bluuebunny/crossref_metadata_2025 huggingface dataset:
Doxycycline interferes with tau amyloid aggregation abolishing its associated neuronal toxicity
Authors: Medina Luciana , González-Lizárraga Florencia , Dominguez-Meijide Antonio , Ploper Diego , Parrales Valeria , Sequeira Sabrina , Cima-Omori Maria Sol , Zweckstetter Markus , Del Bel Elaine , Michel Patrick P. , Outeiro Tiago Fleming , Raisman-Vozari Rita , Chehín Rosana , Socias Sergio B.
Published: November 2020

Tauopathies are neurodegenerative disorders with increasing incidence and still without cure. The extensive time required for development and approval of novel therapeutics highlights the need for testing and repurposing known safe molecules. Since doxycycline impacts α-synuclein aggregation and toxicity, herein we tested its effect on tau. We found that doxycycline reduces amyloid aggregation of the different isoforms of tau protein in a dose-dependent manner, remodeling the resultant species. Furthermore, doxycycline interacts with tau microtubule-binding domain preventing its aggregation. In a cell free system doxycycline also prevents tau seeding and in cell culture reduces toxicity of tau aggregates. Overall, our results expand the spectrum of action of doxycycline against aggregation-prone proteins, opening novel perspectives for its repurposing as a disease-modifying drug for tauopathies.
Optimal density of bacterial cells
Authors: Pang Tin Yau , Lercher Martin J.
Published: November 2020

A substantial fraction of the bacterial cytosol is occupied by catalysts and their substrates. While a higher volume density of catalysts and substrates might boost biochemical fluxes, the resulting molecular crowding can slow down diffusion, perturb the reactions’ Gibbs free energies, and reduce the catalytic efficiency of proteins. Due to these tradeoffs, dry mass density likely possesses an optimum that facilitates maximal cellular growth and that is interdependent on the cytosolic molecule size distribution. Here, we analyze the balanced growth of a model cell, accounting systematically for crowding effects on reaction kinetics. Its optimal cytosolic volume occupancy depends on the nutrient-dependent resource allocation into large ribosomal vs. small metabolic macromolecules, reflecting a tradeoff between the saturation of metabolic enzymes, favoring larger occupancies with higher encounter rates, and the inhibition of the ribosomes, favoring lower occupancies with unhindered diffusion of tRNAs. Our predictions across growth rates are quantitatively consistent with the experimentally observed reduction in volume occupancy on rich media compared to minimal media inE. coli.Strong deviations from optimal cytosolic occupancy only lead to minute reductions in growth rate, which are nevertheless evolutionarily relevant due to large bacterial population sizes. In sum, cytosolic density variation in bacterial cells appears to be consistent with an optimality principle of cellular efficiency.
Diel Investments in Phytoplankton Metabolite Production Influenced by Associated Heterotrophic Bacteria
Authors: Uchimiya Mario , Schroer William , Olofsson Malin , Edison Arthur S. , Moran Mary Ann
Published: November 2020

Organic carbon transfer between photoautotrophic and heterotrophic microbes in the surface ocean mediated through metabolites dissolved in seawater is a central but poorly understood process in the global carbon cycle. In a synthetic microbial community in which diatom extracellular release of organic molecules sustained growth of a co-cultured bacterium, metabolite transfer was assessed over two diel cycles based on per cell quantification of phytoplankton endometabolites and bacterial transcripts. Of 31 phytoplankton endometabolites identified and classified into temporal abundance patterns, eight could be matched to patterns of bacterial transcripts mediating their uptake and catabolism. A model simulating the coupled endometabolite-transcription relationships hypothesized that one category of outcomes required an increase in phytoplankton metabolite synthesis in response to the presence of the bacterium. An experimental test of this hypothesis confirmed higher endometabolome accumulation in the presence of bacteria for all five compounds assigned to this category – leucine, glycerol-3-phosphate, glucose, and the organic sulfur compounds dihydroxypropanesulfonate and dimethylsulfoniopropionate. Partitioning of photosynthate into rapidly-cycling dissolved organic molecules at the expense of phytoplankton biomass production has implications for carbon sequestration in the deep ocean. That heterotrophic bacteria can impact this partitioning suggests a previously unrecognized influence on the ocean’s carbon reservoirs.

Significance Statement

Microbes living in the surface ocean are critical players in the global carbon cycle, carrying out a particularly key role in the flux of carbon between the ocean and atmosphere. The release of metabolites by marine phytoplankton and their uptake by heterotrophic bacteria is one of the major routes of microbial carbon turnover. Yet the identity of these metabolites, their concentration in seawater, and the factors that affect their synthesis and release are poorly known. Here we provide experimental evidence that marine heterotrophic bacteria can affect phytoplankton production and extracellular release of metabolites. This microbial interaction has relevance for the partitioning of photosynthate between dissolved and particulate carbon reservoirs in the ocean, an important factor in oceanic carbon sequestration.
AMPGAN v2: Machine Learning Guided Design of Antimicrobial Peptides
Authors: Van Oort Colin M. , Ferrell Jonathon B. , Remington Jacob M. , Wshah Safwan , Li Jianing
Published: November 2020

Antibiotic resistance is a critical public health problem. Each year ~2.8 million resistant infections lead to more than 35,000 deaths in the U.S. alone. Antimicrobial peptides (AMPs) show promise in treating resistant infections. However, applications of known AMPs have encountered issues in development, production, and shelf-life. To drive the development of AMP-based treatments it is necessary to create design approaches with higher precision and selectivity towards resistant targets.

