Update citations (#1273)

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

_bibliography/citations-eu.bib

@@ -2127,27 +2127,6 @@ @article{chanama_comparative_2023
  year = {2023}
 }
 
-@article{chanama_comparative_2023,
- abstract = {Actinobacteria are well known as a rich source of diversity of bioactive secondary metabolites. Kutzneria, a rare actinobacteria belonging to the family Pseudonocardiaceae has abundance of secondary metabolite biosynthetic gene clusters (BGCs) and is one of important source of natural products and worthy of priority investigation. Currently, Kutzneria chonburiensis SMC256T has been the latest type-strain of the genus and its genome sequence has not been reported yet. Therefore, we present the first report of new complete genome sequence of SMC256T (genome size of 10.4 Mbp) with genome annotation and feature comparison between SMC256T and other publicly available Kutzneria species. The results from comparative and functional genomic analyses regarding the phylogenomic and the clusters of orthologous groups of proteins (COGs) analyses indicated that SMC256T is most closely related to Kutzneria sp. 744, Kutzneria kofuensis, Kutzneria sp. CA-103260 and Kutzneria buriramensis. Furthermore, a total of 322 BGCs were also detected and showed diversity among the Kutzneria genomes. Out of which, 38 clusters showing the best hit to the most known BGCs were predicted in the SMC256Tgenome. We observed that six clusters responsible for biosynthesis of antimicrobials/antitumor metabolites were strain-specific in Kutzneria chonburiensis. These putative metabolites include virginiamycin S1, lysolipin I, esmeraldin, rakicidin, aclacinomycin and streptoseomycin. Based on these findings, the genome of Kutzneria chonburiensis contains distinct and unidentified BGCs different from other members of the genus, and the use of integrative genomic-based approach would be a useful alternative effort to target, isolate and identify putative and undiscovered secondary metabolites suspected to have new and/or specific bioactivity in the Kutzneria.},
- author = {Chanama, Manee and Prombutara, Pinidphon and Chanama, Suchart},
- copyright = {2023 The Author(s)},
- doi = {10.1038/s41598-023-36039-x},
- issn = {2045-2322},
- journal = {Scientific Reports},
- keywords = {{\textgreater}UseGalaxy.eu, Bacteria, Comparative genomics, Phylogenomics},
- language = {en},
- month = {May},
- note = {Number: 1
-Publisher: Nature Publishing Group},
- number = {1},
- pages = {8794},
- title = {Comparative genome features and secondary metabolite biosynthetic potential of {Kutzneria} chonburiensis and other species of the genus {Kutzneria}},
- url = {https://www.nature.com/articles/s41598-023-36039-x},
- urldate = {2023-06-05},
- volume = {13},
- year = {2023}
-}
-
 @article{chen_first_2021,
  author = {Chen, Dong-Bin and Zhang, Ru-Song and Jin, Xiang-Dong and Yang, Jian and Li, Peng and Liu, Yan-Qun},
  doi = {10.1017/s0007485321000808},
@@ -5660,24 +5639,6 @@ @article{kocsmar_proteome_2023
  year = {2023}
 }
 
