Biology subjects

Ma, K.

Publications and source records attributed to Ma, K..

At least 55 records · Page 3Linked to original sources

bioRxiv2024

Incomplete lineage sorting of segmental duplications defines the human chromosome 2 fusion site early during African great ape speciation

All great apes differ karyotypically from humans due to the fusion of chromosomes 2a and 2b, resulting in human chromosome 2. Yet, the structure, function, and evolutionary history of the genomic regions associated with this fusion remain poorly understood. Here, we analyze finished telomere-to-telomere chromosomes in great apes and macaques to show that the fusion was associated with multiple pericentric inversions, segmental duplications (SDs), and the rapid turnover of subterminal repetitive DNA. We characterized the fusion site at single-base-pair resolution and identified three distinct SDs that originated more than 5 million years ago. These three distinct SDs were differentially distributed among African great apes as a result of incomplete lineage sorting (ILS) and lineage-specific duplication. Most conspicuously, one of these SDs shares homology to a hypomethylated SD spacer sequence present in hundreds of copies in the subterminal heterochromatin of chimpanzees and bonobos. The fusion in human was accompanied by a systematic degradation of the three divergent -satellite arrays representing the ancestral centromere creating five distinct structural haplotypes in humans. CRISPR/Cas9-mediated depletion of the fusion site in human cell lines significantly alters the expression of 108 genes, indicating a potential regulatory consequence to this human-specific karyotypic change.

evolutionary biology↗

bioRxiv2024

Separating three variability and noise sources in the response fluctuation of brain stimulation

Motor-evoked potentials (MEPs) are among the few directly observable responses to suprathreshold brain stimulation and serve a variety of applications. If the MEP size is graphed over the stimulation strength, they form an input-output (IO), recruitment, or dose-response curve. Previous statistical models with two variability sources inherently consider the small MEPs at the low plateau as part of the neural recruitment properties. However, recent studies demonstrated that small MEP responses are contaminated and over-shadowed by background noise of mostly technical quality and suggested that the recruitment curve should continue below this noise level. This work intends to separate physiological variability from background noise and improve the description of recruitment behaviour. We developed a model with three variability sources and a logarithmic logistic function without a lower plateau. Compared to previous models, we incorporated an additional source for background noise from amplifiers, electrode impedance, and remote bioelectric activity, which form the obesrved low-side plateau. Compared to the dual-variability source modes, our approach better described IO characteristics, evidenced by lower Bayesian Information Criterion scores across all subjects and pulse shapes. The model independently extracted hidden variability information across the stimulated neural system and isolated it from background noise, which led to an accurate estimation of the IO curve parameters. This new model offers a robust tool to analyse brain stimulation IO curves in clinical and experimental neuroscience, reducing the risk of spurious results from inappropriate statistical methods. By providing a more accurate representation of MEP responses and variability sources, this approach advances our understanding of cortical excitability and may improve the assessment of neuromodulation effects.

neuroscience↗

bioRxiv2024

Single-Cell and Spatial Multi-omics Reveal Interferon Signaling in the Pathogenesis of Perianal Fistulizing Crohn's Disease

Background & AimsPerianal fistulizing Crohns disease (PCD) is a common and debilitating complication with elusive pathophysiology. We examined mucosal cells from patients with PCD and related conditions using a multi-omics approach. MethodsWe recruited patients with PCD (n = 24), CD without perianal disease (NPCD, n = 10), and idiopathic perianal fistulas (IPF, n = 29). Biopsies were taken from fistula tracts, fistula opening, and rectal mucosa. Single-cell RNA-sequencing (scRNA-seq), mass cytometry (CyTOF), spatial transcriptomics (ST), immunohistochemistry, and integrated analysis were performed. ResultsScRNA-seq, CyTOF, and ST unraveled immune and non-immune cell compartments in PCD and IPF fistula tracts. PCD fistulas showed hyperactivated pathogenic pathways including interferon (IFN)G response and TNF signaling in myeloid and stromal cells. Intestinal cells from PCD patients also expressed greater levels of IFNG-responsive and EMT genes compared to NPCD patients. Furthermore, both fistula tracts and ileal mucosa from PCD patients harbored expanded IFNG+ pathogenic Th17 cells, which expressed elevated inflammatory mediators. CyTOF also identified skewed immune cell phenotypes in the fistula tracts, fistula opening, and rectum in PCD patients including expanded Th17 cells, increased pathogenic myeloid cells, and altered T cell exhaustion markers. Further analysis also revealed cellular modules associated with anti-TNF therapy in PCD patients. ConclusionMulti-omics analysis revealed immune, stromal, and epithelial cell landscapes of PCD, which highlight the pathogenic role of hyperactivated IFNG signaling in both fistula tracts and luminal mucosa. This study identified IFNG as a potential therapeutic target for PCD.

