bluuebunny/crossref_metadata_2025 huggingface dataset:
SHIMS 3.0: Highly efficient single-haplotype iterative mapping and sequencing using ultra-long nanopore reads
Authors: Bellott Daniel W. , Cho Ting-Jan , Jackson Emily K. , Skaletsky Helen , Hughes Jennifer F. , Page David C.
Published: September 2020

The reference sequence of structurally complex regions can only be obtained through a highly accurate clone-based approach that we call Single-Haplotype Iterative Mapping and Sequencing (SHIMS). In recent years, improvements to SHIMS have reduced the cost and time required by two orders of magnitude, but internally repetitive clones still require extensive manual effort to transform draft assemblies into reference-quality finished sequences. Here we describe SHIMS 3.0, an extension of our SHIMS sequencing strategy, using ultra-long nanopore reads to augment the Illumina data from SHIMS 2.0 assemblies and resolve internally repetitive structures. This greatly minimizes the need for manual finishing of Illumina-based draft assemblies, allowing a small team with no prior finishing experience to sequence challenging targets with high accuracy. This protocol proceeds from clone-picking to finished assemblies in 2 weeks for about 80 dollars per clone. We recently used this protocol to produce reference sequence of structurally complex palindromes on chimpanzee and rhesus macaque X chromosomes; as a further demonstration of the capabilities of SHIMS 3.0, we finish the TSPY array on the human Y chromosome, which could not be resolved by previous sequencing methods. Our protocol provides access to structurally complex regions that would otherwise be inaccessible from whole-genome shotgun data or require an impractical amount of manual effort to generate an accurate assembly.
A convolutional neural network for common coordinate registration of high-resolution histology images
Authors: Daly Aidan C. , Geras Krzysztof J. , Bonneau Richard A.
Published: September 2020

Registration of histology images from multiple sources is a pressing problem in large-scale studies of spatial -omics data. Researchers often perform “common coordinate registration,” akin to segmentation, in which samples are partitioned based on tissue type to allow for quantitative comparison of similar regions across samples. Accuracy in such registration requires both high image resolution and global awareness, which mark a difficult balancing act for contemporary deep learning architectures. We present a novel convolutional neural network (CNN) architecture that combines (1) a local classification CNN that extracts features from image patches sampled sparsely across the tissue surface, and (2) a global segmentation CNN that operates on these extracted features. This hybrid network can be trained in an end-to-end manner, and we demonstrate its relative merits over competing approaches on a reference histology dataset as well as two published spatial transcriptomics datasets. We believe that this paradigm will greatly enhance our ability to process spatial -omics data, and has general purpose applications for the processing of high-resolution histology images on commercially available GPUs.
Multi-Objective Approach for Identifying Cancer Subnetwork Markers
Authors: Bayat Faezeh , Davoodi Mansoor
Published: September 2020

Identifying genetic markers for cancer is one of the main challenges in the recent researches. Between different cohorts of genetic markers such as genes or a group of genes like pathways or sub-network, identifying functional modules like subnetwork markers has been more challenging. Network-based classification methods have been successfully used for finding effective cancer subnetwork markers. Combination of metabolic networks and molecular profiles of tumor samples has led researchers to a more accurate prediction of subnetwork markers. However, topological features of the network have not been considered in the activity of the subnetwork. Here, we apply a novel protein-protein interaction network-based classification method that considers topological features of the network in addition to the expression profiles of the samples. We have considered the problem of identifying cancer subnetwork markers as a multi-objective problem which in this approach, each subnetwork’s activity level is measured according to both objectives of the problem; Differential expression level of the genes and topological features of the nodes in the network. We found that the subnetwork markers identified by this method achieve higher performance in the classification of cancer outcome in comparison to the other subnetwork markers.
Bayesian Inference with Incomplete Knowledge Explains Perceptual Confidence and its Deviations from Accuracy
Authors: Khalvati Koosha , Kiani Roozbeh , Rao Rajesh P. N.
Published: September 2020

In perceptual decisions, subjects infer hidden states of the environment based on noisy sensory information. Here we show that both choice and its associated confidence are explained by a Bayesian framework based on partially observable Markov decision processes (POMDPs). We test our model on monkeys performing a direction-discrimination task with post-decision wagering, demonstrating that the model explains objective accuracy and predicts subjective confidence. Further, we show that the model replicates well-known discrepancies of confidence and accuracy, including the hard-easy effect, opposing effects of stimulus volatility on confidence and accuracy, dependence of confidence ratings on simultaneous or sequential reports of choice and confidence, apparent difference between choice and confidence sensitivity, and seemingly disproportionate influence of choice-congruent evidence on confidence. These effects may not be signatures of sub-optimal inference or discrepant computational processes for choice and confidence. Rather, they arise in Bayesian inference with incomplete knowledge of the environment.
Age and Sex Effects on Advanced White Matter Microstructure Measures in 15,628 Older Adults: A UK Biobank Study
Authors: Lawrence Katherine E. , Nabulsi Leila , Santhalingam Vigneshwaran , Abaryan Zvart , Villalon-Reina Julio E. , Nir Talia M. , Gari Iyad Ba , Zhu Alyssa H. , Haddad Elizabeth , Muir Alexandra M. , Laltoo Emily , Jahanshad Neda , Thompson Paul M.
Published: September 2020

