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Phillips, D.

Publications and source records attributed to Phillips, D..

At least 19 recordsLinked to original sources

Title: The Cyanobacterial dnaX Intein Encodes an Out-of-Frame Homing Endonuclease and is Sporadically Distributed in the Phylum

Inteins are self-splicing proteins with a wide distribution in single-celled organisms, viruses, and plastids. The function of inteins remains an unanswered question. They may be regulatory elements as they must splice out of their host protein. However, recent research findings point to inteins likely being mobile selfish genetic elements capable of horizontal transfer. Here the intein inhabiting cyanobacterial DNA Polymerase III gamma/tau subunit (dnaX) serves as a case study into the conservation and phylogenetics of the intein compared to the host extein. Phylogenetic analysis reveals a sporadic distribution of intein alleles having an evolutionary history that is incongruent with the extein that may reticulate independently across clades. The dnaX intein can also contain an out-of-frame homing endonuclease (HE), a rarity for annotated inteins, that may have been the result of secondary invasion of an HE into a mini-intein. The simultaneous presence of intein-free and intein-containing alleles in populations of Microcystis aeruginosa challenges current theories about the life cycles of homing endonuclease containing selfish genetic elements and suggests that alternatives to the homing cycle need to be considered for intein persistence. Our analysis reveals an incongruent, disjointed distribution of this specific intein, suggesting that it is neither conserved among individual cyanobacterial lineages nor a critical component of dnaX functionality yet is able to persist in populations without being lost.

microbiology↗

Early life adversity shapes adult behavior in a free-ranging primate

Early life adversity (ELA) causes lasting psychological and behavioral consequences in humans, with parallel stress and fear responses observed in captive animals. How naturally occurring ELA shapes behavior in non-captive animals remains poorly understood. Investigating these effects across socioecological environments is important for identifying the evolutionary pressures shaping early life sensitivities, and determining whether these behavioral syndromes have deep evolutionary roots. Here, we tested the effects of eight forms of ELA on adult behavior using a large dataset (N=313 males, 346 females) from a free-ranging population of rhesus macaques (Macaca mulatta). We measured adult behaviors indicative of stress and the tenor of social interactions, including agonism, vigilance, self-directed behaviors, and affiliation. Individuals exposed to more ELA received more aggression and less grooming, were more submissive, and were less vigilant. While high status buffered the effects of ELA on grooming, it amplified effects on aggression. Our findings demonstrate that in a large sample of a free-ranging primate, early life environments impact behavior into adulthood. While some behaviors are consistent with patterns in humans and captive animals, suggesting an evolutionarily conserved ELA syndrome, other findings add new insights into the various ways individuals interact with their environment as a function of ELA.

evolutionary biology↗

The influence of captivity on cardiac structure and function across age, in rhesus macaques

BackgroundCaptive non-human primates are widely used as models of human aging, yet the conditions they live in differ markedly from their naturalistic environment. Differences between captive and free-ranging environments may impact how the cardiovascular system adapts with age, potentially confounding studies of natural aging. This study characterized age-related cardiac phenotypes in free-ranging rhesus macaques and compared these patterns with their captive-housed counterparts to assess the influence of living environment on cardiac health across the lifespan. MethodologyWe performed transthoracic echocardiography in a cross-sectional cohort of 133 free-ranging rhesus macaques (Macaca mulatta, aged 7 - 25 years, 41 % female) living on Cayo Santiago, Puerto Rico. First, we compared structural and functional cardiac parameters between young (7 - 12 years; n = 48, 60% female) and old (18-26 years, n = 33, 42% female) free-ranging macaques. We then performed an ANCOVA, with age as a covariate, to compare cardiac structural and functional parameters between free-ranging and captive-housed macaques (n = 347, aged 7 - 32 years, 71% female). ResultsIn our free-ranging cohort, older macaques had greater interventricular septal thickness and relative wall thickness (RWT) than young. Males exhibited larger left ventricular (LV) internal dimensions, wall thickness, LV mass, and LV volumes than females, but these differences were attenuated when indexed to body mass. Diastolic function was lower with advanced age in both sexes, reflected by a lower E/A ratio, reduced myocardial tissue velocities during early diastole (e') and greater myocardial tissue velocities during atrial contraction (a). Compared with captive macaques, free-ranging animals exhibited better diastolic function, including a significantly higher E/A ratio, greater e, and lower a. Captive macaques also had significantly greater relative wall thickness across age and between sexes. Conclusions and implicationsOur study provides the first comprehensive characterization of age-related cardiac differences in free-ranging rhesus macaques, which show structural and functional cardiac differences similar to those observed with human aging. Captive macaques exhibited a more pronounced age-related cardiac phenotype than their free-ranging counterparts, including thicker left ventricular walls and lower diastolic function for a given age. These findings highlight the importance of considering the ecological context when interpreting animal models of cardiovascular aging.

