From 27ba5d94e15eca722e561095d6171327213eeb2f Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Mon, 20 May 2024 10:01:28 +0200 Subject: [PATCH] Update citations (#1259) Co-authored-by: bgruening --- _bibliography/citations-eu.bib | 206 +++++++-------------------------- 1 file changed, 40 insertions(+), 166 deletions(-) diff --git a/_bibliography/citations-eu.bib b/_bibliography/citations-eu.bib index 52371ebc..6f9ee74f 100644 --- a/_bibliography/citations-eu.bib +++ b/_bibliography/citations-eu.bib @@ -1217,24 +1217,6 @@ @article{blomberg_connecting_2020 } @article{bode_catecholamine_2024, - abstract = {Catecholamines are commonly used as therapeutic drugs in intensive care medicine to maintain sufficient organ perfusion during shock. However, excessive or sustained adrenergic activation drives detrimental cardiac remodeling and may lead to heart failure. Whether catecholamine treatment in absence of heart failure causes persistent cardiac injury, is uncertain. In this experimental study, we assessed the course of cardiac remodeling and recovery during and after prolonged catecholamine treatment and investigated the molecular mechanisms involved.}, - author = {Bode, Christine and Preissl, Sebastian and Hein, Lutz and Lother, Achim}, - doi = {10.1186/s40635-024-00632-9}, - issn = {2197-425X}, - journal = {Intensive Care Medicine Experimental}, - keywords = {{\textgreater}UseGalaxy.eu, Adrenergic receptors, Cardiomyocyte, Endothelin, Gene expression, Intensive care medicine}, - language = {en}, - month = {May}, - number = {1}, - pages = {48}, - title = {Catecholamine treatment induces reversible heart injury and cardiomyocyte gene expression}, - url = {https://doi.org/10.1186/s40635-024-00632-9}, - urldate = {2024-05-17}, - volume = {12}, - year = {2024} -} - -@article{bode_catecholamine_2024-1, abstract = {Catecholamines are commonly used as therapeutic drugs in intensive care medicine to maintain sufficient organ perfusion during shock. However, excessive or sustained adrenergic activation drives detrimental cardiac remodeling and may lead to heart failure. Whether catecholamine treatment in absence of heart failure causes persistent cardiac injury, is uncertain. In this experimental study, we assessed the course of cardiac remodeling and recovery during and after prolonged catecholamine treatment and investigated the molecular mechanisms involved.}, author = {Bode, Christine and Preissl, Sebastian and Hein, Lutz and Lother, Achim}, doi = {10.1186/s40635-024-00632-9}, @@ -2143,27 +2125,6 @@ @article{chetverikov_molecular_2024 year = {2024} } -@article{chetverikov_molecular_2024-1, - abstract = {Gall mites (Eriophyoidea) are cosmopolitan microscopic phytoparasites that often transmit viruses and induce gallogenesis. The tribe Calacarini is diagnosed by a set of plesiomorphic and homoplastic traits, including elimination of setae sc shared with other lineages of Eriophyoidea. We reviewed data on the generic diversity of calacarines, revised the concept of the type genus Calacarus Keifer 1940, and proposed three zones (MZ, SMZ, LZ) in the prodorsal shields of calacarines to simplify descriptions of their shield patterns. We describe three new calacarine species (Calacarus baviensisn. sp., C. burchelliaen. sp., and Viginticus searsiaen. sp.) from indigenous dicotyledonous trees from South Africa and Vietnam and report on new findings of Paracalacarus podocarpi Keifer in Brazil, Jiangsuacarus sp. in the USA, and Calacarus pusillus Pye in Latvia and Russia. The latter represents the new most northern locality of Calacarini. Reinvestigating the type species of Jaranasia Chandrapatya \& Boczek 2000 revealed that absence of setae l’’ II is the only character separating it from Jiangsuacarus Xue 2009. We proposed two new combinations: Jiangsuacarus sesleriae (Skoracka 2004) n. comb. (transferred from Jaranasia) and Procalacarus mussaendae (Keifer 1977) n. comb. (transferred from Calacarus). Partial sequences of Cox1 and 28S genes were obtained for six calacarines, some of them originating from old ethanol material kept at room temperature. Molecular phylogenetics revealed a stable cluster of “true” calacarine sequences comprising Calacarus, Jaranasia, Latitudo, and Viginticus and a polyphyletic group of erroneous sequences assigned to Calacarini in GenBank. All investigated females of calacarines have a pair of genital tubules associated with the vestibulum and hypothesized to participate in fertilization. This finding may contribute to resolving the question on how the fusion of gametes happens in gall mites.