bluuebunny/crossref_metadata_2025 huggingface dataset:
MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic eventsin vivo
Authors: Zhang Xiaomin , Schlögl Alois , Vandael David , Jonas Peter
Published: July 2020

To understand the mechanisms of information coding in single neurons, it is necessary to analyze subthreshold synaptic events, action potentials (APs), and the interrelation between these two forms of activity in different behavioral states. However, detecting excitatory postsynaptic potentials (EPSPs) or currents (EPSCs) in awake, behaving animals remains challenging, because of unfavorable signal-to-noise ratio, high frequency, fluctuating amplitude, and variable time course of synaptic events. Here, we developed a new method for synaptic event detection, termed MOD (Machine-learningOptimal-filteringDetection-procedure), which combines concepts of supervised machine learning and optimal Wiener filtering. First, experts were asked to manually score short epochs of data. Second, the algorithm was trained to obtain the optimal filter coefficients of a Wiener filter and the optimal detection threshold. Third, scored and unscored data were processed with the optimal filter, and events were detected as peaks above threshold. Finally, the area under the curve (AUC) of the receiver operating characteristics (ROC) curve was used to quantify accuracy and efficiency of detection. Additionally, cross-validation was performed to exclude overfitting of the scored data, a potential concern with machine-learning approaches. We then challenged the new detection method with EPSP tracesin vivoin mice during spatial navigation and EPSC tracesin vitroin slices under conditions of enhanced transmitter release. When benchmarked using a (1−AUC)−1metric, MOD outperformed previous methods (template-fit and deconvolution) by a factor of up to 3. Thus, MOD may become an important tool for large-scale analysis of synaptic activityin vivoandin vitro.

Highlights

A new method for detection of synaptic events, termed MOD, is described

The method combines the concepts of supervised machine learning and optimal filtering

The method is useful for analysis of bothin vitroandin vivodata sets

MOD outperforms previously published methods for synaptic event detection by a factor of up to 3
Connective-Tissue Growth Factor (CTGF/CCN2) Contributes to TGF-β1-Induced Lung Fibrosis
Authors: Yanagihara Toyoshi , Chong Sy Giin , Gholiof Mahsa , Lipson Kenneth E. , Zhou Quan , Scallan Ciaran , Upagupta Chandak , Tikkanen Jussi , Keshavjee Shaf , Ask Kjetil , Kolb Martin RJ
Published: July 2020

Idiopathic pulmonary fibrosis (IPF) is a fatal lung disease characterized by progressive and excessive accumulation of myofibroblasts and extracellular matrix in the lung. Connective-tissue growth factor (CTGF) is known to exacerbate pulmonary fibrosis in radiation-induced lung fibrosis, and in this study, we show the upregulation of CTGF from a rat lung fibrosis model induced by adenovirus vector encoding active TGF-β1 (AdTGF-β1), and also in patients with IPF. The expression of CTGF was upregulated in vascular smooth muscle cells cultured from fibrotic lungs on days 7 or 14 as well as endothelial cells sorted from fibrotic lungs on day 14 or 28 respectively. These findings suggest the role of different cells in maintaining the fibrotic phenotype during fibrogenesis. Treatment of fibroblasts with recombinant CTGF along with TGF-β increases pro-fibrotic markers in fibroblasts, confirming the synergistic effect of recombinant CTGF with TGF-β in inducing pulmonary fibrosis. Also, fibrotic extracellular matrix upregulated the expression of CTGF, as compared to normal extracellular matrix, suggesting that not only profibrotic mediators but also a profibrotic environment contributes to fibrogenesis. We also showed that pamrevlumab, a CTGF inhibitory antibody, partially attenuates fibrosis in the model. These results suggest that pamrevlumab could be an option for the treatment of pulmonary fibrosis.
Harnessing the central dogma for stringent multi-level control of gene expression
Authors: Greco F. Veronica , Pandi Amir , Erb Tobias J. , Grierson Claire S. , Gorochowski Thomas E.
Published: July 2020

Strictly controlled inducible gene expression is crucial when engineering biological systems where even tiny amounts of a protein have a large impact on function or host cell viability. In these cases, leaky protein production must be avoided at all costs, but ideally without affecting the achievable range of expression. Here, we demonstrate how the central dogma offers a simple way to effectively address this challenge. By simultaneously regulating both transcription and translation, we show how relative basal expression of an inducible system can be greatly reduced, with minimal impact on the maximum induced expression rate. Using this approach, we create several stringent expression systems displaying >1000-fold change in their output after inductionin vivoand up to a 350-fold change when used in a cell-free expression system. Furthermore, we find that multi-level regulation is able to suppress transcriptional noise and creates a digital-like switch when transitioning between ‘on’ and ‘off’ states. This work provides foundational knowledge and a genetic toolkit of parts to create multi-level gene expression controllers for those working with toxic genes or requiring precise regulation and propagation of cellular signals. It also demonstrates the value of exploring more complex and diverse regulatory designs for synthetic biology.
CRISPR/Cas9-based silencing of theATXN1gene in Spinocerebellar ataxia type 1 (SCA1) fibroblasts
Authors: Salvatori Francesca , Pappadà Mariangela , Sicurella Mariaconcetta , Buratto Mattia , Simioni Valentina , Tugnoli Valeria , Marconi Peggy
Published: July 2020

