Biology subjects

Lacey, M.

Publications and source records attributed to Lacey, M..

7 recordsLinked to original sources

bioRxiv2026

Aquatic respiratory rates in red devil vampire crabs (Geosesarma hagen) are dependent on interactions between temperature, sex, and body size

The shift to terrestrial environments in ancestrally aquatic animals is often associated with key physiological and physical changes, including shifts in respiratory physiology and in some cases, even the evolution of completely novel respiratory structures. Examining how respiration operates across a gradient of submersion states in ancestrally aquatic terrestrial animals may shed light on how complex biological traits shift under different selective regimes. In this work, we begin exploring respiration in terrestrially-adapted land crabs that still use their gills to respire while underwater. We tested the relationship between aquatic respiratory rates, body size, and sex in red devil vampire crabs (Geosesarma hagen) at two ecologically-relevant temperatures. We found small females respire more than small males at 28{degrees}C, while large females respire more than large males at 21{degrees}C. Additionally, body size is a significant factor affecting respiratory rates of both sexes at 21{degrees}C and warmer temperatures significantly increase respiration in small crabs of both sexes. Interactions between these factors also led to emerging trends that can be explained by both physiological rules, such as reproductive investment and surface-to-volume ratios and heat transfer. We also report a temperature coefficient (Q10) of 1.52 for this species, showing an expected 52% change in respiratory and metabolic rate for every 10{degrees}C increase. This work also demonstrates the importance of understanding how and to what extent biological variables like sex and body size interact with abiotic environmental factors when measuring physiological traits in ectothermic invertebrate animals. What is already knownAs crabs colonize terrestrial environments, they undergo adaptive physical and physiological changes in their respiratory abilities. Few studies have examined these respiratory shifts in individual terrestrial crab species using modern respirometry tools and techniques and across different submersion states and biotic and abiotic factors. We quantify how temperature, body size, and sex affect aquatic respiratory rates in adult terrestrial vampire crabs. What this study addsWe found small females respire more than small males at 28{degrees}C, while large females respire more than large males at 21{degrees}C. Additionally, body size is a significant factor affecting respiratory rates of both sexes at 21{degrees}C and warmer temperatures significantly increase respiration in small crabs of both sexes. Interactions between these factors also led to emerging trends that can be explained by both physiological rules, such as reproductive investment and surface-to-volume ratios and heat transfer. We also report a temperature coefficient (Q10) of 1.52 for this species, showing an expected 52% change in respiratory and metabolic rate for every 10{degrees}C increase.

physiology↗

bioRxiv2022

Promoter-adjacent DNA hypermethylation can downmodulate gene expression: TBX15 in the muscle lineage

TBX15, which encodes a differentiation-related transcription factor, displays promoter-adjacent DNA hypermethylation in myoblasts and skeletal muscle (psoas) that is absent from non-expressing cells in other lineages. By whole-genome bisulfite sequencing (WGBS) and enzymatic methyl-seq (EM-seq), these hypermethylated regions were found to border both sides of a constitutively unmethylated promoter. To understand the functionality of this DNA hypermethylation, we cloned the differentially methylated sequences (DMRs) in CpG-free reporter vectors and tested them for promoter or enhancer activity upon transient transfection. These cloned regions exhibited strong promoter activity and, when placed upstream of a weak promoter, strong enhancer activity specifically in myoblast host cells. In vitro CpG methylation targeted to the DMR sequences in the plasmids resulted in 86 - 100% loss of promoter or enhancer activity, depending on the insert sequence. These results as well as chromatin epigenetic and transcription profiles for this gene in various cell types support the hypothesis that DNA hypermethylation immediately upstream and downstream of the unmethylated promoter region suppresses enhancer/extended promoter activity, thereby downmodulating, but not silencing, expression in myoblasts and certain kinds of skeletal muscle. This promoter-border hypermethylation is not found in cell types with a silent TBX15 gene probably because they have no transcription to modulate. TBX18, TBX2, TBX3 and TBX1 display TBX15-like hypermethylated DMRs at their promoter borders and preferential expression in myoblasts. Therefore, promoter-adjacent DNA hypermethylation for downmodulating transcription to prevent overexpression may be used more frequently for transcription regulation than currently appreciated.

