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Fagan PJ, Krusic PJ, Evans DH, Lerke SA, Johnston E. Synthesis, chemistry, and properties of a monoalkylated buckminsterfullerene derivative, tert-BuC60 anion. J Am Chem Soc 2002. [DOI: 10.1021/ja00050a081] [Citation(s) in RCA: 196] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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196 |
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Johnston E, Crawford J, Blackwell S, Bjurstrom T, Lockbaum P, Roskos L, Yang BB, Gardner S, Miller-Messana MA, Shoemaker D, Garst J, Schwab G. Randomized, dose-escalation study of SD/01 compared with daily filgrastim in patients receiving chemotherapy. J Clin Oncol 2000; 18:2522-8. [PMID: 10893282 DOI: 10.1200/jco.2000.18.13.2522] [Citation(s) in RCA: 189] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE To explore the use of SD/01 (a polyethylene glycol-conjugated filgrastim shown in preclinical studies to have a prolonged half-life) in patients with chemotherapy-induced neutropenia. PATIENTS AND METHODS Thirteen patients with non-small-cell lung cancer were randomized to receive daily filgrastim (5 microg/kg/d) or a single injection of SD/01 (30, 100, or 300 microg/kg) 2 weeks before chemotherapy and again 24 hours after administration of carboplatin and paclitaxel. Pharmacodynamic, pharmacokinetic, and safety analyses were performed. RESULTS Peak serum concentrations of SD/01 and the duration of increased serum concentrations were dependent on the SD/01 dose. SD/01 concentrations remained increased longer in patients with chemotherapy-induced neutropenia. Prechemotherapy median absolute neutrophil counts (ANCs) in patients receiving SD/01 were increased in a dose-dependent fashion, with the duration of this effect also being dose dependent. After chemotherapy, median ANC nadirs were similar in the filgrastim cohort and the cohort receiving SD/01 30 microg/kg, with higher nadirs seen in the cohorts receiving SD/01 100 or 300 microg/kg. Dose-limiting toxicities were not noted. CD34(+) cells were mobilized in all cohorts. CONCLUSION A single dose of SD/01 increases the serum concentration of SD/01 for several days in a dose-dependent fashion and is not associated with significant toxicity. The effects of SD/01 on ANC and CD34(+) cell mobilization are comparable or greater than those achieved with daily filgrastim. The self-regulation of this molecule provides a potential therapeutic advantage in a variety of clinical settings associated with neutropenia.
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Clinical Trial |
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189 |
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Boyce BF, Smith L, Fogelman I, Johnston E, Ralston S, Boyle IT. Focal osteomalacia due to low-dose diphosphonate therapy in Paget's disease. Lancet 1984; 1:821-4. [PMID: 6143140 DOI: 10.1016/s0140-6736(84)92272-4] [Citation(s) in RCA: 158] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Transiliac bone biopsies carried out on 13 patients with Paget's disease to evaluate the effects of low-dose diphosphonate (disodium etidronate) therapy showed focal osteomalacia in the 9 patients in whom post-therapy specimens were taken through pagetic bone. Active bone resorption persisted in 5 of these. A mineralisation defect not amounting to osteomalacia--ie, osteoid of increased thickness but of normal extent--was present in the 4 specimens taken through non-pagetic bone. Although 9 patients experienced symptomatic improvement, 2 suffered fissure fractures in affected lower limbs. In Paget's disease, the combination of osteomalacia and continuing active resorption within a lytic lesion may increase the risk of fracture in a weight-bearing bone. It is suggested that although disodium etidronate often provides effective pain relief it should be administered with caution until the optimum dose and duration of therapy are further evaluated.
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Stone J, Johnston E. The topography of primate retina: a study of the human, bushbaby, and new- and old-world monkeys. J Comp Neurol 1981; 196:205-23. [PMID: 7217355 DOI: 10.1002/cne.901960204] [Citation(s) in RCA: 150] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The distribution of ganglion cells has been studied in the retinas of four primates: the prosimian bushbaby, the New-World squirrel monkey, the Old-World crab-eating cynamolgous monkey, and the human. The sizes of ganglion cell somas were also measured at a number of retinal locations and compared with similar measurements in the cat retina to test for the presence in primates of retinal specializations such as the visual streak, and for gradients in retinal structure, such as that between temporal and nasal retina. In all four primates, ganglion cell somas in peripheral retina ranged considerably in diameter (6-16 micrometer in the bushbaby, 8-22 micrometer in the squirrel monkey, 8-23 micrometer in the cynamolgous monkey, 8-26 micrometer in the human). It seems likely that the strong physiological correlates of soma size which have been described among cat retinal ganglion cells and among the relay cells of the macaque lateral geniculate nucleus are generally present in primates. In all four primates, evidence was also obtained of a visual streak specialization; the isodensity lines in ganglion cell density maps were horizontally elongated, and small-bodied ganglion cells were relatively more common in the region of the proposed streak than in other areas of peripheral retina. However, the visual streak seems less well developed than in the cat; among the four primate species examined it was best developed in the bushbaby, at least as assessed by the shape of the isodensity lines. All four primates showed a clear foveal specialization, but this feature seemed least developed in the bushbaby. At the fovea, ganglion cells are smaller in soma size than in peripheral retina; they also seemed more uniform in size, although some distinctly larger cells persist in the human and bushbaby. Soma size measurements also provided evidence of a difference between nasal and temporal areas of peripheral retina comparable to that reported for the cat and other species. Thus the primate retinas examined show features, such as the foveal specialization, which seem unique to them among mammals. They also show features, such as nasal-temporal differences in ganglion cell size, and (though weakly developed) a visual streak, which they have in common with other mammals with widely different phylogenetic histories.
