Publications by authors named "James Allen"

322 Publications

Human neutralizing antibodies against SARS-CoV-2 require intact Fc effector functions for optimal therapeutic protection.

Cell 2021 04 12;184(7):1804-1820.e16. Epub 2021 Feb 12.

Department of Medicine, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA. Electronic address:

SARS-CoV-2 has caused the global COVID-19 pandemic. Although passively delivered neutralizing antibodies against SARS-CoV-2 show promise in clinical trials, their mechanism of action in vivo is incompletely understood. Here, we define correlates of protection of neutralizing human monoclonal antibodies (mAbs) in SARS-CoV-2-infected animals. Whereas Fc effector functions are dispensable when representative neutralizing mAbs are administered as prophylaxis, they are required for optimal protection as therapy. When given after infection, intact mAbs reduce SARS-CoV-2 burden and lung disease in mice and hamsters better than loss-of-function Fc variant mAbs. Fc engagement of neutralizing antibodies mitigates inflammation and improves respiratory mechanics, and transcriptional profiling suggests these phenotypes are associated with diminished innate immune signaling and preserved tissue repair. Immune cell depletions establish that neutralizing mAbs require monocytes and CD8 T cells for optimal clinical and virological benefit. Thus, potently neutralizing mAbs utilize Fc effector functions during therapy to mitigate lung infection and disease.
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http://dx.doi.org/10.1016/j.cell.2021.02.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7879018PMC
April 2021

Next generation methodology for updating HA vaccines against emerging human seasonal influenza A(H3N2) viruses.

Sci Rep 2021 Mar 2;11(1):4554. Epub 2021 Mar 2.

Center for Vaccines and Immunology, University of Georgia, 501 D.W. Brooks Drive, CVI Room 1504, Athens, GA, 30602, USA.

While vaccines remain the best tool for preventing influenza virus infections, they have demonstrated low to moderate effectiveness in recent years. Seasonal influenza vaccines typically consist of wild-type influenza A and B viruses that are limited in their ability to elicit protective immune responses against co-circulating influenza virus variant strains. Improved influenza virus vaccines need to elicit protective immune responses against multiple influenza virus drift variants within each season. Broadly reactive vaccine candidates potentially provide a solution to this problem, but their efficacy may begin to wane as influenza viruses naturally mutate through processes that mediates drift. Thus, it is necessary to develop a method that commercial vaccine manufacturers can use to update broadly reactive vaccine antigens to better protect against future and currently circulating viral variants. Building upon the COBRA technology, nine next-generation H3N2 influenza hemagglutinin (HA) vaccines were designed using a next generation algorithm and design methodology. These next-generation broadly reactive COBRA H3 HA vaccines were superior to wild-type HA vaccines at eliciting antibodies with high HAI activity against a panel of historical and co-circulating H3N2 influenza viruses isolated over the last 15 years, as well as the ability to neutralize future emerging H3N2 isolates.
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http://dx.doi.org/10.1038/s41598-020-79590-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7925519PMC
March 2021

The utility of head CT scans in geriatric patients with hip fractures following a low energy injury mechanism: A retrospective review.

Injury 2021 Jun 26;52(6):1462-1466. Epub 2020 Dec 26.

Department of Orthopaedic Surgery, London Health Sciences Centre, University Hospital, 339 Windermere Road, London, ON Canada N6A 5A5. Electronic address:

Objectives: Hip fractures are common low-energy orthopaedic injuries in the geriatric population. The purpose of this study is to determine the frequency of CT head exams and the incidence of clinically significant intracranial bleed in patients with low energy hip fractures.

Design: A retrospective cross-sectional review was completed to identify hip fractures presenting to an academic health centre between 2006 and 2015. Our inclusion criteria were those patients with low energy hip fractures and medical records were reviewed to determine whether a CT head scan was utilized as part of their workup.

Results: A total of 2114 patients were reviewed with an average age of 83.2 years. Hip fractures were treated with a hemiarthroplasty in 59.1% of the patients and with a dynamic hip screw in 40.9% of the patients. 26.9% (n = 502) of the patients received a CT head scan as part of their workup. Sixty-two patients (12.3% of patients who received a CT scan or 2.9% of the study population) were found to have had an acute intracranial bleed. None of these patients required neurosurgical intervention and only 9 (14.5% of patients with a positive CT head) had a modification to their thromboprophylaxis post-op. Of the 15 (26.4%) patient on home anticoagulation for a pre-existing medical condition, 10 (67%) had a delay in reinitiating their anticoagulation greater than 24 h post-operatively.

Conclusion: During the study period, 26.7% of patients received a CT scan, with only 2.9% of patients suffering from a concurrent intracranial bleed. None of the patients with a positive scan required neurosurgical intervention, and scan results did not routinely alter DVT prophylaxis. Resuming home anticoagulation was delayed greater than 24 h post-operatively in ten (67%) of cases. With the challenges of resource allocation, potential delays to surgery and costs associated with CT scans, these investigations should be reserved for patients who have a history or physical exam findings of head trauma or are on anticoagulation pre-injury in the low energy hip fracture population.

Level Of Evidence: Level III.
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http://dx.doi.org/10.1016/j.injury.2020.12.022DOI Listing
June 2021

The utility of head CT scans in geriatric patients with hip fractures following a low energy injury mechanism: A retrospective review.