Previously we developed AMPGAN and obtained proof-of-concept evidence for the generative approach to design AMPs with experimental validation. Building on the success of AMPGAN, we present AMPGAN v2 a bidirectional conditional generative adversarial network (BiCGAN) based approach for rational AMP design. AMPGAN v2 uses generator-discriminator dynamics to learn data driven priors and controls generation using conditioning variables. The bidirectional component, implemented using a learned encoder to map data samples into the latent space of the generator, aids iterative manipulation of candidate peptides. These elements allow AMPGAN v2 to generate of candidates that are novel, diverse, and tailored for specific applications—making it an efficient AMP design tool.
Cas12a-Capture: a novel, low-cost, and scalable method for targeted sequencing
Authors: Mighell Taylor L. , Nishida Andrew , O’Connell Brendan L. , Miller Caitlin V. , Grindstaff Sally , Thornton Casey A. , Adey Andrew C. , Doherty Daniel , O’Roak Brian J.
Published: November 2020

Targeted sequencing remains a valuable technique for clinical and research applications. However, many existing technologies suffer from pervasive GC sequence content bias, high input DNA requirements, and high cost for custom panels. We have developed Cas12a-Capture, a low-cost and highly scalable method for targeted sequencing. The method utilizes preprogramed guide RNAs to direct CRISPR-Cas12a cleavage of double stranded DNAin vitroand then takes advantage of the resulting four to five nucleotide overhangs for selective ligation with a custom sequencing adapter. Addition of a second sequencing adapter and enrichment for ligation products generates a targeted sequence library. We first performed a pilot experiment with 7,176 guides targeting 3.5 megabases of DNA. Using these data, we modeled the sequence determinants of Cas12a-Capture efficiency, then designed an optimized set of 11,438 guides targeting 3.0 megabases. The optimized guide set achieves an average 64-fold enrichment of targeted regions with minimal GC bias. Cas12a-Capture variant calls had strong concordance with Illumina Platinum Genome calls, especially for SNVs, which could be improved by applying basic variant quality heuristics. We believe Cas12a-Capture has a wide variety of potential clinical and research applications and is amendable for selective enrichment for any double stranded DNA template or genome.
Taxonomic sampling and rare genomic changes overcome long-branch attraction in the phylogenetic placement of pseudoscorpions
Authors: Ontano Andrew Z. , Gainett Guilherme , Aharon Shlomi , Ballesteros Jesús A. , Benavides Ligia R. , Corbett Kevin F. , Gavish-Regev Efrat , Harvey Mark S. , Monsma Scott , Santibáñez-López Carlos E. , Setton Emily V.W. , Zehms Jakob T. , Zeh Jeanne A. , Zeh David W. , Sharma Prashant P.
Published: November 2020

Long-branch attraction is a systematic artifact that results in erroneous groupings of fast-evolving taxa. The combination of short, deep internodes in tandem with LBA artifacts has produced empirically intractable parts of the Tree of Life. One such group is the arthropod subphylum Chelicerata, whose backbone phylogeny has remained unstable despite improvements in phylogenetic methods and genome-scale datasets. Pseudoscorpion placement is particularly variable across datasets and analytical frameworks, with this group either clustering with other long-branch orders or with Arachnopulmonata (scorpions and tetrapulmonates). To surmount LBA, we investigated the effect of taxonomic sampling via sequential deletion of basally branching pseudoscorpion superfamilies, as well as varying gene occupancy thresholds in supermatrices. We show that concatenated supermatrices and coalescent-based summary species tree approaches support a sister group relationship of pseudoscorpions and scorpions, when more of the basally branching taxa are sampled. Matrix completeness had demonstrably less influence on tree topology. As an external arbiter of phylogenetic placement, we leveraged the recent discovery of an ancient genome duplication in the common ancestor of Arachnopulmonata as a litmus test for competing hypotheses of pseudoscorpion relationships. We generated a high-quality developmental transcriptome and the first genome for pseudoscorpions to assess the incidence of arachnopulmonate-specific duplications (e.g., homeobox genes and miRNAs). Our results support the inclusion of pseudoscorpions in Arachnopulmonata, as the sister group of scorpions. Panscorpiones (new name) is proposed for the clade uniting Scorpiones and Pseudoscorpiones.
Precise spatiotemporal control of voltage-gated sodium channels by photocaged saxitoxin
Authors: Elleman Anna V. , Devienne Gabrielle , Makinson Christopher D. , Haynes Allison L. , Huguenard John R. , Du Bois J.
Published: November 2020

