bluuebunny/crossref_metadata_2025 huggingface dataset:
An adipocyte light-Opsin 3 pathway regulates the circadian clock and energy balance
Authors: Vemaraju Shruti , Nayak Gowri , Buhr Ethan D. , Odaka Yoshinobu , Zhang Kevin X. , Mocko Julie A , Smith April N. , Upton Brian A. , Zhan Jesse J. , Borra Vishnupriya J. , Bernhard Elise , Murakami Kazutoshi , Nguyen Minh-Thanh , Gordon Shannon A. , Wu Gang , Schmidt Robert , Mei Xue , Petts Nathan T. , Batie Matthew , Rao Sujata , Hogenesch John B. , Nakamura Takahisa , Van Gelder Russell N. , Lang Richard A.
Published: July 2018

Almost all life forms can detect and decode light information for adaptive advantage. Examples include the visual system, where photoreceptor signals are processed into virtual images, and the circadian system, where light entrains a physiological clock. Here we describe a pathway in mice that employs encephalopsin (OPN3, a 480 nm light responsive opsin) to mediate light responses in murine adipocytes. The adipocyte light-OPN3 pathway regulates neonatal growth in mice and is required for at least three important functions including (1) photoentrainment of a local circadian clock, (2) extracellular matrix deposition, and (3) regulation of mitochondrial content and the proportion of “brite” adipocytes. Furthermore, we show that the light-OPN3 pathway is required for normal levels of uncoupling protein 1 (UCP1) in white and brown adipose tissue. Consequently, neonatalOpn3germ-line and adipocyte-conditional null mice show a reduced ability to maintain their body temperature under cold stress. This was also observed in wild-type mice deprived of blue light. We hypothesize that the adipocyte light-OPN3 pathway provides a dynamically responsive, circadian clock-integrated mechanism for regulating adipocyte function and in turn directing metabolism to thermogenesis rather than anabolism. These data indicate an important role for peripheral light sensing in mammals and may have broad implications for human health given the unnatural lighting conditions in which we live.
Fibroblast growth factor is predicted to dominate MAPK activation by pro-angiogenic factors
Authors: Song Min , Finley Stacey D.
Published: July 2018

Angiogenesis is important in physiological and pathological conditions, as blood vessels provide nutrients and oxygen needed for tissue growth and survival. Therefore, targeting angiogenesis is a prominent strategy in both tissue engineering and cancer treatment. However, not all of the approaches to promote or inhibit angiogenesis lead to successful outcomes. Angiogenesis-based therapies primarily target pro-angiogenic factors such as vascular endothelial growth factor-A (VEGF) or fibroblast growth factor (FGF) in isolation, and there is a limited understanding of how these promoters combine together to stimulate angiogenesis. Thus, more quantitative insight is needed to understand their interactions. In this study, we have trained and validated a detailed mathematical model to quantitatively characterize the crosstalk of FGF and VEGF intracellular signaling. The model focuses on FGF- and VEGF-induced mitogen-activated protein kinase (MAPK) signaling and phosphorylation of extracellular regulated kinase (ERK), which promote cell proliferation. We apply the model to predict the dynamics of phosphorylated ERK (pERK) in response to the stimulation by FGF and VEGF individually and in combination. The model predicts that FGF plays a dominant role in promoting ERK phosphorylation, compared to VEGF. The modeling predictions show that VEGFR2 density and trafficking parameters significantly influence the level of VEGF-induced pERK. The model matches experimental data and is a framework to synthesize and quantitatively explain experimental studies. Ultimately, the model provides mechanistic insight into FGF and VEGF interactions needed to identify potential targets for pro-or anti-angiogenic therapies.
Local Enrichment of HP1alpha at Telomeres Alters Their Structure and Regulation of Telomere Protection
Authors: Chow Tracy T. , Shi Xiaoyu , Wei Jen-Hsuan , Guan Juan , Stadler Guido , Huang Bo , Blackburn Elizabeth H.
Published: July 2018

Enhanced telomere maintenance is evident in malignant cancers. While telomeres are thought to be inherently heterochromatic, detailed mechanisms of how epigenetic modifications impact telomere protection and structures are largely unknown in human cancers. Here we develop a molecular tethering approach to experimentally enrich heterochromatin protein HP1α specifically at telomeres. This results in increased deposition of H3K9me3 at cancer cell telomeres. Telomere extension by telomerase is attenuated, and damage-induced foci at telomeres are reduced, indicating augmentation of telomere stability. Super resolution STORM imaging shows an unexpected increase in irregularity of telomeric structure. Telomere-tethered chromo shadow domain (CSD) mutant I165A of HP1α abrogates both the inhibition of telomere extension and the irregularity of telomeric structure, suggesting the involvement of at least one HP1α-ligand in mediating these effects. This work presents a new approach to specifically manipulate the epigenetic status locally at telomeres to uncover insights into molecular mechanisms underlying telomere structural dynamics.
Quantification of differential transcription factor activity and multiomics-based classification into activators and repressors:diffTF
Authors: Berest Ivan , Arnold Christian , Reyes-Palomares Armando , Palla Giovanni , Rasmussen Kasper Dindler , Helin Kristian , Zaugg Judith B.
Published: July 2018