systems biology↗

bioRxiv2024

Multi-dimensionality of tree communities structure host-parasitoid networks and their phylogenetic composition

Environmental factors can influence ecological networks, but these effects are poorly understood in the realm of the phylogeny of host-parasitoid interactions. Especially, we lack a comprehensive understanding of the ways that biotic factors, including plant species richness, overall community phylogenetic and functional composition of consumers, and abiotic factors such as microclimate, determining host-parasitoid network structure and host-parasitoid community dynamics. To address this, we leveraged a five-year dataset of trap-nesting bees and wasps and their parasitoids collected in a highly-controlled, large-scale subtropical tree biodiversity experiment. We tested for effects of tree species richness, tree phylogenetic and functional diversity, and species and phylogenetic composition on species and phylogenetic diversity of both host and parasitoid communities and the composition of their interaction networks. We show that multiple components of tree diversity and canopy cover impacted both, species and phylogenetic composition of hosts and parasitoids. Generally, phylogenetic associations between hosts and parasitoids reflected non-randomly structured interactions between phylogenetic trees of hosts and parasitoids. Further, host-parasitoid network structure was influenced by tree species richness, tree phylogenetic diversity, and canopy cover. Our study indicates that the composition of higher trophic levels and corresponding interaction networks are determined by plant diversity and canopy cover especially via trophic links in species-rich ecosystems.

ecology↗

bioRxiv2024

Leeches Predate on Fast-Escaping and Entangling Blackworms by Spiral Entombment

We investigate how the Helobdella spp. freshwater leeches capture and consume Lumbriculus variegatus blackworms despite the blackworms ultrafast helical swimming escape reflex and ability to form large tangled blobs. We describe our discovery of a unique spiral entombment strategy used by these leeches to overcome the blackworms active and collective defenses. Unlike their approach to less reactive and solitary prey like mollusks, where leeches simply attach and suck, Helobdella leeches employ this spiral entombment strategy specifically adapted for blackworms. Our findings highlight the complex interactions between predator and prey in freshwater ecosystems, providing insights into ecological adaptability and predator-prey dynamics.

animal behavior and cognition↗

bioRxiv2024

Nicotine Ameliorates α-synuclein Pre-formed Fibril-Induced Behavioral Deficits and Pathological Features in Mice

BackgroundEpidemiologic study suggests nicotine reduces risk of PD, could be potential treatment for Parkinsons disease. ObjectiveTo study the effect of nicotine on behavioral phenotypes and pathological characteristics of mice induced by human alpha-synuclein preformed fibers (-syn-PFF). MethodsMice were injected with 5 g of human -syn-PFF in the hippocampus while administering nicotine-containing drinking water (200g/mL). After 1 month, the motor ability, mood, spatial learning, and memory ability of the Parkinsons disease(PD)phenotype-like model were detected using open field, rotarod, Y maze, and O maze tests. The expression of pathological -syn, apoptotic proteins and the numbers of glial cells and neural stem cells in the hippocampus of mice were detected using western blotting and immunofluorescence. ResultsNicotine significantly reduced pathological -syn accumulation, -syn serine 129 phosphorylation and cell death caused by PFF injection in the hippocampus of mice, inhibited the increase of glial, microglia and apoptotic cells, decreased the expression levels of PI3K and Akt. ConclusionsNicotine may have inhibitory effects on human -syn-PFF-induced neuroinflammation and apoptosis. Thus, it reduces human -syn-PFF-induced behavioral deficits and pathological changes in mice.

animal behavior and cognition↗

bioRxiv2024

Comparative genomics of macaques and integrated insights into genetic variation and population history

