Biology subjects

Anand, A.

Publications and source records attributed to Anand, A..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Enhanced respiratory electron dissipation promotes mycobacterial biofilm longevity

Mycobacterium tuberculosis organizes as multicellular structures like granuloma and biofilm within human lungs and these lifestyles are critical for the pathophysiological outcomes. Granuloma has been the hallmark of M. tuberculosis infection and has been studied extensively. However, the metabolic interplay dictating biofilm development remains poorly understood. We show that supplementation of immunometabolites, nitrate or fumarate, extends mycobacterial biofilm lifespan dramatically. This longevity is enabled by suppression of dormancy regulons and maintenance of active metabolic state. These results establish that access to alternative electron acceptors directly influences mycobacterial biofilm fate. By linking dormancy suppression to prolonged structural integrity, our study identifies respiratory flexibility as a determinant of mycobacterial biofilm persistence. These findings reveal a central metabolic lever that dictates biofilm survival and open new avenues for targeting mycobacterial biofilms in clinical settings.

microbiology↗

bioRxiv2025

Comprehensive gene heritability estimation reveals the genetic architecture of rare coding variants underlying complex traits

Whole-exome sequencing (WES) enables high-resolution interrogation of the contribution of rare coding variants to complex trait variation. However, existing methods for heritability estimation attributed to rare-coding variants are often limited by the effects of linkage disequilibrium (LD) and by the sparse nature of rare variant data. We introduce FLEX (Fast, LD-aware Estimation of eXome-wide and gene-level heritability), a scalable and flexible framework for estimating and partitioning heritability across genes or sets of genes using WES data. FLEX integrates all coding variants- from common to ultra-rare - within a unifled model and corrects for LD-induced effects to improve the accuracy of heritability estimates. In addition, FLEX supports both individual-level and summary statistic data and is computationally efflcient for biobank-scale datasets. Through extensive simulations, we show that FLEX is well-calibrated while providing accurate heritability estimates. We applied FLEX to WES data across N = 153, 351 unrelated European ancestry individuals and 20 quantitative traits in the UK Biobank. We identifled 64 gene-trait pairs with signiflcant gene-level heritability (p < 0.05/18, 624 accounting for the number of protein-coding genes tested), among which rare coding variants explained 38% of gene-level heritability, on average. Compared to heritability estimates from genome-wide imputed SNPs, incorporation of rare and ultra-rare coding variants led to a 24.8% increase in heritability on average, while effect sizes at rare and ultra-rare variants are substantially larger ({approx} 18x on average). Partitioning across variant effect annotations, we flnd that predicted loss-of-function variants had stronger individual effects than missense variants (24% on average) while missense variants accounted for a greater share of rare coding heritability. Together, FLEX provides an adaptable and accurate approach for quantifying gene-level heritability, advancing our understanding of the genetic architecture of complex traits, and facilitating the discovery of trait-relevant genes.

genetics↗

bioRxiv2025

Mitochondrial DNA damage in substantia nigra parscompacta astrocytes exacerbates dopaminergic neuron lossin a 6-hydroxydopamine mouse model of parkinsonism

