Biology subjects

Anderson, S.

Publications and source records attributed to Anderson, S..

51 records · Page 3Linked to original sources

bioRxiv2019

Exaggerated Cortical Representation of Speech in Older Listeners: Mutual Information Analysis

Aging is associated with an exaggerated representation of the speech envelope in auditory cortex. The relationship between this age-related exaggerated response and a listeners ability to understand speech in noise remains an open question. Here, information-theory-based analysis methods are applied to magnetoencephalography (MEG) recordings of human listeners, investigating their cortical responses to continuous speech, using the novel non-linear measure of phase-locked mutual information between the speech stimuli and cortical responses. The cortex of older listeners shows an exaggerated level of mutual information, compared to younger listeners, for both attended and unattended speakers. The mutual information peaks for several distinct latencies: early ([~]50 ms), middle ([~]100 ms) and late ([~]200 ms). For the late component, the neural enhancement of attended over unattended speech is affected by stimulus SNR, but the direction of this dependency is reversed by aging. Critically, in older listeners and for the same late component, greater cortical exaggeration is correlated with decreased behavioral inhibitory control. This negative correlation also carries over to speech intelligibility in noise, where greater cortical exaggeration in older listeners is correlated with worse speech intelligibility scores. Finally, an age-related lateralization difference is also seen for the [~]100 ms latency peaks, where older listeners show a bilateral response compared to younger listeners right-lateralization. Thus, this information-theory-based analysis provides new, and less coarse-grained, results regarding age-related change in auditory cortical speech processing, and its correlation with cognitive measures, compared to related linear measures. New & NoteworthyCortical representations of natural speech are investigated using a novel non-linear approach based on mutual information. Cortical responses, phase-locked to the speech envelope, show an exaggerated level of mutual information associated with aging, appearing at several distinct latencies ([~]50, [~]100 and [~]200 ms). Critically, for older listeners only, the [~]200 ms latency response components are correlated with specific behavioral measures, including behavioral inhibition and speech comprehension.

neuroscience↗

bioRxiv2019

High-resolution MEMRI characterizes laminar specific ascending and descending spinal cord pathways in rats

Manganese Enhanced MRI (MEMRI) utilizing different manganese chloride (MnCl2) delivery methods, has yielded valuable architectural, functional and connection information about the brain. MEMRI also has the potential in characterizing neural pathways in the spinal cord. The spinal cord grey matter is anatomically composed of nine distinct cellular laminae, where each of the laminae receives input from a specific type of neuronal population and process or serves as a relay region in a specific sensory or motor pathway. This type of laminar arrangement in the spinal cord is currently only visualized by histological methods. It is of significant interest to determine whether laminar specific enhancement by Mn2+ can be achieved in the spinal cord, as has been reported in the brain and olfactory pathway. Here we focus on using MEMRI to determine the specific laminae of the thoracic region of the spinal cord. We focus on MnCl2 changes in the ascending and descending tracts of the spinal cord. Major factors in applying this technique in the spinal cord are the ability to acquire high-resolution spinal cord images and to determine a noninvasive route of administration which will result in uptake by the central nervous system.\n\nWe have applied the MEMRI approach by intraperitoneal (i.p). delivery of MnCl2 and imaged lumbar and thoracic spinal cord levels in rats to determine whether T1 weighted MRI can detect spinal cord laminae 48 hours following MnCl2 administration. T1 weighted images of the lower lumbar level were obtained from MnCl2 injected and control rats. Here we demonstrate laminar specific signal enhancement in the spinal cord of rats administered with MnCl2 vs. controls in MRI of the cord with ultra-high, 69 m in-plane resolution. We also report reduced T1 values over time in MnCl2 groups across laminae I-IX. The regions with the largest T1 enhancements were observed to correspond to laminae that contain either high cell density or large motor neurons, making MEMRI an excellent tool for studying spinal cord architecture, physiology and function in different animal models.

neuroscience↗

bioRxiv2019

Single Cell Spatial Chromatin Analysis of Fixed Immunocytochemically Identified Neuronal Cells