Injury 2021 Jun 26;52(6):1462-1466. Epub 2020 Dec 26.

Department of Orthopaedic Surgery, London Health Sciences Centre, University Hospital, 339 Windermere Road, London, ON Canada N6A 5A5. Electronic address:

Objectives: Hip fractures are common low-energy orthopaedic injuries in the geriatric population. The purpose of this study is to determine the frequency of CT head exams and the incidence of clinically significant intracranial bleed in patients with low energy hip fractures.

Design: A retrospective cross-sectional review was completed to identify hip fractures presenting to an academic health centre between 2006 and 2015. Our inclusion criteria were those patients with low energy hip fractures and medical records were reviewed to determine whether a CT head scan was utilized as part of their workup.

Results: A total of 2114 patients were reviewed with an average age of 83.2 years. Hip fractures were treated with a hemiarthroplasty in 59.1% of the patients and with a dynamic hip screw in 40.9% of the patients. 26.9% (n = 502) of the patients received a CT head scan as part of their workup. Sixty-two patients (12.3% of patients who received a CT scan or 2.9% of the study population) were found to have had an acute intracranial bleed. None of these patients required neurosurgical intervention and only 9 (14.5% of patients with a positive CT head) had a modification to their thromboprophylaxis post-op. Of the 15 (26.4%) patient on home anticoagulation for a pre-existing medical condition, 10 (67%) had a delay in reinitiating their anticoagulation greater than 24 h post-operatively.

Conclusion: During the study period, 26.7% of patients received a CT scan, with only 2.9% of patients suffering from a concurrent intracranial bleed. None of the patients with a positive scan required neurosurgical intervention, and scan results did not routinely alter DVT prophylaxis. Resuming home anticoagulation was delayed greater than 24 h post-operatively in ten (67%) of cases. With the challenges of resource allocation, potential delays to surgery and costs associated with CT scans, these investigations should be reserved for patients who have a history or physical exam findings of head trauma or are on anticoagulation pre-injury in the low energy hip fracture population.

Level Of Evidence: Level III.
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http://dx.doi.org/10.1016/j.injury.2020.12.022DOI Listing
June 2021

Human neutralizing antibodies against SARS-CoV-2 require intact Fc effector functions and monocytes for optimal therapeutic protection.

bioRxiv 2020 Dec 28. Epub 2020 Dec 28.

SARS-CoV-2 has caused the global COVID-19 pandemic. Although passively delivered neutralizing antibodies against SARS-CoV-2 show promise in clinical trials, their mechanism of action is incompletely understood. Here, we define correlates of protection of neutralizing human monoclonal antibodies (mAbs) in SARS-CoV-2-infected animals. Whereas Fc effector functions are dispensable when representative neutralizing mAbs are administered as prophylaxis, they are required for optimal protection as therapy. When given after infection, intact mAbs reduce SARS-CoV-2 burden and lung disease in mice and hamsters better than loss-of-function Fc variant mAbs. Fc engagement of neutralizing antibodies mitigates inflammation and improves respiratory mechanics, and transcriptional profiling suggests these phenotypes are associated with diminished innate immune signaling and preserved tissue repair. Immune cell depletions establish that neutralizing mAbs require monocytes for therapeutic efficacy. Thus, potently neutralizing mAbs require Fc effector functions for maximal therapeutic benefit during therapy to modulate protective immune responses and mitigate lung disease.
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http://dx.doi.org/10.1101/2020.12.28.424554DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7781307PMC
December 2020

Pulmonary Fibrosis Uncovered during Evaluation for Orthotopic Liver Transplantation.

Ann Am Thorac Soc 2020 12;17(12):1629-1632

Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio.

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http://dx.doi.org/10.1513/AnnalsATS.202003-248CCDOI Listing
December 2020

Ensembl 2021.

Nucleic Acids Res 2021 01;49(D1):D884-D891

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

The Ensembl project (https://www.ensembl.org) annotates genomes and disseminates genomic data for vertebrate species. We create detailed and comprehensive annotation of gene structures, regulatory elements and variants, and enable comparative genomics by inferring the evolutionary history of genes and genomes. Our integrated genomic data are made available in a variety of ways, including genome browsers, search interfaces, specialist tools such as the Ensembl Variant Effect Predictor, download files and programmatic interfaces. Here, we present recent Ensembl developments including two new website portals. Ensembl Rapid Release (http://rapid.ensembl.org) is designed to provide core tools and services for genomes as soon as possible and has been deployed to support large biodiversity sequencing projects. Our SARS-CoV-2 genome browser (https://covid-19.ensembl.org) integrates our own annotation with publicly available genomic data from numerous sources to facilitate the use of genomics in the international scientific response to the COVID-19 pandemic. We also report on other updates to our annotation resources, tools and services. All Ensembl data and software are freely available without restriction.
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http://dx.doi.org/10.1093/nar/gkaa942DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7778975PMC
January 2021

Revision Hip Arthroplasty Using a Porous-coated or Taper ZMR Implant: Minimum 10-year Follow-up of Implant Survivorship.

J Am Acad Orthop Surg 2021 Jan;29(1):e41-e50

Mount Sinai Hospital, Division of Orthopaedics - Joseph and Wolf Lebovic Health Complex, Toronto, Ontario, Canada.