Parkinsons disease (PD) is the fastest growing neurological disorder with no known cure. Our ability to develop disease-modifying treatments that slow down the loss of substantia nigra pars compacta (SNc) dopaminergic (DA) neurons is hindered by a dearth of knowledge on roles for non-neuronal elements such as astrocytes during PD pathogenesis. More specifically, the extent to which mitochondrial DNA (mtDNA) damage in SNc astrocytes contributes to SNc DA neuron loss during PD remains unknown. To address this knowledge gap, we utilized an adeno-associated virus (AAV) called Mito-PstI that expresses the restriction enzyme PstI as an approach to damage mtDNA in SNc astrocytes and assess the effect of astrocytic mtDNA damage on SNc DA neuron function and viability in mice. Mito-PstI-induced mtDNA damage in SNc astrocytes disrupted mitochondrial morphology, caused increased wrapping of SNc astrocytic processes around SNc DA neurons, and abnormally increased dopamine release by SNc DA neuron axonal terminals within the dorsolateral striatum (DLS). In addition, mice injected with Mito-PstI in the SNc showed increased spontaneous and apomorphine-induced rotations contralateral to the side with SNc Mito-PstI injections. In further experiments, we used a parkinsonian mouse model with low dose 6-hydroxydopamine (6-OHDA) injection into the DLS to show that Mito-PstI expression in SNc astrocytes caused a worsening of 6-OHDA-induced spontaneous contralateral rotational behavior, and exacerbated SNc DA neuron loss. These results suggest that mitochondria in SNc astrocytes are not only critical for the function of SNc DA neurons, but are also a new target for developing disease-modifying strategies against PD. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=157 SRC="FIGDIR/small/673287v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@b4a98aorg.highwire.dtl.DTLVardef@e6e2fcorg.highwire.dtl.DTLVardef@402b93org.highwire.dtl.DTLVardef@ecdfd2_HPS_FORMAT_FIGEXP M_FIG C_FIG Main PointsO_LIMito-PstI expression in mouse SNc astrocytes increases dopamine release C_LIO_LIMito-PstI expression in SNc astrocytes worsens contralateral rotational behavior in mice C_LIO_LIMito-PstI expression in SNc astrocytes increases DA neuron loss in 6-OHDA mice C_LI

neuroscience↗

bioRxiv2025

Ectopic expression of the sensor CovS cytosolic domain confers phosphatase activity and full virulence to the M1T1 CovSY39H attenuated variant of group A Streptococcus

Group A Streptococcus (GAS) causes a wide variety of diseases ranging from mild, noninvasive, such as pharyngitis and impetigo, to life-threatening infections, such as necrotizing fasciitis (NF) and streptococcal toxic shock syndrome (STSS). The two-component CovR/S system, comprising the sensor kinase CovS and transcription factor CovR, is a central regulator of GAS virulence. An attenuated pharyngeal colonizing variant (S126) possessing a single-nucleotide polymorphism (SNP) in CovS (Y39H) was recovered in France from a member of a family in which another individual developed NF and STSS caused by the M1T1 WT strain (S119). We employed transcriptome analyses (RNA-seq), quantitative determinations of CovR phosphorylation, measurements of virulence factor activity, and a murine model of human NF to demonstrate that CovS of strain S126 almost lost its entire phosphatase activity but retained its kinase and phosphotransfer activities. Moreover, we reversed its attenuated phenotype by ectopically expressing the cytosolic domain of wild-type CovS. Culturing the corresponding strain S126covS-3 in a chemically defined medium (CDM) supplemented with asparagine (Asn), conditions that produce an excess of cytosolic ADP over ATP, stimulated the ectopically expressed phosphatase activity. Consequently, this led to dephosphorylation of CovR[~]P and increased the expression of virulence factors. Most importantly, S126covS-3 reverted to the wild-type phenotype of S119 in the mouse model of human GAS NF. Our study provides a new mechanistic tool that enables the manipulation of CovS phosphatase activity both in vitro and in vivo. IMPORTANCEThe shift from high to low virulence and back in GAS is critical for understanding its pathogenesis and developing new treatments to control GAS infections. The two-component CovR/S system, comprising the sensor kinase/phosphatase CovS and the transcription regulator CovR, regulates the degree of GAS virulence. In the M1T1 serotype, covR/S mutations are typically associated with a loss of CovR/S function, leading to hypervirulent phenotypes. However, an attenuated pharyngeal-colonizing variant possessing a single-nucleotide polymorphism (SNP) in CovS (Y39H strain S126) was isolated in France. Here, we demonstrate that S126 is attenuated because the mutation in CovS inhibits its phosphatase activity but preserves its kinase and phosphotransfer activities. By expressing the cytosolic domain of WT CovS in the S126 background, we endowed the resulting strain, S126covS-3, with phosphatase activity, which was further stimulated by ADP when formed in chemically defined medium (CDM) supplemented with asparagine (Asn). Most importantly, S126covS-3 switched to full virulence, similar to that of S119 in a mouse model of human GAS NF. These findings underscore the importance of comprehensive analyses of disease-related covR/S mutants in understanding the virulence and persistence of GAS.