Assays examining the open-chromatin landscape in single cells require isolation of the nucleus, resulting in the loss of spatial/microenvironment information. Here we describe CHEX-seq (CHromatin EXposed) for identifying single-stranded open-chromatin DNA regions in paraformaldehyde-fixed single cells. CHEX-seq uses light-activated DNA probes that binds to single-stranded DNA in open chromatin. In situ laser activation of the annealed probes 3-Lightning Terminator in selected cells permits the probe to act as a primer for in situ enzymatic copying of single-stranded DNA that is then sequenced. CHEX-seq is benchmarked with human K562 cells and its utility is demonstrated in dispersed primary mouse and human brain cells, and immunostained cells in mouse brain sections. Further, CHEX-seq queries the openness of mitochondrial DNA in single cells. Evaluation of an individual cells chromatin landscape in its tissue context enables \"spatial chromatin analysis\".\n\nOne Sentence SummaryA new method, CHEX-seq (CHromatin eXposed), identifies the open-chromatin landscape in single fixed cells thereby allowing spatial chromatin analysis of selected cells in complex cellular environments.

neuroscience↗

bioRxiv2019

Single-cell analyses reveal aberrant pathways for megakaryocyte-biased hematopoiesis in myelofibrosis and identify mutant clone-specific targets

Myelofibrosis is a severe myeloproliferative neoplasm characterised by increased numbers of abnormal bone marrow megakaryocytes that induce progressive fibrosis, destroying the hematopoietic microenvironment. To determine the cellular and molecular basis for aberrant megakaryopoiesis in myelofibrosis, we performed high-throughput single-cell transcriptome profiling of 50,538 hematopoietic stem/progenitor cells (HSPCs), single-cell proteomics, genomics and functional assays. We identified an aberrant pathway for direct megakaryocyte differentiation from the earliest stages of hematopoiesis in myelofibrosis and associated aberrant molecular signatures, including surface antigens selectively expressed by JAK2-mutant HSPCs. Myelofibrosis megakaryocyte progenitors were heterogeneous, with distinct expression of fibrosis and proliferation-associated genes and putative therapy targets. We validated the immunoglobulin receptor G6B as a promising JAK2-mutant clone-specific antigen warranting further development as an immunotherapy target. Our study paves the way for selective targeting of the myelofibrosis clone and more broadly illustrates the power of single-cell multi-omics to discover tumor-specific therapeutic targets and mediators of tissue fibrosis.

cancer biology↗

bioRxiv2019

Well-Differentiated Papillary Mesothelioma of the Peritoneum is Genetically Distinct from Malignant Mesothelioma

Well-differentiated papillary mesothelioma (WDPM) is an uncommon mesothelial proliferation that is most commonly encountered as an incidental finding in the peritoneal cavity. There is controversy in the literature about whether WDPM is a neoplasm or a reactive process, and if neoplastic, whether it is a variant or precursor of epithelial malignant mesothelioma or is a different entity. Using whole exome sequencing of five WDPM of the peritoneum, we have identified distinct mutations in EHD1, ATM, FBXO10, SH2D2A, CDH5, MAGED1, and TP73 shared by WDPM cases but not reported in malignant mesotheliomas. Furthermore, we show that WDPM is strongly enriched with C>A transversion substitution mutations, a pattern that is also not found in malignant mesotheliomas. The WDPMs lacked alterations involving BAP1, SETD2, NF2, CDKN2A/B, LASTS1/2, PBRM1, and SMARCC1 that are frequently altered in malignant mesotheliomas. We conclude that WDPMs are neoplasms that are genetically distinct from malignant mesotheliomas, and based on observed mutations do not appear to be precursors of malignant mesotheliomas.

cancer biology↗

bioRxiv2019

Mutual Information Analysis of Neural Representations of Speech in Noise in the Aging Midbrain