Introduction: The Zimmer Modular Revision hip (ZMR) system is available in two stem options, a porous-coated cylindrical (PCM) and a taper (TM) stem. Several concerns have been reported regarding modular implants. Specifically, because of early junctional fractures, the ZMR system was redesigned with a wider modular interface. As such, we designed a study assessing long-term ZMR survivorship and functional and radiographic outcomes.

Methods And Materials: A search of our institutional research database was performed. A minimum 10-year follow-up was selected. The following two cohorts were created: PCM and TM stems. The Kaplan-Meier survival analysis was performed, and causes of stem failure requiring revision surgery were collected. Functional outcomes as per the Harris Hip Score and radiographic stem stability were assessed as per the Engh classification.

Results: A total of 146 patients meeting the inclusion criteria were available for follow-up (PCM = 68, TM = 78). The mean follow-up was 13.4 years clinically and 11.1 years radiographically for the PCM cohort. Similarly, the TM cohort had a follow-up of 11.1 years clinically and 10.5 years radiographically. The Kaplan-Meier survivorships were 87.1% and 87.8% at 15 years for the PCM and TM cohorts, respectively. The most common cause of failure requiring revision surgery overall was aseptic loosening (PCM = 1.4%, TM = 5.6%). The mean postoperative Harris Hip Score was as follows: PCM = 71.2 and TM = 64.7. Engh type I or II stem ingrowth was as follows: PCM = 85% and TM = 68%.

Discussion: Good survivorship using the ZMR stem system can be expected at up to 15 years. Aseptic loosening remains the most commonly encountered problem for both PCM and TM stems. Previously identified modular junctional weakness seem to have been addressed.
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http://dx.doi.org/10.5435/JAAOS-D-19-00512DOI Listing
January 2021

Low Risk of Progression of Barrett's Esophagus to Neoplasia in Women.

J Clin Gastroenterol 2021 04;55(4):321-326

Department of Gastroenterology and Hepatology, University of Kansas Medical Center, Kansas City, KS.

Background And Aims: Men are at a higher risk for Barrett's esophagus (BE) and esophageal adenocarcinoma (EAC), but little is known about BE progression to dysplasia and EAC in women. We performed a retrospective, multicenter cohort study to assess risk of BE progression to dysplasia and EAC in women compared with men. We also investigated comorbidities, medication use, and endoscopic features that contribute to sex differences in risk of BE progression.

Methods: We collected data from large cohort of patients with BE seen at 6 centers in the United States and Europe, followed for a median 5.7 years. We obtained demographic information (age, sex, ethnicity), clinical history (tobacco use, body mass index, comorbidities), endoscopy results (procedure date, BE segment length), and histopathology findings. Neoplasia was graded as low-grade dysplasia, high-grade dysplasia (HGD), or EAC. Rates of disease progression between women and men were compared using χ2 analysis and the Student t test. Multivariable logistic regression was used to assess the association between sex and disease progression after adjusting for possible confounding variables.

Results: Of the total 4263 patients in the cohort, 2145 met the inclusion criteria, including 324 (15%) women. There was a total of 34 (1.6%) incident EACs, with an overall annual incidence of 0.3% (95% confidence interval: 0.2%-0.4%). We found significant differences between women and men in annual incidence rates of EAC (0.05% for women vs. 0.3% in men; P=0.04) and in the combined endpoint of HGD or EAC (0.1% for women vs. 1.1% for men; P<0.001). Female gender was an independent predictor for reduced progression to HGD or EAC when rates of progression were adjusted for body mass index, smoking history, race, use of aspirin, nonsteroidal anti-inflammatory drugs, proton-pump inhibitors, or statins, hypertriglyceridemia, BE length, and histology findings at baseline (hazard ratio: 0.11; 95% confidence interval: 0.03-0.45; P=0.002).

Conclusions: In a multicenter study of men versus women with BE, we found a significantly lower risk of disease progression to cancer and HGD in women. The extremely low risk of EAC in women with BE (0.05%/y) indicates that surveillance endoscopy may not be necessary for this subgroup of patients with BE.
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http://dx.doi.org/10.1097/MCG.0000000000001362DOI Listing
April 2021

Self DNA perpetuates IPF lung fibroblast senescence in a cGAS-dependent manner.

Clin Sci (Lond) 2020 04;134(7):889-905

School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia.