Spinocerebellar Ataxia type 1 (SCA1) is an autosomal dominant neurodegenerative disorder caused by a gain-of-function protein with toxic activities, containing an expanded polyQ tract in the coding region. Actually, there are no treatments available to delay the onset, stop or slow down the progression of this pathology. Many approaches developed over the years involve the use of siRNAs and antisense oligonucleotides (ASOs). Here we develop and validate a CRISPR/Cas9 therapeutic strategy in fibroblasts isolated from SCA1 patients. We started from the screening of 10 different sgRNAs able to recognize regions upstream and downstream the CAG repeats, in exon 8 ofATXN1gene. The two most promising sgRNAs, G3 and G8, whose efficiency was evaluated with anin vitrosystem, significantly downregulated the ATXN 1 protein expression. This downregulation was due to the introduction of indels mutations into theATXN1gene. Notably, with an RNA-seq analysis, we demonstrated minimal off-target effects of our sgRNAs. These preliminary results support CRISPR/Cas9 as a promising approach for treated polyQ-expanded diseases.
Gender, race and parenthood impact academic productivity during the COVID-19 pandemic: from survey to action
Authors: Staniscuaski Fernanda , Kmetzsch Livia , Zandonà Eugenia , Reichert Fernanda , Soletti Rossana C. , Ludwig Zelia M.C , Lima Eliade F. , Neumann Adriana , Schwartz Ida V.D. , Mello-Carpes Pamela B. , Tamajusuku Alessandra S.K. , Werneck Fernanda P. , Ricachenevsky Felipe K. , Infanger Camila , Seixas Adriana , Staats Charley C. , de Oliveira Leticia
Published: July 2020

While the Coronavirus disease 2019 (COVID-19) pandemic is altering academia dynamics, those juggling remote work and domestic demands – including childcare - have already felt the impacts on productivity. Female authors are facing a decrease in papers submission rates since the beginning of the pandemic period. The reasons for this decline in women productivity need to be further investigated. Here we show the influence of gender, parenthood and race in academics productivity during the pandemic period, based on a survey answered by 3,345 Brazilian academics from various knowledge areas and research institutions. Findings revealed that male academics - especially childless ones - were the least affected group, whereas female academics, especially Black women and mothers, were the most impacted group. This scenario will leave long-term effects on the career progression of the most affected groups. The results presented here are crucial for the development of actions and policies that aim to avoid further deepening the gender gap in science. This particular situation we are facing during the pandemic demands institutional flexibility and academia should foster the discussion about actions to benefit Black scientists and academics with families in the post-pandemic scenario.
Global proteome and phosphoproteome alterations in third generation EGFR TKI resistance reveal drug targets to circumvent resistance
Authors: Zhang Xu , Maity Tapan K. , Ross Karen E. , Qi Yue , Cultraro Constance M. , Gao Shaojian , Nguyen Khoa Dang , Cowart Julie , Kirkali Fatos , Wu Cathy , Guha Udayan
Published: July 2020

Lung cancer is the leading cause of cancer mortality worldwide. The treatment of lung cancer patients harboring mutant EGFR with orally administered EGFR TKIs has been a paradigm shift. Osimertinib and rociletinib are 3rdgeneration irreversible EGFR TKIs targeting the EGFR T790M mutation. Osimertinib is the current standard care for patients with EGFR mutations due to increased efficacy, lower side effects, and enhanced brain penetrance. Unfortunately, all patients develop resistance. Genomic approaches have primarily been used to interrogate resistance mechanisms. Here, we have characterized the proteome and phosphoproteome of a series of isogenic EGFR mutant lung adenocarcinoma cell lines that are either sensitive or resistant to these drugs. To our knowledge, this is the most comprehensive proteomic dataset resource to date to investigate 3rdgeneration EGFR TKI resistance in lung adenocarcinoma. We have interrogated this unbiased global quantitative mass spectrometry dataset to uncover alterations in signaling pathways, reveal a proteomic signature of epithelial mesenchymal transition (EMT) and identify kinases and phosphatases with altered expression and phosphorylation in TKI resistant cells. Decreased tyrosine phosphorylation of key sites in the phosphatase SHP2 suggests its inhibition resulting in inhibition of RAS/MAPK and activation of PI3K/AKT pathways. Furthermore, we performed anticorrelation analyses of this phosphoproteomic dataset with the published drug-induced P100 phosphoproteomic datasets from the Library of Integrated Network-Based Cellular Signatures (LINCS) program to predict drugs with the potential to overcome EGFR TKI resistance. We identified dactolisib, a PI3K/mTOR inhibitor, which in combination with osimertinib overcomes resistance bothin vitroandin vivo.

