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Article: Beyond Genomes and the Covid-19 Pandemic.

Kostrouch, Z

2020 Volume 66, Issue 3, Page(s) 85

MeSH term(s)	Betacoronavirus ; COVID-19 ; Coronavirus Infections ; Genome ; Humans ; Pandemics ; Phylogeny ; Pneumonia, Viral ; SARS-CoV-2
Keywords	covid19
Language	English
Publishing date	2020-10-15
Publishing country	Czech Republic
Document type	Journal Article ; Comment
ZDB-ID	419223-0
ISSN	0015-5500
ISSN	0015-5500
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Beyond Genomes and the Covid-19 Pandemic

Kostrouch, Z.

Folia Biologica

Abstract: In the field of the host-infectious agent interaction, this translates to tracing the origin of effector proteins to the genomes of the hosts or infectious agents Despite the sound data that support the existence of transfer factors and availability of ... ...

Abstract	In the field of the host-infectious agent interaction, this translates to tracing the origin of effector proteins to the genomes of the hosts or infectious agents Despite the sound data that support the existence of transfer factors and availability of their protein sequences in some cases, the search in genomes using bioinformatic tools fails to confirm their existence both in the species that produced them and in the genomes of infectious agents in cases linked to infections The fact that large numbers of infected people seem to undergo the Covid-19 infection without symptoms or have very light progression of the disease while severe morbidity and mortality occurs in others points at the need to better understand the mechanisms underlying this and related infections
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #827265
Database	COVID19

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Article: The power of informatics.

Kostrouch, Z

Folia biologica

2007 Volume 53, Issue 6, Page(s) 193

MeSH term(s)	Humans ; Hydroxymethylbilane Synthase/genetics ; Informatics ; Internet ; Mutation/genetics ; Porphyria, Acute Intermittent/enzymology ; Porphyria, Acute Intermittent/therapy
Chemical Substances	Hydroxymethylbilane Synthase (EC 2.5.1.61)
Language	English
Publishing date	2007
Publishing country	Czech Republic
Document type	Editorial
ZDB-ID	419223-0
ISSN	0015-5500
ISSN	0015-5500
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Nuclear receptors in nematode development: Natural experiments made by a phylum.

Kostrouchova, Marta / Kostrouch, Zdenek

Biochimica et biophysica acta

2015 Volume 1849, Issue 2, Page(s) 224–237

Abstract: The development of complex multicellular organisms is dependent on regulatory decisions that are necessary for the establishment of specific differentiation and metabolic cellular states. Nuclear receptors (NRs) form a large family of transcription ... ...

Abstract	The development of complex multicellular organisms is dependent on regulatory decisions that are necessary for the establishment of specific differentiation and metabolic cellular states. Nuclear receptors (NRs) form a large family of transcription factors that play critical roles in the regulation of development and metabolism of Metazoa. Based on their DNA binding and ligand binding domains, NRs are divided into eight NR subfamilies from which representatives of six subfamilies are present in both deuterostomes and protostomes indicating their early evolutionary origin. In some nematode species, especially in Caenorhabditis, the family of NRs expanded to a large number of genes strikingly exceeding the number of NR genes in vertebrates or insects. Nematode NRs, including the multiplied Caenorhabditis genes, show clear relation to vertebrate and insect homologues belonging to six of the eight main NR subfamilies. This review summarizes advances in research of nematode NRs and their developmental functions. Nematode NRs can reveal evolutionarily conserved mechanisms that regulate specific developmental and metabolic processes as well as new regulatory adaptations. They represent the results of a large number of natural experiments with structural and functional potential of NRs for the evolution of the phylum. The conserved and divergent character of nematode NRs adds a new dimension to our understanding of the general biology of regulation by NRs. This article is part of a Special Issue entitled: Nuclear receptors in animal development.
MeSH term(s)	Animals ; Caenorhabditis elegans/embryology ; Caenorhabditis elegans/genetics ; Conserved Sequence ; Evolution, Molecular ; Nematoda/embryology ; Nematoda/genetics ; Nematoda/growth & development ; Receptors, Cytoplasmic and Nuclear/classification ; Receptors, Cytoplasmic and Nuclear/physiology
Chemical Substances	Receptors, Cytoplasmic and Nuclear
Language	English
Publishing date	2015-02
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	60-7
ISSN	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
ISSN (online)	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650
ISSN	0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
DOI	10.1016/j.bbagrm.2014.06.016
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: SKIP and BIR-1/Survivin have potential to integrate proteome status with gene expression.