A comprehensive characterization of the brain’s white matter is critical for improving our understanding of healthy and diseased aging. Here we used diffusion-weighted magnetic resonance imaging (dMRI) to estimate age and sex effects on white matter microstructure in a cross-sectional sample of 15,628 adults aged 45-80 years old (47.6% male, 52.4% female). Microstructure was assessed using the following four models: a conventional single-shell model, diffusion tensor imaging (DTI); a more advanced single-shell model, the tensor distribution function (TDF); an advanced multi-shell model, neurite orientation dispersion and density imaging (NODDI); and another advanced multi-shell model, mean apparent propagator MRI (MAPMRI). Age was modeled using a data-driven statistical approach, and normative centile curves were created to provide sex-stratified white matter reference charts. Participant age and sex substantially impacted many aspects of white matter microstructure across the brain, with the advanced dMRI models TDF and NODDI detecting such effects the most sensitively. These findings and the normative reference curves provide an important foundation for the study of healthy and diseased brain aging.
Beware of UVC sanitizers: not all are good
Authors: Arines Justo , Bao-Varela Carmen
Published: September 2020

Disinfection is now one of the major concerns of society. Soap, or hydroalcohol are two known ways of sanitizing different objects. Now we can find in the market more sophisticated systems, which provide more confidence on their sanitizing effects, or that allows disinfection of objects that cannot be sanitized with soap or hydroalcoholic solutions. In this work we analyze a commercially available sanitizing device that claims the use of UVC radiation. We will show that this device is not suitable for complete disinfection of the objects introduced on the cabin. We provide spectral characterization of the sources, as well as irradiance measurements inside the cabin. We conclude that the cabin cannot be used for sanitizing most of the objects that are included in the documentation of the device.
The distribution of common-variant effect sizes
Authors: O’Connor Luke Jen
Published: September 2020

The genetic effect-size distribution describes the number of variants that affect disease risk and the range of their effect sizes. Accurate estimates of this distribution would provide insights into genetic architecture and set sample-size targets for future genome-wide association studies. We developed Fourier Mixture Regression (FMR) to estimate common-variant effect-size distributions from GWAS summary statistics. We validated FMR in simulations and in analyses of UK Biobank data, using interim-release summary statistics (max N=145k) to predict the results of the full release (N=460k). Analyzing summary statistics for 10 diseases (avg Neff=169k) and 22 other traits, we estimated the sample size required for genome-wide significant SNPs to explain 50% of SNP-heritability. For most diseases the requisite number of cases is 100k-1M, an attainable number; ten times more would be required to explain 90% of heritability. In well-powered GWAS, genome-wide significance is a conservative threshold, and loci at less stringent thresholds have true positive rates that remain close to 1 if confounding is controlled. Analyzing the shape of the effect-size distribution, we estimate that heritability accumulates across many thousands of SNPs with a wide range of effect sizes: the largest effects (at the 90thpercentile of heritability) are 100 times larger than the smallest (10thpercentile), and while the midpoint of this range varies across traits, its size is similar. These results suggest attainable sample size targets for future GWAS, and they underscore the complexity of genetic architecture.
Perinatal fentanyl exposure leads to long-lasting impairments in somatosensory circuit function and behavior
Authors: Alipio Jason , Haga Catherine , Fox Megan E , Arakawa Keiko , Balaji Rakshita , Cramer Nathan , Lobo Mary Kay , Keller Asaf
Published: September 2020

One consequence of the opioid epidemic are lasting neurodevelopmental sequelae afflicting adolescents exposed to opioids in the womb. A translationally relevant and developmentally accurate preclinical model is needed to understand the behavioral, circuit, network, and molecular abnormalities resulting from this exposure. By employing a novel preclinical model of perinatal fentanyl exposure, our data reveal that fentanyl has several dose-dependent, developmental consequences to somatosensory function and behavior. Newborn male and female mice exhibit signs of withdrawal and sensory-related deficits that extend at least to adolescence. As fentanyl exposure does not affect dams' health or maternal behavior, these effects result from the direct actions of perinatal fentanyl on the pups' developing brain. At adolescence, exposed mice exhibit reduced adaptation to sensory stimuli, and a corresponding impairment in primary somatosensory (S1) function. In vitro electrophysiology demonstrates a long-lasting reduction in S1 synaptic excitation, evidenced by decreases in release probability, NMDA receptor-mediated postsynaptic currents, and frequency of miniature excitatory postsynaptic currents, as well as increased frequency of miniature inhibitory postsynaptic currents. In contrast, anterior cingulate cortical neurons exhibit an opposite phenotype, with increased synaptic excitation. Consistent with these changes, electrocorticograms reveal suppressed ketamine-evoked γ oscillations. Morphological analysis of S1 pyramidal neurons indicate reduced dendritic complexity, dendritic length, and soma size. Further, exposed mice exhibited abnormal cortical mRNA expression of key receptors and neuronal growth and development, changes that were consistent with the electrophysiological and morphological changes. These findings demonstrate the lasting sequelae of perinatal fentanyl exposure on sensory processing and function.
Prophage-dependent neighbor predation fosters horizontal gene transfer by natural transformation
Authors: Molina-Quiroz Roberto C. , Dalia Triana N. , Camilli Andrew , Dalia Ankur B. , Silva-Valenzuela Cecilia A.
Published: September 2020