}, - author = {Chetverikov, Philipp E. and Craemer, Charnie and Gankevich, Vladimir D. and Le, Nhung Thi Tuyet and Nguyen, Viet Duc and Trinh, Hoat Xuan and Amrine, James}, - copyright = {http://creativecommons.org/licenses/by/3.0/}, - doi = {10.3390/f15020329}, - issn = {1999-4907}, - journal = {Forests}, - keywords = {\textit{28S}, \textit{Calacarus}, \textit{Cox1}, {\textgreater}UseGalaxy.eu, Acari, arthropod structure, endemic, erroneous sequences, female genitalia, phytoparasite diversity, phytophagous mite, reproductive system}, - language = {en}, - month = {February}, - note = {Number: 2 -Publisher: Multidisciplinary Digital Publishing Institute}, - number = {2}, - pages = {329}, - title = {Molecular {Phylogenetics} and {Light} {Microscopy} {Reveal} “{True}” and “{False}” {Calacarines} and {Novel} {Genital} {Structures} in {Gall} {Mites} ({Acariformes}, {Eriophyoidea})}, - url = {https://www.mdpi.com/1999-4907/15/2/329}, - urldate = {2024-05-17}, - volume = {15}, - year = {2024} -} - @article{chiara_next_2020, author = {Chiara, Matteo and D'Erchia, Anna Maria and Gissi, Carmela and Manzari, Caterina and Parisi, Antonio and Resta, Nicoletta and Zambelli, Federico and Picardi, Ernesto and Pavesi, Giulio and Horner, David S. and Pesole, Graziano}, doi = {10.1093/bib/bbaa297}, @@ -2195,25 +2156,6 @@ @article{chiara_next_2021 } @article{choudalakis_repentools_2024, - abstract = {Repeat elements (REs) play important roles for cell function in health and disease. However, RE enrichment analysis in short-read high-throughput sequencing (HTS) data, such as ChIP-seq, is a challenging task.}, - author = {Choudalakis, Michel and Bashtrykov, Pavel and Jeltsch, Albert}, - doi = {10.1186/s13100-024-00315-y}, - issn = {1759-8753}, - journal = {Mobile DNA}, - keywords = {{\textgreater}UseGalaxy.eu, Chromatin modification, Repeat element analysis, Repeat element enrichment, Repeat elements, UHRF1}, - language = {en}, - month = {April}, - number = {1}, - pages = {6}, - shorttitle = {{RepEnTools}}, - title = {{RepEnTools}: an automated repeat enrichment analysis package for {ChIP}-seq data reveals {hUHRF1} {Tandem}-{Tudor} domain enrichment in young repeats}, - url = {https://doi.org/10.1186/s13100-024-00315-y}, - urldate = {2024-04-28}, - volume = {15}, - year = {2024} -} - -@article{choudalakis_repentools_2024-1, abstract = {Repeat elements (REs) play important roles for cell function in health and disease. However, RE enrichment analysis in short-read high-throughput sequencing (HTS) data, such as ChIP-seq, is a challenging task.}, author = {Choudalakis, Michel and Bashtrykov, Pavel and Jeltsch, Albert}, doi = {10.1186/s13100-024-00315-y}, @@ -2756,6 +2698,26 @@ @article{dorone_prion-like_2021 year = {2021} } +@article{dossmann_specific_2024, + abstract = {The DNA methyltransferase DNMT3C appeared as a duplication of the DNMT3B gene in muroids and is required for silencing of young retrotransposons in the male germline. Using specialized assay systems, we investigate the flanking sequence preferences of DNMT3C and observe characteristic preferences for cytosine at the -2 and -1 flank that are unique among DNMT3 enzymes. We identify two amino acids in the catalytic domain of DNMT3C (C543 and V547) that are responsible for the DNMT3C-specific flanking sequence preferences and evolutionary conserved in muroids. Reanalysis of published data shows that DNMT3C flanking preferences are consistent with genome-wide methylation patterns in mouse ES cells only expressing DNMT3C. Strikingly, we show that CpG sites with the preferred flanking sequences of DNMT3C are enriched in murine retrotransposons that were previously identified as DNMT3C targets. Finally, we demonstrate experimentally that DNMT3C has elevated methylation activity on substrates derived from these biological targets. Our data show that DNMT3C flanking sequence preferences match the sequences of young murine retrotransposons which facilitates their methylation. By this, our data provide mechanistic insights into the molecular co-evolution of repeat elements and (epi)genetic defense systems dedicated to maintain genomic stability in mammals.