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Article: Plant Production Protocols from Seeds of Threatened

Copete, Elena / Copete, Miguel A / Martínez-Duro, Esmeralda / Santiago, Alejandro / Ferrandis, Pablo / Herranz, José M

2023 Volume 13, Issue 11

Abstract: Members of the ... ...

Abstract	Members of the genus
Language	English
Publishing date	2023-11-08
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662250-6
ISSN	2075-1729
ISSN	2075-1729
DOI	10.3390/life13112181
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Article ; Online: Corrigendum to "Species delimitation using genomic data to resolve taxonomic uncertainties in a speciation continuum of pelagic seabirds" [Mol. Phylogenet. Evol. 179 (2023) 107671].

Obiol, Joan Ferrer / Herranz, Jose M / Paris, Josephine R / Whiting, James R / Rozas, Julio / Riutort, Marta / González-Solís, Jacob

Molecular phylogenetics and evolution

2023 Volume 187, Page(s) 107888

Language	English
Publishing date	2023-07-26
Publishing country	United States
Document type	Published Erratum
ZDB-ID	33610-5
ISSN	1095-9513 ; 1055-7903
ISSN (online)	1095-9513
ISSN	1055-7903
DOI	10.1016/j.ympev.2023.107888
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Article: Seed germination in

Copete, Elena / Copete, Miguel A / Ferrandis, Pablo / Herranz, José M

AoB PLANTS

2020 Volume 12, Issue 6, Page(s) plaa060

Abstract: Seed dormancy classes determine both population and species-level processes which can be crucial in the life cycle of many plants. However, there are no studies of a dormancy cline between levels of morphophysiological dormancy (MPD). We aimed to ... ...

Abstract	Seed dormancy classes determine both population and species-level processes which can be crucial in the life cycle of many plants. However, there are no studies of a dormancy cline between levels of morphophysiological dormancy (MPD). We aimed to determine the class of seed dormancy of
Language	English
Publishing date	2020-11-17
Publishing country	England
Document type	Journal Article
ISSN	2041-2851
ISSN	2041-2851
DOI	10.1093/aobpla/plaa060
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Article ; Online: Species delimitation using genomic data to resolve taxonomic uncertainties in a speciation continuum of pelagic seabirds.

Ferrer Obiol, Joan / Herranz, Jose M / Paris, Josephine R / Whiting, James R / Rozas, Julio / Riutort, Marta / González-Solís, Jacob

Molecular phylogenetics and evolution

2022 Volume 179, Page(s) 107671

Abstract: Speciation is a continuous and complex process shaped by the interaction of numerous evolutionary forces. Despite the continuous nature of the speciation process, the implementation of conservation policies relies on the delimitation of species and ... ...

Abstract	Speciation is a continuous and complex process shaped by the interaction of numerous evolutionary forces. Despite the continuous nature of the speciation process, the implementation of conservation policies relies on the delimitation of species and evolutionary significant units (ESUs). Puffinus shearwaters are globally distributed and threatened pelagic seabirds. Due to remarkable morphological status the group has been under intense taxonomic debate for the past three decades. Here, we use double digest Restriction-Site Associated DNA sequencing (ddRAD-Seq) to genotype species and subspecies of North Atlantic and Mediterranean Puffinus shearwaters across their entire geographical range. We assess the phylogenetic relationships and population structure among and within the group, evaluate species boundaries, and characterise the genomic landscape of divergence. We find that current taxonomies are not supported by genomic data and propose a more accurate taxonomy by integrating genomic information with other sources of evidence. Our results show that several taxon pairs are at different stages of a speciation continuum. Our study emphasises the potential of genomic data to resolve taxonomic uncertainties, which can help to focus management actions on relevant taxa, even if they do not necessarily coincide with the taxonomic rank of species.
MeSH term(s)	Animals ; Phylogeny ; Species Specificity ; Genome ; Genomics ; Birds/genetics
Language	English
Publishing date	2022-11-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	33610-5
ISSN	1095-9513 ; 1055-7903
ISSN (online)	1095-9513
ISSN	1055-7903
DOI	10.1016/j.ympev.2022.107671
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Article ; Online: MCPIP1 Inhibits Hepatic Stellate Cell Activation in Autocrine and Paracrine Manners, Preventing Liver Fibrosis.