Natural transformation is a broadly conserved mechanism of horizontal gene transfer (HGT) in bacteria (1) that can shape their evolution through the acquisition of genes that promote virulence, antibiotic resistance, and other traits (2). Recent work has established that neighbor predation via Type VI secretion systems (3), bacteriocins (4) and virulent phages (5), play an important role in promoting HGT. Here, we demonstrate that in chitin estuary microcosms,Vibrio choleraeK139 lysogens exhibit prophage-dependent neighbor predation of non-lysogens to enhance HGT. Through predation of non-lysogens, K139 lysogens also have a fitness advantage in these microcosm conditions. The ecological strategy revealed by our work provides a better understanding of the evolutionary mechanisms used by bacteria to adapt in their natural setting and contributes to our understanding of the selective pressures that may drive prophage maintenance in bacterial genomes.

IMPORTANCE

Prophages are nearly ubiquitous in bacterial species. These integrated phage elements have previously been implicated in horizontal gene transfer (HGT) largely through their ability to carry out transduction (generalized or specialized). Here, we show that prophage-encoded viral particles promote neighbor predation leading to enhanced HGT by natural transformation in the water-borne pathogenVibrio cholerae. Our findings contribute to a comprehensive understanding of the dynamic forces involved in prophage maintenance which ultimately drive the evolution of naturally competent bacteria in their natural environment.
How to use online tools to generate new hypotheses for mammary gland biology research: a case study forWnt7b
Authors: van de Grift Yorick Bernardus Cornelis , Heijmans Nika , van Amerongen Renée
Published: September 2020

An increasing number of ‘-omics’ datasets, generated by labs all across the world, are becoming available. They contain a wealth of data that are largely unexplored. Not every scientist, however, will have access to the required resources and expertise to analyze such data from scratch. Luckily, a growing number of investigators is dedicating their time and effort to the development of user friendly, online applications that allow researchers to use and investigate these datasets. Here, we will illustrate the usefulness of such an approach.

Using regulation ofWnt7bas an example, we will highlight a selection of accessible tools and resources that are available to researchers in the area of mammary gland biology. We show how they can be used forin silicoanalyses of gene regulatory mechanisms, resulting in new hypotheses and providing leads for experimental follow up. We also call out to the mammary gland community to join forces in a coordinated effort to generate and share additional tissue-specific ‘-omics’ datasets and thereby expand thein silicotoolbox.
Comparison of multiple tractography methods for reconstruction of the retinogeniculate visual pathway using diffusion MRI
Authors: He Jianzhong , Zhang Fan , Xie Guoqiang , Yao Shun , Feng Yuanjing , Bastos Dhiego C. A. , Rathi Yogesh , Makris Nikos , Kikinis Ron , Golby Alexandra J. , O’Donnell Lauren J.
Published: September 2020

The retinogeniculate visual pathway (RGVP) conveys visual information from the retina to the lateral geniculate nucleus. The RGVP has four subdivisions, including two decussating and two non-decussating pathways that cannot be identified on conventional structural magnetic resonance imaging (MRI). Diffusion MRI tractography has the potential to trace these subdivisions and is increasingly used to study the RGVP. However, it is not yet known which fiber tracking strategy is most suitable for RGVP reconstruction. In this study, four tractography methods are compared, including constrained spherical deconvolution (CSD) based probabilistic (iFOD1) and deterministic (SD-Stream) methods, and multi-fiber (UKF-2T) and single-fiber (UKF-1T) unscented Kalman filter (UKF) methods. Experiments use diffusion MRI data from 57 subjects in the Human Connectome Project. The RGVP is identified using regions of interest created by two clinical experts. Quantitative anatomical measurements and expert anatomical judgment are used to assess the advantages and limitations of the four tractography methods. Overall, we conclude that UKF-2T and iFOD1 produce the best RGVP reconstruction results. The iFOD1 method can better quantitatively estimate the percentage of decussating fibers, while the UKF-2T method produces reconstructed RGVPs that are judged to better correspond to the known anatomy and have the highest spatial overlap across subjects. Overall, we find that it is challenging for current tractography methods to both accurately track RGVP fibers that correspond to known anatomy and produce an approximately correct percentage of decussating fibers. We suggest that future algorithm development for RGVP tractography should take consideration of both of these two points.
A plausible mechanism forDrosophilalarva intermittent behavior
Authors: Sakagiannis Panagiotis , Aguilera Miguel , Nawrot Martin Paul
Published: September 2020

