatic and anti-viral assays. In this study, we screened a collection of 23 ebselen derivatives for SARS-CoV-2 PLproand Mproinhibitors. Our studies revealed that ebselen derivatives are potent inhibitors of both the proteases. We identified three PLproand four Mproinhibitors superior to ebselen. Our work shows that ebselen constitutes a promising platform for development of new antiviral agents targeting both SARS-CoV-2 PLproand Mpro.
Two distinct phases of chloroplast biogenesis during de-etiolation in Arabidopsis thaliana
Authors: Pipitone Rosa , Eicke Simona , Pfister Barbara , Glauser Gaetan , Falconet Denis , Uwizeye Clarisse , Pralon Thibaut , Zeeman Samuel , Kessler Felix , Demarsy Emilie
Published: September 2020

Light triggers chloroplast differentiation whereby the etioplast transforms into a photosynthesizing chloroplast and the thylakoid rapidly emerges. However, the sequence of events during chloroplast differentiation remains poorly understood. Using Serial Block Face Scanning Electron Microscopy (SBF-SEM), we generated a series of chloroplast 3D reconstructions during differentiation, revealing chloroplast number and volume and the extent of envelope and thylakoid membrane surfaces. Furthermore, we used quantitative lipid and whole proteome data to complement the (ultra)structural data, providing a time-resolved, multi-dimensional description of chloroplast differentiation. This showed two distinct phases of chloroplast biogenesis: an initial photosynthesis-enabling ‘Structure Establishment Phase’ followed by a ‘Chloroplast Proliferation Phase’ during cell expansion. Moreover, these data detail thylakoid membrane expansion during de-etiolation at the seedling level and the relative contribution and differential regulation of proteins and lipids at each developmental stage. Altogether, we establish a roadmap for chloroplast differentiation, a critical process for plant photoautotrophic growth and survival.
DIAFree enables untargeted open-search identification for Data-Independent Acquisition data
Authors: Xu Iris
Published: September 2020

As a reliable and high-throughput proteomics strategy, data-independent acquisition (DIA) has shown great potential for protein analysis. However, DIA also imposes stress on the data processing algorithm by generating complex multiplexed spectra. Traditionally, DIA data is processed using spectral libraries refined from experiment histories, which requires stable experiment conditions and additional runs. Furthermore, scientists still need to use library-free tools to generate spectral libraries from additional runs. To lessen those burdens, here we present DIAFree(https://github.com/xuesu/DIAFree), a library-free, tag-index-based software suite that enables both restrict search and open search on DIA data using the information of MS1 scans in a precursor-centric and spectrum-centric style. We validate the quality of detection by publicly available data. We further evaluate the quality of spectral libraries produced by DIAFree.
On-rate modulation of cadherin interactions by chemical fragments
Authors: Senoo Akinobu , Ito Sho , Nagatoishi Satoru , Saito Yutaro , Ueno Go , Yoshida Kouhei , Tashima Takumi , Kudo Shota , Sando Shinsuke , Tsumoto Kouhei
Published: September 2020

Many cadherin family proteins are associated with diseases such as cancer. Since cell adhesion requires homodimerization of cadherin molecules, a small-molecule regulator of dimerization would have therapeutic potential. Herein, we describe identification of a P-cadherin-specific chemical fragment that inhibits P-cadherin-mediated cell adhesion. Although the identified molecule is a fragment compound, it binds to a cavity of P-cadherin that has not previously been targeted, indirectly prevents formation of hydrogen bonds necessary for formation of an intermediate called the X dimer and thus modulates the on-rate of X dimerization. Our findings will impact on a strategy for kinetic regulation of protein-protein interactions and stepwise assembly of protein complexes using small molecules.
Effect of time delay on the synchronization of excitatory-inhibitory neural networks
Authors: Ryu Hwayeon , Campbell Sue Ann
Published: September 2020