Transcription factor (TF) activity is an important read-out of cellular signalling pathways and thus to assess regulatory differences across conditions. However, current technologies lack the ability to simultaneously assess activity changes for multiple TFs and in particular to determine whether a specific TF acts globally as transcriptional repressor or activator. To this end, we introduce a widely applicable genome-wide methoddiffTFto assess differential TF activity and to classify TFs as activator or repressor (available athttps://git.embl.de/grp-zaugg/diffTF). This is done by integrating any type of genome-wide chromatin accessibility data with RNA-Seq data and in-silico predicted TF binding sites. We corroborated the classification of TFs into repressors and activators by three independent analyses based on enrichments of active/repressive chromatin states, correlation of TF activity with gene expression, and activator-and repressor-specific chromatin footprints. To show the power ofdiffTF, we present two case studies: First, we applieddiffTFin to a large ATAC-Seq/RNA-Seq dataset comparing mutated and unmutated chronic lymphocytic leukemia samples, where we identified dozens of known (40%) and potentially novel (60%) TFs that are differentially active. We were also able to classify almost half of them as either repressor and activator. Second, we applieddiffTFto a small ATAC-Seq/RNA-Seq data set comparing two cell types along the hematopoietic differentiation trajectory (multipotent progenitors – MPP – versus granulocyte-macrophage progenitors – GMP). Here we identified the known drivers of differentiation and found that the majority of the differentially active TFs are transcriptional activators. Overall,diffTFwas able to recover the known TFs in both case studies, additionally identified TFs that have been less well characterized in the given condition, and provides a classification of the TFs into transcriptional activators and repressors.
Dorsal Premotor Contributions to Auditory Rhythm Perception: Causal Transcranial Magnetic Stimulation Studies of Interval, Tempo, and Phase
Authors: Ross Jessica , Iversen John , Balasubramaniam Ramesh
Published: July 2018

It has been suggested that movement planning networks are critical for time perception. The Action Simulation for Auditory Prediction (ASAP) hypothesis proposes that the dorsal auditory stream is involved in predictive beat-based timing through bidirectional interchange between auditory perception and dorsal premotor (dPMC) prediction via parietal regions, as has been supported by brain imaging and transcranial magnetic stimulation (TMS). However, causal impact of dPMC on time perception has not been tested directly. We used a TMS protocol that down-regulates cortical activity, continuous theta burst stimulation (cTBS), to test for causal contributions of left dPMC to time perception. Three experiments measured (1) discrete interval timing perception, and relative beat-based musical timing for (2) tempo perception and (3) phase perception. Perceptual acuity was tested pre- and post-cTBS using a test of sub-second interval discrimination and the Adaptive Beat Alignment Test (A-BAT). We show (N = 30) that cTBS down-regulation of left dPMC interferes with interval timing perception and the ability to detect differences in musical tempo, but not phase. Our data support causal involvement of premotor networks in perceptual timing, supporting a causal role of the left dPMC in accurate interval and musical tempo perception, possibly via dorsal stream interactions with auditory cortex.
Parl Deficiency in Mouse Causes Coenzyme Q Depletion, Complex III Defects, and Leigh-like Syndrome
Authors: Spinazzi Marco , Radaelli Enrico , Horré Katrien , Arranz Amaia M. , Gounko Natalia , Agostinis Patrizia , Impens Francis , Alexandra Morais Vanessa , Lopez-Lluch Guillermo , Serneels Lutgarde , Navas Placido , De Strooper Bart
Published: July 2018

The mitochondrial intramembrane rhomboid protease Parl has been implicated in diverse functions in vitro, but its physiological role in vivo remains unclear. Here we show that Parl ablation in mouse causes a striking necrotizing encephalomyelopathy similar to Leigh syndrome, a mitochondrial disease characterized by disrupted energy production. Mice with conditional Parl deficiency in the nervous system, but not in muscle, develop a similar phenotype as germline Parl knockouts demonstrating the vital role of Parl in neurological homeostasis. Genetic modification of two major Parl substrates, Pink1 and Pgam5, do not modify this severe neurological phenotype. Parl-/- brain mitochondria are affected by defects in Complex III activity and in coenzyme Q biosynthesis. Parl is necessary for the stable expression of Ttc19, required for Complex III activity, and of Coq4, essential in coenzyme Q biosynthesis. Thus, Parl plays a previously overseen constitutive role in the maintenance of the respiratory chain in the nervous system, and its deficiency causes progressive mitochondrial dysfunction and Leigh-like syndrome.
High-throughput yeast two-hybrid library screening using next generation sequencing
Authors: Erffelinck Marie-Laure , Ribeiro Bianca , Perassolo Maria , Pauwels Laurens , Pollier Jacob , Storme Veronique , Goossens Alain
Published: July 2018

