Recent Submissions

  • A multiplex qPCR approach for detection of pfhrp2 and pfhrp3 gene deletions in multiple strain infections of Plasmodium falciparum

    Schindler, T.; Deal A.C.; Moser, K.A. (Nature Publishing Group, 2019)
    The rapid and accurate diagnosis of Plasmodium falciparum malaria infection is an essential factor in malaria control. Currently, malaria diagnosis in the field depends heavily on using rapid diagnostic tests (RDTs) many of which detect circulating parasite-derived histidine-rich protein 2 antigen (PfHRP2) in capillary blood. P. falciparum strains lacking PfHRP2, due to pfhrp2 gene deletions, are an emerging threat to malaria control programs. The novel assay described here, named qHRP2/3-del, is well suited for high-throughput screening of P. falciparum isolates to identify these gene deletions. The qHRP2/3-del assay identified pfhrp2 and pfhrp3 deletion status correctly in 93.4% of samples with parasitemia levels higher than 5 parasites/µL when compared to nested PCR. The qHRP2/3-del assay can correctly identify pfhrp2 and pfhrp3 gene deletions in multiple strain co-infections, particularly prevalent in Sub-Saharan countries. Deployment of this qHRP2/3-del assay will provide rapid insight into the prevalence and potential spread of P. falciparum isolates that escape surveillance by RDTs.
  • Increased overall and bacterial infections following myeloablative allogeneic HCT for patients with AML in CR1

    Ustun, C.; Kim, S.; Yared, J.A. (American Society of Hematology, 2019)
    Presumably, reduced-intensity/nonmyeloablative conditioning (RIC/NMA) for allogeneic hematopoietic cell transplantation (alloHCT) results in reduced infections compared with myeloablative conditioning (MAC) regimens; however, published evidence is limited. In this Center for International Blood and Marrow Transplant Research study, 1755 patients (aged ≥40 years) with acute myeloid leukemia in first complete remission were evaluated for infections occurring within 100 days after T-cell replete alloHCT. Patients receiving RIC/NMA (n = 777) compared with those receiving MAC (n = 978) were older and underwent transplantation more recently; however, the groups were similar regarding Karnofsky performance score, HCT-comorbidity index, and cytogenetic risk. One or more infections occurred in 1045 (59.5%) patients (MAC, 595 [61%]; RIC/NMA, 450 [58%]; P = .21) by day 100. The median time to initial infection after MAC conditioning occurred earlier (MAC, 15 days [range, <1-99 days]; RIC/NMA, 21 days [range, <1-100 days]; P < .001). Patients receivingMAC were more likely to experience at least 1 bacterial infection by day 100 (MAC, 46% [95% confidence interval (CI), 43-49]; RIC/NMA, 37% [95% CI, 34-41]; P = .0004), whereas at least a single viral infection was more prevalent in the RIC/NMA cohort (MAC, 34% [95% CI, 31-37]; RIC/NMA, 39% [95%CI, 36-42]; P5.046). MAC remained a risk factor for bacterial infections in multivariable analysis (relative risk, 1.44; 95% CI, 1.23-1.67; P < .0001). Moreover, the rate of any infection per patient-days at risk in the first 100 days (infection density) after alloHCTwas greater for the MAC cohort (1.21; 95% CI, 1.11-1.32; P < .0001). RIC/NMA was associated with reduced infections, especially bacterial infections, in the first 100 days after alloHCT.
  • Genome-wide association meta-analyses and fine-mapping elucidate pathways influencing albuminuria

