• A novel nonlinear dimension reduction approach to infer population structure for low-coverage sequencing data

      Zhang, M.; Liu, Y.; Zhou, H.; Watkins, J.; Zhou, J.; Interdisciplinary Program in Statistics and Data Science, University of Arizona; Department of Mathematics, University of Arizona; Department of Epidemiology and Biostatistics, University of Arizona (NLM (Medline), 2021)
      BACKGROUND: Low-depth sequencing allows researchers to increase sample size at the expense of lower accuracy. To incorporate uncertainties while maintaining statistical power, we introduce MCPCA_PopGen to analyze population structure of low-depth sequencing data. RESULTS: The method optimizes the choice of nonlinear transformations of dosages to maximize the Ky Fan norm of the covariance matrix. The transformation incorporates the uncertainty in calling between heterozygotes and the common homozygotes for loci having a rare allele and is more linear when both variants are common. CONCLUSIONS: We apply MCPCA_PopGen to samples from two indigenous Siberian populations and reveal hidden population structure accurately using only a single chromosome. The MCPCA_PopGen package is available on https://github.com/yiwenstat/MCPCA_PopGen .
    • An integrative re-evaluation of Typhlatya shrimp within the karst aquifer of the Yucatán Peninsula, Mexico

      Ballou, L.; Brankovits, D.; Chávez-Solís, E.M.; Chávez Díaz, J.M.; Gonzalez, B.C.; Rohret, S.; Salinas, A.; Liu, A.; Simões, N.; Álvarez, F.; et al. (NLM (Medline), 2022)
      The Yucatán Peninsula, Mexico is a carbonate platform well-known for extensive karst networks of densely stratified aquifer ecosystems. This aquifer supports diverse anchialine fauna, including species of the globally distributed anchialine shrimp genus Typhlatya (Atyidae). Four species (T. campecheae, T. pearsei, T. dzilamensis and T. mitchelli) are endemic to the Peninsula, of which three are federally listed in Mexico. This first integrative evaluation (i.e., molecular, morphological, broad geographic and type locality sampling, and environmental data) of Yucatán Typhlatya reveals considerable species identity conflict in prior phylogenetic assessments, broad species ranges, syntopy within cave systems and five genetic lineages (of which two are new to science). Despite sampling from the type locality of endangered T. campecheae, specimens (and molecular data) were indistinguishable from vulnerable T. pearsei. Ancestral/divergence reconstructions support convergent evolution of a low-salinity ancestor for a post-Paleogene arc Yucatán + Cuba Typhlatya clade within the anchialine Atyidae clade. A secondary adaptation for the coastal-restricted euryhaline (2-37 psu), Typhlatya dzilamensis (unknown conservation status) was identified, while remaining species lineages were low-salinity (< 5 psu) adapted and found within the meteoric lens of inland and coastal caves. This study demonstrates the need for integrative/interdisciplinary approaches when conducting biodiversity assessments in complex and poorly studied aquifers. © 2022. The Author(s).
    • Androgen-Binding Protein (Abp) Evolutionary History: Has Positive Selection Caused Fixation of Different Paralogs in Different Taxa of the Genus Mus?

      Karn, R.C.; Yazdanifar, G.; Pezer, Ž.; Boursot, P.; Laukaitis, C.M.; Department of Medicine, College of Medicine, University of Arizona (NLM (Medline), 2021)
      Comparison of the androgen-binding protein (Abp) gene regions of six Mus genomes provides insights into the evolutionary history of this large murid rodent gene family. We identified 206 unique Abp sequences and mapped their physical relationships. At least 48 are duplicated and thus present in more than two identical copies. All six taxa have substantially elevated LINE1 densities in Abp regions compared with flanking regions, similar to levels in mouse and rat genomes, although nonallelic homologous recombination seems to have only occurred in Mus musculus domesticus. Phylogenetic and structural relationships support the hypothesis that the extensive Abp expansion began in an ancestor of the genus Mus. We also found duplicated Abpa27's in two taxa, suggesting that previously reported selection on a27 alleles may have actually detected selection on haplotypes wherein different paralogs were lost in each. Other studies reported that a27 gene and species trees were incongruent, likely because of homoplasy. However, L1MC3 phylogenies, supposed to be homoplasy-free compared with coding regions, support our paralog hypothesis because the L1MC3 phylogeny was congruent with the a27 topology. This paralog hypothesis provides an alternative explanation for the origin of the a27 gene that is suggested to be fixed in the three different subspecies of Mus musculus and to mediate sexual selection and incipient reinforcement between at least two of them. Finally, we ask why there are so many Abp genes, especially given the high frequency of pseudogenes and suggest that relaxed selection operates over a large part of the gene clusters. © The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
    • Asymmetric electron acceptor enables highly luminescent organic solar cells with certified efficiency over 18

