Biology subjects

Myers, J.

Publications and source records attributed to Myers, J..

At least 19 recordsLinked to original sources

bioRxiv2026

LYNX: a deep generative model for linking spatial dynamics and cellinteractions in multimodal spatial data

Tissues are spatially organized systems in which cell states, functions and interactions vary across spatial coordinates, forming compartments or gradients shaped by local microenvironments. Understanding how molecular features and cell-cell interactions change across space and time is central to studying development, homeostasis and disease. Addressing these questions increasingly requires the integration of multi-modal spatial data, which provides complementary views of cellular and structural organization. However, existing computational approaches typically combine modalities by weighting them equally, overlooking domain-specific technical artifacts, differences in spatial resolution and non-overlapping feature spaces. In addition, methods for spatial cell-cell communication analysis are largely developed for single-modality settings and do not model how interactions vary across the tissue. To address these gaps, we introduce LYNX, a deep generative framework that learns a shared latent representation of spatial dynamics from joint-measured modalities in the 2D or 3D domain, to provide a unified coordinate system for modeling how cell-cell interactions, phenotypes, and molecular programs vary along continuous spatial gradients. LYNX identifies spatial programs difficult to resolve with existing approaches, including metabolically coupled porto-central interaction remodeling in liver, recovery of degraded proteomic signals along the cortico-medullary axis in thymus, and branching trajectories towards DCIS and invasive niches marked by distinct stromal activation-states and immune-tumor crosstalk in breast tumor microenvironment. We demonstrate that LYNX robustly infers spatially resolved gradients, maps functional compartments and cell-cell interactions along spatial axes and is compatible across diverse spatial profiling technologies, modalities, and resolution disparities. LYNX provides a foundational and scalable framework to advance our understanding of healthy tissue physiology and to decode temporal evolution of complex diseases.

bioengineering↗

bioRxiv2026

Epistasis of two classical color genes, B and L-2, synergistically controls carotenoid accumulation in squash

Carotenoid accumulation underlies fruit color and nutritional quality in squash (Cucurbita pepo). One pair of dominant genes, B and L-2, have been long known to interact epistatically, substantially boosting carotenoid accumulation and producing intensely orange-fleshed fruit. However, their molecular identities and regulatory mechanism are unknown. Here, we show that B encodes a truncated H subunit of magnesium chelatase (CpCHLHB) and L-2 encodes a homolog of Arabidopsis Pseudo-Response Regulator 2 (CpAPRR2-A). Significantly, expression of phytoene synthase (CpPSY-A), which encodes the major rate-limiting enzyme in carotenoid biosynthesis, was dramatically upregulated in fruit of B/B L-2/L-2 plants compared with b/b L-2/L-2 or B/B l-2/l-2, showing that the B and L-2 interaction affects CpPSY-A transcription. A similar upregulation was also observed in Arabidopsis gun5 L-2 transgenic plants, where gun5 is a genetic mimic of the C. pepo B gene. The wild-type CpCHLHb physically interacted with CpAPRR2-A, attenuating the CpAPRR2-A-mediated activation of CpPSY-A. In contrast, the truncated CpCHLHB lost its ability to interact with CpAPRR2-A, enabling CpAPRR2-A to activate CpPSY-A and produce intensely orange fruit. These findings uncover the mechanism underlying the epistatic interaction through which B and L-2 act synergistically to boost carotenoid production, offering novel mechanistic insights and key targets for improving crop quality. One-sentence summarySynergistic epistasis between B and L-2 arises from loss of interaction between their encoded proteins, resulting in dramatically upregulating the key rate-limiting enzyme in carotenoid biosynthesis pathway to produce intensely orange-fleshed fruit in squash.

plant biology↗

bioRxiv2026

Maternal hypertension and cardiovascular medications dysregulate placental arterial tone

