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M2-lon Channel Specific Chimeric Antibodies as a Universal and Escape Mutant-Resistant Therapeutic for Influenza A
No full textGenetic mapping and characterization of nmf364a, a chemically-induced mutation leading to retinal degeneration
No full textThe objective of this study was to characterize and identify the gene mutated in nmf364a, a heritable chemically-induced inherited recessive mutation leading to retinal degeneration. Fundus imaging and histological analysis revealed progressive loss of photoreceptors (PRs) starting from one month of age, while ultrastructural and immunohistochemical analysis showed shortening of the PR outer segments, an accumulation of extracellular vesicles in the PR inner segments, and mis-localization of rhodopsin present at post-natal day 14 (P14). Genetic mapping localized the gene on mouse chromosome 5 and recombination analysis refined the critical region down to a 12,921,653 bp interval between D5Mit394 at 54,500,177 bp and rs13469874 at 67,421,830 bp. Sanger sequencing of candidate genes within the critical interval identified a point mutation in exon 34 of Wdr19 in nmf364a retinas. Wdr19 is a ciliary gene that encodes IFT144, a protein component of the IFT-A intra-cellular transport complex expressed in photoreceptor cells. In humans, mutations in Wdr19 have been most commonly associated with Senior-Loken syndrome, nephronophthisis, and short-rib thoracic dysplasia. Identification and characterization of this mutant variant of Wdr19 and its association with retinal degeneration without multisystemic involvement highlights the importance of genetic screening of Wdr19 in patients with arRP
Understanding the Growth of Xenografted Tumors
No full textThe prognosis of the same cancer does not have a one treatment fits all. After observing different growth patterns in five genetically diverse mice with subcutaneous engraftments from a triple-negative breast cancer (TNBC) cell line, MDA-MB-231/Luc (MDA), Dr. Muneer Hasham\u27s lab at The Jackson Laboratory published that the genetic background of a mouse determines protein expression of the xenografted neoplastic cells, in respect to growth. As our next step, we will investigate if the resulting tumor growth has changed the neoplastic cells intrinsically, thus producing cells independent of a different tumor microenvironment (TME). We will examine two immunodeficient strains, NOD/ShiltJ Rag1-1 - (NR) and C57BL/6J Rag1-1 - (B6R), by extracting cell line-derived tumors from NR and implanting them in both NR and B6R mice. Conversely, tumors from B6R will be implanted in both NR and B6R mice. Previously, B6R has shown slower tumor growth compared to NR. For this study, it can be hypothesized that tumor growth occurs through adaptation to the TME because it provides enriching nutrients to the neoplastic cells. Therefore, we expect NR mice engrafted with B6R cells to demonstrate fast tumor growth, and B6R mice engrafted with NR cells to demonstrate slow tumor growth. However, results suggest the TME of both mouse strains, also known as a non-conducive and conducive environment, respectively, did not affect how the passaged cells developed (P\u3e0.05). The rationale underlying this investigation is to examine if passaged cancer cells are affected by the TME. This will provide a better understanding to using diverse mouse models and improve early detection therapeutics
Comparing Deleterious Mutation Load Between Classical Inbred Mice and Wild-Caught Mice
No full textInbred strains of the house mouse, Mus musculus, are widely used in biological research for studying human disease (1). However, the extreme inbreeding of these strains raises concerns about the deleterious impact it may have in the genomes. In contrast, wild mice harbor greater genetic variation, making their genomes more representative of human genetic diversity (2-3). The aim of this project is to compare inbred mice genomes with wild-caught mice genomes to assess how their deleterious mutation load differs. We predicted that the inbred strains would have more mildly deleterious variants than wild mice, as the lack of natural selection would allow slightly harmful mutations to accumulate (4). We utilized variant effect predictor tools, calculated allele frequencies, and applied conservation scores to both groups, finding overall support for our prediction. Based on these findings, future research should be conducted to better understand the differences between inbred and wild mice, which would have implications for the use of mice in research and the importance of genetic diversity
Determining function for core and strain specific genes in Staphylococcus epidermidis using CRISPRi
No full textStaphylococcus epidermidis is a bacterium that is ubiquitous to human skin. It plays a vital role in skin health and protection from pathogens but is also an opportunistic pathogen and one of the most common sources of blood borne infections. Different strains of S. epidermidis are genetically diverse, with about 20% of genetic content differing between strains. This diversity makes it difficult to find common genes that make certain S. epidermidis strains virulent. The goal of this project is to understand S. epidermidis’ role in skin health and infection by assessing the essentiality of strain-specific and conserved genes across diverse strains using CRISPR interference (CRISPRi). We screened 48 genetically diverse strains of S. epidermidis using pidCas9. Ten of those strains were candidates for gene targeting as there were sufficient colonies present during the primary screen. We focused on S. epidermidis strain NIHLM031 to conduct growth assays to test for gene essentiality based on differences in guide abundance. This research on S. epidermidis will be used to understand gene function of S. epidermidis strains and why some commensal strains become pathogenic in certain conditions
Spencer Lens Microscope
No full textSpencer Lens Microscope #58, Buffalo, NY. America’s first microscope maker. Used by Dr. Paul Swain from 1947-1965. Displayed in its carrying case with manual, “How to Use and Care for the Microscope.”https://mouseion.jax.org/homepage-images/1003/thumbnail.jp
The DO-KB Knowledgebase: a 20-year journey developing the disease open science ecosystem.
