bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cell-type specific transcriptional adaptations of nucleus accumbens interneurons to amphetamine
Authors: Gallegos David A. , Minto Melyssa , Liu Fang , Hazlett Mariah F. , Yousefzadeh S. Aryana , Bartelt Luke C. , West Anne E. 
Published: July 2021

AbstractParvalbumin-expressing (PV+) interneurons of the nucleus accumbens (NAc) play an essential role in the addictive-like behaviors induced by psychostimulant exposure. To identify molecular mechanisms of PV+ neuron plasticity, we isolated interneuron nuclei from the NAc of male and female mice following acute or repeated exposure to amphetamine (AMPH) and sequenced for cell type-specific RNA expression and chromatin accessibility. AMPH regulated the transcription of hundreds of genes in PV+ interneurons, and this program was largely distinct from that regulated in other NAc GABAergic neurons. Chromatin accessibility at enhancers predicted cell-type specific gene regulation, identifying transcriptional mechanisms of differential AMPH responses. Finally, we observed dysregulation of multiple PV-specific, AMPH-regulated genes in an Mecp2 mutant mouse strain that shows heightened behavioral sensitivity to psychostimulants, suggesting the functional importance of this transcriptional program. Together these data provide novel insight into the cell-type specific programs of transcriptional plasticity in NAc neurons that underlie addictive-like behaviors.
Ultra-slow fMRI fluctuations in the fourth ventricle as a marker of drowsiness
Authors: Gonzalez-Castillo Javier , Fernandez Isabel S. , Handwerker Daniel A. , Bandettini Peter A. 
Published: July 2021

AbstractWakefulness levels modulate estimates of functional connectivity (FC), and, if unaccounted for, can become a substantial confound in resting-state fMRI. Unfortunately, wakefulness is rarely monitored due to the need for additional concurrent recordings (e.g., eye tracking, EEG). Recent work has shown that strong fluctuations around 0.05Hz, hypothesized to be CSF inflow, appear in the fourth ventricle (FV) when subjects fall asleep, and that they correlate significantly with the global signal. The analysis of these fluctuations could provide an easy way to evaluate wakefulness in fMRI-only data and improve our understanding of FC during sleep. Here we evaluate this possibility using the 7T resting-state sample from the Human Connectome Project (HCP). Our results replicate the observation that fourth ventricle ultra-slow fluctuations (∼0.05Hz) with inflow-like characteristics (decreasing in intensity for successive slices) are present in scans during which subjects did not comply with instructions to keep their eyes open (i.e., drowsy scans). This is true despite the HCP data not being optimized for the detection of inflow-like effects. In addition, time-locked BOLD fluctuations of the same frequency could be detected in large portions of grey matter with a wide range of temporal delays and contribute in significant ways to our understanding of how FC changes during sleep. First, these ultra-slow fluctuations explain half of the increase in global signal that occurs during descent into sleep. Similarly, global shifts in FC between awake and sleep states are driven by changes in this slow frequency band. Second, they can influence estimates of inter-regional FC. For example, disconnection between frontal and posterior components of the Defulat Mode Network (DMN) typically reported during sleep were only detectable after regression of these ultra-slow fluctuations. Finally, we report that the temporal evolution of the power spectrum of these ultra-slow FV fluctuations can help us reproduce sample-level sleep patterns (e.g., a substantial number of subjects descending into sleep 3 minutes following scanning onset), partially rank scans according to overall drowsiness levels, and predict individual segments of elevated drowsiness (at 60 seconds resolution) with 71% accuracy.
Multifactorial chromatin regulatory landscapes at single cell resolution
Authors: Meers Michael P. , Llagas Geneva , Janssens Derek H. , Codomo Christine A. , Henikoff Steven 
Published: July 2021

