bluuebunny/crossref_metadata_2025 huggingface dataset:
Spike activity regulates vesicle filling at a glutamatergic synapse
Authors: Li Dainan , Zhu Yun , Huang Hai
Published: December 2019

Synaptic vesicles need to be recycled and refilled rapidly to maintain high-frequency synaptic transmission. However, little is known about the control of transport of neurotransmitter into synaptic vesicles, which determines the contents of synaptic vesicles and the strength of synaptic transmission. Here we report that Na+substantially accumulated in the calyx of Held terminals of mouse during high-frequency spiking. The activity-induced elevation of cytosolic Na+activated vesicular Na+/H+exchanger, facilitated glutamate loading into synaptic vesicles and increased quantal size of asynchronous released vesicles, but did not affect the vesicle pool size or release probability. Consequently, presynaptic Na+increased the excitatory postsynaptic currents and was required to maintain the reliable high-frequency signal transmission from the presynaptic calyces to the postsynaptic MNTB neurons. Blocking Na+/H+activity with EIPA decreased the postsynaptic current and caused failures in postsynaptic firing. Therefore, during high-frequency synaptic transmission, when large amounts of glutamate are released, Na+accumulated in the terminals, activated vesicular Na+/H+exchanger, and regulated glutamate loading as a function of the level of vesicle release.

Significant statement

Auditory information is encoded by action potentials phase-locked to sound frequency at high rates. Large amount of synaptic vesicles are released during high-frequency synaptic transmission, accordingly, synaptic vesicles need to be recycled and refilled rapidly. We have recently found that a Na+/H+exchanger expressed on synaptic vesicles promotes vesicle filling with glutamate. Here we showed that during high-frequency signaling, when massive vesicles are released, Na+accumulates in terminals and facilitates glutamate uptake into synaptic vesicle. Na+thus accelerates vesicle replenishment and sustains reliable synaptic transmission.
A map of transcriptional heterogeneity and regulatory variation in human microglia
Authors: Young Adam MH , Kumasaka Natsuhiko , Calvert Fiona , Hammond Timothy R. , Knights Andrew , Panousis Nikolaos , Schwartzentruber Jeremy , Liu Jimmy , Kundu Kousik , Segel Michael , Murphy Natalia , McMurran Christopher E , Bulstrode Harry , Correia Jason , Budohoski Karol P , Joannides Alexis , Guilfoyle Mathew R , Trivedi Rikin , Kirollos Ramez , Morris Robert , Garnett Matthew R , Fernandes Helen , Timofeev Ivan , Jalloh Ibrahim , Holland Katherine , Mannion Richard , Mair Richard , Watts Colin , Price Stephen J , Kirkpatrick Peter J , Santarius Thomas , Soranzo Nicole , Stevens Beth , Hutchinson Peter J , Franklin Robin JM , Gaffney Daniel J
Published: December 2019

Microglia, the tissue resident macrophages of the CNS, are implicated in a broad range of neurological pathologies, from acute brain injury to dementia. Here, we profiled gene expression variation in primary human microglia isolated from 141 patients undergoing neurosurgery. Using single cell and bulk RNA sequencing, we defined distinct cellular populations of acutelyin vivo-activated microglia, and characterised a dramatic switch in microglial population composition in patients suffering from acute brain injury. We mapped expression quantitative trait loci (eQTLs) in human microglia and show that many disease-associated eQTLs in microglia replicate well in a human induced pluripotent stem cell (hIPSC) derived macrophage model system. Using ATAC-seq from 95 individuals in this hIPSC model we fine-map candidate causal variants at risk loci for Alzheimer’s disease, the most prevalent neurodegenerative condition in acute brain injury patients. Our study provides the first population-scale transcriptional map of a critically important cell for neurodegenerative disorders.
Sex chromosome and sex locus characterization in the goldfish, Carassius auratus
Authors: Wen Ming , Feron Romain , Pan Qiaowei , Guguin Justine , Jouanno Elodie , Herpin Amaury , Klopp Christophe , Cabau Cedric , Zahm Margot , Parrinello Hugues , Journot Laurent , Burgess Shawn M. , Omori Yoshihiro , Postlethwait John H. , Schartl Manfred , Guiguen Yann
Published: December 2019

Background

Goldfish is an important model for various areas of research, including neural development and behavior and a species of significant importance in aquaculture, especially as an ornamental species. It has a male heterogametic (XX/XY) sex determination system that relies on both genetic and environmental factors, with high temperatures being able to produce female-to-male sex reversal. Little, however, is currently known on the molecular basis of genetic sex determination in this important cyprinid model. We used sequencing approaches to better characterize sex determination and sex-chromosomes in goldfish.

Results

Our results confirmed that sex determination in goldfish is a mix of environmental and genetic factors and that its sex determination system is male heterogametic (XX/XY). Using reduced representation (RAD-seq) and whole genome (pool-seq) approaches, we characterized sex-linked polymorphisms and developed male specific genetic markers. These male specific markers were used to distinguish sex-reversed XX neomales from XY males and to demonstrate that XX female-to-male sex reversal could even occur at a relatively low rearing temperature (18°C), for which sex reversal has been previously shown to be close to zero. We also characterized a relatively large non-recombining region (∼11.7 Mb) on goldfish linkage group 22 (LG22) that contained a high-density of male-biased genetic polymorphisms. This large LG22 region harbors 373 genes, including a single candidate as a potential master sex gene, i.e., the anti-Mullerian hormone gene (amh). However, no sex-linked polymorphisms were detected in the goldfish amh gene or its 5 kb proximal promoter sequence.

