bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of Circulating Exosomes Reveals a Peripheral Signature of Astrocytic Pathology in Schizophrenia
Authors: Ranganathan Mohini , Rahman Mohamed , Ganesh Suhas , D’Souza Deepak C , Skosnik Patrick D , Radhakrishnan Rajiv , Pathania Surbhi , Mohanakumar Thalachallour
Published: February 2020

Background

There is considerable interest in identifying peripheral biomarkers that reflect neuropathological changes in schizophrenia. Extracellular vesicles, including exosomes can cross the blood brain barrier with their contents intact and their cargo, including lipids, proteins and genetic materials can be assayed peripherally. Circulating exosomes have been studied in other neurodegenerative disorders, but there is scarce data in schizophrenia.

Methods

We examined neuropathology relevant protein biomarkers in circulating exosomes from patients with schizophrenia and age and gender matched healthy controls using methods consistent with the recommended “Minimal information for studies of extracellular vesicles 2018” (MISEV2018) guidelines. Nanoparticle tracking analysis was used to determine the size and concentration of exosomes. Exosomal membrane marker (CD9) and specific target cargo proteins (glial fibrillary acid protein[GFAP], synaptophysin and α-II-spectrin) immunopositivity was examined using Western blot analyses and band intensity quantified.

Results

No group differences were observed between schizophrenia and control samples in plasma exosomal concentration and size or in CD9 or calnexin positivity. Exosomal GFAP concentration was significantly higher and α-II-spectrin expression significantly lower in schizophrenia samples and there were no group differences observed for exosomal synaptophysin concentration.

Conclusions

Our results demonstrate for the first time, a differential pattern of exosomal protein expression in schizophrenia compared to matched healthy controls, consistent with the hypothesized astro-glial pathology in this disorder. These results warrant further examination of circulating exosomes as vehicles of novel peripheral biomarkers of disease in schizophrenia and other neuropsychiatric disorders.
Human-specific staphylococcal virulence factors enhance pathogenicity in a humanised zebrafish C5a receptor model
Authors: Buchan Kyle D. , van Gent Michiel , Prajsnar Tomasz K. , Ogryzko Nikolay V. , de Jong Nienke W.M. , Kolata Julia , Foster Simon J. , van Strijp Jos A.G. , Renshaw Stephen A.
Published: February 2020

Staphylococcus aureusinfects approximately 30% of the human population and causes a spectrum of pathologies ranging from mild skin infections to life-threatening invasive diseases. The strict host specificity of its virulence factors has severely limited the accuracy ofin vivomodels for the development of vaccines and therapeutics. To resolve this, we generated a humanised zebrafish model and determined that neutrophil-specific expression of the human C5a receptor conferred susceptibility to theS. aureustoxins PVL and HlgCB, leading to reduced neutrophil numbers at the site of infection and increased infection-associated mortality as a direct result of the interaction betweenS. aureusand the receptor. These results show that humanised zebrafish provide a valuable platform to study the contribution of human-specificS. aureusvirulence factors to infectionin vivothat could facilitate the development of novel therapeutic approaches and essential vaccines.
“Sulcus Sink”: A Compact Binary and Semi-Automated Inverse Dijkstra-based System for Describing Sulcal Trajectories
Authors: Pienaar Rudolph , Hasselgrove Christian , Im Kiho , Kennedy David , Grant P Ellen , Boriel Denise , Tang Lena , Makris Nikos
Published: February 2020

We present a description of a system that uses a compact binary representation to describe and trace sulci on a reconstructed human cortical surface, based on a set of human-generated targets. The inputs to the system were manually created on a training set of 20 normal subjects (11 females, 9 males) with ages 22 – 40 years. T1 weighted MPRAGE images were collected on a Siemens 3T Trio scanner, with TR/TE = 2530/3.3, matrix = 256×256, FOV = 256mm, slice thickness 1.33mm. The resultant images were reconstructed with Freesurfer, and 10 sulci on each hemisphere were traced by an expert human operator and independently assessed for accuracy. Presented with these input trajectories in its training phase, the system attempted to determine a compact binary feature vector of each sulcus on each subject using as descriptor a binary parametrized function of several surface-geometry variables (such as mean curvature, sulcal depth, edge length, etc.). This function was optimized in a supervised learning fashion using a Dijkstra-based graph theory formulation, in which the binary weights were used to define graph edge costs. In the setup phase, the system was presented with sulcal trajectories already defined on surfaces, and then adjusted its parametrized weights in a binary fashion to minimize differences between the training input path and its Dijkstra-generated output path. Once the setup phase was complete and sulci had been described in a per-sulcus, per-subject manner, we generalized the per-sulcus description across all the subjects to construct a template binary word for each specific sulcus. The performance of the system for each subject and each sulcus, and for each template sulcus group was measured against the original human reference in both a quantitative and qualitative manner. Individual subjects generally showed very good optimization to their manually traced training samples across all sulci, with 91% average overlap within 4mm of the human target. Generalized group results, as expected, showed less overlap with the original human targets, but still performed on average with 80% overlap. Quantitatively, the group results were nonetheless for the most part quite acceptable to an independent human evaluator. The parametrized binary weight description that drives the Dijkstra path optimization is presented as a mechanism to succinctly and compactly describe individual human sulci and groups of sulci.
Deep sequencing of nonenzymatic RNA primer extension
Authors: Duzdevich Daniel , Carr Christopher E. , Szostak Jack W.
Published: February 2020