Senescence and mitochondrial stress are mutually reinforcing age-related processes that contribute to idiopathic pulmonary fibrosis (IPF); a lethal disease that manifests primarily in the elderly. Whilst evidence is accumulating that GMP-AMP synthase (cGAS) is crucial in perpetuating senescence by binding damaged DNA released into the cytosol, its role in IPF is not known. The present study examines the contributions of cGAS and self DNA to the senescence of lung fibroblasts from IPF patients (IPF-LFs) and age-matched controls (Ctrl-LFs). cGAS immunoreactivity was observed in regions of fibrosis associated with fibroblasts in lung tissue of IPF patients. Pharmacological inhibition of cGAS or its knockdown by silencing RNA (siRNA) diminished the escalation of IPF-LF senescence in culture over 7 days as measured by decreased p21 and p16 expression, histone 2AXγ phosphorylation and/or IL-6 production (P < 0.05, n = 5-8). The targeting of cGAS also attenuated etoposide-induced senescence in Ctrl-LFs (P < 0.05, n = 5-8). Levels of mitochondrial DNA (mDNA) detected by qPCR in the cytosol and medium of IPF-LFs or senescence-induced Ctrl-LFs were higher than Ctrl-LFs at baseline (P < 0.05, n = 5-7). The addition of DNAse I (100 U/ml) deaccelerated IPF-LF senescence (P < 0.05, n = 5), whereas ectopic mDNA or the induction of endogenous mDNA release augmented Ctrl-LF senescence in a cGAS-dependent manner (P < 0.05, n = 5). In conclusion, we provide evidence that cGAS reinforces lung fibroblast senescence involving damaged self DNA. The targeting of cGAS to supress senescent-like responses may have potential important therapeutic implications in the treatment of IPF.
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http://dx.doi.org/10.1042/CS20191160DOI Listing
April 2020

Enhanced Photocatalytic Hydrogen Production by Hybrid Streptavidin-Diiron Catalysts.

Chemistry 2020 May 28;26(28):6240-6246. Epub 2020 Apr 28.

School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.

Hybrid protein-organometallic catalysts are being explored for selective catalysis of a number of reactions, because they utilize the complementary strengths of proteins and of organometallic complex. Herein, we present an artificial hydrogenase, StrepH2, built by incorporating a biotinylated [Fe-Fe] hydrogenase organometallic mimic within streptavidin. This strategy takes advantage of the remarkable strength and specificity of biotin-streptavidin recognition, which drives quantitative incorporation of the biotinylated diironhexacarbonyl center into streptavidin, as confirmed by UV/Vis spectroscopy and X-ray crystallography. FTIR spectra of StrepH2 show characteristic peaks at shift values indicative of interactions between the catalyst and the protein scaffold. StrepH2 catalyzes proton reduction to hydrogen in aqueous media during photo- and electrocatalysis. Under photocatalytic conditions, the protein-embedded catalyst shows enhanced efficiency and prolonged activity compared to the isolated catalyst. Transient absorption spectroscopy data suggest a mechanism for the observed increase in activity underpinned by an observed longer lifetime for the catalytic species Fe Fe when incorporated within streptavidin compared to the biotinylated catalyst in solution.
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http://dx.doi.org/10.1002/chem.202000204DOI Listing
May 2020

Ensembl 2020.

Nucleic Acids Res 2020 01;48(D1):D682-D688

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

The Ensembl (https://www.ensembl.org) is a system for generating and distributing genome annotation such as genes, variation, regulation and comparative genomics across the vertebrate subphylum and key model organisms. The Ensembl annotation pipeline is capable of integrating experimental and reference data from multiple providers into a single integrated resource. Here, we present 94 newly annotated and re-annotated genomes, bringing the total number of genomes offered by Ensembl to 227. This represents the single largest expansion of the resource since its inception. We also detail our continued efforts to improve human annotation, developments in our epigenome analysis and display, a new tool for imputing causal genes from genome-wide association studies and visualisation of variation within a 3D protein model. Finally, we present information on our new website. Both software and data are made available without restriction via our website, online tools platform and programmatic interfaces (available under an Apache 2.0 license) and data updates made available four times a year.
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http://dx.doi.org/10.1093/nar/gkz966DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145704PMC
January 2020

GABA-A receptor and mitochondrial TSPO signaling act in parallel to regulate melanocyte stem cell quiescence in larval zebrafish.

Pigment Cell Melanoma Res 2020 05 11;33(3):416-425. Epub 2019 Nov 11.

Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.

Tissue regeneration and homeostasis often require recruitment of undifferentiated precursors (adult stem cells; ASCs). While many ASCs continuously proliferate throughout the lifetime of an organism, others are recruited from a quiescent state to replenish their target tissue. A long-standing question in stem cell biology concerns how long-lived, non-dividing ASCs regulate the transition between quiescence and proliferation. We study the melanocyte stem cell (MSC) to investigate the molecular pathways that regulate ASC quiescence. Our prior work indicated that GABA-A receptor activation promotes MSC quiescence in larval zebrafish. Here, through pharmacological and genetic approaches we show that GABA-A acts through calcium signaling to maintain MSC quiescence. Unexpectedly, we identified translocator protein (TSPO), a mitochondrial membrane-associated protein that regulates mitochondrial function and metabolic homeostasis, as a parallel regulator of MSC quiescence. We found that both TSPO-specific ligands and induction of gluconeogenesis likely act in the same pathway to promote MSC activation and melanocyte production in larval zebrafish. In contrast, TSPO and gluconeogenesis appear to act in parallel to GABA-A receptor signaling to regulate MSC quiescence and vertebrate pigment patterning.
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http://dx.doi.org/10.1111/pcmr.12836DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7176537PMC
May 2020

Bound manganese oxides capable of reducing the bacteriochlorophyll dimer of modified reaction centers from Rhodobacter sphaeroides.

Photosynth Res 2020 Feb 22;143(2):129-141. Epub 2019 Oct 22.

School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.

