bluuebunny/crossref_metadata_2025 huggingface dataset:
Differential responses of transplanted stem cells to the diseased environment unveiled by a single molecular NIR II cell tracker
Authors: Chen Hao , Yang Huaxiao , Zhang Chen , Chen Si , Zhao Xin , Zhu Mark , Wang Zhiming , Zhang Xun , Wang Yuebing , Wo Hung-Ta , Li Kai , Cheng Zhen
Published: March 2020

Stem cell therapy holds high promises in regenerative medicine. The major challenge of clinical translation is to precisely and quantitatively evaluate thein vivocell distribution, migration, and engraftment, which cannot be easily achieved by current techniques. To address this issue, for the first time, we have developed a single molecular cell tracker with a strong fluorescence signal in the second near-infrared (NIR-II) window (1000-1700 nm) for real-time monitoring ofin vivocell behaviors in both healthy and diseased animal models. The NIR-II tracker (CelTrac1000) has shown complete cell labeling with low cytotoxicity and profound long-term tracking ability for 30 days in high temporospatial resolution for semi-quantification of the biodistribution of primary mesenchymal stem cell and induced pluripotent stem cell-derived endothelial cells. Taking advantage of the unique merits of CelTrac1000, the responses of transplanted stem cells to different diseased environments have been discriminated and unveiled. Furthermore, we also demonstrate CelTrac1000 as a universal and effective technique for ultrafast real-time tracking of the cellular migration and distribution in a single cell cluster resolution, along with the lung contraction and heart beating. As such, this single molecular NIR-II tracker will shift the optical cell tracking into a single cell cluster and millisecond temporospatial resolution for better evaluating and understanding stem cell therapy, affording optimal doses and efficacy.

Significance Statement

For the first time, we synthesized a NIR-II tracker (CelTrac1000) for ultrafast real-time tracking of the migration trajectory of transplanted mesenchymal stem cells in the circulatory system with a single cell cluster resolution. Taking advantage of the merits of CelTrac1000, the responses of transplanted stem cells to different diseased environments, including acute lung injury, myocardial infarction, and middle cerebral artery occlusion, have been discriminated and unveiled in mice models. As such, our approach can help correlate critical biomedical information in stem cell therapies, such as stem cell dosing and engraftment and their relationships with efficacy, providing more accurate therapeutic treatment and outcomes in certain diseases during a long evaluation period (>30 days) in comparison with the commercial Qtracker (7-10 days).
The architecture of SARS-CoV-2 transcriptome
Authors: Kim Dongwan , Lee Joo-Yeon , Yang Jeong-Sun , Kim Jun Won , Kim V. Narry , Chang Hyeshik
Published: March 2020

SARS-CoV-2 is a betacoronavirus that is responsible for the COVID-19 pandemic. The genome of SARS-CoV-2 was reported recently, but its transcriptomic architecture is unknown. Utilizing two complementary sequencing techniques, we here present a high-resolution map of the SARS-CoV-2 transcriptome and epitranscriptome. DNA nanoball sequencing shows that the transcriptome is highly complex owing to numerous recombination events, both canonical and noncanonical. In addition to the genomic RNA and subgenomic RNAs common in all coronaviruses, SARS-CoV-2 produces a large number of transcripts encoding unknown ORFs with fusion, deletion, and/or frameshift. Using nanopore direct RNA sequencing, we further find at least 41 RNA modification sites on viral transcripts, with the most frequent motif being AAGAA. Modified RNAs have shorter poly(A) tails than unmodified RNAs, suggesting a link between the internal modification and the 3′ tail. Functional investigation of the unknown ORFs and RNA modifications discovered in this study will open new directions to our understanding of the life cycle and pathogenicity of SARS-CoV-2.

Highlights

We provide a high-resolution map of SARS-CoV-2 transcriptome and epitranscriptome using nanopore direct RNA sequencing and DNA nanoball sequencing.

The transcriptome is highly complex owing to numerous recombination events, both canonical and noncanonical.

In addition to the genomic and subgenomic RNAs common in all coronaviruses, SARS-CoV-2 produces transcripts encoding unknown ORFs.

We discover at least 41 potential RNA modification sites with an AAGAA motif.
Nucleotide Analogues as Inhibitors of SARS-CoV Polymerase
Authors: Ju Jingyue , Li Xiaoxu , Kumar Shiv , Jockusch Steffen , Chien Minchen , Tao Chuanjuan , Morozova Irina , Kalachikov Sergey , Kirchdoerfer Robert N. , Russo James J.
Published: March 2020

SARS-CoV-2, a member of the coronavirus family, has caused a global public health emergency.1 Based on our analysis of hepatitis C virus and coronavirus replication, and the molecular structures and activities of viral inhibitors, we previously reasoned that the FDA-approved heptatitis C drug EPCLUSA (Sofosbuvir/Velpatasvir) should inhibit coronaviruses, including SARS-CoV-2.2 Here, using model polymerase extension experiments, we demonstrate that the activated triphosphate form of Sofosbuvir is incorporated by low-fidelity polymerases and SARS-CoV RNA-dependent RNA polymerase (RdRp), and blocks further incorporation by these polymerases; the activated triphosphate form of Sofosbuvir is not incorporated by a host-like high-fidelity DNA polymerase. Using the same molecular insight, we selected two other anti-viral agents, Alovudine and AZT (an FDA approved HIV/AIDS drug) for evaluation as inhibitors of SARS-CoV RdRp. We demonstrate the ability of two HIV reverse transcriptase inhibitors, 3’-fluoro-3’-deoxythymidine triphosphate and 3’-azido-3’-deoxythymidine triphosphate (the active triphosphate forms of Alovudine and AZT), to be incorporated by SARS-CoV RdRp where they also terminate further polymerase extension. Given the 98% amino acid similarity of the SARS-CoV and SARS-CoV-2 RdRps, we expect these nucleotide analogues would also inhibit the SARS-CoV-2 polymerase. These results offer guidance to further modify these nucleotide analogues to generate more potent broad-spectrum anti-coronavirus agents.
Denoising large-scale biological data using network filters
Authors: Kavran Andrew J. , Clauset Aaron
Published: March 2020

