bluuebunny/crossref_metadata_2025 huggingface dataset:
High-resolution influenza mapping of a city reveals socioeconomic determinants of transmission within and between urban quarters
Authors: Egli Adrian , Goldman Nina , Müller Nicola F. , Brunner Myrta , Wüthrich Daniel , Tschudin-Sutter Sarah , Hodcroft Emma , Neher Richard , Saalfrank Claudia , Hadfield James , Bedford Trevor , Syedbasha Mohammedyaseen , Vogel Thomas , Augustin Noémie , Bauer Jan , Sailer Nadine , Amar-Sliwa Nadezhda , Lang Daniela , Seth-Smith Helena M.B. , Blaich Annette , Hollenstein Yvonne , Dubuis Olivier , Nägele Michael , Buser Andreas , Nickel Christian H. , Ritz Nicole , Zeller Andreas , Stadler Tanja , Battegay Manuel , Schneider-Sliwa Rita
Published: April 2020

With two-thirds of the global population projected to be living in urban areas by 2050, understanding the transmission patterns of viral pathogens within cities is crucial for effective prevention strategies. Here, in unprecedented spatial resolution, we analysed the socioeconomic determinants of influenza transmission in a European city. We combined geographical and epidemiological data with whole genome sequencing of influenza viruses at the scale of urban quarters and statistical blocks, the smallest geographic subdivisions within a city. We observed annually re-occurring geographic clusters of influenza incidences, mainly associated with net income, and independent of population density and living space. Vaccination against influenza was also mainly associated with household income and was linked to the likelihood of influenza-like illness within an urban quarter. Transmissions patterns within and between quarters were complex. High-resolution city-level epidemiological studies combined with social science surveys such as this will be essential for understanding seasonal and pandemic transmission chains and delivering tailored public health information and vaccination programs at the municipal level.
The effect of noise trauma and high-frequency stimulation on thalamic sensory gating in rodents
Authors: Zare Aryo , van Zwieten Gusta , Kotz Sonja A. , Temel Yasin , Schultz Benjamin G. , Schwartze Michael , Janssen Marcus L.F.
Published: April 2020

Background

The medial geniculate body (MGB) of the thalamus plays a central role in tinnitus pathophysiology. Breakdown of sensory gating in this part of the auditory thalamus is a potential mechanism underlying tinnitus. The alleviation of tinnitus-like behavior by high-frequency stimulation (HFS) of the MGB might mitigate dysfunctional sensory gating.

Objective

The study aims at exploring the role of the MGB in sensory gating as a mandatory relay area in auditory processing in noise-exposed and control subjects, and to assess the effect of MGB HFS on this function.

Methods

Noise-exposed rats and controls were tested. Continuous auditory sequences were presented to allow assessment of sensory gating effects associated with pitch, binary grouping, and temporal regularity. Evoked potentials (EP) were recorded from the MGB and acquired before and after HFS (100 Hz).

Results

Noise-exposed rats showed differential modulation of MGB EP amplitudes, confirmed by significant main effects of stimulus type, pair position and temporal regularity. Noise-exposure selectively abolished the effect of temporal regularity on EP amplitudes. A significant three-way interaction between HFS phase, temporal regularity and rat condition (noise-exposed, control) revealed that only noise-exposed rats showed significantly reduced EP amplitudes following MGB HFS.

Conclusion

This is the first report that shows thalamic filtering of incoming auditory signals based on different sound features. Noise-exposed rats further showed higher EP amplitudes in most conditions and did not differentiate the temporal regularity. Critically, MGB HFS was effective in reducing amplitudes of the EP responses in noise-exposed animals.

Highlights

EP findings indicate sensory gating in the MGB in rats.

Noise exposure alters EP amplitudes in the MGB.

HFS selectively suppresses EP responses in noise-exposed animals.
Engineering of critical enzymes and pathways for improved triterpenoid biosynthesis in yeast
Authors: Guo Hao , Wang Huiyan , Huo Yi-xin
Published: April 2020

Triterpenoids represent a diverse group of phytochemicals, widely distributed in the plant kingdom with many biological activities. Recently, the heterologous production of triterpenoids inSaccharomyces cerevisiaehas been successfully implemented by introducing various triterpenoids biosynthetic pathways. By engineering related enzymes as well as yeast metabolism, the yield of various triterpenoids is significantly improved from milligram-scale per liter to gram-scale level per liter. This achievement demonstrates that engineering of critical enzymes is considered as a potential strategy to overcome the main hurdles of translation of these potent natural products into industry. Here, we review strategies for designing enzymes to improve the yield of triterpenoids inS. cerevisiae, which is mainly separated into three aspects: 1. elevating the supply of the precursor—2,3-oxidosqualene, 2. optimizing triterpenoid-involved reactions, 3. lowering the competition of the native sterol pathway. And then we provide challenges and prospects on further enhancing the triterpenoid production inS. cerevisiae.
Direct Electrical Detection of sub-aM DNA Concentrations
Authors: Guo Maoxiang , Madaboosi Narayanan , Neumann Felix , Nilsson Mats , van der Wijngaart Wouter
Published: April 2020