      He, C.; Chen, Z.; Wang, T.; Shen, Z.; Li, Y.; Zhou, J.; Yu, J.; Fang, H.; Li, Y.; Li, S.; et al. (NLM (Medline), 2022)
      Enhancing the luminescence property without sacrificing the charge collection is one key to high-performance organic solar cells (OSCs), while limited by the severe non-radiative charge recombination. Here, we demonstrate efficient OSCs with high luminescence via the design and synthesis of an asymmetric non-fullerene acceptor, BO-5Cl. Blending BO-5Cl with the PM6 donor leads to a record-high electroluminescence external quantum efficiency of 0.1%, which results in a low non-radiative voltage loss of 0.178 eV and a power conversion efficiency (PCE) over 15%. Importantly, incorporating BO-5Cl as the third component into a widely-studied donor:acceptor (D:A) blend, PM6:BO-4Cl, allows device displaying a high certified PCE of 18.2%. Our joint experimental and theoretical studies unveil that more diverse D:A interfacial conformations formed by asymmetric acceptor induce optimized blend interfacial energetics, which contributes to the improved device performance via balancing charge generation and recombination. © 2022. The Author(s).
    • Chronic Hypoxia Decreases Endothelial Connexin 40, Attenuates Endothelium-Dependent Hyperpolarization-Mediated Relaxation in Small Distal Pulmonary Arteries, and Leads to Pulmonary Hypertension

      Si, R.; Zhang, Q.; Cabrera, J.T.O.; Zheng, Q.; Tsuji-Hosokawa, A.; Watanabe, M.; Hosokawa, S.; Xiong, M.; Jain, P.P.; Ashton, A.W.; et al. (NLM (Medline), 2020)
      Background Abnormal endothelial function in the lungs is implicated in the development of pulmonary hypertension; however, there is little information about the difference of endothelial function between small distal pulmonary artery (PA) and large proximal PA and their contribution to the development of pulmonary hypertension. Herein, we investigate endothelium-dependent relaxation in different orders of PAs and examine the molecular mechanisms by which chronic hypoxia attenuates endothelium-dependent pulmonary vasodilation, leading to pulmonary hypertension. Methods and Results Endothelium-dependent relaxation in large proximal PAs (second order) was primarily caused by releasing NO from the endothelium, whereas endothelium-dependent hyperpolarization (EDH)-mediated vasodilation was prominent in small distal PAs (fourth-fifth order). Chronic hypoxia abolished EDH-mediated relaxation in small distal PAs without affecting smooth muscle-dependent relaxation. RNA-sequencing data revealed that, among genes related to EDH, the levels of Cx37, Cx40, Cx43, and IK were altered in mouse pulmonary endothelial cells isolated from chronically hypoxic mice in comparison to mouse pulmonary endothelial cells from normoxic control mice. The protein levels were significantly lower for connexin 40 (Cx40) and higher for connexin 37 in mouse pulmonary endothelial cells from hypoxic mice than normoxic mice. Cx40 knockout mice exhibited significant attenuation of EDH-mediated relaxation and marked increase in right ventricular systolic pressure. Interestingly, chronic hypoxia led to a further increase in right ventricular systolic pressure in Cx40 knockout mice without altering EDH-mediated relaxation. Furthermore, overexpression of Cx40 significantly decreased right ventricular systolic pressure in chronically hypoxic mice. Conclusions These data suggest that chronic hypoxia-induced downregulation of endothelial Cx40 results in impaired EDH-mediated relaxation in small distal PAs and contributes to the development of pulmonary hypertension.
    • Determining Progression in Ectatic Corneal Disease