We study a model for a network of synaptically coupled, excitable neurons to identify the role of coupling delays in generating different network behaviors. The network consists of two distinct populations, each of which contains one excitatory-inhibitory neuron pair. The two pairs are coupled via delayed synaptic coupling between the excitatory neurons, while each inhibitory neuron is connected only to the corresponding excitatory neuron in the same population. We show that multiple equilibria can exist depending on the strength of the excitatory coupling between the populations. We conduct linear stability analysis of the equilibria and derive necessary conditions for delay-induced Hopf bifurcation. We show that these can induce two qualitatively different phase-locked behaviors, with the type of behavior determined by the sizes of the coupling delays. Numerical bifurcation analysis and simulations supplement and confirm our analytical results. Our work shows that the resting equilibrium point is unaffected by the coupling, thus the network exhibits bistability between a rest state and an oscillatory state. This may help understand how rhythms spontaneously arise neuronal networks.
Ecological specialization promotes diversity and diversification in the East Mediterranean genusRicotia(Brassicaceae)
Authors: Özüdoğru Barış , Karacaoğlu Çağaşan , Akaydın Galip , Erik Sadık , Mummenhoff Klaus , Sağlam İsmail Kudret
Published: September 2020

Despite its amazing biodiversity, the Eastern Mediterranean remains a highly understudied region especially when compared to the Western Mediterranean. Scarcity of such studies restrict our understanding of the processes shaping diversity across the entire Mediterranean. To this end we used a combination of molecular markers and presence/absence data from all species of the Eastern Mediterrranean genusRicotiacollected across its full geographic range to determine historical, ecological and evolutionary factors responsible for lineage-specific diversification in this genus. Network analysis based on nuclear ribosomal and chloroplast DNA revealed high genetic structure within all lineages and phylogenetic reconstructions based on the multispecies coalescent showed that within lineage diversification corresponded to the onset of the Mediterranean climate. Reconstruction of ancestral histories indicate the genus originated within Anatolia and slowly spread across the Eastern Mediterranean and Levant using the Taurus mountains. Ecological niche models based on climatic and environmental variables suggest local populations did not go through any major distributional shifts and have persisted in present day habitats since the LGM. Furthermore, niche differentiation tests revealed significant niche differences between closely related species and showed the main variables predicting species limits to be different for each species. Our results give crucial information on the patterns and processes shaping diversity in the Eastern Mediterranean and show the main factor promoting diversification to be local environmental dynamics and ecological specialization and not large scale latitudinal movements as often reported for southern Europe. By determining regional and global patterns of diversification in an eastern Mediterranean genus we further our understanding of the major trends influencing plant diversity in the Mediterranean basin as a whole.
Population Structure Discovery in Meta-Analyzed Microbial Communities and Inflammatory Bowel Disease
Authors: Ma Siyuan , Shungin Dmitry , Mallick Himel , Schirmer Melanie , Nguyen Long H. , Kolde Raivo , Franzosa Eric , Vlamakis Hera , Xavier Ramnik , Huttenhower Curtis
Published: September 2020

Microbial community studies in general, and of the human microbiome in inflammatory bowel disease (IBD) in particular, have now achieved a scale at which it is practical to associate features of the microbiome with environmental exposures and health outcomes across multiple large-scale populations. This permits the development of rigorous meta-analysis methods, of particular importance in IBD as a means by which the heterogeneity of disease etiology and treatment response might be explained. We have thus developed MMUPHin (Meta-analysis Methods with a Uniform Pipeline for Heterogeneity in microbiome studies) for joint normalization, meta-analysis, and population structure discovery using microbial community taxonomic and functional profiles. Applying this method to ten IBD cohorts (5,151 total samples), we identified a single consistent axis of microbial associations among studies, including newly associated taxa such asAcinetobacterandTuricibacterdetected due to the sensitivity of meta-analysis. Linear random effects models further revealed associations with medications, disease location, and interaction effects consistent within and between studies. Finally, multiple unsupervised clustering metrics and dissimilarity measures agreed on a lack of discrete microbiome “types” in the IBD gut microbiome. These results thus provide a benchmark for consistent characterization of the IBD gut microbiome and a general framework applicable to meta-analysis of any microbial community types.
Database and deep learning toolbox for noise-optimized, generalized spike inference from calcium imaging
Authors: Rupprecht Peter , Carta Stefano , Hoffmann Adrian , Echizen Mayumi , Blot Antonin , Kwan Alex C. , Dan Yang , Hofer Sonja B. , Kitamura Kazuo , Helmchen Fritjof , Friedrich Rainer W.
Published: September 2020