Sensors for detecting ultra-low concentrations are limited by the efficient transport of target molecules from large sample volumes to small detection regions. We here report a small-format digital DNA sensor in the shape of a microporous membrane that electrically detects DNA substrates with a concentration as low as 790 zM. This ultra-high sensitivity follows from optimising the mass transport of target DNA to specific receptors on the membrane across multiple spatial scales. mm-sized membranes support the rapid convection of a large sample volume to the detection zone; µm-sized pores ensure that DNA diffusion to the surface-based receptors dominates over convective loss through the pores (low Péclet number), and; at the nm-scale, target-receptor binding dominates over diffusive transport (high Damköhler number). After their efficient capture, the DNA molecules are converted with high specificity into trans-membrane gold nanowires that are detected using a simple, high signal-to-noise, electrical resistance measurement. This sensor design is of interest for detecting low-abundant target molecules without the need for sample amplification or up-concentration, and the mass-transport strategy could be adapted to other surface-based sensing schemes.
Stimulation Artifact Source Separation (SASS) for assessing electric brain oscillations during transcranial alternating current stimulation (tACS)
Authors: Haslacher David , Nasr Khaled , Robinson Stephen E. , Braun Christoph , Soekadar Surjo R.
Published: April 2020

Brain oscillations, e.g. measured by electro- or magnetoencephalography (EEG/MEG), are causally linked to brain functions that are fundamental for perception, cognition and learning. Recent advances in neurotechnology provide means to non-invasively target these oscillations using frequency-tuned amplitude-modulated transcranial alternating current stimulation (AM-tACS). However, online adaptation of stimulation parameters to ongoing brain oscillations remains an unsolved problem due to stimulation artifacts that impede such adaptation, particularly at the target frequency. Here, we introduce a real-time compatible artifact rejection algorithm (Stimulation Artifact Source Separation, SASS) that overcomes this limitation. SASS is a spatial filter (linear projection) removing EEG signal components that are maximally different in the presence versus absence of stimulation. This enables the reliable removal of stimulation-specific signal components, while leaving physiological signal components unaffected. For validation of SASS, we evoked brain activity with known phase and amplitude using 10 Hz visual flickers across 7 healthy human volunteers. 64-channel EEG was recorded during and in absence of 10 Hz AM-tACS targeting the visual cortex. Phase differences between AM-tACS and the visual stimuli were randomized, so that steady-state visually evoked potentials (SSVEPs) were phase-locked to the visual stimuli but not to the AM-tACS signal. For validation, distributions of single-trial amplitude and phase of EEG signals recorded during and in absence of AM-tACS were compared for each participant. When no artifact rejection method was applied, AM-tACS stimulation artifacts impeded assessment of single-trial SSVEP amplitude and phase. Using SASS, amplitude and phase of single trials recorded during and in absence of AM-tACS were comparable. These results indicate that SASS can be used to establish adaptive (closed-loop) AM-tACS, a potentially powerful tool to target various brain functions, and to investigate how AM-tACS interacts with electric brain oscillations.

Highlights

- Stimulation Artifact Source Separation (SASS), a real-time compatible signal decomposition algorithm for separating electric brain activity and stimulation signal artifacts related to amplitude-modulated transcranial alternating current stimulation (AM-tACS), is introduced

- Employing SASS, phase and amplitude of single-trial steady state visual evoked potentials (SSVEPs) were reliably recovered from electroencephalography (EEG) recordings at the frequency targeted with AM-tACS

- SASS enables assessment of single-trial oscillatory brain activity at the target frequency during stimulation and paves the way for online adaptation of stimulation parameters to ongoing brain oscillations
TINC - a method to dissect transcriptional complexes at single locus resolution - reveals novelNanogregulators in mouse embryonic stem cells
Authors: Knaupp AS , Mohenska M , Larcombe MR , Ford E , Lim SM , Wong K , Chen J , Firas J , Huang C , Liu X , Nguyen T , Sun YBY , Holmes ML , Tripathi P , Rossello FJ , Schröder J , Nefzger CM , Das PP , Haigh JJ , Lister R , Schittenhelm RB , Polo JM
Published: April 2020

Cellular identity is ultimately controlled by transcription factors (TFs), which bind to specific regulatory elements (REs) within the genome to regulate gene expression and cell fate changes. While recent advances in genome-wide epigenetic profiling techniques have significantly increased our understanding of which REs are utilized in which cell type, it remains largely unknown which TFs and cofactors interact with these REs to modulate gene expression. A major hurdle in dissecting the whole composition of a multi-protein complex formed at a specific RE is the shortage of appropriate techniques. We have developed a novel method termed TALE-mediated Isolation of Nuclear Chromatin (TINC). TINC utilizes epitope-tagged TALEs to isolate a specific genomic region from the mammalian genome and includes a nuclei isolation and chromatin enrichment step for increased specificity. Upon cross-linking of the cells and isolation of the chromatin, the target region is purified based on affinity purification of the TALE and associated nucleic acid and protein molecules can be subjected to further analyses. A key TF in the pluripotency network and therefore in embryonic stem cells (ESCs) is NANOG. It is currently not fully understood howNanogexpression is regulated and consequently it remains unclear how the ESC state is maintained. Using TINC we dissected the protein complex formed at theNanogpromoter in mouse ESCs and identified many known and numerous novel factors.
Degradation modeling of water environmental DNA: Experiments on multiple DNA sources in pond and seawater
Authors: Saito Tatsuya , Doi Hideyuki
Published: April 2020