AbstractChromatin profiling at locus resolution uncovers gene regulatory features that define cell types and developmental trajectories, but it remains challenging to map and compare distinct chromatin-associated proteins within the same sample. Here we describe a scalable antibody barcoding approach for profiling multiple chromatin features simultaneously in the same individual cells, Multiple Target Identification by Tagmentation (MulTI-Tag). MulTI-Tag is optimized to retain high sensitivity and specificity of enrichment for multiple chromatin targets in the same assay. We use MulTI-Tag in a combinatorial barcoding approach to resolve distinct cell types and developmental trajectories using multiple chromatin features, and to distinguish unique, coordinated patterns of active and repressive element regulatory usage in the same individual cells that are associated with distinct differentiation outcomes. Multifactorial profiling allows us to detect novel associations between histone marks in single cells and holds promise for comprehensively characterizing cell-specific gene regulatory landscapes in development and disease.
Therapeutic efficacy of CT-P59 against P.1 variant of SARS-CoV-2
Authors: Ryu Dong-Kyun , Kang Bobin , Woo Sun-Je , Lee Min-Ho , Tijsma Aloys SL , Noh Hanmi , Kim Jong-In , Seo Ji-Min , Kim Cheolmin , Kim Minsoo , Yang Eunji , Lim Gippeum , Kim Seong-Gyu , Eo Su-Kyeong , Choi Jung-ah , Oh Sang-Seok , Nuijten Patricia M , Song Manki , Chung Hyo-Young , van Baalen Carel A , Kwon Ki-Sung , Lee Soo-Young 
Published: July 2021

AbstractP.1. or gamma variant also known as the Brazil variant, is one of the variants of concern (VOC) which appears to have high transmissibility and mortality. To explore the potency of the CT-P59 monoclonal antibody against P.1 variant, we tried to conduct binding affinity, in vitro neutralization, and in vivo animal tests. In in vitro assays revealed that CT-P59 is able to neutralize P.1 variant in spite of reduction in its binding affinity against a RBD (receptor binding domain) mutant protein including K417T/E484K/N501Y and neutralizing activity against P.1 pseudoviruses and live viruses. In contrast, in vivo hACE2 (human angiotensin-converting enzyme 2)-expressing TG (transgenic) mouse challenge experiment demonstrated that a clinically relevant or lower dosages of CT-P59 is capable of lowering viral loads in the respiratory tract and alleviates symptoms such as body weight losses and survival rates. Therefore, a clinical dosage of CT-P59 could compensate for reduced in vitro antiviral activity in P.1-infected mice, implying that CT-P59 has therapeutic potency for COVID-19 patients infected with P.1 variant.HighlightsCT-P59 could bind to and neutralize P.1 variant, but CT-P59 showed reduced susceptibility in in vitro tests.The clinical dosage of CT-P59 demonstrated in vivo therapeutic potency against P.1 variants in hACE2-expressing mice challenge study.CT-P59 ameliorates their body weight loss and prevents the lethality in P.1 variant-infected mice.
Organization of cortical and thalamic input to inhibitory neurons in mouse motor cortex
Authors: Okoro Sandra U. , Goz Roman U. , Njeri Brigdet W. , Harish Madhumita , Ruff Catherine F. , Ross Sarah E. , Gerfen Charles R. , Hooks Bryan M. 
Published: July 2021

ABSTRACTIntracortical inhibition in motor cortex (M1) regulates movement and motor learning. If inhibitory cell types and cortical laminae targeted by cortical and thalamic afferents differ, then these afferents play different roles in regulating M1 output. We quantified input to two classes of M1 interneurons, parvalbumin+ (PV) fast-spiking cells and somatostatin+ (SOM) low-threshold-spiking cells, using monosynaptic rabies tracing. We then compared anatomical connectivity and functional connectivity based on synaptic strength from sensory cortex and thalamus. Functionally, each input innervated M1 interneurons with a unique laminar profile. Different interneuron types were excited in a distinct, complementary manner, suggesting feedforward inhibition proceeds selectively via distinct circuits. Specifically, somatosensory cortex (S1) inputs primarily targeted PV+ neurons in upper layers (L2/3) but SOM+ neurons in middle layers (L5). Somatosensory thalamus (PO) inputs targeted PV+ neurons in middle layers (L5). In contrast to sensory cortical areas, thalamic input to SOM+ neurons was equivalent to PV+ neurons. Thus, long-range excitatory inputs target inhibitory neurons in an area and cell type-specific manner which contrasts with input to neighboring pyramidal cells. In contrast to feedforward inhibition providing generic inhibitory tone in cortex, circuits are selectively organized to recruit inhibition matched to incoming excitatory circuits.
Visualizing the pH inEscherichia colicoloniesviathe sensor protein mCherryEA allows high-throughput screening of mutant libraries
Authors: Franz Hartmann Fabian Stefan , Weiss Tamara , Shen Jing , Smahajcsik Dóra , Seibold Gerd Michael 
Published: July 2021

