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Article ; Online: The impact of non-coding RNAs: workshop on new functions of regulatory RNAs in pro- & eukaryotes.

Boots, Jennifer L / Moll, Isabella

2009 Volume 10, Issue 6, Page(s) 563–567

MeSH term(s)	Animals ; DNA/metabolism ; Education ; Eukaryotic Cells/metabolism ; Gene Expression Regulation ; Prokaryotic Cells/metabolism ; RNA Stability ; RNA, Untranslated/metabolism ; Transcription, Genetic
Chemical Substances	RNA, Untranslated ; DNA (9007-49-2)
Language	English
Publishing date	2009-05-22
Publishing country	England
Document type	Congress ; Research Support, Non-U.S. Gov't
ZDB-ID	2020896-0
ISSN	1469-3178 ; 1469-221X
ISSN (online)	1469-3178
ISSN	1469-221X
DOI	10.1038/embor.2009.100
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Article ; Online: RNA polymerase II-binding aptamers in human ACRO1 satellites disrupt transcription

Boots, Jennifer L / von Pelchrzim, Frederike / Weiss, Adam / Zimmermann, Bob / Friesacher, Theres / Radtke, Maximilian / Żywicki, Marek / Chen, Doris / Matylla-Kulińska, Katarzyna / Zagrovic, Bojan / Schroeder, Renée

Transcription

2020 Volume 11, Issue 5, Page(s) 217–229

Abstract: Transcription elongation is a highly regulated process affected by many proteins, RNAs and the underlying DNA. Here we show that the nascent RNA can interfere with transcription in human cells, extending our previous findings from bacteria and yeast. We ... ...

Abstract	Transcription elongation is a highly regulated process affected by many proteins, RNAs and the underlying DNA. Here we show that the nascent RNA can interfere with transcription in human cells, extending our previous findings from bacteria and yeast. We identified a variety of Pol II-binding aptamers (RAPs), prominent in repeat elements such as ACRO1 satellites, LINE1 retrotransposons and CA simple repeats, and also in several protein-coding genes. ACRO1 repeat, when translated
MeSH term(s)	Aptamers, Nucleotide/genetics ; Aptamers, Nucleotide/metabolism ; Binding Sites/genetics ; Humans ; RNA Polymerase II/genetics ; RNA Polymerase II/metabolism ; Transcription, Genetic/genetics
Chemical Substances	Aptamers, Nucleotide ; RNA Polymerase II (EC 2.7.7.-)
Language	English
Publishing date	2020-07-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2646974-1
ISSN	2154-1272 ; 2154-1264
ISSN (online)	2154-1272
ISSN	2154-1264
DOI	10.1080/21541264.2020.1790990
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Article ; Online: Finding aptamers and small ribozymes in unexpected places.

Matylla-Kulinska, Katarzyna / Boots, Jennifer L / Zimmermann, Bob / Schroeder, Renée

Wiley interdisciplinary reviews. RNA

2012 Volume 3, Issue 1, Page(s) 73–91

Abstract: The discovery of the catalytic properties of RNAs was a milestone for our view of how life emerged and forced us to reformulate many of our dogmas. The urge to grasp the whole spectrum of potential activities of RNA molecules stimulated two decades of ... ...

