Class III Phosphatidylinositol-3 Kinase/Vacuolar Protein Sorting 34 in Cardiovascular Health and Disease.

Phosphatidylinositol-3 kinases (PI3Ks) play a critical role in maintaining cardiovascular health and the development of cardiovascular diseases (CVDs). Specifically, vacuolar Protein Sorting 34 (VPS34) or PIK3C3, the only member of Class III PI3K, plays an important role in CVD progression. The main function of VPS34 is inducing the production of phosphatidylinositol 3-phosphate, which, together with other essential structural and regulatory proteins in forming VPS34 complexes, further regulates the mammalian target of rapamycin activation, autophagy, and endocytosis.

Zonal patterning of extracellular matrix and stromal cell populations along a perfusable cellular microchannel.

The spatial organization of biophysical and biochemical cues in the extracellular matrix (ECM) in concert with reciprocal cell-cell signaling is vital to tissue patterning during development. However, elucidating the role an individual microenvironmental factor plays using existing models is difficult due to their inherent complexity. In this work, we have developed a microphysiological system to spatially pattern the biochemical, biophysical, and stromal cell composition of the ECM along an epithelialized 3D microchannel.

Live and carcass production traits for progeny of an F1 USDA Prime-Yield Grade 1 carcass clone sire compared to progeny of popular beef terminal sires.

The cloning of beef carcasses that grade United States Department of Agriculture (USDA) Prime-yield grade (YG) 1 (P1) has produced a sire that ranked well against high-performing bulls from multiple breeds. An F1 (P1 × P1 - first generation offspring) sire would ideally outperform its high-performing parents. A terminal sire study was conducted comparing progeny of an F1 (P1 × P1) sire (AxG1) against progeny (heifers and steers) of four high-performing sires of varying breeds {P1 (ALPHA); Angus; Simmental; Angus × Simmental}.

A straightforward cell culture insert model to incorporate biochemical and biophysical stromal properties into transplacental transport studies.

The placental extracellular matrix (ECM) dynamically remodels over pregnancy and in disease. How these changes impact placental barrier function is poorly understood as there are limited in vitro models of the placenta with a modifiable stromal compartment to mechanistically investigate these extracellular factors. We developed a straightforward method to incorporate uniform hydrogels into standard cell culture inserts for transplacental transport studies.

Annotation Vocabulary (Might Be) All You Need.

Protein Language Models (pLMs) have revolutionized the computational modeling of protein systems, building numerical embeddings that are centered around structural features. To enhance the breadth of biochemically relevant properties available in protein embeddings, we engineered the , a transformer readable language of protein properties defined by structured ontologies. We trained (AT) from the ground up to recover masked protein property inputs without reference to amino acid sequences, building a new numerical feature space on protein descriptions alone.

Zonal Patterning of Extracellular Matrix and Stromal Cell Populations Along a Perfusable Cellular Microchannel.

The spatial organization of biophysical and biochemical cues in the extracellular matrix (ECM) in concert with reciprocal cell-cell signaling is vital to tissue patterning during development. However, elucidating the role an individual microenvironmental factor plays using existing models is difficult due to their inherent complexity. In this work, we have developed a microphysiological system to spatially pattern the biochemical, biophysical, and stromal cell composition of the ECM along an epithelialized 3D microchannel.

Quantifying Spatial Patterns of Tissue Stiffness Within the Embryonic Mouse Kidney.

Biophysical factors, including changes in mechanical stiffness, have been shown to influence the morphogenesis of developing organs. There is a lack of experimental techniques, however, that can probe the mechanical properties of embryonic tissues-especially those which are not mechanically or optically accessible, such as the visceral organs of the developing mouse embryo. Here, using the embryonic kidney as a model system, we describe a method to use microindentation to quantify tissue-level regional differences in the mechanical properties of an embryonic organ.

Stochastic to Deterministic: A straightforward approach to create serially perfusable multiscale capillary beds.

Generation of tissue models with serially perfused hierarchical vasculature would allow greater control of fluid perfusion throughout the network and enable direct mechanistic investigation of vasculogenesis, angiogenesis, and vascular remodeling. In this work, we have developed a method to produce a closed, serially perfused, multiscale vessel network embedded within an acellular hydrogel. We confirmed that the acellular and cellular gel-gel interface was functionally annealed without preventing or biasing cell migration and endothelial self-assembly.

Systematic development of ionizable lipid nanoparticles for placental mRNA delivery using a design of experiments approach.

Ionizable lipid nanoparticles (LNPs) have gained attention as mRNA delivery platforms for vaccination against COVID-19 and for protein replacement therapies. LNPs enhance mRNA stability, circulation time, cellular uptake, and preferential delivery to specific tissues compared to mRNA with no carrier platform. However, LNPs are only in the beginning stages of development for safe and effective mRNA delivery to the placenta to treat placental dysfunction.

cdsBERT - Extending Protein Language Models with Codon Awareness.

Recent advancements in Protein Language Models (pLMs) have enabled high-throughput analysis of proteins through primary sequence alone. At the same time, newfound evidence illustrates that codon usage bias is remarkably predictive and can even change the final structure of a protein. Here, we explore these findings by extending the traditional vocabulary of pLMs from amino acids to codons to encapsulate more information inside CoDing Sequences (CDS).

A Large-format Polyacrylamide Gel with Controllable Matrix Mechanics for Mammalian Cell Culture and Conditioned Media Production.

Tissue culture plastic has been used for routine cell culture and in vitro experiments for over 50 years. However, cells are mechanically responsive and behave differently on hard surfaces than they do on softer substrates. Polyacrylamide gels have become a popular hydrogel of choice for controlling surface stiffness and ligand density for cell adhesion.

