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Article ; Online: Domain Cell Theory supports the independent evolution of the Eukarya, Bacteria and Archaea and the Nuclear Compartment Commonality hypothesis.

Staley, James T

2017 Volume 7, Issue 6

Abstract: ... of the Eukarya and Bacteria from nucleated ancestors (Staley 2013 ...

Abstract	In 2015, the Royal Society of London held a meeting to discuss the various hypotheses regarding the origin of the Eukarya. Although not all participants supported a hypothesis, the proposals that did fit into two broad categories: one group favoured 'Prokaryotes First' hypotheses and another addressed 'Eukaryotes First' hypotheses. Those who proposed Prokaryotes First hypotheses advocated either a fusion event between a bacterium and an archaeon that produced the first eukaryote or the direct evolution of the Eukarya from the Archaea. The Eukaryotes First proponents posit that the eukaryotes evolved initially and then, by reductive evolution, produced the Bacteria and Archaea. No mention was made of another previously published hypothesis termed the Nuclear Compartment Commonality (NuCom) hypothesis, which proposed the evolution of the Eukarya and Bacteria from nucleated ancestors (Staley 2013
MeSH term(s)	Archaea/classification ; Archaea/cytology ; Bacteria/classification ; Bacteria/cytology ; Biological Evolution ; Cell Nucleus ; Eukaryota/classification ; Eukaryota/cytology ; Models, Theoretical ; Phylogeny
Language	English
Publishing date	2017-06-28
Publishing country	England
Document type	Journal Article
ZDB-ID	2630944-0
ISSN	2046-2441 ; 2046-2441
ISSN (online)	2046-2441
ISSN	2046-2441
DOI	10.1098/rsob.170041
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: An approach for determining the reliability of manual and digital scoring of sleep stages.

Gerardy, Bethany / Kuna, Samuel T / Pack, Allan / Kushida, Clete A / Walsh, James K / Staley, Bethany / Pien, Grace W / Younes, Magdy

Sleep

2024 Volume 46, Issue 11

Abstract: Study objectives: Inter-scorer variability in sleep staging is largely due to equivocal epochs that contain features of more than one stage. We propose an approach that recognizes the existence of equivocal epochs and evaluates scorers accordingly.: ... ...

Abstract	Study objectives: Inter-scorer variability in sleep staging is largely due to equivocal epochs that contain features of more than one stage. We propose an approach that recognizes the existence of equivocal epochs and evaluates scorers accordingly. Methods: Epoch-by-epoch staging was performed on 70 polysomnograms by six qualified technologists and by a digital system (Michele Sleep Scoring [MSS]). Probability that epochs assigned the same stage by only two of the six technologists (minority score) resulted from random occurrence of two errors was calculated and found to be <5%, thereby indicating that the stage assigned is an acceptable variant for the epoch. Acceptable stages were identified in each epoch as stages assigned by at least two technologists. Percent agreement between each technologist and the other five technologists, acting as judges, was determined. Agreement was considered to exist if the stage assigned by the tested scorer was one of the acceptable stages for the epoch. Stage assigned by MSS was likewise considered in agreement if included in the acceptable stages made by the technologists. Results: Agreement of technologists tested against five qualified judges increased from 80.8% (range 70.5%-86.4% among technologists) when using the majority rule, to 96.1 (89.8%-98.5%) by the proposed approach. Agreement between unedited MSS and same judges was 90.0% and increased to 92.1% after brief editing. Conclusions: Accounting for equivocal epochs provides a more accurate estimate of a scorer's (human or digital) competence in scoring sleep stages and reduces inter-scorer disagreements. The proposed approach can be implemented in sleep-scoring training and accreditation programs.
MeSH term(s)	Humans ; Reproducibility of Results ; Observer Variation ; Sleep Stages ; Sleep ; Polysomnography/methods ; Electroencephalography
Language	English
Publishing date	2024-01-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	424441-2
ISSN	1550-9109 ; 0161-8105
ISSN (online)	1550-9109
ISSN	0161-8105
DOI	10.1093/sleep/zsad248
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Article ; Online: Domain Cell Theory supports the independent evolution of the Eukarya, Bacteria and Archaea and the Nuclear Compartment Commonality hypothesis

James T. Staley

Open Biology, Vol 7, Iss

2017 Volume 6

Abstract: ... of the Eukarya and Bacteria from nucleated ancestors (Staley 2013 Astrobiol Outreach 1, 105 (doi:10.4172/2332 ...