Calcium imaging is a key method to record patterns of neuronal activity across populations of identified neurons. Inference of temporal patterns of action potentials (‘spikes’) from calcium signals is, however, challenging and often limited by the scarcity of ground truth data containing simultaneous measurements of action potentials and calcium signals. To overcome this problem, we compiled a large and diverse ground truth database from publicly available and newly performed recordings. This database covers various types of calcium indicators, cell types, and signal-to-noise ratios and comprises a total of >35 hours from 298 neurons. We then developed a novel algorithm for spike inference (CASCADE) that is based on supervised deep networks, takes advantage of the ground truth database, infers absolute spike rates, and outperforms existing model-based algorithms. To optimize performance for unseen imaging data, CASCADE retrains itself by resampling ground truth data to match the respective sampling rate and noise level. As a consequence, no parameters need to be adjusted by the user. To facilitate routine application of CASCADE we developed systematic performance assessments for unseen data, we openly release all resources, and we provide a user-friendly cloud-based implementation.
In silico Drosophila Patient ModelReveals Optimal Combinatorial Therapies for Colorectal Cancer
Authors: Gondal Mahnoor Naseer , Butt Rida Nasir , Shah Osama Shiraz , Nasir Zainab , Hussain Risham , Khawar Huma , Tariq Muhammad , Faisal Amir , Chaudhary Safee Ullah
Published: September 2020

In silicomodels of biomolecular regulation in cancer, annotated with patient-specific gene expression data can aid in the development of novel personalized cancer therapeutics strategies.Drosophila melanogasteris a well-established animal model that is increasingly being employed to evaluate preclinical personalized cancer therapies. Here, we report five Boolean network models of biomolecular regulation in cells lining theDrosophilamidgut epithelium and annotate them with patient-specific mutation data to develop anin silico Drosophila Patient Model(DPM). The network models were validated against cell-type-specific RNA-seq gene expression data from the FlyGut-seqdatabase and through three literature-based case studies on colorectal cancer. The results obtained from the study help elucidate cell fate evolution in colorectal tumorigenesis, validate cytotoxicity of nine FDA-approved cancer drugs, and devise optimal personalized drug treatment combinations. The proposed personalized therapeutics approach also helped identify synergistic combinations of chemotherapy (paclitaxel) with targeted therapies (pazopanib, or ruxolitinib) for treating colorectal cancer. In conclusion, this work provides a novel roadmap for decoding colorectal tumorigenesis and in the development of personalized cancer therapeutics through a DPM.
Activation of the Cpx-envelope stress response system promotes tolerance to antibacterials delivered by arginine-rich peptides and aminoglycosides inEscherichia coli
Authors: Frimodt-Møller Jakob , Koulouktsis Andreas , Charbon Godefroid , Otterlei Marit , Nielsen Peter E. , Løbner-Olesen Anders
Published: September 2020

Cell penetrating peptides (CPP) are increasingly used for cellular drug delivery in both pro- and eukaryotic cells, and oligoarginines have attracted special attention. However; their mechanism of action, particularly for prokaryotes is still unknown. Arginine-rich CPPs (R-CPP) efficiently delivers the antimicrobial peptide nucleic acid (PNA) into bacteria. Here, we show that resistance to an R-CPP PNA conjugate inEscherichia colirequires multiple genetic modifications and is specific to R-CPP and not to the PNA-part. An integral part of the resistance was the constitutively activated Cpx-envelope stress response system (cpx*), which decreased the cytoplasmic membrane potential and thereby indicates an indirectly energy dependent uptake mechanism. Interestingly,cpx* mutants also showed increased tolerance to aminoglycosides and R-CPP conjugated to a peptide targeting the DNA sliding clamp; i.e., similar uptake inE. colifor these antimicrobial compounds. We speculate that thecpx* phenotype could create an evolutionary opportunity to adapt and evolve in the presence of either compounds.