Environmental DNA (eDNA) methods have been developed to detect organism distribution and abundance/biomass in various environments. eDNA degradation is critical for eDNA evaluation. However, the dynamics and mechanisms of eDNA degradation are largely unknown, especially when considering different eDNA sources, e.g., cells and fragmental DNA. We experimentally evaluated the degradation rates of eDNA derived from multiple sources, including fragmental DNA, free cells, and inhabiting species. We conducted the experiment with pond and seawater to evaluate the differences between freshwater and marine habitats. We quantified the eDNA copies of free cells, fragmental DNA, and inhabiting species (Cyprinus carpio in the pond and Trachurus japonicus in the sea). Our results show that eDNA derived from both cells and fragmental DNA decreased exponentially in both the sea and pond samples. The degradation of eDNA from inhabiting species showed similar behavior to the cell-derived eDNA. We evaluated three degradation models with different assumptions and degradation steps and found that a simple exponential model is effective in most cases. Our findings on cell- and fragmental DNA-derived eDNA provide fundamental information about the eDNA degradation process and can be applied to elucidate eDNA behavior in natural environments.
Codon usage bias in prokaryotic genomes and environmental adaptation
Authors: Arella Davide , Dilucca Maddalena , Giansanti Andrea
Published: April 2020

In each genome synonymous codons are used with different frequencies; this phenomenon is known as codon usage bias. The preferred codons tend to correspond to the most highly expressed tRNAs. It had been known that codon usage bias can influence the cellular fitness and that might be associated with the lifestyle of the organism. To test the impact of environments on genome evolution we studied the relationship between codon usage bias and the phenotypic traits of 615 prokaryotic organisms. Principal component analysis revealed that prokaryotes with a specific phenotypic characteristic and living in similar environmental conditions have similar codon preferences, accessed by the Relative Synonymous Codon Usage (RSCU), and a similar tRNA availability gauged by the tRNA gene copy number (tGCN). In addition, by measuring the average tRNA adaptation index (tAI) for each genome, we discovered that organisms able to live in multiple habitats, including facultative organisms, mesophiles and pathogenic bacteria, exhibit lower extents of translational efficiency, consistent with their need to adapt to different environments.

This is the first large-scale study that examines the role of translational efficiency in the environmental adaptation of prokaryotes. Our results show that synonymous codon choices might be under strong translational selection, adapting the codons to the tRNA pool to different extents depending on the organism’s lifestyle needs.
Minimizing biosignal recording sites for hybrid noninvasive brain/neural robot control
Authors: Cavallo Alessia , Roth Vincent , Haslacher David , Nann Marius , Soekadar Surjo R.
Published: April 2020

Noninvasive brain/neural controlled robots are promising tools to improve autonomy and quality of life in severe paralysis, but require biosignal recordings, such as electroencephalography (EEG) and electrooculography (EOG), from various sites distributed over the user’s head. This limits the applicability and practicality of noninvasive brain/neural robot control on an everyday basis. It would thus be very desirable to minimize the number of necessary recording sites paving the way for miniaturized, headset-like EEG/EOG systems that users with hemiplegia can mount by themselves. Here, we introduce a novel EEG/EOG brain/neural robot control strategy using only scalp electrodes placed near cortical sensorimotor areas. The strategy was tested across 16 healthy volunteers engaging in an EEG/EOG brain/neural control task. Classification accuracies were compared using scalp electrodes only vs. the conventional electrode placements across the scalp and face. To evaluate whether cranial muscle artifacts impede classification accuracy, participants were asked to chew during the task. We found that brain/neural classification accuracy was comparable and that chewing did not impact classification accuracies when using scalp electrodes only. Our results suggest that the proposed new strategy allows for reliable EEG/EOG-based brain/neural robot control, a critical prerequisite to broaden the use of noninvasive brain/neural assistive and rehabilitative technologies.
Dynamic changes in the urine proteome of tumor-bearing mouse models of B16 melanoma and RM-1 prostate cancer
Authors: Li Lujun , Pan Xuanzhen , Liu Yongtao , Wang Ting , Gao Youhe
Published: April 2020

Urine can accumulate changes and reflect early physiological and pathological changes of various diseases, such as tumors. Therefore, urine is an ideal source for identification of early biomarkers. In this study, melanoma and prostate cancer-bearing mouse models were established by subcutaneous injection of B16 and RM-1 cells, respectively. Urine samples were collected at four time points during tumor growth. Based on data-independent acquisition (DIA) technology, liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used for quantitative analysis. Compared with those before the injection of B16 cells, 38 human homologous differential proteins were identified, and 18 proteins were reported to be related to melanoma. Before the tumor was visible, there were 4 differential proteins, and all were reported to be related to melanoma. Compared with that before the injection of RM-1 cells, a total of 14 human homologous differential proteins were identified, and 9 proteins were reported to be associated with prostate cancer. Before the tumor was palpable, 9 proteins showed significant differences. There were significant differences between the two tumor-bearing models. Through the above experiments and analysis, we found that the urine proteome can reflect the changes in the development and provide early biomarkers of the two tumors and provide clues for the early clinical diagnosis of these diseases.
A Region of UNC-89 (obscurin) Lying Between Two Protein Kinase Domains is a Highly Elastic Spring Required for Proper Sarcomere Assembly
Authors: Qadota Hiroshi , Moody Jasmine C. , Lesanpezeshki Leila , Moncrief Taylor , Kitzler Deborah , Bhat Purnima Devaki , Vanapalli Siva A. , Oberhauser Andres F. , Benian Guy M.
Published: April 2020

