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Book ; Online ; Thesis: Heterosis in yeast hybrids

2018

Author's details	Joana P. Bernardes
Keywords	Biowissenschaften, Biologie ; Life Science, Biology
Subject code	sg570
Language	English
Publisher	Universitätsbibliothek Kiel
Publishing place	Kiel
Document type	Book ; Online ; Thesis
Database	Digital theses on the web

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Article ; Online: The evolution of convex trade-offs enables the transition towards multicellularity.

Bernardes, Joana P / John, Uwe / Woltermann, Noemi / Valiadi, Martha / Hermann, Ruben J / Becks, Lutz

Nature communications

2021 Volume 12, Issue 1, Page(s) 4222

Abstract: The evolutionary transition towards multicellular life often involves growth in groups of undifferentiated cells followed by differentiation into soma and germ-like cells. Theory predicts that germ soma differentiation is facilitated by a convex trade- ... ...

Abstract	The evolutionary transition towards multicellular life often involves growth in groups of undifferentiated cells followed by differentiation into soma and germ-like cells. Theory predicts that germ soma differentiation is facilitated by a convex trade-off between survival and reproduction. However, this has never been tested and these transitions remain poorly understood at the ecological and genetic level. Here, we study the evolution of cell groups in ten isogenic lines of the unicellular green algae Chlamydomonas reinhardtii with prolonged exposure to a rotifer predator. We confirm that growth in cell groups is heritable and characterized by a convex trade-off curve between reproduction and survival. Identical mutations evolve in all cell group isolates; these are linked to survival and reducing associated cell costs. Overall, we show that just 500 generations of predator selection were sufficient to lead to a convex trade-off and incorporate evolved changes into the prey genome.
MeSH term(s)	Animals ; Biological Evolution ; Cell Survival/physiology ; Chlamydomonas reinhardtii/physiology ; Models, Biological ; Predatory Behavior ; Rotifera/physiology
Language	English
Publishing date	2021-07-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-021-24503-z
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The evolution of convex trade-offs enables the transition towards multicellularity

Joana P. Bernardes / Uwe John / Noemi Woltermann / Martha Valiadi / Ruben J. Hermann / Lutz Becks

Nature Communications, Vol 12, Iss 1, Pp 1-

2021 Volume 9

Abstract: Multicellularity is a major evolutionary transition that remains poorly characterized at the ecological and genetic level. Exposing unicellular green algae to a rotifer predator showed that just 500 generations of predator selection were sufficient to ... ...

Abstract	Multicellularity is a major evolutionary transition that remains poorly characterized at the ecological and genetic level. Exposing unicellular green algae to a rotifer predator showed that just 500 generations of predator selection were sufficient to lead to a convex trade-off and incorporate evolved changes into the prey genome.
Keywords	Science ; Q
Language	English
Publishing date	2021-07-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Phenotyping of Adaptive Immune Responses in Inflammatory Diseases.

Humrich, Jens Y / Bernardes, Joana P / Ludwig, Ralf J / Klatzmann, David / Scheffold, Alexander

Frontiers in immunology

2020 Volume 11, Page(s) 604464

Abstract: Immunophenotyping on the molecular and cellular level is a central aspect for characterization of patients with inflammatory diseases, both to better understand disease etiopathogenesis and based on this to develop diagnostic and prognostic biomarkers ... ...

Abstract	Immunophenotyping on the molecular and cellular level is a central aspect for characterization of patients with inflammatory diseases, both to better understand disease etiopathogenesis and based on this to develop diagnostic and prognostic biomarkers which allow patient stratification and tailor-made treatment strategies. Technology-driven developments have considerably expanded the range of analysis tools. Especially the analysis of adaptive immune responses, often regarded as central though mostly poorly characterized disease drivers, is a major focus of personalized medicine. The identification of the disease-relevant antigens and characterization of corresponding antigen-specific lymphocytes in individual patients benefits significantly from recent developments in cytometry by sequencing and proteomics. The aim of this workshop was to identify the important developments for state-of-the-art immunophenotyping for clinical application and precision medicine. We focused here on recent key developments in analysis of antigen-specific lymphocytes, sequencing, and proteomics approaches, their relevance in precision medicine and the discussion of the major challenges and opportunities for the future.
MeSH term(s)	Adaptive Immunity ; Animals ; B-Lymphocytes/immunology ; B-Lymphocytes/metabolism ; Congresses as Topic ; High-Throughput Nucleotide Sequencing ; Humans ; Immunophenotyping ; Inflammation/genetics ; Inflammation/immunology ; Inflammation/metabolism ; Phenotype ; Proteomics ; Receptors, Antigen, T-Cell/genetics ; Receptors, Antigen, T-Cell/metabolism ; T-Lymphocytes/immunology ; T-Lymphocytes/metabolism
Chemical Substances	Receptors, Antigen, T-Cell
Language	English
Publishing date	2020-11-25
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2020.604464
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Article: The hemodynamic response function as a type 2 diabetes biomarker: a data-driven approach.