Conclusions

These results show that goldfish have a relatively large sex locus on LG22, which is likely the goldfish Y chromosome. The presence of a few XX males even at low temperature also suggests that other environmental factors in addition to temperature could trigger female-to-male sex reversal. Finally, we also developed sex-linked genetic markers in goldfish, which will be important for future research on sex determination and aquaculture applications in this species.
Enhancer hijacking determines intra- and extrachromosomal circularMYCNamplicon architecture in neuroblastoma
Authors: Helmsauer Konstantin , Valieva Maria , Ali Salaheddine , Gonzalez Rocio Chamorro , Schöpflin Robert , Röefzaad Claudia , Bei Yi , Garcia Heathcliff Dorado , Rodriguez-Fos Elias , Puiggròs Montserrat , Kasack Katharina , Haase Kerstin , Kuschel Luis P. , Euskirchen Philipp , Heinrich Verena , Robson Michael , Rosswog Carolina , Tödling Jörn , Szymansky Annabell , Hertwig Falk , Fischer Matthias , Torrents David , Eggert Angelika , Schulte Johannes H. , Mundlos Stefan , Henssen Anton G. , Koche Richard P.
Published: December 2019

MYCNamplification drives one in six cases of neuroblastoma. The supernumerary gene copies are commonly found on highly rearranged, extrachromosomal circular DNA. The exact amplicon structure has not been described thus far and the functional relevance of its rearrangements is unknown. Here, we analyzed theMYCNamplicon structure and its chromatin landscape. This revealed two distinct classes of amplicons which explain the regulatory requirements forMYCNoverexpression. The first class always co-amplified a proximal enhancer driven by the noradrenergic core regulatory circuit (CRC). The second class ofMYCNamplicons was characterized by high structural complexity, lacked key local enhancers, and instead contained distal chromosomal fragments, which harbored CRC-driven enhancers. Thus, ectopic enhancer hijacking can compensate for the loss of local gene regulatory elements and explains a large component of the structural diversity observed inMYCNamplification.
Recurrent acquisition of alien ribotoxin encoding genes by insect genomes
Authors: Lapadula Walter J. , Mascotti María L. , Ayub Maximiliano Juri
Published: December 2019

Ribosome inactivating proteins (RIPs) are RNAN-glycosidases that depurinate a specific adenine residue in the conserved sarcin/ricin loop of 28S rRNA. These enzymes are widely distributed among plants and bacteria. Recently, we have described RIP genes in mosquitoes belonging to the Culicinae subfamily (AediniandCulicini tribes). We have also shown that these genes are derived from a single event of horizontal gene transfer (HGT) from a prokaryotic donor. In the present work, we show the existence of two RIP encoding genes in the genome of the whiteflyBemisia tabaci(a hemiptera species belonging to the Aleyrodidae family, distantly related to mosquitoes). Contamination artifacts were ruled out analyzing three independentBemisia tabacigenome databases. In contrast to mosquitoes RIPs, the whitefly genes harbor introns and, according to transcriptomic evidence, are transcribed and spliced. Interestingly, phylogenetic inference combined with taxonomic distribution strongly supports that whitefly RIP genes are derived from an independent HGT event from a plant source. Our results suggest that RIP genes fill a functional niche in insects.
Optimization and functionalization of red-shifted rhodamine dyes
Authors: Grimm Jonathan B. , Tkachuk Ariana N. , Choi Heejun , Mohar Boaz , Falco Natalie , Patel Ronak , Lippincott-Schwartz Jennifer , Brown Timothy A. , Lavis Luke D.
Published: December 2019

Expanding the palette of fluorescent dyes is vital for pushing the frontier of biological imaging. Although rhodamine dyes remain the premier type of small-molecule fluorophore due to their bioavailability and brightness, variants excited with far-red or near-infrared light suffer from poor performance due to their propensity to adopt a lipophilic, nonfluorescent form. We report a general chemical modification for rhodamines that optimizes long-wavelength variants and enables facile functionalization with different chemical groups.
Bovine breed-specific augmented reference graphs facilitate accurate sequence read mapping and unbiased variant discovery
Authors: Crysnanto Danang , Pausch Hubert
Published: December 2019

Background

The current bovine genomic reference sequence was assembled from the DNA of a Hereford cow. The resulting linear assembly lacks diversity because it does not contain allelic variation. Lack of diversity is a drawback of linear references that causes reference allele bias. High nucleotide diversity and the separation of individuals by hundreds of breeds make cattle ideally suited to investigate the optimal composition of variation-aware references.

Results

We augment the bovine linear reference sequence (ARS-UCD1.2) with variants filtered for allele frequency in dairy (Brown Swiss, Holstein) and dual-purpose (Fleckvieh, Original Braunvieh) cattle breeds to construct either breed-specific or pan-genome reference graphs using thevg toolkit. We find that read mapping is more accurate to variation-aware than linear references if pre-selected variants are used to construct the genome graphs. Graphs that contain random variants do not improve read mapping over the linear reference sequence. Breed-specific augmented and pan-genome graphs enable almost similar mapping accuracy improvements over the linear reference. We construct a whole-genome graph that contains the Hereford-based reference sequence and 14 million alleles that have alternate allele frequency greater than 0.03 in the Brown Swiss cattle breed. We show that our novel variation-aware reference facilitates accurate read mapping and unbiased sequence variant genotyping for SNPs and Indels.