Molecular insights using spatial transcriptomics of the distal lung in congenital diaphragmatic hernia.

Abnormal pulmonary vascular development and function in congenital diaphragmatic hernia (CDH) is a significant factor leading to pulmonary hypertension. The lung is a very heterogenous organ and has marked cellular diversity that is differentially responsive to injury and therapeutic agents. Spatial transcriptomics provides the unmatched capability of discerning the differences in the transcriptional signature of these distinct cell subpopulations in the lung with regional specificity.

Delivery and short-term maternal and fetal safety of vaginally administered PEG-PLGA nanoparticles.

At the onset of pregnancy, people with preexisting conditions face additional challenges in carrying their pregnancy to term, as the safety of the developing fetus and pregnant person is a significant factor of concern. Nanoparticle (NP)-based therapies have displayed success against various conditions and diseases in non-pregnant patients, but the use of NPs in maternal-fetal health applications needs to be better established. Local vaginal delivery of NPs is a promising administration route with the potential to yield high cargo retention in the vagina and improved therapeutic efficacy compared to systemic administration that results in rapid NP clearance by the hepatic first-pass effect.

Lung Development in a Dish: Models to Interrogate the Cellular Niche and the Role of Mechanical Forces in Development.

Over the past decade, emphasis has been placed on recapitulating in vitro the architecture and multicellular interactions found in organs in vivo [1, 2]. Whereas traditional reductionist approaches to in vitro models enable teasing apart the precise signaling pathways, cellular interactions, and response to biochemical and biophysical cues, model systems that incorporate higher complexity are needed to ask questions about physiology and morphogenesis at the tissue scale. Significant advancements have been made in establishing in vitro models of lung development to understand cell-fate specification, gene regulatory networks, sexual dimorphism, three-dimensional organization, and how mechanical forces interact to drive lung organogenesis [3-5].

Connecting clinical, environmental, and genetic factors point to an essential role for vitamin A signaling in the pathogenesis of congenital diaphragmatic hernia.

Congenital diaphragmatic hernia (CDH) is a developmental disorder that results in incomplete diaphragm formation, pulmonary hypoplasia, and pulmonary hypertension. Although a variety of genes have been linked to its etiology, CDH is not a monogenetic disease, and the cause of the condition is still unclear in the vast majority of clinical cases. By comparing human clinical data and experimental rodent data from the literature, we present clear support demonstrating the importance of vitamin A (vitA) during the early window of pregnancy when the diaphragm and lung are forming.

Lipid Nanoparticle Composition Drives mRNA Delivery to the Placenta.

Ionizable lipid nanoparticles (LNPs) have gained attention as mRNA delivery platforms for vaccination against COVID-19 and for protein replacement therapies. LNPs enhance mRNA stability, circulation time, cellular uptake, and preferential delivery to specific tissues compared to mRNA with no carrier platform. However, LNPs have yet to be developed for safe and effective mRNA delivery to the placenta as a method to treat placental dysfunction.

Secretion of the disulfide bond generating catalyst QSOX1 from pancreatic tumor cells into the extracellular matrix: association with extracellular vesicles and matrix proteins.

Quiescin sulfhydryl oxidase 1 (QSOX1) is a disulfide bond generating catalyst that is overexpressed in solid tumors. Expression of QSOX1 is linked to cancer cell invasion, tumor grade, and extracellular matrix (ECM) protein deposition. While the secreted version of QSOX1 is known to be present in various fluids and secretory tissues, its presence in the ECM of cancer is less understood.

Sex-related external factors influence pulmonary vascular angiogenesis in a sex-dependent manner.

Bronchopulmonary dysplasia (BPD) is a disease with a significant sexual dimorphism where males have a disadvantage compared with their female counterparts. Although mechanisms behind this sexual dimorphism are poorly understood, sex differences in angiogenesis have been identified as one possible source of the male disadvantage in BPD. Pulmonary angiogenesis was assessed in vitro using a bead sprouting assay with pooled male or female human pulmonary microvascular endothelial cells (HPMECs, 18-19 wk gestation, canalicular stage of human lung development) in standard (sex-hormone containing) and hormone-stripped medium.

Focal sources of FGF-10 promote the buckling morphogenesis of the embryonic airway epithelium.

During airway branching morphogenesis, focal regions of FGF-10 expression in the pulmonary mesenchyme are thought to provide a local guidance cue, which promotes chemotactically the directional outgrowth of the airway epithelium. Here, however, we show that an ectopic source of FGF-10 induces epithelial buckling morphogenesis and the formation of multiple new supernumerary buds. FGF-10-induced budding can be modulated by altered epithelial tension and luminal fluid pressure.

Three-dimensional models of the cervicovaginal epithelia to study host-microbiome interactions and sexually transmitted infections.

2D cell culture systems have historically provided controlled, reproducible means to analyze host-pathogen interactions observed in the human reproductive tract. Although inexpensive, straightforward, and requiring a very short time commitment, these models recapitulate neither the functionality of multilayered cell types nor the associated microbiome that occurs in a human. Animal models have commonly been used to recreate the complexity of human infections.

The Cellular and Molecular Effects of Fetoscopic Endoluminal Tracheal Occlusion in Congenital Diaphragmatic Hernia.

Congenital diaphragmatic hernia (CDH) is a complex disease associated with pulmonary hypoplasia and pulmonary hypertension. Great strides have been made in our ability to care for CDH patients, specifically in the prenatal improvement of lung volume and morphology with fetoscopic endoluminal tracheal occlusion (FETO). While the anatomic effects of FETO have been described in-depth, the changes it induces at the cellular and molecular level remain a budding area of CDH research.