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Case Reports |
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O'Brien SL, Gibbons SM, Owens SM, Hampton-Marcell J, Johnston ER, Jastrow JD, Gilbert JA, Meyer F, Antonopoulos DA. Spatial scale drives patterns in soil bacterial diversity. Environ Microbiol 2016; 18:2039-51. [PMID: 26914164 DOI: 10.1111/1462-2920.13231] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 01/17/2016] [Indexed: 01/16/2023]
Abstract
Soil microbial communities are essential for ecosystem function, but linking community composition to biogeochemical processes is challenging because of high microbial diversity and large spatial variability of most soil characteristics. We investigated soil bacterial community structure in a switchgrass stand planted on soil with a history of grassland vegetation at high spatial resolution to determine whether biogeographic trends occurred at the centimeter scale. Moreover, we tested whether such heterogeneity, if present, influenced community structure within or among ecosystems. Pronounced heterogeneity was observed at centimeter scales, with abrupt changes in relative abundance of phyla from sample to sample. At the ecosystem scale (> 10 m), however, bacterial community composition and structure were subtly, but significantly, altered by fertilization, with higher alpha diversity in fertilized plots. Moreover, by comparing these data with data from 1772 soils from the Earth Microbiome Project, it was found that 20% of bacterial taxa were shared between their site and diverse globally sourced soil samples, while grassland soils shared approximately 40% of their operational taxonomic units with the current study. By spanning several orders of magnitude, the analysis suggested that extreme patchiness characterized community structure at smaller scales but that coherent patterns emerged at larger length scales.
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Journal Article |
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122 |
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Gogol EP, Johnston E, Aggeler R, Capaldi RA. Ligand-dependent structural variations in Escherichia coli F1 ATPase revealed by cryoelectron microscopy. Proc Natl Acad Sci U S A 1990; 87:9585-9. [PMID: 2148209 PMCID: PMC55217 DOI: 10.1073/pnas.87.24.9585] [Citation(s) in RCA: 87] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The Escherichia coli F1 ATPase, ECF1, has been examined by cryoelectron microscopy after reaction with Fab' fragments generated from monoclonal antibodies to the alpha and epsilon subunits. The enzyme-antibody complexes appeared triangular due to the superposition of three anti-alpha Fab' fragments on alternating densities of the hexagonally arranged alpha and beta subunits. The Fab' to the epsilon subunit superimposed on a beta subunit. A density was observed near the center of the structure in the internal cavity. The position of this central density with respect to peripheral sites was not fixed. Sorting of images of ECF1 labeled with the combination of three anti-alpha Fab' fragments plus an Fab' directed to the epsilon subunit gave three classes in each of which the central density was closest to a different beta subunit. The distribution of the central density among the three classes was measured for different ligand-binding conditions. When ATP was present in catalytic sites under conditions where there was no enzyme turnover (i.e., without Mg2+ present), there were approximately equal numbers of images in each of three classes. When ATP and Mg2+ were added and ATP hydrolysis was allowed to proceed, almost two-thirds of the images were in the class in which the central density was closest to the beta subunit superimposed by the epsilon subunit. We conclude that domains within the ECF1 structure, either the central mass or a domain including the epsilon subunit, move in the enzyme in response to ligand binding. We suggest that this movement is involved in coupling catalytic sites to the proton channel in the F0 part of the ATP synthase.
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Keshgegian AA, Johnston E, Cnaan A. Bcl-2 oncoprotein positivity and high MIB-1 (Ki-67) proliferative rate are independent predictive markers for recurrence in prostate carcinoma. Am J Clin Pathol 1998; 110:443-9. [PMID: 9763029 DOI: 10.1093/ajcp/110.4.443] [Citation(s) in RCA: 77] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Predicting the clinical behavior of prostate carcinoma can be difficult; one approach is to identify molecular prognostic markers. We evaluated proliferative rate (MIB-1 antibody) and expression of bcl-2, p53, and retinoblastoma (pRB) proteins, which have cell cycle-related functions, in 208 consecutive radical prostatectomy specimens. Values were correlated with histopathologic parameters (Gleason tumor score, tumor amount, capsule invasion, and involvement of surgical margins, seminal vesicles, or lymph nodes) and with recurrence-free survival (4-year median follow-up). A high MIB-1 proliferative rate was associated with all of the measured histopathologic parameters, p53 overexpression with tumor amount, and pRB expression with positive lymph nodes. pRB and p53 expression levels were not associated with differences in recurrence-free survival. A high MIB-1 proliferative rate and bcl-2 positivity were associated with increased recurrence, both considered individually, and also independently and additively when examined together and with the most predictive histopathologic factors (Gleason tumor score and seminal vesicle involvement). MIB-1 proliferative rate and bcl-2 positivity may prove to be useful markers for poor prognosis in prostate carcinoma.
