Biology subjects

Allen, J. M.

Publications and source records attributed to Allen, J. M..

15 recordsLinked to original sources

bioRxiv2026

A phylogenomic framework for avian feather lice (Phthiraptera: Ischnocera)

Comprehensive phylogenies serve as foundations for taxonomic, comparative, and coevolutionary studies. Avian feather lice comprise the most diverse Parvorder (Ischnocera) of parasitic lice (Phthiraptera). Convergence and reduction of morphological features in this group have made past attempts at understanding the evolutionary relationships of feather lice challenging. Several recent phylogenomic studies have begun shedding light on the broader scale evolutionary tree of this group. However, additional taxonomic sampling is needed for a more complete understanding of the phylogeny and for higher statistical power in comparative studies. Here we investigate the higher-level relationships of feather lice based on the most comprehensive taxon sample to date. We leverage genome sequences of 260 samples of feather lice and 25 outgroup taxa to reconstruct a phylogenomic tree based on 2,395 target nuclear ortholog genes, using both concatenated and coalescent methods. These trees provide high support across nearly all branches of the topology, resolving backbone relationships as well as more detailed relationships within major groups. These phylogenies provide a framework for future comparative studies of feather lice, including comparisons with avian phylogeny and investigating patterns of diversification.

evolutionary biology↗

bioRxiv2025

Rational Design and Optimization of a Potent IDO1 Proteolysis Targeting Chimera (PROTAC)

Indoleamine 2,3-dioxygenase 1 (IDO1) is a potently immunosuppressive protein that inhibits antitumor immunity through both tryptophan metabolism and non-enzymatic functions. Pharmacological therapies targeting IDO1 enzyme activity have generally failed to improve the overall survival of patients with cancer. Developing new therapeutic agents that are capable of neutralizing both enzyme-and non-enzyme-derived immunosuppressive IDO1 effects is therefore of high interest. We previously described the development of a novel Proteolysis Targeting Chimera (PROTAC), NU223612, that degrades IDO1 in cultured human glioblastoma (GBM) cells, as well as in well-established brain tumors, in vivo. In this study, we rationally optimized the composition, rigidity, and linker orientation of the PROTAC structure to create NU227326, which degrades IDO1 with a DC50 of 5 nM in human GBM cells. Mechanistic studies showed that IDO1 degradation occurred through the ubiquitin-proteasome system and was sustained for at least 2 days, supporting NU227326 as a highly potent IDO1 PROTAC suitable for further studies in GBM and other human cancers.

biochemistry↗

bioRxiv2024

Aging amplifies a gut microbiota immunogenic signature linked to heightened inflammation

Aging is associated with low-grade inflammation that increases the risk of infection and disease, yet the underlying mechanisms remain unclear. Gut microbiota composition shifts with age, harboring microbes with varied immunogenic capacities. We hypothesized the gut microbiota acts as an active driver of low-grade inflammation during aging. Microbiome patterns in aged mice strongly associated with signs of bacterial-induced barrier disruption and immune infiltration, including marked increased levels of circulating lipopolysaccharide (LPS)-binding protein (LBP) and colonic calprotectin. Ex vivo immunogenicity assays revealed that both colonic contents and mucosa of aged mice harbored increased capacity to activate toll-like receptor 4 (TLR4) whereas TLR5 signaling was unchanged. We found patterns of elevated innate inflammatory signaling (colonic Il6, Tnf, Tlr4) and endotoxemia (circulating LBP) in young germ-free mice after 4 weeks of colonization with intestinal contents from aged mice compared with young counterparts, thus providing a direct link between aging-induced shifts in microbiota immunogenicity and host inflammation. Additionally, we discovered that the gut microbiota of aged mice exhibited unique responses to a broad-spectrum antibiotic challenge (Abx), with sustained elevation in Escherichia (Proteobacteria) and altered TLR5 immunogenicity 7 days post-Abx cessation. Together, these data indicate that old age results in a gut microbiota that differentially acts on TLR signaling pathways of the innate immune system. We found that these age-associated microbiota immunogenic signatures are less resilient to challenge and strongly linked to host inflammatory status. Gut microbiota immunogenic signatures should be thus considered as critical factors in mediating chronic inflammatory diseases disproportionally impacting older populations.

immunology↗

bioRxiv2023

Microbial aromatic amino acid metabolism is modifiable in fermented food matrices to promote bioactivity