Abstract	The discovery of the catalytic properties of RNAs was a milestone for our view of how life emerged and forced us to reformulate many of our dogmas. The urge to grasp the whole spectrum of potential activities of RNA molecules stimulated two decades of fervent research resulting in a deep understanding of RNA-based phenomena. Most ribozymes were discovered by serendipity during the analysis of chemical processes, whereas RNA aptamers were identified through meticulous design and selection even before their discovery in nature. The desire to obtain aptamers led to the development of sophisticated technology and the design of efficient strategies. With the new notion that transcriptomes cover a major part of genomes and determine the identity of cells, it is reasonable to speculate that many more aptamers and ribozymes are awaiting their discovery in unexpected places. Now, in the genomic era with the development of powerful bioinformatics and sequencing methods, we are overwhelmed with tools for studying the genomes of all living and possibly even extinct organisms. Genomic SELEX (systematic evolution of ligands by exponential enrichment) coupled with deep sequencing and sophisticated computational analysis not only gives access to unexplored parts of sequenced genomes but also allows screening metagenomes in an unbiased manner.
MeSH term(s)	Aptamers, Nucleotide/genetics ; Humans ; RNA, Catalytic/genetics ; Riboswitch/genetics ; SELEX Aptamer Technique
Chemical Substances	Aptamers, Nucleotide ; RNA, Catalytic ; Riboswitch
Language	English
Publishing date	2012-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2634714-3
ISSN	1757-7012 ; 1757-7004
ISSN (online)	1757-7012
ISSN	1757-7004
DOI	10.1002/wrna.105
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Article: Adapting to the impact of the COVID-19 pandemic on a randomized controlled trial examining lifestyle behaviors on cognitive functioning in obese African American adults: Building Research in Diet and Cognition (BRIDGE).

Fitzgibbon, Marian / Blumstein, Lara / Schiffer, Linda / Antonic, Mirjana A / McLeod, Andrew / Dakers, Roxanne / Restrepo, Leo / Boots, Elizabeth A / Sanchez-Flack, Jennifer C / Tussing-Humphreys, Lisa / Lamar, Melissa

Research square

2021

Language	English
Publishing date	2021-04-26
Publishing country	United States
Document type	Preprint
DOI	10.21203/rs.3.rs-290482/v1
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Article ; Online: Adapting to the COVID-19 pandemic on Building Research in Diet and Cognition (BRIDGE) trial.

Trials

2021 Volume 22, Issue 1, Page(s) 459

Abstract: Background: The COVID-19 pandemic has altered the research landscape for clinical trials, requiring thoughtful consideration regarding how to handle the risks and benefits of continuing them.: Design: This brief report describes the experience of ... ...

Abstract	Background: The COVID-19 pandemic has altered the research landscape for clinical trials, requiring thoughtful consideration regarding how to handle the risks and benefits of continuing them. Design: This brief report describes the experience of adapting the Building Research in Diet and Cognition (BRIDGE) study, a randomized clinical trial examining the effects of the Mediterranean diet, with and without weight loss, on cognitive functioning in 185 older obese African American adults during the COVID-19 pandemic. Measurement: The University of Illinois at Chicago (UIC) developed an expedited amendment process for research shifting to remote data collection. We conducted the study in three consecutive groups. For group 3, 14-month data collection period, we adapted our protocol to allow data collection via telephone and e-mail. We were unable to collect certain measures that required face-to-face contact. Results: For measures that could be collected remotely, 14-month retention was similar for group 3 compared to groups 1 and 2: data were collected for 86.9% of group 3 (remote) and 87.9% of groups 1 and 2 (face to face), p = .84. Conclusions: In order to preserve the integrity of our clinical trial and ensure the safety of our participants and staff during the COVID-19 pandemic, we had to carefully and efficiently adapt our data collection procedures. The procedures put in place allowed us to collect our primary outcomes and the majority of our secondary outcomes and will enable us to examine the role of dietary intake, with and without weight loss, on cognitive functioning in a vulnerable and high-risk population. Trial registration: ClinicalTrials.gov NCT3129048. Registration Date: 4/17/2017.
MeSH term(s)	Adult ; COVID-19 ; Chicago ; Cognition ; Diet, Mediterranean ; Humans ; Pandemics/prevention & control ; SARS-CoV-2
Language	English
Publishing date	2021-07-16
Publishing country	England
Document type	Letter ; Randomized Controlled Trial
ZDB-ID	2040523-6
ISSN	1745-6215 ; 1468-6694 ; 1745-6215
ISSN (online)	1745-6215
ISSN	1468-6694 ; 1745-6215
DOI	10.1186/s13063-021-05383-6
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Article ; Online: A new marker of sepsis post burn injury?*.

