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Article ; Online: SMC5/6 complex-mediated SUMOylation stimulates DNA-protein cross-link repair in Arabidopsis.

Dvořák Tomaštíková, Eva / Prochazkova, Klara / Yang, Fen / Jemelkova, Jitka / Finke, Andreas / Dorn, Annika / Said, Mahmoud / Puchta, Holger / Pecinka, Ales

The Plant cell

2023 Volume 35, Issue 5, Page(s) 1532–1547

Abstract: DNA-protein cross-links (DPCs) are highly toxic DNA lesions consisting of proteins covalently attached to chromosomal DNA. Unrepaired DPCs physically block DNA replication and transcription. Three DPC repair pathways have been identified in Arabidopsis ( ... ...

Abstract	DNA-protein cross-links (DPCs) are highly toxic DNA lesions consisting of proteins covalently attached to chromosomal DNA. Unrepaired DPCs physically block DNA replication and transcription. Three DPC repair pathways have been identified in Arabidopsis (Arabidopsis thaliana) to date: the endonucleolytic cleavage of DNA by the structure-specific endonuclease MUS81; proteolytic degradation of the crosslinked protein by the metalloprotease WSS1A; and cleavage of the cross-link phosphodiester bonds by the tyrosyl phosphodiesterases TDP1 and TDP2. Here we describe the evolutionary conserved STRUCTURAL MAINTENANCE OF CHROMOSOMEs SMC5/6 complex as a crucial component involved in DPC repair. We identified multiple alleles of the SMC5/6 complex core subunit gene SMC6B via a forward-directed genetic screen designed to identify the factors involved in the repair of DPCs induced by the cytidine analog zebularine. We monitored plant growth and cell death in response to DPC-inducing chemicals, which revealed that the SMC5/6 complex is essential for the repair of several types of DPCs. Genetic interaction and sensitivity assays showed that the SMC5/6 complex works in parallel to the endonucleolytic and proteolytic pathways. The repair of zebularine-induced DPCs was associated with SMC5/6-dependent SUMOylation of the damage sites. Thus, we present the SMC5/6 complex as an important factor in plant DPC repair.
MeSH term(s)	Arabidopsis/genetics ; Arabidopsis/metabolism ; Sumoylation ; DNA Repair/genetics ; DNA Damage ; Proteins/metabolism ; DNA/metabolism ; Cell Cycle Proteins/genetics ; Cell Cycle Proteins/metabolism
Chemical Substances	Proteins ; DNA (9007-49-2) ; Cell Cycle Proteins
Language	English
Publishing date	2023-01-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	623171-8
ISSN	1532-298X ; 1040-4651
ISSN (online)	1532-298X
ISSN	1040-4651
DOI	10.1093/plcell/koad020
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Book ; Online: List Locally Surjective Homomorphisms in Hereditary Graph Classes

Dvořák, Pavel / Krawczyk, Monika / Masařík, Tomáš / Novotná, Jana / Rzążewski, Paweł / Żuk, Aneta

2022

Abstract: ... graphs that exclude a fixed graph $F$ as an induced subgraph. We aim to understand for which pairs $(H,F ... from its list. In this paper, we study the complexity of the LLSHom($H$) problem in $F$-free graphs, i.e ... from $V(G)$ to $V(H)$ that is surjective in the neighborhood of each vertex in $G$. In the list locally ...

Abstract	A locally surjective homomorphism from a graph $G$ to a graph $H$ is an edge-preserving mapping from $V(G)$ to $V(H)$ that is surjective in the neighborhood of each vertex in $G$. In the list locally surjective homomorphism problem, denoted by LLSHom($H$), the graph $H$ is fixed and the instance consists of a graph $G$ whose every vertex is equipped with a subset of $V(H)$, called list. We ask for the existence of a locally surjective homomorphism from $G$ to $H$, where every vertex of $G$ is mapped to a vertex from its list. In this paper, we study the complexity of the LLSHom($H$) problem in $F$-free graphs, i.e., graphs that exclude a fixed graph $F$ as an induced subgraph. We aim to understand for which pairs $(H,F)$ the problem can be solved in subexponential time. We show that for all graphs $H$, for which the problem is NP-hard in general graphs, it cannot be solved in subexponential time in $F$-free graphs unless $F$ is a bounded-degree forest or the ETH fails. The initial study reveals that a natural subfamily of bounded-degree forests $F$ that might lead to some tractability results is the family $\mathcal S$ consisting of forests whose every component has at most three leaves. In this case, we exhibit the following dichotomy theorem: besides the cases that are polynomial-time solvable in general graphs, the graphs $H \in \{P_3,C_4\}$ are the only connected ones that allow for a subexponential-time algorithm in $F$-free graphs for every $F \in \mathcal S$ (unless the ETH fails). Comment: 26 pages, 8 figures
Keywords	Computer Science - Data Structures and Algorithms ; Computer Science - Computational Complexity
Subject code	511
Publishing date	2022-02-24
Publishing country	us
Document type	Book ; Online
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Article ; Online: Sustainable green roofs: a comprehensive review of influential factors.

