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Article ; Online: m

Benavides-Serrato, Angelica / Saunders, Jacquelyn T / Kumar, Sunil / Holmes, Brent / Benavides, Kennedy E / Bashir, Muhammad T / Nishimura, Robert N / Gera, Joseph

Cancer letters

2023 Volume 562, Page(s) 216178

Abstract: ... events regulating cyclin D1 and c-myc IRES activity. Here we describe the requirement for m ...

Abstract	A major mechanism conferring resistance to mTOR inhibitors is activation of a salvage pathway stimulating internal ribosome entry site (IRES)-mediated mRNA translation, driving the synthesis of proteins promoting resistance of glioblastoma (GBM). Previously, we found this pathway is stimulated by the requisite IRES-trans-acting factor (ITAF) hnRNP A1, which itself is subject to phosphorylation and methylation events regulating cyclin D1 and c-myc IRES activity. Here we describe the requirement for m
MeSH term(s)	Humans ; Cyclin D1/genetics ; Cyclin D1/metabolism ; Glioblastoma/drug therapy ; Glioblastoma/genetics ; Glioblastoma/metabolism ; Heterogeneous Nuclear Ribonucleoprotein A1/genetics ; Heterogeneous Nuclear Ribonucleoprotein A1/metabolism ; Internal Ribosome Entry Sites ; Methyltransferases/metabolism ; Protein Biosynthesis ; TOR Serine-Threonine Kinases/metabolism ; Genes, myc
Chemical Substances	Cyclin D1 (136601-57-5) ; Heterogeneous Nuclear Ribonucleoprotein A1 ; Internal Ribosome Entry Sites ; Methyltransferases (EC 2.1.1.-) ; METTL3 protein, human (EC 2.1.1.62) ; MTOR protein, human (EC 2.7.1.1) ; TOR Serine-Threonine Kinases (EC 2.7.11.1)
Language	English
Publishing date	2023-04-14
Publishing country	Ireland
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
ZDB-ID	195674-7
ISSN	1872-7980 ; 0304-3835
ISSN (online)	1872-7980
ISSN	0304-3835
DOI	10.1016/j.canlet.2023.216178
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Article: M

Walsh, Kevin / Calder, Nuala / Olupot-Olupot, Peter / Ssenyondo, Tonny / Okiror, William / Okalebo, Charles Bernard / Muhindo, Rita / Mpoya, Ayub / Holmes, Elaine / Marchesi, Julian / Delamare de la Villenaise de Chenevarin, Gael / Frost, Gary / Maitland, Kathryn

Wellcome open research

2018 Volume 3, Page(s) 95

Abstract: Background: ...

Abstract	Background:
Language	English
Publishing date	2018-08-02
Publishing country	England
Document type	Journal Article
ISSN	2398-502X
ISSN	2398-502X
DOI	10.12688/wellcomeopenres.14706.1
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Article ; Online: HIV-1 Group M Capsid Amino Acid Variability: Implications for Sequence Quality Control of Genotypic Resistance Testing.

Tao, Kaiming / Rhee, Soo-Yon / Tzou, Philip L / Osman, Zachary A / Pond, Sergei L Kosakovsky / Holmes, Susan P / Shafer, Robert W

Viruses

2023 Volume 15, Issue 4

Abstract: ... sequence data.: Methods: We analyzed published HIV-1 group M capsid sequences from 21,012 capsid ... mutations, defined as amino acid differences from the group M consensus, with a prevalence ≥ 0.1%. Co ...

Abstract	Background: With the approval of the HIV-1 capsid inhibitor, lenacapavir, capsid sequencing will be required for managing lenacapavir-experienced individuals with detectable viremia. Successful sequence interpretation will require examining new capsid sequences in the context of previously published sequence data. Methods: We analyzed published HIV-1 group M capsid sequences from 21,012 capsid-inhibitor naïve individuals to characterize amino acid variability at each position and influence of subtype and cytotoxic T lymphocyte (CTL) selection pressure. We determined the distributions of usual mutations, defined as amino acid differences from the group M consensus, with a prevalence ≥ 0.1%. Co-evolving mutations were identified using a phylogenetically-informed Bayesian graphical model method. Results: 162 (70.1%) positions had no usual mutations (45.9%) or only conservative usual mutations with a positive BLOSUM62 score (24.2%). Variability correlated independently with subtype-specific amino acid occurrence (Spearman rho = 0.83; Conclusions: Knowing the distribution of usual capsid mutations is essential for sequence quality control. Comparing capsid sequences from lenacapavir-treated and lenacapavir-naïve individuals will enable the identification of additional mutations potentially associated with lenacapavir therapy.
MeSH term(s)	Humans ; Capsid/chemistry ; HIV-1/genetics ; HIV-1/chemistry ; Amino Acids/genetics ; Bayes Theorem ; HIV Infections/drug therapy ; HIV Infections/genetics ; Mutation ; Capsid Proteins/genetics ; Capsid Proteins/analysis ; HIV Seropositivity ; Anti-HIV Agents/pharmacology
Chemical Substances	Amino Acids ; Capsid Proteins ; Anti-HIV Agents
Language	English
Publishing date	2023-04-18
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v15040992
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Article ; Online: Structural vulnerability and new perspectives in social medicine on the health of immigrants: Interview with James Quesada and Seth M. Holmes.

