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Article ; Online ; Research data: (with research data) Assembly and comparative analysis of transposable elements from low coverage genomic sequence data in Asparagales.

Hertweck, Kate L

2013 Volume 56, Issue 9, Page(s) 487–494

Abstract: The research field of comparative genomics is moving from a focus on genes to a more holistic view including the repetitive complement. This study aimed to characterize relative proportions of the repetitive fraction of large, complex genomes in a ... ...

Abstract	The research field of comparative genomics is moving from a focus on genes to a more holistic view including the repetitive complement. This study aimed to characterize relative proportions of the repetitive fraction of large, complex genomes in a nonmodel system. The monocotyledonous plant order Asparagales (onion, asparagus, agave) comprises some of the largest angiosperm genomes and represents variation in both genome size and structure (karyotype). Anonymous, low coverage, single-end Illumina data from 11 exemplar Asparagales taxa were assembled using a de novo method. Resulting contigs were annotated using a reference library of available monocot repetitive sequences. Mapping reads to contigs provided rough estimates of relative proportions of each type of transposon in the nuclear genome. The results were parsed into general repeat types and synthesized with genome size estimates and a phylogenetic context to describe the pattern of transposable element evolution among these lineages. The major finding is that although some lineages in Asparagales exhibit conservation in repeat proportions, there is generally wide variation in types and frequency of repeats. This approach is an appropriate first step in characterizing repeats in evolutionary lineages with a paucity of genomic resources.
MeSH term(s)	Base Sequence ; Computational Biology/methods ; DNA Transposable Elements/genetics ; Evolution, Molecular ; Genome Size ; Genome, Plant ; Genomics/methods ; Karyotype ; Magnoliopsida/classification ; Magnoliopsida/genetics ; Molecular Sequence Annotation ; Phylogeny ; Repetitive Sequences, Nucleic Acid
Chemical Substances	DNA Transposable Elements
Language	English
Publishing date	2013-09
Publishing country	Canada
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	639031-6
ISSN	1480-3321 ; 0831-2796 ; 0831-2796
ISSN (online)	1480-3321
ISSN	0831-2796
DOI	10.1139/gen-2013-0042
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Article: The Landscape of mtDNA Modifications in Cancer: A Tale of Two Cities.

Hertweck, Kate L / Dasgupta, Santanu

Frontiers in oncology

2017 Volume 7, Page(s) 262

Abstract: Mitochondria from normal and cancerous cells represent a tale of two cities, wherein both execute similar processes but with different cellular and molecular effects. Given the number of reviews currently available which describe the functional ... ...

Abstract	Mitochondria from normal and cancerous cells represent a tale of two cities, wherein both execute similar processes but with different cellular and molecular effects. Given the number of reviews currently available which describe the functional implications of mitochondrial mutations in cancer, this article focuses on documenting current knowledge in the abundance and distribution of somatic mitochondrial mutations, followed by elucidation of processes which affect the fate of mutations in cancer cells. The conclusion includes an overview of translational implications for mtDNA mutations, as well as recommendations for future research uniting mitochondrial variants and tumorigenesis.
Language	English
Publishing date	2017-11-02
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2649216-7
ISSN	2234-943X
ISSN	2234-943X
DOI	10.3389/fonc.2017.00262
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Article ; Online: Random Genetic Drift and Selective Pressures Shaping the Blattabacterium Genome.

Alleman, Austin / Hertweck, Kate L / Kambhampati, Srini

Scientific reports

2018 Volume 8, Issue 1, Page(s) 13427

Abstract: Estimates suggest that at least half of all extant insect genera harbor obligate bacterial mutualists. Whereas an endosymbiotic relationship imparts many benefits upon host and symbiont alike, the intracellular lifestyle has profound effects on the ... ...