Shahmohammad, Mohsen / Hosseinzadeh, Majid / Dvorak, Bruce / Bordbar, Farzaneh / Shahmohammadmirab, Hamid / Aghamohammadi, Nasrin

Environmental science and pollution research international

2022 Volume 29, Issue 52, Page(s) 78228–78254

Abstract: Green roofs have gained much attention as a modern roofing surface due to their potential to deliver many environmental and social benefits. Studies have indicated that different GR designs deliver different ecosystem services, and there are important ... ...

Abstract	Green roofs have gained much attention as a modern roofing surface due to their potential to deliver many environmental and social benefits. Studies have indicated that different GR designs deliver different ecosystem services, and there are important factors that affect GR performance. This article reviewed significant factors that influence GR performance and sustainability. Substrate and drainage layer material choice significantly affects stormwater retention potential, leachate quality, plant survival, and determines GR environmental footprints. Subsequently, type of plants, their form, and kinds used on GRs impact GR ecosystem function. Leaf area is the most studied trait due to its influence on the cooling potential and energy performance. In order to achieve a sustainable GR, it is essential to select the type of plants that have a high survival rate. Perennial herbs, particularly forbs and grass as dominant groups, are heat and drought tolerant, which make them suitable in GR experiment. Furthermore, selecting a suitable irrigation system is as important as two other factors for having a sustainable GR. Irrigation is essential for plant survival, and due to the current pressure on valuable water sources, it is important to select a sustainable irrigation system. This review presents three sustainable irrigation methods: (i) employing alternative water sources such as rainwater, greywater, and atmospheric water; (ii) smart irrigation and monitoring; and (iii) using adaptive materials and additives that improve GR water use. This review sheds new insights on the design of high-performance, sustainable GRs and provides guidance for the legislation of sustainable GR.
MeSH term(s)	Ecosystem ; Conservation of Natural Resources ; Plants ; Water ; Smart Materials
Chemical Substances	Water (059QF0KO0R) ; Smart Materials
Language	English
Publishing date	2022-10-03
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	1178791-0
ISSN	1614-7499 ; 0944-1344
ISSN (online)	1614-7499
ISSN	0944-1344
DOI	10.1007/s11356-022-23405-x
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Article ; Online: Monoterpenoid aryl hydrocarbon receptor allosteric antagonists protect against ultraviolet skin damage in female mice.

Nature communications

2023 Volume 14, Issue 1, Page(s) 2728

Abstract: The human aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that is a pivotal regulator of human physiology and pathophysiology. Allosteric inhibition of AhR was previously thought to be untenable. Here, we identify carvones as ... ...

