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Article ; Online: Alloteropsis semialata as a study system for C4 evolution in grasses.

Pereira, Lara / Bianconi, Matheus E / Osborne, Colin P / Christin, Pascal-Antoine / Dunning, Luke T

2024 Volume 132, Issue 3, Page(s) 365–382

Abstract: Background: Numerous groups of plants have adapted to CO2 limitations by independently evolving C4 photosynthesis. This trait relies on concerted changes in anatomy and biochemistry to concentrate CO2 within the leaf and thereby boost productivity in ... ...

Abstract	Background: Numerous groups of plants have adapted to CO2 limitations by independently evolving C4 photosynthesis. This trait relies on concerted changes in anatomy and biochemistry to concentrate CO2 within the leaf and thereby boost productivity in tropical conditions. The ecological and economic importance of C4 photosynthesis has motivated intense research, often relying on comparisons between distantly related C4 and non-C4 plants. The photosynthetic type is fixed in most species, with the notable exception of the grass Alloteropsis semialata. This species includes populations exhibiting the ancestral C3 state in southern Africa, intermediate populations in the Zambezian region and C4 populations spread around the palaeotropics. Scope: We compile here the knowledge on the distribution and evolutionary history of the Alloteropsis genus as a whole and discuss how this has furthered our understanding of C4 evolution. We then present a chromosome-level reference genome for a C3 individual and compare the genomic architecture with that of a C4 accession of A. semialata. Conclusions: Alloteropsis semialata is one of the best systems in which to investigate the evolution of C4 photosynthesis because the genetic and phenotypic variation provides a fertile ground for comparative and population-level studies. Preliminary comparative genomic investigations show that the C3 and C4 genomes are highly syntenic and have undergone a modest amount of gene duplication and translocation since the different photosynthetic groups diverged. The background knowledge and publicly available genomic resources make A. semialata a great model for further comparative analyses of photosynthetic diversification.
MeSH term(s)	Poaceae/genetics ; Carbon Dioxide ; Plants ; Photosynthesis/genetics ; Phenotype
Chemical Substances	Carbon Dioxide (142M471B3J)
Language	English
Publishing date	2024-02-14
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1461328-1
ISSN	1095-8290 ; 0305-7364
ISSN (online)	1095-8290
ISSN	0305-7364
DOI	10.1093/aob/mcad078
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Lateral gene transfer generates accessory genes that accumulate at different rates within a grass lineage.

Raimondeau, Pauline / Bianconi, Matheus E / Pereira, Lara / Parisod, Christian / Christin, Pascal-Antoine / Dunning, Luke T

The New phytologist

2023 Volume 240, Issue 5, Page(s) 2072–2084

Abstract: Lateral gene transfer (LGT) is the movement of DNA between organisms without sexual reproduction. The acquired genes represent genetic novelties that have independently evolved in the donor's genome. Phylogenetic methods have shown that LGT is widespread ...

Abstract	Lateral gene transfer (LGT) is the movement of DNA between organisms without sexual reproduction. The acquired genes represent genetic novelties that have independently evolved in the donor's genome. Phylogenetic methods have shown that LGT is widespread across the entire grass family, although we know little about the underlying dynamics. We identify laterally acquired genes in five de novo reference genomes from the same grass genus (four Alloteropsis semialata and one Alloteropsis angusta). Using additional resequencing data for a further 40 Alloteropsis individuals, we place the acquisition of each gene onto a phylogeny using stochastic character mapping, and then infer rates of gains and losses. We detect 168 laterally acquired genes in the five reference genomes (32-100 per genome). Exponential decay models indicate that the rate of LGT acquisitions (6-28 per Ma) and subsequent losses (11-24% per Ma) varied significantly among lineages. Laterally acquired genes were lost at a higher rate than vertically inherited loci (0.02-0.8% per Ma). This high turnover creates intraspecific gene content variation, with a preponderance of them occurring as accessory genes in the Alloteropsis pangenome. This rapid turnover generates standing variation that can ultimately fuel local adaptation.
MeSH term(s)	Humans ; Phylogeny ; Poaceae/genetics ; Gene Transfer, Horizontal ; Genome ; Evolution, Molecular
Language	English
Publishing date	2023-10-04
Publishing country	England
Document type	Journal Article
ZDB-ID	208885-x
ISSN	1469-8137 ; 0028-646X
ISSN (online)	1469-8137
ISSN	0028-646X
DOI	10.1111/nph.19272
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Article ; Online: A high coverage Mesolithic aurochs genome and effective leveraging of ancient cattle genomes using whole genome imputation.