      Belin, M.W.; Alizadeh, R.; Torres-Netto, E.A.; Hafezi, F.; Ambrósio, R., Jr; Pajic, B.; University of Arizona, Department of Ophthalmology & Visual Science (NLM (Medline), 2020)
      Before the advent of modern tomographic imaging and corneal cross-linking (CXL), diagnosis and treatment of ectatic disease were limited to disease severity where changes on the anterior corneal surface lead to visual complaints. Rigid contact lenses and/or penetrating keratoplasty addressed late stage disease, as identifying early or subclinical disease was not possible, or its need appreciated. The emergence of CXL as a viable treatment to alter the natural progression of keratoconus heightened the need for improved diagnostics.Several methods have been described in the literature to evaluate and document progression in keratoconus, but there has been no consistent definition of ectasia progression. Newer imaging techniques (ie, tomography) allowed the detection of earlier ectatic disease, before visual loss and subjective complaints. The Belin ABCD classification/staging system was introduced on a Scheimpflug imaging system [Pentacam, (Oculus GmbH, Wetzlar, Germany)] to address previous shortcomings. The ABCD system utilizes 4 parameters: Anterior ("A") and posterior ("B" for Back) radius of curvature taken from a 3.0 mm optical zone centered on the thinnest point, "C" is minimal Corneal thickness, and "D" best spectacle Distance visual acuity. The first 3 parameters (A, B, C) are machine-generated objective measurements that can be used to determine progressive change.The staging system is not limited to a specific commercial entity and can be incorporated in any tomographic imaging system. The ABCD Progression Display graphically displays each parameter and shows when statistical change above measurement noise is reached. This should allow the clinician the ability to diagnose progressive disease at a much earlier stage than was previously possible, with the confidence that earlier intervention could prevent visual loss.
    • Factors associated with cancer treatment delay: a protocol for a systematic review and meta-analysis

      Morrill, K.E.; Robles-Morales, R.; Lopez-Pentecost, M.; Martínez Portilla, R.J.; Saleh, A.A.; Skiba, M.B.; Riall, T.S.; Austin, J.D.; Hirschey, R.; Jacobs, E.T.; et al. (NLM (Medline), 2022)
      INTRODUCTION: Treatment delays are significantly associated with increased mortality risk among adult cancer patients; however, factors associated with these delays have not been robustly evaluated. This review and meta-analysis will evaluate factors associated with treatment delays among patients with five common cancers. METHODS AND ANALYSIS: Scientific databases including Ovid MEDLINE, Elsevier Embase, EBSCOhost CINAHL Plus Full Text, Elsevier Scopus and ProQuest Dissertations and Theses Global will be searched to identify relevant articles published between January 2000 and October 2021. Research articles published in the USA evaluating factors associated with treatment delay among breast, lung, prostate, cervical or colorectal adult cancer patients will be included. The primary outcome of the meta-analysis will be the pooled adjusted and unadjusted odds of treatment delay for patient, disease, provider and system-level factors defined according to specified time intervals. The secondary outcomes will be mean or median treatment delay for each cancer site according to first treatment and the influence of factors on the pooled mean treatment delay for each cancer site (via meta-regression analyses). Results from qualitative and mixed-methods studies will be narratively synthesised. Three reviewers will independently screen records generated from the search and two reviewers will independently extract data following a consensus agreement. Statistical heterogeneity will be assessed with a standard I2 test and funnel plots will be conducted to evaluate publication bias. Risk of bias will be assessed independently by two authors using validated tools according to the article's study design. ETHICS AND DISSEMINATION: Formal ethical approval is not required because the work is being carried out on publicly accessible studies. The findings of this review will be disseminated through a peer-reviewed scientific journal, academic conferences, social media, and key stakeholders. PROSPERO REGISTRATION NUMBER: CRD42021293131. © Author(s) (or their employer(s)) 2022. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.
    • Further progress in understanding of myofibrillar function in health and disease