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77 |
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Zhang X, Johnston ER, Liu W, Li L, Han X. Environmental changes affect the assembly of soil bacterial community primarily by mediating stochastic processes. GLOBAL CHANGE BIOLOGY 2016; 22:198-207. [PMID: 26340501 DOI: 10.1111/gcb.13080] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 08/27/2015] [Indexed: 06/05/2023]
Abstract
Both 'species fitness difference'-based deterministic processes, such as competitive exclusion and environmental filtering, and 'species fitness difference'-independent stochastic processes, such as birth/death and dispersal/colonization, can influence the assembly of soil microbial communities. However, how both types of processes are mediated by anthropogenic environmental changes has rarely been explored. Here we report a novel and general pattern that almost all anthropogenic environmental changes that took place in a grassland ecosystem affected soil bacterial community assembly primarily through promoting or restraining stochastic processes. We performed four experiments mimicking 16 types of environmental changes and separated the compositional variation of soil bacterial communities caused by each environmental change into deterministic and stochastic components, with a recently developed method. Briefly, because the difference between control and treatment communities is primarily caused by deterministic processes, the deterministic change was quantified as (mean compositional variation between treatment and control) - (mean compositional variation within control). The difference among replicate treatment communities is primarily caused by stochastic processes, so the stochastic change was estimated as (mean compositional variation within treatment) - (mean compositional variation within control). The absolute of the stochastic change was greater than that of the deterministic change across almost all environmental changes, which was robust for both taxonomic and functional-based criterion. Although the deterministic change may become more important as environmental changes last longer, our findings showed that changes usually occurred through mediating stochastic processes over 5 years, challenging the traditional determinism-dominated view.
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63 |
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Johnston E, Scranton P, Pfeffer GB. Chronic disorders of the Achilles tendon: results of conservative and surgical treatments. Foot Ankle Int 1997; 18:570-4. [PMID: 9310768 DOI: 10.1177/107110079701800907] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We reviewed our results of nonoperative and operative treatment of chronic Achilles tenosynovitis to further define outcomes and treatment parameters. Forty-one patients presented with an average of 14 weeks of Achilles tendon symptoms. All patients received nonsurgical treatment initially, and 21 patients (51%) recovered after an average of 18 weeks of therapy. Three additional patients improved after brisement of the tendon/peritenon interspace. Seventeen of 41 patients eventually underwent soft tissue tenolysis and/or excision of degenerative tendon cysts. Those patients who responded to nonoperative therapy tended to be younger (average age, 33 years) than those who had degenerative tendon changes requiring surgery (average age, 48 years). All surgical patients were able to return to unrestricted activity after 31 weeks (range, 27-48 weeks). We believe 4 to 6 months of nonsurgical therapy is appropriate for middle aged patients or athletes with chronic Achilles tenosynovitis. Those that fail this treatment will improve with a limited debridement of diseased tissue without excessive soft tissue dissection of the tendon.
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10
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Sims B, Johnston E. Examining Public Opinion about Crime and Justice: A Statewide Study. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/0887403403252668] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
As noted by Flanagan (1996), public opinion polls about crime and justice can act as a social barometer providing important data to policy makers regarding what the public is willing, or is not willing, to accept when it comes to proposed legislation and/or intervention programming. This paper reports findings from the 2001 Penn State Poll, a random telephone survey of Pennsylvanians, 18 years of age or older, in which citizens were asked about their attitudes toward and perceptions of such issues as fear of crime, capital punishment, the most important goal of prison, and where they would most like to see their tax dollars spent (building more prisons vs. early intervention programs with troubled youth). Significant differences were found within certain demographic groups across these sets of questions, and in a predictive model, gender, race/ethnicity, and education had a greater impact on citizens’ support for capital punishment than did their fear of crime. Overall, findings suggest that the public is not as punitive as it is sometimes believed to be by legislators and policy makers.
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DeNise S, Johnston E, Halverson J, Marshall K, Rosenfeld D, McKenna S, Sharp T, Edwards J. Power of exclusion for parentage verification and probability of match for identity in American kennel club breeds using 17 canine microsatellite markers. Anim Genet 2004; 35:14-7. [PMID: 14731224 DOI: 10.1046/j.1365-2052.2003.01074.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
DNA analysis of microsatellite markers has become a common tool for verifying parentage in breed registries and identifying individual animals that are linked to a database or owner. Panels of markers have been developed in canines, but their utility across and within a wide range of breeds has not been reported. The American Kennel Club (AKC) authorized a study to determine the power to exclude non-parents and identify individuals using DNA genotypes of 17 microsatellite markers in two panels. Cheek swab samples were voluntarily collected at Parent Breed Club National Specialty dog shows and 9561 samples representing 108 breeds were collected, averaging 88.5 dogs per breed. The primary panel of 10 markers exceeded 99% power of exclusion for canine parentage verification of 61% of the breeds. In combination with the secondary panel of seven markers, 100% of the tested breeds exceeded 99% power of exclusion. The minimum probability match rate of the first panel was 3.6 x 10(-5) averaged across breeds, and with the addition of the second panel, the probability match rate was 3.2 x 10(-8); thus the probability of another random, unrelated dog with the same genotype is very low. The results of this analysis indicated that, on average, the primary panel meets the AKC's needs for routine parentage testing, but that a combination of 10-15 genetic markers from the two panels could yield a universal canine panel with enhanced processing efficiency, reliability and informativeness.
