bluuebunny/crossref_metadata_2025 huggingface dataset:
Measuring brain beats: cardiac-aligned fast fMRI signals
Authors: Hermes Dora , Wu Hua , Kerr Adam B. , Wandell Brian
Published: February 2022

Blood and cerebrospinal fluid (CSF) pulse and flow throughout the brain, driven by the cardiac cycle. These fluid dynamics, which are essential to healthy brain function, are characterized by several noninvasive magnetic resonance imaging (MRI) methods. Recent developments in fast MRI, specifically simultaneous multislice (SMS) acquisition methods, provide a new opportunity to rapidly and broadly assess cardiac-driven flow, including CSF spaces, surface vessels and parenchymal vessels. We use these techniques to assess blood and CSF flow dynamics in brief (3.5 minute) scans on a conventional 3T MRI scanner. Cardiac pulses are measured with a photoplethysmograph (PPG) on the index finger, along with fMRI signals in the brain. We retrospectively analyze the fMRI signals gated to the heart beat. Highly reliable cardiac-gated fMRI temporal signals are observed in CSF and blood on the timescale of one heartbeat (test-retest reliability within subjects R2>0.50). Cardiac pulsations with a local minimum following systole are observed in blood vessels, with earlier extrema in the carotid and basilar arteries and in branches of the anterior, posterior and middle cerebral arteries and extrema ∼200 ms later in the superior sagittal, transverse and straight sinuses. CSF spaces in the ventricles and subarachnoid space showed cardiac pulsations with a local maximum following systole instead. Similar responses are observed, with less temporal detail, in slower resting state scans with slice timing retrospectively aligned to the cardiac pulse in the same manner. The SMS measurements rapidly, noninvasively and reliably sample brain-wide fMRI signal pulsations aligned to the heartbeat. The measurements estimate the amplitude and phase of cardiac driven fMRI pulsations in the CSF relative to those in the arteries, which is thought to be an estimate of the local intracranial impedance. Cardiac aligned fMRI signals can provide new insights about fluid dynamics or diagnostics for diseases where these dynamics are important.
Self-organization, quality control, and preclinical studies of human iPSC-derived retinal sheets for tissue-transplantation therapy
Authors: Watari Kenji , Yamasaki Suguru , Tu Hung-Ya , Shikamura Masayuki , Kamei Tatsuya , Adachi Hideki , Tochitani Tomoaki , Kita Yasuyuki , Nakamura Aya , Ueyama Kazuki , Ono Keiichi , Morinaga Chikako , Matsuyama Take , Sho Junki , Nakamura Miyuki , Fujiwara Masayo , Hori Yoriko , Tanabe Anna , Hirai Rina , Terai Orie , Ohno Osamu , Ohara Hidetaka , Hayama Tetsuya , Ikeda Atsushi , Nukaya Daiki , Matsushita Keizo , Takahashi Masayo , Kishino Akiyoshi , Kimura Toru , Kawamata Shin , Mandai Michiko , Kuwahara Atsushi
Published: February 2022

Three-dimensional retinal organoids (3D-retinas) are a promising graft source for transplantation therapy. We previously developed self-organizing culture for 3D-retina generation from human pluripotent stem cells (hPSCs). Here we present a quality control method and preclinical studies for tissue-sheet transplantation. Self-organizing hPSCs differentiated into both retinal and off-target tissues. Gene expression analyses identified the major off-target tissues as eye-related, cortex-like, and spinal cord-like tissues. For quality control, we developed a qPCR-based test in which each hPSC-derived neuroepithelium was dissected into two tissue-sheets: inner-central sheet for transplantation and outer-peripheral sheet for qPCR to ensure retinal tissue selection. During qPCR, tissue-sheets were stored for 3–4 days using a newly developed preservation method. In a rat tumorigenicity study, no transplant-related adverse events were observed. In retinal degeneration model rats, retinal transplants differentiated into mature photoreceptors and exhibited light responses in electrophysiology assays. These results demonstrate our rationale toward self-organizing retinal sheet transplantation therapy.
Resolving drug selection and migration in an inbred South American Plasmodium falciparum population with identity-by-descent analysis
Authors: Carrasquilla Manuela , Early Angela M , Taylor Aimee R , Knudson Angélica , Echeverry Diego F , Anderson Timothy JC , Mancilla Elvira , Aponte Samanda , Cárdenas Pablo , Buckee Caroline O , Rayner Julian C , Sáenz Fabián E , Neafsey Daniel E , Corredor Vladimir
Published: February 2022

