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Guo, F.

Publications and source records attributed to Guo, F..

At least 91 records · Page 5Linked to original sources

Morphological changes and two Nodal paralogs drive left-right asymmetry in the squamate veiled chameleon (C. calyptratus).

The ancestral mode of left-right (L-R) patterning involves cilia in the L-R organizer. However, the mechanisms regulating L-R patterning in non-avian reptiles remains an enigma, since most squamate embryos are undergoing organogenesis at oviposition. In contrast, veiled chameleon (Chamaeleo calyptratus) embryos are pre-gastrula at oviposition, making them an excellent organism for studying L-R patterning evolution. Here we show that veiled chameleon embryos lack motile cilia in their L-R organizer, consistent with the loss of motile cilia being a synapomorphy of all reptiles. Furthermore, in contrast to avians, geckos and turtles, which have one Nodal gene, veiled chameleon exhibits expression of two paralogs of Nodal in the left lateral plate mesoderm, albeit in non-identical patterns. Using live imaging, we observed asymmetric morphological changes that precede, and likely trigger, asymmetric expression of the Nodal cascade. Thus, veiled chameleons are a new and unique model for studying the evolution of L-R patterning.

developmental biology↗

Expanding the diversity of Accumulibacter with a novel type and deciphering the transcriptional and morphological features among co-occurring strains

Accumulibacter is the major polyphosphate-accumulating organism (PAO) in global wastewater treatment systems. Its phylogenetic and functional diversity has been continuously updated in recent years. In addition to its widely recognized two sublineages, Types I and II, here we discovered a novel type enriched in laboratory bioreactors. Core gene- and machine learning-based gene feature profiling supported that Type III Accumulibacter was potential PAO with the unique function of using dimethyl sulfoxide as electron acceptor. On the basis of the correlation between the similarity of ppk1 and genome, the number of ppk1-represented Accumulibacter species was estimated to be over one hundred, suggesting that the currently recognized species are only the tip of the iceberg. Meanwhile, multiple Accumulibacter strains co-occurring in a bioreactor were investigated for their inter-strain transcriptional and morphological features. Metatranscriptomics of seven co-occurring strains indicated that the expression level and interphasic dynamics of PAO phenotype-related genes had minimal correlation with their phylogeny. In particular, expression of denitrifying and poly-P metabolism genes had higher inter-strain and interphasic divergence compared with glycogen and polyhydroxyalkanoates metabolic genes. A strategy of cloning rRNA genes from different strains based on similar genomic synteny was successfully applied to differentiate their morphology via fluorescence in situ hybridization. Our study further expanded the phylogenetic and functional diversity of Accumulibacter. We also proposed that deciphering the function and capability of certain Accumulibacter should be environment- and population-specific. ImportanceAccumulibacter, as the core functional but uncultured taxa for enhanced biological phosphorus removal, has attracted much attentions on its phylogenetic and functional diversity and intra-genus niche differentiation in the last two decades. It was well-known that this genus had two sub-lineages (Type I and II) since 2002. In this study, a novel type (Type III) with proposed novel functional feature was discovered by the metagenomic approach. By linking average nucleotide identity of Accumulibacter genomes and the similarity of the ppk1 sequences, a phylogenetic biomarker that has been largely deposited in database, we estimated that its global species-level diversity was higher than 100. Moreover, as we found the co-occurrence of multiple Accumulibacter strains in one bioreactor, the simultaneous transcriptional divergence of the co-occurring strains was interesting for understanding their niche differentiation in a single community. The results suggested the decoupling feature between transcriptional pattern with phylogeny for co-occurring strains.

microbiology↗

JMJD3 is a Key Regulator of Dopamine Synthesis in Ventral Tegmental Area Dopamine Neurons.

