Biology subjects

Jennings, T.

Publications and source records attributed to Jennings, T..

3 recordsLinked to original sources

bioRxiv2026

An Integrated Multiphoton Imaging Workflow for Quantitative Analysis of Aortic Tissue Microstructure

Quantitative, reproducible characterization of aortic microstructure is essential for advancing vascular biomechanics and mechanobiology. To address this need, we present a comprehensive image-analysis workflow that extracts quantitative descriptors of tissue microstructure from multiphoton microscopy stacks of the murine thoracic aorta. Channel-specific signals are acquired for fibrillar collagen (second harmonic generation), elastin (two-photon autofluorescence), and cell nuclei (two-photon excited fluorescence). Following reorientation into the XZ plane, individual elastic lamellae are traced to quantify lamellar thickness and interlamellar spacing using circle-based geometry (Taubin fitting). After correction for vessel wall curvature via a cylindrical transformation, segmented nuclei are assigned to medial or adventitial compartments based on visual estimates of adventitial volume fraction, and nuclear morphology is characterized via ellipsoidal fitting in terms of nuclear aspect ratio and major-axis orientation. Collagen organization is resolved in XY sections by extracting fiber centerlines to quantify straightness and amplitude; traces from serial sections are then combined to reconstruct the three-dimensional collagen network and estimate porosity and linear fiber density, while fiber orientation distributions are derived from principal component analysis-based angles and fit using a von Mises mixture model. Finally, collagen and elastin volume fractions are computed via a two-stage fixed-threshold approach calibrated on a balanced training subset. Overall, this modular and robust workflow provides an integrated framework for studying aortic wall remodeling across physiological and pathological processes. Non-Technical SummaryAs the main blood vessel in our body, the aorta needs to be both strong and flexible. This balance comes from three main parts: elastic layers that allow the aorta to stretch, strong fibers that prevent tearing, and cells that sense and respond to changes in blood pressure and other signals. When any of these components are altered, the aorta may stiffen or weaken, which can interfere with normal blood flow. In this study, we developed a clear and consistent way to measure the structure of the aortic wall using microscope images. The approach examines how thick the elastic layers are and how far apart they lie, the size and orientation of cell centers, and how straight or wavy structural fibers appear. It also estimates how much of each component is present in the aortic wall. Because the same steps are applied each time, results can be fairly compared across different conditions. Overall, this tool transforms detailed images into simple measurements, helping scientists understand how the aorta changes in health and disease.

bioengineering↗

bioRxiv2019

Transcription factor NF-κB in a basal metazoan, the sponge, has conserved and unique sequences, activities, and regulation

Biological and biochemical functions of immunity transcription factor NF-{kappa}B in basal metazoans are largely unknown. Herein, we characterize transcription factor NF-{kappa}B from the demosponge Amphimedon queenslandica (Aq), in the phylum Porifera. Structurally and phylogenetically, the Aq-NF-{kappa}B protein is most similar to NF-{kappa}B p100 and p105 among vertebrate proteins, with an N-terminal DNA-binding/dimerization domain, a C-terminal Ankyrin (ANK) repeat domain, and a DNA binding-site profile more similar to human NF-{kappa}B proteins than Rel proteins. Aq-NF-{kappa}B also resembles the mammalian NF-{kappa}B protein p100 in that C-terminal truncation results in translocation of Aq-NF-{kappa}B to the nucleus and increases its transcriptional activation activity. Overexpression of a human or sea anemone I{kappa}B kinase (IKK) can induce C-terminal processing of Aq-NF-{kappa}B in vivo, and this processing requires C-terminal serine residues in Aq-NF-{kappa}B. Unlike human NF-{kappa}B p100, however, the C-terminal sequences of Aq-NF-{kappa}B do not effectively inhibit its DNA-binding activity when expressed in human cells. Tissue of another demosponge, a black encrusting sponge, contains NF-{kappa}B site DNA-binding activity and an NF-{kappa}B protein that appears mostly processed and in the nucleus of cells. NF-{kappa}B DNA-binding activity and processing is increased by treatment of sponge tissue with LPS. By transcriptomic analysis of A. queenslandica we identified likely homologs to many upstream NF-{kappa}B pathway components. These results present a functional characterization of the most ancient metazoan NF-{kappa}B protein to date, and show that many characteristics of mammalian NF-{kappa}B are conserved in sponge NF-{kappa}B, but the mechanism by which NF-{kappa}B functions and is regulated in the sponge may be somewhat different.

cell biology↗

bioRxiv2017

The phylogeography of westslope cutthroat trout

Identifying units of conservation of aquatic species is fundamental to informed natural resources science and management. We used a combination of mitochondrial and nuclear molecular methods to identify potential units of conservation of westslope cutthroat trout, a taxon native to montane river basins of the northwestern U.S. and southwestern Canada. Mitogenomic sequencing identified two major lineages composed of nine monophyletic clades, and a well-supported subclade within one of these, largely delineated by river basins. Analyses of microsatellites and single nucleotide polymorphisms corroborated most of these groupings, sometimes with less resolution but demonstrating more complex connections among clades. The mitochondrial and nuclear analyses revealed that Pleistocene glacial cycles profoundly influenced the distribution and divergence of westslope cutthroat trout, that this taxon crossed the Continental Divide in two separate events, and that genetically pure but nonindigenous fish were widely distributed. Herein, we recognize nine geographically discrete, cytonuclear lineages largely circumscribed by major river basins as potential units of conservation: 1) John Day; 2) Coeur dAlene; 3) St. Joe; 4) North Fork Clearwater; 5) Salmon; 6) Clearwater headwaters; 7) Clearwater-eastern Cascades; 8) neoboreal, consisting of most of the Columbia upstream from central Washington, the Fraser in British Columbia, and the South Saskatchewan in Alberta; and 9) Missouri.

evolutionary biology↗