Here we report the pharmacologic blockade of voltage-gated sodium ion channels (NaV) by a synthetic saxitoxin derivative affixed to a photocleavable protecting group. We demonstrate that a functionalized saxitoxin (STX-eac) enables exquisite spatiotemporal control of NaV blockade to interrupt action potentials (APs) in dissociated neurons and nerve fiber bundles. The photo-uncaged inhibitor (STX-ea) is a nanomolar potent, reversible binder of NaVs. We use STX-eac to reveal differential susceptibility of myelinated and unmyelinated axons in the corpus callosum to NaV-dependent alterations in AP propagation, with unmyelinated axons preferentially showing reduced AP fidelity under conditions of partial NaV blockade. These results validate STX-eac as a high precision tool for robust photocontrol of neuronal excitability and AP generation.
Recurrent circuit based neural population codes for stimulus representation and inference
Authors: Zhang Wen-Hao , Wu Si , Josić Krešimir , Doiron Brent
Published: November 2020

A large part of the synaptic input received by cortical neurons comes from local cortico-cortical connectivity. Despite their abundance, the role of local recurrent connections in cortical function is unclear, and in simple coding schemes it is often the case that a circuit with no recurrent connections performs optimally. We consider a recurrent excitatory-inhibitory circuit model of a cortical hypercolumn which performs sampling-based Bayesian inference to infer latent hierarchical stimulus features. We show that local recurrent connections can store an internal model of the correlations between stimulus features that are present in the external world. When the resulting recurrent input is combined with feedforward input it produces a population code from which the posterior over the stimulus features can be linearly read out. Internal Poisson spiking variability provides the proper fluctuations for the population to sample stimulus features, yet the resultant population variability is aligned along the stimulus feature direction, producingdifferential correlations. Importantly, the amplitude of these internally generated differential correlations is determined by the associative prior in the model stored in the recurrent connections. This provides experimentally testable predictions for how population connectivity and response variability are related to the structure of latent external stimuli.
Two new hybrid zones expand the swordtail hybridization model system
Authors: Powell Daniel L. , Moran Ben , Kim Bernard , Banerjee Shreya M. , Aguillon Stepfanie M. , Fascinetto-Zago Paola , Langdon Quinn , Schumer Molly
Published: November 2020

Natural hybridization events provide unique windows into the barriers that keep species apart as well as the consequences of their breakdown. Here we characterize hybrid populations formed between the northern swordtail fishXiphophorus corteziandX. birchmannifrom collection sites on two rivers. We develop sensitive and accurate local ancestry calling for this system based on low coverage whole genome sequencing. Strikingly, we find that hybrid populations on both rivers consist of two genetically distinct subpopulations: a cluster of nearly pureX. birchmanniindividuals and one of phenotypically intermediate hybrids that derive ~85-90% of their genome fromX. cortezi. Simulations and empirical data suggest that at both sites initial hybridization occurred ~150 generations ago, with little evidence for contemporary gene flow between subpopulations, likely due to strong assortative mating. The patterns of population structure uncovered here mirror those seen in hybridization betweenX. birchmanniand its sister species,X. malinche. Future comparisons will provide a window into the repeatability of the outcomes of hybridization not only across independent hybridization events between the same species but also across distinct species pairs.
Pupil dilation predicts individual success in emotion regulation and dietary self-control
Authors: Maier Silvia , Grueschow Marcus
Published: November 2020

Multiple theories have proposed that increasing central arousal through the brain’s locus coeruleus – norepinephrine system may facilitate cognitive control and memory. However, for emotion research this hypothesis poses a puzzle, because conventionally, successful emotion regulation is associated with a decrease in arousal.

Pupil diameter is a proxy to infer upon the central arousal state. We employed an emotion regulation paradigm with a combination of design features that allowed us to dissociate regulation- from stimulus-associated arousal in the pupil diameter time course of healthy adults. A pupil diameter increase during regulation predicted individual differences in emotion regulation success beyond task difficulty. Moreover, the extent of this individual arousal boost predicted performance in another self-control task, dietary health challenges. Participants who harnessed more regulation-associated arousal during emotion regulation were also more successful in choosing healthier foods. These results suggest that a common arousal-based facilitation mechanism may support an individual’s self-control across domains.
Mapping the common and distinct neural correlates of visual, rule and motor conflict
Authors: Mew Bryony Goulding , Custovic Darije , Soreq Eyal , Lorenz Romy , Violante Ines , Sandrone Stefano , Hampshire Adam
Published: November 2020

Flexible behaviour requires cognitive-control mechanisms to efficiently resolve conflict between competing information and alternative actions. Whether a global neural resource mediates all forms of conflict or this is achieved within domainspecific systems remains debated. We use a novel fMRI paradigm to orthogonally manipulate rule, response and stimulus-based conflict within a full-factorial design. Whole-brain voxelwise analyses show that activation patterns associated with these conflict types are distinct but partially overlapping within Multiple Demand Cortex (MDC), the brain regions that are most commonly active during cognitive tasks. Region of interest analysis shows that most MDC sub-regions are activated for all conflict types, but to significantly varying levels. We propose that conflict resolution is an emergent property of distributed brain networks, the functional-anatomical components of which place on a continuous, not categorical, scale from domain-specialised to domain general. MDC brain regions place towards one end of that scale but display considerable functional heterogeneity.
Complement Component 3 expressed by the endometrial ectopic tissue is involved in the endometriotic lesion formation through mast cell activation
Authors: Agostinis C. , Zorzet S. , Balduit A. , Zito G. , Mangogna A. , Macor Paolo , Romano F. , Toffoli M. , Belmonte B. , Martorana A. , Borelli V. , Ricci G. , Kishore U. , Bulla R.
Published: November 2020

