Biology subjects

Wilson, P.

Publications and source records attributed to Wilson, P..

31 records · Page 2Linked to original sources

bioRxiv2023

A novel protocol for magnetoencephalographic mapping of speech motor control regions during speech production.

Neuroimaging protocols for mapping of expressive speech centres employ several standard speech tasks including object naming, rhyming, and covert word production (Agarwal et al., 2019). These tasks reliably elicit activation of distributed speech centres in prefrontal, precentral and cingulate motor cortices and are widely used for presurgical mapping and in research studies of language production. In the present study we used an alternative speech protocol employing reiterated productions of simple disyllabic nonwords (VCV; Anastasopoulou et al., 2022; van Lieshout et al., 2007). Here we show that this task elicits highly focal and highly lateralised activations of speech motor control areas centred on the precentral gyrus and adjacent portions of the middle frontal gyrus. 10 healthy adults, 19 typically developing children and 7 children with CAS participated in the study. MEG scans were carried out with a whole-head MEG system consisting of 160 first-order axial gradiometers with a 50 mm baseline (Model PQ1160R-N2, KIT, Kanazawa, Japan). MEG data were acquired with analog filter settings of 0.03 Hz high-pass, 1,000 Hz low-pass, 4,000 Hz sampling rate. Measurements were carried out with participants in supine position in a magnetically shielded room (Fujihara Co. Ltd., Tokyo, Japan). Time-aligned speech acoustics were recorded in an auxiliary channel of the MEG setup at the same sample rate as the MEG recordings. Brain activity was recorded while participants produced reiterated utterances of /ipa/ and /api/, at normal and speeded rates in addition to a button press task (right index finger) to elicit activity in the hand region of sensorimotor cortex (e.g. Johnson et al., 2020). MEG data were co-registered with individual structural MRI scans obtained in a separate scanning session. Source reconstruction was performed with synthetic aperture magnetometry (SAM) beamformer implemented in Matlab (Jobst et al., 2018) and group statistics performed with permutation tests (p < 0.05). Button press map shows clusters encompassing dorsal precentral and postcentral gyri (Brodmann areas 4 and 6), corresponding to hand sensorimotor cortices. Speech map shows clusters encompassing precentral gyrus immediately ventral to hand motor cortex (BA6), and an immediately adjacent portion of the posterior middle frontal gyrus. Both button press and speech result in a robust desynchronisation restricted within a frequency band of about 13-30 Hz (beta band). Our results show that the reiterated speech task results in robust beta-band desynchronisation in a highly focal region of the precentral gyrus, located immediately ventral to the hand motor region of the precentral gyrus. In adults, speech motor -related brain activity was predominantly observed in the left hemisphere. Typically developing children, on the other hand, exhibited bilateral activation and in the case of individuals with CAS exhibited only right-hemisphere activation. Taken together the present findings provide a non-invasive and highly selective window on a crucial node of the expressive speech network that has previously been accessed only with invasive electrophysiological means and lesion studies.

neuroscience↗

bioRxiv2023

Skeletal progenitor LRP1-mediated endocytosis is critical for synovial joint formation and bone growth

Low-density lipoprotein receptor-related protein 1 (LRP1) is a multifunctional endocytic receptor whose dysfunction is linked to developmental dysplasia of the hip, osteoporosis and osteoarthritis. Our work addresses the critical question of how these skeletal pathologies emerge. Here, we show the abundant expression of LRP1 in skeletal progenitor cells at mouse embryonic stage E13.5 and onwards, especially in the perichondrium, the stem cell layer surrounding developing limbs essential for bone formation. Lrp1 deficiency in these stem cells causes joint fusion, malformation of cartilage/bone template and markedly delayed or lack of primary ossification along with aberrant accumulation of some of the LRP1 ligands at as early as E16.5. These early abnormalities result in multiple and persistent skeletal defects including a severe deficit in hip joint and patella, and markedly deformed and low-density long bones leading to dwarfism and impaired mobility. Mechanistically, we show that LRP1 regulates core non-canonical WNT/planar cell polarity (PCP) components that may explain the malformation of long bones. LRP1 directly binds to Wnt5a, facilitates its cell-association and endocytic recycling. Using Xenopus as a model system we show that loss or gain of LRP1 function leads to shortened tadpoles similar to Wnt5a and Wnt11 overexpression, indicating a role for LRP1 in WNT/PCP signalling. Finally, we show the colocalisation LRP1 and Wnt5a in the developing mouse limbs and that Lrp1 deficiency diminishes graded distribution of Wnt5a and Vangl2. We propose that skeletal progenitor LRP1 plays a critical role in formation and maturity of multiple bones and joints by regulating morphogen signalling, providing novel insights into the fundamental processes of morphogenesis and the emergence of skeletal pathologies.

