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Article ; Online: Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota.

Shibata, Takeo / Nakagawa, Mayumi / Coleman, Hannah N / Owens, Sarah M / Greenfield, William W / Sasagawa, Toshiyuki / Robeson, Michael S

PloS one

2021 Volume 16, Issue 8, Page(s) e0237556

Abstract: Cervical microbiota (CM) are considered an important factor affecting the progression of cervical intraepithelial neoplasia (CIN) and are implicated in the persistence of human papillomavirus (HPV). Collection of liquid-based cytology (LBC) samples is ... ...

Abstract	Cervical microbiota (CM) are considered an important factor affecting the progression of cervical intraepithelial neoplasia (CIN) and are implicated in the persistence of human papillomavirus (HPV). Collection of liquid-based cytology (LBC) samples is routine for cervical cancer screening and HPV genotyping and can be used for long-term cytological biobanking. We sought to determine whether it is possible to access microbial DNA from LBC specimens, and compared the performance of four different extraction protocols: (ZymoBIOMICS DNA Miniprep Kit; QIAamp PowerFecal Pro DNA Kit; QIAamp DNA Mini Kit; and IndiSpin Pathogen Kit) and their ability to capture the diversity of CM from LBC specimens. LBC specimens from 20 patients (stored for 716 ± 105 days) with CIN values of 2 or 3 were each aliquoted for each of the four kits. Loss of microbial diversity due to long-term LBC storage could not be assessed due to lack of fresh LBC samples. Comparisons with other types of cervical sampling were not performed. We observed that all DNA extraction kits provided equivalent accessibility to the cervical microbial DNA within stored LBC samples. Approximately 80% microbial genera were shared among all DNA extraction protocols. Potential kit contaminants were observed as well. Variation between individuals was a significantly greater influence on the observed microbial composition than was the method of DNA extraction. We also observed that HPV16 was significantly associated with community types that were not dominated by Lactobacillus iners.
MeSH term(s)	Adult ; Biological Specimen Banks ; Cervix Uteri/microbiology ; Cervix Uteri/virology ; Cytodiagnosis/methods ; DNA/genetics ; Early Detection of Cancer/methods ; Female ; Humans ; Lactobacillus/genetics ; Microbiota/genetics ; Uterine Cervical Neoplasms/diagnosis ; Uterine Cervical Neoplasms/genetics ; Uterine Cervical Neoplasms/microbiology ; Uterine Cervical Neoplasms/virology
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2021-08-30
Publishing country	United States
Document type	Clinical Trial, Phase II ; Journal Article ; Randomized Controlled Trial ; Research Support, N.I.H., Extramural ; 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.0237556
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota.

Takeo Shibata / Mayumi Nakagawa / Hannah N Coleman / Sarah M Owens / William W Greenfield / Toshiyuki Sasagawa / Michael S Robeson

PLoS ONE, Vol 16, Iss 8, p e

2021 Volume 0237556

Abstract	Cervical microbiota (CM) are considered an important factor affecting the progression of cervical intraepithelial neoplasia (CIN) and are implicated in the persistence of human papillomavirus (HPV). Collection of liquid-based cytology (LBC) samples is routine for cervical cancer screening and HPV genotyping and can be used for long-term cytological biobanking. We sought to determine whether it is possible to access microbial DNA from LBC specimens, and compared the performance of four different extraction protocols: (ZymoBIOMICS DNA Miniprep Kit; QIAamp PowerFecal Pro DNA Kit; QIAamp DNA Mini Kit; and IndiSpin Pathogen Kit) and their ability to capture the diversity of CM from LBC specimens. LBC specimens from 20 patients (stored for 716 ± 105 days) with CIN values of 2 or 3 were each aliquoted for each of the four kits. Loss of microbial diversity due to long-term LBC storage could not be assessed due to lack of fresh LBC samples. Comparisons with other types of cervical sampling were not performed. We observed that all DNA extraction kits provided equivalent accessibility to the cervical microbial DNA within stored LBC samples. Approximately 80% microbial genera were shared among all DNA extraction protocols. Potential kit contaminants were observed as well. Variation between individuals was a significantly greater influence on the observed microbial composition than was the method of DNA extraction. We also observed that HPV16 was significantly associated with community types that were not dominated by Lactobacillus iners.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Alternative Means of Estimating

Nichols, Kenneth J / Robeson, William / Yoshida-Hay, Miyuki / Zanzonico, Pat B / Leveque, Fritzgerald / Bhargava, Kuldeep K / Tronco, Gene G / Palestro, Christopher J

Journal of nuclear medicine : official publication, Society of Nuclear Medicine

2017 Volume 58, Issue 10, Page(s) 1588–1595

Abstract: To protect bone marrow from overirradiation, the maximum permissible activity (MPA) ... ...