One Sentence Summary

Global quantitative proteome and phosphoproteome analyses to examine altered signaling pathways in isogenic 3rdgeneration EGFR TKI sensitive and resistant cells.
Improved detection of tumor suppressor events in single-cell RNA-Seq data
Authors: Teschendorff Andrew E. , Wang Ning
Published: July 2020

Tissue-specific transcription factors are frequently inactivated in cancer. To fully dissect the heterogeneity of such tumor suppressor events requires single-cell resolution, yet this is challenging because of the high dropout rate. Here we propose a simple yet effective computational strategy called SCIRA to infer regulatory activity of tissue-specific transcription factors at single-cell resolution and use this tool to identify tumor suppressor events in single-cell RNA-Seq cancer studies. We demonstrate that tissue-specific transcription factors are preferentially inactivated in the corresponding cancer cells, suggesting that these are driver events. For many known or suspected tumor suppressors, SCIRA predicts inactivation in single cancer cells where differential expression does not, indicating that SCIRA improves the sensitivity to detect changes in regulatory activity. We identify NKX2-1 and TBX4 inactivation as early tumor suppressor events in normal non-ciliated lung epithelial cells from smokers. In summary, SCIRA can help chart the heterogeneity of tumor suppressor events at single-cell resolution.
Natural selection acts on epigenetic marks
Authors: Boukas Leandros , Razi Afrooz , Bjornsson Hans T. , Hansen Kasper D.
Published: July 2020

In the study of molecular features like epigenetic marks, it is appealing to ascribe observed patterns to the action of natural selection. However, this conclusion requires a test for selection based on a well-defined notion of neutrality. Here, focusing on epigenetic marks at gene loci, we formalize what it means for an epigenetic mark to be neutral, and develop a test for selection. Our test respects the foundational aspect of epigenetics:trans-regulation by transcription factors and chromatin modifiers. It also enables adjustment for confounders. We establish that promoter DNA methylation, promoter H3K4me3 and exonic H3K36me3 are all under selection, and that this is unlikely to be a passive consequence of selection on gene expression. The effect of these epigenetic marks on fitness is arguably partly explained by a causal involvement in gene regulation. However, we also investigate the complementary explanation that DNA methylation and H3K36me3 are under selection in part because they modify the mutation rate of important genomic regions. We show that this explanation is consistent with empirical observations as well as population genetics theory, because of thetrans-regulation. Exemplifying the protection of important regions from high mutability, we demonstrate that in humans the more intolerant to loss-of-function mutations a gene is, the lower its coding mutation rate is. Our framework for selection inference is simple but general, and we speculate that its core ideas will be useful for additional molecular features beyond epigenetic marks.
Measurement of hindered diffusion in complex geometries for high-speed single-molecule experiments
Authors: Bartsch Tobias F. , Villasante Camila M. , Touré Ahmed , Firester Daniel M. , Hengel Felicitas E. , Oswald Aaron , Hudspeth A. J.
Published: July 2020

In a high-speed single-molecule experiment, a protein is tethered between two substrates that are manipulated to exert force on the system. To avoid nonspecific interactions between the protein and nearby substrates, the protein is usually attached to the substrates through long, flexible linkers. This approach precludes measurements of mechanical properties with high spatial and temporal resolution, for rapidly exerted forces are dissipated into the linkers. Because mammalian hearing operates at frequencies reaching tens to hundreds of kilohertz, the mechanical processes that occur during transduction are of very short duration. Single-molecule experiments on the relevant proteins therefore cannot involve long tethers. We previously characterized the mechanical properties of protocadherin 15 (PCDH15), a protein essential for human hearing, by tethering an individual monomer through very short linkers between a probe bead held in an optical trap and a pedestal bead immobilized on a glass coverslip. Because the two confining surfaces were separated by only the length of the tethered protein, hydrodynamic coupling between those surfaces complicated the interpretation of the data. To facilitate our experiments, we characterize here the anisotropic and position-dependent diffusion coefficient of a probe in the presence of an effectively infinite wall, the coverslip, and of the immobile pedestal.
The Internal Structure of Metacommunities
Authors: Leibold Mathew A. , Rudolph F. Javiera , Blanchet F. Guillaume , De Meester Luc , Gravel Dominique , Hartig Florian , Peres-Neto Pedro , Shoemaker Lauren , Chase Jonathan M.
Published: July 2020

Current analyses of metacommunity data largely focus on global attributes across the entire metacommunity, such as mean alpha, beta, and gamma diversity, as well as the partitioning of compositional variation into single estimates of contributions of space and environmental effects and, more recently, possible contributions of species interactions. However, this view neglects the fact that different species and sites in the landscape can vary widely in how they contribute to these metacommunity-wide attributes. We argue for a new conceptual framework with matched analytics with the goals of studying the complex and interactive relations between process and pattern in metacommunities that is focused on the variation among species and among sites which we call the ‘internal structure’ of the metacommunity. To demonstrate how the internal structure could be studied, we create synthetic data using a process-based colonization-extinction metacommunity model. We then use Joint Species Distribution Models to estimate how the contributions of space, environment and biotic interactions driving metacommunity assembly differ among species and sites. We find that this approach to the internal structure of metacommunities provides useful information about the distinct ways that different species and different sites contribute to metacommunity structure. Although it has limitations, our work points at a more general approach to understand how other possible complexities might affect internal structure and might thus be incorporated into a more cohesive metacommunity theory.
Neurofeedback training of auditory selective attention enhances speech-in-noise perception
Authors: Kim Subong , Emory Caroline , Choi Inyong
Published: July 2020