Kostrouch, David / Kostrouchová, Markéta / Yilma, Petr / Chughtai, Ahmed Ali / Novotný, Jan Philipp / Novák, Petr / Kostrouchová, Veronika / Kostrouchová, Marta / Kostrouch, Zdeněk

Journal of proteomics

2014 Volume 110, Page(s) 93–106

Abstract: SKIP and BIR are evolutionarily conserved proteins; SKIP (SKP-1) is a known transcription and splicing cofactor while BIR-1/Survivin regulates cell division, gene expression and development. Their loss of function induces overlapping developmental ... ...

Abstract	SKIP and BIR are evolutionarily conserved proteins; SKIP (SKP-1) is a known transcription and splicing cofactor while BIR-1/Survivin regulates cell division, gene expression and development. Their loss of function induces overlapping developmental phenotypes. We searched for SKP-1 and BIR-1 interaction on protein level using yeast two-hybrid screens and identified partially overlapping categories of proteins as SKIP-1 and BIR-1 interactors. The interacting proteins included ribosomal proteins, transcription factors, translation factors and cytoskeletal and motor proteins suggesting involvement in multiple protein complexes. To visualize the effect of BIR-1 on the proteome in Caenorhabditis elegans we induced a short time pulse BIR-1 overexpression in synchronized L1 larvae. This led to a dramatic alteration of the whole proteome pattern indicating that BIR-1 alone has the capacity to alter the chromatographic profile of many target proteins including proteins found to be interactors in yeast two hybrid screens. The results were validated for ribosomal proteins RPS3 and RPL5, non-muscle myosin and TAC-1, a transcription cofactor and a centrosome associated protein. Together, these results suggest that SKP-1 and BIR-1 are multifunctional proteins that form multiple protein complexes in both shared and distinct pathways and have the potential to connect proteome signals with the regulation of gene expression. Biological significance: The genomic organization of the genes encoding BIR-1 and SKIP (SKP-1) in C. elegans have suggested that these two factors, each evolutionarily conserved, have related functions. However, these functional connections have remained elusive and underappreciated in light of limited information from C. elegans and other biological systems. Our results provide further evidence for a functional link between these two factors and suggest they may transmit proteome signals towards the regulation of gene expression.
MeSH term(s)	Animals ; Caenorhabditis elegans/metabolism ; Caenorhabditis elegans Proteins/metabolism ; Gene Expression Regulation/physiology ; Nuclear Proteins/metabolism ; Proteome/metabolism ; Signal Transduction/physiology ; Survivors ; Ubiquitin-Protein Ligase Complexes
Chemical Substances	Caenorhabditis elegans Proteins ; Nuclear Proteins ; Proteome ; bir-1 protein, C elegans ; Ubiquitin-Protein Ligase Complexes (EC 2.3.2.23) ; skp-1 protein, C elegans (EC 2.3.2.23)
Language	English
Publishing date	2014-08-01
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2400835-7
ISSN	1876-7737 ; 1874-3919
ISSN (online)	1876-7737
ISSN	1874-3919
DOI	10.1016/j.jprot.2014.07.023
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: The nematode homologue of Mediator complex subunit 28, F28F8.5, is a critical regulator of

Kostrouchová, Markéta / Kostrouch, David / Chughtai, Ahmed A / Kaššák, Filip / Novotný, Jan P / Kostrouchová, Veronika / Benda, Aleš / Krause, Michael W / Saudek, Vladimír / Kostrouchová, Marta / Kostrouch, Zdeněk

PeerJ

2017 Volume 5, Page(s) e3390

Abstract: The evolutionarily conserved Mediator complex is a critical player in regulating transcription. Comprised of approximately two dozen proteins, the Mediator integrates diverse regulatory signals through direct protein-protein interactions that, in turn, ... ...