Abstract	To protect bone marrow from overirradiation, the maximum permissible activity (MPA) of
MeSH term(s)	Female ; Humans ; Iodine Radioisotopes/adverse effects ; Iodine Radioisotopes/therapeutic use ; Kidney/physiology ; Kidney/radiation effects ; Male ; Middle Aged ; Radiation Dosage ; Retrospective Studies ; Thyroid Neoplasms/radiotherapy
Chemical Substances	Iodine Radioisotopes
Language	English
Publishing date	2017-04-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	80272-4
ISSN	1535-5667 ; 0097-9058 ; 0161-5505 ; 0022-3123
ISSN (online)	1535-5667
ISSN	0097-9058 ; 0161-5505 ; 0022-3123
DOI	10.2967/jnumed.117.192278
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Article: Transcriptome assembly and candidate genes involved in nutritional programming in the swordtail fish

Lu, Yuan / Klimovich, Charlotte M / Robeson, Kalen Z / Boswell, William / Ríos-Cardenas, Oscar / Walter, Ronald B / Morris, Molly R

PeerJ

2017 Volume 5, Page(s) e3275

Abstract: Background: Nutritional programming takes place in early development. Variation in the quality and/or quantity of nutrients in early development can influence long-term health and viability. However, little is known about the mechanisms of nutritional ... ...

Abstract	Background: Nutritional programming takes place in early development. Variation in the quality and/or quantity of nutrients in early development can influence long-term health and viability. However, little is known about the mechanisms of nutritional programming. The live-bearing fish Methods: We first examined the influence of both juvenile environment (varied in nutrition and density) and adult environment (varied in nutrition) on behaviors involved in energy acquisition and energy expenditure in adult male Results: We found that both the juvenile and adult environments influenced the energy intake behavior, while only the adult environment influenced energy expenditure. In addition, there were significant interactions between the genetically influenced size classes and the environments that influenced energy intake and energy expenditure, with males from one of the four size classes (Y-II) responding in the opposite direction as compared to the other males examined. When we compared the brains of males of the Y-II size class reared in a low quality juvenile environment to males from the same size class reared in high quality juvenile environment, 131 genes were differentially expressed, including metabolism and appetite master regulator Discussion: Our study provides evidence for nutritional programming in
Language	English
Publishing date	2017-05-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.3275
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Article ; Online: Radiation absorbed dose to the basal ganglia from dopamine transporter radioligand 18F-FPCIT.

Robeson, William / Dhawan, Vijay / Ma, Yilong / Bjelke, David / Margouleff, Claude / Chaly, Thomas / Eidelberg, David

BioMed research international

2014 Volume 2014, Page(s) 498072

Abstract: Our previous dosimetry studies have demonstrated that for dopaminergic radiotracers, (18)F-FDOPA and (18)F-FPCIT, the urinary bladder is the critical organ. As these tracers accumulate in the basal ganglia (BG) with high affinity and long residence times, ...