Selective attention enhances cortical responses to attended sensory inputs while suppressing others, which can be an effective strategy for speech-in-noise (SiN) understanding. Here, we introduce a training paradigm designed to reinforce attentional modulation of auditory evoked responses. Subjects attended one of two speech streams while our EEG-based attention decoder provided online feedback. After four weeks of this neurofeedback training, subjects exhibited enhanced cortical response to target speech and improved performance during a SiN task. Such training effects were not found in the Placebo group that underwent attention training without neurofeedback. These results suggest an effective rehabilitation for SiN deficits.
Angiotensin-converting enzyme 2 (ACE2) expression increases with age in patients requiring mechanical ventilation
Authors: Baker Steven Andrew , Kwok Shirley , Berry Gerald J. , Montine Thomas J.
Published: July 2020

Mortality due to Covid-19 is highly associated with advanced age, owing in large part to severe lower respiratory tract infection. SARS-CoV-2 utilizes the host ACE2 receptor for infection. Whether ACE2 abundance in the lung contributes to age-associated vulnerability is currently unknown. We set out to characterize the RNA and protein expression profiles of ACE2 in aging human lung in the context of phenotypic parameters likely to affect lung physiology. Examining publicly available RNA sequencing data, we discovered that mechanical ventilation is a critical variable affecting lung ACE2 levels. Therefore, we investigated ACE2 protein abundance in patients either requiring mechanical ventilation or spontaneously breathing. ACE2 distribution and expression were determined in archival lung samples by immunohistochemistry (IHC). Tissues were selected from the specimen inventory at a large teaching hospital collected between 2010-2020. Twelve samples were chosen from patients receiving mechanical ventilation for acute hypoxic respiratory failure (AHRF). Twenty samples were selected from patients not requiring ventilation. We compared samples across age, ranging from 40-83 years old in the ventilated cohort and 14-80 years old in the non-ventilated cohort. Within the alveolated parenchyma, ACE2 expression is predominantly observed in type II pneumocytes (or alveolar type II / AT2 cells) and alveolar macrophages. All 12 samples from our ventilated cohort showed histologic features of diffuse alveolar damage including reactive, proliferating AT2 cells. In these cases, ACE2 was strongly upregulated with age when normalized to lung area (p = 0.004) or cellularity (p = 0.003), associated with prominent expression in AT2 cells. In non-ventilated individuals, AT2 cell reactive changes were not observed and ACE2 expression did not change with age when normalized to lung area (p = 0.231) or cellularity (p = 0.349). Additionally, we observed prominent pulmonary endothelial ACE2 expression in 2 patients on either an angiotensin-converting enzyme inhibitor (ACEI) or angiotensin receptor blocker (ARB). In summary, ACE2 expression increases with age in the setting of alveolar damage observed in patients on mechanical ventilation, providing a potential mechanism for higher Covid-19 mortality in the elderly.
An SEIR Model with Contact Tracing and Age-Structured Social Mixing for COVID-19 outbreak
Authors: Teimouri Ali
Published: July 2020

In December 2019 a severe acute respiratory syndrome now known as SARS-CoV-2 began to surge in Wuhan, China. The virus soon spread throughout the world to become a pandemic. Since the outbreak various measures were put in place to contain and control the spread, these interventions were mostly based on compartmental models in epidemiology with the main goal of controlling and monitoring the rate of the basic and effective reproduction number. In this paper, we propose an SEIR model where we incorporate contact tracing and age-structured social mixing. We show the explicit relation between contact tracing and social mixing and other relevant parameters of the proposed model. We derive a formula for the effective reproduction number which is expressed in terms of reported cases, tracing quantities and social mixing. We use this formula to determine the expectation value of the effective reproduction number in London, UK.
Racial segregation, testing sites access, and COVID-19 incidence rate in Massachusetts, USA
Authors: Hu Tao , Yue Han , Wang Changzhen , She Bing , Ye Xinyue , Liu Regina , Zhu Xinyan , Bao Shuming
Published: July 2020

The U.S. has merely 4% of the world population but 25% of the world’s COVID-19 cases. Massachusetts has been in the leading position of total cases since the outbreak in the U.S. Racial residential segregation is a fundamental cause of racial disparities in health. Moreover, disparities of access to health care have a large impact on COVID-19 cases. Thus, this study estimates racial segregation and disparities in testing sites access and employs economic, demographic, and transportation variables at the city/town level in Massachusetts. Spatial regression models are applied to evaluate the relationships between COVID-19 incidence rate and related variables. This is the first study to apply spatial analysis methods across neighborhoods in the U.S. to examine the COVID-19 incidence rate. The findings are: 1) residential segregations of Hispanic and Non-Hispanic Black/African Americans have a significantly positive association with COVID-19 incidence rate, indicating the higher susceptibility of COIVD-19 infections among minority; 2) The Black has the shortest drive time to testing sites, followed by Hispanic, Asian, and Whites. The drive time to testing sites is significantly negatively associated with the COVID-19 incidence rate, implying the importance of testing location being accessed by all populations; 3) Poverty rate and road density are significant explanatory variables. Importantly, overcrowding represented by more than one person per room is a significant variable found to be positively associated with COVID-19 incidence rate, suggesting the effectiveness of social distancing for reducing infection; 4) Different from previous studies, elderly population rate is not statistically significant with incidence rate because the elderly population in Massachusetts is less distributed in the hot spot regions of COVID-19 infections. The findings in this study provide useful insights for policymakers to propose new strategies to contain the COVID-19 transmissions in Massachusetts.
Organization of Primary Health Care in pandemics: a rapid systematic review of the literature in times of COVID-19
Authors: Sarti Thiago Dias , Lazarini Welington Serra , Fontenelle Leonardo Ferreira , Almeida Ana Paula Santana Coelho
Published: July 2020