The behavior of many living organisms is not continuous. Rather, activity emerges in bouts that are separated by epochs of rest, a phenomenon known as intermittent behavior. Although intermittency is ubiquitous across phyla, empirical studies are scarce and the underlying neural mechanisms remain unknown. Here we present the first empirical evidence of intermittency duringDrosophilalarva free exploration. We report power-law distributed rest-bout and log-normal distributed activity-bout durations. We show that a stochastic network model can transition between power-law and non-power-law distributed states and we suggest a plausible neural mechanism for the alternating rest and activity in the larva. Finally, we discuss possible implementations in behavioral simulations extending spatial Levy-walk or coupled-oscillator models with temporal intermittency.
Mechanical compartmentalization of the intestinal organoid enables crypt folding and collective cell migration
Authors: Pérez-González Carlos , Ceada Gerardo , Greco Francesco , Matejcic Marija , Gómez-González Manuel , Castro Natalia , Kale Sohan , Álvarez-Varela Adrián , Roca-Cusachs Pere , Batlle Eduard , Vignjevic Danijela Matic , Arroyo Marino , Trepat Xavier
Published: September 2020

Intestinal organoids capture essential features of the intestinal epithelium such as folding of the crypt, spatial compartmentalization of different cell types, and cellular movements from crypt to villus-like domains. Each of these processes and their coordination in time and space requires patterned physical forces that are currently unknown. Here we map the three-dimensional cell-ECM and cell-cell forces in mouse intestinal organoids grown on soft hydrogels. We show that these organoids exhibit a non-monotonic stress distribution that defines mechanical and functional compartments. The stem cell compartment pushes the ECM and folds through apical constriction, whereas the transit amplifying zone pulls the ECM and elongates through basal constriction. Tension measurements establish that the transit amplifying zone isolates mechanically the stem cell compartment and the villus-like domain. A 3D vertex model shows that the shape and force distribution of the crypt can be largely explained by cell surface tensions following the measured apical and basal actomyosin density. Finally, we show that cells are pulled out of the crypt along a gradient of increasing tension, rather than pushed by a compressive stress downstream of mitotic pressure as previously assumed. Our study unveils how patterned forces enable folding and collective migration in the intestinal crypt.
Common genetic variation in humans impactsin vitrosusceptibility to SARS-CoV-2 infection
Authors: Dobrindt Kristina , Hoagland Daisy A. , Seah Carina , Kassim Bibi , O’Shea Callan P. , Iskhakova Marina , Fernando Michael B. , Deans P.J. Michael , Powell Samuel K. , Javidfar Ben , Murphy Aleta , Peter Cyril , Møeller Rasmus , Garcia Meilin Fernandez , Kimura Masaki , Iwasawa Kentaro , Crary John , Kotton Darrell N. , Takebe Takanori , Huckins Laura M. , tenOever Benjamin R. , Akbarian Schahram , Brennand Kristen J.
Published: September 2020

The host response to SARS-CoV-2, the etiologic agent of the COVID-19 pandemic, demonstrates significant inter-individual variability. In addition to showing more disease in males, the elderly, and individuals with underlying co-morbidities, SARS-CoV-2 can seemingly render healthy individuals with profound clinical complications. We hypothesize that, in addition to viral load and host antibody repertoire, host genetic variants also impact vulnerability to infection. Here we apply human induced pluripotent stem cell (hiPSC)-based models and CRISPR-engineering to explore the host genetics of SARS-CoV-2. We demonstrate that a single nucleotide polymorphism (rs4702), common in the population at large, and located in the 3’UTR of the protease FURIN, impacts alveolar and neuron infection by SARS-CoV-2in vitro. Thus, we provide a proof-of-principle finding that common genetic variation can impact viral infection, and thus contribute to clinical heterogeneity in SARS-CoV-2. Ongoing genetic studies will help to better identify high-risk individuals, predict clinical complications, and facilitate the discovery of drugs that might treat disease.
Single-nucleus RNA-seq resolves spatiotemporal developmental trajectories in the tomato shoot apex
Authors: Tian Caihuan , Du Qingwei , Xu Mengxue , Du Fei , Jiao Yuling
Published: September 2020

Single cell transcriptomics is revolutionizing our understanding of development and response to environmental cues1–3. Recent advances in single cell RNA sequencing (scRNA-seq) technology have enabled profiling gene expression pattern of heterogenous tissues and organs at single cellular level and have been widely applied in human and animal research4,5. Nevertheless, the existence of cell walls significantly encumbered its application in plant research. Protoplasts have been applied for scRNA-seq analysis, but mostly restricted to tissues amenable for wall digestion, such as root tips6–10. However, many cell types are resistant to protoplasting, and protoplasting may yield ectopic gene expression and bias proportions of cell types. Here we demonstrate a method with minimal artifacts for high-throughput single-nucleus RNA sequencing (snRNA-Seq) that we use to profile tomato shoot apex cells. The obtained high-resolution expression atlas identifies numerous distinct cell types covering major shoot tissues and developmental stages, delineates developmental trajectories of mesophyll cells, vasculature cells, epidermal cells, and trichome cells. In addition, we identify key developmental regulators and reveal their hierarchy. Collectively, this study demonstrates the power of snRNA-seq to plant research and provides an unprecedented spatiotemporal gene expression atlas of heterogeneous shoot cells.
A network algorithm for the X chromosomal exact test for Hardy-Weinberg equilibrium with multiple alleles
Authors: Graffelman Jan , Ortoleva Leonardo
Published: September 2020

