Biology subjects

Harris, R.

Publications and source records attributed to Harris, R..

At least 19 recordsLinked to original sources

bioRxiv2026

APOBEC3G Splicing Defects in Nonhuman Primate Models Result in Disparate Viral Mutational Profiles Relative to Humans

Nonhuman primates (NHPs), particularly macaques, are indispensable models for studying human infectious diseases due to their close immunological and physiological similarities. Understanding species-specific molecular differences is essential for maximizing the translational value of these models. Here we report that APOBEC3G (A3G), a potent antiviral restriction factor and the major source of genetic variations in HIV, exhibits a widespread mRNA splicing defect in the Cercopithecinae subfamily, which includes the commonly used NHP models. Driven by intronic polymorphisms, this splicing defect substantially reduces A3G protein levels and consequently results in a markedly reduced A3G-mediated mutation signatures, fewer defective viral genomes, and greater viral diversification in SIV compared to HIV. This species-specific effect is not restricted to lentiviruses: reduced A3G signatures have also been reported in simian foamy virus and simian T-cell leukemia virus, suggesting broader effects across primate retroviruses. These findings reveal a lineage-specific alteration in a major antiviral restriction factor, with important implications for viral restriction, evolution, drug resistance, and immune evasion. They also highlight the importance of incorporating naturally occurring genetic variation into NHP model selection to improve the reproducibility, translational fidelity, and biological relevance of preclinical research.

genomics↗

bioRxiv2026

Endogenous APOBEC3B Promotes CHK1 Inhibitor Sensitivity

APOBEC3B (A3B) is a single-stranded DNA cytosine deaminase overexpressed in cancer, where it causes genomic DNA damage and mutations associated with tumor evolution. Enforced A3B overexpression triggers a dependency on the replication-stress response in different cellular models. However, whether endogenous A3B in cancer cells might yield a similar vulnerability is unclear. Here, we investigate how endogenous A3B expression and catalytic activity affect sensitivity to CHK1 inhibition, using two cancer cell lines, JHOC5 and U2OS. A3B-expressing cancer cells are sensitive to two chemically distinct CHK1 inhibitors, GDC-0575 and Prexasertib. CHK1 inhibitor sensitivity is reduced by A3B CRISPR knockout and restored by re-expressing wildtype A3B in knockout cells. Moreover, an endogenous A3B-E255A catalytic mutant generated by homology-directed repair phenocopies the reduced CHK1 inhibitor sensitivity of A3B-null cells, demonstrating a DNA deamination-dependent mechanism. CHK1 inhibition induces replication-associated DNA damage and cell-cycle perturbation dependent on A3B expression. As a result, A3B-expressing cells accumulate more pan-nuclear {gamma}H2AX, aberrant DNA-content profiles, and an expanded EdU-negative S-phase population, which are hallmarks of stalled DNA replication. In comparison, A3B-null and A3B-E255A cells retain defined cell-cycle distributions and are less sensitive to CHK1 inhibition. Together, these findings identify endogenous A3B-catalyzed deamination as a therapeutically actionable source of replication-associated DNA damage that renders tumor cells selectively dependent on CHK1 function. Statement of significanceAPOBEC3B causes mutations in cancer cells and simultaneously imposes DNA replication stress. This combines to sensitize tumor cells to chemical inhibitors of the DNA damage response kinase CHK1.