AbstractCytoplasmic pH is tightly regulated by diverse active mechanisms and interconnected regulatory processes in bacteria. Many processes and regulators underlying pH-homeostasis have been identifiedviaphenotypic screening of strain libraries towards non-growth at low or high pH values. Direct screens with respect to changes of the internal pH in mutant strain collections are limited by laborious methods including fluorescent dyes or radioactive probes. Genetically encoded biosensors equip single organisms or strain libraries with an internal sensor molecule already during the generation of the strain. In this study, we used the pH-sensitive mCherry variant mCherryEA as ratiometric pH biosensor. We visualized the internal pH ofE. colicolonies on agar plates by the use of a Gel-Doc imaging system. Combining this imaging technology with robot-assisted colony picking and spotting allowed us to screen and select mutants with altered internal pH values from a small transposon mutagenesis derivedE. colilibrary. Identification of the TN- insertion sites in strains with altered internal pH levels revealed that the transposon was inserted intotrkH(encoding a transmembrane protein of the potassium uptake system) or therssBgene (encoding the anti-adaptor protein RssB which mediates the proteolytic degradation of the general stress response regulator RpoS), two genes known to be associated with pH-homeostasis and pH stress adaptation. This successful screening approach demonstrates that the pH- sensor based analysis of arrayed colonies on agar plates is a sensitive approach for the fast identification of genes involved in pH-homeostasis or pH stress adaptation inE. coli.ImportancePhenotypic screening of strain libraries on agar plates has become a versatile tool to understand gene functions and to optimize biotechnological platform organisms. Screening is supported by genetically encoded biosensors that allow to easily measure intracellular processes. For this purpose, transcription-factor-based biosensors have emerged as the sensor-type of choice. Here, the target stimulus initiates the activation of a response gene (e.g. a fluorescent protein) followed by transcription, translation and maturation. Due to this mechanistic principle, biosensor readouts are delayed and cannot report the actual intracellular state of the cell in real-time. To capture fast intracellular processes adequately, fluorescent reporter proteins are extensively applied. But these sensor-types are not utilized for phenotypic screenings so far. To take advantage of their properties, we here established an imaging method, which allows to apply a fast ratiometric sensor protein for assessing the internal pH of colonies in a high-thoughput manner.
Monitoring SARS-CoV-2 variants alterations in Nice neighborhoods by wastewater nanopore sequencing
Authors: Rios Géraldine , Lacoux Caroline , Leclercq Vianney , Diamant Anna , Lebrigand Kévin , Lazuka Adèle , Soyeux Emmanuel , Lacroix Sébastien , Fassy Julien , Couesnon Aurélie , Thiery Richard , Mari Bernard , Pradier Christian , Waldmann Rainer , Barbry Pascal 
Published: July 2021

AbstractBackgroundWastewater surveillance has been proposed as an epidemiological tool to define the prevalence and evolution of the SARS-CoV-2 epidemics. However, most implemented SARS-CoV-2 wastewater surveillance projects were relying on qPCR measurement of virus titers and did not address the mutational spectrum of SARS-CoV-2 circulating in the population.MethodsWe have implemented a nanopore RNA sequencing monitoring system in the city of Nice (France, 550,000 inhabitants). Between October 2020 and March 2021, we monthly analyzed the SARS-CoV-2 variants in 113 wastewater samples collected in the main wastewater treatment plant and 20 neighborhoods.FindingsWe initially detected the lineages predominant in Europe at the end of 2020 (B.1.160, B.1.177, B.1.367, B.1.474, and B.1.221). In January, a localized emergence of a variant (Spike:A522S) of the B.1.1.7 lineage occurred in one neighborhood. It rapidly spread and became dominant all over the city. Other variants of concern (B.1.351, P.1) were also detected in some neighborhoods, but at low frequency. Comparison with individual clinical samples collected during the same week showed that wastewater sequencing correctly identified the same lineages as those found in COVID-19 patients.InterpretationWastewater sequencing allowed to document the diversity of SARS-CoV-2 sequences within the different neighborhoods of the city of Nice. Our results illustrate how sequencing of sewage samples can be used to track pathogen sequence diversity in the current pandemics and in future infectious disease outbreaks.
End-to-end computational approach to the design of RNA biosensors for miRNA biomarkers of cervical cancer
Authors: Baabu Priyannth Ramasami S. , Srinivasan Shivaramakrishna , Nagarajan Swetha , Muthamilselvan Sangeetha , Suresh Raghavv R. , Selvi Thamarai , Palaniappan Ashok 
Published: July 2021