Statistical methodology for testing Hardy-Weinberg equilibrium at X chromosomal variants has recently experienced considerable development. Up to a few years ago, testing X chromosomal variants for equilibrium was basically done by applying autosomal test procedures to females only. At present, male alleles can be taken into account in asymptotic and exact test procedures for both the bi- and multiallelic case. However, current X chromosomal exact procedures for multiple alleles rely on a classical full enumeration algorithm and are computationally expensive, and in practice not feasible for more than three alleles. In this article we extend the autosomal network algorithm for exact Hardy-Weinberg testing with multiple alleles to the X chromosome, achieving considerable reduction in computation times for multiallelic variants with up to five alleles. The performance of the X-chromosomal network algorithm is assessed in a simulation study. Beyond four alleles, a permutation test is, in general, the more feasible approach. A detailed description of the algorithm is given and examples of X chromosomal indels and microsatellites are discussed.
The transcription factor ZEB1 regulates stem cell self-renewal and astroglial fate in the adult hippocampus
Authors: Gupta B , Errington AC , Brabletz S , Stemmler MP , Brabletz T , Siebzehnrubl FA
Published: September 2020

Radial glia-like (RGL) cells persist in the adult mammalian hippocampus where they give rise to new neurons and astrocytes throughout life. Many studies have investigated the process of adult neurogenesis, but factors deciding between neuronal and astroglial fate are incompletely understood. Here, we evaluate the functions of the transcription factor zinc finger E-box binding homeobox 1 (ZEB1) in adult hippocampal RGL cells using a conditional-inducible mouse model. We find that ZEB1 is necessary for self-renewal of active RGL cells as well as for astroglial lineage specification. Genetic deletion ofZeb1causes differentiation-coupled depletion of RGL cells resulting in an increase of newborn neurons at the expense of newly generated astrocytes. This is due to a shift towards symmetric cell divisions that consume the RGL cell and generate pro-neuronal progenies. We identify ZEB1 as a regulator of stem cell self-renewal and lineage specification in the adult hippocampus.
Fast and easy single-molecule pulldown assay based on agarose microbeads
Authors: Zhao Qirui , Shen Yusheng , Li Xiaofen , Tian Fang , Yu Xiaojie , Yobas Levent , Park Hyokeun , Huang Pingbo
Published: September 2020

The recently developed single-molecule pulldown (SiMPull) assay by Jain and colleagues is a highly innovative technique but its wide application is hindered by the high technical barrier and time consumption. We report an innovative, agarose microbead-based approach for SiMPull. We used commercially available, pre-surface-functionalized agarose microbeads to capture the protein of interest together with its binding partners specifically from cell extracts and observed these interactions under a microscope at the single-molecule level. Relative to the original method, microbead-based SiMPull is considerably faster, easier to use, and more reproducible and yet provides similar sensitivity and signal-to-noise ratio; specifically, with the new method, sample-preparation time is substantially decreased (from ∼10 to ∼3 h). These crucial features should facilitate wide application of powerful and versatile SiMPull in common biological and clinical laboratories. Notably, by exploiting the simplicity and ultrahigh sensitivity of microbead-based SiMPull, we used this method in the study of rare auditory hair cells for the first time.
Development of LSTM&CNN Based Hybrid Deep Learning Model to Classify Motor Imagery Tasks
Authors: Uyulan Caglar
Published: September 2020

Recent studies underline the contribution of brain-computer interface (BCI) applications to the enhancement process of the life quality of physically impaired subjects. In this context, to design an effective stroke rehabilitation or assistance system, the classification of motor imagery (MI) tasks are performed through deep learning (DL) algorithms. Although the utilization of DL in the BCI field remains relatively premature as compared to the fields related to natural language processing, object detection, etc., DL has proven its effectiveness in carrying out this task. In this paper, a hybrid method, which fuses the one-dimensional convolutional neural network (1D CNN) with the long short-term memory (LSTM), was performed for classifying four different MI tasks, i.e. left hand, right hand, tongue, and feet movements. The time representation of MI tasks is extracted through the hybrid deep learning model training after principal component analysis (PCA)-based artefact removal process. The performance criteria given in the BCI Competition IV dataset A are estimated. 10-folded Cross-validation (CV) results show that the proposed method outperforms in classifying electroencephalogram (EEG)-electrooculogram (EOG) combined motor imagery tasks compared to the state of art methods and is robust against data variations. The CNN-LSTM classification model reached 95.62 % (±1.2290742) accuracy and 0.9462 (±0.01216265) kappa value for datasets with four MI-based class validated using 10-fold CV. Also, the receiver operator characteristic (ROC) curve, the area under the ROC curve (AUC) score, and confusion matrix are evaluated for further interpretations.
Forest fire survival in young, denseBetula ermaniistands on soil scarification sites
Authors: Hayamizu Masato , Nakata Yasutaka , Torita Hiroyuki
Published: September 2020

