Using Blockchain Technology for The Organ Procurement and Transplant Network

The organ donation system in the United States is centralized and difficult to audit by the general public. This centralized approach may lead to data integrity issues in the future. The Organ Procurement and Transplant Network (OPTN) was built and maintained by a non-governmental organization called the United Network for Organ Sharing (UNOS) under its proprietary UNet(SM) umbrella platform. This platform is made up of proprietary closed source software and does not provide the general public easy access to the organ transplant data for auditing. This study investigates the feasibility, challenges, and advantages of a blockchain-based OPTN. A prototype of a blockchain-based OPTN was created using the Hyperledger Fabric framework. The policies and guidelines issued by the United States Department of Health and Human Services for UNOS and the OPTN were used as the basis of this prototype. Four factors were identified to have a direct effect on the performance of this system, viz. max batch time out, max block size, endorsement policy, and transaction rate. Additionally, two variants of the blockchain chaincode were also developed. The first variant performed the organ-candidate matching inside the blockchain (Scheme A), and the second variant performed it outside the blockchain (Scheme B). Analysis of these data showed that Scheme A outperformed Scheme B in all experiments for write-operations. However, the read operations remained unaffected by any of the experiment variables in the given environment. Based on these results, it is recommended to perform the organ-candidate matching on the blockchain with the max batch time out close to the transaction rate

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage.

Tissue fibrosis is a major cause of mortality that results from the deposition of matrix proteins by an activated mesenchyme. Macrophages accumulate in fibrosis, but the role of specific subgroups in supporting fibrogenesis has not been investigated in vivo. Here, we used single-cell RNA sequencing (scRNA-seq) to characterize the heterogeneity of macrophages in bleomycin-induced lung fibrosis in mice. A novel computational framework for the annotation of scRNA-seq by reference to bulk transcriptomes (SingleR) enabled the subclustering of macrophages and revealed a disease-associated subgroup with a transitional gene expression profile intermediate between monocyte-derived and alveolar macrophages. These CX3CR1+SiglecF+ transitional macrophages localized to the fibrotic niche and had a profibrotic effect in vivo. Human orthologs of genes expressed by the transitional macrophages were upregulated in samples from patients with idiopathic pulmonary fibrosis. Thus, we have identified a pathological subgroup of transitional macrophages that are required for the fibrotic response to injury

Wochenende — modular and flexible alignment-based shotgun metagenome analysis

Background: Shotgun metagenome analysis provides a robust and verifiable method for comprehensive microbiome analysis of fungal, viral, archaeal and bacterial taxonomy, particularly with regard to visualization of read mapping location, normalization options, growth dynamics and functional gene repertoires. Current read classification tools use non-standard output formats, or do not fully show information on mapping location. As reference datasets are not perfect, portrayal of mapping information is critical for judging results effectively. Results: Our alignment-based pipeline, Wochenende, incorporates flexible quality control, trimming, mapping, various filters and normalization. Results are completely transparent and filters can be adjusted by the user. We observe stringent filtering of mismatches and use of mapping quality sharply reduces the number of false positives. Further modules allow genomic visualization and the calculation of growth rates, as well as integration and subsequent plotting of pipeline results as heatmaps or heat trees. Our novel normalization approach additionally allows calculation of absolute abundance profiles by comparison with reads assigned to the human host genome. Conclusion: Wochenende has the ability to find and filter alignments to all kingdoms of life using both short and long reads, and requires only good quality reference genomes. Wochenende automatically combines multiple available modules ranging from quality control and normalization to taxonomic visualization. Wochenende is available at https://github.com/MHH-RCUG/nf_wochenende

Consistent changes in the intestinal microbiota of Atlantic salmon fed insect meal diets

Background Being part of fish's natural diets, insects have become a practical alternative feed ingredient for aquaculture. While nutritional values of insects have been extensively studied in various fish species, their impact on the fish microbiota remains to be fully explored. In an 8-week freshwater feeding trial, Atlantic salmon (Salmo salar) were fed either a commercially relevant reference diet or an insect meal diet wherein black soldier fly (Hermetia illucens) larvae meal comprised 60% of total ingredients. Microbiota of digesta and mucosa origin from the proximal and distal intestine were collected and profiled along with feed and water samples. Results The insect meal diet markedly modulated the salmon intestinal microbiota. Salmon fed the insect meal diet showed similar or lower alpha-diversity indices in the digesta but higher alpha-diversity indices in the mucosa. A group of bacterial genera, dominated by members of the Bacillaceae family, was enriched in salmon fed the insect meal diet, which confirms our previous findings in a seawater feeding trial. We also found that microbiota in the intestine closely resembled that of the feeds but was distinct from the water microbiota. Notably, bacterial genera associated with the diet effects were also present in the feeds. Conclusions We conclude that salmon fed the insect meal diets show consistent changes in the intestinal microbiota. The next challenge is to evaluate the extent to which these alterations are attributable to feed microbiota and dietary nutrients, and what these changes mean for fish physiology and health.publishedVersio

Innovative Approaches To Identify Regulators Of Liver Regeneration

The mammalian liver possesses a remarkable ability to regenerate after injury to prevent immediate organ failure. However, amid a rising global burden of liver disease, the only curative treatment for patients with end-stage liver disease is transplantation. Elucidating the mechanisms underlying tissue repair and regrowth will enable identification of therapeutic targets to stimulate native liver regeneration, thereby circumventing the great paucity of available transplant organs. Here, utilizing the Fah-/- mouse model of liver repopulation, I applied transcriptomic and epigenomic techniques to investigate the changes occurring as hepatocytes restore organ mass following toxic injury. By labeling ribosomal or nuclear envelope proteins, I performed the first extensive characterization of gene expression and chromatin landscape changes specifically in repopulating hepatocytes in response to injury. Transcriptomic analysis showed that repopulating hepatocytes highly upregulate Slc7a11, a gene that encodes the cystine/glutamate antiporter. I demonstrated that ectopic Slc7a11 expression promotes liver regeneration and Slc7a11 mutation inhibits hepatocyte replication. Integrative bioinformatics analyses of chromatin accessibility revealed dynamic changes at promoters and liver-enriched enhancer regions that correlate with the activation of proliferation-associated genes and the repression of transcripts expressed in mature, quiescent hepatocytes. Furthermore, changes in chromatin accessibility and gene expression are associated with increased promoter binding of CCCTC-binding factor (CTCF) and decreased enhancer occupancy of hepatocyte nuclear factor 4α (HNF4α). In summary, my thesis work identifies Slc7a11 as a potential driver of liver regeneration, and provides insights into the complex crosstalk between chromatin accessibility and transcription factor occupancy to regulate gene expression in repopulating hepatocytes