Large-scale biological data sets, e.g., transcriptomic, proteomic, or ecological, are often contaminated by noise, which can impede accurate inferences about underlying processes. Such measurement noise can arise from endogenous biological factors like cell cycle and life history variation, and from exogenous technical factors like sample preparation and instrument variation. Here we describe a general method for automatically reducing noise in large-scale biological data sets. This method uses an interaction network to identify groups of correlated or anti-correlated measurements that can be combined or “filtered” to better recover an underlying biological signal. Similar to the process of denoising an image, a single network filter may be applied to an entire system, or the system may be first decomposed into distinct modules and a different filter applied to each. Applied to synthetic data with known network structure and signal, network filters accurately reduce noise across a wide range of noise levels and structures. Applied to a machine learning task of predicting changes in human protein expression in healthy and cancerous tissues, network filtering prior to training increases accuracy up to 58% compared to using unfiltered data. These results indicate the broad potential utility of network-based filters to applications in systems biology.

Author Summary

System-wide measurements of many biological signals, whether derived from molecules, cells, or entire organisms, are often noisy. Removing or mitigating this noise prior to analysis can improve our understanding and predictions of biological phenomena. We describe a general way to denoise biological data that can account for both correlation and anti-correlation between different measurements. These “network filters” take as input a set of biological measurements, e.g., metabolite concentration, animal traits, neuron activity, or gene expression, and a network of how those measurements are biologically related, e.g., a metabolic network, food web, brain connectome, or protein-protein interaction network. Measurements are then “filtered” for correlated or anti-correlated noise using a set of other measurements that are identified using the network. We investigate the accuracy of these filters in synthetic and real-world data sets, and find that they can substantially reduce noise of different levels and structure. By denoising large-scale biological data sets, network filters have the potential to improve the analysis of many types of biological data.
Limited correspondence in visual representation between the human brain and convolutional neural networks
Authors: Xu Yaoda , Vaziri-Pashkam Maryam
Published: March 2020

Convolutional neural networks (CNNs) have achieved very high object categorization performance recently. It has increasingly become a common practice in human fMRI research to regard CNNs as working model of the human visual system. Here we reevaluate this approach by comparing fMRI responses from the human brain in three experiments with those from 14 different CNNs. Our visual stimuli included original and filtered versions of real-world object images and images of artificial objects. Replicating previous findings, we found a brain-CNN correspondence in a number of CNNs with lower and higher levels of visual representations in the human brain better resembling those of lower and higher CNN layers, respectively. Moreover, the lower layers of some CNNs could fully capture the representational structure of human early visual areas for both the original and filtered real-world object images. Despite these successes, no CNN examined could fully capture the representational structure of higher human visual processing areas. They also failed to capture that of artificial object images in all levels of visual processing. The latter is particularly troublesome, as decades of vision research has demonstrated that the same algorithms used in the processing of natural images would support the processing of artificial visual stimuli in the primate brain. Similar results were obtained when a CNN was trained with stylized object images that emphasized shape representation. CNNs likely represent visual information in fundamentally different ways from the human brain. Current CNNs thus may not serve as sound working models of the human visual system.

Significance Statement

Recent CNNs have achieved very high object categorization performance, with some even exceeding human performance. It has become common practice in recent neuroscience research to regard CNNs as working models of the human visual system. Here we evaluate this approach by comparing fMRI responses from the human brain with those from 14 different CNNs. Despite CNNs’ ability to successfully perform visual object categorization like the human visual system, they appear to represent visual information in fundamentally different ways from the human brain. Current CNNs thus may not serve as sound working models of the human visual system. Given the current dominating trend of incorporating CNN modeling in visual neuroscience research, our results question the validity of such an approach.
Systematically optimized BCMA/CS1 bispecific CAR-T cells robustly control heterogeneous multiple myeloma
Authors: Zah Eugenia , Nam Eunwoo , Bhuvan Vinya , Tran Uyen , Ji Brenda Y. , Gosliner Stanley B. , Wang Xiuli , Brown Christine E. , Chen Yvonne Y.
Published: March 2020

