Biology subjects

Porter, C.

Publications and source records attributed to Porter, C..

14 recordsLinked to original sources

bioRxiv2026

Burn Wound Excision Drives Acute Hypermetabolism in Mice with Scald Burns

Hypermetabolism (elevated resting energy expenditure) is a hallmark of the pathophysiological response to burns. The contribution of wound excision to acute burn-induced hypermetabolism remains unclear. Importantly, while burn wound excision is a standard component of clinical burn care, it is not typically included in rodent models of burn injury. Here, we tested the hypothesis that burn wound excision drives the acute hypermetabolic response to burn trauma. C57BL/6J mice (n=12-18 per group; ~6-weeks old; 50% male) were acclimated to thermoneutral housing (30C) for 6-weeks. All mice underwent baseline body composition scans and metabolic phenotyping to determine total (TEE) and resting energy expenditure (REE). Mice were then randomized to either sham (control), scald burn (burn), wound excision (excision), or scald burn followed by immediate wound excision (burn+excision) groups. Burns and wound excisions involved ~15% of the body surface area. Mice then recovered for 14 days while individually housed in metabolic phenotyping cages. At day 14 post-injury, mice underwent a second body composition scan prior to euthanasia. There were no fatalities in the control or burn groups, whereas 23% (n=7) and 34% (n=11) of mice in the excision and burn+excision groups died or were euthanized during the 14-day recovery period. Male and female mice exhibited broadly similar responses to injury in terms of REE and TEE. Compared to control, REE was greater in burn (47%), excision (102%), and burn+excision groups (136%) during the first week post-injury (P<0.001 for all). Compared to control mice, wound excision (alone or following burns) resulted in a greater acute loss in body mass than burn injury alone. However, this cachectic response was more sustained in male mice compared to females. Similarly, wound excision (alone or following burns) resulted in greater bone mineral content and density loss compared to sham and burn alone in both sexes. Wound excision is a key contributor to the hypermetabolic and cachectic response to burn trauma in mice. We posit that rodent studies aiming to recapitulate burn-induced hypermetabolism and cachexia should include burn wound excision to better model the clinical sequelae to burns.

physiology↗

bioRxiv2026

Quantification of Mouse Total Body Surface Area: Implications for Preclinical Burn Research

Clinically, burn severity is reported as the size (and depth) of burn wounds relative to total body surface area (TBSA). This nomenclature is also often used in rodent models of burns. Accordingly, accurate determination and reporting of rodent TBSA is required to ensure the rigor and reproducibility of preclinical burn research. Rodent TBSA is typically estimated indirectly as a function of body mass. Further, empirical quantification of rodent TBSA through pelt dissection does not consider differences in rodent and human anatomy, making comparison of relative burn size in rodents and humans a challenge. Here, we compared commonly used approaches to directly determine or indirectly estimate rodent TBSA to demonstrate the impact different approaches can have on the calculation of relative burn size. A total of n=48 C57BL/6J background mice (55% male) ranging from 4 to 45 weeks of age and 17 to 40 grams were used. Mice were weighed prior to euthanasia. After euthanasia, mouse length was measured from the nose to anus. Mice were then placed into clear polypropylene sheet protectors (21.6 x 27.9 cm) to trace the areas of both the dorsal and ventral surfaces as well as all four limbs (dorsal-ventral (DV) tracing). Next, the pelt was carefully excised from the body through cutting a lateral line from the mouth to the genitalia, then again proximally to distally on all four limbs. The pelt was gently placed on a sheet protector and traced when both relaxed and stretched. The ears and tail were removed and traced separately. Photographs were taken of all tracings next to a ruler for scale and analyzed in ImageJ. Stretched pelt measurements of TBSA were 34% (79.4{+/-}7.6 vs. 57.5{+/-}7.5 cm2, P<0.001) and 30% (70.6{+/-}10.9 vs. 52.7{+/-}8.1 cm2, P<0.001) greater than relaxed pelt TBSA measurements in male and female mice respectively. TBSA estimated by DV tracing was 9% greater in males (62.5{+/-}10.9 vs. 57.5{+/-}7.5 cm2) and 15% in females (60.6{+/-}12.3 vs. 52.7{+/-}8.1 cm2) compared to TBSA measurements made on relaxed pelts. Accordingly, empirically derived Meeh constants (k) from DV tracing were greater than those derived from relaxed pelt measurements for both males (7.14{+/-}0.59 vs. 6.58{+/-}0.72) and females (7.72{+/-}0.58 vs. 6.78{+/-}0.80). In contrast k values derived from stretched pelt measures of TBSA were significantly greater than those determined in relaxed pelts for males (8.91{+/-}0.87 vs. 6.58{+/-}0.72, P<0.001) and females (8.85{+/-}1.25 vs. 6.78{+/-}0.80, P>0.001). The combined ears and tail represent approximately 7% and 8% of the TBSA measured by the relaxed pelt approach, respectively. Exclusion of the tail and ears from the calculated TBSA results in derived k values that are [~]16-17% lower. The approach used to determine TBSA in mice significantly influences measured areas and thus derived k values. We suggest that stretching the pelt prior to tracing inflates TBSA values, where measurements made from relaxed pelts or by DV tracing likely provide more accurate estimates of actual TBSA. Further, exclusion of the tail and ears (the latter of which is not typically considered in estimates of TBSA in humans) may be a useful approach relating relative burn sizes of mice to those of humans.