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53 |
12
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Yamamoto T, Kabus S, Lorenz C, Johnston E, Maxim PG, Diehn M, Eclov N, Barquero C, Loo BW, Keall PJ. 4D CT lung ventilation images are affected by the 4D CT sorting method. Med Phys 2013; 40:101907. [PMID: 24089909 PMCID: PMC3785523 DOI: 10.1118/1.4820538] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 07/01/2013] [Accepted: 08/17/2013] [Indexed: 11/07/2022] Open
Abstract
PURPOSE Four-dimensional (4D) computed tomography (CT) ventilation imaging is a novel promising technique for lung functional imaging. The current standard 4D CT technique using phase-based sorting frequently results in artifacts, which may deteriorate the accuracy of ventilation imaging. The purpose of this study was to quantify the variability of 4D CT ventilation imaging due to 4D CT sorting. METHODS 4D CT image sets from nine lung cancer patients were each sorted by the phase-based method and anatomic similarity-based method, designed to reduce artifacts, with corresponding ventilation images created for each method. Artifacts in the resulting 4D CT images were quantified with the artifact score which was defined based on the difference between the normalized cross correlation for CT slices within a CT data segment and that for CT slices bordering the interface between adjacent CT data segments. The ventilation variation was quantified using voxel-based Spearman rank correlation coefficients for all lung voxels, and Dice similarity coefficients (DSC) for the spatial overlap of low-functional lung volumes. Furthermore, the correlations with matching single-photon emission CT (SPECT) ventilation images (assumed ground truth) were evaluated for three patients to investigate which sorting method provides higher physiologic accuracy. RESULTS Anatomic similarity-based sorting reduced 4D CT artifacts compared to phase-based sorting (artifact score, 0.45 ± 0.14 vs 0.58 ± 0.24, p = 0.10 at peak-exhale; 0.63 ± 0.19 vs 0.71 ± 0.31, p = 0.25 at peak-inhale). The voxel-based correlation between the two ventilation images was 0.69 ± 0.26 on average, ranging from 0.03 to 0.85. The DSC was 0.71 ± 0.13 on average. Anatomic similarity-based sorting yielded significantly fewer lung voxels with paradoxical negative ventilation values than phase-based sorting (5.0 ± 2.6% vs 9.7 ± 8.4%, p = 0.05), and improved the correlation with SPECT ventilation regionally. CONCLUSIONS The variability of 4D CT ventilation imaging due to 4D CT sorting was moderate overall and substantial in some cases, suggesting that 4D CT artifacts are an important source of variations in 4D CT ventilation imaging. Reduction of 4D CT artifacts provided more physiologically convincing and accurate ventilation estimates. Further studies are needed to confirm this result.
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Research Support, N.I.H., Extramural |
12 |
50 |
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ter Horst AM, Santos-Medellín C, Sorensen JW, Zinke LA, Wilson RM, Johnston ER, Trubl G, Pett-Ridge J, Blazewicz SJ, Hanson PJ, Chanton JP, Schadt CW, Kostka JE, Emerson JB. Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations. MICROBIOME 2021; 9:233. [PMID: 34836550 PMCID: PMC8626947 DOI: 10.1186/s40168-021-01156-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/02/2021] [Indexed: 05/31/2023]
Abstract
BACKGROUND Peatlands are expected to experience sustained yet fluctuating higher temperatures due to climate change, leading to increased microbial activity and greenhouse gas emissions. Despite mounting evidence for viral contributions to these processes in peatlands underlain with permafrost, little is known about viruses in other peatlands. More generally, soil viral biogeography and its potential drivers are poorly understood at both local and global scales. Here, 87 metagenomes and five viral size-fraction metagenomes (viromes) from a boreal peatland in northern Minnesota (the SPRUCE whole-ecosystem warming experiment and surrounding bog) were analyzed for dsDNA viral community ecological patterns, and the recovered viral populations (vOTUs) were compared with our curated PIGEON database of 266,125 vOTUs from diverse ecosystems. RESULTS Within the SPRUCE experiment, viral community composition was significantly correlated with peat depth, water content, and carbon chemistry, including CH4 and CO2 concentrations, but not with temperature during the first 2 years of warming treatments. Peat vOTUs with aquatic-like signatures (shared predicted protein content with marine and/or freshwater vOTUs) were significantly enriched in more waterlogged surface peat depths. Predicted host ranges for SPRUCE vOTUs were relatively narrow, generally within a single bacterial genus. Of the 4326 SPRUCE vOTUs, 164 were previously detected in other soils, mostly peatlands. None of the previously identified 202,371 marine and freshwater vOTUs in our PIGEON database were detected in SPRUCE peat, but 0.4% of 80,714 viral clusters (VCs, grouped by predicted protein content) were shared between soil and aquatic environments. On a per-sample basis, vOTU recovery was 32 times higher from viromes compared with total metagenomes. CONCLUSIONS Results suggest strong viral "species" boundaries between terrestrial and aquatic ecosystems and to some extent between peat and other soils, with differences less pronounced at higher taxonomic levels. The significant enrichment of aquatic-like vOTUs in more waterlogged peat suggests that viruses may also exhibit niche partitioning on more local scales. These patterns are presumably driven in part by host ecology, consistent with the predicted narrow host ranges. Although more samples and increased sequencing depth improved vOTU recovery from total metagenomes, the substantially higher per-sample vOTU recovery after viral particle enrichment highlights the utility of soil viromics. Video abstract The importance of Minnesota peat viromes in revealing terrestrial and aquatic niche partitioning for viral populations.