Abstract	Estimates suggest that at least half of all extant insect genera harbor obligate bacterial mutualists. Whereas an endosymbiotic relationship imparts many benefits upon host and symbiont alike, the intracellular lifestyle has profound effects on the bacterial genome. The obligate endosymbiont genome is a product of opposing forces: genes important to host survival are maintained through physiological constraint, contrasted by the fixation of deleterious mutations and genome erosion through random genetic drift. The obligate cockroach endosymbiont, Blattabacterium - providing nutritional augmentation to its host in the form of amino acid synthesis - displays radical genome alterations when compared to its most recent free-living relative Flavobacterium. To date, eight Blattabacterium genomes have been published, affording an unparalleled opportunity to examine the direction and magnitude of selective forces acting upon this group of symbionts. Here, we find that the Blattabacterium genome is experiencing a 10-fold increase in selection rate compared to Flavobacteria. Additionally, the proportion of selection events is largely negative in direction, with only a handful of loci exhibiting signatures of positive selection. These findings suggest that the Blattabacterium genome will continue to erode, potentially resulting in an endosymbiont with an even further reduced genome, as seen in other insect groups such as Hemiptera.
MeSH term(s)	Animals ; Cockroaches/microbiology ; Evolution, Molecular ; Flavobacteriaceae/genetics ; Genetic Drift ; Genome, Bacterial ; Symbiosis
Language	English
Publishing date	2018-09-07
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-018-31796-6
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Article ; Online: Clinicopathological significance of unraveling mitochondrial pathway alterations in non-small-cell lung cancer.

Hertweck, Kate L / Vikramdeo, Kunwar S / Galeas, Jose N / Marbut, Stephen M / Pramanik, Paramahansa / Yunus, Furhan / Singh, Seema / Singh, Ajay P / Dasgupta, Santanu

FASEB journal : official publication of the Federation of American Societies for Experimental Biology

2023 Volume 37, Issue 7, Page(s) e23018

Abstract: Early detection, accurate monitoring, and therapeutics are major problems in non-small-cell lung cancer (NSCLC) patients. We identified genomic copy number variation of a unique panel of 40 mitochondria-targeted genes in NSCLCs (GEOGSE #29365). ... ...

Abstract	Early detection, accurate monitoring, and therapeutics are major problems in non-small-cell lung cancer (NSCLC) patients. We identified genomic copy number variation of a unique panel of 40 mitochondria-targeted genes in NSCLCs (GEOGSE #29365). Validation of mRNA expression of these molecules revealed an altered panel of 34 genes in lung adenocarcinomas (LUAD) and 36 genes in lung squamous cell carcinomas (LUSC). In the LUAD subtype (n = 533), we identified 29 upregulated and 5 downregulated genes, while in the LUSC subtype (n = 502), a panel of 30 upregulated and 6 downregulated genes were discovered. The majority of these genes are associated with mitochondrial protein transport, ferroptosis, calcium signaling, metabolism, OXPHOS function, TCA cycle, apoptosis, and MARylation. Altered mRNA expression of SLC25A4, ACSF2, MACROD1, and GCAT was associated with poor survival of the NSCLC patients. Progressive loss of SLC25A4 protein expression was confirmed in NSCLC tissues (n = 59), predicting poor survival of the patients. Forced overexpression of SLC25A4 in two LUAD cell lines inhibited their growth, viability, and migration. A significant association of the altered mitochondrial pathway genes with LC subtype-specific classical molecular signatures was observed, implicating the existence of nuclear-mitochondrial cross-talks. Key alteration signatures shared between LUAD and LUSC subtypes including SLC25A4, ACSF2, MACROD1, MDH2, LONP1, MTHFD2, and CA5A could be helpful in developing new biomarkers and therapeutics.
MeSH term(s)	Humans ; Carcinoma, Non-Small-Cell Lung/genetics ; DNA Copy Number Variations ; Lung Neoplasms/genetics ; Adenocarcinoma of Lung ; Carcinoma, Squamous Cell/genetics ; Calcium Signaling ; DNA, Mitochondrial ; RNA, Messenger ; Mitochondrial Proteins/genetics ; ATP-Dependent Proteases
Chemical Substances	DNA, Mitochondrial ; RNA, Messenger ; LONP1 protein, human (EC 3.4.21.-) ; Mitochondrial Proteins ; ATP-Dependent Proteases (EC 3.4.21.-)
Language	English
Publishing date	2023-06-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	639186-2
ISSN	1530-6860 ; 0892-6638
ISSN (online)	1530-6860
ISSN	0892-6638
DOI	10.1096/fj.202201724RR
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Zs.A 2266: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Thesis ; Online: Genome evolution in monocots

Hertweck, Kate L.

2011

Abstract: Monocotyledonous plants are a well-circumscribed lineage comprising 25% of all angiosperm species, including many agriculturally and ecologically important species (e.g., grasses, gingers, palms, orchids, lilies, yams, pondweeds, seagrasses, aroids). ... ...