physiology↗

bioRxiv2026

Inborn cardiorespiratory fitness and exercise training modulate brown adipose tissue function and plasticity in early life

This study aimed to determine the impact of inborn metabolic fitness and early life exercise training on whole body and brown adipose tissue (BAT) energetics. We carried out comprehensive metabolic phenotyping on 4-week old rats bred for high (high-capacity runner, HCR) and low (low-capacity runner, LCR) running capacity following randomization to voluntary wheel running (VWR) or control (CRTL) for 6-weeks. High-resolution respirometry and untargeted proteomics were then employed to determine the impact of inborn fitness and early life exercise on BAT function. When accounting for differences in body mass, early life exercise (VWR) resulted in greater basal and total energy expenditure, irrespective of strain (P < 0.0001 for both). Both leak and uncoupling protein 1 (UCP1) dependent respiratory capacities in isolated BAT mitochondria were greater in rats randomized to VWR compared to CTRL in both HCR (P < 0.01) and LCR (P < 0.05) strains. Similarly, mitochondrial sensitivity to the UCP1 inhibitor GDP was greater in both HCR (P < 0.01) and LCR (P < 0.05) rats randomized to VWR versus control. The BAT proteome differed in CTRL HCR and LCR rats, were there was enrichment in proteins related to branched chain oxidation and mitochondrial fatty acid oxidation in HCR rats. VWR remodeled the BAT proteome, where 151 proteins were differentially expressed in LCR BAT and 209 differentially expressed in LCR BAT following VWR. In both stains, there was an enrichment in proteins related to metabolism mitochondrial function in response to VWR. However, when comparing strains, 39 proteins were differentially expressed in BAT in HCR rats compared to LCR rats in response to VWR. These proteins were related to carboxylic acid and amino acid metabolism. Collectively, inborn fitness impacts body mass and composition, exercise behaviors, and the BAT proteome in early life. Early life exercise alters whole body and BAT energetics irrespective of inborn fitness, augmenting basal and total energy expenditure and BAT thermogenic capacity and function.