Chronic pain is associated with midbrain dopamine levels. The molecules and mechanisms modulating this association remain to be elucidated. By using conditional knockout mice, we report that JMJD3 deficiency in midbrain dopamine neurons causes prolonged mechanical hyperalgesia regardless of sex and age. Both genetic defect and pharmaceutical inhibition of JMJD3 decrease dopamine level in midbrain and striatum, resulting from reduced tyrosine hydroxylase expression in midbrain dopamine neurons. Furthermore, epigenetic experiments reveal that JMJD3 is indispensable for the transcription of tyrosine hydroxylase through direct and indirect manners. These findings suggest JMJD3 and midbrain dopamine neurons as novel players and pharmaceutical targets for chronic pain regulation.

neuroscience↗

rRNA transcription is integral to liquid-liquid phase separation and maintenance of nucleolar structure

Beginning with transcription of ribosomal RNA (rRNA) by RNA Polymerase (Pol) I in the nucleolus, ribosome biogenesis is intimately tied to cell growth and proliferation. Perturbation of ribosome biogenesis has been previously shown to affect nucleolar structure, yet the underlying mechanism is unknown. We generated loss-of-function mouse mutants of Pol I subunits, Polr1a, Polr1b, Polr1c and Polr1d, thereby genetically inhibiting rRNA transcription and ribosome biogenesis. Pol I mutant embryos are preimplantation lethal and have fewer nucleoli. Using hiPSCs triple labeled for the three nucleolar compartments, we observe two phenotypes upon Pol I inhibition: a single condensed nucleolus, and fragmented nucleoli. We find that when rRNA transcription is inhibited, the viscosity of the granular compartment of the nucleolus is increased disrupting its liquid-liquid phase separation properties, which results in a condensed nucleolus. Taken together, our data suggests that Pol I function and rRNA transcription are required for maintaining nucleolar structure and integrity.

developmental biology↗

Distinct structure and gating mechanism in diverse NMDA receptors with GluN2C and GluN2D subunits

N-Methyl-D-Aspartate (NMDA) receptors are essential for many brain functions. These receptors are heterotetramers typically comprising two GluN1 subunits and two GluN2 subunits. The latter could alternate among four subtypes (N2A-N2D) and determine the functional diversity of NMDA receptors1, 2. For example, receptors containing N2C or N2D exhibit 50-fold lower channel open probability (Po) than those containing N2A (ref.3-5). Structures of N2A- and N2B-containing receptors have been extensively characterized, providing molecular basis for understanding NMDA receptor function6-14. Here we report the cryo-EM structures of N1-N2D and N1-N2C di-heterotetramers (di-receptors), and N1-N2A-N2C tri-heterotetramer (tri-receptor) at a resolution up to 3.0 [A]. Structural analysis showed that the bilobate N-terminal domain (NTD) in N2D adopted an intrinsic closed conformation, leading to a compact NTD tetramer in N1-N2D receptor. Functional studies further demonstrated that, in di-receptors containing N2D but not N2A or N2B, crosslinking NTD at the tetrameric interface had no effect on channel activity, while crosslinking ligand-binding domain (LBD) of two N1 protomers significantly elevated Po. Surprisingly, we found that the N1-N2C di-receptors spontaneously oscillated between symmetric and asymmetric conformation. The later one occupied a predominant population, whereby two N2C protomers exhibited distinct conformation. This asymmetry, which was also found to a lesser extent in N1-N2A di-receptor10, was further locked by the binding of an N2C-specific allosteric potentiator PYD-106 to a unique binding pocket between NTD and LBD in only one N2C protomer. Finally, N2A and N2C in the N1-N2A-N2C tri-receptor displayed the conformation close to that found in one protomer of N1-N2A and N1-N2C di-receptors, respectively. These findings provide a comprehensive structural understanding of diverse functional properties of major NMDA receptor subtypes.

neuroscience↗

A novel antidepressant acting via allosteric inhibition of GluN2D-incorporated NMDA receptors at GABAergic interneurons