Life emerging in an RNA world is expected to propagate RNA as hereditary information, requiring some form of primitive replication without enzymes. Nonenzymatic template-directed RNA primer extension is a model of the polymerisation step in this posited form of replication. The sequence space accessed by primer extension dictates potential pathways to self-replication and, eventually, ribozymes. Which sequences can be accessed? What is the fidelity of the reaction? Does the recently-illuminated mechanism of primer extension affect the distribution of sequences that can be copied? How do sequence features respond to experimental conditions and prebiotically relevant contexts? To help answer these and related questions, we here introduce a deep-sequencing methodology for studying RNA primer extension. We have designed and vetted special RNA constructs for this purpose, honed a protocol for sample preparation and developed custom software that sorts and analyses raw sequencing data. We apply this new methodology to proof-of-concept controls, and demonstrate that it works as expected and reports on key features of the sequences accessed by primer extension.
Sex moderates the relationship between aortic stiffness, cognition and cerebrovascular reactivity in healthy older adults
Authors: Sabra Dalia , Intzandt Brittany , Desjardins-Crepeau Laurence , Langeard Antoine , Steele Christopher J. , Frouin Frédérique , Hoge Richard D. , Bherer Louis , Gauthier Claudine J.
Published: February 2020

It is well established that sex differences exist in the manifestation of cardiovascular diseases. Arterial stiffness (AS) has been associated with changes in cerebrovascular reactivity (CVR) and cognitive decline in aging. Specifically, older adults with increased AS show a decline on executive function (EF) tasks. Interestingly, the relationship between AS and CVR is more complex, where some studies show decreased CVR with increased AS, and others demonstrate preserved CVR despite higher AS. We investigated the possible role of sex and hematocrit (HCT) on these hemodynamic relationships. Acquisitions were completed in 48 older adults. Dual-echo pCASL data were collected during a hypercapnia challenge. Aortic PWV data was acquired using cine phase contrast velocity series. A moderation model test revealed that sex moderated the relationship between PWV and CVR and PWV and EF. In addition, there was a significant effect of HCT on the sex differences observed in the moderation effect on EF. Together, our results indicate that the relationships between PWV, CVR and EF are in part mediated by sex and HCT.

Highlights

This study investigates the role of sex on cerebrovascular measures of brain health and congition

Sex moderates the relationship between PWV, cerebrovascular reactivity and cognition

Hematocrit influences the sex differences observed
Prevalence and global distribution ofblaKPC-2andblaNDM-1genes inKlebsiella Pneumoniae
Authors: Zhang Xiufeng , Li Fangping , Cui Shiyun , Mao Lisha , Li Xiaohua , Furqan Awan , Lv Weibiao , Zeng Zhenling
Published: February 2020

Carbapene-resistantKlebsiella pneumoniaeinfections have caused a major concern and posed a global health threat to public.blaKPC-2andblaNDM-1genes are the most widely reported of carbapenem resistance genes inK. pneumoniae. In this study, we investigated phylogenetic relationships of carbapene-resistantK. pneumoniaefrom a tertiary hospital between 2013 and 2018 in China and analyzed the global epidemiology and distribution ofblaKPC-2andblaNDM-1gene inK. pneumoniaebased on 1579 NGS genomes. We found that 19 carbapene-resistantK. pneumoniaeisolated were divided into five lineages and all had high genotypic and phenotypic resistance. Two lineages (mostly ST11 and ST25) were the major type detected carryingblaKPC-2andblaNDM-1gene, respectively. Among global genomes data, 147 known ST types have been identified and ST11 and ST258 were the globally prevalent clones. Genetic environment analysis showed that theISKpn27-blaKPC-2-ISKpn6andblaNDM-1-ble-trpf-nagAmay be the core structure in the horizontal transfer ofblaKPC-2andblaNDM-1, respectively. In addition, DNA transferase (hin) may be involved in the horizontal transfer or the expression ofblaNDM-1. This study sheds some light on the genetic environment ofblaKPC-2andblaNDM-1and should foster further studies about the mechanism of carbapene-resistantK. pneumoniaedissemination.
Neural network features distinguish chemosensory stimuli inCaenorhabditis elegans
Authors: How Javier J. , Navlakha Saket , Chalasani Sreekanth H.
Published: February 2020

Nervous systems extract and process information from their environment to alter animal behavior and physiology. Despite progress in understanding how different stimuli are represented by changes in neuronal activity, less is known about how they affect broader neural network properties. We developed a framework to use graph-theoretic features of neural network activity and predict ecologically-relevant stimulus properties – namely, stimulus identity and valence. Specifically, we used the transparent nematode,Caenorhabditis elegans, with its small nervous system, to define neural network features associated with various chemosensory stimuli. We trapped animals using a microfluidic device and exposed their noses to chemical stimuli known to be attractive or repellent, while monitoring changes in neural activity in more than 40 neurons in their heads. We found that repellents trigger higher average neural activity across the network, and that the tastant salt increases neural variability. In contrast, graph-theoretic features, which capture patterns of interactions between neurons, are better suited to decode stimulus identity than measures of neural activity. Furthermore, we show that a simple machine learning classifier trained using graph-theoretic features alone or in combination with neural activity features can accurately predict stimulus identity. These results indicate that graph theory reveals network characteristics that are distinct from neural activity, confirming its utility in extracting stimulus properties from neural population data.