A biohybrid model system is described that interfaces synthetic Mn-oxides with bacterial reaction centers to gain knowledge concerning redox reactions by metal clusters in proteins, in particular the MnCaO cluster of photosystem II. The ability of Mn-oxides to bind to modified bacterial reaction centers and transfer an electron to the light-induced oxidized bacteriochlorophyll dimer, P, was characterized using optical spectroscopy. The environment of P was altered to obtain a high P/P midpoint potential. In addition, different metal-binding sites were introduced by substitution of amino acid residues as well as extension of the C-terminus of the M subunit with the C-terminal region of the D1 subunit of photosystem II. The Mn-compounds MnO, αMnO, MnO, CaMnO, and Mn(PO) were tested and compared to MnCl. In general, addition of the Mn-compounds resulted in a decrease in the amount of P while the reduced quinone was still present, demonstrating that the Mn-compounds can serve as secondary electron donors. The extent of P reduction for the Mn-oxides was largest for αMnO and CaMnO and smallest for MnO and MnO. The addition of Mn(PO) resulted in nearly complete P reduction, similar to MnCl. Overall, the activity was correlated with the initial oxidation state of the Mn-compound. Transient optical measurements showed a fast kinetic component, assigned to reduction of P by the Mn-oxide, in addition to a slow component due to charge recombination. The results support the conjecture that the incorporation of Mn-oxides by ancient anoxygenic phototrophs was a step in the evolution of oxygenic photosynthesis.
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http://dx.doi.org/10.1007/s11120-019-00680-3DOI Listing
February 2020

Ensembl Genomes 2020-enabling non-vertebrate genomic research.

Nucleic Acids Res 2020 01;48(D1):D689-D695

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of interfaces to genomic data across the tree of life, including reference genome sequence, gene models, transcriptional data, genetic variation and comparative analysis. Data may be accessed via our website, online tools platform and programmatic interfaces, with updates made four times per year (in synchrony with Ensembl). Here, we provide an overview of Ensembl Genomes, with a focus on recent developments. These include the continued growth, more robust and reproducible sets of orthologues and paralogues, and enriched views of gene expression and gene function in plants. Finally, we report on our continued deeper integration with the Ensembl project, which forms a key part of our future strategy for dealing with the increasing quantity of available genome-scale data across the tree of life.
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http://dx.doi.org/10.1093/nar/gkz890DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6943047PMC
January 2020

Influence of Hydrogen Bonds on the Electron-Phonon Coupling Strength/Marker Mode Structure and Charge Separation Rates in Reaction Centers from .

J Phys Chem B 2019 10 2;123(41):8717-8726. Epub 2019 Oct 2.

School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States.

Low-temperature persistent and transient hole-burning (HB) spectra are presented for the triple hydrogen-bonded L131LH + M160LH + M197FH mutant of These spectra expose the heterogeneous nature of the P-, B-, and H-bands, consistent with a distribution of electron transfer (ET) times and excitation energy transfer (EET) rates. Transient PQ holes are observed for fast (tens of picoseconds or faster) ET times and reveal strong coupling to phonons and marker mode(s), while the persistent holes are bleached in a fraction of reaction centers with long-lived excited states characterized by much weaker electron-phonon coupling. Exposed differences in electron-phonon coupling strength, as well as a different coupling to the marker mode(s), appear to affect the ET times. Both resonantly and nonresonantly burned persistent HB spectra show weak blue- (∼150 cm) and large, red-shifted (∼300 cm) antiholes of the P band. Slower EET times from the H- and B-bands to the special pair dimer provide new insight on the influence of hydrogen bonds on mutation-induced heterogeneity.
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http://dx.doi.org/10.1021/acs.jpcb.9b08388DOI Listing
October 2019

Influence of Hydrogen Bonds on the Electron-Phonon Coupling Strength/Marker Mode Structure and Charge Separation Rates in Reaction Centers from .

J Phys Chem B 2019 10 2;123(41):8717-8726. Epub 2019 Oct 2.

School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States.

Low-temperature persistent and transient hole-burning (HB) spectra are presented for the triple hydrogen-bonded L131LH + M160LH + M197FH mutant of These spectra expose the heterogeneous nature of the P-, B-, and H-bands, consistent with a distribution of electron transfer (ET) times and excitation energy transfer (EET) rates. Transient PQ holes are observed for fast (tens of picoseconds or faster) ET times and reveal strong coupling to phonons and marker mode(s), while the persistent holes are bleached in a fraction of reaction centers with long-lived excited states characterized by much weaker electron-phonon coupling. Exposed differences in electron-phonon coupling strength, as well as a different coupling to the marker mode(s), appear to affect the ET times. Both resonantly and nonresonantly burned persistent HB spectra show weak blue- (∼150 cm) and large, red-shifted (∼300 cm) antiholes of the P band. Slower EET times from the H- and B-bands to the special pair dimer provide new insight on the influence of hydrogen bonds on mutation-induced heterogeneity.
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http://dx.doi.org/10.1021/acs.jpcb.9b08388DOI Listing
October 2019

Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes.

Genome Biol 2019 09 2;20(1):187. Epub 2019 Sep 2.

McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.