Conclusions

We developed the first variation-aware reference graph for an agricultural animal:https://doi.org/10.5281/zenodo.3759712. Our novel reference structure improves sequence read mapping and variant genotyping over the linear reference. Our work is a first step towards the transition from linear to variation-aware reference structures in species with high genetic diversity and many sub-populations.
Mechanistic Basis for Microhomology Identification and Genome Scarring by Polymerase Theta
Authors: Carvajal-Garcia Juan , Cho Jang-Eun , Carvajal-Garcia Pablo , Feng Wanjuan , Wood Richard D. , Sekelsky Jeff , Gupta Gaorav P. , Roberts Steven A. , Ramsden Dale A.
Published: December 2019

DNA Polymerase Theta mediates an end joining pathway (TMEJ) that repairs chromosome breaks. It requires resection of broken ends to generate long, 3’ single stranded DNA tails, annealing of complementary sequence segments (microhomologies) in these tails, followed by microhomology-primed synthesis sufficient to resolve broken ends. The means by which microhomologies are identified is thus a critical step in this pathway, but is not understood. Here we show microhomologies are identified by a scanning mechanism initiated from the 3’ terminus and favoring bi-directional progression into flanking DNA, typically to a maximum of 15 nucleotides into each flank. Polymerase theta is frequently insufficiently processive to complete repair of breaks in microhomology-poor, AT-rich regions. Aborted synthesis leads to one or more additional rounds of microhomology search, annealing, and synthesis; this promotes complete repair in part because earlier rounds of synthesis generate microhomologiesde novothat are sufficiently long that synthesis is more processive. Aborted rounds of synthesis are evident in characteristic genomic scars as insertions of 3-30 bp of sequence that is identical to flanking DNA (“templated” insertions). Templated insertions are present at higher levels in breast cancer genomes from patients with germlineBRCA1/2mutations, consistent with an addiction to TMEJ in these cancers. Our work thus describes the mechanism for microhomology identification, and shows both how it mitigates limitations implicit in the microhomology requirement, and generates distinctive genomic scars associated with pathogenic genome instability.
Repression of LKB1 bymiR-17∼92sensitizesMYC-dependent lymphoma to biguanide treatment
Authors: Izreig Said , Gariepy Alexandra , Donayo Ariel O. , Bridon Gaëlle , Avizonis Daina , Sheldon Ryan D. , Laister Rob , Minden Mark D. , Johnson Nathalie A. , Williams Kelsey S. , Rudoltz Marc S. , Duchaine Thomas F. , Yoo Sanghee , Pollak Michael N. , Jones Russell G.
Published: December 2019

Cancer cells display metabolic plasticity to survive metabolic and energetic stresses in the tumor microenvironment, prompting the need for tools to target tumor metabolism. Cellular adaptation to energetic stress is coordinated in part by signaling through the Liver Kinase B1 (LKB1)-AMP-activated protein kinase (AMPK) pathway. Reducing LKB1-AMPK signaling exposes metabolic vulnerabilities in tumor cells with potential for therapeutic targeting. Here we describe that miRNA-mediated silencing of LKB1 (mediated by the oncogenic miRNA clustermiR-17∼92) confers sensitivity of lymphoma cells to mitochondrial inhibition by biguanides. Using both classic (phenformin) and novel (IM156) biguanides, we demonstrate thatMyc+lymphoma cells with elevatedmiR-17∼92expression display increased sensitivity to biguanide treatment both in cell viability assaysin vitroand tumor growth assaysin vivo. This increased biguanide sensitivity is driven bymiR-17-dependent silencing of LKB1, which results in reduced AMPK activation in response to bioenergetic stress. Mechanistically, biguanide treatment inhibits TCA cycle metabolism and mitochondrial respiration inmiR-17∼92-expressing tumor cells, targeting their metabolic vulnerability. Finally, we demonstrate a direct correlation betweenmiR-17∼92expression and biguanide sensitivity in human cancer cells. Our results identifymiR-17∼92expression as a potential biomarker for biguanide sensitivity in hematological malignancies and solid tumors.

One Sentence Summary

miR-17∼92 expression inMyc+tumors sensitizes cancer cells to biguanide treatment by disrupting bioenergetic stability in lymphoma cells.
Homologous laminar organization of the mouse and human subiculum
Authors: Bienkowski Michael S. , Sepehrband Farshid , Kurniawan Nyoman D. , Stanis Jim , Korobkova Laura , Khanjani Neda , Hintiryan Houri , Miller Carol A. , Dong Hong-Wei
Published: December 2019