Erven, Jolijn A M / Scheu, Amelie / Pereira Verdugo, Marta / Cassidy, Lara / Chen, Ningbo / Gehlen, Birgit / Street, Martin / Madsen, Ole / Mullin, Victoria E

Molecular biology and evolution

2024

Abstract: Ancient genomic analyses are often restricted to utilising pseudo-haploid data due to low genome coverage. Leveraging low coverage data by imputation to calculate phased diploid genotypes that enable haplotype-based interrogation and SNP calling at ... ...

Abstract	Ancient genomic analyses are often restricted to utilising pseudo-haploid data due to low genome coverage. Leveraging low coverage data by imputation to calculate phased diploid genotypes that enable haplotype-based interrogation and SNP calling at unsequenced positions is highly desirable. This has not been investigated for ancient cattle genomes despite these being compelling subjects for archaeological, evolutionary and economic reasons. Here we test this approach by sequencing a Mesolithic European aurochs (18.49x; 9852-9376 calBCE), an Early Medieval European cow (18.69x; 427-580 calCE), and combine these with published individuals; two ancient and three modern. We downsample these genomes (0.25x, 0.5x, 1.0x, 2.0x) and impute diploid genotypes, utilising a reference panel of 171 published modern cattle genomes that we curated for 21.7 million (Mn) phased single-nucleotide polymorphisms (SNPs). We recover high densities of correct calls with an accuracy of >99.1% at variant sites for the lowest downsample depth of 0.25x, increasing to >99.5% for 2.0x (transversions only, minor allele frequency (MAF) ≥ 2.5%). The recovery of SNPs correlates with coverage, on average 58% of sites are recovered for 0.25x increasing to 87% for 2.0x, utilising an average of 3.5 million (Mn) transversions (MAF ≥2.5%), even in the aurochs, despite the highest temporal distance from the modern reference panel. Our imputed genomes behave similarly to directly called data in allele-frequency-based analyses; for example consistently identifying runs of homozygosity >2mb, including a long homozygous region in the Mesolithic European aurochs.
Language	English
Publishing date	2024-04-25
Publishing country	United States
Document type	Journal Article
ZDB-ID	998579-7
ISSN	1537-1719 ; 0737-4038
ISSN (online)	1537-1719
ISSN	0737-4038
DOI	10.1093/molbev/msae076
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Article ; Online: Leaf anatomy explains the strength of C

Alenazi, Ahmed S / Bianconi, Matheus E / Middlemiss, Ella / Milenkovic, Vanja / Curran, Emma V / Sotelo, Graciela / Lundgren, Marjorie R / Nyirenda, Florence / Pereira, Lara / Christin, Pascal-Antoine / Dunning, Luke T / Osborne, Colin P

Plant, cell & environment

2023 Volume 46, Issue 8, Page(s) 2310–2322

Abstract: ... ...

