Initiation of hnRNPA1 Low-Complexity Domain Condensation Monitored by Dynamic Light Scattering.

Biomolecular condensates (BMCs) exhibit physiological and pathological relevance in biological systems. Both liquid and solid condensates play significant roles in the spatiotemporal regulation and organization of macromolecules and their biological activities. Some pathological solid condensates, such as Lewy Bodies and other fibrillar aggregates, have been hypothesized to originate from liquid condensates. With the prevalence of BMCs having functional and dysfunctional roles, it is imperative to understand the mechanism of biomolecular condensate formation and initiation. Using the low-complexity domain (LCD) of heterogenous ribonuclear protein A1 (hnRNPA1) as our model, we monitored initial assembly events using dynamic light scattering (DLS) while modulating pH and salt conditions to perturb macromolecule and condensate properties. We observed the formation of nanometer-sized BMCs (nano-condensates) distinct from protein monomers and micron-sized condensates. We also observed that conditions that solubilize micron-sized protein condensates do not solubilize nano-condensates, indicating that the balance of forces that stabilize nano-condensates and micron-sized condensates are distinct. These findings provide insight into the forces that drive protein phase separation and potential nucleation structures of macromolecular condensation.

Stereospecific NANOG PEST Stabilization by Pin1.

NANOG protein levels correlate with stem cell pluripotency. NANOG concentrations fluctuate constantly with low NANOG levels leading to spontaneous cell differentiation. Previous literature implicated Pin1, a phosphorylation-dependent prolyl isomerase, as a key player in NANOG stabilization. Here, using NMR spectroscopy, we investigate the molecular interactions of Pin1 with the NANOG unstructured N-terminal domain that contains a PEST sequence with two phosphorylation sites. Phosphorylation of NANOG PEST peptides increases affinity to Pin1. By systematically increasing the amount of cis PEST conformers, we show that the peptides bind tighter to the prolyl isomerase domain (PPIase) of Pin1. Phosphorylation and cis Pro enhancement at both PEST sites lead to a 5-10-fold increase in NANOG binding to the Pin1 WW domain and PPIase domain, respectively. The cis-populated NANOG PEST peptides can be potential inhibitors for disrupting Pin1-dependent NANOG stabilization in cancer stem cells.

Aggregation of Disordered Proteins Associated with Neurodegeneration.

Cellular deposition of protein aggregates, one of the hallmarks of neurodegeneration, disrupts cellular functions and leads to neuronal death. Mutations, posttranslational modifications, and truncations are common molecular underpinnings in the formation of aberrant protein conformations that seed aggregation. The major proteins involved in neurodegeneration include amyloid beta (Aß) and tau in Alzheimer's disease, α-synuclein in Parkinson's disease, and TAR DNA-binding protein (TDP-43) in amyotrophic lateral sclerosis (ALS). These proteins are described as intrinsically disordered and possess enhanced ability to partition into biomolecular condensates. In this review, we discuss the role of protein misfolding and aggregation in neurodegenerative diseases, specifically highlighting implications of changes to the primary/secondary (mutations, posttranslational modifications, and truncations) and the quaternary/supramolecular (oligomerization and condensation) structural landscapes for the four aforementioned proteins. Understanding these aggregation mechanisms provides insights into neurodegenerative diseases and their common underlying molecular pathology.

Fluorescence Lifetime Imaging Microscopy of Biomolecular Condensates.