physiology↗

Endocannabinoid signaling is a critical link between circadian desynchronization and metabolic dysfunction

It is well documented that disruption of circadian rhythms can cause metabolic dysregulation, but the specific mechanisms involved remain unclear. Our findings demonstrate that the negative metabolic effects of environmental circadian desynchronization (ECD) are dependent upon the cannabinoid receptor 1 (CB1r). The endocannabinoid system has not previously been implicated in mediating the effects of circadian disruption. We showed that ECD induced a positive correlation between the levels of the endocannabinoids AEA and 2-AG in both plasma and liver. While global CB1r knockout protects against the metabolic effects of ECD, behavioral and physiological response to ECD was strikingly similar between WT and CB1r KO mice and could not account for their distinct metabolic outcomes. Using liver-specific CB1r KO mice, we further specified that the ECD-induced metabolic hormone disruption, but not weight gain, is mediated through liver CB1r signaling. Finally, we showed that ECD upregulated transcription of genes involved in oxidative phosphorylation in the liver of WT, but not liver-specific CB1r KO mice. In summary, ECD led to modular metabolic dysfunction through CB1r signaling in multiple tissues, with the liver playing a critical role.

physiology↗

An aqueous watercress extract with topical anti-inflammatory properties in inflamed human skin

Watercress (Nasturtium officinale) is a species of the Brassicaceae plant family, with a biochemical composition which suggests potential uses in anti-inflammatory skincare applications. Watercress has a high content of both anti-inflammatory compounds (e.g., polyphenols) and compounds which upregulate the Nrf2-mediated antioxidant gene response (e.g., isothiocyanates) in human tissues. We have developed a process to manufacture an aqueous watercress extract that contains isothiocyanates and flavonoid-type polyphenols, some of which are known anti-inflammatory compounds. We partially characterized the chemical composition of our extract (LC-QTOF-MS), and we demonstrated in a cultured full-thickness human skin model, that the extract was non-cytotoxic and non-irritant, as monitored by cell viability and IL1 concentrations, respectively. In human trials, in vivo, we showed by visual clinical scoring of inflammation that the extract had anti-inflammatory properties. The anti-inflammatory properties of the aqueous watercress extract may provide a treatment for inflammatory skin diseases such as eczema.

biochemistry↗

Sex chromosome pairing and multivalent associations during meiosis in diploid and polyploid Silene latifolia

Sex chromosomes undergo various modifications that affect their synapsis during meiosis. While most of the genome achieves full synapsis by the end of pachytene, the non-recombining regions of XY (or ZW) chromosomes often remain asynaptic, and fail to form physical associations at metaphase I. Despite significant progress in animal models, the meiotic behaviour dynamics of plant sex chromosomes remain largely unexplored. In this study, we employed super-resolution microscopy to analyse 3D chromosome organization and the localization of key meiotic proteins. Namely, we studied the dynamics of ASY1, ZYP1, and HEI10, across the leptotene to pachytene stages, and compared sex chromosome behaviour in dioecious Silene latifolia with related gynodioecious S. vulgaris. Our findings show that both exhibits a class I crossover (CO) frequency comparable to mammals, indicating moderate COs per bivalent and their similar genetic determinants. We document variation in sex chromosome configurations, from rod bivalents in diploids to open-ring tetravalents in autopolyploids, and characterize Y chromosome behaviour across XXY, XXXY, and XXYY karyotypes. These results reveal pronounced variation in pairing and synaptic patterns, even within a shared genetic background. We discuss how these patterns reflect the evolutionary trajectory of the non-recombining region and provide the most detailed cytogenetic analysis of sex chromosome pairing in a plant with evolutionary young sex chromosomes.