cancer biology↗

bioRxiv2026

Collapsing retroviruses for efficient delivery of viro-toxic cargoes

Retroviruses are excellent tools for delivering and expressing transgenic cargoes with broad utility in research and therapy. However, many cargoes including virus restriction factors can dramatically limit virus production and/or infectivity. An extreme viro-toxic cargo is the DNA cytosine deaminase APOBEC3B, which potently restricts retrovirus infectivity by a direct cDNA deamination-dependent mechanism. To overcome viro-toxicity, an APOBEC3B minigene cargo is disrupted by a translation stop cassette flanked by a direct repeat of its own sequence. The integrity of the minigene is reconstituted naturally by retroviral recombination during transduction. Efficiency can be improved from 90% to nearly 100% by coupling the minigene to the translation of a downstream selectable marker. Collapsing retrovirus (CRV) technology enables the functional delivery of APOBEC3B to a target cell population and may have broad utility for delivering viro-toxic cargoes. MotivationMany different proteins are detrimental to retrovirus production and/or to virus-producing cells. This problem can be circumvented by interrupting the genetic cargo with a direct repeat-flanked translation stop cassette and allowing transgene integrity to be restored naturally by recombination during reverse transcription. As exemplified by the retrovirus restriction factor APOBEC3B, this process is very efficient. HighlightsO_LICollapsing retroviruses (CRVs) prevent retrovirus restriction by viro-toxic proteins C_LIO_LITruncated tandem repeats recombine during transduction and restore virus integrity C_LIO_LITranslation-coupled selection enables near 100% transduction efficiency C_LIO_LICRVs have broad utility for delivering viro-toxic cargoes such as APOBEC3B C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=186 SRC="FIGDIR/small/735095v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@e96092org.highwire.dtl.DTLVardef@1c343f9org.highwire.dtl.DTLVardef@a3b53dorg.highwire.dtl.DTLVardef@1cfeb69_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2026

Defined Mars Media (DMM), a chemically defined simulant of the soluble macro- and micro- nutrients in Mars regolith for use in biological research

Mars harsh yet workable surface conditions, such as manageable temperatures, availability of solar energy, and in situ resources like water ice, carbon dioxide, and mineral-rich regolith, make it a compelling target for supporting life beyond Earth. However, existing experiments testing chemical habitability in Mars conditions generally rely on leachates of physical regolith simulants, which vary in composition across simulant types, leaching conditions, and production batches. We introduce a defined Mars media (DMM) that accurately simulates the biologically relevant nutrients (nitrogen, phosphorus, and sulfur) and stressors (perchlorates, heavy metals) in Martian regolith when it is leached in water at neutral pH. We formulated DMM by combining direct rover and lander measurements from Mars with laboratory measurements of regolith simulant leachates. We validate DMM from a 1x to 20x concentrate, equivalent to 40 g/L to 800 g/L of leached regolith. Using DMM with acetate as a Mars atmosphere-derived carbon source, we grew eight bacteria, demonstrating that organisms can source all essential nutrients from Martian resources. We also demonstrate that microbial growth in DMM is robust to uncertainties in Martian regolith composition: sensitivity experiments can identify limiting trace element nutrients and toxins in DMM, and show that bacterial growth is maintained across at least an order of magnitude variation in their concentrations. This is the first defined Mars regolith media recipe containing both macro- and micro-nutrients, and designed specifically for biological experimentation. By shifting from variable leachate-based approaches to a defined aqueous analog, we enable controlled hypothesis testing of microbial survival, growth, and function in a Martian chemical environment. DMM will enable further research on astrobiology, biological in situ resource utilization, large-scale soil remediation, and terraforming. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=121 SRC="FIGDIR/small/719001v2_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@37408forg.highwire.dtl.DTLVardef@16fabfforg.highwire.dtl.DTLVardef@84fa43org.highwire.dtl.DTLVardef@4a7c5e_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2026

Targeting Protease-activated Receptor 4 (PAR4) Protects Against Acute Kidney Injury (AKI) in Ischemia Reperfusion Injury

Acute kidney injury (AKI) is a serious and common clinical syndrome that currently has no effective treatment. Emerging evidence links coagulation pathways to kidney injury, particularly through coagulation proteases. Protease-activated receptors (PARs) are a family of G-protein coupled receptors (GPCRs) that are activated by proteolytic cleavage of their N termini, exposing a tethered ligand that initiates receptor signaling. PARs have been shown to play a major role in inflammation, vascular regulation, and tissue injury. PARs play key roles in inflammation, vascular regulation, and tissue injury. Previous work from the Hamm laboratory demonstrated that PAR4 contributes to AKI progression, as PAR4 knockout mice were protected in both unilateral ureteral obstruction and ischemia-reperfusion-based models of kidney disease. In this study, we investigated the potential of a PAR4 antagonist, VU6073819, at mitigating AKI progression in an ischemia-reperfusion injury (IRI) mouse model. PAR4 antagonism not only alleviated kidney injury and inflammatory response, but it significantly improved the survival. These findings identify PAR4 as a promising therapeutic target for AKI.