InC. elegans, unc-89encodes a set of giant multi-domain proteins (up 8,081 residues) localized to the M-lines of muscle sarcomeres and required for normal sarcomere organization and whole-animal locomotion. Multiple UNC-89 isoforms contain two protein kinase domains. There is conservation in arrangement of domains between UNC-89 and its two mammalian homologs, obscurin and SPEG: kinase, a non-domain region of 647-742 residues, Ig domain, Fn3 domain and a second kinase domain. In all three proteins, this non-domain “interkinase region” has low sequence complexity, high proline content and lacks predicted secondary structure. We report that a major portion of this interkinase (571 residues out of 647 residues) when examined by single molecule force spectroscopyin vitrodisplays the properties of a random coil and acts as an entropic spring. We used CRISPR/Cas9 to create nematodes carrying an in-frame deletion of the same 571-residue portion of the interkinase. These animals express normal levels of giant internally deleted UNC-89 proteins, and yet show severe disorganization of all portions of the sarcomere in body wall muscle. Super-resolution microscopy reveals extra, short-A-bands lying close to the outer muscle cell membrane and between normally spaced A-bands. Nematodes with this in-frame deletion show defective locomotion and muscle force generation. We designed our CRISPR-generated in-frame deletion to contain an HA tag at the N-terminus of the large UNC-89 isoforms. This HA tag results in normal organization of body wall muscle, but dis-organization of pharyngeal muscle, small body size, and reduced muscle force, likely due to poor nutritional uptake.

Highlights

The giant muscle proteins UNC-89 and its mammalian homologs have an ∼700 aa non-domain region lying between two protein kinase domains

By single molecule force spectroscopy UNC-89 non-domain region is an elastic random coil

Nematodes lacking this non-domain region have disorganized sarcomeres and reduced whole animal locomotion

UNC-89 non-domain region is required for proper assembly of A-bands from thick filaments
Obtusaquinone is a cysteine modifying compound that targets Keap1 for degradation
Authors: Badr Christian E. , da Hora Cintia Carla , Kirov Aleksandar B. , Tabet Elie , Amante Romain , Nibbs Antoinette E. , Fitzsimons Evelyn , Chen John W. , Chiu Norman , Nakano Ichiro , Haas Wilhelm , Mazitschek Ralph , Tannous Bakhos A.
Published: April 2020

We have previously identified the natural product Obtusaquinone (OBT) as a potent antineoplastic agent with promising in vivo activity in glioblastoma and breast cancer through the activation of oxidative stress; however, the molecular properties of this compound remained elusive. We used a multidisciplinary approach comprising medicinal chemistry, quantitative mass spectrometry-based proteomics, functional studies in cancer cells, pharmacokinetic analysis, as well as mouse xenograft models to develop and validate novel OBT analogs and charaterize the molecular mechanism of action of OBT. We here show that OBT and analogs, which have improved pharmacological properties, bind to cysteine residues with particular affinity to cysteine-rich Keap1, a member of the CUL3 ubiquitin ligase complex. This binding promotes an overall stress response and results in ubiquitination and proteasomal degradation of Keap1 and downstream activation of the Nrf2 pathway.
Hydrogen-deuterium exchange mass spectrometry captures distinct dynamics upon substrate and inhibitor binding to a transporter
Authors: Jia Ruyu , Martens Chloe , Shekhar Mrinal , Pant Shashank , Pellowe Grant A. , Lau Andy M. , Findlay Heather E. , Harris Nicola J. , Tajkhorshid Emad , Booth Paula J. , Politis Argyris
Published: April 2020

Proton-coupled transporters use transmembrane proton gradients to power active transport of nutrients inside the cell. High-resolution structures often fail to capture the coupling between proton and ligand binding, and conformational changes associated with transport. We combine HDX-MS with mutagenesis and MD simulations to dissect the molecular mechanism of the prototypical transporter XylE. We show that protonation of a conserved aspartate triggers conformational transition from outward-facing to inward-facing state. This transition only occurs in the presence of substrate xylose, while the inhibitor glucose locks the transporter in the outward-facing state. MD simulations corroborate the experiments by showing that only the combination of protonation and xylose binding, and not glucose, sets up the transporter for conformational switch. Overall, we demonstrate the unique ability of HDX-MS to distinguish between the conformational dynamics of inhibitor and substrate binding, and show that a specific allosteric coupling between substrate binding and protonation is a key step to initiate transport.
Programmable RNA Targeting using CasRx in Flies
Authors: Buchman Anna , Brogan Dan J. , Sun Ruichen , Yang Ting , Hsu Patrick , Akbari Omar S.
Published: April 2020