The subiculum is the major output structure of the hippocampal formation and one of the brain regions most affected by Alzheimer’s disease. Our previous work revealed a hidden laminar architecture within the mouse subiculum. However, the rotation of the hippocampal longitudinal axis across species makes it unclear how the laminar organization is represented in human subiculum. Usingin situhybridization data from the Allen Human Brain Atlas, we demonstrate that the human subiculum also contains complementary laminar gene expression patterns similar to the mouse. In addition, we provide evidence that the molecular domain boundaries in human subiculum correspond to microstructural differences observed in high resolution MRI and fiber density imaging. Finally, we show both similarities and differences in the gene expression profile of subiculum pyramidal cells within homologous lamina. Overall, we present a new 3D model of the anatomical organization of human subiculum and its evolution from the mouse.
Ankylosis homologue (ANKH) controls extracellular citrate and pyrophosphate homeostasis and affects bone mechanical performance
Authors: Szeri Flora , Lundkvist Stefan , Donnelly Sylvia , Engelke Udo F.H. , Rhee Kyu , Williams Charlene , Sundberg John P. , Wevers Ron A. , Tomlinson Ryan E. , Jansen Robert , van de Wetering Koen
Published: December 2019

The membrane protein Ankylosis homologue (ANKH, mouse orthologue: ANK) prevents mineralization of joint-space and articular cartilage. The accepted view is that ANKH mediates cellular release of inorganic pyrophosphate (PPi), a strong physiological inhibitor of mineralization. Using global metabolite profiling, we identified citrate as the most prominent metabolite leaving HEK293 cells in an ANKH-dependent manner. Although PPi levels were increased in culture medium of HEK293-ANKH cells, PPi was formed extracellularly after release of ATP and other nucleoside triphosphates.Ankank/ankmice, which lack functional ANK, had substantially reduced concentrations of citrate in plasma and urine, while citrate was undetectable in urine of a human patient lacking functional ANKH. Bone hydroxyapatite ofAnkank/ankmice also contained markedly reduced levels of citrate and PPi and displayed diminished strength. Together, our data show that ANKH is a crucial factor in extracellular citrate and PPi homeostasis that is essential for normal bone development.
A sub+ cortical fMRI-based surface parcellation
Authors: Lewis John D. , Bezgin Gleb , Fonov Vladimir S. , Collins D. Louis , Evans Alan C.
Published: December 2019

Both the cortex and the subcortical structures are organized into a large number of distinct areas reflecting functional and cytoarchitectonic differences. Mapping these areas is of fundamental importance to neuroscience. A central obstacle to this task is the inaccuracy associated with mapping results from individuals into a common space. The vast individual differences in morphology pose a serious problem for volumetric registration. Surface-based approaches fare substantially better, but have thus far been used only for cortical parcellation. We extend this surface-based approach to include also the subcortical deep gray-matter structures. Using the life-span data from the Enhanced Nathan Klein Institute - Rockland Sample, comprised of data from 590 individuals from 6 to 85 years of age, we generate a functional parcellation of both the cortical and subcortical surfaces. To assess this extended parcellation, we show that our extended functional parcellation provides greater homogeneity of functional connectivity patterns than do arbitrary parcellations matching in the number and size of parcels. We also show that our subcortical parcels align with known subnuclei. Further, we show that this parcellation is appropriate for use with data from other modalities; we generate cortical and subcortical white/gray contrast measures for this same dataset, and draw on the fact that areal differences are evident in the relation of white/gray contrast to age, to sex, to brain volume, and to interactions of these terms; we show that our extended functional parcellation provides an improved fit to the complexity of the life-span changes in the white/gray contrast data compared to arbitrary parcellations matching in the number and size of parcels. We provide our extended functional parcellation for the use of the neuroimaging community.
Dnmt3aknockout in excitatory neurons impairs postnatal synapse maturation and is partly compensated by repressive histone modification H3K27me3
Authors: Li Junhao , Pinto-Duarte Antonio , Zander Mark , Lai Chi-Yu , Osteen Julia , Fang Linjing , Luo Chongyuan , Lucero Jacinta D. , Gomez-Castanon Rosa , Nery Joseph R. , Silva-Garcia Isai , Pang Yan , Sejnowski Terrence J. , Powell Susan B. , Ecker Joseph R. , Mukamel Eran A. , Behrens M. Margarita
Published: December 2019

Two epigenetic pathways of repression, DNA methylation and Polycomb repressive complex 2 (PRC2) mediated gene silencing, regulate neuron development and function, but their respective contributions are unknown. We found that conditional loss of thede novoDNA methyltransferaseDnmt3ain mouse excitatory neurons altered expression of synapse-related genes, stunted synapse maturation, and impaired working memory and social interest. Loss ofDnmt3aabolished postnatal accumulation of CG and non-CG DNA methylation, leaving neurons with an unmethylated, fetal-like epigenomic pattern at −140,000 genomic regions. The PRC2-associated histone modification H3K27me3 increased at many of these sites, partially compensating for the loss of DNA methylation. Our data support a dynamic interaction between two fundamental modes of epigenetic repression during postnatal maturation of excitatory neurons, which together confer robustness on neuronal regulation.
A genomic view of coral-associatedProsthecochlorisand a companion sulfate-reducing bacterium
Authors: Chen Yu-Hsiang , Yang Shan-Hua , Tandon Kshitij , Lu Chih-Ying , Chen Hsing-Ju , Shih Chao-Jen , Tang Sen-Lin
Published: December 2019