Biomolecular condensates of ribonucleoproteins (RNPs) such as the transactivation response element (TAR) DNA-binding protein 43 (TDP-43) arise from liquid-liquid phase separation (LLPS) and play vital roles in various biological processes including the formation-dissolution of stress granules (SGs). These condensates are thought to be directly linked to neurodegenerative diseases, providing a depot of aggregation-prone proteins and serving as a cauldron of protein aggregation and fibrillation. Despite recent research efforts, biochemical processes and rearrangements within biomolecular condensates that trigger subsequent protein misfolding and aggregation remain to be elucidated. Fluorescence lifetime imaging microscopy (FLIM) provides a minimally intrusive high-sensitivity and high-resolution imaging method to monitor in-droplet spatiotemporal changes that initiate and lead to protein aggregation. In this chapter, we describe a FLIM application for characterizing chemical chaperone-assisted decoupling of TDP-43 liquid-liquid phase separation and aggregation/fibrillation, highlighting potential therapeutic strategies to combat pathological RNP-associated aggregates without compromising cellular stress responses.

Machine learning approaches used to analyze auditory evoked responses from the human auditory brainstem: A systematic review.

BACKGROUND: The application of machine learning algorithms for assessing the auditory brainstem response has gained interest over recent years with a considerable number of publications in the literature. In this systematic review, we explore how machine learning has been used to develop algorithms to assess auditory brainstem responses. A clear and comprehensive overview is provided to allow clinicians and researchers to explore the domain and the potential translation to clinical care. METHODS: The systematic review was performed based on PRISMA guidelines. A search was conducted of PubMed, IEEE-Xplore, and Scopus databases focusing on human studies that have used machine learning to assess auditory brainstem responses. The duration of the search was from January 1, 1990, to April 3, 2021. The Covidence systematic review platform (www.covidence.org) was used throughout the process. RESULTS: A total of 5812 studies were found through the database search and 451 duplicates were removed. The title and abstract screening process further reduced the article count to 89 and in the proceeding full-text screening, 34 articles met our full inclusion criteria. CONCLUSION: Three categories of applications were found, namely neurologic diagnosis, hearing threshold estimation, and other (does not relate to neurologic or hearing threshold estimation). Neural networks and support vector machines were the most commonly used machine learning algorithms in all three categories. Only one study had conducted a clinical trial to evaluate the algorithm after development. Challenges remain in the amount of data required to train machine learning models. Suggestions for future research avenues are mentioned with recommended reporting methods for researchers.

NANOG prion-like assembly mediates DNA bridging to facilitate chromatin reorganization and activation of pluripotency.

Human NANOG expression resets stem cells to ground-state pluripotency. Here we identify the unique features of human NANOG that relate to its dose-sensitive function as a master transcription factor. NANOG is largely disordered, with a C-terminal prion-like domain that phase-transitions to gel-like condensates. Full-length NANOG readily forms higher-order oligomers at low nanomolar concentrations, orders of magnitude lower than typical amyloids. Using single-molecule Förster resonance energy transfer and fluorescence cross-correlation techniques, we show that NANOG oligomerization is essential for bridging DNA elements in vitro. Using chromatin immunoprecipitation sequencing and Hi-C 3.0 in cells, we validate that NANOG prion-like domain assembly is essential for specific DNA recognition and distant chromatin interactions. Our results provide a physical basis for the indispensable role of NANOG in shaping the pluripotent genome. NANOG's unique ability to form prion-like assemblies could provide a cooperative and concerted DNA bridging mechanism that is essential for chromatin reorganization and dose-sensitive activation of ground-state pluripotency.

Hydroxyapatite-decorated Fmoc-hydrogel as a bone-mimicking substrate for osteoclast differentiation and culture.