Paratz, Jennifer D / Lipman, Jeffrey / Boots, Robert J / Muller, Michael J / Paterson, David L

Critical care medicine

2014 Volume 42, Issue 9, Page(s) 2029–2036

Abstract: Objectives: Accurate diagnosis of sepsis is difficult in patients post burn due to the large inflammatory response produced by the major insult. We aimed to estimate the values of serum N-terminal pro-B-type natriuretic peptide and procalcitonin and the ...

Abstract	Objectives: Accurate diagnosis of sepsis is difficult in patients post burn due to the large inflammatory response produced by the major insult. We aimed to estimate the values of serum N-terminal pro-B-type natriuretic peptide and procalcitonin and the changes in hemodynamic variables as markers of sepsis in critically ill burn patients. Design: Prospective, observational study. Setting: A quaternary-level university-affiliated ICU. Patients: Fifty-four patients with burns to total body surface area of greater than or equal to 15%, intubated with no previous cardiovascular comorbidities, were enrolled. Interventions: At admission, a FloTrac/Vigileo system was attached and daily blood samples taken from the arterial catheter. Infection surveillance was carried out daily with patients classified as septic/nonseptic according to American Burns Consensus criteria. Measurements and main results: N-terminal pro-B-type natriuretic peptide, procalcitonin, and waveform analysis of changes in stroke volume index and systemic vascular resistance index were measured within the first 24 hours after burn and daily thereafter for the length of the ICU stay or until their first episode of sepsis. Prevalences of stroke volume variation less than 12% (normovolemia) with hypotension (systolic blood pressure < 90 mm Hg) were recorded. Patients with sepsis differed significantly from "no sepsis" for N-terminal pro-B-type natriuretic peptide, systemic vascular resistance index, and stroke volume index on days 3-7. Procalcitonin did not differ between sepsis and "no sepsis" except for day 3. Area under the receiver operating characteristic curves showed excellent discriminative power for B-type natriuretic peptide (p = 0.001; 95% CI, 0.99-1.00), systemic vascular resistance index (p < 0.001; 95% CI, 0.97-0.99), and stroke volume index (p < 0.01; 95% CI, 0.96-0.99) in predicting sepsis but not for procalcitonin (not significant; 95% CI, 0.29-0.46). A chi-square crosstab found that there was no relationship between hypotension with normovolemia (stroke volume variation < 12%) and sepsis. Conclusions: Serum N-terminal pro-B-type natriuretic peptide levels and certain hemodynamic changes can be used as an early indicator of sepsis in patients with burn injury. Procalcitonin did not assist in the early diagnosis of sepsis.
MeSH term(s)	Adolescent ; Adult ; Biomarkers ; Burns/blood ; Burns/epidemiology ; Burns/physiopathology ; Calcitonin/blood ; Calcitonin Gene-Related Peptide ; Critical Illness ; Female ; Hemodynamics ; Hospital Mortality ; Hospitals, University ; Humans ; Intensive Care Units ; Male ; Middle Aged ; Natriuretic Peptide, Brain/blood ; Peptide Fragments/blood ; Prognosis ; Prospective Studies ; Protein Precursors/blood ; Sepsis/blood ; Sepsis/epidemiology ; Sepsis/physiopathology ; Young Adult
Chemical Substances	Biomarkers ; CALCA protein, human ; Peptide Fragments ; Protein Precursors ; pro-brain natriuretic peptide (1-76) ; Natriuretic Peptide, Brain (114471-18-0) ; Calcitonin Gene-Related Peptide (83652-28-2) ; Calcitonin (9007-12-9)
Language	English
Publishing date	2014-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	197890-1
ISSN	1530-0293 ; 0090-3493
ISSN (online)	1530-0293
ISSN	0090-3493
DOI	10.1097/CCM.0000000000000400
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Article ; Online: Cardiorespiratory fitness attenuates age-associated aggregation of white matter hyperintensities in an at-risk cohort.