physiology↗

bioRxiv2026

Carnitine deficiency alters fuel metabolism and voluntary wheel running in mice

BackgroundCarnitine plays an obligatory role in energetics owing to its role in the translocation of long-chain fatty acids into the mitochondrion for oxidation. Here, we determined the metabolic and behavioral consequences of systemic carnitine deficiency (SCD) in mice. MethodsFemale C57BL/6J mice were randomized to receive normal drinking water (control, n = 8) or drinking water supplemented with mildronate 4g.L-1 (mildronate, n = 8) for 21 days. Body composition was assessed at baseline and post treatment. Metabolic and behavioral phenotyping was performed continuously over 72 hours following 14 days of control or mildronate treatment. Stable isotope were used to assess whole-body substrate oxidation. Carnitine subfractions were quantified in skeletal muscle and liver, as was mitochondrial respiratory function. Liver and muscle samples also underwent proteomic analysis. ResultsMildronate treatment depleted total carnitine in muscle and liver by [~]97% (P < 0.001) and [~]90% (P < 0.001), respectively. Carnitine depletion was accompanied by lower total energy expenditure (P = 0.01), attributable to lower voluntary wheel running (P = 0.01). Oxidation rates of palmitate (P < 0.01) but not octanoate were lower whereas rates of glucose oxidation were greater in carnitine depleted mice (P < 0.01). Mitochondrial respiratory capacity was unaltered by carnitine deficiency. Carnitine deficiency remodeled muscle and liver proteomes to support lipid oxidation and energy production. SummaryIn mice, carnitine deficiency is characterized by decreased long-chain fatty acid oxidation despite preserved mitochondrial respiratory capacity. Carnitine deficiency resulted in lower voluntary exercise and a concomitant reduction in energy expenditure.

physiology↗

bioRxiv2025

Modified self-amplifying RNAs mediate robust and prolonged gene expression in the mammalian brain

Facile, non-genomic integrating gene delivery technologies are lacking for rapid onset and prolonged protein expression in the brain. Here we report the protein expression and cell type tropism for an advanced messenger ribonucleic acid (mRNA) technology, modified 5-hydroxymethylcytidine (hm5C) self-amplifying ribonucleic acid (saRNA), when injected into the mouse brain or applied to ex vivo human cortical brain slices. saRNA, encoding fluorescent proteins, encapsulated in an LNP formulation comprising ALC-0315 (present in Comirnaty(R)) efficiently mediates long-lasting protein expression in mouse brain cells beyond five weeks, with detectable expression in some neurons at three months. hm5C saRNA substantially outperforms N1m{Psi} mRNA. In addition to transfecting astrocytes and neurons at the injection site, hm5C saRNA-LNPs label neurons retrogradely. Excitingly, hm5C saRNA-LNPs afford protein expression in human cortical brain slices, with expression emerging within 24 hours and lasting beyond 76 days. Modified saRNA provides new opportunities for mechanistic neuroscience research and therapeutic development.

neuroscience↗

bioRxiv2025

Two-Phase Coding Strategy by CA1 Pyramidal Neurons: Linking Spatiotemporal Integration to Predictive Behavior

Space and time are fundamental components of memory, yet how the brain encodes these dimensions to guide behavior remains unclear. Using virtual-reality environments, we uncovered a two-phase neural code in hippocampus CA1 that represents time or distance through two functional pyramidal subpopulations, PyrUp and PyrDown. In Phase I, PyrUp activity synchronously increases to mark the initiation of encoding; In Phase II, their activity decays at heterogeneous, neuron-specific rates, creating a gradual divergence in across-population firing rates that scales with elapsed time. Conversely, PyrDown activity initially decreases before gradually rising. The crossover point, where rising PyrDown activity surpasses declining PyrUp activity, precedes predictive licking behavior. Combining optogenetics and computational modeling, we provided circuit-level evidence that PyrUp neurons primarily process locomotion-related inputs regulated by somatostatin-positive interneurons, whereas PyrDown neurons mainly receive reward-related inputs gated by parvalbumin-positive interneurons. These findings advance our understanding of how hippocampal circuits compute spatiotemporal information to inform behavior.

neuroscience↗

bioRxiv2025

Utility of a quantitative approach to microbial dysbiosis using machine learning in an African American cohort with self-reported hair loss