Yeast two-hybrid (Y2H) is a well-established genetics-based system that uses yeast to selectively display binary protein-protein interactions (PPIs). To meet the current need to unravel complex PPI networks, several adaptations have been made to establish medium- to high-throughput Y2H screening platforms, with several having successfully incorporated the use of the next-generation sequencing (NGS) technology to increase the scale and sensitivity of the method. However, these have been to date mainly restricted to the use of fully annotated custom-made open reading frame (ORF) libraries and subject to complex downstream data processing. Here, a streamlined high-throughput Y2H library screening strategy, based on integration of Y2H with NGS, called Y2H-seq, was developed, which allows efficient and reliable screening of Y2H cDNA libraries. To generate proof of concept, the method was applied to screen for interaction partners of two key components of the jasmonate signaling machinery in the model plantArabidopsis thaliana, resulting in the identification of several previously reported as well as hitherto unknown interactors. Our Y2H-seq method offers a user-friendly, specific and sensitive screening method that allows high-throughput identification of PPIs without prior knowledge of the organism’s ORFs, thereby extending the method to organisms of which the genome has not entirely been annotated yet. The quantitative NGS readout and the incorporation of background controls allow to increase genome coverage and ultimately dispose of recurrent false positives, thereby overcoming some of the bottlenecks of current Y2H technologies, which will further strengthen the value of the Y2H technology as a discovery platform.
Occidiofungin, an actin binding antifungal within vivoefficacy in a vulvovaginal candidiasis infection
Authors: Ravichandran Akshaya , Geng Mengxin , Hull Kenneth G. , Romo Daniel , Lu Shi-En , Albee Aaron , Nutter Christopher , Gordon Donna M. , Ghannoum Mahmoud A. , Lockless Steve W. , Smith Leif
Published: July 2018

Current antifungal treatment options are plagued with rapidly increasing occurrence of resistance, high degree of toxicity and a limited spectrum of activity. The need to develop a novel antifungal with a unique target, wider spectrum of activity, and reduced toxicity to the host, is urgent. We have identified and characterized one such compound named occidiofungin that is produced by the soil bacteriumBurkholderia contaminansMS14. This study identifies the primary cellular target of the antifungal, which was determined to be actin. Actin binding metabolites are generally characterized by their ability to inhibit polymerization or depolymerization of actin filaments, which presumably accounts for their severe toxicity. Occidiofungin, instead, has a subtler effect on actin dynamics that triggers apoptotic cell death. We were able to demonstrate the effectiveness of the antifungal in treating a vulvovaginal yeast infection in a murine model. This discovery puts occidiofungin in a unique class of actin-binding antifungal compounds with minimal reported toxicity to the host. The results of this study are important for the development of a novel class of antifungals that could fill the existing gap in treatment options for fungal infections.

Author summary

Widespread resistance to antifungal compounds currently in use has been alarming. Identification and development of a new class of antifungals with a novel cellular target is desperately needed. This study describes the assays carried out to determine the molecular target and evaluate efficacy of one such novel antifungal compound called occidiofungin. Occidiofungin modified with a functional alkyne group enabled affinity purification assays and localization studies in yeast. These studies led to the identification of the actin binding property of occidiofungin. Actin-binding by secondary metabolites often exhibit severe host toxicity, but this does not appear to be the case for occidiofungin. We have previously been able to administer occidiofungin to mice at concentrations in the range of 5 mg/kg without any serious complications. We were able to demonstrate the effectiveness of the antifungal in treating a vaginal fungal infection in a murine model. The results outlined in this manuscript establish that occidiofungin is an efficacious compound with a novel molecular target, putting it in a completely new class of antifungals.
Myoglianin triggers the pre-metamorphosis stage in hemimetabolan insects
Authors: Kamsoi Orathai , Belles Xavier
Published: July 2018

Insect metamorphosis is triggered by a decrease in juvenile hormone (JH) in the final juvenile instar. What induces this decline is therefore a very relevant question. Working with the cockroachBlattella germanica, we found that Myoglianin (Myo), a ligand in the TGF-β signaling pathway, is highly expressed in the corpora allata (CA, the JH producing glands) and prothoracic glands (PG, which produce ecdysone) during the penultimate nymphal instar (N5). In the CA, high Myo levels during N5 repress the expression ofjhamt, a JH biosynthesis gene. In the PG, decreasing JH levels trigger gland degeneration, mediated by the factors Kr-h1, FTZ-F1, E93 and IAP1. Also in the PG, a peak ofmyoexpression in N5 stimulates the expression of ecdysone biosynthesis genes, such asnvd, thus enhancing the production of the metamorphic ecdysone pulse in N6. Themyoexpression peak in N5 also represses cell proliferation, which can contribute to enhance ecdysone production. The data indicate that Myo triggers the pre-metamorphic nymphal instar inB. germanica, and possibly in other hemimetabolan insects.
The Female Heart: Sex Differences in the Dynamics of ECG in Response to Stress
Authors: Adjei Tricia , Xue Jingwen , Mandic Danilo P.
Published: July 2018