Background: Tsetse flies (Glossina sp.) are the vectors of human and animal trypanosomiasis throughout sub-Saharan Africa. Tsetse flies are distinguished from other Diptera by unique adaptations, including lactation and the birthing of live young (obligate viviparity), a vertebrate blood-specific diet by both sexes, and obligate bacterial symbiosis. This work describes the comparative analysis of six Glossina genomes representing three sub-genera: Morsitans (G. morsitans morsitans, G. pallidipes, G. austeni), Palpalis (G. palpalis, G. fuscipes), and Fusca (G. brevipalpis) which represent different habitats, host preferences, and vectorial capacity.

Results: Genomic analyses validate established evolutionary relationships and sub-genera. Syntenic analysis of Glossina relative to Drosophila melanogaster shows reduced structural conservation across the sex-linked X chromosome. Sex-linked scaffolds show increased rates of female-specific gene expression and lower evolutionary rates relative to autosome associated genes. Tsetse-specific genes are enriched in protease, odorant-binding, and helicase activities. Lactation-associated genes are conserved across all Glossina species while male seminal proteins are rapidly evolving. Olfactory and gustatory genes are reduced across the genus relative to other insects. Vision-associated Rhodopsin genes show conservation of motion detection/tracking functions and variance in the Rhodopsin detecting colors in the blue wavelength ranges.

Conclusions: Expanded genomic discoveries reveal the genetics underlying Glossina biology and provide a rich body of knowledge for basic science and disease control. They also provide insight into the evolutionary biology underlying novel adaptations and are relevant to applied aspects of vector control such as trap design and discovery of novel pest and disease control strategies.
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http://dx.doi.org/10.1186/s13059-019-1768-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6721284PMC
September 2019

Maintenance of Melanocyte Stem Cell Quiescence by GABA-A Signaling in Larval Zebrafish.

Genetics 2019 10 23;213(2):555-566. Epub 2019 Aug 23.

Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110

In larval zebrafish, melanocyte stem cells (MSCs) are quiescent, but can be recruited to regenerate the larval pigment pattern following melanocyte ablation. Through pharmacological experiments, we found that inhibition of γ-aminobutyric acid (GABA)-A receptor function, specifically the GABA-A ρ subtype, induces excessive melanocyte production in larval zebrafish. Conversely, pharmacological activation of GABA-A inhibited melanocyte regeneration. We used clustered regularly interspaced short palindromic repeats/Cas9 to generate two mutant alleles of , a subtype of GABA-A receptors. Both alleles exhibited robust melanocyte overproduction, while conditional overexpression of inhibited larval melanocyte regeneration. Our data suggest that signaling is necessary to maintain MSC quiescence and sufficient to reduce, but not eliminate, melanocyte regeneration in larval zebrafish.
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http://dx.doi.org/10.1534/genetics.119.302416DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6781893PMC
October 2019

Substance Use Research with Indigenous Communities: Exploring and Extending Foundational Principles of Community Psychology.

Am J Community Psychol 2019 09 31;64(1-2):146-158. Epub 2019 Jul 31.

Department of Family Medicine and Biobehavioral Health, University of Minnesota Medical School, Duluth Campus, Duluth, MN, USA.

Many Indigenous communities are concerned with substance use (SU) problems and eager to advance effective solutions for their prevention and treatment. Yet these communities also are concerned about the perpetuation of colonizing, disorder-focused, stigmatizing approaches to mental health, and social narratives related to SU problems. Foundational principles of community psychology-ecological perspectives, empowerment, sociocultural competence, community inclusion and partnership, and reflective practice-provide useful frameworks for informing ethical community-based research pertaining to SU problems conducted with and by Indigenous communities. These principles are explored and extended for Indigenous community contexts through themes generated from seven collaborative studies focused on understanding, preventing, and treating SU problems. These studies are generated from research teams working with Indigenous communities across the United States and Canada-inclusive of urban, rural, and reservation/reserve populations as well as adult and youth participants. Shared themes indicate that Indigenous SU research reflects community psychology principles, as an outgrowth of research agendas and processes that are increasingly guided by Indigenous communities. At the same time, this research challenges these principles in important ways pertaining to Indigenous-settler relations and Indigenous-specific considerations. We discuss these challenges and recommend greater synergy between community psychology and Indigenous research.
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http://dx.doi.org/10.1002/ajcp.12363DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6777961PMC
September 2019

Substance Use Research with Indigenous Communities: Exploring and Extending Foundational Principles of Community Psychology.

Am J Community Psychol 2019 09 31;64(1-2):146-158. Epub 2019 Jul 31.

Department of Family Medicine and Biobehavioral Health, University of Minnesota Medical School, Duluth Campus, Duluth, MN, USA.

Many Indigenous communities are concerned with substance use (SU) problems and eager to advance effective solutions for their prevention and treatment. Yet these communities also are concerned about the perpetuation of colonizing, disorder-focused, stigmatizing approaches to mental health, and social narratives related to SU problems. Foundational principles of community psychology-ecological perspectives, empowerment, sociocultural competence, community inclusion and partnership, and reflective practice-provide useful frameworks for informing ethical community-based research pertaining to SU problems conducted with and by Indigenous communities. These principles are explored and extended for Indigenous community contexts through themes generated from seven collaborative studies focused on understanding, preventing, and treating SU problems. These studies are generated from research teams working with Indigenous communities across the United States and Canada-inclusive of urban, rural, and reservation/reserve populations as well as adult and youth participants. Shared themes indicate that Indigenous SU research reflects community psychology principles, as an outgrowth of research agendas and processes that are increasingly guided by Indigenous communities. At the same time, this research challenges these principles in important ways pertaining to Indigenous-settler relations and Indigenous-specific considerations. We discuss these challenges and recommend greater synergy between community psychology and Indigenous research.
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http://dx.doi.org/10.1002/ajcp.12363DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6777961PMC
September 2019

An Intervention Science to Advance Underrepresented Perspectives and Indigenous Self-Determination in Health.