Chimeric antigen receptor (CAR)-T cell therapy has shown remarkable clinical efficacy against B-cell malignancies but also demonstrated marked vulnerability to antigen escape and tumor relapse. Here, we report the rational design and systematic optimization of bispecific CAR-T cells with robust activity against multiple myeloma (MM), including heterogeneous MM that is resistant to conventional CAR-T cell therapy targeting B-cell maturation antigen (BCMA). We demonstrate that BCMA/CS1 bispecific CAR-T cells exhibit significantly higher CAR expression levels and greater antigen-stimulated proliferation compared to T cells that co-express individual BCMA and CS1 CARs. Compared to single-input BCMA- or CS1-targeting CAR-T cells, BCMA/CS1 bispecific CAR-T cells significantly prolong the survival of animals bearing heterogeneous MM tumors. Combination therapy with anti–PD-1 antibody further accelerates the rate of initial tumor clearancein vivo, but CAR-T cell treatment alone was able to achieve durable tumor-free survival even upon tumor re-challenge. Taken together, the BCMA/CS1 bispecific CAR presents a promising treatment approach to prevent antigen escape in CAR-T cell therapy against MM, and the vertically integrated optimization process can be used to develop robust cell-based therapy against novel disease targets.
TNPO3-mediated nuclear entry of the Rous sarcoma virus Gag protein is independent of the cargo-binding domain
Authors: Rice Breanna L. , Stake Matthew S. , Parent Leslie J.
Published: March 2020

Retroviral Gag polyproteins orchestrate the assembly and release of nascent virus particles from the plasma membranes of infected cells. Although it was traditionally thought that Gag proteins trafficked directly from the cytosol to the plasma membrane, we discovered that the oncogenic avian alpharetrovirus Rous sarcoma virus (RSV) Gag protein undergoes transient nucleocytoplasmic transport as an intrinsic step in virus assembly. Using a genetic approach in yeast, we identified three karyopherins that engage the two independent nuclear localization signals (NLS) in Gag. The primary NLS is in the nucleocapsid (NC) domain of Gag and binds directly to importin-α, which recruits importin-β to mediate nuclear entry. The second NLS, which resides in the matrix (MA) domain, is dependent on importin-11 and transportin-3 (TNPO3), known as MTR10p and Kap120p in yeast, although it is not clear whether these import factors are independent or additive. The functionality of importin α/β and importin-11 has been verified in avian cells, whereas the role of TNPO3 has not been studied. In this report, we demonstrate that TNPO3 mediates nuclear entry of Gag and directly binds to Gag. To our surprise, this interaction did not require the cargo-binding domain of TNPO3, which typically mediates nuclear entry for other binding partners of TNPO3 including SR-domain containing splicing factors and tRNAs that re-enter the nucleus. These results suggest that RSV hijacks the host nuclear import pathway using a unique mechanism, potentially allowing other cargo to bind TNPO3 simultaneously.

Importance

RSV Gag nuclear entry is facilitated using three distinct host import factors that interact with nuclear localization signals in the Gag MA and NC domains. Here we show that the MA region is required for nuclear import of Gag through the TNPO3 pathway. Gag nuclear entry does not require the cargo binding domain of TNPO3. Understanding the molecular basis for TNPO3-mediated nuclear trafficking of the RSV Gag protein may lead to a deeper appreciation for whether different import factors play distinct roles in retrovirus replication.
Angioplasty-induced epigenomic remodeling entails BRD4 and EZH2 hierarchical regulations
Authors: Zhang Mengxue , Wang Bowen , Urabe Go , Ozer Hatice Gulcin , Han Renzhi , Kent K. Craig , Guo Lian-Wang
Published: March 2020

Atherosclerosis is commonly treated with angioplasty which, however, evokes neointimal hyperplasia (IH) and recurrent stenotic diseases. Epigenomic investigation was lacking on post-angioplasty IH. The histone acetylation reader BRD4 and H3K27me3 writer EZH2 are potent epigenetic factors; their relationship is little understood. Through genome-wide survey in the rat angioplasty model, we studied BRD4 and EZH2 functional regulations involved in IH.

We performed chromatin immunoprecipitation sequencing (ChIPseq) using rat carotid arteries. While H3K27me3 ChIPseq signal prevalently intensified in balloon-injured (vsuninjured) arteries, BRD4 and H3K27ac became more enriched atEzh2. Indeed, BRD4-siRNA or CRISPR-deletion of BRD4-associated enhancer abated the smooth muscle cell (SMC) expression of EZH2, and SMC-specific BRD4 knockout inBRD4fl/fl;Myh11CreERT2mice reduced both H3K27me3 and IH in wire-injured femoral arteries. In accordance, post-angioplasty IH was exacerbated and mitigated, respectively, by lentiviral expression and pharmacological inhibition of EZH2/1; EZH2 (or EZH1) loss- and gain-of-function respectively attenuated and aggravated pro-IH SMC proliferative behaviors. Furthermore, while H3K27me3 ChIPseq signal magnified atP57and ebbed atCcnd1andUhrf1after injury, silencing either EZH2 or EZH1 in SMCs up-regulatedP57and down-regulatedCcnd1andUhrf1.

In summary, our results reveal an upsurge of EZH2/H3K27me3 after angioplasty, BRD4’s control over EZH2 expression, and non-redundant EZH2/1 functions. As such, this study unravels angioplasty-induced loci-specific H3K27me3/ac redistribution in the epigenomic landscape rationalizing BRD4/EZH2-governed pro-IH regulations.
Systematics of the oil bee genusLanthanomelissaand its implications to the biogeography of southern grasslands
Authors: Ribeiro Taís M. A. , Martins Aline C. , Silva Daniel P. , Aguiar Antonio J. C.
Published: March 2020