Younger adults with normal hearing can typically understand speech in the presence of a competing speaker without much effort, but this ability to understand speech in challenging conditions deteriorates with age. Older adults, even with clinically normal hearing, often have problems understanding speech in noise. Earlier auditory studies using the frequency-following response (FFR), primarily believed generated by the midbrain, have demonstrated age-related neural deficits when analyzed using traditional measures. Here we use a mutual information paradigm to analyze the FFR to speech (masked by a competing speech signal) by estimating the amount of stimulus information contained in the FFR. Our results show, first, a broad-band informational loss associated with aging for both FFR amplitude and phase. Second, this age-related loss of information is more severe in higher frequency FFR bands (several hundred Hz). Third, the mutual information between the FFR and the stimulus decreases as noise level increases for both age groups. Fourth, older adults benefit neurally, i.e., show a reduction in loss of information, when the speech masker is changed from meaningful (talker speaking a language that they can comprehend, such as English) to meaningless (talker speaking a language that they cannot comprehend, such as Dutch). This benefit is not seen in younger listeners, which suggests age-related informational loss may be more severe when the speech masker is meaningful than when it is meaningless. In summary, as a method, mutual information analysis can unveil new results that traditional measures may not have enough statistical power to assess.\n\nNew & NoteworthyOlder adults, even with clinically normal hearing, often have problems understanding speech in noise. Auditory studies using the frequency-following response (FFR) have demonstrated age-related neural deficits using traditional methods. Here we use a mutual information paradigm to analyze the FFR to speech masked by competing speech. Results confirm those using traditional analysis, but additionally show that older adults benefit neurally when the masker changes from a language that they comprehend to a language they cannot.

neuroscience↗

bioRxiv2018

The High-throughput WAFFL System for Treating and Monitoring Individual Drosophila melanogaster Adults

Non-mammalian model organisms have been essential for our understanding of the mechanisms and control of development, disease, and physiology, but are underutilized in pharmacological phenotypic screening assays due to low throughput compared to cell-based systems. To increase the utility of using Drosophila melanogaster in screening, we have designed the whole animal feeding flat (WAFFL), a novel, flexible, and complete system for feeding, monitoring, and assaying flies in a high throughput format. Our system was conceived keeping in mind the use of off-the-shelf, commercial, 96-well consumables and equipment in order to be amenable to experimental needs. Here we provide an overview of the design and 3-D printing manufacture specifications.

pharmacology and toxicology↗

bioRxiv2018

Measuring Illumina Size Bias Using REcount: A Novel Method for Highly Accurate Quantification of Engineered Genetic Constructs

Quantification of DNA sequence tags associated with engineered genetic constructs underlies many genomics measurements. Typically, such measurements are done using PCR to enrich sequence tags and add adapters, followed by next-generation sequencing (NGS). However, PCR amplification can introduce significant quantitative error into these measurements. Here we describe REcount, a novel PCR-free direct counting method for NGS-based quantification of engineered genetic constructs. By comparing measurements of defined plasmid pools to droplet digital PCR data, we demonstrate that this method is highly accurate and reproducible. We further demonstrate that the REcount approach is amenable to multiplexing through the use of orthogonal restriction enzymes. Finally, we use REcount to provide new insights into clustering biases due to molecule length across different Illumina sequencing platforms.

genomics↗

bioRxiv2018

DISC1 regulates N-Methyl-D-Aspartate receptor dynamics: Abnormalities induced by a Disc1 mutation modelling a translocation linked to major mental illness

The neuromodulatory gene DISC1 is disrupted by a t(1;11) translocation that is highly penetrant for schizophrenia and affective disorders, but how this translocation affects DISC1 function is incompletely understood. N-Methyl-D-Aspartate receptors (NMDAR) play a central role in synaptic plasticity and cognition, and are implicated in the pathophysiology of schizophrenia through genetic and functional studies. We show that the NMDAR subunit GluN2B complexes with DISC1-associated trafficking factor TRAK1, while DISC1 interacts with the GluN1 subunit and regulates dendritic NMDAR motility in cultured mouse neurons. Moreover, in the first mutant mouse that models DISC1 disruption by the translocation, the pool of NMDAR transport vesicles and surface/synaptic NMDAR expression are increased. Since NMDAR cell surface/synaptic expression is tightly regulated to ensure correct function, these changes in the mutant mouse are likely to affect NMDAR signalling and synaptic plasticity. Consistent with these observations, RNASeq analysis of translocation carrier-derived human neurons indicates abnormalities of excitatory synapses and vesicle dynamics. RNASeq analysis of the human neurons also identifies many differentially expressed genes previously highlighted as putative schizophrenia and/or depression risk factors through large-scale genome-wide association and copy number variant studies, indicating that the translocation triggers common disease pathways that are shared with unrelated psychiatric patients. Altogether our findings suggest that translocation-induced disease mechanisms are likely to be relevant to mental illness in general, and that such disease mechanisms include altered NMDAR dynamics and excitatory synapse function. This could contribute to the cognitive disorders displayed by translocation carriers.