Prev Sci 2020 01;21(Suppl 1):83-92

Department of Family Medicine and Biobehavioral Health & Memory Keepers Medical Discovery Team - American Indian and Rural Health Equity, University of Minnesota Medical School, Duluth Campus, 624 E. 1st St., Suite 201, Duluth, MN, 55805, USA.

This concluding article to the Supplemental Issue on Promoting Health Equity through Rigorous, Culturally Informed Intervention Science: Innovations with Indigenous Populations in the United States draws themes and conclusions from the innovative practices implemented by the National Institutes of Health Intervention Research to Improve Native American Health (IRINAH) consortium. The IRINAH work highlights promising practices for advancing the diverse and underrepresented perspectives essential to develop and test culturally appropriate, effective health interventions in American Indian, Alaska Native, and Native Hawaiian settings. Four emergent themes appear through the IRINAH work. First, community-based participatory research (CBPR) has provided projects an intersectional worldview for bridging cultures and informing an ethics of local control. Second, culture is fundamental as a central organizing principle in IRINAH research and intervention implementation. Third, crucial demands for sustainability of interventions in Indigenous intervention science require a rethinking of the intervention development process. Finally, tensions persist in Indigenous health research, even as significant strides are made in the field. These themes collectively inform an ethical and rigorous Indigenous intervention science. Collectively, they suggest a roadmap for advancing Indigenous perspectives and self-determination in health intervention research. IRINAH studies are leading innovation in intervention science by advancing applications of CBPR in intervention science, promoting new directions in small populations health research, and demonstrating value of participatory team science.
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http://dx.doi.org/10.1007/s11121-019-01025-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6885107PMC
January 2020

Wave energy converter geometry for coastal flooding mitigation.

Sci Total Environ 2019 Jun 6;668:1232-1241. Epub 2019 Mar 6.

MaREI, Environmental Research Institute & School of Engineering, University College Cork, College Road, Cork, Ireland; School of Engineering, University of Plymouth, Plymouth PL4 8AA, UK.

Wave farms, i.e., arrays of wave energy converters (WECs), have been proposed to fulfil the dual function of carbon-free energy generation and coastal protection. The objective of this work is to investigate, for the first time, how the coastal protection performance against flooding is affected by WEC geometry. This is done by means of a case study with WaveCat WECs (floating, overtopping WECs) deployed off the Playa Granada beach (Spain). To this end, two models of WaveCat WECs with different geometries are tested in a laboratory tank at a 1:30 scale under low-, mid- and high-energy sea states representative of the wave conditions of Playa Granada. The geometries differed in the angle between the twin hulls (wedge angle) of WaveCat: 30° and 60°. The reflection and transmission coefficients thus obtained are used in a coupled numerical modelling approach, combining wave and coastal processes models (SWAN and XBeach-G, respectively). We find that WECs with an angle of 60° provide more (less) protection for long (short) wave periods in terms of reductions in wave height and run-up on the beach. As for the flooded dry beach areas, they are generally smaller for WECs with 60°, with only some exceptions under mild conditions. Thus, considering that beach inundation usually occurs under high-energy, storm conditions, we conclude that the wave farm composed by WECs with a wedge angle of 60° is more efficient against coastal flooding.
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http://dx.doi.org/10.1016/j.scitotenv.2019.03.022DOI Listing
June 2019

Wave energy converter geometry for coastal flooding mitigation.

Sci Total Environ 2019 Jun 6;668:1232-1241. Epub 2019 Mar 6.

MaREI, Environmental Research Institute & School of Engineering, University College Cork, College Road, Cork, Ireland; School of Engineering, University of Plymouth, Plymouth PL4 8AA, UK.

Wave farms, i.e., arrays of wave energy converters (WECs), have been proposed to fulfil the dual function of carbon-free energy generation and coastal protection. The objective of this work is to investigate, for the first time, how the coastal protection performance against flooding is affected by WEC geometry. This is done by means of a case study with WaveCat WECs (floating, overtopping WECs) deployed off the Playa Granada beach (Spain). To this end, two models of WaveCat WECs with different geometries are tested in a laboratory tank at a 1:30 scale under low-, mid- and high-energy sea states representative of the wave conditions of Playa Granada. The geometries differed in the angle between the twin hulls (wedge angle) of WaveCat: 30° and 60°. The reflection and transmission coefficients thus obtained are used in a coupled numerical modelling approach, combining wave and coastal processes models (SWAN and XBeach-G, respectively). We find that WECs with an angle of 60° provide more (less) protection for long (short) wave periods in terms of reductions in wave height and run-up on the beach. As for the flooded dry beach areas, they are generally smaller for WECs with 60°, with only some exceptions under mild conditions. Thus, considering that beach inundation usually occurs under high-energy, storm conditions, we conclude that the wave farm composed by WECs with a wedge angle of 60° is more efficient against coastal flooding.
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http://dx.doi.org/10.1016/j.scitotenv.2019.03.022DOI Listing
June 2019

Recent innovations in membrane-protein structural biology.