A forest fire in a cool-temperate broad-leaved forest in northern Japan, from 26 May to 19 June 2019, provided an opportunity to examine its effects on young and dense birch (Betula ermaniiCham.) stands in soil scarification sites. To characterise post-fire responses (survival and resprouting) of birch, we set up two plots, 6 months post fire. We investigated trunk diameter at breast height and burn marks on tree trunks (scorch height and charring percentage around the tree bole) of allB. ermaniitrees in both plots. Survival and resprouting of each tree were monitored over 2 years (6 and 16 months post fire). To quantify post-fire vegetation recovery in the forest floor, we manually mapped the dominant understory plant, dwarf bamboo (i.e.Sasa kurilensis(Rupr.) Makino et Shibata), from orthomosaic images obtained by an unmanned aircraft vehicle, and estimated the recovery rate in the second year post fire. Additionally, seedlings of woody species were counted in both plots. Size-dependent survival rates of plants in both plots were similar in the first year post fire. AllB. ermaniitrees died without resprouting in the second year post fire, indicating the lethal effects of fire on young birch trees. Moreover, a high recovery rate of dwarf bamboos over 2 years in both plots and limited seedling establishment of woody plants suggest that the fire resulted in regeneration failure of young stands in the scarification sites. On the basis of these findings, we propose future management of stands in soil scarification sites post fire, considering the vulnerability of young trees and the rapid change in vegetation from young forest to dense birch cover post fire.
Global Profiling of the Lysine Crotonylome in Different Pluripotent States
Authors: Lv Yuan , Bu Chen , Meng Jin , Ward Carl , Volpe Giacomo , Hu Jieyi , Jiang Mengling , Guo Lin , Chen Jiekai , Esteban Miguel A. , Bao Xichen , Cheng Zhongyi
Published: September 2020

Pluripotent stem cells (PSCs) can be expandedin vitroin different culture conditions, resulting in a spectrum of cell states with distinct properties. Understanding how PSCs transition from one state to another, ultimately leading to lineage-specific differentiation, is important for developmental biology and regenerative medicine. Although there is significant information regarding gene expression changes controlling these transitions, less is known about post-translational modifications of proteins. Protein crotonylation is a newly discovered post-translational modification where lysine residues are modified with a crotonyl group. Here, we employed affinity purification of crotonylated peptides and liquid chromatography-tandem mass spectrometry (LC-MS/MS) to systematically profile protein crotonylation in mouse PSCs in different states including ground, metastable and primed state, as well as metastable PSCs undergoing early pluripotency exit. We successfully identified 3628 high-confidence sites in 1426 proteins. These crotonylated proteins are enriched for factors involved in functions related to pluripotency such as RNA biogenesis, central carbon metabolism and proteasome function. Moreover, we found that increasing the cellular levels of crotonyl-CoA through crotonic acid treatment promotes proteasome activity in metastable PSCs and delays their differentiation, consistent with previous observations showing that enhanced proteasomal activity helps to sustain pluripotency. Our atlas of protein crotonylation will be valuable for further studies of pluripotency regulation and may also provide insights into the role of metabolism in other cell fate transitions.
Critical Interactions Between the SARS-CoV-2 Spike Glycoprotein and the Human ACE2 Receptor
Authors: Taka Elhan , Yilmaz Sema Z. , Golcuk Mert , Kilinc Ceren , Aktas Umut , Yildiz Ahmet , Gur Mert
Published: September 2020

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects human cells upon binding of its spike (S) glycoproteins to ACE2 receptors and causes the coronavirus disease 2019 (COVID-19). Therapeutic approaches to prevent SARS-CoV-2 infection are mostly focused on blocking S-ACE2 binding, but critical residues that stabilize this interaction are not well understood. By performing all-atom molecular dynamics (MD) simulations, we identified an extended network of salt bridges, hydrophobic and electrostatic interactions, and hydrogen bonding between the receptor-binding domain (RBD) of the S protein and ACE2. Mutagenesis of these residues on the RBD was not sufficient to destabilize binding but reduced the average work to unbind the S protein from ACE2. In particular, the hydrophobic end of RBD serves as the main anchor site and unbinds last from ACE2 under force. We propose that blocking the hydrophobic surface of RBD via neutralizing antibodies could prove an effective strategy to inhibit S-ACE2 interactions.
Determining the inherent reaction-diffusion properties of actin-binding proteins in cells by incorporating genetic engineering to FRAP-based framework
Authors: Saito Takumi , Matsunaga Daiki , Matsui Tsubasa S. , Noi Kentaro , Deguchi Shinji
Published: September 2020

Proteins in cells undergo repeated association to other molecules, thereby reducing the apparent extent of their intracellular diffusion. While much effort has been made to analytically decouple these combined effects of pure diffusion and chemical reaction, it is difficult to attribute the measured quantities to the nature of specific domains of the probed proteins particularly if, as is often the case, the protein has multiple domains to independently interact with the same types but different molecules. Motivated by the common goal in cell signaling research aimed at identifying the protein domains responsible for particular intermolecular interactions, here we describe a new approach to determining the domain-level reaction and pure diffusion properties. To validate this methodology, we apply it to transgelin-2, an actin-binding protein whose intracellular dynamics remains elusive. We develop a fluorescence recovery after photobleaching (FRAP)-based framework, in which comprehensive combinations of domain-deletion mutants are created with genetic engineering, and the difference among the mutants in FRAP response is analyzed. We demonstrate that transgelin-2 in cells interacts with F-actin via two separate domains, and the chemical equilibrium constant of the interaction is determined at the individual domain levels. Its pure diffusion properties independent of the association to F-actin is also obtained. This approach requires some effort to construct the mutants, but instead enables in situ domain-level determination of the physicochemical properties, which will be useful, as specifically shown here for transgelin-2, in addressing the signaling mechanism of cellular proteins.
Overlapping activities of ELAV/Hu RNA binding proteins specify multiple neural alternative splicing programs
Authors: Lee Seungjae , Zhang Binglong , Wei Lu , Goering Raeann , Majumdar Sonali , Taliaferro J. Matthew , Lai Eric C.
Published: September 2020