The world is experiencing one of the greatest public health emergencies in history with the global spread of COVID-19. Health systems, including Primary Health Care (PHC) services, are pillars of pandemic coping strategies, and there are important gaps in the literature on the best ways to organize PHC in health crisis scenarios such as the one currently experienced. Given the urgency of responses, we performed a rapid systematic literature review on MEDLINE (via PubMed), EMBASE and LILACS (via VHL), in order to analyze empirical studies on the effectiveness of PHC organization strategies in the context of epidemics to improve access and reduce morbidity and mortality. We selected seven articles, which studied the responses to different epidemics in different parts of the world. In terms of access, the studies suggest positive results with the adoption of adjustments of work processes of the teams and the structure of the services, combined with diversification of actions (including call center), adequate provision of inputs and personal protective equipment, adequate action plans and communication strategies, and effective integration with public health services and other levels of care. No study analyzed population morbidity and mortality. The included studies suggest also that community-oriented PHC is more effective in crisis scenarios, indicating the necessity of strengthening of the Family Health Strategy in the Brazilian context.
A robust method for generating, quantifying and testing large amounts ofEscherichia colipersisters
Authors: Vedelaar Silke R. , Radzikowski Jakub L. , Heinemann Matthias
Published: July 2020

Bacteria can exhibit phenotypes, which makes them tolerant against antibiotics. However, often only a few cells of a bacterial population show such so-called persister phenotype, which makes it difficult to study this health-threatening phenotype. We recently found that certain abrupt nutrient-shifts generateE. colipopulations that consist of almost only antibiotic tolerant persister cells. Such nearly homogeneous persister cell populations enable assessment with population-averaging experimental methods, such as high-throughput methods. In this paper, we provide a detailed protocol of how to generate such large fraction of tolerant cells using the nutrient-switch approach. Furthermore, we describe how to determine the fraction of cells that enter the tolerant state upon a sudden nutrient shift and describe a new way to assess antibiotic tolerance with flow cytometry. We envision that these methods facilitate research into the important and exciting phenotype of bacterial cells.
Sexually divergent development of depression-related brain networks during healthy human adolescence
Authors: Dorfschmidt L. , Bethlehem R.A.I. , Seidlitz J. , Váša F. , White S.R. , Romero-García R. , Kitzbichler M.G. , Aruldass A. , Morgan S.E. , Goodyer I.M. , Fonagy P. , Jones P.B. , Dolan R.J. ,   the NSPN consortium, Harrison N.A. , Vértes P.E. , Bullmore E.T.
Published: July 2020

We hypothesized that there are sexual differences in human brain network development underlying the female > male divergence in adolescent depression. We tested for sex differences in parameters of brain network development (accelerated longitudinal fMRI, N=298 healthy adolescents, each scanned 1 to 3 times). Sexually divergent development of functional connectivity was located in default mode network (DMN), limbic cortex, and subcortical nuclei. Females had a more “disruptive” pattern of development, where weak functional connectivity at age 14 became stronger during adolescence. This fMRI-derived map of divergent adolescent development was co-located with (i) a map of functional dysconnectivity associated with adult major depressive disorder (MDD); and (ii) an adult brain gene expression pattern enriched for genes on the X chromosome, neurodevelopmental genes, and risk genes for MDD. Sexual divergence in disruptive development of DMN, limbic and subcortical functional networks is potentially relevant to the increased risk of depression in adolescent females.
Sleep Identification Enabled by Supervised Training Algorithms (SIESTA): An open-source platform for automatic sleep staging of rodent polysomnographic data
Authors: Caldart Carlos S. , Sanchez Raymond E. A. , Ben-Hamo Miriam , Beck Asad I. , Weil Tenley A. , Perez Jazmine G. , Kalume Franck , Brunton Bingni W. , de la Iglesia Horacio O.
Published: July 2020

The temporal distribution of sleep stages is critical for the study of sleep function, regulation, and disorders in higher vertebrates. This temporal distribution is typically determined polysomnographically. In laboratory rodents, scoring of electrocorticography (ECoG) and electromyography (EMG) recordings is usually performed manually, where 5-10 second epochs are categorized as one of three specific stages: wakefulness, rapid-eye-movement (REM) sleep and non-REM (NREM) sleep. This process is laborious, time-consuming, and particularly impractical for large experimental cohorts with recordings lasting longer than 24 hours.

To circumvent this problem, we developed an open-source Python toolkit,Sleep Identification Enabled by Supervised Training Algorithms(SIESTA), that automates the detection of these three main behavioral stages in mice. Our supervised machine learning algorithm extracts features from the ECoG and EMG signals, then automatically scores recordings with a hierarchical classifier based on Bagging Random Forest approaches. We evaluated this approach on data collected from wild-type mice housed under both normal and different lighting conditions, as well as from a mutant mouse line with abnormal sleep phenotypes. To validate its performance on test data, we compared SIESTA with manually scored data and obtained F1scores of 0.92 for wakefulness, 0.81 for REM, and 0.93 for NREM.