The pathophysiology of endometriosis (EM) is an excellent example of immune dysfunction, reminiscent of tumor microenvironment as well. Here, we report that an interplay between C3 and mast cells (MCs) is involved in the pathogenesis of ectopic EM. C3 is at the epicenter of the regulatory feed forward loop, amplifying the inflammatory microenvironment, in which the MCs are protagonists. Thus, C3 can be considered a marker of EM and its local synthesis can promote the engraftment of the endometriotic cysts. We generated a murine model of EM via injection of minced uterine tissue from a donor mouse, into the peritoneum of the recipient mice. The wild type mice showed greater amount of cyst formation in the peritoneum compared to C3 knock-out mice. This study offers an opportunity for novel therapeutic intervention in EM, a difficult to treat gynecological condition.

C3 produced by the endometriotic tissue is involved in the lesion development through mast cell activation
Paracrine regulation of neural crest EMT by placodal MMP28
Authors: Gouignard Nadège , Bibonne Anne , Mata Joao F , Bajanca Fernanda , Berki Bianka , Barriga Elias H , Saint-Jeannet Jean-Pierre , Theveneau Eric
Published: November 2020

Epithelial-Mesenchymal Transition (EMT) is an early event in cell dissemination from epithelial tissues. EMT endows cells with migratory, and sometimes invasive, capabilities and is thus a key process in embryo morphogenesis and cancer progression. So far, Matrix Metalloproteinases (MMPs) have not been considered as key players in EMT but rather studied for their role in matrix remodelling in later events such as cell migrationper se. Here we usedXenopusneural crest cells to assess the role of MMP28 in EMT and migrationin vivo. We provide strong evidence indicating that MMP28 produced by neighbouring placode cells is imported in the nucleus of neural crest cells for EMT and migration to occur.
MR1-restricted MAIT cells from the human lung mucosal surface have distinct phenotypic, functional, and transcriptomic features that are preserved in HIV infection
Authors: Khuzwayo Sharon , Mthembu Maphe , Meermeier Erin W. , Prakadan Sanjay M. , Kazer Samuel W. , Bassett Thierry , Nyamande Kennedy , Khan Dilshaad Fakey , Maharaj Priya , Mitha Mohammed , Suleman Moosa , Mhlane Zoey , Ramjit Dirhona , Karim Farina , Shalek Alex K. , Lewinsohn David M. , Ndung’u Thumbi , Wong Emily B.
Published: November 2020

Mucosal associated invariant T (MAIT) cells are a class of innate-like T cells that utilize a semi-invariant αβ T cell receptor to recognize small molecule ligands produced by bacteria and fungi. Despite growing evidence that immune cells at mucosal surfaces are often phenotypically and functionally distinct from those in the peripheral circulation, knowledge about the characteristics of MAIT cells at the lung mucosal surface, the site of exposure to respiratory pathogens, is limited. HIV infection has been shown to have a profound effect on the number and function of MAIT cells in the peripheral blood, but its effect on lung mucosal MAIT cells is unknown. We examined the phenotypic, functional, and transcriptomic features of MR1 restricted MAIT cells from the peripheral blood and bronchoalveolar compartments of otherwise healthy individuals with latentMycobacterium tuberculosis (Mtb)infection who were either HIV uninfected or HIV infected. Peripheral blood MAIT cells consistently co-expressed typical MAIT cell surface markers CD161 and CD26 in healthy individuals, while paired bronchoalveolar MAIT cells displayed heterogenous expression of these markers. Bronchoalveolar MAIT cells produced lower levels of pro-inflammatory cytokine IFN-γ and expressed higher levels of co-inhibitory markers PD-1 and TIM-3 than peripheral MAIT cells. HIV infection resulted in decreased frequencies and pro-inflammatory function of peripheral blood MAIT cells, while in the bronchoalveolar compartment MAIT cell frequency was decreased but phenotype and function were not significantly altered. Single-cell transcriptomic analysis demonstrated greater heterogeneity among bronchoalveolar compared to peripheral blood MAIT cells and suggested a distinct subset in the bronchoalveolar compartment. The transcriptional features of this bronchoalveolar subset were associated with atypical MAIT cells and tissue repair functions. In summary, we found previously undescribed phenotypic and transcriptional heterogeneity of bronchoalveolar MAIT cells in healthy people. In HIV infection, we found numeric depletion of MAIT cells in both anatomical compartments but preservation of the novel phenotypic and transcriptional features of bronchoalveolar MAIT cells.
Dramatic changes in mitochondrial substrate use at critically high temperatures: a comparative study usingDrosophila
Authors: Jørgensen Lisa Bjerregaard , Overgaard Johannes , Hunter-Manseau Florence , Pichaud Nicolas
Published: November 2020