Get PDFIn 2003, the Human Disease Ontology (DO, https://disease-ontology.org/) was established at Northwestern University. In the intervening 20 years, the DO has expanded to become a highly-utilized disease knowledge resource. Serving as the nomenclature and classification standard for human diseases, the DO provides a stable, etiology-based structure integrating mechanistic drivers of human disease. Over the past two decades the DO has grown from a collection of clinical vocabularies, into an expertly curated semantic resource of over 11300 common and rare diseases linking disease concepts through more than 37000 vocabulary cross mappings (v2023-08-08). Here, we introduce the recently launched DO Knowledgebase (DO-KB), which expands the DO\u27s representation of the diseaseome and enhances the findability, accessibility, interoperability and reusability (FAIR) of disease data through a new SPARQL service and new Faceted Search Interface. The DO-KB is an integrated data system, built upon the DO\u27s semantic disease knowledge backbone, with resources that expose and connect the DO\u27s semantic knowledge with disease-related data across Open Linked Data resources. This update includes descriptions of efforts to assess the DO\u27s global impact and improvements to data quality and content, with emphasis on changes in the last two years
Small polymorphisms are a source of ancestral bias in structural variant breakpoint placement.
Get PDFHigh-quality genome assemblies and sophisticated algorithms have increased sensitivity for a wide range of variant types, and breakpoint accuracy for structural variants (SVs, ≥50 bp) has improved to near base pair precision. Despite these advances, many SV breakpoint locations are subject to systematic bias affecting variant representation. To understand why SV breakpoints are inconsistent across samples, we reanalyzed 64 phased haplotypes constructed from long-read assemblies released by the Human Genome Structural Variation Consortium (HGSVC). We identify 882 SV insertions and 180 SV deletions with variable breakpoints not anchored in tandem repeats (TRs) or segmental duplications (SDs). SVs called from aligned sequencing reads increase breakpoint disagreements by 2×-16×. Sequence accuracy had a minimal impact on breakpoints, but we observe a strong effect of ancestry. We confirm that SNP and indel polymorphisms are enriched at shifted breakpoints and are also absent from variant callsets. Breakpoint homology increases the likelihood of imprecise SV calls and the distance they are shifted, and tandem duplications are the most heavily affected SVs. Because graph genome methods normalize SV calls across samples, we investigated graphs generated by two different methods and find the resulting breakpoints are subject to other technical biases affecting breakpoint accuracy. The breakpoint inconsistencies we characterize affect ∼5% of the SVs called in a human genome and can impact variant interpretation and annotation. These limitations underscore a need for algorithm development to improve SV databases, mitigate the impact of ancestry on breakpoints, and increase the value of callsets for investigating breakpoint features
Complex regulatory networks influence pluripotent cell state transitions in human iPSCs.
Get PDFStem cells exist in vitro in a spectrum of interconvertible pluripotent states. Analyzing hundreds of hiPSCs derived from different individuals, we show the proportions of these pluripotent states vary considerably across lines. We discover 13 gene network modules (GNMs) and 13 regulatory network modules (RNMs), which are highly correlated with each other suggesting that the coordinated co-accessibility of regulatory elements in the RNMs likely underlie the coordinated expression of genes in the GNMs. Epigenetic analyses reveal that regulatory networks underlying self-renewal and pluripotency are more complex than previously realized. Genetic analyses identify thousands of regulatory variants that overlapped predicted transcription factor binding sites and are associated with chromatin accessibility in the hiPSCs. We show that the master regulator of pluripotency, the NANOG-OCT4 Complex, and its associated network are significantly enriched for regulatory variants with large effects, suggesting that they play a role in the varying cellular proportions of pluripotency states between hiPSCs. Our work bins tens of thousands of regulatory elements in hiPSCs into discrete regulatory networks, shows that pluripotency and self-renewal processes have a surprising level of regulatory complexity, and suggests that genetic factors may contribute to cell state transitions in human iPSC lines
Astaxanthin and meclizine extend lifespan in UM-HET3 male mice; fisetin, SG1002 (hydrogen sulfide donor), dimethyl fumarate, mycophenolic acid, and 4-phenylbutyrate do not significantly affect lifespan in either sex at the doses and schedules used.
Get PDFIn genetically heterogeneous (UM-HET3) mice produced by the CByB6F1 × C3D2F1 cross, the Nrf2 activator astaxanthin (Asta) extended the median male lifespan by 12% (p = 0.003, log-rank test), while meclizine (Mec), an mTORC1 inhibitor, extended the male lifespan by 8% (p = 0.03). Asta was fed at 1840 ± 520 (9) ppm and Mec at 544 ± 48 (9) ppm, stated as mean ± SE (n) of independent diet preparations. Both were started at 12 months of age. The 90th percentile lifespan for both treatments was extended in absolute value by 6% in males, but neither was significant by the Wang-Allison test. Five other new agents were also tested as follows: fisetin, SG1002 (hydrogen sulfide donor), dimethyl fumarate, mycophenolic acid, and 4-phenylbutyrate. None of these increased lifespan significantly at the dose and method of administration tested in either sex. Amounts of dimethyl fumarate in the diet averaged 35% of the target dose, which may explain the absence of lifespan effects. Body weight was not significantly affected in males by any of the test agents. Late life weights were lower in females fed Asta and Mec, but lifespan was not significantly affected in these females. The male-specific lifespan benefits from Asta and Mec may provide insights into sex-specific aspects of aging