      Cremo, C.; Moss, R.L.; Granzier, H.; Cellular and Molecular Medicine, University of Arizona (NLM (Medline), 2021)
    • Genome Evolution in Bacteria Isolated from Million-Year-Old Subseafloor Sediment

      Orsi, W.D.; Magritsch, T.; Vargas, S.; Coskun, ÖK.; Vuillemin, A.; Höhna, S.; Wörheide, G.; D'Hondt, S.; Shapiro, B.J.; Carini, P.; et al. (NLM (Medline), 2021)
      Beneath the seafloor, microbial life subsists in isolation from the surface world under persistent energy limitation. The nature and extent of genomic evolution in subseafloor microbes have been unknown. Here, we show that the genomes of Thalassospira bacterial populations cultured from million-year-old subseafloor sediments evolve in clonal populations by point mutation, with a relatively low rate of homologous recombination and elevated numbers of pseudogenes. Ratios of nonsynonymous to synonymous substitutions correlate with the accumulation of pseudogenes, consistent with a role for genetic drift in the subseafloor strains but not in type strains of Thalassospira isolated from the surface world. Consistent with this, pangenome analysis reveals that the subseafloor bacterial genomes have a significantly lower number of singleton genes than the type strains, indicating a reduction in recent gene acquisitions. Numerous insertion-deletion events and pseudogenes were present in a flagellar operon of the subseafloor bacteria, indicating that motility is nonessential in these million-year-old subseafloor sediments. This genomic evolution in subseafloor clonal populations coincided with a phenotypic difference: all subseafloor isolates have a lower rate of growth under laboratory conditions than the Thalassospira xiamenensis type strain. Our findings demonstrate that the long-term physical isolation of Thalassospira, in the absence of recombination, has resulted in clonal populations whereby reduced access to novel genetic material from neighbors has resulted in the fixation of new mutations that accumulate in genomes over millions of years. IMPORTANCE The nature and extent of genomic evolution in subseafloor microbial populations subsisting for millions of years below the seafloor are unknown. Subseafloor populations have ultralow metabolic rates that are hypothesized to restrict reproduction and, consequently, the spread of new traits. Our findings demonstrate that genomes of cultivated bacterial strains from the genus Thalassospira isolated from million-year-old abyssal sediment exhibit greatly reduced levels of homologous recombination, elevated numbers of pseudogenes, and genome-wide evidence of relaxed purifying selection. These substitutions and pseudogenes are fixed into the population, suggesting that the genome evolution of these bacteria has been dominated by genetic drift. Thus, reduced recombination, stemming from long-term physical isolation, resulted in small clonal populations of Thalassospira that have accumulated mutations in their genomes over millions of years.
    • Genomic population structure associated with repeated escape of Salmonella enterica ATCC14028s from the laboratory into nature

      Achtman, M.; Van den Broeck, F.; Cooper, K.K.; Lemey, P.; Parker, C.T.; Zhou, Z.; ATCC14028s Study, Group; School of Animal and Comparative Biomedical Sciences, University of Arizona (NLM (Medline), 2021)
      Salmonella enterica serovar Typhimurium strain ATCC14028s is commercially available from multiple national type culture collections, and has been widely used since 1960 for quality control of growth media and experiments on fitness ("laboratory evolution"). ATCC14028s has been implicated in multiple cross-contaminations in the laboratory, and has also caused multiple laboratory infections and one known attempt at bioterrorism. According to hierarchical clustering of 3002 core gene sequences, ATCC14028s belongs to HierCC cluster HC20_373 in which most internal branch lengths are only one to three SNPs long. Many natural Typhimurium isolates from humans, domesticated animals and the environment also belong to HC20_373, and their core genomes are almost indistinguishable from those of laboratory strains. These natural isolates have infected humans in Ireland and Taiwan for decades, and are common in the British Isles as well as the Americas. The isolation history of some of the natural isolates confirms the conclusion that they do not represent recent contamination by the laboratory strain, and 10% carry plasmids or bacteriophages which have been acquired in nature by HGT from unrelated bacteria. We propose that ATCC14028s has repeatedly escaped from the laboratory environment into nature via laboratory accidents or infections, but the escaped micro-lineages have only a limited life span. As a result, there is a genetic gap separating HC20_373 from its closest natural relatives due to a divergence between them in the late 19th century followed by repeated extinction events of escaped HC20_373.
    • Hypertension, cholesterol and diabetes medication adherence, health care utilization and expenditure in a Medicare Supplemental sample