The human malaria parasite Plasmodium falciparum is globally widespread, but its prevalence varies significantly between and even within countries. Most population genetic studies in P. falciparum focus on regions of high transmission where parasite populations are large and genetically diverse, such as sub-Saharan Africa. Understanding population dynamics in low transmission settings, however, is of particular importance as these are often where drug resistance first evolves. Here, we use the Pacific Coast of Colombia and Ecuador as a model for understanding the population structure and evolution of Plasmodium parasites in small populations harboring low genetic diversity. The combination of low transmission and a high proportion of monoclonal infections means there are few outcrossing events and clonal lineages persist for long periods of time. Yet despite this, the population is evolutionarily labile and has successfully adapted to multiple drug regimes. Using 166 newly sequenced whole genomes, we measure relatedness between parasites, calculated as identity by descent (IBD), and find 17 distinct but highly related clonal lineages, six of which have persisted in the region for at least a decade. This inbred population structure is captured in more detail with IBD than with other common population structure analyses like PCA, ADMIXTURE, and distance-based trees. We additionally use patterns of intra-chromosomal IBD and an analysis of haplotypic variation to explore the role of recombination in spreading drug resistance mutations throughout the region. Two genes associated with chloroquine resistance, crt and aat1, show evidence of hard selective sweeps, while selection appears soft and/or incomplete at three other key resistance loci (dhps, mdr1, and dhfr). Overall, this work highlights the strength of IBD analyses for studying parasite population structure and resistance evolution in regions of low transmission, and emphasizes that drug resistance can evolve and spread in extremely small populations, as will occur in any region nearing malaria elimination.
Complete sequences of the velvet worm slime proteins reveal that slime formation is enabled by disulfide bonds and intrinsically disordered regions
Authors: Lu Yang , Sharma Bhargy , Soon Wei Long , Shi Xiangyan , Zhao Tianyun , Lim Yan Ting , Sobota Radoslaw M. , Hoon Shawn , Pilloni Giovanni , Usadi Adam , Pervushin Konstantin , Miserez Ali
Published: February 2022

The slime of velvet worms (Onychophora) is a strong and fully biodegradable protein material, which upon ejection undergoes a fast liquid-to-solid transition to ensnare prey. However, the molecular mechanisms of slime self-assembly are still not well understood, notably because the primary structures of slime proteins are yet unknown. Combining transcriptomic and proteomic studies, we have obtained the complete primary sequences of slime proteins and identified key features for slime self-assembly. The high molecular weight slime proteins contain Cys residues at the N- and C-termini that mediate the formation of multi-protein complexes via disulfide bonding. Low complexity domains in the N-termini were also identified and their propensity for liquid-liquid phase separation established, which may play a central role for slime biofabrication. Using solid-state nuclear magnetic resonance, rigid and flexible domains of the slime proteins were mapped to specific peptide domains. The complete sequencing of major slime proteins is an important step towards sustainable fabrication of polymers inspired by the velvet worm slime.
Human regulatory T-cells locally differentiate and are functionally heterogeneous within the inflamed arthritic joint
Authors: Lutter Lisanne , van der Wal M. Marlot , Brand Eelco C. , Maschmeyer Patrick , Vastert Sebastiaan , Mashreghi Mir-Farzin , van Loosdregt Jorg , van Wijk Femke
Published: February 2022

Objective

Tregs are crucial for immune regulation, and environment-driven adaptation of effector (e)Tregs is essential for local functioning. However, the extent of human Treg heterogeneity in inflammatory settings is unclear.

Methods

We combined single-cell RNA- and TCR-sequencing on Tregs derived from 4-6 patients with juvenile idiopathic arthritis (JIA) to investigate the functional heterogeneity of human synovial fluid (SF)-derived Tregs from inflamed joints. Confirmation and suppressive function of the identified Treg clusters was assessed by flow cytometry.

Results

Four Treg clusters were identified; incoming, activated eTregs with either a dominant suppressive or cytotoxic profile, and GPR56+CD161+CXCL13+ Tregs. Pseudotime analysis showed differentiation towards either classical eTreg profiles or GPR56+CD161+CXCL13+ Tregs supported by TCR data. Despite its most differentiated phenotype GPR56+CD161+CXCL13+ Tregs were shown to be suppressive. Furthermore, BATF was identified as an overarching eTreg regulator, with the novel Treg-associated regulon BHLHE40 driving differentiation towards GPR56+CD161+CXCL13+ Tregs, and JAZF1 towards classical eTregs.

Conclusion

Our study reveals a heterogeneous population of Tregs at the site of inflammation in JIA. SF Treg differentiate to a classical eTreg profile with a more dominant suppressive or cytotoxic profile that share a similar TCR repertoire, or towards GPR56+CD161+CXCL13+ Tregs with a more distinct TCR repertoire. Genes characterizing GPR56+CD161+CXCL13+ Tregs were also mirrored in other T-cell subsets in both the tumor and autoimmune setting. Finally, the identified key regulators driving SF Treg adaptation may be interesting targets for autoimmunity or tumor interventions.
ERROR MODELLED GENE EXPRESSION ANALYSIS (EMOGEA) PROVIDES A SUPERIOR OVERVIEW OF TIME COURSE RNA-SEQ MEASUREMENTS AND LOW COUNT GENE EXPRESSION
Authors: Karakach Tobias K. , Taverna Federico , Barra Jasmine
Published: February 2022