Ectotherm thermal tolerance is critical to species distribution, but at present the physiological underpinnings of heat tolerance remain poorly understood. Mitochondrial function is perturbed at critically high temperatures in some ectotherms, including insects, suggesting that heat tolerance of these animals is linked to failure of oxidative phosphorylation (OXPHOS) and/or ATP production. To test this hypothesis we measured mitochondrial oxygen consumption rates in sixDrosophilaspecies with different heat tolerance using high-resolution respirometry. Using a substrate-uncoupler-inhibitor titration protocol we examined specific steps of the electron transport system to study how temperatures below, bracketing and above organismal heat limits affected mitochondrial function and substrate oxidation. At benign temperatures (19 and 30°C), complex I-supported respiration (CI-OXPHOS) was the most significant contributor to maximal OXPHOS. At higher temperatures (34, 38, 42 and 46°C), CI-OXPHOS decreased considerably, ultimately to very low levels at 42 and 46°C. The enzymatic catalytic capacity of complex I was intact across all temperatures and accordingly the decreased CI-OXPHOS is unlikely to be caused directly by hyperthermic denaturation/inactivation of complex I. Despite the reduction in CI-OXPHOS, maximal OXPHOS capacities were maintained in all species, through oxidation of alternative substrates; proline, succinate and, particularly, glycerol-3-phosphate, suggesting important mitochondrial flexibility at temperatures exceeding the organismal heat limit. Interestingly, this compensatory oxidation of alternative substrates occurred at temperatures that tended to correlate with species heat tolerance, such that heat-tolerant species could defend “normal” mitochondrial function at higher temperatures than sensitive species. Future studies should investigate why CI-OXPHOS is perturbed and how this potentially affects ATP production rates.
Loss of active neurogenesis in the adult shark retina
Authors: Hernández-Núñez Ismael , Robledo Diego , Mayeur Hélène , Mazan Sylvie , Sánchez Laura , Adrio Fátima , Barreiro-Iglesias Antón , Candal Eva
Published: November 2020

Neurogenesis is the process by which progenitor cells generate new neurons. As development progresses neurogenesis becomes restricted to concrete neurogenic niches, where it persists during postnatal life. The retina of teleost fishes is thought to proliferate and produce new cells throughout life. Whether this capacity may be an ancestral characteristic of jawed vertebrates, shared with chondrichthyans, which diverged from osteichthyans prior to the gnathostome radiation is completely unknown. Previous work from our group revealed that the juvenile retina of the catshark Scyliorhinus canicula shows active proliferation and neurogenesis. Here, we compared the morphology and proliferative status of the retina between catshark juveniles and adults. Histological analyses revealed an important reduction in the size of the peripheral retina (where progenitor cells are mainly located), an increase in the thickness of the plexiform layers and a decrease in the thickness of the inner nuclear layer in adults. Contrary to what has been reported in teleost fish, we did not observe active mitotic activity in the catshark retina after sexual maturation, suggesting that there is no significant proliferation and neurogenesis in adult specimens. Based on these results, we carried out RNA-Sequencing (RNA-Seq) analyses comparing the retinal transcriptome of juveniles and adults, which revealed a statistically significant decrease in the expression of many genes involved in cell proliferation and neurogenesis in adult catsharks. Our RNA-Seq data provides an excellent resource to identify new signaling pathways controlling neurogenesis in the vertebrate retina.
TimeCycle: Topology Inspired MEthod for the Detection of Cycling Transcripts in Circadian Time-Series Data
Authors: Ness-Cohn Elan , Braun Rosemary
Published: November 2020

Motivation

The circadian rhythm drives the oscillatory expression of thousands of genes across all tissues. The recent revolution in high-throughput transcriptomics, coupled with the significant implications of the circadian clock for human health, has sparked an interest in circadian profiling studies to discover genes under circadian control.

Result

We present TimeCycle: a topology-based rhythm detection method designed to identify cycling transcripts. For a given time-series, the method reconstructs the state space using time-delay embedding, a data transformation technique from dynamical systems theory. In the embedded space, Takens’ theorem proves that the dynamics of a rhythmic signal will exhibit circular patterns. The degree of circularity of the embedding is calculated as a persistence score using persistent homology, an algebraic method for discerning the topological features of data. By comparing the persistence scores to a bootstrapped null distribution, cycling genes are identified. Results in both synthetic and biological data highlight Time-Cycle’s ability to identify cycling genes across a range of sampling schemes, number of replicates, and missing data. Comparison to competing methods highlights their relative strengths, providing guidance as to the optimal choice of cycling detection method.

Availability and Implementation

A fully documented open-source R package implementing Time-Cycle is available at:https://nesscoder.github.io/TimeCycle/.
Deep neural network models reveal interplay of peripheral coding and stimulus statistics in pitch perception
Authors: Saddler Mark R. , Gonzalez Ray , McDermott Josh H.
Published: November 2020

Perception is thought to be shaped by the environments for which organisms are optimized. These influences are difficult to test in biological organisms but may be revealed by machine perceptual systems optimized under different conditions. We investigated environmental and physiological influences on pitch perception, whose properties are commonly linked to peripheral neural coding limits. We first trained artificial neural networks to estimate fundamental frequency from biologically faithful cochlear representations of natural sounds. The best-performing networks replicated many characteristics of human pitch judgments. To probe the origins of these characteristics, we then optimized networks given altered cochleae or sound statistics. Human-like behavior emerged only when cochleae had high temporal fidelity and when models were optimized for naturalistic sounds. The results suggest pitch perception is critically shaped by the constraints of natural environments in addition to those of the cochlea, illustrating the use of artificial neural networks to reveal underpinnings of behavior.
Design of an imaging probe to monitor real-time redistribution of L-type voltage gated calcium channels in astrocytic glutamate signalling
Authors: Sadat Tabatabaee Mitra , Kerkovius Jeff , Menard Frederic
Published: November 2020

Purpose

In the brain, astrocytes are non-excitable cells that undergo rapid morphological changes when stimulated by the excitatory neurotransmitter glutamate. We developed a chemical probe to monitor how glutamate affects the density and distribution of astrocytic L-type voltage-gated calcium channels (LTCC).