cell biology↗

IR spectroscopy: from experimental spectra to high-resolution structural analysis by integrating simulations and machine learning

Understanding biomolecular function at the atomic scale requires detailed insight into the structural changes underlying dynamic processes. Vibrational infrared (IR) spectroscopy--when paired with biomolecular simulations and quantum-chemical calculations--determines bond length variations on the order of 0.01 [A], providing insights into these structutral changes. Here, we address the forward problem in IR spectroscopy: predicting high-accuracy vibrational spectra from known molecular structures identified by biomolecular simulations. Solving this problem lays the groundwork for the inverse problem: inferring structural ensembles directly from experimental IR spectra. We evaluate two computational approaches, normal mode analysis and Fourier-transformed dipole autocorrelation, against experimental IR spectra of N-Methylacetamide, a prototypical model for peptide bond vibrations. Spectra are derived from simulation models at multiple levels of theory, including hybrid quantum mechanics/molecular mechanics, machine-learned and classical molecular mechanics approaches. Our results highlight the capabilities and limitations of current theoretical biophysical approaches to decode structural information from experimental vibrational spectroscopy data. These insights underscore the potential of future artificial intelligence (AI)-enhanced models to enable direct IR-based structure determination. For example, resolving the so far experimentally inaccessible structures of toxic oligomers involved in neurodegenerative diseases, enabling improved disease diagnostics and targeted therapies. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/665767v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@6603d3org.highwire.dtl.DTLVardef@1852c85org.highwire.dtl.DTLVardef@2ddaccorg.highwire.dtl.DTLVardef@77b554_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

Age and early life adversity shape heterogeneity of the epigenome across tissues in macaques

Age and early life adversity (ELA) are both key determinants of health, but whether they target similar physiological mechanisms across the body is unknown due to limited multi-tissue datasets from well-characterized cohorts. We generated DNA methylation (DNAm) profiles across 14 tissues in 237 semi-free ranging rhesus macaques, with records of naturally occurring ELA. We show that age-associated DNAm variation is predominantly tissue-dependent, yet tissue-specific epigenetic clocks reveal that the pace of epigenetic aging is relatively consistent within individuals. ELA effects on loci are adversity-dependent, but a given ELA has a coordinated impact across tissues. Finally, ELA targeted many of the same loci as age, but the direction of these effects varied, indicating that ELA does not uniformly contribute to accelerated age in the epigenome. ELA thus imprints a coordinated, tissue-spanning epigenetic signature that is both distinct from and intertwined with age-related change, advancing our understanding of how early environments sculpt the molecular foundations of aging and disease.

genomics↗

EEG Functional Connectivity as a Marker of Evolution from Infantile Epileptic Spasms Syndrome to Lennox-Gastaut Syndrome

Background and ObjectivesTimely diagnosis and effective treatment of Lennox-Gastaut Syndrome (LGS) improve prognosis and lower healthcare costs, but the transition from infantile epileptic spasms syndrome (IESS) to LGS is highly variable and insidious. Objective biomarkers are needed to monitor this progression and guide clinical decision making. MethodsWe retrospectively collected longitudinal EEG data at the Childrens Hospital of Orange County from fifteen children who were diagnosed with IESS and later with LGS between 2012 and 2021. EEGs were from IESS and LGS diagnoses, between the two diagnoses, and following LGS diagnosis. Functional connectivity networks were calculated using a cross-correlation-based method and assessed relative to diagnostic timepoint, treatment response, presence of clinical markers of disease, age, and amplitude of interictal spikes. ResultsConnectivity strength was high at LGS diagnosis and decreased after favorable response to treatment, but it remained stable or increased when response was unfavorable. In all subjects, connectivity strength was higher at the time of LGS diagnosis than at the preceding timepoint. Presence of clinical markers of LGS were associated with high connectivity strength, but no single marker predicted connectivity strength. DiscussionComputational EEG analysis can be used to map the evolution from IESS to LGS. Changes in connectivity may enable prediction of impending LGS and treatment response monitoring, thus facilitating earlier LGS treatment and guiding medical management. Key pointsO_LIEEG functional connectivity analysis can track progression from infantile epileptic spasms syndrome (IESS) to Lennox-Gastaut Syndrome (LGS). C_LIO_LIHigh connectivity strength at LGS diagnosis decreases with favorable treatment response but remains high with poor response. C_LIO_LIClinical LGS markers correlate with high connectivity, but no single marker predicts connectivity strength. C_LIO_LIEEG functional connectivity analysis may help predict LGS onset, enabling early intervention and improving prognosis. C_LI