The crab-eating macaques (Macaca fascicularis) and rhesus macaques (M. mulatta) are widely studied nonhuman primates in biomedical and evolutionary research. Despite their significance, the current understanding of the complex genomic structure in macaques and the differences between species requires substantial improvement. Here, we present a complete genome assembly of a crab-eating macaque and 20 haplotype-resolved macaque assemblies to investigate the complex regions and major genomic differences between species. Segmental duplication in macaques is [~]42% lower, while centromeres are [~]3.7 times longer than those in humans. The characterization of [~]2 Mbp fixed genetic variants and [~]240 Mbp complex loci highlights potential associations with metabolic differences between the two macaque species (e.g., CYP2C76 and EHBP1L1). Additionally, hundreds of alternative splicing differences show post-transcriptional regulation divergence between these two species (e.g., PNPO). We also characterize 91 large-scale genomic differences between macaques and humans at a single-base-pair resolution and highlight their impact on gene regulation in primate evolution (e.g., FOLH1 and PIEZO2). Finally, population genetics recapitulates macaque speciation and selective sweeps, highlighting potential genetic basis of reproduction and tail phenotype differences (e.g., STAB1, SEMA3F, and HOXD13). In summary, the integrated analysis of genetic variation and population genetics in macaques greatly enhances our comprehension of lineage-specific phenotypes, adaptation, and primate evolution, thereby improving their biomedical applications in human diseases.

genomics↗

bioRxiv2024

Monocyte to macrophage differentiation and changes in cellular redox homeostasis promote cell type-specific HIV latency reactivation

Human Immunodeficiency Virus (HIV) latency regulation in monocytes and macrophages can vary according to signals directing differentiation, polarization, and function. To investigate these processes, we generated an HIV latency model in THP-1 monocytes and showed differential levels of HIV reactivation among clonal populations. Monocyte-to-macrophage differentiation of HIV-infected primary human CD14+ and THP-1 cells induced HIV reactivation and showed that virus production increased concomitant with macrophage differentiation. We applied the HIV-infected THP-1 monocyte-to- macrophage (MLat) model to assess the biological mechanisms regulating HIV latency dynamics during monocyte-to-macrophage differentiation. We pinpointed PKC signaling pathway activation and Cyclin T1 upregulation as inherent differentiation mechanisms that regulate HIV latency reactivation. Macrophage polarization regulated latency, revealing pro-inflammatory M1 macrophages suppressed HIV reactivation while M2 macrophages promoted HIV reactivation. Because macrophages rely on reactive- oxygen species (ROS) to exert numerous cellular functions, we disrupted redox pathways and discovered that inhibitors of the thioredoxin (Trx) system acted as latency promoting agents (LPAs) in T-cells and monocytes, but opposingly acted as latency reversing agents (LRAs) in macrophages. We explored this mechanism with Auranofin, a clinical candidate for reducing HIV reservoirs, and demonstrated Trx reductase (TrxR) inhibition led to ROS induced NF-{kappa}B activity, which promoted HIV reactivation in macrophages, but not in T-cells and monocytes. Collectively, cell type-specific differences in HIV latency regulation could pose a barrier to HIV eradication strategies.

microbiology↗

bioRxiv2024

A user-friendly input-output (IO) curve analysis tool for variable brain stimulation responses, particularly evoked potentials in transcranial magnetic stimulation (TMS)

BackgroundMotor-evoked potentials (MEPs) are among the few readily observable direct responses to suprathreshold stimuli administered to the brain. They serve for a variety of applications, often in the form of dose-response curves, also called recruitment or input-output (IO) curves. However, MEPs and thus IO curves demonstrate extreme trial-to-trial variability that can exceed more than two decimal orders of magnitude. Recent studies have identified issues in previous statistical analysis of IO curves and introduced better methods, others could quantitatively separate several widely independent variability sources. However, research has failed providing the field with a user-friendly implementation of the methods for analysing such IO curves statistically sound and separating variability so that they were limited to a few research groups. ObjectiveThis work intends to provide the latest methods for analysing IO curves and extract variability information in an open-source package so that the community can easily use and adapt them to their own needs. MethodsWe implemented recent IO curve methods with a graphical user interface and provided the code as well as compiled versions for Mac, Linux, and Windows. ResultsThe application imports typical IO data of individual stimulus-response sets, guides users step by step through the analysis, and allows exporting of the results including figures for post-hoc analysis and documentation. ConclusionThis graphical application offers a user-friendly environment for analysing the variability of evoked potentials and its various contributions, catering to the needs of clinical and experimental neuroscientists.

