bluuebunny/crossref_metadata_2025 huggingface dataset:
Sensitive period-regulating genetic pathways and exposure to adversity shape risk for depression
Authors: Zhu Yiwen , Wang Min-Jung , Crawford Katherine M. , Ramírez-Tapia Juan Carlos , Lussier Alexandre A. , Davis Kathryn A. , de Leeuw Christiaan , Takesian Anne E. ,   Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, Hensch Takao K. , Smoller Jordan W. , Dunn Erin C.
Published: May 2021

Animal and human studies have documented the existence of developmental windows (or sensitive periods) when experience can have lasting effects in shaping brain structure or function, behavior, and disease risk. Sensitive periods for depression likely arise through a complex interplay of genes and experience, though this possibility has not been explored. We examined the effect of sensitive period-regulating genetic pathways identified in preclinical animal studies, alone and in interaction with socioeconomic disadvantage, a common childhood adversity, on depression risk. Using a translational approach, we: (1) performed gene-set association analyses using summary data from a genome-wide association study of depression (n=807,553) to assess the effects of three gene sets (60 genes) shown in animal studies to regulate sensitive periods; (2) evaluated the developmental expression patterns of these sensitive period-regulating genes using data from BrainSpan (n=31), a transcriptional atlas of postmortem brain samples; and (3) tested gene-by-development interplay by analyzing the combined effect of common variants in sensitive period genes and timing of exposure to socioeconomic disadvantage within a population-based birth cohort (n=6254). The gene set regulating sensitive period opening associated with increased depression risk. Notably, six of the 15 genes in this set showed developmentally regulated gene-level expression. A genome-wide polygenic risk score-by-environment analysis showed socioeconomic disadvantage during ages 1-5 years were independently associated with depression risk, but no gene-by-development interactions were found. Genes involved in regulating sensitive periods may be implicated in depression vulnerability and differentially expressed across the life course, though larger studies are needed to identify developmental interplays.
Real-time genomics to track COVID-19 post-elimination border incursions in Aotearoa New Zealand
Authors: Douglas Jordan , Geoghegan Jemma L. , Hadfield James , Bouckaert Remco , Storey Matthew , Ren Xiaoyun , de Ligt Joep , French Nigel , Welch David
Published: May 2021

There have been thirteen known COVID-19 community outbreaks in Aotearoa New Zealand since the virus was first eliminated in May 2020, two of which led to stay-at-home orders being issued by health officials. These outbreaks originated at the border; via isolating returnees, airline workers, and cargo vessels. With a public health system informed by real-time viral genomic sequencing which typically had complete genomes within 12 hours after a community-based positive COVID-19 test, every outbreak was well-contained with a total of 225 community cases, resulting in three deaths. Real-time genomics were essential for establishing links between cases when epidemiological data could not, and for identifying when concurrent outbreaks had different origins. By reconstructing the viral transmission history from genomic sequences, here we recount all thirteen community outbreaks and demonstrate how genomics played a vital role in containing them.

The authors recount the role of real-time viral genomics in containing the COVID-19 community outbreaks of Aotearoa New Zealand.
BK polyomavirus (BKPyV) is a risk factor for bladder cancer through induction of APOBEC3-mediated genomic damage
Authors: Baker Simon C. , Mason Andrew S. , Slip Raphael G. , Skinner Katie T. , Macdonald Andrew , Masood Omar , Harris Reuben S. , Fenton Tim R. , Periyasamy Manikandan , Ali Simak , Southgate Jennifer
Published: May 2021

Limited understanding of bladder cancer aetiopathology hampers progress in reducing incidence. BK polyomavirus (BKPyV) is a common childhood infection that can be reactivated in the adult kidney leading to viruria. Here we used a mitotically-quiescent, differentiated, normal human urothelial in vitro model to study BKPyV infection. BKPyV infection led to significantly elevated APOBEC3A and APOBEC3B protein, increased deaminase activity and greater numbers of apurinic/apyrimidinic sites in the host urothelial genome. BKPyV Large T antigen (LT-Ag) stimulated re-entry into the cell cycle via inhibition of Retinoblastoma protein and activation of EZH2, E2F1 and FOXM1, which combined to push urothelial cells from G0 into an arrested G2 cell cycle state. The single-stranded DNA displacement loops formed during BKPyV-infection, provide a substrate for APOBEC3 enzymes where they interacted with LT-Ag. These results support reactivated BKPyV infections in adults as a risk factor for bladder cancer in immune-insufficient populations, including transplant patients and the elderly.
Phase 2 Randomized Trial of an AS03 Adjuvanted Plant-Based Virus-Like Particle Vaccine for Covid-19 in Healthy Adults, Older Adults and Adults with Comorbidities
Authors: Gobeil Philipe , Pillet Stéphane , Boulay Iohann , Séguin Annie , Makarkov Alexander , Heizer Gretchen , Bhutada Kapil , Mahmood Asif , Charland Nathalie , Trépanier Sonia , Hager Karen , Jiang-Wright Julia , Atkins Judith , Cheng Matthew P. , Vinh Donald C. , Boutet Philippe , Roman François , Van Der Most Robbert , Ceregido Maria Angeles , Dionne Marc , Tellier Guy , Gauthier Jean-Sébastien , Essink Brandon , Libman Michael , Haffizulla Jason , Fréchette André , D’Aoust Marc-André , Landry Nathalie , Ward Brian J.
Published: May 2021

