OrthoList, a compendium of
genes with human orthologs compiled in 2011 by a meta-analysis of four orthology-prediction methods, has been a popular tool for identifying conserved genes for research ...into biological and disease mechanisms. However, the efficacy of orthology prediction depends on the accuracy of gene-model predictions, an ongoing process, and orthology-prediction algorithms have also been updated over time. Here we present OrthoList 2 (OL2), a new comparative genomic analysis between
and humans, and the first assessment of how changes over time affect the landscape of predicted orthologs between two species. Although we find that updates to the orthology-prediction methods significantly changed the landscape of
-human orthologs predicted by individual programs and-unexpectedly-reduced agreement among them, we also show that our meta-analysis approach "buffered" against changes in gene content. We show that adding results from more programs did not lead to many additions to the list and discuss reasons to avoid assigning "scores" based on support by individual orthology-prediction programs; the treatment of "legacy" genes no longer predicted by these programs; and the practical difficulties of updating due to encountering deprecated, changed, or retired gene identifiers. In addition, we consider what other criteria may support claims of orthology and alternative approaches to find potential orthologs that elude identification by these programs. Finally, we created a new web-based tool that allows for rapid searches of OL2 by gene identifiers, protein domains InterPro and SMART (Simple Modular Architecture Research Tool, or human disease associations (OMIM (Online Mendelian Inheritence in Man, and also includes available RNA-interference resources to facilitate potential translational cross-species studies.
Intestinal epithelial cells are subject to attack by a diverse array of microbes, including intracellular as well as extracellular pathogens. While defense in epithelial cells can be triggered by ...pattern recognition receptor-mediated detection of microbe-associated molecular patterns, there is much to be learned about how they sense infection via perturbations of host physiology, which often occur during infection. A recently described host defense response in the nematode C. elegans called the Intracellular Pathogen Response (IPR) can be triggered by infection with diverse natural intracellular pathogens, as well as by perturbations to protein homeostasis. From a forward genetic screen, we identified the C. elegans ortholog of purine nucleoside phosphorylase pnp-1 as a negative regulator of IPR gene expression, as well as a negative regulator of genes induced by extracellular pathogens. Accordingly, pnp-1 mutants have resistance to both intracellular and extracellular pathogens. Metabolomics analysis indicates that C. elegans pnp-1 likely has enzymatic activity similar to its human ortholog, serving to convert purine nucleosides into free bases. Classic genetic studies have shown how mutations in human purine nucleoside phosphorylase cause immunodeficiency due to T-cell dysfunction. Here we show that C. elegans pnp-1 acts in intestinal epithelial cells to regulate defense. Altogether, these results indicate that perturbations in purine metabolism are likely monitored as a cue to promote defense against epithelial infection in the nematode C. elegans.
Immune genes are under intense, pathogen-induced pressure, which causes these genes to diversify over evolutionary time and become species-specific. Through a forward genetic screen we recently ...described a C. elegans-specific gene called pals-22 to be a repressor of "Intracellular Pathogen Response" or IPR genes. Here we describe pals-25, which, like pals-22, is a species-specific gene of unknown biochemical function. We identified pals-25 in a screen for suppression of pals-22 mutant phenotypes and found that mutations in pals-25 suppress all known phenotypes caused by mutations in pals-22. These phenotypes include increased IPR gene expression, thermotolerance, and immunity against natural pathogens, including Nematocida parisii microsporidia and the Orsay virus. Mutations in pals-25 also reverse the reduced lifespan and slowed growth of pals-22 mutants. Transcriptome analysis indicates that pals-22 and pals-25 control expression of genes induced not only by natural pathogens of the intestine, but also by natural pathogens of the epidermis. Indeed, in an independent forward genetic screen we identified pals-22 as a repressor and pals-25 as an activator of epidermal defense gene expression. In summary, the species-specific pals-22 and pals-25 genes act as a switch to regulate a program of gene expression, growth, and defense against diverse natural pathogens in C. elegans.