Sex differences in the study of the human physiological response to mental stress are often erroneously ignored. To this end, we set out to show that our understanding of the stress response is fundamentally altered once sex differences are taken into account. This is achieved by comparing the heart rate variability (HRV) signals acquired during mental maths tests from ten females and ten males of similar maths ability; all females were in the follicular phase of their menstrual cycle. For rigour, the HRV signals from this pilot study were analysed using temporal, spectral and nonlinear signal processing techniques, which all revealed significant statistical differences between the sexes, with the stress-induced increases in the heart rates from the males being significantly larger than those from the females (p-value=2.2×10−3). In addition, mental stress produced an overall increase in the power of the low frequency component of HRV in the males, but caused an overall decrease in the females. The stress-induced changes in the power of the high frequency component were even more profound; it greatly decreased in the males, but increased in the females. We also show that mental stress was followed by the expected decrease in sample entropy, a nonlinear measure of signal regularity, computed from the males’ HRV signals, while overall, stress manifested in an increase in the sample entropy computed from the females’ HRV signals. This finding is significant, since mental stress is commonly understood to be manifested in the decreased entropy of HRV signals, however, the significant difference (p-value=2×10−9) in the changes in the entropies from the males and females highlights the pitfalls in ignoring sex in the formation of a physiological hypothesis. Furthermore, it has been argued that oestrogen attenuates the effect of catecholamine stress hormones; the findings from this investigation suggest for the first time that the conventionally cited cardiac changes, attributed to the fight-or-flight stress response, are not universally applicable to females. Instead, this pilot study provides an alternative interpretation of cardiac responses to stress in females, which indicates a closer alignment to the evolutionary tend-and-befriend response.
Exocyst subunit Sec6 is positioned by microtubule overlaps in the moss phragmoplast prior to the arrival of cell plate membrane
Authors: Tang Han , de Keijzer Jeroen , Overdijk Elysa , Sweep Els , Steentjes Maikel , Vermeer Joop E. , Janson Marcel E. , Ketelaar Tijs
Published: July 2018

During plant cytokinesis a radially expanding membrane-enclosedcell plateis formed from fusing vesicles that compartmentalizes the cell in two. How fusion is spatially restricted to the site of cell plate formation is unknown. Aggregation of cell-plate membrane starts near regions of microtubule overlap within the bipolar phragmoplast apparatus of the mossPhyscomitrella patens. Since vesicle fusion generally requires coordination of vesicle tethering and subsequent fusion activity we analysed the subcellular localization of several subunits of the exocyst, a tethering complex active during plant cytokinesis. We found that Sec6, but neither Sec3 or Sec5 subunits localized to microtubule overlap regions in advance of cell plate construction started in moss. Moreover, Sec6 exhibited a conserved physical interaction with an orthologue of the Sec1/Munc18 protein KEULE, an important regulator for cell-plate membrane vesicle fusion in Arabidopsis. Recruitment of PpKEULE and vesicles to the early cell plate was delayed upon Sec6 gene silencing. Our findings thus suggest that vesicle-vesicle fusion is in part enabled by a pool of exocyst subunits at microtubule overlaps that is recruited independent of the delivery of vesicles.

Summary statement

We performed a time-resolved localization screen of multiple subunits of the exocyst complex throughout moss cytokinesis and show that each subunit has a unique spatiotemporal recruitment pattern.
The Feeding Connectome: Convergence of Monosynaptic and Polysynaptic Sensory Paths onto Common Motor Outputs
Authors: Miroschnikow Anton , Schlegel Philipp , Schoofs Andreas , Hückesfeld Sebastian , Li Feng , Schneider-Mizell Casey M , Fetter Richard D , Truman James , Cardona Albert , Pankratz Michael J
Published: July 2018

Little is known about the organization of central circuits by which external and internal sensory inputs act on motor outputs to regulate fundamental behaviors such as feeding. We reconstructed, from a whole CNS EM volume, the synaptic map of input and output neurons that underlie food intake behavior ofDrosophilalarvae. The input neurons originate from enteric, pharyngeal and external sensory organs and converge onto seven distinct sensory synaptic compartments within the CNS, as defined by distribution patterns of their presynaptic sites. The output neurons consist of pharyngeal motor neurons, serotonergic modulatory neurons, and neuroendocrine neurons that target the ring gland, a key endocrine organ. Monosynaptic connections from a set of sensory synaptic compartments cover the motor and endocrine targets in overlapping domains. Polysynaptic routes can be superimposed on top of the monosynaptic connections, resulting in divergent sensory paths that converge on common motor outputs. A completely different set of sensory compartments is connected to the mushroom body calyx of the memory circuits. Our results illustrate a circuit architecture in which monosynaptic and multisynaptic connections from sensory inputs traverse onto output neurons via a series of converging paths.
Regional diversity in the postsynaptic proteome of the mouse brain
Authors: Roy Marcia , Sorokina Oksana , McLean Colin , Tapia-González Silvia , DeFelipe Javier , Armstrong J. Douglas , Grant Seth G. N.
Published: July 2018

The proteome of the postsynaptic terminal of excitatory synapses comprises over one thousand proteins in vertebrate species and plays a central role in behavior and brain disease. The brain is organized into anatomically distinct regions and whether the synapse proteome differs across these regions is poorly understood. Postsynaptic proteomes were isolated from seven forebrain and hindbrain regions in mice and their composition determined using proteomic mass spectrometry. Seventy-four percent of proteins showed differential expression and each region displayed a unique compositional signature. These signatures correlated with the anatomical divisions of the brain and their embryological origins. Biochemical pathways controlling plasticity and disease, protein interaction networks and individual proteins involved with cognition all showed differential regional expression. Combining proteomic and connectomic data shows that interconnected regions have specific proteome signatures. Diversity in synapse proteome composition is key feature of mouse and human brain structure.
Novel bir’s-foot trefoil RNA viruses provide insights into a clade of legume associated enamoviruses
Authors: Debat Humberto J. , Bejerman Nicolas
Published: July 2018