The rapid spread of SARS-CoV-2 continues to impact humanity on a global scale with rising total morbidity and mortality. Despite the development of several effective vaccines, new products are needed to supply ongoing demand and the needs of specific populations. We report herein a pre-specified interim analysis of the phase 2 portion of an ongoing Phase 2/3, randomized, placebo-controlled trial of a coronavirus virus-like particle (CoVLP) vaccine candidate produced in plants that displays the SARS-CoV-2 spike glycoprotein adjuvanted with AS03 (NCT04636697). A total of 753 subjects were recruited between 25 November 2020 and 24 March 2021 into three groups: Healthy Adults (18-64 years: N=306), Older Adults (≥ 65 years: N=282) and Adults with Comorbidities (≥18 years: N=165) and randomized 5:1 to receive two intramuscular doses of either vaccine CoVLP (3.75 μg/dose + AS03) or placebo 21 days apart. This report presents safety, tolerability and immunogenicity data collected up to 21 days after the second dose. The immune outcomes presented include neutralizing antibody (NAb) titres and cellular (IFN-γ and IL-4 ELISpot) responses. In this study, CoVLP+AS03 was well-tolerated and adverse events (AE) after each dose were generally mild to moderate and transient. Solicited AEs in Older Adults and Adults with Comorbidities were generally less frequent than in Healthy Adults. CoVLP+AS03 induced seroconversion in >35% of subjects in each group after the first dose and in ∼98% of subjects 21 days after the second dose. In all treatment groups, NAb levels were ∼10-fold higher than those in a panel of convalescent sera. A significant minority (∼20%) of subjects had evidence of a pre-existing IFN-γ response to the S protein and almost all subjects in all groups (>88%) had detectable cellular responses (IFN-γ, IL-4 or both) at 21 days after the second dose. A Th1-biased response was most evident after the first dose and was still present after dose two. These data demonstrated that CoVLP+AS03 will likely be well-tolerated and highly immunogenic in adults ≥18 years of age with and without comorbidities.
Single cell analysis of RA synovial B cells reveals a dynamic spectrum of ectopic lymphoid B cell activation and hypermutation characterized by NR4A nuclear receptor expression
Authors: Meednu Nida , Rangel-Moreno Javier , Zhang Fan , Escalera-Rivera Katherine , Corsiero Elisa , Prediletto Edoardo , DiCarlo Edward , Goodman Susan , Donlin Laura T , Raychauduri Soumya , Bombardieri Michele , Pitzalis Costantino , Orange Dana E ,   Accelerating Medicines Partnership Rheumatoid Arthritis and Systemic Lupus Erythematosus (AMP RA/SLE) Network, McDavid Andrew , Anolik Jennifer H
Published: May 2021

Ectopic lymphoid structures (ELS) can develop in rheumatoid arthritis (RA) synovial tissue, but the precise pathways of B cell activation and selection are not well understood. Here, we identified a unique B cell population in the synovium characterized by co-expression of a family of orphan nuclear receptors, NR4A1 (also known as NUR77), NR4A2 (NURR1) and NR4A3 (NOR1), that is highly enriched at both early and late stages of RA. NR4A B cells are rare in healthy peripheral blood, RA blood, and SLE kidney, but share markers with blood transcriptomic signatures that peak during RA disease flare. Using combined single cell transcriptomics and B cell receptor (BCR) sequencing, we demonstrate that NR4A synovial B cells have an activated transcriptomic profile that significantly overlaps with germinal center (GC) light zone (LZ) B cells and an accrual of somatic hypermutation that correlates with loss of naïve B cell status. NR4A B cells uniquely co-express lymphotoxinβand IL6, supporting important functions in ELS promotion and pro-inflammatory cytokine production. Further, the presence of shared clones in this activated B cell state and NR4A expressing synovial plasma cells (PC) and the rapid up-regulation with BCR stimulation points toin situdifferentiation. Taken together, we identified a dynamic progression of B cell activation in RA synovial ELS, with NR4A transcription factors having an important role in antigen activation and local adaptive immune responses.

One sentence summary

B cells in the rheumatoid arthritis synovium undergo a spectrum of in situ activation, with the NR4A family of transcription factors having an important role in antigen stimulation, local adaptive immunity, and pathological B cell responses.
riboviz 2: A flexible and robust ribosome profiling data analysis and visualization workflow
Authors: Cope Alexander L. , Anderson Felicity , Favate John , Jackson Michael , Mok Amanda , Kurowska Anna , MacKenzie Emma , Shivakumar Vikram , Tilton Peter , Winterbourne Sophie M. , Xue Siyin , Kavoussanakis Kostas , Lareau Liana F. , Shah Premal , Wallace Edward W.J.
Published: May 2021

Motivation

Ribosome profiling, or Ribo-seq, is the state of the art method for quantifying protein synthesis in living cells. Computational analysis of Ribo-seq data remains challenging due to the complexity of the procedure, as well as variations introduced for specific organisms or specialized analyses. Many bioinformatic pipelines have been developed, but these pipelines have key limitations in terms of functionality or usability.