Guimarães, Pedro / Serranho, Pedro / Duarte, João V / Crisóstomo, Joana / Moreno, Carolina / Gomes, Leonor / Bernardes, Rui / Castelo-Branco, Miguel

Frontiers in neuroinformatics

2024 Volume 17, Page(s) 1321178

Abstract: Introduction: There is a need to better understand the neurophysiological changes associated with early brain dysfunction in Type 2 diabetes mellitus (T2DM) before vascular or structural lesions. Our aim was to use a novel unbiased data-driven approach ... ...

Abstract	Introduction: There is a need to better understand the neurophysiological changes associated with early brain dysfunction in Type 2 diabetes mellitus (T2DM) before vascular or structural lesions. Our aim was to use a novel unbiased data-driven approach to detect and characterize hemodynamic response function (HRF) alterations in T2DM patients, focusing on their potential as biomarkers. Methods: We meshed task-based event-related (visual speed discrimination) functional magnetic resonance imaging with DL to show, from an unbiased perspective, that T2DM patients' blood-oxygen-level dependent response is altered. Relevance analysis determined which brain regions were more important for discrimination. We combined explainability with deconvolution generalized linear model to provide a more accurate picture of the nature of the neural changes. Results: The proposed approach to discriminate T2DM patients achieved up to 95% accuracy. Higher performance was achieved at higher stimulus (speed) contrast, showing a direct relationship with stimulus properties, and in the hemispherically dominant left visual hemifield, demonstrating biological interpretability. Differences are explained by physiological asymmetries in cortical spatial processing (right hemisphere dominance) and larger neural signal-to-noise ratios related to stimulus contrast. Relevance analysis revealed the most important regions for discrimination, such as extrastriate visual cortex, parietal cortex, and insula. These are disease/task related, providing additional evidence for pathophysiological significance. Our data-driven design allowed us to compute the unbiased HRF without assumptions. Conclusion: We can accurately differentiate T2DM patients using a data-driven classification of the HRF. HRF differences hold promise as biomarkers and could contribute to a deeper understanding of neurophysiological changes associated with T2DM.
Language	English
Publishing date	2024-01-05
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2452979-5
ISSN	1662-5196
ISSN	1662-5196
DOI	10.3389/fninf.2023.1321178
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Article ; Online: Phenotyping of Adaptive Immune Responses in Inflammatory Diseases

Jens Y. Humrich / Joana P. Bernardes / Ralf J. Ludwig / David Klatzmann / Alexander Scheffold

Frontiers in Immunology, Vol

2020 Volume 11

Abstract	Immunophenotyping on the molecular and cellular level is a central aspect for characterization of patients with inflammatory diseases, both to better understand disease etiopathogenesis and based on this to develop diagnostic and prognostic biomarkers which allow patient stratification and tailor-made treatment strategies. Technology-driven developments have considerably expanded the range of analysis tools. Especially the analysis of adaptive immune responses, often regarded as central though mostly poorly characterized disease drivers, is a major focus of personalized medicine. The identification of the disease-relevant antigens and characterization of corresponding antigen-specific lymphocytes in individual patients benefits significantly from recent developments in cytometry by sequencing and proteomics. The aim of this workshop was to identify the important developments for state-of-the-art immunophenotyping for clinical application and precision medicine. We focused here on recent key developments in analysis of antigen-specific lymphocytes, sequencing, and proteomics approaches, their relevance in precision medicine and the discussion of the major challenges and opportunities for the future.
Keywords	immunophenotyping ; sequencing ; proteomics ; inflammation ; precision medicine ; TCR repertoire ; Immunologic diseases. Allergy ; RC581-607
Subject code	610
Language	English
Publishing date	2020-11-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Diazaborines Are a Versatile Platform to Develop ROS-Responsive Antibody Drug Conjugates*.

António, João P M / Carvalho, Joana Inês / André, Ana S / Dias, Joana N R / Aguiar, Sandra I / Faustino, Hélio / Lopes, Ricardo M R M / Veiros, Luis F / Bernardes, Gonçalo J L / da Silva, Frederico A / Gois, Pedro M P

Angewandte Chemie (International ed. in English)

2021 Volume 60, Issue 49, Page(s) 25914–25921

Abstract: Antibody-drug conjugates (ADCs) are a new class of therapeutics that combine the lethality of potent cytotoxic drugs with the targeting ability of antibodies to selectively deliver drugs to cancer cells. In this study we show for the first time the ... ...