      Campbell, P.J.; Axon, D.R.; Taylor, A.M.; Smith, K.; Pickering, M.; Black, H.; Warholak, T.; Chinthammit, C.; University of Arizona College of Pharmacy (NLM (Medline), 2021)
      ABSTRACT: Limited evidence exists regarding the relationships between adherence, as defined in Pharmacy Quality Alliance (PQA) medication adherence measures, health care utilization, and economic outcomes. PQA adherence measures for hypertension, cholesterol, and diabetes are of particular interest given their use in Medicare Star Ratings to evaluate health plan performance.The objective of this study was to assess the relationship between adherence and utilization and cost among Medicare Supplemental beneficiaries included in the aforementioned PQA measures over a 1-year period.Retrospective cohort study.Three cohorts (hypertension, cholesterol, and diabetes) of eligible individuals from the Truven Health MarketScan Commercial Claims and Encounters Research Databases (2009-2015) were used to assess associations between adherence and health care expenditure and utilization for Medicare Supplemental beneficiaries.Generalized linear models with log link and negative binomial (utilization) or gamma (expenditure) distributions assessed relationships between adherence (≥80% proportion of days covered) and health care utilization and expenditure (in 2015 US dollars) while adjusting for confounding variables. Beta coefficients were used to compute cost ratios and rate ratios.Adherence for all 3 disease cohorts was associated with lower outpatient and inpatient visits. During the 1-year study period, adherence was associated with lower outpatient, inpatient, and total expenditures across the cohorts, ranging from 9% lower outpatient costs (diabetes cohort) to 41.9% lower inpatient costs (hypertension cohort). Savings of up to $324.53 per member per month in total expenditure were observed for the hypertension cohort.Our findings indicate adherence is associated with lower health care utilization and expenditures within 1 year. Copyright © 2021 the Author(s). Published by Wolters Kluwer Health, Inc.
    • Independent and Synergistic Effects of Knocking out Two ABC Transporter Genes on Resistance to Bacillus thuringiensis Toxins Cry1Ac and Cry1Fa in Diamondback Moth

      Zhao, S.; Jiang, D.; Wang, F.; Yang, Y.; Tabashnik, B.E.; Wu, Y.; Department of Entomology, University of Arizona (NLM (Medline), 2020)
      Insecticidal proteins from Bacillus thuringiensis (Bt) are used widely in sprays and transgenic crops to control insect pests. However, evolution of resistance by pests can reduce the efficacy of Bt toxins. Here we analyzed resistance to Bt toxins Cry1Ac and Cry1Fa in the diamondback moth (Plutella xylostella), one of the world's most destructive pests of vegetable crops. We used CRISPR/Cas9 gene editing to create strains with knockouts of the ATP-binding cassette (ABC) transporter genes PxABCC2, PxABCC3, or both. Bioassay results show that knocking out either gene alone caused at most 2.9-fold resistance but knocking out both caused >10,320-fold resistance to Cry1Ac and 380-fold resistance to Cry1Fa. Cry1Ac resistance in the double knockout strain was recessive and genetically linked with the PxABCC2/PxABCC3 loci. The results provide insight into the mechanism of cross-resistance to Cry1Fa in diamondback moth. They also confirm previous work with this pest showing that mutations disrupting both genes cause higher resistance to Cry1Ac than mutations affecting either PxABCC2 or PxABCC3 alone. Together with previous work, the results here highlight the value of using single and multiple gene knockouts to better understand the independent and synergistic effects of putative Bt toxin receptors on resistance to Bt toxins.
    • Metabolomic and lipidomic changes triggered by lipopolysaccharide-induced systemic inflammation in transgenic APdE9 mice