Results

We present riboviz 2, an updated riboviz package, for the comprehensive transcript-centric analysis and visualization of Ribo-seq data. riboviz 2 includes an analysis workflow built on the Nextflow workflow management system, combining freely available software with custom code. The package is extensively documented and provides example configuration files for organisms spanning the domains of life. riboviz 2 is distinguished by clear separation of concerns between annotation and analysis: prior to a run, the user chooses a transcriptome in FASTA format, paired with annotation for the CDS locations in GFF3 format. The user is empowered to choose the relevant transcriptome for their biological question, or to run alternative analyses that address distinct questions. riboviz 2 has been extensively tested on various library preparation strategies, including multiplexed samples. riboviz 2 is flexible and uses open, documented file formats, allowing users to integrate new analyses with the pipeline.

Availability

riboviz 2 is freely available at github.com/riboviz/riboviz.

Supplementary information
Ranking Reprogramming Factors for Directed Differentiation
Authors: Hammelman Jennifer , Patel Tulsi , Closser Michael , Wichterle Hynek , Gifford David
Published: May 2021

Transcription factor over-expression is a proven method for reprogramming cells to a desired cell type for regenerative medicine and therapeutic discovery. However, a general method for the identification of reprogramming factors to create an arbitrary cell type is an open problem. We examine the success rate of methods and data for directed differentiation by testing the ability of nine computational methods (CellNet, GarNet, EBSeq, AME, DREME, HOMER, KMAC, diffTF, and DeepAccess) to correctly discover and rank candidate factors for eight target cell types with known reprogramming solutions. We compare methods that utilize gene expression, biological networks, and chromatin accessibility data to identify eight sets of known reprogramming factors and comprehensively test parameter and pre-processing of input data to optimize performance of these methods. We find the best factor identification methods can identify an average of 50-60% of reprogramming factors within the top 10 candidates, and methods that use chromatin accessibility perform the best. Among the chromatin accessibility methods, complex methods DeepAccess and diffTF are more likely to consistently correctly rank the significance of transcription factor candidates within reprogramming protocols for differentiation. We provide evidence that AME and DeepAccess are optimal methods for transcription factor recovery and ranking which will allow for systematic prioritization of transcription factor candidates to aid in the design of novel reprogramming protocols.
Visual Comparison of Phylogenetic Trees Through iPhyloC, a New Interactive Web-based Framework
Authors: Hammoud Muhsen , Santos Charles Morphy D. , Gois João Paulo
Published: May 2021

Current side-by-side phylogenetic trees comparison frameworks face two issues: (1) accepting binary trees as input, and (2) assuming input trees having identical or highly overlapping taxa. We present a task abstraction of the problem of side-by-side comparison of two phylogenetic trees and propose a set-based measure for detailed structural comparison between two phylogenetic trees, which can be non-binary and not highly overlapping. iPhyloC is an interactive web-based framework including automatic identification of the common taxa in both trees, comparing input trees in several modes, intuitive design, high usability, scalability to large trees, and cross-platform support. iPhyloC was tested in hypothetical and real biological examples.
SENIES: DNA Shape Enhanced Two-layer Deep Learning Predictor for the Identification of Enhancers and Their Strength
Authors: Li Ye , Kong Fanhui , Cui Hui , Li Chunquan , Ma Jiquan
Published: May 2021

The identification of enhancers has always been an important task in bioinformatics owing to their major role in regulating gene expression. For this reason, many computational algorithms devoted to enhancer identification have been put forward over the years. To boost the performance of their methods, more features are extracted from the single DNA sequences and integrated to develop an ensemble classifier. Nevertheless, the sequence-derived features used in previous studies can hardly provide the 3D structure information of DNA sequences, which is regarded as an important factor affecting the binding preferences of transcription factors to regulatory elements like enhancers. Given that, we here propose SENIES, a DNA shape enhanced deep learning predictor, for the identification of enhancers and their strength. The predictor consists of two layers where the first layer is for enhancer and non-enhancer identification, and the second layer is for predicting the strength of enhancers. Besides utilizing two common sequence-derived features (i.e. one-hot and k-mer) as input, it introduces DNA shape for describing the 3D structures of DNA sequences. Performance comparison with state-of-the-art methods conducted on the same datasets demonstrates the effectiveness and robustness of our method. The code implementation of our predictor is publicly available at https://github.com/hlju-liye/SENIES.
A contraction-reaction-diffusion model for circular pattern formation in embryogenesis
Authors: Zhao Tiankai , Sun Yubing , Li Xin , Baghaee Mehdi , Wang Yuenan , Yuan Hongyan
Published: May 2021

Reaction-diffusion models have been widely used to elucidate pattern formation in developmental biology. More recently, they have also been applied in modeling cell fate patterning that mimic early-stage human development events utilizing geometrically confined pluripotent stem cells. However, the traditional reaction-diffusion equations could not satisfactorily explain the concentric ring distributions of various cell types, as they do not yield circular patterns even for circular domains. In previous mathematical models that yield ring patterns, certain conditions that lack biophysical understandings had been considered in the reaction-diffusion models. Here we hypothesize that the circular patterns are the results of the coupling of the mechanobiological factors with the traditional reaction-diffusion model. We propose two types of coupling scenarios: tissue tension-dependent diffusion flux and traction stress-dependent activation of signaling molecules. By coupling reaction-diffusion equations with the elasticity equations, we demonstrate computationally that the contraction-reaction-diffusion model can naturally yield the circular patterns.
Large-scale digital traces of university students show that morning classes are bad for attendance, sleep, and academic performance
Authors: Yeo Sing Chen , Lai Clin K.Y. , Tan Jacinda , Lim Samantha , Chandramoghan Yuvan , Gooley Joshua J.
Published: May 2021