Six initially equivalent, multipotential Vulval Precursor Cells (VPCs) in
adopt distinct cell fates in a precise spatial pattern, with each fate associated with transcription of different target ...genes. The pattern is centered on a cell that adopts the "1°" fate through Epidermal Growth Factor Receptor (EGFR) activity, and produces a lateral signal composed of ligands that activate LIN-12/Notch in the two flanking VPCs to cause them to adopt "2°" fate. Here, we investigate orthologs of a transcription complex that acts in mammalian EGFR signaling-
/Elk1,
Med23, and the Cdk8 Kinase module (CKM)-previously implicated in aspects of 1° fate in
and show they act in different combinations for different processes for 2° fate. When EGFR is inactive, the CKM, but not SUR-2, helps to set a threshold for LIN-12/Notch activity in all VPCs. When EGFR is active, all three factors act to resist LIN-12/Notch, as revealed by the reduced ability of ectopically-activated LIN-12/Notch to activate target gene reporters. We show that overcoming this resistance in the 1° VPC leads to repression of lateral signal gene reporters, suggesting that resistance to LIN-12/Notch helps ensure that P6.p becomes a robust source of the lateral signal. In addition, we show that
Med23 and
/Elk1, and not the CKM, are required to promote endocytic downregulation of LIN-12-GFP in the 1° VPC. Finally, our analysis using cell fate reporters reveals that both EGFR and LIN-12/Notch signal transduction pathways are active in all VPCs in
/Elk1 mutants, and that
/Elk1 is important for integrating EGFR and
/Notch signaling inputs in the VPCs so that the proper gene complement is transcribed.
During animal development, ligand binding releases the intracellular domain of LIN-12/Notch by proteolytic cleavage to translocate to the nucleus, where it associates with the DNA-binding protein ...LAG-1/CSL to activate target gene transcription. We investigated the spatiotemporal regulation of LAG-1/CSL expression in
and observed that an increase in endogenous LAG-1 levels correlates with LIN-12/Notch activation in different cell contexts during reproductive system development. We show that this increase is via transcriptional upregulation by creating a synthetic endogenous operon, and identified an enhancer region that contains multiple LAG-1 binding sites (LBSs) embedded in a more extensively conserved high occupancy target (HOT) region. We show that these LBSs are necessary for upregulation in response to LIN-12/Notch activity, indicating that
engages in direct positive autoregulation. Deletion of the HOT region from endogenous
reduced LAG-1 levels and abrogated positive autoregulation, but did not cause hallmark cell fate transformations associated with loss of
/
or
activity. Instead, later somatic reproductive system defects suggest that proper transcriptional regulation of
confers robustness to somatic reproductive system development.
Low-temperature cryogenics open the door for a range of interesting technologies based on features like superconductivity and superfluidity, low-temperature phase transitions or the low heat capacity ...of non-metals in the milli-Kelvin range. Devices based on these technologies are often sensitive to small energy depositions as can be caused by environmental radiation. The Cryogenic Underground TEst facility (CUTE) at SNOLAB is a platform for testing and operating cryogenic devices in an environment with low levels of background. The large experimental chamber (
O
(10) L) reaches a base temperature of ∼ 12 mK; it can hold a payload of up to ∼ 20 kg and provides a radiogenic background event rate as low as a few events/kg/keV/day in the energy range below about 100 keV, as well as a negligible muon rate (
O
1)/month). CUTE was designed and built in the context of the Super Cryogenic Dark Matter Search experiment (SuperCDMS) that uses cryogenic detectors to search for interactions of dark matter particles with ordinary matter. The facility has been used to test SuperCDMS detectors since its commissioning in 2019. In 2021, it was handed over to SNOLAB to become a SNOLAB user facility after the completion of the testing of detectors for SuperCDMS. The facility will be available for projects that benefit from these special conditions, based on proposals assessed for their scientific and technological merits. This article describes the main design features and operating parameters of CUTE.