Hydrogels are water-swollen networks with great potential for tissue engineering applications. However, their use in bone regeneration is often hampered due to a lack of materials' mineralization and poor mechanical properties. Moreover, most studies are focused on osteoblasts (OBs) for bone formation, while osteoclasts (OCs), cells involved in bone resorption, are often overlooked. Yet, the role of OCs is pivotal for bone homeostasis and aberrant OC activity has been reported in several pathological diseases, such as osteoporosis and bone cancer. For these reasons, the aim of this work is to develop customised, reinforced hydrogels to be used as material platform to study cell function, cell-material interactions and ultimately to provide a substrate for OC differentiation and culture. Here, Fmoc-based RGD-functionalised peptide hydrogels have been modified with hydroxyapatite nanopowder (Hap) as nanofiller, to create nanocomposite hydrogels. Atomic force microscopy showed that Hap nanoparticles decorate the peptide nanofibres with a repeating pattern, resulting in stiffer hydrogels with improved mechanical properties compared to Hap- and RGD-free controls. Furthermore, these nanocomposites supported adhesion of Raw 264.7 macrophages and their differentiation in 2D to mature OCs, as defined by the adoption of a typical OC morphology (presence of an actin ring, multinucleation, and ruffled plasma membrane). Finally, after 7 days of culture OCs showed an increased expression of TRAP, a typical OC differentiation marker. Collectively, the results suggest that the Hap/Fmoc-RGD hydrogel has a potential for bone tissue engineering, as a 2D model to study impairment or upregulation of OC differentiation. STATEMENT OF SIGNIFICANCE: Altered osteoclasts (OC) function is one of the major cause of bone fracture in the most commonly skeletal disorders (e.g. osteoporosis). Peptide hydrogels can be used as a platform to mimic the bone microenvironment and provide a tool to assess OC differentiation and function. Moreover, hydrogels can incorporate different nanofillers to yield hybrid biomaterials with enhanced mechanical properties and improved cytocompatibility. Herein, Fmoc-based RGD-functionalised peptide hydrogels were decorated with hydroxyapatite (Hap) nanoparticles to generate a hydrogel with improved rheological properties. Furthermore, they are able to support osteoclastogenesis of Raw264.7 cells in vitro as confirmed by morphology changes and expression of OC-markers. Therefore, this Hap-decorated hydrogel can be used as a template to successfully differentiate OC and potentially study OC dysfunction.

Verification of a Mobile Psychoacoustic Test System.

Many hearing difficulties can be explained as a loss of audibility, a problem easily detected and treated using standard audiological procedures. Yet, hearing can be much poorer (or more impaired) than audibility predicts because of deficits in the suprathreshold mechanisms that encode the rapidly changing, spectral, temporal, and binaural aspects of the sound. The ability to evaluate these mechanisms requires well-defined stimuli and strict adherence to rigorous psychometric principles. This project reports on the comparison between a laboratory-based and a mobile system's results for psychoacoustic assessment in adult listeners with normal hearing. A description of both systems employed is provided. Psychoacoustic tests include frequency discrimination, amplitude modulation detection, binaural encoding, and temporal gap detection. Results reported by the mobile system were not significantly different from those collected with the laboratory-based system for most of the tests and were consistent with those reported in the literature. The mobile system has the potential to be a feasible option for the assessment of suprathreshold auditory encoding abilities.

Assessment of cochlear electrophysiology in typically developing children and children with auditory processing disorder.

OBJECTIVE: Children with auditory processing disorder (APD) are reported to have abnormal auditory brainstem responses (ABR) but little is understood about their cochlear integrity. Poor cochlear integrity can affect neural responses. In this study, cochlear and auditory brainstem integrity was investigated in children with APD. METHOD: Twenty children with APD, sixteen typically developing children and twenty adults participated in this study. Click evoked electrocochleography (ECochG) and ABRs were recorded from all the participants. Cochlear responses were analyzed using a) latency and amplitude of summating potential; action potential, b) transmission time between summating potential and action potential, c) summating potential/action potential amplitude ratio and d) action potential latency difference to condensation and rarefaction polarity. Amplitude in the ABR components was examined. RESULTS: Children with APD showed similar cochlear function to the typically developing children. There were no significant differences in wave I amplitude between children with APD and typically developing children. However, wave V amplitude was significantly reduced in children with APD compared to typically developing children. CONCLUSION: In the absence of any functional differences in the cochlea, children with APD can show poor amplitude in the later components of the ABR. The ABR anomalies observed in children with APD arise due to poor neural processing, possibly after the first auditory synapse.

OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies.

