Supplemental Table S2

Supplemental Table 2. Top 10 significantly (p<0.05) enriched Ingenuity Canonical Pathways for the 193 transcripts that were differentially expressed in the HFD:control comparison of liver transcriptomes but not the HFD+DHA:control comparison (total of 24 enriched pathways), and for the 179 transcripts differentially expressed in the HFD+DHA:control comparison of liver transcriptomes, but not the HFD:Control comparison (total of 16 enriched pathways). Transcriptomic analysis was performed on N=4 for each group. Ratio = number of differentially expressed genes/total genes in pathway. Red indicates predicted positive activation of the pathway and upregulation of an individual transcript and blue indicates downregulation.</p

Supplemental Table S6

Supplemental Table 6. Top 10 significantly (p-value <0.05) enriched Ingenuity Canonical Pathways in the HFD:HFD+DHA (14 total enriched pathways), the HFD:HFD+EPA (9 enriched pathways), and the HFD+DHA:HFD+EPA (15 enriched pathways) comparisons of liver transcriptomes. Transcriptomic analysis was performed on N=4 for each group. Ratio = number of differentially expressed genes/total genes in pathway. Red indicates predicted positive activation of the pathway and upregulation of an individual transcript in the reference group (listed first) and blue indicates downregulation.</p

Supplemental Table S1

Supplemental Table 1. Dietary composition of the purified diets for the control, HFD, HFD+EPA, and HFD+DHA groups

Supplemental Table S5

Supplemental Table 5. Top 10 significantly (p<0.05) enriched Ingenuity Canonical Pathways for the 76 transcripts that were differentially expressed in the HFD:control comparison of skeletal muscle transcriptomes but not the HFD+EPA:control comparison (total of 21 enriched pathways), and for the 216 transcripts differentially expressed in the HFD+EPA:control comparison of skeletal muscle transcriptomes, but not the HFD:Control comparison (total of 116 enriched pathways). Transcriptomic analysis was performed on N=4 for each group. Ratio = number of differentially expressed genes/total genes in pathway. Red indicates predicted positive activation of the pathway and upregulation of an individual transcript and blue indicates downregulation.</p

Supplemental Table S4

Supplemental Table 4. Top 10 significantly (p<0.05) enriched Ingenuity Canonical Pathways for the 152 transcripts that were differentially expressed in the HFD:control comparison of skeletal muscle transcriptomes but not the HFD+DHA:control comparison (total of 59 enriched pathways), and for the 67 transcripts differentially expressed in the HFD+DHA:control comparison of skeletal muscle transcriptomes, but not the HFD:Control comparison (total of 44 enriched pathways). Transcriptomic analysis was performed on N=4 for each group. Ratio = number of differentially expressed genes/total genes in pathway. Red indicates predicted positive activation of the pathway and upregulation of an individual transcript and blue indicates downregulation.</p

Supplemental Table S3

Supplemental Table 3. Top 10 significantly (p<0.05) enriched Ingenuity Canonical Pathways for the 92 transcripts that were differentially expressed in the HFD:control comparison of liver transcriptomes but not the HFD+EPA:control comparison (total of 25 enriched pathways), and for the 264 transcripts differentially expressed in the HFD+EPA:control comparison of liver transcriptomes, but not the HFD:Control comparison (total of 33 enriched pathways). Transcriptomic analysis was performed on N=4 for each group. Ratio = number of differentially expressed genes/total genes in pathway. Red indicates predicted positive activation of the pathway and upregulation of an individual transcript and blue indicates downregulation.</p

Supplemental Table S7

Supplemental Table 7. Top 10 significantly (p-value <0.05) enriched Ingenuity Canonical Pathways in the HFD:HFD+DHA (39 total enriched pathways), the HFD:HFD+EPA (5 total enriched pathways), and the HFD+DHA:HFD+EPA (61 enriched pathways) comparisons of skeletal muscle transcriptomes. Transcriptomic analysis was performed on N=4 for each group. Ratio = number of differentially expressed genes/total genes in pathway. Red indicates predicted positive activation of the pathway and upregulation of an individual transcript and blue indicates downregulation.</p

DataSheet1_Basement Membrane of Tissue Engineered Extracellular Matrix Scaffolds Modulates Rapid Human Endothelial Cell Recellularization and Promote Quiescent Behavior After Monolayer Formation.PDF