Abstract	C
MeSH term(s)	Poaceae/metabolism ; Plants/metabolism ; Photosynthesis/physiology ; Carbon/metabolism ; Carbon Isotopes/metabolism ; Plant Leaves/metabolism ; Carbon Dioxide/metabolism
Chemical Substances	Carbon (7440-44-0) ; Carbon Isotopes ; Carbon Dioxide (142M471B3J)
Language	English
Publishing date	2023-05-15
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	391893-2
ISSN	1365-3040 ; 0140-7791
ISSN (online)	1365-3040
ISSN	0140-7791
DOI	10.1111/pce.14607
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Article ; Online: Lateral gene transfer generates accessory genes that accumulate at different rates within a grass lineage

Raimondeau, Pauline / Bianconi, Matheus E. / Pereira, Lara / Parisod, Christian / Christin, Pascal‐Antoine / Dunning, Luke T.

New Phytologist. 2023 Dec., v. 240, no. 5 p.2072-2084

2023

Abstract	Lateral gene transfer (LGT) is the movement of DNA between organisms without sexual reproduction. The acquired genes represent genetic novelties that have independently evolved in the donor's genome. Phylogenetic methods have shown that LGT is widespread across the entire grass family, although we know little about the underlying dynamics. We identify laterally acquired genes in five de novo reference genomes from the same grass genus (four Alloteropsis semialata and one Alloteropsis angusta). Using additional resequencing data for a further 40 Alloteropsis individuals, we place the acquisition of each gene onto a phylogeny using stochastic character mapping, and then infer rates of gains and losses. We detect 168 laterally acquired genes in the five reference genomes (32–100 per genome). Exponential decay models indicate that the rate of LGT acquisitions (6–28 per Ma) and subsequent losses (11–24% per Ma) varied significantly among lineages. Laterally acquired genes were lost at a higher rate than vertically inherited loci (0.02–0.8% per Ma). This high turnover creates intraspecific gene content variation, with a preponderance of them occurring as accessory genes in the Alloteropsis pangenome. This rapid turnover generates standing variation that can ultimately fuel local adaptation.
Keywords	Alloteropsis ; DNA ; genes ; grasses ; horizontal gene transfer ; phylogeny ; sexual reproduction
Language	English
Dates of publication	2023-12
Size	p. 2072-2084.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	208885-x
ISSN	1469-8137 ; 0028-646X
ISSN (online)	1469-8137
ISSN	0028-646X
DOI	10.1111/nph.19272
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Myocardial Injury Progression after Radiofrequency Ablation in School-Age Children.

Melo, Sissy Lara de / Ferraz, Alberto Pereira / Lemouche, Stephanie Ondracek / Devido, Marcela Santana / Sousa, Gabriela Liberato de / Rochitte, Carlos E / Pisani, Cristiano Faria / Hachul, Denise Tessariol / Scanavacca, Mauricio

Arquivos brasileiros de cardiologia

2024 Volume 121, Issue 1, Page(s) e20220727

Abstract: Background: The past decades have seen the rapid development of the invasive treatment of arrhythmias by catheter ablation procedures. Despite its safety and efficacy being well-established in adults, to date there has been little data in pediatric ... ...

