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Article ; Online: New Mechanistic Insights into Purine Biosynthesis with Second Messenger c-di-AMP in Relation to Biofilm-Related Persistent Methicillin-Resistant Staphylococcus aureus Infections.

Li, Liang / Li, Yi / Zhu, Fengli / Cheung, Ambrose L / Wang, Genzhu / Bai, Guangchun / Proctor, Richard A / Yeaman, Michael R / Bayer, Arnold S / Xiong, Yan Q

mBio

2021 Volume 12, Issue 6, Page(s) e0208121

Abstract: ... demonstrated that purine biosynthesis plays an important role in such persistent infections. Cyclic di-AMP (c ... in bacteria. However, whether there is a regulatory connection between the purine biosynthesis pathway and c ...

Abstract	Persistent methicillin-resistant Staphylococcus aureus (MRSA) endovascular infections represent a significant clinically challenging subset of invasive, life-threatening S. aureus infections. We have recently demonstrated that purine biosynthesis plays an important role in such persistent infections. Cyclic di-AMP (c-di-AMP) is an essential and ubiquitous second messenger that regulates many cellular pathways in bacteria. However, whether there is a regulatory connection between the purine biosynthesis pathway and c-di-AMP impacting persistent outcomes was not known. Here, we demonstrated that the purine biosynthesis mutant MRSA strain, the Δ
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Biofilms/drug effects ; Biosynthetic Pathways ; Cyclic AMP/metabolism ; Daptomycin/pharmacology ; Humans ; Methicillin-Resistant Staphylococcus aureus/drug effects ; Methicillin-Resistant Staphylococcus aureus/genetics ; Methicillin-Resistant Staphylococcus aureus/metabolism ; Persistent Infection/microbiology ; Purines/biosynthesis ; Second Messenger Systems ; Staphylococcal Infections/microbiology
Chemical Substances	Anti-Bacterial Agents ; Bacterial Proteins ; Purines ; Cyclic AMP (E0399OZS9N) ; Daptomycin (NWQ5N31VKK) ; purine (W60KTZ3IZY)
Language	English
Publishing date	2021-11-02
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mBio.02081-21
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Using genome scans to identify genes used repeatedly for adaptation.

Booker, Tom R / Yeaman, Sam / Whitlock, Michael C

Evolution; international journal of organic evolution

2023 Volume 77, Issue 3, Page(s) 801–811

Abstract: Adaptation occurring in similar genes or genomic regions in distinct lineages provides evolutionary biologists with a glimpse at the fundamental opportunities for and constraints to diversification. With the widespread availability of high-throughput ... ...

Abstract	Adaptation occurring in similar genes or genomic regions in distinct lineages provides evolutionary biologists with a glimpse at the fundamental opportunities for and constraints to diversification. With the widespread availability of high-throughput sequencing technologies and the development of population genetic methods to identify the genetic basis of adaptation, studies have begun to compare the evidence for adaptation at the molecular level among distinct lineages. However, methods to study repeated adaptation are often oriented toward genome-wide testing to identify a set of genes with signatures of repeated use, rather than evaluating the significance at the level of an individual gene. In this study, we propose PicMin, a novel statistical method derived from the theory of order statistics that can test for repeated molecular evolution to estimate significance at the level of an individual gene, using the results of genome scans. This method is generalizable to any number of lineages and, indeed, statistical power to detect repeated adaptation increases with the number of lineages that have signals of repeated adaptation of a given gene in multiple lineages. An implementation of the method written for R can be downloaded from https://github.com/TBooker/PicMin.
MeSH term(s)	Adaptation, Physiological/genetics ; Genome ; Genomics ; Biological Evolution ; Evolution, Molecular
Language	English
Publishing date	2023-01-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2036375-8
ISSN	1558-5646 ; 0014-3820
ISSN (online)	1558-5646
ISSN	0014-3820
DOI	10.1093/evolut/qpac063
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Article ; Online: Tensor-based insights into systems immunity and infectious disease.

Chin, Jackson L / Chan, Liana C / Yeaman, Michael R / Meyer, Aaron S

Trends in immunology

2023 Volume 44, Issue 5, Page(s) 329–332

Abstract: Profiling immune responses across several dimensions, including time, patients, molecular features, and tissue sites, can deepen our understanding of immunity as an integrated system. These studies require new analytical approaches to realize their full ... ...