Author summary

The emergence of multidrug resistant bacteria is raising the need for new classes of antibiotics. Peptide nucleic acids (PNAs) may fill this requirement by their ability to block translation of essential mRNAs and hence inhibit growth. PNA needs conjugation to a delivery peptide (cell penetrating peptide; CPP) to enter the bacteria. Arginine-rich CPPs (CPPR) are receiving a lot of attention for use as delivery vessels. Here, we show, for the first time, CPPR-PNA resistance inEscherichia colidirected towards the delivery peptide. Consequently, resistance also applies to other antimicrobial compounds delivered by the same carrier. An integral part of CPPRresistance is due to a constitutive active Cpx-response system, which leads to a decreased electric potential (ΔΨ) across the inner membrane. The decreased ΔΨis a result of down-regulation of two aerobic respiratory operons, namely NADH:ubiquinone oxidoreductase complex I and cytochrome bo3ubiquinol oxidase. The decreased ΔΨalso led to increased tolerance to aminoglycosides. This shows that a (large) negative ΔΨis important for providing sufficient free energy for membrane translocation of both CPPRand that the inner membrane is the main barrier for entry of both arginine-rich delivery peptides and aminoglycosides.
Head-direction coding in the hippocampal formation of birds
Authors: Ben-Yishay Elhanan , Krivoruchko Ksenia , Ron Shaked , Ulanovsky Nachum , Derdikman Dori , Gutfreund Yoram
Published: September 2020

Birds strongly rely on spatial memory and navigation. Therefore, it is of utmost interest to reveal how space is represented in the avian brain. Here we used tetrodes to record neurons from the hippocampal formation of Japanese quails – a ground-dwelling species – while the quails roamed a 1×1-meter arena (>2,100 neurons from 23 birds). Whereas spatially-modulated cells (place-cells, border-cells, etc.) were generally not encountered, the firing-rate of 12% of the neurons was unimodally and significantly modulated by the head-azimuth – i.e. these were head-direction cells (HD cells). Typically, HD cells were maximally active at one preferred-direction and minimally at the opposite null-direction, with preferred-directions spanning all 360°. The HD tuning was relatively broad (mean width ∼130°), independent of the animal’s position and speed, and was stable during the recording-session. Similarly to findings in rodents, the HD tuning usually rotated with the rotation of a salient visual cue in the arena. These findings support the existence of an allocentric head-direction representation in the quail hippocampal formation, and provide the first demonstration of head-direction cells in birds.
Pervasive compartment-specific regulation of gene expression during homeostatic synaptic scaling
Authors: Colameo David , Rajman Marek , Soutschek Michael , Bicker Silvia , von Ziegler Lukas , Bohacek Johannes , Germain Pierre-Luc , Dieterich Christoph , Schratt Gerhard
Published: September 2020

Synaptic scaling is a form of homeostatic plasticity which allows neurons to adjust their action potential firing rate in response to chronic alterations in neural activity. Synaptic scaling requires profound changes in gene expression, but the relative contribution of local and cell-wide mechanisms is controversial. Here we performed a comprehensive multi-omics characterization of the somatic and process compartments of primary rat hippocampal neurons during synaptic scaling. Thereby, we uncovered both highly compartment-specific and correlated changes in the neuronal transcriptome and proteome. Whereas downregulation of crucial regulators of neuronal excitability occurred primarily in the somatic compartment, structural components of excitatory postsynapses were mostly downregulated in processes. Motif analysis further suggests an important role for trans-acting post-transcriptional regulators, including RNA-binding proteins and microRNAs, in the local regulation of the corresponding mRNAs. Altogether, our study indicates that compartmentalized gene expression changes are widespread in synaptic scaling and might co-exist with neuron-wide mechanisms to allow synaptic computation and homeostasis.
Selection favors adaptive plasticity in a long-term reciprocal transplant experiment
Authors: Anderson Jill , Jameel M. Inam , Geber Monica A.
Published: September 2020

