24 research outputs found
Molecular modeling and simulation of bacterial chemosensory arrays
No full textThe movement of an organism in response to environmental chemical cues is known as chemotaxis. Motile bacteria use chemotaxis to navigate through their environments, enabling cells to efficiently locate favorable growing conditions while avoiding harmful ones. Central to this ability, bacteria posses a universally conserved sensory apparatus, known as the chemosensory array, which involves the clustering of thousands of proteins into a highly cooperative signaling network. The present dissertation will present my work using techniques in computational modeling and simulation to investigate the molecular structure and function of the bacterial chemosensory array. A brief overview of each chapter follows.
Chapter 1 provides an introduction to the systems-level features of chemotaxis in the model organism Escherichia coli as well as an overview of the molecular organization and function of the chemosensory array.
Chapter 2 gives an outline of the core methodologies used in my work, specifically all-atom molecular dynamics (MD) simulation and Molecular Dynamics Flexible Fitting (MDFF). In addition, two of the primary techniques used to analyze the MD simulations presented in this dissertation are sketched out, namely structural clustering based on root- mean-square displacement (RMSD) and Principal Component Analysis (PCA).
Chapter 3 reports my work, in collaboration with Peijun Zhang’s Lab, to investigate the structural and dynamical features of the extended chemosensory array. Using computational techniques to synthesize multi-scale structural data from X-ray crystallography and cryo-electron tomography (cryo-ET), an atomic model of the cytoplasmic portion of the chemosensory array from Thermotoga maritima is constructed and refined. Through the use of large-scale MD simulations, a novel conformational change in a key signaling protein is identified and subsequently shown to be critical for chemotaxis signaling in live E. coli cells.
Chapter 4 details the construction of an atomic model of a complete, transmembrane (TM) chemoreceptor. In particular, I use homology modeling and MD simulations, in- formed by biochemical and X-ray crystallographic data, to derive a model of the E. coli serine receptor (Tsr), including the previously uncharacterized TM four-helix bundle and HAMP domains. In addition, I report a series of MD simulations of a fragment of the resulting Tsr model, investigating the structural and dynamical effects of mutations on a key control cable residue. Preliminary MD simulations of the intact Tsr model are also presented.
Chapter 5 reports work in collaboration with Michael Eisenbach’s Lab at the Weizmann Institute, exploring the role of acetylation on CheY activation and the generation of clockwise (CW) flagellar motor rotation. Specifically, I present a series of MD simulations that investigate the effect of a hyperactivating mutation at a key acetylation site and offer a molecular explanation of acetylation-dependent generation of CW flagellar motor rotation.
I conclude with a brief description of recent work, expanding upon the results of the previous chapters, which has resulted in the first atomically resolved model of the E. coli transmembrane chemosensory array.Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2019-05-01The student, C. Cassidy, accepted the attached license on 2017-01-09 at 12:41.The student, C. Cassidy, submitted this Dissertation for approval on 2017-01-09 at 13:01.This Dissertation was approved for publication on 2017-01-10 at 08:48.DSpace SAF Submission Ingestion Package generated from Vireo submission #10534 on 2017-08-10 at 15:04:11Made available in DSpace on 2017-08-10T20:32:24Z (GMT). No. of bitstreams: 3
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Amiota zaliskoi Jones & Grimaldi 2022, sp. nov.