The rapid pace of innovation in biological imaging and the diversity of its applications have prevented the establishment of a community-agreed standardized data format. We propose that complementing established open formats such as OME-TIFF and HDF5 with a next-generation file format such as Zarr will satisfy the majority of use cases in bioimaging. Critically, a common metadata format used in all these vessels can deliver truly findable, accessible, interoperable and reusable bioimaging data.

Liquid condensation of reprogramming factor KLF4 with DNA provides a mechanism for chromatin organization.

Expression of a few master transcription factors can reprogram the epigenetic landscape and three-dimensional chromatin topology of differentiated cells and achieve pluripotency. During reprogramming, thousands of long-range chromatin contacts are altered, and changes in promoter association with enhancers dramatically influence transcription. Molecular participants at these sites have been identified, but how this re-organization might be orchestrated is not known. Biomolecular condensation is implicated in subcellular organization, including the recruitment of RNA polymerase in transcriptional activation. Here, we show that reprogramming factor KLF4 undergoes biomolecular condensation even in the absence of its intrinsically disordered region. Liquid-liquid condensation of the isolated KLF4 DNA binding domain with a DNA fragment from the NANOG proximal promoter is enhanced by CpG methylation of a KLF4 cognate binding site. We propose KLF4-mediated condensation as one mechanism for selectively organizing and re-organizing the genome based on the local sequence and epigenetic state.

Electrostatic modulation of hnRNPA1 low-complexity domain liquid-liquid phase separation and aggregation.

Membrane-less organelles and RNP granules are enriched in RNA and RNA-binding proteins containing disordered regions. Heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1), a key regulating protein in RNA metabolism, localizes to cytoplasmic RNP granules including stress granules. Dysfunctional nuclear-cytoplasmic transport and dynamic phase separation of hnRNPA1 leads to abnormal amyloid aggregation and neurodegeneration. The intrinsically disordered C-terminal domain (CTD) of hnRNPA1 mediates both dynamic liquid-liquid phase separation (LLPS) and aggregation. While cellular phase separation drives the formation of membrane-less organelles, aggregation within phase-separated compartments has been linked to neurodegenerative diseases. To understand some of the underlying mechanisms behind protein phase separation and LLPS-mediated aggregation, we studied LLPS of hnRNPA1 CTD in conditions that probe protein electrostatics, modulated specifically by varying pH conditions, and protein, salt and RNA concentrations. In the conditions investigated, we observed LLPS to be favored in acidic conditions, and by high protein, salt and RNA concentrations. We also observed that conditions that favor LLPS also enhance protein aggregation and fibrillation, which suggests an aggregation pathway that is LLPS-mediated. The results reported here also suggest that LLPS can play a direct role in facilitating protein aggregation, and that changes in cellular environment that affect protein electrostatics can contribute to the pathological aggregation exhibited in neurodegeneration.

A Simple Method for Creating a High-Content Microscope for Imaging Multiplexed Tissue Microarrays.

High-throughput, high-content imaging technologies and multiplex slide scanning have become widely used. Advantages of these approaches include the ability to archive digital copies of slides, review slides as teams using virtual microscopy software, and standardize analytical approaches. The cost and hardware and software inflexibility of dedicated slide scanning devices can, however, complicate implementation. Here, we describe a simple method that allows any microscope to be used for slide scanning. The only requirements are that the microscope be equipped with a motorized filter turret or wheels (for multi-channel fluorescence) and a motorized xyz stage. This example uses MetaMorph software, but the same principles can be used with any microscope control software that includes a few standard functions and allows programming of simple command routines, or journals. The series of journals that implement the method perform key functions, including assistance in defining an unlimited number of regions of interest (ROI) and imaging parameters. Fully automated acquisition is rapid, taking less than 3 hr to image fifty 2.5-mm ROIs in four channels. Following acquisition, images can be easily stitched and displayed using open-source or commercial image-processing and virtual microscope applications. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Hardware and software configuration Basic Protocol 2: Create a preliminary scan Basic Protocol 3: Select, save, and position ROIs Basic Protocol 4: Determine and set autofocus parameters Basic Protocol 5: Acquire tiled images Basic Protocol 6: Review the scans Basic Protocol 7: Reimage ROIs as needed Basic Protocol 8: Stitch, stack, and assemble images Basic Protocol 9: Repeat scanning for multiplex immunostaining or background subtraction.