Spatial and temporal environmental variation can favor the evolution of adaptive phenotypic plasticity, such that genotypes alter their phenotypes in response to local conditions to maintain fitness across heterogeneous landscapes. When individuals show greater fitness in one habitat than another, asymmetric migration can restrict adaptive responses to selection in the lower quality environment. In these cases, selection is predicted to favor traits that enhance fitness in the higher-quality source habitat at the expense of fitness in the marginal habitat, resulting in specialization to the high-quality environment. Here, we test whether plasticity is adaptive in a system regulated by demographic source-sink dynamics.Vaccinium elliottii(Ericaceae) occurs in dry upland and flood-prone bottomland forests throughout the southeastern United States, and shows patterns consistent with source-sink dynamics. We conducted a multi-year field experiment to evaluate whether plasticity in foliar morphology is advantageous. Both across habitats and within the high-quality upland environment, selection favored plasticity in specific leaf area and stomatal density. Stabilizing selection acted on plasticity in these traits, suggesting that extreme levels of plasticity are disadvantageous. We conclude that even in systems driven by source-sink dynamics, temporal and spatial variation in conditions can favor the evolution of plasticity.
Oleic acid protectsCaenorhabditismothers from mating-induced death
Authors: Choi Leo S. , Shi Cheng , Murphy Coleen T.
Published: September 2020

Reproduction comes at a cost, including death. Previous studies of the interconnections between reproduction, lifespan, and fat metabolism inC. eleganswere predominantly performed in low-reproduction conditions. To understand how increased reproduction affects lifespan and fat metabolism, we examined mated worms; we find that a Δ9 desaturase, FAT-7, is significantly up-regulated. Dietary supplementation of oleic acid (OA), the immediate downstream product of FAT-7 activity, restores fat storage and completely rescues mating-induced death, while other fatty acids cannot. OA-mediated lifespan restoration is also observed inC. elegansmutants suffering increased death from short-term mating, and in matedC. remaneifemales, indicating a conserved role of oleic acid in post-mating lifespan regulation. Because OA supplementation does not further increase the reproductive span or the brood size of matedC. elegansmothers, our results suggest that altering specific fat metabolism uncouples reproduction and somatic lifespan regulation, providing potent targets to ameliorate the cost of reproduction.
DNA methylation signatures of duplicate gene evolution in angiosperms
Authors: Kenchanmane Raju Sunil K. , Ledford S. Marshall , Niederhuth Chad E.
Published: September 2020

Gene duplication is a source of evolutionary novelty. DNA methylation may play a role in the evolution of duplicate genes through its association with gene expression. While this relationship is examined to varying extent in a few individual species, the generalizability of these results at either a broad phylogenetic scale with species of differing duplication histories or across a population, remains unknown. We apply a comparative epigenomics approach to 43 angiosperm species across the phylogeny and a population of 928Arabidopsis thalianaaccessions, examining the association of DNA methylation with paralog evolution. Genic DNA methylation is differentially associated with duplication type, the age of duplication, sequence evolution, and gene expression. Whole genome duplicates are typically enriched for CG-only gene-body methylated or unmethylated genes, while single-gene duplications are typically enriched for non-CG methylated or unmethylated genes. Non-CG methylation, in particular, was characteristic of more recent single-gene duplicates. Core angiosperm gene families are differentiated into those which preferentially retain paralogs and ‘duplication-resistant’ families, which convergently revert to singletons following duplication. Duplication-resistant families which still have paralogous copies are, uncharacteristically for core angiosperm genes, enriched for non-CG methylation. Non-CG methylated paralogs have higher rates of sequence evolution, higher frequency of presence-absence variation, and more limited expression. This suggests that silencing by non-CG methylation may be important to maintaining dosage following duplication and be a precursor to fractionation. Our results indicate that genic methylation marks differing evolutionary trajectories and fates between paralogous genes and have a role in maintaining dosage following duplication.
Flow cytometry with cell sorting and sequencing as a tool for the study of the Humboldt Current krill stomach microbiota
Authors: Henriquez-Castillo Carlos , Franco-Cisterna Belén , Murillo Alejandro A. , Ulloa Osvaldo , Riquelme-Bugueño Ramiro
Published: September 2020

Euphausiids (or krill) are important contributors to marine biomass and key players in marine pelagic trophic webs. Euphausiids stomachs represent a specific niche for microbes that participate in the digestion of the host dietary components. To date, methods for the study of the diversity and function of these microorganisms remain complex. Often, bacterial ribosomal sequences obtained from lysates of stomachs are overrepresented by organisms from the surrounding environment. Flow cytometry with cell sorting (FC-CS) have become a powerful technique to study microbial community structure but also for the study of population genomics of gut-associated bacteria, even at a single-cell level.