Significance Statement

Changes in the external environment (stimuli) alter patterns of neural activity in animal nervous systems. A central challenge in computational neuroscience is to identify how stimulus properties alter interactions between neurons. We recorded neural activity data fromC. eleganshead neurons while the animal experienced various chemosensory stimuli. We then used a combination of activity statistics (i.e., average, standard deviation, and several frequency-based measures) and graph-theoretic features of network structure (e.g., modularity – the extent to which a network can be divided into independent clusters) to define neural properties that can accurately predict stimulus identity. Our method is general and can be used across species.
CasRx-mediated RNA targeting prevents choroidal neovascularization in a mouse model of age-related macular degeneration
Authors: Zhou Changyang , Hu Xinde , Tang Cheng , Liu Wenjia , Wang Shaoran , Zhou Yingsi , Zhao Qimeng , Bo Qiyu , Shi Linyu , Sun Xiaodong , Zhou Haibo , Yang Hui
Published: February 2020

The smallest Cas13 family protein, CasRx, has a high cleavage activity and targeting specificity, offering attractive opportunity for therapeutic applications. Here we report that delivery of CasRx by adeno-associated virus via intravitreal injection could efficiently knockdownVegfatranscripts and significantly reduce the area of laser-induced choroidal neovascularization in a mouse model of age-related macular degeneration. Thus, RNA-targeting CRISPR system could be used forin vivogene therapy.
Brain Injury after Transcatheter Aortic Valve Replacement for Bicuspid Versus Tricuspid Aortic Valve Stenosis
Authors: Fan Jiaqi , Fang Xian , Liu Chunhui , Zhu Gangjie , Hou Cody R. , Jiang Jubo , Lin Xinping , Wang Lihan , He Yuxin , Zhu Qifeng , Ng Stella , Chen Zexin , Hu Haitao , Tse Hungfat , Liu Xianbao , Wang Jian’an
Published: February 2020

Backgrounds

The risk of brain injury in bicuspid aortic valve (BAV) patients following transcatheter aortic valve replacement (TAVR) is currently unknown.

Methods and Results

A total of 204 consecutive severe aortic stenosis patients who underwent TAVR were enrolled. 83 (40.7%) patients were BAV patients and the other 121 patients were tricuspid aortic valve (TAV) patients. All patients received diffusion-weighted magnetic resonance imaging (DW-MRI) at baseline, 2 to 7 days after TAVR. Mean ages (mean ± SD: 75.8 ± 6.7 years vs. 78.9 ± 6.6 years, p = 0.004) and STS scores (6.0 ± 3.7 vs. 7.1 ± 4.2, p = 0.044) of the BAV and TAV patients were significantly different, while the stroke rates (2.4% vs. 1.7%, p = 0.704) were comparable between two groups. BAV patients were associated with higher number of new lesions (5.69 ± 6.22 vs. 3.50 ± 4.16, p = 0.008), total lesion volume [median(interquartile range): 290(70-930) mm3 vs. 140(35-480) mm3, p = 0.008], and the volume per lesion [70.0(45.0-115.0) mm3 vs. 57.5(24.5-93.0) mm3, p = 0.037] in DW-MRI. Moreover, the proportion of patients with lesions larger than 1cm3 (28.6% vs. 10.9%, p = 0.005) and the number of new lesions in the middle cerebral arteries zone (1.46 ± 2.07 vs. 0.98 ± 1.84, p = 0.039) and intermediate zone between the anterior cerebral and middle cerebral arteries (ACA/MCA) (1.07 ± 1.68 vs. 0.50 ± 1.05, p = 0.007), and between the vertebral artery and basilar artery (VA/BA) (1.01 ± 1.35 vs. 0.77 ± 1.44, p = 0.033) were higher in BAV patients than in TAV patients.

Conclusions

BAV patients may encounter more severe brain injuries not only due to greater number of lesions but also due to larger lesion size, especially in the ACA/MCA, MCA and VA/BA lesions zone.
Rewinding the molecular clock in the genusCarabus(Coleoptera: Carabidae) in light of fossil evidence and the Gondwana split: a re-analyses
Authors: Opgenoorth Lars , Hofmann Sylvia , Schmidt Joachim
Published: February 2020

1

Background

Molecular clocks have become powerful tools given increasing sequencing and fossil resources. However, outcome of calibration analyses depend on choosing priors. Here we revisit a seminal dating study of the genusCarabusby Andujar et al. proposing that their prior choices need re-evaluation with the hypothesis that reflecting fossil evidence and the Gondwanan split properly rewinds the molecular clock significantly. We used the same dataset including five mitochondrial and four nuclear DNA fragments with 7888 nt total length. We set the root age based on the fossil evidence of Harpalinae ground beetles in the Upper Cretaceous and introduce the Paleogene divergence of the outgroup taxaCeroglossus(endemic to South-America) andPamborus+Maoripamborus(Australia, New Zealand) as a new prior based on current paleontological and geological literature.