No full textAmiota zaliskoi, sp. nov. Figures 18E–F, 19J–K, 28, 85C DIAGNOSIS: Small to medium-sized fly (ThL 0.98–1.38 mm); dark brown, glossy; facial marking small, width 0.3× length; subepandrial sclerite cantilevered, compartmentalizing surstyli; outer paraphyses laterally flattened, with short subapical dorsal hook and pair of large, symmetrical, dorsomedial spines; inner paraphysis composed of 4 asymmetrical spines, including large, prominent one with preapical tooth, extending over complex. DESCRIPTION: Small to medium-sized fly (ThL 0.98–1.38 mm), almost black, slightly glossy, grading lighter ventrally; legs yellow. Frons black, shiny ventrally, especially ventrolateral corners. Cheek small (EL/CW 9.6–13.75), yellow to brown. Facial marking small, width 0.3× length. Palp brown. Arista: Medium, plumose; longest branch D3; A.R. 0.38.; 4 long dorsal, 2 long ventral branches; D4 pointed laterad, V1 mediad; arista trunk with long microtrichia along entire length. Male genitalia: Epandrium fused at midline, this margin faintly grading into surrounding membrane. Cercus long, pendulous, nearly diamond-shaped; dorsal margins grading into surrounding membrane. Surstylus rounded; 11 prensisetae, apices blunt, closely arranged, comblike; distinctive paddle-shaped process, curving dorsomedially, extending beyond prensisetae; distal end of process with rough, textured cuticle; row of setulae along process, curving medially in semicircular pattern to midregion of surstylus. Subepandrial sclerite distinctive; cantilevered, distal corners curving downward slightly; central membrane forming septum, surrounding surstylus. Outer paraphysis long, laterally flattened, distal end rounded; very small preapical dorsal apical hook, arising on mesal surface; 2 large, heavily sclerotized, perpendicular spines present, proximal to preapical dorsal hook, with sensilla between; 4–5 sensilla in row between large spine and inner paraphysis. Inner paraphysis composed of 4 asymmetrical spines; prominent spine, large, with preapical tooth, extending over complex. Aedeagal apodeme slightly longer than wide; distal end only slightly flared, lobes distinct; distal notch very small, shallow. Hypandrium simple, of relatively uniform thickness, anterior end narrowed. Ejaculatory apodeme not studied. Head and thorax measurements: (n = 5; Am 29, 32, 529, 638, 1168) FL/ FW 0.77 (0.70–0.85), EL/EW 1.29 (1.17–1.40), EL/ CW 11.2 (9.6–13.75), FML/FMW 0.27 (0.24–0.30), PR /RR 0.58 (0.45–0.77), ThL 1.25 (0.98–1.38 mm). TYPE MATERIAL: Holotype: male: NEW YORK: Tompkins Co., Texas Hollow, [42.386486, -76.773090], VII/26/83, D. Grimaldi and L.L Pechuman, flying about head, Am 32, [specimen glued to paper point, dissected]. Deposited in the American Museum of Natural History (AMNH). Paratypes: NEW YORK: Tompkins Co., Texas Hollow, VII/26/83, D. Grimaldi and L.L Pechuman, flying about head, 3♂ (Am 21, 29*, 30*, AMNH). OTHER MATERIAL EXAMINED: Canada: Ontario: Algonquin Provincial Park, Swan Lake Station, Scott Lake Survey, 1995-05-29 through 1995-06-16, leg. S.A. Marshall, A transect bracket. Pans on debarked snag, 1♂ (Am 576, DEBU). Lambton Co., Port Franks, 1996-08-02, leg. J. Skevington, 1♂ (Am 638*, DEBU). Quebec: Old Chelsea, 1959-09-29, leg. J. R. Vockeroth, 1♂ (Am 1437*, CNC); 1150′, 1966-07-05, leg. D.D. Monroe, 1♂ (Am 1258*, CNC); 1150′, 1966-07-08, leg. D.D. Monroe, 1♂ (Am 1259*, CNC); 1150′, 1966-08-09, leg. D.D. Monroe, 1♂ (Am 1261*, CNC); Old Chelsea, King Mt., 1969-08-13, leg. B. V. Peterson, 1♂ (Am 1582*, CNC); Old Cheslea, Summit King Mtn., 1965-06-20, leg. D.M. Wood, 2♂ (Am 1462*, 1541*, CNC); Summit King Mt. Old Chelsea, 1980- 06-23, leg. K.N. Barber, 1♂ (Am 529*, DEBU). USA: New York: Monroe Co., Rochester, Highland Pk., 43.132600, -77.602784, 2018-09-17, leg. John Jaenike, 1♂ (Am 1168*, AMNH). North Carolina: Wayah Bald, 5300′, 1957-07-14, leg. J.G. Chillcott, “ Paratype,” [never published], 1♂ (Am 1375*, CNC). ETYMOLOGY: Named for Edward Zalisko (1958–), outstanding teacher and professor of biology at Blackburn College in Carlinville, Illinois. In appreciation for introducing the first author to phylogenies and evolution while he was an undergraduate at Blackburn. Zalisko once said in class, “I am the world’s authority on something that absolutely nobody cares about!” a sentiment now understood by the first author. DISTRIBUTION: Amiota zaliskoi is found in the Great Lakes region, but one record as far south as North Carolina is known. COMMENTS: This species exhibits the characteristic behavior of attraction to the eyes and face common in many Amiota.Published as part of Jones, Lance E. & Grimaldi, David A., 2022, Revision Of The Nearctic Species Of The Genus Amiota Loew (Diptera: Drosophilidae), pp. 1-181 in Bulletin of the American Museum of Natural History 2022 (458) on pages 49-50, DOI: 10.1206/0003-0090.458.1.1, http://zenodo.org/record/740002