}, + author = {Dossmann, Leonie and Emperle, Max and Dukatz, Michael and de Mendoza, Alex and Bashtrykov, Pavel and Jeltsch, Albert}, + copyright = {2024 The Author(s)}, + doi = {10.1038/s42003-024-06252-z}, + issn = {2399-3642}, + journal = {Communications Biology}, + keywords = {{\textgreater}UseGalaxy.eu, DNA methylation, Enzyme mechanisms, Transferases}, + language = {en}, + month = {May}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {1--12}, + title = {Specific {DNMT3C} flanking sequence preferences facilitate methylation of young murine retrotransposons}, + url = {https://www.nature.com/articles/s42003-024-06252-z}, + urldate = {2024-05-19}, + volume = {7}, + year = {2024} +} + @article{dugar_chromosomal_2022, author = {Dugar, Gaurav and Hofmann, Andreas and Heermann, Dieter W and Hamoen, Leendert W}, journal = {Nature Genetics}, @@ -2835,6 +2797,26 @@ @informatik.uni-freiburg.de year = {2018} } +@article{ehle_downregulation_2024, + abstract = {The hepatic acute-phase response is characterized by a massive upregulation of serum proteins, such as haptoglobin and serum amyloid A, at the expense of liver homeostatic functions. Although the transcription factor hepatocyte nuclear factor 4 alpha (HNF4A) has a well-established role in safeguarding liver function and its cistrome spans around 50\% of liver-specific genes, its role in the acute-phase response has received little attention so far. We demonstrate that HNF4A binds to and represses acute-phase genes under basal conditions. The reprogramming of hepatic transcription during inflammation necessitates loss of HNF4A function to allow expression of acute-phase genes while liver homeostatic genes are repressed. In a pre-clinical liver organoid model overexpression of HNF4A maintained liver functionality in spite of inflammation-induced cell damage. Conversely, HNF4A overexpression potently impaired the acute-phase response by retaining chromatin at regulatory regions of acute-phase genes inaccessible to transcription. Taken together, our data extend the understanding of dual HNF4A action as transcriptional activator and repressor, establishing HNF4A as gatekeeper for the hepatic acute-phase response.}, + author = {Ehle, Charlotte and Iyer-Bierhoff, Aishwarya and Wu, Yunchen and Xing, Shaojun and Kiehntopf, Michael and Mosig, Alexander S. and Godmann, Maren and Heinzel, Thorsten}, + copyright = {2024 The Author(s)}, + doi = {10.1038/s42003-024-06288-1}, + issn = {2399-3642}, + journal = {Communications Biology}, + keywords = {{\textgreater}UseGalaxy.eu, Hepatology, Transcription}, + language = {en}, + month = {May}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {1--14}, + title = {Downregulation of {HNF4A} enables transcriptomic reprogramming during the hepatic acute-phase response}, + url = {https://www.nature.com/articles/s42003-024-06288-1}, + urldate = {2024-05-19}, + volume = {7}, + year = {2024} +} + @article{eisenhardt_genotyping_2022, abstract = {Background: Synovial sarcoma (SS) is a malignant soft tissue tumor of mesenchymal origin that frequently occurs in young adults. Translocation of the SYT gene on chromosome 18 to the SSX genes on chromosome X leads to the formation of oncogenic fusion genes, which lead to initiation and proliferation of tumor cells. The detection and quantification of circulating tumor DNA (ctDNA) can serve as a non-invasive method for diagnostics of local or distant tumor recurrence, which could improve survival rates due to early detection. Methods: We developed a subtype-specific targeted next-generation sequencing (NGS) approach specifically targeting SS t(X;18)(p11;q11), which fuses SS18 (SYT) in chromosome 18 to SSX1 or SSX2 in chromosome x, and recurrent point mutations. In addition, patient-specific panels were designed from tumor exome sequencing. Both approaches were used to quantify ctDNA in patients’ plasma. Results: The subtype-specific assay allowed detection of somatic mutations from 25/25 tumors with a mean of 1.68 targetable mutations. The