Ingestion of fermented foods impacts human immune function, yet the bioactive food components underlying these effects are not understood. Here, we interrogated whether fermented food bioactivity could be traced to a class of microbial metabolites derived from aromatic amino acids (ArAA), termed aryl-lactates. Using targeted metabolomics, we established that the aryl-lactates phenyllactic acid (PLA), 4-hydroxyphenyllactic acid (4-HPLA), and indole-3-lactic acid (ILA), are present in varying concentrations across a wide range of commercially available fermented foods, including many vegetable and dairy ferments. After pinpointing fermented food-associated lactic acid bacteria (LAB) that produce high levels of aryl-lactates (e.g., Lactiplantibacillus plantarum), we utilized our knowledge of LAB metabolism to identify fermentation conditions (added cultures [e.g., L. plantarum] and metabolic co-factors [e.g., aryl-pyruvates]) to increase aryl-lactate production in food matrices up to 5x103 fold vs. standard fermentation conditions. Next, using ex vivo reporter assays, we found that a variety of food matrix conditions optimized for aryl-lactate production exhibited enhanced agonist activity for the human aryl-hydrocarbon receptor (AhR) as compared to standard fermentation conditions and/or commercial brands. Moreover, we determined that strategies to enhance aryl-lactates effectively maintained food matrix AhR bioactivity across 4 weeks of storage. Reduced microbial-induced AhR activity has emerged as a hallmark of many chronic inflammatory diseases, thus we envision strategies to enhance microbially produced aryl-lactates and thus AhR bioactivity of fermented foods can be leveraged to improve human health.

microbiology↗

bioRxiv2023

Influenza A virus during pregnancy disrupts maternal intestinal immunity and fetal cortical development in a dose- and time-dependent manner

Epidemiological studies link neurodevelopmental disorders (NDDs) with exposure to maternal viral infection in utero. It is hypothesized that the mechanism governing this link involves the activation of maternal intestinal T helper 17 (TH17) cells, which produce effector cytokine interleukin (IL)-17. While IL-17 is implicated as a major driver of fetal brain abnormalities, this inflammation-induced TH17 pathway has not been thoroughly examined in models of live viral infection during pregnancy. Influenza A virus (IAV) infection is consistently linked to offspring NDDs and can result in host intestinal dysregulation. Therefore, it is possible that intestinal TH17 cells and subsequent production of IL-17 could drive fetal brain abnormalities during gestational IAV infection. To test this, we inoculated pregnant mice with two infectious doses of IAV and evaluated peak innate and adaptive immune responses in the dam and fetus. While respiratory IAV infection led to dose-dependent maternal colonic shortening and microbial dysregulation, there was no elevation in intestinal TH17 cells nor IL-17. Fetal cortical abnormalities and global changes in fetal brain transcripts were observable in the high-dose IAV group, despite a lack of IL-17 signaling. Profiling fetal microglia and border-associated macrophages (BAMs) -potential cellular mediators of IAV-induced cortical abnormalities -revealed dose-dependent differences in the numbers of BAMs but not microglia. Overall, our data support the idea of an infection severity threshold for downstream maternal inflammation and fetal cortical abnormalities, confirming the use of live pathogens in NDD modeling to better evaluate the complete immune response and to improve translation to the clinic.

neuroscience↗

bioRxiv2023

Nano-computed tomography reveals repeated phenotypic divergence in parasites to escape host defense

Understanding how selective pressures drive morphological change is a central question in evolutionary biology. Feather lice have repeatedly diversified into convergent ecomorphs, based on how they escape from host defenses in different microhabitats. Here, we used nano-computed tomography scan data of 89 specimens of feather lice, belonging to four ecomorph groups to quantify variation of functional traits, including mandibular muscle volume, limb length, and three-dimensional head shape data in these tiny insects. The results suggest that the shape of the head, the proportional volume of the chewing muscles, and the length of the leg segments in feather lice are all strongly associated with specific host-habitats. Further, species that co-occur on hosts have increased rates of morphological evolution, suggesting competition for host space is one of the drivers of morphology. This supports previous work indicating that the phenotypic diversity of feather lice is the result of repeated convergence resulting from resource partitioning, microhabitat specialization, and selection pressures imposed by host defense.

evolutionary biology↗

bioRxiv2021

Psychological stress disrupts intestinal epithelial cell function and mucosal integrity through microbe and host-directed processes

