1,690 research outputs found
Cwbr Author Interview: Reluctant Rebels: The Confederates Who Joined The Army After 1861
No full textInterview with Dr. Kenneth W. Noe, Professor of History at Auburn University Interviewed by Nathan Buman Civil War Book Review (CWBR): I\u27m here today with Kenneth Noe, author of Reluctant Rebels: The Confederates Who Joined the Army after 1861. Professor Noe, thank you for joining me. Kenneth Noe (KN): I\u27m happy to be here Nathan
Diet-derived microRNAs: unicorn or silver bullet?
No full textIn ancient lore, a bullet cast from silver is the only effective weapon against monsters. The uptake of active diet-derived microRNAs (miRNAs) in consumers may be the silver bullet long sought after in nutrition and oral therapeutics. However, the majority of scientists consider the transfer and regulation of consumer’s gene activity by these diet-derived miRNAs to be a fantasy akin to spotting a unicorn. Nevertheless, groups like Dr. Chen-Yu Zhang’s lab in Nanjing University have stockpiled breathtaking amounts of data to shoot down these naysayers. Meanwhile, Dr. Ken Witwer at John Hopkins has steadfastly cautioned the field to beware of fallacies caused by contamination, technical artifacts, and confirmation bias. Here, Dr. Witwer and Dr. Zhang share their realities of dietary miRNAs by answering five questions related to this controversial field
Kenneth W. Ashley
No full textImage submitted by author for Poetry Spotlight 2023.https://digitalcommons.odu.edu/vapoets-images/1083/thumbnail.jp
Modification of nektonic fish distribution by piers and pile fields in an urban estuary
No full textLarge urban piers degrade habitat value for several estuarine benthic fish species by shading, but their effects on mobile nektonic species is less well understood due to sampling challenges. Dual Frequency Identification Sonar (DIDSON) allowed equal access to sampling in the water column of structured shaded and unshaded vs. open environments in both dark and light conditions by methods similar to video but without light. Sampling (n = 228, 5-minute transects) occurred under and around four large municipal piers of varying dimensions in the Hudson River estuary during day and night from summer and fall in 2007 - 2009. The distribution of small (5 - 25 cm in length) and large (25 – 850 cm) fishes were analyzed separately in recognition of functional guild differences. Small fishes occupied open water, shaded under-pier, and un-decked relict piling habitats, but were significantly more abundant during the day in open unshaded water than under adjacent piers or in piling habitats.. Small fish occurred under 3 of 4 piers of varying size and configuration at 10 - 20% of the median abundances of adjacent open water. However, while schools were rare under piers they could be very large, so that abundance greatly exceeded mean open water abundance variance so as to preclude confidence in differences among piers. The differences among habitats was not significant at night, and the difference among piers was also not significant at night. School membership for small fish appeared to mitigate adverse effects of shading and may influence scaling of their response to shading and could therefore influence pier design. Large (>25 cm) predatory fish were uncommon but responded similarly to habitat effects as did small fish. Habitats did not segregate fish by guild as small forage fish co-occurred in 65.8% of samples with large piscivores. Studies that provide species-specific and mechanistic interpretation of dynamic habitat use as well as further quantification of scaling effects could improve our understanding of how fishes respond to piers and other structures on urban shorelines.Peer reviewed
High-resolution characterization of HIV and extracellular vesicles by STORM-FISHing: combining dSTORM and smFISH
No full textOver the last two decades, advancements in optical microscopy have led to the development of a variety of super-resolution microscopy (SRM) methods, each with the capacity to examine subcellular structures at high resolution, including the virions of exogenous viruses such as human immunodeficiency virus (HIV) and host extracellular vesicles (EVs). Accurately identifying and characterizing complete virions within complex biological samples is essential for advancing our understanding of the structural diversity of virions and virus-like particles. However, few approaches take advantage of the detailed structural insights that SRM can offer to characterize free-floating virions and multiple types of molecules associated with them. In this study, we evaluate STORM-FISH, a dual-labeling technique that combines antibody-based HIV protein labeling and smFISH-based HIV RNA labeling with dSTORM for accurate, high-resolution characterization of HIV virions. Using smFISH probes specific to BaL HIV vRNA, we observed high specificity for virion labeling in dSTORM imaging, with minimal levels of binding in control samples (DCL4 plant probes and non-BaL HIV strains). While individual labeling of viral proteins (gp120) alone resulted in considerable non-specific binding to host-derived