Abstract	The evolutionarily conserved Mediator complex is a critical player in regulating transcription. Comprised of approximately two dozen proteins, the Mediator integrates diverse regulatory signals through direct protein-protein interactions that, in turn, modulate the influence of Mediator on RNA Polymerase II activity. One Mediator subunit, MED28, is known to interact with cytoplasmic structural proteins, providing a potential direct link between cytoplasmic dynamics and the control of gene transcription. Although identified in many animals and plants, MED28 is not present in yeast; no bona fide MED28 has been described previously in
Language	English
Publishing date	2017-06-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.3390
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Article: Trichoplax adhaerens

Novotný, Jan Philipp / Chughtai, Ahmed Ali / Kostrouchová, Markéta / Kostrouchová, Veronika / Kostrouch, David / Kaššák, Filip / Kaňa, Radek / Schierwater, Bernd / Kostrouchová, Marta / Kostrouch, Zdenek

PeerJ

2017 Volume 5, Page(s) e3789

Abstract: Trichoplax ... ...

Abstract	Trichoplax adhaerens
Language	English
Publishing date	2017-09-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.3789
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Valproic acid, a molecular lead to multiple regulatory pathways.

Kostrouchová, M / Kostrouch, Z

Folia biologica

2007 Volume 53, Issue 2, Page(s) 37–49

Abstract: Valproic acid (2-propyl pentanoic acid) is a drug used for the treatment of epilepsy and bipolar disorder. Although very rare, side effects such as spina bifida and other defects of neural tube closure indicate that valproic acid interferes with ... ...

Abstract	Valproic acid (2-propyl pentanoic acid) is a drug used for the treatment of epilepsy and bipolar disorder. Although very rare, side effects such as spina bifida and other defects of neural tube closure indicate that valproic acid interferes with developmental regulatory pathways. Recently obtained data show that valproic acid affects cell growth, differentiation, apoptosis and immunogenicity of cultured cancer cells and tumours. Focused studies uncovered the potential of valproic acid to interfere with multiple regulatory mechanisms including histone deacetylases, GSK3 alpha and beta, Akt, the ERK pathway, the phosphoinositol pathway, the tricarboxylic acid cycle, GABA, and the OXPHOS system. Valproic acid is emerging as a potential anticancer drug and may also serve as a molecular lead that can help design drugs with more specific and more potent effects on the one side and drugs with wide additive but weaker effects on the other. Valproic acid is thus a powerful molecular tool for better understanding and therapeutic targeting of pathways that regulate the behaviour of cancer cells.
MeSH term(s)	Animals ; Antineoplastic Agents/administration & dosage ; Antineoplastic Agents/pharmacology ; Antineoplastic Agents/therapeutic use ; Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; Gene Expression Regulation, Neoplastic/drug effects ; Humans ; Neoplasms/drug therapy ; Neoplasms/genetics ; Teratogens/toxicity ; Valproic Acid/analogs & derivatives ; Valproic Acid/chemistry ; Valproic Acid/pharmacology ; Valproic Acid/therapeutic use
Chemical Substances	Antineoplastic Agents ; Teratogens ; Valproic Acid (614OI1Z5WI)
Language	English
Publishing date	2007
Publishing country	Czech Republic
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	419223-0
ISSN	0015-5500
ISSN	0015-5500
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: SMED-TLX-1 (NR2E1) is critical for tissue and body plan maintenance in Schmidtea mediterranea in fasting/feeding cycles.

Raška, O / Kostrouchová, V / Behenský, F / Yilma, P / Saudek, V / Kostrouch, Z / Kostrouchová, M

Folia biologica

2011 Volume 57, Issue 6, Page(s) 223–231

Abstract: Nuclear receptors (NRs), or nuclear hormone receptors (NHRs), are transcription factors that regulate development and metabolism of most if not all animal species. Their regulatory networks include ... ...