Abstract	Antibody-drug conjugates (ADCs) are a new class of therapeutics that combine the lethality of potent cytotoxic drugs with the targeting ability of antibodies to selectively deliver drugs to cancer cells. In this study we show for the first time the synthesis of a reactive-oxygen-species (ROS)-responsive ADC (VL-DAB31-SN-38) that is highly selective and cytotoxic to B-cell lymphoma (CLBL-1 cell line, IC
MeSH term(s)	Antineoplastic Agents/chemistry ; Antineoplastic Agents/metabolism ; Antineoplastic Agents/pharmacology ; Boron Compounds/chemistry ; Boron Compounds/pharmacology ; Cell Proliferation/drug effects ; Cell Survival/drug effects ; Drug Screening Assays, Antitumor ; Humans ; Immunoconjugates/chemistry ; Immunoconjugates/metabolism ; Immunoconjugates/pharmacology ; Lymphoma, B-Cell/drug therapy ; Lymphoma, B-Cell/metabolism ; Lymphoma, B-Cell/pathology ; Molecular Structure ; Reactive Oxygen Species/metabolism
Chemical Substances	Antineoplastic Agents ; Boron Compounds ; Immunoconjugates ; Reactive Oxygen Species
Language	English
Publishing date	2021-11-05
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2011836-3
ISSN	1521-3773 ; 1433-7851
ISSN (online)	1521-3773
ISSN	1433-7851
DOI	10.1002/anie.202109835
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Article ; Online: Targeted deletion of von-Hippel-Lindau in the proximal tubule conditions the kidney against early diabetic kidney disease.

Kunke, Madlen / Knöfler, Hannah / Dahlke, Eileen / Zanon Rodriguez, Luis / Böttner, Martina / Larionov, Alexey / Saudenova, Makhabbat / Ohrenschall, Gerrit M / Westermann, Magdalena / Porubsky, Stefan / Bernardes, Joana P / Häsler, Robert / Magnin, Jean-Luc / Koepsell, Hermann / Jouret, François / Theilig, Franziska

Cell death & disease

2023 Volume 14, Issue 8, Page(s) 562

Abstract: Diabetic kidney disease (DKD) is the leading cause of end-stage renal disease. Glomerular hyperfiltration and albuminuria subject the proximal tubule (PT) to a subsequent elevation of workload, growth, and hypoxia. Hypoxia plays an ambiguous role in the ... ...

Abstract	Diabetic kidney disease (DKD) is the leading cause of end-stage renal disease. Glomerular hyperfiltration and albuminuria subject the proximal tubule (PT) to a subsequent elevation of workload, growth, and hypoxia. Hypoxia plays an ambiguous role in the development and progression of DKD and shall be clarified in our study. PT-von-Hippel-Lindau (Vhl)-deleted mouse model in combination with streptozotocin (STZ)-induced type I diabetes mellitus (DM) was phenotyped. In contrary to PT-Vhl-deleted STZ-induced type 1 DM mice, proteinuria and glomerular hyperfiltration occurred in diabetic control mice the latter due to higher nitric oxide synthase 1 and sodium and glucose transporter expression. PT Vhl deletion and DKD share common alterations in gene expression profiles, including glomerular and tubular morphology, and tubular transport and metabolism. Compared to diabetic control mice, the most significantly altered in PT Vhl-deleted STZ-induced type 1 DM mice were Ldc-1, regulating cellular oxygen consumption rate, and Zbtb16, inhibiting autophagy. Alignment of altered genes in heat maps uncovered that Vhl deletion prior to STZ-induced DM preconditioned the kidney against DKD. HIF-1α stabilization leading to histone modification and chromatin remodeling resets most genes altered upon DKD towards the control level. These data demonstrate that PT HIF-1α stabilization is a hallmark of early DKD and that targeting hypoxia prior to the onset of type 1 DM normalizes renal cell homeostasis and prevents DKD development.
MeSH term(s)	Animals ; Mice ; Diabetic Nephropathies/genetics ; Kidney ; Kidney Tubules, Proximal ; Kidney Glomerulus ; Diabetes Mellitus, Type 1/complications ; Diabetes Mellitus, Type 1/genetics ; Diabetes Mellitus, Experimental/complications ; Diabetes Mellitus, Experimental/genetics
Language	English
Publishing date	2023-08-26
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2541626-1
ISSN	2041-4889 ; 2041-4889
ISSN (online)	2041-4889
ISSN	2041-4889
DOI	10.1038/s41419-023-06074-7
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Plastia em Z modificada do ligamento patelar com reforço de tendão quadricipital no tratamento da patela baixa

Costa, Tiago António Almeida Orange / Bernardes, Francisco / Miradouro, José / Pereira, Joana / Barreira, Pedro / Carvalho, João

Revista Brasileira de Ortopedia

2024

Abstract: A Patela Baixa é uma patologia do joelho pouco frequente, mas limitante devido à rigidez articular e dor localizada na região anterior do joelho. Pode decorrer após trauma, imobilização prolongada ou intervenção cirúrgica local. O achado patológico ... ...