N-methyl-D-aspartate receptors (NMDARs) are glutamate-gated calcium-permeable excitatory channels. They have attracted great interest as potential targets for the treatment of depression in recent years. NMDARs typically assemble as heterotetramers composed of two GluN1 and two alternative GluN2 (2A-2D) subunits, the latter of which endow various subtypes with diverse gating and pharmacological properties. To date, limited molecules with GluN2 specificity have been identified to show antidepressant effects. Here, we identify a compound termed YY-23 extracted from Rhizoma Anemarrhenae allosterically inhibited the channel activities of GluN2C- or GluN2D-incorporated NMDARs, an effect that was presumably influenced by the S2 segment in the ligand-binding domain of the GluN2 subunit. We found that prefrontal GluN2D-containing NMDARs were predominantly expressed at GABAergic interneurons rather than pyramidal neurons. Furthermore, we revealed that YY-23 suppressed the activity of GluN2D-containing NMDARs and GABAergic neurotransmission in the medial prefrontal cortex (mPFC). As a consequence, this GABAergic disinhibition facilitated the excitatory transmission. Behavioural experiments showed that YY-23 acted as a rapid antidepressant in both stress-naive and stressed animal models, which was abolished in Grin2d-knockout mice. Together, our findings suggest that GluN2D-incorporated NMDARs on GABAergic interneurons might be promising therapeutic targets for the treatment of depression.

neuroscience↗

(Z, Z, Z)-3,6,9-nonadecadiene, a potential inhibitor of sex pheromone of Ectropis grisescens Warren (Lepidoptera: Geometridae): electroantennogram test, wind tunnel, and in silico study

Application of sex pheromone is the most environmental-friendly technique to control pests. Moreover, it has been discovered that pheromone analogs can disturb or inhibit mating communication in some species of moths. Ectropis grisescens Warren (Lepidoptera: Geometridae), is the most severe tea defoliator in China. Thus, in our study, an analog of the pest sex pheromone component, (Z, Z, Z)-3,6,9-nonadecadiene (Z3Z6Z9-19:Hy), was selected to determine its potential activity in controlling the pest. Electroantennogram (EAG), Y-tube olfactometer, and wind tunnel experiments separately showed potential inhibition of Z3Z6Z9-19:Hy. The response elicited by Z3Z6Z9-19:Hy displayed a dose-dependent way in EAG test. Furthermore, in Y-tube olfactometer, percentage of positive response of E. grisescens males was significantly (P<0.01) reduced by Z3Z6Z9-19:Hy up to 70%. In wind tunnel, all types of behavioral response were significantly (P<0.01) inhibited by Z3Z6Z9-19:Hy, percentage of contacting source was utterly inhibited at the lowest dose tested. Based on these results, the combination of the analog and SNMP1 protein was also studied. Our study revealed the potential of Z3Z6Z9-19:Hy as a sex pheromone inhibitor, which would provide new perspectives in monitoring and mating disruption of E. grisescens in pest-control strategies.

ecology↗

Engineering human spinal microphysiological systems to model opioid-induced tolerance

Opioids are commonly used for treating chronic pain. However, with continued use, they may induce tolerance and/or hyperalgesia, which limits therapeutic efficacy. The human mechanisms of opioid-induced hyperalgesia are significantly understudied, in part, because current models cannot fully recapitulate human pathology. Here, we engineered novel human spinal microphysiological systems (MPSs) integrated with plug-and-play neural activity sensing for modeling human nociception and opioid-induced tolerance. Each spinal MPS consists of a flattened human spinal cord organoid derived from human stem cells and a 3D printed organoid holder device for plug-and-play neural activity measurement. We found that the flattened organoid design of MPSs not only reduces hypoxia and necrosis in the organoids, but also promotes their neuron maturation, neural activity, and functional development. We further demonstrated that prolonged opioid exposure resulted in neurochemical correlates of opioid tolerance and hyperalgesia, as measured by altered neural activity, reduced densities of glutamate transporter levels and downregulation of -opioid receptor expression of human spinal MPSs. The MPSs are scalable, cost-effective, easy-to-use, and compatible with commonly-used well-plates, thus allowing plug-and-play measurements of neural activity. We believe the MPSs hold a promising translational potential for studying human pain etiology, screening new treatments, and validating novel therapeutics for human pain medicine.

bioengineering↗

Acrylamide Induces Protein Aggregation in CNS through Suppression of FoxO1-mediated Autophagy.