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Video-Audio Media |
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47 |
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Snyder JR, Johnston ER, Serianni AS. D-Talose anomerization: NMR methods to evaluate the reaction kinetics. J Am Chem Soc 2002. [DOI: 10.1021/ja00189a050] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Johnston ER, Radke K. The SU and TM envelope protein subunits of bovine leukemia virus are linked by disulfide bonds, both in cells and in virions. J Virol 2000; 74:2930-5. [PMID: 10684314 PMCID: PMC111788 DOI: 10.1128/jvi.74.6.2930-2935.2000] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
After the polyprotein precursor of retroviral envelope proteins is proteolytically cleaved, the surface (SU) and transmembrane (TM) subunits remain associated with each other by noncovalent interactions or by disulfide bonds. Disulfide linkages confer a relatively stable association between the SU and TM envelope protein subunits of Rous sarcoma virus and murine leukemia virus. In contrast, the noncovalent association between SU and TM of human immunodeficiency virus leads to significant shedding of SU from the surface of infected cells. The SU and TM proteins of bovine leukemia virus (BLV) initially were reported to be disulfide linked but later were concluded not to be, since TM is often lost during purification of SU protein. Here, we show that SU and TM of BLV do, indeed, associate through disulfide bonds, whether the envelope proteins are overexpressed in transfected cells, are produced in virus-infected cells, or are present in newly produced virions.
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25 |
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Linch M, Goh G, Hiley C, Shanmugabavan Y, McGranahan N, Rowan A, Wong YNS, King H, Furness A, Freeman A, Linares J, Akarca A, Herrero J, Rosenthal R, Harder N, Schmidt G, Wilson GA, Birkbak NJ, Mitter R, Dentro S, Cathcart P, Arya M, Johnston E, Scott R, Hung M, Emberton M, Attard G, Szallasi Z, Punwani S, Quezada SA, Marafioti T, Gerlinger M, Ahmed HU, Swanton C. Intratumoural evolutionary landscape of high-risk prostate cancer: the PROGENY study of genomic and immune parameters. Ann Oncol 2017; 28:2472-2480. [PMID: 28961847 PMCID: PMC5815564 DOI: 10.1093/annonc/mdx355] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Intratumoural heterogeneity (ITH) is well recognised in prostate cancer (PC), but its role in high-risk disease is uncertain. A prospective, single-arm, translational study using targeted multiregion prostate biopsies was carried out to study genomic and T-cell ITH in clinically high-risk PC aiming to identify drivers and potential therapeutic strategies. PATIENTS AND METHODS Forty-nine men with elevated prostate-specific antigen and multiparametric-magnetic resonance imaging detected PC underwent image-guided multiregion transperineal biopsy. Seventy-nine tumour regions from 25 patients with PC underwent sequencing, analysis of mutations, copy number and neoepitopes combined with tumour infiltrating T-cell subset quantification. RESULTS We demonstrated extensive somatic nucleotide variation and somatic copy number alteration heterogeneity in high-risk PC. Overall, the mutational burden was low (0.93/Megabase), but two patients had hypermutation, with loss of mismatch repair (MMR) proteins, MSH2 and MSH6. Somatic copy number alteration burden was higher in patients with metastatic hormone-naive PC (mHNPC) than in those with high-risk localised PC (hrlPC), independent of Gleason grade. Mutations were rarely ubiquitous and mutational frequencies were similar for mHNPC and hrlPC patients. Enrichment of focal 3q26.2 and 3q21.3, regions containing putative metastasis drivers, was seen in mHNPC patients. We found evidence of parallel evolution with three separate clones containing activating mutations of β-catenin in a single patient. We demonstrated extensive intratumoural and intertumoural T-cell heterogeneity and high inflammatory infiltrate in the MMR-deficient (MMRD) patients and the patient with parallel evolution of β-catenin. Analysis of all patients with activating Wnt/β-catenin mutations demonstrated a low CD8+/FOXP3+ ratio, a potential surrogate marker of immune evasion. CONCLUSIONS The PROGENY (PROstate cancer GENomic heterogeneitY) study provides a diagnostic platform suitable for studying tumour ITH. Genetic aberrations in clinically high-risk PC are associated with altered patterns of immune infiltrate in tumours. Activating mutations of Wnt/β-catenin signalling pathway or MMRD could be considered as potential biomarkers for immunomodulation therapies. CLINICAL TRIALS.GOV IDENTIFIER NCT02022371.