microbiology↗

bioRxiv2025

Integrated genetic screening reveals FEN1 as a driver of stemness and temozolomide resistance in glioblastoma

Glioblastoma (GBM) is a lethal brain tumor with limited response to standard of care chemoradiotherapy. In this study, we conducted genome-wide CRISPR knockout screening in patient-derived glioblastoma stem cells (GSCs) to identify genetic dependencies of cell survival and therapy resistance. Our screening identified flap endonuclease 1 (FEN1) as a key driver of GSC survival, with enhanced dependency under temozolomide (TMZ) treatment. Genetic perturbation of FEN1 reduced GSC self-renewal and proliferation in vitro, and prolonged survival in a patient-derived xenograft model of GBM. FEN1 inhibition (FEN1i) preferentially affected highly aggressive or recurrent GBM models compared with less aggressive GBMs and healthy neural stem cells. Moreover, FEN1 inhibition synergized with TMZ only in these aggressive FEN1i-sensitive GSCs, providing cancer-selective killing and TMZ sensitization in the most untreatable of GBMs. Mechanistically, FEN1i-sensitive GSCs exhibited greater proliferation and sphere formation, while stalling their proliferation conferred resistance to FEN1 inhibition. Single-cell transcriptomics further linked FEN1 expression to stemness and the DNA damage response, elucidating broader determinants of FEN1 dependency. These findings establish FEN1 as a promising therapeutic target in GBM, offering a strategy for both selective targeting and enhancement of TMZ efficacy in aggressive cancers. Statement of SignificanceThis study identifies FEN1 as a key vulnerability of glioblastoma stem cells, revealing its role in therapy resistance and stemness, and proposes FEN1 inhibition as a strategy to enhance temozolomide efficacy.

cancer biology↗

bioRxiv2025

A single MHCII neoepitope mRNA vaccine elicits CD4 T- and B- cell responses promoting endogenous CD8 anti-tumor immunity

Recent progress in therapeutic cancer vaccines has shown promising clinical activity, especially when targeting MHC class I (MHCI) neoantigen-specific CD8+ T cell responses in post-surgical patients. To explore the role of CD4+ T cells in vaccine-dependent tumor rejection, we constructed an mRNA lipoplex vaccine encoding a single MHCII-restricted neoantigen. The vaccine elicited Tfh and Th1 cell responses while decreasing Tregs, leading to rejection of established tumors in mice. IL-21 and IFN-{gamma}, crucial for Tfh and Th1 function respectively, contributed to anti-tumor activity. B cells and neoantigen-specific antibodies were also shown to participate in vaccine efficacy. Additionally, conventional type 1 dendritic cells (cDC1s) were essential for eliciting vaccine-induced CD4+ T cells, and both cDC1s and CD4+ T cells were required to enhance endogenous CD8+ responses, which were crucial for tumor control. Our results suggest that immunizing against MHCII neoantigens alone is sufficient to orchestrate a potent and cooperative immune response against cancer.

immunology↗

bioRxiv2025

Characterization of Sex-Based Differences in Integrin-Mediated Endothelial Cel Adhesion to Bioactive Hydrogels

Endothelialization promotes thromboresistance in blood-contacting devices, but biomaterial designs often overlook sex differences in endothelialization processes. In this study, we elucidated sex differences in endothelial cell-material interactions through investigation of the integrin-ligand interplay with biomaterial substrates and the corollary effects on cell adhesion and spreading. First, integrin expression of human coronary artery endothelial cells (HCAECs) was characterized for age-matched donors (3 male, 3 female). Sex-based differences in integrin expression were identified, with notably higher 2{beta}1, 5{beta}1, and V{beta}3 expression in female cells and higher 1{beta}1 expression in male cells. On polyethylene glycol (PEG)-based hydrogel incorporating collagen or gelatin, female cells showed increased attachment on stiff substrates as compared to male HCAECs, likely driven by increased 2{beta}1, 5{beta}1, and V{beta}3 expression in female cells. Collectively, these results demonstrate sex-biased endothelial cell responses to bioactive hydrogels mediated by integrin interactions and highlight the importance of incorporating biological sex as a design variable in the development of blood-contacting biomaterials. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=72 SRC="FIGDIR/small/656802v2_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@41bfb9org.highwire.dtl.DTLVardef@921619org.highwire.dtl.DTLVardef@e8df4corg.highwire.dtl.DTLVardef@9c0faa_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2025