CRISPR-Cas genome editing technologies have revolutionized the fields of functional genetics and genome engineering, but with the recent discovery and optimization of RNA-targeting Cas ribonucleases, we may soon see a similar revolution in the study of RNA function and transcriptome engineering. However, to date, successful proof-of-principle for Cas ribonuclease RNA targeting in eukaryotic systems has been limited. Only recently has successful modification of RNA expression by a Cas ribonuclease been demonstrated in animal embryos. This previous work, however, did not evaluate endogenous expression of Cas ribonucleases and only focused on Cas ribonuclease function in early developmental stages. A more comprehensive evaluation of this technology is needed to assess its potential impact in the field. Here we report on our efforts to develop a programmable platform for RNA-targeting using a Cas ribonuclease, CasRx, in the model organismDrosophila melanogaster. By genetically encoding CasRx in flies, we demonstrate moderate transcript targeting of known phenotypic genes in addition to unexpected toxicity and lethality. We also report on the off-target effects following on-target transcript cleavage by CasRx. Taken together, our results present the current state and limitations of a genetically encoded programmable RNA-targeting Cas system inDrosophila melanogaster, paving the way for future optimization of the system.
Myosin VI moves on nuclear actin filaments and supports long-range chromatin rearrangements
Authors: Große-Berkenbusch Andreas , Hettich Johannes , Kuhn Timo , Fili Natalia , Cook Alexander W. , Hari-Gupta Yukti , Palmer Anja , Streit Lisa , Ellis Peter J.I. , Toseland Christopher P. , Gebhardt J. Christof M.
Published: April 2020

Nuclear myosin VI (MVI) enhances RNA polymerase II – dependent transcription, but the molecular mechanism is unclear. We used live cell single molecule tracking to follow individual MVI molecules inside the nucleus and observed micrometer-long motion of the motor. Besides static chromatin interactions lasting for tens of seconds, ATPase-dependent directed motion occurred with a velocity of 2 µm/s. The movement was frequently interrupted by short periods of slow restricted diffusion and increased in frequency upon stimulation of transcription. Mutagenesis and perturbation experiments demonstrated that nuclear MVI motion is independent of dimerization and occurs on nuclear actin filaments, which we also observed by two-color imaging. Using chromosome paint to quantify distances between chromosomes, we found that MVI is required for transcription-dependent long-range chromatin rearrangements. Our measurements reveal a transcription-coupled function of MVI in the nucleus, where it actively undergoes directed movement along nuclear actin filaments. Motion is potentially mediated by cooperating monomeric motors and might assist in enhancing transcription by supporting long-range chromatin rearrangements.
Whole-Brain opto-fMRI Map of Mouse VTA Dopaminergic Activation Reflects Structural Projections with Small but Significant Deviations
Authors: Ioanas Horea-Ioan , Saab Bechara John , Rudin Markus
Published: April 2020

Ascending dopaminergic projections from neurons located in the Ventral Tegmental Area (VTA) are key to the etiology, dysfunction, and control of motivation, learning, and addiction. Due to evolutionary conservation of this nucleus and the extensive use of mice as disease models, establishing an assay for VTA dopaminergic signalling in the mouse brain is crucial for the translational investigation of motivational control as well as of neuronal function phenotypes for diseases and interventions. In this article we use optogenetic stimulation directed at VTA dopaminergic neurons in combination with functional Magnetic Resonance Imaging (fMRI), a method widely used in human deep brain imaging. We present a comprehensive assay producing the first whole-brain opto-fMRI map of dopaminergic activation in the mouse, and show that VTA dopaminergic system function is consistent with its structural VTA projections, diverging only in a few key aspects. While the activation map predominantly highlights target areas according to their relative projection densities (e.g. strong activation of the nucleus accumbens and low activation of the hippocampus), it also includes areas for which a structural connection is not well established (such as the dorsomedial striatum). We further detail the variability of the assay with regard to multiple experimental parameters, including stimulation protocol and implant position, and provide evidence-based recommendations for assay reuse, publishing both reference results and a reference analysis workflow implementation.
FlexDotPlot: a universal and modular dot plot visualization tool for complex multifaceted data
Authors: Leonard Simon , Lardenois Aurélie , Tarte Karin , Rolland Antoine , Chalmel Frédéric
Published: April 2020

Motivation

Dot plots are heatmap-like charts that provide a compact way to simultaneously display two quantitative information by means of dots of different sizes and colours. Despite the popularity of this visualization method, particularly in single-cell RNA-seq studies, existing tools used to make dot plots are limited in terms of functionality and usability.

Results

We developed FlexDotPlot, an R package for generating dot plots from multifaceted data, including single-cell RNA-seq data. It provides a universal and easy-to-use solution with a high versatility. An interactive R Shiny application is also available allowing non-R users to easily generate dot plots with several tunable parameters.