Attending classes and sleeping well are important for students’ academic success. However, early classes might impede learning by contributing to absenteeism and insufficient sleep. We used big datasets collected passively from university students to test the hypothesis that morning classes are associated with poorer attendance, shorter sleep, and lower grades. Wi-Fi connection data were used to estimate attendance rates of 24,678 students enrolled in lecture courses with start times ranging from 08:00 to 16:00. Students’ interactions with the university’s Learning Management System (LMS) were used to estimate nocturnal sleep opportunities by compiling 17.4 million logins from 39,458 students with data sorted by students’ first class of the day. Objective sleep behavior was assessed in 181 students who took part in a 6-week actigraphy study. We found that Wi-Fi confirmed attendance was about 15 percentage points lower in students taking classes at 08:00 compared with later start times. Actigraphy data revealed that students frequently slept past the start of morning classes. LMS and actigraphy data showed that nocturnal sleep opportunities and total sleep time decreased with earlier class start times due to students waking up earlier. Analyses of grades in 27,281 students showed that having morning classes on more days of the week resulted in a lower grade point average. These findings suggest cumulative negative effects of morning classes on learning. Early morning classes force many students to decide to either sleep more and skip class, or sleep less to attend class. Therefore, universities should avoid scheduling early morning classes.

Significance Statement

We show that morning classes are associated with lower attendance, shorter nocturnal sleep, and lower grade point average in university students. Scalable methods for measuring attendance and sleep were developed using students’ Wi-Fi connection data and interactions with the Learning Management System. Students had lower attendance rates and frequently slept past the start of early morning classes. However, students still lost about an hour of sleep on average when they had early morning classes due to waking up earlier than usual. Students who had morning classes on more days of the week had a lower grade point average. Our results suggest cumulative negative effects of morning classes on students’ academic performance. Universities should avoid scheduling early morning classes.
A multiple-causal-gene-cluster model underlying GWAS signals of Alzheimer’s disease
Authors: Xu Min , Liu Qianjin , Bi Rui , Li Yu , Zeng Chunhua , Yan Zhongjiang , Zheng Quanzhen , Li Xiao , Sun Chunli , Ye Maosen , Luo Xiong-Jian , Li Ming , Zhang Deng-Feng , Yao Yong-Gang
Published: May 2021

Genome-wide association studies (GWASs) have identified dozens of genetic susceptibility loci for Alzheimer’s disease (AD). Nevertheless, the underlying causal variants and biological mechanisms remain elusive. Here, we systematically integrated AD GWAS with comprehensive multi-omics data, and distilled 304 potentially functional variants and 166 causal genes from 49 loci. Intriguingly, we found that most of AD GWAS loci contain multiple functional variants and causal genes. In vitro assays showed that one functional variant regulated multiple genes in the 11p11.2 locus (the CELF1/SPI1 locus) and alteration of these target genes contributed to AD-related molecular processes, supporting the co-existence of multiple functional variants and AD-relevant causal genes within a single locus. We thus proposed a multiple-causal-gene-cluster model that co-dysregulation of a cluster of genes within a single GWAS loci individually or synergistically contribute to AD development. This model provides a novel insight into the biological mechanisms underlying the GWAS loci of complex traits.
The quality of dissolved organic matter shapes the biogeography of the active bathypelagic microbiome
Authors: Sebastián Marta , Sánchez Pablo , Salazar Guillem , Álvarez-Salgado Xosé A. , Reche Isabel , Morán Xosé Anxelu G , Sala M Montserrat , Duarte Carlos M. , Acinas Silvia G. , Gasol Josep M.
Published: May 2021

The bathypelagic ocean (1000-4000 m depth) is the largest aquatic biome on Earth but it is still largely unexplored. Due to its prevalent low dissolved organic carbon concentrations, most of the prokaryotic metabolic activity is assumed to be associated to particles. The role of free-living prokaryotes has thus been mostly ignored, except that of some chemolithoautotrophic lineages. Here we used a global bathypelagic survey of size-fractionated metagenomic and 16S (genes and transcripts) data and performed a differential abundance analysis to explore the functional traits of the different prokaryotic life-strategies, their contribution to the active microbiome, and the role that the quality of the dissolved organic matter (DOM) plays in driving this contribution. We found that free-living prokaryotes have limited capacity to uplift their metabolism in response to environmental changes and display comparatively lower growth rates than particle associated prokaryotes, but are responsible for the synthesis of vitamins in the bathypelagic. Furthermore, their contribution to the active prokaryotic microbiome increased towards waters depleted of labile DOM, which represented a large fraction of the tropical and subtropical ocean sampled stations. This points to a relevant yet overlooked role of free-living prokaryotes in DOM cycling in the vast bathypelagic desert.
OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis
Authors: Baltoumas Fotis A. , Zafeiropoulou Sofia , Karatzas Evangelos , Paragkamian Savvas , Thanati Foteini , Iliopoulos Ioannis , Eliopoulos Aristides G. , Schneider Reinhard , Jensen Lars Juhl , Pafilis Evangelos , Pavlopoulos Georgios A.
Published: May 2021

