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Article ; Online: syntenyPlotteR: a user-friendly R package to visualize genome synteny, ideal for both experienced and novice bioinformaticians.

Quigley, Sarah / Damas, Joana / Larkin, Denis M / Farré, Marta

Bioinformatics advances

2023 Volume 3, Issue 1, Page(s) vbad161

Abstract: Motivation: The rapid increase in the number of chromosome-scale genome assemblies has renewed interest in chromosome evolution studies. The visualization of syntenic relationships between genomes is a crucial initial step in the study of chromosome ... ...

Abstract	Motivation: The rapid increase in the number of chromosome-scale genome assemblies has renewed interest in chromosome evolution studies. The visualization of syntenic relationships between genomes is a crucial initial step in the study of chromosome rearrangements and evolution. There are few tools available that serve this purpose, and they can be difficult to learn. Moreover, these tools are limited in the number of species comparisons that can be visualized and the size of chromosome rearrangements identified. Thus, the development of novel visualization tools is in strong need. Results: Here, we present syntenyPlotteR, an R package developed to visualize homologous synteny blocks in a pairwise or multispecies manner. This package contains three functions that allow users to generate publication-quality representations of syntenic relationships easily and quickly between genomes of interest. Availability and implementation: SyntenyPlotteR can be installed from CRAN with the documentation found in https://farre-lab.github.io/syntenyPlotteR/.
Language	English
Publishing date	2023-11-08
Publishing country	England
Document type	Journal Article
ISSN	2635-0041
ISSN (online)	2635-0041
DOI	10.1093/bioadv/vbad161
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Article ; Online: Conservation of chromatin conformation in carnivores.

Corbo, Marco / Damas, Joana / Bursell, Madeline G / Lewin, Harris A

Proceedings of the National Academy of Sciences of the United States of America

2022 Volume 119, Issue 9

Abstract: High throughput chromatin conformation capture (Hi-C) of leukocyte DNA was used to investigate the evolutionary stability of chromatin conformation at the chromosomal level in 11 species from three carnivore families: Felidae, Canidae, and Ursidae. ... ...

Abstract	High throughput chromatin conformation capture (Hi-C) of leukocyte DNA was used to investigate the evolutionary stability of chromatin conformation at the chromosomal level in 11 species from three carnivore families: Felidae, Canidae, and Ursidae. Chromosome-scale scaffolds (C-scaffolds) of each species were initially used for whole-genome alignment to a reference genome within each family. This approach established putative orthologous relationships between C-scaffolds among the different species. Hi-C contact maps for all C-scaffolds were then visually compared and found to be distinct for a given reference chromosome or C-scaffold within a species and indistinguishable for orthologous C-scaffolds having a 1:1 relationship within a family. The visual patterns within families were strongly supported by eigenvectors from the Hi-C contact maps. Analysis of Hi-C contact maps and eigenvectors across the three carnivore families revealed that most cross-family orthologous subchromosomal fragments have a conserved three-dimensional (3D) chromatin structure and thus have been under strong evolutionary constraint for ∼54 My of carnivore evolution. The most pronounced differences in chromatin conformation were observed for the X chromosome and the red fox genome, whose chromosomes have undergone extensive rearrangements relative to other canids. We also demonstrate that Hi-C contact map pattern analysis can be used to accurately identify orthologous relationships between C-scaffolds and chromosomes, a method we termed "3D comparative scaffotyping." This method provides a powerful means for estimating karyotypes in de novo sequenced species that have unknown karyotype and no physical mapping information.
MeSH term(s)	Animals ; Carnivora/genetics ; Chromatin/genetics ; Chromosomes ; Evolution, Molecular
Chemical Substances	Chromatin
Language	English
Publishing date	2022-03-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2120555119
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Article ; Online: Vertebrate Chromosome Evolution.

Damas, Joana / Corbo, Marco / Lewin, Harris A

Annual review of animal biosciences

2020 Volume 9, Page(s) 1–27

Abstract: The study of chromosome evolution is undergoing a resurgence of interest owing to advances in DNA sequencing technology that facilitate the production of chromosome-scale whole-genome assemblies de novo. This review focuses on the history, methods, ... ...