neuroscience↗

bioRxiv2018

Muscle Stem Cell Niche Dysregulation in Volumetric Muscle Loss Injury

Skeletal muscle has a remarkable regenerative capacity; however, after volumetric muscle loss (VML) due to traumatic injury or surgery this regenerative response is significantly diminished, causing chronic functional deficits. The critical defect size at which the muscle will not functionally recover has not yet been established and subsequently, the relative contribution of crucial muscle components, including muscle stem cells and the muscle stem cell niche, are unknown. In this study, we created VML injuries of 2, 3, or 4 mm diameter, full-thickness defects in the mouse quadriceps. The 2, 3, and 4 mm injuries resulted in a defect of 5, 15, or 30% of the quadriceps mass, respectively. At 14 and 28 days after injury, histological analyses revealed injury size-dependent differences in myofiber morphology and fibrosis; the number of small myofibers increased with increasing injury size. The results showed that the 3 mm injury was at a threshold point, as myofibers were unable to bridge the defect, there was persistent fibrosis and inflammation, and significantly increased number of myofibers with centrally located nuclei. We then further investigated the 3 mm VML for nerve and vascular regeneration. These injured muscles were accompanied by a drastic increase in denervated neuromuscular junctions (NMJ), while assessment of angiogenesis via micro-CT analysis revealed a significant increase in vascular volume primarily from small diameter vessels after VML injury. Collectively, these data indicate that the spatial and temporal control of the fibrotic and neuromotor response are critical to regeneration and could be potential therapeutic targets, as they are the most dysregulated components of the muscle stem cell niche after VML.

bioengineering↗

bioRxiv2018

Increased speech representation in older adults originates from early response in higher order auditory cortex

1Previous research has found that, paradoxically, while older adults have more difficulty comprehending speech in challenging circumstances than younger adults, their brain responses track the acoustic signal more robustly. Here we investigate this puzzle by using magnetoencephalography (MEG) source localization to determine the anatomical origin of this difference. Our results indicate that this robust tracking in older adults does not arise merely from having the same responses as younger adults but with larger amplitudes; instead they recruit additional regions, inferior to core auditory cortex, as part of an early response peak at ~ 30 ms relative to the acoustic signal.

neuroscience↗

bioRxiv2018

BAP1 Loss Predicts Therapeutic Vulnerability in Malignant Peritoneal Mesothelioma

BackgroundMalignant Peritoneal Mesothelioma (PeM) is a rare but frequently fatal cancer that originates from the peritoneal lining of the abdomen. Standard treatment of PeM is limited to cytoreductive surgery and/or chemotherapy, and no effective targeted therapies for PeM yet exist. In the search for novel therapeutic target candidates in PeM, we performed a comprehensive integrative multi-omics analysis of 19 treatment-naive PeM tumors.\n\nResultsThe analysis identified PeM tumors with BAP1 loss to form a distinct molecular subtype characterized by distinct expression patterns of genes involved in chromatin remodeling, DNA repair pathway, and immune checkpoint receptor activation. This PeM subtype could potentially benefit from immune checkpoint, PARP, or HDAC inhibition therapies.\n\nConclusionsOur findings uncover BAP1 as a trackable prognostic and predictive biomarker, and refine PeM disease classification. This integrated molecular characterization provides a comprehensive foundation for developing PeM precision medicine.