Nuclear Phase Separation Drives NPM1-mutant Acute Myeloid Leukemia

During cancer development, mutations promote gene expression changes that cause transformation. Leukemia is frequently associated with aberrant HOXA expression driven by translocations in nucleoporin genes or KMT2A, and mutations in NPM1. How disparate mutations converge on this regulatory pathway is not understood. Here we demonstrate that mutant NPM1 (NPM1c) forms nuclear condensates in multiple human cell lines, mouse models, and primary patient samples. We show NPM1c phase separation is necessary and sufficient to coordinate the recruitment of NUP98 and KMT2A to condensates. Through extensive mutagenesis and pharmacological destabilization of phase separation, we find that NPM1c condensates are necessary for regulating gene expression, promoting in vivo expansion, and maintaining the undifferentiated leukemic state. Finally, we show that nucleoporin and KMT2A fusion proteins form condensates that are biophysically indistinguishable from NPM1c condensates. Together, these data define a new condensate underlying leukemias that we term coordinating bodies (C-bodies), and propose C-bodies as a therapeutic vulnerability.

biophysics↗

bioRxiv2025

Intratumoral cDC1-T Cell Clusters Serve as Sites of Local Costimulation to Enhance CTL-Mediated Tumor Rejection

T cells are essential for anti-tumor immunity, but their ability to eliminate tumors depends on coordinated interactions with type 1 conventional dendritic cells (cDC1s). While cDC1s are known for cross-presenting tumor-derived antigens in lymph nodes to prime CD8+ T cells, their role within the tumor itself remains less well understood. Here, we use the Skin Tumor Array by Micro-Poration (STAMP) model to investigate how cDC1-T cell interactions shape immune responses and influence tumor fate. Our data reveal that it is the spatial distribution of both cDC1s and T cells that determines whether a tumor can be rejected. We defined three primary immunotypes based on the spatial distribution of T cells and cDC1s: T cell-inflamed/dendritic cell-inflamed (TC-In/DC-In) tumors, where T cells and cDC1s co-infiltrate the tumor; T cell-inflamed/dendritic cell-excluded (TC-In/DC-Ex) tumors, where T cells infiltrate but cDC1s remain at the periphery; and T cell-excluded/dendritic cell-excluded (TC-Ex/DC-Ex) tumors, which lack both cDC1 and T cell infiltration. Notably, TC-In/DC-In tumors are more likely to undergo rejection, whereas TC-In/DC-Ex tumors persist despite T cell infiltration. Within TC-In/DC-In tumors, cDC1s engage in direct interactions with T cells, upregulate co-stimulatory molecules, and sustain effector T cell responses, while cDC1s in TC-In/DC-Ex tumors express higher migration-associated genes, suggesting a propensity to exit the tumor. We further show that chemokine modulation, particularly through CXCL9, CCL5, and XCL1, can reshape immune infiltration patterns to promote intra-tumoral cDC1-T cell clustering and improve tumor rejection. These findings underscore the unexpectedly important role of cDC1 positioning and function in sustaining effective anti-tumor immunity and highlight spatially organized cDC1-T cell clusters as critical hubs for local T cell activation.

immunology↗

bioRxiv2025

Aerobicity stimulon in Escherichia coli revealed using multi-scale computational systems biology of adapted respiratory variants