Abstract	A Patela Baixa é uma patologia do joelho pouco frequente, mas limitante devido à rigidez articular e dor localizada na região anterior do joelho. Pode decorrer após trauma, imobilização prolongada ou intervenção cirúrgica local. O achado patológico marcante é o encurtamento e o aumento na espessura do ligamento patelar. Foram descritas várias técnicas cirúrgicas para o seu tratamento, não existindo nenhum tratamento padronizado. Descrevemos o caso de uma doente de 73 anos de idade que apresentava rigidez do joelho, deficit funcional importante e patela baixa após artroplastia total do joelho. Foi submetida a um procedimento cirúrgico de partes moles recentemente descrito, com excelente evolução funcional, melhorando de um Lysholm Knee Score de 16 para 81 pontos, permitindo a mobilização e regresso às atividades de vida diárias precocemente. Patella Baixa is an infrequent knee pathology, but it is limiting due to joint stiffness and localized pain in the anterior region of the knee. It may occur after trauma, prolonged immobilization or local surgical intervention. The striking pathological finding is the shortening and increase in thickness of the patellar ligament. Several surgical techniques have been described for its treatment, and there is no standardized treatment. We describe the case of a 73-year-old female patient who presented with knee stiffness, significant functional deficit, and patella baja after total knee arthroplasty. She underwent a recently described soft tissue surgical procedure, with excellent functional evolution, improving from a Lysholm Knee Score of 16 to 81 points, allowing early mobilization and return to daily life activities.
Keywords	artroplastia do joelho ; articulação do joelho ; ligamento patelar ; patela ; tendões ; arthroplasty, replacement, knee ; knee joint ; patellar tendon ; patella ; tendons
Language	Portuguese
Publishing date	2024-04-19
Publisher	Thieme Revinter Publicações Ltda.
Publishing place	Stuttgart ; New York
Document type	Article
ZDB-ID	2411301-3
ISSN	1982-4378 ; 0102-3616 ; 1982-4378
ISSN (online)	1982-4378
ISSN	0102-3616 ; 1982-4378
DOI	10.1055/s-0043-1770967
Database	Thieme publisher's database

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Article ; Online: FixNCut: single-cell genomics through reversible tissue fixation and dissociation.

Jiménez-Gracia, Laura / Marchese, Domenica / Nieto, Juan C / Caratù, Ginevra / Melón-Ardanaz, Elisa / Gudiño, Victoria / Roth, Sara / Wise, Kellie / Ryan, Natalie K / Jensen, Kirk B / Hernando-Momblona, Xavier / Bernardes, Joana P / Tran, Florian / Sievers, Laura Katharina / Schreiber, Stefan / van den Berge, Maarten / Kole, Tessa / van der Velde, Petra L / Nawijn, Martijn C /

Rosenstiel, Philip / Batlle, Eduard / Butler, Lisa M / Parish, Ian A / Plummer, Jasmine / Gut, Ivo / Salas, Azucena / Heyn, Holger / Martelotto, Luciano G

Genome biology

2024 Volume 25, Issue 1, Page(s) 81

Abstract: The use of single-cell technologies for clinical applications requires disconnecting sampling from downstream processing steps. Early sample preservation can further increase robustness and reproducibility by avoiding artifacts introduced during specimen ...

Abstract	The use of single-cell technologies for clinical applications requires disconnecting sampling from downstream processing steps. Early sample preservation can further increase robustness and reproducibility by avoiding artifacts introduced during specimen handling. We present FixNCut, a methodology for the reversible fixation of tissue followed by dissociation that overcomes current limitations. We applied FixNCut to human and mouse tissues to demonstrate the preservation of RNA integrity, sequencing library complexity, and cellular composition, while diminishing stress-related artifacts. Besides single-cell RNA sequencing, FixNCut is compatible with multiple single-cell and spatial technologies, making it a versatile tool for robust and flexible study designs.
MeSH term(s)	Humans ; Animals ; Mice ; Tissue Fixation/methods ; Reproducibility of Results ; Sequence Analysis, RNA/methods ; RNA/genetics ; Genomics/methods ; Single-Cell Analysis/methods
Chemical Substances	RNA (63231-63-0)
Language	English
Publishing date	2024-03-29
Publishing country	England
Document type	Journal Article
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-024-03219-5
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