Abstract	Profiling immune responses across several dimensions, including time, patients, molecular features, and tissue sites, can deepen our understanding of immunity as an integrated system. These studies require new analytical approaches to realize their full potential. We highlight recent applications of tensor methods and discuss several future opportunities.
MeSH term(s)	Humans ; Communicable Diseases ; Immunity
Language	English
Publishing date	2023-03-29
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2036831-8
ISSN	1471-4981 ; 1471-4906
ISSN (online)	1471-4981
ISSN	1471-4906
DOI	10.1016/j.it.2023.03.003
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Article ; Online: The WZA: A window-based method for characterizing genotype-environment associations.

Booker, Tom R / Yeaman, Sam / Whiting, James R / Whitlock, Michael C

Molecular ecology resources

2023 Volume 24, Issue 2, Page(s) e13768

Abstract: Genotype-environment association (GEA) studies have the potential to identify the genetic basis of local adaptation in natural populations. Specifically, GEA approaches look for a correlation between allele frequencies and putatively selective features ... ...

Abstract	Genotype-environment association (GEA) studies have the potential to identify the genetic basis of local adaptation in natural populations. Specifically, GEA approaches look for a correlation between allele frequencies and putatively selective features of the environment. Genetic markers with extreme evidence of correlation with the environment are presumed to be tagging the location of alleles that contribute to local adaptation. In this study, we propose a new method for GEA studies called the Weighted-Z Analysis (WZA) that combines information from closely linked sites into analysis windows in a way that was inspired by methods for calculating F
MeSH term(s)	Humans ; Adaptation, Physiological/genetics ; Gene Frequency ; Genotype ; Polymorphism, Single Nucleotide ; Genetics, Population
Language	English
Publishing date	2023-03-10
Publishing country	England
Document type	Journal Article
ZDB-ID	2406833-0
ISSN	1755-0998 ; 1755-098X
ISSN (online)	1755-0998
ISSN	1755-098X
DOI	10.1111/1755-0998.13768
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Article ; Online: International Iohexol Shortage: Alternative Contrast Agents and Imaging Procedures for the Urologist.

Lardieri, Grant / Kennady, Emmett H / Yeaman, Clinton / Schenkman, Noah

Urology practice

2023 Volume 10, Issue 3, Page(s) 271–277

Abstract: Introduction: In April 2022, GE Healthcare announced a COVID-19-related interruption in iohexol manufacturing, leading to an international iodinated contrast shortage. The shortage greatly impacted urological practice, highlighting the value of ... ...

Abstract	Introduction: In April 2022, GE Healthcare announced a COVID-19-related interruption in iohexol manufacturing, leading to an international iodinated contrast shortage. The shortage greatly impacted urological practice, highlighting the value of alternative contrast agents and imaging/procedure alternatives. These alternatives are reviewed in this work. Methods: A review of existing literature describing the use of alternative contrast agents, alternative imaging procedures, and contrast conservation strategies in urological care was performed using the PubMed database. The review was not performed systematically. Results: Older iodinated contrast agents such as ioxaglate and diatrizoate can replace iohexol for intravascular imaging in patients without renal impairment. These agents, along with gadolinium-based agents such as Gadavist, have been used intraluminally for urological procedures and diagnostic imaging. Several lesser-known imaging and procedure alternatives are described and include air contrast pyelography, contrast-enhanced ultrasound, voiding urosonography, and low tube voltage CT urography. Conservation strategies include contrast dose reductions and use of contrast management devices for contrast vial splitting. Conclusions: The COVID-19-related iohexol shortage caused significant hardship for urological care internationally, leading to delayed contrasted imaging studies and urological procedures. Alternative contrast agents, imaging/procedure alternatives, and conservation strategies are reviewed in this work with the goal of equipping the urologist to mitigate the current iodinated contrast shortage and to prepare in the event of a future shortage.
MeSH term(s)	Humans ; Iohexol ; Contrast Media ; Urologists ; COVID-19 ; Diatrizoate
Chemical Substances	Iohexol (4419T9MX03) ; Contrast Media ; Diatrizoate (117-96-4)
Language	English
Publishing date	2023-03-16
Publishing country	United States
Document type	Review ; Journal Article
ISSN	2352-0787
ISSN (online)	2352-0787
DOI	10.1097/UPJ.0000000000000396
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Article ; Online: Predictors of pelvic pain in a general urology clinic population.