    Connell, J.O; Ryan, K.A; Parsa, A. (Nature Publishing Group, 2019)
    Increased levels of the urinary albumin-to-creatinine ratio (UACR) are associated with higher risk of kidney disease progression and cardiovascular events, but underlying mechanisms are incompletely understood. Here, we conduct trans-ethnic (n = 564,257) and European-ancestry specific meta-analyses of genome-wide association studies of UACR, including ancestry- and diabetes-specific analyses, and identify 68 UACR-associated loci. Genetic correlation analyses and risk score associations in an independent electronic medical records database (n = 192,868) reveal connections with proteinuria, hyperlipidemia, gout, and hypertension. Fine-mapping and trans-Omics analyses with gene expression in 47 tissues and plasma protein levels implicate genes potentially operating through differential expression in kidney (including TGFB1, MUC1, PRKCI, and OAF), and allow coupling of UACR associations to altered plasma OAF concentrations. Knockdown of OAF and PRKCI orthologs in Drosophila nephrocytes reduces albumin endocytosis. Silencing fly PRKCI further impairs slit diaphragm formation. These results generate a priority list of genes and pathways for translational research to reduce albuminuria.
  • Ciliary exclusion of Polycystin-2 promotes kidney cystogenesis in an autosomal dominant polycystic kidney disease model

    Walker, R.V.; Keynton, J.L.; Grimes, D.T. (Nature Publishing Group, 2019)
    The human PKD2 locus encodes Polycystin-2 (PC2), a TRPP channel that localises to several distinct cellular compartments, including the cilium. PKD2 mutations cause Autosomal Dominant Polycystic Kidney Disease (ADPKD) and affect many cellular pathways. Data underlining the importance of ciliary PC2 localisation in preventing PKD are limited because PC2 function is ablated throughout the cell in existing model systems. Here, we dissect the ciliary role of PC2 by analysing mice carrying a non-ciliary localising, yet channel-functional, PC2 mutation. Mutants develop embryonic renal cysts that appear indistinguishable from mice completely lacking PC2. Despite not entering the cilium in mutant cells, mutant PC2 accumulates at the ciliary base, forming a ring pattern consistent with distal appendage localisation. This suggests a two-step model of ciliary entry; PC2 first traffics to the cilium base before TOP domain dependent entry. Our results suggest that PC2 localisation to the cilium is necessary to prevent PKD. Copyright 2019, The Author(s).
  • Human genome-edited hematopoietic stem cells phenotypically correct Mucopolysaccharidosis type I

    Gomez-Ospina, N.; Scharenberg, S.G.; Aurelian, L. (Nature Publishing Group, 2019)
    Lysosomal enzyme deficiencies comprise a large group of genetic disorders that generally lack effective treatments. A potential treatment approach is to engineer the patient’s own hematopoietic system to express high levels of the deficient enzyme, thereby correcting the biochemical defect and halting disease progression. Here, we present an efficient ex vivo genome editing approach using CRISPR-Cas9 that targets the lysosomal enzyme iduronidase to the CCR5 safe harbor locus in human CD34+ hematopoietic stem and progenitor cells. The modified cells secrete supra-endogenous enzyme levels, maintain long-term repopulation and multi-lineage differentiation potential, and can improve biochemical and phenotypic abnormalities in an immunocompromised mouse model of Mucopolysaccharidosis type I. These studies provide support for the development of genome-edited CD34+ hematopoietic stem and progenitor cells as a potential treatment for Mucopolysaccharidosis type I. The safe harbor approach constitutes a flexible platform for the expression of lysosomal enzymes making it applicable to other lysosomal storage disorders. Copyright 2019, The Author(s).
  • Emergency Declarations for Public Health Issues: Expanding Our Definition of Emergency

    Sunshine, G.; Barrera N.; Corcoran A.J.; Penn, M. (SAGE Publications Inc., 2019)
    Emergency declarations are a vital legal authority that can activate funds, personnel, and material and change the legal landscape to aid in the response to a public health threat. Traditionally, declarations have been used against immediate and unforeseen threats such as hurricanes, tornadoes, wildfires, and pandemic influenza. Recently, however, states have used emergency declarations to address public health issues that have existed in communities for months and years and have risk factors such as poverty and substance misuse. Leaders in these states have chosen to use emergency powers that are normally reserved for sudden catastrophes to address these enduring public health issues. This article will explore emergency declarations as a legal mechanism for response; describe recent declarations to address hepatitis A and the opioid overdose epidemic; and seek to answer the question of whether it is appropriate to use emergency powers to address public health issues that are not traditionally the basis for an emergency declaration.
  • Development of a multiple-antigen protein fusion vaccine candidate that confers protection against Bacillus anthracis and Yersinia pestis