Energy homeostasis facilitated by the interplay of substrate-level and oxidative phosphorylation is crucial for bacterial adaptation to diverse substrates and environments. To investigate how bioenergetic systems optimize under restrictive conditions, we evolved ETS variants with distinct proton-pumping efficiencies (1, 2, 3, or 4 proton(s) per electron) on succinate and glycerol. These substrates impose unique metabolic constraints: succinate requires complete gluconeogenesis, while glycerol supports mixed glycolytic and gluconeogenic fluxes. Multi-scale computational analysis of the strains revealed (a) Growth optimization across carbon substrates for multiple ETS variants, (b) A conserved aerobicity stimulon comprising seven independently regulated gene groups that are co-regulated with increasing aerobic capacities, (c) Proteome reallocation linked to aerobicity, validated using genome-scale metabolism and expression modeling, and (d) Carbon source-specific compensatory mutations in succinate transporters and regulatory elements. These findings define the aerobicity stimulon and establish a unifying framework for understanding bacterial respiratory flexibility, demonstrating how transcriptional networks and metabolic systems integrate to achieve energy homeostasis and bioenergetic resilience.

systems biology↗

bioRxiv2025

Hidden Markov Model-Based Prokaryotic Genome Space Mining Reveals the Widespread Pervasiveness of Complex I and Its Potential Evolutionary Scheme

Most cellular reactions are interdependent; however, a subset of reactions often associates more closely to form a defined reaction pathway. An extreme arrangement of interdependent reactions occurs when the cognate proteins physically associate to constitute a complex. Respiratory complex I is one of the largest membrane resident protein assemblies. Besides being the hallmark of bioenergetics, this enzyme complex is critical for redox homeostasis and transport. The evolutionary scheme for the development of this enzyme complex is poorly understood due to associated challenges like complications in delineating close homologs and diverse subunit ancestry. We used custom Hidden Markov Model profiles to examine the available prokaryotic genome space to trace the distribution pattern of fourteen core Nuo subunits of Complex I. We report: (a) a sensitive HMMER-based workflow for comprehensively annotating and analyzing the Nuo subunits, which can be adapted to multiple such analyses; (b) the first curated species-level distribution of Nuo subunits; (c) multiple variants of Complex I across [~]11,000 species with 51.2% species having complete complex; (d) presence of Complex I variants on plasmids which potentially facilitated the evolutionary distribution; (e) extension of our workflow for examining distribution of mitochondrial Complex I accessory subunits among prokaryotes highlighting their evolutionary roots. We have also developed a web application to facilitate the convenient dissemination of our compiled resources. The knowledge of bioenergetic repertoire is critical in the successful targeting of energy metabolism for antimicrobial development.

microbiology↗

bioRxiv2025

Nanometer condensate organization in live cells derived from partitioning measurements

Biomolecules self-organize into membrane-less organelles known as condensates that compartmentalize essential biochemical processes, such as ribosome biogenesis in the nucleolus1-3. Molecular dynamics within condensates are governed by chemical preferences and interaction networks that can imbue nanoscale structure4-7. Such organization is typically inferred from ensemble-averaged measurements, such as scattering and electron microscopy, which reveal molecular arrangements8-14. However, the complexity of cells obscures the interpretability of these techniques, limiting insight into condensate internal structure and roles in macromolecular assembly and transport. Here, we develop an approach to quantify the average microenvironment surrounding specific proteins within condensates in live cells, using thermodynamic principles to interpret the partitioning of designed protein probes. Using this approach, we find that condensates in cells, including the nucleolus, stress granule, and nuclear pore, exhibit spatial inhomogeneity, aligning with emerging views of condensates as networked fluids5,6,15-18. Within the nucleolus, we link spatial inhomogeneity to ribosome biogenesis, which progressively loosens the average local meshwork, facilitating transport of assembled ribosomal subunits. Within the nuclear pore, we find that transporters experience a weaker local meshwork than nucleoporins, consistent with the selective phase model19,20. Together, our approach uncovers a distinct mode of biomolecular control arising from nanoscale structure, which we term microenvironment coupling, whereby internal interaction landscapes shape transport to enable regulation and proofreading.