Extracting and processing information from documents is of great importance as lots of experimental results and findings are stored in local files. Therefore, extracting and analysing biomedical terms from such files in an automated way is absolutely necessary. In this article, we present OnTheFly2.0, a web application for extracting biomedical entities from individual files such as plain texts, Office documents, PDF files or images. OnTheFly2.0can generate informative summaries in popup windows containing knowledge related to the identified terms along with links to various databases. It uses the EXTRACT tagging service to perform Named Entity Recognition (NER) for genes/proteins, chemical compounds, organisms, tissues, environments, diseases, phenotypes and Gene Ontology terms. Multiple files can be analysed, whereas identified terms such as proteins or genes can be explored through functional enrichment analysis or be associated with diseases and PubMed entries. Finally, protein-protein and protein-chemical networks can be generated with the use of STRING and STITCH services. To demonstrate its capacity for knowledge discovery, we interrogated published meta-analyses of clinical biomarkers of severe COVID-19 and uncovered inflammatory and senescence pathways that impact disease pathogenesis. OnTheFly2.0currently supports 197 species and is available athttp://onthefly.pavlopouloslab.info.
Nitric oxide signalling underlies salicylate-induced increases in neuronal firing in the inferior colliculus: a central mechanism of tinnitus?
Authors: Olthof Bas MJ , Lyzwa Dominika , Gartside Sarah E , Rees Adrian
Published: May 2021

The tinnitus-inducing agent salicylate reduces cochlear output but causes hyperactivity in higher auditory centres, including the inferior colliculus (the auditory midbrain). Using multi-electrode recording in anaesthetised guinea pigs (Cavia porcellus), we addressed the hypothesis that salicylate-induced hyperactivity in the inferior colliculus involves nitric oxide signalling secondary to increased ascending excitatory input.

In the inferior colliculus, systemic salicylate (200 mg/kg i.p., 0 h) markedly increased spontaneous and sound-driven neuronal firing (3-6 h post drug) with both onset and sustained responses to pure tones being massively increased. Reverse microdialysis of increasing concentrations of salicylate directly into the inferior colliculus (100 µM-10 mM, from 0 h) failed to mimic systemic salicylate. In contrast, it caused a small, transient, increase in sound-driven firing (1 h), followed by a larger sustained decrease in both spontaneous and sound-driven firing (2-5 h). When salicylate was given systemically, reverse microdialysis of the neuronal nitric oxide synthase inhibitor L-methyl arginine into the inferior colliculus (500 mM, 2-6 h) completely blocked the salicylate-induced increase in spontaneous and sound-driven neuronal firing.

Our data indicate that systemic salicylate induces neuronal hyperactivity in the auditory midbrain via a mechanism outside the inferior colliculus, presumably upstream in the auditory pathway; and that the mechanism is ultimately dependent on nitric oxide signalling within the inferior colliculus.

Given that nitric oxide is known to mediate NMDA receptor signalling in the inferior colliculus, we propose that salicylate activates an ascending glutamatergic input to the inferior colliculus and that this is an important mechanism underlying salicylate-induced tinnitus.

Graphical abstract

Tinnitus is associated with increased activity in the central auditory pathway, an effect replicated by high dose sodium salicylate. Here we show that salicylate-induced increases in neuronal activity in the auditory midbrain are mediated by nitric oxide signalling within this region. Nitric oxide is a key mediator of neuronal responses to NMDA receptor stimulation in this region. Our data support the hypothesis that tinnitus is mediated by increased ascending glutamatergic input to the auditory midbrain.
Effect of charge on protein preferred orientation at the air–water interface in cryo-electron microscopy
Authors: Li Bufan , Zhu Dongjie , Shi Huigang , Zhang Xinzheng
Published: May 2021

The air–water interface (AWI) tends to absorb proteins and frequently causes preferred orientation problems in cryo-electron microscopy (cryo-EM). Here, we examined cryo-EM data from protein samples frozen with different detergents and found that both anionic and cationic detergents promoted binding of proteins to the AWI. By contrast, nonionic and zwitterionic detergents tended to prevent proteins from attaching to the AWI. This ability was positively associated with the critical micelle concentration of the detergent. The protein orientation distributions with different anionic detergents were similar and resembled that obtained without detergent. By contrast, cationic detergents gave distinct orientation distributions. The AWI is negatively charged and the absorption of cationic detergents to the AWI alters its charge. Our results indicates that proteins absorb to charged interface and the negative charge of the AWI plays an important role in absorbing proteins in the conventional cryo-EM sample preparation. According to these findings, a new method was developed to modify the charge distribution of the AWI by adding a very low concentration of anionic detergent. Using this method, the protein particles exhibited a more evenly distributed orientations and still absorbed to the AWI enabling them embedding in a thin layer of ice, which will benefit the cryo-EM structural determination.
Ultra-Rapid Somatic Variant Detection via Real-Time Threshold Sequencing
Authors: Wadden Jack , Newell Brandon , Bugbee Joshua , Dickson Robert P. , Koschmann Carl , Blaauw David , Narayanasamy Satish , Das Reetuparna
Published: May 2021