ELAV/Hu factors are conserved RNA binding proteins that play diverse roles in mRNA processing and regulation. The founding member,DrosophilaElav, was recognized as a vital neural factor 35 years ago. Nevertheless, still little is known about its impacts on the transcriptome, and potential functional overlap with its paralogs. Building on our recent findings that neural-specific lengthened 3’ UTR isoforms are co-determined by ELAV/Hu factors, we address their impacts on splicing. In ectopic contexts, all three members (Elav, Fne and Rbp9) induce similar and broad changes to cassette exon and alternative last exon (ALE) splicing. Reciprocally, double mutants ofelav/fne, but notelavalone, have opposite effects on both types of mRNA processing events in the larval CNS. Accordingly, whilefnemutants are normal,fneloss strongly enhanceselavmutants with respect to neuronal differentiation. While manipulation ofDrosophilaELAV/Hu factors induces both exon skipping and inclusion, motif analysis indicates their major direct effects are to suppress cassette exon usage. Moreover, we find direct analogies in their roles in global promotion of distal ALE splicing and terminal 3’ UTR extension, since both involve local suppression of proximal polyadenylation signals via ELAV/Hu binding sites downstream of cleavage sites. Finally, we provide evidence for analogous co-implementation of distal ALE and APA lengthening programs in mammalian neurons, linked to ELAV/Hu motifs downstream of regulated polyadenylation sites. Overall, ELAV/Hu proteins orchestrate multiple conserved programs of neuronal mRNA processing by suppressing alternative exons and polyadenylation sites.
Antioxidant enriched fraction fromPueraria tuberosaalleviates ovariectomized-induced osteoporosis in rats, and inhibits growth of breast and ovarian cancer cell linesin vitro
Authors: Satpathy Swaha , Patra Arjun , Hussain Muhammad Delwar , Kazi Mohsin , Aldughaim Mohammed S , Ahirwar Bharti
Published: September 2020

Pueraria tuberosa(P. tuberosa), known as Indian Kudzu belongs to family Fabaceae and it is solicited as “Rasayana” drugs in Ayurveda. In the present study, we analyzed the efficacy an antioxidant enriched fraction (AEF) from the tuber extract ofP. tuberosaagainst menopausal osteoporosis and breast and ovarian cancer cell lines. The AEF fromP. tuberosawas identified by determining phenolic composition (total phenolic and flavonoid amount). Antioxidant property (in vitroassays) was also carried out followed by analysis of the AEF for its antiosteoporotic and anticancer potentials. Antiosteoporotic activity of AEF was investigated in ovariectomy-induced osteoporosis in rats andin vitroanticancer activity by MTT assay. Also, the GC/MS analysis of AEF was performed to determine various phytoconstituents. A docking analysis was performed to verify the interaction of bioactive molecules with estrogen receptors (ERs). Ethyl acetate fraction of the mother extract was proved as the AEF. AEF significantly improved various biomechanical and biochemical parameters in a dose dependent manner in the ovariectomized animals. AEF also controlled the increased body weight and decreased uterus weight following ovariectomy. Histopathology of femur revealed the restoration of typical bone structure and trabecular width in ovariectomized animals after AEF and raloxifene treatment. AEF also exhibitedin vitrocytotoxicity in breast (MCF-7 and MDA-MB-231) and ovarian (SKOV-3) cancer cells. Further, genistein and daidzein exhibited a high affinity towards both estrogen receptors (α and β) in docking study revealing the probable mechanism of the antiosteoporotic activity. GC/MS analysis confirmed the presence of bioactive molecules such as stigmasterol, β-sitosterol, and stigmasta-3,5-dien-7-one. The observations of this study vindicate the potency of AEF fromP. tuberosain the treatment of menopausal osteoporosis and cancer.
A comparative genomics and immunoinformatics approach to identify epitope-based peptide vaccine candidates against bovine hemoplasmosis
Authors: Quiroz-Castañeda Rosa Estela , Aguilar-Díaz Hugo , Flores-García Diana Laura , Martínez-Ocampo Fernando , Amaro-Estrada Itzel
Published: September 2020

Mycoplasma wenyoniiand ‘CandidatusMycoplasma haemobos’ have been described as major hemoplasmas that infect cattle worldwide. Currently, three bovine hemoplasma genomes are known. The aim of this work was to know the main genomic characteristics and the evolutionary relationships between hemoplasmas, as well as to provide a list of epitopes identified by immunoinformatics that could be used as vaccine candidates against bovine hemoplasmosis. So far, there is not a vaccine to prevent this disease that impact economically in cattle production around the world.