Rivera, Carlos Piñones / Quesada, James / Holmes, Seth M

Salud colectiva

2019 Volume 15, Page(s) e2146

Abstract: A decade ago, a number of English-speaking authors focused mainly on the analysis and intervention of processes of social determination of health of migrants developed the concept of structural vulnerability as a way to combat individualism, biologism, ... ...

Title translation	La vulnerabilidad estructural y las nuevas perspectivas en medicina social sobre la salud de los migrantes: entrevista a James Quesada y Seth M. Holmes.
Abstract	A decade ago, a number of English-speaking authors focused mainly on the analysis and intervention of processes of social determination of health of migrants developed the concept of structural vulnerability as a way to combat individualism, biologism, the invisibilization of processes of structural determination and the blaming of victims. As part of the historical contributions of social medicine, the current developments of the structural vulnerability approach have been disconnected from the discussions of the collective health movement and Latin American social medicine in general, among other reasons due to linguistic barriers associated with the scarcity of publications in Spanish. The present interview, conducted with two of the primary representatives of the structural vulnerability approach, investigates its historical origins and seeks to explore the specific contributions that are being made today, as a way to bring them closer to Spanish-speaking readers and so enable dialogue with the proposals of Latin American social medicine.
MeSH term(s)	Anthropology, Medical ; Emigrants and Immigrants ; Humans ; Latin America ; Social Determinants of Health ; Social Medicine ; Vulnerable Populations
Language	Spanish
Publishing date	2019-08-15
Publishing country	Argentina
Document type	Interview
ZDB-ID	2394313-0
ISSN	1851-8265 ; 1669-2381
ISSN (online)	1851-8265
ISSN	1669-2381
DOI	10.18294/sc.2019.2146
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Article: Mammalian research honoring the educational contributions of Grinnell Awardee Robert M. Timm

Anderson, Robert P / Eifler, Maria A / Lanier, Hayley C / Holmes, Thorvald

Journal of mammalogy. 2020 June 4, v. 100, no. 6

2020

Abstract: This Special Feature honors Robert M. (Bob) Timm, who was recognized by the American Society ...

Abstract	This Special Feature honors Robert M. (Bob) Timm, who was recognized by the American Society of Mammalogists in 2017 with the Joseph Grinnell Award for his contributions to education in mammalogy. Bob has made great educational contributions through formal classroom and field instruction, interactions with researchers, public outreach, and mentorship of graduate students. Bob also has promoted equity and human diversity in mammalogy and joyfully assisted international colleagues (especially Latin Americans). In this Festschrift, many of his Ph.D. students offer the results of their recent mammalian research on topics as diverse as taxonomy and species identification, functional morphology, and biogeography and conservation on an environmentally dynamic planet.
Keywords	anatomy and morphology ; biogeography ; education ; humans ; mammalogy ; outreach ; species identification
Language	English
Dates of publication	2020-0604
Size	p. 1710-1712.
Publishing place	American Society of Mammalogists
Document type	Article
Note	NAL-light
ZDB-ID	218314-6
ISSN	0022-2372
ISSN	0022-2372
DOI	10.1093/jmammal/gyz159
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: The role of selection in shaping diversity of natural M. tuberculosis populations.

Pepperell, Caitlin S / Casto, Amanda M / Kitchen, Andrew / Granka, Julie M / Cornejo, Omar E / Holmes, Edward C / Holmes, Eddie C / Birren, Bruce / Galagan, James / Feldman, Marcus W

PLoS pathogens

2013 Volume 9, Issue 8, Page(s) e1003543

Abstract: Mycobacterium tuberculosis (M.tb), the cause of tuberculosis (TB), is estimated to infect a new ... host every second. While analyses of genetic data from natural populations of M.tb have emphasized ... of diversity in 63 globally extant genomes of M.tb and related pathogenic mycobacteria. We found evidence ...