Procedures

The imaging probe FluoBar1 was created from a barbiturate ligand modified with a fluorescent coumarin moiety. The probe selectivity was examined with colocalization analyses of confocal fluorescence imaging in U118-MG and transfected COS-7 cells. Living cells treated with 50 nM FluoBar1 were imaged in real time to reveal changes in density and distribution of astrocytic LTCCs upon exposure to glutamate.

Results

FluoBar1 was synthesized in ten steps. The selectivity of the probe was demonstrated with immunoblotting and confocal imaging of immunostained cells expressing the CaV1.2 isoform of LTCCs proteins. Applying FluoBar1 to astrocyte model cells U118-MG allowed us to measure a 5-fold increase in fluorescence density of LTCCs upon glutamate exposure.

Conclusions

Imaging probe FluoBar1 allows the real-time monitoring of LTCCs in living cells, revealing for first time that glutamate causes a rapid increase of LTCC membranar density in astrocyte model cells. FluoBar1 may help tackle previously intractable questions about LTCC dynamics in cellular events.
Passive visual stimulation induces fatigue or improvement depending on cognitive load
Authors: Ioannucci Stefano , Borragán Guillermo , Zénon Alexandre
Published: November 2020

Theories of mental fatigue disagree on whether performance decrement is caused by motivational or functional alterations. We tested the assumption that keeping neural networks active for an extensive period of time entrains consequences at the subjective and objective level – the defining characteristics of fatigue – when confounds such as motivation, boredom and level of skill are controlled. We reveal that passive visual stimulation affects the performance of a subsequent task that is carried out in the same portion of visual space. This outcome, consisting either in an enhancement or deterioration of performance, was determined by the participants’ level of cognitive load and arousal, which were manipulated through variations in the difficulty of concurrent auditory tasks. Thus, repeated stimulation of neural networks leads to their altered functional performance, a mechanism which may play a role in the development of global mental fatigue.
Migraine Attacks as a Result of Hypothalamic Loss of Control
Authors: Stankewitz Anne , Keidel Leonie , Rehm Mathias , Irving Stephanie , Kaczmarz Stephan , Preibisch Christine , Witkovsky Viktor , Zimmer Claus , Schulz Enrico , Toelle Thomas R
Published: November 2020

To assess the natural trajectory of brain activity over the migraine cycle, we assessed (1) the cerebral perfusion and (2) the hypothalamic connectivity during spontaneous headache attacks with follow-up recordings towards the next migraine attack. Using pseudo-continuous arterial spin labelling and resting-state functional magnetic resonance imaging, 12 migraine patients were examined in 82 sessions. We detected cyclic changes of brain perfusion in the limbic circuit (insula, hippocampus, and nucleus accumbens), with the highest perfusion during headache attacks. In addition, we found an increase of hypothalamic connectivity to the limbic system over the interictal interval, then collapsing during the headache. Our data provide strong evidence for the predominant role of the hypothalamus as a zeitgeber for generating migraine attacks. Our findings suggest that migraine attacks are the result of the hypothalamus losing control over the limbic system.
Copper Containing Glass-Based Bone Adhesives for Orthopaedic Applications: Glass Characterization and Advanced Mechanical Evaluation
Authors: Mokhtari Sahar. , Wren Anthony.W.
Published: November 2020

This study addresses issues with currently used bone adhesives, by producing novel glass based skeletal adhesives through modification of the base glass composition to include copper (Cu) and by characterizing each glass with respect to structural changes. Bioactive glasses have found applications in fields such as orthopedics and dentistry, where they have been utilized for the restoration of bone and teeth. The present work outlines the formation of flexible organic-inorganic polyacrylic acid (PAA) – glass hybrids, commercial forms are known as glass ionomer cements (GICs). Initial stages of this research will involve characterization of the Cu-glasses, significant to evaluate the properties of the resulting adhesives. Scanning electron microscopy (SEM) of annealed Cu glasses indicates the presence of partial crystallization in the glass. The structural analysis of the glass using Raman suggests the formation of CuO nanocrystals on the surface. X-ray diffraction (XRD) pattern and X-ray photoelectron spectroscopy (XPS) further confirmed the formation of crystalline CuO phases on the surface of the annealed Cu-glass. The setting reaction was studied using Fourier transform infrared spectroscopy (ATR-FTIR). The mechanical properties of the Cu containing adhesives exhibited gel viscoelastic behavior and enhanced mechanical properties when compared to the control composition. Compression data indicated the Cu glass adhesives were efficient at energy dissipation due to the reversible interactions between CuO nano particles and PAA polymer chains.
BETA- AND GAMMA-SYNUCLEINS MODULATE SYNAPTIC VESICLE-BINDING OF ALPHA-SYNUCLEIN
Authors: Carnazza Kathryn E. , Komer Lauren , Pineda André , Na Yoonmi , Ramlall Trudy , Buchman Vladimir L. , Eliezer David , Sharma Manu , Burré Jacqueline
Published: November 2020