AbstractCervical cancer is a global public health subject as it affects women in the reproductive ages, and accounts for the second largest burden among cancer patients worldwide with an unforgiving 50% mortality rate. Poor awareness and access to effective diagnosis have led to this enormous disease burden, calling for point-of-care, minimally invasive diagnosis methods. Here, an end-to-end quantitative approach for a new kind of diagnosis has been developed, comprising identification of optimal biomarkers, design of the sensor, and simulation of the diagnostic circuit. Using miRNA expression data in the public domain, we identified circulating miRNA biomarkers specific to cervical cancer using multi-tier screening. Synthetic riboregulators called toehold switches specific for the biomarker panel were then designed. To predict the dynamic range of toehold switches for use in genetic circuits as biosensors, we developed a generic grammar of these switches, and built a multivariate linear regression model using thermodynamic features derived from RNA secondary structure and interaction. The model yielded predictions of toehold efficacy with an adjusted R2 = 0.59. Reaction kinetics modelling was performed to predict the sensitivity of the second-generation toehold switches to the miRNA biomarkers. Simulations showed a linear response between 10nM and 100nM before saturation. Our study demonstrates an end-to-end workflow for the efficient design of genetic circuits geared towards the effective detection of unique genomic signatures that would be increasingly important in today’s world. The approach has the potential to direct experimental efforts and minimise costs. All resources including the machine learning toolkit, reaction kinetics simulation, designed toehold sequences, genetic circuits, data and sbml files for replicating and utilizing our study are provided open-source with the iGEM Foundation (https://github.com/igem2019) under GNU GPLv3 licence.
Using Domain-Knowledge to Assist Lead Discovery in Early-Stage Drug Design
Authors: Dash Tirtharaj , Srinivasan Ashwin , Vig Lovekesh , Roy Arijit 
Published: July 2021

AbstractWe are interested in generating new small molecules which could act as inhibitors of a biological target, when there is limited prior information on target-specific inhibitors. This form of drug-design is assuming increasing importance with the advent of new disease threats for which known chemicals only provide limited information about target inhibition. In this paper, we propose the combined use of deep neural networks and Inductive Logic Programming (ILP) that allows the use of symbolic domain-knowledge (B) to explore the large space of possible molecules. Assuming molecules and their activities to be instances of random variablesXandY, the problem is to draw instances from the conditional distribution ofX, givenY, B(DX|Y,B). We decompose this into the constituent parts of obtaining the distributionsDX|BandDY|X,B, and describe the design and implementation of models to approximate the distributions. The design consists of generators (to approximateDX|BandDX|Y,B) and a discriminator (to approximateDY|X,B). We investigate our approach using the well-studied problem of inhibitors for the Janus kinase (JAK) class of proteins. We assume first that if no data on inhibitors are available for a target protein (JAK2), but a small numbers of inhibitors are known for homologous proteins (JAK1, JAK3 and TYK2). We show that the inclusion of relational domain-knowledge results in a potentially more effective generator of inhibitors than simple random sampling from the space of molecules or a generator without access to symbolic relations. The results suggest a way of combining symbolic domain-knowledge and deep generative models to constrain the exploration of the chemical space of molecules, when there is limited information on target-inhibitors. We also show how samples from the conditional generator can be used to identify potentially novel target inhibitors.
Neural encoding of phrases and sentences in spoken language comprehension
Authors: Bai Fan , Meyer Antje S. , Martin Andrea E. 
Published: July 2021