molecular biology↗

bioRxiv2021

Evaluating Differences in Elastic Modulus of Regenerated and Uninjured Mouse Digit Bone through microCT Density-Elasticity Calculation and Nanoindentation Testing

Bone is an essential, healing structure in vertebrates that ensures daily function. However, the regenerative capacity of bone declines with age, compromising quality of life in the elderly and increasing cost of care. Here, for the first time, the elasticity of regenerated bone in a mouse digit amputation model is evaluated in order to better investigate biomechanics of skeletal regeneration. Amputation of the distal one third of the digit (third phalangeal element - P3) results in de novo regeneration of the digit, where analyzing the structural quality of this regenerated bone is a challenging task due to its small scale and triangular shape. To date, the evaluation of structural quality of the P3 bone has primarily focused on mineral density and bone architecture. This work describes an image-processing based method for assessment of elasticity in the whole P3 bone by using microcomputed tomography-generated mineral density data to calculate spatially discrete elastic modulus values across the entire P3 bone volume. Further, we validate this method through comparison to nanoindentation-measured values for elastic modulus. Application to a set of regenerated and unamputated digits shows that regenerated bone has a lower elastic modulus compared to the uninjured digit, with a similar trend for experimental hardness values. This method will be impactful in predicting and evaluating the regenerative outcomes of potential treatments and heightens the utility of the P3 regenerative model.

bioengineering↗

bioRxiv2020

The SEQC2 Epigenomics Quality Control (EpiQC) Study: Comprehensive Characterization of Epigenetic Methods, Reproducibility, and Quantification

Cytosine modifications in DNA such as 5-methylcytosine (5mC) underlie a broad range of developmental processes, maintain cellular lineage specification, and can define or stratify cancer and other diseases. However, the wide variety of approaches available to interrogate these modifications has created a need for harmonized materials, methods, and rigorous benchmarking to improve genome-wide methylome sequencing applications in clinical and basic research. Here, we present a multi-platform assessment and a global resource for epigenetics research from the FDAs Epigenomics Quality Control (EpiQC) Group. The study design leverages seven human cell lines that are designated as reference materials and publicly available from the National Institute of Standards and Technology (NIST) and Genome in a Bottle (GIAB) consortium. These samples were subject to a variety of genome-wide methylation interrogation approaches across six independent laboratories, with a primary focus was on 5-methylcytosine modifications. Each sample was processed in two or more technical replicates by three whole-genome bisulfite sequencing (WGBS) protocols (TruSeq DNA methylation, Accel-NGS MethylSeq, and SPLAT), oxidative bisulfite sequencing (TrueMethyl), one enzymatic deamination method (EMseq), targeted methylation sequencing (Illumina Methyl Capture EPIC), and single-molecule long-read nanopore sequencing from Oxford Nanopore Technologies. After rigorous quality assessment and comparison to Illumina EPIC methylation microarrays and testing on a range of algorithms (Bismark, BitmapperBS, BWAMeth, and GemBS), we found overall high concordance between assays (R=0.87-R0.93), differences in efficency of read mapping and CpG capture and coverage, and platform performance. The data provided herein can guide continued used of these reference materials in epigenomics assays, as well as provide best practices for epigenomics research and experimental design in future studies.

genomics↗

bioRxiv2020

Epigenetics and expression of key genes associated with cardiac fibrosis: NLRP3, MMP2, MMP9, CCN2/CTGF, and AGT