Endolithic microbial symbionts in the coral skeleton may play a pivotal role in maintaining coral health. However, compared to aerobic microorganisms, research on the roles of endolithic anaerobic microorganisms and microbe-microbe interactions in the coral skeleton are still in their infancy. In our previous study, we showed that a group of coral-associatedProsthecochloris(CAP), a genus of anaerobic green sulfur bacteria, was dominant in the skeleton of the coralIsopora palifera. Though CAP is diverse, the 16S rRNA phylogeny presents it as a distinct clade separate from other free-livingProsthecochloris. In this study, we build on previous research and further characterize the genomic and metabolic traits of CAP by recovering two new near-complete CAP genomes—CandidatusProsthecochloris isoporaea andCandidatusProsthecochloris sp. N1—from coralIsopora paliferaendolithic cultures. Genomic analysis revealed that these two CAP genomes have high genomic similarities compared with otherProsthecochlorisand harbor several CAP-unique genes. Interestingly, different CAP species harbor various pigment synthesis and sulfur metabolism genes, indicating that individual CAPs can adapt to a diversity of coral microenvironments. A novel near-complete SRB genome—CandidatusHalodesulfovibrio lyudaonia—was also recovered from the same culture. The fact that CAP and various sulfate-reducing bacteria (SRB) co-exist in coral endolithic cultures and coral skeleton highlights the importance of SRB in the coral endolithic community. Based on functional genomic analysis ofCa. P. sp. N1 andCa. H. lyudaonia, we also propose a syntrophic relationship between the SRB and CAP in the coral skeleton.

Importance

Little is known about the ecological roles of endolithic microbes in the coral skeleton; one potential role is as a nutrient source for their coral hosts. Here, we identified a close ecological relationship between CAP and SRB. Recovering novel near-complete CAP and SRB genomes from endolithic cultures in this study enabled us to understand the genomic and metabolic features of anaerobic endolithic bacteria in coral skeletons. These results demonstrate that CAP members with similar functions in carbon, sulfur, and nitrogen metabolisms harbor different light-harvesting components, suggesting that CAP in the skeleton adapts to niches with different light intensities. Our study highlights the potential ecological roles of CAP and SRB in coral skeletons and paves the way for future investigations into how coral endolithic communities will respond to environmental changes.
Expansions of adaptive-like NK cells with a tissue-resident phenotype in human lung and blood
Authors: Marquardt Nicole , Scharenberg Marlena , Mold Jeffrey E. , Hård Joanna , Kekäläinen Eliisa , Buggert Marcus , Nguyen Son , Wilson Jennifer N. , Al-Ameri Mamdoh , Ljunggren Hans-Gustaf , Michaëlsson Jakob
Published: December 2019

Human adaptive-like “memory” CD56dimCD16+ NK cells in peripheral blood from cytomegalovirus-seropositive individuals have been extensively investigated in recent years and are currently explored as a treatment strategy for hematological cancers. However, treatment of solid tumors remains limited due to insufficient NK cell tumor infiltration, and it is unknown whether large expansions of adaptive-like NK cells that are equipped for tissue-residency and tumor-homing exist in peripheral tissues. Here, we show that human lung and blood contains adaptive-like CD56brightCD16− NK cells with hallmarks of tissue-residency, including expression of CD49a. Expansions of adaptive-like lung tissue-resident (tr)NK cells were found to be present independently of adaptive-like CD56dimCD16+ NK cells and to be hyperresponsive towards target cells. Together, our data demonstrate that phenotypically, functionally, and developmentally distinct subsets of adaptive-like NK cells exist in human lung and blood. Given their tissue-related character and hyperresponsiveness, human lung adaptive-like trNK cells might represent a suitable alternative for therapies targeting solid tumors.
Whole-body imaging of neural and muscle activity during behavior inHydra: bidirectional effects of osmolarity on contraction bursts
Authors: Yamamoto Wataru , Yuste Rafael
Published: December 2019

The neural code relates the activity of the nervous system to the activity of the muscles to the generation of behavior. To decipher it, it would be ideal to comprehensively measure the activity of the entire nervous system and musculature in a behaving animal. As a step in this direction, we used the cnidarianHydra vulgaristo explore how physiological and environmental conditions alter the activity of the entire neural and muscle tissue and affect behavior. We used whole-body calcium imaging of neurons and muscle cells and studied the effect of temperature, media osmolarity, nutritional state and body size on body contractions.

In mountedHydra, changes in temperature, nutrition or body size did not have a major effect on neural or muscle activity, or on behavior. But changes in media osmolarity altered body contractions, increasing them in hipo-osmolar media solutions and decreasing them in hyperosmolar media. Similar effects were seen in ectodermal, but not in endodermal muscle. Osmolarity also bidirectionally changed the activity of contraction bursts neurons, but not of rhythmic potential neurons.

These findings show osmolarity-dependent changes in neuronal activity, muscle activity, and contractions, consistent with the hypothesis that contraction burst neurons respond to media osmolarity, activating ectodermal muscle to generate contraction bursts. This dedicated circuit could serve as an excretory system to prevent osmotic injury. This work demonstrates the feasibility of studying the entire neuronal and muscle activity of behaving animals.