SIESTA has a user-friendly interface that can be used without coding expertise. To our knowledge, this is the first time that such a strategy has been developed using all open-source and freely available resources, and our aim is that SIESTA becomes a useful tool that facilitates further research of sleep in rodent models.
Self-assembling shell proteins PduA and PduJ have essential and redundant roles in bacterial microcompartment assembly
Authors: Kennedy Nolan W. , Ikonomova Svetlana P. , Lee Marilyn Slininger , Raeder Henry W. , Tullman-Ercek Danielle
Published: July 2020

Protein self-assembly is a common and essential biological phenomenon, and bacterial microcompartments present a promising model system to study this process. Bacterial microcompartments are large, protein-based organelles which natively carry out processes important for carbon fixation in cyanobacteria and the survival of enteric bacteria. These structures are increasingly popular with biological engineers due to their potential utility as nanobioreactors or drug delivery vehicles. However, the limited understanding of the assembly mechanism of these bacterial microcompartments hinders efforts to repurpose them for non-native functions. Here, we comprehensively investigate proteins involved in the assembly of the 1,2-propanediol utilization bacterial microcompartment fromSalmonella entericaserovar Typhimurium LT2, one of the most widely studied microcompartment systems. We first demonstrate that two shell proteins, PduA and PduJ, have a high propensity for self-assembly upon overexpression, and we provide a novel method for self-assembly quantification. Using genomic knock-outs and knock-ins, we systematically show that these two proteins play an essential and redundant role in bacterial microcompartment assembly that cannot be compensated by other shell proteins. At least one of the two proteins PduA and PduJ must be present for the bacterial microcompartment shell to assemble. We also demonstrate that assembly-deficient variants of these proteins are unable to rescue microcompartment formation, highlighting the importance of this assembly property. Our work provides insight into the assembly mechanism of these bacterial organelles and will aid downstream engineering efforts.
Tracking Age Differences in Neural Distinctiveness across Representational Levels
Authors: Kobelt Malte , Sommer Verena R. , Keresztes Attila , Werkle-Bergner Markus , Sander Myriam C.
Published: July 2020

The authors have withdrawn the preprint due to two errors in the analyses: The first error was a failure to account for three dummy volumes (TR = 2s) collected at the beginning of each experimental run. The second error was a coding error related to the definition of the category-selective clusters. Since correcting for these errors drastically altered the results and conclusions of this paper, the authors have withdrawn the preprint and retracted the published paper. More information as well as a report comparing original and corrected results can be found onhttps://osf.io/t8dpv/. If you have any questions please contact the corresponding author (sander@mpib-berlin.mpg.de).
Addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq
Authors: Gustafsson Johan , Robinson Jonathan , Nielsen Jens , Pachter Lior
Published: July 2020

The incorporation of unique molecular identifiers (UMIs) in single-cell RNA-seq assays allows for the removal of amplification bias in the estimation of gene abundances. We show that UMIs can also be used to address a problem resulting from incomplete sequencing of amplified molecules in sequencing libraries that can lead to bias in gene abundance estimates. Our method, called BUTTERFLY, is based on a zero truncated negative binomial estimator and is implemented in the kallisto bustools single-cell RNA-seq workflow. We demonstrate its efficacy using a range of datasets and show that it can invert the relative abundance of certain genes in cases of a pooled amplification paradox.
Faunistic study on the freshwater ciliates from Delhi, India
Authors: Abraham Jeeva Susan , Gupta Renu , Somasundaram Sripoorna , Naqvi Ilmas , Maurya Swati , Toteja Ravi , Makhija Seema
Published: July 2020

The ciliated protist communities show richness as well as uniqueness. This is true both for aquatic and soil ciliates. Delhi region lies in the subtropical semi-arid zone wherein the temperatures are highest in May-June and lowest in January. It also receives its monsoonal rainfall during the month of July-August. Thus, the region offers ideal conditions for the growth and proliferation of aquatic living beings. During the past three decades, a series of investigation has been carried out on the freshwater free-living ciliate fauna from fourteen sites at the river Yamuna and different freshwater bodies in Delhi. Samples were brought to the laboratory, ciliates were identified using live-cell observations and silver staining methods. A large number of Spirotrich species and a lower proportion belonging to class Heterotrichea, Litostomaea, Phyllopharyngea, Oligohymenophorea, Prostomatea, and Colpodea were identified. A total of 55 species belonging to 7 classes, 16 orders, 26 families, 40 genera were identified and documented. Ciliate diversity was found to be highest in the water sample from Okhla bird sanctuary (OBS). All ciliate species recorded during the present study have been listed and their general characteristics have been discussed.
Towards a taxonomically unbiased EU Biodiversity Strategy for 2030
Authors: Mammola Stefano , Riccardi Nicoletta , Prié Vincent , Correia Ricardo , Cardoso Pedro , Lopes-Lima Manuel , Sousa Ronaldo
Published: July 2020