Psychological stress alters the gut microbiota and predisposes individuals to increased risk for enteric infections and chronic bowel conditions. Intestinal epithelial cells (IECs) are responsible for maintaining homeostatic interactions between the gut microbiota and its host. In this study, we hypothesized that disruption to colonic IECs is a key factor underlying stress-induced disturbances to intestinal homeostasis. Conventionally raised (CONV-R) and germ-free (GF) mice were exposed to a social disruption stressor (Str) to ascertain how stress modifies colonic IECs, the mucosal layer, and the gut microbiota. RNA sequencing of IECs isolated from CONV-R mice revealed a robust pro-inflammatory (Saa1, Il18), pro-oxidative (Duox2, Nos2), and antimicrobial (Reg3b/g) transcriptional profile as a result of Str. This response occurred concomitant to mucus layer thinning and signs of microbial translocation. In contrast to their CONV-R counterparts, IECs from GF mice or mice treated with broad spectrum antibiotics exhibited no detectable transcriptional changes in response to Str. Nevertheless, IECs from Str-exposed GF mice exhibited an altered response to ex vivo bacterial challenge (increased dual Oxidase-2 [Duox2] and nitric oxide synthase-2 (Nos2)), indicating that STR primes host IEC pro-oxidative responses. In CONV-R mice stress-induced increases in colonic Duox2 and Nos2 (ROS generating enzymes) strongly paralleled changes to microbiome composition and function, evidencing Str-mediated ROS production as a primary factor mediating gut-microbiota dysbiosis. In conclusion, a mouse model of social stress disrupts colonic epithelial and mucosal integrity, a response dependent on an intact microbiota and host stress signals. Together these preclinical findings may provide new insight into mechanisms of stress-associated bowel pathologies in humans.

immunology↗

bioRxiv2021

RNAi screening of RING/U-box domain ubiquitin ligases identifies critical regulators of stem cells and tissue regeneration in planarians

Regenerative processes depend on the interpretation of signals to coordinate cell behaviors. The role of ubiquitin-mediated signaling is known to be important in many cellular and biological contexts, but its role in regeneration is not well understood. To investigate how ubiquitylation impacts tissue regeneration in vivo, we are studying planarians that are capable of regenerating after nearly any injury using a population of stem cells. Here we used RNAi to screen RING/U-box E3 ubiquitin ligases that are highly expressed in planarian stem cells and stem cell progeny. RNAi screening identified nine genes with functions in regeneration, including the spliceosomal factor prpf19 and histone modifier rnf2; based on their known roles in developmental processes, we further investigated these two genes. We found that prpf19 was required for animal survival but not for stem cell maintenance, suggesting a role in promoting cell differentiation. Because RNF2 is the catalytic subunit of the Polycomb Repressive Complex 1 (PRC1), we also examined other putative members of this complex (CBX and PHC). We observed a striking phenotype of regional tissue misspecification in cbx and phc RNAi planarians. To identify genes regulated by PRC1, we performed RNA-seq after knocking down rnf2 or phc. Although these proteins are predicted to function in the same complex, we found that the set of genes differentially expressed in rnf2 versus phc RNAi were largely non-overlapping. Using in situ hybridization, we showed that rnf2 regulates gene expression levels within a tissue type, whereas phc is necessary for the spatial restriction of gene expression, findings consistent with their respective in vivo phenotypes. This work not only uncovered roles for RING/U-box E3 ligases in stem cell regulation and regeneration, but also identified differential gene targets for two putative PRC1 factors required for maintaining cell-type-specific gene expression in planarians.

developmental biology↗

bioRxiv2021

Long-distance dispersal of pigeons and doves generated new ecological opportunities for host-switching and adaptive radiation by their parasites

Adaptive radiation is an important mechanism of organismal diversification, and can be triggered by new ecological opportunities. Although poorly studied in this regard, parasites present an ideal system to study adaptive radiations because of their close associations with host species. Both experimental and comparative studies suggest that the ectoparasitic wing lice of pigeons and doves have undergone an adaptive radiation, resulting in differences in both body size and overall coloration. Here we show that long-distance dispersal by dove hosts was important for parasite diversification, providing new ecological opportunities for parasites to speciate by host-switching. We further show that these new opportunities for host-switching decreased over time, and cospeciation became the more dominant mode of parasite speciation. Taken together, our results suggest that host dispersal, followed by host-switching, provided novel ecological opportunities that facilitated adaptive radiation by parasites.

evolutionary biology↗

bioRxiv2020

Spatial phylogenetics of butterflies in relation to environmental drivers and angiosperm diversity across North America