Molecular markers are becoming increasingly important for cancer diagnosis, proper clinical trial enrollment, and even surgical decision making, motivating ultra-rapid, intraoperative variant detection. Sequencing-based detection is considered the gold standard approach, but typically takes hours to perform. In this work, we present Threshold Sequencing, a methodology for designing protocols for targeted variant detection on real-time sequencers with a minimal time to result. Threshold Sequencing analytically identifies a time-optimal threshold to stop target amplification and begin sequencing. To further reduce diagnostic time, we explore targeted Loop-mediated Isothermal Amplification (LAMP) and design a LAMP-specific bioinformatics tool—LAMPrey—to process sequenced LAMP product. LAMPrey’s concatemer aware alignment algorithm is designed to maximize recovery of diagnostically relevant information leading to a more rapid detection versus standard read alignment approaches. Coupled with time-optimized DNA extraction and library preparation, we demonstrate confirmation of a hot-spot mutation (250x support) from tumor tissue in less than 30 minutes.
Waveform detection by deep learning reveals multi-area spindles that are selectively modulated by memory load
Authors: Mofrad Maryam H. , Gilmore Greydon , Mirsattari Seyed M. , Burneo Jorge G. , Steven David A. , Khan Ali , Marti Ana Suller , Muller Lyle
Published: May 2021

Sleep is generally considered to be a state of large-scale synchrony across thalamus and neocortex; however, recent work has challenged this idea by reporting isolated sleep rhythms such as slow-oscillations and spindles. What is the spatial scale of sleep rhythms? To answer this question, we adapted deep learning algorithms initially developed for detecting earthquakes and gravitational waves in high-noise settings for analysis of neural recordings in sleep. We then studied sleep spindles in non-human primate ECoG, human EEG, and clinical intracranial recordings (iEEG) in the human. We find a widespread extent of spindles, which has direct implications for the spatiotemporal dynamics we have previously studied in spindle oscillations (Muller et al., 2016) and the distribution of memory engrams in the primate.
Dissection of N-, O- and glycosphingolipid glycosylation changes in PaTu-S pancreatic adenocarcinoma cells upon TGF-β challenge
Authors: Zhang Jing , Zhang Zejian , Holst Stephanie , Blöchl Constantin , Madunic Katarina , Wuhrer Manfred , ten Dijke Peter , Zhang Tao
Published: May 2021

Pancreatic ductal adenocarcinoma (PDAC) is characterized by poor prognosis and high mortality. Transforming growth factor-β (TGF-β) plays a key role in tumor progression, which is often associated with aberrant glycosylation. How PDAC cells respond to TGF-β and the role of glycosylation therein is, however, not well known. Here, we investigated the TGF-β-mediated response and glycosylation changes in SMAD4-deficient PaTu-8955S (PaTu-S) cell line. PaTu-S cells responded to TGF-β by upregulating SMAD2 phosphorylation and target gene expression. TGF-β induced expression of the mesenchymal marker N-cadherin, but did not significantly affect epithelial marker E-cadherin expression. The differences of N-glycans, O-glycans and glycosphingolipid (GSL) glycans in PaTu-S cells with TGF-β stimulation were examined. TGF-β treatment primarily induced N-glycome aberrations involving elevated levels of branching, core fucosylation, and sialylation in PaTu-S cells, in line with TGF-β-induced changes in the expression of glycosylation-related genes. In addition, we observed differences in O- and GSL-glycosylation profiles after TGF-β treatment, including lower levels of sialylated Tn antigen, and neoexpression of globosides. Furthermore, SOX4 expression was upregulated upon TGF-β stimulation, and its depletion blocked the TGF-β-induced N-glycomic changes. Thus, our study provides a mechanism by which TGF-β-induced N-glycosylation changes in SOX4 dependent and SMAD4 independent manner in pancreatic cancer cells. Our results open up avenues to study the relevance of glycosylation in TGF-β signaling in SMAD4 inactivated PDAC.
Processing of Pain by the Developing Brain: Evidence of Differences Between Adolescent and Adult Females
Authors: Tong Han , Maloney Thomas C. , Payne Michael F. , King Christopher D. , Ting Tracy V. , Kashikar-Zuck Susmita , Coghill Robert C. , López-Solà Marina
Published: May 2021