Results

The ultrametric time-calibrated tree of the extended nd5 dataset resulted in a median TMRCACarabusage of 58.48 Ma (HPD95% 46.61-72.04), roughly 35 Ma older than in the Andujar study. The splits betweenC. rugosusandC. morbillosus(A), betweenC. riffensisfrom the EuropeanMesocarabus(B), and betweenEurycarabusandNesaeocarabus(C) were dated to 19.19 (13.54-25.87), 25.95 (18.8-34.62), and 23.98 (17.28-31.47) Ma and were thus decidedly older than previously reported (7.48, 10.93, and 9.51 Ma). These changes were driven solely by constraining the Carabidae time tree root with Harpalinae amber fossils at ∼99 Ma. Utilizing the nd5 dating results of three well supportedCarabusclades as secondary calibration points for the complete MIT-NUC data set lead to a TMRCA ofCarabusof 53.56 (41.25-67.05) Ma compared to 25.16 (18.41-33.04) in Andujar’s study.

Conclusion

Taking into account the Gondwanan split as a new prior, together with the fossil evidence of the outgroup taxon Harpalini in the Late Cretaceous, our new approach supports an origin of the genusCarabusin the Paleocene-Early Eocene. Our results are preliminary due to the heavy reliance on the nd5 gene and thus will have to be tested with sufficient set of nuclear markers. In addition, uncertainties arise from dating the root age of the tree based on a single fossil and outgroup taxon which has a major effect on the results. Improvement of the fossil data base particularly in the supertribe Carabitae is thus strongly needed to reduce the currently large uncertainties in datingCarabusphylogeny.
Urethral luminal epithelia are castration-insensitive progenitors of the proximal prostate
Authors: Joseph Diya B. , Henry Gervaise H. , Malewska Alicia , Iqbal Nida S. , Ruetten Hannah M. , Turco Anne E. , Abler Lisa L. , Sandhu Simran K. , Cadena Mark T. , Malladi Venkat S. , Reese Jeffrey C. , Mauck Ryan J. , Gahan Jeffrey C. , Hutchinson Ryan C. , Roehrborn Claus G. , Baker Linda A. , Vezina Chad M. , Strand Douglas W.
Published: February 2020

Castration-insensitive epithelial progenitors capable of regenerating the prostate are concentrated in the proximal region close to the urethra, but the identification of these cells has been limited to individual cell surface markers. Here, we use single cell RNA sequencing (scRNA-seq) to obtain a cellular anatomy of the mouse prostate and urethra and create a comparative map with the human. These data reveal that previously identified facultative progenitors marked by TROP2, Sca-1, KRT4, and PSCA are actually luminal epithelia of the urethra that extend into the proximal prostate. These mouse urethral cells are the human equivalent of previously identified club and hillock urethral cells. Castration decreases androgen-dependent prostate luminal epithelia as expected, but TROP2+ urethral luminal epithelia survive and expand into the prostate. Benign prostatic hyperplasia (BPH) has long been considered an ‘embryonic reawakening’, but the cellular origin of peri-urethral growth is unclear. We use scRNA-seq and flow cytometry to demonstrate an increase in urethral luminal epithelia within glandular nodules from patients with BPH, which are further enriched in patients treated with a 5 alpha reductase inhibitor. These data demonstrate that the putative prostate progenitors enriched by castration in the proximal prostate are an expansion of urethral luminal epithelia and that these cells may play an important role in the etiology of human BPH.

Significance Statement

The prostate involutes after castration, but regrows to its original size with androgen replenishment. This observation prompted the search for a castration-insensitive prostate progenitor. Here, Josephet al. produce a comparative cellular atlas of the prostate and urethra in the mousevs.human, discovering an equivalent urethral luminal epithelial cell type that extends into the proximal prostatic ducts and expresses previously identified markers of facultative prostate progenitors. Urethral luminal epithelia are established before prostate budding in human and mouse development, and expand after castration in the mouse and after 5 alpha reductase inhibitor treatment in human BPH. These data suggest that luminal epithelia of the urethra are castration-insensitive cells of proximal ducts that may act as progenitors in human BPH.
Input connectivity reveals additional heterogeneity of dopaminergic reinforcement inDrosophila
Authors: Otto Nils , Pleijzier Markus W. , Morgan Isabel C. , Edmondson-Stait Amelia J. , Heinz Konrad J. , Stark Ildiko , Dempsey Georgia , Ito Masayoshi , Kapoor Ishaan , Hsu Joseph , Schlegel Philipp M. , Bates Alexander S. , Feng Li , Costa Marta , Ito Kei , Bock Davi D. , Rubin Gerald M , Jefferis Gregory S. X. E. , Waddell Scott
Published: February 2020

Different types ofDrosophiladopaminergic neurons (DANs) reinforce memories of unique valence and provide state-dependent motivational control [1]. Prior studies suggest that the compartment architecture of the mushroom body (MB) is the relevant resolution for distinct DAN functions [2, 3]. Here we used a recent electron microscope volume of the fly brain [4] to reconstruct the fine anatomy of individual DANs within three MB compartments. We find the 20 DANs of the γ5 compartment, at least some of which provide reward teaching signals, can be clustered into 5 anatomical subtypes that innervate different regions within γ5. Reconstructing 821 upstream neurons reveals input selectivity, supporting the functional relevance of DAN sub-classification. Only one PAM-γ5 DAN subtype γ5(fb) receives direct recurrent input from γ5β’2a mushroom body output neurons (MBONs) and behavioral experiments distinguish a role for these DANs in memory revaluation from those reinforcing sugar memory. Other DAN subtypes receive major, and potentially reinforcing, inputs from putative gustatory interneurons or lateral horn neurons, which can also relay indirect feedback from MBONs. We similarly reconstructed the single aversively reinforcing PPL1-γ1pedc DAN. The γ1pedc DAN inputs mostly differ from those of γ5 DANs and they cluster onto distinct dendritic branches, presumably separating its established roles in aversive reinforcement and appetitive motivation [5, 6]. Tracing also identified neurons that provide broad input to γ5, β’2a and γ1pedc DANs suggesting that distributed DAN populations can be coordinately regulated. These connectomic and behavioral analyses therefore reveal further complexity of dopaminergic reinforcement circuits between and within MB compartments.