developmental biology↗

bioRxiv2023

A hybrid single-cell demultiplexing strategy that increases both cell recovery rate and calling accuracy

Recent advances in single cell RNA sequencing allow users to pool multiple samples and demultiplex in downstream analysis, which greatly increase experimental efficiency and cost-effectiveness. Among all the demultiplexing methods, nucleotide barcode-based cell hashing has gained widespread popularity due to its compatibility and simplicity. Despite these advantages, certain issues of this technic remain to be solved, such as challenges in distinguishing true positive from background, high reagent cost for samples with large cell numbers, and unpredictable false negative and false doublet rates. Here, we propose a hybrid demultiplexing strategy that increases calling accuracy and cell recovery of cell hashing without adding experimental cost. In this approach, we computationally cluster all single cells based on their natural genetic variations and assign donor identity by finding the dominant hashtag in each genotype cluster. This hybrid strategy assigns donor identity to any cell that is identified as singlet by either genotype clustering or cell hashing, which allows us to demultiplex most majority of cells even if only a small fraction of cells are labeled with hashtags. When comparing its performance with cell hashing on multiple real-world datasets, this hybrid approach consistently generates reliable demultiplexing results with increased cell recovery and accuracy. Key PointsO_LIThe improved cut-off calling tool, HTOreader, accurately distinguishes true positive from background signal for each individual hashtag. C_LIO_LIThe hybrid demultiplexing strategy increases cell recovery of cell hashing by increasing cut-off calling accuracy and decreasing false negative and false double rates. C_LIO_LIThe hybrid strategy enhances cost-effectiveness of cell hashing and consistently produces reliable demultiplexing results, regardless of hashtag staining quality. C_LIO_LIThe hybrid strategy can be seamlessly integrated into a variety of single-cell experimental protocols and analytic pipelines. C_LI

bioinformatics↗

bioRxiv2023

A standard protocol to report discrete stage-structured demographic information

O_LIStage-based demographic methods, such as matrix population models (MPMs), are powerful tools used to address a broad range of fundamental questions in ecology, evolutionary biology, and conservation science. Accordingly, MPMs now exist for over 3,000 species worldwide. These data are being digitised as an ongoing process and periodically released into two large open-access online repositories: the COMPADRE Plant Matrix Database and the COMADRE Animal Matrix Database. During the last decade, data archiving and curation of COMPADRE and COMADRE, and subsequent comparative research, have revealed pronounced variation in how MPMs are parameterized and reported. C_LIO_LIHere, we summarise current issues related to the parameterisation and reporting of MPMs that arise most frequently and outline how they affect MPM construction, analysis, and interpretation. To quantify variation in how MPMs are reported, we present results from a survey identifying key aspects of MPMs that are frequently unreported in manuscripts. We then screen COMPADRE and COMADRE to quantify how often key pieces of information are omitted from manuscripts using MPMs. C_LIO_LIOver 80% of surveyed researchers (n=60) state a clear benefit to adopting more standardised methodologies for reporting MPMs. Furthermore, over 85% of the 300 MPMs assessed from COMPADRE and COMADRE omitted one or more elements that are key to their accurate interpretation. Based on these insights, we identify fundamental issues that can arise from MPM construction and communication and provide suggestions to improve clarity, reproducibility, and future research utilising MPMs and their required metadata. To fortify reproducibility and empower researchers to take full advantage of their demographic data, we introduce a standardized protocol to present MPMs in publications. This standard is linked to www.compadre-db.org, so that authors wishing to archive their MPMs can do so prior to submission of publications, following examples from other open-access repositories such as DRYAD, Figshare, and Zenodo. C_LIO_LICombining and standardising MPMs parameterized from populations around the globe and across the tree of life opens up powerful research opportunities in evolutionary biology, ecology, and conservation research. However, this potential can only be fully realised by adopting standardised methods to ensure reproducibility. C_LI