Title translation	Progressão da Lesão Miocárdica após Ablação por Radiofrequência em Crianças em Idade Escolar.
Abstract	Background: The past decades have seen the rapid development of the invasive treatment of arrhythmias by catheter ablation procedures. Despite its safety and efficacy being well-established in adults, to date there has been little data in pediatric scenarios. One of the main concerns is the possible expansion of the ablation procedure scar in this population and its consequences over the years. Objectives: This study aimed to analyze the risk of myocardial injury progression after radiofrequency catheter ablation in pediatric patients. Methods: This is a retrospective study of 20 pediatric patients with previous ablation for treatment of supraventricular arrhythmia that underwent cardiac magnetic resonance and coronary angiography for evaluation of myocardial fibrosis and the integrity of the coronary arteries during follow-up. Results: The median age at ablation procedure was 15.1 years (Q1 12.9, Q3 16.6) and 21 years (Q1 20, Q3 23) when the cardiac magnetic resonance was performed. Fourteen of them were women. Nodal reentry tachycardia and Wolf-Parkinson-White Syndrome were the main diagnosis (19 patients), with one patient with atrial tachycardia. Three patients had ventricular myocardial fibrosis, but with a volume < 0.6 cm 3 . None of them developed ventricular dysfunction and no patient had coronary lesions on angiography. Conclusion: Radiofrequency catheter ablation did not show to increase the risk of myocardial injury progression or coronary artery lesions.
MeSH term(s)	Adult ; Humans ; Child ; Female ; Male ; Retrospective Studies ; Tachycardia, Supraventricular/surgery ; Arrhythmias, Cardiac ; Atrioventricular Node ; Catheter Ablation/adverse effects ; Catheter Ablation/methods ; Heart Injuries/diagnostic imaging ; Heart Injuries/etiology ; Fibrosis
Language	English
Publishing date	2024-02-05
Publishing country	Brazil
Document type	Journal Article
ZDB-ID	730261-7
ISSN	1678-4170 ; 0066-782X
ISSN (online)	1678-4170
ISSN	0066-782X
DOI	10.36660/abc.20220727
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Article ; Online: Apolipoprotein E-ε2 and Resistance to Atherosclerosis in Midlife: The PESA Observational Study.

Circulation research

2024 Volume 134, Issue 4, Page(s) 411–424

Abstract: Background: APOE is a known genetic contributor to cardiovascular disease, but the differential role : Methods: The PESA (Progression of Early Subclinical Atherosclerosis) is an observational cohort study that recruited 4184 middle-aged asymptomatic ... ...

Abstract	Background: APOE is a known genetic contributor to cardiovascular disease, but the differential role Methods: The PESA (Progression of Early Subclinical Atherosclerosis) is an observational cohort study that recruited 4184 middle-aged asymptomatic individuals to be screened for cardiovascular risk and multiterritorial subclinical atherosclerosis. Participants were Results: In the PESA study, the frequencies for Conclusions: This work sheds light on the role of APOE in cardiovascular disease development with important therapeutic and prevention implications on cardiovascular health, especially in early midlife. Registration: URL: https://www.clinicaltrials.gov: NCT01410318.
MeSH term(s)	Male ; Middle Aged ; Humans ; Female ; Apolipoprotein E2/genetics ; Genetic Predisposition to Disease ; Apolipoproteins E/genetics ; Cardiovascular Diseases/genetics ; Genotype ; Atherosclerosis/epidemiology ; Atherosclerosis/genetics ; Cholesterol, LDL ; Alleles
Chemical Substances	Apolipoprotein E2 ; Apolipoproteins E ; Cholesterol, LDL
Language	English
Publishing date	2024-01-23
Publishing country	United States
Document type	Observational Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80100-8
ISSN	1524-4571 ; 0009-7330 ; 0931-6876
ISSN (online)	1524-4571
ISSN	0009-7330 ; 0931-6876
DOI	10.1161/CIRCRESAHA.123.323921
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Article ; Online: Evaluation of the effect of extended refrigerated storage of serum and plasma specimens on syphilis serologic test results.

Sun, Yongcheng / Shukla, Mayur R / Deutsch, John / Cao, Weiping / Fakile, Yetunde / Kersh, Ellen N / Pereira, Lara E

Diagnostic microbiology and infectious disease

2021 Volume 102, Issue 2, Page(s) 115588

Abstract: The effect of extended refrigerated storage of 14 serum and plasma specimens on 5 syphilis serologic tests was evaluated for 16 weeks. Higher stability of nontreponemal and treponemal antibodies in serum was recorded compared to plasma. Described work ... ...