AbstractSpeech stands out in the natural world as a biological signal that communicates formally-specifiable complex meanings. However, the acoustic and physical dynamics of speech do not injectively mark the linguistic structure and meaning that we perceive. Linguistic structure must therefore be inferred through the human brain’s endogenous mechanisms, which remain poorly understood. Using electroencephalography, we investigated the neural response to synthesized spoken phrases and sentences that were closely physically-matched but differed in syntactic structure, under either linguistic or non-linguistic task conditions. Differences in syntactic structure were well-captured in theta band (∼ 2 to 7 Hz) phase coherence, phase connectivity degree at low frequencies (< ∼ 2 Hz), and in both intensity and degree of power connectivity of induced neural response in the alpha band (∼ 7.5 to 13.5 Hz). Theta-gamma phase-amplitude coupling was found when participants listened to speech, but it did not discriminate between syntactic structures. Spectral-temporal response function modelling suggested different encoding states in both temporal and spectral dimensions as a function of the amount and type of linguistic structure perceived, over and above the acoustically-driven neural response. Our findings provide a comprehensive description of how the brain separates linguistic structures in the dynamics of neural responses, and imply that phase synchronization and strength of connectivity can be used as readouts for constituent structure, providing a novel basis for future neurophysiological research on linguistic structure in the brain.
Experimental evolution ofBacillus subtilisonArabidopsis thalianaroots reveals fast adaptation and improved root colonization in the presence of soil microbes
Authors: Nordgaard Mathilde , Blake Christopher , Maróti Gergely , Hu Guohai , Wang Yue , Strube Mikael Lenz , Kovács Ákos T. 
Published: July 2021

SummaryThe soil ubiquitousBacillus subtilisis known to promote plant growth and protect plants against disease. These characteristics makeB. subtilishighly relevant in an agricultural perspective, fueling the interest in studyingB. subtilis-plant interactions. Here, we employ an experimental evolution approach to explore adaptation ofB. subtilistoArabidopsis thalianaroots. We found thatB. subtilisrapidly adapted to the plant root environment, as evidenced by improved root colonizers observed already after 12 consecutive transfers between seedlings in a hydroponic setup. In addition, two selected evolved isolates from independent populations from transfer 30 outcompeted the ancestor during root colonization. Re-sequencing of single evolved isolates and endpoint populations revealed mutations in genes related to different bacterial traits. Further, phenotypic characterization of evolved isolates from transfer 30 showed that increased root colonization was associated with robust biofilm formation in response to the plant polysaccharide xylan. Additionally, several evolved isolates across independent populations were impaired in motility, a redundant trait in the selective environment. Interestingly, two evolved isolates suffered a fitness disadvantage in a non-selective environment, demonstrating an evolutionary cost of adaptation to the plant root. Finally, increased root colonization by a selected evolved isolate was also demonstrated in the presence of resident soil microbes. Our findings provide novel insights into how a well-known plant growth-promoting rhizobacterium rapidly adapts to an ecologically relevant environment and reveal evolutionary consequences that are fundamental to consider when evolving strains for biocontrol purposes.
Transient accumulation and bidirectional movement of KIF13B in primary cilia
Authors: Juhl Alice Dupont , Anvarian Zeinab , Kuhns Stefanie , Berges Julia , Andersen Jens S. , Wüstner Daniel , Pedersen Lotte B. 
Published: July 2021

AbstractPrimary cilia are microtubule-based sensory organelles whose assembly and function rely on the conserved bidirectional intraflagellar transport (IFT) system, which is powered by anterograde kinesin-2 and retrograde cytoplasmic dynein 2 motors. Nematodes additionally employ a cell type-specific kinesin-3 motor, KLP-6, which moves within cilia independently of IFT and regulates ciliary content and function. Here we provide evidence that a KLP-6 homolog, KIF13B, undergoes bursts of bidirectional movement within primary cilia of cultured immortalized human retinal pigment epithelial (hTERT-RPE1) cells. Anterograde and retrograde intraciliary velocities of KIF13B were similar to those of IFT (IFT172-eGFP), but intraciliary movement of KIF13B required its own motor domain and appeared to be cell-type specific. Our work provides the first demonstration of motor-driven, intraciliary movement by a vertebrate kinesin other than kinesin-2 motors.