Vesperman, Clayton J / Pozorski, Vincent / Dougherty, Ryan J / Law, Lena L / Boots, Elizabeth / Oh, Jennifer M / Gallagher, Catherine L / Carlsson, Cynthia M / Rowley, Howard A / Ma, Yue / Bendlin, Barbara B / Asthana, Sanjay / Sager, Mark A / Hermann, Bruce P / Johnson, Sterling C / Cook, Dane B / Okonkwo, Ozioma C

Alzheimer's research & therapy

2018 Volume 10, Issue 1, Page(s) 97

Abstract: Background: Age is the cardinal risk factor for Alzheimer's disease (AD), and white matter hyperintensities (WMH), which are more prevalent with increasing age, may contribute to AD. Higher cardiorespiratory fitness (CRF) has been shown to be associated ...

Abstract	Background: Age is the cardinal risk factor for Alzheimer's disease (AD), and white matter hyperintensities (WMH), which are more prevalent with increasing age, may contribute to AD. Higher cardiorespiratory fitness (CRF) has been shown to be associated with cognitive health and decreased burden of AD-related brain alterations in older adults. Accordingly, the aim of this study was to determine whether CRF attenuates age-related accumulation of WMH in middle-aged adults at risk for AD. Methods: One hundred and seven cognitively unimpaired, late-middle-aged adults from the Wisconsin Registry for Alzheimer's Prevention underwent 3 T magnetic resonance imaging and performed graded maximal treadmill exercise testing from which we calculated the oxygen uptake efficiency slope (OUES) as our measure of CRF. Total WMH were quantified using the Lesion Segmentation Tool and scaled to intracranial volume. Linear regression adjusted for APOE4 carriage, family history, body mass index, systolic blood pressure, and sex was used to examine relationships between age, WMH, and CRF. Results: As expected, there was a significant association between age and WMH (p < .001). Importantly, there was a significant interaction between age and OUES on WMH (p = .015). Simple main effects analyses revealed that the effect of age on WMH remained significant in the Low OUES group (p < .001) but not in the High OUES group (p = .540), indicating that higher CRF attenuates the deleterious age association with WMH. Conclusions: Higher CRF tempers the adverse effect of age on WMH. This suggests a potential pathway through which increased aerobic fitness facilitates healthy brain aging, especially among individuals at risk for AD.
MeSH term(s)	Aged ; Aging ; Alzheimer Disease/prevention & control ; Brain/diagnostic imaging ; Cardiorespiratory Fitness ; Cohort Studies ; Female ; Humans ; Magnetic Resonance Imaging ; Male ; Middle Aged ; Risk Factors ; White Matter/diagnostic imaging
Language	English
Publishing date	2018-09-24
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2506521-X
ISSN	1758-9193 ; 1758-9193
ISSN (online)	1758-9193
ISSN	1758-9193
DOI	10.1186/s13195-018-0429-0
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Article ; Online: Launching a saliva-based SARS-CoV-2 surveillance testing program on a university campus.

Ehrenberg, Alexander J / Moehle, Erica A / Brook, Cara E / Doudna Cate, Andrew H / Witkowsky, Lea B / Sachdeva, Rohan / Hirsh, Ariana / Barry, Kerrie / Hamilton, Jennifer R / Lin-Shiao, Enrique / McDevitt, Shana / Valentin-Alvarado, Luis / Letourneau, Kaitlyn N / Hunter, Lauren / Keller, Amanda / Pestal, Kathleen / Frankino, Phillip A / Murley, Andrew / Nandakumar, Divya /