Abstract	Mycobacterium tuberculosis (M.tb), the cause of tuberculosis (TB), is estimated to infect a new host every second. While analyses of genetic data from natural populations of M.tb have emphasized the role of genetic drift in shaping patterns of diversity, the influence of natural selection on this successful pathogen is less well understood. We investigated the effects of natural selection on patterns of diversity in 63 globally extant genomes of M.tb and related pathogenic mycobacteria. We found evidence of strong purifying selection, with an estimated genome-wide selection coefficient equal to -9.5 × 10(-4) (95% CI -1.1 × 10(-3) to -6.8 × 10(-4)); this is several orders of magnitude higher than recent estimates for eukaryotic and prokaryotic organisms. We also identified different patterns of variation across categories of gene function. Genes involved in transport and metabolism of inorganic ions exhibited very low levels of non-synonymous polymorphism, equivalent to categories under strong purifying selection (essential and translation-associated genes). The highest levels of non-synonymous variation were seen in a group of transporter genes, likely due to either diversifying selection or local selective sweeps. In addition to selection, we identified other important influences on M.tb genetic diversity, such as a 25-fold expansion of global M.tb populations coincident with explosive growth in human populations (estimated timing 1684 C.E., 95% CI 1620-1713 C.E.). These results emphasize the parallel demographic histories of this obligate pathogen and its human host, and suggest that the dominant effect of selection on M.tb is removal of novel variants, with exceptions in an interesting group of genes involved in transportation and defense. We speculate that the hostile environment within a host imposes strict demands on M.tb physiology, and thus a substantial fitness cost for most new mutations. In this respect, obligate bacterial pathogens may differ from other host-associated microbes such as symbionts.
MeSH term(s)	Evolution, Molecular ; Genome, Bacterial ; Humans ; Mycobacterium tuberculosis/classification ; Mycobacterium tuberculosis/genetics ; Phylogeny ; Polymorphism, Genetic/genetics ; Recombination, Genetic ; Selection, Genetic/genetics ; Tuberculosis/genetics ; Tuberculosis/microbiology
Language	English
Publishing date	2013-08-15
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2205412-1
ISSN	1553-7374 ; 1553-7366
ISSN (online)	1553-7374
ISSN	1553-7366
DOI	10.1371/journal.ppat.1003543
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Article: Reply from j.B. Jones and R.m. Holmes.

Jones, J B / Holmes, R M

Trends in ecology & evolution

2011 Volume 11, Issue 10, Page(s) 430

Language	English
Publishing date	2011-01-14
Publishing country	England
Document type	Letter
ZDB-ID	284965-3
ISSN	1872-8383 ; 0169-5347
ISSN (online)	1872-8383
ISSN	0169-5347
DOI	10.1016/0169-5347(96)91649-3
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Zs Bio TEE: Show issues
Z 2005/711: Show issues

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Article ; Online: First structurally characterized tricyanomanganate(III) and its magnetic {Mn(III)(2)M(II)(2)} complexes (M(II) = Mn, Ni).

Tang, Minao / Li, Dongfeng / Mallik, Uma Prasad / Withers, Jeffrey R / Brauer, Shari / Rhodes, Michael R / Clérac, Rodolphe / Yee, Gordon T / Whangbo, Myung-Hwan / Holmes, Stephen M

Inorganic chemistry

2010 Volume 49, Issue 11, Page(s) 4753–4755

Abstract: ... 2'-bipyridine (bpy) affords {Mn(III)(2)M(II)(2)} complexes (M(II) = Mn, 2; Ni, 3). Magnetic ...

Abstract	Treatment of tris(3-cyano-2,4-pentanedionato)manganese(III) with KTp, followed by [NEt(4)]CN affords [NEt(4)][(Tp)Mn(III)(CN)(3)] (1); subsequent treatment of 1 with divalent triflates (OTf) and 2,2'-bipyridine (bpy) affords {Mn(III)(2)M(II)(2)} complexes (M(II) = Mn, 2; Ni, 3). Magnetic measurements show that 1-3 exhibit S(T) = 1, 3, and 4 spin ground states, respectively.
Language	English
Publishing date	2010-06-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	1484438-2
ISSN	1520-510X ; 0020-1669
ISSN (online)	1520-510X
ISSN	0020-1669
DOI	10.1021/ic1006605
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Article ; Online: Urban primate ranging patterns: GPS-collar deployments for Macaca fascicularis and M. sylvanus.