Proteotoxic stress is a major stimulus and risk factor for the neuropathogenesis in central nervous system (CNS), which is tightly associated with neurodegenerative diseases. Here, we identify acrylamide (ACR), a type-2 alkene that is commonly detected in deep-fried starch food and used in water industry and biomedical laboratories, as a potent and universal inducer of proteotoxic stress in mouse brain, as well as in cultured mouse neural stem cells, neurons and astrocytes, three major cell types in CNS. Aggregations of ubiquitin-labeled misfolded proteins and neurodegeneration-related proteins including amyloid precursor protein and presenilin 1 were drastically induced by ACR, leading to cell-defensive aggresome formation that was able to temporarily counteract with ACR toxicity. However, a defected clearance of aggresomes eventually led to apoptotic cell death, which was largely attributed to the breakdown of cytoskeleton and impairment of macroautophagy/autophagy, as evidenced by an aggregation of filament actin and an almost complete loss of LC3-positive autophagosomes. A series of core autophagy-related genes responsible for autophagosome formation were down-regulated, indicating an ACR-induced transcriptional suppression of autophagy. In addition, FoxO1, the master transactivator of these genes, were both transcriptionally repressed and nuclear excluded by ACR. Overexpression of FoxO1 rescued ACR-induced autophagy defects and attenuated the proteotoxicity. In summary, we spotlight proteotoxic stress as a novel feature of ACR neurotoxicity in CNS, and implicate FoxO1 as a critical therapeutic target.

pathology↗

Simulation study of Cell Transmembrane Potential and Electroporation Induced by Time-Varying Magnetic Fields

In this work, an improved simulation model was proposed to assess the transmembrane potential (TMP) evolution on the cellular membrane exposed to time-varying magnetic fields (TMFs). Comparatively, we extended the research on TMP induced by TMF to the electroporation phenomenon by introducing the Smoluchowski function, thereby predicting the occurrence of electroporation. The simulation results based on our numerical model showed that with exposure to the sub-microsecond trapezoidal pulsed magnetic field (PMF), the pore density did not reach the conventional electroporation criterion (1014 m-2) even if the TMP exceeded the electroporation threshold ([~]1V); however, with the same energy import, it was easier for the nanosecond pulse to electroporate the membrane evidenced by higher pore density. Further, the capability of predicting the occurrence of electroporation was verified by extending our simulation model to compare experimental results. The comparative analysis showed that our simulation model has predictive and guiding significance for experimental studies and practical applications.

biophysics↗

All atom molecular dynamics simulation of the combinedeffects of different phospholipids and cholesterolcontents on electroporation

The electroporation mechanism could be related to the composition of the plasma membrane, and the combined effect of different phospholipids molecules and cholesterol contents on electroporation is rarely studied and concluded. In this paper, we applied all-atom molecular dynamics (MD) simulation to study the effects of phospholipids and cholesterol contents on bilayer membrane electroporation. The palmitoyl-oleoyl-phosphatidylcholine (POPC) model, palmitoyl-oleoyl-phosphatidylethanolamine (POPE) model and 1:1 mixed model of POPC and POPE called PEPC were three basic models. An electric field of 0.45 V/nm was applied to nine models including three basic models with cholesterol contents of 0%, 24%, and 40%. The interfacial water molecules moved under the electric field, and once the first water bridge formed, the rest of the water molecules would dramatically flood into the membrane. The simulation showed that a rapid rise in the Z component of the average dipole moment of interfacial water (Z-DM) indicated the occurrence of electroporation, and the same increment of Z-DM represented the similar change in the size of water bridge. With the same cholesterol content, the formation of the first water bridge was the most rapid in POPC model regarding the average electroporation time (tep), and the average tep of the PEPC model was close to that of the POPE model. We speculate that the difference in membrane thickness and initial hydrogen bonds of interfacial water affecting the average tep among different membrane composition. Our results reveal the influence of membrane composition on electroporation mechanism at the molecular level.