α-Synuclein (αSyn), β-synuclein (βSyn), and γ-synuclein (γSyn) are abundantly expressed in the vertebrate nervous system. αSyn functions in neurotransmitter release via binding to and clustering synaptic vesicles and chaperoning of SNARE-complex assembly. The functions of βSyn and γSyn are unknown. Functional redundancy of the three synucleins and mutual compensation when one synuclein is deleted have been proposed, but with conflicting evidence. Here, we demonstrate that βSyn and γSyn have a reduced affinity towards membranes compared to αSyn, and that direct interaction of βSyn or γSyn with αSyn results in reduced membrane binding of αSyn. Our data suggest that all three synucleins affect synapse function, but only αSyn mediates the downstream function of vesicle clustering and SNARE-complex assembly, while βSyn and γSyn modulate the activity of αSyn through regulating its binding to synaptic vesicles.
Cancer cells are sensitive to wild-type IDH1 inhibition under nutrient limitation
Authors: Vaziri-Gohar Ali , Hue Jonathan J. , Graor Hallie J. , Prendergast Erin , Chen Vanessa , Cassel Joel , Mohammed Farheen S. , Abbas Ata , Dukleska Katerina , Khokhar Imran , Hajhassani Omid , Zarei Mahsa , Wang Rui , Rothermel Luke D. , Bederman Ilya , Browers Jessica , Getts Robert , Brunengraber Henri , Salvino Joseph M. , Brody Jonathan R. , Winter Jordan M.
Published: November 2020

Pancreatic cancer cells alter their metabolism to survive cancer-associated stress (1-4). For example, cancer cells must adapt to steep nutrient gradients that characterize the natural tumor microenvironment (TME) (5-7). In the absence of adaptive strategies, harsh metabolic conditions promote the generation of free radicals (8) and impair energy production in tumor cells. Towards this end, wild-type isocitrate dehydrogenase 1 (IDH1) activity is a metabolic requirement for cancer cells living in a harsh metabolic milieu. The cytosolic enzyme interconverts isocitrate and alpha-ketoglutarate, and uses NADP(H) as a cofactor. We show that under low nutrient conditions, the enzymatic reaction favors oxidative decarboxylation to yield NADPH and alpha-ketoglutarate. Metabolic studies showed that the IDH1 products directly support antioxidant defense and mitochondrial function in stressed cancer cells. Genetic IDH1 suppression reduced growth of pancreatic cancer cells in vitro under low nutrient conditions and in mouse models of pancreatic cancer. Surprisingly, allosteric inhibitors of mutant IDH1 proved to be potent wild-type IDH1 inhibitors under conditions specific to the TME, highlighting a natural therapeutic window. The presence of low magnesium enhanced allosteric inhibition by the drug, and ambient low glucose levels enhanced cancer cells’ dependence on wild-type IDH1. Thus, intrinsic TME conditions sensitized wild-type IDH1 to FDA-approved AG-120 (ivosidenib), and revealed the drug to be a potent single-agent therapeutic in cell culture and diverse in vivo cancer models. This work identified a potentially new repertoire of safe cancer therapies, including a clinically available compound, for the treatment of multiple wild-type IDH1 cancers (e.g., pancreatic).
Are fleas highly modified Mecoptera? Phylogenomic resolution of Antliophora (Insecta: Holometabola)
Authors: Meusemann Karen , Trautwein Michelle , Friedrich Frank , Beutel Rolf G. , Wiegmann Brian M. , Donath Alexander , Podsiadlowski Lars , Petersen Malte , Niehuis Oliver , Mayer Christoph , Bayless Keith M. , Shin Seunggwan , Liu Shanlin , Hlinka Ondrej , Minh Bui Quang , Kozlov Alexey , Morel Benoit , Peters Ralph S. , Bartel Daniela , Grove Simon , Zhou Xin , Misof Bernhard , Yeates David K.
Published: November 2020

Insect orders have been defined and stable for decades, with few notable exceptions (e.g., Blattodea and Psocoptera). One of the few remaining questions of order-level monophyly is that of Mecoptera in respect to the phylogenetic placement of Siphonaptera (fleas). We used a large set of transcriptomic nucleotide sequence data representing 56 species and more than 3,000 single-copy genes to resolve the evolutionary history of Antliophora, including fleas (Siphonaptera), scorpionflies and relatives (Mecoptera), and true flies (Diptera). We find that fleas and mecopterans together are the sister group of flies. However, our data and/or analyses are unable to distinguish whether fleas are sister to a monophyletic Mecoptera, or whether they arose from within extant mecopteran families, rendering Mecoptera paraphyletic. We did not detect parameter bias in our dataset after applying a broad range of detection methods. Counter to a previous hypothesis that placed fleas within Mecoptera as the sister group to wingless boreids (snow fleas), we found a potential sister group relationship between fleas and the enigmatic family Nannochoristidae. Although we lack conclusive evidence, it seems possible that fleas represent the most-species rich group of modern mecopterans and that their parasitic lifestyle and morphological adaptations have simply made them unrecognizable in respect to their order-level classification.
Encoding of odor information and reward anticipation in anterior cortical amygdaloid nucleus
Authors: Shiotani Kazuki , Tanisumi Yuta , Hirokawa Junya , Sakurai Yoshio , Manabe Hiroyuki
Published: November 2020