Serial RNA-seq studies of bulk samples are widespread and provide an opportunity for improved understanding of gene regulation during e.g., development or response to an incremental dose of a pharmacotherapeutic. In addition, the widely popular single cell RNA-seq (scRNA-seq) data implicitly exhibit serial characteristics because measured gene expression values recapitulate cellular transitions. Unfortunately serial RNA-seq data continue to be analyzed by methods that ignore this ordinal structure and yield results that are difficult to interpret. Here, we present Error Modelled Gene Expression Analysis (EMOGEA), a principled framework for analyzing RNA-seq data that incorporates measurement uncertainty in the analysis, while introducing a special formulation for modelling data that are acquired as a function of time or other continuous variable. By incorporating uncertainties in the analysis, EMOGEA is specifically suited for RNA-seq studies in which low-count transcripts with small fold-changes lead to significant biological effects. Such transcripts include signaling mRNAs and non-coding RNAs (ncRNA) that are known to exhibit low levels of expression. Through this approach, missing values are handled by associating with them disproportionately large uncertainties which makes it particularly useful for single cell RNA-seq data. We demonstrate the utility of this framework by extracting a cascade of gene expression waves from a well-designed RNA-seq study of zebrafish embryogenesis and, a scRNA-seq study of mouse pre-implantation and provide unique biological insights into the regulation of genes in each wave. For non-ordinal measurements, we show that EMOGEA has a much higher rate of true positive calls and a vanishingly small rate for false negative discoveries compared to common approaches. Finally, we provide an R package (https://github.com/itikadi/EMOGEA) that is self-contained and easy to use.
Graphical Abstract:

Graphical representation of EMOGEA indicating the incorporation of measurement errors in modeling RNA-seq data to generate superior results in exploratory analysis, differential gene expression analyses and, scRNA-seq and Time Course analyses.
A Methodological Framework to Assess the Accuracy of Virtual Reality Hand-Tracking Systems: A case study with the Oculus Quest 2
Authors: Abdlkarim Diar , Di Luca Massimiliano , Aves Poppy , Yeo Sang-Hoon , Miall R. Chris , Holland Peter , Galea Joseph M.
Published: February 2022

Optical marker-less hand-tracking systems incorporated into virtual reality (VR) headsets are transforming the ability to assess motor skills, including hand movements, in VR. This promises to have far-reaching implications for the increased applicability of VR across scientific, industrial and clinical settings. However, so far, there is little data regarding the accuracy, delay and overall performance of these types of hand-tracking systems. Here we present a novel methodological framework which can be easily applied to measure these systems’ absolute positional error, temporal delay and finger joint-angle accuracy. We used this framework to evaluate the Meta Quest 2 hand-tracking system. Our results showed an average fingertip positional error of 1.1cm, an average finger joint angle error of 9.6oand an average temporal delay of 38.0ms. Finally, a novel approach was developed to correct for these positional errors based on a lens distortion model. This methodological framework provides a powerful tool to ensure the reliability and validity of data originating from VR-based, marker-less hand-tracking systems.
Hyperflexion is unlikely to be the primary cervical spine injury mechanism in accidental head-on rugby tackling
Authors: Silvestros Pavlos , Preatoni Ezio , Gill Harinderjit S. , Cazzola Dario
Published: February 2022

In Rugby a high proportion of catastrophic cervical spine injuries occur during tackling. In the injury prevention literature, there is still an open debate on the injury mechanisms related to such injuries, with hyperflexion and buckling being under scrutiny. The aims of this study were to determine the primary cervical spine injury mechanism during head-on rugby tackling, and evaluate the effect of tackling technique on cervical spine intervertebral loading. We conducted an in silico study to examine the dynamic response of the cervical spine under loading conditions representative of accidental head-on rugby tackles by using a subject-specific musculoskeletal model of a rugby player. The computer simulations were driven by experimental in vivo data of an academy rugby player tackling a punchbag, and in vitro data of head-first impacts using a dummy head. Results showed that: i) the earlier generation of high compression and anterior shear loads with low values of flexion moments provides evidence that hyperflexion is unlikely to be the primary injury mechanism in the sub-axial cervical spine (C3-C7) during central and posterior head impact locations; ii) a higher degree of neck flexion at impact poses the cervical spine in a more hazardous position. These findings provide objective evidence to inform injury prevention strategies or rugby law changes, with the final view of improving the safety of the game of rugby.
Differential binding of salicylic acid, phenolic acid derivatives and co-factors determines the roles of Arabidopsis NPR1 to NPR4 in plant immunity
Authors: Konopka Evelyn , Saur Mathias , Pfitzner Artur J.P. , Pfitzner Ursula M.
Published: February 2022

Genetic studies have demonstrated that NPR1 is the key positive regulator of salicylic acid (SA)-induced PR-1 gene induction and systemic acquired resistance (SAR). In Arabidopsis, family members NPR1 to NPR4 share domain architecture.

Yeast hybrid assays were used to explore biochemical capabilities of NPR1 to NPR4.

All NPR1 to NPR4 are responsive to SA. SA perception proceeds via the conserved arginine embedded in a C-terminal LENRV-like motif. Clade 2 proteins NPR3 and NPR4 perceive SA directly, while clade 1 members NPR1 and NPR2 require interaction with partner proteins NIMIN1/NIMIN2 and TGA factors, respectively, to enable SA sensing. Intriguingly, NPR3 is considerably more sensitive to the synthetic analog 3,5-dichloroanthranilic acid than to SA, and all NPR1 to NPR4 are able to sense the microbial metabolite 6-methyl SA.