BackgroundAntihypertensive and cardioprotective medications are prescribed to pregnant women and include Ca2+ channel blockers (CCBs; amlodipine, nifedipine), - (doxazosin) and {beta}-(labetalol, bisoprolol, nebivolol) adrenergic receptor antagonists, and -adrenergic receptor agonists (methyldopa). These vasoactive drugs enter the fetal circulation, with unknown effects on the fetoplacental vasculature. We aimed to investigate whether cardiovascular medications modulate human fetoplacental vascular tone, which may impair or enhance placental perfusion. MethodsChorionic plate arteries (CPAs) were obtained from the placentas of women with normotensive pregnancy (N=28), with unmedicated hypertension (N=14), and those chronically medicated (N=61) with either amlodipine, nifedipine, labetalol or bisoprolol, or a combination of CCBs and labetalol. Using wire myography, ex vivo effects of amlodipine, nifedipine, labetalol, methyldopa, doxazosin, bisoprolol and nebivolol were tested in a concentration-dependent manner (10-11-10-5M) in pre-constricted CPAs isolated from the placentas of normotensive women. Differences in CPA vascular reactivity in response to chronic exposure to hypertension and/or cardiovascular medications was assessed by vasoconstriction to high potassium physiological solution (KPSS; 120mM) and to the thromboxane A2 mimetic (U46619; 10-10-2x10-6M), and relaxation to the nitric oxide donor, sodium nitroprusside (SNP; 10-10-10-5M). ResultsIn pre-constricted CPAs isolated from normotensive women, acute exposure to amlodipine, nifedipine, doxazosin and nebivolol promoted significant vasorelaxation (P<0.05). CPAs acutely exposed to labetalol, methyldopa (P<0.05) and bisoprolol (P<0.001) exhibited increased vasoconstriction compared to their respective diluent controls. CPAs from women with chronic hypertension and from those who had chronic labetalol treatment exhibited significantly reduced vasoconstriction to KPSS (P<0.05). CPAs from women with chronic hypertension and exposure to bisoprolol also had significantly attenuated vascular responses to U46619 and SNP (P<0.01 and P<0.01, respectively), compared to normal pregnancy. ConclusionsMaternal hypertension impairs vascular responses of the placenta. Cardiovascular medications prescribed during pregnancy may dysregulate placental vascular function. Further research is warranted to evaluate the relative safety of cardiovascular medications in pregnancy, as their distinct effects on fetoplacental vascular function may have important implications for maternal and fetal outcomes. Mechanistic studies alongside clinical correlations are essential to guide evidence-based prescribing.

physiology↗

bioRxiv2026

Impaired trophoblast efferocytosis by decidual macrophages in early-onset preeclampsia

Preeclampsia (PE) is a hypertensive disorder of pregnancy associated with inadequate trophoblast invasion, impaired spiral artery remodelling and increased trophoblast apoptosis, leading to malplacentation. Decidual macrophages are through to be key in clearing these apoptotic cells via efferocytosis, a process that normally promotes an anti-inflammatory phenotype. In PE, however, transcriptomic studies have shown that decidual macrophages exhibit a pro-inflammatory phenotype, suggesting their ability to efferocytose may be impaired. This study investigated whether PE alters ex vivo decidual macrophage function in placentas obtained from healthy pregnancies (n=11) or with early-onset PE (n=9). Macrophages isolated from both the decidua basalis and decidua parietalis of PE placentas demonstrated significantly reduced efferocytosis of apoptotic trophoblasts compared to healthy controls, accompanied by increased release of CXCL-8 and IL-6. Similarly, phagocytosis of Streptococcus agalactiae was significantly impaired by both macrophage subtypes. Analysis of macrophage scavenger receptors revealed that efferocytic macrophages upregulate receptors for eat me signals, whereas non-efferocytic macrophages fail to do so. These findings demonstrate that decidual macrophages in the preeclamptic placenta exhibit impaired efferocytosis and phagocytosis, which may contribute to the accumulation of apoptotic trophoblasts and increased pro-inflammatory signaling. Further analysis of this defective function is vital to identify novel immunomodulatory treatments for PE. Graphical abstractIn healthy pregnancy, decidual macrophage efferocytosis of apoptotic trophoblasts prevents inflammation through release of anti-inflammatory IL-10. In early-onset preeclampsia, failure to efferocytose causes a build up of apoptotic trophoblasts, and promotes inflammation through release of pro-inflammatory CXCL-8 and IL-6. Targeting decidual macrophage function may be beneficial in preeclampsia. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=164 SRC="FIGDIR/small/708195v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@ca7b24org.highwire.dtl.DTLVardef@15a9289org.highwire.dtl.DTLVardef@14a6631org.highwire.dtl.DTLVardef@17b4ff1_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