Comparison of machine learning models to classify Auditory Brainstem Responses recorded from children with Auditory Processing Disorder.

INTRODUCTION: Auditory brainstem responses (ABRs) offer a unique opportunity to assess the neural integrity of the peripheral auditory nervous system in individuals presenting with listening difficulties. ABRs are typically recorded and analyzed by an audiologist who manually measures the timing and quality of the waveforms. The interpretation of ABRs requires considerable experience and training, and inappropriate interpretation can lead to incorrect judgments about the integrity of the system. Machine learning (ML) techniques may be a suitable approach to automate ABR interpretation and reduce human error. OBJECTIVES: The main objective of this paper was to identify a suitable ML technique to automate the analysis of ABR responses recorded as a part of the electrophysiological testing in the Auditory Processing Disorder clinical test battery. METHODS: ABR responses recorded during routine clinical assessment from 136 children being evaluated for auditory processing difficulties were analyzed using several common ML algorithms: Support Vector Machines (SVM), Random Forests (RF), Decision Trees (DT), Gradient Boosting (GB), Extreme Gradient Boosting (Xgboost), and Neural Networks (NN). A variety of signal feature extraction techniques were used to extract features from the ABR waveforms as inputs to the ML algorithms. Statistical significance testing and confusion matrices were used to identify the most robust model capable of accurately identifying neurological abnormalities present in ABRs. RESULTS: Clinically significant features in the time-frequency representation of the signal were identified. The ML model trained using the Xgboost algorithm was identified as the most robust model with an accuracy of 92% compared to other models. CONCLUSION: The findings of the present study demonstrate that it is possible to develop accurate ML models to automate the process of analyzing ABR waveforms recorded at suprathreshold levels. There is currently no ML-based application to screen children with listening difficulties. Therefore, it is expected that this work will be translated into an evaluation tool that can be used by audiologists in the clinic. Furthermore, this work may aid future researchers in exploring ML paradigms to improve clinical test batteries used by audiologists in achieving accurate diagnoses.

Perceptual and Objective Assessment of Envelope Enhancement for Children With Auditory Processing Disorder.

This paper evaluated the performance of an envelope enhancement (EE) algorithm subjectively by children with auditory processing disorder (APD), and objectively through computational models. Speech intelligibility data was collected from children with APD, for unprocessed and envelope-enhanced speech in the presence of stationary and non-stationary background noise at different signal to noise ratios (SNRs), both with and without noise reduction (NR) algorithms as a front-end to the EE algorithm. Furthermore, intrusive and non-intrusive objective speech intelligibility metrics were derived to predict the perceptual impact of this EE algorithm. Subjective data for stationary noise conditions revealed that the combination of NR and EE algorithms significantly improved the speech intelligibility scores at poor SNRs. In contrast, the same combination was ineffective in improving speech intelligibility in non-stationary noise conditions. Taken together, subjective results suggest that exaggerating the envelope cues improves speech identification scores for children with APD. However, the benefit obtained varies depending upon the type and level of the background noise. Both intrusive and non-intrusive objective speech intelligibility estimators exhibited good correlation with the subjective data, with the intrusive metric demonstrating better generalization capabilities. Implications of these results for hearing aid applications for children with APD is discussed.

The SINEB1 element in the long non-coding RNA Malat1 is necessary for TDP-43 proteostasis.