Abstract	The study of chromosome evolution is undergoing a resurgence of interest owing to advances in DNA sequencing technology that facilitate the production of chromosome-scale whole-genome assemblies de novo. This review focuses on the history, methods, discoveries, and current challenges facing the field, with an emphasis on vertebrate genomes. A detailed examination of the literature on the biology of chromosome rearrangements is presented, specifically the relationship between chromosome rearrangements and phenotypic evolution, adaptation, and speciation. A critical review of the methods for identifying, characterizing, and visualizing chromosome rearrangements and computationally reconstructing ancestral karyotypes is presented. We conclude by looking to the future, identifying the enormous technical and scientific challenges presented by the accumulation of hundreds and eventually thousands of chromosome-scale assemblies.
MeSH term(s)	Animals ; Chromosome Aberrations ; Chromosomes/genetics ; Evolution, Molecular ; Genetic Speciation ; Genomics ; Vertebrates/genetics
Language	English
Publishing date	2020-11-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2700164-7
ISSN	2165-8110 ; 2165-8102
ISSN (online)	2165-8110
ISSN	2165-8102
DOI	10.1146/annurev-animal-020518-114924
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Article ; Online: Adenovirus Infection in a Kidney-Pancreatic Transplant Recipient: Case Report.

Damas, Juliana / Vida, Ana Carlota / Marques, Joana / Caeiro, Fernando / Aires, Inês / Dias, Joana Monteiro / Vieira, Miguel Bigotte / Cotovio, Patrícia / Magriço, Rita / Ferreira, Aníbal

Transplantation proceedings

2023 Volume 55, Issue 6, Page(s) 1441–1443

Abstract: Adenovirus infection in transplant recipients may present from asymptomatic viremia to multisystemic involvement. Most frequently, it occurs in the first year after a kidney transplant, and it is secondary to the reactivation of latent disease. However, ... ...

Abstract	Adenovirus infection in transplant recipients may present from asymptomatic viremia to multisystemic involvement. Most frequently, it occurs in the first year after a kidney transplant, and it is secondary to the reactivation of latent disease. However, primary infection may occur, and disseminated disease is more common when related to primary infection. Kidney involvement may be confirmed by biopsy, although diagnosis may be presumptive. Reduction of immunosuppression and supportive care are important components of therapy. CASE DESCRIPTION: A 41-year-old female renal-pancreatic recipient 12 years before with chronic renal graft dysfunction and a functional pancreatic graft had a history of cytomegalovirus and polyoma virus infection 2 years after transplantation. She was taking tacrolimus, mycophenolate mofetil, and prednisolone. The patient was admitted after persistent uncharacteristic diarrhea 3 weeks before hospitalization without any relevant epidemiologic context. She was dehydrated, and the lab results showed worsened kidney function and leucocytosis. The viral culture revealed adenovirus. Vigorous hydration was implemented, and the mycophenolate mofetil dose was reduced. The patient was discharged, and renal function returned to previous values. DISCUSSION AND CONCLUSION: Adenovirus infection has a wide clinical presentation, and multisystemic involvement may occur in transplant recipients. Supportive care is paramount. The clinical features and viral culture confirm the diagnosis, although tissue samples and quantitative polymerase chain reaction may be required in more severe cases.
MeSH term(s)	Female ; Humans ; Adult ; Immunosuppressive Agents/adverse effects ; Mycophenolic Acid/adverse effects ; Transplant Recipients ; Kidney/pathology ; Adenoviridae Infections/diagnosis ; Graft Rejection
Chemical Substances	Immunosuppressive Agents ; Mycophenolic Acid (HU9DX48N0T)
Language	English
Publishing date	2023-07-22
Publishing country	United States
Document type	Case Reports ; Journal Article
ZDB-ID	82046-5
ISSN	1873-2623 ; 0041-1345
ISSN (online)	1873-2623
ISSN	0041-1345
DOI	10.1016/j.transproceed.2023.06.005
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Article ; Online: Augmin-dependent microtubule self-organization drives kinetochore fiber maturation in mammals.

Almeida, Ana C / Soares-de-Oliveira, Joana / Drpic, Danica / Cheeseman, Liam P / Damas, Joana / Lewin, Harris A / Larkin, Denis M / Aguiar, Paulo / Pereira, António J / Maiato, Helder

Cell reports

2022 Volume 39, Issue 1, Page(s) 110610

Abstract: Chromosome segregation in mammals relies on the maturation of a thick bundle of kinetochore-attached microtubules known as k-fiber. How k-fibers mature from initial kinetochore microtubule attachments remains a fundamental question. By combining ... ...