Excessive inflammatory signaling and pathological remodeling of the extracellular matrix are important contributors to cardiac fibrosis and involve major changes in gene expression. We examined the relationships between tissue-specific expression and the epigenetics of five genes involved in these pathways, NLRP3, MMP2, MMP9, CCN2/CTGF, and AGT. The proteins encoded by these genes play major fibrosis-related roles in inflammasome formation, degradation of extracellular matrix proteins and remodeling of the extracellular matrix and vasculature, autocrine regulation of fibrosis, or cell signaling. Our analyses showed that the first four of these genes had super-enhancers (unusually strong enhancer clusters) that correlate with their very high expression in monocytes, neutrophils, fibroblasts, or venous cells. Expression of the gene encoding miR-223, a micro-RNA that plays an important role in downregulating NLRP3 protein levels, is also probably driven by the super-enhancer in which it is embedded. Enhancer chromatin for all these genes was inside as well as outside the gene body. While AGT, which encodes precursors of angiotensin II, lacked a super-enhancer, its tissue-specific expression profile correlates with the tissue-specific enhancer chromatin extending into its distant silent gene neighbor (CAPN9). Tissue-specific peaks of DNA hypomethylation, open chromatin (DNaseI hypersensitivity), and transcription factor binding were detected in subregions of these super-enhancers/enhancers that are likely to be the main drivers of expression of their associated gene. We found that CCN2/CTGF is co-expressed with its far-upstream neighbor LINC01013, a noncoding RNA gene, specifically in vein endothelial cells (HUVEC) and chondrocytes. Evidence from chromatin looping profiling (Hi-C) suggests coregulation of these genes in HUVEC. Our findings indicate the importance of understanding the often-overlooked roles of enhancers and their hypomethylated, transcription factor-binding subregions in the regulation of expression of fibrosis-related genes in normal and fibrotic tissue.

genomics↗

bioRxiv2019

Epigenetics of skeletal muscle-associated genes in the ASB, LRRC, TMEM, and OSBPL gene families

Much remains to be discovered about the intersection of tissue-specific transcription control and the epigenetics of skeletal muscle (SkM), a very complex and dynamic organ. From four gene families, ASB, LRRC, TMEM, and OSBPL, we chose 21 genes that are preferentially expressed in human SkM relative to 52 other tissue types and analyzed relationships between their tissue-specific epigenetics and expression. We also compared their genetics, proteomics, and descriptions in the literature. For this study, we identified genes with little or no previous descriptions of SkM functionality (ASB4, ASB8, ASB10, ASB12, ASB16, LRRC14B, LRRC20, LRRC30, TMEM52, TMEM233, OSBPL6/ORP6, and OSBPL11/ORP11) and included genes whose SkM functions had been previously addressed (ASB2, ASB5, ASB11, ASB15, LRRC2, LRRC38, LRRC39, TMEM38A/TRIC-A, and TMEM38B/TRIC-B). Among the transcription-related SkM epigenetic features that we identified were super-enhancers, promoter DNA hypomethylation, lengthening of constitutive low-methylated promoter regions, and SkM-related enhancers for one gene embedded in a neighboring gene (e.g., ASB8-PFKM, LRRC39-DBT, and LRRC14B-PLEKHG4B gene-pairs). In addition, highly or lowly co-expressed long non-coding RNA (lncRNA) genes probably regulate several of these genes. Our findings give insights into tissue-specific epigenetic patterns and functionality of related genes in a gene family and can elucidate normal and disease-related regulation of gene expression in SkM.

genomics↗

bioRxiv2017

Hypermethylation of human DNA: Fine-tuning transcription associated with development

Tissue-specific gene transcription can be affected by DNA methylation in ways that are difficult to discern from studies focused on genome-wide analyses of differentially methylated regions (DMRs). We studied 95 genes in detail using available epigenetic and transcription databases to detect and elucidate less obvious associations between development-linked hypermethylated DMRs in myoblasts (Mb) and cell-and tissue-specific expression. Many of these genes encode developmental transcription factors and display DNA hypermethylation also in skeletal muscle (SkM) and a few heterologous samples (e.g., aorta, mammary epithelial cells, or brain) among the 38 types of human cell cultures or tissues examined. Most of the DMRs overlapped transcription regulatory elements, including canonical, alternative, or cryptic promoters; enhancers; CTCF binding sites; and long-noncoding RNA (lncRNA) gene regions. Among the prominent relationships between DMRs and expression was promoter-region hypermethylation accompanying repression in Mb but not in many other repressed samples (26 genes). Another surprising relationship was down-modulated (but not silenced) expression in Mb associated with DNA hypermethylation at cryptic enhancers in Mb although such methylation was absent in both non-expressing samples and highly expressing samples (24 genes). The tissue-specificity of DNA hypermethylation can be explained for many of the genes by their roles in prenatal development or by the tissue-specific expression of neighboring genes. Besides elucidating developmental epigenetics, our study provides insights into the roles of abnormal DNA methylation in disease, e.g., cancer, Duchenne muscular dystrophy, and congenital heart malformations.

genomics↗