bioinformatics↗

bioRxiv2023

MolPad: An R-Shiny Package for Cluster Co-Expression Analysis in Longitudinal Microbiomics

The R-Shiny package MolPad provides an interactive dashboard for understanding the dynamics of longitudinal molecular co-expression in microbiomics. The main idea for addressing the issue is first to use a network to overview major patterns among their predictive relationships and then zoom into specific clusters of interest. It is designed with a focus-plus-context analysis strategy and automatically generates links to online curated annotations. The dashboard consists of a cluster-level network, a bar plot of taxonomic composition, a line plot of data modalities, and a table for each pathway. Further, the package includes functions that handle the data processing for creating the dashboard. This makes it beginner-friendly for users with less R programming experience. We illustrate these methods with a case study on a longitudinal metagenomics analysis of the cheese microbiome.

microbiology↗

bioRxiv2023

Anti-adipogenic properties of clock activator chlorhexidine and a new derivative

BackgroundThe circadian clock exerts temporal control of metabolic pathways to maintain homeostasis, and its disruption leads to the development of obesity and insulin resistance. In adipose tissue, key regulators of clock machinery orchestrate adipogenic processes via the Wnt signaling pathway to impact mature adipocyte development. MethodsBased on the recent finding of chlorhexidine as a new clock activator, we determined its potential anti-adipogenic activities in distinct adipogenic progenitor models. Furthermore, we report the structural optimization of chlorhexidine leading to the discovery of analogs with improved efficacy in inhibiting adipogenesis. ResultsIn adipogenic progenitors with Per2::dLuc luciferase reporter, Chlorhexidine shortened clock period length with induction of core clock components. Consistent with its clock-activating function, Chlorhexidine robustly suppressed the lineage commitment and maturation of adipogenic mesenchymal precursors, with comparable effect on inhibiting preadipocyte terminal differentiation. Mechanistically, we show that Chlorhexidine induces signaling components of the Wnt pathway resulting in activation of Wnt activity. Via modification of its chemical scaffold, we generated analogs of chlorhexidine that led to the identification of CM002 as a new clock- activating molecule with improved anti-adipogenic activity. ConclusionsCollectively, our findings uncovered the anti-adipogenic functions of a new class of small molecule clock activators. These compounds provide novel chemical probes to dissect clock function in maintaining metabolic homeostasis and may have therapeutic implications in obesity and associated metabolic disorders.

cell biology↗

bioRxiv2023

The clinical, genomic, and transcriptomic landscape of BRAF mutant cancers

BackgroundBRAF mutations are classified into 4 molecularly distinct groups, and Class 1 (V600) mutant tumors are treated with targeted therapies. Effective treatment has not been established for Class 2/3 or BRAF Fusions. We investigated whether BRAF mutation class differed according to clinical, genomic, and transcriptomic variables in cancer patients. MethodsUsing the AACR GENIE (v.12) cancer database, the distribution of BRAF mutation class in adult cancer patients was analyzed according to sex, age, primary race, and tumor type. Genomic alteration data and transcriptomic analysis was performed using The Cancer Genome Atlas. ResultsBRAF mutations were identified in 9515 (6.2%) samples among 153,834, with melanoma (31%), CRC (20.7%), and NSCLC (13.9%) being the most frequent cancer types. Class 1 harbored co-mutations outside of the MAPK pathway (TERT, RFN43) vs Class 2/3 mutations (RAS, NF1). Across all tumour types, Class 2/3 were enriched for alterations in genes involved in UV response and WNT/{beta}-catenin. Pathway analysis revealed enrichment of WNT/{beta}-catenin and Hedgehog signaling in non-V600 mutated CRC. Males had a higher proportion of Class 3 mutations vs. females (17.4% vs 12.3% q = 0.003). Non-V600 mutations were generally more common in older patients (aged 60+) vs younger (38% vs 15% p<0.0001), except in CRC (15% vs 30% q = 0.0001). Black race was associated with non-V600 BRAF alterations (OR: 1.58; p<0.0001). ConclusionsClass 2/3 BRAF are more present in Black, male patients with co-mutations outside of the MAPK pathway, likely requiring additional oncogenic input for tumorigenesis. Improving access to NGS and trial enrollment will help development of targeted therapies for non-V600 BRAF mutations. Statement of Translational RelevanceBRAF mutations are classified in 4 categories based on molecular characteristics, but only Class 1 BRAF V600 have effective targeted treatment strategies. With increasing access to next-generation sequencing, oncologists are more frequently uncovering non-V600 BRAF mutations, where there remains a scarcity of effective therapies. Responsiveness to MAPK pathway inhibitors differs according to BRAF mutation class and primary tumor type. For this reason, we sought to determine whether key demographic, genomic, and transcriptomic differences existed between classes. This cross-sectional study analyzes the largest dataset of BRAF-mutated cancers to date. Our findings propose insights to optimize clinical trial design and patient selection in the pursuit of developing effective treatment strategies for patients whose tumors harbor non-V600 BRAF mutations. This study also offers insights into the potential of targeting alternative pathways in addition to the MAPK pathway as part of combinatorial treatment strategies.