The neural basis of emotional generalization in empathy

The essence of empathy is generalization of emotion across persons. Here, we leverage recent theoretical advances in the neuroscience of generalization to help us understand empathy. We measured brain activity in human neurosurgical patients performing two tasks, one focused on identifying their own emotional response and one identifying emotional responses in others. We quantified the representational geometry of local field potential (LFP) high-gamma activity in four regions: the medial temporal lobe, anterior cingulate cortex, orbitofrontal cortex, and insula. We found encoding of both self- and other-emotions in all four regions, but codes for emotion and person are disentangled (that is, factorized) in the insula, but not the other regions. This factorized representation allows for cross-person generalization of emotion in a way that tangled (non-factorized) representations do not. Together, these results support the hypothesis that the insula uniquely contributes to social mirroring processes by which we understand emotions across individuals.

neuroscience↗

bioRxiv2025

Targeting Endothelial PERK Accelerates Lymphoid Regeneration by Enhancing DLL4-NOTCH3 Signaling at the Pre-B Niche

Delayed immune recovery after hematopoietic stem cell (HSC) transplantation is associated with a poor clinical outcome, yet strategies to enhance lymphocyte regeneration are limited. We studied the role of unfolded protein response (ER stress) in hematopoietic regeneration within the bone marrow (BM) microenvironment. We revealed that PERK activation is a prominent feature of BM endothelium in leukemia patients and is a hallmark response in mouse BM following ionizing irradiation. Ablating endothelial Perk boosted Notch ligand DLL4 expression and promoted DLL4-dependent early HSC and B progenitor regeneration. Single-cell analysis shows that endothelial DLL4 activates NOTCH3 expressed by mesenchymal stroma cells, and that the PERK-DLL4 axis coordinates the regulation of lymphoid commitment and niche cytokine production. NOTCH3 is critical for the upregulation of IL7 following irradiation and for supporting the expansion of lymphoid progenitors in mesenchymal sphere cultures. These findings not only unveil a previously unrecognized ER stress-controlled vascular-stroma signaling mechanism in regenerative hematopoiesis but also highlight PERK blockade as a promising therapeutic strategy to improve immune recovery after myeloablative transplantation. SummaryZou et al unravel that the adaptive ER stress response in bone marrow blood vessels restricts the post-transplant regeneration of immune progenitor cells by attenuating the expression of Notch ligand DLL4. Targeting ER stress sensor PERK can accelerate immune recovery after transplantation by enhancing DLL4-NOTCH3 signaling and IL7 cytokine production.

cell biology↗

bioRxiv2025

Senolytics Restore Hematopoietic Stem Cells Function in Sickle Cell Disease

Sickle Cell Disease (SCD) is a blood disorder affecting millions worldwide. Emerging evidence reveals that SCD pathophysiology increases risk of myeloid malignancies and hematopoietic stem cell (HSC) dysfunction, possibly due to pathological stress on bone marrow. To investigate this further, we interrogated mice and individuals with SCD and observed extended cell cycle times, oxidative stress, DNA damage, senescence, and dysregulation of molecular programs associated with these processes in bone marrow hematopoietic stem and progenitor cells (HSPCs). Human SCD HSPCs displayed poor hematopoietic potential ex vivo. SCD mice displayed a dramatic loss of transplantable bone marrow HSPCs, which was reversed upon treatment of SCD mice with the senolytic agent, ABT-263 (navitoclax). Thus, senolytics restore bone marrow function during SCD in mice and represent a novel strategy to improve bone marrow health in individuals with SCD and improve the safety of potentially curative gene therapies that utilize autologous HSPCs from individuals with SCD.

cell biology↗

bioRxiv2024

From Cardiac Myosin to the Beta Receptor: Autoantibodies Promote a Fibrotic Transcriptome and Reduced Ventricular Recovery in Human Myocarditis