EVs, the combined use of gp120 antibodies and BaL smFISH probes allowed clear identification of complete BaL HIV virions, as demonstrated by distinct populations of double-positive (BaL smFISH+/gp120+) and triple-positive (BaL smFISH+/gp120+/CD63+) particles. Interestingly, the smFISH probes sometimes localized externally to gp120+ particles, raising questions about the origin of this potential external vRNA. The high-resolution imaging capabilities of STORM-FISH allow for detailed analysis of virion structure, protein localization, and component orientation, facilitating deeper insights into the structural dynamics of HIV. Our results validate STORM-FISH as an effective technique for dual protein/RNA labeling of free-floating virions in dSTORM microscopy and could translate well into furthering virological research and characterization of therapeutic extracellular vesicles or virus-mediated gene delivery systems
High-resolution characterization of HIV and extracellular vesicles by STORM-FISHing: combining dSTORM and smFISH
No full textOver the last two decades, advancements in optical microscopy have led to the development of a variety of super-resolution microscopy (SRM) methods, each with the capacity to examine subcellular structures at high resolution, including the virions of exogenous viruses such as human immunodeficiency virus (HIV) and host extracellular vesicles (EVs). Accurately identifying and characterizing complete virions within complex biological samples is essential for advancing our understanding of the structural diversity of virions and virus-like particles. However, few approaches take advantage of the detailed structural insights that SRM can offer to characterize free-floating virions and multiple types of molecules associated with them. In this study, we evaluate STORM-FISH, a dual-labeling technique that combines antibody-based HIV protein labeling and smFISH-based HIV RNA labeling with dSTORM for accurate, high-resolution characterization of HIV virions. Using smFISH probes specific to BaL HIV vRNA, we observed high specificity for virion labeling in dSTORM imaging, with minimal levels of binding in control samples (DCL4 plant probes and non-BaL HIV strains). While individual labeling of viral proteins (gp120) alone resulted in considerable non-specific binding to host-derived EVs, the combined use of gp120 antibodies and BaL smFISH probes allowed clear identification of complete BaL HIV virions, as demonstrated by distinct populations of double-positive (BaL smFISH+/gp120+) and triple-positive (BaL smFISH+/gp120+/CD63+) particles. Interestingly, the smFISH probes sometimes localized externally to gp120+ particles, raising questions about the origin of this potential external vRNA. The high-resolution imaging capabilities of STORM-FISH allow for detailed analysis of virion structure, protein localization, and component orientation, facilitating deeper insights into the structural dynamics of HIV. Our results validate STORM-FISH as an effective technique for dual protein/RNA labeling of free-floating virions in dSTORM microscopy and could translate well into furthering virological research and characterization of therapeutic extracellular vesicles or virus-mediated gene delivery systems
RNA Landscapes of Brain and Brain-Derived Extracellular Vesicles in Simian Immunodeficiency Virus Infection and Central Nervous System Pathology
No full textThis is a pre-copyedited, author-produced version of an article accepted for publication in The Journal of Infectious Diseases following peer review. The version of record Yiyao Huang, Ahmed Abdelgawad, Andrey Turchinovich, Suzanne Queen, Celina Monteiro Abreu, Xianming Zhu, Mona Batish, Lei Zheng, Kenneth W Witwer, RNA Landscapes of Brain and Brain-Derived Extracellular Vesicles in Simian Immunodeficiency Virus Infection and Central Nervous System Pathology, The Journal of Infectious Diseases, 2023;, jiad563, https://doi.org/10.1093/infdis/jiad563 is available online at: https://doi.org/10.1093/infdis/jiad563. © The Author(s) 2023. Published by Oxford University Press on behalf of Infectious Diseases Society of America. All rights reserved. For permissions, please e-mail: [email protected]. This article will be embargoed until 12/11/2024.Background
Brain tissue-derived extracellular vesicles (bdEVs) act locally in the central nervous system (CNS) and may indicate molecular mechanisms in human immunodeficiency virus (HIV) CNS pathology. Using brain homogenate (BH) and bdEVs from a simian immunodeficiency virus (SIV) model of HIV disease, we identified RNA networks in SIV infection and neuroinflammation.
Methods
Postmortem occipital cortex samples were obtained from uninfected controls and SIV-infected subjects (acute and chronic phases with or without CNS pathology [SIV encephalitis]). bdEVs were separated and characterized per international consensus guidelines. RNAs from bdEVs and BH were sequenced and quantitative polymerase chain reaction (qPCR)-amplified to detect levels of small RNAs (sRNAs, including microRNAs [miRNAs]) and longer RNAs including messenger RNAs (mRNAs) and circular RNAs (circRNAs).