neuroscience↗

Social ageing can protect against infectious disease in a group-living primate

The benefits of social living are well established, but sociality also comes with costs, including infectious disease risk. This cost-benefit ratio of sociality is expected to change across individuals lifespans, which may drive changes in social behaviour with age. To explore this idea, we combine data from a group-living primate for which social ageing has been described with epidemiological models to show that having lower social connectedness when older can protect against the costs of a hypothetical, directly transmitted endemic pathogen. Assuming no age differences in epidemiological characteristics (susceptibility to, severity, and duration of infection), older individuals suffered lower infection costs, which was explained largely because they were less connected in their social networks than younger individuals. This benefit of social ageing depended on epidemiological characteristics and was greatest when infection severity increased with age. When infection duration increased with age, social ageing was beneficial only when pathogen transmissibility was low. Older individuals benefited most from having a lower frequency of interactions (strength) and network embeddedness (closeness) and benefited less from having fewer social partners (degree). Our study provides a first examination of the epidemiology of social ageing, demonstrating the potential for pathogens to influence evolutionary dynamics of social ageing in natural populations.

animal behavior and cognition↗

SbPIP2 Mediated Improvements in Plant Resilience: Physiological and Molecular Insights into Abiotic Stress Response

Understanding the mechanisms behind plant resilience to abiotic stresses is essential for enhancing crop yield and sustainability. This study integrates findings from a comprehensive investigation into the function of the SbPIP2 gene, which encodes an aquaporin protein, in improving the abiotic stress tolerance of transgenic plants. Our integrated approach revealed that transgenic plants overexpressing SbPIP2 significantly reduce reactive oxygen species (ROS) accumulation and exhibit enhanced physiological attributes, including higher seed germination rates, improved growth, early flowering, and better seed setting under stress conditions. Notably, these plants also showed a quicker recovery and completion of their lifecycle post-stress treatment. The transcriptomic analysis provided a deeper understanding of the genetic modifications contributing to stress resilience, highlighting the involvement of genes associated with oxidative stress response, calcium and sugar signaling pathways, stomatal regulation, phytohormone biosynthesis, and flower development. Additionally, the study underscores the central role of abscisic acid (ABA) in mediating stress responses through hormonal regulation, with transgenic plants displaying increased ABA levels due to the upregulation of biosynthesis genes and downregulation of catabolism genes. This hormonal adjustment is critical for stomatal closure, reducing water loss, and enhancing tolerance to abiotic stresses. Our findings elucidate the complex genetic and molecular pathways that underpin abiotic stress tolerance in plants, offering valuable insights for future research aimed at improving crop resilience through genetic engineering, thereby addressing the challenges of climate change and environmental stressors.

plant biology↗

The impact of kinship composition on social structure

The relatedness between group members is a potential driver of variation in social structure. Relatedness predicts biases in partner choice and formation of strong relationships among group members. As such, groups that differ in their percentage of non-kin dyads, i.e., in their kinship composition, should therefore differ in the structure of their social networks. Yet the relationship between kinship composition and social structure remains unclear. Here, we used long-term social and pedigree data from a population of rhesus macaques to investigate the relationship between kinship composition and the connectivity, cohesion, potential for transmission and social differentiation of the social networks of adult female macaques. We found no evidence that the social structure of groups composed of greater proportion of unrelated females differ from that of groups with a lower proportion of non-kin. To investigate this unexpected finding, we built agent-based models parameterised with the empirical data to further explore (1) the expected relationship between kinship composition and social structure and (2) why we did not find such a relationship in the empirical data. Agent-based models showed that kinship composition can influence social structure in populations similar to the one studied, but that this effect may only be detectable with a sample size even larger than ours (19 group-years) and with greater variance in kinship composition (proportion of non-kin varied between 0.830-0.922 in the empirical data). The relationship between kinship composition and social structure might be more apparent when comparing data from species that differ strongly in their social organisation, translating into marked differences in kinship composition. This further emphasises the importance of reporting existing and future kinship composition data to deepen our understanding of the evolution of sociality and highlights the potential of agent-based models to better understand empirical results.