-@article{kocsmar_proteome_2023,
- abstract = {Protein expression is a primary area of interest for routine histological diagnostics and tissue-based research projects, but the limitations of its post-mortem applicability remain largely unclear. On the other hand, tissue specimens obtained during autopsies can provide unique insight into advanced disease states, especially in cancer research. Therefore, we aimed to identify the maximum post-mortem interval (PMI) which is still suitable for characterizing protein expression patterns, to explore organ-specific differences in protein degradation, and to investigate whether certain proteins follow specific degradation kinetics. Therefore, the proteome of human tissue samples obtained during routine autopsies of deceased patients with accurate PMI (6, 12, 18, 24, 48, 72, 96 h) and without specific diseases that significantly affect tissue preservation, from lungs, kidneys and livers, was analyzed by liquid chromatography–tandem mass spectrometry (LC–MS/MS). For the kidney and liver, significant protein degradation became apparent at 48 h. For the lung, the proteome composition was rather static for up to 48 h and substantial protein degradation was detected only at 72 h suggesting that degradation kinetics appear to be organ specific. More detailed analyses suggested that proteins with similar post-mortem kinetics are not primarily shared in their biological functions. The overrepresentation of protein families with analogous structural motifs in the kidney indicates that structural features may be a common factor in determining similar postmortem stability. Our study demonstrates that a longer post-mortem period may have a significant impact on proteome composition, but sampling within 24 h may be appropriate, as degradation is within acceptable limits even in organs with faster autolysis.},
- author = {Kocsmár, Éva and Schmid, Marlene and Cosenza-Contreras, Miguel and Kocsmár, Ildikó and Föll, Melanie and Krey, Leah and Barta, Bálint András and Rácz, Gergely and Kiss, András and Werner, Martin and Schilling, Oliver and Lotz, Gábor and Bronsert, Peter},
- doi = {10.1007/s00018-023-04754-3},
- issn = {1420-9071},
- journal = {Cellular and Molecular Life Sciences},
- keywords = {{\textgreater}UseGalaxy.eu, Autopsy, Degradation, Proteomics},
- language = {en},
- month = {April},
- number = {5},
- pages = {117},
- title = {Proteome alterations in human autopsy tissues in relation to time after death},
- url = {https://doi.org/10.1007/s00018-023-04754-3},
- urldate = {2023-06-05},
- volume = {80},
- year = {2023}
-}
-
 @article{koeppel_sars-cov-2_2022,
  author = {Koeppel, Katja Natalie and Mendes, Adriano and Strydom, Amy and Rotherham, Lia and Mulumba, Misheck and Venter, Marietjie},
  doi = {10.3390/v14010120},
@@ -7005,6 +6966,26 @@ @article{mcgowan_multi-omics_2020
  year = {2020}
 }
 
+@article{mcvey_genetic_2024,
+ abstract = {Vascular smooth muscle cell (VSMC) proliferation, migration, and apoptosis play important roles in many physiological processes and pathological conditions. To identify genetic influences on VSMC behavior, we measured these traits and undertook genome-wide association studies in primary umbilical artery-derived VSMCs from {\textgreater}2000 individuals. Although there were no genome-wide significant associations for VSMC proliferation or migration, genetic variants at two genomic loci (7p15.3 and 7q32.3) showed highly significant associations with VSMC apoptosis (P = 1.95 × 10−13 and P = 7.47 × 10−9, respectively). The lead variant at the 7p51.3 locus was associated with increased expression of the GSDME and PALS2 genes in VSMCs. Knockdown of GSDME or PALS2 in VSMCs attenuated apoptotic cell death. A protein co-immunoprecipitation assay indicated that GSDME complexed with PALS2. PALS2 knockdown attenuated activated caspase-3 and GSDME fragmentation, whilst GSDME knockdown also reduced activated caspase-3. These findings provide new insights into the genetic regulation of VSMC apoptosis, with potential utility for therapeutic development.},
+ author = {McVey, David G. and Andreadi, Catherine and Gong, Peng and Stanczyk, Paulina J. and Solomon, Charles U. and Turner, Lenka and Yan, Liu and Chen, Runji and Cao, Junjun and Nelson, Christopher P. and Thompson, John R. and Yu, Haojie and Webb, Tom R. and Samani, Nilesh J. and Ye, Shu},
+ copyright = {2024 The Author(s)},
+ doi = {10.1038/s41419-024-06799-z},
+ issn = {2041-4889},
+ journal = {Cell Death \& Disease},
+ keywords = {{\textgreater}UseGalaxy.eu, Apoptosis, Cell death},
+ language = {en},
+ month = {June},
+ note = {Publisher: Nature Publishing Group},
+ number = {6},
+ pages = {1--12},
+ title = {Genetic influence on vascular smooth muscle cell apoptosis},
+ url = {https://www.nature.com/articles/s41419-024-06799-z},
+ urldate = {2024-07-09},
+ volume = {15},
+ year = {2024}
+}
+
 @article{meem_exploring_2024,
  abstract = {This study investigates the potential of 2-(4-butylbenzyl)-3-hydroxynaphthalene-1,4-dione (11) and its 12 derivatives as anticancer and biofilm formation inhibitors for methicillin-resistant staphylococcus aureus using in silico methods. The study employed various computational methods, including molecular dynamics simulation molecular docking, density functional theory, and global chemical descriptors, to evaluate the interactions between the compounds and the target proteins. The docking results revealed that compounds 9, 11, 13, and ofloxacin exhibited binding affinities of −7.6, −7.9, −7.5, and −7.8 kcal mol−1, respectively, against peptide methionine sulfoxide reductase msrA/msrB (PDB: 3E0M). Ligand (11) showed better inhibition for methicillin-resistant staphylococcus aureus msrA/msrB enzyme. The complex of the 3E0M-ligand 11 remained highly stable across all tested temperatures (300, 305, 310, and 320 K). Principal Component Analysis (PCA) was employed to evaluate the behavior of the complex at various temperatures (300, 305, 310, and 320 K), demonstrating a total variance of 85\%. Convergence was confirmed by the eigenvector’s cosine content value of 0.43, consistently displaying low RMSD values, with the minimum observed at 310 K. Furthermore, ligand 11 emerges as the most promising candidate among the compounds examined, showcasing notable potential when considering a combination of in vitro, in vivo, and now in silico data. While the naphthoquinone derivative (11) remains the primary candidate based on comprehensive in silico studies, further analysis using Frontier molecular orbital (FMO) suggests while the Egap value of compound 11 (2.980 eV) and compound 13 (2.975 eV) is lower than ofloxacin (4.369 eV), indicating their potential, so it can be a statement that compound 13 can also be investigated in further research.},
  author = {Meem, Mehnaz Hossain and Yusuf, Sumaiya Binte and Al Abbad, Sanaa S. and Rahman, Shofiur and Al-Gawati, Mahmoud and Albrithen, Hamad and Alodhayb, Abdullah N. and Uddin, Kabir M.},
@@ -9029,6 +9010,26 @@ @article{riediger_analysis_2020
  year = {2020}
 }
 