ecology↗

bioRxiv2022

Defining transcription factor nucleosome binding with Pioneer-seq

Gene expression requires the targeting of transcription factors (TFs) to regulatory sequences often occluded within nucleosomes. To comprehensively examine TF nucleosome binding, we developed Pioneer-Seq. In Pioneer-seq a library of nucleosomes containing thousands of DNA sequences with TF binding sites in all possible nucleosome orientations is bound to a TF and the protein-nucleosome complex is isolated and quantified. To demonstrate Pioneer-seq we examined nucleosome binding by OCT4, SOX2, KLF4, and c-MYC. Our results demonstrate that KLF4 and SOX2 can bind close to the nucleosome dyad with nucleosome sequence being the major factor regulating TF binding across all studied TFs.

molecular biology↗

bioRxiv2022

Visual Perception of 3D Space and Shape in Time - Part I: 2D Space Perception by 2D Linear Translation

Visual perception plays a critical role in navigating space and extracting useful semantic information crucial to survival. To identify distant landmarks, we constantly shift gaze vectors through saccades, while still maintaining the visual perception of stable allocentric space. How can we sustain stable allocentric space so effortlessly? To solve this question, we have developed a new concept of NHT (Neural Holography Tomography). This model states that retinotopy is invisible (not available to consciousness) and must be converted to a time code by traveling alpha brainwaves to perceive objects consciously. According to this framework, if identical alpha phases are continually assigned to a landmark, we perceive its exact and consistent allocentric location. To test this hypothesis, we designed reaction time (RT) experiments to observe evidence of the predicted space-to-time conversion. Various visual stimuli were generated at a wide range of eccentricities either on a large TV (up to 40{degrees}) or by LED strips on a hemispherical dome (up to 60{degrees}). Participants were instructed to report the observed patterns promptly under either covert (no eye movement) or overt (with eye movement) conditions. As predicted, stimuli presented at the center of fixation always produced the fastest RTs. The additional RT delay was precisely proportional to the eccentricity of the peripheral stimulus presentation. Furthermore, both covert and overt attention protocols created the same RT delays, and trajectories of saccadic eye motions were in parallel to the overt RT vs. eccentricity. These findings strongly support our NHT model, in which the observed RT-eccentricity dependence is indicative of the spatiotemporal conversion required for maintaining a stable allocentric frame of reference. That is, we perceive space by time.

neuroscience↗

bioRxiv2022

Visual Perception of 3D Space and Shape in Time - Part III: 2D Shape Recognition by Log-Scaling