Highlights

Nanoscale anatomy reveals additional subtypes of rewarding dopaminergic neurons.

Connectomics reveals extensive input specificity to subtypes of dopaminergic neurons.

Axon morphology implies dopaminergic neurons provide subcompartment-level function.

Unique dopaminergic subtypes serve aversive memory extinction and sugar learning.
Museum phylogenomics of extinctOryctesbeetles from the Mascarene Islands
Authors: Latorre Sergio M. , Herrmann Matthias , Paulsen M.J. , Rödelsperger Christian , Dréau Andreea , Röseler Waltraud , Sommer Ralf J. , Burbano Hernán A.
Published: February 2020

The evolution of island systems is characterized by processes that result in extreme morphological diversity, high endemism and high extinction rates. These dynamics can make phylogenetic reconstruction difficult, i.e. the extinct flightless Dodo from Mauritius was assigned to the family of doves only through DNA analysis of subfossils. Many insect species on islands have gone extinct through habitat loss, and face similar challenges to decipher their evolutionary history, however historical specimens have not yet been harnessed for phylogenomic reconstructions. Here, we employed historical museum specimens from the Mascarene Islands to generate the first whole-genome based phylogeny of three presumably extinct species of the rhinoceros beetle genusOryctes. We compared their genomes with those of an extantOryctesspecies from the island of Réunion, as well as a flightless Réunion-based species previously placed into the supposedly unrelated genusMarronus. We found thatMarronus borbonicusbelongs instead to the genusOryctesand that the two Réunion-based species (O. borbonicusandM. borbonicus) are not sister taxa, suggesting two independent colonizations. The divergence time between them (<3Myr) overlaps with the volcanic formation of Réunion, likely indicating thatM. borbonicusbecame flightlessin situ. Our study showcases the power of genomes from insect museum specimens to address evolutionary questions in light of increasing extinction rates.
Myeloid-derived suppressor cell subsets drive glioblastoma growth in a sex-specific manner
Authors: Bayik Defne , Zhou Yadi , Park Chihyun , Hong Changjin , Vail Daniel , Silver Daniel J. , Lauko Adam J. , Roversi Gustavo A. , Watson Dionysios C. , Lo Alice , Alban Tyler J. , McGraw Mary , Sorensen Mia D. , Grabowski Matthew M. , Otvos Balint , Vogelbaum Michael A. , Horbinski Craig M. , Kristensen Bjarne Winther , Khalil Ahmad M. , Hwang Tae Hyun , Ahluwalia Manmeet S. , Cheng Feixiong , Lathia Justin D.
Published: February 2020

Myeloid-derived suppressor cells (MDSCs) that block anti-tumor immunity are elevated in glioblastoma (GBM) patients. However, the distinct contribution of monocytic (mMDSC) versus granulocytic (gMDSC) subsets has yet to be determined. We observed that mMDSCs were enriched in the male tumor microenvironment, while gMDSCs were elevated in the circulation of female GBM models. Depletion of peripheral gMDSCs extended the survival only in female mice. Using gene expression signatures coupled with network medicine analysis, we demonstrated in pre-clinical models that mMDSCs could be targeted with anti-proliferative agents in males, whereas gMDSC function in females could be inhibited by IL-1β blockade. Analysis of patient data confirmed that proliferating mMDSCs were the predominant population in male tumors, and that a high gMDSC/IL-1β gene signature correlated with poor prognosis of female patients. These findings demonstrate that MDSC subsets differentially drive immune suppression in a sex-specific manner and can be leveraged for therapeutic intervention in GBM.

Statement of Significance

Sexual dimorphism at the level of MDSC subset prevalence, localization and gene expression profile comprises a therapeutic opportunity. Our results indicate that chemotherapy can be used to target mMDSC in males, while IL-1 pathway inhibitors can provide benefit to females through blockade of gMDSC function.
Ras-GRF1 in CRF Cells Controls the Early Adolescent Female Response to Repeated Stress
Authors: Jin Shan-xue , Dickson David A. , Maguire Jamie , Feig Larry A.
Published: February 2020