Abstract	The human aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that is a pivotal regulator of human physiology and pathophysiology. Allosteric inhibition of AhR was previously thought to be untenable. Here, we identify carvones as noncompetitive, insurmountable antagonists of AhR and characterize the structural and functional consequences of their binding. Carvones do not displace radiolabeled ligands from binding to AhR but instead bind allosterically within the bHLH/PAS-A region of AhR. Carvones do not influence the translocation of ligand-activated AhR into the nucleus but inhibit the heterodimerization of AhR with its canonical partner ARNT and subsequent binding of AhR to the promoter of CYP1A1. As a proof of concept, we demonstrate physiologically relevant Ahr-antagonism by carvones in vivo in female mice. These substances establish the molecular basis for selective targeting of AhR regardless of the type of ligand(s) present and provide opportunities for the treatment of disease processes modified by AhR.
MeSH term(s)	Animals ; Female ; Mice ; Aryl Hydrocarbon Receptor Nuclear Translocator/genetics ; Aryl Hydrocarbon Receptor Nuclear Translocator/metabolism ; Cytochrome P-450 CYP1A1/genetics ; Ligands ; Promoter Regions, Genetic ; Receptors, Aryl Hydrocarbon/genetics ; Receptors, Aryl Hydrocarbon/metabolism ; Skin/metabolism ; Skin/radiation effects ; Ultraviolet Rays/adverse effects
Chemical Substances	Aryl Hydrocarbon Receptor Nuclear Translocator (138391-32-9) ; Cytochrome P-450 CYP1A1 (EC 1.14.14.1) ; Ligands ; Receptors, Aryl Hydrocarbon
Language	English
Publishing date	2023-05-11
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/s41467-023-38478-6
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Book ; Online: Parameterized Inapproximability of Independent Set in $H$-Free Graphs

Dvořák, Pavel / Feldmann, Andreas Emil / Rai, Ashutosh / Rzążewski, Paweł

2020

Abstract: ... alpha(H))}$ algorithm in $H$-free graphs and under Gap-ETH there is no $d/k^{o(1)}$-approximation for $K ... We study the Independent Set (IS) problem in $H$-free graphs, i.e., graphs excluding some fixed ... graph $H$ as an induced subgraph. We prove several inapproximability results both for polynomial-time ...

Abstract	We study the Independent Set (IS) problem in $H$-free graphs, i.e., graphs excluding some fixed graph $H$ as an induced subgraph. We prove several inapproximability results both for polynomial-time and parameterized algorithms. Halld\'orsson [SODA 1995] showed that for every $\delta>0$ IS has a polynomial-time $(\frac{d-1}{2}+\delta)$-approximation in $K_{1,d}$-free graphs. We extend this result by showing that $K_{a,b}$-free graphs admit a polynomial-time $O(\alpha(G)^{1-1/a})$-approximation, where $\alpha(G)$ is the size of a maximum independent set in $G$. Furthermore, we complement the result of Halld\'orsson by showing that for some $\gamma=\Theta(d/\log d),$ there is no polynomial-time $\gamma$-approximation for these graphs, unless NP = ZPP. Bonnet et al. [IPEC 2018] showed that IS parameterized by the size $k$ of the independent set is W[1]-hard on graphs which do not contain (1) a cycle of constant length at least $4$, (2) the star $K_{1,4}$, and (3) any tree with two vertices of degree at least $3$ at constant distance. We strengthen this result by proving three inapproximability results under different complexity assumptions for almost the same class of graphs (we weaken condition (2) that $G$ does not contain $K_{1,5}$). First, under the ETH, there is no $f(k)\cdot n^{o(k/\log k)}$ algorithm for any computable function $f$. Then, under the deterministic Gap-ETH, there is a constant $\delta>0$ such that no $\delta$-approximation can be computed in $f(k) \cdot n^{O(1)}$ time. Also, under the stronger randomized Gap-ETH there is no such approximation algorithm with runtime $f(k)\cdot n^{o(\sqrt{k})}$. Finally, we consider the parameterization by the excluded graph $H$, and show that under the ETH, IS has no $n^{o(\alpha(H))}$ algorithm in $H$-free graphs and under Gap-ETH there is no $d/k^{o(1)}$-approximation for $K_{1,d}$-free graphs with runtime $f(d,k) n^{O(1)}$. Comment: Preliminary version of the paper in WG 2020 proceedings
Keywords	Computer Science - Computational Complexity ; F.2
Subject code	511
Publishing date	2020-06-18
Publishing country	us
Document type	Book ; Online
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Article ; Online: Fertility Preservation Practices at Pediatric Oncology Institutions in the United States: A Report From the Children's Oncology Group.

Frederick, Natasha N / Klosky, James L / Meacham, Lillian / Quinn, Gwendolyn P / Kelvin, Joanne F / Cherven, Brooke / Freyer, David R / Dvorak, Christopher C / Brackett, Julienne / Ahmed-Winston, Sameeya / Bryson, Elyse / Su, H Irene / Chow, Eric J / Levine, Jennifer

JCO oncology practice

2023 Volume 19, Issue 4, Page(s) e550–e558

Abstract: Purpose: Fertility discussions are an integral part of comprehensive care for pediatric, adolescent, and young adult patients newly diagnosed with cancer and are supported by national guidelines. Current institutional practices are poorly understood.: ...