    Gallagher, T.B.; Mellado-Sanchez, G.; Jorgensen, A.L.; Moore, S.; Pasetti, M.F. (Public Library of Science, 2019)
    Bacillus anthracis and Yersinia pestis are zoonotic bacteria capable of causing severe and sometimes fatal infections in animals and humans. Although considered as diseases of antiquity in industrialized countries due to animal and public health improvements, they remain endemic in vast regions of the world disproportionally affecting the poor. These pathogens also remain a serious threat if deployed in biological warfare. A single vaccine capable of stimulating rapid protection against both pathogens would be an extremely advantageous public health tool. We produced multiple-antigen fusion proteins (MaF1 and MaF2) containing protective regions from B. anthracis protective antigen (PA) and lethal factor (LF), and from Y. pestis V antigen (LcrV) and fraction 1 (F1) capsule. The MaF2 sequence was also expressed from a plasmid construct (pDNA-MaF2). Immunogenicity and protective efficacy were investigated in mice following homologous and heterologous prime-boost immunization. Antibody responses were determined by ELISA and anthrax toxin neutralization assay. Vaccine efficacy was determined against lethal challenge with either anthrax toxin or Y. pestis. Both constructs elicited LcrV and LF-specific serum IgG, and MaF2 elicited toxin-neutralizing antibodies. Immunizations with MaF2 conferred 100% and 88% protection against Y. pestis and anthrax toxin, respectively. In contrast, pDNA-MaF2 conferred only 63% protection against Y. pestis and no protection against anthrax toxin challenge. pDNA-MaF2-prime MaF2-boost induced 75% protection against Y. pestis and 25% protection against anthrax toxin. Protection was increased by the molecular adjuvant CARDif. In conclusion, MaF2 is a promising multi-antigen vaccine candidate against anthrax and plague that warrants further investigation.
  • White matter disturbances in major depressive disorder: a coordinated analysis across 20 international cohorts in the ENIGMA MDD working group

    van, Velzen, L.S.; Kelly, S.; Kochunov, P (Nature Publishing Group, 2019)
    Alterations in white matter (WM) microstructure have been implicated in the pathophysiology of major depressive disorder (MDD). However, previous findings have been inconsistent, partially due to low statistical power and the heterogeneity of depression. In the largest multi-site study to date, we examined WM anisotropy and diffusivity in 1305 MDD patients and 1602 healthy controls (age range 12–88 years) from 20 samples worldwide, which included both adults and adolescents, within the MDD Working Group of the Enhancing Neuroimaging Genetics through Meta-Analysis (ENIGMA) consortium. Processing of diffusion tensor imaging (DTI) data and statistical analyses were harmonized across sites and effects were meta-analyzed across studies. We observed subtle, but widespread, lower fractional anisotropy (FA) in adult MDD patients compared with controls in 16 out of 25 WM tracts of interest (Cohen’s d between 0.12 and 0.26). The largest differences were observed in the corpus callosum and corona radiata. Widespread higher radial diffusivity (RD) was also observed (all Cohen’s d between 0.12 and 0.18). Findings appeared to be driven by patients with recurrent MDD and an adult age of onset of depression. White matter microstructural differences in a smaller sample of adolescent MDD patients and controls did not survive correction for multiple testing. In this coordinated and harmonized multisite DTI study, we showed subtle, but widespread differences in WM microstructure in adult MDD, which may suggest structural disconnectivity in MDD. Copyright 2019, The Author(s).
  • STUB1 suppresseses tumorigenesis and chemoresistance through antagonizing YAP1 signaling