Availability and implementation

Source code, detailed manual, and code to reproduce figures are available athttps://github.com/Simon-Leonard/FlexDotPlot. A Shiny app is available as a stand-alone application within the package.
Investigation in scanning beampattern generated by resonance cavities
Authors: Lu Hongwang , Ma Xin
Published: April 2020

The previous study has reported that the presence of a small flap in the Brown Long-Eared Bat (Plecotus auritus) generate useful spatial information by the frequency-driven beam scanning. However, it did not investigate the beampattern generating mechanism of the flap. In this study, according to the dipole equivalence principle, the two resonance cavities split by the flap are simplified to a dipole source with certain vibration orientation. The analytical solution of the dipole shows obvious frequency-driven sidelobe scanning in the beampattern, which matches the numerical results obtained from the pinna quite well. The results support the hypothesis that the frequency-driven sidelobe scanning is generated by the resonance in the two cavities split by the flap. This method can be applied to design a reflector antenna with small geometric structures for splitting existent resonance cavities to meet requirements of beam scanning.
Facile Synthesis and Metabolic Incorporation ofm-DAP Bioisosteres Into Cell Walls of Live Bacteria
Authors: Apostolos Alexis J. , Nelson Julia M. , Pires Marcos M.
Published: April 2020

Bacterial cell walls contain peptidoglycan (PG), a scaffold that provides proper rigidity to resist lysis from internal osmotic pressure and a barrier to protect cells against external stressors. It consists of repeating sugar units with a linkage to a stem peptide that becomes highly crosslinked by cell wall transpeptidases (TP). Because it is an essential component of the bacterial cell, the PG biosynthetic machinery is often the target of antibiotics. For this reason, cellular probes that advance our understanding of PG biosynthesis and its maintenance can be powerful tools to reveal novel drug targets. While synthetic PG fragments containing L-Lysine in the 3rdposition on the stem peptide are easier to access, those withmeso-diaminopimelic acid (m-DAP) pose a severe synthetic challenge. Herein, we describe a solid phase synthetic scheme based on the widely available Fmoc-protected L-Cysteine building block to assemblemeso-cystine (m-CYT), which mimics key structural features ofm-DAP. To demonstrate proper mimicry ofm-DAP, cell wall probes were synthesized withm-CYT in place ofm-DAP and evaluated for their metabolic processing in live bacterial cells. We found thatm-CYT-based cell wall probes were properly processed by TPs in various bacterial species that endogenously containm-DAP in their PG. We anticipate that this strategy, which is based on the use of inexpensive and commercially available building blocks, can be widely adopted to provide greater accessibility of PG mimics form-DAP containing organisms.
Spatio-temporal responses of butterflies to global warming on a Mediterranean island over two decades
Authors: Colom Pau , Traveset Anna , Carreras David , Stefanescu Constantí
Published: April 2020

In recent decades, efforts have been made to understand how global warming affects biodiversity and in this regard butterflies have emerged as a model group. The most conspicuous sign that warming is affecting the ecology of butterflies are the phenological advances occurring in many species. Moreover, rising temperatures are having a notable impact – both negative and positive – on population abundances. To date, patterns have generally been analysed at species level without taking into account possible differences between populations, which, when they are noted, are mostly attributed to large-scale climate differences across a latitudinal gradient. In this work, we use a long-term database of butterflies from the island of Menorca (Balearic Islands, Spain) to investigate how phenology and population dynamics have been affected by climate warming during the past two decades. In addition, we assess how responses are modulated by habitat characteristics and by species’ biological cycles. Our results show that species respond differently to warming at a local scale depending on season and habitat, and that coastal habitats in the Mediterranean region are particularly sensitive to the effects of climate change. Furthermore, our findings suggest that the effects of temperature could be partially offset in more inland habitats such as forests and deep ravines. The positive effect of temperature on ravine populations during the summer suggests that butterflies disperse across habitats as a response to rising temperatures during the season. This type of dispersal behaviour as a response to warming could be especially important in island ecosystems where the possibilities of modifying altitudinal or latitudinal distributions are often severely limited.
Genetic interaction between profilin and myosin II reveals a potential role for myosin II in actin filament disassemblyin vivo
Authors: Zambon Paola , Palani Saravanan , Jadhav Shekhar Sanjay , Gayathri Pananghat , Balasubramanian Mohan K.
Published: April 2020

The actin cytoskeleton plays a variety of roles in eukaryotic cell physiology, ranging from cell polarity and migration to cytokinesis. Key to the function of the actin cytoskeleton is the mechanisms that control its assembly, stability, and turnover. Through genetic analyses in fission yeast, we found that,myo2-S1(myo2-G515D), a myosin II mutant allele was capable of rescuing lethality caused by compromise of mechanisms involved in actin cable / ring assembly and stability. The mutation inmyo2-S1 affects the activation loop of Myosin II, which is involved in physical interaction with subdomain 1 of actin and in stimulating the ATPase activity of Myosin. Consistently, actomyosin rings inmyo2-S1 cell ghosts were severely compromised in contraction upon ATP addition, suggesting that Myo2-S1p was defective in actin binding and / or motor activity. These studies strongly suggest a role for Myo2p in actin cytoskeletal disassembly and turnover, and that compromise of this activity leads to genetic suppression of mutants defective in actin cable assembly / stability.
Analysis of Endothelial-to-Haematopoietic Transition at the Single Cell Level identifies Cell Cycle Regulation as a Driver of Differentiation
Authors: Canu Giovanni , Athanasiadis Emmanouil , Grandy Rodrigo A. , Garcia-Bernardo Jose , Strzelecka Paulina M. , Vallier Ludovic , Ortmann Daniel , Cvejic Ana
Published: April 2020