ObjectiveHair loss is a common issue that affects a large proportion of the population, leading to lower self-confidence and quality of life. Microbial dysbiosis of the scalp has been shown to be associated with several different disorders leading to hair loss. Though several "microbiome friendly" cosmetic treatments are currently on the market, there is no agreement on the best technique for assessing dysbiosis leading to a lack of scientific rigor for quantifying the effective treatments. To help address this, the association between self-perceived hair loss and the scalp microbiome in an African-American cohort (n=36) was investigated. MethodsUsing a self-controlled design, swabs were collected from both "sparse" and "normal" scalp sites. The scalp microbiome was characterized via 16S rRNA gene sequencing and a dysbiosis score was calculated based on the proportion of all taxa within the samples. Further, we identified the taxa that contributed most to abnormal or dysbiotic hair sites using a machine learning random forest classifier and a negative binomial mixed effects model. ResultsThe dysbiosis index is sensitive to participants self-assessment of hair loss and interindividual variation. We found a core set of operational taxonomic units (OTUs) assigned to 7 genera that significantly contributed to increased scalp dysbiosis. ConclusionThis study demonstrates that self-perceived hair loss is associated with significant and measurable alterations in the scalp microbiome using, making the reported dysbiosis index a practical tool that may be used to assess microbiome changes following cosmetic or medical interventions for hair loss and other microbiome-associated disorders.

microbiology↗

bioRxiv2025

Prenatal maternal infection promotes maternal microchimeric cells to alter infection risk in male offspring

Vertically transferred maternal cells or maternal microchimeric cells (MMCs) engraft the fetus and persist in offspring for long periods of time. How altered maternal immune states arising from infection affect MMCs and their function in offspring is poorly understood. Here, we show that pregnancy-associated transient maternal infection alters MMCs to differentially regulate immunity in offspring. In male offspring of dams previously infected with Yersinia pseudotuberculosis, MMCs confer a pro-inflammatory type 17 T effector phenotype that leads to enhanced protective immunity to an unrelated Salmonella infection. Thus, acquired maternal cells imprinted by microbial exposure during pregnancy exert an antigen agnostic and sex-differential effect on offspring immunity, and may potentially be targeted to deliver immune benefits to infants in the vulnerable early life period.

immunology↗

bioRxiv2024

Shared and distinct adaptations to early-life exercise training based on inborn fitness

BackgroundLow cardiorespiratory fitness due to genetics increases the risk for cardiometabolic disease. Endurance exercise training promotes cardiorespiratory fitness and improves cardiometabolic risk factors, but with great heterogeneity. Here, we tested the hypothesis that the metabolic phenotype imparted by low parental (inborn) cardiorespiratory fitness would be overcome by early-life exercise training, and that exercise adaptations would be influenced in part by inborn fitness. MethodsAt 26 days of age, male and female rat low-capacity runners (LCR, n=20) and high-capacity runners (HCR, n=20) generated by artificial selection were assigned to either sedentary control (CTRL, n=10) or voluntary wheel running (VWR, n=10) for 6 weeks. Post-intervention, whole-body metabolic phenotyping was performed, and the respiratory function of isolated skeletal muscle and liver mitochondria assayed. Transcriptomics and proteomics were performed on skeletal muscle and liver tissue using RNA-sequencing and mass spectrometry, respectively. ResultsDaily VWR volume was 1.8-fold higher in HCR-VWR compared to LCR-VWR. In LCR, VWR reduced adiposity and enhanced glucose tolerance, coincident with elevated total energy expenditure. While intrinsic skeletal muscle mitochondrial respiratory function was unaffected by VWR, estimated skeletal muscle oxidative capacity increased in VWR groups owing to greater mitochondrial content. In the liver, both maximal oxidative capacity and ATP-linked respiration were higher in HCR-VWR than HCR-CTRL. Transcriptomic and proteomic profiling revealed extensive remodeling of skeletal muscle and liver tissue by VWR, elements of which were both shared and distinct based on inborn fitness. SummaryEarly-life exercise training partially overcomes the metabolic phenotype imparted by low inborn cardiorespiratory fitness. However, molecular adaptations to VWR are partly influenced by inborn fitness, which may have implications for personalized exercise medicine.

physiology↗

bioRxiv2021

CHARM: COVID-19 Health Action Response for Marines - association of antigen-specific interferon-gamma and IL2 responses with asymptomatic and symptomatic infections after a positive qPCR SARS-CoV-2 test