    Tang, D.-E.; Dai, Y.,Xu, S.-H. (Blackwell Publishing Ltd, 2019)
    Yes-associated protein (YAP) is a component of the canonical Hippo signaling pathway that is known to play essential roles in modulating organ size, development, and tumorigenesis. Activation or upregulation of YAP1, which contributes to cancer cell survival and chemoresistance, has been verified in different types of human cancers. However, the molecular mechanism of YAP1 upregulation in cancer is still unclear. Here we report that the E3 ubiquitin ligase STUB1 ubiquitinates and destabilizes YAP1, thereby inhibiting cancer cell survival. Low levels of STUB1 expression were correlated with increased protein levels of YAP1 in human gastric cancer cell lines and patient samples. Moreover, we revealed that STUB1 ubiquitinates YAP1 at the K280 site by K48-linked polyubiquitination, which in turn increases YAP1 turnover and promotes cellular chemosensitivity. Overall, our study establishes YAP1 ubiquitination and degradation mediated by the E3 ligase STUB1 as an important regulatory mechanism in gastric cancer, and provides a rationale for potential therapeutic interventions. Copyright 2019 The Authors.
  • Comparison of two rotary systems in bacteria/lps removal from endodontic infections: randomized clinical trial

    Machado, C.A.D.; Souza, A.C.A.; Martinho, F.C. (The Scientific Electronic Library Online, 2019)
    This clinical study compared the effectiveness of two rotary systems: HyFlex CM (Coltene-Whaledent, Altstetten, Switzerland) and ProTaper Next (Dentsply Sirona, Ballaigues, Switzerland) on the removal of cultivable bacteria and endotoxins from primarily infected root canals. This study was designed as a randomized single-blinded, 2-arm, clinical trial. Twenty-four primarily infected root canals were selected and randomly divided into 2 groups: HyFlex CM (n = 12); and ProTaper Next (n = 12). Samples were collected before and after the biomechanical preparation and inoculated in specific flasks. Irrigation was performed using 2.5% sodium hypochlorite. A kinetic turbidimetric lysate assay of limulus amoebocytes was used to quantify endotoxins. Microbiological culture technique was used to determine the count of bacterial colony forming units (CFU/mL). Data collected were statistically analyzed using SigmaPlot 12.0 for Windows. The Two-Way ANOVA statistical test was performed and the level of significance was 5%. In the samples before the biomechanical preparation, cultivable bacteria and endotoxins were evidenced in 100% of the cases. The culture analysis revealed that there was no statistically significant difference in the bacterial reduction between the two instrumentation systems. Endotoxins were present in 100% of the canals after instrumentation and there was no statistical difference between the two systems in endotoxin reduction. Thus, it was concluded that both instrumentation systems were effective in reducing root canal bacteria and endotoxins with primary endodontic infection and that there was no statistical difference between them. However, no system was able to eliminate 100% of the bacteria and their by-products.
  • An Innovative Disease-Drug-Trial Framework to Guide Binge Eating Disorder Drug Development: A Case Study for Topiramate

    Kalaria, S.N.; Gobburu, J.; Gopalakrishnan, M. (Blackwell Publishing Ltd, 2019)
    As with other psychiatric disorders, development of drugs to treat binge-eating disorder (BED) has been hampered by high placebo response and dropout rates in randomized controlled trials (RCTs). Although not approved for use in BED, several RCTs have suggested that topiramate is efficacious for BED in obese individuals. Using data from a positive investigator-initiated RCT of topiramate in 61 obese individuals with BED, the objective of the present study is (i) to develop a quantitative disease-drug-trial framework to inform future BED clinical trial designs, and (ii) to determine the optimal topiramate dose to achieve therapeutic efficacy. Disease-drug-trial models were developed separately for the two efficacy measures, namely, longitudinal normalized weekly binge-eating episode frequency (BEF) and binge day frequency (BDF). Model building consisted of (i) developing a placebo effect model that describes response from the placebo group, (ii) adding a drug effect to the placebo model to describe dose-response relationships, and (iii) developing a parametric time to event model to characterize patient dropout patterns. The placebo effect on normalized BEF and BDF over time demonstrated a maximum decrease of ~ 57% by 5 weeks. Participants had a higher dropout probability if no weight loss occurred during the trial period. The identified dose-response relationship demonstrated a daily dose of 125 mg was needed to exhibit a marked reduction in weekly BEF. The developed comprehensive disease-drug-trial model will be utilized to simulate different clinical trial designs to increase the success for future BED drug development programs. Copyright 2019 The Authors.
  • The Reply