Off-the-shelf small diameter vascular grafts are an attractive alternative to eliminate the shortcomings of autologous tissues for vascular grafting. Bovine saphenous vein (SV) extracellular matrix (ECM) scaffolds are potentially ideal small diameter vascular grafts, due to their inherent architecture and signaling molecules capable of driving repopulating cell behavior and regeneration. However, harnessing this potential is predicated on the ability of the scaffold generation technique to maintain the delicate structure, composition, and associated functions of native vascular ECM. Previous de-cellularization methods have been uniformly demonstrated to disrupt the delicate basement membrane components of native vascular ECM. The antigen removal (AR) tissue processing method utilizes the protein chemistry principle of differential solubility to achieve a step-wise removal of antigens with similar physiochemical properties. Briefly, the cellular components of SV are permeabilized and the actomyosin crossbridges are relaxed, followed by lipophilic antigen removal, sarcomeric disassembly, hydrophilic antigen removal, nuclease digestion, and washout. Here, we demonstrate that bovine SV ECM scaffolds generated using the novel AR approach results in the retention of native basement membrane protein structure, composition (e.g., Collagen IV and laminin), and associated cell modulatory function. Presence of basement membrane proteins in AR vascular ECM scaffolds increases the rate of endothelial cell monolayer formation by enhancing cell migration and proliferation. Following monolayer formation, basement membrane proteins promote appropriate formation of adherence junction and apicobasal polarization, increasing the secretion of nitric oxide, and driving repopulating endothelial cells toward a quiescent phenotype. We conclude that the presence of an intact native vascular basement membrane in the AR SV ECM scaffolds modulates human endothelial cell quiescent monolayer formation which is essential for vessel homeostasis.</p

Correction to Mapping Serum Albumin Adducts of the Food-Borne Carcinogen 2‑Amino-1-methyl-6-phenylimidazo[4,5‑<i>b</i>]pyridine by Data-Dependent Tandem Mass Spectrometry

Correction to Mapping Serum Albumin Adducts of the Food-Borne Carcinogen 2‑Amino-1-methyl-6-phenylimidazo[4,5‑b]pyridine by Data-Dependent Tandem Mass Spectrometr

Mapping Serum Albumin Adducts of the Food-Borne Carcinogen 2‑Amino-1-methyl-6-phenylimidazo[4,5‑<i>b</i>]pyridine by Data-Dependent Tandem Mass Spectrometry

2-Amino-1-methyl-6-phenylimidazo­[4,5-<i>b</i>]­pyridine (PhIP) is a heterocyclic aromatic amine that is formed during the cooking of meats. PhIP is a potential human carcinogen: it undergoes metabolic activation to form electrophilic metabolites that bind to DNA and proteins, including serum albumin (SA). The structures of PhIP-SA adducts formed in vivo are unknown and require elucidation before PhIP protein adducts can be implemented as biomarkers in human studies. We previously examined the reaction of genotoxic N-oxidized metabolites of PhIP with human SA in vitro and identified covalent adducts formed at cysteine³⁴ (Cys³⁴); however, other adduction products were thought to occur. We have now identified adducts of PhIP formed at multiple sites of SA reacted with isotopic mixtures of electrophilic metabolites of PhIP and 2-amino-1-methyl-6-[²H₅]-phenylimidazo­[4,5-<i>b</i>]­pyridine ([²H₅]-PhIP). The metabolites used for study were 2-nitro-1-methyl-6-phenylimidazo­[4,5-<i>b</i>]­pyridine (NO₂-PhIP), 2-hydroxyamino-1-methyl-6-phenylimidazo­[4,5-<i>b</i>]­pyridine (HONH-PhIP), or <i>N</i>-acetyloxy-2-amino-1-methyl-6-phenylimidazo­[4,5-<i>b</i>]­pyridine (<i>N</i>-acetoxy-PhIP). Following proteolytic digestion, PhIP-adducted peptides were separated by ultra performance liquid chromatography and characterized by ion trap mass spectrometry, employing isotopic data-dependent scanning. Analysis of the tryptic or tryptic/chymotryptic digests of SA modified with NO₂-PhIP revealed that adduction occurred at Cys³⁴, Lys¹⁹⁵, Lys¹⁹⁹, Lys³⁵¹, Lys⁵⁴¹, Tyr¹³⁸, Tyr¹⁵⁰, Tyr⁴⁰¹, and Tyr⁴¹¹, whereas the only site of HONH-PhIP adduction was detected at Cys³⁴. <i>N</i>-Acetoxy-PhIP, a penultimate metabolite of PhIP that reacts with DNA to form covalent adducts, did not appear to form stable adducts with SA; instead, PhIP and 2-amino-1-methyl-6-(5-hydroxy)-phenylimidazo­[4,5-<i>b</i>]­pyridine, an aqueous reaction product of the proposed nitrenium ion of PhIP, were recovered during the proteolysis of <i>N</i>-acetoxy-PhIP-modified SA. Some of these SA adduction products of PhIP may be implemented in molecular epidemiology studies to assess the role of well-done cooked meat, PhIP, and the risk of cancer