biochemistry↗

Molecular dynamics study of phospholipid membrane electroporation induced by bipolar pulses with different intervals

In this study, PM-EP induced by bipolar pulses with different intervals was investigated by all-atom molecular dynamics simulation. Firstly, PM-EP was formed during the positive pulse of 2ns and 0.5V/nm, then the effects of various intervals of 0, 1, 5, 10ns on PM-EP evolution were investigated, and the dynamic changes of different degrees of PM-EP induced by following negative pulses of 2ns and 0.5V/nm were analyzed. The elimination of the PM-EP during the interval of bipolar pulses were determined and it was related to the degrees of PM-EP and the time of intervals, then the degrees of PM-EP at the end of the intervals were classified and quantitatively defined, namely, Resealing, Destabilizing and Retaining state. These three states appeared due to the combined effect of both the preceding positive pulse and the interval. Furthermore, the evolution of PM-EP in resealing state under negative pulses was similar to that of positive pulses as evidenced by EP formation time and degree of PM-EP, the destabilizing state had the same trends as the resealing state except that the re-electroporation of phospholipid membrane appeared faster and larger degree of EP obtained with the same pulse exposure time. Regarding the retaining state, the negative pulses enhanced PM-EP with more profound water bridges, which can be considered as the effect of electric field superposition. These results can improve our understanding of the fundamental mechanism of bipolar pulse-induced PM-EP. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=163 SRC="FIGDIR/small/501059v1_ufig1.gif" ALT="Figure 1"> View larger version (87K): org.highwire.dtl.DTLVardef@9a1d36org.highwire.dtl.DTLVardef@1f3f6ccorg.highwire.dtl.DTLVardef@1d0068dorg.highwire.dtl.DTLVardef@5e1e2b_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIQuantitative and qualitative definition of the three states of the phospholipid membrane electroporation at the end of the intervals. C_LIO_LIClarification that the states of phospholipid membrane electroporation were generated due to the combined effect of positive pulses and intervals. C_LIO_LIQuantitative and qualitative comparison the evolution of the states of phospholipid membrane electroporation during the negative pulses. C_LI

biochemistry↗

Starvation Induces Diverse Autophagic Response in Cardiomyocytes and Noncardiomyocytes.

Cardiac autophagy serves as a potential mechanism to be genetically, epigenetically and pharmaceutically manipulated to prevent or alleviate pathological conditions in heart diseases. One of the complexities of this manipulation comes from the cellular heterogeneity of the heart. In this study, we assessed the dynamics of nutrient deprivation-induced autophagy activation in four major cardiac cell types in vitro and in vivo and found a major difference between cardiomyocyte and other three types of noncardiomyocyte. In comparison to the constant increase and maintenance of autophagic activity in noncardiomyocytes, cardiomyocyte undergoes rapid gain and loss of autophagic activity. This difference contributes to at least two aspects of cardiomyocyte pathophysiology: high vulnerability to nutrient deprivation-induced cell death and unresponsiveness to pharmaceutical regulation of autophagy. Our present findings support a cell type-specific targeting of autophagy for therapeutic intervention of cardiac diseases.

cell biology↗

Inhibition of c-Jun in AgRP neurons mediates chronic stress-induced anxiety-like behaviors and colitis susceptibility