Results
Dysregulated RNAs in BH and bdEVs were identified in acute and chronic infection with pathology groups, including mRNAs, miRNAs, and circRNAs. Most dysregulated mRNAs in bdEVs reflected dysregulation in source BH. These mRNAs are disproportionately involved in inflammation and immune responses. Based on target prediction, several circRNAs that were differentially abundant in source tissue might be responsible for specific differences in sRNA levels in bdEVs during SIV infection.
Conclusions
RNA profiling of bdEVs and source tissues reveals potential regulatory networks in SIV infection and SIV-related CNS pathology.This work was supported by the National Institutes of Health (NIH), National Institute on Drug Abuse (grant numbers DA040385 and DA047807 to K. W. W.); by 2 pilot grants awarded to Y. H. through the Johns Hopkins National Institute of Mental Health (NIMH) Center (supported by National Institute of Mental Health MH075673) and the Johns Hopkins University Center for AIDS Research (supported by National Institutes of Health/National Institute of Allergy and Infectious Diseases P30AI094189-01A1); and the National Science Foundation (grant number 2244127 to M. B.). The Witwer laboratory is also supported in part by National Cancer Institute/Common Fund (grant number CA241694); National Institute of Allergy and Infectious Diseases (grant number AI144997); National Institute of Mental Health (NIMH) (grant number MH118164); and the Johns Hopkins University Richman Family Precision Medicine Center of Excellence in Alzheimer’s Disease. Samples used in this study were derived in part from research supported by National Institutes of Health (NIH) (grant number U42OD013117 to Johns Hopkins pigtailed macaque breeding colony); National Institute of Neurological Disorders and Stroke (grant number NS089482 to Joseph L. Mankowski); and National Institute of Mental Health (NIMH) (grant number MH070306 to Janice E. Clements)
Upcoming Post: Similarities in the Prison-Themed Messages of Kenneth W. Hagin and F.F. Bosworth
No full textCopyright © 2018 by Roscoe Barnes III
#FFBosworthThis blog post is as an
announcement of a forthcoming post/article on the writings of Kenneth W. Hagin and
F.F. Bosworth. The author suggests that Hagin’s minibook, The Prison Door is Open: What Are You Still Doing Inside?, seems to
borrow from Bosworth’s article, "The Opening of the Prison," without
proper attribution.For more information on F.F. Bosworth, follow the Bosworth
Matters blog at: http://ffbosworth.strikingly.com#ChristTheHealer #BosworthMatters #BosworthMention</p
Fig. 1 in The Life History Of Ostrocerca Dimicki (Frison) In A Short-Flow, Summer-Dry Oregon Stream
No full textFig. 1. Outgate Beck stream channel obscured by grass, looking upstream from the emergence trap; author Anderson straddling the stream.Published as part of Stewart, Kenneth W. & Anderson, Norman H., 2010, The Life History Of Ostrocerca Dimicki (Frison) In A Short-Flow, Summer-Dry Oregon Stream, pp. 52-57 in Illiesia 6 (6) on page 53, DOI: 10.5281/zenodo.475962
Advances in Extracellular Vesicle Research Over the Past Decade: Source and Isolation Method are Connected with Cargo and Function
No full textThe evolution of extracellular vesicle (EV) research has introduced nanotechnology into biomedical cell communication science while recognizing what is formerly considered cell "dust" as constituting an entirely new universe of cell signaling particles. To display the global EV research landscape, a systematic review of 20 364 original research articles selected from all 40 684 EV-related records identified in PubMed 2013-2022 is performed. Machine-learning is used to categorize the high-dimensional data and further dissected significant associations between EV source, isolation method, cargo, and function. Unexpected correlations between these four categories indicate prevalent experimental strategies based on cargo connectivity with function of interest being associated with certain EV sources or isolation strategies. Conceptually relevant association of size-based EV isolation with protein cargo and uptake function will guide strategic conclusions enhancing future EV research and product development. Based on this study, an open-source database is built to facilitate further analysis with conventional or AI tools to identify additional causative associations of interest.A total of 20 364 original extracellular vesicle (EV) research articles for the decade 2013-2022 are analyzed for the presence or absence of 36 selected parameters in the four categories EV source, isolation, cargo, and function. The results are displayed in machine-learning-based 2D landscapes and further dissected by correlation analysis to identify conceptually relevant associations and draw strategic conclusions. imag
- …