Civil society and political change in Morocco
No full textEThOS - Electronic Theses Online ServiceGBUnited Kingdo
Comparative evaluation of ten lateral flow immunoassays to detect SARS-CoV-2 antibodies
No full textBackground: Rapid mobilisation from industry and academia following the outbreak of the novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), led to the development and availability of SARS-CoV-2 lateral flow immunoassays (LFAs). High quality LFAs are urgently needed at the point of care to add to currently available diagnostic tools. In this study, we provide evaluation data for ten LFAs suitable for use at the point of care. Methods: : COVID-19 positive patients (N=45), confirmed by reverse transcription – quantitative polymerase chain reaction (RT-qPCR), were recruited through the International Severe Acute Respiratory and Emerging Infection Consortium - Coronavirus Clinical Characterisation Consortium (ISARIC4C) study. Sera collected from patients with influenza A (N=20), tuberculosis (N=5), individuals with previous flavivirus exposure (N=21), and healthy sera (N=4), collected pre-pandemic, were used as negative controls. Ten LFAs manufactured or distributed by ASBT Holdings Ltd, Cellex, Fortress Diagnostics, Nantong Egens Biotechnology, Mologic, NG Biotech, Nal von Minden and Suzhou Herui BioMed Co. were evaluated. Results: : Compared to RT-qPCR, sensitivity of LFAs ranged from 87.0-95.7%. Specificity against pre-pandemic controls ranged between 92.0-100%. Compared to IgG ELISA, sensitivity and specificity ranged between 90.5-100% and 93.2-100%, respectively. Percentage agreement between LFAs and IgG ELISA ranged from 89.6-92.7%. Inter-test agreement between LFAs and IgG ELISA ranged between kappa=0.792-0.854. Conclusions: : LFAs may serve as a useful tool for rapid confirmation of ongoing or previous infection in conjunction with clinical suspicion of COVID-19 in patients attending hospital. Impartial validation prior to commercial sale provides users with data that can inform best use settings
Open Access Bibliography: Liberating Scholarly Literature with E-Prints and Open Access Journals
No full textThe Open Access Bibliography: Liberating Scholarly Literature with E-Prints and Open Access Journals provides an overview of open access concepts, and it presents over 1,300 selected English-language books, conference papers (including some digital video presentations), debates, editorials, e-prints, journal and magazine articles, news articles, technical reports, and other printed and electronic sources that are useful in understanding the open access movement's efforts to provide free access to and unfettered use of scholarly literature. Most sources have been published between 1999 and August 31, 2004; however, a limited number of key sources published prior to 1999 are also included. Where possible, links are provided to sources that are freely available on the Internet (approximately 78 percent of the bibliography's references have such links). The 129-page bibliography has been published in print and PDF formats by the Association of Research Libraries (ARL). The print version is available from ARL. The book is licensed under the Creative Commons Attribution-NonCommercial License
HLA-E-restricted SARS-CoV-2-specific T cells from convalescent COVID-19 patients suppress virus replication despite HLA class Ia down-regulation