biophysics↗

bioRxiv2025

CK2 directly controls CARD9 protein homeostasis

CARD9 is an attractive target for therapeutic intervention because the human genetic data provides strong evidence for the causal role of CARD9 in both protection and susceptibility to autoimmune disease. Expression quantitative trait loci (eQTLs) link higher CARD9 expression to increased disease risk and lower CARD9 expression to protection. Additionally, a rare allele variant leading to a C-terminal truncation of CARD9 (CARD9{Delta}11) and subsequent loss-of-function is also protective for inflammatory bowel disease (IBD). The mechanism of CARD9-driven inflammation through scaffold assembly with BCL10 and MALT1 (CBM complex) suggests a durable inflammatory signal driven by increasing levels of CARD9. Therefore, CARD9 depletion is a desired therapeutic strategy for drug discovery, yet a difficult one due to the nature of CARD9 as an adaptor protein target and the limited number of chemical tools available to engage it. Here, we uncover through a protein homeostasis screen that casein kinase 2 (CK2/CSNK2) inhibition leads to cellular CARD9 depletion. Following up with arrayed CRISPR screening, we identify key casein kinase isoforms/subunits responsible for CARD9 depletion. We find that CK2 directly binds to CARD9 and phosphorylates S424/S425 as well as S483/S484. Orthosteric CK2 inhibition prevents CK2 binding to CARD9 and leads to CARD9 destabilization. We show that the interaction between CK2 and CARD9{Delta}11 is significantly attenuated and not sensitive to CK2-mediated protein stabilization. The CK2-driven CARD9 depletion mechanism is preserved outside of immortalized cell lines and conserved between primary, differentiated mouse and human dendritic cells. Finally, we demonstrate therapeutic proof of concept in vivo using CK2 inhibition to deplete CARD9 in murine whole blood, peritoneum, and colon. Our study expands the scope of cellular consequences dealt by kinase inhibition, offers an unconventional approach for engaging a therapeutically intractable target, and identifies a novel mechanism that could contribute to disease protection conferred by the CARD9{Delta}11 allele.

immunology↗

bioRxiv2025

Discovering Symbolic Cognitive Models from Human and Animal Behavior

Symbolic models play a key role in cognitive science, expressing computationally precise hypotheses about how the brain implements a cognitive process. Identifying an appropriate model typically requires a great deal of effort and ingenuity on the part of a human scientist. Here, we adapt FunSearch Romera-Paredes et al. (2024), a recently developed tool that uses Large Language Models (LLMs) in an evolutionary algorithm, to automatically discover symbolic cognitive models that accurately capture human and animal behavior. We consider datasets from three species performing a classic reward-learning task that has been the focus of substantial modeling effort, and find that the discovered programs outperform state-of-the-art cognitive models for each. The discovered programs can readily be interpreted as hypotheses about human and animal cognition, instantiating interpretable symbolic learning and decision-making algorithms. Broadly, these results demonstrate the viability of using LLM-powered program synthesis to propose novel scientific hypotheses regarding mechanisms of human and animal cognition.

animal behavior and cognition↗

bioRxiv2024

Biocultural vulnerability of traditional crops in the Indian Trans Himalaya

Traditional agricultural landscapes are critical for conserving biocultural and ecological diversity. Despite their significance, traditional systems have often been overlooked, leading to genetic erosion of crop landraces. Using the fragile ecosystems of northwest Himalaya as case study, we examine the ecological and genetic resilience of an understudied and lesser-known traditional crop, black pea, and barley (Hordeum vulgare) and compare them to the introduced cash crop of green pea (Pisum sativum L.). We co-designed field experiments with local farmers to assess survival and reproductive traits for the crops. We performed whole-genome sequencing to investigate the genetic diversity of black pea and describe their nutritional profile. Our findings indicate that traditional crops are better adapted to local climatic conditions and hold considerable genetic diversity and nutritional potential. We emphasize the importance of integrating traditional knowledge with scientific research to promote sustainable food systems and socio-ecological stability in vulnerable mountain regions.