Transposable elements (TEs) comprise a large proportion of long non-coding RNAs (lncRNAs). Here, we employed CRISPR to delete a short interspersed nuclear element (SINE) in Malat1, a cancer-associated lncRNA, to investigate its significance in cellular physiology. We show that Malat1 with a SINE deletion forms diffuse nuclear speckles and is frequently translocated to the cytoplasm. SINE-deleted cells exhibit an activated unfolded protein response and PKR and markedly increased DNA damage and apoptosis caused by dysregulation of TDP-43 localization and formation of cytotoxic inclusions. TDP-43 binds stronger to Malat1 without the SINE and is likely 'hijacked' by cytoplasmic Malat1 to the cytoplasm, resulting in the depletion of nuclear TDP-43 and redistribution of TDP-43 binding to repetitive element transcripts and mRNAs encoding mitotic and nuclear-cytoplasmic regulators. The SINE promotes Malat1 nuclear retention by facilitating Malat1 binding to HNRNPK, a protein that drives RNA nuclear retention, potentially through direct interactions of the SINE with KHDRBS1 and TRA2A, which bind to HNRNPK. Losing these RNA-protein interactions due to the SINE deletion likely creates more available TDP-43 binding sites on Malat1 and subsequent TDP-43 aggregation. These results highlight the significance of lncRNA TEs in TDP-43 proteostasis with potential implications in both cancer and neurodegenerative diseases.

Ligand interactions and the protein order-disorder energetic continuum.

Intrinsically disordered proteins as computationally predicted account for ∼1/3 of eukaryotic proteomes, are involved in a plethora of biological functions, and have been linked to several human diseases as a result of their dysfunctions. Here, we present a picture wherein an energetic continuum describes protein structural and conformational propensities, ranging from the hyperstable folded proteins on one end to the hyperdestabilized and sometimes functionally disordered proteins on the other. We distinguish between proteins that are folding-competent but disordered because of marginal stability and those that are disordered due mainly to the absence of folding code-completing structure-determining interactions, and postulate that disordered proteins that are unstructured by way of partial population of protein denatured states represent a sizable proportion of the proteome.

Bringing Open Data to Whole Slide Imaging.

Faced with the need to support a growing number of whole slide imaging (WSI) file formats, our team has extended a long-standing community file format (OME-TIFF) for use in digital pathology. The format makes use of the core TIFF specification to store multi-resolution (or "pyramidal") representations of a single slide in a flexible, performant manner. Here we describe the structure of this format, its performance characteristics, as well as an open-source library support for reading and writing pyramidal OME-TIFFs.

The Medial Olivocochlear Reflex Is Unlikely to Play a Role in Listening Difficulties in Children.

The medial olivocochlear reflex (MOCR) has been implicated in several auditory processes. The putative role of the MOCR in improving speech perception in noise is particularly relevant for children who complain of listening difficulties (LiD). The hypothesis that the MOCR may be impaired in individuals with LiD or auditory processing disorder has led to several investigations but without consensus. In two related studies, we compared the MOCR functioning of children with LiD and typically developing (TD) children in the same age range (7-17 years). In Study 1, we investigated ipsilateral, contralateral, and bilateral MOCR using forward-masked click-evoked otoacoustic emissions (CEOAEs; n = 17 TD, 17 LiD). In Study 2, we employed three OAE types: CEOAEs (n = 16 TD, 21 LiD), stimulus frequency OAEs (n = 21 TD, 30 LiD), and distortion product OAEs (n = 17 TD, 22 LiD) in a contralateral noise paradigm. Results from both studies suggest that the MOCR functioning is not significantly different between the two groups. Some likely reasons for differences in findings among published studies could stem from the lack of strict data quality measures (e.g., high signal-to-noise ratio, control for the middle ear muscle reflex) that were enforced in the present study. The inherent variability of the MOCR, the subpar reliability of current MOCR methods, and the heterogeneity in auditory processing deficits that underlie auditory processing disorder make detecting clinically relevant differences in MOCR function impractical using current methods.