Lanthanomelissais a controversial taxonomic group of bees that was treated as subgenus ofChalepogenusor an independent genus. All of its species are endemic to the south-eastern grasslands of South America, an endangered and still poorly known environment. We aimed to understand the origin of this group of bees in time and space as well as the influence of Quaternary climatic fluctuations on its current distribution and possible link to the history of the Southern Grasslands. We inferred phylogenetic relationships ofLanthanomelissaspecies using 37 terminals and 3430 nucleotides of three mitochondrial and two nuclear markers and estimated divergence times and ancestral geographic range. We performed an ensemble with the algorithms SVM, Maxent, and Random Forest in a dataset of 192 georeferenced occurrence points using 19 WorldClim bioclimatic variables to analyse species distribution during the current and two past climatic scenarios (LIG, ∼120 kya and LGM, ∼21 kya). The results support the monophyly of the genus and taxonomic changes including the speciesLanthanomelissa parvan. comb. onLanthanomelissa, and the treatment of thegoeldianusgroup ofChalepogenusas the genusLanthanella.The genus originated at the Oligocene-Miocene border in the Chacoan-Pampean region, and the glacial-interglacial models indicated expansion in Last Glacial Maximum and retraction in Last Interglacial. Expansion and retraction ofLanthanomelissadistribution in the last glacial-interglacial indicated grasslands distributional shifts during periods of climate cooling and warming. The diversification ofLanthanomelissasupported the estimated expansion of southern grasslands in South America concurrently with the origin of Cerrado during the late Miocene. Their origin was approximately synchronized with their exclusive floral host,Sisyrinchium(Iridaceae).
Signaling input from divergent pathways subverts malignant B-cell transformation
Authors: Chan Lai N. , Murakami Mark A. , Robinson Mark E. , Caeser Rebecca , Sadras Teresa , Lee Jaewoong , Cosgun Kadriye Nehir , Kume Kohei , Khairnar Vishal , Xiao Gang , Ahmed Mohamed , Aghania Eamon , Deb Gauri , Hurtz Christian , Shojaee Seyedmehdi , Hong Chao , Pölönen Petri , Nix Matthew A. , Chen Zhengshan , Chen Chun Wei , Chen Jianjun , Vogt Andreas , Heinäniemi Merja , Lohi Olli , Wiita Arun P. , Izraeli Shai , Geng Huimin , Weinstock David M. , Müschen Markus
Published: March 2020

Malignant transformation typically involves multiple genetic lesions whose combined activity gives rise to cancer1. Our analysis of 1,148 patient-derived B-cell leukemia (B-ALL) samples revealed that individual mutations did not promote leukemogenesis unless they converged on one single oncogenic pathway characteristic for the differentiation status of these transformed B cells. Specifically, we show here the JAK/STAT5 signaling pathway supports the developmental stage-specific expansion of pro-B ALL whereas the ERK-pathway that of pre-B ALL. Mutations that were not aligned with the central oncogenic driver would activate divergent pathways and subvert malignant transformation. Oncogenic lesions in B-ALL frequently mimic survival and proliferation signals downstream of cytokine receptors (through activation of STAT5)2-7or the pre-B cell receptor (through activation of ERK)8-13. STAT5- (372 cases) and ERK- (386 cases) activating lesions were frequently found but only co-occurred in ∼3% (37) of cases (P=2.2E-16). Single-cell mutation and phosphoprotein analyses revealed that even in these rare cases, oncogenic STAT5- or ERK-activation were mutually exclusive and segregated to competing clones. STAT5 and ERK engaged opposing biochemical and transcriptional programs orchestrated by MYC and BCL6, respectively. Genetic reactivation of the divergent (suppressed) pathway came at the expense of the principal oncogenic driver and reversed malignant transformation. Conversely, Cre-mediated deletion of divergent pathway components triggered leukemia-initiation and accelerated development of fatal disease. Thus, persistence of divergent signaling pathways represents a powerful barrier to malignant transformation while convergence on one principal driver defines a key event during leukemia-initiation. Proof-of-concept studies in patient-derived B-ALL cells revealed that pharmacological reactivation of suppressed divergent circuits strongly synergized with direct inhibition of the principal oncogenic driver. Hence, pharmacological reactivation of divergent pathways can be leveraged as a previously unrecognized strategy to deepen treatment responses and to overcome drug-resistance. Current treatment approaches for drug-resistant cancer are focused on drug-combinations to suppress the central oncogenic driver and multiple alternative pathways14-17. Here, we introduce a concept based on inhibition of the principal driver combined with pharmacological reactivation of divergent pathways.
Sensitive spatial genome wide expression profiling at cellular resolution
Authors: Stickels Robert R. , Murray Evan , Kumar Pawan , Li Jilong , Marshall Jamie L. , Di Bella Daniela , Arlotta Paola , Macosko Evan Z. , Chen Fei
Published: March 2020

The precise spatial localization of molecular signals within tissues richly informs the mechanisms of tissue formation and function. Previously, we developed Slide-seq, a technology which enables transcriptome-wide measurements with 10-micron spatial resolution. Here, we report new modifications to Slide-seq library generation, bead synthesis, and array indexing that markedly improve the mRNA capture sensitivity of the technology, approaching the efficiency of droplet-based single-cell RNAseq techniques. We demonstrate how this modified protocol, which we have termed Slide-seqV2, can be used effectively in biological contexts where high detection sensitivity is important. First, we deploy Slide-seqV2 to identify new dendritically localized mRNAs in the mouse hippocampus. Second, we integrate the spatial information of Slide-seq data with single-cell trajectory analysis tools to characterize the spatiotemporal development of the mouse neocortex. The combination of near-cellular resolution and high transcript detection will enable broad utility of Slide-seq across many experimental contexts.
Cholinergic basal forebrain degeneration due to obstructive sleep apnoea increases Alzheimer’s pathology in mice
Authors: Qian Lei , Kasas Leda , Milne Michael R , Rawashdeh Oliver , Marks Nicola , Sharma Aanchal , Bellingham Mark C , Coulson Elizabeth J
Published: March 2020