Bird’s-foot trefoil (Lotus corniculatus) is a nutritious forage crop, employed for livestock foraging around the world. Here, we report the identification and characterization of two novel viruses associated with bird’s-foot trefoil. Virus sequences with affinity to enamoviruses (ssRNA (+);Luteoviridae; Enamovirus) and nucleorhabdoviruses (ssRNA (-);Rhabdoviridae; Nucleorhabdovirus) were detected inL. corniculatustranscriptome data. The tentatively named birds-foot trefoil associated virus 1 (BFTV-1) genome organization is characterized by 13,626 nt long negative-sense ssRNA. BFTV-1 presents in its antigenome orientation six predicted gene products in the canonical order 3′-N-P-P3-M-G-L-5′. The proposed birds-foot trefoil associated virus 2 (BFTV-2) 5,736 nt virus sequence presents a typical 5′-PO-P1-2-IGS-P3-P5-3′ enamovirus genome structure. Phylogenetic analysis suggests that BFTV-1 is closely related toDatura yellow vein nucleorhabdovirus, and that BFTV-2 clusters into a monophyletic cluster of legumes-associated enamoviruses. This sub-clade of highly related and co-divergent legume associated viruses provides insights on the evolutionary history of the enamoviruses. The bioinformatic reanalysis of SRA libraries deposited in the NCBI database constitutes an emerging approach to the discovery of novel plant viruses which should be important for both quarantine purposes and disease management.
A central control circuit for encoding perceived food value
Authors: Crossley Michael , Staras Kevin , Kemenes György
Published: July 2018

Hunger state can substantially alter the perceived value of a stimulus, even to the extent that the same sensory cue can trigger antagonistic behaviors. How the nervous system uses such graded perceptual shifts to select between opposed motor patterns remains enigmatic. Here we challenged food-deprived and satiatedLymnaeato choose between two mutually exclusive behaviors, ingestion or egestion, produced by the same feeding central pattern generator. Decoding the underlying neural circuit reveals that the activity of central dopaminergic interneurons defines hunger state and drives network reconfiguration, biasing satiated animals towards the rejection of stimuli deemed palatable by food-deprived ones. By blocking the action of these neurons, satiated animals can be reconfigured to exhibit a hungry animal phenotype. This centralized mechanism occurs in the complete absence of sensory retuning and generalizes across different sensory modalities, allowing food-deprived animals to increase their perception of food value in a stimulus-independent manner to maximize potential calorific intake.
Distribution and asymptotic behavior of the phylogenetic transfer distance
Authors: Dávila Felipe Miraine , Entfellner Jean-Baka Domelevo , Lemoine Frédéric , Truszkowski Jakub , Gascuel Olivier
Published: July 2018

Thetransfer distance(TD) was introduced in the classification framework and studied in the context of phylogenetic tree matching. Recently, Lemoine et al. (2018) showed that TD can be a powerful tool to assess the branch support of phylogenies with large data sets, thus providing a relevant alternative to Felsenstein’s bootstrap. This distance allows areference branch βin a reference tree 𝒯 to be compared to a branchbfrom another treeT, both on the same set ofntaxa. The TD between these branches is the number of taxa that must be transferred from one side ofbto the other in order to obtainβ. By taking the minimum TD fromβto all branches inTwe define thetransfer index, denoted byϕ(β, T), measuring the degree of agreement ofβwithT. Let us consider a reference branchβhavingptips on its light side and define thetransfer support(TS) as 1 –ϕ(β, T)/(p –1). The aim of this article is to provide evidence thatp1 is a meaningful normalization constant in the definition of TS, and measure the statistical significance of TS, assuming thatβis compared to a tree T drawn according to a null model. We obtain several results that shed light on these questions in a number of settings. In particular, we study the asymptotic behavior of TS whenntends to ∞, and fully characterize the distribution ofϕwhenTis a caterpillar tree.
Tau protein aggregation induces cellular senescence in the brain
Authors: Musi Nicolas , Valentine Joseph M. , Sickora Kathryn R. , Baeuerle Eric , Thompson Cody S. , Zapata Ashley , Shen Qiang , Orr Miranda E.
Published: July 2018

Tau protein accumulation is the most common pathology among degenerative brain diseases, including Alzheimer’s disease (AD), progressive supranuclear palsy (PSP), traumatic brain injury (TBI) and over twenty others1. Tau-containing neurofibrillary tangle (NFT) accumulation is the closest correlate with cognitive decline and cell loss, yet the mechanisms mediating tau toxicity are poorly understood. NFT-containing neurons do not die, which suggests secondary mechanisms are driving toxicity2. We evaluated gene expression patterns of NFT-containing neurons microdissected from AD patient brains3 and found they develop an expression profile consistent with cellular senescence described in dividing cells. This complex stress response induces a near permanent cell cycle arrest, adaptations to maintain survival, cellular remodeling, and metabolic dysfunction4. Moreover, senescent cells induce chronic degeneration of surrounding tissue through the secretion of pro-inflammatory, pro-apoptotic molecules termed the senescence-associated secretory phenotype (SASP)5. Using transgenic mouse models of tau-associated pathogenesis we found that NFTs induced a senescence-like phenotype including DNA damage, karyomegaly, mitochondrial dysfunction and SASP. Cdkn2a transcript level, a hallmark measure of senescence, directly correlated with brain atrophy and NFT load. This relationship extended to postmortem brain tissue from humans with PSP to indicate a phenomenon common to tau toxicity. Tau transgenic mice with late stage pathology were treated with senolytics to remove senescent cells. Despite the advanced age and disease progression, senolytic treatment reduced total NFT burden, neuron loss and ventricular enlargement; and normalized cerebral blood flow to that of non-transgenic control mice. Collectively, these findings indicate that NFTs induce cellular senescence in the brain, which contributes to neurodegeneration and brain dysfunction. Moreover, given the prevalence of tau protein deposition among neurodegenerative diseases, these findings have broad implications for understanding, and potentially treating, dozens of brain diseases.
Computational fluid dynamic analysis reveals the underlying physical forces playing a role in 3D multiplex brain organoid cultures
Authors: Goto-Silva Livia , Ayad Nadia M. E. , Herzog Iasmin L. , Silva Nilton P. , Lamien Bernard , Orlande Helcio R. B. , Costa Souza Annie da , Ribeiro Sidarta , Martins Michele , Domont Gilberto B. , Junqueira Magno , Tovar-Moll Fernanda , Rehen Stevens K.
Published: July 2018