      Puris, E.; Kouřil, Š.; Najdekr, L.; Loppi, S.; Korhonen, P.; Kanninen, K.M.; Malm, T.; Koistinaho, J.; Friedecký, D.; Gynther, M.; et al. (NLM (Medline), 2021)
      Peripheral infections followed by systemic inflammation may contribute to the onset of Alzheimer`s disease (AD) and accelerate the disease progression later in life. Yet, the impact of systemic inflammation on the plasma and brain tissue metabolome and lipidome in AD has not been investigated. In this study, targeted metabolomic and untargeted lipidomic profiling experiments were performed on the plasma, cortices, and hippocampi of wild-type (WT) mice and transgenic APdE9 mice after chronic lipopolysaccharide (LPS) treatment, as well as saline-treated APdE9 mice. The lipidome and the metabolome of these mice were compared to saline-treated WT animals. In the brain tissue of all three models, the lipidome was more influenced than the metabolome. The LPS-treated APdE9 mice had the highest number of changes in brain metabolic pathways with significant alterations in levels of lysine, myo-inositol, spermine, phosphocreatine, acylcarnitines and diacylglycerols, which were not observed in the saline-treated APdE9 mice. In the WT mice, the effect of the LPS administration on metabolome and lipidome was negligible. The study provided exciting information about the biochemical perturbations due to LPS-induced inflammation in the transgenic AD model, which can significantly enhance our understanding of the role of systemic inflammation in AD pathogenesis.
    • Muscle ankyrin repeat protein 1 (MARP1) locks titin to the sarcomeric thin filament and is a passive force regulator

      van der Pijl, R.J.; van den Berg, M.; van de Locht, M.; Shen, S.; Bogaards, S.J.P.; Conijn, S.; Langlais, P.; Hooijman, P.E.; Labeit, S.; Heunks, L.M.A.; et al. (NLM (Medline), 2021)
      Muscle ankyrin repeat protein 1 (MARP1) is frequently up-regulated in stressed muscle, but its effect on skeletal muscle function is poorly understood. Here, we focused on its interaction with the titin-N2A element, found in titin's molecular spring region. We show that MARP1 binds to F-actin, and that this interaction is stronger when MARP1 forms a complex with titin-N2A. Mechanics and super-resolution microscopy revealed that MARP1 "locks" titin-N2A to the sarcomeric thin filament, causing increased extension of titin's elastic PEVK element and, importantly, increased passive force. In support of this mechanism, removal of thin filaments abolished the effect of MARP1 on passive force. The clinical relevance of this mechanism was established in diaphragm myofibers of mechanically ventilated rats and of critically ill patients. Thus, MARP1 regulates passive force by locking titin to the thin filament. We propose that in stressed muscle, this mechanism protects the sarcomere from mechanical damage. © 2021 van der Pijl et al.
    • NCBI's Virus Discovery Codeathon: Building "FIVE" -The Federated Index of Viral Experiments API Index

      Martí-Carreras, J.; Gener, A.R.; Miller, S.D.; Brito, A.F.; Camacho, C.E.; Connor, R.; Deboutte, W.; Glickman, C.; Kristensen, D.M.; Meyer, W.K.; et al. (NLM (Medline), 2020)
      Viruses represent important test cases for data federation due to their genome size and the rapid increase in sequence data in publicly available databases. However, some consequences of previously decentralized (unfederated) data are lack of consensus or comparisons between feature annotations. Unifying or displaying alternative annotations should be a priority both for communities with robust entry representation and for nascent communities with burgeoning data sources. To this end, during this three-day continuation of the Virus Hunting Toolkit codeathon series (VHT-2), a new integrated and federated viral index was elaborated. This Federated Index of Viral Experiments (FIVE) integrates pre-existing and novel functional and taxonomy annotations and virus-host pairings. Variability in the context of viral genomic diversity is often overlooked in virus databases. As a proof-of-concept, FIVE was the first attempt to include viral genome variation for HIV, the most well-studied human pathogen, through viral genome diversity graphs. As per the publication of this manuscript, FIVE is the first implementation of a virus-specific federated index of such scope. FIVE is coded in BigQuery for optimal access of large quantities of data and is publicly accessible. Many projects of database or index federation fail to provide easier alternatives to access or query information. To this end, a Python API query system was developed to enhance the accessibility of FIVE.
    • Network analysis reveals dysregulated functional patterns in type II diabetic skin