Epidemiological studies indicate that obstructive sleep apnoea is a strong risk factor for the development of Alzheimer’s disease but the mechanisms of the risk remain unclear. We developed a method of modelling obstructive sleep apnoea in mice that replicates key features of human obstructive sleep apnoea: altered breathing during sleep, sleep disruption, moderate intermittent hypoxemia and cognitive impairment. When we induced obstructive sleep apnoea in a familial Alzheimer’s disease model, the mice displayed exacerbation of cognitive impairment and pathological features of Alzheimer’s disease, including increased levels of amyloid-beta and inflammatory markers, as well as selective degeneration of cholinergic basal forebrain neurons. These pathological features were not induced by chronic hypoxia or sleep disruption alone. Our results also revealed that the neurodegeneration was mediated by the oxygen-sensitive p75 neurotrophin receptor and hypoxia inducible factor 1 alpha activity. Furthermore, restoring blood oxygen levels during sleep to prevent intermittent hypoxia prevented the pathological changes induced by the OSA. These findings provide a signalling mechanism by which obstructive sleep apnoea induces cholinergic basal forebrain degeneration and could thereby increase the risk of developing Alzheimer’s disease, as well as providing a rationale for testing a range of possible prophylactic treatment options for people with obstructive sleep apnoea and hypoxia including increased compliance of continuous positive airway pressure therapy.
Nanopore long-read transcriptome data of fungal pathogen of chalkbrood disease,Ascosphaera apis
Authors: Du Yu , Chen Huazhi , Wang Jie , Zhu Zhiwei , Xiong Cuiling , Zheng Yanzhen , Chen Dafu , Guo Rui
Published: March 2020

Ascosphaera apisis a fungal pathogen that exclusively infects honeybee larvae, leading to chalkbrood disease, which damages the number of adult honeybees and colony productivity. In this article,A. apismecylia and spores were respectively purified followed by Oxford Nanopore sequencing via PromethION platform. In total, 6,321,704 and 6,259,727 raw reads were generated from Aam and Aas, with a length distribution among 1 kb~10 kb. The quality (Q) scores of majority of raw reads were Q9 (Aam) and Q11 (Aas). Additionally, 5,669,436 and 6,233,159 clean reads were gained, among them 79.32% and 79.62% were identified as being full-length. The lengths of redundant reads-removed full-length transcripts were among 1 kb~8 kb and 1 kb~9 kb, and most abundant length for both was 1 kb. Furthermore, the length of redundant transcripts-removed clean reads was ranged from 1 kb~7 kb, with the largest group of 1 kb. The data reported here provides a beneficial genetic resource for improving genome and transcriptome annotations ofA. apisand for exploring alternative splicing and polyadenylation ofA. apismRNAs.

Value of the result

Current dataset enables better understanding of the complexity ofA. apistranscriptome.

The long-read transcriptome data can be used to identify of genes and transcripts associated withA. apisinfection mechanism.

The accessible data provides full-length transcripts for improving gene structure and functional annotation ofA. apistranscriptome.

This dataset could be utilized for investigation of alternative splicing and polyadenylation ofA. apismRNAs.
Scalable method for micro-CT analysis enables large scale quantitative characterization of brain lesions and implants
Authors: Kastner David B. , Kharazia Viktor , Nevers Rhino , Astudillo-Maya Daniela A. , Williams Greer M. , Yang Zhounan , Smyth Clay , Santina Luca Della , Parkinson Dilworth Y. , Frank Loren M.
Published: March 2020

Anatomic evaluation is an important aspect of many studies in neuroscience; however, it often lacks information about the three-dimensional structure of the brain. Micro-CT imaging provides an excellent, nondestructive, method for the evaluation of brain structure, but current applications to neurophysiological or lesions studies require removal of the skull and hazardous chemicals, dehydration or embedding, limiting their scalability and utility. Here we present a protocol using eosin in combination with bone decalcification to enhance contrast in the tissue and then employ monochromatic and propagation phase-contrast micro-CT imaging to enable the imaging of brain structure with the preservation of the surrounding skull. Instead of relying on descriptive, time-consuming, or subjective methods, we develop simple quantitative analyses to map the locations of recording electrodes and to characterize the presence and extent of brain lesions.
Selective gating of retinal information by arousal
Authors: Liang Liang , Fratzl Alex , Mansour Omar El , Reggiani Jasmine D.S. , Chen Chinfei , Andermann Mark L.
Published: March 2020