Klegarth, Amy R / Hollocher, Hope / Jones-Engel, Lisa / Shaw, Eric / Lee, Benjamin P Y-H / Feeney, Tessa / Holmes, Damian / Laguea, Dale / Fuentes, Agustín

American journal of primatology

2017 Volume 79, Issue 5

Abstract: The global increase in urbanization is leading to heavier interface between humans and wildlife. Within these anthropogenic landscapes, little is known about ranging patterns, particularly with regard to urban primates. Here we present the results of the ...

Abstract	The global increase in urbanization is leading to heavier interface between humans and wildlife. Within these anthropogenic landscapes, little is known about ranging patterns, particularly with regard to urban primates. Here we present the results of the first long-term deployment of multiple GPS collars on two species of macaques to investigate the impacts of urbanization on urban primate ranging patterns in Singapore and Gibraltar. Collars data acquisition were excellent with respect to the amount, quality, and accuracy of data collected; however, remote connectivity and drop-off functionality was poor across all deployments. Analyses highlighted high variability in ranging patterns between individuals within each species that aligned with access to human food resources and patterns of tourism. Individuals from troops with less access to human food had much larger home, core, and day ranges relative to those with regular provisioning or raiding opportunities. Almost no temporal range overlap was observed between any focal individuals at either site and spatial overlap was low for all but two troops at each site. We found no relationship between anthropogenic schedules and changes in ranging patterns. Significant seasonal variation existed for daily path length and day range size for both the Singapore long-tailed and the Gibraltar Barbary macaques, with long-tailed macaques increasing their range during the equatorial monsoon season and Barbary macaques increasing their range during drier, summer months. This study highlights how the behavioral plasticity found within the genus Macaca is reflected in ranging pattern variability within urban environments.
MeSH term(s)	Animal Distribution ; Animals ; Cities ; Ethology/instrumentation ; Female ; Geographic Information Systems ; Gibraltar ; Homing Behavior ; Macaca/physiology ; Macaca fascicularis/physiology ; Male ; Seasons ; Singapore
Language	English
Publishing date	2017-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	1495834-x
ISSN	1098-2345 ; 0275-2565
ISSN (online)	1098-2345
ISSN	0275-2565
DOI	10.1002/ajp.22633
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Article ; Online: The role of selection in shaping diversity of natural M. tuberculosis populations.

Caitlin S Pepperell / Amanda M Casto / Andrew Kitchen / Julie M Granka / Omar E Cornejo / Edward C Holmes / Bruce Birren / James Galagan / Marcus W Feldman

PLoS Pathogens, Vol 9, Iss 8, p e

2013 Volume 1003543

Abstract	Mycobacterium tuberculosis (M.tb), the cause of tuberculosis (TB), is estimated to infect a new host every second. While analyses of genetic data from natural populations of M.tb have emphasized the role of genetic drift in shaping patterns of diversity, the influence of natural selection on this successful pathogen is less well understood. We investigated the effects of natural selection on patterns of diversity in 63 globally extant genomes of M.tb and related pathogenic mycobacteria. We found evidence of strong purifying selection, with an estimated genome-wide selection coefficient equal to -9.5 × 10(-4) (95% CI -1.1 × 10(-3) to -6.8 × 10(-4)); this is several orders of magnitude higher than recent estimates for eukaryotic and prokaryotic organisms. We also identified different patterns of variation across categories of gene function. Genes involved in transport and metabolism of inorganic ions exhibited very low levels of non-synonymous polymorphism, equivalent to categories under strong purifying selection (essential and translation-associated genes). The highest levels of non-synonymous variation were seen in a group of transporter genes, likely due to either diversifying selection or local selective sweeps. In addition to selection, we identified other important influences on M.tb genetic diversity, such as a 25-fold expansion of global M.tb populations coincident with explosive growth in human populations (estimated timing 1684 C.E., 95% CI 1620-1713 C.E.). These results emphasize the parallel demographic histories of this obligate pathogen and its human host, and suggest that the dominant effect of selection on M.tb is removal of novel variants, with exceptions in an interesting group of genes involved in transportation and defense. We speculate that the hostile environment within a host imposes strict demands on M.tb physiology, and thus a substantial fitness cost for most new mutations. In this respect, obligate bacterial pathogens may differ from other host-associated microbes such as symbionts.
Keywords	Immunologic diseases. Allergy ; RC581-607 ; Biology (General) ; QH301-705.5
Subject code	612
Language	English
Publishing date	2013-08-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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