No full textPathogen-specific CD8+ T cell responses restricted by the nonpolymorphic nonclassical class Ib molecule human leukocyte antigen E (HLA-E) are rarely reported in viral infections. The natural HLA-E ligand is a signal peptide derived from classical class Ia HLA molecules that interact with the NKG2/CD94 receptors to regulate natural killer cell functions, but pathogen-derived peptides can also be presented by HLA-E. Here, we describe five peptides from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that elicited HLA-E–restricted CD8+ T cell responses in convalescent patients with coronavirus disease 2019. These T cell responses were identified in the blood at frequencies similar to those reported for classical HLA-Ia–restricted anti–SARS-CoV-2 CD8+ T cells. HLA-E peptide–specific CD8+ T cell clones, which expressed diverse T cell receptors, suppressed SARS-CoV-2 replication in Calu-3 human lung epithelial cells. SARS-CoV-2 infection markedly down-regulated classical HLA class I expression in Calu-3 cells and primary reconstituted human airway epithelial cells, whereas HLA-E expression was not affected, enabling T cell recognition. Thus, HLA-E–restricted T cells could contribute to the control of SARS-CoV-2 infection alongside classical T cells
A haemagglutination test for rapid detection of antibodies to SARS-CoV-2
No full textAbstract Serological detection of antibodies to SARS-CoV-2 is essential for establishing rates of seroconversion in populations, detection of seroconversion after vaccination, and for seeking evidence for a level of antibody that may be protective against COVID-19 disease. Several high-performance commercial tests have been described, but these require centralised laboratory facilities that are comparatively expensive, and therefore not available universally. Red cell agglutination tests have a long history in blood typing, and general serology through linkage of reporter molecules to the red cell surface. They do not require special equipment, are read by eye, have short development times, low cost and can be applied as a Point of Care Test (POCT). We describe a red cell agglutination test for the detection of antibodies to the SARS-CoV-2 receptor binding domain (RBD). We show that the Haemagglutination Test (HAT) has a sensitivity of 90% and specificity of 99% for detection of antibodies after a PCR diagnosed infection. The HAT can be titrated, detects rising titres in the first five days of hospital admission, correlates well with a commercial test that detects antibodies to the RBD, and can be applied as a point of care test. The developing reagent is composed of a previously described nanobody to a conserved glycophorin A epitope on red cells, linked to the RBD from SARS-CoV-2. It can be lyophilised for ease of shipping. We have scaled up production of this reagent to one gram, which is sufficient for ten million tests, at a cost of ~0.27 UK pence per test well. Aliquots of this reagent are ready to be supplied to qualified groups anywhere in the world that need to detect antibodies to SARS-CoV-2, but do not have the facilities for high throughput commercial tests.</p
Risk stratification of patients admitted to hospital with covid-19 using the ISARIC WHO Clinical Characterisation Protocol: development and validation of the 4C Mortality Score
No full textObjectives To develop and validate a pragmatic risk score to predict mortality for patients admitted to hospital with covid-19. Design Prospective observational cohort study: ISARIC WHO CCP-UK study (ISARIC Coronavirus Clinical Characterisation Consortium [4C]). Model training was performed on a cohort of patients recruited between 6 February and 20 May 2020, with validation conducted on a second cohort of patients recruited between 21 May and 29 June 2020. Setting 260 hospitals across England, Scotland, and Wales. Participants Adult patients (≥18 years) admitted to hospital with covid-19 admitted at least four weeks before final data extraction. Main outcome measures In-hospital mortality. Results There were 34 692 patients included in the derivation dataset (mortality rate 31.7%) and 22 454 in the validation dataset (mortality 31.5%). The final 4C Mortality Score included eight variables readily available at initial hospital assessment: age, sex, number of comorbidities, respiratory rate, peripheral oxygen saturation, level of consciousness, urea, and C-reactive protein (score range 0-21 points). The 4C risk stratification score demonstrated high discrimination