Prillaman, Grace / Zillioux, Jacqueline / Beller, Haerin / Yeaman, Clinton / Rapp, David

BJUI compass

2023 Volume 4, Issue 6, Page(s) 668–672

Abstract: Objectives: To assess the prevalence and predictors of chronic pelvic pain in a general urology population presenting for evaluation of unrelated non-painful complaints.Generalized pelvic pain is estimated to afflict between 6% and 26% of women and is ... ...

Abstract	Objectives: To assess the prevalence and predictors of chronic pelvic pain in a general urology population presenting for evaluation of unrelated non-painful complaints.Generalized pelvic pain is estimated to afflict between 6% and 26% of women and is often multifactorial in aetiology. A paucity of prospective research exists to characterize chronic pelvic pain patterns and to understand related predictors. Materials and methods: This is a prospective, cross-sectional survey-based study of female patients presenting to a general urology clinic over a 10-month period (7/2018-5/2019). Patients completed a 32-item survey with questions pertaining to demographics, comorbidities and chronic pelvic pain characteristics. Comparison tests (chi-squared, Fisher's exact) and stepwise multivariable logistic modelling were performed to assess for predictors of chronic pelvic pain. Results: A total of 181 women completed the survey, with a mean age of 56 years. Overall, 75 (41%) women reported chronic pelvic pain. Those with chronic pelvic pain were younger compared to those without (52 vs 59 years, Conclusions: Our study is one of the few studies that has prospectively analysed chronic pelvic pain and its predictors. The present study identified significant associations with overactive bladder, fibromyalgia and bowel symptoms. Further research is needed to better understand the aetiologies of chronic pelvic pain and the possible relationship with identified clinical predictors.
Language	English
Publishing date	2023-07-01
Publishing country	United States
Document type	Journal Article
ISSN	2688-4526
ISSN (online)	2688-4526
DOI	10.1002/bco2.262
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Article ; Online: (with research data) Conservation and divergence of gene expression plasticity following c. 140 million years of evolution in lodgepole pine (Pinus contorta) and interior spruce (Picea glauca×Picea engelmannii).

Yeaman, Sam / Hodgins, Kathryn A / Suren, Haktan / Nurkowski, Kristin A / Rieseberg, Loren H / Holliday, Jason A / Aitken, Sally N

The New phytologist

2014 Volume 203, Issue 2, Page(s) 578–591

Abstract: Species respond to environmental stress through a combination of genetic adaptation and phenotypic plasticity, both of which may be important for survival in the face of climatic change. By characterizing the molecular basis of plastic responses and ... ...

Abstract	Species respond to environmental stress through a combination of genetic adaptation and phenotypic plasticity, both of which may be important for survival in the face of climatic change. By characterizing the molecular basis of plastic responses and comparing patterns among species, it is possible to identify how such traits evolve. Here, we used de novo transcriptome assembly and RNAseq to explore how patterns of gene expression differ in response to temperature, moisture, and light regime treatments in lodgepole pine (Pinus contorta) and interior spruce (a natural hybrid population of Picea glauca and Picea engelmannii). We found wide evidence for an effect of treatment on expression within each species, with 6413 and 11,658 differentially expressed genes identified in spruce and pine, respectively. Comparing patterns of expression among these species, we found that 74% of all orthologs with differential expression had a pattern that was conserved in both species, despite 140 million yr of evolution. We also found that the specific treatments driving expression patterns differed between genes with conserved versus diverged patterns of expression. We conclude that natural selection has probably played a role in shaping plastic responses to environment in these species.
MeSH term(s)	Acclimatization/genetics ; Biological Evolution ; Gene Expression Regulation, Plant ; Gene Ontology ; Picea/genetics ; Pinus/genetics ; Seedlings/genetics ; Seedlings/physiology
Language	English
Publishing date	2014-04-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	208885-x
ISSN	1469-8137 ; 0028-646X
ISSN (online)	1469-8137
ISSN	0028-646X
DOI	10.1111/nph.12819
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Article ; Research data: (with research data) Conservation and divergence of gene expression plasticity following c. 140� million years of evolution in lodgepole pine (Pinus contorta) and interior spruce (Picea glauca� ×� Picea engelmannii)