Abstract	Monocotyledonous plants are a well-circumscribed lineage comprising 25% of all angiosperm species, including many agriculturally and ecologically important species (e.g., grasses, gingers, palms, orchids, lilies, yams, pondweeds, seagrasses, aroids). These taxa possess nearly the full breadth of vegetative and floral morphology seen across angiosperms, dominate a variety of ecosystems, and exhibit considerable genomic complexity, including the largest genome sizes of all plants. The opportunities afforded by this wealth of variation include evaluating patterns of morphological evolution, genomic change, and geographic radiation. This same variation, however, presents unique challenges to establishing an accurate phylogenetic framework as the foundation for evolutionary analysis. This dissertation documents three vignettes in monocot evolution, each highlighting different taxonomic scales and relevant questions to the diversification and significance of both organismal (life history, biogeography, morphology) and genomic (genome size, molecular evolution) characteristics. Chapter 2 uses molecular sequence data from all three genomic partitions (nuclear and both organellar genomes) to infer evolutionary relationships in monocots. Subsequent divergence time and diversification analysis suggests that radiation of major monocot lineages was highly dependent on the origin of other plant and animal lineages. Chapter 3 evaluates a taxonomic classification system in the Tradescantia alliance (Commelinaceae, Commelinales), a group of closely related genera exhibiting kaleidoscopic variation in life history and genomic traits. The phylogeny developed for the alliance is used to re-interpret evolution of taxonomically relevant morphological characters and to test for correlations between genome size and life history/biogeography. Finally, Chapter 4 evaluates a methodological approach to genome sequencing in two lineages of monocots. Grasses (Poaceae, Poales) as a model system are used to test the efficacy of such methods. Non-model Asparagales (agave, onion, asparagus), with large genomes and a paucity of published sequence data, are used to support the ability of these genome sequencing methods to provide ample data for ecological and evolutionary studies. Each of these examples highlights the ability of monocots to serve as test cases for different types of evolutionary questions.
Keywords	Genetics\|Evolution and Development\|Systematic
Subject code	590
Language	ENG
Publishing date	2011-01-01 00:00:01.0
Publisher	University of Missouri - Columbia
Publishing country	us
Document type	Thesis ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Conservation biology of a southwestern endemic, the texas garter snake, thamnophis sirtalis annectens: an integrative perspective

Key, Kayla N / Banta, Joshua A / Gluesenkamp, Andrew G / Hertweck, Kate L / Placyk, John S

Southwestern naturalist. 2019 Dec. 19, v. 64, no. 1

2019

Abstract: We investigate the taxonomic status of the Texas garter snake, Thamnophis sirtalis annectens, a species of greatest conservation need in Texas. We broadly test the hypothesis that an integrative approach to species conservation has greater utility than ... ...

Abstract	We investigate the taxonomic status of the Texas garter snake, Thamnophis sirtalis annectens, a species of greatest conservation need in Texas. We broadly test the hypothesis that an integrative approach to species conservation has greater utility than using only a single data type (e.g., molecular, morphological, behavioral, or ecological) by demonstrating how ecological niche modeling and molecular genetics can be used synergistically to resolve taxonomic classifications. Using a phylogenetic analysis based on molecular data, we found that some putative T. s. annectens specimens actually represent a co-occurring subspecies (the red-sided garter snake, Thamnophis sirtalis parietalis), which is not of conservation concern. However, both T. s. annectens and T. s. parietalis are genetically distinctive from another co-occurring subspecies, Thamnophis sirtalis sirtalis, and the ecological distinctness of T. s. annectens from T. s. parietalis suggests that T. s. annectens is, in fact, a distinct evolutionary subunit. Only when both genetic and ecological information were included was the distinctiveness of T. s. annectens apparent, thus highlighting the need for integrative approaches in conservation management regardless of the taxa in question.
Keywords	Thamnophis sirtalis ; molecular genetics ; niches ; phylogeny ; snakes ; wildlife management ; Texas
Language	English
Dates of publication	2019-1219
Size	p. 8-19.
Publishing place	Southwestern Association of Naturalists
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	2175917-0
ISSN	0038-4909
ISSN	0038-4909
DOI	10.1894/0038-4909-64-1-8
Database	NAL-Catalogue (AGRICOLA)

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Article: Systematics and Evolution of Inflorescence Structure in the Tradescantia Alliance (Commelinaceae)

Hertweck, Kate L / Pires, J. Chris

Systematic botany. 2014 May, v. 39, no. 1

2014

Abstract: The Tradescantia alliance (subtribes Tradescantiinae and Thyrsantheminae of tribe Tradescantieae, family Commelinaceae) comprises a group of closely related New World genera exhibiting considerable variation in morphological, life history, and genomic ... ...

