Enzymatically Degradable Mussel-Inspired Adhesive Hydrogel

Mussel-inspired adhesive hydrogels represent innovative candidate medical sealants or glues. In the present work, we describe an enzyme-degradable mussel-inspired adhesive hydrogel formulation, achieved by incorporating minimal elastase substrate peptide Ala-Ala into the branched poly(ethylene glycol) (PEG) macromonomer structure. The system takes advantage of neutrophil elastase expression upregulation and secretion from neutrophils upon recruitment to wounded or inflamed tissue. By integrating adhesive degradation behaviors that respond to cellular cues, we expand the functional range of our mussel-inspired adhesive hydrogel platforms. Rapid (<1 min) and simultaneous gelation and adhesion of the proteolytically active, catechol-terminated precursor macromonomer was achieved by addition of sodium periodate oxidant. Rheological analysis and equilibrium swelling studies demonstrated that the hydrogel is appropriate for soft tissue-contacting applications. Notably, hydrogel storage modulus (G) achieved values on the order of 10 kPa, and strain at failure exceeded 200% strain. Lap shear testing confirmed the materials adhesive behavior (shear strength: 30.4 ± 3.39 kPa). Although adhesive hydrogel degradation was not observed during short-term (27 h) in vitro treatment with neutrophil elastase, in vivo degradation proceeded over several months following dorsal subcutaneous implantation in mice. This work represents the first example of an enzymatically degradable mussel-inspired adhesive and expands the potential biomedical applications of this family of materials

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Migration and Evolution of giant ExoPlanets (MEEP) I: Nine Newly Confirmed Hot Jupiters from the TESS Mission

Hot Jupiters were many of the first exoplanets discovered in the 1990s, but in the decades since their discovery, the mysteries surrounding their origins remain. Here, we present nine new hot Jupiters (TOI-1855 b, TOI-2107 b, TOI-2368 b, TOI-3321 b, TOI-3894 b, TOI-3919 b, TOI-4153 b, TOI-5232 b, and TOI-5301 b) discovered by NASA's TESS mission and confirmed using ground-based imaging and spectroscopy. These discoveries are the first in a series of papers named the Migration and Evolution of giant ExoPlanets (MEEP) survey and are part of an ongoing effort to build a complete sample of hot Jupiters orbiting FGK stars, with a limiting Gaia $G$-band magnitude of 12.5. This effort aims to use homogeneous detection and analysis techniques to generate a set of precisely measured stellar and planetary properties that is ripe for statistical analysis. The nine planets presented in this work occupy a range of masses (0.55 Jupiter masses (M$_{\rm{J}}$) $<$ M$_{\rm{P}}$ $<$ 3.88 M$_{\rm{J}}$) and sizes (0.967 Jupiter radii (R$_{\rm{J}}$) $<$ R$_{\rm{P}}$ $<$ 1.438 R$_{\rm{J}}$) and orbit stars that range in temperature from 5360 K $<$ Teff $<$ 6860 K with Gaia $G$-band magnitudes ranging from 11.1 to 12.7. Two of the planets in our sample have detectable orbital eccentricity: TOI-3919 b ($e = 0.259^{+0.033}_{-0.036}$) and TOI-5301 b ($e = 0.33^{+0.11}_{-0.10}$). These eccentric planets join a growing sample of eccentric hot Jupiters that are consistent with high-eccentricity tidal migration, one of the three most prominent theories explaining hot Jupiter formation and evolution.Comment: 35 pages, 7 tables, and 14 figures. Submitted to AAS Journals on 2023 Dec 2

Another Shipment of Six Short-Period Giant Planets from TESS

We present the discovery and characterization of six short-period, transiting giant planets from NASA's Transiting Exoplanet Survey Satellite (TESS) -- TOI-1811 (TIC 376524552), TOI-2025 (TIC 394050135), TOI-2145 (TIC 88992642), TOI-2152 (TIC 395393265), TOI-2154 (TIC 428787891), & TOI-2497 (TIC 97568467). All six planets orbit bright host stars (8.9 <G< 11.8, 7.7 <K< 10.1). Using a combination of time-series photometric and spectroscopic follow-up observations from the TESS Follow-up Observing Program (TFOP) Working Group, we have determined that the planets are Jovian-sized (R$_{P}$ = 1.00-1.45 R$_{J}$), have masses ranging from 0.92 to 5.35 M$_{J}$, and orbit F, G, and K stars (4753 $<$ T$_{eff}$ $<$ 7360 K). We detect a significant orbital eccentricity for the three longest-period systems in our sample: TOI-2025 b (P = 8.872 days, $e$ = $0.220\pm0.053$), TOI-2145 b (P = 10.261 days, $e$ = $0.182^{+0.039}_{-0.049}$), and TOI-2497 b (P = 10.656 days, $e$ = $0.196^{+0.059}_{-0.053}$). TOI-2145 b and TOI-2497 b both orbit subgiant host stars (3.8 $<$ $\log$ g $<$4.0), but these planets show no sign of inflation despite very high levels of irradiation. The lack of inflation may be explained by the high mass of the planets; $5.35^{+0.32}_{-0.35}$ M$_{\rm J}$ (TOI-2145 b) and $5.21\pm0.52$ M$_{\rm J}$ (TOI-2497 b). These six new discoveries contribute to the larger community effort to use {\it TESS} to create a magnitude-complete, self-consistent sample of giant planets with well-determined parameters for future detailed studies.Comment: 20 Pages, 6 Figures, 8 Tables, Accepted by MNRA

Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome

Most of our understanding of plant genome structure and evolution has come from the careful annotation of small (e.g., 100 kb) sequenced genomic regions or from automated annotation of complete genome sequences. Here, we sequenced and carefully annotated a contiguous 22 Mb region of maize chromosome 4 using an improved pseudomolecule for annotation. The sequence segment was comprehensively ordered, oriented, and confirmed using the maize optical map. Nearly 84% of the sequence is composed of transposable elements (TEs) that are mostly nested within each other, of which most families are low-copy. We identified 544 gene models using multiple levels of evidence, as well as five miRNA genes. Gene fragments, many captured by TEs, are prevalent within this region. Elimination of gene redundancy from a tetraploid maize ancestor that originated a few million years ago is responsible in this region for most disruptions of synteny with sorghum and rice. Consistent with other sub-genomic analyses in maize, small RNA mapping showed that many small RNAs match TEs and that most TEs match small RNAs. These results, performed on ∼1% of the maize genome, demonstrate the feasibility of refining the B73 RefGen_v1 genome assembly by incorporating optical map, high-resolution genetic map, and comparative genomic data sets. Such improvements, along with those of gene and repeat annotation, will serve to promote future functional genomic and phylogenomic research in maize and other grasses