    El, Chaer, F.; El, Sahly, H.M. (Elsevier Inc., 2019)
  • Clarin-2 is essential for hearing by maintaining stereocilia integrity and function

    Dunbar, L.A.; Patni, P.; Hertzano, R. (Blackwell Publishing Ltd, 2019)
    Hearing relies on mechanically gated ion channels present in the actin-rich stereocilia bundles at the apical surface of cochlear hair cells. Our knowledge of the mechanisms underlying the formation and maintenance of the sound-receptive structure is limited. Utilizing a large-scale forward genetic screen in mice, genome mapping and gene complementation tests, we identified Clrn2 as a new deafness gene. The Clrn2clarinet/clarinet mice (p.Trp4* mutation) exhibit a progressive, early-onset hearing loss, with no overt retinal deficits. Utilizing data from the UK Biobank study, we could show that CLRN2 is involved in human non-syndromic progressive hearing loss. Our in-depth morphological, molecular and functional investigations establish that while it is not required for initial formation of cochlear sensory hair cell stereocilia bundles, clarin-2 is critical for maintaining normal bundle integrity and functioning. In the differentiating hair bundles, lack of clarin-2 leads to loss of mechano-electrical transduction, followed by selective progressive loss of the transducing stereocilia. Together, our findings demonstrate a key role for clarin-2 in mammalian hearing, providing insights into the interplay between mechano-electrical transduction and stereocilia maintenance. Copyright 2019 The Authors.
  • Contribution of Functional Antimalarial Immunity to Measures of Parasite Clearance in Therapeutic Efficacy Studies of Artemisinin Derivatives

    O'Flaherty, K.; Ata�de; R.; Dhorda, M. (Oxford Academic, 2019)
    BACKGROUND: Antibodies to the blood stages of malaria parasites enhance parasite clearance and antimalarial efficacy. The antibody subclass and functions that contribute to parasite clearance during antimalarial treatment and their relationship to malaria transmission intensity have not been characterized. METHODS: Levels of immunoglobulin G (IgG) subclasses and C1q fixation in response to Plasmodium falciparum merozoite antigens (erythrocyte-binding antigen [EBA] 175RIII-V, merozoite surface protein 2 [MSP-2], and MSP-142) and opsonic phagocytosis of merozoites were measured in a multinational trial assessing the efficacy of artesunate therapy across 11 Southeast Asian sites. Regression analyses assessed the effects of antibody seropositivity on the parasite clearance half-life (PC½), having a PC½ of ≥5 hours, and having parasitemia 3 days after treatment. RESULTS: IgG3, followed by IgG1, was the predominant IgG subclass detected (seroprevalence range, 5%-35% for IgG1 and 27%-41% for IgG3), varied across study sites, and was lowest in study sites with the lowest transmission intensity and slowest mean PC½. IgG3, C1q fixation, and opsonic-phagocytosis seropositivity were associated with a faster PC½ (range of the mean reduction in PC½, 0.47-1.16 hours; P range, .001-.03) and a reduced odds of having a PC½ of ≥5 hours and having parasitemia 3 days after treatment. CONCLUSIONS: The prevalence of IgG3, complement-fixing antibodies, and merozoite phagocytosis vary according to transmission intensity, are associated with faster parasite clearance, and may be sensitive surrogates of an augmented clearance capacity of infected erythrocytes. Determining the functional immune mechanisms associated with parasite clearance will improve characterization of artemisinin resistance. Copyright The Author(s) 2019.
  • Future-proofing your microbiology resource announcements genome assembly for reproducibility and clarity

    Baltrus, D.A.; Cuomo, C.A.; Dunning, Hotopp, J.C. (American Society for Microbiology, 2019)
    Descriptions of resources, like the genome assemblies reported in Microbiology Resource Announcements, are often frozen at their time of publication, yet they will need to be interpreted in the midst of continually evolving technologies. It is therefore important to ensure that researchers accessing published resources have access to all of the information required to repeat, interpret, and extend these original analyses. Here, we provide a set of suggestions to help make certain that published resources remain useful and repeatable for the foreseeable future. Copyright 2019 Baltrus et al.
  • Ideology and Scientific Progress: First-Rank Symptoms