Abstract	In 2015, the Royal Society of London held a meeting to discuss the various hypotheses regarding the origin of the Eukarya. Although not all participants supported a hypothesis, the proposals that did fit into two broad categories: one group favoured ‘Prokaryotes First’ hypotheses and another addressed ‘Eukaryotes First’ hypotheses. Those who proposed Prokaryotes First hypotheses advocated either a fusion event between a bacterium and an archaeon that produced the first eukaryote or the direct evolution of the Eukarya from the Archaea. The Eukaryotes First proponents posit that the eukaryotes evolved initially and then, by reductive evolution, produced the Bacteria and Archaea. No mention was made of another previously published hypothesis termed the Nuclear Compartment Commonality (NuCom) hypothesis, which proposed the evolution of the Eukarya and Bacteria from nucleated ancestors (Staley 2013 Astrobiol Outreach 1, 105 (doi:10.4172/2332-2519.1000105)). Evidence from two studies indicates that the nucleated Planctomycetes–Verrucomicrobia–Chlamydia superphylum members are the most ancient Bacteria known (Brochier & Philippe 2002 Nature 417, 244 (doi:10.1038/417244a); Jun et al. 2010 Proc. Natl Acad. Sci. USA 107, 133–138 (doi:10.1073/pnas.0913033107)). This review summarizes the evidence for the NuCom hypothesis and discusses how simple the NuCom hypothesis is in explaining eukaryote evolution relative to the other hypotheses. The philosophical importance of simplicity and its relationship to truth in hypotheses such as NuCom and Domain Cell Theory is presented. Domain Cell Theory is also proposed herein, which contends that each of the three cellular lineages of life, the Archaea, Bacteria and Eukarya domains, evolved independently, in support of the NuCom hypothesis. All other proposed hypotheses violate Domain Cell Theory because they posit the evolution of different cellular descendants from ancestral cellular types.
Keywords	evolution ; cell theory ; tree of life ; Biology (General) ; QH301-705.5
Subject code	160
Language	English
Publishing date	2017-01-01T00:00:00Z
Publisher	The Royal Society
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Ancient, highly conserved proteins from a LUCA with complex cell biology provide evidence in support of the nuclear compartment commonality (NuCom) hypothesis.

Staley, James T / Fuerst, John A

Research in microbiology

2017 Volume 168, Issue 5, Page(s) 395–412

Abstract: The nuclear compartment commonality (NuCom) hypothesis posits a complex last common ancestor (LUCA) with membranous compartments including a nuclear membrane. Such a LUCA then evolved to produce two nucleated lineages of the tree of life: the ... ...

Abstract	The nuclear compartment commonality (NuCom) hypothesis posits a complex last common ancestor (LUCA) with membranous compartments including a nuclear membrane. Such a LUCA then evolved to produce two nucleated lineages of the tree of life: the Planctomycetes-Verrucomicrobia-Chlamydia superphylum (PVC) within the Bacteria, and the Eukarya. We propose that a group of ancient essential protokaryotic signature proteins (PSPs) originating in LUCA were incorporated into ancestors of PVC Bacteria and Eukarya. Tubulins, ubiquitin system enzymes and sterol-synthesizing enzymes are consistent with early origins of these features shared between the PVC superphylum and Eukarya.
Language	English
Publishing date	2017-06
Publishing country	France
Document type	Journal Article ; Review
ZDB-ID	1004220-9
ISSN	1769-7123 ; 0923-2508
ISSN (online)	1769-7123
ISSN	0923-2508
DOI	10.1016/j.resmic.2017.01.001
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Article ; Online: Archaea-First and the Co-Evolutionary Diversification of Domains of Life.

Staley, James T / Caetano-Anollés, Gustavo

BioEssays : news and reviews in molecular, cellular and developmental biology

2018 Volume 40, Issue 8, Page(s) e1800036

Abstract: The origins and evolution of the Archaea, Bacteria, and Eukarya remain controversial. Phylogenomic-wide studies of molecular features that are evolutionarily conserved, such as protein structural domains, suggest Archaea is the first domain of life to ... ...