for mortality (derivation cohort: AUROC 0.79; 95% CI 0.78 − 0.79; validation cohort 0.78, 0.77-0.79) with excellent calibration (slope = 1.0). Patients with a score ≥15 (n = 2310, 17.4%) had a 67% mortality (i.e., positive predictive value 67%) compared with 1.0% mortality for those with a score ≤3 (n = 918, 7%; negative predictive value 99%). Discriminatory performance was higher than 15 pre-existing risk stratification scores (AUROC range 0.60-0.76), with scores developed in other covid-19 cohorts often performing poorly (range 0.63-0.73). Conclusions We have developed and validated an easy-to-use risk stratification score based on commonly available parameters at hospital presentation. This outperformed existing scores, demonstrated utility to directly inform clinical decision making, and can be used to stratify inpatients with covid-19 into different management groups. The 4C Mortality Score may help clinicians identify patients with covid-19 at high risk of dying during current and subsequent waves of the pandemic. Study registration ISRCTN6672626
Clinical characteristics of children and young people admitted to hospital with covid-19 in United Kingdom: prospective multicentre observational cohort study
No full textObjective To characterise the clinical features of children and young people admitted to hospital with laboratory-confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in the UK, and explore factors associated with admission to critical care, mortality, and development of multisystem inflammatory syndrome in children and adolescents temporarily related to covid-19 (MIS-C). Design Prospective observational cohort study with rapid data gathering and near real time analysis. Setting 260 acute care hospitals in England, Wales, and Scotland between 17th January and 5th June 2020, with a minimal follow-up time of two weeks (to 19th June 2020). Participants 451 children and young people aged less than 19 years admitted to 116 hospitals and enrolled into the International Severe Acute Respiratory and emergency Infections Consortium (ISARIC) WHO Clinical Characterisation Protocol UK study with laboratory-confirmed SARS-CoV-2. Main Outcome Measures Admission to critical care (high dependency or intensive care), in-hospital mortality, or meeting the WHO preliminary case definition for MIS-C. Results Median age was 3.9 years [interquartile range (IQR) 0.3-12.9 years], 36% (162/451) were under 12 months old, and 57% (256/450) were male. 56% (224/401) were White, 12% (49/401) South Asian and 10% (40/401) Black. 43% (195/451) had at least one recorded comorbidity. A muco-enteric cluster of symptoms was identified, closely mirroring the WHO MIS-C criteria. 17% of children (72/431) were admitted to critical care. On multivariable analysis this was associated with age under one month odds ratio 5.05 (95% confidence interval 1.69 to 15.72, p=0.004), age 10 to 14 years OR 3.11 (1.21 to 8.55, p=0.022) and Black ethnicity OR 3.02 (1.30 to 6.84, p=0.008). Three young people died (0.7 %, 3/451) aged 16 to 19 years, all of whom had profound comorbidity. Twelve percent of children (36/303) met the WHO MIS-C criteria, with the first patient developing symptoms in mid-March. Those meeting MIS-C criteria were older, (median age 10.8 years ([IQR 8.4-14.1] vs 2.0 [0.2-12.6]), p<0.001) and more likely to be of non-White ethnicity (70% (23/33) vs 43% (101/237), p=0.005). Children with MIS-C were four times more likely to be admitted to critical care (61% (22/36) vs 15% (40/267, p<0.001). In addition to the WHO criteria, children with MIS-C were more likely to present with headache (45% (13/29) vs 11% (19/171), p<0.001), myalgia (39% (11/28) vs 7% (12/170), p<0.001), sore throat (37% (10/27) vs (13% (24/183, p = 0.004) and fatigue (57% (17/30) vs 31% (60/192), p =0.012) than children who did not and to have a platelet count of less than 150 x109/L (30% (10/33) vs 10% (24/232), p=0.004). Conclusions Our data confirms less severe covid-19 in children and young people than in adults and we provide additional evidence for refining the MIS-C case definition. The identification of a muco-enteric symptom cluster also raises the suggestion that MIS-C is the severe end of a spectrum of disease. Study registration ISRCTN6672626