Abstract	Chromosome segregation in mammals relies on the maturation of a thick bundle of kinetochore-attached microtubules known as k-fiber. How k-fibers mature from initial kinetochore microtubule attachments remains a fundamental question. By combining molecular perturbations and phenotypic analyses in Indian muntjac fibroblasts containing the lowest known diploid chromosome number in mammals (2N = 6) and distinctively large kinetochores, with fixed/live-cell super-resolution coherent-hybrid stimulated emission depletion (CH-STED) nanoscopy and laser microsurgery, we demonstrate a key role for augmin in kinetochore microtubule self-organization and maturation, regardless of pioneer centrosomal microtubules. In doing so, augmin promotes kinetochore and interpolar microtubule turnover and poleward flux. Tracking of microtubule growth events within individual k-fibers reveals a wide angular dispersion, consistent with augmin-mediated branched microtubule nucleation. Augmin depletion reduces the frequency of kinetochore microtubule growth events and hampers efficient repair after acute k-fiber injury by laser microsurgery. Together, these findings underscore the contribution of augmin-mediated microtubule amplification for k-fiber self-organization and maturation in mammals.
MeSH term(s)	Animals ; Chromosome Segregation ; Kinetochores ; Mammals/genetics ; Microtubules ; Mitosis ; Spindle Apparatus/genetics
Language	English
Publishing date	2022-03-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2022.110610
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Article ; Online: Analytical Assessment and Nutritional Adequacy of School Lunches in Sintra's Public Primary Schools.

Nogueira, Telma / Ferreira, Raquel J / Dias da Silva, Vitória / Liñan Pinto, Mariana / Damas, Carlos / Sousa, Joana

Nutrients

2021 Volume 13, Issue 6

Abstract: School meals present several cost benefits overtime at the short, medium, and long term for individuals and society. This cross-sectional study aims to analyse the nutritional composition and evaluate the adequacy of school lunches. One hundred and fifty- ...

Abstract	School meals present several cost benefits overtime at the short, medium, and long term for individuals and society. This cross-sectional study aims to analyse the nutritional composition and evaluate the adequacy of school lunches. One hundred and fifty-eight samples were collected and analysed from 10 primary schools in Sintra's municipality, served during one week. On average, energy (27.7% daily energetic requirements) and carbohydrate (48.1%) contents did not reach the reference values, and the content of protein (19.5%) exceeded the reference value (
Language	English
Publishing date	2021-06-05
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2518386-2
ISSN	2072-6643 ; 2072-6643
ISSN (online)	2072-6643
ISSN	2072-6643
DOI	10.3390/nu13061946
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Article ; Online: A genomic timescale for placental mammal evolution.

Foley, Nicole M / Mason, Victor C / Harris, Andrew J / Bredemeyer, Kevin R / Damas, Joana / Lewin, Harris A / Eizirik, Eduardo / Gatesy, John / Karlsson, Elinor K / Lindblad-Toh, Kerstin / Springer, Mark S / Murphy, William J

Science (New York, N.Y.)

2023 Volume 380, Issue 6643, Page(s) eabl8189

Abstract: The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis of genetic variation across an alignment of 241 placental mammal genome assemblies, ... ...

Abstract	The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis of genetic variation across an alignment of 241 placental mammal genome assemblies, addressing prior concerns regarding limited genomic sampling across species. We compared neutral genome-wide phylogenomic signals using concatenation and coalescent-based approaches, interrogated phylogenetic variation across chromosomes, and analyzed extensive catalogs of structural variants. Interordinal relationships exhibit relatively low rates of phylogenomic conflict across diverse datasets and analytical methods. Conversely, X-chromosome versus autosome conflicts characterize multiple independent clades that radiated during the Cenozoic. Genomic time trees reveal an accumulation of cladogenic events before and immediately after the Cretaceous-Paleogene (K-Pg) boundary, implying important roles for Cretaceous continental vicariance and the K-Pg extinction in the placental radiation.
MeSH term(s)	Animals ; Female ; Biological Evolution ; Eutheria/classification ; Eutheria/genetics ; Evolution, Molecular ; Fossils ; Genomics/methods ; Phylogeny ; Genetic Variation ; Time Factors
Language	English
Publishing date	2023-04-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.abl8189
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Zs.MG 77: Show issues

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Book ; Online: Broad Host Range of SARS-CoV-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates

Damas, Joana / Karlsson, Elinor K. / Lewin, Harris A.

University of Massachusetts Medical School Faculty Publications

2020

Abstract: The novel coronavirus SARS-CoV-2 is the cause of Coronavirus Disease-2019 (COVID-19). The main receptor of SARS-CoV-2, angiotensin I converting enzyme 2 (ACE2), is now undergoing extensive scrutiny to understand the routes of transmission and sensitivity ...