Adolescence is a sensitive period for both brain development and the emergence of chronic pain particularly in females. However, the brain mechanisms supporting pain perception during adolescence remain unclear. This study compares perceptual and brain responses to pain in female adolescents and adults to characterize pain processing in the developing brain. Thirty adolescent (ages 13-17) and thirty adult (ages 35-55) females underwent a functional MRI scan involving acute experimental pain. Participants received 12 ten-second noxious pressure stimuli which were applied to the left thumbnail at 2.5 and 4 kg/cm2, and rated pain intensity and unpleasantness on a visual analogue scale. We found a significant group-by-stimulus intensity interaction on pain ratings. Compared to adults, adolescents reported greater pain intensity and unpleasantness in response to 2.5 kg/cm2, but not 4 kg/cm2. Adolescents showed greater medial-lateral prefrontal cortex (PFC) and supramarginal gyrus activation in response to 2.5 kg/cm2, and greater medial PFC and rostral anterior cingulate responses to 4 kg/cm2. Adolescents showed augmented pain-evoked responses in the Neurologic Pain Signature and greater activation in the default mode (DMN) and ventral attention (VAN) networks. Also, the amygdala and associated regions played a stronger role in predicting pain intensity in adolescents, and activity in DMN and VAN regions more strongly mediated the relationship between stimulus intensity and pain ratings. This study provides the first evidence of augmented pain-evoked brain responses in healthy female adolescents involving regions important for nociceptive, affective and cognitive processing, in line with their augmented sensitivity to low-intensity noxious stimuli.
Septin function tunes lipid kinase activity and phosphatidylinositol 4,5 bisphosphate turnover during G-protein coupled PLC signaling in vivo
Authors: Kumari Aastha , Ghosh Avishek , Kolay Sourav , Raghu Padinjat
Published: May 2021

The hydrolysis of phosphatidylinositol 4,5− bisphosphate [PI(4,5)P2] at the plasma membrane by receptor activated phospholipase C (PLC) activity is a conserved mechanism of signal transduction. Given the low abundance of PI(4,5)P2 at the plasma membrane, its hydrolysis needs to be coupled to lipid resynthesis to ensure continued PLC activity during receptor activation. However, the mechanism by which PI(4,5)P2 depletion during signalling is coupled to its resynthesis remains unknown. PI(4,5)P2 synthesis is catalyzed by lipid kinase activity and the phosphorylation of phosphatidylinositol 4 phosphate (PI4P) by phosphatidylinositol 4 phosphate 5 kinase (PIP5K) is the final step in this process. In Drosophila photoreceptors, sensory transduction of photon absorption is transduced into PLC activity leading to an electrical response to light. During this process, PI(4,5)P2 is resynthesized by a PIP5K activity but the mechanism by which the activity of this enzyme is coupled to PLC signalling is not known. In this study, we identify a unique protein isoform of dPIP5K, dPIP5KL that is both necessary and sufficient to mediate PI(4,5)P2 synthesis during phototransduction. The activity of dPIP5KLin vitro is enhanced by depletion of PNUT, a non-redundant subunit of the septin family of GTP binding proteins and in vivo, depletion of pnut rescues the effect of dPIP5KL depletion on the light response and PI(4,5)P2 resynthesis during PLC signalling. Lastly we find that depletion of Septin Interacting Protein 1 (Sip1), previously shown to bind PNUT, phenocopies the effect of dPIP5KL depletion in vivo. Thus, our work defines a septin 7 and Sip1 mediated mechanism through which PIP5K activity is coupled to ongoing PLC mediated PI(4,5)P2 depletion.
Loss of imprinting of the Igf2-H19 ICR1 enhances placental endocrine capacity via sex-specific alterations in signalling pathways in the mouse
Authors: Aykroyd Bethany R. L. , Tunster Simon J. , Sferruzzi-Perri Amanda N.
Published: May 2021

Imprinting control region (ICR1) controls the expression of the Igf2 and H19 genes in a parent-of-origin specific manner. Appropriate expression of the Igf2-H19 locus is fundamental for normal fetal development, yet the importance of ICR1 in the placental production of hormones that promote maternal nutrient allocation to the fetus is unknown. To address this, we used a novel mouse model to selectively delete ICR1 in the endocrine junctional zone (Jz) of the mouse placenta (Jz-ΔICR1). The Jz-ΔICR1 mice exhibit increased Igf2 and decreased H19 expression specifically in the Jz. This was accompanied by an expansion of Jz endocrine cell types due to enhanced rates of proliferation and increased expression of pregnancy-specific glycoprotein 23 in the placenta of both fetal sexes. However, changes in the endocrine phenotype of the placenta were related sexually-dimorphic alterations to the abundance of IGF2 receptors and downstream signalling pathways (PI3K-AKT and MAPK). There was no effect of Jz-ΔICR1 on the expression of targets of the H19 embedded miR-675 or on fetal weight. Our results demonstrate that ICR1 controls placental endocrine capacity via sex-dependant changes in signalling.

Summary statement

Imprinting at Igf2-H19 ICR1 regulates endocrine cell formation and function via sexually-dimorphic changes in PI3K-AKT and MAPK signalling in the mouse.
Pepsickle rapidly and accurately predicts proteasomal cleavage sites for improved neoantigen identification
Authors: Weeder Benjamin R. , Wood Mary A. , Li Ellysia , Nellore Abhinav , Thompson Reid F.
Published: May 2021

Proteasomal cleavage is a key component in protein turnover, as well as antigen presentation and subsequent immune response. Herein we present pepsickle, an open-source tool for proteasomal cleavage prediction with better in vivo prediction performance (AUC) and computational speed than current models available in the field, and with the ability to predict sites based on both constitutive and immunoproteasome profiles. Post-hoc filtering of predicted patient neoepitopes using pepsickle significantly enriches for immune-responsive epitopes and may represent a significant opportunity to improve current epitope prediction and vaccine development pipelines.
Structure-Function Relationships of the Vertebral Endplate
Authors: Wu Yuanqiao , Loaiza Johnfredy , Banerji Rohin , Blouin Olivia , Morgan Elise F.
Published: May 2021

Background

Although deformation and fracture of the vertebral endplate have been implicated in spinal conditions such as vertebral fracture and disc degeneration, few biomechanical studies of this structure are available. The goal of this study was to quantify the mechanical behavior of the vertebral endplate.