We suggest that the plant´s ability to track SA and phenolic acid derivatives through NPR proteins has evolved to support diverse defense signaling outputs that are activated in parallel by agonists which may be of microbial or plant origin. In this line, NPR1-NIMIN2/NIMIN1 complex is the prime receptor for SA synthesized by plants in response to microbial attack, while NPR3 induces defense different from SAR primarily via unrecognized signal molecules.
Progressive maturation of the root apical meristem inArabidopsis thalianalateral roots
Authors: Berthet Béatrice , Bald Lotte , Louveaux Marion , Maizel Alexis
Published: February 2022

Meristems are stem cells niches that support the formation of all plant organs and are either set during embryogenesis and maintained throughout the plant life or specified de novo, post-embryonically. The embryo-derived root apical meristem is organized around a group of infrequently dividing cells, the quiescent centre, that maintains the stem cells, organizes growth along two axes and owing to its resistance to 3ic stress can replace damaged stem cells. In most cases, lateral roots post-embryonically branch off the primary and establish a new root meristem which organization is identical to the primary root one. The cellular and molecular processes underpinning the emergence of new stem cell niches are not well known. Here, we characterize the de novo establishment of the root apical meristem in lateral roots. While the position of the new stem cell niche is set early during morphogenesis, its cellular layout, unique gene expression profile and mitotic quiescence are only acquired after emergence concomitant to the establishment of two diverging growth axis. Our results show that the intertwined attributes of the mature root stem cell niche are progressively acquired during lateral root formation, and support a model in which the position of the stem cell niche emerges from the establishment of diverging growth axis.

Highlight

Analyze of the ontogeny of the quiescent center during lateral root ontogeny reveal its late formation and supports that its emergence results from the establishment of two diverging growth axis.
SpheroidAnalyseR – an online platform for analysing data from 3D spheroids or organoids grown in 96-well plates
Authors: Barrow Rhiannon , Wilkinson Joseph N , He Yichen , Callaghan Martin , Brüning-Richardson Anke , Dunning Mark , Stead Lucy F
Published: February 2022

Spheroids and organoids are increasingly popular three-dimensional (3D) cell culture models. Spheroid models are more physiologically relevant to a tumour compared to two-dimensional (2D) cultures and organoids are a simplified version of an organ with similar composition. Both can be used in cell migration studies, disease modelling and drug discovery. A drawback of these models is, however, the lack of appropriate analytical tools for high throughput imaging and analysis over a time course. To address this, we have developed an R Shiny app called SpheroidAnalyseR: a simple, fast, effective open-source app that allows the analysis of spheroid or organoid size data generated in a 96-well format. SpheroidAnalyseR processes and analyses datasets of image measurements that can be obtained via a bespoke software, described herein, that automates spheroid imaging and quantification using the Nikon A1R Confocal Laser Scanning Microscope. However, templates are provided to enable users to input spheroid image measurements obtained by user-preferred methods. SpheroidAnalyseR facilitates outlier identification and removal followed by graphical visualisation of spheroid measurements across multiple predefined parameters such as time, cell-type and treatment(s). Spheroid imaging and analysis can, thus, be reduced from hours to minutes, removing the requirement for substantial manual data manipulation in a spreadsheet application. The combination of spheroid generation in 96-well ultra-low attachment microplates, imaging using our bespoke software, and analysis using SpheroidAnalyseR toolkit allows high throughput, longitudinal quantification of 3D spheroid growth whilst minimising user input and significantly improving the efficiency and reproducibility of data analysis. Our bespoke imaging software is available from https://github.com/GliomaGenomics. SpheroidAnalyseR is available at https://spheroidanalyser7.azurewebsites.net, and the source code found at https://github.com/GliomaGenomics.

Abstract Figure

Graphical abstract - SpheroidAnalyseR main steps.

A summary of the process followed within the SpheroidAnalyseR app. Dotted boxes are the steps required to produce the input data for SpheroidAnalyseR. Solid boxes show the 5 main steps of SpheroidAnalyseR: Data input, Preview, Outlier removal, Merging and Plotting.
An assessment of bioinformatics tools for the detection of human endogenous retroviral insertions in short-read genome sequencing data
Authors: Bowles Harry , Kabiljo Renata , Jones Ashley , Al Khleifat Ahmad , Quinn John P , Dobson Richard JB , Swanson Chad M , Al-Chalabi Ammar , Iacoangeli Alfredo
Published: February 2022

There is a growing interest in the study of human endogenous retroviruses (HERVs) given the substantial body of evidence that implicates them in many human diseases. Although their genomic characterization presents numerous technical challenges, next-generation sequencing (NGS) has shown potential to detect HERV insertions and their polymorphisms in humans, and a number of computational tools to detect them in short-read NGS data exist. In order to design optimal analysis pipelines, an independent evaluation of the currently available tools is required. We evaluated the performance of a set of such tools using a variety of experimental designs and types of NGS datasets. These included 50 human short read whole-genome sequencing samples, matching long and short read NGS data, and simulated short-read NGS data. Our results highlight the performance variability of the tools across the datasets and suggest that different tools might be suitable for different study designs. Using multiple tools and a consensus approach is advisable if computationally feasible and wet-lab validation via PCR is advisable where biological samples are available.
Sample preparation and warping accuracy for correlative multimodal imaging in the mouse olfactory bulb using 2-photon, synchrotron X-ray and volume electron microscopy
Authors: Zhang Yuxin , Ackels Tobias , Pacureanu Alexandra , Zdora Marie-Christine , Bonnin Anne , Schaefer Andreas T. , Bosch Carles
Published: February 2022