A significant barrier to the success of engineered tissues is the inadequate transport of nutrients and gases to, and waste away from, cells within the constructs, after implantation. Generation of ...microtubular networks by endothelial cells in engineered constructs to mimic the in vivo transport scheme is essential for facilitating tissue survival by promoting the in vitro formation of microvessels that integrate with host microvasculature, after implantation. Previously, we reported that select pressures stimulate endothelial proliferation involving protubulogenic molecules such as fibroblast growth factor-2 (FGF-2) and vascular endothelial growth factor-C (VEGF-C). Based on this, we investigated fluid pressure as a selective modulator of early tubulogenic activity with the intent of assessing the potential utility of this mechanical stimulus as a tissue-engineering control parameter. For this purpose, we used a custom pressure system to expose two-dimensional (2D) and three-dimensional (3D) cultures of endothelial cells to static pressures of 0 (controls), 20, or 40 mmHg for 3 days. Compared to controls, 2D endothelial cultures exposed to 20, but not 40 mmHg, exhibited significantly (p<0.05) enhanced cell growth that depended on VEGF receptor-3 (VEGFR-3), a receptor for VEGF-C. Moreover, endothelial cells grown on microbeads and suspended in 3D collagen gels under 20 mmHg, but not 40 mmHg, displayed significantly (p<0.05) increased sprout formation. Interestingly, pressure-dependent proliferation and sprout formation occurred in parallel with pressure-sensitive upregulation of VEGF-C and VEGFR-3 expression and were sensitive to local FGF-2 levels. Collectively, the results of the present study provided evidence that early endothelial-related tubulogenic activity depends on local hydrostatic pressure levels in the context of local growth factor conditions. In addition to relevance to microvascular diseases associated with interstitial hypertension (e.g., cancer and glaucoma), these findings provided first insight into the potential utility of hydrostatic pressure as a fine-tune control parameter to optimize microvascularization of tissue-engineering constructs in the in vitro setting before their implantation.
Two novel genotypes of species human mastadenovirus D designated 109 and 110 were isolated from three epidemiologically unrelated cases of acute respiratory disease detected in January 2018 by ...surveillance efforts at the California/Mexico border. Both genotypes represent examples of intertypic recombination. Genotype D109 is most closely related to genotype D56 (97.68% genomic similarity) and features a type D22‐like penton base, a type D19‐like hexon gene, and a type D9‐like fiber P22/H19/F9. On the other hand, genotype D110 is most closely related to type D22 (96.94% genomic similarity) and features a type D67‐like penton base, a novel hexon gene, and a type D9‐like fiber P67/H110/F9. Importantly, the fibers of both novel genotypes are highly similar to those of genotypes D56 and D59, which have also been isolated from a few cases of respiratory infections. The present report shows data contributing to the understanding of the molecular determinants of the expanded tissue tropism of certain members of species HAdV‐D.
The Super Cryogenic Dark Matter Search (SuperCDMS) uses germanium and silicon semiconductor detectors to search for dark matter. Particle interactions with these detectors create observable signals ...in the form of phonons and electron-hole pair. We apply a voltage bias across these detectors, utilising the Neganov-Trofimov-Luke (NTL) effect to amplify the charge signal into phonons and search for the rare low-energy depositions of light dark matter. In CDMSlite Run 3, my work on a fiducial volume cut was a primary factor in being able to set at-the-time world-leading dark matter limits for WIMPs in the 1.6 to 5.5 GeV range.The Cryogenic Underground TEst facility (CUTE) is a detector testing facility operated at SNOLAB that has been used to test SuperCDMS detectors. One such de-tector is PD2, which when operated at a surface facility set leading WIMP exclusions. My work operating PD2 at CUTE and exploring the backgrounds and capabilities of CUTE using PD2 and other detectors paves the way for SuperCDMS detector testing at SNOLAB.
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