Stahl, Elizabeth C / Tsuchida, Connor A / Gildea, Holly K / Murdock, Andrew G / Hochstrasser, Megan L / O'Brien, Elizabeth / Ciling, Alison / Tsitsiklis, Alexandra / Worden, Kurtresha / Dugast-Darzacq, Claire / Hays, Stephanie G / Barber, Colin C / McGarrigle, Riley / Lam, Emily K / Ensminger, David C / Bardet, Lucie / Sherry, Carolyn / Harte, Anna / Nicolette, Guy / Giannikopoulos, Petros / Hockemeyer, Dirk / Petersen, Maya / Urnov, Fyodor D / Ringeisen, Bradley R / Boots, Mike / Doudna, Jennifer A

PloS one

2021 Volume 16, Issue 5, Page(s) e0251296

Abstract: Regular surveillance testing of asymptomatic individuals for SARS-CoV-2 has been center to SARS-CoV-2 outbreak prevention on college and university campuses. Here we describe the voluntary saliva testing program instituted at the University of California, ...

Abstract	Regular surveillance testing of asymptomatic individuals for SARS-CoV-2 has been center to SARS-CoV-2 outbreak prevention on college and university campuses. Here we describe the voluntary saliva testing program instituted at the University of California, Berkeley during an early period of the SARS-CoV-2 pandemic in 2020. The program was administered as a research study ahead of clinical implementation, enabling us to launch surveillance testing while continuing to optimize the assay. Results of both the testing protocol itself and the study participants' experience show how the program succeeded in providing routine, robust testing capable of contributing to outbreak prevention within a campus community and offer strategies for encouraging participation and a sense of civic responsibility.
MeSH term(s)	Adult ; Aged ; COVID-19/diagnosis ; COVID-19/epidemiology ; COVID-19/virology ; COVID-19 Testing/methods ; Female ; Humans ; Male ; Middle Aged ; Program Evaluation ; RNA, Viral/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; SARS-CoV-2/genetics ; SARS-CoV-2/isolation & purification ; Saliva/virology ; Social Norms ; Surveys and Questionnaires ; Universities ; Young Adult
Chemical Substances	RNA, Viral
Language	English
Publishing date	2021-05-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0251296
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Article ; Online: Metal ion specificities for folding and cleavage activity in the Schistosoma hammerhead ribozyme.

Boots, Jennifer L / Canny, Marella D / Azimi, Ehsan / Pardi, Arthur

RNA (New York, N.Y.)

2008 Volume 14, Issue 10, Page(s) 2212–2222

Abstract: The effects of various metal ions on cleavage activity and global folding have been studied in the extended Schistosoma hammerhead ribozyme. Fluorescence resonance energy transfer was used to probe global folding as a function of various monovalent and ... ...

Abstract	The effects of various metal ions on cleavage activity and global folding have been studied in the extended Schistosoma hammerhead ribozyme. Fluorescence resonance energy transfer was used to probe global folding as a function of various monovalent and divalent metal ions in this ribozyme. The divalent metals ions Ca(2+), Mg(2+), Mn(2+), and Sr(2+) have a relatively small variation (less than sixfold) in their ability to globally fold the hammerhead ribozyme, which contrasts with the very large difference (>10,000-fold) in apparent rate constants for cleavage for these divalent metal ions in single-turnover kinetic experiments. There is still a very large range (>4600-fold) in the apparent rate constants for cleavage for these divalent metal ions measured in high salt (2 M NaCl) conditions where the ribozyme is globally folded. These results demonstrate that the identity of the divalent metal ion has little effect on global folding of the Schistosoma hammerhead ribozyme, whereas it has a very large effect on the cleavage kinetics. Mechanisms by which the identity of the divalent metal ion can have such a large effect on cleavage activity in the Schistosoma hammerhead ribozyme are discussed.
MeSH term(s)	Animals ; Base Sequence ; Cations, Divalent/chemistry ; Metals/chemistry ; Nucleic Acid Conformation ; RNA, Catalytic/chemistry ; Schistosoma mansoni/enzymology
Chemical Substances	Cations, Divalent ; Metals ; RNA, Catalytic ; hammerhead ribozyme
Language	English
Publishing date	2008-08-28
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1241540-6
ISSN	1469-9001 ; 1355-8382
ISSN (online)	1469-9001
ISSN	1355-8382
DOI	10.1261/rna.1010808
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Zs.A 4777: Show issues

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Article ; Online: Moderate Physical Activity is Associated with Cerebral Glucose Metabolism in Adults at Risk for Alzheimer's Disease.