Integrating physiology with structural insights of the same neuronal circuit provides a unique approach to understanding how the mammalian brain computes information. However, combining the techniques that provide both streams of data represents an experimental challenge. When studying glomerular column circuits in the mouse olfactory bulb, this approach involves e.g. recording the neuronal activity with in vivo 2-photon (2P) calcium imaging, retrieving the circuit structure with synchrotron X-ray computed tomography with propagation-based phase contrast (SXRT) and/or serial block-face electron microscopy (SBEM) and correlating these datasets. Sample preparation and dataset correlation are two key bottlenecks in this correlative workflow. Here, we first quantify the occurrence of different artefacts when staining tissue slices with heavy metals to generate X-ray or electron contrast. We report improvements in the staining procedure, ultimately achieving perfect staining in ∼67% of the 0.6 mm thick olfactory bulb slices that were previously imaged in vivo with 2P. Secondly, we characterise the accuracy of the spatial correlation between functional and structural datasets. We demonstrate that direct, single-cell precise correlation between in vivo 2P and SXRT tissue volumes is possible and as reliable as correlating between 2P and SBEM. Altogether, these results pave the way for experiments that require retrieving physiology, circuit structure and synaptic signatures in targeted regions. These correlative function-structure studies will bring a more complete understanding of mammalian olfactory processing across length scales and time.
Exploring the link between Parkinson’s disease and Diabetes Mellitus in Drosophila
Authors: Sanz Francisco José , Solana-Manrique Cristina , Lilao-Garzón Joaquín , Brito-Casillas Yeray , Muñoz-Descalzo Silvia , Paricio Nuria
Published: February 2022

Parkinson’s disease (PD) is the second most common neurodegenerative disease. Diabetes mellitus (DM) is a metabolic disease characterized by high levels of glucose in blood. Recent epidemiological studies are highlighting the link between both diseases; it is even considered that DM might be a risk factor for PD. To further investigate the likely relation of these diseases, we have used a Drosophila PD model based on inactivation of the DJ-1β gene (ortholog of human DJ-1), and diet-induced Drosophila and mouse T2DM models, together with human neuron-like cells. T2DM models were obtained by feeding flies with a high sugar containing medium, and mice with a high fat diet. Our results showed that both fly models exhibit common phenotypes such as alterations in carbohydrate homeostasis, mitochondrial dysfunction or motor defects, among others. In addition, we demonstrated that T2DM might be a risk factor of developing PD since our diet-induced fly and mouse T2DM models present DA neurodegeneration, a hallmark of PD. We have also confirmed that neurodegeneration is caused by increased glucose levels, which has detrimental effects in human neuron-like cells by triggering apoptosis and leading to cell death. Besides, the observed phenotypes were exacerbated in DJ-1β mutants cultured in the high sugared medium, indicating that DJ-1 might have a role in carbohydrate homeostasis. Finally, we have confirmed that metformin, an antidiabetic drug, is a potential candidate for PD treatment and that it could prevent PD onset in T2DM model flies. This result supports antidiabetic drugs as promising PD therapeutics.
Is Over-parameterization a Problem for Profile Mixture Models?
Authors: Baños Hector , Susko Edward , Roger Andrew J.
Published: February 2022

Biochemical constraints on the admissible amino acids at specific sites in proteins leads to heterogeneity of the amino acid substitution process over sites in alignments. It is well known that phylogenetic models of protein sequence evolution that do not account for site heterogeneity are prone to long-branch attraction (LBA) artifacts. Profile mixture models were developed to model heterogeneity of preferred amino acids at sites via a finite distribution of site classes each with a distinct set of equilibrium amino acid frequencies. However, it is unknown whether the large number of parameters in such models associated with the many amino acid frequency classes can adversely affect tree topology estimates because of over-parameterization. Here we demonstrate theoretically that for long sequences, over-parameterization does not create problems for estimation with profile mixture models. Under mild conditions, tree, amino acid frequencies and other model parameters converge to true values as sequence length increases, even when there are large numbers of components in the frequency profile distributions. Because large sample theory does not necessarily imply good behavior for shorter alignments we explore performance of these models with short alignments simulated with tree topologies that are prone to LBA artifacts. We find that over-parameterization is not a problem for complex profile mixture models even when there are many amino acid frequency classes. In fact, simple models with few site classes behave poorly. Interestingly, we also found that misspecification of the amino acid frequency classes does not lead to increased LBA artifacts as long as the estimated cumulative distribution function of the amino acid frequencies at sites adequately approximates the true one. In contrast, misspecification of the amino acid exchangeability rates can severely negatively affect parameter estimation. Finally, we explore the effects of including in the profile mixture model an additional ‘F-class’ representing the overall frequencies of amino acids in the data set. Surprisingly, the F-class does not help parameter estimation significantly, and can decrease the probability of correct tree estimation, depending on the scenario, even though it tends to improve likelihood scores.
Ethanol exposure alters Alzheimer’s-related pathology, behavior, and metabolism in APP/PS1 mice
Authors: Gironda Stephen C. , Day Stephen M. , Clarke Caitlin W. , Snipes J. Andy , Nicol Noelle I. , Kamran Hana , Vaughn Warner , Macauley Shannon L. , Weiner Jeff L.
Published: February 2022