Abstract	The novel coronavirus SARS-CoV-2 is the cause of Coronavirus Disease-2019 (COVID-19). The main receptor of SARS-CoV-2, angiotensin I converting enzyme 2 (ACE2), is now undergoing extensive scrutiny to understand the routes of transmission and sensitivity in different species. Here, we utilized a unique dataset of 410 vertebrates, including 252 mammals, to study cross-species conservation of ACE2 and its likelihood to function as a SARS-CoV-2 receptor. We designed a five-category ranking score based on the conservation properties of 25 amino acids important for the binding between receptor and virus, classifying all species from very high to very low. Only mammals fell into the medium to very high categories, and only catarrhine primates in the very high category, suggesting that they are at high risk for SARS-CoV-2 infection. We employed a protein structural analysis to qualitatively assess whether amino acid changes at variable residues would be likely to disrupt ACE2/SARS-CoV-2 binding, and found the number of predicted unfavorable changes significantly correlated with the binding score. Extending this analysis to human population data, we found only rare (<0.1%) variants in 10/25 binding sites. In addition, we observed evidence of positive selection in ACE2 in multiple species, including bats. Utilized appropriately, our results may lead to the identification of intermediate host species for SARS-CoV-2, justify the selection of animal models of COVID-19, and assist the conservation of animals both in native habitats and in human care.
Keywords	ACE2 ; COVID-19 ; SARS-CoV-2 ; comparative genomics ; evolution ; host range ; species conservation ; Amino Acids ; Peptides ; and Proteins ; Biochemistry ; Biophysics ; and Structural Biology ; Biodiversity ; Ecology and Evolutionary Biology ; Enzymes and Coenzymes ; Genomics ; Immunology and Infectious Disease ; Virology ; Virus Diseases ; covid19
Subject code	590
Publishing date	2020-04-18T07:00:00Z
Publisher	eScholarship@UMMS
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Augmin-dependent microtubule self-organization drives kinetochore fiber maturation in mammals

Ana C. Almeida / Joana Soares-de-Oliveira / Danica Drpic / Liam P. Cheeseman / Joana Damas / Harris A. Lewin / Denis M. Larkin / Paulo Aguiar / António J. Pereira / Helder Maiato

Cell Reports, Vol 39, Iss 1, Pp 110610- (2022)

2022

Abstract: Summary: Chromosome segregation in mammals relies on the maturation of a thick bundle of kinetochore-attached microtubules known as k-fiber. How k-fibers mature from initial kinetochore microtubule attachments remains a fundamental question. By combining ...

Abstract	Summary: Chromosome segregation in mammals relies on the maturation of a thick bundle of kinetochore-attached microtubules known as k-fiber. How k-fibers mature from initial kinetochore microtubule attachments remains a fundamental question. By combining molecular perturbations and phenotypic analyses in Indian muntjac fibroblasts containing the lowest known diploid chromosome number in mammals (2N = 6) and distinctively large kinetochores, with fixed/live-cell super-resolution coherent-hybrid stimulated emission depletion (CH-STED) nanoscopy and laser microsurgery, we demonstrate a key role for augmin in kinetochore microtubule self-organization and maturation, regardless of pioneer centrosomal microtubules. In doing so, augmin promotes kinetochore and interpolar microtubule turnover and poleward flux. Tracking of microtubule growth events within individual k-fibers reveals a wide angular dispersion, consistent with augmin-mediated branched microtubule nucleation. Augmin depletion reduces the frequency of kinetochore microtubule growth events and hampers efficient repair after acute k-fiber injury by laser microsurgery. Together, these findings underscore the contribution of augmin-mediated microtubule amplification for k-fiber self-organization and maturation in mammals.
Keywords	CP: Cell biology ; Biology (General) ; QH301-705.5
Subject code	571
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Analytical Assessment and Nutritional Adequacy of School Lunches in Sintra’s Public Primary Schools

Nogueira, Telma / Ferreira, Raquel J. / Dias da Silva, Vitória / Liñan Pinto, Mariana / Damas, Carlos / Sousa, Joana

Nutrients. 2021 June 05, v. 13, no. 6

2021

Abstract	School meals present several cost benefits overtime at the short, medium, and long term for individuals and society. This cross-sectional study aims to analyse the nutritional composition and evaluate the adequacy of school lunches. One hundred and fifty-eight samples were collected and analysed from 10 primary schools in Sintra’s municipality, served during one week. On average, energy (27.7% daily energetic requirements) and carbohydrate (48.1%) contents did not reach the reference values, and the content of protein (19.5%) exceeded the reference value (p < 0.05). The mean total fat (28.8%) and saturated fatty acids (5.4%) content complied with the recommendations. The mean salt (1.7 g) and dietary fibre (8.3 g) content exceeded the reference value but did not differ significantly from the recommendations. Addressing school canteens is crucial, not only in a nutritional approach, but also as an opportunity to achieve healthier, sustainable, and accessible food systems, aligned with the Sustainable Development Goals 2030. We highlighted the importance of evaluating evidence-based practices and disseminated practice-based evidence regarding the adequacy of school lunches.
Keywords	carbohydrates ; cross-sectional studies ; dietary fiber ; energy ; nutrient content ; nutritional adequacy ; sustainable development
Language	English
Dates of publication	2021-0605
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2518386-2
ISSN	2072-6643
ISSN	2072-6643
DOI	10.3390/nu13061946
Database	NAL-Catalogue (AGRICOLA)

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