Broad-scale quantitative assessments of biodiversity and the factors shaping it remain particularly poorly explored in insects. Here, we undertook a spatial phylogenetic analysis of North American butterflies via assembly of a time-calibrated phylogeny of the region coupled with a unique, complete range assessment for ~75% of the known species. We utilized a suite of phylodiversity metrics and associated environmental data to test whether climate stability and temperature gradients have shaped North American butterfly phylogenetic diversity and endemism. We also undertook the first direct, quantitative comparisons of spatial phylogenetic patterns between butterflies and flowering plants in North America. We expected concordance between butterflies and angiosperms based on both shared historical environmental drivers and presumed strong butterfly-host plant specializations. We instead found that biodiversity patterns in butterflies are strikingly different from flowering plants in some regions of the continent. In particular, the warm desert regions of the southwestern United States and Mexico showed surprisingly high butterfly phylogenetic diversity and endemism, in contrast to much lower values for angiosperms. Butterflies did not show patterns of phylogenetic clustering as found in flowering plants, suggesting differences in habitat conservation between the two groups. Finally, we found weak relationships and spatially structured biases in relative branching timing between angiosperms and butterflies. These results suggest that shared biogeographic histories and trophic associations do not necessarily assure similar diversity outcomes. The work has applied value in conservation planning, documenting warm deserts as an important North American butterfly biodiversity hotspot.

ecology↗

bioRxiv2019

Comparison of mechanical sorting and DNA metabarcoding for diet analysis with degraded wolf scats

DNA metabarcoding has become a powerful technique for identifying species and profiling biodiversity with the potential to improve efficiency, reveal rare prey species, and correct mistaken identification error in diet studies. However, the extent to which molecular approaches agree with traditional approaches is unknown for many species. Here, we compare diets from wolf scats profiled using both mechanical sorting and metabarcoding of amplified vertebrate DNA sequences. Our objectives were: (1) compare findings from mechanical sorting and metabarcoding as a method of diet profiling and (2) use results to better understand diets of wolves on Prince of Wales Island, a population of conservation concern. We predicted metabarcoding would reveal both higher diversity of prey and identify rare species that are overlooked with mechanical sorting. We also posited that the relative contribution of Sitka black-tailed deer (Odocoileus hemionus sitkensis) and beaver (Castor canadensis) would be overestimated with mechanical sorting methods because of the failure to account for the full diet diversity of these wolves. We found that there was substantial overlap in the diets revealed using both methods, indicating that deer, beaver, and black bear (Ursus americanus) were the primary prey species. However, there was a large discrepancy in the occurrence of beaver in scats (54% and 24% from mechanical sorting and metabarcoding, respectively) explained by the high rate of false positives with mechanical sorting methods. Metabarcoding revealed more diet diversity than mechanical sorting, thus supporting our initial predictions. Prince of Wales Island wolves appear to have a more diverse diet with greater occurrence of rare species than previously described including 14 prey species that contribute to wolf diet. Metabarcoding is an effective method for profiling carnivore diet and enhances our knowledge concerning the full diversity of wolf diets, even in the extremely wet conditions of southeast Alaska, which can lead to DNA degradation. Given the increasingly efficient and cost-effective nature of collecting eDNA, we recommend incorporating these molecular methods into field-based projects to further examine questions related to increased use of alternate prey coinciding with changes in abundance of primary prey and habitat alteration.

ecology↗

bioRxiv2019

Environmental DNA for indigenous-led monitoring of a culturally important fish

Although environmental DNA shed from an organism is now widely used for species detection in a wide variety of contexts, mobilizing environmental DNA for management requires estimation of population size and trends rather than simply assessing presence or absence. However, the efficacy of environmental-DNA-based indices of abundance for long-term population monitoring have not yet been assessed. Here we report on the relationship between six years of mark-recapture population estimates for eulachon (Thaleichthys pacificus) and eDNA rates, which are calculated from the product of stream flow and DNA concentration. Eulachon are a culturally and biologically important anadromous fish that have significantly declined in the southern part of their range but were historically rendered into oil and traded. Both the peak eDNA rate and the area under the curve of the daily eDNA rate were highly predictive of the mark-recapture population estimate, explaining 84.96% and 92.53% of the deviance respectively. Even in the absence of flow correction, the peak of the daily eDNA concentration explained an astonishing 89.53% while the area under the curve explained 90.74% of the deviance. These results support the use of eDNA to monitor eulachon population trends and represent a >80% cost savings over mark-recapture, which could be further increased with automated water sampling, reduced replication, and focused temporal sampling. Due to its logistical ease and affordability, eDNA sampling can facilitate monitoring a larger number of rivers and in remote locations where mark-recapture is infeasible.

ecology↗

bioRxiv2018

Genomic sequence capture of haemosporidian parasites: Methods and prospects for enhanced study of host-parasite evolution