Abstract	The Tradescantia alliance (subtribes Tradescantiinae and Thyrsantheminae of tribe Tradescantieae, family Commelinaceae) comprises a group of closely related New World genera exhibiting considerable variation in morphological, life history, and genomic traits. Despite ecological and cytogenetic significance of the Tradescantia alliance, phylogenetic relationships among genera and species remain uncertain. In particular, variation in inflorescence morphology has confounded classification and taxonomy. We inferred phylogenetic relationships using two plastid loci (rpL16, trnL-trnF) for 85 taxa in Commelinaceae, with sampling focused in the Tradescantia alliance. Constraint tests supported only subtribe Tradescantiinae, Tripogandra and Tinantia as monophyletic, with Tripogandra nested within Callisia. We estimated ancestral states for both breeding system and inflorescence condensation and tested for a correlation. Inflorescence morphology, an important character for generic identification, is more labile than previously expected, with condensed inflorescences evolving twice with three subsequent reversals. Breeding system evolution is more complex, with many more switches between self compatibility and self incompatibility and more uncertainty in ancestral state estimates. The presence of self compatible and incompatible species allowed us to test the hypothesis that self compatible species will have condensed inflorescences, as less allocation to floral display is necessary. While we did not find a correlation between self compatibility and inflorescence condensation, we propose additional floral and inflorescence characteristics that may have contributed to variation in breeding system.
Keywords	Callisia ; Tradescantia ; breeding ; condensation ; inflorescences ; life history ; loci ; monophyly ; plant taxonomy ; testing ; uncertainty
Language	English
Dates of publication	2014-05
Size	p. 105-116.
Publishing place	American Society of Plant Toxonomists
Document type	Article
ZDB-ID	2052625-8
ISSN	1548-2324 ; 0363-6445
ISSN (online)	1548-2324
ISSN	0363-6445
DOI	10.1600%2F036364414X677991
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Genetic Mutation and Exosome Signature of Human Papilloma Virus Associated Oropharyngeal Cancer.

Kannan, Anbarasu / Hertweck, Kate L / Philley, Julie V / Wells, Robert B / Dasgupta, Santanu

Scientific reports

2017 Volume 7, Page(s) 46102

Abstract: Human papilloma virus-16 (HPV-16) associated oropharyngeal cancer (HPVOPC) is increasing alarmingly in the United States. We performed whole genome sequencing of a 44 year old, male HPVOPC subject diagnosed with moderately differentiated tonsillar ... ...

Abstract	Human papilloma virus-16 (HPV-16) associated oropharyngeal cancer (HPVOPC) is increasing alarmingly in the United States. We performed whole genome sequencing of a 44 year old, male HPVOPC subject diagnosed with moderately differentiated tonsillar carcinoma. We identified new somatic mutation in MUC16 (A.k.a. CA-125), MUC12, MUC4, MUC6, MUC2, SIRPA, HLA-DRB1, HLA-A and HLA-B molecules. Increased protein expression of MUC16, SIRPA and decreased expression of HLA-DRB1 was further demonstrated in this HPVOPC subject and an additional set of 15 HPVOPC cases. Copy number gain (3 copies) was also observed for MUC2, MUC4, MUC6 and SIRPA. Enhanced expression of MUC16, SIRPA and HPV-16-E7 protein was detectable in the circulating exosomes of numerous HPVOPC subjects. Treatment of non-tumorigenic mammary epithelial cells with exosomes derived from aggressive HPVOPC cells harboring MUC16, SIRPA and HPV-16-E7 proteins augmented invasion and induced epithelial to mesenchymal transition (EMT) accompanied by an increased expression ratio of the EMT markers Vimentin/E-cadherin. Exosome based screening of key HPVOPC associated molecules could be beneficial for early cancer diagnosis, monitoring and surveillance.
MeSH term(s)	Adult ; DNA Copy Number Variations/genetics ; Epithelial-Mesenchymal Transition ; Exosomes/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Genome, Human ; Human papillomavirus 16/genetics ; Humans ; Male ; Mutation/genetics ; Neoplasm Invasiveness ; Neoplasm Proteins/genetics ; Neoplasm Proteins/metabolism ; Oropharyngeal Neoplasms/pathology ; Oropharyngeal Neoplasms/virology ; Papillomaviridae/genetics ; Reproducibility of Results
Chemical Substances	Neoplasm Proteins
Language	English
Publishing date	2017-04-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/srep46102
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Article: Host Identity Impacts Rhizosphere Fungal Communities Associated with Three Alpine Plant Species