pharmacology and toxicology↗

bioRxiv2025

Murine models for triple-negative breast cancer with differential responsiveness to immunotherapy

Breast cancer is the most common cancer diagnosis in women. Clinical studies with triple-negative breast cancer (TNBC) are encouraging for immunotherapy combined with chemotherapy (anti-PD-1 with paclitaxel and/or carboplatin). However, additional clinical advances may be pursued more rapidly with assistance from preclinical TNBC models including syngeneic mammary tumor cell lines. Here, we report two mammary tumor cell lines that exhibit differential responsiveness to immunotherapy in vivo. Spontaneous mammary tumors from C57BL/6J MMTV-Cre Trp53fl/+ animals were passaged serially in cell culture and in vivo in the mammary fat pad of fully wildtype animals. The resulting lines, MM001i and MM008i, lost Trp53 and formed 1000 mm3 tumors in the mammary fat pad within 21-28 days. Despite originating from the same genetic background, these lines exhibit differential responses to immunotherapy. For anti-PD-1 therapy, MM001i is poorly responsive and MM008i is strongly responsive with near-complete tumor regression. In comparison, both MM001i and MM008i respond rapidly to anti-CTLA-4 therapy. Both models express unique tumor antigens as evidenced by immunity to subsequent engraftments. Primary MM008i tumors exhibit greater T cell infiltration, and CD8-positive T lymphocytes are required for anti-PD-1 responses. These TNBC models are promising for further mechanistic studies and testing future single and combinatorial therapies.

cancer biology↗

bioRxiv2025

Utilising multi-modal data-driven network analysis to identify monotherapy and combinational therapy targets in SOX2-dependent squamous cell lung cancer

Drug discovery requires a deep understanding of disease mechanisms, making the integration and analysis of diverse, multi-modal data types essential. These data types, spanning omics types, disease- associated, and biological pathway information, often originate from disparate sources and must be combined to uncover critical insights. We have developed iPANDDA (in-silico Pipeline for Agnostic Network-based Drug Discovery Analysis), a computational pipeline that integrates multi-modal data through a network-based approach to predict candidate drug target proteins for specific diseases. We applied iPANDDA to lung squamous cell carcinoma (LUSC), a subtype of non-small cell lung cancer (NSCLC) that accounts for approximately 25% of all lung cancer cases globally. Despite advances in cancer therapeutics, targeted therapies specifically approved for LUSC remain lacking, exacerbated by the shortage of robust models for studying LUSC carcinogenesis and therapeutic responses. The SOX2 gene, amplified in about 50% of LUSC patients, plays a critical role in driving and maintaining the cancer phenotype. Using iPANDDA, we identified relevant therapeutic targets for SOX2-dependent LUSC. Selected candidate drug targets were validated in vitro using cell-based models. We conducted target inhibition studies in both SOX2-dependent and non-SOX2-dependent cell lines, evaluating the effects of inhibition and knockout through cell viability assays. Our findings confirmed key monotherapy and combination therapy targets for SOX2-focused models. Specifically, we validated the AKT and mTOR complexes as promising therapeutic targets for LUSC. Additionally, we identified potential pathways for developing novel combination therapies targeting SOX2-dependent LUSC. iPANDDA offers a robust approach to refining and focusing therapeutic strategies for diseases with unmet clinical needs.