Significance Statement

We imaged whole-body muscle and neuronal activity inHydrain response to different physiological and environmental conditions. Osmolarity bidirectionally alteredHydracontractile behavior. These changes were accompanied by corresponding changes in the activity of one neuronal circuit and one set of muscles. This work is a step toward comprehensive deciphering of the mechanisms of animal behavior by measuring the activity of all neurons and muscle cells.
A single-cell transcriptomic atlas of the adultDrosophilaventral nerve cord
Authors: Allen Aaron M. , Neville Megan C. , Birtles Sebastian , Croset Vincent , Treiber Christoph D. , Waddell Scott , Goodwin Stephen F.
Published: December 2019

TheDrosophilaventral nerve cord (VNC) receives and processes descending signals from the brain to produce a variety of coordinated locomotor outputs. It also integrates sensory information from the periphery and sends ascending signals to the brain. We used single-cell transcriptomics to generate an unbiased classification of cellular diversity in the VNC of five-day old adult flies. We produced an atlas of 26,000 high-quality cells, representing more than 100 transcriptionally distinct cell types. The predominant gene signatures defining neuronal cell types reflect shared developmental histories based on the neuroblast from which cells were derived, as well as their birth order. Cells could also be assigned to specific neuromeres using adult Hox gene expression. This single-cell transcriptional atlas of the adult fly VNC will be a valuable resource for future studies of neurodevelopment and behavior.
Sequence heterochrony led to a gain of functionality in an immature stage of the central complex: a fly-beetle insight
Authors: Farnworth Max S. , Eckermann Kolja N. , Bucher Gregor
Published: December 2019

Animal behavior is guided by the brain. Therefore, adaptations of brain structure and function are essential for animal survival, and each species differs in such adaptations. The brain of one individual may even differ between life stages, for instance as adaptation to the divergent needs of larval and adult life of holometabolous insects. All such differences emerge during development but the cellular mechanisms behind the diversification of brains between taxa and life stages remain enigmatic. In this study, we investigated holometabolous insects, where larvae differ dramatically from the adult in both behavior and morphology. As consequence, the central complex, mainly responsible for spatial orientation, is conserved between species at the adult stage, but differs between larvae and adults as well as between larvae of different taxa. We used genome editing and established transgenic lines to visualize cells expressing the conserved transcription factorretinal homeobox,thereby marking homologousgenetic neural lineagesin both the flyDrosophila melanogasterand the beetleTribolium castaneum. This approach allowed us for the first time to compare the development of homologous neural cells between taxa from embryo to the adult. We found complex heterochronic changes including shifts of developmental events between embryonic and pupal stages. Further, we provide, to our knowledge, the first example ofsequence heterochronyin brain development, where certain developmental steps changed their position within the ontogenetic progression. We show that through thissequence heterochrony, an immature developmental stage of the central complex gains functionality inTriboliumlarvae. We discuss the bearing of our results on the evolution of holometabolous larval central complexes by regression to a form present in an ancestor.
Increasing motor skill acquisition by driving theta-gamma coupling
Authors: Akkad Haya , Dupont-Hadwen Joshua , Frese Amba , Tetkovic Irena , Barrett Liam , Bestmann Sven , Stagg Charlotte J
Published: December 2019

Skill learning is a fundamental adaptive process, but the mechanisms remain poorly understood. Hippocampal learning is closely associated with gamma activity, which is amplitude-modulated by the phase of underlying theta activity. Whether such nested activity patterns also underpin skill acquisition in non-hippocampal tasks is unknown. Here we addressed this question by using transcranial alternating current stimulation (tACS) over sensorimotor cortex to modulate theta-gamma activity during motor skill acquisition, as an exemplar of a non-hippocampal-dependent task. We demonstrated, and then replicated, a significant improvement in skill acquisition with theta-gamma tACS, which outlasted the stimulation by an hour. Our results suggest that theta-gamma activity may be a common mechanism for learning across the brain and provides a putative novel intervention for optimising functional improvements in response to training or therapy.
Testing relationships between multimodal modes of brain structural variation and age, sex and polygenic scores for neuroticism in children and adolescents
Authors: Norbom Linn B. , Rokicki Jaroslav , van der Meer Dennis , Alnæs Dag , Doan Nhat Trung , Moberget Torgeir , Kaufmann Tobias , Andreassen Ole A. , Westlye Lars T. , Tamnes Christian K.
Published: December 2019

Human brain development involves spatially and temporally heterogeneous changes, detectable across a wide range of magnetic resonance imaging (MRI) measures. Investigating the interplay between multimodal MRI and polygenic scores (PGS) for personality traits associated with mental disorders in youth may provide new knowledge about typical and atypical neurodevelopment. We derived independent components across cortical thickness, cortical surface area, and gray/white matter contrast (GWC) (n=2596, 3-23 years), and tested for associations between these components and age, sex and-, in a subsample (n=878), PGS for neuroticism. Age was negatively associated with a single-modality component reflecting higher global GWC, and additionally with components capturing common variance between global thickness and GWC, and several multimodal regional patterns. Sex differences were found for components primarily capturing global and regional surface area (boys>girls), but also regional cortical thickness. For PGS for neuroticism, we found weak and bidirectional associations with a component reflecting right prefrontal surface area. These results indicate that multimodal fusion is sensitive to age and sex differences in brain structure in youth, but only weakly to polygenic load for neuroticism.
The spatial Muller’s ratchet: surfing of deleterious mutations during range expansion
Authors: Foutel-Rodier Félix , Etheridge Alison
Published: December 2019