animal behavior and cognition↗

Socioecological drivers of injuries in female and male rhesus macaques (Macaca mulatta)

Competition over access to resources, such as food and mates, is believed to be one of the major costs associated with group living. Two socioecological factors suggested to predict the intensity of competition are group size and the relative abundance of sexually active individuals. However, empirical evidence linking these factors to injuries and survival costs is scarce. Here, we leveraged 10 years of data from free-ranging rhesus macaques where injuries inflicted by conspecifics are associated with a high mortality risk. We tested if group size and adult sex ratio predicted the occurrence of injuries and used data on physical aggression to contextualise these results. We found that males were less likely to be injured when living in larger groups, potentially due to advantages in intergroup encounters. Females, instead, had higher injury risk when living in larger groups but this was not explained by within-group aggression among females. Further, male-biased sex ratios predicted a weak increase in injury risk in females and were positively related to male-female aggression, indicating that male coercion during mating competition may be a cause of injuries in females. Overall, our results provide insights into sex differences in the fitness-related costs of competition and empirical evidence for long-standing predictions on the evolution of group living.

evolutionary biology↗

Early life adversity has sex-dependent effects on survival across the lifespan in rhesus macaques

Exposure to adversity during early life is linked to lasting detrimental effects on evolutionary fitness across many taxa. However, due to the challenges of collecting longitudinal data, especially in species where one sex disperses, direct evidence from long-lived species remains relatively scarce. Here we test the effects of early life adversity on male and female longevity in a free-ranging population of rhesus macaques (Macaca mulatta) at Cayo Santiago, Puerto Rico. We leveraged six decades of data to quantify the relative importance of ten forms of early life adversity for 6,599 macaques (3,230 male, 3,369 female), with a smaller sample size (N=299) for one form of adversity (maternal social isolation) which required high-resolution behavioral data. We found that individuals who experienced more early life adversity died earlier than those who experienced less adversity. Mortality risk was highest during early life, defined as birth to four years old, suggesting acute survival effects of adversity, but heightened mortality risk was also present in macaques who survived to adulthood. Females and males were affected differently by some forms of adversity, and these differences might be driven by varying energetic demands, female philopatry, and male dispersal. By leveraging data on thousands of macaques collected over decades, our results show that the fitness consequences of early life adversity are not uniform across individuals but vary as a function of the type of adversity, timing, and social context, and thus contribute to our limited but growing understanding of the evolution of early life sensitivities in long-lived species. Significance Statement Exposure to early life adversity, even when conditions subsequently improve, can have profound and persistent consequences for human health. Negative effects of early life adversity appear widespread across the animal kingdom. To date, however, direct evidence from long-lived species is relatively scarce due to the difficulties of collecting data from early life till death. We leverage six decades of observations on thousands of free-ranging male and female rhesus macaques to examine the complex ways early life adversity impacts survival. Our results suggest that the type of adversity and life history factors intersect to impact immediate and downstream survival. By studying early life adversity across environments, cultures, contexts, and species, we can better understand the evolutionary underpinnings of early life sensitivities.

animal behavior and cognition↗

Multiple axes of visual system diversity in Ithomiini, an ecologically diverse tribe of mimetic butterflies