bioinformatics↗

bioRxiv2025

Tobacco smoke carcinogens exacerbate APOBEC mutagenesis and carcinogenesis

Mutational processes are thought to act independently and additively. We challenge this view by demonstrating that DNA-adducting agents sensitize the genome to mutagenesis by APOBEC enzymes. A model tobacco carcinogen (NQO) triggers a 100-fold increase in APOBEC3B- catalyzed signature mutations and elevates oral carcinoma levels in vivo. A hallmark of this unidirectional synergy is strand-coordinated pairs of APOBEC signature mutations within 32nt of each other (didyma). Biochemical experiments show that APOBEC3B can catalyze didyma formation, and genetic studies demonstrate requirements for APOBEC3B and functional nucleotide excision repair (XPA in human cells and Rad14 in yeast). Analyses of lung and head & neck cancers show that APOBEC mutagenesis and didyma are elevated in tumors from smokers compared to non-smokers. Additional tumor types with links to DNA-adducting agents also exhibit didyma. These studies support a model in which DNA-adducting carcinogens activate nucleotide excision repair and amplify mutagenesis by APOBEC enzymes in cancer.

cancer biology↗

bioRxiv2025

Pseudozyma aphidis bio-active extract inhibit plant pathogens and activate induce resistance in tomato plants

The constant growth in the world population demands a constant increase in agricultural yields. One of the main ways to increase agricultural yields is by improving the control of pests and pathogens. Human health and environmental concerns regarding the traditional synthetic pesticides challenge the scientific community to discover new and less harmful ways to control pests, such as the development of biocontrol agents and natural-based pesticides. Previous studies have established that application of live P. aphidis can be used for biocontrol of diverse fungal and bacterial phytopathogens. Here demonstrate activity of two semi-purified fractions from P. aphidis, one containing the antimicrobial metabolites and the other containing the resistance inducing metabolites. Our results from the in vitro experiments with the antimicrobial extract show that P. aphidis metabolites strongly inhibit important fungal and bacterial phytopathogens. In planta experiments demonstrated a significant, dose-dependent reduction in disease infection when a spore suspension of B. cinerea was treated or exposed to the extracted metabolites. From the other hand, our results showed that the application a semi-purified aqueous fraction from P. aphidis on tomato plants rapidly up-regulated the expression of defense-related genes, which are associated with both the induced systemic resistance and the systemic acquired resistance pathways. In conclusion, this study further enhances our understanding of the biochemical mechanisms behind P. aphidis main modes of action: antibiosis and induced resistance. It also demonstrates the great potential of this unique biocontrol agent as a source for new natural-based pesticides and/or enhanced resistance substances.

microbiology↗

bioRxiv2025

Selective degradation of BRD9 by a DCAF16-recruiting targeted glue: mode of action elucidation and in vivo proof of concept

Prospective discovery of molecular glues degraders for a specific therapeutic target protein of interest is an emerging strategy in drug discovery. Modification of pre-existing ligands with fragments that can alter the protein surface can lead to the creation of novel compounds ( targeted glues) able to induce neo-interactions between the target and an E3 ligase, resulting in targeted protein degradation. By screening a library of potential BRD9 targeted glue compounds, we have discovered a potent and selective, reversibly covalent BRD9 degrader, AMPTX-1. Co-immunoprecipitation-mass spectrometry experiments demonstrated that cell treatment with AMPTX-1 induces selective recruitment of BRD9 to the E3 ligase DCAF16. Degradation is dependent on the engagement of the surface Cys58 of DCAF16 and formation of a covalent adduct to DCAF16 is facilitated by the ternary complex formation with BRD9. BRD9 degradation is achieved in vivo after oral dosing, demonstrating that covalent recruitment of DCAF16 is a viable strategy for targeted protein degradation and can be achieved with drug-like, orally bioavailable compounds with promising in vivo activity.