Ras-GRF1 (GRF1) is a calcium-stimulated guanine-nucleotide exchange factor that activates Ras and Rac GTPases. In hippocampal neurons, it mediates the action of NMDA and calcium-permeable AMPA glutamate receptors on specific forms of synaptic plasticity, learning, and memory in both male and female mice. Recently, we showed that GRF1 also regulates the HPA axis response to restraint stress, but only in female mice before puberty. In particular, we found that after exposure to 7-days of restraint-stress (7DRS) (30 min/day) elevation of serum CORT levels are suppressed in early adolescent (EA) female, but not EA male or adult female GRF1 knockdown mice. Here, we show that this phenotype is due, at least in part, to the loss of GRF1 expression in CRF cells of the paraventricular nucleus of the hypothalamus, as GRF1 knockdown specifically in these cells also reduces serum CORT response to 7DRS in EA females, but not EA males or adult females. Moreover, it reduces females CORT levels to those to found in comparably stressed control male mice. GRF1 knockdown in CRF cells also blocks the anxiolytic phenotype normally found in EA females 24 hrs after 7DRS. Interestingly, loss of GRF1 in these cells has no effect after only 3 exposures to restraint stress, revealing a role for GRF1 in repeated stress-induced CRF cell plasticity that appears to be specific to EA female mice. Overall, these findings indicate that GRF1 in CRF cells makes a key contribution to the distinct response early-adolescent female display to repeated stress.
Fast retrograde access to projection neuron circuits underlying vocal learning in songbirds
Authors: Düring DN , Dittrich F , Rocha MD , Tachibana RO , Mori C , Okanoya K , Boehringer R , Ehret B , Grewe BF , Rauch M , Paterna JC , Kasper R , Gahr M , Hahnloser RHR
Published: February 2020

Understanding the structure and function of neural circuits underlying speech and language is a vital step towards better treatments for diseases of these systems. Songbirds, among the few animal orders that share with humans the ability to learn vocalizations from a conspecific, have provided many insights into the neural mechanisms of vocal development. However, research into vocal learning circuits has been hindered by a lack of tools for rapid genetic targeting of specific neuron populations to meet the quick pace of developmental learning. Here, we present a new viral tool that enables fast and efficient retrograde access to projection neuron populations. In zebra finches, Bengalese finches, canaries, and mice, we demonstrate fast retrograde labeling of cortical or dopaminergic neurons. We further demonstrate the suitability of our construct for detailed morphological analysis, forin vivoimaging of calcium activity, and for multicolor brainbow labeling.
Portuguese wild grapevine genome re-sequencing (Vitis vinifera sylvestris)
Authors: Ramos Miguel J N , Coito João L , Silva David F , Cunha Jorge , Costa M Manuela R , Amâncio Sara , Rocheta Margarida
Published: February 2020

Vitisis a relevant genus worldwide. The genome of aVitis viniferarepresentative (PN40024) published in 2007 boosted grapevine related studies. While this reference genome is a suitable tool for the overall studies in the field, it lacks the ability to unveil changes accumulated duringV. viniferadomestication. Considering that grapevines for wine production (V. v. vinifera, hereaftervinifera) have evolved fromV. v. sylvestris(hereaftersylvestris), or from a shared no-longer existing ancestor, both subspecies are quite close, butsylvestrishas not been domesticated and still exist nowadays, preserving wild characteristics, making it a good material to provide insights intoviniferadomestication. The difference in the reproductive strategy between both subspecies is one of the characteristics that sets them apart. Whileviniferaflowers are hermaphrodite with functional male and female organs,sylvestrisis mostly dioecious. Male plants present flowers lacking functional carpels unable to produce grapes and female individuals have flowers with reflexed stamens producing infertile pollen but able to exhibit small and acidic grapes. In this paper, we describe the re-sequencing of the genomes from a male and a female individual of the wildsylvestrisand its comparison against the referenceviniferagenome.
Simple models including energy and spike constraints reproduce complex activity patterns and metabolic disruptions
Authors: Fardet Tanguy , Levina Anna
Published: February 2020

In this work, we introduce new phenomenological neuronal models (eLIF and mAdExp) that account for energy supply and demand in the cell as well as the inactivation of spike generation how these interact with subthreshold and spiking dynamics. Including these constraints, the new models reproduce a broad range of biologically-relevant behaviors that are identified to be crucial in many neurological disorders, but were not captured by commonly used phenomenological models. Because of their low dimensionalityeLIF and mAdExp open the possibility of future large-scale simulations for more realistic studies of brain circuits involved in neuronal disorders. The new models enable both more accurate modeling and the possibility to study energy-associated disorders over the whole time-course of disease progression instead of only comparing the initially healthy status with the final diseased state. These models, therefore, provide new theoretical and computational methods to assess the opportunities of early diagnostics and the potential of energy-centered approaches to improve therapies.

Author summary

Neurons, even “at rest”, require a constant supply of energy to function. They cannot sustain high-frequency activity over long periods because of regulatory mechanisms, such as adaptation or sodium channels inactivation, and metabolic limitations. These limitations are especially severe in many neuronal disorders, where energy can become insufficient and make the neuronal response change drastically, leading to increased burstiness, network oscillations, or seizures. Capturing such behaviors and impact of energy constraints on them is an essential prerequisite to study disorders such as Parkinson’s disease and epilepsy. However, energy and spiking constraints are not present in any of the standard neuronal models used in computational neuroscience. Here we introduce models that provide a simple and scalable way to account for these features, enabling large-scale theoretical and computational studies of neurological disorders and activity patterns that could not be captured by previously used models. These models provide a way to study energy-associated disorders over the whole time-course of disease progression, and they enable a better assessment of energy-centered approaches to improve therapies.
Prediction of Essential Binding Domains for the Endocannabinoid N-Arachidonoylethanolamine (AEA) in the Brain Cannabinoid CB1 receptor
Authors: Shim Joong-Youn
Published: February 2020