Abstract	The effect of extended refrigerated storage of 14 serum and plasma specimens on 5 syphilis serologic tests was evaluated for 16 weeks. Higher stability of nontreponemal and treponemal antibodies in serum was recorded compared to plasma. Described work may provide insights on refrigerated specimens' stability and suitability for syphilis tests.
MeSH term(s)	Antibodies, Bacterial/analysis ; Antibodies, Bacterial/blood ; Humans ; Plasma/microbiology ; Refrigeration/methods ; Serum/microbiology ; Specimen Handling/methods ; Syphilis/blood ; Syphilis/diagnosis ; Syphilis/microbiology ; Syphilis Serodiagnosis/methods
Chemical Substances	Antibodies, Bacterial
Language	English
Publishing date	2021-10-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	604920-5
ISSN	1879-0070 ; 0732-8893
ISSN (online)	1879-0070
ISSN	0732-8893
DOI	10.1016/j.diagmicrobio.2021.115588
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Article ; Online: Nursing Care of an Adolescent with Toxic Epidermal Necrolysis

Gabriela Maria Lara de Paulo / Ana Caroliny da Silva / Mykaella Cristina Araujo Margarida / Carlos Matheus Pierson Colares / Thainara Lorraine Costa e Silva Pereira / Lais Lara Silva Xavier / Lorena Morena Rosa Melchior

REVISA, Vol 10, Iss 2, Pp 224-

A Case Report

2021 Volume 228

Abstract: Objective: To report nursing care facing a case of an adolescent diagnosed with Toxic Epidermal Necrolysis (TEN) hospitalized in a Burns Intensive Care Unit. Method: This is a case report on the nursing interventions performed on a teenager diagnosed ... ...

Abstract	Objective: To report nursing care facing a case of an adolescent diagnosed with Toxic Epidermal Necrolysis (TEN) hospitalized in a Burns Intensive Care Unit. Method: This is a case report on the nursing interventions performed on a teenager diagnosed with TEN, who was hospitalized for a month in 2020 at the Burn Intensive Care Unit in the state of Goiás. The information was collected from the patient's medical record. Results: We present clinical practices to assist the management of patients with TEN. The case presented had a positive outcome. Conclusion: Nursing care is essential for the positive prognosis of the patient. In this case, nursing acted mainly in wound care, medication administration, laser therapy and surveillance to prevent infections.
Keywords	necrólise epidérmica tóxica ; net ; cuidados de enfermagem ; queimadura ; Medicine (General) ; R5-920
Language	Portuguese
Publishing date	2021-04-01T00:00:00Z
Publisher	Faculdade de Ciências e Educação Sena Aires
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Hybridization boosts dispersal of two contrasted ecotypes in a grass species.

Curran, Emma V / Scott, Matilda S / Olofsson, Jill K / Nyirenda, Florence / Sotelo, Graciela / Bianconi, Matheus E / Manzi, Sophie / Besnard, Guillaume / Pereira, Lara / Christin, Pascal-Antoine

Proceedings. Biological sciences

2022 Volume 289, Issue 1967, Page(s) 20212491

Abstract: Genetic exchanges between closely related groups of organisms with different adaptations have well-documented beneficial and detrimental consequences. In plants, pollen-mediated exchanges affect the sorting of alleles across physical landscapes and ... ...

Abstract	Genetic exchanges between closely related groups of organisms with different adaptations have well-documented beneficial and detrimental consequences. In plants, pollen-mediated exchanges affect the sorting of alleles across physical landscapes and influence rates of hybridization. How these dynamics affect the emergence and spread of novel phenotypes remains only partially understood. Here, we use phylogenomics and population genomics to retrace the origin and spread of two geographically overlapping ecotypes of the African grass
MeSH term(s)	Alleles ; Ecotype ; Gene Flow ; Hybridization, Genetic ; Poaceae/genetics
Language	English
Publishing date	2022-01-26
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209242-6
ISSN	1471-2954 ; 0080-4649 ; 0962-8452 ; 0950-1193
ISSN (online)	1471-2954
ISSN	0080-4649 ; 0962-8452 ; 0950-1193
DOI	10.1098/rspb.2021.2491
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