SARS-CoV-2 T cell responses are associated with COVID-19 recovery, and Class I- and Class II-restricted epitopes have been identified in the spike (S), nucleocapsid (N) and membrane (M) proteins and others. This prospective COVID-19 Health Action Response for Marines (CHARM) study enabled assessment of T cell responses in symptomatic and asymptomatic SARS-CoV-2 infected participants. At enrollment all participants were negative by qPCR; follow-up occurred biweekly and then bimonthly for the next 6 weeks. Study participants who tested positive by qPCR SARS-CoV-2 test were asked to enroll in an immune response sub-study. FluoroSpot interferon-gamma (IFN-{gamma}) and IL2 responses following qPCR-confirmed infection at enrollment (day 0), day 7 and 14 and more than 28 days later were measured using pools of 17mer peptides covering S, N, and M proteins, or CD4+CD8 peptide pools containing predicted epitopes from multiple SARS-CoV-2 antigens. Among 124 asymptomatic and 105 symptomatic participants, SARS-CoV-2 infection generated IFN-{gamma} responses to the S, N and M proteins that persisted longer in asymptomatic cases. IFN-{gamma} responses were significantly (p=0.001) more frequent to the N pool (51.4%) than the M pool (18.9%) among asymptomatic subjects; however, the difference was not statistically significant (p=0.06) for symptomatic subjects (N pool: 44.4%; M pool: 25.9%). In asymptomatic participants IFN-{gamma} responders to the CD4+CD8 pool responded more frequently to the S pool (55.6%) and N pool (57.1%), than the M pool (7.1%), but symptomatic participants, IFN-{gamma} responses were more frequent to the S pool (75.0%) than N pool (33.3%) and M pool (33.3%). The frequencies of IFN-{gamma} responses to the S and N+M pools peaked 7 days after the positive qPCR test among asymptomatic (S pool: 22.2%; N+M pool: 28.7%) and symptomatic (S pool: 15.3%; N+M pool 21.9%) participants and dropped by >28 days. Magnitudes of post-infection IFN-{gamma} and IL2 responses to the N+M pool were significantly correlated with IFN-{gamma} and IL2 responses to the N and M pools. These data further support the central role of Th1-biased cell mediated immunity IFN-{gamma} and IL2 responses, particularly to the N protein, in controlling COVID-19 symptoms, and justify T cell-based COVID-19 vaccines that include the N and S proteins.

immunology↗

bioRxiv2020

Single-nucleus and spatial transcriptomics of archival pancreatic cancer reveals multi-compartment reprogramming after neoadjuvant treatment

Pancreatic ductal adenocarcinoma (PDAC) remains a treatment-refractory disease. Characterizing PDAC by mRNA profiling remains particularly challenging. Previously identified bulk expression subtypes were influenced by contaminating stroma and have not yet informed clinical management, whereas single cell RNA-seq (scRNA-seq) of fresh tumors under-represented key cell types. Here, we developed a robust single-nucleus RNA-seq (snRNA-seq) technique for frozen archival PDAC specimens and used it to study both untreated tumors and those that received neoadjuvant chemotherapy and radiotherapy (CRT). Gene expression programs learned across untreated malignant cell and fibroblast profiles uncovered a clinically relevant molecular taxonomy with improved prognostic stratification compared to prior classifications. Moreover, in the increasingly-adopted neoadjuvant treatment context, there was a depletion of classical-like phenotypes in malignant cells in favor of basal-like phenotypes associated with TNF-NFkB and interferon signaling as well as the presence of novel acinar and neuroendocrine classical-like states, which may be more resilient to cytotoxic treatment. Spatially-resolved transcriptomics revealed an association between malignant cells expressing these basal-like programs and higher immune infiltration with increased lymphocytic content, whereas those exhibiting classical-like programs were linked to sparser macrophage-predominant microniches, perhaps pointing to susceptibility to distinct therapeutic strategies. Our refined molecular taxonomy and spatial resolution can help advance precision oncology in PDAC through informative stratification in clinical trials and insights into differential therapeutic targeting leveraging the immune system.

genomics↗

bioRxiv2018

xMD-miRNA-seq to generate near in vivo miRNA expression estimates in colon epithelial cells