BackgroundMyocarditis leads to dilated cardiomyopathy (DCM) with one-third failing to recover normal ejection fraction (EF50%), and there is a critical need for prognostic biomarkers to assess risk of nonrecovery. Cardiac myosin (CM) autoantibodies (AAbs) cross-reactive with the {beta}-adrenergic receptor ({beta}AR) are associated with myocarditis/DCM, but their potential for prognosis and functional relevance is not fully understood. MethodsCM AAbs and myocarditis-derived human monoclonal antibodies (mAbs) were investigated to define pathogenic mechanisms and CM epitopes of nonrecovery. Myocarditis patients who do not recover ejection fraction (EF<50%) by one year were studied in a longitudinal (n=41) cohort. Sera IgG and human mAbs were investigated for autoreactivity with CM and CM peptides by ELISA, protein kinase A (PKA) activation, and transcriptomic analysis in H9c2 heart cell line. ResultsCM AAbs were significantly elevated in nonrecovered compared to recovered patients and correlated with reduced EF (<50%). CM epitopes specific to nonrecovery were identified. Transcriptomic analysis revealed serum IgG and mAb 2C.4 induced fibrosis/apoptosis pathways in vitro similar to isoproterenol treated cells. Sera IgG and 2C.4 activated PKA in an IgG and {beta}AR-dependent manner. Endomyocardial biopsies from myocarditis/DCM revealed IgG+ trichrome+ tissues. ConclusionsCM AAbs were significantly elevated in nonrecovered patients, suggesting novel prognostic relevance. CM AAbs correlated with lower EF, and Ab-induced fibrosis/apoptosis pathways suggested a role for CM AAbs in patients who do not recover and develop irreversible heart failure. Homology between CM and {beta}ARs supports mechanisms related to cross-reactivity of CM AAbs with the {beta}AR, a potential AAb target in nonrecovery.

immunology↗

bioRxiv2024

Insula uses overlapping codes for emotion in self and others

In daily life, we must recognize others emotions so we can respond appropriately. This ability may rely, at least in part, on neural responses similar to those associated with our own emotions. We hypothesized that the insula, a cortical region near the junction of the temporal, parietal, and frontal lobes, may play a key role in this process. We recorded local field potential (LFP) activity in human neurosurgical patients performing two tasks, one focused on identifying their own emotional response and one on identifying facial emotional responses in others. We found matching patterns of gamma- and high-gamma band activity for the two tasks in the insula. Three other regions (MTL, ACC, and OFC) clearly encoded both self- and other-emotions, but used orthogonal activity patterns to do so. These results support the hypothesis that the insula plays a particularly important role in mediating between experienced vs. observed emotions.

neuroscience↗

bioRxiv2024

Large DNA viruses in early diverging fungal genomes are relics of past and present infections

Giant viruses of the phylum Nucleocytoviricota have emerged as particularly notable due to their increasingly recognized impacts on eukaryotic genome evolution. Their origins are hypothesized to predate or coincide with the diversification of eukaryotes, and they have been detected in hosts that span the eukaryotic tree of life. But surprisingly, such viruses have not been definitively found in Kingdom Fungi, though earlier genomic and metagenomic work suggests putative associations. Here we report both "viral fossils" and active infection by giant viruses in fungi, particularly in the zoosporic phyla Blastocladiomycota and Chytridiomycota. The recovered viral assemblies span up to 350 kb, encode over 300 genes, and form a monophyletic family-level clade within the Nucleocytoviricota related to orders Imitervirales and Algavirales, which we name Mycodnaviridae. We observed variation in infection status among the isolates including apparent active infection and transcriptionally suppressed states, suggesting that viral activation may be constrained to certain life stages of the host. Our experimental findings add to the limited natural virus-host systems available in culture for the study of giant viruses and expand the known host range of Nucleocytoviricota into a new kingdom that contains many model species. Mycodnaviridae have a global distribution, which invites inquiry into the implications of these infections for host traits, host genome evolution, and the metabolic impacts on ecosystems.

microbiology↗

bioRxiv2023

Investigating the Association Between Nitrate Dosing and Nitrite Generation by the Human Oral Microbiota in Continuous Culture

The generation of nitrite by the oral microbiota is believed to contribute to healthy cardiovascular function, with oral nitrate reduction to nitrite associated with systemic blood pressure regulation. There is the potential to manipulate the composition or activities of the oral microbiota to a higher nitrate-reducing state through nitrate supplementation. The current study examined microbial community composition and enzymatic responses to nitrate supplementation in in sessile oral microbiota grown in continuous culture. Nitrate reductase activity and nitrite concentrations were not significantly different to tongue-derived inocula in model biofilms. These were generally dominated by Streptococcus spp., initially, and a single nitrate supplementation resulted in the increased relative abundance of the nitrate-reducing genera Veillonella, Neisseria and Proteus spp. Nitrite concentrations increased concomitantly and continued to increase throughout oral microbiota development. Continuous nitrate supplementation, over a 7-day period, was similarly associated with an elevated abundance of nitrate-reducing taxa and increased nitrite concentration in the perfusate. In experiments in which the models were established in continuous low or high nitrate environments, there was an initial elevation in nitrate reductase, and nitrite concentrations reached a relatively constant concentration over time similar to the acute nitrate challenge with a similar expansion of Veillonella and Neisseria. In summary, we have investigated nitrate metabolism in continuous culture oral biofilms, showing that nitrate addition increases nitrate reductase activity and nitrite concentrations in oral microbiota with the expansion of putatively NaR-producing taxa. ImportanceClinical evidence suggests that blood pressure regulation can be promoted by nitrite generated through the reduction of supplemental dietary nitrate by the oral microbiota. We have utilised oral microbiota models to investigate the mechanisms responsible, demonstrating that nitrate addition increases nitrate reductase activity and nitrite concentrations in oral microbiota with the expansion of nitrate-reducing taxa.