Haematopoietic stem cells (HSC) first arise during development in the aorta-gonad-mesonephros (AGM) region of the embryo from a population of haemogenic endothelial cells which undergo endothelial-to-haematopoietic transition (EHT). Despite the progress achieved in recent years, the molecular mechanisms driving EHT are still poorly understood, especially in human where the AGM region is not easily accessible. In this study, we took advantage of a human pluripotent stem cell (hPSC) differentiation system and single-cell transcriptomics to recapitulate EHTin vitroand uncover mechanisms by which the haemogenic endothelium generates early haematopoietic cells. We show that most of the endothelial cells reside in a quiescent state and progress to the haematopoietic fate within a defined time window, within which they need to re-enter into the cell cycle. If cell cycle is blocked, haemogenic endothelial cells lose their EHT potential and adopt a non-haemogenic identity. Furthermore, we demonstrated that CDK4/6 and CDK1 play a key role not only in the transition but also in allowing haematopoietic progenitors to establish their full differentiation potential. Therefore, we propose a direct link between the molecular machineries that control cell cycle progression and EHT.
Hypergraphs for predicting essential genes using multiprotein complex data
Authors: Klimm Florian , Deane Charlotte M. , Reinert Gesine
Published: April 2020

Protein-protein interactions are crucial in many biological pathways and facilitate cellular function. Investigating these interactions as a graph of pairwise interactions can help to gain a systemic understanding of cellular processes. It is known, however, that proteins interact with each other not exclusively in pairs but also in polyadic interactions and they can formmultiprotein complexes, which are stable interactions between multiple proteins. In this manuscript, we usehypergraphsto investigate multiprotein complex data. We investigate two random null models to test which hypergraph properties occur as a consequence of constraints, such as the size and the number of multiprotein complexes. We find that assortativity, the number of connected components, and clustering differ from the data to these null models. Our main finding is that projecting a hypergraph of polyadic interactions onto a graph of pairwise interactions leads to the identification of different proteins as hubs than the hyper-graph. We find in our data set that the hypergraph degree is a more accurate predictor for gene-essentiality than the degree in the pairwise graph. We find that analysing a hypergraph as pairwise graph drastically changes the distribution of the local clustering coefficient. Furthermore, using a pairwise interaction representing multiprotein complex data may lead to a spurious hierarchical structure, which is not observed in the hypergraph. Hence, we illustrate that hypergraphs can be more suitable than pairwise graphs for the analysis of multiprotein complex data.
The evolution of red blood cell shape in a continental radiation of fishes
Authors: Martins Brenda Oliveira , Franco-Belussi Lilian , Siqueira Mayara Schueroff , Fernandes Carlos E. , Provete Diogo B.
Published: April 2020

The size and shape of Red Blood Cells (RBC) can provide key information on life history strategies in vertebrates. However, little is known about how RBC shape evolved in response to environmental factors and the role of phylogenetic relationship. Here, we analyzed RBC morphometrics in a continental radiation of fishes testing the hypothesis that phylogenetic relationship determines species occupation of morphospace. We collected blood samples of five specimens of 15 freshwater fish species from six orders and used basic stereological methods to measure cell and nucleus area, perimeter, and diameter, cell and nucleus volume, nucleus:cytoplasm ratio, and shape factor of 50 cells per specimen. Then, we conducted a phylogenetic Principal Components Analysis using a dated phylogeny and built a phylomorphospace. To test if the phylogenetic relationship predicted the phenotypic similarity of species, we calculated multivariate phylogenetic signal. We also estimated the evolution rate of RBC shape for each node and tip using ridge regression. Finally, we tested if the position in the water column influenced RBC shape using a phylogenetic GLS. RBC shape seems to have evolved in a non-stationary way because the distribution pattern of species in the phylomorphospace is independent of the phylogeny. Accordingly, the rate of evolution for shape was highly heterogeneous, with an increase in the genusPygocentrus. Water column position does not influence RBC shape. In conclusion, RBC shape seem to have evolved in response to multiple selective pressures independent of life history characters.
High-affinity agonist binding to C5aR results from a cooperative two-site binding mechanism
Authors: Dumitru Andra C. , Krishna Deepak R. N. V. , Liu Heng , Koehler Melanie , Zhang Cheng , Fan Hao , Alsteens David
Published: April 2020

A current challenge in the field of life sciences is to decipher, in their native environment, the functional activation of cell surface receptors upon binding of complex ligands. Lack of suitable nanoscopic methods has hampered our ability to meet this challenge in an experimental manner. Here, we use for the first time the interplay between atomic force microscopy, steered molecular dynamics and functional assays to elucidate the complex ligand-binding mechanism of C5a with the human G protein-coupled C5a receptor (C5aR). We have identified two independent binding sites acting in concert where the N-terminal C5aR serves as kinetic trap and the transmembrane domain as functional site. Our results corroborate the two-site binding model and clearly identify a cooperative effect between two binding sites within the C5aR. We anticipate that our methodology could be used for development and design of new therapeutic agents to negatively modulate C5aR activity.
Cells and gene expression programs in the adult human heart
Authors: Litviňuková Monika , Talavera-López Carlos , Maatz Henrike , Reichart Daniel , Worth Catherine L. , Lindberg Eric L. , Kanda Masatoshi , Polanski Krzysztof , Fasouli Eirini S. , Samari Sara , Roberts Kenny , Tuck Liz , Heinig Matthias , DeLaughter Daniel M. , McDonough Barbara , Wakimoto Hiroko , Gorham Joshua M. , Nadelmann Emily R. , Mahbubani Krishnaa T. , Saeb-Parsy Kourosh , Patone Giannino , Boyle Joseph J. , Zhang Hongbo , Zhang Hao , Viveiros Anissa , Oudit Gavin Y. , Bayraktar Omer , Seidman J. G. , Seidman Christine , Noseda Michela , Hübner Norbert , Teichmann Sarah A.
Published: April 2020