biochemistry↗

bioRxiv2024

KegAlign: Optimizing pairwise alignments with diagonal partitioning

Our ability to generate sequencing data and assemble it into high quality complete genomes has rapidly advanced in recent years. These data promise to advance our understanding of organismal biology and answer longstanding evolutionary questions. Multiple genome alignment is a key tool in this quest. It is also the area which is lagging: today we can generate genomes faster than we can construct and update multiple alignments containing them. The bottleneck is in considerable computational time required to generate accurate pairwise alignments between divergent genomes, an unavoidable precursor to multiple alignments. This step is typically performed with lastZ, a very sensitive and yet equally slow tool. Here we describe an optimized GPU-enabled pairwise aligner KegAlign. It incorporates a new parallelization strategy, diagonal partitioning, with the latest features of modern GPUs. With KegAlign a typical human/mouse alignment can be computed in under 6 hours on a machine containing a single NVidia A100 GPU and 80 CPU cores without the need for any pre-partitioning of input sequences: a [~]150x improvement over lastZ. While other pairwise aligners can complete this task in a fraction of that time, none achieves the sensitivity of KegAligns main alignment engine, lastZ, and thus may not be suitable for comparing divergent genomes. In addition to providing the source code and a Conda package for KegAlign we also provide a Galaxy workflow that can be readily used by anyone.

genomics↗

bioRxiv2024

APOBEC shapes tumor evolution and age at onset of lung cancer in smokers

APOBEC enzymes are part of the innate immunity and are responsible for restricting viruses and retroelements by deaminating cytosine residues1,2. Most solid tumors harbor different levels of somatic mutations attributed to the off-target activities of APOBEC3A (A3A) and/or APOBEC3B (A3B)3-6. However, how APOBEC3A/B enzymes shape the tumor evolution in the presence of exogenous mutagenic processes is largely unknown. Here, by combining deep whole-genome sequencing with multi-omics profiling of 309 lung cancers from smokers with detailed tobacco smoking information, we identify two subtypes defined by low (LAS) and high (HAS) APOBEC mutagenesis. LAS are enriched for A3B-like mutagenesis and KRAS mutations, whereas HAS for A3A-like mutagenesis and TP53 mutations. Unlike APOBEC3A, APOBEC3B expression is strongly associated with an upregulation of the base excision repair pathway. Hypermutation by unrepaired A3A and tobacco smoking mutagenesis combined with TP53-induced genomic instability can trigger senescence7, apoptosis8, and cell regeneration9, as indicated by high expression of pulmonary healing signaling pathway, stemness markers and distal cell-of-origin in HAS. The expected association of tobacco smoking variables (e.g., time to first cigarette) with genomic/epigenomic changes are not observed in HAS, a plausible consequence of frequent cell senescence or apoptosis. HAS have more neoantigens, slower clonal expansion, and older age at onset compared to LAS, particularly in heavy smokers, consistent with high proportions of newly generated, unmutated cells and frequent immuno-editing. These findings show how heterogeneity in mutational burden across co-occurring mutational processes and cell types contributes to tumor development, with important clinical implications.

genomics↗

bioRxiv2023

Elevation-dependent patterns of snow-gum dieback are moderated by trait differences between montane and subalpine forests.

Subalpine forests worldwide face the synergistic threats of global warming and increased biotic attack, and the collapse or transition of subalpine forests is predicted in south-eastern Australia under future climates. The recent widespread dieback of subalpine snow gum forests due to increased activity of a native wood-boring longicorn beetle suggests this process may already be underway. We investigated how variation in tree tissue traits and environmental conditions correlated with elevation-dependent spatial patterns of forest mortality. We hypothesised that increased vulnerability of subalpine snow gums to wood-borer-mediated dieback at intermediate elevations was associated with poorly-resolved differences in traits between montane (Eucalyptus pauciflora subsp. pauciflora) and subalpine (E. pauciflora subsp. niphophila) snow-gum subspecies. We first sought to characterise variation and elevation-dependent transitions in 20 structural and drought-related functional traits among 120 healthy trees distributed along a 1000m elevation transect which spanned the subspecies transition zone. Secondly, we surveyed 774 trees across 53 sites between 1280-1980m asl. to explore associations between borer-damage severity, elevation, subspecies, and a subset of traits that differed between subspecies. These snow-gum subspecies exhibited mean differences and/or divergent elevation responses in 25% of traits surveyed, indicating contrasting suites of traits between montane and subalpine subspecies. Increased borer-damage severity across the montane-to-subalpine subspecies transition was correlated with lower bark thickness, whereas reduced borer damage at the highest elevations was associated with greater precipitation and lower temperatures. Our results suggest that due to possessing distinct traits associated with increased borer susceptibility, subalpine snow-gum forests will be subject to increased risk of severe borer-mediated forest dieback under warmer and drier future climates. Identifying traits contributing to species distribution limits and biotic-agent vulnerability remains critical for predicting, monitoring, and possibly mitigating forest and vegetation declines under future climates.