cancer biology↗

bioRxiv2017

Video Assessment of Head Impact Exposure in American Football

Previous research has sought to quantify head impact exposure using wearable kinematic sensors. However, many sensors suffer from poor accuracy in estimating impact kinematics and count, motivating the need for additional independent impact exposure quantification for comparison. Here, we equipped seven collegiate American football players with instrumented mouthguards, and video recorded practices and games to compare video-based and sensor-based exposure rates and impact location distributions. Over 50 player-hours, we identified 271 helmet contact periods in video, while the instrumented mouthguard sensor recorded 2,032 discrete head impacts. Matching video and mouthguard real-time stamps yielded 193 video-identified helmet contact periods and 217 sensor-recorded impacts. To compare impact locations, we binned matched impacts into frontal, rear, side, oblique, and top locations based on video observations and sensor kinematics. While both video-based and sensor-based methods found similar location distributions, our best method utilizing integrated linear and angular position only correctly predicted 81 of 217 impacts. Finally, based on the activity timeline from video assessment, we also developed a new exposure metric unique to American football quantifying number of cross-verified sensor impacts per player-play. We found significantly higher exposure during games (0.35, 95% CI: 0.29-0.42) than practices (0.20, 95% CI: 0.17-0.23) (p<0.05). In the traditional impacts per player-hour metric, we observed higher exposure during practices (4.7) than games (3.7) due to increased player activity in practices. Thus, our exposure metric accounts for variability in on-field participation. While both video-based and sensor-based exposure datasets have limitations, they can complement one another to provide more confidence in exposure statistics.

bioengineering↗

bioRxiv2017

Representation of speech in noise in the aging midbrain and cortex: aging may dominate over hearing-loss

ObjectiveTo understand the effect of peripheral hearing loss on the representation of speech in noise in the aging midbrain and cortex.\n\nMethodsSubjects comprised 17 normal-hearing younger adults, 15 normal-hearing older adults and 14 hearing-impaired older adults. The midbrain response, measured with Frequency-Following Responses (FFRs), and the cortical response, measured with magnetoencephalography (MEG) responses, were recorded from subjects listening to speech in quiet and noise at varying signal to noise ratios (SNRs).\n\nResultsBoth groups of older listeners showed both weaker midbrain response amplitudes and overrepresentation of cortical responses compared to younger listeners. However, significant differences between the older groups were found in both midbrain-cortex relationships and in cortical processing durations, suggesting that hearing loss may alter reciprocal connections between lower and higher levels of the auditory pathway.\n\nConclusionsThe paucity of differences in midbrain or cortical responses between the two older groups suggest that age-related temporal processing deficits may contribute to older adults communication difficulties beyond what might be predicted from peripheral hearing loss alone.\n\nSignificanceClinical devices, such as hearing aids, should not ignore age-related temporal processing deficits in the design of algorithms to maximize user benefit.\n\nHIGHLIGHTSO_LIMild sensorineural hearing loss does not appear to significantly exacerbate already appreciable age-related deficits in midbrain speech-in-noise encoding.\nC_LIO_LIMild sensorineural hearing loss also does not appear to significantly exacerbate already appreciable age-related deficits in most measures of cortical speech-in-noise encoding.\nC_LIO_LICentral processing deficits caused by peripheral hearing loss in older adults are seen only in more subtle measures, including altered relationships between midbrain and cortex.\nC_LI

neuroscience↗

bioRxiv2017

A toolbox of immunoprecipitation-grade monoclonal antibodies against human transcription factors.

A key component to overcoming the reproducibility crisis in biomedical research is the development of readily available, rigorously validated and renewable protein affinity reagents. As part of the NIH Protein Capture Reagents Program (PCRP), we have generated a collection of 1406 highly validated, immunoprecipitation (IP) and/or immunoblotting (IB) grade, mouse monoclonal antibodies (mAbs) to 736 human transcription factors. We used HuProt human protein microarrays to identify mAbs that recognize their cognate targets with exceptional specificity. Using an integrated production and validation pipeline, we validated these mAbs in multiple experimental applications, and have distributed them to the Developmental Studies Hybridoma Bank (DSHB) and several commercial suppliers. This study allowed us to perform a meta-analysis that identified critical variables that contribute to the generation of high quality mAbs. We find that using full-length antigens for immunization, in combination with HuProt analysis, provides the highest overall success rates. The efficiencies built into this pipeline ensure substantial cost savings compared to current standard practices.

biochemistry↗