Through the Habitats Directive (92/43/EEC) and the LIFE projects financial investments, Europe has been the world’s experimental arena for biological conservation. With an estimated budget of €20 billion/year, the EU Biodiversity Strategy for 2030 has set an ambitious goal of reaching 30% Protected Areas and ensure no deterioration in conservation trends and status of all protected species. We analyzed LIFE projects focused on animals from 1992 to 2018 and we found that investment towards vertebrates has been six times higher than that for invertebrates (€970 vs €150 million), with birds and mammals alone accounting for 72% species and 75% total budget. Budget allocation is primarily explained by species’ popularity. We propose a roadmap to achieve unbiased conservation targets for 2030 and beyond.
UvrD helicase–RNA polymerase interactions are governed by UvrD’s carboxy-terminal Tudor domain
Authors: Kawale Ashish A. , Burmann Björn M.
Published: July 2020

All living organisms have to cope with the constant threat of genome damage by UV light and other toxic reagents. To maintain the integrity of their genomes, organisms developed a variety of DNA repair pathways. One of these, theTranscriptionCoupled DNA-Repair (TCR) pathway, is triggered by stalled RNA Polymerase (RNAP) complexes at DNA damage sites on actively transcribed genes. A recently elucidated bacterial TCR pathway employs the UvrD helicase pulling back stalled RNAP complexes from the damage, stimulating recruitment of the DNA-repair machinery. However, structural and functional aspects of UvrD’s interaction with RNA Polymerase remain elusive. Here we used advanced solution NMR spectroscopy to investigate UvrD’s role within the TCR, identifying that the carboxy-terminal region of the UvrD helicase facilitates RNAP interactions by adopting a Tudor-domain like fold. Subsequently, we functionally analyzed this domain, identifying it as a crucial component for the UvrD–RNAP interaction besides having nucleic-acid affinity.
Ghat: An R package for identifying adaptive polygenic traits
Authors: Mahmoud Medhat , Tost Mila , Ha Ngoc-Thuy , Simianer Henner , Beissinger Timothy
Published: July 2020

Identifying selection on polygenic complex traits in crops and livestock is important for understanding evolution and helps prioritize important characteristics for breeding. The QTL that contribute to polygenic trait variation often exhibit small or infinitesimal effects. This hinders the ability to detect QTL controlling polygenic traits because enormously high statistical power is needed for their detection. Recently, we circumvented this challenge by introducing a method to identify selection on complex traits by evaluating the relationship between genome-wide changes in allele frequency and estimates of effect-size. The approach involves calculating a composite-statistic across all markers that captures this relationship, followed by implementing a linkage disequilibrium-aware permutation test to evaluate if the observed pattern differs from that expected due to drift during evolution and population stratification. In this manuscript, we describe “Ghat”, an R package developed to implement this method to test for selection on polygenic traits. We demonstrate the package by applying it to test for polygenic selection on 15 published European wheat traits including yield, biomass, quality, morphological characteristics, and disease resistance traits. Moreover, we applied Ghat to different simulated populations with different breeding history and genetic architecture. The results highlight the power of Ghat to identify selection on complex traits. The Ghat package is accessible on CRAN, the Comprehensive R Archival Network, and on GitHub.
Sodium Diethyldithiocarbamate antiparasitic activity against differentTrypanosoma cruzistrains: Insights of its biological activity
Authors: de Freitas Oliveira Johny Wysllas , Torres Taffarel Melo , Gonçalves Moreno Cláudia Jassica , Amorim-Carmo Bruno , Damasceno Igor Zumba , Cruz Soares Ana Katarina Menezes , da Silva Barbosa Jefferson , Oliveira Rocha Hugo Alexandre , Silva Marcelo Sousa
Published: July 2020

Background

Chagas disease is caused by the protozoanTrypanosoma cruzi, a neglected tropical disease that affects thousands of people, mainly in Latin America. The drugs currently used in therapy are toxic and have therapeutic limitations during treatment. In addition, the genetic diversity ofT. cruzirepresents an important variable and challenge with regard to the pathogenesis of the infection, the epidemiological profile of the cases, and the therapeutic control of the infection. Sodium diethyldithiocarbamate (DETC) is a compound of high pharmacological versatility acting as metal chelators and producing reactive oxygen species. Thus, the objective of this work is to characterize the antiparasitic action of DETC against different strains and evolutionary forms ofT. cruzi, as well as the characterization of the mechanism of antiparasitic action.

Methodology/Principal findings

The different strains and evolutionary forms ofT. cruziwere grown in LIT medium. To evaluate the antiparasitic activity of DETC, the evolutionary forms epimastigote and trypomastigote ofT. cruziwere used by resazurin reduction methods and by counting under optical microscopy. Different response patterns were obtained between the strains and an IC50of DETC ranging from 9.44 ± 3,181µM to 60.49 ± 7.62 µM. Cell cytotoxicity against cell lines 3T3 and RAW and evaluated by MTT, demonstrated that DETC in high concentration (2222 µM) reduces around 60% the cell capacity of MTT reduction. The antiparasitic activity of DETC has been demonstrated through damage caused in the mitochondria ofT. cruzi, a reduction of up to 80% in the mitochondrial potential of the parasites, as well as through damage caused in the membrane of the parasite.