Pydyn, Natalia / Ferenc, Anna / Trzos, Katarzyna / Pospiech, Ewelina / Wilamowski, Mateusz / Mucha, Olga / Major, Piotr / Kadluczka, Justyna / Rodrigues, Pedro M / Banales, Jesus M / Herranz, Jose M / Avila, Matias A / Hutsch, Tomasz / Malczak, Piotr / Radkowiak, Dorota / Budzynski, Andrzej / Jura, Jolanta / Kotlinowski, Jerzy

Cellular and molecular gastroenterology and hepatology

2024 Volume 17, Issue 6, Page(s) 887–906

Abstract: Background & aims: Hepatic fibrosis is characterized by enhanced deposition of extracellular matrix (ECM), which results from the wound healing response to chronic, repeated injury of any etiology. Upon injury, hepatic stellate cells (HSCs) activate and ...

Abstract	Background & aims: Hepatic fibrosis is characterized by enhanced deposition of extracellular matrix (ECM), which results from the wound healing response to chronic, repeated injury of any etiology. Upon injury, hepatic stellate cells (HSCs) activate and secrete ECM proteins, forming scar tissue, which leads to liver dysfunction. Monocyte-chemoattractant protein-induced protein 1 (MCPIP1) possesses anti-inflammatory activity, and its overexpression reduces liver injury in septic mice. In addition, mice with liver-specific deletion of Zc3h12a develop features of primary biliary cholangitis. In this study, we investigated the role of MCPIP1 in liver fibrosis and HSC activation. Methods: We analyzed MCPIP1 levels in patients' fibrotic livers and hepatic cells isolated from fibrotic murine livers. In vitro experiments were conducted on primary HSCs, cholangiocytes, hepatocytes, and LX-2 cells with MCPIP1 overexpression or silencing. Results: MCPIP1 levels are induced in patients' fibrotic livers compared with their nonfibrotic counterparts. Murine models of fibrosis revealed that its level is increased in HSCs and hepatocytes. Moreover, hepatocytes with Mcpip1 deletion trigger HSC activation via the release of connective tissue growth factor. Overexpression of MCPIP1 in LX-2 cells inhibits their activation through the regulation of TGFB1 expression, and this phenotype is reversed upon MCPIP1 silencing. Conclusions: We demonstrated that MCPIP1 is induced in human fibrotic livers and regulates the activation of HSCs in both autocrine and paracrine manners. Our results indicate that MCPIP1 could have a potential role in the development of liver fibrosis.
Language	English
Publishing date	2024-02-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	2819778-1
ISSN	2352-345X ; 2352-345X
ISSN (online)	2352-345X
ISSN	2352-345X
DOI	10.1016/j.jcmgh.2024.01.021
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Article ; Online: Optimization of Plant Production by Seed Treatment in Two Wild Subspecies of

Herranz, Raquel / Copete, Miguel A / Herranz, José M / Copete, Elena / Ferrandis, Pablo

Molecules (Basel, Switzerland)

2020 Volume 25, Issue 19

Abstract: ... The ... ...

Abstract	The daffodil
MeSH term(s)	Alkaloids/metabolism ; Germination ; Narcissus/classification ; Narcissus/growth & development ; Plant Dormancy ; Seedlings/classification ; Seedlings/growth & development ; Seeds/growth & development
Chemical Substances	Alkaloids
Language	English
Publishing date	2020-09-27
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/molecules25194439
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Article ; Online: New insights into the regulation of bile acids synthesis during the early stages of liver regeneration: A human and experimental study.

Uriarte, Iker / Santamaria, Eva / López-Pascual, Amaya / Monte, María J / Argemí, Josepmaria / Latasa, M Ujue / Adán-Villaescusa, Elena / Irigaray, Ainara / Herranz, Jose M / Arechederra, María / Basualdo, Jorge / Lucena, Felipe / Corrales, Fernando J / Rotellar, Fernando / Pardo, Fernando / Merlen, Gregory / Rainteau, Dominique / Sangro, Bruno / Tordjmann, Thierry /

Berasain, Carmen / Marín, Jose J G / Fernández-Barrena, Maite G / Herrero, Ignacio / Avila, Matias A

Biochimica et biophysica acta. Molecular basis of disease

2024 Volume 1870, Issue 5, Page(s) 167166

Abstract: Background and aims: Liver regeneration is essential for the preservation of homeostasis and survival. Bile acids (BAs)-mediated signaling is necessary for liver regeneration, but BAs levels need to be carefully controlled to avoid hepatotoxicity. We ... ...