    Carpenter, W.T.; Strauss, J.S. (Oxford Academic, 2019)
  • An asymmetry that leads to activity

    Varney, K.M.; Cook, M.E.; Weber, D.J. (PNAS, 2019)
  • Renal effects of sodium-glucose cotransporter-2 inhibitors in patients with type 2 diabetes and renal impairment

    Weir, M.R. (Taylor and Francis Inc., 2019)
    In patients with type 2 diabetes (T2D), microvascular changes in the kidney often result in diabetic kidney disease (DKD), the progression of which is associated with an increased risk of cardiovascular (CV) and all-cause mortality. Sodium-glucose cotransporter-2 inhibitors (SGLT-2is) are a newer class of oral glucose-lowering therapies that were associated with significant reductions in the risk of major adverse CV events, CV death, and hospitalization for heart failure compared with placebo in CV outcomes trials (CVOTs) of patients with T2D and established CV disease or varying levels of CV risk. In addition, SGLT-2is reduced the risks of clinically relevant renal outcomes in these large randomized studies, indicating the potential for renoprotective effects in patients with T2D and DKD. This review discussed the non-glycemic effects of SGLT-2is in patients with T2D and renal impairment, including reductions in systolic and diastolic blood pressure, decreases in albuminuria and plasma uric acid, changes in estimated glomerular filtration rate, and minimal changes in electrolytes. Potential mechanisms for the renoprotective effects of SGLT-2is observed in CVOTs were considered, including the likely incremental benefits of SGLT-2is when added to renin-aldosterone-angiotensin system inhibitors (RAASis). The possibility of extending the use of SGLT-2is to patients with non-DKD was also discussed. Although the exact mechanisms by which SGLT-2is improve renal outcomes are not fully understood, they are likely to be multifactorial and additive when these drugs are used in combination with RAASis in patients with DKD. Copyright 2019 The Author(s).
  • Rehabilitation After Hip Fracture for Nursing Home Residents: A Controlled Feasibility Trial

    Beaupre, L.A.; Magaziner, J.S.; Jones, C.A. (Oxford Academic, 2019)
    BACKGROUND: This study compared functional outcomes at 3 months after hip fracture surgery between nursing home residents participating in a 10-week outreach rehabilitation program and those receiving usual care. Function, health-related quality of life, and mortality were also compared over 12 months, and outreach program feasibility was assessed. METHODS: A feasibility trial was undertaken in Canadian nursing homes; of 77 participants, 46 were allocated to Outreach and 31 to Control prior to assessing function or cognition. Outreach participants received 10 weeks of rehabilitation (30 sessions), and Control participants received usual posthospital fracture care in their nursing homes. The primary outcome was the Functional Independence Measure Physical Domain (FIMphysical) score 3 months post-fracture; we also explored FIM Locomotion and Mobility. Secondary outcomes were FIM scores, EQ-5D-3L scores, and mortality over 12 months. Program feasibility was also evaluated. RESULTS: The mean age was 88.7 ± 7.0 years, 55 (71%) were female, and 58 (75%) had severe cognitive impairment with no significant group differences (p > .14). Outreach participants had significantly higher FIM Locomotion than usual care (p = .02), but no significant group differences were seen in FIMphysical or FIM Mobility score 3 months post-fracture. In adjusted analyses, Outreach participants reported significant improvements in all FIM and EQ-5D-3L scores compared with Control participants over 12 months (p < .05). Mortality did not differ by group (p = .80). Thirty (65%) Outreach participants completed the program. CONCLUSIONS: Our feasibility trial demonstrated that Outreach participants achieved better locomotion by 3 months post-fracture compared with participants receiving usual postfracture care; benefits were sustained to 12 months post-fracture. In adjusted analyses, Outreach participants also showed sustained benefits in physical function and health-related quality of life. Copyright The Author(s) 2019.

View more