Abstract	Our previous dosimetry studies have demonstrated that for dopaminergic radiotracers, (18)F-FDOPA and (18)F-FPCIT, the urinary bladder is the critical organ. As these tracers accumulate in the basal ganglia (BG) with high affinity and long residence times, radiation dose to the BG may become significant, especially in normal control subjects. We have performed dynamic PET measurements using (18)F-FPCIT in 16 normal adult subjects to determine if in fact the BG, although not a whole organ, but a well-defined substructure, receives the highest dose. Regions of interest were drawn over left and right BG structures. Resultant time-activity curves were generated and used to determine residence times for dosimetry calculations. S-factors were computed using the MIRDOSE3 nodule model for each caudate and putamen. For (18)F-FPCIT, BG dose ranged from 0.029 to 0.069 mGy/MBq. In half of all subjects, BG dose exceeded 85% of the published critical organ (bladder) dose, and in three of those, the BG dose exceeded that for the bladder. The BG can become the dose-limiting organ in studies using dopamine transporter ligands. For some normal subjects studied with F-18 or long half-life radionuclide, the BG may exceed bladder dose and become the critical structure.
MeSH term(s)	Adult ; Basal Ganglia/diagnostic imaging ; Dopamine Plasma Membrane Transport Proteins/chemistry ; Fluorodeoxyglucose F18/administration & dosage ; Humans ; Ligands ; Positron-Emission Tomography ; Radiation Dosage ; Radiography ; Radiopharmaceuticals/administration & dosage ; Urinary Bladder/diagnostic imaging ; Urinary Bladder/metabolism
Chemical Substances	Dopamine Plasma Membrane Transport Proteins ; Ligands ; Radiopharmaceuticals ; Fluorodeoxyglucose F18 (0Z5B2CJX4D)
Language	English
Publishing date	2014-06-30
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2698540-8
ISSN	2314-6141 ; 2314-6133
ISSN (online)	2314-6141
ISSN	2314-6133
DOI	10.1155/2014/498072
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Article ; Online: Cervical Microbiome and Response to a Human Papillomavirus Therapeutic Vaccine for Treating High-Grade Cervical Squamous Intraepithelial Lesion.

Ravilla, Rahul / Coleman, Hannah N / Chow, Cheryl-Emiliane / Chan, Luisa / Fuhrman, Barbara J / Greenfield, William W / Robeson, Michael Scott / Iverson, Kathryn / Spencer, Horace / Nakagawa, Mayumi

Integrative cancer therapies

2019 Volume 18, Page(s) 1534735419893063

Abstract: Human papillomavirus (HPV) infection is associated with the vast majority of cervical cancer cases as well as with other anogenital cancers. PepCan is an investigational HPV therapeutic vaccine for treating cervical high-grade squamous intraepithelial ... ...

Abstract	Human papillomavirus (HPV) infection is associated with the vast majority of cervical cancer cases as well as with other anogenital cancers. PepCan is an investigational HPV therapeutic vaccine for treating cervical high-grade squamous intraepithelial lesions. The present study was performed to test whether the cervical microbiome influences vaccine responses and to explore host factors as determinants of the cervical microbiome composition in women with biopsy-proven high-grade squamous intraepithelial lesions. In a recently completed Phase I clinical trial of PepCan, histological response rate of 45% (14 of 31 patients), a significant increase in circulating T-helper type 1 cells, and a significant decrease in HPV 16 viral load were reported. DNA, extracted from liquid cytology specimens collected before and after vaccinations, were amplified and then hybridized to a G4 PhyloChip assay to characterize the microbiome. We describe trends that certain bacterial taxa in the cervix may be enriched in non-responders in comparison to responders (
MeSH term(s)	Adult ; Cervix Uteri/immunology ; Cervix Uteri/microbiology ; Female ; Human papillomavirus 16/immunology ; Humans ; Microbiota/immunology ; Middle Aged ; Papillomavirus Infections/immunology ; Papillomavirus Infections/microbiology ; Papillomavirus Vaccines/immunology ; Squamous Intraepithelial Lesions/immunology ; Squamous Intraepithelial Lesions/microbiology ; Uterine Cervical Neoplasms/immunology ; Uterine Cervical Neoplasms/microbiology ; Viral Load/immunology ; Young Adult
Chemical Substances	Papillomavirus Vaccines
Language	English
Publishing date	2019-12-17
Publishing country	United States
Document type	Clinical Trial, Phase I ; Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2182320-0
ISSN	1552-695X ; 1534-7354
ISSN (online)	1552-695X
ISSN	1534-7354
DOI	10.1177/1534735419893063
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Article ; Online: Genomic characterization of mumps viruses from a large-scale mumps outbreak in Arkansas, 2016.

Alkam, Duah / Jenjaroenpun, Piroon / Wongsurawat, Thidathip / Udaondo, Zulema / Patumcharoenpol, Preecha / Robeson, Michael / Haselow, Dirk / Mason, William / Nookaew, Intawat / Ussery, David / Jun, Se-Ran

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases

2019 Volume 75, Page(s) 103965

Abstract: In 2016, a year-long large-scale mumps outbreak occurred in Arkansas among a highly-vaccinated population. A total of 2954 mumps cases were identified during this outbreak. The majority of cases (1676 (57%)) were school-aged children (5-17 years), 1536 ( ... ...