During a range expansion, deleterious mutations can “surf” on the colonisation front. The resultant decrease in fitness is known as expansion load. An Allee effect is known to reduce the loss of genetic diversity of expanding populations, by changing the nature of the expansion from “pulled” to “pushed”. We study the impact of an Allee effect on the formation of an expansion load with a new model, in which individuals have the genetic structure of a Muller’s ratchet. A key feature of Muller’s ratchet is that the population fatally accumulates deleterious mutations due to the stochastic loss of the fittest individuals, an event called a click of the ratchet. We observe fast clicks of the ratchet at the colonization front owing to small population size, followed by a slow fitness recovery due to migration of fit individuals from the bulk of the population, leading to a transient expansion load. For large population size, we are able to derive quantitative features of the expansion wave, such as the wave speed and the frequency of individuals carrying a given number of mutations. Using simulations, we show that the presence of an Allee effect reduces the rate at which clicks occur at the front, and thus reduces the expansion load.
Nuclear upregulation of PI3K p110β correlates with increased rRNA transcription in endometrial cancer cells
Authors: Gavgani Fatemeh Mazloumi , Karlsson Thomas , Tangen Ingvild L , Papdiné Morovicz Andrea , Arnesen Victoria Smith , Turcu Diana C. , Krakstad Camilla , Guillermet-Guibert Julie , Lewis Aurélia E
Published: December 2019

Genes encoding for components of the phosphoinositide 3-kinase (PI3K) pathway are frequently mutated in cancer, including inactivating mutations ofPTENand activating mutations ofPIK3CA, encoding the PI3K catalytic subunit p110α.PIK3CB, encoding p110β, is rarely mutated, but can contribute to tumourigenesis in some PTEN-deficient tumours. The underlying molecular mechanisms are however poorly understood. By analysing cell lines and annotated clinical samples, we have previously found that p110β is highly expressed in endometrial cancer (EC) cell lines and thatPIK3CBmRNA levels increase early in primary tumours correlating with lower survival. Selective inhibition of p110α and p110β led to different effects on cell signalling and cell function, p110α activity being correlated to cell survival inPIK3CAmutant cells and p110β with cell proliferation in PTEN-deficient cells. To understand the mechanisms governing the differential roles of these isoforms, we assessed their sub-cellular localisation. p110α was cytoplasmic whereas p110β was both cytoplasmic and nuclear with increased levels in both compartments in cancer cells. Immunohistochemistry of p110β in clinically annotated patient tumour sections revealed high nuclear/cytoplasmic staining ratio, which correlated significantly with higher grades. Consistently, the presence of high levels of p110β in the nuclei of EC cells, correlated with high levels of its product phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3) in the nucleus. Using immunofluorescence labelling, we observed both p110β and PtdIns(3,4,5)P3in the nucleoli of EC cell lines. The production of nucleolar PtdIns(3,4,5)P3was dependent upon p110β activity. EC cells with high levels of nuclear PtdIns(3,4,5)P3and p110β showed elevated nucleolar activity as assessed by the increase in 47S pre-rRNA transcriptional levels in a p110β-dependent manner. Altogether, these results present a nucleolar role for the PI3K pathway that may contribute to tumour progression in endometrial cancer.
Langerhans cells immunocompetency is critical for IDO1-dependent ability to induce tolerogenic T cells
Authors: Davies James , Sirvent Sofia , Vallejo Andres F. , Clayton Kalum , Porter Gemma , Stumpf Patrick , West Jonathan , Ardern-Jones Michael , Singh Harinder , MacArthur Ben , Polak Marta E
Published: December 2019

Human epidermal Langerhans cells (LCs) can coordinate both immunogenic and tolerogenic immune responses, creating an attractive opportunity for immunomodulation strategies. To investigate transcriptional determinants of human primary LC tolerance we applied single cells RNA-sequencing combined with transcriptional network modelling and functional analysis. Unsupervised clustering of single cell transcriptomes revealed that steady-state LCs exist in immature and immunocompetent states, and become fully immunocompetent on migration. Interestingly, LC migration, which has been shown to result in upregulation of the transcription factor IRF4, led in parallel to increased expression of a tolerogenic gene module includingIDO1,LGALS1,LAMTOR1andIL10RA,which translated to efficient induction of regulatory T cells in co-culture assays by immunocompetent LCs. Using protein expression analysis and perturbation with inhibitors, we confirmed the role of IDO1 as a mediator of LC tolerogenic responses induced during LC migration. Computational analysis of regulons and Partial Information Decomposition analyses identifiedIRF4as a key driver for LC tolerogenic programmes. The predicted IRF4-regulated genes were confirmed by analysis of CRISPR-Cas9 edited LCs. These findings suggest that efficient priming of tolerogenic responses by LCs requires upregulation of a migration-coupled maturation program which is superimposed with a tolerance-inducing genomic module.
TENET: Gene network reconstruction using transfer entropy reveals key regulatory factors from single cell transcriptomic data
Authors: Kim Junil , Jakobsen Simon Toftholm , Natarajan Kedar Nath , Won Kyoung Jae
Published: December 2019

Accurate prediction of gene regulatory rules is important towards understanding of cellular processes. Existing computational algorithms devised for bulk transcriptomics typically require a large number of time points to infer gene regulatory networks (GRNs), are applicable for a small number of genes, and fail to detect potential causal relationships effectively. Here, we propose a novel approach ‘TENET’ to reconstruct GRNs from single cell RNA sequencing (scRNAseq) datasets. Employing transfer entropy (TE) to measure the amount of causal relationships between genes, TENET predicts large-scale gene regulatory cascades/relationships from scRNAseq data. TENET showed better performance than other GRN reconstructors, in identifying key regulators from public datasets. Specifically from scRNAseq, TENET identified key transcriptional factors in embryonic stem cells (ESCs) and during direct cardiomyocytes reprogramming, where other predictors failed. We further demonstrate that known target genes have significantly higher TE values, and TENET predicted higher TE genes were more influenced by the perturbation of their regulator. Using TENET, we identified and validated that Nme2 is a culture condition specific stem cell factor. These results indicate that TENET is uniquely capable of identifying key regulators from scRNAseq data.