Abstract	Purpose: Fertility discussions are an integral part of comprehensive care for pediatric, adolescent, and young adult patients newly diagnosed with cancer and are supported by national guidelines. Current institutional practices are poorly understood. Methods: A cross-sectional survey was distributed to 220 Children's Oncology Group member institutions regarding fertility discussion practices. Descriptive statistics were calculated for all variables. The association between specific practices and selected outcomes on the basis of sex was examined via multivariable logistic regression. Results: One hundred forty-four programs (65.5%) returned surveys. Of these, 65 (45.1%) reported routine discussions of fertility with all female patients and 55 (38.5%) all male patients ( Conclusion: Despite recommended guidelines, fertility discussions with patients/families before treatment initiation are not routine at Children's Oncology Group institutions. Standard criteria to determine which options should be offered to patients are more common for males than females.
MeSH term(s)	Adolescent ; Young Adult ; Humans ; Male ; Female ; Child ; United States ; Fertility Preservation ; Cross-Sectional Studies ; Semen ; Medical Oncology ; Neoplasms/complications ; Neoplasms/therapy
Language	English
Publishing date	2023-02-10
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	3028198-2
ISSN	2688-1535 ; 2688-1527
ISSN (online)	2688-1535
ISSN	2688-1527
DOI	10.1200/OP.22.00349
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Article ; Online: Immune activation by microbiome shapes the colon mucosa: Comparison between healthy rat mucosa under conventional and germ-free conditions.

Čaja, Fabián / Stakheev, Dmitry / Chernyavskiy, Oleksander / Křížan, Jiří / Dvořák, Jiří / Rossmann, Pavel / Štěpánková, Renata / Makovický, Peter / Makovický, Pavol / Kozáková, Hana / Vannucci, Luca

Journal of immunotoxicology

2021 Volume 18, Issue 1, Page(s) 37–49

Abstract: Germ-free animals (GF) are those without a microbiome since birth. This particular biological model has become one of special interest with the growing evidence of importance of the microbiome in the life, development, adaptation, and immunity of humans ... ...

Abstract	Germ-free animals (GF) are those without a microbiome since birth. This particular biological model has become one of special interest with the growing evidence of importance of the microbiome in the life, development, adaptation, and immunity of humans and animals in the environments in which they live. Anatomical differences observed in GF compared with conventionally-reared animals (CV) has given rise to the question of the influence of commensal microflora on the development of structure and function (even immunological) of the bowel. Only recently, thanks to achievements in microscopy and associated methods, structural differences can be better evaluated and put in perspective with the immunological characteristics of GF vs. CV animals. This study, using a GF rat model, describes for the first time the possible influence that the presence of commensal microflora, continuously stimulating mucosal immunity, has on the collagen scaffold organization of the colon mucosa. Significant differences were found between CV and GF mucosa structure with higher complexity in the CV rats associated to a more activated immune environment. The immunological data suggest that, in response to the presence of a microbiome, an effective homeostatic regulation in developed by the CV rats in healthy conditions to avoid inflammation and maintain cytokine levels near the spontaneous production found in the GF animals. The results indicated that collagen scaffold adapted to the immune microenvironment; therefore, it is apparent that the microbiome was able to condition the structure of the colon mucosa.
MeSH term(s)	Animals ; Colon ; Germ-Free Life ; Immunity, Mucosal ; Intestinal Mucosa ; Microbiota ; Rats
Language	English
Publishing date	2021-03-05
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2205064-4
ISSN	1547-6901 ; 1547-691X
ISSN (online)	1547-6901
ISSN	1547-691X
DOI	10.1080/1547691X.2021.1887412
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Article: Angiogenesis: update 2005.

Dvorak, H F

Journal of thrombosis and haemostasis : JTH

2005 Volume 3, Issue 8, Page(s) 1835–1842

Abstract: Angiogenesis has critical roles in normal vascular development and in important pathologies including cancer, wound healing and inflammation. This brief article will review the angiogenic response induced by the vascular permeability factor/vascular ... ...