Abstract	The origins and evolution of the Archaea, Bacteria, and Eukarya remain controversial. Phylogenomic-wide studies of molecular features that are evolutionarily conserved, such as protein structural domains, suggest Archaea is the first domain of life to diversify from a stem line of descent. This line embodies the last universal common ancestor of cellular life. Here, we propose that ancestors of Euryarchaeota co-evolved with those of Bacteria prior to the diversification of Eukarya. This co-evolutionary scenario is supported by comparative genomic and phylogenomic analyses of the distributions of fold families of domains in the proteomes of free-living organisms, which show horizontal gene recruitments and informational process homologies. It also benefits from the molecular study of cell physiologies responsible for membrane phospholipids, methanogenesis, methane oxidation, cell division, gas vesicles, and the cell wall. Our theory however challenges popular cell fusion and two-domain of life scenarios derived from sequence analysis, demanding phylogenetic reconciliation. Also see the video abstract here: https://youtu.be/9yVWn_Q9faY.
MeSH term(s)	Archaea/genetics ; Archaea/physiology ; Archaeal Proteins/chemistry ; Archaeal Proteins/genetics ; Archaeal Proteins/metabolism ; Bacteria/cytology ; Bacteria/genetics ; Biological Evolution ; Cell Membrane/metabolism ; Cell Wall/chemistry ; Cell Wall/metabolism ; Eukaryota/cytology ; Eukaryota/genetics ; Eukaryota/physiology ; Gene Transfer, Horizontal ; Genomics ; Methane/metabolism ; Phospholipids/metabolism ; Phylogeny ; Proteome
Chemical Substances	Archaeal Proteins ; Phospholipids ; Proteome ; Methane (OP0UW79H66)
Language	English
Publishing date	2018-06-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	50140-2
ISSN	1521-1878 ; 0265-9247
ISSN (online)	1521-1878
ISSN	0265-9247
DOI	10.1002/bies.201800036
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Article: Archaea‐First and the Co‐Evolutionary Diversification of Domains of Life

Staley, James T / Caetano‐Anollés, Gustavo

BioEssays. 2018 Aug., v. 40, no. 8

2018

Abstract: The origins and evolution of the Archaea, Bacteria, and Eukarya remain controversial. Phylogenomic‐wide studies of molecular features that are evolutionarily conserved, such as protein structural domains, suggest Archaea is the first domain of life to ... ...

Abstract	The origins and evolution of the Archaea, Bacteria, and Eukarya remain controversial. Phylogenomic‐wide studies of molecular features that are evolutionarily conserved, such as protein structural domains, suggest Archaea is the first domain of life to diversify from a stem line of descent. This line embodies the last universal common ancestor of cellular life. Here, we propose that ancestors of Euryarchaeota co‐evolved with those of Bacteria prior to the diversification of Eukarya. This co‐evolutionary scenario is supported by comparative genomic and phylogenomic analyses of the distributions of fold families of domains in the proteomes of free‐living organisms, which show horizontal gene recruitments and informational process homologies. It also benefits from the molecular study of cell physiologies responsible for membrane phospholipids, methanogenesis, methane oxidation, cell division, gas vesicles, and the cell wall. Our theory however challenges popular cell fusion and two‐domain of life scenarios derived from sequence analysis, demanding phylogenetic reconciliation. Also see the video abstract here: https://youtu.be/9yVWn_Q9faY.
Keywords	ancestry ; bacteria ; cell division ; cell fusion ; cell walls ; coevolution ; Euryarchaeota ; genes ; genomics ; methane ; methane production ; oxidation ; phospholipids ; phylogeny ; proteome ; sequence analysis
Language	English
Dates of publication	2018-08
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	REVIEW
ZDB-ID	50140-2
ISSN	1521-1878 ; 0265-9247
ISSN (online)	1521-1878
ISSN	0265-9247
DOI	10.1002/bies.201800036
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Article ; Online: Universal species concept: pipe dream or a step toward unifying biology?