∆9-tetrahydrocannabinol (∆9-THC), the main active ingredient ofCannabis sativa(marijuana), interacts with the human brain cannabinoid (CB1) receptor and mimics pharmacological effects of endocannabinoids (eCBs)N-arachidonylethanolamide (AEA) and 2-arachidonoylglycerol (2-AG). Given recent intriguing findings that some allosteric modulators can enhance selectively the AEA-activated CB1 receptor, it is imperative to determine the structure of the AEA-bound CB1 receptor. However, due to its highly flexible nature of AEA, establishing its binding mode to the CB1 receptor is elusive. The aim of the present study was to explore many possible binding conformations of AEA within the binding pocket of the CB1 receptor that is confirmed in the recently available X-ray crystal structures of the agonist-bound CB1 receptors and predict essential AEA binding domains. We performed long time molecular dynamics stimulations of plausible AEA docking poses until its receptor binding interactions became optimally established. Our simulation results revealed that AEA favors to bind to the hydrophobic channel of the CB1 receptor, suggesting that the hydrophobic channel holds essential significance in AEA binding to the CB1 receptor. Our results also suggest that the H2/H3 region of the CB1 receptor is an AEA binding subsite privileged possibly over the H7 region. The results of the present study contribute to identifying the (hidden) allosteric site(s) of the CB1 receptor in our immediate future study.
Endonuclease activity of RecJ from extremely alkaliphilic Bacillus alcalophilus
Authors: Zheng Minggang , Wang Wen , Ma Liya , Wang Ling , Qu Lingyun , Liu Xipeng , Liu Hailiang
Published: February 2020

At present, all documented RecJs are exonucleases, degrading single-stranded nucleic acids. Here, we report a novel RecJ, from the extremely alkaliphilic bacteriumBacillus alcalophilus(BaRecJ), which possesses endonuclease activity and can cleave supercoiled DNA. BaRecJ contains the typical DHH and DHHA1 domains, which are conserved in all RecJs, and a functionally unknown PIWI-like domain at the C-terminus. The endonuclease activity originates from the C-terminal domain of BaRecJ which contains PIWI-like domain, and the exonuclease activity from the DHH and DHHA1 domains. Mutational analysis reveals that several important residues affect the endonuclease activity of BaRecJ. Moreover, BaRecJ cleaves specific target sequences at moderate temperature when directed by a phosphorothioate-modified single-stranded DNA (S-modified ssDNA) guide. These findings suggest that BaRecJ is substantially different from any reported RecJs and has the potential to be developed as a new gene editing tool.
A novel drug-combination screen in zebrafish identifies epigenetic small molecule candidates for Duchenne muscular dystrophy
Authors: Farr Gist H. , Morris Melanie , Gomez Arianna , Pham Thao , Parker Elizabeth U. , Kilroy Elisabeth , Said Shery , Henry Clarissa , Maves Lisa
Published: February 2020

Duchenne muscular dystrophy (DMD) is a severe neuromuscular disorder and is one of the most common muscular dystrophies. There are currently few effective therapies to treat the disease, although many small-molecule approaches are being pursued. Specific histone deacetylase inhibitors (HDACi) can ameliorate DMD phenotypes in mouse and zebrafish animal models and have also shown promise for DMD in clinical trials. However, beyond these HDACi, other classes of epigenetic small molecules have not been broadly and systematically studied for their benefits for DMD. Here, we performed a novel chemical screen of a library of epigenetic compounds using the zebrafishdmdmodel. We identified candidate pools of epigenetic compounds that improve skeletal muscle structure indmdzebrafish. We then identified a specific combination of two drugs, oxamflatin and salermide, that significantly rescueddmdzebrafish skeletal muscle degeneration. Furthermore, we validated the effects of oxamflatin and salermide in an independent laboratory. Our results provide novel, effective methods for performing a combination small-molecule screen in zebrafish. Our results also add to the growing evidence that epigenetic small molecules may be promising candidates for treating DMD.
Sox17 and β-catenin co-occupy Wnt-responsive enhancers to govern the endodermal gene regulatory network
Authors: Mukherjee Shreyasi , Chaturvedi Praneet , Rankin Scott A. , Fish Margaret B. , Wlizla Marcin , Paraiso Kitt D. , MacDonald Melissa , Chen Xiaoting , Weirauch Matthew T. , Blitz Ira L. , Cho Ken W. Y. , Zorn Aaron M.
Published: February 2020

Lineage specification is governed by gene regulatory networks (GRNs) that integrate the activity of signaling effectors and transcription factors (TFs) on enhancers. Sox17 is a key transcriptional regulator of definitive endoderm development, and yet, its genomic targets remain largely uncharacterized. Here, using genomic approaches and epistasis experiments, we define the Sox17-governed endoderm GRN inXenopusgastrulae. We show that Sox17 functionally interacts with the canonical Wnt pathway to specify and pattern the endoderm while repressing alternative mesectoderm fates. Sox17 and β-catenin co-occupy hundreds of key enhancers. In some cases, Sox17 and β-catenin synergistically activate transcription independent of Tcfs, whereas on other enhancers, Sox17 represses ß-catenin/Tcf-mediated transcription to spatially restrict gene expression domains. Our findings establish Sox17 as a tissue-specific modifier of Wnt responses and point to a novel paradigm where genomic specificity of Wnt/ß-catenin transcription is determined through functional interactions between lineage-specific Sox TFs and ß-catenin/Tcf transcriptional complexes. Given the ubiquitous nature of Sox TFs and Wnt signaling, this mechanism has important implications across a diverse range of developmental and disease contexts.