Cardiovascular disease is the leading cause of death worldwide. Advanced insights into disease mechanisms and strategies to improve therapeutic opportunities require deeper understanding of the molecular processes of the normal heart. Knowledge of the full repertoire of cardiac cells and their gene expression profiles is a fundamental first step in this endeavor. Here, using large-scale single cell and nuclei transcriptomic profiling together with state-of-the-art analytical techniques, we characterise the adult human heart cellular landscape covering six anatomical cardiac regions (left and right atria and ventricles, apex and interventricular septum). Our results highlight the cellular heterogeneity of cardiomyocytes, pericytes and fibroblasts, revealing distinct subsets in the atria and ventricles indicative of diverse developmental origins and specialized properties. Further we define the complexity of the cardiac vascular network which includes clusters of arterial, capillary, venous, lymphatic endothelial cells and an atrial-enriched population. By comparing cardiac cells to skeletal muscle and kidney, we identify cardiac tissue resident macrophage subsets with transcriptional signatures indicative of both inflammatory and reparative phenotypes. Further, inference of cell-cell interactions highlight a macrophage-fibroblast-cardiomyocyte network that differs between atria and ventricles, and compared to skeletal muscle. We expect this reference human cardiac cell atlas to advance mechanistic studies of heart homeostasis and disease.
α-Synuclein-112 impairs synaptic vesicle recycling consistent with its enhanced membrane binding properties
Authors: Soll Lindsey G. , Eisen Julia N. , Vargas Karina J. , Medeiros Audrey T. , Hammar Katherine M. , Morgan Jennifer R.
Published: April 2020

Synucleinopathies are neurological disorders associated with α-synuclein overexpression and aggregation. While it is well established that overexpression of wild type α-synuclein (α-syn-140) leads to cellular toxicity and neurodegeneration, much less is known about other naturally occurring α-synuclein splice isoforms. In this study we provide the first detailed examination of the synaptic effects caused by one of these splice isoforms, α-synuclein-112 (α-syn-112). α-Syn-112 is produced by an in-frame excision of exon 5, resulting in deletion of amino acids 103-130 in the C-terminal region. α-Syn-112 is upregulated in the substantia nigra, frontal cortex, and cerebellum of parkinsonian brains and is correlated with susceptibility to sporadic Parkinson’s disease (PD), dementia with Lewy bodies (DLB) and multiple systems atrophy (MSA). We report here that α-syn-112 binds strongly to anionic phospholipids when presented in highly-curved liposomes, similar to α-syn-140. However, α-syn-112 bound significantly stronger to all phospholipids tested, including the phosphoinositides. α-Syn-112 also dimerized and trimerized on isolated synaptic membranes, while α-syn-140 remained largely monomeric. When introduced acutely to lamprey synapses, α-syn-112 robustly inhibited synaptic vesicle recycling. Interestingly, α-syn-112 produced effects on the plasma membrane and clathrin-mediated synaptic vesicle endocytosis that were phenotypically intermediate between those caused by monomeric and dimeric α-syn-140. These findings indicate that α-syn-112 exhibits enhanced phospholipid binding and oligomerizationin vitroand consequently interferes with synaptic vesicle recyclingin vivoin ways that are consistent with its biochemical properties. This study provides additional evidence suggesting that impaired vesicle endocytosis is a cellular target of excess α-synuclein and advances our understanding of potential mechanisms underlying disease pathogenesis in the synucleinopathies.
Accumulation of dead cells from contact killing facilitates coexistence in bacterial biofilms
Authors: Steinbach Gabi , Crisan Cristian , Ng Siu Lung , Hammer Brian , Yunker Peter
Published: April 2020

Bacterial communities govern their composition using a wide variety of social interactions, some of which are antagonistic. Many antagonistic mechanisms, such as the Type VI Secretion System (T6SS), require killer cells to directly contact target cells. The T6SS is hypothesized to be a highly potent weapon, capable of facilitating the invasion and defense of bacterial populations. However, we find that the efficacy of the T6SS is severely limited by the material consequences of cell death. Through experiments withVibrio choleraestrains that kill via the T6SS, we show that dead cell debris quickly accumulates at the interface that forms between competing strains, preventing contact and thus preventing killing. While previous experiments have shown that T6SS killing can reduce a population of target cells by as much as one-million-fold, we find that as a result of the formation of dead cell debris barriers, the impact of T6SS killing depends sensitively on the initial concentrations of killer and target cells. Therefore, while the T6SS provides defense against contacting competitors on a single cell level, it is incapable of facilitating invasion or the elimination of competitors on a community level.