Staley, James T

Journal of industrial microbiology & biotechnology

2009 Volume 36, Issue 11, Page(s) 1331–1336

Abstract: The Universal Tree of Life, which is based on phylogenetic analysis of the RNA sequence from the small ribosomal subunit, was a breakthrough in understanding the relatedness among all living organisms. The result has had a major impact on taxonomy by ... ...

Abstract	The Universal Tree of Life, which is based on phylogenetic analysis of the RNA sequence from the small ribosomal subunit, was a breakthrough in understanding the relatedness among all living organisms. The result has had a major impact on taxonomy by separating life into three domains: Eukarya, Bacteria, and Archaea. Indeed, microbiologists have used the 16S ribosomal RNA (rRNA) of the small ribosomal subunit to construct the hierarchical classification of Bacteria and Archaea from the level of domain to genus. However, the 16S rRNA of the Bacteria and Archaea and the corresponding 18S rRNA of the Eukarya are too highly conserved to be useful phylogenetically at the species level. For this reason, I propose that biologists adopt a phylogenomic species concept that utilizes both phylogenetic analyses of less highly conserved genes and proteins as well as genomic analyses for the circumscription of species. If biologists adopt a phylogenomic concept for species, the classification of all living organisms from domain to species could be completed. Furthermore, this universal species concept could help provide a more equitable circumscription among all species, as well as aid in the unification of biologists and biology.
MeSH term(s)	Archaea/classification ; Bacteria/classification ; Genetic Speciation ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 5S/chemistry ; RNA, Ribosomal, 5S/genetics ; Species Specificity
Chemical Substances	RNA, Ribosomal, 5S
Language	English
Publishing date	2009-09-25
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1482484-X
ISSN	1476-5535 ; 1367-5435
ISSN (online)	1476-5535
ISSN	1367-5435
DOI	10.1007/s10295-009-0642-8
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Article ; Online: The Efficacy and Safety of Treating Acquired MET Resistance Through Combinations of Parent and MET Tyrosine Kinase Inhibitors in Patients With Metastatic Oncogene-Driven NSCLC.

JTO clinical and research reports

2024 Volume 5, Issue 2, Page(s) 100637

Abstract: Introduction: Acquired : Methods: Multi-institutional retrospective chart review identified 83 patients with metastatic oncogene-driven NSCLC that were separated into the following two pairwise matched cohorts: (1) MET cohort (n = 41)-patients with ... ...

Abstract	Introduction: Acquired Methods: Multi-institutional retrospective chart review identified 83 patients with metastatic oncogene-driven NSCLC that were separated into the following two pairwise matched cohorts: (1) MET cohort (n = 41)-patients with acquired MET resistance continuing their parent TKI with a MET TKI added or (2) Chemotherapy cohort (n = 42)-patients without any actionable resistance continuing their parent TKI with a platinum-pemetrexed added. Clinicopathologic features, radiographic response (by means of Response Evaluation Criteria in Solid Tumors version 1.1), survival outcomes, adverse events (AEs) (by means of Common Terminology Criteria for Adverse Events version 5.0), and genomic data were collected. Survival outcomes were assessed using Kaplan-Meier methods. Multivariate modeling adjusted for lines of therapy, brain metastases, TP53 mutations, and oligometastatic disease. Results: Within the MET cohort, median age was 56 years (range: 36-83 y). Most patients were never smokers (28 of 41, 68.3%). Baseline brain metastases were common (21 of 41, 51%). The most common oncogenes in the MET cohort were Conclusions: The efficacy and safety of combining MET TKIs (crizotinib, capmatinib, or tepotinib) with parent TKIs for acquired MET resistance are efficacious. Radiographic response and AEs did not differ significantly on the basis of the underlying MET TKI used. Loss of
Language	English
Publishing date	2024-01-18
Publishing country	United States
Document type	Journal Article
ISSN	2666-3643
ISSN (online)	2666-3643
DOI	10.1016/j.jtocrr.2024.100637
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Article: Ancient, highly conserved proteins from a LUCA with complex cell biology provide evidence in support of the nuclear compartment commonality (NuCom) hypothesis