How sensory information is processed by the brain can depend on behavioral state. In the visual thalamus and cortex, arousal/locomotion is associated with changes in the magnitude of responses to visual stimuli. Here, we asked whether such modulation of visual responses might already occur at an earlier stage in this visual pathway. We measured neural activity of retinal axons using wide-field and two-photon calcium imaging in awake mouse thalamus across arousal states associated with different pupil sizes. Surprisingly, visual responses to drifting gratings in retinal axonal boutons were robustly modulated by arousal level, in a manner that varied across stimulus dimensions and across functionally distinct subsets of boutons. At low and intermediate spatial frequencies, the majority of boutons were suppressed by arousal. In contrast, at high spatial frequencies, the proportions of boutons showing enhancement or suppression were more similar, particularly for boutons tuned to regions of visual space ahead of the mouse. Arousal-related modulation also varied with a bouton’s sensitivity to luminance changes and direction of motion, with greater response suppression in boutons tuned to luminance decrements vs. increments, and in boutons preferring motion along directions or axes of optic flow. Together, our results suggest that differential filtering of distinct visual information channels by arousal state occurs at very early stages of visual processing, before the information is transmitted to neurons in visual thalamus. Such early filtering may provide an efficient means of optimizing central visual processing and perception of state-relevant visual stimuli.
A Clock-Driven Neural Network Critical for Arousal
Authors: Bell Benjamin J. , Liu Qiang , Kim Dong Won , Lee Sang Soo , Liu Qili , Blum Ian D. , Wang Annette A. , Bedont Joseph L. , Chang Anna J. , Issa Habon , Cohen Jeremiah Y. , Blackshaw Seth , Wu Mark N.
Published: March 2020

The daily cycling of sleep and arousal states is among the most prominent biological rhythms under circadian control. While much is known about the core circadian clock1,2, how this clock tunes sleep and arousal remains poorly understood3. InDrosophila, we previously characterized WIDE AWAKE (WAKE), a clock-output molecule that promotes sleep at night4,5. Here, we show that the function of WAKE in regulating circadian-dependent neural excitability and arousal is conserved in mice.mWake+cells are found in the suprachiasmatic nucleus (SCN) and dorsomedial hypothalamus (DMH).mWakeDMHneurons drive wakefulness and exhibit rhythmic spiking, with greater firing during the night vs the day. Loss of mWAKE leads to increased spiking ofmWake+SCN and DMH neurons and prominent behavioural arousal, specifically during the night. Single-cell sequencing, imaging, and patch-clamp experiments reveal thatmWakeDMHneurons constitute a glutamatergic/GABAergic population that projects widely, receives neuromodulatory input, and acts on neuromodulatory neurons. Strikingly, broad chemogenetic silencing ofmWake+cells leads to profound loss of behavioural responsiveness and low amplitude, low frequency electroencephalography waveforms. These findings suggest that the genetic mechanisms regulating circadian control of sleep and arousal are conserved across >500 million years of evolution and define a clock-regulated neural network critical for arousal.
RNA sequencing reveals interacting key determinants of osteoarthritis acting in subchondral bone and articular cartilage
Authors: Tuerlings Margo , van Hoolwerff Marcella , Houtman Evelyn , Suchiman Eka (H.E.D.) , Lakenberg Nico , Mei Hailiang , van der Linden Enrike (H.M.J.) , Nelissen Rob (R.G.H.H.) , Ramos Yolande (Y.F.M.) , de Almeida Rodrigo Coutinho , Meulenbelt Ingrid
Published: March 2020

Objective

The aim of this study was to identify key determinants of the interactive osteoarthritis (OA) pathophysiological processes of subchondral bone and cartilage.

Methods

We performed RNA sequencing on macroscopically preserved and lesioned OA subchondral bone of patients that underwent joint replacement surgery due to OA (N=24 pairs; 6 hips, 18 knees, RAAK-study). Unsupervised hierarchical clustering and differential expression analyses were performed. Results were combined with previously identified, differentially expressed genes in cartilage (partly overlapping samples) as well as with recently identified OA risk genes.

Results

We identified 1569 genes significantly differentially expressed between lesioned and preserved subchondral bone, includingCNTNAP2(FC=2.4, FDR=3.36×10−5) andSTMN2(FC=9.6, FDR=3.36×10−3). Among the identified genes, 305 were also differentially expressed and with same direction of effects in cartilage, includingIL11andCHADL, recently acknowledged OA susceptibility genes. Upon differential expression analysis stratifying for joint site, we identified 509 genes exclusively differentially expressed in subchondral bone of the knee, such asKLF11andWNT4. These exclusive knee genes were enriched for involvement in epigenetic processes, characterized by for instanceHIST1H3JandHIST1H3H.

Conclusion

To our knowledge, we are the first to report on differential gene expression patterns of paired OA subchondral bone tissue using RNA sequencing. Among the most consistently differentially expressed genes with OA pathophysiology in both bone and cartilage wereIL11andCHADL.As these genes were recently also identified as robust OA risk genes they classify as attractive druggable targets acting on two OA disease relevant tissues.
Large-scale Proteomic and Phosphoproteomic Analysis of Maize Seedling Leaves During De-etiolation
Authors: Gao Zhi-Fang , Shen Zhuo , Chao Qing , Yan Zhen , Ge Xuan-Liang , Lu Tiancong , Zheng Haiyan , Qian Chun-Rong , Wang Bai-Chen
Published: March 2020