ecology↗

bioRxiv2023

Mesoscale DNA Features Impact APOBEC3A and APOBEC3B Deaminase Activity and Shape Tumor Mutational Landscapes

Antiviral DNA cytosine deaminases APOBEC3A and APOBEC3B are major sources of mutations in cancer by catalyzing cytosine-to-uracil deamination. APOBEC3A preferentially targets singlestranded DNAs, with a noted affinity for DNA regions that adopt stem-loop secondary structures. However, the detailed substrate preferences of APOBEC3A and APOBEC3B have been fully established, and the specific influence of the DNA sequence on APOBEC3A APOBEC3B deaminase activity remains to be investigated. Here, we find that APOBEC3B selectively targets DNA stem-loop structures, and they are distinct from those subjected deamination by APOBEC3A. We develop Oligo-seq, a novel in vitro sequencing-based to identify specific sequence contexts promoting APOBEC3A and APOBEC3B activity. Through this approach, we demonstrate that APOBEC3A an APOBEC3B deaminase activity is strongly regulated by specific sequences surrounding the targeted cytosine. Moreover, we identify structural features of APOBEC3B and APOBEC3A responsible for their substrate preferences. Importantly, we determine that APOBEC3B-induced mutations in hairpin-forming sequences within tumor genomes differ from the DNA stem-loop sequences mutated by APOBEC3A. Together, our study provides evidence that APOBEC3A and APOBEC3B can generate mutation landscapes in cancer genomes, driven by their unique substrate selectivity.

biochemistry↗

bioRxiv2023

Inhibition of Retinoic Acid Signaling in Proximal Tubular Epithelial cells Protects against Acute Kidney Injury by Enhancing Kim-1-dependent Efferocytosis

Retinoic acid receptor (RAR) signaling is essential for mammalian kidney development, but in the adult kidney is restricted to occasional collecting duct epithelial cells. We now show there is widespread reactivation of RAR signaling in proximal tubular epithelial cells (PTECs) in human sepsis-associated acute kidney injury (AKI), and in mouse models of AKI. Genetic inhibition of RAR signaling in PTECs protects against experimental AKI but is associated with increased expression of the PTEC injury marker, Kim-1. However, Kim-1 is also expressed by de-differentiated, proliferating PTECs, and protects against injury by increasing apoptotic cell clearance, or efferocytosis. We show that the protective effect of inhibiting PTEC RAR signaling is mediated by increased Kim-1 dependent efferocytosis, and that this is associated with de-differentiation, proliferation, and metabolic reprogramming of PTECs. These data demonstrate a novel functional role that reactivation of RAR signaling plays in regulating PTEC differentiation and function in human and experimental AKI. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC="FIGDIR/small/545113v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@140ba6borg.highwire.dtl.DTLVardef@8f02f0org.highwire.dtl.DTLVardef@10a123eorg.highwire.dtl.DTLVardef@33b564_HPS_FORMAT_FIGEXP M_FIG C_FIG

pathology↗

bioRxiv2023

Introgression underlies phylogenetic uncertainty but not parallel plumage evolution in a recent songbird radiation