Methods

Eight-five rectangular specimens were dissected from the superior and/or inferior central endplates of human lumbar spine segments L1-L4. Micro-computed tomography (μCT) imaging, four-point-bend testing, and ashing were performed to quantify the apparent elastic modulus and yield stress (modulus and yield stress, respectively, of the porous vertebral endplate), tissue yield stress (yield stress of the tissue of the vertebral endplate, excluding pores), ultimate strain, fracture strain, bone volume fraction (BV/TV), bone mineral density (BMD), and various measures of tissue density and composition (tissue mineral density, ash fraction, and ash density). Regression was used to assess the dependence of mechanical properties on density and composition.

Results

Wide variations in elastic and failure properties, and in density and tissue composition, were observed. BMD and BV/TV were good predictors of many of the apparent-level mechanical properties, including modulus, yield stress, and in the case of the inferior vertebral endplate, failure strains. Similar values of the mechanical properties were noted between superior and inferior vertebral endplates. In contrast to the dependence of apparent stiffness and strength on BMD and BV/TV, none of the mechanical properties depended on any of the tissue-level density measurements.

Conclusion

The dependence of many of the mechanical properties of the vertebral endplate on BV/TV and BMD suggests possibilities for non-invasive assessment of how this region of the spine behaves during habitual and injurious loading. Further study of the non-mineral components of the endplate tissue is required to understand how the composition of this tissue may influence the overall mechanical behavior of the vertebral endplate.
Herpetologists’ Conservation Research Focus Drives Their Intentions to Participate in Future Public Engagement
Authors: Hecht Kirsten A , Stofer Kathryn A. , Monroe Martha , Klarenberg Geraldine , Nickerson Max A.
Published: May 2021

Public Engagement with Science (PES) is a popular topic in the science community due to general concerns about public support for science, attitudes toward science, and changes in scientific funding requirements. PES may be especially relevant in conservation disciplines as the public plays an important role in conservation practice. Herpetofauna specifically stand to benefit, as PES activities can help improve attitudes and conservation behavior of participants toward uncharismatic species. We assessed the current scope of herpetologists’ PES activities and investigated factors associated with their participation in PES. We used a closed-ended question survey distributed via the listservs of four American herpetological organizations. Herpetologists’ intentions to engage at least 10 hours in the next 12 months significantly differed between herpetologists with high and low conservation research focuses, but hours of engagement in the past 12 months was not significantly different among these groups. Despite most responding herpetologists having limited formal training, time, resources, and institutional support, many participated in a variety of PES activities, often utilizing partnerships and their own resources. Sampled herpetologists rarely evaluated their PES activities or considered publishing about their engagement activities. Some respondents expressed unease with the idea of message framing. Respondents were interested in evaluation training and providing accessible opportunities, and grant funds were the most likely interventions to increase herpetologists’ participation in PES. These results provide reference data and insight into the public engagement practices and needs of practicing herpetologists and conservation scientists.

Author statement

We informed participants of their rights and protections as approved by University of Florida IRB201800258. None of the authors have conflicts of interest related to this research. Funding for the research was provided by a Roger Conant Grant from the Society for the Study of Amphibians and Reptiles (SSAR). SSAR had no role in interpretation of data, the writing of the report, or the decision to submit the article for publication.
Soil chemistry determines whether defensive plant secondary metabolites promote or suppress herbivore growth
Authors: Hu Lingfei , Wu Zhenwei , Robert Christelle A.M. , Ouyang Xiao , Züst Tobias , Mestrot Adrien , Xu Jianming , Erb Matthias
Published: May 2021

Specialized metabolites mediate important interactions in both the rhizosphere and the phyllosphere. How this compartmentalized multifunctionality influences plant-environment interactions is unknown. Here, we investigated how the dual role of maize benzoxazinoids as leaf defenses and root siderophores shapes the interaction between maize and a major global insect pest, the fall armyworm. We find that benzoxazinoids suppress fall armyworm growth in soils with low bioavailable iron but enhance growth in soils with higher bioavailable iron. Manipulation experiments confirm that benzoxazinoids suppress herbivore growth under iron-deficient conditions but enhance herbivore growth when iron is present in its free form. This reversal of the protective effect of benzoxazinoids is not associated with major changes in plant primary metabolism. Plant defense activation is modulated by the interplay between soil iron and benzoxazinoids but does not explain fall armyworm performance. Instead, increased iron supply to the fall armyworm by benzoxazinoids in the presence of free iron enhances larval performance. This work identifies soil chemistry as a decisive factor for the impact of plant secondary metabolites on herbivore growth. It also demonstrates how the multifunctionality of plant secondary metabolites drives interactions between abiotic and biotic factors, with major consequences for plant health in variable environments.