plant biology↗

bioRxiv2024

Small DNA elements that act as both insulators and silencers in plants

Insulators are cis-regulatory elements that separate transcriptional units, whereas silencers are elements that repress transcription regardless of their position. In plants, these elements remain largely uncharacterized. Here, we use the massively parallel reporter assay Plant STARR-seq with short fragments of eight large insulators to identify more than 100 fragments that block enhancer activity. The short fragments can be combined to generate more powerful insulators that abolish the capacity of the strong viral 35S enhancer to activate the 35S minimal promoter. Unexpectedly, when tested upstream of weak enhancers, these fragments act as silencers and repress transcription. Thus, these elements are capable of both insulating or repressing transcription dependent upon regulatory context. We validate our findings in stable transgenic Arabidopsis, maize, and rice plants. The short elements identified here should be useful building blocks for plant biotechnology efforts.

plant biology↗

bioRxiv2024

Metapipeline-DNA: A Comprehensive Germline & Somatic Genomics Nextflow Pipeline

SummaryThe price, quality and throughout of DNA sequencing continue to improve. Algorithmic innovations have allowed inference of a growing range of features from DNA sequencing data, quantifying nuclear, mitochondrial and evolutionary aspects of both germline and somatic genomes. To automate analyses of the full range of genomic characteristics, we created an extensible Nextflow meta-pipeline called metapipeline-DNA. Metapipeline-DNA analyzes targeted and whole-genome sequencing data from raw reads through pre-processing, feature detection by multiple algorithms, quality-control and data- visualization. Each step can be run independently and is supported robust software engineering including automated failure-recovery, robust testing and consistent verifications of inputs, outputs and parameters. Metapipeline-DNA is cloud-compatible and highly configurable, with options to subset and optimize each analysis. Metapipeline-DNA facilitates high-scale, comprehensive analysis of DNA sequencing data. AvailabilityMetapipeline-DNA is an open-source Nextflow pipeline under the GPLv2 license and is available at https://github.com/uclahs-cds/metapipeline-DNA.

bioinformatics↗

bioRxiv2024

Burst Estimation through Atomic Decomposition (BEAD): A Toolbox to find Oscillatory Bursts in Brain Signals

Recent studies have shown that brain signals often show oscillatory bursts of short durations, which have been linked to various aspects of computation and behavior. Traditional methods often use direct spectral estimators to estimate the power of brain signals in spectral and temporal domains, from which bursts are identified. However, direct spectral estimators are known to be noisy, such that even stable oscillations may appear bursty. We have previously shown that the Matching Pursuit (MP) algorithm, which uses a large overcomplete dictionary of basis functions (called "atoms") to decompose the signal directly in the time domain, partly addresses this concern and robustly finds long bursts in synthetic as well as real data. However, MP is a greedy algorithm that can give non-optimal solutions and requires a large-sized dictionary. To address these concerns, we extended two other algorithms - orthogonal MP (OMP) and OMP using Multiscale Adaptive Gabor Expansion (OMP-MAGE), to perform burst duration estimation. We also develop a novel algorithm, called OMP using Gabor Expansion with Atom Reassignment (OMP-GEAR). These algorithms overcome the limitations of MP and can work with a significantly smaller dictionary size. We find that, in synthetic data, OMP, OMP-MAGE and OMP-GEAR converge faster than MP. Also, OMP-MAGE and OMP-GEAR outperform both MP and OMP when the dictionary size is small. Finally, OMP-GEAR significantly outperforms OMP-MAGE when the bursts are overlapping. Importantly, the burst durations obtained using MP and OMP with a very large-sized dictionary are comparable to that obtained using OMP-MAGE with a much smaller-sized dictionary in real data obtained from two monkeys passively viewing static gratings which induced gamma bursts in the primary visual cortex. OMP-GEAR yields slightly smaller burst durations, but all the estimated burst durations are still significantly larger than the duration estimated using traditional methods. These results suggest that gamma bursts are longer than previously reported. Raw data from two monkeys, as well as codes for both traditional and new methods, are publicly available as part of this toolbox.

neuroscience↗