minimal limit of detection was determined at a variant allele frequency of 0.05\%. Analysis of 29 plasma samples from 15 tumor patients identified breakpoint ctDNA in 6 patients (sensitivity: 40\%, specificity 100\%). The addition of more mutations further increased assay sensitivity. Quantification of ctDNA in plasma samples (n = 11) from one patient collected over 3 years, with a patient-specific panel based on tumor exome sequencing, correlated with the clinical course, response to treatment and tumor volume. Conclusions: Targeted NGS allows for highly sensitive tumor profiling and non-invasive detection of ctDNA in SS patients, enabling non-invasive monitoring of tumor dynamics.}, author = {Eisenhardt, Anja E. and Brugger, Zacharias and Lausch, Ute and Kiefer, Jurij and Zeller, Johannes and Runkel, Alexander and Schmid, Adrian and Bronsert, Peter and Wehrle, Julius and Leithner, Andreas and Liegl-Atzwanger, Bernadette and Giunta, Riccardo E. and Eisenhardt, Steffen U. and Braig, David}, @@ -5426,45 +5408,6 @@ @article{kruse_synaptopodin_2024 language = {en}, month = {January}, note = {Number: 2 -Publisher: Multidisciplinary Digital Publishing Institute}, - number = {2}, - pages = {114}, - title = {Synaptopodin {Regulates} {Denervation}-{Induced} {Plasticity} at {Hippocampal} {Mossy} {Fiber} {Synapses}}, - url = {https://www.mdpi.com/2073-4409/13/2/114}, - urldate = {2024-04-28}, - volume = {13}, - year = {2024} -} - -@article{kruse_synaptopodin_2024, - abstract = {Neurological diseases can lead to the denervation of brain regions caused by demyelination, traumatic injury or cell death. The molecular and structural mechanisms underlying lesion-induced reorganization of denervated brain regions, however, are a matter of ongoing investigation. In order to address this issue, we performed an entorhinal cortex lesion (ECL) in mouse organotypic entorhino-hippocampal tissue cultures of both sexes and studied denervation-induced plasticity of mossy fiber synapses, which connect dentate granule cells (dGCs) with CA3 pyramidal cells (CA3-PCs) and play important roles in learning and memory formation. Partial denervation caused a strengthening of excitatory neurotransmission in dGCs, CA3-PCs and their direct synaptic connections, as revealed by paired recordings (dGC-to-CA3-PC). These functional changes were accompanied by ultrastructural reorganization of mossy fiber synapses, which regularly contain the plasticity-regulating protein synaptopodin and the spine apparatus organelle. We demonstrate that the spine apparatus organelle and synaptopodin are related to ribosomes in close proximity to synaptic sites and reveal a synaptopodin-related transcriptome. Notably, synaptopodin-deficient tissue preparations that lack the spine apparatus organelle failed to express lesion-induced synaptic adjustments. Hence, synaptopodin and the spine apparatus organelle play a crucial role in regulating lesion-induced synaptic plasticity at hippocampal mossy fiber synapses.}, - author = {Kruse, Pia and Brandes, Gudrun and Hemeling, Hanna and Huang, Zhong and Wrede, Christoph and Hegermann, Jan and Vlachos, Andreas and Lenz, Maximilian}, - doi = {10.3390/cells13020114}, - issn = {2073-4409}, - journal = {Cells}, - keywords = {{\textgreater}UseGalaxy.eu, Animals, Cell Death, Denervation, Female, Hippocampus, Male, Mice, Mossy Fibers, Hippocampal, Neuronal Plasticity, Synapses, denervation, lesion-induced plasticity, local protein synthesis, synaptopodin}, - language = {eng}, - month = {January}, - number = {2}, - pages = {114}, - pmcid = {PMC10814840}, - pmid = {38247806}, - title = {Synaptopodin {Regulates} {Denervation}-{Induced} {Plasticity} at {Hippocampal} {Mossy} {Fiber} {Synapses}}, - volume = {13}, - year = {2024} -} - -@article{kruse_synaptopodin_2024-1, - abstract = {Neurological diseases can lead to the denervation of brain regions caused by demyelination, traumatic injury or cell death. The molecular and structural mechanisms underlying lesion-induced reorganization of denervated brain regions, however, are a matter of ongoing investigation. In order to address this issue, we performed an entorhinal cortex lesion (ECL) in mouse organotypic entorhino-hippocampal tissue cultures of both