Accurate, RNA-seq based, microRNA (miRNA) expression estimates from primary cells have recently been described. However, this in vitro data is mainly obtained from cell culture, which is known to alter cell maturity/differentiation status, significantly changing miRNA levels. What is needed is a robust method to obtain in vivo miRNA expression values directly from cells. We introduce expression microdissection miRNA small RNA sequencing (xMD-miRNA-seq), a method to isolate cells directly from formalin fixed paraffin-embedded (FFPE) tissues. xMD-miRNA-seq is a low-cost, high-throughput, immunohistochemistry-based method to capture any cell type of interest. As a proof-of-concept, we isolated colon epithelial cells from two specimens and performed low-input small RNA-seq. We generated up to 600,000 miRNA reads from the samples. Isolated epithelial cells, had abundant epithelial-enriched miRNA expression (miR-192; miR-194; miR-200b; miR-200c; miR-215; miR-375) and overall similar miRNA expression patterns to other epithelial cell populations (colonic enteroids and flow-isolated colon epithelium). xMD-derived epithelial cells were generally not contaminated by other adjacent cells of the colon as noted by t-SNE analysis. xMD-miRNA-seq allows for simple, economical, and efficient identification of cell-specific miRNA expression estimates. Further development will enhance rapid identification of cell-specific miRNA expression estimates in health and disease for nearly any cell type using archival FFPE material.

molecular biology↗

bioRxiv2017

Compensatory evolution via cryptic genetic variation: Distinct trajectories to phenotypic and fitness recovery

Populations are constantly exposed to deleterious alleles, most of which are purged via natural selection. However, deleterious fitness effects of alleles can also be suppressed by compensatory adaptation. Compensatory mutations can act directly to reduce deleterious effects of an allele. Alternatively, compensation may also occur by altering other aspects of an organisms phenotype or performance, without suppressing the phenotypic effects of the deleterious allele. Moreover, the origin of allelic variation contributing to compensatory adaptation remains poorly understood. Compensatory evolution driven by mutations that arise during the selective process are well studied. However less is known about the role standing (cryptic) genetic variation plays in compensatory adaptation. To address these questions, we examined evolutionary trajectories of natural populations of Drosophila melanogaster fixed for mutations that disrupt wing morphology, resulting in deleterious effects on several components of fitness. Lineages subjected only to natural selection, evolved modifications to courtship behavior and several life history traits without compensation in wing morphology. Yet, we observed rapid phenotypic compensation of wing morphology under artificial selection, consistent with segregating variation for compensatory alleles. We show that alleles contributing to compensation of wing morphology have deleterious effects on other fitness components. These results demonstrate the potential for multiple independent avenues for rapid compensatory adaptation from standing genetic variation, which ultimately may reveal novel adaptive trajectories.

evolutionary biology↗

bioRxiv2017

How Well Do You Know Your Mutation? Complex Effects Of Genetic Background On Expressivity, Complementation, And Ordering Of Allelic Effects

For a given gene, different mutations influence organismal phenotypes to varying degrees. However, the expressivity of these variants not only depends on the DNA lesion associated with the mutation, but also on factors including the genetic background and rearing environment. The degree to which these factors influence related alleles, genes, or pathways similarly, and whether similar developmental mechanisms underlie variation in the expressivity of a single allele across conditions and variation across alleles is poorly understood. Besides their fundamental biological significance, these questions have important implications for the interpretation of functional genetic analyses, for example, if these factors alter the ordering of allelic series or patterns of complementation. We examined the impact of genetic background and rearing environment for a series of mutations spanning the range of phenotypic effects for both the scalloped and vestigial genes, which influence wing development in Drosophila melanogaster. Genetic background and rearing environment influenced the phenotypic outcome of mutations, including intra-genic interactions, particularly for mutations of moderate expressivity. We examined whether cellular correlates (such as cell proliferation during development) of these phenotypic effects matched the observed phenotypic outcome. While cell proliferation decreased with mutations of increasingly severe effects, surprisingly it did not co-vary strongly with the degree of background dependence. We discuss these findings and propose a phenomenological model to aid in understanding the biology of genes, and how this influences our interpretation of allelic effects in genetic analysis.

genetics↗