Organoid cultivation in suspension culture requires agitation at low shear stress to allow for nutrient diffusion, which preserves tissue structure. Multiplex systems for organoid cultivation have been proposed, but whether they meet similar shear stress parameters as the regularly used spinner flask and its correlation with the successful generation of brain organoids, has not been determined. Herein, we used computational fluid dynamics (CFD) analysis to compare two multiplex culture conditions: steering plates on an orbital shaker and the use of a previously described bioreactor. The bioreactor had low speed and high shear stress regions that may affect cell aggregate growth, depending on volume, whereas the CFD parameters of the steering plates were closest to the parameters of the spinning flask. Our protocol improves the initial steps of the standard brain organoid formation, and organoids produced therefrom displayed regionalized brain structures, including retinal pigmented cells. Overall, we conclude that suspension culture on orbital steering plates is a cost-effective practical alternative to previously described platforms for the cultivation of brain organoids for research and multiplex testing.

Highlights

Improvements to organoid preparation protocol

Multiplex suspension culture protocol successfully generate brain organoids

Computational fluid dynamics (CFD) reveals emerging properties of suspension cultures

CFD of steering plates is equivalent to that of spinner flask cultures
Multi-scale analysis of schizophrenia risk loci: Integrating centenarian genomes and spatio-temporal expression profiles suggests the need for adjunctive therapeutic interventions for neuropsychiatric disorders
Authors: Anirudh Chellappa S , Pathak Ankit Kumar , Sinha Prashant , Jainarayanan Ashwin K. , Jain Sanjeev , Brahmachari Samir K.
Published: July 2018

Schizophrenia (SZ) is a debilitating mental illness with multigenic etiology and significant heritability. Despite extensive genetic studies the molecular etiology has remained enigmatic. A recent systems biology study suggested a protein-protein interaction (PPI) network for SZ with 504 novel interactions. The onset of psychiatric disorders is predominantly during adolescence often accompanied by subtle structural abnormalities in multiple regions of the brain. The availability of BrainSpan atlas data allowed us to re-examine the genes present in SZ interactome as a function of space and time. The availability of genomes of healthy centenarians and non-psychiatric ExAC database allowed us to identify thevariants of criticality. The expression of SZ candidate genes responsible for cognition and disease onset were studied in different brain regions during particular developmental stages. A subset of novel interactors detected in the network was further validated using gene-expression data of post-mortem brains of patients with psychiatric illness. We have narrowed down the list of drug targets proposed by the previous interactome study to 10 proteins. These proteins belonging to 81 biological pathways, are targeted by 34 known FDA approved drugs that have distinct potential for treatment of neuropsychiatric disorders. We also report the possibility of targeting key genes belonging to Celecoxib pharmacodynamics, Gα signaling and cGMP-PKG signaling pathways, that are non-specific to schizophrenia etiology.
Estrogen-independent molecular actions of mutant estrogen receptor alpha in endometrial cancer
Authors: Blanchard Zannel , Vahrenkamp Jeffery M. , Berrett Kristofer C. , Arnesen Spencer , Gertz Jason
Published: July 2018

Estrogen receptor 1 (ESR1) mutations have been identified in hormone therapy resistant breast cancer and primary endometrial cancer. Analyses in breast cancer suggests that mutant ESR1 exhibits estrogen independent activity. In endometrial cancer, ESR1 mutations are associated with worse outcomes and less obesity, however experimental investigation of these mutations has not been performed. Using a unique CRISPR/Cas9 strategy, we introduced the D538G mutation, a common endometrial cancer mutation that alters the ligand binding domain of ESR1, while epitope tagging the endogenous locus. We discovered estrogen-independent mutant ESR1 genomic binding that is significantly altered from wildtype ESR1. The D538G mutation impacted expression, including a large set of non-estrogen regulated genes, and chromatin accessibility, with most affected loci bound by mutant ESR1. Mutant ESR1 is unique from constitutive ESR1 activity as mutant-specific changes are not recapitulated with prolonged estrogen exposure. Overall, D538G mutant ESR1 confers estrogen-independent activity while causing additional regulatory changes in endometrial cancer cells that are distinct from breast cancer cells.
Male and female mice demonstrate divergent cellular responses in the bed nucleus of stria terminalis (BNST) following morphine withdrawal
Authors: Luster Brennon R. , Cogan Elizabeth S. , Schmidt Karl T. , Pati Dipanwita , Pina Melanie M. , Dange Kedar , McElligott Zoé A.
Published: July 2018