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Jiang L, Johnston E, Aberg KM, Nilsson U, Ilag LL. Strategy for quantifying trace levels of BMAA in cyanobacteria by LC/MS/MS. Anal Bioanal Chem 2012. [PMID: 23180086 DOI: 10.1007/s00216-012-6550-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cyanobacterial neurotoxin β-N-methylamino-L-alanine (BMAA) is an amino acid that is putatively associated with the pathology of amyotrophic lateral sclerosis/Parkinsonism-dementia complex (ALS-PDC) disease. It raises serious health risk concerns since cyanobacteria are ubiquitous thus making human exposure almost inevitable. The identification and quantification of BMAA in cyanobacteria is challenging because it is present only in trace amounts and occurs alongside structurally similar compounds such as BMAA isomers. This work describes an enhanced liquid chromatography/tandem mass spectrometry platform that can distinguish BMAA from its isomers β-amino-N-methyl-alanine, N-(2-aminoethyl) glycine (AEG), and 2,4-diaminobutyric acid, thus ensuring confident identification of BMAA. The method's sensitivity was improved fourfold by a post-column addition of acetonitrile. The instrument and method limits of detection were shown to be 4.2 fmol/injection (or 0.5 pg/one column) and 0.1 μg/g dry weight of cyanobacteria, respectively. The quantification method uses synthesized deuterated BMAA as an internal standard and exhibits good linearity, accuracy, and precision. Matrix effects were also investigated, revealing an ion enhancement of around 18 %. A lab-cultured cyanobacterial sample (Leptolyngbya PCC73110) was analyzed and shown to contain about 0.73 μg/g dry weight BMAA. The isomer AEG, whose chromatographic properties closely resemble those of BMAA, was also detected. These results highlight the importance of distinguishing BMAA from its isomers for reliable identification as well as providing a sensitive and accurate quantification method for measuring trace levels of BMAA in cyanobacterial samples.
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Franzblau A, Werner RA, Albers JW, Grant CL, Olinski D, Johnston E. Workplace surveillance for carpal tunnel syndrome using hand diagrams. JOURNAL OF OCCUPATIONAL REHABILITATION 1994; 4:185-198. [PMID: 24234506 DOI: 10.1007/bf02331615] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Four hundred and eleven workers from 4 different companies participated in a worksite screening program designed, in part, to estimate the prevalence of carpal tunnel syndrome (CTS). Each worker completed a discomfort survey and underwent limited nerve conduction testing of the median and ulnar sensory nerves in both wrists. The discomfort survey included a hand diagram which allowed subjects to shade in area(s) affected by numbness, burning, tingling, or pain. The discomfort survey also asked each worker to indicate whether she or he had experienced neuropathic symptoms (i.e., numbness, burning, tingling, or pain) in the wrist, hand or fingers of each hand, without regard to localization (i.e., median versus ulnar versus radial distribution), and also nocturnal occurrence of symptoms. Analyses involved comparing hand diagram scores and non localized wrist/hand/finger symptoms with electrodiagnostic test results. All configurations of hand diagram scores of the dominant hands had a statistically significant association with electrophysiologically determined median nerve dysfunction, but so did non localized symptom reports. The sensitivity, specificity, and positive predicted values of hand diagrams were poorer than those reported previously. While some test performance characteristics of hand diagrams were better than those for non localized distal extremity symptoms consistent with CTS, some were worse. Overall, our data suggest that hand diagrams are no better than using a questionnaire to determine if workers have experienced symptoms consistent with CTS in their wrists, hands or fingers without regard to localization. The choice of screening tool would depend on the goal of screening, in particular, whether it is more desirable to have slightly higher sensitivity or positive predictive value.
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Aussedat B, Fasching B, Johnston E, Sane N, Nagorny P, Danishefsky SJ. Total synthesis of the α-subunit of human glycoprotein hormones: toward fully synthetic homogeneous human follicle-stimulating hormone. J Am Chem Soc 2012; 134:3532-41. [PMID: 22280541 PMCID: PMC3288947 DOI: 10.1021/ja2111459] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Described herein is the first total chemical synthesis of the unique α-subunit of the human glycoprotein hormone (α-hGPH). Unlike the biologically derived glycoprotein hormones, which are isolated as highly complex mixtures of glycoforms, α-hGPH obtained by chemical synthesis contains discrete homogeneous glycoforms. Two such systems have been prepared. One contains the disaccharide chitobiose at the natural N-glycosylation sites. The other contains dodecamer oligosaccharides at these same sites. The dodecamer sugar is a consensus sequence incorporating the key features associated with human glycoproteins.