De-etiolation consists of a series of developmental and physiological changes that a plant undergoes in response to light. During this process light, an important environmental signal, triggers the inhibition of mesocotyl elongation and the production of photosynthetically active chloroplasts, and etiolated leaves transition from the “sink” stage to the “source” stage. De-etiolation has been extensively studied in maize (Zea mays L). However, little is known about how this transition is regulated. In this study, we describe a quantitative proteomic and phosphoproteomic atlas of the de-etiolation process in maize. We identified 16,420 proteins and quantified 14,168. In addition, 8,746 phosphorylation sites within 3,110 proteins were identified. From the proteomic and phosphoproteomic data combined, we identified a total of 17,436 proteins, 27.6% of which are annotated protein coding genes in theZea_maysAGPv3.28 database. Only 6% of proteins significantly changed in abundance during de-etiolation. In contrast, the phosphorylation levels of more than 25% of phosphoproteins significantly changed; these included proteins involved in gene expression and homeostatic pathways and rate-limiting enzymes involved in photosynthesis light and carbon reactions. Based on phosphoproteomic analysis, 34% (1,057) of all phosphoproteins identified in this study contained more than three phosphorylation sites, and 37 proteins contained more than 16 phosphorylation sites, which shows that multi-phosphorylation is ubiquitous during the de-etiolation process. Our results suggest that plants might preferentially regulate the level of PTMs rather than protein abundance for adapting to changing environments. The study of PTMs could thus better reveal the regulation of de-etiolation.
Different Proteins Mediate Step-wise Chromosome Architectures inThermoplasma acidophilumandPyrobaculum calidifontis
Authors: Maruyama Hugo , Prieto Eloise I. , Nambu Takayuki , Mashimo Chiho , Kashiwagi Kosuke , Okinaga Toshinori , Atomi Haruyuki , Takeyasu Kunio
Published: March 2020

Archaeal species encode a variety of distinct lineage-specific chromosomal proteins. We have previously shown that inThermococcus kodakarensis, histone, Alba, and TrmBL2 play distinct roles in chromosome organization. Although our understanding of individual archaeal chromosomal proteins has been advancing, how archaeal chromosomes are folded into higher-order structures and how they are regulated are largely unknown. Here, we investigated the primary and higher-order structures of archaeal chromosomes from different archaeal lineages. Atomic force microscopy of chromosome spreads out ofThermoplasma acidophilumandPyrobaculum calidifontiscells revealed 10-nm fibers and 30–40-nm globular structures, suggesting the occurrence of higher-order chromosomal folding. Our results also indicated that chromosome compaction occurs toward the stationary phase. Micrococcal nuclease digestion indicated that fundamental structural units of the chromosome exist inT. acidophilumandT. kodakarensisbut not inP. calidifontisorSulfolobus solfataricus. In vitro reconstitution showed that, inT. acidophilum,the bacterial HU protein homolog HTa formed a 6-nm fiber by wrapping DNA, and that Alba was responsible for the formation of the 10-nm fiber by binding along the DNA without wrapping. Remarkably, Alba could form different higher-order complexes with histone or HTa on DNA in vitro. Mass spectrometry detected HTa in theT. acidophilumchromosome but not in other species. A putative transcriptional regulator of the AsnC/Lrp family (Pcal_1183) was detected on theP. calidifontischromosome, but not on that of other species studied. Putative membrane-associated proteins were detected in the chromosomes of the three archaeal species studied, includingT. acidophilum,P. calidifontis, andT. kodakarensis. Collectively, our data show that Archaea use different combinations of proteins to achieve chromosomal architecture and functional regulation.
Human and macaque pairs employ different coordination strategies in a transparent decision game
Authors: Möller Sebastian , Unakafov Anton M. , Fischer Julia , Gail Alexander , Treue Stefan , Kagan Igor
Published: March 2020

Many real-world decisions in social contexts are made while observing a partner’s actions. To study dynamic interactions during such decisions, we developed a setup where two agents seated face-to-face engage in game-theoretical tasks on a shared transparent touchscreen display (“transparent games”). We compared human and macaque pairs in a transparent version of the coordination game “Bach-or-Stravinsky”, which entails a conflict about which of two individually-preferred opposing options to choose to achieve coordination. Most human pairs developed coordinated behavior and adopted dynamic turn-taking to equalize the payoffs. All macaque pairs converged on simpler, static coordination. Remarkably, two animals learned to coordinate dynamically after training with a human confederate. This pair selected the faster agent’s preferred option, exhibiting turn-taking behavior that was captured by modeling the visibility of the partner’s action before one’s own movement. Such competitive turn-taking was unlike the prosocial turn-taking in humans, who equally often initiated switches to and from their preferred option. Thus, the dynamic coordination is not restricted to humans, but can occur on the background of different social attitudes and cognitive capacities in rhesus monkeys. Overall, our results illustrate how action visibility promotes emergence and maintenance of coordination when agents can observe and time their mutual actions.
Assessing the perceived reverberation in different rooms for a set of musical instrument sounds
Authors: Vecchi Alejandro Osses , McLachlan Glen , Kohlrausch Armin
Published: March 2020

Previous research has shown that the perceived reverberation in a room, or reverberance, depends on the sound source that is being listened to. In a study by Osses et al. [(2017) J. Acoust. Soc. Am.141(4), EL381-EL387], reverberance estimates obtained from an auditory model for 23 musical instrument sounds in 8 rooms supported this sound-source dependency. As a follow-up to that study, a listening experiment with 24 participants was conducted using a subset of the original sounds with the purpose of mapping each test sound onto a reverberance scale. The experimentally-obtained reverberance estimates were significantly correlated with the simulated reverberance, providing further evidence that the sensation of reverberance is sound-source dependent.
Mapping the influence of the gut microbiota on small molecules in the brain through mass spectrometry imaging
Authors: Hulme Heather , Meikle Lynsey M. , Strittmatter Nicole , Swales John , Hamm Gregory , Brown Sheila L. , Milling Simon , MacDonald Andrew S. , Goodwin Richard J.A. , Burchmore Richard , Wall Daniel M.
Published: March 2020

Background

The gut microbiota is known to influence virtually all facets of human health. Recent work has highlighted a potential role for the gut microbiota in neurological health through the microbiome-gut-brain axis. Microbes can influence the brain both directly and indirectly; through neurotransmitter production, induction of host immunomodulators, or through the release or induction of other microbial or host molecules.