The United States is experiencing an opioid epidemic of significant proportions, imposing enormous fiscal and societal costs. While prescription opioid analgesics are essential for treating pain, the cessation of these drugs can induce a withdrawal syndrome, and thus opioid use often persists to alleviate or avoid these symptoms. Therefore, it is essential to understand the neurobiology underlying this critical window of withdrawal from opioid analgesics to prevent continued usage. To model this, we administered a low dose of morphine, and precipitated withdrawal with naloxone to investigate the behavioral and cellular responses in C57BL/6J male and female mice. Following 3 days of administration, both male and female mice sensitized to the repeated bouts of withdrawal, as evidenced by their composite global withdrawal score. Female mice exhibited increased withdrawal symptoms on some individual measures, but did not show characteristic weight loss observed in male mice. Because of its role in mediating withdrawal-associated behaviors, we examined neuronal excitability and inhibitory synaptic transmission in the bed nucleus of the stria terminalis (BNST) 24 hours following the final precipitated withdrawal. In male mice, morphine withdrawal increased spontaneous GABAergic signaling compared to controls. In contrast, morphine withdrawal decreased spontaneous GABAergic signaling, and increased BNST projection neuron excitability in female mice. Intriguingly, these opposing GABAergic effects were dependent on within slice excitability. Our findings suggest that male and female mice manifest divergent cellular responses in the BNST following morphine withdrawal, and alterations in BNST inhibitory signaling may be a significant factor contributing to the expression of behaviors following opioid withdrawal.
A novel virtual plus-maze for studying electrophysiological correlates of spatial reorientation
Authors: Török Ágoston , Kóbor Andrea , Honbolygó Ferenc , Baker Travis
Published: July 2018

Quick reorientation is an essential part of successful navigation. Despite growing attention to this ability, little is known about how reorientation happens in humans. To this aim, we recorded EEG from 34 participants. Participants were navigating a simple virtual reality plus-maze where at the beginning of each trial they were randomly teleported to either the North or the South alley. Results show that the teleportation event caused a quick reorientation effect over occipito-parietal areas as early as 100 msec; meaning that despite the known stochastic nature of the teleportation, participants built up expectations for their place of arrival. This result has important consequences for the optimal design of Virtual reality locomotion.
transcranial Direct Current Stimulation Studies Open Database (tDCS-OD)
Authors: Grossman Pnina , Alekseichuk Ivan , de Lara Gabriel , Paneri Kunal , Kunz Patrik , Turi Zsolt , Bikson Marom , Paulus Walter , Antal Andrea
Published: July 2018

Transcranial direct current stimulation (tDCS) is increasingly evaluated for a myriad of clinical indications and performance enhancement mainly related to cognitive and motor applications. As a result tDCS has been tested with diverse inclusion criteria and subject populations. tDCS is customized for applications by many factors, including stimulation dose (montage, current, time), associated training and subject inclusion/exclusion criteria. The rapid proliferation of applications, technological advancements and emerging scientific discoveries presents challenges to the organization and consolidation of tDCS data – which can lead to scientific, clinical and public confusions. In this paper, we develop a system to summarize and consolidate methodological aspects of tDCS, concentrating on study design and the physical parameters of the stimulation. We introduce a community-driven, open access database, where these parameters, including stimulation intensities, duration, electrode sizes, montages, and subject information, are noted for relevant tDCS publications. The transcranial Direct Current Stimulation Studies Open Database (tDCS-OD) (http://tdcsdatabase.com) will support constructive dialogue on research and clinical tDCS applications, critical evaluation of past work, and identification of promising protocols, while reducing ambiguity about stimulation methodology. The database design allows ongoing updates and editing, with transparent version control. At the moment, the database includes information about 56,613 tDCS sessions.
Brd4 and P300 regulate zygotic genome activation through histone acetylation
Authors: Chan Shun Hang , Tang Yin , Miao Liyun , Darwich-Codore Hiba , Vejnar Charles E. , Beaudoin Jean-Denis , Musaev Damir , Fernandez Juan P. , Moreno-Mateos Miguel A. , Giraldez Antonio J.
Published: July 2018

The awakening of the zygote genome, signaling the transition from maternal transcriptional control to zygotic control, is a watershed in embryonic development, but the factors and mechanisms controlling this transition are still poorly understood. By combining CRISPR-Cas9-mediated live imaging of the first transcribed genes (miR-430), chromatin and transcription analysis during zebrafish embryogenesis, we observed that genome activation is gradual and stochastic, and the active state is inherited in daughter cells. We discovered that genome activation is regulated through both translation of maternal mRNAs and the effects of these factors on the chromatin. We show that chemical inhibition of H3K27Ac writer (P300) and reader (Brd4) block genome activation, while induction of a histone acetylation prematurely activates transcription, and restore genome activation in embryos where translation of maternal mRNAs is impaired, demonstrating that they are limiting factors for the activation of the genome. In contrast to current models, we do not observe triggering of genome activation by a reduction of the nuclear-cytoplasmic (N/C) ratio or slower cell division. We conclude that genome activation is controlled by a time-dependent mechanism involving the translation of maternal mRNAs and the regulation of histone acetylation through P300 and Brd4. This mechanism is critical to initiating zygotic development and developmental reprogramming.
CRISPR-Cas9 human gene replacement and phenomic characterization inCaenorhabditis elegansto understand the functional conservation of human genes and decipher variants of uncertain significance
Authors: McDiarmid Troy A. , Au Vinci , Loewen Aaron D. , Liang Joseph , Mizumoto Kota , Moerman Donald G. , Rankin Catharine H.
Published: July 2018