Authors:
James P Allen

F1000Res 2019 22;8. Epub 2019 Feb 22.

School of Molecular Sciences, Arizona State University, Tempe, AZ, USA.

Innovations are expanding the capabilities of experimental investigations of the structural properties of membrane proteins. Traditionally, three-dimensional structures have been determined by measuring x-ray diffraction using protein crystals with a size of least 100 μm. For membrane proteins, achieving crystals suitable for these measurements has been a significant challenge. The availabilities of micro-focus x-ray beams and the new instrumentation of x-ray free-electron lasers have opened up the possibility of using submicrometer-sized crystals. In addition, advances in cryo-electron microscopy have expanded the use of this technique for studies of protein crystals as well as studies of individual proteins as single particles. Together, these approaches provide unprecedented opportunities for the exploration of structural properties of membrane proteins, including dynamical changes during protein function.
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http://dx.doi.org/10.12688/f1000research.16234.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6392159PMC
June 2020

Decreasing Endoscopy No-Shows Using a Lean Improvement Framework.

Clin Gastroenterol Hepatol 2019 06 5;17(7):1224-1227.e3. Epub 2019 Feb 5.

Durham VA Medical Center, Durham, North Carolina; Division of Gastroenterology, Duke University School of Medicine, Durham, North Carolina; The Cooperative Studies Program Epidemiology Center-Durham, Durham, North Carolina. Electronic address:

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http://dx.doi.org/10.1016/j.cgh.2019.02.002DOI Listing
June 2019

Development of Novel Micro-dystrophins with Enhanced Functionality.

Mol Ther 2019 03 1;27(3):623-635. Epub 2019 Feb 1.

Molecular and Cellular Biology Program, University of Washington School of Medicine, Seattle, WA 98195, USA; Department of Neurology, University of Washington School of Medicine, Seattle, WA 98195, USA; Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington School of Medicine, Seattle, WA 98195, USA; Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA. Electronic address:

Gene therapies using adeno-associated viral (AAV) vectors have advanced into clinical trials for several diseases, including Duchenne muscular dystrophy (DMD). A limitation of AAV is the carrying capacity (∼5 kb) available for genes and regulatory cassettes (RCs). These size constraints are problematic for the 2.2-Mb dystrophin gene. We previously designed a variety of miniaturized micro-dystrophins (μDys) that displayed significant, albeit incomplete, function in striated muscles. To develop μDys proteins with improved performance, we explored structural modifications of the dystrophin central rod domain. Eight μDys variants were studied that carried unique combinations of between four and six of the 24 spectrin-like repeats present in the full-length protein, as well as various hinge domains. Expression of μDys was regulated by a strong but compact muscle-restricted RC (CK8e) or by the ubiquitously active cytomegalovirus (CMV) RC. Vectors were evaluated by intramuscular injection and systemic delivery to dystrophic mdx mice, followed by analysis of skeletal muscle pathophysiology. Two μDys designs were identified that led to increased force generation compared with previous μDys while also localizing neuronal nitric oxide synthase to the sarcolemma. An AAV vector expressing the smaller of these (μDys5) from the CK8e RC is currently being evaluated in a DMD clinical trial.
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http://dx.doi.org/10.1016/j.ymthe.2019.01.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6403485PMC
March 2019

Development of Novel Micro-dystrophins with Enhanced Functionality.

Mol Ther 2019 03 1;27(3):623-635. Epub 2019 Feb 1.

Molecular and Cellular Biology Program, University of Washington School of Medicine, Seattle, WA 98195, USA; Department of Neurology, University of Washington School of Medicine, Seattle, WA 98195, USA; Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington School of Medicine, Seattle, WA 98195, USA; Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA. Electronic address:

Gene therapies using adeno-associated viral (AAV) vectors have advanced into clinical trials for several diseases, including Duchenne muscular dystrophy (DMD). A limitation of AAV is the carrying capacity (∼5 kb) available for genes and regulatory cassettes (RCs). These size constraints are problematic for the 2.2-Mb dystrophin gene. We previously designed a variety of miniaturized micro-dystrophins (μDys) that displayed significant, albeit incomplete, function in striated muscles. To develop μDys proteins with improved performance, we explored structural modifications of the dystrophin central rod domain. Eight μDys variants were studied that carried unique combinations of between four and six of the 24 spectrin-like repeats present in the full-length protein, as well as various hinge domains. Expression of μDys was regulated by a strong but compact muscle-restricted RC (CK8e) or by the ubiquitously active cytomegalovirus (CMV) RC. Vectors were evaluated by intramuscular injection and systemic delivery to dystrophic mdx mice, followed by analysis of skeletal muscle pathophysiology. Two μDys designs were identified that led to increased force generation compared with previous μDys while also localizing neuronal nitric oxide synthase to the sarcolemma. An AAV vector expressing the smaller of these (μDys5) from the CK8e RC is currently being evaluated in a DMD clinical trial.
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http://dx.doi.org/10.1016/j.ymthe.2019.01.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6403485PMC
March 2019