In this work, we used comparative genomics to analyze the genomes of the hemoplasmas so far reported. As a result, we confirm that ‘Ca. M haemobos’ INIFAP01 is a divergent species fromM. wenyoniiINIFAP02 andM. wenyoniiMassachusetts. Although both strains ofM. wenyoniihave genomes with similar characteristics (length, G+C content, tRNAs and position of rRNAs) they have different structures (alignment coverage and identity of 51.58 and 79.37%, respectively).

The correct genomic characterization of bovine hemoplasmas, never studied before, will allow to develop better molecular detection methods, to understand the possible pathogenic mechanisms of these bacteria and to identify epitopes sequences that could be used in the vaccine design.
Applications of spatial models to ordinal data
Authors: Xu Zhanyou , Cannon Steven B. , Beavis William D.
Published: September 2020

Models have been developed to account for heterogeneous spatial variation in field trials. These spatial models have been shown to successfully increase the quality of phenotypic data resulting in improved effectiveness of selection by plant breeders. The models were developed for continuous data types such as grain yield and plant height, but data for most traits, such as in iron deficiency chlorosis (IDC), are recorded on ordinal scales. Is it reasonable to make spatial adjustments to ordinal data by simply applying methods developed for continuous data? The objective of the research described herein is to evaluate methods for spatial adjustment on ordinal data, using soybean IDC as an example. Spatial adjustment models are classified into three different groups: group I, moving average grid adjustment; group II, geospatial autoregressive regression (SAR) models; and group III, tensor product penalized P-splines. Comparisons of eight models sampled from these three classes demonstrate that spatial adjustments depend on severity of field heterogeneity, the irregularity of the spatial patterns, and the model used. SAR models generally produce better performance metrics than other classes of models. However, none of the eight evaluated models fully removed spatial patterns indicating that there is a need to either adjust existing models or develop novel models for spatial adjustments of ordinal data collected in fields exhibiting discontinuous transitions between heterogeneous patches.
Mecamylamine inhibits seizure-like activity in CA1-CA3 hippocampus through antagonism to nicotinic receptors
Authors: Zapukhliak Olha , Netsyk Olga , Romanov Artur , Maximyuk Oleksandr , Oz Murat , Holmes Gregory L. , Krishtal Oleg , Isaev Dmytro
Published: September 2020

Cholinergic modulation of hippocampal network function is implicated in multiple behavioral and cognitive states. Activation of nicotinic and muscarinic acetylcholine receptors affects neuronal excitability, synaptic transmission and rhythmic oscillations in the hippocampus. In this work, we study the ability of the cholinergic system to sustain hippocampal epileptiform activity independently from glutamate and GABA transmission. Simultaneous CA3 and CA1 field potential recordings were obtained during the perfusion of hippocampal slices with the aCSF containing AMPA, NMDA and GABA receptor antagonists. Under these conditions, recurrent field discharges synchronous between CA3 and CA1 were recorded. Field discharges were blocked by addition of calcium-channel blocker Cd2+and disappeared in CA1 after a surgical cut between CA3 and CA1. Cholinergic antagonist mecamylamine abolished CA3-CA1 synchronous field discharges, while antagonists of α7 and α4β2 nAChRs – MLA and DhβE had no effect. Our results suggest that activation of nicotinic acetylcholine receptors is able to sustain CA3-CA1 synchronous epileptiform activity independently from AMPA NMDA and GABA transmission. In addition, mecamylamine but not α7 and α4β2 nAChRs antagonists reduce bicuculline-induced seizure-like activity. The ability of mecamylamine to decrease hippocampal network synchronization might be associated with its therapeutic effects in a wide variety of CNS disorders including addiction, depression and anxiety.
Temporal scaling inC. eleganslarval development
Authors: Filina Olga , Haagmans Rik , van Zon Jeroen S.
Published: September 2020

It is essential that correct temporal order of cellular events is maintained during animal development. During post-embryonic development, the rate of development depends on external conditions, such as food availability, diet and temperature. How timing of cellular events is impacted when the rate of development is changed at the organism-level is not known. We used a novel time-lapse microscopy approach to simultaneously measure timing of oscillatory gene expression, hypodermal stem cell divisions and cuticle shedding in individual animals, duringC. eleganslarval development from hatching to adulthood. This revealed strong variability in timing between isogenic individuals under the same conditions. However, this variability obeyed ‘temporal scaling’, meaning that events occurred at the same time when measured relative to the duration of development in each individual. We also observed pervasive changes in population-averaged timing when temperature, diet or genotype were varied, but with larval development divided in ‘epochs’ that differed in how the timing of events was impacted. Yet, these variations in timing were still explained by temporal scaling when timing was rescaled by the duration of the respective epochs in each individual. Surprisingly, timing obeyed temporal scaling even in mutants lackinglin-42/Period, presumed a core regulator of timing of larval development, that exhibited strongly delayed, heterogeneous timing and growth arrest. Timing of larval development is likely controlled by timers based on protein degradation or protein oscillations, but such mechanisms do not inherently generate temporal scaling. Hence, our observations will put strong constraints on models to explain timing of larval development.