      Liu, C.; Ram, S.; Hurwitz, B.L.; Department of Biosystems Engineering, BIO5 Institute, University of Arizona; Department of Management Information Systems, BIO5 Institute, University of Arizona (NLM (Medline), 2022)
      Skin disorders are one of the most common complications of type II diabetes (T2DM). Long-term effects of high blood glucose leave individuals with T2DM more susceptible to cutaneous diseases, but its underlying molecular mechanisms are unclear. Network-based methods consider the complex interactions between genes which can complement the analysis of single genes in previous research. Here, we use network analysis and topological properties to systematically investigate dysregulated gene co-expression patterns in type II diabetic skin with skin samples from the Genotype-Tissue Expression database. Our final network consisted of 8812 genes from 73 subjects with T2DM and 147 non-T2DM subjects matched for age, sex, and race. Two gene modules significantly related to T2DM were functionally enriched in the pathway lipid metabolism, activated by PPARA and SREBF (SREBP). Transcription factors KLF10, KLF4, SP1, and microRNA-21 were predicted to be important regulators of gene expression in these modules. Intramodular analysis and betweenness centrality identified NCOA6 as the hub gene while KHSRP and SIN3B are key coordinators that influence molecular activities differently between T2DM and non-T2DM populations. We built a TF-miRNA-mRNA regulatory network to reveal the novel mechanism (miR-21-PPARA-NCOA6) of dysregulated keratinocyte proliferation, differentiation, and migration in diabetic skin, which may provide new insights into the susceptibility of skin disorders in T2DM patients. Hub genes and key coordinators may serve as therapeutic targets to improve diabetic skincare. © 2022. The Author(s).
    • New Consideration for Old Conditions

      Jeng, B.H.; Belin, M.W.; Department of Ophthalmology and Vision Science, University of Arizona (NLM (Medline), 2020)
    • New World Cactaceae Plants Harbor Diverse Geminiviruses

      Fontenele, R.S.; Salywon, A.M.; Majure, L.C.; Cobb, I.N.; Bhaskara, A.; Avalos-Calleros, J.A.; Argüello-Astorga, G.R.; Schmidlin, K.; Khalifeh, A.; Smith, K.; et al. (NLM (Medline), 2021)
      The family Cactaceae comprises a diverse group of typically succulent plants that are native to the American continent but have been introduced to nearly all other continents, predominantly for ornamental purposes. Despite their economic, cultural, and ecological importance, very little research has been conducted on the viral community that infects them. We previously identified a highly divergent geminivirus that is the first known to infect cacti. Recent research efforts in non-cultivated and asymptomatic plants have shown that the diversity of this viral family has been under-sampled. As a consequence, little is known about the effects and interactions of geminiviruses in many plants, such as cacti. With the objective to expand knowledge on the diversity of geminiviruses infecting cacti, we used previously acquired high-throughput sequencing results to search for viral sequences using BLASTx against a viral RefSeq protein database. We identified two additional sequences with similarity to geminiviruses, for which we designed abutting primers and recovered full-length genomes. From 42 cacti and five scale insects, we derived 42 complete genome sequences of a novel geminivirus species that we have tentatively named Opuntia virus 2 (OpV2) and 32 genomes of an Opuntia-infecting becurtovirus (which is a new strain of the spinach curly top Arizona virus species). Interspecies recombination analysis of the OpV2 group revealed several recombinant regions, in some cases spanning half of the genome. Phylogenetic analysis demonstrated that OpV2 is a novel geminivirus more closely related to viruses of the genus Curtovirus, which was further supported by the detection of three recombination events between curtoviruses and OpV2. Both OpV2 and Opuntia becurtoviruses were identified in mixed infections, which also included the previously characterized Opuntia virus 1. Viral quantification of the co-infected cactus plants compared with single infections did not show any clear trend in viral dynamics that might be associated with the mixed infections. Using experimental Rhizobium-mediated inoculations, we found that the initial accumulation of OpV2 is facilitated by co-infection with OpV1. This study shows that the diversity of geminiviruses that infect cacti is under-sampled and that cacti harbor diverse geminiviruses. The detection of the Opuntia becurtoviruses suggests spill-over events between viruses of cultivated species and native vegetation. The threat this poses to cacti needs to be further investigated.
    • Pediatric Emergency Medicine Didactics and Simulation (PEMDAS) Telesimulation Series: Hyperleukocytosis