Psychiatric disorders, such as anxiety, are frequently associated with inflammatory bowel diseases (IBD), however, the neural mechanisms are unknown. Here, we showed that hypothalamic agouti-related protein (AgRP) neuronal activity was suppressed under chronic restraint stress (CRS), a condition known to induce anxiety-like behaviors and increase colitis susceptibility. Consistently, chemogenic activation (inhibition) of AgRP neurons reversed (mimicked) CRS-induced anxiety-like behaviors and colitis susceptibility. Furthermore, CRS inhibited AgRP neuronal activity by suppressing the expression of c-Jun. As expected, overexpression of c-Jun in these neurons protected against the CRS-induced these effects and knockdown of c-Jun in AgRP neurons (c-Jun{Delta}AgRP) promoted anxiety-like behaviors and colitis. Moreover, relieving the anxiety with cyamemazine (an anxiolytic drug) alleviated colitis susceptibility in c-Jun{Delta}AgRP mice. Finally, according to a proteomic analysis, the levels of the secreted protein thrombospondin 1 (THBS1) were negatively associated with the increased anxiety-like behaviors and colitis susceptibility, supplementing recombinant THBS1 rescued colitis in c-Jun{Delta}AgRP mice. Taken together, these results reveal a critical role of hypothalamic AgRP neuron-derived c-Jun in orchestrating chronic stress-induced anxiety-like behaviors and colitis susceptibility. These results provide a new perspective for understanding the neuronal mechanisms and potential therapeutic target for the comorbidity of psychiatric disorders, such as anxiety, and IBD.

neuroscience↗

Functional autapses form in striatal parvalbumin interneurons but not medium spiny neurons

Autapses (or self-synapses) selectively form in specific cell types in many brain regions including the neocortex and the hippocampus, where they provide feedback control over self-spiking activities. Previous morphological studies also found putative autapses in medium spiny neurons (MSNs) of the striatum. However, it remains unclear whether striatal neurons indeed form physiologically functional autapses. We performed whole-cell recordings from striatal neurons in acute mouse brain slices, and identify autaptic neurons by the occurrence of prolonged asynchronous release (AR) of neurotransmitter after high-frequency burst of action potentials (APs) in the same cell. To our surprise, we found no autaptic release in all recorded MSNs after the AP burst, even in the presence of Sr2+ that should desynchronize and thus prolong synaptic vesicle release. In sharp contrast, we observed robust autaptic AR events in half of the recorded parvalbumin (PV)-positive neurons. Autaptic responses in PV cells were mediated by GABAA receptors, and the AR strength was dependent on the frequency and the number of APs during the burst. Further simulation results show that autapses regulate burst spiking in PV cells by providing self-inhibition and thus shape network oscillation at certain frequencies. Together, we reveal that, distinct from MSNs, striatal PV neurons form functional autapses, activation of which would regulate self-activities in PV cells, and thereby shape MSN firing and network oscillations. Author summarySynapses, which usually occur between two neurons, are key structures for signal communication in the nervous system. However, some types of neurons form autapses, where a neuron synapses onto itself. Autaptic transmission provides feedback signal regulating self-spiking activities. Neuronal and network activities in the striatum play critical roles in motor control and other brain functions. Previous studies suggest formation of autapses in striatal principal MSNs, but it remains unclear whether striatal neurons form functional autapses. We performed direct recordings from striatal neurons and examined the occurrence of autaptic transmission in acute brain slices. Surprisingly, we did not detect any autaptic responses in MSNs. A large proportion of striatal PV neurons, however, produced robust autaptic GABA release upon high-frequency stimulation, indicating selective formation of autapses in striatal PV cells. Our computation simulations suggest that autapses provide self-inhibition in PV cells and thereby shape activities in MSNs and striatal network, particularly when PV cells discharge at high frequencies corresponding to a high dopamine state. Together, our findings indicate that PV cells, but not MSNs, in the striatum form physiologically functional autapses. Autapses in PV cells could be essential circuit elements in the striatum and contribute to striatal functions, such as motor control.