Olfactory information directly reaches the amygdala through the olfactory cortex, without the involvement of thalamic areas, unlike other sensory systems. The anterior cortical amygdaloid nucleus (ACo) is one of the olfactory cortices that receives olfactory sensory input, and is part of the olfactory cortical amygdala, which relays olfactory information to the amygdala. To examine its electrophysiological features, we recorded individual ACo neurons during the odor-guided go/no-go task to obtain a water reward. Many ACo neurons exhibited odor-evoked go cue-preferred during the late phase of odor-sampling supporting the population dynamics that differentiate go/no-go responses before executing the odor-evoked behaviors. We observed two types of neurons with different anticipation signals: one neuron type exhibited gradual increases of activity toward reward delivery, while another type exhibited a phasic go cue-preferred activity during odor sampling as well as another phasic anticipatory activity for rewards. These results suggest that the ACo may be involved in reward-related behavioral learning by associating the olfactory information with reward anticipation.
Assessing and Maximizing Cultivated Diversity with Plate-Wash PCR and High Throughput Sequencing
Authors: Junkins Emily N. , Stevenson Bradley S.
Published: November 2020

Molecular techniques continue to reveal a growing disparity between the immense diversity of microbial life and the small proportion that is in pure culture. The disparity, originally dubbed “the great plate count anomaly” by Staley and Konopka, has become even more vexing given our increased understanding of the importance of microbiomes to a host and the role of microorganisms in the vital biogeochemical functions of our biosphere. Searching for novel antimicrobial drug targets often focuses on screening a broad diversity of microorganisms. If diverse microorganisms are to be screened, they need to be cultivated. Recent innovative research has used molecular techniques to assess the efficacy of cultivation efforts, providing invaluable feedback to cultivation strategies for isolating targeted and/or novel microorganisms. Here, we aimed to determine the efficiency of cultivating representative microorganisms from a non-human, mammalian microbiome, identify those microorganisms, and determine the bioactivity of isolates. Molecular methods indicated that around 57% of the ASVs detected in the original inoculum were cultivated in our experiments, but nearly 53% of the total ASVs that were present in our cultivation experiments werenotdetected in the original inoculum. In light of our controls, our data suggests that when molecular tools were used to characterize our cultivation efforts, they provided a more complete, albeit more complex, understanding of which organisms were present compared to what was eventually cultivated. Lastly, about 3% of the isolates collected from our cultivation experiments showed inhibitory bioactivity against a multidrug-resistant pathogen panel, further highlighting the importance of informing and directing future cultivation efforts with molecular tools.

Importance

Cultivation is the definitive tool to understand a microorganism’s physiology, metabolism, and ecological role(s). Despite continuous efforts to hone this skill, researchers are still observing yet-to-be cultivated organisms through high-throughput sequencing studies. Here, we use the very same tool that highlights biodiversity to assess cultivation efficiency. When applied to drug discovery, where screening a vast number of isolates for bioactive metabolites is common, cultivating redundant organisms is a hindrance. However, we observed that cultivating in combination with molecular tools can expand the observed diversity of an environment and its community, potentially increasing the number of microorganisms to be screened for natural products.
Sex of donor cell and reprogramming conditions predict the extent and nature of imprinting defects in mouse iPSCs
Authors: Arez Maria , Eckersley-Maslin Melanie , Klobučar Tajda , von Gilsa Lopes João , Krueger Felix , Raposo Ana Cláudia , Gendrel Anne-Valerie , de Jesus Bruno Bernardes , da Rocha Simão Teixeira
Published: November 2020

Reprogramming of somatic cells into induced Pluripotent Stem Cells (iPSCs) is a major leap towards personalized approaches to disease modelling and cell-replacement therapies. However, we still lack the ability to fully control the epigenetic status of iPSCs, which is a major hurdle for their downstream applications. A sensible indicator for epigenetic fidelity is genomic imprinting, a phenomenon dependent on DNA methylation, which is frequently perturbed in iPSCs by yet unidentified reasons. By using a secondary reprogramming system with murine hybrid donor cells, we conducted a thorough imprinting analysis using IMPLICON in multiple female and male iPSCs generated under different culture conditions. Our results show that imprinting defects are remarkably common in mouse iPSCs causing dysregulation of the typical monoallelic expression of imprinted genes. Interestingly, the nature of imprinting defects depends on the sex of the donor cell and their respective response to culture conditions. Under serum-free conditions, male iPSCs show global hypomethylation at imprinted regions, whereas in serum conditions show focal hypermethylation at specific loci. In contrast, female iPSCs always exhibit hypomethylation defects regardless of culture conditions. These imprinting defects are more severe than the global changes in DNA methylation, highlighting the sensitivity of imprinting loci to current iPSC generation protocols. Our results reveal clear predictors underlying different types of imprinting defects in mouse iPSCs. This knowledge is essential to devise novel reprogramming strategies aiming at generating epigenetically faithful iPSCs.