microbiology↗

bioRxiv2022

Nodavirus RNA Replication Crown Architecture Reveals Proto-Crown Precursor and Viral Protein A Conformational Switching

Positive-strand RNA viruses replicate their genomes in virus-induced membrane vesicles, and the resulting RNA replication complexes are a major target for virus control. Nodavirus studies first revealed viral RNA replication proteins forming a 12-fold symmetric "crown" at the vesicle opening to the cytosol, an arrangement recently confirmed to extend to distantly related alphaviruses. Using cryo-electron microscopy (cryo-EM), we show that mature nodavirus crowns comprise two stacked 12-mer rings of multi-domain viral RNA replication protein A. Each ring contains an ~19 nm circle of C-proximal polymerase domains, differentiated by strikingly diverged positions of N-proximal RNA capping/membrane binding domains. The lower ring is a "proto-crown" precursor that assembles prior to RNA template recruitment, RNA synthesis and replication vesicle formation. In this proto-crown, the N-proximal segments interact to form a toroidal central floor, whose 3.1 [A] resolution structure reveals many mechanistic details of the RNA capping/membrane binding domains. In the upper ring, cryo-EM fitting indicates that the N-proximal domains extend radially outside the polymerases, forming separated, membrane-binding "legs." The polymerase and N-proximal domains are connected by a long linker accommodating the conformational switch between the two rings and possibly also polymerase movements associated with RNA synthesis and non-symmetric electron density in the lower center of mature crowns. The results reveal remarkable viral protein multifunctionality, conformational flexibility and evolutionary plasticity and new insights into (+)RNA virus replication and control. SignificancePositive-strand RNA viruses - including coronaviruses, alphaviruses, flaviviruses and many other medically and economically important pathogens - replicate their RNA genomes by virus-encoded machinery that has been poorly characterized. Using an advanced nodavirus model, we identify a major precursor in RNA replication complex assembly and show it to be a 12-mer ring of viral RNA replication protein A, whose single particle cryo-EM structure reveals functional features of its membrane interaction, assembly, polymerase and RNA capping domains. We further show that fully functional RNA replication complexes acquire a second 12-mer ring of protein A in alternate conformation atop the first, and a central density likely to represent another polymerase conformation. These findings provide strong foundations for understanding, controlling and beneficially using such viruses.

microbiology↗

bioRxiv2022

Loss of pod strings in common bean is associated with gene duplication, retrotransposon insertion, and overexpression of PvIND

Regulation of fruit development has been central in the evolution and domestication of flowering plants. In common bean (Phaseolus vulgaris L.), a major global staple crop, the two main economic categories are distinguished by differences in fiber deposition in pods: a) dry beans with fibrous and stringy pods; and b) stringless snap/green beans with reduced fiber deposition, but which frequently revert to the ancestral stringy state. To better understand control of this important trait, we first characterized developmental patterns of gene expression in four phenotypically diverse varieties. Then, using isogenic stringless/revertant pairs of six snap bean varieties, we identified strong overexpression of the common bean ortholog of INDEHISCENT (PvIND) in non-stringy types compared to their string-producing counterparts. Microscopy of these pairs indicates that PvIND overexpression is associated with overspecification of weak dehiscence zone cells throughout the entire pod vascular sheath. No differences in PvIND DNA methylation were correlated with pod string phenotype. Sequencing of a 500 kb region surrounding PvIND in the stringless snap bean cultivar Hystyle revealed that PvIND had been duplicated into two tandem repeats, and that a Ty1-copia retrotransposon was inserted between these tandem repeats, possibly driving PvIND overexpression. Further sequencing of stringless/revertant isogenic pairs and diverse materials indicated that these sequence features had been uniformly lost in revertant types and were strongly predictive of pod phenotype, supporting their role in PvIND overexpression and pod string phenotype. SignificanceFruit dehiscence is a key trait for seed dissemination. In legumes, e.g., common bean, dehiscence relies on the presence of fibers, including pod "strings". Selections during domestication and improvement have decreased (dry beans) or eliminated (snap beans) fibers, but reversion to the fibrous state occurs frequently in snap beans. In this article, we document that fiber loss or gain is controlled by structural changes at the PvIND locus, a homolog of the Arabidopsis INDEHISCENT gene. These changes include a duplication of the locus and insertion/deletion of a retrotransposon, which are associated with significant changes in PvIND expression. Our findings shed light on the molecular basis of unstable mutations and provide potential solutions to an important pod quality issue. Competing Interest StatementThe authors have no competing interests.