In this study, we used FC-CS and sequencing of the bacterial 16S rRNA gene to study the microorganisms inhabiting the stomach of the Humboldt Current krill,Euphausia mucronata. This approach was complemented with DNA extraction and sequencing from whole lysate stomachs as described for other crustacean species.

Non-specific amplification was not retrieved in the polymerase chain reaction (PCR) from cells sorted, opposite to the observed using the DNA from the whole lysate. Sequences obtained from the whole stomach DNA were enriched in picocyanobacteria, meanwhile, sequences retrieved from cells sorted belonged almost exclusively toBalneolasp. of the new phylum, Balneolaeota. This study represents, to our knowledge, the first report ofBalneolasp. in the stomach for any organism inhabiting the Humboldt Current System (HCS).

Our results suggest that the stomach-associated microbiota can be characterized by FC-CS and sequencing by manual scraping of the stomach coupled with the DNA extraction and sequencing. This work represents a baseline for similar studies of other mesozooplankton groups. The implementation of this technique might complement future studies on host-microbes’ interaction and their implications on the marine pelagic food web.
A COVID-19 vaccine candidate using SpyCatcher multimerization of the SARS-CoV-2 spike protein receptor-binding domain induces potent neutralising antibody responses
Authors: Tan Tiong Kit , Rijal Pramila , Rahikainen Rolle , Keeble Anthony H. , Schimanski Lisa , Hussain Saira , Harvey Ruth , Hayes Jack W.P. , Edwards Jane. C. , McLean Rebecca K. , Martini Veronica , Pedrera Miriam , Thakur Nazia , Conceicao Carina , Dietrich Isabelle , Shelton Holly , Ludi Anna , Wilsden Ginette , Browning Clare , Zagrajek Adrian K. , Bialy Dagmara , Bhat Sushant , Stevenson-Leggett Phoebe , Hollinghurst Philippa , Tully Matthew , Moffat Katy , Chiu Chris , Waters Ryan , Gray Ashley , Azhar Mehreen , Mioulet Valerie , Newman Joseph , Asfor Amin S. , Burman Alison , Crossley Sylvia , Hammond John A. , Tchilian Elma , Charleston Bryan , Bailey Dalan , Tuthill Tobias J. , Graham Simon P. , Malinauskas Tomas , Huo Jiandong , Tree Julia A. , Buttigieg Karen R. , Owens Raymond J. , Caroll Miles W. , Daniels Rodney S. , McCauley John W. , Huang Kuan-Ying A. , Howarth Mark , Townsend Alain R.
Published: September 2020

There is dire need for an effective and affordable vaccine against SARS-CoV-2 to tackle the ongoing pandemic. In this study, we describe a modular virus-like particle vaccine candidate displaying the SARS-CoV-2 spike glycoprotein receptor-binding domain (RBD) using SpyTag/SpyCatcher technology (RBD-SpyVLP). Low doses of RBD-SpyVLP in a prime-boost regimen induced a strong neutralising antibody response in mice and pigs that was superior to convalescent human sera. We evaluated antibody quality using ACE2 blocking and neutralisation of cell infection by pseudovirus or wild-type SARS-CoV-2. Using competition assays with a monoclonal antibody panel, we showed that RBD-SpyVLP induced a polyclonal antibody response that recognised all key epitopes on the RBD, reducing the likelihood of selecting neutralisation-escape mutants. The induction of potent and polyclonal antibody responses by RBD-SpyVLP provides strong potential to address clinical and logistic challenges of the COVID-19 pandemic. Moreover, RBD-SpyVLP is highly resilient, thermostable and can be lyophilised without losing immunogenicity, to facilitate global distribution and reduce cold-chain dependence.
STABILITY ANALYSIS OF A SIGNALING CIRCUIT WITH DUAL SPECIES OF GTPASE SWITCHES
Authors: Stolerman Lucas M. , Ghosh Pradipta , Rangamani Padmini
Published: September 2020