Dougherty, Ryan J / Schultz, Stephanie A / Kirby, Taylor K / Boots, Elizabeth A / Oh, Jennifer M / Edwards, Dorothy / Gallagher, Catherine L / Carlsson, Cynthia M / Bendlin, Barbara B / Asthana, Sanjay / Sager, Mark A / Hermann, Bruce P / Christian, Bradley T / Johnson, Sterling C / Cook, Dane B / Okonkwo, Ozioma C

Journal of Alzheimer's disease : JAD

2017 Volume 58, Issue 4, Page(s) 1089–1097

Abstract: The objective of this study was to investigate the relationship between accelerometer-measured physical activity (PA) and glucose metabolism in asymptomatic late-middle-aged adults. Ninety-three cognitively healthy late-middle-aged adults from the ... ...

Abstract	The objective of this study was to investigate the relationship between accelerometer-measured physical activity (PA) and glucose metabolism in asymptomatic late-middle-aged adults. Ninety-three cognitively healthy late-middle-aged adults from the Wisconsin Registry for Alzheimer's Prevention participated in this cross-sectional study. They underwent 18F-fluorodeoxyglucose positron emission tomography (FDG-PET) imaging and wore an accelerometer (ActiGraph GT3X+) to measure free-living PA. Accelerometer data yielded measures of light (LPA), moderate (MPA), and vigorous (VPA) intensity PA. FDG-PET images were scaled to the cerebellum and pons, and cerebral glucose metabolic rate was extracted from specific regions of interest (ROIs) known to be hypometabolic in AD, i.e., hippocampus, posterior cingulate, inferior temporal cortex, and angular gyrus. Regression analyses were utilized to examine the association between PA and glucose metabolism, while adjusting for potential confounds. There were associations between MPA and glucose metabolism in all ROIs examined. In contrast, LPA was not associated with glucose uptake in any ROI and VPA was only associated with hippocampal FDG uptake. Secondary analyses did not reveal associations between sedentary time and glucose metabolism in any of the ROIs. Exploratory voxel-wise analysis identified additional regions where MPA was significantly associated with glucose metabolism including the precuneus, supramarginal gyrus, amygdala, and middle frontal gyrus. These findings suggest that the intensity of PA is an important contributor to neuronal function in a late-middle-aged cohort, with MPA being the most salient. Prospective studies are necessary for fully elucidating the link between midlife engagement in PA and later life development of AD.
MeSH term(s)	Accelerometry ; Aged ; Alzheimer Disease/diagnostic imaging ; Alzheimer Disease/metabolism ; Alzheimer Disease/pathology ; Alzheimer Disease/physiopathology ; Cerebral Cortex/diagnostic imaging ; Cerebral Cortex/metabolism ; Cross-Sectional Studies ; Exercise/physiology ; Female ; Fluorodeoxyglucose F18/pharmacokinetics ; Glucose/metabolism ; Humans ; Male ; Middle Aged ; Positron-Emission Tomography ; Registries
Chemical Substances	Fluorodeoxyglucose F18 (0Z5B2CJX4D) ; Glucose (IY9XDZ35W2)
Language	English
Publishing date	2017-05-18
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1440127-7
ISSN	1875-8908 ; 1387-2877
ISSN (online)	1875-8908
ISSN	1387-2877
DOI	10.3233/JAD-161067
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