Abstract	Nuclear receptors (NRs), or nuclear hormone receptors (NHRs), are transcription factors that regulate development and metabolism of most if not all animal species. Their regulatory networks include conserved mechanisms that are shared in-between species as well as mechanisms that are restricted to certain phyla or even species. In search for conserved members of the NHR family in Schmidtea mediterranea, we identified a molecular signature of a class of NRs, NR2E1, in the S. mediterranea genome and cloned its complete cDNA coding sequence. The derived amino acid sequence shows a high degree of conservation of both DNA-binding domain and ligand- binding domain and a remarkably high homology to vertebrate NR2E1 and C. elegans NHR-67. Quantitative PCR detected approximately ten-fold higher expression of Smed-tlx-1 in the proximal part of the head compared to the tail region. The expression of Smed-tlx-1 is higher during fed state than during fasting. Smed-tlx-1 down-regulation by RNA interference affects the ability of the animals to maintain body plan and induces defects of brain, eyes and body shape during fasting and re-growing cycles. These results suggest that SMED-TLX-1 is critical for tissue and body plan maintenance in planaria.
MeSH term(s)	Amino Acid Sequence ; Animals ; Body Patterning/genetics ; Cloning, Molecular ; Fasting/physiology ; Feeding Behavior/physiology ; Gene Expression Regulation ; Helminth Proteins/chemistry ; Helminth Proteins/genetics ; Helminth Proteins/metabolism ; Humans ; Molecular Sequence Data ; Organ Specificity/genetics ; Phylogeny ; RNA Interference ; Receptors, Cytoplasmic and Nuclear/chemistry ; Receptors, Cytoplasmic and Nuclear/genetics ; Receptors, Cytoplasmic and Nuclear/metabolism ; Sequence Alignment ; Turbellaria/embryology ; Turbellaria/genetics ; Turbellaria/physiology
Chemical Substances	Helminth Proteins ; Receptors, Cytoplasmic and Nuclear
Language	English
Publishing date	2011-05-05
Publishing country	Czech Republic
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	419223-0
ISSN	0015-5500
ISSN	0015-5500
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Article: Perilipin-related protein regulates lipid metabolism in C. elegans.

Chughtai, Ahmed Ali / Kaššák, Filip / Kostrouchová, Markéta / Novotný, Jan Philipp / Krause, Michael W / Saudek, Vladimír / Kostrouch, Zdenek / Kostrouchová, Marta

PeerJ

2015 Volume 3, Page(s) e1213

Abstract: Perilipins are lipid droplet surface proteins that contribute to fat metabolism by controlling the access of lipids to lipolytic enzymes. Perilipins have been identified in organisms as diverse as metazoa, fungi, and amoebas but strikingly not in ... ...

Abstract	Perilipins are lipid droplet surface proteins that contribute to fat metabolism by controlling the access of lipids to lipolytic enzymes. Perilipins have been identified in organisms as diverse as metazoa, fungi, and amoebas but strikingly not in nematodes. Here we identify the protein encoded by the W01A8.1 gene in Caenorhabditis elegans as the closest homologue and likely orthologue of metazoan perilipin. We demonstrate that nematode W01A8.1 is a cytoplasmic protein residing on lipid droplets similarly as human perilipins 1 and 2. Downregulation or elimination of W01A8.1 affects the appearance of lipid droplets resulting in the formation of large lipid droplets localized around the dividing nucleus during the early zygotic divisions. Visualization of lipid containing structures by CARS microscopy in vivo showed that lipid-containing structures become gradually enlarged during oogenesis and relocate during the first zygotic division around the dividing nucleus. In mutant embryos, the lipid containing structures show defective intracellular distribution in subsequent embryonic divisions and become gradually smaller during further development. In contrast to embryos, lipid-containing structures in enterocytes and in epidermal cells of adult animals are smaller in mutants than in wild type animals. Our results demonstrate the existence of a perilipin-related regulation of fat metabolism in nematodes and provide new possibilities for functional studies of lipid metabolism.
Language	English
Publishing date	2015-09-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.1213
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