Becklin, Katie M / Hertweck, Kate L / Jumpponen, Ari

Microbial ecology. 2012 Apr., v. 63, no. 3

2012

Abstract: Fungal diversity and composition are still relatively unknown in many ecosystems; however, host identity and environmental conditions are hypothesized to influence fungal community assembly. To test these hypotheses, we characterized the richness, ... ...

Abstract	Fungal diversity and composition are still relatively unknown in many ecosystems; however, host identity and environmental conditions are hypothesized to influence fungal community assembly. To test these hypotheses, we characterized the richness, diversity, and composition of rhizosphere fungi colonizing three alpine plant species, Taraxacum ceratophorum, Taraxacum officinale, and Polemonium viscosum. Roots were collected from open meadow and willow understory habitats at treeline on Pennsylvania Mountain, Colorado, USA. Fungal small subunit ribosomal DNA was sequenced using fungal-specific primers, sample-specific DNA tags, and 454 pyrosequencing. We classified operational taxonomic units (OTUs) as arbuscular mycorrhizal (AMF) or non-arbuscular mycorrhizal (non-AMF) fungi and then tested whether habitat or host identity influenced these fungal communities. Approximately 14% of the sequences represented AMF taxa (44 OTUs) with the majority belonging to Glomus groups A and B. Non-AMF sequences represented 186 OTUs belonging to Ascomycota (58%), Basidiomycota (26%), Zygomycota (14%), and Chytridiomycota (2%) phyla. Total AMF and non-AMF richness were similar between habitats but varied among host species. AMF richness and diversity per root sample also varied among host species and were highest in T. ceratophorum compared with T. officinale and P. viscosum. In contrast, non-AMF richness and diversity per root sample were similar among host species except in the willow understory where diversity was reduced in T. officinale. Fungal community composition was influenced by host identity but not habitat. Specifically, T. officinale hosted a different AMF community than T. ceratophorum and P. viscosum while P. viscosum hosted a different non-AMF community than T. ceratophorum and T. officinale. Our results suggest that host identity has a stronger effect on rhizosphere fungi than habitat. Furthermore, although host identity influenced both AMF and non-AMF, this effect was stronger for the mutualistic AMF community.
Keywords	Ascomycota ; Basidiomycota ; Chytridiomycota ; DNA ; Glomus ; Polemonium ; Taraxacum officinale ; Zygomycota ; alpine plants ; community structure ; ecosystems ; environmental factors ; fungal communities ; hosts ; meadows ; mountains ; nucleotide sequences ; rhizosphere ; rhizosphere fungi ; roots ; understory ; vesicular arbuscular mycorrhizae ; Colorado
Language	English
Dates of publication	2012-04
Size	p. 682-693.
Publishing place	Springer-Verlag
Document type	Article
ZDB-ID	1462065-0
ISSN	1432-184X ; 0095-3628
ISSN (online)	1432-184X
ISSN	0095-3628
DOI	10.1007/s00248-011-9968-7
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Ten simple rules for collaborative lesson development.

Devenyi, Gabriel A / Emonet, Rémi / Harris, Rayna M / Hertweck, Kate L / Irving, Damien / Milligan, Ian / Wilson, Greg

PLoS computational biology

2018 Volume 14, Issue 3, Page(s) e1005963

MeSH term(s)	Cooperative Behavior ; Databases, Factual ; Humans ; Informatics/education ; Software
Language	English
Publishing date	2018-03-01
Publishing country	United States
Document type	Editorial
ZDB-ID	2193340-6
ISSN	1553-7358 ; 1553-734X
ISSN (online)	1553-7358
ISSN	1553-734X
DOI	10.1371/journal.pcbi.1005963
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