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Research Support, N.I.H., Extramural |
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Johnston ER, Rodriguez-R LM, Luo C, Yuan MM, Wu L, He Z, Schuur EAG, Luo Y, Tiedje JM, Zhou J, Konstantinidis KT. Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem. Front Microbiol 2016; 7:579. [PMID: 27199914 PMCID: PMC4842900 DOI: 10.3389/fmicb.2016.00579] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 04/08/2016] [Indexed: 01/19/2023] Open
Abstract
How soil microbial communities contrast with respect to taxonomic and functional composition within and between ecosystems remains an unresolved question that is central to predicting how global anthropogenic change will affect soil functioning and services. In particular, it remains unclear how small-scale observations of soil communities based on the typical volume sampled (1-2 g) are generalizable to ecosystem-scale responses and processes. This is especially relevant for remote, northern latitude soils, which are challenging to sample and are also thought to be more vulnerable to climate change compared to temperate soils. Here, we employed well-replicated shotgun metagenome and 16S rRNA gene amplicon sequencing to characterize community composition and metabolic potential in Alaskan tundra soils, combining our own datasets with those publically available from distant tundra and temperate grassland and agriculture habitats. We found that the abundance of many taxa and metabolic functions differed substantially between tundra soil metagenomes relative to those from temperate soils, and that a high degree of OTU-sharing exists between tundra locations. Tundra soils were an order of magnitude less complex than their temperate counterparts, allowing for near-complete coverage of microbial community richness (~92% breadth) by sequencing, and the recovery of 27 high-quality, almost complete (>80% completeness) population bins. These population bins, collectively, made up to ~10% of the metagenomic datasets, and represented diverse taxonomic groups and metabolic lifestyles tuned toward sulfur cycling, hydrogen metabolism, methanotrophy, and organic matter oxidation. Several population bins, including members of Acidobacteria, Actinobacteria, and Proteobacteria, were also present in geographically distant (~100-530 km apart) tundra habitats (full genome representation and up to 99.6% genome-derived average nucleotide identity). Collectively, our results revealed that Alaska tundra microbial communities are less diverse and more homogenous across spatial scales than previously anticipated, and provided DNA sequences of abundant populations and genes that would be relevant for future studies of the effects of environmental change on tundra ecosystems.
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Franzblau A, Werner R, Valle J, Johnston E. Workplace surveillance for carpal tunnel syndrome: A comparison of methods. JOURNAL OF OCCUPATIONAL REHABILITATION 1993; 3:1-14. [PMID: 24243148 DOI: 10.1007/bf01076738] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A variety of screening procedures for carpal tunnel syndrome (CTS) were applied among workers in a manufacturing plant, and results were compared. The test procedures included a symptom survey, physical examination, limited electrodiagnostic testing at the wrists, quantitative vibratory threshold testing, 2-point discrimination, palmar pinch grip, and hand grip strength testing. When electrodiagnostic testing alone was used as "gold standard," the sensitivity and positive predictive value (PPV) of physical examination findings and quantitative test procedures were no better than, and usually worse than, the results on the symptom survey alone. Variation of the constellation of symptoms (i.e., numbness, tingling, pain or burning) and the anatomic distribution of reported symptoms (i.e., fingers, hand, wrist, or forearm) for inclusion in the screening symptom definition of CTS yielded modest changes in the sensitivity and PPV of the symptom survey. However, addition of the requirement for nocturnal symptoms as part of the screening symptom definition for CTS resulted in substantially higher PPV with only slight reduction in sensitivity. These results suggest that, in the absence of electrodiagnostic testing, the simplest test, and the procedure with the highest sensitivity and PPV for CTS is a symptom survey alone. Quantitative test procedures (vibrometry, pinch grip strength, hand grip strength) and physical examination for findings consistent with CTS (e.g., Phalen's test, Tinel's test, thenar muscle wasting, 2-point discrimination) appear to contribute little, if any, additional information when screening subjects in the work setting.
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Zhang X, Johnston ER, Li L, Konstantinidis KT, Han X. Experimental warming reveals positive feedbacks to climate change in the Eurasian Steppe. ISME JOURNAL 2016; 11:885-895. [PMID: 27996978 DOI: 10.1038/ismej.2016.180] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Revised: 10/20/2016] [Accepted: 10/28/2016] [Indexed: 02/01/2023]
Abstract
Identifying soil microbial feedbacks to increasing temperatures and moisture alterations is critical for predicting how terrestrial ecosystems will respond to climate change. We performed a 5-year field experiment manipulating warming, watering and their combination in a semiarid temperate steppe in northern China. Warming stimulated the abundance of genes responsible for degrading recalcitrant soil organic matter (SOM) and reduced SOM content by 13%. Watering, and warming plus watering also increased the abundance of recalcitrant SOM catabolism pathways, but concurrently promoted plant growth and increased labile SOM content, which somewhat offset SOM loss. The treatments also increased microbial biomass, community complexity and metabolic potential for nitrogen and sulfur assimilation. Both microbial and plant community composition shifted with the treatment conditions, and the sample-to-sample compositional variations of the two communities (pairwise β-diversity distances) were significantly correlated. In particular, microbial community composition was substantially correlated with the dominant plant species (~0.54 Spearman correlation coefficient), much more than with measured soil indices, affirming a tight coupling between both biological communities. Collectively, our study revealed the direction and underlying mechanisms of microbial feedbacks to warming and suggested that semiarid regions of northern steppes could act as a net carbon source under increased temperatures, unless precipitation increases concurrently.
