Update citations (#1312)

Co-authored-by: bgruening <469983+bgruening@users.noreply.github.com>

_bibliography/citations-eu.bib

@@ -7278,6 +7278,26 @@ @article{kowalski_eplerenone_2021
  year = {2021}
 }
 
+@article{kramer_cyclic_2024,
+ abstract = {In nature plants constantly experience changes in light intensities. Low illumination limits photosynthesis and growth. However, also high light intensities are a threat to plants as the photosynthetic machinery gets damaged when the incoming energy surpasses the capacity of photochemistry. One limitation of photochemistry is the constant resupply of stromal electron (e-) acceptors, mainly NADP. NADP is reduced at the acceptor-side of photosystem I. The resulting NADPH is utilized by the Calvin–Benson–Bassham cycle (CBBC) and the malate valve to ensure sufficient oxidized NADP ready to accept e- from PSI. Lately, additional pathways, which function as stromal e- sinks under abiotic stress conditions, were discovered. One such reaction in Arabidopsis thaliana is catalyzed by PHOSPHOGLYCERATE DEHYDROGENASE 3 (PGDH3), which diverts e- from the CBBC into NADH. pgdh3 loss-of-function mutants exhibit elevated non-photochemical quenching (NPQ) and fluctuating light susceptibility. To optimize plant photosynthesis in challenging environments knowledge on PGDH3’s metabolic integration is needed. We used the source of high NPQ in pgdh3 as a starting point. Our study reveals that increased NPQ originates from high cyclic electron flow (CEF). Interestingly, PGDH3 function seems very important when the CEF-generator PROTON GRADIENT REGULATION5 (PGR5) is lost. Consequently, pgr5pgdh3 double mutants are more sensitive to fluctuating light.},
+ author = {Krämer, Moritz and Blanco, Nicolás E. and Penzler, Jan-Ferdinand and Davis, Geoffry A. and Brandt, Benjamin and Leister, Dario and Kunz, Hans-Henning},
+ copyright = {2024 The Author(s)},
+ doi = {10.1038/s41598-024-80836-x},
+ issn = {2045-2322},
+ journal = {Scientific Reports},
+ keywords = {{\textgreater}UseGalaxy.eu, Light responses, Non-photochemical quenching},
+ language = {en},
+ month = {November},
+ note = {Publisher: Nature Publishing Group},
+ number = {1},
+ pages = {29274},
+ title = {Cyclic electron flow compensates loss of {PGDH3} and concomitant stromal {NADH} reduction},
+ url = {https://www.nature.com/articles/s41598-024-80836-x},
+ urldate = {2024-11-29},
+ volume = {14},
+ year = {2024}
+}
+
 @article{kruk_integrated_2024,
  author = {Kruk, Monica E. and Mehta, Subina and Murray, Kevin and Higgins, LeeAnn and Do, Katherine and Johnson, James E. and Wagner, Reid and Wendt, Chris H. and O’Connor, John B. and Harris, J. Kirk and Laguna, Theresa A. and Jagtap, Pratik D. and Griffin, Timothy J.},
  doi = {10.1128/msystems.00929-23},
@@ -10747,6 +10767,21 @@ @article{pelos_fast_2023
  year = {2023}
 }
 