Abstract	Angiogenesis has critical roles in normal vascular development and in important pathologies including cancer, wound healing and inflammation. This brief article will review the angiogenic response induced by the vascular permeability factor/vascular endothelial growth factor (VPF/VEGF) family of proteins and particularly VEGF-A, thought to be the single most important angiogenic factor. It will also review the steps and mechanisms by which VEGF-A induces the formation of new blood vessels and will provide an initial classification of the abnormal blood vessels that form in pathological angiogenesis. Finally, it will touch on the exciting relationships that are emerging between angiogenesis and the hemostatic and nervous systems.
MeSH term(s)	Animals ; Blood Coagulation ; Cell Proliferation ; Endothelial Growth Factors/metabolism ; Humans ; Models, Biological ; Neovascularization, Pathologic ; Neovascularization, Physiologic ; Signal Transduction ; Vascular Endothelial Growth Factor A/metabolism
Chemical Substances	Endothelial Growth Factors ; Vascular Endothelial Growth Factor A
Language	English
Publishing date	2005-07-08
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S. ; Review
ZDB-ID	2112661-6
ISSN	1538-7836 ; 1538-7933
ISSN (online)	1538-7836
ISSN	1538-7933
DOI	10.1111/j.1538-7836.2005.01361.x
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Article ; Online: Bidirectional Modulation of the Voltage-Gated Sodium (Nav1.6) Channel by Rationally Designed Peptidomimetics.

Dvorak, Nolan M / Wadsworth, Paul A / Wang, Pingyuan / Chen, Haiying / Zhou, Jia / Laezza, Fernanda

Molecules (Basel, Switzerland)

2020 Volume 25, Issue 15

Abstract: Disruption of protein:protein interactions (PPIs) that regulate the function of voltage-gated ... ...

Abstract	Disruption of protein:protein interactions (PPIs) that regulate the function of voltage-gated Na
MeSH term(s)	Allosteric Regulation ; Binding Sites ; Drug Design ; Fibroblast Growth Factors/chemistry ; Fibroblast Growth Factors/metabolism ; HEK293 Cells ; Humans ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Docking Simulation ; Molecular Structure ; NAV1.6 Voltage-Gated Sodium Channel/chemistry ; NAV1.6 Voltage-Gated Sodium Channel/metabolism ; Peptidomimetics/chemical synthesis ; Peptidomimetics/chemistry ; Peptidomimetics/pharmacology ; Protein Binding/drug effects ; Protein Structure, Secondary
Chemical Substances	NAV1.6 Voltage-Gated Sodium Channel ; Peptidomimetics ; SCN8A protein, human ; fibroblast growth factor 14 ; Fibroblast Growth Factors (62031-54-3)
Language	English
Publishing date	2020-07-24
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules25153365
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Article ; Online: The Berlin 2016 process: a summary of methodology for the 5th International Consensus Conference on Concussion in Sport.

Meeuwisse, Willem H / Schneider, Kathryn J / Dvořák, Jiří / Omu, Onutobor Tobi / Finch, Caroline F / Hayden, K Alix / McCrory, Paul

British journal of sports medicine

2017 Volume 51, Issue 11, Page(s) 873–876

Abstract: The purpose of this paper is to summarise the methodology for the 5th International Consensus Conference on Concussion in Sport. The 18 months of preparation included engagement of a scientific committee, an expert panel of 33 individuals in the field of ...

Abstract	The purpose of this paper is to summarise the methodology for the 5th International Consensus Conference on Concussion in Sport. The 18 months of preparation included engagement of a scientific committee, an expert panel of 33 individuals in the field of concussion and a modified Delphi technique to determine the primary questions to be answered. The methodology also involved the writing of 12 systematic reviews to inform the consensus conference and submission and review of scientific abstracts. The meeting itself followed a 2-day open format, a 1-day closed expert panel meeting and two additional half day meetings to develop the Concussion Recognition Tool 5 (Pocket CRT5), Sport Concussion Assessment Tool 5 (SCAT5) and Child SCAT5.
Language	English
Publishing date	2017-06
Publishing country	England
Document type	Journal Article
ZDB-ID	600592-5
ISSN	1473-0480 ; 0306-3674
ISSN (online)	1473-0480
ISSN	0306-3674
DOI	10.1136/bjsports-2017-097569
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