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Gustafson G, Vicini F, Freedman L, Johnston E, Edmundson G, Sherman S, Pursel S, Komic M, Chen P, Borrego JC. High dose rate endobronchial brachytherapy in the management of primary and recurrent bronchogenic malignancies. Cancer 1995; 75:2345-50. [PMID: 7712446 DOI: 10.1002/1097-0142(19950501)75:9<2345::aid-cncr2820750925>3.0.co;2-m] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
BACKGROUND The clinical, radiographic, and bronchoscopic records of patients treated with out-patient high dose rate (HDR) endobronchial brachytherapy were reviewed to determine its effectiveness in patients with malignant airway obstruction (with or without prior external beam radiation). In addition, quality of life and acute and chronic morbidity were evaluated. METHODS From January 1, 1989 to June 30, 1993, 46 patients received 128 HDR endobronchial treatments employing a high activity Ir-192 source with a remote afterloader. Patients treated had a total of 22 primary and 17 recurrent bronchogenic carcinomas, 7 of which were metastatic nonpulmonary tumors. Three separate fractions of 7.0 Gy were prescribed to a depth of 1.0 cm. and given 1 week apart. Twelve patients (30%) received prior external beam irradiation (median dose, 58 Gy). RESULTS Median follow-up for the entire group was 5 months (17.5 for surviving patients). Of the eight asymptomatic patients, five (62%) remained asymptomatic for the remainder of their lives. Of the 38 symptomatic patients, 28 (74%) had significant clinical improvement, and 12 of them remained improved for the duration of their lives. Of thirty-six (78%) patients examined for radiographic response, 25 (69%) had a partial or complete response to this treatment. In patients without prior irradiation, there was a tendency for a higher percentage of clinical and radiographic response. Two patients (4%) experienced mild, transient dysphagia, four patients developed self-limited radiation pneumonitis (9%), and three patients (7%) suffered fatal hemoptysis (all of these patients received prior or concurrent external beam radiotherapy). No factor (i.e., prior radiation therapy, number of catheters placed, surgery, or chemotherapy) predicted an increased risk of complications (P = NS). CONCLUSIONS Outpatient HDR endobronchial brachytherapy is effective in both preventing and relieving endobronchial obstruction in patients with or without prior irradiation, recurrent lesions, or metastatic nonpulmonary disease. A significant proportion of patients can be rendered asymptomatic for the duration of their lives, hence were provided with improved quality of life. These treatments are well tolerated and safe, and result in minimal long term morbidity.
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Kanthaswamy S, Tom BK, Mattila AM, Johnston E, Dayton M, Kinaga J, Joy-Alise Erickson B, Halverson J, Fantin D, DeNise S, Kou A, Malladi V, Satkoski J, Budowle B, Glenn Smith D, Koskinen MT. Canine Population Data Generated from a Multiplex STR Kit for Use in Forensic Casework. J Forensic Sci 2009; 54:829-40. [DOI: 10.1111/j.1556-4029.2009.01080.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Tao X, Feng J, Yang Y, Wang G, Tian R, Fan F, Ning D, Bates CT, Hale L, Yuan MM, Wu L, Gao Q, Lei J, Schuur EAG, Yu J, Bracho R, Luo Y, Konstantinidis KT, Johnston ER, Cole JR, Penton CR, Tiedje JM, Zhou J. Winter warming in Alaska accelerates lignin decomposition contributed by Proteobacteria. MICROBIOME 2020; 8:84. [PMID: 32503635 PMCID: PMC7275452 DOI: 10.1186/s40168-020-00838-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 04/15/2020] [Indexed: 06/01/2023]
Abstract
BACKGROUND In a warmer world, microbial decomposition of previously frozen organic carbon (C) is one of the most likely positive climate feedbacks of permafrost regions to the atmosphere. However, mechanistic understanding of microbial mediation on chemically recalcitrant C instability is limited; thus, it is crucial to identify and evaluate active decomposers of chemically recalcitrant C, which is essential for predicting C-cycle feedbacks and their relative strength of influence on climate change. Using stable isotope probing of the active layer of Arctic tundra soils after depleting soil labile C through a 975-day laboratory incubation, the identity of microbial decomposers of lignin and, their responses to warming were revealed. RESULTS The β-Proteobacteria genus Burkholderia accounted for 95.1% of total abundance of potential lignin decomposers. Consistently, Burkholderia isolated from our tundra soils could grow with lignin as the sole C source. A 2.2 °C increase of warming considerably increased total abundance and functional capacities of all potential lignin decomposers. In addition to Burkholderia, α-Proteobacteria capable of lignin decomposition (e.g. Bradyrhizobium and Methylobacterium genera) were stimulated by warming by 82-fold. Those community changes collectively doubled the priming effect, i.e., decomposition of existing C after fresh C input to soil. Consequently, warming aggravates soil C instability, as verified by microbially enabled climate-C modeling. CONCLUSIONS Our findings are alarming, which demonstrate that accelerated C decomposition under warming conditions will make tundra soils a larger biospheric C source than anticipated. Video Abstract.
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