      Koff, A.; Burns, R.; Auerbach, M.; Lee, B.; Pearce, J.; Ciener, D.; Augenstein, J.; Yeung, C.; Thomas, A.; University of Arizona College of Medicine (NLM (Medline), 2021)
      Introduction: Hyperleukocytosis, an infrequent presentation of new-onset leukemia, is a medical emergency requiring prompt recognition and treatment. It can include altered mental status, fever, critical electrolyte derangements, and coagulopathies. Due to the COVID-19 pandemic, this simulation was created as a telesimulation in order to adhere to mandatory physical distancing guidelines while addressing learning objectives. Methods: This simulation was designed for pediatric emergency medicine fellows and featured a pediatric patient presenting with fever, altered mental status, and respiratory distress. After an initial assessment and appropriate workup, the patient developed tumor lysis syndrome, coagulopathies, and new-onset neurologic changes requiring appropriate interventions. A debriefing guide and participant evaluation form were utilized. Results: This telesimulation was implemented at five different institutions, with evaluation surveys completed by 22 pediatric emergency medicine fellows. The scenario was rated on a 5-point Likert scale (1 = strongly disagree, 5 = strongly agree) and was generally well received, with participants rating the simulation as effective in teaching the recognition (M = 4.8) and management (M = 4.6) of hyperleukocytosis. Participants felt that virtual telesimulation was effective compared to other distance learning methods (M = 3.9). Discussion: This simulation-based curriculum allows learners to practice identifying and managing hyperleukocytosis. We found that it was well received in both in-person and virtual formats. © 2021 Koff et al.
    • Plastome Structural Evolution and Homoplastic Inversions in Neo-Astragalus (Fabaceae)

      Charboneau, J.L.M.; Cronn, R.C.; Liston, A.; Wojciechowski, M.F.; Sanderson, M.J.; Department of Ecology and Evolutionary Biology, University of Arizona (NLM (Medline), 2021)
      The plastid genomes of photosynthetic green plants have largely maintained conserved gene content and order as well as structure over hundreds of millions of years of evolution. Several plant lineages, however, have departed from this conservation and contain many plastome structural rearrangements, which have been associated with an abundance of repeated sequences both overall and near rearrangement endpoints. We sequenced the plastomes of 25 taxa of Astragalus L. (Fabaceae), a large genus in the inverted repeat-lacking clade of legumes, to gain a greater understanding of the connection between repeats and plastome inversions. We found plastome repeat structure has a strong phylogenetic signal among these closely related taxa mostly in the New World clade of Astragalus called Neo-Astragalus. Taxa without inversions also do not differ substantially in their overall repeat structure from four taxa each with one large-scale inversion. For two taxa with inversion endpoints between the same pairs of genes, differences in their exact endpoints indicate the inversions occurred independently. Our proposed mechanism for inversion formation suggests the short inverted repeats now found near the endpoints of the four inversions may be there as a result of these inversions rather than their cause. The longer inverted repeats now near endpoints may have allowed the inversions first mediated by shorter microhomologous sequences to propagate, something that should be considered in explaining how any plastome rearrangement becomes fixed regardless of the mechanism of initial formation. © The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.