cancer biology↗

bioRxiv2023

Tree diversity increases forest temperature buffering

Global warming is increasing the frequency and intensity of climate extremes. Forests may buffer such extreme events by creating their own microclimate below their canopy via cooling hot and insulating against cold macroclimate air temperatures. This buffering capacity of forests may be increased by tree diversity and may itself maintain forest functioning and biodiversity. However, despite its relevance for many ecosystem processes, the effect of tree diversity on temperature buffering is largely unexplored. Here, we show that tree species richness consistently increases forest temperature buffering across daily, monthly, and annual scales over six years. This finding is based on data from a large-scale tree diversity experiment covering a species richness gradient of 1 to 24 tree species. We found that species richness strengthened both components of forest temperature buffering: the attenuation of hot and of cold macroclimate air temperatures, with the cooling effect being more pronounced. The buffering effect of tree species richness was mediated by canopy density and structural diversity, assessed as leaf area index and stand structural complexity index, respectively. Safeguarding and planting diverse forests may thus mitigate negative effects of global warming and climate extremes on ecosystem functions and communities below the tree canopy.

ecology↗

bioRxiv2023

Using Saturation Mutagenesis-Reinforced Functional Assays (SMuRF) to improve the variant interpretation for alpha-dystroglycan glycosylation enzymes

Interpretation of disease-causing genetic variants remains a challenge in human genetics. Current costs and complexity of deep mutational scanning methods hamper crowd-sourcing approaches toward genome-wide resolution of variants in disease-related genes. Our framework, Saturation Mutagenesis-Reinforced Functional assays (SMuRF), addresses these issues by offering simple and cost-effective saturation mutagenesis, as well as streamlining functional assays to enhance the interpretation of unresolved variants. Applying SMuRF to neuromuscular disease genes FKRP and LARGE1, we generated functional scores for all possible coding single nucleotide variants, which aid in resolving clinically reported variants of uncertain significance. SMuRF also demonstrates utility in predicting disease severity, resolving critical structural regions, and providing training datasets for the development of computational predictors. Our approach opens new directions for enabling variant-to-function insights for disease genes in a manner that is broadly useful for crowd-sourcing implementation across standard research laboratories.

genetics↗

bioRxiv2023

Exploring the Dose-Dependency of After-Effects: A Computational Model for Theta-Burst Transcranial Magnetic Stimulation

Transcranial magnetic stimulation (TMS) is a non-invasive neurostimulation and neuromodulation technique that is widely applied in brain research and clinical applications. However, the optimal parameters of neuromodulating TMS protocols describing the specific rhythms, such as number of pulses, frequency, and stimulation strength, are widely unknown. Improving previous rather limited and ad-hoc models, we aimed to investigate the dose-dependency of theta-burst stimulation (TBS) protocols with a more elaborate but still parsimonious quantitative model representing the non-linearities of the mechanisms of synaptic plasticity and metaplasticity during repetitive magnetic stimulation. Our model, which considers the interaction between facilitatory and inhibitory processes, successfully reproduced results from TBS experiments and provide testable predictions for prolonged TBS protocols. Moreover, we suggested that the activation of kinases and phosphatases could be potential candidates for later TMS modelling research. Although this model still simplifies the complex dynamics of cellular and molecular processes, it offers a starting basis for future studies to incorporate more intricate mechanisms. By further refining our understanding of the underlying mechanisms and improving the accuracy of prediction models, we can advance the efficacy and clinical application of TBS protocols in various neurological and psychiatric conditions.