Conclusion

In this study we can conclude that DETC has antiparasitic activity against different genotypes and evolutionary forms ofT. cruzi, representing a promising molecule as a drug for the treatment of Chagas disease.
Mus musculuspopulations in Western Australia lack VKORC1 mutations conferring resistance to first generation anticoagulant rodenticides: Implications for conservation and biosecurity
Authors: Duncan Bridget J.M.L. , Koenders Annette , Burnham Quinton , Lohr Michael T.
Published: July 2020

Background

Humans routinely attempt to manage pest rodent populations with anticoagulant rodenticides (ARs). We require information on resistance to ARs within rodent populations to have effective eradication programs that minimise exposure in non-target species. Mutations to the VKORC1 gene have been shown to confer resistance in rodents with high proportions of resistance in mice found in all European populations tested. We screened mutations inMus musculuswithin Western Australia, by sampling populations from the capital city (Perth) and a remote island (Browse Island). These are the first Australian mouse populations screened for resistance using this method. Additionally, the mitochondrial D-loop of house mice was sequenced to explore population genetic structure, identify the origin of Western Australian mice, and to elucidate whether resistance was linked to certain haplotypes.

Results

No resistance-related VKORC1 mutations were detected in either house mouse population. A genetic introgression in the intronic sequence of the VKORC1 gene of Browse Island house mouse was detected which is thought to have originated through hybridisation with the Algerian mouse (Mus spretus). Analysis of the mitochondrial D-loop reported two haplotypes in the house mouse population of Perth, and two haplotypes in the population of Browse Island.

Conclusions

Both house mouse populations exhibited no genetic resistance to ARs, in spite of free use of ARs in Western Australia. Therefore weaker anticoagulant rodenticides can be employed in pest control and eradication attempts, which will result in reduced negative impacts on non-target species. Biosecurity measures must be in place to avoid introduction of resistant house mice, and new house mouse subspecies to Western Australia.
Identification of oxygen-independent pathways for pyridine-nucleotide and Coenzyme-A synthesis in anaerobic fungi by expression of candidate genes in yeast
Authors: Perli Thomas , Vos Aurin M. , Bouwknegt Jonna , Dekker Wijb J. C. , Wiersma Sanne J. , Mooiman Christiaan , Ortiz-Merino Raúl A. , Daran Jean-Marc , Pronk Jack T.
Published: July 2020

Neocallimastigomycetes are rare examples of strictly anaerobic eukaryotes. This study investigates how these anaerobic fungi bypass reactions involved in synthesis of pyridine nucleotide cofactors and coenzyme A that, in canonical fungal pathways, require molecular oxygen. Analysis of Neocallimastigomycete proteomes identified a candidate L-aspartate-decarboxylase (AdcA), and L-aspartate oxidase (NadB) and quinolinate synthase (NadA), constituting putative oxygen-independent bypasses for coenzyme A synthesis and pyridine nucleotide cofactor synthesis, respectively. The corresponding gene sequences indicated acquisition by ancient horizontal gene transfer event involving bacterial donors. To test whether these enzymes suffice to bypass corresponding oxygen-requiring reactions, they were introduced intofms1Δandbna2Δ Sacharomyces cerevisiaestrains. Expression ofnadAandnadB, andadcAfrom the NeocallimastigomycetesPiromyces finnisandNeocallimastix californiae, respectively, conferred cofactor prototrophy under aerobic and anaerobic conditions. This study simulates how horizontal gene transfer can drive eukaryotic adaptation to anaerobiosis, and provides a basis for elimination of auxotrophic requirements in anaerobic industrial applications of yeasts and fungi.
A simple and rapid method for isolating high-quality RNA from kenaf containing high polysaccharide and polyphenol contents
Authors: Liao Xiaofang , Li Hongwei , Khan Aziz , Zhao Yanhong , Hou Wenhuan , Tang Xingfu , Akhtar Kashif , Zhou Ruiyang
Published: July 2020

The isolation of high-quality RNA from kenaf is crucial for genetic and molecular biology studies. However, high levels of polysaccharide and polyphenol compounds in kenaf tissues could irreversibly bind to and coprecipitate with RNA, which complicates RNA extraction. In the present study, we proposed a simplified, time-saving and low-cost extraction method for isolating high quantities of high-quality RNA from several different kenaf tissues. RNA quality was measured for yield and purity, and the proposed protocol yielded high quantities of RNA (10.1-12.9 μg/g·FW). Spectrophotometric analysis showed that A260/280ratios of RNA samples were in the range of 2.11 to 2.13, and A260/230ratios were in the range of 2.04-2.24, indicating that the RNA samples were free of polyphenols, polysaccharides, and protein contaminants after isolation. The method of RNA extraction presented here was superior to the conventional CTAB method in terms of RNA isolation efficiency and was more sample-adaptable and cost-effective than commercial kits. Furthermore, to confirm downstream amenability, the high-quality RNA obtained from this method was successfully used for RT-PCR, real-time RT-PCR and Northern blot analysis. We provide an efficient and low-cost method for extracting high quantities of high-quality RNA from plants that are rich in polyphenols and polysaccharides, and this method was also validated for the isolation of high-quality RNA from other plants.