Abstract	Background and aims: Liver regeneration is essential for the preservation of homeostasis and survival. Bile acids (BAs)-mediated signaling is necessary for liver regeneration, but BAs levels need to be carefully controlled to avoid hepatotoxicity. We studied the early response of the BAs-fibroblast growth factor 19 (FGF19) axis in healthy individuals undergoing hepatectomy for living donor liver transplant. We also evaluated BAs synthesis in mice upon partial hepatectomy (PH) and acute inflammation, focusing on the regulation of cytochrome-7A1 (CYP7A1), a key enzyme in BAs synthesis from cholesterol. Methods: Serum was obtained from twelve human liver donors. Mice underwent 2/3-PH or sham-operation. Acute inflammation was induced with bacterial lipopolysaccharide (LPS) in mice fed control or antoxidant-supplemented diets. BAs and 7α-hydroxy-4-cholesten-3-one (C4) levels were measured by HPLC-MS/MS; serum FGF19 by ELISA. Gene expression and protein levels were analyzed by RT-qPCR and western-blot. Results: Serum BAs levels increased after PH. In patients with more pronounced hypercholanemia, FGF19 concentrations transiently rose, while C4 levels (a readout of CYP7A1 activity) dropped 2 h post-resection in all cases. Serum BAs and C4 followed the same pattern in mice 1 h after PH, but C4 levels also dropped in sham-operated and LPS-treated animals, without marked changes in CYP7A1 protein levels. LPS-induced serum C4 decline was attenuated in mice fed an antioxidant-supplemented diet. Conclusions: In human liver regeneration FGF19 upregulation may constitute a protective response from BAs excess during liver regeneration. Our findings suggest the existence of post-translational mechanisms regulating CYP7A1 activity, and therefore BAs synthesis, independent from CYP7A1/Cyp7a1 gene transcription.
Language	English
Publishing date	2024-04-19
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	60-7
ISSN	1879-260X ; 1879-2596 ; 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)	1879-260X ; 1879-2596 ; 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.bbadis.2024.167166
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Article ; Online: Comprehensive analysis of epigenetic and epitranscriptomic genes' expression in human NAFLD.

Herranz, Jose M / López-Pascual, Amaya / Clavería-Cabello, Alex / Uriarte, Iker / Latasa, M Ujúe / Irigaray-Miramon, Ainara / Adán-Villaescusa, Elena / Castelló-Uribe, Borja / Sangro, Bruno / Arechederra, María / Berasain, Carmen / Avila, Matías A / Fernández-Barrena, Maite G

Journal of physiology and biochemistry

2023 Volume 79, Issue 4, Page(s) 901–924

Abstract: Non-alcoholic fatty liver disease (NAFLD) is a multifactorial condition with a complex etiology. Its incidence is increasing globally in parallel with the obesity epidemic, and it is now considered the most common liver disease in Western countries. The ... ...

Abstract	Non-alcoholic fatty liver disease (NAFLD) is a multifactorial condition with a complex etiology. Its incidence is increasing globally in parallel with the obesity epidemic, and it is now considered the most common liver disease in Western countries. The precise mechanisms underlying the development and progression of NAFLD are complex and still poorly understood. The dysregulation of epigenetic and epitranscriptomic mechanisms is increasingly recognized to play pathogenic roles in multiple conditions, including chronic liver diseases. Here, we have performed a comprehensive analysis of the expression of epigenetic and epitranscriptomic genes in a total of 903 liver tissue samples corresponding to patients with normal liver, obese patients, and patients with non-alcoholic fatty liver (NAFL) and non-alcoholic steatohepatitis (NASH), advancing stages in NAFLD progression. We integrated ten transcriptomic datasets in an unbiased manner, enabling their robust analysis and comparison. We describe the complete landscape of epigenetic and epitranscriptomic genes' expression along the course of the disease. We identify signatures of genes significantly dysregulated in association with disease progression, particularly with liver fibrosis development. Most of these epigenetic and epitranscriptomic effectors have not been previously described in human NAFLD, and their altered expression may have pathogenic implications. We also performed a comprehensive analysis of the expression of enzymes involved in the metabolism of the substrates and cofactors of epigenetic and epitranscriptomic effectors. This study provides novel information on NAFLD pathogenesis and may also guide the identification of drug targets to treat this condition and its progression towards hepatocellular carcinoma.
MeSH term(s)	Humans ; Non-alcoholic Fatty Liver Disease/metabolism ; Carcinoma, Hepatocellular/pathology ; Liver Cirrhosis/genetics ; Obesity/genetics ; Obesity/metabolism ; Liver Neoplasms/pathology ; Epigenesis, Genetic
Language	English
Publishing date	2023-08-25
Publishing country	Spain
Document type	Journal Article
ZDB-ID	1325104-1
ISSN	1877-8755 ; 0034-9402 ; 1138-7548
ISSN (online)	1877-8755
ISSN	0034-9402 ; 1138-7548
DOI	10.1007/s13105-023-00976-y
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Article ; Online: Impact of Liver Inflammation on Bile Acid Side Chain Shortening and Amidation.