Yeaman, Sam / Hodgins, Kathryn A / Suren, Haktan / Nurkowski, Kristin A / Rieseberg, Loren H / Holliday, Jason A / Aitken, Sally N

New phytologist. 2014 July, v. 203, no. 2

2014

Abstract	Species respond to environmental stress through a combination of genetic adaptation and phenotypic plasticity, both of which may be important for survival in the face of climatic change. By characterizing the molecular basis of plastic responses and comparing patterns among species, it is possible to identify how such traits evolve. Here, we used de novo transcriptome assembly and RNAseq to explore how patterns of gene expression differ in response to temperature, moisture, and light regime treatments in lodgepole pine (Pinus contorta) and interior spruce (a natural hybrid population of Picea glauca and Picea engelmannii). We found wide evidence for an effect of treatment on expression within each species, with 6413 and 11� 658 differentially expressed genes identified in spruce and pine, respectively. Comparing patterns of expression among these species, we found that 74% of all orthologs with differential expression had a pattern that was conserved in both species, despite 140� million yr of evolution. We also found that the specific treatments driving expression patterns differed between genes with conserved versus diverged patterns of expression. We conclude that natural selection has probably played a role in shaping plastic responses to environment in these species.
Keywords	Picea engelmannii ; Picea glauca ; Pinus contorta var. latifolia ; climate change ; gene expression ; gene expression regulation ; genes ; hybrids ; natural selection ; phenotypic plasticity ; photoperiod ; temperature ; transcriptome
Language	English
Dates of publication	2014-07
Size	p. 578-591.
Publishing place	William Wesley and Son
Document type	Article ; Research data
ZDB-ID	208885-x
ISSN	1469-8137 ; 0028-646X ; 0028-646X
ISSN (online)	1469-8137
ISSN	0028-646X
DOI	10.1111/nph.12819
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Global adaptation complicates the interpretation of genome scans for local adaptation.

Booker, Tom R / Yeaman, Sam / Whitlock, Michael C

Evolution letters

2020 Volume 5, Issue 1, Page(s) 4–15

Abstract: Spatially varying selection promotes variance in allele frequencies, increasing genetic differentiation between the demes of a metapopulation. For that reason, outliers in the genome-wide distribution of summary statistics measuring genetic ... ...

Abstract	Spatially varying selection promotes variance in allele frequencies, increasing genetic differentiation between the demes of a metapopulation. For that reason, outliers in the genome-wide distribution of summary statistics measuring genetic differentiation, such as
Language	English
Publishing date	2020-12-15
Publishing country	England
Document type	Journal Article
ISSN	2056-3744
ISSN (online)	2056-3744
DOI	10.1002/evl3.208
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Article ; Online: Variation in recombination rate affects detection of outliers in genome scans under neutrality.

Booker, Tom R / Yeaman, Sam / Whitlock, Michael C

Molecular ecology

2020 Volume 29, Issue 22, Page(s) 4274–4279

Abstract: Genome scans can potentially identify genetic loci involved in evolutionary processes such as local adaptation and gene flow. Here, we show that recombination rate variation across a neutrally evolving genome gives rise to mixed sampling distributions of ...

Abstract	Genome scans can potentially identify genetic loci involved in evolutionary processes such as local adaptation and gene flow. Here, we show that recombination rate variation across a neutrally evolving genome gives rise to mixed sampling distributions of mean F
MeSH term(s)	Animals ; Drosophila melanogaster/genetics ; Gene Flow ; Genome ; Recombination, Genetic ; Selection, Genetic
Language	English
Publishing date	2020-07-02
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1126687-9
ISSN	1365-294X ; 0962-1083
ISSN (online)	1365-294X
ISSN	0962-1083
DOI	10.1111/mec.15501
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