Staley, James T / John A. Fuerst

Institut Pasteur Research in microbiology. 2017 June, v. 168, no. 5

2017

Abstract	The nuclear compartment commonality (NuCom) hypothesis posits a complex last common ancestor (LUCA) with membranous compartments including a nuclear membrane. Such a LUCA then evolved to produce two nucleated lineages of the tree of life: the Planctomycetes–Verrucomicrobia–Chlamydia superphylum (PVC) within the Bacteria, and the Eukarya. We propose that a group of ancient essential protokaryotic signature proteins (PSPs) originating in LUCA were incorporated into ancestors of PVC Bacteria and Eukarya. Tubulins, ubiquitin system enzymes and sterol-synthesizing enzymes are consistent with early origins of these features shared between the PVC superphylum and Eukarya.
Keywords	ancestry ; bacteria ; enzymes ; nuclear membrane ; tubulin ; ubiquitin
Language	English
Dates of publication	2017-06
Size	p. 395-412.
Publishing place	Elsevier Masson SAS
Document type	Article
ZDB-ID	1004220-9
ISSN	1769-7123 ; 0923-2508
ISSN (online)	1769-7123
ISSN	0923-2508
DOI	10.1016/j.resmic.2017.01.001
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Article ; Online: Stakeholder selected strategies for obesity prevention in childcare: results from a small-scale cluster randomized hybrid type III trial.

Swindle, Taren / McBride, Nicole M / Selig, James P / Johnson, Susan L / Whiteside-Mansell, Leanne / Martin, Janna / Staley, Audra / Curran, Geoffrey M

Implementation science : IS

2021 Volume 16, Issue 1, Page(s) 48

Abstract: ... Strategies were assessed using examination of data distributions and unadjusted comparisons (t tests) as well ...

Abstract	Background: Together, We Inspire Smart Eating (WISE) is an intervention for the early care and education setting to support children's exposure to and intake of fruits and vegetables. WISE emphasizes 4 evidence-based practices (EBPs): (1) use of a mascot; (2) educators' role modeling; (3) positive feeding practices; and (4) hands-on exposures. The current study reports on a small-scale implementation trial aimed at improving the use of WISE EBPs by teachers. Methods: A Hybrid Type III Cluster Randomized Design compared a Basic and Enhanced implementation strategy. The Basic Strategy included training and reminders only; the Enhanced strategy was a multi-faceted package of stakeholder-selected strategies including a leadership commitment, an implementation blueprint, a local champion, an environmental reminder of the EBPs, facilitation, and tailored educational resources and incentives. All study sites were Head Starts. Sites were randomized using a balancing technique that considered site characteristics; 4 sites (20 classrooms, 39 educators, 305 children) received Enhanced support; 5 sites (18 classrooms, 36 educators, 316 children) received Basic support. RE-AIM guided the evaluation, and implementation fidelity was the primary outcome. Strategies were assessed using examination of data distributions and unadjusted comparisons (t tests) as well as general linear and mixed effects models controlling for covariates. Results: For the primary outcome of fidelity, the Enhanced group had significantly higher means for 3 of 4 EBPs. Multivariate models explained a significant portion of variance for both mascot use and hands-on exposure with a significant positive effect observed for treatment condition. The Enhanced group also had higher rates of Appropriateness and Organizational Readiness for Implementing Change (as indicators of implementation and adoption, respectively). There was no significant difference between groups for indicators of Reach, Effectiveness or Maintenance. Formative interviews indicated key targets for iteration and potential mechanisms. Key events were catalogued to provide context for interpretation (e.g., 61% of classrooms with turnover). Conclusions: Findings were mixed but suggested promise for the Enhanced strategy, especially considering key events of the study. Implementation fidelity improvements occurred mainly in the last 3 months of the school year; additional time may be needed to translate to improvements in child outcomes. Trial registration: NCT03075085 Registered 20 February 2017.
MeSH term(s)	Child ; Child Health ; Evidence-Based Practice ; Humans ; Obesity
Language	English
Publishing date	2021-05-01
Publishing country	England
Document type	Journal Article ; Randomized Controlled Trial ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2225822-X
ISSN	1748-5908 ; 1748-5908
ISSN (online)	1748-5908
ISSN	1748-5908
DOI	10.1186/s13012-021-01119-x
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