+@article{peresh_carbon_2024,
+ abstract = {Carbon quantum dots (CQDs) are promising therapeutic agent due to their pro-oxidant, antioxidant, antiviral, antibacterial, and anticancer properties when exposed to visible light irradiation. Oxidative stress in bacteria is the main reason for bacteria death after exposure to blue light photoexcited quantum dots. Herein, we present the antibacterial activities of hydrophobic carbon quantum dots/polydimethylsiloxane nanocomposites, hydrophilic citric acid CQDs, and combinations of CQDs with methylene blue. We investigated the antirickettsial effect of hydrophilic and hydrophobic CQDs against Rickettsia slovaca, a tick-borne bacterial pathogen. Photodynamic activity against on rickettsiae reached 99.66\% using CQDs with 470 nm blue light irradiation. Combining methylene blue with CQDs further enhanced the effect on rickettsial infection, achieving 99,98\% efficacy. The obtained results reveal the in vitro antirickettsial properties of CQDs. Sequencing analysis on the genomic level of control and treated samples showed single nucleotide variants (SNVs). Based on snippy analysis SNVs were assigned to the rRNA genes, 16S rRNA and 30S rRNA genes. By freebayes analysis in treated samples, a stop-lost mutation was detected in pseudogene (RSL\_RS06070), while the possible effect on down-stream genes including tsaD, acyl-CoA-desaturase, 30S ribosomal protein S6 and DUF424 family protein. The frameshift mutation was localized within clpB pseudogene belonging to stress-response heat-shock proteins.},
+ author = {Peresh, Yevheniy-Yuliy and Šoltys, Katarína and Kľúčár, Ľuboš and Beke, Gábor and Kováčová, Mária and Špitalský, Zdenko and Špitalská, Eva},
+ doi = {10.1016/j.pdpdt.2024.104402},
+ issn = {1572-1000},
+ journal = {Photodiagnosis and Photodynamic Therapy},
+ keywords = {{\textgreater}UseGalaxy.eu, Carbon quantum dots/polydimethylsiloxane nanocomposites, Citric-acid carbon nanodots, Methylene blue, Photodynamic therapy},
+ month = {November},
+ pages = {104402},
+ title = {Carbon nanodots as photosensitizer in photodynamic inactivation of \textit{{Rickettsia} slovaca}},
+ url = {https://www.sciencedirect.com/science/article/pii/S1572100024004393},
+ urldate = {2024-11-20},
+ year = {2024}
+}
+
 @article{perez-schindler_characterization_2022,
  abstract = {Non-alcoholic fatty liver disease is a continuum of disorders among which non-alcoholic steatohepatitis (NASH) is particularly associated with a negative prognosis. Hepatocyte lipotoxicity is one of the main pathogenic factors of liver fibrosis and NASH. However, the molecular mechanisms regulating this process are poorly understood. The main aim of this study was to dissect transcriptional mechanisms regulated by lipotoxicity in hepatocytes. We achieved this aim by combining transcriptomic, proteomic and chromatin accessibility analyses from human liver and mouse hepatocytes. This integrative approach revealed several transcription factor networks deregulated by NASH and lipotoxicity. To validate these predictions, genetic deletion of the transcription factors MAFK and TCF4 was performed, resulting in hepatocytes that were better protected against saturated fatty acid oversupply. MAFK- and TCF4-regulated gene expression profiles suggest a mitigating effect against cell stress, while promoting cell survival and growth. Moreover, in the context of lipotoxicity, some MAFK and TCF4 target genes were to the corresponding differentially regulated transcripts in human liver fibrosis. Collectively, our findings comprehensively profile the transcriptional response to lipotoxicity in hepatocytes, revealing new molecular insights and providing a valuable resource for future endeavours to tackle the molecular mechanisms of NASH.},
  author = {Pérez-Schindler, Joaquín and Vargas-Fernández, Elyzabeth and Karrer-Cardel, Bettina and Ritz, Danilo and Schmidt, Alexander and Handschin, Christoph},
@@ -14229,6 +14264,17 @@ @article{vaquero-sedas_epigenetic_2022
  year = {2022}
 }
 
+@inproceedings{varshney_madland_2024,
+ author = {Varshney, D. and Hiltemann, S. and Petroll, R. and Fernandez-Pozo, N. and Grüning, B. A. and Rensing, S. A.},
+ keywords = {{\textgreater}UseGalaxy.eu},
+ month = {October},
+ pages = {10--11},
+ title = {{MAdLand} computational resources for the {Plant} community},
+ url = {https://pure.mpg.de/pubman/faces/ViewItemOverviewPage.jsp?itemId=item_3620708},
+ urldate = {2024-12-01},
+ year = {2024}
+}
+
 @article{vecchi_mitogenome_2024,
  abstract = {Ramazzottius is a widespread genus of tardigrades with extreme cryptobiotic capabilities. Thanks to its ability to survive desiccation and freezing, this genus is usually recorded from harsh habitats such as exposed mosses and lichens and rock pools. In the last years, research focused on both describing Ramazzottius diversity and revealing the molecular mechanisms behind their cryptobiotic capabilities. Despite the research efforts in these fields, much still remains to be discovered. Here we describe a new Ramazzottius species from an Italian rock pool by means of integrative taxonomy (morphology, morphometry, and DNA sequencing) and sequenced its genome with Nanopore technology to provide an assembled mitogenome and annotate its Temperature and Desiccation Resistance Proteins (TDPR) repertoire. The new gonochoric species is phylogenetically close to the parthenogenetic R. varieornatus, a strain of which (YOKOZUNA-1) has been adopted as model organism for the study of cryptobiosis. The mitogenome of the new species shows perfect synteny with R. varieornatus and shares with it most of the TDPR genes. The relative genetic similarity of the new species to the model R. varieornatus, combined with unique biological traits (for example the difference in reproductive mode and the unique habitat it colonizes), makes the new species a potential new addition to the range of model tardigrade species.},
  author = {Vecchi, Matteo and Stec, Daniel},
@@ -15794,6 +15840,23 @@ @article{zhang_complete_2024
  year = {2024}
 }
 