Chronic ethanol exposure can increase amyloid-β (Aβ) and tau in rodent models of Alzheimer’s-disease (AD)-like pathology, yet the underlying mechanisms are poorly understood. In this study, a moderate two-bottle choice drinking paradigm was used to identify how chronic ethanol exposure alters Aβ-related pathology, metabolism, and behavior. Complementary in vivo microdialysis experiments were used to measure how acute ethanol directly modulates Aβ in the hippocampal interstitial fluid (ISF). Ethanol-exposed APPswe/PSEN1dE9 (APP/PS1) mice showed increased brain atrophy and an increased number of amyloid plaques. Further analysis revealed that ethanol exposure led to a shift in the distribution of plaque size in the cortex and hippocampus. Ethanol-exposed mice developed a greater number of smaller plaques, potentially setting the stage for increased plaque proliferation in later life. Ethanol also induced changes in N-methyl-D-aspartate and γ-aminobutyric acid type-A receptor (NMDAR and GABAAR, respectively) expression, possibly reflecting changes in the excitatory and inhibitory (E/I) balance in the brain. Ethanol exposure also led to a diurnal shift in feeding behavior which was associated with changes in glucose homeostasis and glucose intolerance. Ethanol exposure also exacerbated alterations in the open-field test and deficits in nest-building behaviors in APP/PS1mice. Lastly, an acute dose of ethanol bidirectionally altered hippocampal ISF Aβ levels – decreasing during the initial exposure and increasing during withdrawal. Acute ethanol exposure increased hippocampal ISF glucose levels, suggesting changes in cerebral glucose metabolism occur in response to ethanol. These experiments indicate that ethanol exacerbates an AD-like phenotype by altering Aβ deposition, behavior, and metabolism. Here, even a moderate drinking paradigm culminates in an interaction between alcohol use and AD-related phenotypes with a potentiation of AD-related pathology, behavioral dysfunction, and metabolic impairment.

Highlights

Chronic ethanol exposure increases brain atrophy in APP/PS1 mice.

Chronic ethanol exposure increased the number of plaques in the brains of APP/PS1 mice.

Chronic ethanol exposure led to dysregulated metabolism in APP/PS1 mice.

Chronic ethanol exposure altered anxiety- and dementia-related behaviors in APP/PS1 mice.

Acute ethanol exposure bidirectionally alters interstitial fluid (ISF) levels of amyloid-β in APP/PS1 mice during exposure and withdrawal.
An increase in serial sarcomere number induced via weighted downhill running improves work loop performance in the rat soleus
Authors: Hinks Avery , Jacob Kaitlyn , Mashouri Parastoo , Medak Kyle D. , Franchi Martino V. , Wright David C. , Brown Stephen H. M. , Power Geoffrey A.
Published: February 2022

Increased serial sarcomere number (SSN) has been observed in rats via downhill running training due to the emphasis on active lengthening contractions; however, little is known about the influence on dynamic contractile function. Therefore, we employed 4 weeks of weighted downhill running training in rats, then assessed soleus SSN and work loop performance. We hypothesized trained rats would produce greater net work output during faster, higher-strain work loops due to a greater SSN. Thirty-one Sprague-Dawley rats were assigned to a control or training group. Weight was added during downhill running via a custom-made vest, progressing from 5-15% body mass. Following sacrifice, the soleus was dissected, and a force-length relationship was constructed. Work loops (active shortening followed by passive lengthening) were then performed about optimal muscle length (LO) at 1.5-3-Hz cycle frequencies and 1-7-mm strains to assess net work output. Muscles were then fixed in formalin at LO. Fascicle lengths and sarcomere lengths were measured and used to calculate SSN. Intramuscular collagen content and crosslinking were quantified via a hydroxyproline content and pepsin-solubility assay. Trained rats had longer fascicle lengths (+13%), greater SSN (+8%), greater specific active forces (+50%), and lower passive forces (–45-62%) than controls (P<0.05). There were no differences in collagen parameters (P>0.05). Net work output was greater (+101-424%) in trained than control rats for the 1.5-Hz loops at 1, 3, and 5-mm strains (P<0.05) and showed relationships with fascicle length (R2=0.14-0.24, P<0.05). These results suggest training-induced longitudinal muscle growth may improve dynamic performance.
Integrated epigenome and transcriptome analysis of normal and arrested meiotic initiation during mouse spermatogenesis
Authors: Zhang Xiaoyu , Gunewardena Sumedha , Wang Ning
Published: February 2022

The transition from mitotic to meiotic cell cycles is a transcriptional event that entails the activation of genes important for meiosis and requires germline-specific retinoic acid (RA) signaling target, Stra8. To identify novel transcription factors underlying mammalian meiotic initiation, we conducted integrative snATAC-seq and scRNA-seq analysis using wild-type and Stra8-deficient mouse testicular cells to map the chromatin accessibility and gene expression landscapes of normal and genetically arrested meiotic initiation. Our results identified a cluster of putative inhibitory transcription factors for meiotic initiation, which we consider “meiotic inhibitors”. STRA8 binds to the regulatory sequences of these meiotic inhibitors and represses their expression upon meiotic initiation. In Stra8-deficient cells that suffer meiotic initiation arrest, the chromatin accessibility of these meiotic inhibitors is increased, concurrent with their uncontrolled and sustained expression. Among these meiotic inhibitors include KLF4, MAX, and MAZ. Importantly, by analyzing the single cell transcriptomes of human testes, our data show that these putative meiotic inhibitor genes are upregulated in early germ cells from patients with spermatogenic failure. Our study suggests that proper repression of meiotic inhibitors is essential for both mouse and human spermatogenesis.
Evaluating Impacts of Syntenic Block Detection Strategies on Rearrangement Phylogeny Using M. tuberculosis Isolates
Authors: Elghraoui Afif , Mirarab Siavash , Swenson Krister M. , Valafar Faramarz
Published: February 2022