Key Points

TENET measures putative causal relationships between genes using transfer entropy.

TENET shows outstanding performance in identifying key regulators compared to existing methods.

TENET can reveal previously uncharacterized regulators.
Pyk2 Overexpression in Postsynaptic Neurons Blocks Aβ1-42-induced Synaptotoxicity in a Microfluidic Co-Culture Model
Authors: Kilinc Devrim , Vreulx Anaïs-Camille , Mendes Tiago , Flaig Amandine , Marques-Coelho Diego , Verschoore Maxime , Demiautte Florie , Amouyel Philippe ,   Neuro-CEB Brain Bank, Eysert Fanny , Dourlen Pierre , Chapuis Julien , Costa Marcos Romualdo , Malmanche Nicolas , Checler Frederic , Lambert Jean-Charles
Published: December 2019

Recent meta-analyses of genome-wide association studies identified a number of genetic risk factors of Alzheimer’s disease; however, little is known about the mechanisms by which they contribute to the pathological process. As synapse loss is observed at the earliest stage of Alzheimer’s disease, deciphering the impact of Alzheimer’s risk genes on synapse formation and maintenance is of great interest. In this paper, we report a microfluidic co-culture device that physically isolates synapses from pre- and postsynaptic neurons and chronically exposes them to toxic amyloid-beta (Aβ) peptides secreted by model cell lines overexpressing wild-type or mutated (V717I) amyloid precursor protein (APP). Co-culture with cells overexpressing mutated APP exposed the synapses of primary hippocampal neurons to Aβ1-42molecules at nanomolar concentrations and induced a significant decrease in synaptic connectivity, as evidenced by distance-based assignment of postsynaptic puncta to presynaptic puncta. Treating the cells with antibodies that target different forms of Aβ suggested that low molecular weight oligomers are the likely culprit. As proof of concept, we demonstrate that overexpression of protein tyrosine kinase 2 beta (Pyk2) –an Alzheimer’s disease genetic risk factor involved in synaptic plasticity and shown to decrease in Alzheimer’s disease brains at gene expression and protein levels–selectively in postsynaptic neurons is protective against Aβ1-42-induced synaptotoxicity. In summary, our lab-on-a-chip device provides a physiologically-relevant model of Alzheimer’s disease-related synaptotoxicity, optimal for assessing the impact of risk genes in pre- and postsynaptic compartments.
Intracellular DNA replication and differentiation ofTrypanosoma cruziis asynchronous within individual host cellsin vivoat all stages of infection
Authors: Taylor Martin. C. , Ward Alexander , Olmo Francisco , Jayawardhana Shiromani , Francisco Amanda F. , Lewis Michael D. , Kelly John M.
Published: December 2019

Investigations into intracellular replication and differentiation ofTrypanosoma cruziwithin the mammalian host have been restricted by limitations in our ability to detect parasitized cells throughout the course of infection. We have overcome this problem by generating genetically modified parasites that express a bioluminescent/fluorescent fusion protein. By combiningin vivoimaging and confocal microscopy, this has enabled us to routinely visualise murine infections at the level of individual host cells. These studies reveal that intracellular parasite replication is an asynchronous process, irrespective of tissue location or disease stage. Furthermore, using TUNEL assays and EdU labelling, we demonstrate that within individual infected cells, replication of both mitochondrial (kDNA) and nuclear genomes is not co-ordinated within the parasite population, and that replicating amastigotes and non-replicating trypomastigotes can co-exist in the same cell. Finally, we report the presence of distinct non-canonical morphological forms ofT. cruziin the mammalian host. These appear to represent transitional forms in the amastigote to trypomastigote differentiation process. Therefore, the intracellular life-cycle ofT. cruzi in vivois more complex than previously realised, with potential implications for our understanding of disease pathogenesis, immune evasion and drug development. Dissecting the mechanisms involved will be an important experimental challenge.

AUTHOR SUMMARY

Chagas disease, caused by the protozoan parasite Trypanosoma cruzi, is becoming an emerging threat in non-endemic countries and establishing new foci in endemic countries. The treatment available has not changed significantly in over 40 years. Therefore, there is an urgent need for a greater understanding of parasite biology and disease pathogenesis to identify new therapeutic targets and to maximise the efficient use of existing drugs. We have used genetically modified strains ofT. cruzicarrying a bioluminescence/fluorescence dual reporter fusion gene to monitor parasite replicationin vivoduring both acute and chronic infections in a mouse model. Utilising TUNEL assays for mitochondrial DNA replication and EdU incorporation for total DNA replication, we have found that parasite division within infected cells is asynchronous in all phases of infection. Differentiation also appears to be uncoordinated, with replicating amastigotes co-existing with non-dividing trypomastigotes in the same host cell.