plant biology↗

bioRxiv2021

Spontaneous Neuronal Oscillations in the Human Insula are Hierarchically Organized Traveling Waves

The insula plays a fundamental role in a wide range of adaptive human behaviors, but its electrophysiological dynamics are poorly understood. Here we used human intracranial electroencephalographic recordings to investigate the electrophysiological properties and hierarchical organization of spontaneous neuronal oscillations within the insula. We analyzed the neuronal oscillations of the insula directly and found that rhythms in the theta and beta frequency oscillations are widespread and spontaneously present. These oscillations are largely organized along the anterior-posterior axis of the insula. Both the left and right insula showed anterior-to-posterior decreasing gradients for the power of oscillations in the beta frequency band. The left insula also showed a posterior-to-anterior decreasing frequency gradient and an anterior-to-posterior decreasing power gradient in the theta frequency band. In addition to measuring the power of these oscillations, we also examined the phase of these signals across simultaneous recording channels and found that the insula oscillations in the theta and beta bands are traveling waves. The strength of the traveling waves in each frequency was positively correlated with the amplitude of each oscillation. However, the theta and beta traveling waves were uncoupled to each other in terms of phase and amplitude, which suggested that insula traveling waves in the theta and beta bands operate independently. Our findings provide new insights into the spatiotemporal dynamics and hierarchical organization of neuronal oscillations within the insula, which, given its rich connectivity with widespread cortical regions, indicates that oscillations and traveling waves have an important role in intra- and inter-insula communication.

neuroscience↗

bioRxiv2021

The Spatial Reach of Neuronal Coherence and Spike-field Coupling across the Human Neocortex

Neuronal coherence is thought to be a fundamental mechanism of communication in the brain, where synchronized field potentials coordinate synaptic and spiking events to support plasticity and learning. Although the spread of field potentials has garnered great interest, little is known about the spatial reach of phase synchronization, or neuronal coherence. Functional connectivity between different brain regions is known to occur across long distances, but the locality of coherence within a brain region is understudied. Here we used simultaneous recordings from electrocorticography (ECoG) grids and high-density microelectrode arrays to estimate the spatial reach of neuronal coherence and spike-field coherence (SFC) across frontal, temporal, and occipital cortices during cognitive tasks in humans. We observed the strongest coherence within a 2-3 cm distance from the microelectrode arrays, potentially defining an effective range for local communication. This range was relatively consistent across brain regions, spectral frequencies, and cognitive tasks. The magnitude of coherence showed power law decay with increasing distance from the microelectrode arrays, where the highest coherence occurred between ECoG contacts, followed by coherence between ECoG and deep cortical LFP, and then SFC (i.e., ECoG > LFP > SFC). The spectral frequency of coherence also affected its magnitude. Alpha coherence (8-14 Hz) was generally higher than other frequencies for signals nearest the microelectrode arrays, whereas delta coherence (1-3 Hz) was higher for signals that were farther away. Action potentials in all brain regions were most coherent with the phase of alpha oscillations, which suggests that alpha waves could play a larger, more spatially local role in spike timing than other frequencies. These findings provide a deeper understanding of the spatial and spectral dynamics of neuronal coherence, further advancing knowledge about how activity propagates across the human brain.