Abstract	In 2016, a year-long large-scale mumps outbreak occurred in Arkansas among a highly-vaccinated population. A total of 2954 mumps cases were identified during this outbreak. The majority of cases (1676 (57%)) were school-aged children (5-17 years), 1536 (92%) of these children had completed the mumps vaccination schedule. To weigh the possibility that the mumps virus evaded vaccine-induced immunity in the affected Arkansas population, we established a pipeline for genomic characterization of the outbreak strains. Our pipeline produces whole-genome sequences along with phylogenetic analysis of the outbreak mumps virus strains. We collected buccal swab samples of patients who tested positive for the mumps virus during the 2016 Arkansas outbreak, and used the portable Oxford Nanopore Technology to sequence the extracted strains. Our pipeline identified the genotype of the Arkansas mumps strains as genotype G and presented a genome-based phylogenetic tree with superior resolution to a standard small hydrophobic (SH) gene-based tree. We phylogenetically compared the Arkansas whole-genome sequences to all publicly available mumps strains. While these analyses show that the Arkansas mumps strains are evolutionarily distinct from the vaccine strains, we observed no correlation between vaccination history and phylogenetic grouping. Furthermore, we predicted potential B-cell epitopes encoded by the Arkansas mumps strains using a random forest prediction model trained on antibody-antigen protein structures. Over half of the predicted epitopes of the Jeryl-Lynn vaccine strains in the Hemagglutinin-Neuraminidase (HN) surface glycoprotein (a major target of neutralizing antibodies) region are missing in the Arkansas mumps strains. In-silico analyses of potential epitopes may indicate that the Arkansas mumps strains display antigens with reduced immunogenicity, which may contribute to reduced vaccine effectiveness. However, our in-silico findings should be assessed by robust experiments such as cross neutralization assays. Metadata analysis showed that vaccination history had no effect on the evolution of the Arkansas mumps strains during this outbreak. We conclude that the driving force behind the spread of the mumps virus in the 2016 Arkansas outbreak remains undetermined.
MeSH term(s)	Antibodies, Neutralizing/genetics ; Antibodies, Viral/immunology ; Arkansas/epidemiology ; Disease Outbreaks ; Genome, Viral ; Genotype ; Humans ; Mumps/epidemiology ; Mumps/virology ; Mumps Vaccine ; Mumps virus/genetics ; Neutralization Tests ; Phylogeny
Chemical Substances	Antibodies, Neutralizing ; Antibodies, Viral ; Mumps Vaccine
Language	English
Publishing date	2019-07-15
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2037068-4
ISSN	1567-7257 ; 1567-1348
ISSN (online)	1567-7257
ISSN	1567-1348
DOI	10.1016/j.meegid.2019.103965
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Book ; Online: The East Is Black

Frazier, Robeson Taj

Cold War China in the Black Radical Imagination

2014

Abstract: ... E.B. and Shirley Graham Du Bois, journalist William Worthy, Marxist feminist Vicki Garvin, and ...

Abstract	During the Cold War, several prominent African American radical activist-intellectuals-including W.E.B. and Shirley Graham Du Bois, journalist William Worthy, Marxist feminist Vicki Garvin, and freedom fighters Mabel and Robert Williams-traveled and lived in China. There, they used a variety of media to express their solidarity with Chinese communism and to redefine the relationship between Asian struggles against imperialism and black American movements against social, racial, and economic injustice. In The East Is Black, Taj Frazier examines the ways in which these figures and the Chinese go
Language	English
Size	Online-Ressource (329 p)
Publisher	Duke University Press
Publishing place	Durham
Document type	Book ; Online
Note	Description based upon print version of record
ISBN	9780822357681 ; 0822357682
Database	Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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Article ; Online: STING agonist promotes CAR T cell trafficking and persistence in breast cancer.

Xu, Nuo / Palmer, Douglas C / Robeson, Alexander C / Shou, Peishun / Bommiasamy, Hemamalini / Laurie, Sonia J / Willis, Caryn / Dotti, Gianpietro / Vincent, Benjamin G / Restifo, Nicholas P / Serody, Jonathan S

The Journal of experimental medicine

2021 Volume 218, Issue 2

Abstract: CAR T therapy targeting solid tumors is restrained by limited infiltration and persistence of those cells in the tumor microenvironment (TME). Here, we developed approaches to enhance the activity of CAR T cells using an orthotopic model of locally ... ...