Human vision has a remarkable ability to recognize complex 3D objects such as faces that appear with any size and 3D orientations at any 3D location. If we initially memorize a face only with a normalized size and viewed from directly head on, the direct comparison between the one-sized memory and a new incoming image would demand tremendous mental frame translations in 7D. How can we perform such a demanding task so promptly and reliably as we experience the objects in the world around us? Intriguingly, our primary visual cortex exhibits a 2D retinotopy with a log-polar coordinate system, where scaling up/down of shape is converted to linear frame translation. As a result, mental scaling can be performed by linearly translating the memory or the perceptual image until they overlap with each other. According to our new model of NHT (Neural Holography Tomography), alpha brainwaves traveling at a constant speed can conduct this linear translation. With this scheme, every scaling up/down by a factor of two should take the same amount of extra mental time to recognize a smaller/larger face. To test this hypothesis, we designed a reaction time (RT) experiment, where participants were first asked to memorize sets of unfamiliar faces with a given specific size (4{degrees} or 8{degrees}). Following the memorization phase, similar stimuli with a wide range of sizes (from 1{degrees} to 32{degrees}) were presented, and RTs were recorded. As predicted, the increase in RT was proportional to the scaling factor in the log scale. Furthermore, we observed that RTs were fastest for 8{degrees} faces even if the memorized face was 4{degrees}. This supports our hypothesis that we always memorize faces at the exact size of ~8 {degrees}. To our surprise, the increases in RT were also consistent with the mentally-estimated depth sensation, which indicates that the apparent size of the recognized face can create a proper depth sensation.

neuroscience↗

bioRxiv2022

Visual Perception of 3D Space and Shape In Time - Part IV: 3D Shape Recognition by 3D Rotation

Human vision has a remarkable ability to recognize complex 3D objects such as faces that appear at any size and 3D orientations at any 3D location. If we initially memorize a face only with a normalized size upfront at the object center, the direct comparison between the one-sized memory and an incoming new image would demand tremendous mental frame translations in 7D. How can we perform such a demanding task so promptly as we experience it in our daily lives? This paper specifically addresses the recognition of human faces with arbitrary 3D orientation in the [Roll, Yaw, Pitch] axes. According to our new model of NHT (Neural Holography Tomography), space is represented by time utilizing the phase of the alpha brainwave. This principle should be applicable to any mental rotation in 3D; thus, it predicts that extra time is required to perceive a rotated face to revolve it back to upright by the constant-speed alpha wave. To assess this hypothesis, we designed a reaction time (RT) experiment, where participants were first asked to memorize sets of upright unfamiliar faces. Following the memorization phase, similar stimuli with a wide range of rotating faces in 3D were presented, and RTs were recorded. As expected, the memorized upfront face was the fastest RT. The excess of the RT was observed proportional to the rotating angle in all [Roll, Yaw, Pitch] axes. Roll had the flattest slope, whereas upper Pitch was the steepest. We suspect that Roll is the swiftest mental operation because it can be conducted by the linear frame translation on the log-polar retinotopy of the visual cortex.

neuroscience↗

bioRxiv2021

More sustainable vegetable oil: balancing productivity with carbon storage opportunities

Intensive cultivation and post-harvest vegetable oil production stages are major sources of greenhouse gas (GHG) emissions. Variation between production systems and reporting disparity have resulted in discordance in previous emissions estimates. To assess systems-wide GHG implications of meeting increasing edible oil demand, we performed a unified re-analysis of life cycle input data from diverse oil palm, soybean, rapeseed, and sunflower production systems, from a saturating search of published literature. The resulting dataset reflects almost 6,000 producers in 38 countries, and is representative of over 74% of global vegetable oil production. Determination of the carbon cost of agricultural land occupation revealed that carbon storage potential drives variation in production GHG emissions, and indicates that expansion of production in low carbon storage potential land, whilst reforesting areas of high carbon storage potential, could reduce net GHG emissions whilst boosting productivity. Nevertheless, there remains considerable scope to improve sustainability within current production systems.

ecology↗

bioRxiv2021

Novel epitopes of human monoclonal antibodies targeting the influenza virus N1 neuraminidase