Key findings

Sox17 regulates germ layer segregation by promoting endoderm differentiation while simultaneously repressing mesectoderm fates.

Functional interactions between Sox17 and canonical Wnt-signaling is a major feature of the GRN controlling endoderm specification and patterning.

Sox17 and β-catenin co-occupy a subset of enhancers to synergistically stimulate transcription in the absence of Tcfs.

Sox17 regulates the spatial expression domains of Wnt/β-catenin-responsive transcription in the gastrula.
C. elegansnuclear RNAi factor SET-32 deposits the transgenerational heritable histone modification, H3K23me3
Authors: Schwartz-Orbach Lianna , Zhang Chenzhen , Sidoli Simone , Amin Richa , Kaur Diljeet , Zhebrun Anna , Ni Julie , Gu Sam
Published: February 2020

Nuclear RNAi provides a highly tractable system to study RNA-mediated chromatin changes and epigenetic inheritance. Recent studies have indicated that the regulation and function of nuclear RNAi-mediated heterochromatin are highly complex. Our knowledge of histone modifications and the corresponding histone modifying enzymes involved in the system remains limited. In this study, we show that the heterochromatin mark, H3K23me3, is induced by nuclear RNAi at both exogenous and endogenous targets inC. elegans. In addition, dsRNA-induced H3K23me3 can be inherited for four generations. We demonstrate that the histone methyltransferase SET-32, methylates H3K23in vitro. Bothset-32and the germline nuclear RNAi Argonaute,hrde-1, are required for nuclear RNAi-induced H3K23me3in vivo. Our data poise H3K23me3 as an additional chromatin modification in the nuclear RNAi pathway and provides the field with a new target for uncovering the role of heterochromatin in transgenerational epigenetic silencing.
Units of motor production: Bengalese finches interrupt song within syllables
Authors: Riedner D. , Adam I.
Published: February 2020

Birdsong consists of syllables that are separated by silent intervals. Previous work in zebra finches showed that syllables correspond to the smallest motor production units (Cynx, 1990; Franz and Goller, 2002) by inducing song stops using strobe light. In this study, we interrupted the song of six Bengalese finches experimentally with the bird’s own song as auditory stimulus using an interactive playback approach. Five of the tested males interrupted their ongoing vocalizations within syllables (16 instances of induced interrupted syllables) in response to the playback. Additionally, we observed 9 spontaneous interruptions in our control recordings. This study establishes that birds can interrupt ongoing syllables within extremely short latencies in response to an auditory stimulus, and that auditory stimuli interrupt syllables more effectively than visual stimuli. Even if syllables are the functionally stable production units, the ability to disrupt those units differs between species and individuals, indicating various degrees of vocal control.
Quantitative dialing of gene expression via precision targeting of KRAB repressor
Authors: Wilken Matthew S. , Ciarlo Christie , Pearl Jocelynn , Schanzer Elaine , Liao Hanna , Biber Benjamin Van , Queitsch Konstantin , Bloom Jordan , Federation Alexander , Acosta Reyes , Vong Shinny , Otterman Ericka , Dunn Douglass , Wang Hao , Zrazhevskiy Pavel , Nandakumar Vivek , Bates Daniel , Sandstrom Richard , Urnov Fyodor D. , Funnell Alister , Green Shon , Stamatoyannopoulos John A.
Published: February 2020

Human genes are regulated quantitatively, yet the ability to specify the expression level of a native gene accurately and specifically using a defined reagent has remained elusive. Here we show that precise targeting of KRAB repressive domain within regulatory DNA unlocks an endogenous quantitative ‘dial’ that can be engaged at nucleotide resolution to program expression levels across a wide physiologic range, with single-gene specificity and high reproducibly in primary cells.
Assessment of mitochondrial physiology of murine white adipose tissue by mechanical permeabilization and lipid depletion
Authors: Romeiro Natália C. , Ferreira Caroline M. , Oliveira Marcus F.
Published: February 2020

White adipose tissue (WAT) is classically associated with energy storage in the form of triacylglycerol and is directly associated with metabolic disorders, including obesity. Mitochondria regulates cellular expenditure and are active in WAT. Although isolated mitochondria have been classically used to assess their functions, several artifacts can be introduced by this approach. Although methods to assess mitochondrial physiology in permeabilized WAT were proposed, important limitations that affect organelle function exist. Here, we established and validated a method for functional evaluation of mice mesenteric WAT (mWAT) mitochondria by using mechanical permeabilization in combination with lipid depletion and high-resolution respirometry. We observed that mild stirring of mWAT for 20 minutes at room temperature with 4% fatty acid-free albumin selectively permeabilized white adipocytes plasma membrane. In these conditions, mWAT mitochondria were intact and coupled, exhibiting succinate-induced respiratory rates that were sensitive to classical modulators of oxidative phosphorylation. Finally, the respiratory capacity of mWAT in females was significantly higher than in males, an observation that agrees with reported data using isolated mitochondria. The functional assessment of mWAT mitochondria through mild mechanical permeabilization, lipid depletion and high resolution respirometry proposed here will contribute to a better understanding of WAT biology in several pathophysiological contexts.