Methods

Here we used mass spectrometry imaging (MSI), a label-free imaging tool, to map the molecular changes that occur in the murine gut and brain in germ-free, antibiotic-treated and control mice.

Results

We determined the spatial distribution and relative quantification of neurotransmitters and their precursors across brain and gut sections in response to the microbiome. Using untargeted MSI of small molecules, we detected a significant change in the levels of four identified metabolites in the brains of germ-free animals compared to controls; vitamin B5, 3-hydroxy-3-methylglutaric acid, 3-methyl-4-(trimethylammonio)butanoate and 4-(trimethylammonio)pentanoate. However, antibiotic treatment induced no significant changes in these metabolites in the brain after one week of treatment.

Conclusions

This work exemplifies the utility of MSI as a tool in determining the spatial distribution and quantification of bacterial and host metabolites in the gut and brain whilst also offering the potential for discovery of novel mediators of microbiome-gut-brain axis communication.
Cytoplasmic incompatibility between Old and New World populations of a tramp ant
Authors: Ün Çiğdem , Schultner Eva , Manzano-Marín Alejandro , Flórez Laura V. , Seifert Bernhard , Heinze Jürgen , Oettler Jan
Published: March 2020

As we enter the Anthropocene, the evolutionary dynamics of species will change drastically, and as yet unpredictably, due to human activity. Already today, increases in global human traffic have resulted in the rapid spread of species to new areas, leading to the formation of geographically isolated populations. These go on to evolve in allopatry, which can lead to reproductive isolation, and potentially, the formation of new species. Surprisingly, little is known about such eco-evolutionary processes in ants, even though numerous invasive ant species are globally distributed in geographically isolated populations. Here, we describe the first case of cytoplasmic incompatibility (CI) between populations of a cosmotropic distributed tramp ant with Asian roots,Cardiocondyla obscurior,which has acquired a novelWolbachiastrain in the New World. Our study uncovers the first symbiont-induced mechanism of reproductive isolation in ants, providing a novel perspective on the biology of globally distributed ants.
Facets of individual-specific health signatures determined from longitudinal plasma proteome profiling
Authors: Dodig-Crnković Tea , Hong Mun-Gwan , Thomas Cecilia Engel , Häussler Ragna S. , Bendes Annika , Dale Matilda , Edfors Fredrik , Forsström Björn , Magnusson Patrik K.E. , Schuppe-Koistinen Ina , Odeberg Jacob , Fagerberg Linn , Gummesson Anders , Bergström Göran , Uhlén Mathias , Schwenk Jochen M
Published: March 2020

Background

Precision medicine approaches aim to tackle diseases on an individual level through molecular profiling. Despite the growing knowledge about diseases and the reported diversity of molecular phenotypes, the descriptions of human health on an individual level have been far less elaborate.

Methods

To provide insights into the longitudinal protein signatures of well-being, we profiled blood plasma collected over one year from 101 clinically healthy individuals using multiplexed antibody assays. After applying an antibody validation scheme, we utilized > 700 protein profiles for in-depth analyses of the individuals’ short-term health trajectories.

Findings

We found signatures of circulating proteomes to be highly individual-specific. Considering technical and longitudinal variability, we observed both stable and fluctuating proteins in the circulation, as well as networks of proteins that covaried over time. For each participant, there were unique protein profiles and some of these could be explained by associations to genetic variants.

Interpretation

This study demonstrates that there was noticeable diversity among clinically healthy subjects, and facets of individual-specific signatures emerged by monitoring the variability of the circulating proteomes over time. Longitudinal profiling of circulating proteomes has the potential to enable a more personal hence precise assessment of health states, and thereby provide a valuable component of precision medicine approaches.

Funding

This work was supported by the Erling Persson Foundation for the KTH Centre for Precision Medicine and the Swedish Heart and Lung Foundation for the SCAPIS project. We also acknowledge the Knut and Alice Wallenberg Foundation for funding the Human Protein Atlas project, Science for Life Laboratory for Plasma Profiling Facility, and the Swedish Research Council (Grant no 2017-00641).
MMS2plot: an R package for visualizing multiple MS/MS spectra for groups of modified and non-modified peptides
Authors: Ming Liya , Zou Yang , Zhao Yiming , Zhang Luna , He Ningning , Chen Zhen , Li Shawn S-C. , Li Lei
Published: March 2020

A large number of post-translational modifications (PTMs) in proteins are buried in the unassigned mass spectrometric (MS) spectra in shot-gun proteomics datasets. Because the modified peptide fragments are low in abundance relative to the corresponding non-modified versions, it is critical to develop tools that allow facile evaluation of assignment of PTMs based on the MS/MS spectra. Such tools would preferably have the ability to allow comparison of fragment ion spectra and retention time between the modified and unmodified peptide pairs or group. Herein, we describe MMS2plot, an R package for visualizing peptide-spectrum matches (PSMs) for multiple peptides. MMS2plot features a batch mode and generates the output images in vector graphics file format that facilitate evaluation and publication of the PSM assignment. We expect MMS2plot to play an important role in PTM discovery from large-scale proteomics datasets generated by LC (liquid chromatography)-MS/MS. The MMS2plot package is freely available athttps://github.com/lileir/MMS2plotunder the GPL-3 license.