Influenza virus neuraminidase (NA) targeting antibodies are an independent correlate of protection against infection. Antibodies against the NA act by blocking enzymatic activity, preventing virus release and transmission. As we advance the development of improved influenza virus vaccines that incorporate standard amounts of NA antigen, it is important to identify the antigenic targets of human monoclonal antibodies (mAbs). Additionally, it is important to understand how escape from mAbs changes viral fitness. Here, we describe escape mutants generated by serial passage of A/Netherlands/602/2009 (H1N1) in the presence of human anti-N1 mAbs. We observed escape mutations on the N1 protein around the enzymatic site (S364N, N369T and R430Q) and also detected escape mutations located on the sides and bottom of the NA (N88D, N270D and Q313K/R). We found that a majority of escape mutant viruses had increased fitness in vitro but not in vivo. This work increases our understanding of how human antibody responses target the N1 protein. ImportanceAs improved influenza virus vaccines are being developed, the influenza virus neuraminidase (NA) is becoming an important new target for immune responses. By identifying novel epitopes of anti-NA antibodies, we can improve vaccine design. Additionally, characterizing changes in viruses containing mutations in these epitopes aids in identifying effects of NA antigenic drift.

microbiology↗

bioRxiv2020

Biochemical Patterns of Antibody Polyreactivity Revealed Through a Bioinformatics-Based Analysis of CDR Loops

Antibodies are critical components of adaptive immunity, binding with high affinity to pathogenic epitopes. Antibodies undergo rigorous selection to achieve this high affinity, yet some maintain an additional basal level of low affinity, broad reactivity to diverse epitopes, a phenomenon termed "polyreactivity". While polyreactivity has been observed in antibodies isolated from various immunological niches, the biophysical properties that allow for promiscuity in a protein selected for high affinity binding to a single target remain unclear. Using a database of nearly 1,500 polyreactive and non-polyreactive antibody sequences, we created a bioinformatic pipeline to isolate key determinants of polyreactivity. These determinants, which include an increase in inter-loop crosstalk and a propensity for an "inoffensive" binding surface, are sufficient to generate a classifier able to identify polyreactive antibodies with over 75% accuracy. The framework from which this classifier was built is generalizable, and represents a powerful, automated pipeline for future immune repertoire analysis.

immunology↗

bioRxiv2020

The complete genome sequence of the Staphylococcus bacteriophage Metroid

Phages infecting bacteria of the genus Staphylococcus play an important role in their hosts ecology and evolution. On one hand, horizontal gene transfer from phage can encourage the rapid adaptation of pathogenic Staphylococcus enabling them to escape host immunity or access novel environments. On the other hand, lytic phages are promising agents for the treatment of bacterial infections, especially those resistant to antibiotics. As part of an ongoing effort to gain novel insights into bacteriophage diversity, we characterized the complete genome of the Staphylococcus bacteriophage Metroid, a cluster C phage with a genome size of 151kb, encompassing 254 predicted protein-coding genes as well as 4 tRNAs. A comparative genomic analysis highlights strong similarities - including a conservation of the lysis cassette - with other Staphylococcus cluster C1 bacteriophages, several of which were previously characterized for therapeutic applications.

genomics↗

bioRxiv2020

Cell profiling of mouse acute kidney injury reveals conserved cellular responses to injury

After acute kidney injury (AKI), patients either recover or alternatively develop fibrosis and chronic kidney disease. Interactions between injured epithelia, stroma and inflammatory cells determine whether kidneys repair or undergo fibrosis, but the molecular events that drive these processes are poorly understood. Here, we use single nucleus RNA sequencing of a mouse model of AKI to characterize cell states during repair from acute injury. We identify a distinct proinflammatory and profibrotic proximal tubule cell state that fails to repair. Deconvolution of bulk RNA-seq datasets indicates that this "failed-repair proximal tubule cell" or FR-PTC, state can be detected in other models of kidney injury, increasing in the aging rat kidney and over time in human kidney allografts. We also describe dynamic intercellular communication networks and discern transcriptional pathways driving successful vs. failed repair. Our study provides a detailed description of cellular responses after injury and suggests that the FR-PTC state may represent a therapeutic target to improve repair. Significance StatementSingle nucleus RNA sequencing revealed gene expression changes during repair after acute kidney injury. We describe a small population of proximal tubule cells that fail to repair (FR-PTC). Since this subpopulation expresses abundant pro-inflammatory and profibrotic genes, it may represent a new therapeutic target to improve repair and reduce fibrosis after AKI.

genomics↗