Abstract	CAR T therapy targeting solid tumors is restrained by limited infiltration and persistence of those cells in the tumor microenvironment (TME). Here, we developed approaches to enhance the activity of CAR T cells using an orthotopic model of locally advanced breast cancer. CAR T cells generated from Th/Tc17 cells given with the STING agonists DMXAA or cGAMP greatly enhanced tumor control, which was associated with enhanced CAR T cell persistence in the TME. Using single-cell RNA sequencing, we demonstrate that DMXAA promoted CAR T cell trafficking and persistence, supported by the generation of a chemokine milieu that promoted CAR T cell recruitment and modulation of the immunosuppressive TME through alterations in the balance of immune-stimulatory and suppressive myeloid cells. However, sustained tumor regression was accomplished only with the addition of anti-PD-1 and anti-GR-1 mAb to Th/Tc17 CAR T cell therapy given with STING agonists. This study provides new approaches to enhance adoptive T cell therapy in solid tumors.
MeSH term(s)	3T3 Cells ; Animals ; Antigens, Neoplasm/metabolism ; Breast Neoplasms/metabolism ; Cell Line ; Chemokines/metabolism ; Disease Models, Animal ; Female ; Immunotherapy, Adoptive/methods ; Membrane Proteins/agonists ; Mice ; Receptors, Chimeric Antigen/metabolism ; T-Lymphocytes/metabolism ; Tumor Microenvironment/physiology
Chemical Substances	Antigens, Neoplasm ; Chemokines ; Membrane Proteins ; Receptors, Chimeric Antigen ; Sting1 protein, mouse
Language	English
Publishing date	2021-02-02
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	218343-2
ISSN	1540-9538 ; 0022-1007
ISSN (online)	1540-9538
ISSN	0022-1007
DOI	10.1084/jem.20200844
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Zs.MG 45: Show issues

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Article ; Online: Transcriptome assembly and candidate genes involved in nutritional programming in the swordtail fish Xiphophorus multilineatus

Yuan Lu / Charlotte M. Klimovich / Kalen Z. Robeson / William Boswell / Oscar Ríos-Cardenas / Ronald B. Walter / Molly R. Morris

PeerJ, Vol 5, p e

2017 Volume 3275

Abstract: Background Nutritional programming takes place in early development. Variation in the quality and/or quantity of nutrients in early development can influence long-term health and viability. However, little is known about the mechanisms of nutritional ... ...

Abstract	Background Nutritional programming takes place in early development. Variation in the quality and/or quantity of nutrients in early development can influence long-term health and viability. However, little is known about the mechanisms of nutritional programming. The live-bearing fish Xiphophorus multilineatus has the potential to be a new model for understanding these mechanisms, given prior evidence of nutritional programming influencing behavior and juvenile growth rate. We tested the hypotheses that nutritional programming would influence behaviors involved in energy homeostasis as well gene expression in X. multilineatus. Methods We first examined the influence of both juvenile environment (varied in nutrition and density) and adult environment (varied in nutrition) on behaviors involved in energy acquisition and energy expenditure in adult male X. multilineatus. We also compared the behavioral responses across the genetically influenced size classes of males. Males stop growing at sexual maturity, and the size classes of can be identified based on phenotypes (adult size and pigment patterns). To study the molecular signatures of nutritional programming, we assembled a de novo transcriptome for X. multilineatus using RNA from brain, liver, skin, testis and gonad tissues, and used RNA-Seq to profile gene expression in the brains of males reared in low quality (reduced food, increased density) and high quality (increased food, decreased density) juvenile environments. Results We found that both the juvenile and adult environments influenced the energy intake behavior, while only the adult environment influenced energy expenditure. In addition, there were significant interactions between the genetically influenced size classes and the environments that influenced energy intake and energy expenditure, with males from one of the four size classes (Y-II) responding in the opposite direction as compared to the other males examined. When we compared the brains of males of the Y-II size class reared in a low quality ...
Keywords	RNA-Seq ; Xiphophorus multilineatus ; Transcriptome ; Energy homeostasis ; Medicine ; R
Subject code	590
Language	English
Publishing date	2017-05-01T00:00:00Z
Publisher	PeerJ Inc.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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