Our ability to sequence genomes has vastly surpassed our ability to interpret the genetic variation we discover. This presents a major challenge in the clinical setting, where the recent application of whole exome and whole genome sequencing has uncovered thousands of genetic variants of uncertain significance. Here, we present a strategy for targeted human gene replacement and phenomic characterization based on CRISPR-Cas9 genome engineering in the genetic model organismCaenorhabditis elegansthat will facilitate assessment of the functional conservation of human genes and structure-function analysis of disease-associated variants with unprecedented precision. We validate our strategy by demonstrating that direct single-copy replacement of theC. elegansortholog (daf-18) with the critical human disease-associated gene Phosphatase and Tensin Homolog (PTEN) is sufficient to rescue multiple phenotypic abnormalities caused by complete deletion ofdaf-18, including complex chemosensory and mechanosenory impairments. In addition, we used our strategy to generate animals harboring a single copy of the known pathogenic lipid phosphatase inactive PTEN variant (PTEN-G129E) and showed that our automatedin vivophenotypic assays could accurately and efficiently classify this missense variant as loss-of-function. The integrated nature of the human transgenes allows for analysis of both homozygous and heterozygous variants and greatly facilitates high-throughput precision medicine drug screens. By combining genome engineering with rapid and automated phenotypic characterization, our strategy streamlines identification of novel conserved gene functions in complex sensory and learning phenotypes that can be used asin vivofunctional assays to decipher variants of uncertain significance.
Tube for obtaining crystals in a laboratory furnace
Authors: Janicijevic Aco , Danilovic Nebojsa
Published: July 2018

A design for an air-cooled tube (`crystallization incubator') installed in a laboratory tube furnace is presented. The setup allows regulation and simultaneous crystallization of several substances at different temperature gradients and rate intervals, with the purpose of obtaining crystals.
The nanodiffraction problem
Authors: Xiong Shangmin , Öztürk Hande , Lee Seung-Yub , Mooney Patricia M. , Noyan Ismail Cevdet
Published: July 2018

The results of a systematic rigorous study on the accuracy of lattice parameters computed from X-ray diffraction patterns of ideally perfect nanocrystalline powder and thin-film samples are presented. It is shown that, if the dimensions of such samples are below 20 nm, the lattice parameters obtained from diffraction analysis will deviate from their true values. The relative deviation depends on the relevant size parameter through an inverse power law and, for particular reflections, depends on the angular peak positions. This size-dependent error, Δa/a, is larger than the precision of typical X-ray diffraction measurements for ∼20 nm-thick diffracting domains, and it can be several orders of magnitude larger for particles smaller than 5 nm.
decryst: an efficient software suite for structure determination from powder diffraction
Authors: Liu Yu
Published: July 2018

Presented here isdecryst, a software suite for structure determination from powder diffraction, which uses the direct-space method, and is able to apply anti-bump constraints automatically and efficiently during the procedure of global optimization using the crystallographic collision detection algorithm by Liu [Acta Cryst.(2017), A73, 414–422].decrystemploys incremental computation in its global-optimization cycles, which results in dramatic performance enhancement. It is also designed with parallel and distributed computing in mind, allowing for even better performance by simultaneous use of multiple processors. Owing to the parallelized usage of the equivalent position combination method [Deng & Dong (2009).J. Appl. Cryst.42, 953–958] indecryst, it is particularly suitable for determination of structures with mostly unknown bonding relations, and offers some unprecedented opportunities for these structures.decrystis free and open-source software, and can be obtained at https://gitlab.com/CasperVector/decryst/; it strives to be simple yet flexible, in the hope that the underlying techniques could be adopted in more crystallographic applications.
Polymorphic phase transformations of 3-chloro-trans-cinnamic acid and its solid solution with 3-bromo-trans-cinnamic acid
Authors: Khoj Manal A. , Hughes Colan E. , Harris Kenneth D. M. , Kariuki Benson M.
Published: July 2018

We have investigated the polymorphic phase transformations above ambient temperature for 3-chloro-trans-cinnamic acid (3-ClCA, C9H7ClO2) and a solid solution of 3-ClCA and 3-bromo-trans-cinnamic acid (3-BrCA, C9H7BrO2). At 413 K, the γ polymorph of 3-ClCA transforms to the β polymorph. Interestingly, the structure of the β polymorph of 3-ClCA obtained in this transformation is different from the structure of the β polymorph of 3-BrCA obtained in the corresponding polymorphic transformation from the γ polymorph of 3-BrCA, even though the γ polymorphs of 3-ClCA and 3-BrCA are isostructural. We also report a high-temperature phase transformation from a γ-type structure to a β-type structure for a solid solution of 3-ClCA and 3-BrCA (with a molar ratio close to 1:1). The γ polymorph of the solid solution is isostructural with the γ polymorphs of pure 3-ClCA and pure 3-BrCA, while the β-type structure produced in the phase transformation is structurally similar to the β polymorph of pure 3-BrCA.