The striking structural variation seen in arthropod visual systems can be explained by the overall quantity and spatio-temporal structure of light within habitats coupled with developmental and physiological constraints. However, little is currently known about how fine-scale variation in visual structures arise across shorter evolutionary and ecological scales. In this study, we characterise patterns of interspecific (between species), intraspecific (between sexes) and intraindividual (between eye regions) variation in the visual system of four ithomiine butterfly species. These species are part of a diverse 26-Myr-old Neotropical radiation where changes in mimetic colouration are associated with fine-scale shifts in ecology, such as microhabitat preference. By using a combination of selection analyses on visual opsin sequences, in-vivo ophthalmoscopy, micro-computed tomography (micro-CT), immunohistochemistry, confocal microscopy, and neural tracing, we quantify and describe physiological, anatomical, and molecular traits involved in visual processing. Using these data, we provide evidence of substantial variation within the visual systems of Ithomiini, including: i) relaxed selection on visual opsins, perhaps mediated by habitat preference, ii) interspecific shifts in visual system physiology and anatomy, and iii) extensive sexual dimorphism, including the complete absence of a butterfly-specific optic neuropil in the males of some species. We conclude that considerable visual system variation can exist within diverse insect radiations, hinting at the evolutionary lability of these systems to rapidly develop specialisations to distinct visual ecologies, with selection acting at both the perceptual, processing, and molecular level. Summary statementPhysiological, anatomical, and molecular evidence of extensive visual system variation within a diverse butterfly radiation, hinting at the lability of visual systems to evolve specialisations to distinct visual environments.

evolutionary biology↗

Systematically characterizing the roles of E3-ligase family members in inflammatory responses with massively parallel Perturb-seq

E3 ligases regulate key processes, but many of their roles remain unknown. Using Perturb-seq, we interrogated the function of 1,130 E3 ligases, partners and substrates in the inflammatory response in primary dendritic cells (DCs). Dozens impacted the balance of DC1, DC2, migratory DC and macrophage states and a gradient of DC maturation. Family members grouped into co-functional modules that were enriched for physical interactions and impacted specific programs through substrate transcription factors. E3s and their adaptors co-regulated the same processes, but partnered with different substrate recognition adaptors to impact distinct aspects of the DC life cycle. Genetic interactions were more prevalent within than between modules, and a deep learning model, com{beta}VAE, predicts the outcome of new combinations by leveraging modularity. The E3 regulatory network was associated with heritable variation and aberrant gene expression in immune cells in human inflammatory diseases. Our study provides a general approach to dissect gene function.

genomics↗

Cost and benefits of being social: examining the influence of sociality on faecal parasites in free-ranging rhesus macaques

Parasites and infectious diseases constitute an important challenge to the health of group-living animals. Social contact and shared space can both increase disease transmission risk, while individual differences in social resources can help prevent infections. For example, high social status individuals and those with more or stronger social relationships may have better immunity and, thus, lower parasitic burden. To test for health trade-offs in the costs and benefits of sociality, we quantified how parasitic load varied with an individuals social status, as well as with their weak and strong affiliative relationships in a free-ranging population of rhesus macaques (Macaca mulatta). Social resources may also protect against infection under environmentally challenging situations, such as natural disasters. We additionally examined the impact of a major hurricane on the sociality-parasite relationship in this system. We found that both weak and strong proximity partners, but not grooming partners, were associated with lower protozoa infection risk. Social status was not linked to infection risk, even after the hurricane. Overall, our study highlights the buffering against infection that affiliative partners may provide, suggesting individuals can compensate for the health costs of sociality by having partners who tolerate their presence.

ecology↗

Cell-subtype specific effects of genetic variation in the aging and Alzheimer cortex

The relationship between genetic variation and gene expression in individual brain cell types and subtypes has remained elusive. Here, we generated single-nucleus RNA sequencing data from the dorsolateral prefrontal cortex of 424 individuals of advanced age; analyzing 1.5 million nuclear transcriptomes, we assessed the effect of genetic variants on RNA expression in cis (cis-eQTL) for 7 cell types and 81 cell subtypes. This effort identified 10,004 eGenes at the cell type level and 8,138 eGenes at the cell subtype level. Many eGenes are only detected within cell subtypes. A new variant influences APOE expression only in microglia and is associated with greater cerebral amyloid angiopathy but not Alzheimer pathology, accounting for the effect of APOE{varepsilon}4, providing mechanistic insights into both pathologies. While eQTLs are readily detected, only a TMEM106B variant robustly affects the proportion of cell subtypes. Integration of these results with GWAS highlighted the targeted cell type and likely causal gene within susceptibility loci for Alzheimers, Parkinsons, schizophrenia, and educational attainment.

genomics↗