Instances of parallel phenotypic evolution offer great opportunities to understand the evolutionary processes underlying phenotypic changes. However, confirming parallel phenotypic evolution and studying its causes requires a robust phylogenetic framework. One such example is the "black-and-white wagtails", a group of five species in the songbird genus Motacilla: one species, the White Wagtail (M. alba), shows wide intra-specific plumage variation, while the four others form two pairs of very similar-looking species (African Pied Wagtail M. aguimp + Mekong Wagtail M. samveasnae and Japanese Wagtail M. grandis + White-browed Wagtail M. maderaspatensis, respectively). However, the two species in each of these pairs were not recovered as sisters in previous phylogenetic inferences. Their relationships varied depending on the markers used, suggesting that gene tree heterogeneity might have hampered accurate phylogenetic inference. Here, we use whole genome resequencing data to explore the phylogenetic relationships within this group, with a special emphasis on characterizing the extent of gene tree heterogeneity and its underlying causes. We first used multispecies coalescent methods to generate a "complete evidence" phylogenetic hypothesis based on genome-wide variants, while accounting for incomplete lineage sorting and introgression. We then investigated the variation in phylogenetic signal across the genome, to quantify the extent of discordance across genomic regions, and test its underlying causes. We found that wagtail genomes are mosaics of regions supporting variable genealogies, because of ILS and inter-specific introgression. The most common topology across the genome, supporting M. alba and M. aguimp as sister species, appears to be influenced by ancient introgression. Additionally, we inferred another ancient introgression event, between M. alba and M. grandis. By combining results from multiple analyses, we propose a phylogenetic network for the black-and-white wagtails that confirms that similar phenotypes evolved in non-sister lineages, supporting parallel plumage evolution. Furthermore, the inferred reticulations do not connect species with similar plumage coloration, suggesting that introgression does not underlie parallel plumage evolution in this group. Our results demonstrate the importance of investigation of genome-wide patterns of gene tree heterogeneity to help understanding the mechanisms underlying phenotypic evolution.

evolutionary biology↗

bioRxiv2023

Disrupting microglial TGF-β signaling triggers region-specific pathology in the spinal cord

Transforming growth factor-{beta} (TGF-{beta}) signaling is critical for microglial maturation during development and the maintenance of microglial homeostasis in adulthood. It remains unclear whether regional susceptibilities to the loss of TGF-{beta} signaling in microglia also exist, and the contributing factors have yet to be identified. We find that deletion of Tgfbr2 on microglia leads to microglial activation and demyelination in mouse spinal cords, primarily in the dorsal column (DC). Tgfbr2-deficient microglia exhibit distinct transcriptomic changes, and those sorted from the DC display a more proinflammatory profile compared to those from the ventral column (VC) and grey matter (GM). Single nucleus RNA sequencing (snRNA-seq) of the spinal cord uncovers a microglial subtype that emerges exclusively following Tgfbr2 deletion (termed TGF{beta} signaling-suppressed microglia, TSM), exhibiting high expression of Mmp12, Gpnmb, Lgals3, Mgll, and Alcam, predominantly located in the DC. Phenotypically, disruption of microglial TGF-{beta} signaling results in behavioral deficits that are more severe in female and older mice, whereas young male mice are less affected. Mechanistically, we reveal a significantly higher level of TGF-{beta}1/TGFBR2 in the spinal cords of normal older mice compared to the young mice, with the DC region richer in genes of the TGF-{beta} signaling pathway than the VC and GM regions. This indicates that older mice and the DC region require more TGF{beta}1 to maintain tissue homeostasis and, reciprocally, are more responsive and sensitive to the disruption of TGF-{beta} signaling in microglia. Herein, we report a demyelinating disease with region-specificity and its susceptibility to the loss of microglial TGF-{beta} signaling with gender and age differences. Our findings contribute valuable information to our understanding of the importance of microglia in regulating myelin health, especially during the aging process.

neuroscience↗

bioRxiv2023

Rapid resistance profiling of SARS-CoV-2 protease inhibitors

Resistance to nirmatrelvir (Paxlovid) has been shown by multiple groups and may already exist in clinical SARS-CoV-2 isolates. Here a panel of SARS-CoV-2 main protease (Mpro) variants and a robust cell-based assay are used to compare the resistance profiles of nirmatrelvir, ensitrelvir, and FB2001. The results reveal distinct resistance mechanisms ("fingerprints") and indicate that these next-generation drugs have the potential to be effective against nirmatrelvir-resistant variants and vice versa.

microbiology↗