sexes and studied denervation-induced plasticity of mossy fiber synapses, which connect dentate granule cells (dGCs) with CA3 pyramidal cells (CA3-PCs) and play important roles in learning and memory formation. Partial denervation caused a strengthening of excitatory neurotransmission in dGCs, CA3-PCs and their direct synaptic connections, as revealed by paired recordings (dGC-to-CA3-PC). These functional changes were accompanied by ultrastructural reorganization of mossy fiber synapses, which regularly contain the plasticity-regulating protein synaptopodin and the spine apparatus organelle. We demonstrate that the spine apparatus organelle and synaptopodin are related to ribosomes in close proximity to synaptic sites and reveal a synaptopodin-related transcriptome. Notably, synaptopodin-deficient tissue preparations that lack the spine apparatus organelle failed to express lesion-induced synaptic adjustments. Hence, synaptopodin and the spine apparatus organelle play a crucial role in regulating lesion-induced synaptic plasticity at hippocampal mossy fiber synapses.}, - author = {Kruse, Pia and Brandes, Gudrun and Hemeling, Hanna and Huang, Zhong and Wrede, Christoph and Hegermann, Jan and Vlachos, Andreas and Lenz, Maximilian}, - copyright = {http://creativecommons.org/licenses/by/3.0/}, - doi = {10.3390/cells13020114}, - issn = {2073-4409}, - journal = {Cells}, - keywords = {{\textgreater}UseGalaxy.eu, denervation, lesion-induced plasticity, local protein synthesis, synaptopodin}, - language = {en}, - month = {January}, - note = {Number: 2 Publisher: Multidisciplinary Digital Publishing Institute}, number = {2}, pages = {114}, @@ -5899,27 +5842,6 @@ @article{leavitt_acute_2024 year = {2024} } -@article{leavitt_acute_2024-1, - abstract = {Purpose -Tumor hypoxia is a major cause of treatment resistance, especially to radiation therapy at conventional dose rate (CONV), and we wanted to assess whether hypoxia does alter tumor sensitivity to FLASH. -Methods and Materials -We engrafted several tumor types (glioblastoma [GBM], head and neck cancer, and lung adenocarcinoma) subcutaneously in mice to provide a reliable and rigorous way to modulate oxygen supply via vascular clamping or carbogen breathing. We irradiated tumors using a single 20-Gy fraction at either CONV or FLASH, measured oxygen tension, monitored tumor growth, and sampled tumors for bulk RNAseq and pimonidazole analysis. Next, we inhibited glycolysis with trametinib in GBM tumors to enhance FLASH efficacy. -Results -Using various subcutaneous tumor models, and in contrast to CONV, FLASH retained antitumor efficacy under acute hypoxia. These findings show that in addition to normal tissue sparing, FLASH could overcome hypoxia-mediated tumor resistance. Follow-up molecular analysis using RNAseq profiling uncovered a FLASH-specific profile in human GBM that involved cell-cycle arrest, decreased ribosomal biogenesis, and a switch from oxidative phosphorylation to glycolysis. Glycolysis inhibition by trametinib enhanced FLASH efficacy in both normal and clamped conditions. -Conclusions -These data provide new and specific insights showing the efficacy of FLASH in a radiation-resistant context, proving an additional benefit of FLASH over CONV.}, - author = {Leavitt, Ron J. and Almeida, Aymeric and Grilj, Veljko and Montay-Gruel, Pierre and Godfroid, Céline and Petit, Benoit and Bailat, Claude and Limoli, Charles L. and Vozenin, Marie-Catherine}, - doi = {10.1016/j.ijrobp.2024.02.015}, - issn = {0360-3016}, - journal = {International Journal of Radiation Oncology*Biology*Physics}, - keywords = {{\textgreater}UseGalaxy.eu}, - month = {February}, - title = {Acute {Hypoxia} {Does} {Not} {Alter} {Tumor} {Sensitivity} to {FLASH} {Radiation} {Therapy}}, - url = {https://www.sciencedirect.com/science/article/pii/S0360301624003201}, - urldate = {2024-05-17}, - year = {2024} -} - @article{lee_genomic_2022, abstract = {The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic since 2019. Variants of concern (VOCs) declared by the World Health Organization require continuous monitoring because of their possible changes in transmissibility, virulence, and antigenicity. The Omicron variant, a VOC, has become the dominant variant worldwide