Avian malaria and related haemosporidians (Plasmodium, [Para]Haemoproteus, and Leucocytoozoon) represent an exciting multi-host, multi-parasite system in ecology and evolution. Global research in this field accelerated after 1) the publication in 2000 of PCR protocols to sequence a haemosporidian mitochondrial (mtDNA) barcode, and 2) the development in 2009 of an open-access database to document the geographic and host ranges of parasite mtDNA haplotypes. Isolating haemosporidian nuclear DNA from bird hosts, however, has been technically challenging, slowing the transition to genomic-scale sequencing techniques. We extend a recently-developed sequence capture method to obtain hundreds of haemosporidian nuclear loci from wild bird samples, which typically have low levels of infection, or parasitemia. We tested 51 infected birds from Peru and New Mexico and evaluated locus recovery in light of variation in parasitemia, divergence from reference sequences, and pooling strategies. Our method was successful for samples with parasitemia as low as [~]0.03% (3 of 10,000 blood cells infected) and mtDNA divergence as high as 15.9% (one Leucocytozoon sample), and using the most cost-effective pooling strategy tested. Phylogenetic relationships estimated with >300 nuclear loci were well resolved, providing substantial improvement over the mtDNA barcode. We provide protocols for sample preparation and sequence capture including custom probe kit sequences, and describe our bioinformatics pipeline using aTRAM 2.0, PHYLUCE, and custom Perl and Python scripts. This approach can be applied to the tens of thousands of avian samples that have already been screened for haemosporidians, and greatly improve our understanding of parasite speciation, biogeography, and evolutionary dynamics.

genomics↗

bioRxiv2018

Environmental DNA for the enumeration and management of Pacific salmon

Pacific salmon are a keystone resource in Alaska, generating annual revenues of well over [~]US$500 million/yr. Due to their anadromous life history, adult spawners distribute amongst thousands of streams, posing a huge management challenge. Currently, spawners are enumerated at just a few streams because of reliance on human counters and, rarely, sonar. The ability to detect organisms by shed tissue (environmental DNA, eDNA) promises a more efficient counting method. However, although eDNA correlates generally with local fish abundances, we do not know if eDNA can accurately enumerate salmon. Here we show that daily, and near-daily, flow-corrected eDNA rate closely tracks daily numbers of returning sockeye and coho spawners and outmigrating sockeye smolts. eDNA thus promises accurate and efficient enumeration, but to deliver the most robust numbers will need higher-resolution stream-flow data, at-least-daily sampling, and a focus on species with simple life histories, since shedding rate varies amongst jacks, juveniles, and adults.

ecology↗

bioRxiv2018

For comparing phylogenetic diversity among communities, go ahead and use synthesis phylogenies

Should we build our own phylogenetic trees based on gene sequence data, or can we simply use available synthesis phylogenies? This is a fundamental question that any study involving a phylogenetic framework must face at the beginning of the project. Building a phylogeny from gene sequence data (purpose-built phylogeny) requires more effort, expertise, and cost than subsetting an already available phylogeny (synthesis-based phylogeny). However, we still lack a comparison of how these two approaches to building phylogenetic trees influence common community phylogenetic analyses such as comparing community phylogenetic diversity and estimating trait phylogenetic signal. Here, we generated three purpose-built phylogenies and their corresponding synthesis-based trees (two from Phylomatic and one from the Open Tree of Life [OTL]). We simulated 1,000 communities and 12,000 continuous traits along each purpose-built phylogeny. We then compared the effects of different trees on estimates of phylogenetic diversity (alpha and beta) and phylogenetic signal (Pagels {lambda} and Blombergs K). Synthesis-based phylogenies generally yielded higher estimates of phylogenetic diversity when compared to purpose-built phylogenies. However, resulting measures of phylogenetic diversity from both types of phylogenies were highly correlated (Spearmans{rho} > 0.8 in most cases). Mean pairwise distance (both alpha and beta) is the index that is most robust to the differences in tree construction that we tested. Measures of phylogenetic diversity based on the OTL showed the highest correlation with measures based on the purpose-built phylogenies. Trait phylogenetic signal estimated with synthesis-based phylogenies, especially from the OTL, were also highly correlated with estimates of Blombergs K or close to Pagels {lambda} from purpose-built phylogenies when traits were simulated under Brownian Motion. For commonly employed community phylogenetic analyses, our results justify taking advantage of recently developed and continuously improving synthesis trees, especially the Open Tree of Life.

ecology↗