+@article{zhang_deciphering_2024,
+ abstract = {Plant and animal stem cells receive signals from their surrounding cells to stay undifferentiated. In the Arabidopsis root, the quiescent center (QC) acts as a stem cell organizer, signaling to the neighboring stem cells. WOX5 is a central transcription factor regulating QC function. However, due to the scarcity of QC cells, WOX5 functions in the QC are largely unexplored at a genomic scale. Here, we unveil the transcriptional and epigenetic landscapes of the QC and the role of WOX5 within them. We find that WOX5 functions both as a transcriptional repressor and activator, affecting histone modifications and chromatin accessibility. Our data expand on known WOX5 functions, such as the regulation of differentiation, cell division, and auxin biosynthesis. We also uncover unexpected WOX5-regulated pathways involved in nitrate transport and the regulation of basal expression levels of genes associated with mature root tissues. These data suggest a role for QC cells as reserve stem cells and primed cells for prospective progenitor fates. Taken together, these findings offer insights into the role of WOX5 at the QC and provide a basis for further analyses to advance our understanding of the nature of plant stem cell organizers.},
+ author = {Zhang, Ning and Bitterli, Pamela and Oluoch, Peter and Hermann, Marita and Aichinger, Ernst and Groot, Edwin P and Laux, Thomas},
+ doi = {10.1038/s44318-024-00302-2},
+ issn = {0261-4189},
+ journal = {The EMBO Journal},
+ keywords = {{\textgreater}UseGalaxy.eu, Arabidopsis, Cell-specific Transcriptomic and Epigenetic Profiling, Root, Stem Cells Organizer, WOX5},
+ month = {November},
+ note = {Num Pages: 23
+Publisher: John Wiley \& Sons, Ltd},
+ pages = {1--23},
+ title = {Deciphering the molecular logic of {WOX5} function in the root stem cell organizer},
+ url = {https://www.embopress.org/doi/full/10.1038/s44318-024-00302-2},
+ urldate = {2024-11-21},
+ year = {2024}
+}
+
 @article{zhang_first_2024,
  abstract = {This study presents the complete mitochondrial genome (mitogenome) of Litostrophus scaber, which is the first mitogenome of the genus Litostrophus. The mitogenome is a circular molecule with a length of 15,081 bp. The proportion of adenine and thymine (A + T) was 69.25\%. The gene ND4L used TGA as the initiation codon, while the other PCGs utilized ATN (A, T, G, C) as the initiation codons. More than half of the PCGs used T as an incomplete termination codon. The transcription direction of the L. scaber mitogenome matched Spirobolus bungii, in contrast to most millipedes. Novel rearrangements were found in the L. scaber mitogenome: trnQ -trnC and trnL1- trnP underwent short-distance translocations and the gene block rrnS-rrnL-ND1 moved to a position between ND4 and ND5, resulting in the formation of a novel gene order. The phylogenetic analysis showed that L. scaber is most closely related to S. bungii, followed by Narceus magnum. These findings enhance our understanding of the rearrangement and evolution of Diplopoda mitogenomes.},
  author = {Zhang, Gaoji and Gao, Ming and Chen, Yukun and Wang, Yinuo and Gan, Tianyi and Zhu, Fuyuan and Liu, Hongyi},