since November 2021. In the Republic of Korea (South Korea), the number of confirmed cases increased rapidly after the detection of Omicron VOC on November 24, 2021. In this study, we estimated the underlying epidemiological processes of Omicron VOC in South Korea using time-scaled phylodynamic analysis. Three distinct phylogenetic subgroups (Kor-O1, Kor-O2, and Kor-O3) were detected in South Korea. The Kor-O1 subgroup circulated in the Daegu region, whereas Kor-O2 and Kor-O3 circulated in Incheon and Jeollanam-do, respectively. The viral population size and case number of the Kor-O1 subgroup increased more rapidly than those of the other subgroups, indicating the rapid spread of the virus. The results indicated the multiple introductions of Omicron sub-lineages into South Korea and their subsequent co-circulation. The evolution and transmission of SARS-CoV-2 should be continuously monitored, and control strategies need to be improved to control the multiple variants.}, author = {Lee, Dong-Wook and Kim, Jeong-Min and Park, Ae Kyung and Kim, Da-Won and Kim, Ji-Yun and Lim, Noori and Lee, Hyeokjin and Kim, Il-Hwan and Kim, Jeong-Ah and Lee, Chae young and Kwon, Jung-Hoon and Kim, Eun-Jin}, @@ -10387,38 +10309,6 @@ @article{voelker_terpene_2023 } @article{volkova_multi-omics_2024, - abstract = {Barley is a resilient crop with high nutritional value and adaptability, making it a promising candidate for phytoremediation and space agriculture. The study presents a comprehensive multi-omics analysis of the impact of ionising radiation (IR) on barley seedlings, intending to identify candidate pathways for creating radiation-resilient barley plants. We found that different IR treatments (gamma, electron, proton, neutron) increased the intensity of protein catabolism and led to the attenuation of translation. The impact of IRs on protein synthesis and degradation was accompanied by rearrangements in energy metabolism and reallocation of nitrogen, probably due to enhanced protein catabolism. At least partially, those changes seem to fuel secondary metabolites production, including riboflavin, various phytoalexins, phytosiderophores, ferulic and sinapic acids, kaempferol, quercetin, nictoflorin, gallate, and podophyllotoxin. Many of these compounds have antioxidant or radioprotective properties. To focus on possible targets for gene editing, we identified genes differentially regulated after all types of IR exposure and potential transcription factors regulating secondary metabolism, including AP2/ERF, WRKY, bHLH, bZIP, MYB, and NAC families.}, - author = {Volkova, Polina and Prazyan, Alexandr and Podlutskii, Mikhail and Saburov, Vyacheslav and Kazakova, Elizaveta and Bitarishvili, Sofia and Duarte, Gustavo T. and Shesterikova, Ekaterina and Makarenko, Ekaterina and Lychenkova, Maria and Ben, Cécile and Gentzbittel, Laurent and Kazakov, Evgenii and Moiseev, Alexandr and Diuzhenko, Sergei and Korol, Marina and Bondarenko, Ekaterina}, - doi = {10.1016/j.envexpbot.2023.105600}, - issn = {0098-8472}, - journal = {Environmental and Experimental Botany}, - keywords = {{\textgreater}UseGalaxy.eu, Barley, Ionising radiation, Metabolomics, Multi-omics, Phytoremediation, Proteomics, Radioresistance, Secondary metabolites, Transcriptomics, Translation}, - month = {February}, - pages = {105600}, - title = {Multi-omics responses of barley seedlings to low and high linear energy transfer irradiation}, - url = {https://www.sciencedirect.com/science/article/pii/S0098847223003957}, - urldate = {2024-05-17}, - volume = {218}, - year = {2024} -} - -@article{volkova_multi-omics_2024-1, - abstract = {Barley is a resilient crop with high nutritional value and adaptability, making it a promising candidate for phytoremediation and space agriculture. The study presents a comprehensive multi-omics analysis of the impact of ionising radiation (IR) on barley seedlings, intending to identify candidate pathways for creating radiation-resilient barley plants. We found that different IR treatments (gamma, electron, proton, neutron) increased the intensity of protein catabolism and led to the attenuation of translation. The impact of IRs on protein synthesis and degradation was accompanied by rearrangements in energy metabolism