neuroscience↗

bioRxiv2020

Comparative analysis of single-cell RNA Sequencing Platforms and Methods

Single-cell RNA sequencing (scRNA-seq) offers great new opportunities for increasing our understanding of complex biological processes. In particular, development of an accurate Human Cell Atlas is largely dependent on the rapidly advancing technologies and molecular chemistries employed in scRNA-seq. These advances have already allowed an increase in throughput for scRNA-seq from 96 to 80,000 cells on a single instrument run by capturing cells within nano-liter droplets. While this increase in throughput is critical for many experimental questions, a thorough comparison between microfluidic-, plate-, and droplet-based technologies or between multiple available platforms utilizing these technologies is largely lacking. Here, we report scRNA-seq data from SUM149PT cells treated with the histone deacetylase inhibitor TSA vs. untreated controls across several scRNA-seq platforms (Fluidigm C1, WaferGen iCell8, 10X Genomics Chromium Controller, and Illumina/BioRad ddSEQ). The primary goal of this project was to demonstrate RNA sequencing (RNA-seq) methods for profiling the ultra-low amounts of RNA present in individual cells, and this report discusses the results of the study as well as technical challenges/lesson learned and present general guidelines for best practices in sample preparation and analysis.

genomics↗

bioRxiv2020

Single cell transcriptomic profiling identifies molecular phenotypes of newborn human lung cells

RationaleWhile animal model studies have extensively defined mechanisms controlling cell diversity in the developing mammalian lung, the limited data available from late stage human lung development represents a significant knowledge gap. The NHLBI Molecular Atlas of Lung Development Program (LungMAP) seeks to fill this gap by creating a structural, cellular and molecular atlas of the human and mouse lung. MethodsSingle cell RNA sequencing generated transcriptional profiles of 5500 cells obtained from two one-day old human lungs (born at gestational ages of 39 and 31 weeks) from the LungMAP Human Tissue Core Biorepository at the University of Rochester. Frozen single cell isolates were captured, and library preparation was completed on the Chromium 10X system. Data was analyzed in Seurat, and cellular annotation was performed using the ToppGene functional analysis tool. Single cell sequence data from 32000 postnatal day 1, 3, 7 and 10 mouse lung (n = 2 at each time point) cells generated by the LungMAP Research Center at Cincinnati Childrens Hospital and Medical Center, using Dropseq platform, was integrated with the human data. In situ hybridization was used to confirm the spatial location of cellular phenotypes. ResultsTranscriptional interrogation of donor newborn human lung cells identified distinct clusters representing multiple populations of epithelial, endothelial, fibroblasts, pericytes, smooth muscle, and immune cells and signature genes for each of these populations were identified. Computational integration of newborn human and postnatal mouse lung development cellular transcriptomes facilitated the identification of distinct cellular lineages among all the major cell types. Integration of the human and mouse cellular transcriptomes also demonstrated cell type-specific differences in developmental states of the newborn human lung cells. In particular, matrix fibroblasts could be separated into those representative of younger cells (n=393), or older cells (n=158). This is the first comprehensive molecular map of the cellular landscape of neonatal human lung, including biomarkers for cells at distinct states of development. Our results indicate that integrated single cell RNA profiling of human and mouse lung will help identify common and species-specific mechanisms of lung development and respiratory disease.

genomics↗

bioRxiv2019

Genetic Associations in Four Decades of Multi-Environment Trials Reveal Agronomic Trait Evolution in Common Bean

Multi-environment trials (METs) are widely used to assess the performance of promising crop germplasm. Though seldom designed to elucidate genetic mechanisms, MET datasets are often much larger than could be duplicated for genetic research and, given proper interpretation, may offer valuable insights into the genetics of adaptation across time and space. The Cooperative Dry Bean Nursery (CDBN) is a MET for common bean (Phaseolus vulgaris) grown for over 70 years in the United States and Canada, consisting of 20 to 50 entries each year at 10 to 20 locations. The CBDN provides a rich source of phenotypic data across entries, years, and locations that is amenable to genetic analysis. To study stable genetic effects segregating in this MET, we conducted genome-wide association (GWAS) using best linear unbiased predictions (BLUPs) derived across years and locations for 21 CDBN phenotypes and genotypic data (1.2M SNPs) for 327 CDBN genotypes. The value of this approach was confirmed by the discovery of three candidate genes and genomic regions previously identified in balanced GWAS. Multivariate adaptive shrinkage (mash) analysis, which increased our power to detect significant correlated effects, found significant effects for all phenotypes. The first use of mash on an agricultural dataset discovered two genomic regions with pleiotropic effects on multiple phenotypes, likely selected on in pursuit of a crop ideotype. Overall, our results demonstrate that by applying multiple statistical genomic approaches on data mined from MET phenotypic data sets, significant genetic effects that define genomic regions associated with crop improvement can be discovered.

genomics↗