+@article{riesle_activator-blocker_2023,
+ abstract = {Zygotic genome activation (ZGA) in the development of flies, fish, frogs and mammals depends on pioneer-like transcription factors (TFs). Those TFs create open chromatin regions, promote histone acetylation on enhancers, and activate transcription. Here, we use the panel of single, double and triple mutants for zebrafish genome activators Pou5f3, Sox19b and Nanog, multi-omics and mathematical modeling to investigate the combinatorial mechanisms of genome activation. We show that Pou5f3 and Nanog act differently on synergistic and antagonistic enhancer types. Pou5f3 and Nanog both bind as pioneer-like TFs on synergistic enhancers, promote histone acetylation and activate transcription. Antagonistic enhancers are activated by binding of one of these factors. The other TF binds as non-pioneer-like TF, competes with the activator and blocks all its effects, partially or completely. This activator-blocker mechanism mutually restricts widespread transcriptional activation by Pou5f3 and Nanog and prevents premature expression of late developmental regulators in the early embryo.},
+ author = {Riesle, Aileen Julia and Gao, Meijiang and Rosenblatt, Marcus and Hermes, Jacques and Hass, Helge and Gebhard, Anna and Veil, Marina and Grüning, Björn and Timmer, Jens and Onichtchouk, Daria},
+ copyright = {2023 The Author(s)},
+ doi = {10.1038/s41467-023-41507-z},
+ issn = {2041-1723},
+ journal = {Nature Communications},
+ keywords = {{\textgreater}UseGalaxy.eu, Development, Differential equations, Gastrulation, Gene expression profiling, Transcriptional regulatory elements},
+ language = {en},
+ month = {September},
+ note = {Publisher: Nature Publishing Group},
+ number = {1},
+ pages = {5677},
+ title = {Activator-blocker model of transcriptional regulation by pioneer-like factors},
+ url = {https://www.nature.com/articles/s41467-023-41507-z},
+ urldate = {2024-07-09},
+ volume = {14},
+ year = {2023}
+}
+
 @article{ristinmaa_resin_2023,
  abstract = {The bark is the outermost defense of trees against microbial attack, largely thanks to toxicity and prevalence of extractive compounds. Nevertheless, bark decomposes in nature, though by which species and mechanisms remains unknown. Here, we have followed the development of microbial enrichments growing on spruce bark over six months, by monitoring both chemical changes in the material and performing community and metagenomic analyses. Carbohydrate metabolism was unexpectedly limited, and instead a key activity was metabolism of extractives. Resin acid degradation was principally linked to community diversification with specific bacteria revealed to dominate the process. Metagenome-guided isolation facilitated the recovery of the dominant enrichment strain in pure culture, which represents a new species (Pseudomonas abieticivorans sp. nov.), that can grow on resin acids as a sole carbon source. Our results illuminate key stages in degradation of an abundant renewable resource, and how defensive extractive compounds have major roles in shaping microbiomes.},
  author = {Ristinmaa, Amanda Sörensen and Tafur Rangel, Albert and Idström, Alexander and Valenzuela, Sebastian and Kerkhoven, Eduard J. and Pope, Phillip B. and Hasani, Merima and Larsbrink, Johan},