Alonso-Peña, Marta / Espinosa-Escudero, Ricardo / Hermanns, Heike M / Briz, Oscar / Herranz, Jose M / Garcia-Ruiz, Carmen / Fernandez-Checa, Jose C / Juamperez, Javier / Avila, Matias / Argemi, Josepmaria / Bataller, Ramon / Crespo, Javier / Monte, Maria J / Geier, Andreas / Herraez, Elisa / Marin, Jose J G

Cells

2022 Volume 11, Issue 24

Abstract: Bile acid (BA) synthesis from cholesterol by hepatocytes is inhibited by inflammatory cytokines. Whether liver inflammation also affects BA side chain shortening and conjugation was investigated. In human liver cell lines (IHH, HepG2, and HepaRG), ... ...

Abstract	Bile acid (BA) synthesis from cholesterol by hepatocytes is inhibited by inflammatory cytokines. Whether liver inflammation also affects BA side chain shortening and conjugation was investigated. In human liver cell lines (IHH, HepG2, and HepaRG), agonists of nuclear receptors including the farnesoid X receptor (FXR), liver X receptor (LXR), and peroxisome proliferator-activated receptors (PPARs) did not affect the expression of BA-related peroxisomal enzymes. In contrast, hepatocyte nuclear factor 4α (HNF4α) inhibition down-regulated acyl-CoA oxidase 2 (ACOX2).
Language	English
Publishing date	2022-12-09
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2661518-6
ISSN	2073-4409 ; 2073-4409
ISSN (online)	2073-4409
ISSN	2073-4409
DOI	10.3390/cells11243983
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Article ; Online: Integrated Transcriptomic and Proteomic Analysis Identifies Plasma Biomarkers of Hepatocellular Failure in Alcohol-Associated Hepatitis.

Argemi, Josepmaria / Kedia, Komal / Gritsenko, Marina A / Clemente-Sanchez, Ana / Asghar, Aliya / Herranz, Jose M / Liu, Zhang-Xu / Atkinson, Stephen R / Smith, Richard D / Norden-Krichmar, Trina M / Day, Le Z / Stolz, Andrew / Tayek, John A / Bataller, Ramon / Morgan, Timothy R / Jacobs, Jon M

The American journal of pathology

2022 Volume 192, Issue 12, Page(s) 1658–1669

Abstract: Alcohol-associated hepatitis (AH) is a form of liver failure with high short-term mortality. Recent studies have shown that defective function of hepatocyte nuclear factor 4 alpha (HNF4a) and systemic inflammation are major disease drivers of AH. Plasma ... ...

Abstract	Alcohol-associated hepatitis (AH) is a form of liver failure with high short-term mortality. Recent studies have shown that defective function of hepatocyte nuclear factor 4 alpha (HNF4a) and systemic inflammation are major disease drivers of AH. Plasma biomarkers of hepatocyte function could be useful for diagnostic and prognostic purposes. Herein, an integrative analysis of hepatic RNA sequencing and liquid chromatography-tandem mass spectrometry was performed to identify plasma protein signatures for patients with mild and severe AH. Alcohol-related liver disease cirrhosis, nonalcoholic fatty liver disease, and healthy subjects were used as comparator groups. Levels of identified proteins primarily involved in hepatocellular function were decreased in patients with AH, which included hepatokines, clotting factors, complement cascade components, and hepatocyte growth activators. A protein signature of AH disease severity was identified, including thrombin, hepatocyte growth factor α, clusterin, human serum factor H-related protein, and kallistatin, which exhibited large abundance shifts between severe and nonsevere AH. The combination of thrombin and hepatocyte growth factor α discriminated between severe and nonsevere AH with high sensitivity and specificity. These findings were correlated with the liver expression of genes encoding secreted proteins in a similar cohort, finding a highly consistent plasma protein signature reflecting HNF4A and HNF1A functions. This unbiased proteomic-transcriptome analysis identified plasma protein signatures and pathways associated with disease severity, reflecting HNF4A/1A activity useful for diagnostic assessment in AH.
MeSH term(s)	Humans ; Transcriptome ; Hepatocyte Growth Factor/genetics ; Proteomics ; Thrombin/metabolism ; Carcinoma, Hepatocellular ; Liver Neoplasms ; Hepatitis, Alcoholic/diagnosis ; Proteins/genetics ; Biomarkers
Chemical Substances	Hepatocyte Growth Factor (67256-21-7) ; Thrombin (EC 3.4.21.5) ; Proteins ; Biomarkers
Language	English
Publishing date	2022-10-13
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2943-9
ISSN	1525-2191 ; 0002-9440
ISSN (online)	1525-2191
ISSN	0002-9440
DOI	10.1016/j.ajpath.2022.08.009
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