and reallocation of nitrogen, probably due to enhanced protein catabolism. At least partially, those changes seem to fuel secondary metabolites production, including riboflavin, various phytoalexins, phytosiderophores, ferulic and sinapic acids, kaempferol, quercetin, nictoflorin, gallate, and podophyllotoxin. Many of these compounds have antioxidant or radioprotective properties. To focus on possible targets for gene editing, we identified genes differentially regulated after all types of IR exposure and potential transcription factors regulating secondary metabolism, including AP2/ERF, WRKY, bHLH, bZIP, MYB, and NAC families.}, - author = {Volkova, Polina and Prazyan, Alexandr and Podlutskii, Mikhail and Saburov, Vyacheslav and Kazakova, Elizaveta and Bitarishvili, Sofia and Duarte, Gustavo T. and Shesterikova, Ekaterina and Makarenko, Ekaterina and Lychenkova, Maria and Ben, Cécile and Gentzbittel, Laurent and Kazakov, Evgenii and Moiseev, Alexandr and Diuzhenko, Sergei and Korol, Marina and Bondarenko, Ekaterina}, - doi = {10.1016/j.envexpbot.2023.105600}, - issn = {0098-8472}, - journal = {Environmental and Experimental Botany}, - keywords = {{\textgreater}UseGalaxy.eu, Barley, Ionising radiation, Metabolomics, Multi-omics, Phytoremediation, Proteomics, Radioresistance, Secondary metabolites, Transcriptomics, Translation}, - month = {February}, - pages = {105600}, - title = {Multi-omics responses of barley seedlings to low and high linear energy transfer irradiation}, - url = {https://www.sciencedirect.com/science/article/pii/S0098847223003957}, - urldate = {2024-05-17}, - volume = {218}, - year = {2024} -} - -@article{volkova_multi-omics_2024-2, abstract = {Barley is a resilient crop with high nutritional value and adaptability, making it a promising candidate for phytoremediation and space agriculture. The study presents a comprehensive multi-omics analysis of the impact of ionising radiation (IR) on barley seedlings, intending to identify candidate pathways for creating radiation-resilient barley plants. We found that different IR treatments (gamma, electron, proton, neutron) increased the intensity of protein catabolism and led to the attenuation of translation. The impact of IRs on protein synthesis and degradation was accompanied by rearrangements in energy metabolism and reallocation of nitrogen, probably due to enhanced protein catabolism. At least partially, those changes seem to fuel secondary metabolites production, including riboflavin, various phytoalexins, phytosiderophores, ferulic and sinapic acids, kaempferol, quercetin, nictoflorin, gallate, and podophyllotoxin. Many of these compounds have antioxidant or radioprotective properties. To focus on possible targets for gene editing, we identified genes differentially regulated after all types of IR exposure and potential transcription factors regulating secondary metabolism, including AP2/ERF, WRKY, bHLH, bZIP, MYB, and NAC families.}, author = {Volkova, Polina and Prazyan, Alexandr and Podlutskii, Mikhail and Saburov, Vyacheslav and Kazakova, Elizaveta and Bitarishvili, Sofia and Duarte, Gustavo T. and Shesterikova, Ekaterina and Makarenko, Ekaterina and Lychenkova, Maria and Ben, Cécile and Gentzbittel, Laurent and Kazakov, Evgenii and Moiseev, Alexandr and Diuzhenko, Sergei and Korol, Marina and Bondarenko, Ekaterina}, doi = {10.1016/j.envexpbot.2023.105600}, @@ -10777,22 +10667,6 @@ @article{wichers_common_2021 year = {2021} } -@article{wight_anthropogenic_2024, - author = {Wight, Jordan and Byrne, Alexander S. and Tahlan, Kapil and Lang, Andrew S.}, - doi = {10.1128/aem.01809-23}, - journal = {Applied and Environmental Microbiology}, - keywords = {{\textgreater}UseGalaxy.eu}, - month = {February}, - note = {Publisher: American Society for Microbiology}, - number = {3}, - pages = {e01809--23}, - title = {Anthropogenic contamination sources drive differences in antimicrobial-resistant {Escherichia} coli in three urban lakes}, - url = {https://journals.asm.org/doi/full/10.1128/aem.01809-23}, - urldate = {2024-05-17}, - volume = {90}, - year = {2024} -} - @article{wight_anthropogenic_2024, author = {Wight, Jordan and Byrne, Alexander S. and Tahlan, Kapil and Lang, Andrew S.}, doi = {10.1128/aem.01809-23},