Abstract

GTPases are molecular switches that regulate a wide range of cellular processes, such as organelle biogenesis, position, shape, and function, vesicular transport between organelles, and signal transduction. These hydrolase enzymes operate by toggling between an active “ON”) guanosine triphosphate (GTP)-bound state and an inactive (“OFF”) guanosine diphosphate (GDP)-bound state; such a toggle is regulated by GEFs (guanine nucleotide exchange factors) and GAPs (GTPase activating proteins). Here we propose a model for a network motif between monomeric (m) and trimeric (t) GTPases assembled exclusively in eukaryotic cells of multicellular organisms. We develop a system of ordinary differential equations in which these two classes of GT-Pases are interlinked conditional to their ON/OFF states within a motif through coupling and feedback loops. We provide explicit formulae for the steady states of the system and perform classical local stability analysis to systematically investigate the role of the different connections between the GTPase switches. Interestingly, a coupling of the active mGTPase to the GEF of the tGTPase was sufficient to provide two locally stable states: one where both active/inactive forms of the mGTPase can be interpreted as having low concentrations and the other where both m- and tGTPase have high concentrations. Moreover, when a feedback loop from the GEF of the tGTPase to the GAP of the mGTPase was added to the coupled system, two other locally stable states emerged, both having the tGTPase inactivated and being interpreted as having low active tGTPase concentrations. Finally, the addition of a second feedback loop, from the active tGT-Pase to the GAP of the mGTPase, gives rise to a family of steady states that can be parametrized by a range of inactive tGTPase concentrations. Our findings reveal that the coupling of these two different GTPase motifs can dramatically change their steady state behaviors and shed light on how such coupling may impact signaling mechanisms in eukaryotic cells.
Massively parallel identification of causal variants underlying gene expression differences in a yeast cross
Authors: Renganaath Kaushik , Cheung Rocky , Day Laura , Kosuri Sriram , Kruglyak Leonid , Albert Frank W.
Published: September 2020

Sequence variation in regulatory DNA alters gene expression and shapes genetically complex traits. However, the identification of individual, causal regulatory variants is challenging. Here, we used a massively parallel reporter assay to measure thecis-regulatory consequences of 5,832 natural DNA variants in the promoters of 2,503 genes in the yeastSaccharomyces cerevisiae. We identified 451 causal variants, which underlie genetic loci known to affect gene expression. Several promoters harbored multiple causal variants. In five promoters, pairs of variants showed non-additive, epistatic interactions. Causal variants were enriched at conserved nucleotides, tended to have low derived allele frequency, and were depleted from promoters of essential genes, which is consistent with the action of negative selection. Causal variants were also enriched for alterations in transcription factor binding sites. Models integrating these features provided modest, but statistically significant, ability to predict causal variants. This work revealed a complex molecular basis forcis-acting regulatory variation.
Identifying Isl1 genetic lineage in the developing olfactory system and in GnRH-1 neurons
Authors: Taroc Ed Zandro M. , Katreddi Raghu Ram , Forni Paolo E.
Published: September 2020

During embryonic development, symmetric ectodermal thickenings (olfactory placodes) give rise to several cell types that comprise the olfactory system, such as those that form the terminal nerve ganglion (TN), gonadotropin releasing hormone-1 (GnRH-1) neurons and other migratory neurons in rodents. Even though the genetic heterogeneity among these cell types are documented, unidentified cell populations arising from the olfactory placode remain. One candidate to identify placodal derived neurons in the developing nasal area is the transcription factor Isl1, which was recently identified in GnRH-3 neurons of the terminal nerve in fish, as well as expression in neurons of the nasal migratory mass. Here, we analyzed the Isl1 genetic lineage in chemosensory neuronal populations in the nasal area and migratory GnRH-1 neurons in mice usingin-situhybridization, immunolabeling a Tamoxifen inducible Isl1CreERTand a constitutive Isl1Creknock-in mouse lines. In addition, we also performed conditional Isl1 ablation in developing GnRH neurons. We found Isl1 lineage across non sensory cells of the respiratory epithelium and sustentacular cells of OE and VNO. We identified a population of transient embryonic Isl1+ neurons in the olfactory epithelium and sparse Isl1+ neurons in postnatal VNO. Isl1 is expressed in almost all GnRH neurons and in approximately half of the other neuron populations in the Migratory Mass. However, Isl1 conditional ablation alone does not significantly compromise GnRH-1 neuronal migration or GnRH-1 expression, suggesting compensatory mechanisms. Further studies will elucidate the functional and mechanistic role of Isl1 in development of migratory endocrine neurons.