neuroscience↗

bioRxiv2023

Scalable, cell type-selective in vivo AAV-based CRISPR screens in mice

There is a significant need for scalable CRISPR-based genetic screening methods that can be applied directly in mammalian tissues in vivo while enabling cell type-specific analysis. To address this, we developed an adeno-associated virus (AAV)-based CRISPR screening platform, CrAAVe- seq, that incorporates a Cre-sensitive sgRNA construct for pooled screening within targeted cell populations in mouse tissues. We demonstrate the utility of this approach by screening two distinct large sgRNA libraries, together targeting over 5,000 genes, in mouse brains to create a robust profile of neuron-essential genes. We validate two genes as strongly neuron-essential in both primary mouse neurons and in vivo, confirming the predictive power of our platform. By comparing results from individual mice and across different cell populations, we highlight the reproducibility and scalability of the platform and show that it is highly sensitive even for screening smaller neuronal subpopulations. We systematically characterize the impact of sgRNA library size, mouse cohort size, the size of the targeted cell population, viral titer, and multiplicity of infection on screen performance to establish general guidelines for large-scale in vivo screens.

genomics↗

bioRxiv2023

CRISPR-Cas12a-Based Rapid and Sensitive Detection of rpoBL378R in Mycobacterium tuberculosis

Rifampin is the most effective drug in the treatment of tuberculosis, whose major pathogen is Mycobacterium tuberculosis (MTB), whereas there are still certain MTB strains resistant to the therapy of rifampin. The rpoB mutations play a central role in MTB resistance to the rifampin therapy, so it is crucial to identify these mutations in order to discover novel therapeutic approaches to these drug-resistant MTB strains. Here we show that a CRISPR-Cas12a-based detection platform with recombinase polymerase amplification and fluorescence reporter can be utilized to detect and visualize an MTB drug-resistant point mutation (rpoBL378R) from its rpoB wild type. Notably, this detection system is highly specific because it did not cross-react with contrived reference samples containing the genomes of MTB H37Rv, Mycobacterium smegmatis (M. smegmatis), Mycobacterium aureus (M. aureus), and Escherichia coli (E. coli). Collectively, this strategy based on CRISPR-Cas12a that we show in this report is simple, sensitive as well as specific for detection of the rifampin-resistant MTB H37Rv with the rpoBL378R mutation, indicating that this CRISPR-Cas12a-based detection platform has high potential to be exploited for clinic application to identify MTB mutations.

microbiology↗

bioRxiv2023

Latitudinal scaling of aggregation with abundance and its consequences for coexistence in species rich forests

The search for simple principles underlying the complex spatial structure and dynamics of plant communities is a long-standing challenge in ecology1-6. In particular, the relationship between the spatial distribution of plants and species coexistence is challenging to resolve in species-rich communities7-9. Analysing the spatial patterns of tree species in 21 large forest plots, we find that rare species tend to be more spatially aggregated than common species, and a latitudinal gradient in the strength of this negative correlations that increases from tropical to temperate forests. Our analysis suggests that latitudinal gradients in animal seed dispersal10 and mycorrhizal associations11,12,13 may jointly generate this intriguing pattern. To assess the consequences of negative aggregation-abundance correlations for species coexistence, we present here a framework to incorporate the observed spatial patterns into population models8 along with an analytical solution for the local extinction risk14 of species invading from low abundances in dependence of spatial structure, demographic parameters, and immigration. For example, the stabilizing effect of the observed spatial patterns reduced the local extinction risk of species when rare almost by a factor of two. Our approach opens up new avenues for integrating observed spatial patterns into mathematical theory, and our findings demonstrate that spatial patterns, such as species aggregation and segregation, can contribute substantially to coexistence in species-rich communities. This underscores the need to understand the interactions between multiple ecological processes and spatial patterns in greater detail.

ecology↗