Abstract

Phylogenetic inference based on genomic structural variations, that manipulate the gene order and content of whole chromosomes, promises to inform a more comprehensive understanding of evolution. The first challenge in using such data, the incompleteness of availablede novoassemblies, is easing as long read technologies enable (near-)complete genome assembly, but methodological challenges remain. To obtain the input to rearrangement-based inference methods, we need to detect syntenic blocks of orthologous sequences, a task that can be accomplished in many ways, none of which are obviously preferable. In this paper, we use 94 reference quality genomes of primarilyMycobacterium tuberculosis(Mtb) isolates as a benchmark to evaluate these methods. The clonal nature of Mtb evolution, the manageable genome sizes, along with substantial levels of structural variation make this an ideal benchmarking dataset. We test several methods for detecting homology and obtaining syntenic blocks, and two methods for inferring phylogenies, comparing them to the standard method that uses substitutions for inferring the tree. We find that not only the choice of methods but also their parameters can impact results, especially among branches with lower support. In particular, a method based on an encoding of adjacencies applied to Cactus-defined blocks was fully compatible with the highly supported branches of the substitution-based tree. Thus, we were able tocombinethe two trees to obtain a supertree with high resolution utilizing both SNPs and rearrangements. Furthermore, we observed that the results were much less affected by the choice of the tree inference method than by the method used to determine the underlying syntenic blocks. Overall, our results indicate that accurate trees can be inferred using genome rearrangements, but the choice of the methods for inferring the homology matters and requires care.
Chemical exploration of a highly selective scaffold with activity against intracellular Mycobacterium tuberculosis
Authors: Njikan Samuel , Ahmed Sara , Manning Alyssa , Awasthi Divya , Ovechkina Yulia , Chowdhury Sultan , Butts Arielle , Parish Tanya
Published: February 2022

We previously identified a phenylthiourea series with activity against intracellular Mycobacterium tuberculosis using a high throughput, high content assay. We conducted a catalog structure-activity relationship study with a collection of 35 analogs. We identified several thiourea derivatives with excellent potency against intracellular bacteria and good selectivity over eukaryotic cells. Compounds had much lower activity against extracellular bacteria which was not increased by using cholesterol as the sole carbon source. Compounds were equally active against strains with mutations in QcrB or MmpL3, thereby excluding common, promiscuous targets as the mode of action. The phenylthiourea series represents a good starting point for further exploration to develop novel anti-tubercular agents.
Ovarian carcinosarcoma is a distinct form of ovarian cancer with poorer survival compared to tubo-ovarian high grade serous carcinoma
Authors: Hollis Robert L. , Croy Ian , Churchman Mike , Bartos Clare , Rye Tzyvia , Gourley Charlie , Herrington C. Simon
Published: February 2022

BACKGROUND

Ovarian carcinosarcoma (OCS) is an uncommon, biphasic and highly aggressive ovarian cancer type, which has received relatively little research attention.

METHODS

We curated the largest pathologically-confirmed OCS cohort to date, performing detailed histopathological characterisation, analysis of features associated with survival, and comparison against high grade serous ovarian carcinoma (HGSOC).

RESULTS

82 OCS patients were identified; overall survival was poor (median 12.7 months). 79% demonstrated epithelial components of high grade serous (HGS) type, while 21% were endometrioid. Heterologous elements were common (chondrosarcoma in 32%, rhabdomyosarcoma in 21%, liposarcoma in 2%); chondrosarcoma was more frequent in OCS with carcinomatous components of endometrioid type. Earlier stage, complete surgical resection, and treatment with platinum-containing chemotherapy were associated with prolonged survival; however, risk of relapse and mortality was high across all patient groups. Histological subclassification did not identify subgroups with distinct survival. Compared to HGSOC, OCS patients were older at diagnosis (P<0.0001), more likely to be FIGO stage I (P=0.025), demonstrated lower chemotherapy response rate (P=0.001) and had significantly poorer survival (P<0.0001).