neuroscience↗

A metabolically engineered bacterium controls autoimmunity by remodeling the pro-inflammatory microenvironment

Immunotherapy has led to impressive advances in the treatment of autoimmune and pro-inflammatory disorders; yet, its clinical outcomes remain limited by a variety of factors including the pro-inflammatory microenvironment (IME). Discovering effective immunomodulatory agents, and the mechanisms by which they control disease, will lead to innovative strategies for enhancing the effectiveness of current immunotherapeutic approaches. We have metabolically engineered an attenuated bacterial strain (i.e., Brucella melitensis 16M {Delta}vjbR, Bm{Delta}vjbR) to produce indole, a tryptophan metabolite that controls the fate and function of regulatory T cells (Tregs). We demonstrated that treatment with this strain polarized M2 macrophages (M{varphi}) which produced anti-inflammatory cytokines (e.g., IL-10) and promoted Treg function; moreover, when combined with adoptive cell transfer (ACT) of Tregs, a single treatment with our engineered bacterial strain dramatically reduced the incidence and score of autoimmune arthritis and decreased joint damage. These findings show how a metabolically engineered bacterium can constitute a powerful vehicle for improving the efficacy of immunotherapy, defeating autoimmunity and reducing inflammation by remodeling the IME and augmenting Treg function.

immunology↗

Recombination-aware Phylogeographic Inference Using the Structured Coalescent with Ancestral Recombination

Movement of individuals between populations or demes is often restricted, especially between geographically isolated populations. The structured coalescent provides an elegant theoretical framework for describing how movement between populations shapes the genealogical history of sampled individuals and thereby structures genetic variation within and between populations. However, in the presence of recombination an individual may inherit different regions of their genome from different parents, resulting in a mosaic of genealogical histories across the genome, which can be represented by an Ancestral Recombination Graph (ARG). In this case, different genomic regions may have different ancestral histories and so different histories of movement between populations. Recombination therefore poses an additional challenge to phylogeographic methods that aim to reconstruct the movement of individuals from genealogies, although also a potential benefit in that different loci may contain additional information about movement. Here, we introduce the Structured Coalescent with Ancestral Recombination (SCAR) model, which builds on recent approximations to the structured coalescent by incorporating recombination into the ancestry of sampled individuals. The SCAR model allows us to infer how the migration history of sampled individuals varies across the genome from ARGs, and improves estimation of key population genetic parameters such as population sizes, recombination rates and migration rates. Using the SCAR model, we explore the potential and limitations of phylogeographic inference using full ARGs. We then apply the SCAR to lineages of the recombining fungus Aspergillus flavus sampled across the United States to explore patterns of recombination and migration across the genome.

bioinformatics↗

Understanding immune-driven brain aging by human brain organoid microphysiological analysis platform

The aging of the immune system drives systemic aging and the pathogenesis of age-related diseases. However, a significant knowledge gap remains in understanding immune-driven aging, especially in brain aging, due to the limited current in vitro models of neuro-immune interaction. Here we report the development of a human brain organoid microphysiological analysis platform (MAP) to discover the dynamic process of immune-driven brain aging. We create the organoid MAP by 3D printing that can confine organoid growth and perfuse oxygen and nutrients (and immune cells) to generate standardized human cortical organoids that promote viability, maturation, and commitment to human forebrain identity. Dynamic rocking flow is incorporated for the platform that allows us to perfuse primary monocytes from young (20 to 30-year-old) and aged (>60-year-old) donors and culture human cortical organoids for modeling and analyzing the aged immune cell interacting organoid tissues systematically. We discovered the aged monocytes had increased infiltration and promoted the expression of aging-related markers (e.g., p16 in astrocytes neighboring to monocytes) within human cortical organoids, indicating that aged monocytes may drive brain aging. We believe that our human brain organoid MAP provides promising solutions for basic research and translational applications in aging, neuroimmunological diseases, autoimmune disorders, and cancers.

bioengineering↗