CONCLUSION

OCS represents a distinct, highly lethal form of ovarian cancer for which new treatment strategies are urgently needed. Aggressive adjuvant chemotherapy should be considered for all patients, including those with early stage disease.
Risk of SARS-CoV-2 reinfection 18 months after primary infection: population-level observational study
Authors: Flacco Maria Elena , Soldato Graziella , Martellucci Cecilia Acuti , Di Martino Giuseppe , Carota Roberto , Caponetti Antonio , Manzoli Lamberto
Published: February 2022

Current data suggest that SARS-CoV-2 reinfections are rare, but uncertainties remain on the duration of the natural immunity, its protection against Omicron variant, finally the impact of vaccination to reduce reinfection rates. In this retrospective cohort analysis of the entire population of an Italian Region, we followed 1,293,941 subjects from the beginning of the pandemic to the current scenario of Omicron predominance (up to mid-January 2022). After an average of 334 days, we recorded 260 reinfections among 84,907 previously infected subjects (overall rate: 0.31%), two hospitalizations (2.4 x100,000), and one death. Importantly, the incidence of reinfection did not vary substantially over time: after 18-22 months from the primary infection, the reinfection rate was still 0.32%, suggesting that protection conferred by natural immunity may last beyond 12 months. The risk of reinfection was significantly higher among the unvaccinated subjects, and during the Omicron wave.
A Chromodomain Mutation Identifies Separable Roles for C. elegans MRG-1 in Germline and Somatic Development
Authors: Doronio Christine A. , Ling Huiping , Gleason Elizabeth J. , Kelly William G.
Published: February 2022

The packaging of DNA into chromatin strongly influences gene regulation. Post-translational modifications of histones, and the proteins that bind to them, alter the accessibility of chromatin and contribute to the activation and repression of genes. The human MRG15 (MORF4- Related Gene on chromosome 15) protein is a conserved chromodomain-containing protein that binds to methylated lysine 36 on histone H3 (H3K36me) and plays important roles in development, genome integrity, and gene regulation. MRG15 affects transcriptional regulation through its interactions with both histone acetyltransferase (HAT) and histone deacetylase (HDAC) complexes. MRG-1, its C. elegans homolog, has similarly been shown to have important roles in genomic integrity and development, and has also been shown to co- purify with HDAC complexes. Like MRG15, MRG-1 is predicted to bind to H3K36me through its chromodomain, yet despite mrg-1 mutants displaying developmental and germline phenotypes that overlap with H3K36 methyltransferase mutants, the role of the MRG-1 chromodomain has never been characterized. In this study, we examined meiotic cells lacking H3K36me3 to compare to mrg-1 mutant germ cell phenotypes, and mutated key residues in the MRG-1 chromodomain (CD) to assess its function. The CD mutations cause embryonic lethality but few post-embryonic germline defects, in contrast to mrg-1 deletion mutants which are viable but sterile. The CD mutations therefore disrupt somatic development despite the apparent absence of a requirement for MRG-1 protein in embryogenesis. Furthermore, the CD mutants exhibit a dominant RNAi resistance phenotype that is not seen in other mrg-1 mutant alleles. This suggests that the function of MRG-1, and the chromatin modifying complexes with which it interacts, includes tissue-specific interactions involving different requirements for a functional chromodomain. We propose that the CD mutation disrupts proper guidance of complexes within which it acts, and this guidance defect results in improper HDAC and/or HAT regulation causing an indirect defect in RNAi machinery expression or targeting.
Protein profiling of WERI RB1 and etoposide resistant WERI ETOR reveals new insights into topoisomerase inhibitor resistance in retinoblastoma
Authors: Kakkassery Vinodh , Gemoll Timo , Krämer Miriam M. , Sauer Thorben , Tura Aysegül , Ranjbar Mahdy , Grisanti Salvatore , Joachim Stephanie C. , Mergler Stefan , Reinhard Jacqueline
Published: February 2022

Chemotherapy resistance is one of the reasons for eye loss in patients with retinoblastoma (RB). RB chemotherapy resistance has been studied in different cell culture models such as WERI RB1. In addition, chemotherapy resistant RB subclones like the etoposide resistant WERI ETOR cell line have been established to improve the understanding of chemotherapy resistance in RB. The objective of this study was to characterize cell line models of an etoposide sensitive WERI RB1 and its etoposide resistant subclone WERI ETOR by proteomic analysis. Subsequently, quantitative proteomic data served for correlation analysis with known drug perturbation profiles. Methodically, WERI RB1 and WERI ETOR were cultured and prepared for quantitative mass spectrometry (MS). This was carried out in a data-independent acquisition (DIA) mode (Sequential Window Acquisition of All Theoretical Mass Spectra, SWATH-MS). The raw SWATH files were processed using neural networks in a library free mode along with machine learning algorithms. Pathway enrichment was performed using the REACTOME pathway resource and correlated to the Molecular Signature Database (MSigDB) hallmark gene set collections for functional annotation. Furthermore, a drug connectivity analysis using the L1000 database was used to correlate the mechanism-of-action (MOA) for different anticancer reagents to WERI RB1/WERI ETOR signatures. A total of 4,756 proteins were identified across all samples, showing a distinct clustering between the groups. Of these proteins, 64 were significantly altered (q < 0.05 & log2FC |>2|, 22% higher in WERI ETOR). Pathway analysis revealed an enriched metabolic pathway for “retinoid metabolism and transport” in WERI ETOR and for “sphingolipid de novo biosynthesis” in WERI RB1. In addition, this study revealed similar protein signatures of topoisomerase inhibitors in WERI ETOR as well as ATPase inhibitors, acetylcholine receptor antagonists and vascular endothelial growth factor receptor (VEGFR) inhibitors in WERI RB1. In this study, WERI RB1 and WERI ETOR were analyzed as a cell line model for chemotherapy resistance in RB using data-independent MS. The global proteome identified activation of “sphingolipid de novo biosynthesis” in WERI RB1 and revealed future potential treatment options for etoposide resistance in RB.